Presented at ISMB Berlin July 23, 2013

1. Drug Repurposing Against Infectious
Diseases by Integrating Chemical Genomics
and Structural Systems Biology
Philip E. Bourne1, Lei Xie2
1Skaggs School of Pharmacy and Pharmaceutical Sciences
University of California, San Diego
2Department of Computer Science, Hunter College
Ph.D. Program in Computer Science, Biology, and Biochemistry
The City University of New York

2. Infectious Disease: A Growing Problem
 Infectious diseases account for 25% of deaths worldwide
 Antimicrobial resistance is increasing
 Wide-spread bacteria use antibiotics for nourishment
Clatworthy et al., Nature Chemical Biology, 3(2007), 541 - 548

3. Teaching New Tricks to Old Drugs
Ashburn et al. Nat Rev Drug Disc 3(2004), 673-683

4. Challenges in Drug Repurposing Against
Infectious Diseases
 Phenotype-based methods (e.g. gene expression profiles)
- Difficult to compare phenotypes across organisms
- Unknown targets for a large number of bioactive compounds
 Ligand-based chemoinformatics methods
- Limited target coverage of pathogen genomes in bioassay databases
- Insufficient models for 3D protein-ligand interactions
 Target-based molecular modeling methods (e.g. protein-ligand
docking, MD simulation, structural bioinformatics)
- Not scalable to millions of chemicals and ten thousands of targets
7/22/2013 4

5. Reconstruction of Genome-Scale
3D Drug-Target Interaction Models
Integrating chemical genomics and structural systems biology
7/22/2013 5
MD
simulation
Mj
Q
Refined
interaction
model
Mj
Q
geneSAR SMAP
Protein-ligand
docking
Mj
Q
Mi
3D model
of novel
Target
3D model of
annotated
target
Initial
interaction
model
Query
chemical
Network
modeling
Experimental
support
generalized network
enrichment of Structure-
Activity Relationships

6. Similarity Search Revisit
7/22/2013 6
1
1
0 1
0
0
Query
False
Negative
False
Positive
Query
2.8
2.8
2.2 1.7
1.2
1.2

7. Generalized Network Enrichment of
Structure-Activity Relationship (geneSAR)
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Bioassay
Database
(ChEMBL,
PubChem etc.)
Ti
Tj
Fingerprint
similarity
Q
Random walk
with restart
(RWR)
Ti
Tj
Ligand
Set
Random
Set
Global
Statistics
Score Distribution
Ti Tj
Q
Ti Tj

8. geneSAR Considerably Improves the
Performance of Drug-Target Interactions
 RWR improves both the
sensitivity/specificity and
coverage of chemical similarity
search compared with 2D
fingerprints.
 When false positive ratio < 0.05,
geneSAR detects >3 times more
drug-target interactions than SEA.
 The success of geneSAR comes
from its combination of RWR and
global statistics.
7/22/2013 8

9. Detecting Protein Binding Promiscuity
across Fold Space
35% of biologically active compounds bind to two or more targets
that do not have similar sequences or global shapes
Paolini et al. Nat. Biotechnol. 2006 24:805–815
HASSTRVCTVREPRTSEQAENCE
SMAP v2.0

10. Experimental Validation of SMAP
Predictions on Multiple Organisms
Primary Target Off-target Pharmacology
implication
Publication
Human protein
kinase
Bacteria
carboxylase
Drug repurposing for
antibiotics
Miller et al. Proc Natl Acad Sci
USA 106(2009):1737
HIV Protease Human protein
kinase
Drug repurposing for
cancer
Xie et al. PLoS Comp Biol
7(2011):e1002037
Human ER P. auroginosa
PhzB
Drug repurposing for
anti-virulence
Ho Sui et al. Int. J. of
Antimicrobial Agents
40(2012):246-251
T. brucei
RNA-ligase
Human
MECR/ETR1
Serious side effects Durrant et al PLoS Comp Biol
6(2010):e1000648
Human COMT M. tb InhA Drug repurposing for
MDR TB
Kinings et al. PLoS Comp Biol
5(2009):e1000423
http://www.sdsc.edu/pb/ - Drug Discovery Work

11. Case Studies
 Repurposing selective estrogen receptor
modulators (SERMs) as anti-virulence agents
 Target fishing from the “Malaria Box” and
subsequent drug repurposing
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12. Case Studies
 Repurposing selective estrogen receptor
modulators (SERMs) as anti-virulence agents
 Target fishing from the “Malaria Box” and
subsequent drug repurposing
7/22/2013 12

13. Target Species: Pseudomonas
aeruginosa
 Opportunistic pathogen causes
infections in individuals with
weak immunity, burn victims, and
patients of cystic fibrosis.
 Intrinsic antibiotic resistance
mainly through efflux pump

14. PhzB2 as a Potential Drug Target Interacting with
Selective Estrogen Receptor Modulators
 PhzB2 involved in pyocyanin
biosynthesis although its
molecular function remains
unknown
 Pyocyanin is both a virulence
factor of bacteria that induce
oxidative stress in host cells
and a quorum sensing signaling
molecule
 No human orthologs
 Raloxifene (antagonist of ER,
preventive therapy for
osteoporosis) can be docked
into an uncharacterized pocket
PhzB2

15. Experimental Validation
 Increased survival rate of infected C. elegans
 Reduced virulence factor pyocyanin production
20
30
40
50
60
70
80
90
100
0 39 43 62 67 70 91 95
SurvivalRate(%)
Time (h)
OP50
PAO1
PA01+RAL
PAO1+RAL
PA14
PA14+RAL
(1.6 mg/ml)
(100 mg/ml)
(100 mg/ml)
PA
14
g/m
l)
m
PA
14
+
R
al(12.5
g/m
l)
m
PA
14
+
R
al(25
g/m
l)
m
PA
14
+
R
al(50
g/m
l)
m
PA
14
+
R
al(100
0.0
0.5
1.0
1.5
2.0
2.5
Pyocyanin,mg/mlofculturesupernatant
S.J. Ho Sui, et al. 2012 Int. J. of Antimicrobial Agents (40)3: 246-251

16. Case Studies
 Repurposing selective estrogen receptor
modulators (SERMs) as anti-virulence agents
 Target fishing from the “Malaria Box” and
subsequent drug repurposing
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17. Malaria
 Malaria is a widespread disease, caused by Plasmodium
(P. falciparum and P. vivax)
 219 million cases, 1.2 million deaths in 2010
 Resistance has developed to anti-malaria drugs.
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18. P. falciparum Drugome
 116 drugs, 268 P. falciparum
proteins, and 1120 interactions.
 Antimicrobial drugs are most likely to
be anti-malarial drugs
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P fal Drugome: Y. Zhang et al. 2013 Submitted.
TB Drugome: S.L. Kinnings, et al. 2011 PLoS Comp. Biol. 6(11): e1000976

19. Open Access Malaria Box
 400 diverse compounds with anti-malaria activity (200 drug-like, 200
probe-like) from whole cell screening of ~4 million of compound.
 Molecular targets are unknown.
 in vivo anti-malaria activities are unknown
 Potential side effects are unknown
The identification of molecular targets in both P. fal and human will:
 Optimize these drug-like compounds to be effective therapeutics
 Predict potential side effects
 Provide insight into potential drug resistance
7/22/2013 19

20. Targets of Drug-like Compounds from
Chemical Genomics Data (ChEMBL)
 157 drug-like compounds are predicted to interact with 427 targets from
multiple organisms using geneSAR (FDR<0.05)
 Implication of side effects and drug repurposing for other infectious
diseases
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Target organism phamarcology
Heparanase Human cancer and thrombosis
PDE5A Human Cardiac effect
Dihydroorotate
dehydrogenase
Human inflammation
Sporulation kinase A B. subtilis Gut side effects
hexokinase T. bruci African sleeping sickness
Bontoxilysin-A C. botulinum Neurotoxin

21. Link Approved Drugs with Malaria Box via
Target Interaction Profiling (TIP)
Novel Essential P. fal Target Safe Drug
Dihydroorotate dehydrogenase Leflunomide (anti-inflammation)
Beta-hydroxyacyl-ACP dehydratase Hesperetin ( lowering cholesterol)
Cysteine protease falcipain-3 ?
3-oxoacyl-acyl-carrier protein reductase Desonide (anti-inflammation)
DNA topoisomerase 2 Genistein (cancer prevention)
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genome
Malaria
Box
Drugbank

22. Summary
 A new chemical genomics algorithm to identify
drug-target interactions
 An integrated chemical genomics and structural
systems biology computational pipeline is able to
generate testable hypotheses for drug
repurposing
 This is only the beginning in making a difference

23. Acknowledgement
• Dr. Li Xie (SSPPS, UCSD)
• Mr. Joshua Lerman (Bioengineering, UCSD)
• Ms. Yinliang Zhang (SSPPS, UCSD)
• Ms. Clara Ng (Hunter, CUNY)
• Prof. Fiona Brinkman (Simon Fraser Univ.)
• Dr. Shannan Ho Sui (Harvard University)
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IIS-1242451

24. 7/22/2013 24
lei.xie@hunter.cuny.edu
pbourne@ucsd.edu
http://www.sdsc.edu/pb/ - Drug Discovery Work
Funding: NIH