computational approaches on pbp
TRANSCRIPT
Computational Approaches for
Understanding Penicilling-binding Proteins
and its Inhibitors
Thet Su Win
MTMT/D 5736940
Outline
2
Penicillin-binding Proteins
Different computational approaches
Objectives and Study Design
Outcomes
Discussion and Conclusion 5
4
3
2
1
Penicillin-Binding Proteins (PBPs)
• PBPs are a group of
proteins that are
characterized by their
affinity for and binding
to penicillin
• normal constituent of
many bacteria
3
PBPs
• They are the membrane proteins with molecular
weights ranging from 40,000 to 120,000.
• Found on several Gram-positive and Gram-
negative bacteria.
• Bacteria possess a variable number of PBPs.
• A wide variation in both number and patterns of
PBPs in different bacteria.
• These patterns often correlate with the affinity of
PBPs to penicillin and β-lactam antibiotics.
4
Classification of PBPs
5
PBPs
High molecular weight (HMW)
PBPs
Class A Class B
Low molecular weight (LMW)
PBPs
Class C
Sauvage et al, FEMS Microbiology Rev 32(2008) 234-258.
Examples
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Exam
ple
s o
f ea
ch
cla
ss
of
PB
Ps
Function of PBPs
• PBPs are involved in the final stages of synthesis of
peptidoglycan
7
Function of PBPs
• Inhibition of PBPs lead to irregularities in cell wall
structure, cell death and lysis
8
PBPs and antibiotics
• PBPs bind β-lactam antibiotics
(penicillin, cephalosporin,
ceftazidine)
• They are similar in chemical
structure to the modular pieces
that form the peptidoglycan.
• This is an irreversible reaction
and inactivates the enzyme
• So, it is a very good target for
drugs.
9
PBPs and antibiotics
Changing in PBP
• Polymorphism in PBP
sequence
• formation of PBPs that
have low affinity for
penicillins 10
drug resistance
PDPs and Drug resistance
Four main mechanisms of drug resistance by
microorganisms
1.Drug inactivation or modification
Deactivation of penicillin G through the production of
Beta-lactamases
2.Alteration of target site
Alteration of target site in PBP (e.g. – by encoded mecA
gene in MRSA)
3.Alteration of metabolic pathway
4.Reduction of drug accumulation 11
Spreading Scourge of Drug resistance microbial infection
12
www.go.nature.com/c217ry
Drug Discovery and Computational approaches
C. O’Driscoll. http://www.nature.com/horizon/chemicalspace/background/pdf/odyssey.pdf
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Computational approaches on Drug Targets
• Computational approaches are instrumental for drug
discovery and design efforts.
• These approaches in the context of drug discovery/design
can be divided into 3 major classes:
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Computational
Approach example
1. Ligand-based Quantitative Structure-Activity
Relationships (QSAR)
2. Structure-based Molecular Docking
3. Systems-based Proteochemometric modeling (PCM)
Molecular Docking
A Structure-Based Drug Design (SBDD)
means “using protein structure”
Computational method that predicts the binding affinity or a score representing the strength of binding
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QSAR
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Proteochemometrics Modeling (PCM)
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Comparison of QSAR and PCM
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QSAR PCM
A systematic overview of PCM
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Objectives
• To study the inhibitory effects of the new
compounds as potential PBP inhibitors
• To study the interaction of the existing β-lactam
antibiotics to suggest the further modification to
increase the efficacy of the drug
• To study the effects of PBP mutations on β-
lactam antibiotics
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Study Design
PBPs
New Compounds
(Hamamelitannin derivatives)
Β-lactam antibiotics
Β-lactam antibiotics
21
PCM
QSAR DOCKING
Docking and QSAR studies on
Hamamelitannin derivatives and PBP4
22
Study Design - 1
PBP4
New Compounds
(Hamamelitannin derivatives)
Β-lactam antibiotics
Β-lactam antibiotics
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QSAR DOCKING
Discovery Studio 2.5 Hex 6.3 PBP4 is essential
for beta-lactam
struggle in MRSA
Hamamelitannin derivatives
a natural product found in
the bark and the leaves of
Hamamelis virginiana
(witch hazel)
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Methods Program used
1. structure of PBP4 receptor RCSB protein data bank
2. structure of 14
Hamamelitannin derivatives
Pub Chem database
MDL ISIS draw 2.5
Module Chem3D Ultra 8.0
3. Docking Hux (version 6.3)
4. QSAR Discovery Studio v.2.5
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Summary of Docking Study
Outcome of Docking studies
26
• Energy values were computed using docking software,
Hex (v6.3)
• Cpd 11, 13, 14 exhibited highest inhibitory activity with
lowest energy score.
Interaction and binding energy
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Compound 11
Compound 14
Compound 13
-268.84
-274.11
-317.38
Promising inhibitory activity
QSAR studies
steric Physicochemical
Constitutional
Lipo philic
electrostatic
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electronic
molecular
Hydro
phobic
Discovery Studio 2.5
structural
Fitness plot using Grid based and
PLS based models
29
• QSAR models have Good R2 values
• Good predictive ability
Rsquare=0.958 Rsquare=0.975
Docking study of 19 β–lactam antibiotics
on different PBPs
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Study Design - 2
PBPs
New Compounds
(Hamamelitannin derivatives)
Β-lactam antibiotics
Β-lactam antibiotics
31
DOCKING
PBP1a, PBP1b, PBP2a,
PBP2b, PBP2x, PBP3,
PBP4, PBP5, PBP6
19 new generation beta-lactam antibiotics
and penicillin derivatives
Methods Program used
1. 3D structure of PBPs Protein Data Bank (PDB)
2. 3D structure of β-lactam
antibiotics NCBI PubChem Compound database
3. Active site identification Qsite finder
4. Virtual screening iGEMDOCK
5. Docking Auto-Dock version 4.0
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Summary of Docking Study
• 3D structure of these PBPs were
visualized through PyMOL viewer.
33
Virtual screening results of β-lactam
antibiotics by iGEMDOCK
34 The lower the energy scores represent better protein-ligand binding affinity.
35
PB
P 2
x
PB
P 2
b
PB
P 2
a
PB
P 1
b
Docking results of Ceftobiprole
Formation of more than 5 hydrogen bonds with PBPs
36
PB
P 3
PB
P 6
P
BP
4
PB
P 5
Docking results of Ceftaroline
Formation of more than 5 hydrogen bonds with PBPs
• Molecular properties
of Penicillin
derivatives and
Cephalosporins
obtained from
Molinspiration
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PCM model for predicting Interaction of 50
amino acid mutations in PBP2 with 3 β-
lactam antibiotics
38
Study Design
PBP2
New Compounds
(Hamamelitannin derivatives)
Β-lactam antibiotics
Β-lactam antibiotics
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PCM
Penicillin G
Cefixime
Cefriaxone
50 PBP2 mutant variants
Chemical
Descriptors Chemical
Descriptors
Target
chemical
space
Compound
chemical
space
Interaction
space
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Performance of the PCM models
Interactions
Cross-terms
Targets Compounds
Performance of the PCM models
41
Effects of amino acid mutations on susceptibility to the three
β-lactam antibiotics as calculated from the PCM Model-7
42
Goodness-of-fit for model-7
43
Location of the mutation that associated with
increased resistance to β-lactam
44 A
B
Discussion - 1
• From the Docking study of 14 Hamamelitannin
derivatives, three compounds (Comp11, 13 and
14 exhibited minimum energy value.
• And also have good R2 values in QSAR models.
• The results of QSAR and Docking studies were
supportive to the possibilities of novel PBP
inhibitors.
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Discussion - 2
• Virtual screening and docking results suggested
that Ceftobiprole and Ceftaroline can be potent
inhibitors for all types of PBPs.
• But their molecular weight (more than 500)
decreases their permeability and bioavailability.
• Further modification should be done on these
drugs.
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Discussion - 3
• PCM models provided that;
• Mutation at amino acid position 501 and 551
showed important inter-dependencies with many
ligand descriptors
• This mutation is located near the active site
which markedly decreased the pMIC values.
• Mutation at amino acid position 541 and 541 can
change the hydrogen bonding network.
• Also lead to decrease drug susceptibility.
47
Conclusion - 1
• Results from different computational approaches
on PBPs are useful in nature on interaction
between PBP and its inhibitors such as β-lactam
antibiotics and Hamamelitannin derivatives
• Docking studies allows discerning the molecular
details on how compounds interact with PBPs.
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Conclusion - 2
• QSAR allows discerning the relative importance
and contributions of each and every functional
groups present in the molecular structure of
compounds.
• Such knowledge from docking and QSAR can
use to modify the molecular of compounds to be
use as the more effective drug.
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Conclusion - 3
• PCM supports the big and also molecular details
of how a series of compounds interact with a
series of proteins.
• PCM can assess the important mutation
positions conferring change in antimicrobial
susceptibility by analyzing the cross-terms
between mutated amino acids and antibiotics.
• Computational approaches can provide the
effective suggestion for improving the treatment
on bacterial infection especially for drug
resistance strains.
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Acknowledgement
Assoc. Prof. Dr. Chanin Nantasenamat
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