email: chakravarti@multicase.com
Phone:
+1-216-310-4361
Professional Profile
14+ years of experience in computational
medicinal chemistry, computational toxicology and cheminformatics.
Substantial experience in research,
implementation and application of machine learning and data mining for the
development of better and safer drugs.
In depth knowledge of US FDAs
computational safety assessment of drugs and development of computational
tools of regulatory importance.
Ph.D. in
medicinal and pharmaceutical chemistry with special emphasis in computer-aided
design of anti-inflammatory compounds.
Substantial experience in translating
scientific ideas to algorithms and computer implementation.
Extensive experience of programming
in C++, C#/.net and in the development and maintaining large computational
chemistry/cheminformatics software.
Experience
Vice President, Multicase
Inc., Beachwood,
OH, Oct 2012 - Present
Chief Scientific Officer, Multicase Inc., Beachwood, OH, Apr 2011 -
Present
Played leadership role in the design and
development of company's latest bioactivity prediction software.
Carried out research projects to
significantly improve performance and capabilities of computational toxicity
prediction software.
Successfully
developed novel fragment based toxicity prediction algorithms.
Development
of effective user interfaces for bioactivity prediction software.
Principal Scientist, Multicase
Inc., Beachwood,
OH, Sep 2008 - Mar 2011
Invented novel algorithms for mining
structure - activity relationships from large databases.
Programming and designing of large
software libraries for computational chemistry and cheminformatics
related tasks.
Design and development of anti colon
cancer compounds with minimal toxic effects.
Senior
Research Associate, Case Western Reserve University,
Cleveland, OH, Jan 2005 to Aug 2008
Research on discovery of substructural features of small molecules for differential cytotoxicity of small molecules towards human cancer cell
lines.
Developed an extensive cheminformatics software library which proved crucial in
many future applications.
Developed models for ADME and toxicity
calculations, e.g. a LogP model, a blood brain
barrier permeation model and a rat LD50 model.
Post Doctoral Research Associate, Case Western
Reserve University,
Cleveland, OH, May 2001 to Dec 2004
Developed an algorithm for toxicity
prediction of drugs using multiple rodent models in collaboration with CDER
branch of US FDA.
Developed methodologies for predicting
estrogen disrupter potential of small molecules.
Successfully carried out research
projects on similarity search, substructure search, PLS/PCA projections, fuzzy
set modeling, 2D to 3D chemical structure conversion, descriptor calculations,
neural networks, genetic algorithms etc.
Received extensive training in the use
of MCASE suite of software for toxicity prediction and metabolism/degradation
prediction.
Education
Ph.D. in Pharmacy (Medicinal
and Pharmaceutical Chemistry) Department of Pharmacy, SGSITS,
Indore, India, 1996 to 2000.
Thesis:
Designing of some New Non-Steroidal Anti-inflammatory Compounds using
Molecular Modeling, Synthesis & Biological Evaluation.
Master of Pharmacy in
Medicinal and Pharmaceutical Chemistry, Department of
Pharmacy, SGSITS, Indore, India, 1994 to 1996.
Bachelor of Pharmacy Department
of Pharmacy, SGSITS, Indore, India, 1990 to 1994.
Machine Learning,
April-July 2012 (by Andrew Ng, 10 weeks), Stanford University,
online via Coursera.org.
Human-Computer Interaction,
Apprentice track, May-July 2012 (by Scott Klemmer,
5 weeks), Stanford University, online via Coursera.org.
Writing in the Sciences,
Sep-Nov 2012 (by Kristin Sainani, 8 weeks), Stanford
University, online via Coursera.org.
Developing Innovative Ideas for New
Companies, Jan-Mar 2013 (taught by James
Green, 6 weeks), University of Maryland, online via Coursera.org.
Natural Language Processing, Feb-May
2013 (by Michael Collins, 10 Weeks), Columbia University, online
via Coursera.org.
Skills
Programming/Scripting
Languages: C/C++,
C#, Matlab, Octave.
Software
Development: Graphical user interface design,
development and optimization, object oriented programming, database
development and programming, code optimization, multiple core programming, data
visualization and reporting, total development of scientific software packages.
Machine
Learning: Research, development and implementation of
knowledge extraction algorithms, statistical techniques, expert systems,
artificial neural networks, genetic algorithms, logistic regression, partial
least square regression, support vector machines, principal component analysis
and multidimensional scaling, decision trees, kNN,
K-Means etc.
Medicinal
Chemistry: QSAR, QSPR, QSTR, variable selection
methods, substructure search, descriptor calculations, lead discovery
and optimization, predictive toxicology, molecular database development and
handling.
Patents
Drug for treatment of colon cancer,
Klopman G. and Chakravarti
S. K., US PTO # 8329756, awarded on Dec 11 2012.
Cancer treatment, Klopman
G. and Chakravarti S. K., US PTO Application
#
20120065208, filed on March 15 2012.
Publications
Kim M.T., Sedykh
A., Chakravarti S.K., Saiakhov
R.D., Zhu H. Critical evaluation of human oral bioavailability for
pharmaceutical drugs by using various cheminformatics
approaches, Pharmaceutical Research, 2014, 31(4), 1002-1014.
Saiakhov,
R.D., Chakravarti, S.K. and Klopman,
G. Effectiveness of CASE Ultra Expert System in Evaluating Adverse
Effects of Drugs, Molecular Informatics, 2012, 32, 87-97.
Chakravarti,
S.K., Saiakhov, R.D. and Klopman,
G., Optimizing predictive performance of CASE Ultra expert system
models using the applicability domains of individual toxicity alerts,
Journal of Chemical Information and Modeling, 2012, 52, 2609-2618.
Chakravarti,
S.K. and Klopman, G., Finding Relevant Genes
Involved in the Cytotoxicity Mechanisms of
Anticancer Biophores, Current Computer
Aided Drug Design, 2009, 5, 215-224.
Chakravarti, S.K.
and Klopman, G., A
Structural Analysis of the
Differential
Cytotoxicity of Chemicals in the NCI-60 Cancer Cell
Lines, Bioorganic & Medicinal Chemistry, 2008, 16,
4052-4063.
Zhu, H., Sedykh,
A., Chakravarti, S.K. and Klopman,
G., A new group contribution approach to the calculation of LogP, Current Computer Aided Drug Design, 2005,
2, 563-569.
Gilles
Klopman, Julian Ivanov, Roustem Saiakhov and Suman Chakravarti,
MC4PC-An
Artificial Intelligence Approach to the Discovery of Quantitative StructureToxic
Activity Relationships.
In Predictive Toxicology (C. Helma
Editor), Chapter 12 (p 423-457), Taylor and Francis Group, FL USA, 2005.
Klopman, G., Chakravarti, S.K., Zhu, H., Ivanov,
J.M. and Saiakhov, R.D.,
ESP:
A Method To Predict Toxicity and Pharmacological
Properties of Chemicals Using Multiple MCASE Databases,
Journal of Chemical Information and Computer Science, 2004, 44, 704-715.
Klopman,
G. and Chakravarti, S.K., Structure-activity
relationship study of a diverse set of estrogen receptor ligands (I) using MultiCASE
expert system, Chemosphere, 2003, 51, 445-449.
Klopman,
G. and Chakravarti, S.K., Screening of high
production volume chemicals for estrogen receptor binding activity (II)
by the MultiCASE expert system, Chemosphere,
2003, 51, 461-468.
Klopman,
G., Chakravarti, S.K., Harris, N, Ivanov,
J. and Saiakhov, R.D., In-silico
screening of high production volume chemicals for
mutagenicity
using the MCASE QSAR expert system, SAR and QSAR in Environmental
Research, 2003, 14(2), 165-180.
Chakravarti,
S.K. and Chaturvedi, S.C., Receptor surface
analysis of some antiinflammatory benzimidazoles derivatives, Indian Journal of Pharmaceutical
Sciences, 2000, 62(5), 364-370.
Chakravarti,
S.K. and Chaturvedi, S.C., Molecular shape
analysis of some antiinflammatory benzimidazoles, Indian Journal of Pharmaceutical Sciences,
2000, 4, 281-287.
Chakravarti,
S.K., and Chaturvedi, S.C., A quantitative
structure-activity relationship analysis of some substituted oxazolo pyridines and benzimidazoles
with antiinflammatory activity, Indian Journal of
Pharmaceutical Sciences, 1999, 61(4), 206-212.
Chakravarti,
S.K., Ajmani, S. and Chaturvedi,
S.C., SMRAILS : A lotus 1-2-3 spreadsheet
for stepwise multiple parameter regression analysis applied to QSAR analysis,
Indian Journal of Pharmaceutical Sciences, 1998, 60(6), 371-374.
Chakravarti,
S.K., Ajmani, S., Tiwari,
M. and Chaturvedi, S.C., A quantitative structure-activity
relationship analysis of some Nimesulide analogues
using computer-aided molecular modeling, Indian Journal of
Pharmaceutical Sciences, 1998, 60(4), 216-221.
Recent
Presentations
Suman Chakravarti, Alexander
Sedykh,
and Roustem Saiakhov; An
Improved
Workflow to Perform In Silico Mutagenicity
Assessment of Impurities As Per ICH M7 Guideline; Society
of Toxicology Meeting, Phoenix Arizona, March 2014.
Alexander
Sedykh, Suman Chakravarti, and Roustem Saiakhov; Developing
QSAR
models of major human membrane transporters for the application in drug design
and drug safety evaluations; Society of Toxicology
Meeting, Phoenix Arizona, March 2014.
Lidiya
Stavitskaya, Kevin P. Cross, Naomi L. Kruhlak, Barbara L. Minnier,
David A. Bower, Suman Chakravarti,
Roustem D. Saiakhov, Thomas
J. Colatsky, R. Daniel Benz, Development of
Enhanced QSAR Models for the Rapid Assessment of MCM Drug Safety,
FDA's Medical Countermeasures Symposium, 2012.
S. Chakravarti,
R. D. Saiakhov, M. A. Fuller, and G. Klopman., CASE Ultra: A new in silico tool for quantitative prediction of biological
activity. Presented at Society of Toxicology Meeting 2012, San
Francisco, CA.
M.
A. Fuller, R. D. Saiakhov, S. Chakravarti,
and G. Klopman., CASE Ultra:
Predictive
performance in assessing the potential carcinogenicity, genotoxicity,
developmental toxicity, and adverse effects of new drug candidates, impurities,
and metabolites. Presented at Society of Toxicology Meeting 2012, San
Francisco, CA.
Chakravarti, S.K., Saiakhov, R.D., Fuller, M.A., and Klopman,
G., CASE
Ultra:
An Expert System for In Silico Predictive Toxicology
with a Novel Fragment Based Algorithm, Presented at Society
of Toxicology Meeting 2011, Washington DC.
Awards and
Fellowships
Professor M. L. Khorana award for Best
Research Paper of year 2000 in the field of Medicinal and Pharmaceutical
Chemistry by Indian Journal of Pharmaceutical Sciences.
G. P. Nair Gold Medal Award, Indian Drug
Manufacturers Association, for securing First Position in the University in B.
Pharm program.
Senior Research Fellowship, Council of
Scientific and Industrial Research, New Delhi, India.
Junior Research Fellowship, Ministry of
Human Resource Development, New Delhi, India.