Worldwide Protein Data Bank

www.wwpdb.org

Mining databases for understanding target recognition

Philip E. Bourne

03/12/11 Workshop in Allosteric and Orthosteric Ligands in Drug Action

Worldwide Protein Data Bank

www.wwpdb.org

Mining databases for understanding target recognition – well the PDB anyway

Philip E. Bourne

03/12/11 Workshop in Allosteric and Orthosteric Ligands in Drug Action

Worldwide Protein Data Bank

www.wwpdb.org

“If you remember 3 things from a lecture a week later it was a good lecture”

from Ten Simple Rules for Making Good Oral Presentations

PLoS Comp Biol 2007 3(4): e77

03/12/11 Workshop in Allosteric and Orthosteric Ligands in Drug Action

1. The PDB services almost 200,000 scientists per month, but you are special – take advantage of this offer

03/12/11 Workshop in Allosteric and Orthosteric Ligands in Drug Action

Worldwide Protein Data Bank

www.wwpdb.org“I want to review all multimeric quaternary complexes in the PDB that may be of interest in the understanding of allosteric mechanisms exhibited by such complexes”

Jean-Pierre Changeux

03/12/11 Workshop in Allosteric and Orthosteric Ligands in Drug Action

Its not as easy as it sounds..Group II Chaperonins - Open and Closed Conformation

all chains are sequence identical within one chaperone and 95% similar between the two PDB entries

3KFK 3KFB

Worldwide Protein Data Bank

www.wwpdb.org

Identify biological relatedness even if quaternary structures show variability

Methodology

Take all chains from a PDB95 sequence cluster

Fetch the (1st) Biological Assembly (BA) for the PDB ID of the chain

Align the whole BAs against each other using CE-CP

Prlic et al 2010 Bioinformatics 10.1093/bioinformatics/btq572

Our scores allow to pick out unusual ones:

1Y01

Z-score: 6.23 Coverage 1:22 Coverage 2:59 TM-Score: 0.56

4HHB (self)

Z-score: 8.49Coverage 1:100 Coverage 2:100 TM-Score: 1.0

2W72

Distal site hemoglobin mutant

AHSP bound to Fe(II) alpha-hemoglobin

Z-score: 7.02Coverage 1:76Coverage 2:100 TM-Score: 0.98

Long Term Goal

Characterize all quaternary structures found in the PDB according to level of structural similarity

Where structural similarity exists classify according to ligands bound

Characterize those with drug binding sites at the subunit boundaries

Better characterize allosteric mechanisms associated with quaternary structures

03/12/11 Workshop in Allosteric and Orthosteric Ligands in Drug Action

Worldwide Protein Data Bank

www.wwpdb.org2. We have research tools, not part of the PDB (yet), which are important for discovering and characterizing protein receptors

03/12/11 Workshop in Allosteric and Orthosteric Ligands in Drug Action

• Initially assign C atom with a value that is the distance to the environmental boundary

• Update the value with those of surrounding C atoms dependent on distances and orientation – atoms within a 10A radius define i

0.2

0.1)cos(

0.1

i

Di

PiPGP

neighbors

Conceptually similar to hydrophobicity or electrostatic potential that is dependant on both global and local environments

Characterization of the Ligand Binding Site - The Geometric Potential

Xie and Bourne 2007 BMC Bioinformatics, 8(Suppl 4):S9

Discrimination Power of the Geometric Potential

0

0.5

1

1.5

2

2.5

3

3.5

4

0 11 22 33 44 55 66 77 88 99

Geometric Potential

binding site

non-binding site

Geometric potential can distinguish binding and non-binding sites

100 0

Geometric Potential Scale

Xie and Bourne 2007 BMC Bioinformatics, 8(Suppl 4):S9

L E R

V K D L

L E R

V K D L

Structure A Structure B

• Build an associated graph from the graph representations of two structures being compared. Each of the nodes is assigned with a weight from the similarity matrix

• The maximum-weight clique corresponds to the optimum alignment of the two structures

Xie and Bourne 2008 PNAS, 105(14) 5441

Search for Similar Ligand Binding Sites

http://funsite.sdsc.edu

Worldwide Protein Data Bank

www.wwpdb.org3. We can undertake high-throughput hypothesis generation for protein-drug interactions on a proteome-wide scale

03/12/11 Workshop in Allosteric and Orthosteric Ligands in Drug Action

The TB-Drugome

1. Determine the TB structural proteome

2. Determine all known drug binding sites from the PDB

3. Determine which of the sites found in 2 exist in 1

4. Call the result the TB-drugome

Kinnings et al 2010 PLoS Comp Biol 6(11): e1000976

Workshop in Allosteric and Orthosteric Ligands in Drug Action

03/12/11

1. Determine the TB Structural Proteome

284

1, 446

3, 996 2, 266

TB proteome

homology

models

solve

d

structu

res

High quality homology models from ModBase (http://modbase.compbio.ucsf.edu) increase structural coverage from 7.1% to 43.3%

03/12/11 Workshop in Allosteric and Orthosteric Ligands in Drug Action

2. Determine all Known Drug Binding Sites in the PDB

Searched the PDB for protein crystal structures bound with FDA-approved drugs

268 drugs bound in a total of 931 binding sites

No. of drug binding sites

MethotrexateChenodiol

AlitretinoinConjugated estrogens

DarunavirAcarbose

03/12/11 Workshop in Allosteric and Orthosteric Ligands in Drug Action

Map 2 onto 1 – The TB-Drugomehttp://funsite.sdsc.edu/drugome/TB/

Similarities between the binding sites of M.tb proteins (blue), and binding sites containing approved drugs (red).

From a Drug Repositioning Perspective

Similarities between drug binding sites and TB proteins are found for 61/268 drugs

41 of these drugs could potentially inhibit more than one TB protein

No. of potential TB targets

raloxifenealitretinoin

conjugated estrogens &methotrexate

ritonavir

testosteronelevothyroxine

chenodiol

03/12/11

Top 5 Most Highly Connected Drugs

Drug Intended targets Indications No. of connections TB proteins

levothyroxine transthyretin, thyroid hormone receptor α & β-1, thyroxine-binding globulin, mu-crystallin homolog, serum albumin

hypothyroidism, goiter, chronic lymphocytic thyroiditis, myxedema coma, stupor

14

adenylyl cyclase, argR, bioD, CRP/FNR trans. reg., ethR, glbN, glbO, kasB, lrpA, nusA, prrA, secA1, thyX, trans. reg. protein

alitretinoin retinoic acid receptor RXR-α, β & γ, retinoic acid receptor α, β & γ-1&2, cellular retinoic acid-binding protein 1&2

cutaneous lesions in patients with Kaposi's sarcoma 13

adenylyl cyclase, aroG, bioD, bpoC, CRP/FNR trans. reg., cyp125, embR, glbN, inhA, lppX, nusA, pknE, purN

conjugated estrogens estrogen receptor

menopausal vasomotor symptoms, osteoporosis, hypoestrogenism, primary ovarian failure

10

acetylglutamate kinase, adenylyl cyclase, bphD, CRP/FNR trans. reg., cyp121, cysM, inhA, mscL, pknB, sigC

methotrexatedihydrofolate reductase, serum albumin

gestational choriocarcinoma, chorioadenoma destruens, hydatidiform mole, severe psoriasis, rheumatoid arthritis

10

acetylglutamate kinase, aroF, cmaA2, CRP/FNR trans. reg., cyp121, cyp51, lpd, mmaA4, panC, usp

raloxifeneestrogen receptor, estrogen receptor β

osteoporosis in post-menopausal women 9

adenylyl cyclase, CRP/FNR trans. reg., deoD, inhA, pknB, pknE, Rv1347c, secA1, sigC

03/12/11 Workshop in Allosteric and Orthosteric Ligands in Drug Action

Acknowledgements

Funding Agencies: NSF, NIGMS, DOE, NLM, NCI, NCRR, NIBIB, NINDS, NIDDK

2303/12/11 Workshop in Allosteric and Orthosteric Ligands in Drug Action