GAUDIGAUDI

Jordi Mestres & Tudor Oprea

Chemotargets Chemotargets && Sunset Molecular Sunset Molecular

Drug Reprofiling SymposiumACS Boston, 19 August 2007Copyright © Tudor I. Oprea, 2007. All rights reserved

Molecular Libraries InitiativeMolecular Libraries Initiative

NIH Roadmap InitiativeNIH Roadmap Initiative

         

           

           

           

           

           

           

           

           

           

           

           

250-300 thousand small molecules

Hundreds of HTS Assays

SAR matrix

The NIH Roadmap: Some Numbers The NIH Roadmap: Some Numbers

4 Chemical SynthesisCenters

4 Chemical SynthesisCenters

MLSCN (9+1)9 external centers 1 NIH intramural

20 x 10 = 200 assays

MLSCN (9+1)9 external centers 1 NIH intramural

20 x 10 = 200 assays

PubChem(NLM)

PubChem(NLM)

ECCR (6)ExploratoryCenters

ECCR (6)ExploratoryCenters

CombiChemParallel synthesis

DOS4 centers + DPI

100k–500k compounds

CombiChemParallel synthesis

DOS4 centers + DPI

100k–500k compounds

Predictive ADMET (8)

Predictive ADMET (8)

Slide modified from Alex Tropsha (UNC)

OUTPUT:ChemicalProbes

O

O

O N

O

N

NHO

NO2

N+

N

O

O

F

F

N

H

5,0

5,5

6,0

6,5

7,0

7,5

8,0

m k d OR

L1

A3

a1

D1

D2

D3

D4

D5

H2

M1

M2

5-H

T1

A

5-H

T2

A

5-H

T3

5-H

T5

A

5-H

T6

5-H

T7

Receptor List

pIC

50

1

2

Beyond traditional drug discovery:Beyond traditional drug discovery:Off Target ProfilingOff Target Profiling

Poulain et al. J. Med. Chem. 2001, 44, 3391

The Molecular PharmacopoeiaThe Molecular Pharmacopoeia

• Literature estimates the number of drug targets between 5,000 (high estimate) to 500 (targets hit by current drugs)

– Definition: A target is a macro-molecular structure (defined by at least a molecular mass) that undergoes a specific interaction with therapeutics (chemicals administered to treat or diagnose a disease). The target-drug interaction results in clinical effect(s).

– Imming, Sinning & Meyer considered the ’intended’ (not side-effect) targets for drugs; validation in knock-out models - a plus; receptor (ant)agonism, enzyme inhibition were also considered proof; 1-3 targets/drug were considered [was this OK?!].

– Overington, Al-Lazikani & Hopkins considered protein targets for FDA-approved drugs only (~1200 drugs from the Orange Book). They did make allowances for ”non-intended” drug targets for, e.g., ritonavir – an HIV-protease inhibitor given in combination with other such inhibitors because it slows down their metabolism via CYP3A4 inhibition (thus CYP3A4 was considered a drug target for ritonavir). [this was better].

• Part of the problem: there is no “right” definition for health (e.g, free from dis-ease). In the case of sickness, do we “cure”, do we “treat” patients, or do we heal them?

Drug Targets & Dis-easeDrug Targets & Dis-ease

*) P. Imming, C. Sinning, A. Meyer, Nature Rev. Drug Discov 2006, 5: 821-834

*) J. Overington, B. Al-Lazikani, A.L. Hopkins, Nature Rev. Drug Discov 2006, 5: 993-996

Aspirin – the “first drug”Aspirin – the “first drug”• COX-1; Prostaglandin G/H synthase 1

• COX-2; Prostaglandin G/H synthase 2

Acts as suicide inhibitor; is there a COX-3???

• Platelet glycoprotein IIb of IIb/IIIa complex, or antigen CD41

Acts as competitive antagonist (μM inhibitor)

(used as Baby Aspirin as antiaggregant)

• Phospholipase A2 (PDB code 1OXR)

Acts as competitive antagonist (μM inhibitor)

History: Felix Hoffmann was believed to have developed aspirin for F. Bayer & Co., to help his rheumatic father. Arthur Eichengrün claimed in 1949 that the work had been done under his direction.

Walter Sneader analyzed archival data from Bayer, as well as published material and concluded that Eichengrün's claim is valid. Acetylsalicylic acid was synthesised under Eichengrün's direction, and it would not have been introduced in 1899 without his interventionW. Sneader, British Medical Journal 2000, 321:1591–1594

O

O

O

O

Aripiprazole – a “dirty drug” exampleAripiprazole – a “dirty drug” example

N

N

N

O

Cl

Cl

O

• Target Meas Value Activity

• D2 Ki 0.34 nM partial agonist

• D3 Ki 0.8 nM antagonist

• D4 Ki 44 nM antagonist

• 5HT1A Ki 1.7 nM partial agonist

• 5HT2A Ki 3.4 nM antagonist

• 5HT2C Ki 15 nM antagonist

• 5HT7 Ki 39 nM antagonist

• alpha1AR Ki 57 nM antagonist

• H1 Ki 61 nM antagonist• 5HT reuptake Ki 98 nM antagonist• Aripiprazole is an antipsychotic and neuroleptic with

efficacy in schizophrenia and bipolar disorder. Its mechanism of action is unknown (as per FDA label), although the above activities were observed in vitro.

Tamoxifen – a “clean drug” exampleTamoxifen – a “clean drug” example• Estrogen receptor – intended

drug target. TAM & metabolites antagonize dimer formation; ERα monomer + TAM can act as agonist (NFkB, AP-1)

• ERRγ (estrogen-related response receptors, also class 3 NHRs) – 4OHTAM, antagonist

• Anti-Target (?): GPR30 (estrogen GPCR) – 4-OH TAM, agonist

• Anti-Target: Emopamil binding protein; 3β-hydroxysteroid-Δ7-8 isomerase; cholestenol delta-isomerase (TAM, inhibitor)

• Anti-Target: Type I sigma receptor (TAM & metabolites, antagonists)

• Anti-Target (?): PXR; Pregnane X receptor; Orphan nuclear receptor PXR (activator)

NO CH3

CH3CH3

NHO

CH3CH3

NO

OH

CH3

CH3CH3

NHO

OH

CH3CH3

Endoxifen

4OHTAM

N-desmethylTAM

TAM

CYP3A4/5

CYP2D6, 2B62C9, 2C19, 3A

CYP2D6

CYP3A4/5

Desta, Z et al JPET 2004, 310:1062-1075

Tamoxifen is the gold standard “antiestrogen” therapy, used as the first line therapy in Estrogen positive breast cancers. Although its mechanism of action is “known” (as per FDA label), TAM has in vitro nM affinity to the above targets (except PXR; N/A).

Amantadine – a “simple drug” exampleAmantadine – a “simple drug” example• D1 dopamine receptor agonist

• D2 dopamine receptor agonist

• N-methyl D-aspartate receptor subtype 2D (Glutamate [NMDA] receptor subunit epsilon 4) - antagonist at the Phencyclidine binding site

Used in Parkinson’s disease

• Antiviral against Influenza A virus by interfering with the viral M2 membrane ion channel; appears effective on all Influenza A viral strains

• Antiviral against feline immunodeficiency virus

Used as antiviral

• Side effect 1: hERG (probably). Demonstrated to produce QT-prolongation (with risk for congenital long QT patients)

• Side effect 2: anticholinergic-like effects (dry mouth, urinary retention, and constipation) – do not appear to be mediated by direct binding to cholinergic receptors

NH2

• Imming, Sinning & Meyer counted 218 drug targets; Overington, Al-Lazikani, & Hopkins suggest 186 small-molecule targets

– Discrepancy: Drug targets, as counted by these authors, do not consider unique protein classes, and do not capture each high-affinity target.

• An analysis of 988 drugs (WOMBAT-PK database) shows 410 unique drug targets, of which 299 are human:

– 190 enzymes; 68 GPCRs; 55 ion channels; 21 transporters; 18 NHRs; 44 ’proteins’; 7 ’other’ receptors; and 6 nucleic acids

• From WOMBAT: 68 additional targets, of which 43 are human, are reported in the medicinal chemistry literature, with affinity higher than 10 nM for 171 launched drugs:

– 47 enzymes; 11 receptors (9 GPCRs, 2 NHRs); 4 ion channels; and 6 proteins.

• In total, 498 targets, of which 342 are human, were found• How many Drug Targets? And how many small molecules can we develop

to therapeutically manipulate them?• Part of the difficulty: there is no unique, standardised source to capture

information related to small molecules (including drugs) and the macromolecules (proteins, nucleic acids) that interact with them.

Drug Targets RevisitedDrug Targets Revisited

• A total of 163,134 unique molecules annotated to 576 targets

• Enzymes: 411• G protein-coupled receptors: 120• Nuclear receptors: 29• Integrins: 7• Ion channels: 6• Transporters: 3

• containing 152,158 IC50 values and 107,617 Ki values.

• How can one visualize, classify, and analyze this Chemo-Target Space?

Chemical and Target Spaces Chemical and Target Spaces covered in WOMBATcovered in WOMBAT

WOMBAT HeatmapWOMBAT Heatmap

WOMBAT Descriptors SpaceWOMBAT Descriptors Space

WOMBAT Bioactivity SpaceWOMBAT Bioactivity Space

• A total of 803 unique drugs annotated to 268 targets:

• Enzymes: 166

• G protein-coupled receptors: 73

• Nuclear receptors: 19

• Integrins: 3

• Ion channels: 4

• Transporters: 3

• containing 3,320 IC50 values and 3,047 Ki values.

Chemical and Target Spaces Chemical and Target Spaces of DRUGS covered in WOMBATof DRUGS covered in WOMBAT

WOMBAT Bioactivity SpaceWOMBAT Bioactivity Space

WOMBAT Drugs Descriptor SpaceWOMBAT Drugs Descriptor Space

WOMBAT Drugs Bioactivity SpaceWOMBAT Drugs Bioactivity Space

WOMBAT Drugs HeatmapWOMBAT Drugs Heatmap

WOMBAT Drugs: Fused 5-6 Rings SpaceWOMBAT Drugs: Fused 5-6 Rings Space

WOMBAT Drugs: Fused 5-6 Rings DescriptorsWOMBAT Drugs: Fused 5-6 Rings Descriptors

WOMBAT Drugs: Fused 5-6 Rings ScaffoldsWOMBAT Drugs: Fused 5-6 Rings Scaffolds

WOMBAT “5-6” Drug: Thalidomide PKWOMBAT “5-6” Drug: Thalidomide PK

WOMBAT “5-6” Drug: Thalidomide BioactivityWOMBAT “5-6” Drug: Thalidomide Bioactivity

Drug profiling: Graph Framework of Drug profiling: Graph Framework of PergolidePergolide

Drug profiling: Annotations for PergolideDrug profiling: Annotations for Pergolide

D1

D2D3

5-HT1A

D1D2D35-HT1A5-HT1D

Not reported in literatureMicromolar affinities confirmed

Drug profiling: 322 drugs x 199 Drug profiling: 322 drugs x 199 targetstargets

*

* Reference annotated molecule present in Wombat

* *

ConclusionsConclusions• GAUDI is a tool that mines target and chemical space

simultaneously, given the hierarchical classification that is (or can be) inherent to known targets.

• GAUDI is annotated with in vitro data only. However, the use of scaffold mapping enables the user to “jump” from one target space to another, and make high-level connections, that are otherwise hidden

• GAUDI is designed to move beyond the “traditional query” of (sub)structure / target / text search

• Though current data do not explain the withdrawal symptoms for PERGOLIDE, the opioid activities suggested with GAUDI show a previously unkown activity for this drug

AcknowledgmentsAcknowledgments

• WOMBAT Team: Maria Mracec, Marius Olah, Lili Ostopovici, Ramona Rad, Alina Bora, Nicoleta Hadaruga, Ramona Moldovan, Dan Hadaruga (Romanian Academy Institute of Chemistry, Timisoara, Romania)

• GAUDI was developed by Innova Consulting, Santander, Spain http://innovayconsulting.com/