research article herb network analysis for a famous tcm...
TRANSCRIPT
Research ArticleHerb Network Analysis for a Famous TCM DoctorrsquosPrescriptions on Treatment of Rheumatoid Arthritis
Yan Li1 Rui Li2 Zibo Ouyang2 and Shao Li2
1Yijishan Hospital Wannan Medical College Wuhu 241001 China2MOE Key Lab of Bioinformatics Bioinformatics Division TNLIST Department of AutomationTsinghua University Beijing 100084 China
Correspondence should be addressed to Shao Li shaolimailtsinghuaeducn
Received 28 October 2014 Revised 20 January 2015 Accepted 20 January 2015
Academic Editor Jairo K Bastos
Copyright copy 2015 Yan Li et al This is an open access article distributed under the Creative Commons Attribution License whichpermits unrestricted use distribution and reproduction in any medium provided the original work is properly cited
Traditional Chinese Medicine (TCM) doctors always prescribe various herbal formulae tailored to individual patients Howeverthere is still a lack of appropriate methods to study the rule and potential biological basis underlying the numerous prescriptionsHerewe developed anHerb-Compound-Target-Disease coherent network approach to analyze 871 herbal prescriptions fromaTCMmasterMr Ji-Ren Li in his clinical practice on treatment of rheumatoid arthritis (RA)The core herb networks were extracted fromMr Lirsquos prescriptions Then we predicted target profiles of compounds in core herb networks and calculated potential synergisticactivities among them We further found that the target sets of core herbs overlapped significantly with the RA related biologicalprocesses and pathways Moreover we detected a possible connection between the prescribed herbs with different properties suchas Cold andHot and theWestern drugs with different actions such as immunomodulatory and hormone regulation on treatment ofRA In summary we explored a new application of TCMnetwork pharmacology on the analysis of TCMprescriptions and detectedthe networked core herbs their potential synergistic and biological activities and possible connections with drugsThis work offersa novel way to understand TCM prescriptions in clinical practice
1 Background
Traditional ChineseMedicine (TCM) is one of the most trea-sured cultural heritages in China and is also an inseparablepart of current medical systems Herbal formula (Fang-Ji inMandarin) that consists of two ormoremedicinal herbs is themajor form in TCM clinical practice Nowadays TCM herbalformula has been well known to be effective for the controlof many complex diseases for example rheumatoid arthritis(RA) a common autoimmune disease that leads to a chronicand systemic inflammatory disorder [1 2] Rheumatoidarthritis is manifested by synovial inflammation morningstiffness and pain and may affect many tissues and organs inhuman body especially causing joint deformity Rheumatoidarthritis is a complex disease with limited treatment optionsWithout regular treatment many patients tend to suffer fromhigh probability of disability TCM has been regarded as animportant strategy to inhibit RA development and improve
the life quality of RA patients [3] Actually the treatmentof RA in TCM can be traced up to more than 3000 yearsago RA falls in the scope of the TCM therapeutic conceptldquoBi ZHENGrdquo The etiologies syndrome classification andtreatment of Bi ZHENG had been recorded in the YellowEmperorrsquos Internal Classic one of the earliest treatises inTCM Subsequently TCM practitioners have accumulatedrich clinical experience and numbers of herbal formulae fortreating patients with rheumatoid arthritis As one of the first30 ldquoGrandMasters of TCMrdquo selected byChinese governmentMr Ji-Ren Li at Yijishan Hospital Wannan Medical Collegeis a highly regarded Chinese medicine practitioner who isskilled in the treatment of RA [4 5] Mr Li has accumulatednumerous herbal prescriptions to cure RA patients and earlyaction needs to be taken to understand the professionalexperience embedded in such valuable herbal prescriptions
However quite different from the clinical practice of theWestern medicine herbal formulae are always prescribed by
Hindawi Publishing CorporationEvidence-Based Complementary and Alternative MedicineVolume 2015 Article ID 451319 9 pageshttpdxdoiorg1011552015451319
2 Evidence-Based Complementary and Alternative Medicine
TCMpractitioners specifically tailored to individual patientsTCM doctors treat patients mainly based on syndrome dif-ferentiation For different patients various herbs are groupedand different formulae are prescribed This tradition andfeature make TCM a kind of personalized medicine andcause great difficulty in designing standard protocols suchas the randomized controlled trial in TCM studies Thelack of appropriate methods to analyze the rule as well asscientific basis for TCM-doctor-prescribed herbal formulaeis therefore one of the major frustrations to find clinicalevidence of TCM How to study the characteristics andprescription rule of such flexible TCM formulae is still a greatchallenge and requires widely interdisciplinary efforts
Thanks to the rapid progress of bioinformatics especiallycomplex network theory and technologies recently thenetwork approach has become a new avenue and powerfultool to handle intricate problems such as those in TCMWe have been making efforts to build a TCM networkpharmacology approach over ten years and established aset of network-based methods for TCM study [6ndash9] Forexample to reveal the combination rule and the biologicalbasis of herbal formulae we proposed a global networkanalysis framework consisting of herbcompound networkbiological network (gene protein or target network) anddisease network Several methods are also created suchas a distance-based mutual information model (DMIM)that can identify herb relationships from numerous herbalformulae The good performance of the DMIM method touncover the herbal combination rules has been illustrated inboth 3865 collaterals-related herbal formulae and a classicLiu-Wei-Di-Huang formula [6] Furthermore we proposeda novel concept of ldquonetwork targetrdquo [7] which treats adisease-specific molecular network as a therapeutic targetto help design suitable medical treatments Several methodsfor the network target analysis especially the disease geneprediction target prediction for drugs or herbal compounds[8] the network comodule analysis for drug discovery andthe network-based prioritization of synergistic combinations[7] are developed subsequently These methods have beenapplied in finding bioactive compounds and revealing themechanism of action for herbal formulae including Liu-Wei-Di-Huang pill [9] Now the network-based method inthe context of TCM network pharmacology has become aburgeoning field in the modern studies of TCM [10ndash12] Webelieve the network-based strategy and approaches can alsoprovide good solutions for the herbal prescription analysis
In this work 871 herbal prescriptions from Mr Ji-Ren Lirsquos clinical treatment on patients with rheumatoidarthritis were analyzed from a network point of view TCMnetwork pharmacology methods were employed to detectthe common rules and potential biological basis of theseherbal prescriptions This work is promising as the resultsnicely show the rationality and validity of Mr Lirsquos herbalprescriptions Moreover this work provides a new route tointerpret the professional experience embedded in numerousand precious TCM herbal prescriptions
Herbal prescriptions
Herbnetwork
Compound network
Herb name normalization
Herb relationship byDMIM scoring
Herb compoundcollection
Target prediction by drugCIPHER
Connect compound by target interaction
Disease gene network
Evaluation of synergistic activity by NIMS
Figure 1 The Herb-Compound-Target-Disease coherent networkanalysis framework for studying herbal prescriptions on the treat-ment of certain diseases
2 Methods
21 Herbal Formulae and Herbal Compounds A total of 871herbal prescriptions from Mr Ji-Ren Li in the individuallyclinical treatment of RA patients from 2005 to 2013 were usedin this work The 871 herbal prescriptions were normalizedby substituting the polysemes synonyms and acronyms ofthe herbs in the dataset and resulted in a standardized HerbName list Each formula contains 15 to 29 herbs and the aver-age number is 18 Compounds of herbs were gathered fromthe HerbBioMap database (China Copyright of ComputerSoftware 2011SR076502)TheHerbBioMapdatabase contains10806 compounds for 539 herbs up to now
22 Multilayer Coherent Network Analysis for Herbal Pre-scriptions As shown in Figure 1 we proposed an Herb-Compound-Target-Disease coherent network analysis frame-work to study the prescription rules and potential biologicalbasis for herbal prescriptionsThe principle steps are summa-rized as follows
Herb Network Construction We created a matrix of 871dimensions to represent all collected herbal formulae andthen calculated the frequency of every 343 herbs in allformulae and gave a normalized frequency (NF) NF =AFsum119873
119899=1AF1 where AF is accumulated frequency and 119873
denotes 343-herb species number Next most frequent herbsin 871 herbal prescriptions were selected and subjected tothe DMIM (distance-basedmutual informationmodel) anal-ysis an algorithm for identifying herb relationships amongdifferent formulae and uncovering the combinational rulesof herbs in a network manner [6] The DMIM model isan integrated scoring system combining the mutual infor-mation (MI) entropy characteristics and the ldquobetween-herbdistancerdquo (119889) between herbs by calculating score(119909 119910) =MI(119909 119910)119889(119909 119910) which describes the tendency of herb 119909 and
Evidence-Based Complementary and Alternative Medicine 3
herb 119910 to form an herb pair More importantly the DMIMmodel extracts information from the organization of Jun-Chen-Zuo-Shi (Master-Adviser-Soldier-Guide) herbs in anherbal formula based on which a new parameter ldquobetween-herb distancerdquowas created thatmeans the further the distancebetween two herbs in a formula is the less likely they are tobe relevant to one anotherThus DMIM is suitable to retrieveherb combinational rules achieving a good balance amongthe herbrsquos frequency independence and distance in herbalformulae [6]
Target Prediction for Herbal Compounds and Herbs In thepresent study drugCIPHER a method we developed previ-ously [8] is used to predict the target profile for all availablecompounds collected from each herb in the core herbnetworks drugCIPHER is a regressionmodel that can predictthe links between drugs and target proteins in a genome-wide scale by correlating the drug chemical informationand protein-protein interaction (PPI) from a heterogeneousnetwork By integrating and making full use of all currentFDA-approved drug structures drug-target interactions andhuman protein-protein interactions drugCIPHER can out-put a target profile for any given compound with knownstructure that is calculated from the correlation between thequery ingredientrsquos structure similarity vector in the drugspace and the target-related genersquos closeness vector in thetarget space As the top 100 targets predicted by drugCIPHERcan reach the high prediction accuracy (773) [8] here thetop 100 target profiles predicted for each compound wereselected and the target profiles of all collected compoundswithin a herb were combined to form integrative targetprofiles of this herb The target prediction procedure wasconducted for herbs present in the core herb networks orinvolved in the following studies
Evaluation of Synergistic Actions forHerbNetwork To identifythe potential synergistic effects of herb combinations in thecore herb network at the molecular level and in a highthroughput way we used the network-based identificationof multicomponent synergy (NIMS) method [7] a novelapproach to access the synergistic strength of any combina-tion of herbal compounds by determining their target inter-actions in the protein-protein network The NIMS algorithmconsists of two components topology score and agent scoreThe topology score is generated from the topological featuresof the background network related to disease condition anddrug actions while the agent score is based on the similarityof agent phenotypes Two graph-based measures between-ness and closeness were used to capture the associationsamong targets and the other measure PageRank to verifythe node importance [7] The resulted synergy score is usedto prioritize the synergistic effect of combinations of agentsincluding herbs or herbal compounds
Gene Ontology (GO) and Pathway Analysis for Herb Targetsand RAGenesThe targets of each compound in the top herbswere predicted using drugCIPHER For each compound ofthe top herbs the top 100 proteins were treated as targetsfor the given compound The targets hit by more than five
compounds within an herb were considered herb targets Top15 frequent herbsrsquo targets were subjected to the gene ontology[13] and pathway enrichment analysis One the other handthe 129 RA-related genes with a direct mechanism relation-ship to rheumatoid arthritis were collected from the CTDdatabase [14] For functional analysis we used the ldquoSet Ana-lyzerrdquo tool at the CTD site (httpctdbaseorgtoolsanalyzergo) to analyze the enriched GO terms as well as KEGGpathways for herb targets and RA genes respectively withcorrected 119875 value less than 005 We also mapped the RAgenes and herb targets in the enriched KEGG pathwaynetwork
Compound Network Analysis for Anti-RA Herbs and DrugsFor comparison of the herbal prescriptions and the Westernanti-RA drugs we collected the commonly used anti-RAdrugs and their targets from the DrugBank database [15]Nine immunomodulatory drugs and 7 hormones were selec-ted The immunomodulatory drugs include methotrexateleflunomide ciclosporin thalidomide cyclophosphamideazathioprine mycophenolate mofetil tacrolimus and cyclo-sporine Hormones include dexamethasone hydrocortisonecortisone triamcinolone prednisolone prednisone andmethylprednisolone Based on the targets of each compoundcontained by the top 50 frequent herbs the closeness ofherb compoundrsquos targets and targets of immunomodulatorydrugs and hormones on the RA-related gene network thatconnected by PPI interactions (HPRD Release 7) [16] weremeasuredThe compoundnetworks are then formed inwhichtwo compounds (or drugs) will be linked if their targetsare overlapped or directly connected in the network Herewe paid more attention on the relationship between herbalcompounds with ColdHot property and two types of RAdrugs
3 Results and Discussion
31 Core Herb Networks from Herbal Prescriptions 343 herbswere uniquely identified from all 871 prescriptions ByDMIMscoring [6] we obtained frequently used herbs as well as theircombinations from all available prescriptions with Ji XueTeng as the most frequently used herb The top 15 herbs inMr Lirsquos anti-RA herbal prescription are shown in Table 1 Wecan see that although the prescriptions are written out indi-vidually to patients the commonly used herbs with differentproperties are considered to be the most representative ofthe available herbal prescriptions Therefore to capture thecommon rule of herbal prescriptions here we focused onthe most frequent herbs for the subsequent network analysisThenwe conducted the herb network analysis for these herbalprescriptions A node in herb network refers to an herb andan edge connecting two nodes refers to the two significantcooccurrent herbs in herbal prescriptions By using DMIMscore to evaluate the significance of the edge we constructedtwo types of the core herb networks namely the high-frequency herb network and the intersection herb networkfor Mr Lirsquos 871 prescriptions
For the high-frequency network only the top frequentherbs were treated as nodes and the cooccurrence herbs
4 Evidence-Based Complementary and Alternative Medicine
Table 1 Top 15 herbs in Mr Ji-Ren Lirsquos antirheumatoid arthritis herbal prescriptions
Chinese name Latin name Property Frequency Normalized frequencyJi Xue Teng Millettia reticulata Benth Warm 503 510Huo Xue Teng Sargentodoxa cuneata Neutral 499 506Huang Qi Astragalus membranaceus (Fisch) Bunge Warm 481 487Dang Gui Radix Angelicae sinensis Warm 430 436Quan Xie Scorpio Neutral 399 404Qing Feng Teng Caulis Sinomenii Neutral 396 401Ku Shen Radix Sophorae flavescentis Cold 323 327Wu Tou Aconitum carmichaeli Debx Hot 306 310Wu Gong Scolopendra Warm 287 291Huang Bai Cortex Phellodendri Cold 283 287Bi Xie Rhizoma Dioscoreae Hypoglaucae Neutral 280 284Ren Dong Teng Caulis Lonicerae Cool 257 260Qin Jiao Radix Gentianae macrophyllae Cold 254 257Wu Shao She Zaocys dhumnades Neutral 235 238Pu Gong Ying Taraxacum mongolicumHand-Mazz Cold 227 230
in herbal prescriptions identified by DMIM were treated asedges For example we found that the top 10 frequent herbswith 45 edges are closely interrelatedwith each other formingalmost all connected graphs Among them Ji Xue Teng andHuang Qi (DMIM score = 18627) Huo Xue Teng and Ji XueTeng (DMIM score = 16517) have the highest DMIM scoresThis result suggests that the top 10 herbs are always prescribedin pairs in Mr Lirsquos practice for RA treatment
For the intersection herb network we built every subnet-work by DMIM for each of the top frequent herbs and thenintersected the subnetworks to construct a core networkFor example Figure 2(a) shows the subnetwork around thetop 2 herb Huo Xue Teng (Sargentodoxa cuneata) The topten frequent herb subnetworks contained 21 to 35 nodes and100 to 200 edges and the resulted core intersection networkhas 14 nodes and 29 edges (Figure 2(b)) Interestingly acomplete formula of Mr Li Qing-Luo-Yin [17] is present inthis network
Herbs and herb combinations present in these two typesof herb networks may play a central role in Mr Lirsquos herbalprescriptions for the treatment of RA
32 Potential Synergistic Activities Underlying Core Herb Net-works Taking the core herb networks as examples we fur-ther performed the network target analysis to computation-ally determine whether the DMIM extracted herb networksdisplayed synergistic effects In this step we collected avail-able compounds for the core herb networks identified fromMr Lirsquos prescriptions The target profile of each compoundwas predicted by the drugCIPHER method [8] Then weselected top 100 targets of compounds assembled in eachherb to analyze the synergistic activity by evaluating the tar-get interactions in the protein-protein interaction networkWhen drugCIPHER [8] and NIMS [7] (see Section 2) areapplied to the herb networks we can obviously detect themodular property in themolecular level that denotes the syn-ergistic relationship in the core herb networks (Figure 3(a))From the outputs of the NIMS score we found that in
an herb network not all herbs interact strongly Instead onlycertain herbs or even certain herbal compounds produceclear synergistic effects For example in the high-frequencyherb network Ji Xue Teng and Huo Xue Teng (average NIMSscore = 084) Ku Shen and Qing Feng Teng (average NIMSscore = 057) Ku Shen and Ji Xue Teng (average NIMS score= 04) and Huo Xue Teng and Qing Feng Teng (averageNIMS score = 031) each of the two herbs has a relativelyhigh NIMS score and tends to produce synergistic activity indifferent levels In the intersection herb network the mainconstituent of TCM herbal formulae Qing-Luo-Yin (QLY)also has a good NIMS score A part of the synergistic modulefromQing Feng Teng and Ku Shen was shown in Figure 3(b)This figure further illustrated that different compounds inan herb pair obtained diverse synergistic scores Amongthem the combination of compounds such as Sinomenineand Matrine achieves a relatively high score which agreeswith the previously experimental results on the synergisticeffects in QLY [17] Thus we demonstrate here that thesynergistic effects of herb components may be contributed tothe modular property of the herb network as well as herbalprescriptions
33 Biological Associations between Herb Targets and RAGenes Since the targets of each compound of herbs areavailable by drugCIPHER we further verify the effectivenessof the top 15 frequent herbs in Mr Lirsquos prescriptions (Table 1)by evaluating the herbal compoundsrsquo targets and theirrelationship with RA genes in terms of the GO biologicalprocesses and pathways As shown in Table 2 there are RA-related GO terms resulting from targets of the top 15 herbswhich were also enriched with 129 RA-related genes formthe CTD database For example the overlapped GO termswhich resulted from both herb targets and RA genes includeangiogenesis [18] cytokine production [19] inflammatoryresponse [20] lymphocyte activation [21] and NF-120581B tran-scription factor activity [22] The overlapped GO terms alsoinclude ldquodefense response to bacteriumrdquo which is worthy
Evidence-Based Complementary and Alternative Medicine 5
Lian Qiao
Hu Zhang Dai MaoRou Gui
Ku Shen
Bi Xie
Wu Shao She
Qin Jiao
Man Jing Zi
Han Lian Cao
Chai Hu
Wu Wei Zi
Bai Mao Gen
Wei Ling Xian
Qing Feng Teng
Zhi Mu
Wu Tou
Huo Xue Teng
Lei Gong Teng
Huang Bai
Ji XueTengHuang Qi
Pu Gong Ying
Ren Dong Teng
(a)
Man Jing Zi
Wu Tou
Bi Xie
Ji Xue Teng
Zhi Mu
Qin JiaoWu Shao She
Ku ShenHuo Xue Teng
Qing Feng Teng
Pu Gong Ying
Lei Gong Teng
Huang Bai
Ren Dong Teng
(b)
Figure 2 The core intersection herb networks constructed fromMr Ji-Ren Lirsquos anti-RA herbal prescriptions (a) The herb subnet-works around each top frequent herb for example Huo Xue Teng(Sargentodoxa cuneata the top 2 herb) (b) The intersection herbnetwork created from the intersection herb networks of the top tenfrequent herbs Four herbs circled by the green line are a completeformula of Qing-Luo-Yin
of further study Note that other nonoverlapping GO termsassociated with herbs such as the steroid hormone receptorsignaling pathway also contributed a lot to the progressof RA [23] Moreover by pathway enrichment analysis wefurther found that both the RA genes and herb targetsare significantly enriched in the pathway of ldquorheumatoidarthritisrdquo (KEGG05323) (corrected 119875 = 155119890 minus 15 for RAgenes and 119875 = 283119890 minus 12 for herb targets resp) Figure 4shows the details of the network associations of RA genesandherb targets in theKEGGldquorheumatoid arthritisrdquo pathwayproviding additional evidence for the anti-RA effects of MrLirsquos herbal prescriptions These results suggest that the top15 frequent herbs have a potential to treat RA patients byintervening in the critical biological processes and pathway
Qing Feng Teng
Ku Shen
(a)
1
09
08
07
06
05
04
03
02
01
SinomenineDisinomenine
SinacutineAcutumineTuduranine
MagnoflorineIsosinomenine
MichelalbineBianfugenineStepharanine
Mat
rine
NIM
S sc
ore
Kura
rinon
eKu
rara
min
eBa
ptifo
line
Lehm
anin
eBe
ta-s
itoste
rol
Kush
enol
lCa
mph
orKo
sam
ol a
Gua
ijave
rin
Qin
g Fe
ng T
eng
Ku Shen
(b)
Figure 3 Calculation of synergistic activity among compoundscollected from the core herb networks (a) A part of the synergisticmodule from compounds of Qing Feng Teng (Caulis Sinomenii)and Ku Shen (Radix Sophorae flavescentis) (b) The horizontal andvertical axes show the compounds of herbs and the intervals ofaxis represent herbs The dark areas illustrate a modular featureand indicate strong synergistic interactions of herbs with highsynergistic scores calculated by the NIMS method
of RA which in turn gives evidence for the rationality of thecommonly prescribed herbs in Mr Lirsquos clinical practice
34 Network Connections of Anti-RA Herbs and Drugs InTCM RA patients can be categorized to different syndromes(ZHENG in Mandarin) for example Cold Syndrome andHot Syndrome Accordingly as shown in Table 1 Cold HotWarm Cool and Neutral are the basic properties of herbsreflecting the traditional characteristic of TCM TypicallyTCM doctors always use Cool or Cold herbs to treat patientswith Hot Syndrome whereas they use Warm or Hot herbsto treat patients with Cold Syndrome Cold-tendency andHot-tendency herbs may be combined to treat RA patientswith mixed Hot and Cold Syndromes On the other handin modern medicine immunomodulatory drugs such as
6 Evidence-Based Complementary and Alternative Medicine
Th17 cellTGF120573
Synovial macrophage
T cell receptor
Antigen
DC
Rheumatoid arthritis
CD8086
MHCII
IgGSDF1
VEGF
CCL2 CXCL1CXCL5CCL3
CCL20 Ang1IL8Tie2Flt1
AP1TLR24LPSPeptidoglycan
signaling pathwayToll-like receptor
Autoantibody production
B cell
APRIL
RANKL
CD28CTLA4
TCR
LFA1
ICAM1
IL15
IL6
Synovium
Bone
IL23
MCSF
RANKL
RANKL RANK
CTSKTRAP
CTSLMMP13 Joint destruction
Inflammation
Angiogenesis
Leukocyte migration
Blood vessel
VEGF signaling pathway
Inflammatory
Synovial pannus
Bone resorption
V-ATPase
Osteoblast
Osteoclast
Osteoclast
differentiation
Synovial fibroblast
PTHVitamin D3
IL11
IL17
IL1IL6
IL6
CCL5IL1120573
GMCSF
IL18
BLYS
Self-reactiveTh1 cell
signaling pathwayLT120573
IFN120574
TNF120572
PGE2
H+
cell infiltration
formation
Herb targetRA gene
Figure 4 Network association of RA genes and top 15 frequent herbsrsquo targets in the enriched KEGG ldquorheumatoid arthritisrdquo pathway (KEGG05323)
methotrexate and leflunomide [24 25] and hormones such asglucocorticoids (dexamethasone) [26 27] are two categoriesof medicines for the treatment of patients with rheumatoidarthritis [28] Both categories of medicines can improve thequality of life and delay the disease progression of RA patientsvia independent but interactivemechanism of actions By cal-culating compound networks from the top 50 frequent herbsin Mr Lirsquos prescriptions we obtained the herbs that containingredients similar to RA immunomodulatory drugs andhormones respectively As shown in Figure 5 many herbscontain compounds with targets connected to the selectedanti-RA drugs in the network and may exert similar actionson RA For example 9 out of top 10 herbs with differentproperties such as Cold and Hot (Table 1) have compoundsthat are closely clustered with RA immune and hormonedrugs in the network These results are meaningful sincerecent studies indicated that the metabolism and immuneimbalance are closely associated with patients suffering fromCold Syndrome and Hot Syndrome [29 30] in many diseasesincluding rheumatoid arthritis [31 32] Interestingly it isnoticed that the Cold herbs tend to be enriched in theimmune-herb cluster Hot herbs tend to be enriched inhormone-herb cluster and Warm herbs are enriched in bothclusters Moreover compared with the hormone-herb cluster(Figure 5(b)) the immune-herb cluster is less diverse andonly contains Cold and Warm herbs suggesting these herbstend to exert immunosuppressive or immunoenhancementactions (Figure 5(a)) Although the results are preliminary
the potential connection as well as combinational effectsbetween herbs and drugs is of great importance and deservesfurther investigation in larger samples and clinical or experi-mental studies
4 Conclusions
In summary we developed a TCM network pharmacologystrategy and an Herb-Compound-Target-Disease coherentnetwork analysis framework to study herbal prescriptionsthe main form of TCM clinical practice We extracted twotypes of core herb networks from871 anti-RAherbal formulaeprescribed by a famous TCM doctor From the core herb net-works our network-based strategy identified cooccurrenceherbs and herb pairs with potential synergistic activities Wealso predicted the biological basis of the core herb networkby calculating the compoundrsquos targets from most frequentherbs We detected that targets of the commonly prescribedherbs are enriched together with RA genes in critical bio-logical processes and pathway of RA We also indicated thatherbs with different properties in prescriptions may have apotential connection with RA immunomodulatory drugs orhormones in the compound networks Taken together theseresults could help uncover the prescription rules underlyingherbal formulae in the clinical practice of TCM practitionersMoreover such network-based analyses not only can developa holistic understanding of herbal remedies but also mayfacilitate the following pharmacological evaluation of herbal
Evidence-Based Complementary and Alternative Medicine 7
Ethylsalicylate
Hinesol
Campesterol
Taraxerone
AtractylenolideI
Leflunomide
Chen PiAngelicideBai
Shao
PaeonilactoneC
QiangHuo
Bai Zhu Albiflorin R1Sheng
DiHuang
ChiShao
Mai Ya
ManJing Zi Fang
Feng
KuShen
QingFengTeng
DangGui
Benzothiazole
Adrenocorticotropichormone
Folic acid
Chromone
Methotrexate
Lupenone
Dipterocarpol
Perrimustine
GuaiolIsofucosterol
120573-cryptoxanthin
Herb
Compound or drug
TengJi Xue
JiangHuang
DanShen
WuGong
HuangQi
ChuanXiong
3-Hydroxymugineicacid
Thiolproteaseinhibitor
Listomin S
Pseudocarpaine
Ciclosporin
Goitrin
Dihydro-2-methyl-3(2H)-furanone
Acetamide
Acetoin
Bornylacetate
Sophoranol
Tacrolimus
SandaracopimaricacidViridiflorol
Stigmasterin
Cholesterol
Ro 09-0680Phenylacetaldehyde
DAU 6215 hydrochloride
AC1L7QUY
Levamisolehydrochloride
Thalidomide
Mugineicacid
Benzoyl-dl-leucine
Ethanamine
Permanentorange
acid
Metarene
Laccase
AC1L7VXU
4-Hydroxymephenytoin
NSC673109
Procurcumenol Dehydrocurdione
Zeaxanthin
C09772
Olean-18-en-3-one
45-epoxide
100347-96-4
trans-Sabinenehydrate
CampheneVitamin D3
3-Oxo-1113(18)-oleanadien-28-oicacid
acid
6-Methylcholest-4-en-3-oneAspartylglucosamine
7-Dehydrostigmasterol
Cyclosporine
(4S5S)-(+)-germacrone
(5|A8|A9|A10|A16|A)-16-hydroxykauran-18-oic
(ZZ998400)-diligustilide
120575-terpineol
120573-sitosterol
51205729120572-dihydroxymatrine
2998400-Deoxymugineic
acetate
(a)
Apioglycyrrhizin
UralsaponinB
InflasaponinIV
InflasaponinI
Glycamil
Glycyrrhizicacid
ammoniumsalt
Glyuranolide
Glycyrrhizinicacid
AraboglycyrrhizinLiquoric acid
SophoraflavosideIV
GibberellinA1
CinncassiolA
Napellonine
CinncassiolC3
SophoraflavosideIII
Shanzhisidemethyl ester
Dexamethasone
Palbinone
Triamcinolone
LeiGongTeng
Ge Gen
WeiLingXian
QuanXie
RenDongTeng
Wu Tou
Fu Zi
Sang Ji Sheng
RuXiang
120572-boswellicacid
Rehmannicacid
Loganin
Tutin
acid
Loganic acid
NSC302037
Glycyrrhetinicacid
Prednisone
24-Hydroxyglycyrrheticacid
Corianin
3-Glc-soyasapogenolE
Glabric acidPaeonilactone
B
Cinncassiol E
Ecdysterone
Uralenolide
Asiatic acid
120573-glycyrrhetinicacid
Oleanolicacid
Geigerinin
CinncassiolC2
Tigogenin
Neotigogenin
GlycyrrhetolKatonic acid
Kihadanin A
Cortisone
Triptonide
Bufotoxin
Helixin
Inokosterone
Methylprednisolone
PrednisoloneTriptolideGibberellic
acidCaryoptoside
Triptolideanalog
Hydrocortisone
Gui Zhi
GanCao
XuDuan
Cold
Warm
Hormone drug
Immunomodulatory drug
Hot
Cool
Tu Fu LingHuang
Bai
Neutral
Niu Xi
Du Huo
Zhi Mu
Mu Gua
ShanZha
Pinnatifidin
(25S)-5120573-spirostan-3120573-ol
11-Keto-120573-boswellicacid
Acetyloleanolicacid
Corosolicacid
Boswellicacid
(5xi13|A14|A20s23r24s)-2324-dihydroxy-25-methoxylanost-7-en-3-one
(3|A20|A)-3-hydroxy-11-oxo-olean-12-en-29-oic
Herb
Compound or drug
(b)
Figure 5 Possible connection between RA herbs and drugs in the networks consisting of herbs herbal compounds immunomodulatorydrugs (a) and hormones (b)
8 Evidence-Based Complementary and Alternative Medicine
Table 2 Overlapped RA-related GO terms between top 15 herbtargets and RA genes
Category Enriched GO terms Corrected119875-value
Herbtargets
Response to wounding 238119890 minus 127
Angiogenesis 121119890 minus 26
Inflammatory response 860119890 minus 71
Regulation of cytokine production 612119890 minus 26
Immune response 261119890 minus 88
Leukocyte activation 341119890 minus 38
Regulation of lymphocyte activation 452119890 minus 23
Defense response to bacterium 356119890 minus 10
Positive regulation of NF-120581Btranscription factor activity 604119890 minus 12
RA genes
Response to wounding 148119890 minus 15
Angiogenesis 579119890 minus 6
Inflammatory response 576119890 minus 26
Regulation of cytokine production 165119890 minus 26
Immune response 629119890 minus 39
Leukocyte activation 728119890 minus 30
Regulation of lymphocyte activation 125119890 minus 31
Defense response to bacterium 727119890 minus 12
Positive regulation of NF-120581Btranscription factor activity 254119890 minus 6
treatments Clearly this study is only the first step to learnthe common rule of herbal prescriptions We will continueto conduct in-depth analysis for understanding the scientificbasis of herbal prescriptions in our future work Althoughmore powerful methods more data on TCM prescriptionsand clinical or experimental evaluations are still requiredwe believe that this TCM network pharmacology strategy issuitable to study herbal formulae both in the herb level andin the molecular level and thus can serve as a novel approachto further understand the professional experience embeddedin TCM prescriptions
Abbreviations
DMIM Distance-based mutual information modeldrugCIPHER Drug-target prediction by correlating
protein interaction network andphenotype network
GO Gene ontologyMI Mutual informationNIMS Network-based identification of
multicomponent synergyRA Rheumatoid arthritisPPI Protein-protein interactionQLY Qing-Luo-YinTCM Traditional Chinese Medicine
Conflict of Interests
The authors declare that they have no competing interests
Authorsrsquo Contribution
Shao Li conceived the study Yan Li collected the data Shao LiYan Li Rui Li and Zibo Ouyang analyzed the data and wrotethe paper All authors read and approved the final paper
Acknowledgments
Thanks to Kai Zhang for his help in herbal prescription col-lection This work is supported by NSFC project (81225025)the SATCM key discipline of ldquoTCM Bi-Bingrdquo in YijishanHospital of WannanMedical College the SATCM laboratoryof TCM master Ji-Ren Li the CATCM project and AnhuirsquosKey Technologies RampD project (11010402173)
References
[1] G G Zhang W Lee B Bausell L Lao B Handwerger andB Berman ldquoVariability in the traditional Chinese medicine(TCM) diagnoses and herbal prescriptions provided by threeTCM practitioners for 40 patients with rheumatoid arthritisrdquoJournal of Alternative and Complementary Medicine vol 11 no3 pp 415ndash421 2005
[2] G G Zhang B Singh W Lee B Handwerger L Lao and BBerman ldquoImprovement of agreement in TCMdiagnosis amongTCM practitioners for persons with the conventional diagnosisof rheumatoid arthritis effect of trainingrdquo Journal of Alternativeand Complementary Medicine vol 14 no 4 pp 381ndash386 2008
[3] P Zhang J Li Y Han X W Yu and L Qin ldquoTraditionalChinese medicine in the treatment of rheumatoid arthritis ageneral reviewrdquo Rheumatology International vol 30 no 6 pp713ndash718 2010
[4] Y Li 100 TCM Practitioners in Latest 100 Years Li Ji-ren ampZhang Shun-hua China Press of Traditional Chinese MedicineBeijing China 2004
[5] C Shu Z Li and Y Li ldquoGrand Master of TCM Ji-Ren Lirsquosexperience on the treatment of Bi Zhengrdquo Forum on TraditionalChinese Medicine vol 27 pp 10ndash12 2012
[6] S Li B Zhang D Jiang Y Wei and N Zhang ldquoHerbnetwork construction and co-module analysis for uncoveringthe combination rule of traditional Chinese herbal formulaerdquoBMC Bioinformatics vol 11 supplement 11 article S6 2010
[7] S Li B Zhang and N Zhang ldquoNetwork target for screeningsynergistic drug combinations with application to traditionalChinese medicinerdquo BMC Systems Biology vol 5 supplement 1p S10 2011
[8] S Zhao and S Li ldquoNetwork-based relating pharmacological andgenomic spaces for drug target identificationrdquo PLoS ONE vol5 no 7 Article ID e11764 2010
[9] X Liang H Li and S Li ldquoA novel network pharmacologyapproach to analyse traditional herbal formulae the Liu-Wei-Di-Huang pill as a case studyrdquoMolecular BioSystems vol 10 no5 pp 1014ndash1022 2014
[10] E L Leung Z-W Cao Z-H Jiang H Zhou and L LiuldquoNetwork-based drug discovery by integrating systems biologyand computational technologiesrdquo Briefings in Bioinformaticsvol 14 no 4 pp 491ndash505 2013
[11] V Sharma and I N Sarkar ldquoBioinformatics opportunitiesfor identification and study of medicinal plantsrdquo Briefings inBioinformatics vol 14 no 2 pp 238ndash250 2013
Evidence-Based Complementary and Alternative Medicine 9
[12] S Li and B Zhang ldquoTraditional Chinese medicine networkpharmacology theory methodology and applicationrdquo ChineseJournal of Natural Medicines vol 11 no 2 pp 110ndash120 2013
[13] M Ashburner C A Ball J A Blake et al ldquoGene ontology toolfor the unification of biologyrdquoNature Genetics vol 25 no 1 pp25ndash29 2000
[14] A P Davis B L King S Mockus et al ldquoThe comparativetoxicogenomics database update 2011rdquo Nucleic Acids Researchvol 39 no 1 pp D1067ndashD1072 2011
[15] D S Wishart C Knox A C Guo et al ldquoDrugBank a knowl-edgebase for drugs drug actions and drug targetsrdquoNucleic AcidsResearch vol 36 no 1 pp D901ndashD906 2008
[16] T S Keshava Prasad RGoel K Kandasamy et al ldquoHumanpro-tein reference databasemdash2009 updaterdquo Nucleic Acids Researchvol 37 no 1 pp D767ndashD772 2009
[17] B Zhang X Wang and S Li ldquoAn integrative platform of TCMnetwork pharmacology and its application on a herbal formulaQing-Luo-Yinrdquo Evidence-Based Complementary and AlternativeMedicine vol 2013 Article ID 456747 12 pages 2013
[18] A E Koch ldquoAngiogenesis implications for rheumatoid arthri-tisrdquo Arthritis amp Rheumatism vol 41 no 6 pp 951ndash962 1998
[19] M Feldmann F M Brennan and R N Maini ldquoRole ofcytokines in rheumatoid arthritisrdquo Annual Review of Immunol-ogy vol 14 pp 397ndash440 1996
[20] E H S Choy and G S Panayi ldquoCytokine pathways andjoint inflammation in rheumatoid arthritisrdquo The New EnglandJournal of Medicine vol 344 no 12 pp 907ndash916 2001
[21] G Janossy G Panayi O Duke M Bofill L W Poulterand G Goldstein ldquoRheumatoid arthritis a disease of T-lymphocytemacrophage immunoregulationrdquo The Lancet vol2 no 8251 pp 839ndash842 1981
[22] S S Makarov ldquoNF-120581B in rheumatoid arthritis a pivotal reg-ulator of inflammation hyperplasia and tissue destructionrdquoArthritis Research vol 3 no 4 pp 200ndash206 2001
[23] M Cutolo A Sulli B Villaggio B Seriolo and S AccardoldquoRelations between steroid hormones and cytokines in rheuma-toid arthritis and systemic lupus erythematosusrdquo Annals of theRheumatic Diseases vol 57 no 10 pp 573ndash577 1998
[24] P E Lipsky D M van der Heijde E W St Clair et al ldquoAnti-TumorNecrosis Factor Trial in RheumatoidArthritis with Con-comitant Therapy Study Group Infliximab and methotrexatein the treatment of rheumatoid arthritis Anti-Tumor NecrosisFactor Trial in Rheumatoid Arthritis with Concomitant Ther-apy Study Grouprdquo The New England Journal of Medicine vol343 no 22 pp 1594ndash1602 2000
[25] V Strand S Cohen M Schiff et al ldquoTreatment of activerheumatoid arthritis with leflunomide compared with placeboand methotrexate Leflunomide Rheumatoid Arthritis Investi-gators Grouprdquo Archives of Internal Medicine vol 159 no 21 pp2542ndash2550 1999
[26] J R Kirwan ldquoThe effect of glucocorticoids on joint destructionin rheumatoid arthritisrdquoThe New England Journal of Medicinevol 333 no 3 pp 142ndash146 1995
[27] S R de Antonio H M Blotta R L Mamoni et al ldquoEffects ofdexamethasone on lymphocyte proliferation and cytokine pro-duction in rheumatoid arthritisrdquoThe Journal of Rheumatologyvol 29 no 1 pp 46ndash51 2002
[28] J R OrsquoDell ldquoTherapeutic strategies for rheumatoid arthritisrdquoTheNew England Journal of Medicine vol 350 no 25 pp 2591ndash2602 2004
[29] S Li Z Q Zhang L JWu X G Zhang Y D Li andY YWangldquoUnderstanding ZHENG in traditional Chinese medicine inthe context of neuro-endocrine-immune networkrdquo IET SystemsBiology vol 1 no 1 pp 51ndash60 2007
[30] R Li T Ma J Gu X Liang and S Li ldquoImbalanced networkbiomarkers for traditional Chinese medicine Syndrome ingastritis patientsrdquo Scientific Reports vol 3 article 1543 2013
[31] G Chen C Lu Q Zha et al ldquoA network-based analysis oftraditional Chinese medicine cold and hot patterns in rheuma-toid arthritisrdquo Complementary Therapies in Medicine vol 20no 1-2 pp 23ndash30 2012
[32] H A van Wietmarschen W Dai A J van der Kooij et alldquoCharacterization of rheumatoid arthritis subtypes using symp-tom profiles clinical chemistry and metabolomics measure-mentsrdquo PLoS ONE vol 7 no 9 Article ID e44331 2012
Submit your manuscripts athttpwwwhindawicom
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Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
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Disease Markers
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OncologyJournal of
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Oxidative Medicine and Cellular Longevity
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Parkinsonrsquos Disease
Evidence-Based Complementary and Alternative Medicine
Volume 2014Hindawi Publishing Corporationhttpwwwhindawicom
2 Evidence-Based Complementary and Alternative Medicine
TCMpractitioners specifically tailored to individual patientsTCM doctors treat patients mainly based on syndrome dif-ferentiation For different patients various herbs are groupedand different formulae are prescribed This tradition andfeature make TCM a kind of personalized medicine andcause great difficulty in designing standard protocols suchas the randomized controlled trial in TCM studies Thelack of appropriate methods to analyze the rule as well asscientific basis for TCM-doctor-prescribed herbal formulaeis therefore one of the major frustrations to find clinicalevidence of TCM How to study the characteristics andprescription rule of such flexible TCM formulae is still a greatchallenge and requires widely interdisciplinary efforts
Thanks to the rapid progress of bioinformatics especiallycomplex network theory and technologies recently thenetwork approach has become a new avenue and powerfultool to handle intricate problems such as those in TCMWe have been making efforts to build a TCM networkpharmacology approach over ten years and established aset of network-based methods for TCM study [6ndash9] Forexample to reveal the combination rule and the biologicalbasis of herbal formulae we proposed a global networkanalysis framework consisting of herbcompound networkbiological network (gene protein or target network) anddisease network Several methods are also created suchas a distance-based mutual information model (DMIM)that can identify herb relationships from numerous herbalformulae The good performance of the DMIM method touncover the herbal combination rules has been illustrated inboth 3865 collaterals-related herbal formulae and a classicLiu-Wei-Di-Huang formula [6] Furthermore we proposeda novel concept of ldquonetwork targetrdquo [7] which treats adisease-specific molecular network as a therapeutic targetto help design suitable medical treatments Several methodsfor the network target analysis especially the disease geneprediction target prediction for drugs or herbal compounds[8] the network comodule analysis for drug discovery andthe network-based prioritization of synergistic combinations[7] are developed subsequently These methods have beenapplied in finding bioactive compounds and revealing themechanism of action for herbal formulae including Liu-Wei-Di-Huang pill [9] Now the network-based method inthe context of TCM network pharmacology has become aburgeoning field in the modern studies of TCM [10ndash12] Webelieve the network-based strategy and approaches can alsoprovide good solutions for the herbal prescription analysis
In this work 871 herbal prescriptions from Mr Ji-Ren Lirsquos clinical treatment on patients with rheumatoidarthritis were analyzed from a network point of view TCMnetwork pharmacology methods were employed to detectthe common rules and potential biological basis of theseherbal prescriptions This work is promising as the resultsnicely show the rationality and validity of Mr Lirsquos herbalprescriptions Moreover this work provides a new route tointerpret the professional experience embedded in numerousand precious TCM herbal prescriptions
Herbal prescriptions
Herbnetwork
Compound network
Herb name normalization
Herb relationship byDMIM scoring
Herb compoundcollection
Target prediction by drugCIPHER
Connect compound by target interaction
Disease gene network
Evaluation of synergistic activity by NIMS
Figure 1 The Herb-Compound-Target-Disease coherent networkanalysis framework for studying herbal prescriptions on the treat-ment of certain diseases
2 Methods
21 Herbal Formulae and Herbal Compounds A total of 871herbal prescriptions from Mr Ji-Ren Li in the individuallyclinical treatment of RA patients from 2005 to 2013 were usedin this work The 871 herbal prescriptions were normalizedby substituting the polysemes synonyms and acronyms ofthe herbs in the dataset and resulted in a standardized HerbName list Each formula contains 15 to 29 herbs and the aver-age number is 18 Compounds of herbs were gathered fromthe HerbBioMap database (China Copyright of ComputerSoftware 2011SR076502)TheHerbBioMapdatabase contains10806 compounds for 539 herbs up to now
22 Multilayer Coherent Network Analysis for Herbal Pre-scriptions As shown in Figure 1 we proposed an Herb-Compound-Target-Disease coherent network analysis frame-work to study the prescription rules and potential biologicalbasis for herbal prescriptionsThe principle steps are summa-rized as follows
Herb Network Construction We created a matrix of 871dimensions to represent all collected herbal formulae andthen calculated the frequency of every 343 herbs in allformulae and gave a normalized frequency (NF) NF =AFsum119873
119899=1AF1 where AF is accumulated frequency and 119873
denotes 343-herb species number Next most frequent herbsin 871 herbal prescriptions were selected and subjected tothe DMIM (distance-basedmutual informationmodel) anal-ysis an algorithm for identifying herb relationships amongdifferent formulae and uncovering the combinational rulesof herbs in a network manner [6] The DMIM model isan integrated scoring system combining the mutual infor-mation (MI) entropy characteristics and the ldquobetween-herbdistancerdquo (119889) between herbs by calculating score(119909 119910) =MI(119909 119910)119889(119909 119910) which describes the tendency of herb 119909 and
Evidence-Based Complementary and Alternative Medicine 3
herb 119910 to form an herb pair More importantly the DMIMmodel extracts information from the organization of Jun-Chen-Zuo-Shi (Master-Adviser-Soldier-Guide) herbs in anherbal formula based on which a new parameter ldquobetween-herb distancerdquowas created thatmeans the further the distancebetween two herbs in a formula is the less likely they are tobe relevant to one anotherThus DMIM is suitable to retrieveherb combinational rules achieving a good balance amongthe herbrsquos frequency independence and distance in herbalformulae [6]
Target Prediction for Herbal Compounds and Herbs In thepresent study drugCIPHER a method we developed previ-ously [8] is used to predict the target profile for all availablecompounds collected from each herb in the core herbnetworks drugCIPHER is a regressionmodel that can predictthe links between drugs and target proteins in a genome-wide scale by correlating the drug chemical informationand protein-protein interaction (PPI) from a heterogeneousnetwork By integrating and making full use of all currentFDA-approved drug structures drug-target interactions andhuman protein-protein interactions drugCIPHER can out-put a target profile for any given compound with knownstructure that is calculated from the correlation between thequery ingredientrsquos structure similarity vector in the drugspace and the target-related genersquos closeness vector in thetarget space As the top 100 targets predicted by drugCIPHERcan reach the high prediction accuracy (773) [8] here thetop 100 target profiles predicted for each compound wereselected and the target profiles of all collected compoundswithin a herb were combined to form integrative targetprofiles of this herb The target prediction procedure wasconducted for herbs present in the core herb networks orinvolved in the following studies
Evaluation of Synergistic Actions forHerbNetwork To identifythe potential synergistic effects of herb combinations in thecore herb network at the molecular level and in a highthroughput way we used the network-based identificationof multicomponent synergy (NIMS) method [7] a novelapproach to access the synergistic strength of any combina-tion of herbal compounds by determining their target inter-actions in the protein-protein network The NIMS algorithmconsists of two components topology score and agent scoreThe topology score is generated from the topological featuresof the background network related to disease condition anddrug actions while the agent score is based on the similarityof agent phenotypes Two graph-based measures between-ness and closeness were used to capture the associationsamong targets and the other measure PageRank to verifythe node importance [7] The resulted synergy score is usedto prioritize the synergistic effect of combinations of agentsincluding herbs or herbal compounds
Gene Ontology (GO) and Pathway Analysis for Herb Targetsand RAGenesThe targets of each compound in the top herbswere predicted using drugCIPHER For each compound ofthe top herbs the top 100 proteins were treated as targetsfor the given compound The targets hit by more than five
compounds within an herb were considered herb targets Top15 frequent herbsrsquo targets were subjected to the gene ontology[13] and pathway enrichment analysis One the other handthe 129 RA-related genes with a direct mechanism relation-ship to rheumatoid arthritis were collected from the CTDdatabase [14] For functional analysis we used the ldquoSet Ana-lyzerrdquo tool at the CTD site (httpctdbaseorgtoolsanalyzergo) to analyze the enriched GO terms as well as KEGGpathways for herb targets and RA genes respectively withcorrected 119875 value less than 005 We also mapped the RAgenes and herb targets in the enriched KEGG pathwaynetwork
Compound Network Analysis for Anti-RA Herbs and DrugsFor comparison of the herbal prescriptions and the Westernanti-RA drugs we collected the commonly used anti-RAdrugs and their targets from the DrugBank database [15]Nine immunomodulatory drugs and 7 hormones were selec-ted The immunomodulatory drugs include methotrexateleflunomide ciclosporin thalidomide cyclophosphamideazathioprine mycophenolate mofetil tacrolimus and cyclo-sporine Hormones include dexamethasone hydrocortisonecortisone triamcinolone prednisolone prednisone andmethylprednisolone Based on the targets of each compoundcontained by the top 50 frequent herbs the closeness ofherb compoundrsquos targets and targets of immunomodulatorydrugs and hormones on the RA-related gene network thatconnected by PPI interactions (HPRD Release 7) [16] weremeasuredThe compoundnetworks are then formed inwhichtwo compounds (or drugs) will be linked if their targetsare overlapped or directly connected in the network Herewe paid more attention on the relationship between herbalcompounds with ColdHot property and two types of RAdrugs
3 Results and Discussion
31 Core Herb Networks from Herbal Prescriptions 343 herbswere uniquely identified from all 871 prescriptions ByDMIMscoring [6] we obtained frequently used herbs as well as theircombinations from all available prescriptions with Ji XueTeng as the most frequently used herb The top 15 herbs inMr Lirsquos anti-RA herbal prescription are shown in Table 1 Wecan see that although the prescriptions are written out indi-vidually to patients the commonly used herbs with differentproperties are considered to be the most representative ofthe available herbal prescriptions Therefore to capture thecommon rule of herbal prescriptions here we focused onthe most frequent herbs for the subsequent network analysisThenwe conducted the herb network analysis for these herbalprescriptions A node in herb network refers to an herb andan edge connecting two nodes refers to the two significantcooccurrent herbs in herbal prescriptions By using DMIMscore to evaluate the significance of the edge we constructedtwo types of the core herb networks namely the high-frequency herb network and the intersection herb networkfor Mr Lirsquos 871 prescriptions
For the high-frequency network only the top frequentherbs were treated as nodes and the cooccurrence herbs
4 Evidence-Based Complementary and Alternative Medicine
Table 1 Top 15 herbs in Mr Ji-Ren Lirsquos antirheumatoid arthritis herbal prescriptions
Chinese name Latin name Property Frequency Normalized frequencyJi Xue Teng Millettia reticulata Benth Warm 503 510Huo Xue Teng Sargentodoxa cuneata Neutral 499 506Huang Qi Astragalus membranaceus (Fisch) Bunge Warm 481 487Dang Gui Radix Angelicae sinensis Warm 430 436Quan Xie Scorpio Neutral 399 404Qing Feng Teng Caulis Sinomenii Neutral 396 401Ku Shen Radix Sophorae flavescentis Cold 323 327Wu Tou Aconitum carmichaeli Debx Hot 306 310Wu Gong Scolopendra Warm 287 291Huang Bai Cortex Phellodendri Cold 283 287Bi Xie Rhizoma Dioscoreae Hypoglaucae Neutral 280 284Ren Dong Teng Caulis Lonicerae Cool 257 260Qin Jiao Radix Gentianae macrophyllae Cold 254 257Wu Shao She Zaocys dhumnades Neutral 235 238Pu Gong Ying Taraxacum mongolicumHand-Mazz Cold 227 230
in herbal prescriptions identified by DMIM were treated asedges For example we found that the top 10 frequent herbswith 45 edges are closely interrelatedwith each other formingalmost all connected graphs Among them Ji Xue Teng andHuang Qi (DMIM score = 18627) Huo Xue Teng and Ji XueTeng (DMIM score = 16517) have the highest DMIM scoresThis result suggests that the top 10 herbs are always prescribedin pairs in Mr Lirsquos practice for RA treatment
For the intersection herb network we built every subnet-work by DMIM for each of the top frequent herbs and thenintersected the subnetworks to construct a core networkFor example Figure 2(a) shows the subnetwork around thetop 2 herb Huo Xue Teng (Sargentodoxa cuneata) The topten frequent herb subnetworks contained 21 to 35 nodes and100 to 200 edges and the resulted core intersection networkhas 14 nodes and 29 edges (Figure 2(b)) Interestingly acomplete formula of Mr Li Qing-Luo-Yin [17] is present inthis network
Herbs and herb combinations present in these two typesof herb networks may play a central role in Mr Lirsquos herbalprescriptions for the treatment of RA
32 Potential Synergistic Activities Underlying Core Herb Net-works Taking the core herb networks as examples we fur-ther performed the network target analysis to computation-ally determine whether the DMIM extracted herb networksdisplayed synergistic effects In this step we collected avail-able compounds for the core herb networks identified fromMr Lirsquos prescriptions The target profile of each compoundwas predicted by the drugCIPHER method [8] Then weselected top 100 targets of compounds assembled in eachherb to analyze the synergistic activity by evaluating the tar-get interactions in the protein-protein interaction networkWhen drugCIPHER [8] and NIMS [7] (see Section 2) areapplied to the herb networks we can obviously detect themodular property in themolecular level that denotes the syn-ergistic relationship in the core herb networks (Figure 3(a))From the outputs of the NIMS score we found that in
an herb network not all herbs interact strongly Instead onlycertain herbs or even certain herbal compounds produceclear synergistic effects For example in the high-frequencyherb network Ji Xue Teng and Huo Xue Teng (average NIMSscore = 084) Ku Shen and Qing Feng Teng (average NIMSscore = 057) Ku Shen and Ji Xue Teng (average NIMS score= 04) and Huo Xue Teng and Qing Feng Teng (averageNIMS score = 031) each of the two herbs has a relativelyhigh NIMS score and tends to produce synergistic activity indifferent levels In the intersection herb network the mainconstituent of TCM herbal formulae Qing-Luo-Yin (QLY)also has a good NIMS score A part of the synergistic modulefromQing Feng Teng and Ku Shen was shown in Figure 3(b)This figure further illustrated that different compounds inan herb pair obtained diverse synergistic scores Amongthem the combination of compounds such as Sinomenineand Matrine achieves a relatively high score which agreeswith the previously experimental results on the synergisticeffects in QLY [17] Thus we demonstrate here that thesynergistic effects of herb components may be contributed tothe modular property of the herb network as well as herbalprescriptions
33 Biological Associations between Herb Targets and RAGenes Since the targets of each compound of herbs areavailable by drugCIPHER we further verify the effectivenessof the top 15 frequent herbs in Mr Lirsquos prescriptions (Table 1)by evaluating the herbal compoundsrsquo targets and theirrelationship with RA genes in terms of the GO biologicalprocesses and pathways As shown in Table 2 there are RA-related GO terms resulting from targets of the top 15 herbswhich were also enriched with 129 RA-related genes formthe CTD database For example the overlapped GO termswhich resulted from both herb targets and RA genes includeangiogenesis [18] cytokine production [19] inflammatoryresponse [20] lymphocyte activation [21] and NF-120581B tran-scription factor activity [22] The overlapped GO terms alsoinclude ldquodefense response to bacteriumrdquo which is worthy
Evidence-Based Complementary and Alternative Medicine 5
Lian Qiao
Hu Zhang Dai MaoRou Gui
Ku Shen
Bi Xie
Wu Shao She
Qin Jiao
Man Jing Zi
Han Lian Cao
Chai Hu
Wu Wei Zi
Bai Mao Gen
Wei Ling Xian
Qing Feng Teng
Zhi Mu
Wu Tou
Huo Xue Teng
Lei Gong Teng
Huang Bai
Ji XueTengHuang Qi
Pu Gong Ying
Ren Dong Teng
(a)
Man Jing Zi
Wu Tou
Bi Xie
Ji Xue Teng
Zhi Mu
Qin JiaoWu Shao She
Ku ShenHuo Xue Teng
Qing Feng Teng
Pu Gong Ying
Lei Gong Teng
Huang Bai
Ren Dong Teng
(b)
Figure 2 The core intersection herb networks constructed fromMr Ji-Ren Lirsquos anti-RA herbal prescriptions (a) The herb subnet-works around each top frequent herb for example Huo Xue Teng(Sargentodoxa cuneata the top 2 herb) (b) The intersection herbnetwork created from the intersection herb networks of the top tenfrequent herbs Four herbs circled by the green line are a completeformula of Qing-Luo-Yin
of further study Note that other nonoverlapping GO termsassociated with herbs such as the steroid hormone receptorsignaling pathway also contributed a lot to the progressof RA [23] Moreover by pathway enrichment analysis wefurther found that both the RA genes and herb targetsare significantly enriched in the pathway of ldquorheumatoidarthritisrdquo (KEGG05323) (corrected 119875 = 155119890 minus 15 for RAgenes and 119875 = 283119890 minus 12 for herb targets resp) Figure 4shows the details of the network associations of RA genesandherb targets in theKEGGldquorheumatoid arthritisrdquo pathwayproviding additional evidence for the anti-RA effects of MrLirsquos herbal prescriptions These results suggest that the top15 frequent herbs have a potential to treat RA patients byintervening in the critical biological processes and pathway
Qing Feng Teng
Ku Shen
(a)
1
09
08
07
06
05
04
03
02
01
SinomenineDisinomenine
SinacutineAcutumineTuduranine
MagnoflorineIsosinomenine
MichelalbineBianfugenineStepharanine
Mat
rine
NIM
S sc
ore
Kura
rinon
eKu
rara
min
eBa
ptifo
line
Lehm
anin
eBe
ta-s
itoste
rol
Kush
enol
lCa
mph
orKo
sam
ol a
Gua
ijave
rin
Qin
g Fe
ng T
eng
Ku Shen
(b)
Figure 3 Calculation of synergistic activity among compoundscollected from the core herb networks (a) A part of the synergisticmodule from compounds of Qing Feng Teng (Caulis Sinomenii)and Ku Shen (Radix Sophorae flavescentis) (b) The horizontal andvertical axes show the compounds of herbs and the intervals ofaxis represent herbs The dark areas illustrate a modular featureand indicate strong synergistic interactions of herbs with highsynergistic scores calculated by the NIMS method
of RA which in turn gives evidence for the rationality of thecommonly prescribed herbs in Mr Lirsquos clinical practice
34 Network Connections of Anti-RA Herbs and Drugs InTCM RA patients can be categorized to different syndromes(ZHENG in Mandarin) for example Cold Syndrome andHot Syndrome Accordingly as shown in Table 1 Cold HotWarm Cool and Neutral are the basic properties of herbsreflecting the traditional characteristic of TCM TypicallyTCM doctors always use Cool or Cold herbs to treat patientswith Hot Syndrome whereas they use Warm or Hot herbsto treat patients with Cold Syndrome Cold-tendency andHot-tendency herbs may be combined to treat RA patientswith mixed Hot and Cold Syndromes On the other handin modern medicine immunomodulatory drugs such as
6 Evidence-Based Complementary and Alternative Medicine
Th17 cellTGF120573
Synovial macrophage
T cell receptor
Antigen
DC
Rheumatoid arthritis
CD8086
MHCII
IgGSDF1
VEGF
CCL2 CXCL1CXCL5CCL3
CCL20 Ang1IL8Tie2Flt1
AP1TLR24LPSPeptidoglycan
signaling pathwayToll-like receptor
Autoantibody production
B cell
APRIL
RANKL
CD28CTLA4
TCR
LFA1
ICAM1
IL15
IL6
Synovium
Bone
IL23
MCSF
RANKL
RANKL RANK
CTSKTRAP
CTSLMMP13 Joint destruction
Inflammation
Angiogenesis
Leukocyte migration
Blood vessel
VEGF signaling pathway
Inflammatory
Synovial pannus
Bone resorption
V-ATPase
Osteoblast
Osteoclast
Osteoclast
differentiation
Synovial fibroblast
PTHVitamin D3
IL11
IL17
IL1IL6
IL6
CCL5IL1120573
GMCSF
IL18
BLYS
Self-reactiveTh1 cell
signaling pathwayLT120573
IFN120574
TNF120572
PGE2
H+
cell infiltration
formation
Herb targetRA gene
Figure 4 Network association of RA genes and top 15 frequent herbsrsquo targets in the enriched KEGG ldquorheumatoid arthritisrdquo pathway (KEGG05323)
methotrexate and leflunomide [24 25] and hormones such asglucocorticoids (dexamethasone) [26 27] are two categoriesof medicines for the treatment of patients with rheumatoidarthritis [28] Both categories of medicines can improve thequality of life and delay the disease progression of RA patientsvia independent but interactivemechanism of actions By cal-culating compound networks from the top 50 frequent herbsin Mr Lirsquos prescriptions we obtained the herbs that containingredients similar to RA immunomodulatory drugs andhormones respectively As shown in Figure 5 many herbscontain compounds with targets connected to the selectedanti-RA drugs in the network and may exert similar actionson RA For example 9 out of top 10 herbs with differentproperties such as Cold and Hot (Table 1) have compoundsthat are closely clustered with RA immune and hormonedrugs in the network These results are meaningful sincerecent studies indicated that the metabolism and immuneimbalance are closely associated with patients suffering fromCold Syndrome and Hot Syndrome [29 30] in many diseasesincluding rheumatoid arthritis [31 32] Interestingly it isnoticed that the Cold herbs tend to be enriched in theimmune-herb cluster Hot herbs tend to be enriched inhormone-herb cluster and Warm herbs are enriched in bothclusters Moreover compared with the hormone-herb cluster(Figure 5(b)) the immune-herb cluster is less diverse andonly contains Cold and Warm herbs suggesting these herbstend to exert immunosuppressive or immunoenhancementactions (Figure 5(a)) Although the results are preliminary
the potential connection as well as combinational effectsbetween herbs and drugs is of great importance and deservesfurther investigation in larger samples and clinical or experi-mental studies
4 Conclusions
In summary we developed a TCM network pharmacologystrategy and an Herb-Compound-Target-Disease coherentnetwork analysis framework to study herbal prescriptionsthe main form of TCM clinical practice We extracted twotypes of core herb networks from871 anti-RAherbal formulaeprescribed by a famous TCM doctor From the core herb net-works our network-based strategy identified cooccurrenceherbs and herb pairs with potential synergistic activities Wealso predicted the biological basis of the core herb networkby calculating the compoundrsquos targets from most frequentherbs We detected that targets of the commonly prescribedherbs are enriched together with RA genes in critical bio-logical processes and pathway of RA We also indicated thatherbs with different properties in prescriptions may have apotential connection with RA immunomodulatory drugs orhormones in the compound networks Taken together theseresults could help uncover the prescription rules underlyingherbal formulae in the clinical practice of TCM practitionersMoreover such network-based analyses not only can developa holistic understanding of herbal remedies but also mayfacilitate the following pharmacological evaluation of herbal
Evidence-Based Complementary and Alternative Medicine 7
Ethylsalicylate
Hinesol
Campesterol
Taraxerone
AtractylenolideI
Leflunomide
Chen PiAngelicideBai
Shao
PaeonilactoneC
QiangHuo
Bai Zhu Albiflorin R1Sheng
DiHuang
ChiShao
Mai Ya
ManJing Zi Fang
Feng
KuShen
QingFengTeng
DangGui
Benzothiazole
Adrenocorticotropichormone
Folic acid
Chromone
Methotrexate
Lupenone
Dipterocarpol
Perrimustine
GuaiolIsofucosterol
120573-cryptoxanthin
Herb
Compound or drug
TengJi Xue
JiangHuang
DanShen
WuGong
HuangQi
ChuanXiong
3-Hydroxymugineicacid
Thiolproteaseinhibitor
Listomin S
Pseudocarpaine
Ciclosporin
Goitrin
Dihydro-2-methyl-3(2H)-furanone
Acetamide
Acetoin
Bornylacetate
Sophoranol
Tacrolimus
SandaracopimaricacidViridiflorol
Stigmasterin
Cholesterol
Ro 09-0680Phenylacetaldehyde
DAU 6215 hydrochloride
AC1L7QUY
Levamisolehydrochloride
Thalidomide
Mugineicacid
Benzoyl-dl-leucine
Ethanamine
Permanentorange
acid
Metarene
Laccase
AC1L7VXU
4-Hydroxymephenytoin
NSC673109
Procurcumenol Dehydrocurdione
Zeaxanthin
C09772
Olean-18-en-3-one
45-epoxide
100347-96-4
trans-Sabinenehydrate
CampheneVitamin D3
3-Oxo-1113(18)-oleanadien-28-oicacid
acid
6-Methylcholest-4-en-3-oneAspartylglucosamine
7-Dehydrostigmasterol
Cyclosporine
(4S5S)-(+)-germacrone
(5|A8|A9|A10|A16|A)-16-hydroxykauran-18-oic
(ZZ998400)-diligustilide
120575-terpineol
120573-sitosterol
51205729120572-dihydroxymatrine
2998400-Deoxymugineic
acetate
(a)
Apioglycyrrhizin
UralsaponinB
InflasaponinIV
InflasaponinI
Glycamil
Glycyrrhizicacid
ammoniumsalt
Glyuranolide
Glycyrrhizinicacid
AraboglycyrrhizinLiquoric acid
SophoraflavosideIV
GibberellinA1
CinncassiolA
Napellonine
CinncassiolC3
SophoraflavosideIII
Shanzhisidemethyl ester
Dexamethasone
Palbinone
Triamcinolone
LeiGongTeng
Ge Gen
WeiLingXian
QuanXie
RenDongTeng
Wu Tou
Fu Zi
Sang Ji Sheng
RuXiang
120572-boswellicacid
Rehmannicacid
Loganin
Tutin
acid
Loganic acid
NSC302037
Glycyrrhetinicacid
Prednisone
24-Hydroxyglycyrrheticacid
Corianin
3-Glc-soyasapogenolE
Glabric acidPaeonilactone
B
Cinncassiol E
Ecdysterone
Uralenolide
Asiatic acid
120573-glycyrrhetinicacid
Oleanolicacid
Geigerinin
CinncassiolC2
Tigogenin
Neotigogenin
GlycyrrhetolKatonic acid
Kihadanin A
Cortisone
Triptonide
Bufotoxin
Helixin
Inokosterone
Methylprednisolone
PrednisoloneTriptolideGibberellic
acidCaryoptoside
Triptolideanalog
Hydrocortisone
Gui Zhi
GanCao
XuDuan
Cold
Warm
Hormone drug
Immunomodulatory drug
Hot
Cool
Tu Fu LingHuang
Bai
Neutral
Niu Xi
Du Huo
Zhi Mu
Mu Gua
ShanZha
Pinnatifidin
(25S)-5120573-spirostan-3120573-ol
11-Keto-120573-boswellicacid
Acetyloleanolicacid
Corosolicacid
Boswellicacid
(5xi13|A14|A20s23r24s)-2324-dihydroxy-25-methoxylanost-7-en-3-one
(3|A20|A)-3-hydroxy-11-oxo-olean-12-en-29-oic
Herb
Compound or drug
(b)
Figure 5 Possible connection between RA herbs and drugs in the networks consisting of herbs herbal compounds immunomodulatorydrugs (a) and hormones (b)
8 Evidence-Based Complementary and Alternative Medicine
Table 2 Overlapped RA-related GO terms between top 15 herbtargets and RA genes
Category Enriched GO terms Corrected119875-value
Herbtargets
Response to wounding 238119890 minus 127
Angiogenesis 121119890 minus 26
Inflammatory response 860119890 minus 71
Regulation of cytokine production 612119890 minus 26
Immune response 261119890 minus 88
Leukocyte activation 341119890 minus 38
Regulation of lymphocyte activation 452119890 minus 23
Defense response to bacterium 356119890 minus 10
Positive regulation of NF-120581Btranscription factor activity 604119890 minus 12
RA genes
Response to wounding 148119890 minus 15
Angiogenesis 579119890 minus 6
Inflammatory response 576119890 minus 26
Regulation of cytokine production 165119890 minus 26
Immune response 629119890 minus 39
Leukocyte activation 728119890 minus 30
Regulation of lymphocyte activation 125119890 minus 31
Defense response to bacterium 727119890 minus 12
Positive regulation of NF-120581Btranscription factor activity 254119890 minus 6
treatments Clearly this study is only the first step to learnthe common rule of herbal prescriptions We will continueto conduct in-depth analysis for understanding the scientificbasis of herbal prescriptions in our future work Althoughmore powerful methods more data on TCM prescriptionsand clinical or experimental evaluations are still requiredwe believe that this TCM network pharmacology strategy issuitable to study herbal formulae both in the herb level andin the molecular level and thus can serve as a novel approachto further understand the professional experience embeddedin TCM prescriptions
Abbreviations
DMIM Distance-based mutual information modeldrugCIPHER Drug-target prediction by correlating
protein interaction network andphenotype network
GO Gene ontologyMI Mutual informationNIMS Network-based identification of
multicomponent synergyRA Rheumatoid arthritisPPI Protein-protein interactionQLY Qing-Luo-YinTCM Traditional Chinese Medicine
Conflict of Interests
The authors declare that they have no competing interests
Authorsrsquo Contribution
Shao Li conceived the study Yan Li collected the data Shao LiYan Li Rui Li and Zibo Ouyang analyzed the data and wrotethe paper All authors read and approved the final paper
Acknowledgments
Thanks to Kai Zhang for his help in herbal prescription col-lection This work is supported by NSFC project (81225025)the SATCM key discipline of ldquoTCM Bi-Bingrdquo in YijishanHospital of WannanMedical College the SATCM laboratoryof TCM master Ji-Ren Li the CATCM project and AnhuirsquosKey Technologies RampD project (11010402173)
References
[1] G G Zhang W Lee B Bausell L Lao B Handwerger andB Berman ldquoVariability in the traditional Chinese medicine(TCM) diagnoses and herbal prescriptions provided by threeTCM practitioners for 40 patients with rheumatoid arthritisrdquoJournal of Alternative and Complementary Medicine vol 11 no3 pp 415ndash421 2005
[2] G G Zhang B Singh W Lee B Handwerger L Lao and BBerman ldquoImprovement of agreement in TCMdiagnosis amongTCM practitioners for persons with the conventional diagnosisof rheumatoid arthritis effect of trainingrdquo Journal of Alternativeand Complementary Medicine vol 14 no 4 pp 381ndash386 2008
[3] P Zhang J Li Y Han X W Yu and L Qin ldquoTraditionalChinese medicine in the treatment of rheumatoid arthritis ageneral reviewrdquo Rheumatology International vol 30 no 6 pp713ndash718 2010
[4] Y Li 100 TCM Practitioners in Latest 100 Years Li Ji-ren ampZhang Shun-hua China Press of Traditional Chinese MedicineBeijing China 2004
[5] C Shu Z Li and Y Li ldquoGrand Master of TCM Ji-Ren Lirsquosexperience on the treatment of Bi Zhengrdquo Forum on TraditionalChinese Medicine vol 27 pp 10ndash12 2012
[6] S Li B Zhang D Jiang Y Wei and N Zhang ldquoHerbnetwork construction and co-module analysis for uncoveringthe combination rule of traditional Chinese herbal formulaerdquoBMC Bioinformatics vol 11 supplement 11 article S6 2010
[7] S Li B Zhang and N Zhang ldquoNetwork target for screeningsynergistic drug combinations with application to traditionalChinese medicinerdquo BMC Systems Biology vol 5 supplement 1p S10 2011
[8] S Zhao and S Li ldquoNetwork-based relating pharmacological andgenomic spaces for drug target identificationrdquo PLoS ONE vol5 no 7 Article ID e11764 2010
[9] X Liang H Li and S Li ldquoA novel network pharmacologyapproach to analyse traditional herbal formulae the Liu-Wei-Di-Huang pill as a case studyrdquoMolecular BioSystems vol 10 no5 pp 1014ndash1022 2014
[10] E L Leung Z-W Cao Z-H Jiang H Zhou and L LiuldquoNetwork-based drug discovery by integrating systems biologyand computational technologiesrdquo Briefings in Bioinformaticsvol 14 no 4 pp 491ndash505 2013
[11] V Sharma and I N Sarkar ldquoBioinformatics opportunitiesfor identification and study of medicinal plantsrdquo Briefings inBioinformatics vol 14 no 2 pp 238ndash250 2013
Evidence-Based Complementary and Alternative Medicine 9
[12] S Li and B Zhang ldquoTraditional Chinese medicine networkpharmacology theory methodology and applicationrdquo ChineseJournal of Natural Medicines vol 11 no 2 pp 110ndash120 2013
[13] M Ashburner C A Ball J A Blake et al ldquoGene ontology toolfor the unification of biologyrdquoNature Genetics vol 25 no 1 pp25ndash29 2000
[14] A P Davis B L King S Mockus et al ldquoThe comparativetoxicogenomics database update 2011rdquo Nucleic Acids Researchvol 39 no 1 pp D1067ndashD1072 2011
[15] D S Wishart C Knox A C Guo et al ldquoDrugBank a knowl-edgebase for drugs drug actions and drug targetsrdquoNucleic AcidsResearch vol 36 no 1 pp D901ndashD906 2008
[16] T S Keshava Prasad RGoel K Kandasamy et al ldquoHumanpro-tein reference databasemdash2009 updaterdquo Nucleic Acids Researchvol 37 no 1 pp D767ndashD772 2009
[17] B Zhang X Wang and S Li ldquoAn integrative platform of TCMnetwork pharmacology and its application on a herbal formulaQing-Luo-Yinrdquo Evidence-Based Complementary and AlternativeMedicine vol 2013 Article ID 456747 12 pages 2013
[18] A E Koch ldquoAngiogenesis implications for rheumatoid arthri-tisrdquo Arthritis amp Rheumatism vol 41 no 6 pp 951ndash962 1998
[19] M Feldmann F M Brennan and R N Maini ldquoRole ofcytokines in rheumatoid arthritisrdquo Annual Review of Immunol-ogy vol 14 pp 397ndash440 1996
[20] E H S Choy and G S Panayi ldquoCytokine pathways andjoint inflammation in rheumatoid arthritisrdquo The New EnglandJournal of Medicine vol 344 no 12 pp 907ndash916 2001
[21] G Janossy G Panayi O Duke M Bofill L W Poulterand G Goldstein ldquoRheumatoid arthritis a disease of T-lymphocytemacrophage immunoregulationrdquo The Lancet vol2 no 8251 pp 839ndash842 1981
[22] S S Makarov ldquoNF-120581B in rheumatoid arthritis a pivotal reg-ulator of inflammation hyperplasia and tissue destructionrdquoArthritis Research vol 3 no 4 pp 200ndash206 2001
[23] M Cutolo A Sulli B Villaggio B Seriolo and S AccardoldquoRelations between steroid hormones and cytokines in rheuma-toid arthritis and systemic lupus erythematosusrdquo Annals of theRheumatic Diseases vol 57 no 10 pp 573ndash577 1998
[24] P E Lipsky D M van der Heijde E W St Clair et al ldquoAnti-TumorNecrosis Factor Trial in RheumatoidArthritis with Con-comitant Therapy Study Group Infliximab and methotrexatein the treatment of rheumatoid arthritis Anti-Tumor NecrosisFactor Trial in Rheumatoid Arthritis with Concomitant Ther-apy Study Grouprdquo The New England Journal of Medicine vol343 no 22 pp 1594ndash1602 2000
[25] V Strand S Cohen M Schiff et al ldquoTreatment of activerheumatoid arthritis with leflunomide compared with placeboand methotrexate Leflunomide Rheumatoid Arthritis Investi-gators Grouprdquo Archives of Internal Medicine vol 159 no 21 pp2542ndash2550 1999
[26] J R Kirwan ldquoThe effect of glucocorticoids on joint destructionin rheumatoid arthritisrdquoThe New England Journal of Medicinevol 333 no 3 pp 142ndash146 1995
[27] S R de Antonio H M Blotta R L Mamoni et al ldquoEffects ofdexamethasone on lymphocyte proliferation and cytokine pro-duction in rheumatoid arthritisrdquoThe Journal of Rheumatologyvol 29 no 1 pp 46ndash51 2002
[28] J R OrsquoDell ldquoTherapeutic strategies for rheumatoid arthritisrdquoTheNew England Journal of Medicine vol 350 no 25 pp 2591ndash2602 2004
[29] S Li Z Q Zhang L JWu X G Zhang Y D Li andY YWangldquoUnderstanding ZHENG in traditional Chinese medicine inthe context of neuro-endocrine-immune networkrdquo IET SystemsBiology vol 1 no 1 pp 51ndash60 2007
[30] R Li T Ma J Gu X Liang and S Li ldquoImbalanced networkbiomarkers for traditional Chinese medicine Syndrome ingastritis patientsrdquo Scientific Reports vol 3 article 1543 2013
[31] G Chen C Lu Q Zha et al ldquoA network-based analysis oftraditional Chinese medicine cold and hot patterns in rheuma-toid arthritisrdquo Complementary Therapies in Medicine vol 20no 1-2 pp 23ndash30 2012
[32] H A van Wietmarschen W Dai A J van der Kooij et alldquoCharacterization of rheumatoid arthritis subtypes using symp-tom profiles clinical chemistry and metabolomics measure-mentsrdquo PLoS ONE vol 7 no 9 Article ID e44331 2012
Submit your manuscripts athttpwwwhindawicom
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Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
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Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
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Disease Markers
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
BioMed Research International
OncologyJournal of
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Oxidative Medicine and Cellular Longevity
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PPAR Research
The Scientific World JournalHindawi Publishing Corporation httpwwwhindawicom Volume 2014
Immunology ResearchHindawi Publishing Corporationhttpwwwhindawicom Volume 2014
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Research and TreatmentAIDS
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Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Parkinsonrsquos Disease
Evidence-Based Complementary and Alternative Medicine
Volume 2014Hindawi Publishing Corporationhttpwwwhindawicom
Evidence-Based Complementary and Alternative Medicine 3
herb 119910 to form an herb pair More importantly the DMIMmodel extracts information from the organization of Jun-Chen-Zuo-Shi (Master-Adviser-Soldier-Guide) herbs in anherbal formula based on which a new parameter ldquobetween-herb distancerdquowas created thatmeans the further the distancebetween two herbs in a formula is the less likely they are tobe relevant to one anotherThus DMIM is suitable to retrieveherb combinational rules achieving a good balance amongthe herbrsquos frequency independence and distance in herbalformulae [6]
Target Prediction for Herbal Compounds and Herbs In thepresent study drugCIPHER a method we developed previ-ously [8] is used to predict the target profile for all availablecompounds collected from each herb in the core herbnetworks drugCIPHER is a regressionmodel that can predictthe links between drugs and target proteins in a genome-wide scale by correlating the drug chemical informationand protein-protein interaction (PPI) from a heterogeneousnetwork By integrating and making full use of all currentFDA-approved drug structures drug-target interactions andhuman protein-protein interactions drugCIPHER can out-put a target profile for any given compound with knownstructure that is calculated from the correlation between thequery ingredientrsquos structure similarity vector in the drugspace and the target-related genersquos closeness vector in thetarget space As the top 100 targets predicted by drugCIPHERcan reach the high prediction accuracy (773) [8] here thetop 100 target profiles predicted for each compound wereselected and the target profiles of all collected compoundswithin a herb were combined to form integrative targetprofiles of this herb The target prediction procedure wasconducted for herbs present in the core herb networks orinvolved in the following studies
Evaluation of Synergistic Actions forHerbNetwork To identifythe potential synergistic effects of herb combinations in thecore herb network at the molecular level and in a highthroughput way we used the network-based identificationof multicomponent synergy (NIMS) method [7] a novelapproach to access the synergistic strength of any combina-tion of herbal compounds by determining their target inter-actions in the protein-protein network The NIMS algorithmconsists of two components topology score and agent scoreThe topology score is generated from the topological featuresof the background network related to disease condition anddrug actions while the agent score is based on the similarityof agent phenotypes Two graph-based measures between-ness and closeness were used to capture the associationsamong targets and the other measure PageRank to verifythe node importance [7] The resulted synergy score is usedto prioritize the synergistic effect of combinations of agentsincluding herbs or herbal compounds
Gene Ontology (GO) and Pathway Analysis for Herb Targetsand RAGenesThe targets of each compound in the top herbswere predicted using drugCIPHER For each compound ofthe top herbs the top 100 proteins were treated as targetsfor the given compound The targets hit by more than five
compounds within an herb were considered herb targets Top15 frequent herbsrsquo targets were subjected to the gene ontology[13] and pathway enrichment analysis One the other handthe 129 RA-related genes with a direct mechanism relation-ship to rheumatoid arthritis were collected from the CTDdatabase [14] For functional analysis we used the ldquoSet Ana-lyzerrdquo tool at the CTD site (httpctdbaseorgtoolsanalyzergo) to analyze the enriched GO terms as well as KEGGpathways for herb targets and RA genes respectively withcorrected 119875 value less than 005 We also mapped the RAgenes and herb targets in the enriched KEGG pathwaynetwork
Compound Network Analysis for Anti-RA Herbs and DrugsFor comparison of the herbal prescriptions and the Westernanti-RA drugs we collected the commonly used anti-RAdrugs and their targets from the DrugBank database [15]Nine immunomodulatory drugs and 7 hormones were selec-ted The immunomodulatory drugs include methotrexateleflunomide ciclosporin thalidomide cyclophosphamideazathioprine mycophenolate mofetil tacrolimus and cyclo-sporine Hormones include dexamethasone hydrocortisonecortisone triamcinolone prednisolone prednisone andmethylprednisolone Based on the targets of each compoundcontained by the top 50 frequent herbs the closeness ofherb compoundrsquos targets and targets of immunomodulatorydrugs and hormones on the RA-related gene network thatconnected by PPI interactions (HPRD Release 7) [16] weremeasuredThe compoundnetworks are then formed inwhichtwo compounds (or drugs) will be linked if their targetsare overlapped or directly connected in the network Herewe paid more attention on the relationship between herbalcompounds with ColdHot property and two types of RAdrugs
3 Results and Discussion
31 Core Herb Networks from Herbal Prescriptions 343 herbswere uniquely identified from all 871 prescriptions ByDMIMscoring [6] we obtained frequently used herbs as well as theircombinations from all available prescriptions with Ji XueTeng as the most frequently used herb The top 15 herbs inMr Lirsquos anti-RA herbal prescription are shown in Table 1 Wecan see that although the prescriptions are written out indi-vidually to patients the commonly used herbs with differentproperties are considered to be the most representative ofthe available herbal prescriptions Therefore to capture thecommon rule of herbal prescriptions here we focused onthe most frequent herbs for the subsequent network analysisThenwe conducted the herb network analysis for these herbalprescriptions A node in herb network refers to an herb andan edge connecting two nodes refers to the two significantcooccurrent herbs in herbal prescriptions By using DMIMscore to evaluate the significance of the edge we constructedtwo types of the core herb networks namely the high-frequency herb network and the intersection herb networkfor Mr Lirsquos 871 prescriptions
For the high-frequency network only the top frequentherbs were treated as nodes and the cooccurrence herbs
4 Evidence-Based Complementary and Alternative Medicine
Table 1 Top 15 herbs in Mr Ji-Ren Lirsquos antirheumatoid arthritis herbal prescriptions
Chinese name Latin name Property Frequency Normalized frequencyJi Xue Teng Millettia reticulata Benth Warm 503 510Huo Xue Teng Sargentodoxa cuneata Neutral 499 506Huang Qi Astragalus membranaceus (Fisch) Bunge Warm 481 487Dang Gui Radix Angelicae sinensis Warm 430 436Quan Xie Scorpio Neutral 399 404Qing Feng Teng Caulis Sinomenii Neutral 396 401Ku Shen Radix Sophorae flavescentis Cold 323 327Wu Tou Aconitum carmichaeli Debx Hot 306 310Wu Gong Scolopendra Warm 287 291Huang Bai Cortex Phellodendri Cold 283 287Bi Xie Rhizoma Dioscoreae Hypoglaucae Neutral 280 284Ren Dong Teng Caulis Lonicerae Cool 257 260Qin Jiao Radix Gentianae macrophyllae Cold 254 257Wu Shao She Zaocys dhumnades Neutral 235 238Pu Gong Ying Taraxacum mongolicumHand-Mazz Cold 227 230
in herbal prescriptions identified by DMIM were treated asedges For example we found that the top 10 frequent herbswith 45 edges are closely interrelatedwith each other formingalmost all connected graphs Among them Ji Xue Teng andHuang Qi (DMIM score = 18627) Huo Xue Teng and Ji XueTeng (DMIM score = 16517) have the highest DMIM scoresThis result suggests that the top 10 herbs are always prescribedin pairs in Mr Lirsquos practice for RA treatment
For the intersection herb network we built every subnet-work by DMIM for each of the top frequent herbs and thenintersected the subnetworks to construct a core networkFor example Figure 2(a) shows the subnetwork around thetop 2 herb Huo Xue Teng (Sargentodoxa cuneata) The topten frequent herb subnetworks contained 21 to 35 nodes and100 to 200 edges and the resulted core intersection networkhas 14 nodes and 29 edges (Figure 2(b)) Interestingly acomplete formula of Mr Li Qing-Luo-Yin [17] is present inthis network
Herbs and herb combinations present in these two typesof herb networks may play a central role in Mr Lirsquos herbalprescriptions for the treatment of RA
32 Potential Synergistic Activities Underlying Core Herb Net-works Taking the core herb networks as examples we fur-ther performed the network target analysis to computation-ally determine whether the DMIM extracted herb networksdisplayed synergistic effects In this step we collected avail-able compounds for the core herb networks identified fromMr Lirsquos prescriptions The target profile of each compoundwas predicted by the drugCIPHER method [8] Then weselected top 100 targets of compounds assembled in eachherb to analyze the synergistic activity by evaluating the tar-get interactions in the protein-protein interaction networkWhen drugCIPHER [8] and NIMS [7] (see Section 2) areapplied to the herb networks we can obviously detect themodular property in themolecular level that denotes the syn-ergistic relationship in the core herb networks (Figure 3(a))From the outputs of the NIMS score we found that in
an herb network not all herbs interact strongly Instead onlycertain herbs or even certain herbal compounds produceclear synergistic effects For example in the high-frequencyherb network Ji Xue Teng and Huo Xue Teng (average NIMSscore = 084) Ku Shen and Qing Feng Teng (average NIMSscore = 057) Ku Shen and Ji Xue Teng (average NIMS score= 04) and Huo Xue Teng and Qing Feng Teng (averageNIMS score = 031) each of the two herbs has a relativelyhigh NIMS score and tends to produce synergistic activity indifferent levels In the intersection herb network the mainconstituent of TCM herbal formulae Qing-Luo-Yin (QLY)also has a good NIMS score A part of the synergistic modulefromQing Feng Teng and Ku Shen was shown in Figure 3(b)This figure further illustrated that different compounds inan herb pair obtained diverse synergistic scores Amongthem the combination of compounds such as Sinomenineand Matrine achieves a relatively high score which agreeswith the previously experimental results on the synergisticeffects in QLY [17] Thus we demonstrate here that thesynergistic effects of herb components may be contributed tothe modular property of the herb network as well as herbalprescriptions
33 Biological Associations between Herb Targets and RAGenes Since the targets of each compound of herbs areavailable by drugCIPHER we further verify the effectivenessof the top 15 frequent herbs in Mr Lirsquos prescriptions (Table 1)by evaluating the herbal compoundsrsquo targets and theirrelationship with RA genes in terms of the GO biologicalprocesses and pathways As shown in Table 2 there are RA-related GO terms resulting from targets of the top 15 herbswhich were also enriched with 129 RA-related genes formthe CTD database For example the overlapped GO termswhich resulted from both herb targets and RA genes includeangiogenesis [18] cytokine production [19] inflammatoryresponse [20] lymphocyte activation [21] and NF-120581B tran-scription factor activity [22] The overlapped GO terms alsoinclude ldquodefense response to bacteriumrdquo which is worthy
Evidence-Based Complementary and Alternative Medicine 5
Lian Qiao
Hu Zhang Dai MaoRou Gui
Ku Shen
Bi Xie
Wu Shao She
Qin Jiao
Man Jing Zi
Han Lian Cao
Chai Hu
Wu Wei Zi
Bai Mao Gen
Wei Ling Xian
Qing Feng Teng
Zhi Mu
Wu Tou
Huo Xue Teng
Lei Gong Teng
Huang Bai
Ji XueTengHuang Qi
Pu Gong Ying
Ren Dong Teng
(a)
Man Jing Zi
Wu Tou
Bi Xie
Ji Xue Teng
Zhi Mu
Qin JiaoWu Shao She
Ku ShenHuo Xue Teng
Qing Feng Teng
Pu Gong Ying
Lei Gong Teng
Huang Bai
Ren Dong Teng
(b)
Figure 2 The core intersection herb networks constructed fromMr Ji-Ren Lirsquos anti-RA herbal prescriptions (a) The herb subnet-works around each top frequent herb for example Huo Xue Teng(Sargentodoxa cuneata the top 2 herb) (b) The intersection herbnetwork created from the intersection herb networks of the top tenfrequent herbs Four herbs circled by the green line are a completeformula of Qing-Luo-Yin
of further study Note that other nonoverlapping GO termsassociated with herbs such as the steroid hormone receptorsignaling pathway also contributed a lot to the progressof RA [23] Moreover by pathway enrichment analysis wefurther found that both the RA genes and herb targetsare significantly enriched in the pathway of ldquorheumatoidarthritisrdquo (KEGG05323) (corrected 119875 = 155119890 minus 15 for RAgenes and 119875 = 283119890 minus 12 for herb targets resp) Figure 4shows the details of the network associations of RA genesandherb targets in theKEGGldquorheumatoid arthritisrdquo pathwayproviding additional evidence for the anti-RA effects of MrLirsquos herbal prescriptions These results suggest that the top15 frequent herbs have a potential to treat RA patients byintervening in the critical biological processes and pathway
Qing Feng Teng
Ku Shen
(a)
1
09
08
07
06
05
04
03
02
01
SinomenineDisinomenine
SinacutineAcutumineTuduranine
MagnoflorineIsosinomenine
MichelalbineBianfugenineStepharanine
Mat
rine
NIM
S sc
ore
Kura
rinon
eKu
rara
min
eBa
ptifo
line
Lehm
anin
eBe
ta-s
itoste
rol
Kush
enol
lCa
mph
orKo
sam
ol a
Gua
ijave
rin
Qin
g Fe
ng T
eng
Ku Shen
(b)
Figure 3 Calculation of synergistic activity among compoundscollected from the core herb networks (a) A part of the synergisticmodule from compounds of Qing Feng Teng (Caulis Sinomenii)and Ku Shen (Radix Sophorae flavescentis) (b) The horizontal andvertical axes show the compounds of herbs and the intervals ofaxis represent herbs The dark areas illustrate a modular featureand indicate strong synergistic interactions of herbs with highsynergistic scores calculated by the NIMS method
of RA which in turn gives evidence for the rationality of thecommonly prescribed herbs in Mr Lirsquos clinical practice
34 Network Connections of Anti-RA Herbs and Drugs InTCM RA patients can be categorized to different syndromes(ZHENG in Mandarin) for example Cold Syndrome andHot Syndrome Accordingly as shown in Table 1 Cold HotWarm Cool and Neutral are the basic properties of herbsreflecting the traditional characteristic of TCM TypicallyTCM doctors always use Cool or Cold herbs to treat patientswith Hot Syndrome whereas they use Warm or Hot herbsto treat patients with Cold Syndrome Cold-tendency andHot-tendency herbs may be combined to treat RA patientswith mixed Hot and Cold Syndromes On the other handin modern medicine immunomodulatory drugs such as
6 Evidence-Based Complementary and Alternative Medicine
Th17 cellTGF120573
Synovial macrophage
T cell receptor
Antigen
DC
Rheumatoid arthritis
CD8086
MHCII
IgGSDF1
VEGF
CCL2 CXCL1CXCL5CCL3
CCL20 Ang1IL8Tie2Flt1
AP1TLR24LPSPeptidoglycan
signaling pathwayToll-like receptor
Autoantibody production
B cell
APRIL
RANKL
CD28CTLA4
TCR
LFA1
ICAM1
IL15
IL6
Synovium
Bone
IL23
MCSF
RANKL
RANKL RANK
CTSKTRAP
CTSLMMP13 Joint destruction
Inflammation
Angiogenesis
Leukocyte migration
Blood vessel
VEGF signaling pathway
Inflammatory
Synovial pannus
Bone resorption
V-ATPase
Osteoblast
Osteoclast
Osteoclast
differentiation
Synovial fibroblast
PTHVitamin D3
IL11
IL17
IL1IL6
IL6
CCL5IL1120573
GMCSF
IL18
BLYS
Self-reactiveTh1 cell
signaling pathwayLT120573
IFN120574
TNF120572
PGE2
H+
cell infiltration
formation
Herb targetRA gene
Figure 4 Network association of RA genes and top 15 frequent herbsrsquo targets in the enriched KEGG ldquorheumatoid arthritisrdquo pathway (KEGG05323)
methotrexate and leflunomide [24 25] and hormones such asglucocorticoids (dexamethasone) [26 27] are two categoriesof medicines for the treatment of patients with rheumatoidarthritis [28] Both categories of medicines can improve thequality of life and delay the disease progression of RA patientsvia independent but interactivemechanism of actions By cal-culating compound networks from the top 50 frequent herbsin Mr Lirsquos prescriptions we obtained the herbs that containingredients similar to RA immunomodulatory drugs andhormones respectively As shown in Figure 5 many herbscontain compounds with targets connected to the selectedanti-RA drugs in the network and may exert similar actionson RA For example 9 out of top 10 herbs with differentproperties such as Cold and Hot (Table 1) have compoundsthat are closely clustered with RA immune and hormonedrugs in the network These results are meaningful sincerecent studies indicated that the metabolism and immuneimbalance are closely associated with patients suffering fromCold Syndrome and Hot Syndrome [29 30] in many diseasesincluding rheumatoid arthritis [31 32] Interestingly it isnoticed that the Cold herbs tend to be enriched in theimmune-herb cluster Hot herbs tend to be enriched inhormone-herb cluster and Warm herbs are enriched in bothclusters Moreover compared with the hormone-herb cluster(Figure 5(b)) the immune-herb cluster is less diverse andonly contains Cold and Warm herbs suggesting these herbstend to exert immunosuppressive or immunoenhancementactions (Figure 5(a)) Although the results are preliminary
the potential connection as well as combinational effectsbetween herbs and drugs is of great importance and deservesfurther investigation in larger samples and clinical or experi-mental studies
4 Conclusions
In summary we developed a TCM network pharmacologystrategy and an Herb-Compound-Target-Disease coherentnetwork analysis framework to study herbal prescriptionsthe main form of TCM clinical practice We extracted twotypes of core herb networks from871 anti-RAherbal formulaeprescribed by a famous TCM doctor From the core herb net-works our network-based strategy identified cooccurrenceherbs and herb pairs with potential synergistic activities Wealso predicted the biological basis of the core herb networkby calculating the compoundrsquos targets from most frequentherbs We detected that targets of the commonly prescribedherbs are enriched together with RA genes in critical bio-logical processes and pathway of RA We also indicated thatherbs with different properties in prescriptions may have apotential connection with RA immunomodulatory drugs orhormones in the compound networks Taken together theseresults could help uncover the prescription rules underlyingherbal formulae in the clinical practice of TCM practitionersMoreover such network-based analyses not only can developa holistic understanding of herbal remedies but also mayfacilitate the following pharmacological evaluation of herbal
Evidence-Based Complementary and Alternative Medicine 7
Ethylsalicylate
Hinesol
Campesterol
Taraxerone
AtractylenolideI
Leflunomide
Chen PiAngelicideBai
Shao
PaeonilactoneC
QiangHuo
Bai Zhu Albiflorin R1Sheng
DiHuang
ChiShao
Mai Ya
ManJing Zi Fang
Feng
KuShen
QingFengTeng
DangGui
Benzothiazole
Adrenocorticotropichormone
Folic acid
Chromone
Methotrexate
Lupenone
Dipterocarpol
Perrimustine
GuaiolIsofucosterol
120573-cryptoxanthin
Herb
Compound or drug
TengJi Xue
JiangHuang
DanShen
WuGong
HuangQi
ChuanXiong
3-Hydroxymugineicacid
Thiolproteaseinhibitor
Listomin S
Pseudocarpaine
Ciclosporin
Goitrin
Dihydro-2-methyl-3(2H)-furanone
Acetamide
Acetoin
Bornylacetate
Sophoranol
Tacrolimus
SandaracopimaricacidViridiflorol
Stigmasterin
Cholesterol
Ro 09-0680Phenylacetaldehyde
DAU 6215 hydrochloride
AC1L7QUY
Levamisolehydrochloride
Thalidomide
Mugineicacid
Benzoyl-dl-leucine
Ethanamine
Permanentorange
acid
Metarene
Laccase
AC1L7VXU
4-Hydroxymephenytoin
NSC673109
Procurcumenol Dehydrocurdione
Zeaxanthin
C09772
Olean-18-en-3-one
45-epoxide
100347-96-4
trans-Sabinenehydrate
CampheneVitamin D3
3-Oxo-1113(18)-oleanadien-28-oicacid
acid
6-Methylcholest-4-en-3-oneAspartylglucosamine
7-Dehydrostigmasterol
Cyclosporine
(4S5S)-(+)-germacrone
(5|A8|A9|A10|A16|A)-16-hydroxykauran-18-oic
(ZZ998400)-diligustilide
120575-terpineol
120573-sitosterol
51205729120572-dihydroxymatrine
2998400-Deoxymugineic
acetate
(a)
Apioglycyrrhizin
UralsaponinB
InflasaponinIV
InflasaponinI
Glycamil
Glycyrrhizicacid
ammoniumsalt
Glyuranolide
Glycyrrhizinicacid
AraboglycyrrhizinLiquoric acid
SophoraflavosideIV
GibberellinA1
CinncassiolA
Napellonine
CinncassiolC3
SophoraflavosideIII
Shanzhisidemethyl ester
Dexamethasone
Palbinone
Triamcinolone
LeiGongTeng
Ge Gen
WeiLingXian
QuanXie
RenDongTeng
Wu Tou
Fu Zi
Sang Ji Sheng
RuXiang
120572-boswellicacid
Rehmannicacid
Loganin
Tutin
acid
Loganic acid
NSC302037
Glycyrrhetinicacid
Prednisone
24-Hydroxyglycyrrheticacid
Corianin
3-Glc-soyasapogenolE
Glabric acidPaeonilactone
B
Cinncassiol E
Ecdysterone
Uralenolide
Asiatic acid
120573-glycyrrhetinicacid
Oleanolicacid
Geigerinin
CinncassiolC2
Tigogenin
Neotigogenin
GlycyrrhetolKatonic acid
Kihadanin A
Cortisone
Triptonide
Bufotoxin
Helixin
Inokosterone
Methylprednisolone
PrednisoloneTriptolideGibberellic
acidCaryoptoside
Triptolideanalog
Hydrocortisone
Gui Zhi
GanCao
XuDuan
Cold
Warm
Hormone drug
Immunomodulatory drug
Hot
Cool
Tu Fu LingHuang
Bai
Neutral
Niu Xi
Du Huo
Zhi Mu
Mu Gua
ShanZha
Pinnatifidin
(25S)-5120573-spirostan-3120573-ol
11-Keto-120573-boswellicacid
Acetyloleanolicacid
Corosolicacid
Boswellicacid
(5xi13|A14|A20s23r24s)-2324-dihydroxy-25-methoxylanost-7-en-3-one
(3|A20|A)-3-hydroxy-11-oxo-olean-12-en-29-oic
Herb
Compound or drug
(b)
Figure 5 Possible connection between RA herbs and drugs in the networks consisting of herbs herbal compounds immunomodulatorydrugs (a) and hormones (b)
8 Evidence-Based Complementary and Alternative Medicine
Table 2 Overlapped RA-related GO terms between top 15 herbtargets and RA genes
Category Enriched GO terms Corrected119875-value
Herbtargets
Response to wounding 238119890 minus 127
Angiogenesis 121119890 minus 26
Inflammatory response 860119890 minus 71
Regulation of cytokine production 612119890 minus 26
Immune response 261119890 minus 88
Leukocyte activation 341119890 minus 38
Regulation of lymphocyte activation 452119890 minus 23
Defense response to bacterium 356119890 minus 10
Positive regulation of NF-120581Btranscription factor activity 604119890 minus 12
RA genes
Response to wounding 148119890 minus 15
Angiogenesis 579119890 minus 6
Inflammatory response 576119890 minus 26
Regulation of cytokine production 165119890 minus 26
Immune response 629119890 minus 39
Leukocyte activation 728119890 minus 30
Regulation of lymphocyte activation 125119890 minus 31
Defense response to bacterium 727119890 minus 12
Positive regulation of NF-120581Btranscription factor activity 254119890 minus 6
treatments Clearly this study is only the first step to learnthe common rule of herbal prescriptions We will continueto conduct in-depth analysis for understanding the scientificbasis of herbal prescriptions in our future work Althoughmore powerful methods more data on TCM prescriptionsand clinical or experimental evaluations are still requiredwe believe that this TCM network pharmacology strategy issuitable to study herbal formulae both in the herb level andin the molecular level and thus can serve as a novel approachto further understand the professional experience embeddedin TCM prescriptions
Abbreviations
DMIM Distance-based mutual information modeldrugCIPHER Drug-target prediction by correlating
protein interaction network andphenotype network
GO Gene ontologyMI Mutual informationNIMS Network-based identification of
multicomponent synergyRA Rheumatoid arthritisPPI Protein-protein interactionQLY Qing-Luo-YinTCM Traditional Chinese Medicine
Conflict of Interests
The authors declare that they have no competing interests
Authorsrsquo Contribution
Shao Li conceived the study Yan Li collected the data Shao LiYan Li Rui Li and Zibo Ouyang analyzed the data and wrotethe paper All authors read and approved the final paper
Acknowledgments
Thanks to Kai Zhang for his help in herbal prescription col-lection This work is supported by NSFC project (81225025)the SATCM key discipline of ldquoTCM Bi-Bingrdquo in YijishanHospital of WannanMedical College the SATCM laboratoryof TCM master Ji-Ren Li the CATCM project and AnhuirsquosKey Technologies RampD project (11010402173)
References
[1] G G Zhang W Lee B Bausell L Lao B Handwerger andB Berman ldquoVariability in the traditional Chinese medicine(TCM) diagnoses and herbal prescriptions provided by threeTCM practitioners for 40 patients with rheumatoid arthritisrdquoJournal of Alternative and Complementary Medicine vol 11 no3 pp 415ndash421 2005
[2] G G Zhang B Singh W Lee B Handwerger L Lao and BBerman ldquoImprovement of agreement in TCMdiagnosis amongTCM practitioners for persons with the conventional diagnosisof rheumatoid arthritis effect of trainingrdquo Journal of Alternativeand Complementary Medicine vol 14 no 4 pp 381ndash386 2008
[3] P Zhang J Li Y Han X W Yu and L Qin ldquoTraditionalChinese medicine in the treatment of rheumatoid arthritis ageneral reviewrdquo Rheumatology International vol 30 no 6 pp713ndash718 2010
[4] Y Li 100 TCM Practitioners in Latest 100 Years Li Ji-ren ampZhang Shun-hua China Press of Traditional Chinese MedicineBeijing China 2004
[5] C Shu Z Li and Y Li ldquoGrand Master of TCM Ji-Ren Lirsquosexperience on the treatment of Bi Zhengrdquo Forum on TraditionalChinese Medicine vol 27 pp 10ndash12 2012
[6] S Li B Zhang D Jiang Y Wei and N Zhang ldquoHerbnetwork construction and co-module analysis for uncoveringthe combination rule of traditional Chinese herbal formulaerdquoBMC Bioinformatics vol 11 supplement 11 article S6 2010
[7] S Li B Zhang and N Zhang ldquoNetwork target for screeningsynergistic drug combinations with application to traditionalChinese medicinerdquo BMC Systems Biology vol 5 supplement 1p S10 2011
[8] S Zhao and S Li ldquoNetwork-based relating pharmacological andgenomic spaces for drug target identificationrdquo PLoS ONE vol5 no 7 Article ID e11764 2010
[9] X Liang H Li and S Li ldquoA novel network pharmacologyapproach to analyse traditional herbal formulae the Liu-Wei-Di-Huang pill as a case studyrdquoMolecular BioSystems vol 10 no5 pp 1014ndash1022 2014
[10] E L Leung Z-W Cao Z-H Jiang H Zhou and L LiuldquoNetwork-based drug discovery by integrating systems biologyand computational technologiesrdquo Briefings in Bioinformaticsvol 14 no 4 pp 491ndash505 2013
[11] V Sharma and I N Sarkar ldquoBioinformatics opportunitiesfor identification and study of medicinal plantsrdquo Briefings inBioinformatics vol 14 no 2 pp 238ndash250 2013
Evidence-Based Complementary and Alternative Medicine 9
[12] S Li and B Zhang ldquoTraditional Chinese medicine networkpharmacology theory methodology and applicationrdquo ChineseJournal of Natural Medicines vol 11 no 2 pp 110ndash120 2013
[13] M Ashburner C A Ball J A Blake et al ldquoGene ontology toolfor the unification of biologyrdquoNature Genetics vol 25 no 1 pp25ndash29 2000
[14] A P Davis B L King S Mockus et al ldquoThe comparativetoxicogenomics database update 2011rdquo Nucleic Acids Researchvol 39 no 1 pp D1067ndashD1072 2011
[15] D S Wishart C Knox A C Guo et al ldquoDrugBank a knowl-edgebase for drugs drug actions and drug targetsrdquoNucleic AcidsResearch vol 36 no 1 pp D901ndashD906 2008
[16] T S Keshava Prasad RGoel K Kandasamy et al ldquoHumanpro-tein reference databasemdash2009 updaterdquo Nucleic Acids Researchvol 37 no 1 pp D767ndashD772 2009
[17] B Zhang X Wang and S Li ldquoAn integrative platform of TCMnetwork pharmacology and its application on a herbal formulaQing-Luo-Yinrdquo Evidence-Based Complementary and AlternativeMedicine vol 2013 Article ID 456747 12 pages 2013
[18] A E Koch ldquoAngiogenesis implications for rheumatoid arthri-tisrdquo Arthritis amp Rheumatism vol 41 no 6 pp 951ndash962 1998
[19] M Feldmann F M Brennan and R N Maini ldquoRole ofcytokines in rheumatoid arthritisrdquo Annual Review of Immunol-ogy vol 14 pp 397ndash440 1996
[20] E H S Choy and G S Panayi ldquoCytokine pathways andjoint inflammation in rheumatoid arthritisrdquo The New EnglandJournal of Medicine vol 344 no 12 pp 907ndash916 2001
[21] G Janossy G Panayi O Duke M Bofill L W Poulterand G Goldstein ldquoRheumatoid arthritis a disease of T-lymphocytemacrophage immunoregulationrdquo The Lancet vol2 no 8251 pp 839ndash842 1981
[22] S S Makarov ldquoNF-120581B in rheumatoid arthritis a pivotal reg-ulator of inflammation hyperplasia and tissue destructionrdquoArthritis Research vol 3 no 4 pp 200ndash206 2001
[23] M Cutolo A Sulli B Villaggio B Seriolo and S AccardoldquoRelations between steroid hormones and cytokines in rheuma-toid arthritis and systemic lupus erythematosusrdquo Annals of theRheumatic Diseases vol 57 no 10 pp 573ndash577 1998
[24] P E Lipsky D M van der Heijde E W St Clair et al ldquoAnti-TumorNecrosis Factor Trial in RheumatoidArthritis with Con-comitant Therapy Study Group Infliximab and methotrexatein the treatment of rheumatoid arthritis Anti-Tumor NecrosisFactor Trial in Rheumatoid Arthritis with Concomitant Ther-apy Study Grouprdquo The New England Journal of Medicine vol343 no 22 pp 1594ndash1602 2000
[25] V Strand S Cohen M Schiff et al ldquoTreatment of activerheumatoid arthritis with leflunomide compared with placeboand methotrexate Leflunomide Rheumatoid Arthritis Investi-gators Grouprdquo Archives of Internal Medicine vol 159 no 21 pp2542ndash2550 1999
[26] J R Kirwan ldquoThe effect of glucocorticoids on joint destructionin rheumatoid arthritisrdquoThe New England Journal of Medicinevol 333 no 3 pp 142ndash146 1995
[27] S R de Antonio H M Blotta R L Mamoni et al ldquoEffects ofdexamethasone on lymphocyte proliferation and cytokine pro-duction in rheumatoid arthritisrdquoThe Journal of Rheumatologyvol 29 no 1 pp 46ndash51 2002
[28] J R OrsquoDell ldquoTherapeutic strategies for rheumatoid arthritisrdquoTheNew England Journal of Medicine vol 350 no 25 pp 2591ndash2602 2004
[29] S Li Z Q Zhang L JWu X G Zhang Y D Li andY YWangldquoUnderstanding ZHENG in traditional Chinese medicine inthe context of neuro-endocrine-immune networkrdquo IET SystemsBiology vol 1 no 1 pp 51ndash60 2007
[30] R Li T Ma J Gu X Liang and S Li ldquoImbalanced networkbiomarkers for traditional Chinese medicine Syndrome ingastritis patientsrdquo Scientific Reports vol 3 article 1543 2013
[31] G Chen C Lu Q Zha et al ldquoA network-based analysis oftraditional Chinese medicine cold and hot patterns in rheuma-toid arthritisrdquo Complementary Therapies in Medicine vol 20no 1-2 pp 23ndash30 2012
[32] H A van Wietmarschen W Dai A J van der Kooij et alldquoCharacterization of rheumatoid arthritis subtypes using symp-tom profiles clinical chemistry and metabolomics measure-mentsrdquo PLoS ONE vol 7 no 9 Article ID e44331 2012
Submit your manuscripts athttpwwwhindawicom
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Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
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Disease Markers
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
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OncologyJournal of
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Oxidative Medicine and Cellular Longevity
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PPAR Research
The Scientific World JournalHindawi Publishing Corporation httpwwwhindawicom Volume 2014
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Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Parkinsonrsquos Disease
Evidence-Based Complementary and Alternative Medicine
Volume 2014Hindawi Publishing Corporationhttpwwwhindawicom
4 Evidence-Based Complementary and Alternative Medicine
Table 1 Top 15 herbs in Mr Ji-Ren Lirsquos antirheumatoid arthritis herbal prescriptions
Chinese name Latin name Property Frequency Normalized frequencyJi Xue Teng Millettia reticulata Benth Warm 503 510Huo Xue Teng Sargentodoxa cuneata Neutral 499 506Huang Qi Astragalus membranaceus (Fisch) Bunge Warm 481 487Dang Gui Radix Angelicae sinensis Warm 430 436Quan Xie Scorpio Neutral 399 404Qing Feng Teng Caulis Sinomenii Neutral 396 401Ku Shen Radix Sophorae flavescentis Cold 323 327Wu Tou Aconitum carmichaeli Debx Hot 306 310Wu Gong Scolopendra Warm 287 291Huang Bai Cortex Phellodendri Cold 283 287Bi Xie Rhizoma Dioscoreae Hypoglaucae Neutral 280 284Ren Dong Teng Caulis Lonicerae Cool 257 260Qin Jiao Radix Gentianae macrophyllae Cold 254 257Wu Shao She Zaocys dhumnades Neutral 235 238Pu Gong Ying Taraxacum mongolicumHand-Mazz Cold 227 230
in herbal prescriptions identified by DMIM were treated asedges For example we found that the top 10 frequent herbswith 45 edges are closely interrelatedwith each other formingalmost all connected graphs Among them Ji Xue Teng andHuang Qi (DMIM score = 18627) Huo Xue Teng and Ji XueTeng (DMIM score = 16517) have the highest DMIM scoresThis result suggests that the top 10 herbs are always prescribedin pairs in Mr Lirsquos practice for RA treatment
For the intersection herb network we built every subnet-work by DMIM for each of the top frequent herbs and thenintersected the subnetworks to construct a core networkFor example Figure 2(a) shows the subnetwork around thetop 2 herb Huo Xue Teng (Sargentodoxa cuneata) The topten frequent herb subnetworks contained 21 to 35 nodes and100 to 200 edges and the resulted core intersection networkhas 14 nodes and 29 edges (Figure 2(b)) Interestingly acomplete formula of Mr Li Qing-Luo-Yin [17] is present inthis network
Herbs and herb combinations present in these two typesof herb networks may play a central role in Mr Lirsquos herbalprescriptions for the treatment of RA
32 Potential Synergistic Activities Underlying Core Herb Net-works Taking the core herb networks as examples we fur-ther performed the network target analysis to computation-ally determine whether the DMIM extracted herb networksdisplayed synergistic effects In this step we collected avail-able compounds for the core herb networks identified fromMr Lirsquos prescriptions The target profile of each compoundwas predicted by the drugCIPHER method [8] Then weselected top 100 targets of compounds assembled in eachherb to analyze the synergistic activity by evaluating the tar-get interactions in the protein-protein interaction networkWhen drugCIPHER [8] and NIMS [7] (see Section 2) areapplied to the herb networks we can obviously detect themodular property in themolecular level that denotes the syn-ergistic relationship in the core herb networks (Figure 3(a))From the outputs of the NIMS score we found that in
an herb network not all herbs interact strongly Instead onlycertain herbs or even certain herbal compounds produceclear synergistic effects For example in the high-frequencyherb network Ji Xue Teng and Huo Xue Teng (average NIMSscore = 084) Ku Shen and Qing Feng Teng (average NIMSscore = 057) Ku Shen and Ji Xue Teng (average NIMS score= 04) and Huo Xue Teng and Qing Feng Teng (averageNIMS score = 031) each of the two herbs has a relativelyhigh NIMS score and tends to produce synergistic activity indifferent levels In the intersection herb network the mainconstituent of TCM herbal formulae Qing-Luo-Yin (QLY)also has a good NIMS score A part of the synergistic modulefromQing Feng Teng and Ku Shen was shown in Figure 3(b)This figure further illustrated that different compounds inan herb pair obtained diverse synergistic scores Amongthem the combination of compounds such as Sinomenineand Matrine achieves a relatively high score which agreeswith the previously experimental results on the synergisticeffects in QLY [17] Thus we demonstrate here that thesynergistic effects of herb components may be contributed tothe modular property of the herb network as well as herbalprescriptions
33 Biological Associations between Herb Targets and RAGenes Since the targets of each compound of herbs areavailable by drugCIPHER we further verify the effectivenessof the top 15 frequent herbs in Mr Lirsquos prescriptions (Table 1)by evaluating the herbal compoundsrsquo targets and theirrelationship with RA genes in terms of the GO biologicalprocesses and pathways As shown in Table 2 there are RA-related GO terms resulting from targets of the top 15 herbswhich were also enriched with 129 RA-related genes formthe CTD database For example the overlapped GO termswhich resulted from both herb targets and RA genes includeangiogenesis [18] cytokine production [19] inflammatoryresponse [20] lymphocyte activation [21] and NF-120581B tran-scription factor activity [22] The overlapped GO terms alsoinclude ldquodefense response to bacteriumrdquo which is worthy
Evidence-Based Complementary and Alternative Medicine 5
Lian Qiao
Hu Zhang Dai MaoRou Gui
Ku Shen
Bi Xie
Wu Shao She
Qin Jiao
Man Jing Zi
Han Lian Cao
Chai Hu
Wu Wei Zi
Bai Mao Gen
Wei Ling Xian
Qing Feng Teng
Zhi Mu
Wu Tou
Huo Xue Teng
Lei Gong Teng
Huang Bai
Ji XueTengHuang Qi
Pu Gong Ying
Ren Dong Teng
(a)
Man Jing Zi
Wu Tou
Bi Xie
Ji Xue Teng
Zhi Mu
Qin JiaoWu Shao She
Ku ShenHuo Xue Teng
Qing Feng Teng
Pu Gong Ying
Lei Gong Teng
Huang Bai
Ren Dong Teng
(b)
Figure 2 The core intersection herb networks constructed fromMr Ji-Ren Lirsquos anti-RA herbal prescriptions (a) The herb subnet-works around each top frequent herb for example Huo Xue Teng(Sargentodoxa cuneata the top 2 herb) (b) The intersection herbnetwork created from the intersection herb networks of the top tenfrequent herbs Four herbs circled by the green line are a completeformula of Qing-Luo-Yin
of further study Note that other nonoverlapping GO termsassociated with herbs such as the steroid hormone receptorsignaling pathway also contributed a lot to the progressof RA [23] Moreover by pathway enrichment analysis wefurther found that both the RA genes and herb targetsare significantly enriched in the pathway of ldquorheumatoidarthritisrdquo (KEGG05323) (corrected 119875 = 155119890 minus 15 for RAgenes and 119875 = 283119890 minus 12 for herb targets resp) Figure 4shows the details of the network associations of RA genesandherb targets in theKEGGldquorheumatoid arthritisrdquo pathwayproviding additional evidence for the anti-RA effects of MrLirsquos herbal prescriptions These results suggest that the top15 frequent herbs have a potential to treat RA patients byintervening in the critical biological processes and pathway
Qing Feng Teng
Ku Shen
(a)
1
09
08
07
06
05
04
03
02
01
SinomenineDisinomenine
SinacutineAcutumineTuduranine
MagnoflorineIsosinomenine
MichelalbineBianfugenineStepharanine
Mat
rine
NIM
S sc
ore
Kura
rinon
eKu
rara
min
eBa
ptifo
line
Lehm
anin
eBe
ta-s
itoste
rol
Kush
enol
lCa
mph
orKo
sam
ol a
Gua
ijave
rin
Qin
g Fe
ng T
eng
Ku Shen
(b)
Figure 3 Calculation of synergistic activity among compoundscollected from the core herb networks (a) A part of the synergisticmodule from compounds of Qing Feng Teng (Caulis Sinomenii)and Ku Shen (Radix Sophorae flavescentis) (b) The horizontal andvertical axes show the compounds of herbs and the intervals ofaxis represent herbs The dark areas illustrate a modular featureand indicate strong synergistic interactions of herbs with highsynergistic scores calculated by the NIMS method
of RA which in turn gives evidence for the rationality of thecommonly prescribed herbs in Mr Lirsquos clinical practice
34 Network Connections of Anti-RA Herbs and Drugs InTCM RA patients can be categorized to different syndromes(ZHENG in Mandarin) for example Cold Syndrome andHot Syndrome Accordingly as shown in Table 1 Cold HotWarm Cool and Neutral are the basic properties of herbsreflecting the traditional characteristic of TCM TypicallyTCM doctors always use Cool or Cold herbs to treat patientswith Hot Syndrome whereas they use Warm or Hot herbsto treat patients with Cold Syndrome Cold-tendency andHot-tendency herbs may be combined to treat RA patientswith mixed Hot and Cold Syndromes On the other handin modern medicine immunomodulatory drugs such as
6 Evidence-Based Complementary and Alternative Medicine
Th17 cellTGF120573
Synovial macrophage
T cell receptor
Antigen
DC
Rheumatoid arthritis
CD8086
MHCII
IgGSDF1
VEGF
CCL2 CXCL1CXCL5CCL3
CCL20 Ang1IL8Tie2Flt1
AP1TLR24LPSPeptidoglycan
signaling pathwayToll-like receptor
Autoantibody production
B cell
APRIL
RANKL
CD28CTLA4
TCR
LFA1
ICAM1
IL15
IL6
Synovium
Bone
IL23
MCSF
RANKL
RANKL RANK
CTSKTRAP
CTSLMMP13 Joint destruction
Inflammation
Angiogenesis
Leukocyte migration
Blood vessel
VEGF signaling pathway
Inflammatory
Synovial pannus
Bone resorption
V-ATPase
Osteoblast
Osteoclast
Osteoclast
differentiation
Synovial fibroblast
PTHVitamin D3
IL11
IL17
IL1IL6
IL6
CCL5IL1120573
GMCSF
IL18
BLYS
Self-reactiveTh1 cell
signaling pathwayLT120573
IFN120574
TNF120572
PGE2
H+
cell infiltration
formation
Herb targetRA gene
Figure 4 Network association of RA genes and top 15 frequent herbsrsquo targets in the enriched KEGG ldquorheumatoid arthritisrdquo pathway (KEGG05323)
methotrexate and leflunomide [24 25] and hormones such asglucocorticoids (dexamethasone) [26 27] are two categoriesof medicines for the treatment of patients with rheumatoidarthritis [28] Both categories of medicines can improve thequality of life and delay the disease progression of RA patientsvia independent but interactivemechanism of actions By cal-culating compound networks from the top 50 frequent herbsin Mr Lirsquos prescriptions we obtained the herbs that containingredients similar to RA immunomodulatory drugs andhormones respectively As shown in Figure 5 many herbscontain compounds with targets connected to the selectedanti-RA drugs in the network and may exert similar actionson RA For example 9 out of top 10 herbs with differentproperties such as Cold and Hot (Table 1) have compoundsthat are closely clustered with RA immune and hormonedrugs in the network These results are meaningful sincerecent studies indicated that the metabolism and immuneimbalance are closely associated with patients suffering fromCold Syndrome and Hot Syndrome [29 30] in many diseasesincluding rheumatoid arthritis [31 32] Interestingly it isnoticed that the Cold herbs tend to be enriched in theimmune-herb cluster Hot herbs tend to be enriched inhormone-herb cluster and Warm herbs are enriched in bothclusters Moreover compared with the hormone-herb cluster(Figure 5(b)) the immune-herb cluster is less diverse andonly contains Cold and Warm herbs suggesting these herbstend to exert immunosuppressive or immunoenhancementactions (Figure 5(a)) Although the results are preliminary
the potential connection as well as combinational effectsbetween herbs and drugs is of great importance and deservesfurther investigation in larger samples and clinical or experi-mental studies
4 Conclusions
In summary we developed a TCM network pharmacologystrategy and an Herb-Compound-Target-Disease coherentnetwork analysis framework to study herbal prescriptionsthe main form of TCM clinical practice We extracted twotypes of core herb networks from871 anti-RAherbal formulaeprescribed by a famous TCM doctor From the core herb net-works our network-based strategy identified cooccurrenceherbs and herb pairs with potential synergistic activities Wealso predicted the biological basis of the core herb networkby calculating the compoundrsquos targets from most frequentherbs We detected that targets of the commonly prescribedherbs are enriched together with RA genes in critical bio-logical processes and pathway of RA We also indicated thatherbs with different properties in prescriptions may have apotential connection with RA immunomodulatory drugs orhormones in the compound networks Taken together theseresults could help uncover the prescription rules underlyingherbal formulae in the clinical practice of TCM practitionersMoreover such network-based analyses not only can developa holistic understanding of herbal remedies but also mayfacilitate the following pharmacological evaluation of herbal
Evidence-Based Complementary and Alternative Medicine 7
Ethylsalicylate
Hinesol
Campesterol
Taraxerone
AtractylenolideI
Leflunomide
Chen PiAngelicideBai
Shao
PaeonilactoneC
QiangHuo
Bai Zhu Albiflorin R1Sheng
DiHuang
ChiShao
Mai Ya
ManJing Zi Fang
Feng
KuShen
QingFengTeng
DangGui
Benzothiazole
Adrenocorticotropichormone
Folic acid
Chromone
Methotrexate
Lupenone
Dipterocarpol
Perrimustine
GuaiolIsofucosterol
120573-cryptoxanthin
Herb
Compound or drug
TengJi Xue
JiangHuang
DanShen
WuGong
HuangQi
ChuanXiong
3-Hydroxymugineicacid
Thiolproteaseinhibitor
Listomin S
Pseudocarpaine
Ciclosporin
Goitrin
Dihydro-2-methyl-3(2H)-furanone
Acetamide
Acetoin
Bornylacetate
Sophoranol
Tacrolimus
SandaracopimaricacidViridiflorol
Stigmasterin
Cholesterol
Ro 09-0680Phenylacetaldehyde
DAU 6215 hydrochloride
AC1L7QUY
Levamisolehydrochloride
Thalidomide
Mugineicacid
Benzoyl-dl-leucine
Ethanamine
Permanentorange
acid
Metarene
Laccase
AC1L7VXU
4-Hydroxymephenytoin
NSC673109
Procurcumenol Dehydrocurdione
Zeaxanthin
C09772
Olean-18-en-3-one
45-epoxide
100347-96-4
trans-Sabinenehydrate
CampheneVitamin D3
3-Oxo-1113(18)-oleanadien-28-oicacid
acid
6-Methylcholest-4-en-3-oneAspartylglucosamine
7-Dehydrostigmasterol
Cyclosporine
(4S5S)-(+)-germacrone
(5|A8|A9|A10|A16|A)-16-hydroxykauran-18-oic
(ZZ998400)-diligustilide
120575-terpineol
120573-sitosterol
51205729120572-dihydroxymatrine
2998400-Deoxymugineic
acetate
(a)
Apioglycyrrhizin
UralsaponinB
InflasaponinIV
InflasaponinI
Glycamil
Glycyrrhizicacid
ammoniumsalt
Glyuranolide
Glycyrrhizinicacid
AraboglycyrrhizinLiquoric acid
SophoraflavosideIV
GibberellinA1
CinncassiolA
Napellonine
CinncassiolC3
SophoraflavosideIII
Shanzhisidemethyl ester
Dexamethasone
Palbinone
Triamcinolone
LeiGongTeng
Ge Gen
WeiLingXian
QuanXie
RenDongTeng
Wu Tou
Fu Zi
Sang Ji Sheng
RuXiang
120572-boswellicacid
Rehmannicacid
Loganin
Tutin
acid
Loganic acid
NSC302037
Glycyrrhetinicacid
Prednisone
24-Hydroxyglycyrrheticacid
Corianin
3-Glc-soyasapogenolE
Glabric acidPaeonilactone
B
Cinncassiol E
Ecdysterone
Uralenolide
Asiatic acid
120573-glycyrrhetinicacid
Oleanolicacid
Geigerinin
CinncassiolC2
Tigogenin
Neotigogenin
GlycyrrhetolKatonic acid
Kihadanin A
Cortisone
Triptonide
Bufotoxin
Helixin
Inokosterone
Methylprednisolone
PrednisoloneTriptolideGibberellic
acidCaryoptoside
Triptolideanalog
Hydrocortisone
Gui Zhi
GanCao
XuDuan
Cold
Warm
Hormone drug
Immunomodulatory drug
Hot
Cool
Tu Fu LingHuang
Bai
Neutral
Niu Xi
Du Huo
Zhi Mu
Mu Gua
ShanZha
Pinnatifidin
(25S)-5120573-spirostan-3120573-ol
11-Keto-120573-boswellicacid
Acetyloleanolicacid
Corosolicacid
Boswellicacid
(5xi13|A14|A20s23r24s)-2324-dihydroxy-25-methoxylanost-7-en-3-one
(3|A20|A)-3-hydroxy-11-oxo-olean-12-en-29-oic
Herb
Compound or drug
(b)
Figure 5 Possible connection between RA herbs and drugs in the networks consisting of herbs herbal compounds immunomodulatorydrugs (a) and hormones (b)
8 Evidence-Based Complementary and Alternative Medicine
Table 2 Overlapped RA-related GO terms between top 15 herbtargets and RA genes
Category Enriched GO terms Corrected119875-value
Herbtargets
Response to wounding 238119890 minus 127
Angiogenesis 121119890 minus 26
Inflammatory response 860119890 minus 71
Regulation of cytokine production 612119890 minus 26
Immune response 261119890 minus 88
Leukocyte activation 341119890 minus 38
Regulation of lymphocyte activation 452119890 minus 23
Defense response to bacterium 356119890 minus 10
Positive regulation of NF-120581Btranscription factor activity 604119890 minus 12
RA genes
Response to wounding 148119890 minus 15
Angiogenesis 579119890 minus 6
Inflammatory response 576119890 minus 26
Regulation of cytokine production 165119890 minus 26
Immune response 629119890 minus 39
Leukocyte activation 728119890 minus 30
Regulation of lymphocyte activation 125119890 minus 31
Defense response to bacterium 727119890 minus 12
Positive regulation of NF-120581Btranscription factor activity 254119890 minus 6
treatments Clearly this study is only the first step to learnthe common rule of herbal prescriptions We will continueto conduct in-depth analysis for understanding the scientificbasis of herbal prescriptions in our future work Althoughmore powerful methods more data on TCM prescriptionsand clinical or experimental evaluations are still requiredwe believe that this TCM network pharmacology strategy issuitable to study herbal formulae both in the herb level andin the molecular level and thus can serve as a novel approachto further understand the professional experience embeddedin TCM prescriptions
Abbreviations
DMIM Distance-based mutual information modeldrugCIPHER Drug-target prediction by correlating
protein interaction network andphenotype network
GO Gene ontologyMI Mutual informationNIMS Network-based identification of
multicomponent synergyRA Rheumatoid arthritisPPI Protein-protein interactionQLY Qing-Luo-YinTCM Traditional Chinese Medicine
Conflict of Interests
The authors declare that they have no competing interests
Authorsrsquo Contribution
Shao Li conceived the study Yan Li collected the data Shao LiYan Li Rui Li and Zibo Ouyang analyzed the data and wrotethe paper All authors read and approved the final paper
Acknowledgments
Thanks to Kai Zhang for his help in herbal prescription col-lection This work is supported by NSFC project (81225025)the SATCM key discipline of ldquoTCM Bi-Bingrdquo in YijishanHospital of WannanMedical College the SATCM laboratoryof TCM master Ji-Ren Li the CATCM project and AnhuirsquosKey Technologies RampD project (11010402173)
References
[1] G G Zhang W Lee B Bausell L Lao B Handwerger andB Berman ldquoVariability in the traditional Chinese medicine(TCM) diagnoses and herbal prescriptions provided by threeTCM practitioners for 40 patients with rheumatoid arthritisrdquoJournal of Alternative and Complementary Medicine vol 11 no3 pp 415ndash421 2005
[2] G G Zhang B Singh W Lee B Handwerger L Lao and BBerman ldquoImprovement of agreement in TCMdiagnosis amongTCM practitioners for persons with the conventional diagnosisof rheumatoid arthritis effect of trainingrdquo Journal of Alternativeand Complementary Medicine vol 14 no 4 pp 381ndash386 2008
[3] P Zhang J Li Y Han X W Yu and L Qin ldquoTraditionalChinese medicine in the treatment of rheumatoid arthritis ageneral reviewrdquo Rheumatology International vol 30 no 6 pp713ndash718 2010
[4] Y Li 100 TCM Practitioners in Latest 100 Years Li Ji-ren ampZhang Shun-hua China Press of Traditional Chinese MedicineBeijing China 2004
[5] C Shu Z Li and Y Li ldquoGrand Master of TCM Ji-Ren Lirsquosexperience on the treatment of Bi Zhengrdquo Forum on TraditionalChinese Medicine vol 27 pp 10ndash12 2012
[6] S Li B Zhang D Jiang Y Wei and N Zhang ldquoHerbnetwork construction and co-module analysis for uncoveringthe combination rule of traditional Chinese herbal formulaerdquoBMC Bioinformatics vol 11 supplement 11 article S6 2010
[7] S Li B Zhang and N Zhang ldquoNetwork target for screeningsynergistic drug combinations with application to traditionalChinese medicinerdquo BMC Systems Biology vol 5 supplement 1p S10 2011
[8] S Zhao and S Li ldquoNetwork-based relating pharmacological andgenomic spaces for drug target identificationrdquo PLoS ONE vol5 no 7 Article ID e11764 2010
[9] X Liang H Li and S Li ldquoA novel network pharmacologyapproach to analyse traditional herbal formulae the Liu-Wei-Di-Huang pill as a case studyrdquoMolecular BioSystems vol 10 no5 pp 1014ndash1022 2014
[10] E L Leung Z-W Cao Z-H Jiang H Zhou and L LiuldquoNetwork-based drug discovery by integrating systems biologyand computational technologiesrdquo Briefings in Bioinformaticsvol 14 no 4 pp 491ndash505 2013
[11] V Sharma and I N Sarkar ldquoBioinformatics opportunitiesfor identification and study of medicinal plantsrdquo Briefings inBioinformatics vol 14 no 2 pp 238ndash250 2013
Evidence-Based Complementary and Alternative Medicine 9
[12] S Li and B Zhang ldquoTraditional Chinese medicine networkpharmacology theory methodology and applicationrdquo ChineseJournal of Natural Medicines vol 11 no 2 pp 110ndash120 2013
[13] M Ashburner C A Ball J A Blake et al ldquoGene ontology toolfor the unification of biologyrdquoNature Genetics vol 25 no 1 pp25ndash29 2000
[14] A P Davis B L King S Mockus et al ldquoThe comparativetoxicogenomics database update 2011rdquo Nucleic Acids Researchvol 39 no 1 pp D1067ndashD1072 2011
[15] D S Wishart C Knox A C Guo et al ldquoDrugBank a knowl-edgebase for drugs drug actions and drug targetsrdquoNucleic AcidsResearch vol 36 no 1 pp D901ndashD906 2008
[16] T S Keshava Prasad RGoel K Kandasamy et al ldquoHumanpro-tein reference databasemdash2009 updaterdquo Nucleic Acids Researchvol 37 no 1 pp D767ndashD772 2009
[17] B Zhang X Wang and S Li ldquoAn integrative platform of TCMnetwork pharmacology and its application on a herbal formulaQing-Luo-Yinrdquo Evidence-Based Complementary and AlternativeMedicine vol 2013 Article ID 456747 12 pages 2013
[18] A E Koch ldquoAngiogenesis implications for rheumatoid arthri-tisrdquo Arthritis amp Rheumatism vol 41 no 6 pp 951ndash962 1998
[19] M Feldmann F M Brennan and R N Maini ldquoRole ofcytokines in rheumatoid arthritisrdquo Annual Review of Immunol-ogy vol 14 pp 397ndash440 1996
[20] E H S Choy and G S Panayi ldquoCytokine pathways andjoint inflammation in rheumatoid arthritisrdquo The New EnglandJournal of Medicine vol 344 no 12 pp 907ndash916 2001
[21] G Janossy G Panayi O Duke M Bofill L W Poulterand G Goldstein ldquoRheumatoid arthritis a disease of T-lymphocytemacrophage immunoregulationrdquo The Lancet vol2 no 8251 pp 839ndash842 1981
[22] S S Makarov ldquoNF-120581B in rheumatoid arthritis a pivotal reg-ulator of inflammation hyperplasia and tissue destructionrdquoArthritis Research vol 3 no 4 pp 200ndash206 2001
[23] M Cutolo A Sulli B Villaggio B Seriolo and S AccardoldquoRelations between steroid hormones and cytokines in rheuma-toid arthritis and systemic lupus erythematosusrdquo Annals of theRheumatic Diseases vol 57 no 10 pp 573ndash577 1998
[24] P E Lipsky D M van der Heijde E W St Clair et al ldquoAnti-TumorNecrosis Factor Trial in RheumatoidArthritis with Con-comitant Therapy Study Group Infliximab and methotrexatein the treatment of rheumatoid arthritis Anti-Tumor NecrosisFactor Trial in Rheumatoid Arthritis with Concomitant Ther-apy Study Grouprdquo The New England Journal of Medicine vol343 no 22 pp 1594ndash1602 2000
[25] V Strand S Cohen M Schiff et al ldquoTreatment of activerheumatoid arthritis with leflunomide compared with placeboand methotrexate Leflunomide Rheumatoid Arthritis Investi-gators Grouprdquo Archives of Internal Medicine vol 159 no 21 pp2542ndash2550 1999
[26] J R Kirwan ldquoThe effect of glucocorticoids on joint destructionin rheumatoid arthritisrdquoThe New England Journal of Medicinevol 333 no 3 pp 142ndash146 1995
[27] S R de Antonio H M Blotta R L Mamoni et al ldquoEffects ofdexamethasone on lymphocyte proliferation and cytokine pro-duction in rheumatoid arthritisrdquoThe Journal of Rheumatologyvol 29 no 1 pp 46ndash51 2002
[28] J R OrsquoDell ldquoTherapeutic strategies for rheumatoid arthritisrdquoTheNew England Journal of Medicine vol 350 no 25 pp 2591ndash2602 2004
[29] S Li Z Q Zhang L JWu X G Zhang Y D Li andY YWangldquoUnderstanding ZHENG in traditional Chinese medicine inthe context of neuro-endocrine-immune networkrdquo IET SystemsBiology vol 1 no 1 pp 51ndash60 2007
[30] R Li T Ma J Gu X Liang and S Li ldquoImbalanced networkbiomarkers for traditional Chinese medicine Syndrome ingastritis patientsrdquo Scientific Reports vol 3 article 1543 2013
[31] G Chen C Lu Q Zha et al ldquoA network-based analysis oftraditional Chinese medicine cold and hot patterns in rheuma-toid arthritisrdquo Complementary Therapies in Medicine vol 20no 1-2 pp 23ndash30 2012
[32] H A van Wietmarschen W Dai A J van der Kooij et alldquoCharacterization of rheumatoid arthritis subtypes using symp-tom profiles clinical chemistry and metabolomics measure-mentsrdquo PLoS ONE vol 7 no 9 Article ID e44331 2012
Submit your manuscripts athttpwwwhindawicom
Stem CellsInternational
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
MEDIATORSINFLAMMATION
of
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Behavioural Neurology
EndocrinologyInternational Journal of
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Disease Markers
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
BioMed Research International
OncologyJournal of
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Oxidative Medicine and Cellular Longevity
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
PPAR Research
The Scientific World JournalHindawi Publishing Corporation httpwwwhindawicom Volume 2014
Immunology ResearchHindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Journal of
ObesityJournal of
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Computational and Mathematical Methods in Medicine
OphthalmologyJournal of
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Diabetes ResearchJournal of
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Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Research and TreatmentAIDS
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Gastroenterology Research and Practice
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Parkinsonrsquos Disease
Evidence-Based Complementary and Alternative Medicine
Volume 2014Hindawi Publishing Corporationhttpwwwhindawicom
Evidence-Based Complementary and Alternative Medicine 5
Lian Qiao
Hu Zhang Dai MaoRou Gui
Ku Shen
Bi Xie
Wu Shao She
Qin Jiao
Man Jing Zi
Han Lian Cao
Chai Hu
Wu Wei Zi
Bai Mao Gen
Wei Ling Xian
Qing Feng Teng
Zhi Mu
Wu Tou
Huo Xue Teng
Lei Gong Teng
Huang Bai
Ji XueTengHuang Qi
Pu Gong Ying
Ren Dong Teng
(a)
Man Jing Zi
Wu Tou
Bi Xie
Ji Xue Teng
Zhi Mu
Qin JiaoWu Shao She
Ku ShenHuo Xue Teng
Qing Feng Teng
Pu Gong Ying
Lei Gong Teng
Huang Bai
Ren Dong Teng
(b)
Figure 2 The core intersection herb networks constructed fromMr Ji-Ren Lirsquos anti-RA herbal prescriptions (a) The herb subnet-works around each top frequent herb for example Huo Xue Teng(Sargentodoxa cuneata the top 2 herb) (b) The intersection herbnetwork created from the intersection herb networks of the top tenfrequent herbs Four herbs circled by the green line are a completeformula of Qing-Luo-Yin
of further study Note that other nonoverlapping GO termsassociated with herbs such as the steroid hormone receptorsignaling pathway also contributed a lot to the progressof RA [23] Moreover by pathway enrichment analysis wefurther found that both the RA genes and herb targetsare significantly enriched in the pathway of ldquorheumatoidarthritisrdquo (KEGG05323) (corrected 119875 = 155119890 minus 15 for RAgenes and 119875 = 283119890 minus 12 for herb targets resp) Figure 4shows the details of the network associations of RA genesandherb targets in theKEGGldquorheumatoid arthritisrdquo pathwayproviding additional evidence for the anti-RA effects of MrLirsquos herbal prescriptions These results suggest that the top15 frequent herbs have a potential to treat RA patients byintervening in the critical biological processes and pathway
Qing Feng Teng
Ku Shen
(a)
1
09
08
07
06
05
04
03
02
01
SinomenineDisinomenine
SinacutineAcutumineTuduranine
MagnoflorineIsosinomenine
MichelalbineBianfugenineStepharanine
Mat
rine
NIM
S sc
ore
Kura
rinon
eKu
rara
min
eBa
ptifo
line
Lehm
anin
eBe
ta-s
itoste
rol
Kush
enol
lCa
mph
orKo
sam
ol a
Gua
ijave
rin
Qin
g Fe
ng T
eng
Ku Shen
(b)
Figure 3 Calculation of synergistic activity among compoundscollected from the core herb networks (a) A part of the synergisticmodule from compounds of Qing Feng Teng (Caulis Sinomenii)and Ku Shen (Radix Sophorae flavescentis) (b) The horizontal andvertical axes show the compounds of herbs and the intervals ofaxis represent herbs The dark areas illustrate a modular featureand indicate strong synergistic interactions of herbs with highsynergistic scores calculated by the NIMS method
of RA which in turn gives evidence for the rationality of thecommonly prescribed herbs in Mr Lirsquos clinical practice
34 Network Connections of Anti-RA Herbs and Drugs InTCM RA patients can be categorized to different syndromes(ZHENG in Mandarin) for example Cold Syndrome andHot Syndrome Accordingly as shown in Table 1 Cold HotWarm Cool and Neutral are the basic properties of herbsreflecting the traditional characteristic of TCM TypicallyTCM doctors always use Cool or Cold herbs to treat patientswith Hot Syndrome whereas they use Warm or Hot herbsto treat patients with Cold Syndrome Cold-tendency andHot-tendency herbs may be combined to treat RA patientswith mixed Hot and Cold Syndromes On the other handin modern medicine immunomodulatory drugs such as
6 Evidence-Based Complementary and Alternative Medicine
Th17 cellTGF120573
Synovial macrophage
T cell receptor
Antigen
DC
Rheumatoid arthritis
CD8086
MHCII
IgGSDF1
VEGF
CCL2 CXCL1CXCL5CCL3
CCL20 Ang1IL8Tie2Flt1
AP1TLR24LPSPeptidoglycan
signaling pathwayToll-like receptor
Autoantibody production
B cell
APRIL
RANKL
CD28CTLA4
TCR
LFA1
ICAM1
IL15
IL6
Synovium
Bone
IL23
MCSF
RANKL
RANKL RANK
CTSKTRAP
CTSLMMP13 Joint destruction
Inflammation
Angiogenesis
Leukocyte migration
Blood vessel
VEGF signaling pathway
Inflammatory
Synovial pannus
Bone resorption
V-ATPase
Osteoblast
Osteoclast
Osteoclast
differentiation
Synovial fibroblast
PTHVitamin D3
IL11
IL17
IL1IL6
IL6
CCL5IL1120573
GMCSF
IL18
BLYS
Self-reactiveTh1 cell
signaling pathwayLT120573
IFN120574
TNF120572
PGE2
H+
cell infiltration
formation
Herb targetRA gene
Figure 4 Network association of RA genes and top 15 frequent herbsrsquo targets in the enriched KEGG ldquorheumatoid arthritisrdquo pathway (KEGG05323)
methotrexate and leflunomide [24 25] and hormones such asglucocorticoids (dexamethasone) [26 27] are two categoriesof medicines for the treatment of patients with rheumatoidarthritis [28] Both categories of medicines can improve thequality of life and delay the disease progression of RA patientsvia independent but interactivemechanism of actions By cal-culating compound networks from the top 50 frequent herbsin Mr Lirsquos prescriptions we obtained the herbs that containingredients similar to RA immunomodulatory drugs andhormones respectively As shown in Figure 5 many herbscontain compounds with targets connected to the selectedanti-RA drugs in the network and may exert similar actionson RA For example 9 out of top 10 herbs with differentproperties such as Cold and Hot (Table 1) have compoundsthat are closely clustered with RA immune and hormonedrugs in the network These results are meaningful sincerecent studies indicated that the metabolism and immuneimbalance are closely associated with patients suffering fromCold Syndrome and Hot Syndrome [29 30] in many diseasesincluding rheumatoid arthritis [31 32] Interestingly it isnoticed that the Cold herbs tend to be enriched in theimmune-herb cluster Hot herbs tend to be enriched inhormone-herb cluster and Warm herbs are enriched in bothclusters Moreover compared with the hormone-herb cluster(Figure 5(b)) the immune-herb cluster is less diverse andonly contains Cold and Warm herbs suggesting these herbstend to exert immunosuppressive or immunoenhancementactions (Figure 5(a)) Although the results are preliminary
the potential connection as well as combinational effectsbetween herbs and drugs is of great importance and deservesfurther investigation in larger samples and clinical or experi-mental studies
4 Conclusions
In summary we developed a TCM network pharmacologystrategy and an Herb-Compound-Target-Disease coherentnetwork analysis framework to study herbal prescriptionsthe main form of TCM clinical practice We extracted twotypes of core herb networks from871 anti-RAherbal formulaeprescribed by a famous TCM doctor From the core herb net-works our network-based strategy identified cooccurrenceherbs and herb pairs with potential synergistic activities Wealso predicted the biological basis of the core herb networkby calculating the compoundrsquos targets from most frequentherbs We detected that targets of the commonly prescribedherbs are enriched together with RA genes in critical bio-logical processes and pathway of RA We also indicated thatherbs with different properties in prescriptions may have apotential connection with RA immunomodulatory drugs orhormones in the compound networks Taken together theseresults could help uncover the prescription rules underlyingherbal formulae in the clinical practice of TCM practitionersMoreover such network-based analyses not only can developa holistic understanding of herbal remedies but also mayfacilitate the following pharmacological evaluation of herbal
Evidence-Based Complementary and Alternative Medicine 7
Ethylsalicylate
Hinesol
Campesterol
Taraxerone
AtractylenolideI
Leflunomide
Chen PiAngelicideBai
Shao
PaeonilactoneC
QiangHuo
Bai Zhu Albiflorin R1Sheng
DiHuang
ChiShao
Mai Ya
ManJing Zi Fang
Feng
KuShen
QingFengTeng
DangGui
Benzothiazole
Adrenocorticotropichormone
Folic acid
Chromone
Methotrexate
Lupenone
Dipterocarpol
Perrimustine
GuaiolIsofucosterol
120573-cryptoxanthin
Herb
Compound or drug
TengJi Xue
JiangHuang
DanShen
WuGong
HuangQi
ChuanXiong
3-Hydroxymugineicacid
Thiolproteaseinhibitor
Listomin S
Pseudocarpaine
Ciclosporin
Goitrin
Dihydro-2-methyl-3(2H)-furanone
Acetamide
Acetoin
Bornylacetate
Sophoranol
Tacrolimus
SandaracopimaricacidViridiflorol
Stigmasterin
Cholesterol
Ro 09-0680Phenylacetaldehyde
DAU 6215 hydrochloride
AC1L7QUY
Levamisolehydrochloride
Thalidomide
Mugineicacid
Benzoyl-dl-leucine
Ethanamine
Permanentorange
acid
Metarene
Laccase
AC1L7VXU
4-Hydroxymephenytoin
NSC673109
Procurcumenol Dehydrocurdione
Zeaxanthin
C09772
Olean-18-en-3-one
45-epoxide
100347-96-4
trans-Sabinenehydrate
CampheneVitamin D3
3-Oxo-1113(18)-oleanadien-28-oicacid
acid
6-Methylcholest-4-en-3-oneAspartylglucosamine
7-Dehydrostigmasterol
Cyclosporine
(4S5S)-(+)-germacrone
(5|A8|A9|A10|A16|A)-16-hydroxykauran-18-oic
(ZZ998400)-diligustilide
120575-terpineol
120573-sitosterol
51205729120572-dihydroxymatrine
2998400-Deoxymugineic
acetate
(a)
Apioglycyrrhizin
UralsaponinB
InflasaponinIV
InflasaponinI
Glycamil
Glycyrrhizicacid
ammoniumsalt
Glyuranolide
Glycyrrhizinicacid
AraboglycyrrhizinLiquoric acid
SophoraflavosideIV
GibberellinA1
CinncassiolA
Napellonine
CinncassiolC3
SophoraflavosideIII
Shanzhisidemethyl ester
Dexamethasone
Palbinone
Triamcinolone
LeiGongTeng
Ge Gen
WeiLingXian
QuanXie
RenDongTeng
Wu Tou
Fu Zi
Sang Ji Sheng
RuXiang
120572-boswellicacid
Rehmannicacid
Loganin
Tutin
acid
Loganic acid
NSC302037
Glycyrrhetinicacid
Prednisone
24-Hydroxyglycyrrheticacid
Corianin
3-Glc-soyasapogenolE
Glabric acidPaeonilactone
B
Cinncassiol E
Ecdysterone
Uralenolide
Asiatic acid
120573-glycyrrhetinicacid
Oleanolicacid
Geigerinin
CinncassiolC2
Tigogenin
Neotigogenin
GlycyrrhetolKatonic acid
Kihadanin A
Cortisone
Triptonide
Bufotoxin
Helixin
Inokosterone
Methylprednisolone
PrednisoloneTriptolideGibberellic
acidCaryoptoside
Triptolideanalog
Hydrocortisone
Gui Zhi
GanCao
XuDuan
Cold
Warm
Hormone drug
Immunomodulatory drug
Hot
Cool
Tu Fu LingHuang
Bai
Neutral
Niu Xi
Du Huo
Zhi Mu
Mu Gua
ShanZha
Pinnatifidin
(25S)-5120573-spirostan-3120573-ol
11-Keto-120573-boswellicacid
Acetyloleanolicacid
Corosolicacid
Boswellicacid
(5xi13|A14|A20s23r24s)-2324-dihydroxy-25-methoxylanost-7-en-3-one
(3|A20|A)-3-hydroxy-11-oxo-olean-12-en-29-oic
Herb
Compound or drug
(b)
Figure 5 Possible connection between RA herbs and drugs in the networks consisting of herbs herbal compounds immunomodulatorydrugs (a) and hormones (b)
8 Evidence-Based Complementary and Alternative Medicine
Table 2 Overlapped RA-related GO terms between top 15 herbtargets and RA genes
Category Enriched GO terms Corrected119875-value
Herbtargets
Response to wounding 238119890 minus 127
Angiogenesis 121119890 minus 26
Inflammatory response 860119890 minus 71
Regulation of cytokine production 612119890 minus 26
Immune response 261119890 minus 88
Leukocyte activation 341119890 minus 38
Regulation of lymphocyte activation 452119890 minus 23
Defense response to bacterium 356119890 minus 10
Positive regulation of NF-120581Btranscription factor activity 604119890 minus 12
RA genes
Response to wounding 148119890 minus 15
Angiogenesis 579119890 minus 6
Inflammatory response 576119890 minus 26
Regulation of cytokine production 165119890 minus 26
Immune response 629119890 minus 39
Leukocyte activation 728119890 minus 30
Regulation of lymphocyte activation 125119890 minus 31
Defense response to bacterium 727119890 minus 12
Positive regulation of NF-120581Btranscription factor activity 254119890 minus 6
treatments Clearly this study is only the first step to learnthe common rule of herbal prescriptions We will continueto conduct in-depth analysis for understanding the scientificbasis of herbal prescriptions in our future work Althoughmore powerful methods more data on TCM prescriptionsand clinical or experimental evaluations are still requiredwe believe that this TCM network pharmacology strategy issuitable to study herbal formulae both in the herb level andin the molecular level and thus can serve as a novel approachto further understand the professional experience embeddedin TCM prescriptions
Abbreviations
DMIM Distance-based mutual information modeldrugCIPHER Drug-target prediction by correlating
protein interaction network andphenotype network
GO Gene ontologyMI Mutual informationNIMS Network-based identification of
multicomponent synergyRA Rheumatoid arthritisPPI Protein-protein interactionQLY Qing-Luo-YinTCM Traditional Chinese Medicine
Conflict of Interests
The authors declare that they have no competing interests
Authorsrsquo Contribution
Shao Li conceived the study Yan Li collected the data Shao LiYan Li Rui Li and Zibo Ouyang analyzed the data and wrotethe paper All authors read and approved the final paper
Acknowledgments
Thanks to Kai Zhang for his help in herbal prescription col-lection This work is supported by NSFC project (81225025)the SATCM key discipline of ldquoTCM Bi-Bingrdquo in YijishanHospital of WannanMedical College the SATCM laboratoryof TCM master Ji-Ren Li the CATCM project and AnhuirsquosKey Technologies RampD project (11010402173)
References
[1] G G Zhang W Lee B Bausell L Lao B Handwerger andB Berman ldquoVariability in the traditional Chinese medicine(TCM) diagnoses and herbal prescriptions provided by threeTCM practitioners for 40 patients with rheumatoid arthritisrdquoJournal of Alternative and Complementary Medicine vol 11 no3 pp 415ndash421 2005
[2] G G Zhang B Singh W Lee B Handwerger L Lao and BBerman ldquoImprovement of agreement in TCMdiagnosis amongTCM practitioners for persons with the conventional diagnosisof rheumatoid arthritis effect of trainingrdquo Journal of Alternativeand Complementary Medicine vol 14 no 4 pp 381ndash386 2008
[3] P Zhang J Li Y Han X W Yu and L Qin ldquoTraditionalChinese medicine in the treatment of rheumatoid arthritis ageneral reviewrdquo Rheumatology International vol 30 no 6 pp713ndash718 2010
[4] Y Li 100 TCM Practitioners in Latest 100 Years Li Ji-ren ampZhang Shun-hua China Press of Traditional Chinese MedicineBeijing China 2004
[5] C Shu Z Li and Y Li ldquoGrand Master of TCM Ji-Ren Lirsquosexperience on the treatment of Bi Zhengrdquo Forum on TraditionalChinese Medicine vol 27 pp 10ndash12 2012
[6] S Li B Zhang D Jiang Y Wei and N Zhang ldquoHerbnetwork construction and co-module analysis for uncoveringthe combination rule of traditional Chinese herbal formulaerdquoBMC Bioinformatics vol 11 supplement 11 article S6 2010
[7] S Li B Zhang and N Zhang ldquoNetwork target for screeningsynergistic drug combinations with application to traditionalChinese medicinerdquo BMC Systems Biology vol 5 supplement 1p S10 2011
[8] S Zhao and S Li ldquoNetwork-based relating pharmacological andgenomic spaces for drug target identificationrdquo PLoS ONE vol5 no 7 Article ID e11764 2010
[9] X Liang H Li and S Li ldquoA novel network pharmacologyapproach to analyse traditional herbal formulae the Liu-Wei-Di-Huang pill as a case studyrdquoMolecular BioSystems vol 10 no5 pp 1014ndash1022 2014
[10] E L Leung Z-W Cao Z-H Jiang H Zhou and L LiuldquoNetwork-based drug discovery by integrating systems biologyand computational technologiesrdquo Briefings in Bioinformaticsvol 14 no 4 pp 491ndash505 2013
[11] V Sharma and I N Sarkar ldquoBioinformatics opportunitiesfor identification and study of medicinal plantsrdquo Briefings inBioinformatics vol 14 no 2 pp 238ndash250 2013
Evidence-Based Complementary and Alternative Medicine 9
[12] S Li and B Zhang ldquoTraditional Chinese medicine networkpharmacology theory methodology and applicationrdquo ChineseJournal of Natural Medicines vol 11 no 2 pp 110ndash120 2013
[13] M Ashburner C A Ball J A Blake et al ldquoGene ontology toolfor the unification of biologyrdquoNature Genetics vol 25 no 1 pp25ndash29 2000
[14] A P Davis B L King S Mockus et al ldquoThe comparativetoxicogenomics database update 2011rdquo Nucleic Acids Researchvol 39 no 1 pp D1067ndashD1072 2011
[15] D S Wishart C Knox A C Guo et al ldquoDrugBank a knowl-edgebase for drugs drug actions and drug targetsrdquoNucleic AcidsResearch vol 36 no 1 pp D901ndashD906 2008
[16] T S Keshava Prasad RGoel K Kandasamy et al ldquoHumanpro-tein reference databasemdash2009 updaterdquo Nucleic Acids Researchvol 37 no 1 pp D767ndashD772 2009
[17] B Zhang X Wang and S Li ldquoAn integrative platform of TCMnetwork pharmacology and its application on a herbal formulaQing-Luo-Yinrdquo Evidence-Based Complementary and AlternativeMedicine vol 2013 Article ID 456747 12 pages 2013
[18] A E Koch ldquoAngiogenesis implications for rheumatoid arthri-tisrdquo Arthritis amp Rheumatism vol 41 no 6 pp 951ndash962 1998
[19] M Feldmann F M Brennan and R N Maini ldquoRole ofcytokines in rheumatoid arthritisrdquo Annual Review of Immunol-ogy vol 14 pp 397ndash440 1996
[20] E H S Choy and G S Panayi ldquoCytokine pathways andjoint inflammation in rheumatoid arthritisrdquo The New EnglandJournal of Medicine vol 344 no 12 pp 907ndash916 2001
[21] G Janossy G Panayi O Duke M Bofill L W Poulterand G Goldstein ldquoRheumatoid arthritis a disease of T-lymphocytemacrophage immunoregulationrdquo The Lancet vol2 no 8251 pp 839ndash842 1981
[22] S S Makarov ldquoNF-120581B in rheumatoid arthritis a pivotal reg-ulator of inflammation hyperplasia and tissue destructionrdquoArthritis Research vol 3 no 4 pp 200ndash206 2001
[23] M Cutolo A Sulli B Villaggio B Seriolo and S AccardoldquoRelations between steroid hormones and cytokines in rheuma-toid arthritis and systemic lupus erythematosusrdquo Annals of theRheumatic Diseases vol 57 no 10 pp 573ndash577 1998
[24] P E Lipsky D M van der Heijde E W St Clair et al ldquoAnti-TumorNecrosis Factor Trial in RheumatoidArthritis with Con-comitant Therapy Study Group Infliximab and methotrexatein the treatment of rheumatoid arthritis Anti-Tumor NecrosisFactor Trial in Rheumatoid Arthritis with Concomitant Ther-apy Study Grouprdquo The New England Journal of Medicine vol343 no 22 pp 1594ndash1602 2000
[25] V Strand S Cohen M Schiff et al ldquoTreatment of activerheumatoid arthritis with leflunomide compared with placeboand methotrexate Leflunomide Rheumatoid Arthritis Investi-gators Grouprdquo Archives of Internal Medicine vol 159 no 21 pp2542ndash2550 1999
[26] J R Kirwan ldquoThe effect of glucocorticoids on joint destructionin rheumatoid arthritisrdquoThe New England Journal of Medicinevol 333 no 3 pp 142ndash146 1995
[27] S R de Antonio H M Blotta R L Mamoni et al ldquoEffects ofdexamethasone on lymphocyte proliferation and cytokine pro-duction in rheumatoid arthritisrdquoThe Journal of Rheumatologyvol 29 no 1 pp 46ndash51 2002
[28] J R OrsquoDell ldquoTherapeutic strategies for rheumatoid arthritisrdquoTheNew England Journal of Medicine vol 350 no 25 pp 2591ndash2602 2004
[29] S Li Z Q Zhang L JWu X G Zhang Y D Li andY YWangldquoUnderstanding ZHENG in traditional Chinese medicine inthe context of neuro-endocrine-immune networkrdquo IET SystemsBiology vol 1 no 1 pp 51ndash60 2007
[30] R Li T Ma J Gu X Liang and S Li ldquoImbalanced networkbiomarkers for traditional Chinese medicine Syndrome ingastritis patientsrdquo Scientific Reports vol 3 article 1543 2013
[31] G Chen C Lu Q Zha et al ldquoA network-based analysis oftraditional Chinese medicine cold and hot patterns in rheuma-toid arthritisrdquo Complementary Therapies in Medicine vol 20no 1-2 pp 23ndash30 2012
[32] H A van Wietmarschen W Dai A J van der Kooij et alldquoCharacterization of rheumatoid arthritis subtypes using symp-tom profiles clinical chemistry and metabolomics measure-mentsrdquo PLoS ONE vol 7 no 9 Article ID e44331 2012
Submit your manuscripts athttpwwwhindawicom
Stem CellsInternational
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
MEDIATORSINFLAMMATION
of
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Behavioural Neurology
EndocrinologyInternational Journal of
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Disease Markers
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
BioMed Research International
OncologyJournal of
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Oxidative Medicine and Cellular Longevity
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
PPAR Research
The Scientific World JournalHindawi Publishing Corporation httpwwwhindawicom Volume 2014
Immunology ResearchHindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Journal of
ObesityJournal of
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Computational and Mathematical Methods in Medicine
OphthalmologyJournal of
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Diabetes ResearchJournal of
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Research and TreatmentAIDS
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Gastroenterology Research and Practice
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Parkinsonrsquos Disease
Evidence-Based Complementary and Alternative Medicine
Volume 2014Hindawi Publishing Corporationhttpwwwhindawicom
6 Evidence-Based Complementary and Alternative Medicine
Th17 cellTGF120573
Synovial macrophage
T cell receptor
Antigen
DC
Rheumatoid arthritis
CD8086
MHCII
IgGSDF1
VEGF
CCL2 CXCL1CXCL5CCL3
CCL20 Ang1IL8Tie2Flt1
AP1TLR24LPSPeptidoglycan
signaling pathwayToll-like receptor
Autoantibody production
B cell
APRIL
RANKL
CD28CTLA4
TCR
LFA1
ICAM1
IL15
IL6
Synovium
Bone
IL23
MCSF
RANKL
RANKL RANK
CTSKTRAP
CTSLMMP13 Joint destruction
Inflammation
Angiogenesis
Leukocyte migration
Blood vessel
VEGF signaling pathway
Inflammatory
Synovial pannus
Bone resorption
V-ATPase
Osteoblast
Osteoclast
Osteoclast
differentiation
Synovial fibroblast
PTHVitamin D3
IL11
IL17
IL1IL6
IL6
CCL5IL1120573
GMCSF
IL18
BLYS
Self-reactiveTh1 cell
signaling pathwayLT120573
IFN120574
TNF120572
PGE2
H+
cell infiltration
formation
Herb targetRA gene
Figure 4 Network association of RA genes and top 15 frequent herbsrsquo targets in the enriched KEGG ldquorheumatoid arthritisrdquo pathway (KEGG05323)
methotrexate and leflunomide [24 25] and hormones such asglucocorticoids (dexamethasone) [26 27] are two categoriesof medicines for the treatment of patients with rheumatoidarthritis [28] Both categories of medicines can improve thequality of life and delay the disease progression of RA patientsvia independent but interactivemechanism of actions By cal-culating compound networks from the top 50 frequent herbsin Mr Lirsquos prescriptions we obtained the herbs that containingredients similar to RA immunomodulatory drugs andhormones respectively As shown in Figure 5 many herbscontain compounds with targets connected to the selectedanti-RA drugs in the network and may exert similar actionson RA For example 9 out of top 10 herbs with differentproperties such as Cold and Hot (Table 1) have compoundsthat are closely clustered with RA immune and hormonedrugs in the network These results are meaningful sincerecent studies indicated that the metabolism and immuneimbalance are closely associated with patients suffering fromCold Syndrome and Hot Syndrome [29 30] in many diseasesincluding rheumatoid arthritis [31 32] Interestingly it isnoticed that the Cold herbs tend to be enriched in theimmune-herb cluster Hot herbs tend to be enriched inhormone-herb cluster and Warm herbs are enriched in bothclusters Moreover compared with the hormone-herb cluster(Figure 5(b)) the immune-herb cluster is less diverse andonly contains Cold and Warm herbs suggesting these herbstend to exert immunosuppressive or immunoenhancementactions (Figure 5(a)) Although the results are preliminary
the potential connection as well as combinational effectsbetween herbs and drugs is of great importance and deservesfurther investigation in larger samples and clinical or experi-mental studies
4 Conclusions
In summary we developed a TCM network pharmacologystrategy and an Herb-Compound-Target-Disease coherentnetwork analysis framework to study herbal prescriptionsthe main form of TCM clinical practice We extracted twotypes of core herb networks from871 anti-RAherbal formulaeprescribed by a famous TCM doctor From the core herb net-works our network-based strategy identified cooccurrenceherbs and herb pairs with potential synergistic activities Wealso predicted the biological basis of the core herb networkby calculating the compoundrsquos targets from most frequentherbs We detected that targets of the commonly prescribedherbs are enriched together with RA genes in critical bio-logical processes and pathway of RA We also indicated thatherbs with different properties in prescriptions may have apotential connection with RA immunomodulatory drugs orhormones in the compound networks Taken together theseresults could help uncover the prescription rules underlyingherbal formulae in the clinical practice of TCM practitionersMoreover such network-based analyses not only can developa holistic understanding of herbal remedies but also mayfacilitate the following pharmacological evaluation of herbal
Evidence-Based Complementary and Alternative Medicine 7
Ethylsalicylate
Hinesol
Campesterol
Taraxerone
AtractylenolideI
Leflunomide
Chen PiAngelicideBai
Shao
PaeonilactoneC
QiangHuo
Bai Zhu Albiflorin R1Sheng
DiHuang
ChiShao
Mai Ya
ManJing Zi Fang
Feng
KuShen
QingFengTeng
DangGui
Benzothiazole
Adrenocorticotropichormone
Folic acid
Chromone
Methotrexate
Lupenone
Dipterocarpol
Perrimustine
GuaiolIsofucosterol
120573-cryptoxanthin
Herb
Compound or drug
TengJi Xue
JiangHuang
DanShen
WuGong
HuangQi
ChuanXiong
3-Hydroxymugineicacid
Thiolproteaseinhibitor
Listomin S
Pseudocarpaine
Ciclosporin
Goitrin
Dihydro-2-methyl-3(2H)-furanone
Acetamide
Acetoin
Bornylacetate
Sophoranol
Tacrolimus
SandaracopimaricacidViridiflorol
Stigmasterin
Cholesterol
Ro 09-0680Phenylacetaldehyde
DAU 6215 hydrochloride
AC1L7QUY
Levamisolehydrochloride
Thalidomide
Mugineicacid
Benzoyl-dl-leucine
Ethanamine
Permanentorange
acid
Metarene
Laccase
AC1L7VXU
4-Hydroxymephenytoin
NSC673109
Procurcumenol Dehydrocurdione
Zeaxanthin
C09772
Olean-18-en-3-one
45-epoxide
100347-96-4
trans-Sabinenehydrate
CampheneVitamin D3
3-Oxo-1113(18)-oleanadien-28-oicacid
acid
6-Methylcholest-4-en-3-oneAspartylglucosamine
7-Dehydrostigmasterol
Cyclosporine
(4S5S)-(+)-germacrone
(5|A8|A9|A10|A16|A)-16-hydroxykauran-18-oic
(ZZ998400)-diligustilide
120575-terpineol
120573-sitosterol
51205729120572-dihydroxymatrine
2998400-Deoxymugineic
acetate
(a)
Apioglycyrrhizin
UralsaponinB
InflasaponinIV
InflasaponinI
Glycamil
Glycyrrhizicacid
ammoniumsalt
Glyuranolide
Glycyrrhizinicacid
AraboglycyrrhizinLiquoric acid
SophoraflavosideIV
GibberellinA1
CinncassiolA
Napellonine
CinncassiolC3
SophoraflavosideIII
Shanzhisidemethyl ester
Dexamethasone
Palbinone
Triamcinolone
LeiGongTeng
Ge Gen
WeiLingXian
QuanXie
RenDongTeng
Wu Tou
Fu Zi
Sang Ji Sheng
RuXiang
120572-boswellicacid
Rehmannicacid
Loganin
Tutin
acid
Loganic acid
NSC302037
Glycyrrhetinicacid
Prednisone
24-Hydroxyglycyrrheticacid
Corianin
3-Glc-soyasapogenolE
Glabric acidPaeonilactone
B
Cinncassiol E
Ecdysterone
Uralenolide
Asiatic acid
120573-glycyrrhetinicacid
Oleanolicacid
Geigerinin
CinncassiolC2
Tigogenin
Neotigogenin
GlycyrrhetolKatonic acid
Kihadanin A
Cortisone
Triptonide
Bufotoxin
Helixin
Inokosterone
Methylprednisolone
PrednisoloneTriptolideGibberellic
acidCaryoptoside
Triptolideanalog
Hydrocortisone
Gui Zhi
GanCao
XuDuan
Cold
Warm
Hormone drug
Immunomodulatory drug
Hot
Cool
Tu Fu LingHuang
Bai
Neutral
Niu Xi
Du Huo
Zhi Mu
Mu Gua
ShanZha
Pinnatifidin
(25S)-5120573-spirostan-3120573-ol
11-Keto-120573-boswellicacid
Acetyloleanolicacid
Corosolicacid
Boswellicacid
(5xi13|A14|A20s23r24s)-2324-dihydroxy-25-methoxylanost-7-en-3-one
(3|A20|A)-3-hydroxy-11-oxo-olean-12-en-29-oic
Herb
Compound or drug
(b)
Figure 5 Possible connection between RA herbs and drugs in the networks consisting of herbs herbal compounds immunomodulatorydrugs (a) and hormones (b)
8 Evidence-Based Complementary and Alternative Medicine
Table 2 Overlapped RA-related GO terms between top 15 herbtargets and RA genes
Category Enriched GO terms Corrected119875-value
Herbtargets
Response to wounding 238119890 minus 127
Angiogenesis 121119890 minus 26
Inflammatory response 860119890 minus 71
Regulation of cytokine production 612119890 minus 26
Immune response 261119890 minus 88
Leukocyte activation 341119890 minus 38
Regulation of lymphocyte activation 452119890 minus 23
Defense response to bacterium 356119890 minus 10
Positive regulation of NF-120581Btranscription factor activity 604119890 minus 12
RA genes
Response to wounding 148119890 minus 15
Angiogenesis 579119890 minus 6
Inflammatory response 576119890 minus 26
Regulation of cytokine production 165119890 minus 26
Immune response 629119890 minus 39
Leukocyte activation 728119890 minus 30
Regulation of lymphocyte activation 125119890 minus 31
Defense response to bacterium 727119890 minus 12
Positive regulation of NF-120581Btranscription factor activity 254119890 minus 6
treatments Clearly this study is only the first step to learnthe common rule of herbal prescriptions We will continueto conduct in-depth analysis for understanding the scientificbasis of herbal prescriptions in our future work Althoughmore powerful methods more data on TCM prescriptionsand clinical or experimental evaluations are still requiredwe believe that this TCM network pharmacology strategy issuitable to study herbal formulae both in the herb level andin the molecular level and thus can serve as a novel approachto further understand the professional experience embeddedin TCM prescriptions
Abbreviations
DMIM Distance-based mutual information modeldrugCIPHER Drug-target prediction by correlating
protein interaction network andphenotype network
GO Gene ontologyMI Mutual informationNIMS Network-based identification of
multicomponent synergyRA Rheumatoid arthritisPPI Protein-protein interactionQLY Qing-Luo-YinTCM Traditional Chinese Medicine
Conflict of Interests
The authors declare that they have no competing interests
Authorsrsquo Contribution
Shao Li conceived the study Yan Li collected the data Shao LiYan Li Rui Li and Zibo Ouyang analyzed the data and wrotethe paper All authors read and approved the final paper
Acknowledgments
Thanks to Kai Zhang for his help in herbal prescription col-lection This work is supported by NSFC project (81225025)the SATCM key discipline of ldquoTCM Bi-Bingrdquo in YijishanHospital of WannanMedical College the SATCM laboratoryof TCM master Ji-Ren Li the CATCM project and AnhuirsquosKey Technologies RampD project (11010402173)
References
[1] G G Zhang W Lee B Bausell L Lao B Handwerger andB Berman ldquoVariability in the traditional Chinese medicine(TCM) diagnoses and herbal prescriptions provided by threeTCM practitioners for 40 patients with rheumatoid arthritisrdquoJournal of Alternative and Complementary Medicine vol 11 no3 pp 415ndash421 2005
[2] G G Zhang B Singh W Lee B Handwerger L Lao and BBerman ldquoImprovement of agreement in TCMdiagnosis amongTCM practitioners for persons with the conventional diagnosisof rheumatoid arthritis effect of trainingrdquo Journal of Alternativeand Complementary Medicine vol 14 no 4 pp 381ndash386 2008
[3] P Zhang J Li Y Han X W Yu and L Qin ldquoTraditionalChinese medicine in the treatment of rheumatoid arthritis ageneral reviewrdquo Rheumatology International vol 30 no 6 pp713ndash718 2010
[4] Y Li 100 TCM Practitioners in Latest 100 Years Li Ji-ren ampZhang Shun-hua China Press of Traditional Chinese MedicineBeijing China 2004
[5] C Shu Z Li and Y Li ldquoGrand Master of TCM Ji-Ren Lirsquosexperience on the treatment of Bi Zhengrdquo Forum on TraditionalChinese Medicine vol 27 pp 10ndash12 2012
[6] S Li B Zhang D Jiang Y Wei and N Zhang ldquoHerbnetwork construction and co-module analysis for uncoveringthe combination rule of traditional Chinese herbal formulaerdquoBMC Bioinformatics vol 11 supplement 11 article S6 2010
[7] S Li B Zhang and N Zhang ldquoNetwork target for screeningsynergistic drug combinations with application to traditionalChinese medicinerdquo BMC Systems Biology vol 5 supplement 1p S10 2011
[8] S Zhao and S Li ldquoNetwork-based relating pharmacological andgenomic spaces for drug target identificationrdquo PLoS ONE vol5 no 7 Article ID e11764 2010
[9] X Liang H Li and S Li ldquoA novel network pharmacologyapproach to analyse traditional herbal formulae the Liu-Wei-Di-Huang pill as a case studyrdquoMolecular BioSystems vol 10 no5 pp 1014ndash1022 2014
[10] E L Leung Z-W Cao Z-H Jiang H Zhou and L LiuldquoNetwork-based drug discovery by integrating systems biologyand computational technologiesrdquo Briefings in Bioinformaticsvol 14 no 4 pp 491ndash505 2013
[11] V Sharma and I N Sarkar ldquoBioinformatics opportunitiesfor identification and study of medicinal plantsrdquo Briefings inBioinformatics vol 14 no 2 pp 238ndash250 2013
Evidence-Based Complementary and Alternative Medicine 9
[12] S Li and B Zhang ldquoTraditional Chinese medicine networkpharmacology theory methodology and applicationrdquo ChineseJournal of Natural Medicines vol 11 no 2 pp 110ndash120 2013
[13] M Ashburner C A Ball J A Blake et al ldquoGene ontology toolfor the unification of biologyrdquoNature Genetics vol 25 no 1 pp25ndash29 2000
[14] A P Davis B L King S Mockus et al ldquoThe comparativetoxicogenomics database update 2011rdquo Nucleic Acids Researchvol 39 no 1 pp D1067ndashD1072 2011
[15] D S Wishart C Knox A C Guo et al ldquoDrugBank a knowl-edgebase for drugs drug actions and drug targetsrdquoNucleic AcidsResearch vol 36 no 1 pp D901ndashD906 2008
[16] T S Keshava Prasad RGoel K Kandasamy et al ldquoHumanpro-tein reference databasemdash2009 updaterdquo Nucleic Acids Researchvol 37 no 1 pp D767ndashD772 2009
[17] B Zhang X Wang and S Li ldquoAn integrative platform of TCMnetwork pharmacology and its application on a herbal formulaQing-Luo-Yinrdquo Evidence-Based Complementary and AlternativeMedicine vol 2013 Article ID 456747 12 pages 2013
[18] A E Koch ldquoAngiogenesis implications for rheumatoid arthri-tisrdquo Arthritis amp Rheumatism vol 41 no 6 pp 951ndash962 1998
[19] M Feldmann F M Brennan and R N Maini ldquoRole ofcytokines in rheumatoid arthritisrdquo Annual Review of Immunol-ogy vol 14 pp 397ndash440 1996
[20] E H S Choy and G S Panayi ldquoCytokine pathways andjoint inflammation in rheumatoid arthritisrdquo The New EnglandJournal of Medicine vol 344 no 12 pp 907ndash916 2001
[21] G Janossy G Panayi O Duke M Bofill L W Poulterand G Goldstein ldquoRheumatoid arthritis a disease of T-lymphocytemacrophage immunoregulationrdquo The Lancet vol2 no 8251 pp 839ndash842 1981
[22] S S Makarov ldquoNF-120581B in rheumatoid arthritis a pivotal reg-ulator of inflammation hyperplasia and tissue destructionrdquoArthritis Research vol 3 no 4 pp 200ndash206 2001
[23] M Cutolo A Sulli B Villaggio B Seriolo and S AccardoldquoRelations between steroid hormones and cytokines in rheuma-toid arthritis and systemic lupus erythematosusrdquo Annals of theRheumatic Diseases vol 57 no 10 pp 573ndash577 1998
[24] P E Lipsky D M van der Heijde E W St Clair et al ldquoAnti-TumorNecrosis Factor Trial in RheumatoidArthritis with Con-comitant Therapy Study Group Infliximab and methotrexatein the treatment of rheumatoid arthritis Anti-Tumor NecrosisFactor Trial in Rheumatoid Arthritis with Concomitant Ther-apy Study Grouprdquo The New England Journal of Medicine vol343 no 22 pp 1594ndash1602 2000
[25] V Strand S Cohen M Schiff et al ldquoTreatment of activerheumatoid arthritis with leflunomide compared with placeboand methotrexate Leflunomide Rheumatoid Arthritis Investi-gators Grouprdquo Archives of Internal Medicine vol 159 no 21 pp2542ndash2550 1999
[26] J R Kirwan ldquoThe effect of glucocorticoids on joint destructionin rheumatoid arthritisrdquoThe New England Journal of Medicinevol 333 no 3 pp 142ndash146 1995
[27] S R de Antonio H M Blotta R L Mamoni et al ldquoEffects ofdexamethasone on lymphocyte proliferation and cytokine pro-duction in rheumatoid arthritisrdquoThe Journal of Rheumatologyvol 29 no 1 pp 46ndash51 2002
[28] J R OrsquoDell ldquoTherapeutic strategies for rheumatoid arthritisrdquoTheNew England Journal of Medicine vol 350 no 25 pp 2591ndash2602 2004
[29] S Li Z Q Zhang L JWu X G Zhang Y D Li andY YWangldquoUnderstanding ZHENG in traditional Chinese medicine inthe context of neuro-endocrine-immune networkrdquo IET SystemsBiology vol 1 no 1 pp 51ndash60 2007
[30] R Li T Ma J Gu X Liang and S Li ldquoImbalanced networkbiomarkers for traditional Chinese medicine Syndrome ingastritis patientsrdquo Scientific Reports vol 3 article 1543 2013
[31] G Chen C Lu Q Zha et al ldquoA network-based analysis oftraditional Chinese medicine cold and hot patterns in rheuma-toid arthritisrdquo Complementary Therapies in Medicine vol 20no 1-2 pp 23ndash30 2012
[32] H A van Wietmarschen W Dai A J van der Kooij et alldquoCharacterization of rheumatoid arthritis subtypes using symp-tom profiles clinical chemistry and metabolomics measure-mentsrdquo PLoS ONE vol 7 no 9 Article ID e44331 2012
Submit your manuscripts athttpwwwhindawicom
Stem CellsInternational
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
MEDIATORSINFLAMMATION
of
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Behavioural Neurology
EndocrinologyInternational Journal of
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Disease Markers
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
BioMed Research International
OncologyJournal of
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Oxidative Medicine and Cellular Longevity
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
PPAR Research
The Scientific World JournalHindawi Publishing Corporation httpwwwhindawicom Volume 2014
Immunology ResearchHindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Journal of
ObesityJournal of
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Computational and Mathematical Methods in Medicine
OphthalmologyJournal of
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Diabetes ResearchJournal of
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Research and TreatmentAIDS
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Gastroenterology Research and Practice
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Parkinsonrsquos Disease
Evidence-Based Complementary and Alternative Medicine
Volume 2014Hindawi Publishing Corporationhttpwwwhindawicom
Evidence-Based Complementary and Alternative Medicine 7
Ethylsalicylate
Hinesol
Campesterol
Taraxerone
AtractylenolideI
Leflunomide
Chen PiAngelicideBai
Shao
PaeonilactoneC
QiangHuo
Bai Zhu Albiflorin R1Sheng
DiHuang
ChiShao
Mai Ya
ManJing Zi Fang
Feng
KuShen
QingFengTeng
DangGui
Benzothiazole
Adrenocorticotropichormone
Folic acid
Chromone
Methotrexate
Lupenone
Dipterocarpol
Perrimustine
GuaiolIsofucosterol
120573-cryptoxanthin
Herb
Compound or drug
TengJi Xue
JiangHuang
DanShen
WuGong
HuangQi
ChuanXiong
3-Hydroxymugineicacid
Thiolproteaseinhibitor
Listomin S
Pseudocarpaine
Ciclosporin
Goitrin
Dihydro-2-methyl-3(2H)-furanone
Acetamide
Acetoin
Bornylacetate
Sophoranol
Tacrolimus
SandaracopimaricacidViridiflorol
Stigmasterin
Cholesterol
Ro 09-0680Phenylacetaldehyde
DAU 6215 hydrochloride
AC1L7QUY
Levamisolehydrochloride
Thalidomide
Mugineicacid
Benzoyl-dl-leucine
Ethanamine
Permanentorange
acid
Metarene
Laccase
AC1L7VXU
4-Hydroxymephenytoin
NSC673109
Procurcumenol Dehydrocurdione
Zeaxanthin
C09772
Olean-18-en-3-one
45-epoxide
100347-96-4
trans-Sabinenehydrate
CampheneVitamin D3
3-Oxo-1113(18)-oleanadien-28-oicacid
acid
6-Methylcholest-4-en-3-oneAspartylglucosamine
7-Dehydrostigmasterol
Cyclosporine
(4S5S)-(+)-germacrone
(5|A8|A9|A10|A16|A)-16-hydroxykauran-18-oic
(ZZ998400)-diligustilide
120575-terpineol
120573-sitosterol
51205729120572-dihydroxymatrine
2998400-Deoxymugineic
acetate
(a)
Apioglycyrrhizin
UralsaponinB
InflasaponinIV
InflasaponinI
Glycamil
Glycyrrhizicacid
ammoniumsalt
Glyuranolide
Glycyrrhizinicacid
AraboglycyrrhizinLiquoric acid
SophoraflavosideIV
GibberellinA1
CinncassiolA
Napellonine
CinncassiolC3
SophoraflavosideIII
Shanzhisidemethyl ester
Dexamethasone
Palbinone
Triamcinolone
LeiGongTeng
Ge Gen
WeiLingXian
QuanXie
RenDongTeng
Wu Tou
Fu Zi
Sang Ji Sheng
RuXiang
120572-boswellicacid
Rehmannicacid
Loganin
Tutin
acid
Loganic acid
NSC302037
Glycyrrhetinicacid
Prednisone
24-Hydroxyglycyrrheticacid
Corianin
3-Glc-soyasapogenolE
Glabric acidPaeonilactone
B
Cinncassiol E
Ecdysterone
Uralenolide
Asiatic acid
120573-glycyrrhetinicacid
Oleanolicacid
Geigerinin
CinncassiolC2
Tigogenin
Neotigogenin
GlycyrrhetolKatonic acid
Kihadanin A
Cortisone
Triptonide
Bufotoxin
Helixin
Inokosterone
Methylprednisolone
PrednisoloneTriptolideGibberellic
acidCaryoptoside
Triptolideanalog
Hydrocortisone
Gui Zhi
GanCao
XuDuan
Cold
Warm
Hormone drug
Immunomodulatory drug
Hot
Cool
Tu Fu LingHuang
Bai
Neutral
Niu Xi
Du Huo
Zhi Mu
Mu Gua
ShanZha
Pinnatifidin
(25S)-5120573-spirostan-3120573-ol
11-Keto-120573-boswellicacid
Acetyloleanolicacid
Corosolicacid
Boswellicacid
(5xi13|A14|A20s23r24s)-2324-dihydroxy-25-methoxylanost-7-en-3-one
(3|A20|A)-3-hydroxy-11-oxo-olean-12-en-29-oic
Herb
Compound or drug
(b)
Figure 5 Possible connection between RA herbs and drugs in the networks consisting of herbs herbal compounds immunomodulatorydrugs (a) and hormones (b)
8 Evidence-Based Complementary and Alternative Medicine
Table 2 Overlapped RA-related GO terms between top 15 herbtargets and RA genes
Category Enriched GO terms Corrected119875-value
Herbtargets
Response to wounding 238119890 minus 127
Angiogenesis 121119890 minus 26
Inflammatory response 860119890 minus 71
Regulation of cytokine production 612119890 minus 26
Immune response 261119890 minus 88
Leukocyte activation 341119890 minus 38
Regulation of lymphocyte activation 452119890 minus 23
Defense response to bacterium 356119890 minus 10
Positive regulation of NF-120581Btranscription factor activity 604119890 minus 12
RA genes
Response to wounding 148119890 minus 15
Angiogenesis 579119890 minus 6
Inflammatory response 576119890 minus 26
Regulation of cytokine production 165119890 minus 26
Immune response 629119890 minus 39
Leukocyte activation 728119890 minus 30
Regulation of lymphocyte activation 125119890 minus 31
Defense response to bacterium 727119890 minus 12
Positive regulation of NF-120581Btranscription factor activity 254119890 minus 6
treatments Clearly this study is only the first step to learnthe common rule of herbal prescriptions We will continueto conduct in-depth analysis for understanding the scientificbasis of herbal prescriptions in our future work Althoughmore powerful methods more data on TCM prescriptionsand clinical or experimental evaluations are still requiredwe believe that this TCM network pharmacology strategy issuitable to study herbal formulae both in the herb level andin the molecular level and thus can serve as a novel approachto further understand the professional experience embeddedin TCM prescriptions
Abbreviations
DMIM Distance-based mutual information modeldrugCIPHER Drug-target prediction by correlating
protein interaction network andphenotype network
GO Gene ontologyMI Mutual informationNIMS Network-based identification of
multicomponent synergyRA Rheumatoid arthritisPPI Protein-protein interactionQLY Qing-Luo-YinTCM Traditional Chinese Medicine
Conflict of Interests
The authors declare that they have no competing interests
Authorsrsquo Contribution
Shao Li conceived the study Yan Li collected the data Shao LiYan Li Rui Li and Zibo Ouyang analyzed the data and wrotethe paper All authors read and approved the final paper
Acknowledgments
Thanks to Kai Zhang for his help in herbal prescription col-lection This work is supported by NSFC project (81225025)the SATCM key discipline of ldquoTCM Bi-Bingrdquo in YijishanHospital of WannanMedical College the SATCM laboratoryof TCM master Ji-Ren Li the CATCM project and AnhuirsquosKey Technologies RampD project (11010402173)
References
[1] G G Zhang W Lee B Bausell L Lao B Handwerger andB Berman ldquoVariability in the traditional Chinese medicine(TCM) diagnoses and herbal prescriptions provided by threeTCM practitioners for 40 patients with rheumatoid arthritisrdquoJournal of Alternative and Complementary Medicine vol 11 no3 pp 415ndash421 2005
[2] G G Zhang B Singh W Lee B Handwerger L Lao and BBerman ldquoImprovement of agreement in TCMdiagnosis amongTCM practitioners for persons with the conventional diagnosisof rheumatoid arthritis effect of trainingrdquo Journal of Alternativeand Complementary Medicine vol 14 no 4 pp 381ndash386 2008
[3] P Zhang J Li Y Han X W Yu and L Qin ldquoTraditionalChinese medicine in the treatment of rheumatoid arthritis ageneral reviewrdquo Rheumatology International vol 30 no 6 pp713ndash718 2010
[4] Y Li 100 TCM Practitioners in Latest 100 Years Li Ji-ren ampZhang Shun-hua China Press of Traditional Chinese MedicineBeijing China 2004
[5] C Shu Z Li and Y Li ldquoGrand Master of TCM Ji-Ren Lirsquosexperience on the treatment of Bi Zhengrdquo Forum on TraditionalChinese Medicine vol 27 pp 10ndash12 2012
[6] S Li B Zhang D Jiang Y Wei and N Zhang ldquoHerbnetwork construction and co-module analysis for uncoveringthe combination rule of traditional Chinese herbal formulaerdquoBMC Bioinformatics vol 11 supplement 11 article S6 2010
[7] S Li B Zhang and N Zhang ldquoNetwork target for screeningsynergistic drug combinations with application to traditionalChinese medicinerdquo BMC Systems Biology vol 5 supplement 1p S10 2011
[8] S Zhao and S Li ldquoNetwork-based relating pharmacological andgenomic spaces for drug target identificationrdquo PLoS ONE vol5 no 7 Article ID e11764 2010
[9] X Liang H Li and S Li ldquoA novel network pharmacologyapproach to analyse traditional herbal formulae the Liu-Wei-Di-Huang pill as a case studyrdquoMolecular BioSystems vol 10 no5 pp 1014ndash1022 2014
[10] E L Leung Z-W Cao Z-H Jiang H Zhou and L LiuldquoNetwork-based drug discovery by integrating systems biologyand computational technologiesrdquo Briefings in Bioinformaticsvol 14 no 4 pp 491ndash505 2013
[11] V Sharma and I N Sarkar ldquoBioinformatics opportunitiesfor identification and study of medicinal plantsrdquo Briefings inBioinformatics vol 14 no 2 pp 238ndash250 2013
Evidence-Based Complementary and Alternative Medicine 9
[12] S Li and B Zhang ldquoTraditional Chinese medicine networkpharmacology theory methodology and applicationrdquo ChineseJournal of Natural Medicines vol 11 no 2 pp 110ndash120 2013
[13] M Ashburner C A Ball J A Blake et al ldquoGene ontology toolfor the unification of biologyrdquoNature Genetics vol 25 no 1 pp25ndash29 2000
[14] A P Davis B L King S Mockus et al ldquoThe comparativetoxicogenomics database update 2011rdquo Nucleic Acids Researchvol 39 no 1 pp D1067ndashD1072 2011
[15] D S Wishart C Knox A C Guo et al ldquoDrugBank a knowl-edgebase for drugs drug actions and drug targetsrdquoNucleic AcidsResearch vol 36 no 1 pp D901ndashD906 2008
[16] T S Keshava Prasad RGoel K Kandasamy et al ldquoHumanpro-tein reference databasemdash2009 updaterdquo Nucleic Acids Researchvol 37 no 1 pp D767ndashD772 2009
[17] B Zhang X Wang and S Li ldquoAn integrative platform of TCMnetwork pharmacology and its application on a herbal formulaQing-Luo-Yinrdquo Evidence-Based Complementary and AlternativeMedicine vol 2013 Article ID 456747 12 pages 2013
[18] A E Koch ldquoAngiogenesis implications for rheumatoid arthri-tisrdquo Arthritis amp Rheumatism vol 41 no 6 pp 951ndash962 1998
[19] M Feldmann F M Brennan and R N Maini ldquoRole ofcytokines in rheumatoid arthritisrdquo Annual Review of Immunol-ogy vol 14 pp 397ndash440 1996
[20] E H S Choy and G S Panayi ldquoCytokine pathways andjoint inflammation in rheumatoid arthritisrdquo The New EnglandJournal of Medicine vol 344 no 12 pp 907ndash916 2001
[21] G Janossy G Panayi O Duke M Bofill L W Poulterand G Goldstein ldquoRheumatoid arthritis a disease of T-lymphocytemacrophage immunoregulationrdquo The Lancet vol2 no 8251 pp 839ndash842 1981
[22] S S Makarov ldquoNF-120581B in rheumatoid arthritis a pivotal reg-ulator of inflammation hyperplasia and tissue destructionrdquoArthritis Research vol 3 no 4 pp 200ndash206 2001
[23] M Cutolo A Sulli B Villaggio B Seriolo and S AccardoldquoRelations between steroid hormones and cytokines in rheuma-toid arthritis and systemic lupus erythematosusrdquo Annals of theRheumatic Diseases vol 57 no 10 pp 573ndash577 1998
[24] P E Lipsky D M van der Heijde E W St Clair et al ldquoAnti-TumorNecrosis Factor Trial in RheumatoidArthritis with Con-comitant Therapy Study Group Infliximab and methotrexatein the treatment of rheumatoid arthritis Anti-Tumor NecrosisFactor Trial in Rheumatoid Arthritis with Concomitant Ther-apy Study Grouprdquo The New England Journal of Medicine vol343 no 22 pp 1594ndash1602 2000
[25] V Strand S Cohen M Schiff et al ldquoTreatment of activerheumatoid arthritis with leflunomide compared with placeboand methotrexate Leflunomide Rheumatoid Arthritis Investi-gators Grouprdquo Archives of Internal Medicine vol 159 no 21 pp2542ndash2550 1999
[26] J R Kirwan ldquoThe effect of glucocorticoids on joint destructionin rheumatoid arthritisrdquoThe New England Journal of Medicinevol 333 no 3 pp 142ndash146 1995
[27] S R de Antonio H M Blotta R L Mamoni et al ldquoEffects ofdexamethasone on lymphocyte proliferation and cytokine pro-duction in rheumatoid arthritisrdquoThe Journal of Rheumatologyvol 29 no 1 pp 46ndash51 2002
[28] J R OrsquoDell ldquoTherapeutic strategies for rheumatoid arthritisrdquoTheNew England Journal of Medicine vol 350 no 25 pp 2591ndash2602 2004
[29] S Li Z Q Zhang L JWu X G Zhang Y D Li andY YWangldquoUnderstanding ZHENG in traditional Chinese medicine inthe context of neuro-endocrine-immune networkrdquo IET SystemsBiology vol 1 no 1 pp 51ndash60 2007
[30] R Li T Ma J Gu X Liang and S Li ldquoImbalanced networkbiomarkers for traditional Chinese medicine Syndrome ingastritis patientsrdquo Scientific Reports vol 3 article 1543 2013
[31] G Chen C Lu Q Zha et al ldquoA network-based analysis oftraditional Chinese medicine cold and hot patterns in rheuma-toid arthritisrdquo Complementary Therapies in Medicine vol 20no 1-2 pp 23ndash30 2012
[32] H A van Wietmarschen W Dai A J van der Kooij et alldquoCharacterization of rheumatoid arthritis subtypes using symp-tom profiles clinical chemistry and metabolomics measure-mentsrdquo PLoS ONE vol 7 no 9 Article ID e44331 2012
Submit your manuscripts athttpwwwhindawicom
Stem CellsInternational
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
MEDIATORSINFLAMMATION
of
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Behavioural Neurology
EndocrinologyInternational Journal of
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Disease Markers
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
BioMed Research International
OncologyJournal of
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Oxidative Medicine and Cellular Longevity
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
PPAR Research
The Scientific World JournalHindawi Publishing Corporation httpwwwhindawicom Volume 2014
Immunology ResearchHindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Journal of
ObesityJournal of
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Computational and Mathematical Methods in Medicine
OphthalmologyJournal of
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Diabetes ResearchJournal of
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Research and TreatmentAIDS
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Gastroenterology Research and Practice
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Parkinsonrsquos Disease
Evidence-Based Complementary and Alternative Medicine
Volume 2014Hindawi Publishing Corporationhttpwwwhindawicom
8 Evidence-Based Complementary and Alternative Medicine
Table 2 Overlapped RA-related GO terms between top 15 herbtargets and RA genes
Category Enriched GO terms Corrected119875-value
Herbtargets
Response to wounding 238119890 minus 127
Angiogenesis 121119890 minus 26
Inflammatory response 860119890 minus 71
Regulation of cytokine production 612119890 minus 26
Immune response 261119890 minus 88
Leukocyte activation 341119890 minus 38
Regulation of lymphocyte activation 452119890 minus 23
Defense response to bacterium 356119890 minus 10
Positive regulation of NF-120581Btranscription factor activity 604119890 minus 12
RA genes
Response to wounding 148119890 minus 15
Angiogenesis 579119890 minus 6
Inflammatory response 576119890 minus 26
Regulation of cytokine production 165119890 minus 26
Immune response 629119890 minus 39
Leukocyte activation 728119890 minus 30
Regulation of lymphocyte activation 125119890 minus 31
Defense response to bacterium 727119890 minus 12
Positive regulation of NF-120581Btranscription factor activity 254119890 minus 6
treatments Clearly this study is only the first step to learnthe common rule of herbal prescriptions We will continueto conduct in-depth analysis for understanding the scientificbasis of herbal prescriptions in our future work Althoughmore powerful methods more data on TCM prescriptionsand clinical or experimental evaluations are still requiredwe believe that this TCM network pharmacology strategy issuitable to study herbal formulae both in the herb level andin the molecular level and thus can serve as a novel approachto further understand the professional experience embeddedin TCM prescriptions
Abbreviations
DMIM Distance-based mutual information modeldrugCIPHER Drug-target prediction by correlating
protein interaction network andphenotype network
GO Gene ontologyMI Mutual informationNIMS Network-based identification of
multicomponent synergyRA Rheumatoid arthritisPPI Protein-protein interactionQLY Qing-Luo-YinTCM Traditional Chinese Medicine
Conflict of Interests
The authors declare that they have no competing interests
Authorsrsquo Contribution
Shao Li conceived the study Yan Li collected the data Shao LiYan Li Rui Li and Zibo Ouyang analyzed the data and wrotethe paper All authors read and approved the final paper
Acknowledgments
Thanks to Kai Zhang for his help in herbal prescription col-lection This work is supported by NSFC project (81225025)the SATCM key discipline of ldquoTCM Bi-Bingrdquo in YijishanHospital of WannanMedical College the SATCM laboratoryof TCM master Ji-Ren Li the CATCM project and AnhuirsquosKey Technologies RampD project (11010402173)
References
[1] G G Zhang W Lee B Bausell L Lao B Handwerger andB Berman ldquoVariability in the traditional Chinese medicine(TCM) diagnoses and herbal prescriptions provided by threeTCM practitioners for 40 patients with rheumatoid arthritisrdquoJournal of Alternative and Complementary Medicine vol 11 no3 pp 415ndash421 2005
[2] G G Zhang B Singh W Lee B Handwerger L Lao and BBerman ldquoImprovement of agreement in TCMdiagnosis amongTCM practitioners for persons with the conventional diagnosisof rheumatoid arthritis effect of trainingrdquo Journal of Alternativeand Complementary Medicine vol 14 no 4 pp 381ndash386 2008
[3] P Zhang J Li Y Han X W Yu and L Qin ldquoTraditionalChinese medicine in the treatment of rheumatoid arthritis ageneral reviewrdquo Rheumatology International vol 30 no 6 pp713ndash718 2010
[4] Y Li 100 TCM Practitioners in Latest 100 Years Li Ji-ren ampZhang Shun-hua China Press of Traditional Chinese MedicineBeijing China 2004
[5] C Shu Z Li and Y Li ldquoGrand Master of TCM Ji-Ren Lirsquosexperience on the treatment of Bi Zhengrdquo Forum on TraditionalChinese Medicine vol 27 pp 10ndash12 2012
[6] S Li B Zhang D Jiang Y Wei and N Zhang ldquoHerbnetwork construction and co-module analysis for uncoveringthe combination rule of traditional Chinese herbal formulaerdquoBMC Bioinformatics vol 11 supplement 11 article S6 2010
[7] S Li B Zhang and N Zhang ldquoNetwork target for screeningsynergistic drug combinations with application to traditionalChinese medicinerdquo BMC Systems Biology vol 5 supplement 1p S10 2011
[8] S Zhao and S Li ldquoNetwork-based relating pharmacological andgenomic spaces for drug target identificationrdquo PLoS ONE vol5 no 7 Article ID e11764 2010
[9] X Liang H Li and S Li ldquoA novel network pharmacologyapproach to analyse traditional herbal formulae the Liu-Wei-Di-Huang pill as a case studyrdquoMolecular BioSystems vol 10 no5 pp 1014ndash1022 2014
[10] E L Leung Z-W Cao Z-H Jiang H Zhou and L LiuldquoNetwork-based drug discovery by integrating systems biologyand computational technologiesrdquo Briefings in Bioinformaticsvol 14 no 4 pp 491ndash505 2013
[11] V Sharma and I N Sarkar ldquoBioinformatics opportunitiesfor identification and study of medicinal plantsrdquo Briefings inBioinformatics vol 14 no 2 pp 238ndash250 2013
Evidence-Based Complementary and Alternative Medicine 9
[12] S Li and B Zhang ldquoTraditional Chinese medicine networkpharmacology theory methodology and applicationrdquo ChineseJournal of Natural Medicines vol 11 no 2 pp 110ndash120 2013
[13] M Ashburner C A Ball J A Blake et al ldquoGene ontology toolfor the unification of biologyrdquoNature Genetics vol 25 no 1 pp25ndash29 2000
[14] A P Davis B L King S Mockus et al ldquoThe comparativetoxicogenomics database update 2011rdquo Nucleic Acids Researchvol 39 no 1 pp D1067ndashD1072 2011
[15] D S Wishart C Knox A C Guo et al ldquoDrugBank a knowl-edgebase for drugs drug actions and drug targetsrdquoNucleic AcidsResearch vol 36 no 1 pp D901ndashD906 2008
[16] T S Keshava Prasad RGoel K Kandasamy et al ldquoHumanpro-tein reference databasemdash2009 updaterdquo Nucleic Acids Researchvol 37 no 1 pp D767ndashD772 2009
[17] B Zhang X Wang and S Li ldquoAn integrative platform of TCMnetwork pharmacology and its application on a herbal formulaQing-Luo-Yinrdquo Evidence-Based Complementary and AlternativeMedicine vol 2013 Article ID 456747 12 pages 2013
[18] A E Koch ldquoAngiogenesis implications for rheumatoid arthri-tisrdquo Arthritis amp Rheumatism vol 41 no 6 pp 951ndash962 1998
[19] M Feldmann F M Brennan and R N Maini ldquoRole ofcytokines in rheumatoid arthritisrdquo Annual Review of Immunol-ogy vol 14 pp 397ndash440 1996
[20] E H S Choy and G S Panayi ldquoCytokine pathways andjoint inflammation in rheumatoid arthritisrdquo The New EnglandJournal of Medicine vol 344 no 12 pp 907ndash916 2001
[21] G Janossy G Panayi O Duke M Bofill L W Poulterand G Goldstein ldquoRheumatoid arthritis a disease of T-lymphocytemacrophage immunoregulationrdquo The Lancet vol2 no 8251 pp 839ndash842 1981
[22] S S Makarov ldquoNF-120581B in rheumatoid arthritis a pivotal reg-ulator of inflammation hyperplasia and tissue destructionrdquoArthritis Research vol 3 no 4 pp 200ndash206 2001
[23] M Cutolo A Sulli B Villaggio B Seriolo and S AccardoldquoRelations between steroid hormones and cytokines in rheuma-toid arthritis and systemic lupus erythematosusrdquo Annals of theRheumatic Diseases vol 57 no 10 pp 573ndash577 1998
[24] P E Lipsky D M van der Heijde E W St Clair et al ldquoAnti-TumorNecrosis Factor Trial in RheumatoidArthritis with Con-comitant Therapy Study Group Infliximab and methotrexatein the treatment of rheumatoid arthritis Anti-Tumor NecrosisFactor Trial in Rheumatoid Arthritis with Concomitant Ther-apy Study Grouprdquo The New England Journal of Medicine vol343 no 22 pp 1594ndash1602 2000
[25] V Strand S Cohen M Schiff et al ldquoTreatment of activerheumatoid arthritis with leflunomide compared with placeboand methotrexate Leflunomide Rheumatoid Arthritis Investi-gators Grouprdquo Archives of Internal Medicine vol 159 no 21 pp2542ndash2550 1999
[26] J R Kirwan ldquoThe effect of glucocorticoids on joint destructionin rheumatoid arthritisrdquoThe New England Journal of Medicinevol 333 no 3 pp 142ndash146 1995
[27] S R de Antonio H M Blotta R L Mamoni et al ldquoEffects ofdexamethasone on lymphocyte proliferation and cytokine pro-duction in rheumatoid arthritisrdquoThe Journal of Rheumatologyvol 29 no 1 pp 46ndash51 2002
[28] J R OrsquoDell ldquoTherapeutic strategies for rheumatoid arthritisrdquoTheNew England Journal of Medicine vol 350 no 25 pp 2591ndash2602 2004
[29] S Li Z Q Zhang L JWu X G Zhang Y D Li andY YWangldquoUnderstanding ZHENG in traditional Chinese medicine inthe context of neuro-endocrine-immune networkrdquo IET SystemsBiology vol 1 no 1 pp 51ndash60 2007
[30] R Li T Ma J Gu X Liang and S Li ldquoImbalanced networkbiomarkers for traditional Chinese medicine Syndrome ingastritis patientsrdquo Scientific Reports vol 3 article 1543 2013
[31] G Chen C Lu Q Zha et al ldquoA network-based analysis oftraditional Chinese medicine cold and hot patterns in rheuma-toid arthritisrdquo Complementary Therapies in Medicine vol 20no 1-2 pp 23ndash30 2012
[32] H A van Wietmarschen W Dai A J van der Kooij et alldquoCharacterization of rheumatoid arthritis subtypes using symp-tom profiles clinical chemistry and metabolomics measure-mentsrdquo PLoS ONE vol 7 no 9 Article ID e44331 2012
Submit your manuscripts athttpwwwhindawicom
Stem CellsInternational
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
MEDIATORSINFLAMMATION
of
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Behavioural Neurology
EndocrinologyInternational Journal of
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Disease Markers
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
BioMed Research International
OncologyJournal of
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Oxidative Medicine and Cellular Longevity
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
PPAR Research
The Scientific World JournalHindawi Publishing Corporation httpwwwhindawicom Volume 2014
Immunology ResearchHindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Journal of
ObesityJournal of
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Computational and Mathematical Methods in Medicine
OphthalmologyJournal of
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Diabetes ResearchJournal of
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Research and TreatmentAIDS
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Gastroenterology Research and Practice
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Parkinsonrsquos Disease
Evidence-Based Complementary and Alternative Medicine
Volume 2014Hindawi Publishing Corporationhttpwwwhindawicom
Evidence-Based Complementary and Alternative Medicine 9
[12] S Li and B Zhang ldquoTraditional Chinese medicine networkpharmacology theory methodology and applicationrdquo ChineseJournal of Natural Medicines vol 11 no 2 pp 110ndash120 2013
[13] M Ashburner C A Ball J A Blake et al ldquoGene ontology toolfor the unification of biologyrdquoNature Genetics vol 25 no 1 pp25ndash29 2000
[14] A P Davis B L King S Mockus et al ldquoThe comparativetoxicogenomics database update 2011rdquo Nucleic Acids Researchvol 39 no 1 pp D1067ndashD1072 2011
[15] D S Wishart C Knox A C Guo et al ldquoDrugBank a knowl-edgebase for drugs drug actions and drug targetsrdquoNucleic AcidsResearch vol 36 no 1 pp D901ndashD906 2008
[16] T S Keshava Prasad RGoel K Kandasamy et al ldquoHumanpro-tein reference databasemdash2009 updaterdquo Nucleic Acids Researchvol 37 no 1 pp D767ndashD772 2009
[17] B Zhang X Wang and S Li ldquoAn integrative platform of TCMnetwork pharmacology and its application on a herbal formulaQing-Luo-Yinrdquo Evidence-Based Complementary and AlternativeMedicine vol 2013 Article ID 456747 12 pages 2013
[18] A E Koch ldquoAngiogenesis implications for rheumatoid arthri-tisrdquo Arthritis amp Rheumatism vol 41 no 6 pp 951ndash962 1998
[19] M Feldmann F M Brennan and R N Maini ldquoRole ofcytokines in rheumatoid arthritisrdquo Annual Review of Immunol-ogy vol 14 pp 397ndash440 1996
[20] E H S Choy and G S Panayi ldquoCytokine pathways andjoint inflammation in rheumatoid arthritisrdquo The New EnglandJournal of Medicine vol 344 no 12 pp 907ndash916 2001
[21] G Janossy G Panayi O Duke M Bofill L W Poulterand G Goldstein ldquoRheumatoid arthritis a disease of T-lymphocytemacrophage immunoregulationrdquo The Lancet vol2 no 8251 pp 839ndash842 1981
[22] S S Makarov ldquoNF-120581B in rheumatoid arthritis a pivotal reg-ulator of inflammation hyperplasia and tissue destructionrdquoArthritis Research vol 3 no 4 pp 200ndash206 2001
[23] M Cutolo A Sulli B Villaggio B Seriolo and S AccardoldquoRelations between steroid hormones and cytokines in rheuma-toid arthritis and systemic lupus erythematosusrdquo Annals of theRheumatic Diseases vol 57 no 10 pp 573ndash577 1998
[24] P E Lipsky D M van der Heijde E W St Clair et al ldquoAnti-TumorNecrosis Factor Trial in RheumatoidArthritis with Con-comitant Therapy Study Group Infliximab and methotrexatein the treatment of rheumatoid arthritis Anti-Tumor NecrosisFactor Trial in Rheumatoid Arthritis with Concomitant Ther-apy Study Grouprdquo The New England Journal of Medicine vol343 no 22 pp 1594ndash1602 2000
[25] V Strand S Cohen M Schiff et al ldquoTreatment of activerheumatoid arthritis with leflunomide compared with placeboand methotrexate Leflunomide Rheumatoid Arthritis Investi-gators Grouprdquo Archives of Internal Medicine vol 159 no 21 pp2542ndash2550 1999
[26] J R Kirwan ldquoThe effect of glucocorticoids on joint destructionin rheumatoid arthritisrdquoThe New England Journal of Medicinevol 333 no 3 pp 142ndash146 1995
[27] S R de Antonio H M Blotta R L Mamoni et al ldquoEffects ofdexamethasone on lymphocyte proliferation and cytokine pro-duction in rheumatoid arthritisrdquoThe Journal of Rheumatologyvol 29 no 1 pp 46ndash51 2002
[28] J R OrsquoDell ldquoTherapeutic strategies for rheumatoid arthritisrdquoTheNew England Journal of Medicine vol 350 no 25 pp 2591ndash2602 2004
[29] S Li Z Q Zhang L JWu X G Zhang Y D Li andY YWangldquoUnderstanding ZHENG in traditional Chinese medicine inthe context of neuro-endocrine-immune networkrdquo IET SystemsBiology vol 1 no 1 pp 51ndash60 2007
[30] R Li T Ma J Gu X Liang and S Li ldquoImbalanced networkbiomarkers for traditional Chinese medicine Syndrome ingastritis patientsrdquo Scientific Reports vol 3 article 1543 2013
[31] G Chen C Lu Q Zha et al ldquoA network-based analysis oftraditional Chinese medicine cold and hot patterns in rheuma-toid arthritisrdquo Complementary Therapies in Medicine vol 20no 1-2 pp 23ndash30 2012
[32] H A van Wietmarschen W Dai A J van der Kooij et alldquoCharacterization of rheumatoid arthritis subtypes using symp-tom profiles clinical chemistry and metabolomics measure-mentsrdquo PLoS ONE vol 7 no 9 Article ID e44331 2012
Submit your manuscripts athttpwwwhindawicom
Stem CellsInternational
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
MEDIATORSINFLAMMATION
of
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Behavioural Neurology
EndocrinologyInternational Journal of
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Disease Markers
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
BioMed Research International
OncologyJournal of
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Oxidative Medicine and Cellular Longevity
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
PPAR Research
The Scientific World JournalHindawi Publishing Corporation httpwwwhindawicom Volume 2014
Immunology ResearchHindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Journal of
ObesityJournal of
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Computational and Mathematical Methods in Medicine
OphthalmologyJournal of
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Diabetes ResearchJournal of
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Research and TreatmentAIDS
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Gastroenterology Research and Practice
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Parkinsonrsquos Disease
Evidence-Based Complementary and Alternative Medicine
Volume 2014Hindawi Publishing Corporationhttpwwwhindawicom
Submit your manuscripts athttpwwwhindawicom
Stem CellsInternational
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
MEDIATORSINFLAMMATION
of
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Behavioural Neurology
EndocrinologyInternational Journal of
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Disease Markers
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
BioMed Research International
OncologyJournal of
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Oxidative Medicine and Cellular Longevity
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
PPAR Research
The Scientific World JournalHindawi Publishing Corporation httpwwwhindawicom Volume 2014
Immunology ResearchHindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Journal of
ObesityJournal of
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Computational and Mathematical Methods in Medicine
OphthalmologyJournal of
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Diabetes ResearchJournal of
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Research and TreatmentAIDS
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Gastroenterology Research and Practice
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Parkinsonrsquos Disease
Evidence-Based Complementary and Alternative Medicine
Volume 2014Hindawi Publishing Corporationhttpwwwhindawicom