Download Novel HIVInhibitors

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
HIV/AIDS as a Global Threat
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-1 Replication Cycle
HAART – Highly Active AntiRetroviral Therapy
Problems with the Current Therapy:
-
Adverse/Toxic effects.
- High cost of treatment.
- Multiple drug resistance.
Mechanism of HIV-1 DNA integration into a cellular DNA
integrase
5’ACTGGAA
3’TGACCTT
U3
HIV-1 DNA
R U5
gag pol env
U3
R U5
TAGCAGT 3’
ATCGTCA 5’
integrase
3’-end processing
cytoplasm
5’ACTGGAA
3’ ACCTT
U3
R U5
gag pol env
U3
R U5
TAGCA
3’
ATCGTCA 5’
nucleus
Strand transfer
U3
U5
U3
Cellular DNA
U5
Post-integration
processing
U3
U5
U3
U5
HIV-1 Integrase as Anti-HIV Target
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.
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
HIV/AIDS
Computer-assisted
Svyatoslav Shevelev
IOC RAS (FWS)
discovery of new
HIV-1 integrase
Marina Gottikh
IPCB MSU
inhibitors
Vladimir Poroikov
IBMC RAMS
Marc Nicklaus
NCI/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 treatment
Anabolic
Analgesic
Angiogenesis inhibitor
Angiogenesis stimulant
Antiarrhythmic
Antiarrhythmic Class III
Antiarthritic
Antibacterial
...
Biological Activity Spectrum Represents 3300 kinds
of biological activity (PASS 2007), including:
2755 biochemical mechanisms, e.g.
5 Alpha reductase inhibitor
5 Hydroxytryptamine 1 agonist
5 Hydroxytryptamine 1A antagonist
5 Hydroxytryptamine 1B agonist
5 Lipoxygenase inhibitor
5-Phytase inhibitor
6 Phosphofructokinase inhibitor
Acetaldehyde dehydrogenase inhibitor
Acetate kinase inhibitor
Acetate-CoA ligase inhibitor
...
Biological Activity Spectrum Represents 3300 kinds
of biological activity (PASS 2007), including:
50 adverse effects & toxicity, e.g.
Arrhythmogenic
Carcinogenic
Cardiotoxic
Cytotoxic
DNA damaging
Embryotoxic
Eye irritation, corrasive
Hematotoxic
Hyperglycemic
...
Biological Activity Spectrum Represents 3300 kinds
of biological activity (PASS 2007), including:
121 metabolic terms, e.g.
CYP2 substrate
CYP24 substrate
CYP27 substrate
CYP2A substrate
CYP2A1 substrate
CYP2A10 substrate
CYP2A3 substrate
CYP2A6 substrate
...
How Biological Activity Spectrum Is Predicted?
Cl
Structure of new compound
Cl
O
Estimating the probability that it
has a particular biological activity
Predicted biological
activity spectrum
Anxiolytic
Sedative
5HT1A Inhibitor
Carcinogen
...
O
Pa
Pi
for Activity:
0.853 0.020 Anxiolytic
0.694 0.035 Sedative
...
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
Goel et al.,
2005.
Benzimidazoles
Polyketides
Cyclic nitrones
Anxiolytic
Antihypertensive
Estrada-Soto et
al., 2006.
Phosphatase inhibitor
Seibert et al.,
2006.
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 .
Former Collaboration (CRDF Grant RC1-2064)
Lab. Med. Chem.,
NCI, NIH
Lab. Str.-Funct. Based
Drug Des., IBMC, RAMS
Computer-assisted mechanism-of-action
analysis of large databases including
250,000 chemical compounds
registered by NCI
PASS Predictions Searchable in NCI DB Browser
(http://cactus.nci.nih.gov)
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.
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.
Creating New Medicines Is a High Risk Journey
15
Medicine
10
5
year
s
Idea
3D-TI Conference, Dec. 10-11, 2007
OPTIMIZATION
General Scheme of Search for New HIV-1 Inhibitors
Improvement of PASS
Training Set
Computer Screening of
Diverse Databases
Molecular Modelling
(Target Based Design)
Development of New Synthetic
Routes, Chemical Synthesis
In Vitro Testing
Hits
Testing in Cell Culture
Leads
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
2006
2008
2205 compounds
260 compounds
- Publications
- Publications (only with Mg2+)
- Patents
- Tested in NCI
- NIAID HIV Therapeutics Database
- Tested in IPCB
Name
L-870,810
GS 9137
Exp. IC50 , M
Predictions (2006 database)
Predictions (2008 database)
3’-p
ST
3’-p
ST
3’-p
ST
0.085
0.015
0.589
0.639
0.689
0,765
0.485
0,363
0,898
0.0072
S-1360
0.53
L-870,812
0.04
MK-0518
0.007
0.193
0.19
0,511
0,218
0,724
0,806
From Hits to Leads: Structure Optimization
GS 9137
MK-0518
IOCh-18-47
IOCh-18-76
IC50: 3’-P = 80 M, ST = 80 M
IC50: 3’-P = 0.2 M, ST = 20 M
IOCh-18-74
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
Summary of the Results
• 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).
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
IBMC
Tamara Fedoronchuk
Dmitry Filimonov
Tatyana Gloriozova
Dmitry Druzhilovsky
Alexey Lagunin
Alexander Shkrob
Alexander Veselovsky
Elena Shilova
Antonina Boudunova
IOC
Svyatoslav Shevelev & Associates
IPCB
Marina Gottikh & Associates
NCI
Marc Nicklaus & Associates
Winay Pattak & Associates
Financial support: ISTC/BTEP Project # 3197/111