computer-aided discovery of new hiv-1 integrase inhibitors (istc/btep project # 3197/111) vladimir...

Computer-Aided Discovery of New

HIV-1 Integrase Inhibitors

(ISTC/BTEP Project # 3197/111)

Vladimir Poroikov

Laboratory for Structure-Function Based Drug Design, Institute of Biomedical Chemistry of Rus. Acad. Med. Sci.

Slovenja: The Land of Many Dreams

Acquired immunodeficiency syndrome (AIDS), which is

caused by HIV, is an immunosuppressive disease that

results in life-threatening opportunistic infections and

malignancies. First reported in 1981 in the United States,

AIDS has become a major worldwide epidemic. The United

Nations Program on AIDS (UNAIDS) estimates that at the

end of 2002 nearly 42 million will have died of AIDS.

During 2002, about 3 million people became infected.

AIDS is presently the leading cause of death in Africa and

the fourth leading cause of death worldwide.

Cos P. et al. J. Nat. Prod., 2004, 67, 284-293.

HIV/AIDS as a Global Threat

HIV-1 Replication CycleHAART – Highly Active AntiRetroviral Therapy

Problems with the Current Therapy:

- Adverse/Toxic effects.

- High cost of treatment.

- Multiple drug resistance.

Post-integration processing

U5Cellular DNA

RU3

U3

U5

U3 U3 U5U5

3’-end processing

integraseintegrase

integraseintegrase

HIV-1 DNA

R5’ACTGGAA

3’TGACCTT TAGCAGT 3’ATCGTCA 5’

RU3 gag pol env U3 U5U5

Strand transfer

cytoplasm

nucleus

R5’ACTGGAA

3’ ACCTT TAGCA 3’ATCGTCA 5’

RU3 gag pol env U3 U5U5

Mechanism of HIV-1 DNA integration into a cellular DNA

HIV-1 integrase:

Catalyzes one of the crucial step of HIV

replication.

Has no cellular analogs.

All retroviral integrases have a

conservative structure.

Is a prospective target for treating HIV infection and preventing AIDS.

HIV-1 Integrase as Anti-HIV Target

ISTC/BTEP Project # 3197/111

The purpose of the project is to find new

efficient inhibitors of HIV-1 integrase on the

basis of the latest technologies in bioinformatics

and computer-aided drug discovery.

Duration: April 1, 2005 – March 31, 2008

First Approval of HIV-1 Integrase Inhibitor

Problems with Finding of HIV-1 Integrase Inhibitors

• Viral strains resistant to HIV-1 integrase inhibitors have been already identified.

• Conformation of integrase is rather flexible, it is stabilized in the pre-integration complex.

• Three-dimensional structure of full-length integrase as well as the structure of integrase complex with viral DNA are not known.

Participating Institutions

Institute of Biomedical Chemistry of RAMS (IBMC), Moscow (leading organization – computer-aided drug discovery)

Institute of Organic Chemistry of RAS (IOC), Moscow (chemical synthesis of potential compounds)

Institute of Physical-Chemical Biology of MSU (IPCB), Moscow (testing of potential compounds in vitro)

National Cancer Institute, NIH, Frederick, MD (molecular modelling, testing in cell culture)

ISTC/BTEP Project # 3197/111

Svyatoslav ShevelevIOC RAS (FWS)

Marina GottikhIPCB MSU

Vladimir PoroikovIBMC RAMS

HIV/AIDS

Computer-assisted

discovery of new

HIV-1 integrase

inhibitors

Marc NicklausNCI/NIH

PASS: Prediction of Activity Spectra for Substances

What is the Biological Activity Spectrum?

Biological Activity Spectrum is the

“intrinsic” property of the compound that

reflects all kinds of its biological activity,

which can be found in the compound’s

interaction with biological entity.

Poroikov V. and Filimonov D. In: Predictive Toxicology. Ed. by Christoph Helma. Taylor & Francis, 2005, 459-478.

Biological Activity Spectrum Represents 3300 kinds of biological activity (PASS 2007), including:

374 pharmacotherapeutic effects, e.g.

Alzheimer's disease treatmentAnabolicAnalgesicAngiogenesis inhibitorAngiogenesis stimulantAntiarrhythmicAntiarrhythmic Class IIIAntiarthriticAntibacterial

. . .

Biological Activity Spectrum Represents 3300 kinds of biological activity (PASS 2007), including:

2755 biochemical mechanisms, e.g.

5 Alpha reductase inhibitor5 Hydroxytryptamine 1 agonist5 Hydroxytryptamine 1A antagonist5 Hydroxytryptamine 1B agonist5 Lipoxygenase inhibitor5-Phytase inhibitor6 Phosphofructokinase inhibitorAcetaldehyde dehydrogenase inhibitorAcetate kinase inhibitorAcetate-CoA ligase inhibitor

. . .

50 adverse effects & toxicity, e.g.

ArrhythmogenicCarcinogenicCardiotoxicCytotoxicDNA damagingEmbryotoxicEye irritation, corrasiveHematotoxicHyperglycemic

. . .

Biological Activity Spectrum Represents 3300 kinds of biological activity (PASS 2007), including:

CYP2 substrate

CYP24 substrate

CYP27 substrate

CYP2A substrate

CYP2A1 substrate

CYP2A10 substrate

CYP2A3 substrate

CYP2A6 substrate

. . .

121 metabolic terms, e.g.

Biological Activity Spectrum Represents 3300 kinds of biological activity (PASS 2007), including:

How Biological Activity Spectrum Is Predicted?

Structure of new compound

O

O

Cl

Cl

An

xio

lyti

cS

ed

ati

ve

5H

T1

A In

hib

itor

Carc

inog

en

. .

.

Estimating the probability that it

has a particular biological activity

Pa Pi for Activity:0.853 0.020 Anxiolytic0.694 0.035 Sedative . . .

Predicted biological activity spectrum

Some Examples of PASS INet (www.ibmc.msk.ru/PASS) Predictions, Confirmed by the Experiments

Chemical class Biological activity Reference

Methoxyacridines

Antileishmanial Di Giorgio et al., 2003.

Quinazolines Anxiolytic Goel et al., 2005.

Benzimidazoles Antihypertensive Estrada-Soto et

al., 2006.

Polyketides Phosphatase inhibitor Seibert et al., 2006.

Cyclic nitrones Nootropic Marwaha et al., 2007.

Geronikaki A. et al. Prediction of biological activity via Internet. Medicinal chemist's point of view. SAR & QSAR Environ. Res., 2007, 19, 27-38 .

Lab. Med. Chem., Lab. Str.-Funct. Based NCI, NIH Drug Des., IBMC, RAMS

Computer-assisted mechanism-of-action

analysis of large databases including 250,000 chemical compounds

registered by NCI

Former Collaboration (CRDF Grant RC1-2064)

More than 64 million PASS predictions included.More than 700 activities available.Predictions separately searchable by probabilities of activity and inactivity.Both types combinable by logical AND.Predictions searchable by probability ranges (in subintervals of 0.0 – 1.0).PASS searches combinable with any other search criteria.

PASS Predictions Searchable in NCI DB Browser (http://cactus.nci.nih.gov)

Based on PASS predictions, a fraction of “active” compounds can be increased significantly:

Poroikov et al. J. Chem. Inf. Comput. Sci., 2003, 43, 228-236.

15

10

5

Idea

Medicine

years

Creating New Medicines Is a High Risk Journey

3D-TI Conference, Dec. 10-11, 2007

General Scheme of Search for New HIV-1 Inhibitors

Computer Screening of Diverse Databases

Development of New Synthetic Routes, Chemical Synthesis

Improvement of PASS Training Set

Molecular Modelling (Target Based Design)

In Vitro Testing

Hits

Testing in Cell Culture

Leads

O P

T I

M I

Z A

T I

O N

HIV-1 IN Inhibitors Database Prepared for Input to PASS Training Set

3D Model of HIV-1 Integrase (Karki R. et al. JCAMD, 2004, 18: 739.

Example of HIV-1 Inhibitors Pharmacophore

Optimization of the Specialized PASS Training Set

2205 compounds

2006

260 compounds

2008

- Publications

- Patents

- NIAID HIV Therapeutics Database

- Publications (only with Mg2+)

- Tested in NCI

- Tested in IPCB

Name Exp. IC50 , M Predictions (2006 database) Predictions (2008 database)

  3’-p ST 3’-p ST 3’-p ST

L-870,810 0.085 0.015 0.589 0.639 0.689 0,765

GS 9137   0.0072   0.485 0,363 0,898

S-1360   0.53 0.193 0.19   0,511

L-870,812   0.04     0,218 0,724

MK-0518   0.007       0,806

From Hits to Leads: Structure Optimization

GS 9137 MK-0518

IOCh-18-76

IC50: 3’-P = 80 M, ST = 80 M

IOCh-18-47

IOCh-18-74

IC50: 3’-P = 0.2 M, ST = 20 M

IC50: 3’-P = 0.3 M, ST = 0.5 M

Strand Transfer Inhibition by Compounds IOCh-18-47, IOCh-18-74 and IOCh-18-92

3’-Processing Inhibition by Compounds IOCh-18-47, IOCh-18-74 and IOCh-18-92

•198 compounds were selected as hits, synthesized (or purchased from vendors of commercially available samples)

•176 compounds were tested in vitro on inhibition for strand transfer and 32 compounds were tested on inhibition for 3’-processing.

•15 compounds were identified as HIV-1 integrase

inhibiting agents with IC50 values in the micromolar

and sub-micromolar range.

•For 4 most active compounds results were further confirmed by in vitro testing at NCI.

•The discovered compounds belong to the chemical series where this activity was unknown (NCEs).

Summary of the Results

Some Prospects for a Near Future (BII Supported?)

1. Synthesis and biological testing of additional

rationally designed derivatives from the same

chemical series, to increase potency and

decrease toxicity.

2. Detailed study the mechanism of binding,

specificity, etc. for this classes of compounds.

3. Preparation and submission of patent(s) .

4. Negotiations with pharmaceutical companies

about possibilities of commercialization.

Acknowledgements

IBMCTamara FedoronchukDmitry FilimonovTatyana GloriozovaDmitry DruzhilovskyAlexey LaguninAlexander ShkrobAlexander Veselovsky

Elena ShilovaAntonina Boudunova

IOCSvyatoslav Shevelev & Associates

IPCBMarina Gottikh & Associates

NCIMarc Nicklaus & AssociatesWinay Pattak & Associates

Financial support: ISTC/BTEP Project # 3197/111