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About Sapient Discovery

Sapient Discovery draws upon the extensive knowledge of its expert team of computational chemists and structural biologists who in the past have developed and successfully identified lead molecules for a wide range of protein targets some of which are in clinical trials and others in pre-clinical development. In order to meet the pharmaceutical industry’s need to quickly find drug leads from disease genes, Sapient Discovery computationally defines the molecular structure of potential drug targets from gene sequence information, using validated proprietary algorithms and experimental data from X-ray crystallography.  The resulting protein structures can be used as templates for extremely rapid drug design.  Sapient Discovery provides a unique and practical “operating system” that bridges the gap between novel target discovery and the 3-D structural coordinates required by chemists and biologists in order to discover new drugs from such targets.

Sapient Discovery’s powerful approach to drug discovery combines three technologies the (i) Genes to LeadsTM, virtual screen  (ii) Augmented Homology ModelingTM and (iii) X-ray crystallography to rapidly and inexpensively identify and validate novel, small molecule inhibitor/antagonist leads for protein drug targets.

Collaborative Opportunity for Grants and Contracts
Facilities/Equipment Description

Company Bios

Kal Ramnarayan, Ph.D.
Co-founder President  and Chief Scientific Officer

(Formerly, Vice President and Chief Scientific Officer of Cengent Therapeutics Inc. (formerly (SBI). Structural Bioinformatics, Inc.).  

Dr. Ramnarayan (Dr. Ram) was one of the Co-founders of Structural Bioinformatics, Inc. As part of the senior management team, he participated in raising more than US$ 50M.  At Structural Bioinformatics he established a number of proprietary databases including StructureBankTM – a database of 5,000 drug target and related anti-target 3-D structures; VariomeTM  - a Pharmacogenomics database of structural polymorphisms of over 50,000 patient specific HIV protease and reverse transcriptases;  and CombiLibTM  -  a small molecule combinatorial virtual library for selection of drug leads..  His technology leadership results in several leads for targets like ALF, PTP1B, SHP-2, DER, TNFR, Her-2, ZAP-70, IKKB, CD45, NY2R, etc.  He established Cengent’s Genes to LeadsTM technology and business, which brought in revenues to the tune of several million dollars to the Company.  He has had several successful grants from DARPA and SBIR.  He has collaborated extensively with GSK, Novartis, J and J, DuPont, several Japanese, European and American companies in projects for lead discovery.  Prior to co-founding Structural Bioinfofmatics, Inc., Dr. Ram was Head of Computational Chemistry at ImmunoPharmaceutics Inc., where he designed numerous drug leads, including highly specific endothelin-A receptor antagonists. One of these drugs, Sitaxsentan, a highly promising treatment for chronic heart failure, is currently in Phase III clinical development by Encysive Pharmaceuticals. Dr. Ramnarayan holds a PhD in molecular biophysics from the Indian Institute of Science, Bangalore and has co-authored multiple papers and patents.  While he has several patents pending, his granted patents include, U.S. Patent No. 6,436,933: Inhibitors of Anthrax Lethal Factor Activity; U.S. Patent No. 5,571,821: Sulfonamides and derivatives thereof that modulate the activity of endothelin and  U.S. Patent No. 6,541,498: Benzenesulfonamides and the use thereof to modulate the activity of endothelin. He is on the Advisory Board of the IBM BlueGene Initiative, Strand Genomics and Keck Research Institute.  He is on the Editorial Board of Current Proteomics.  Dr. Ramnarayan is also Co-founder and Chief Scientific Officer of Focus Synthesis, LLC., in San Diego.


Shankari Mylvaganam, Ph.D.
Co-founder and Vice President of Research

(Formerly Associate Director and Head of Crystallography at Cengent Therapeutics).

Dr. Mylvaganam established the Crystallography Department at Structural Bioinformatics, Inc., where she directed the protein production and X-ray-crystallography of therapeutic protein targets for drug discovery (1997-2005).  She grew the team of structural biologists and planned and successfully directed the cloning, expression, purification and crystallography of a number of novel protein targets for customer-based and in-house programs. The customers included Johnson and Johnson, Janssen Pharmaceutica, Atherogenics, Inc., AGY Therapeutics and Pierre Fabre. She played an integral role in the structure-based inhibitor design in the in-house PTP1B Diabetes program and also headed the homology modeling efforts at Cengent. Her key contribution to the Diabetes program was to determine the first and several additional co-crystal structures of Cengent inhibitors bound to PTP1B.  She has determined crystal structures of novel proteins and protein-inhibitor bound complexes of the phosphatase and kinase families. Dr. Mylvaganam determined the high-resolution crystal structures and structure-function mechanisms of the E8 antibody in both its free state and with it bound to cytochrome-c, as well as novel hemoglobin exhibiting the Root Effect.  Her research findings were published in prominent peer-reviewed journals. She has authored many scientific manuscripts in the field of crystallography and homology modeling, and, is a co-author on several PTP1B patents.  Dr. Mylvaganam worked with the School of Pharmacy, University of London, on the structural studies of inhibitor bound viral protease. Her post-doctoral studies were conducted at The Scripps Research Institute. Dr. Mylvaganam holds a Ph.D. in Protein Crystallography from Birkbeck College, University of London, England.



Scientific Advisory Board

Sapient Discovery has assembled a very competent Scientific Advisory Board, with rich and varied experience in Structural biology, Bioinformatics and structure based molecular design.  The list of advisors will continue to grow with us to bring even more experienced guidance to the company.


Hubert Appert, Ph.D. Professor Emeritus, Medical College of Ohio, Ohio.

Prof. Pierre Baldi, Ph.D. Professor, School of  Information and Computer Sciences &
Institute for Genomics and Bioinformatics, University of California, Irvine, CA.

Jakob Bohr, Ph.D.  Professor, Danish Technical University, Denmark.

Soren Brunak, Ph.D., D.Phil., Professor and Director of Center for Biological Sequence Analysis, Professor, Danish Technical University, Denmark.

Deb Chakrabarti, Ph.D. Beckman Professor of Applied Life Sciences, Keck Graduate Institute, Claremont, CA.

Kathryn R. Ely, Ph. D.  Principal Consultant, Protein Connections, San Diego, CA.

Iman Essam Eldin Mohamed, MD, MRCP(UK), FACP, MPH. Chief of Hematology and Oncology Division Medical Director of the Comprehensive Breast Center at the MCO Cancer Institute and Assistant Professor, Medicine Ohio Cancer Institute, Toledo, Ohio.

Gregory V. Nikiforovich, Ph.D., D.Sc. Washington University, St. Louis. MO.

Arthur Olson, Ph.D., Professor, Department of Molecular Biology and Director, Molecular Graphics Laboratory, The Scripps Research Institute, La Jolla, CA.



Collaborative Opportunity for Grants and Contracts

Sapient Discovery scientists are experienced in working on governmental grants and contracts.  The flexible business model is ideal for setting up collaborations with both commercial and non-profit entities to jointly explore grant and contract opportunities. The technology is applicable to conventional drug discovery targets and also to targets of importance in developing counter measures against infectious and pathogenic origin.  Sapient Discovery will explore collaborative opportunities with government agencies, biotech companies and national and international institutions.

Please contact info@sapientdiscovery.com for setting up or discussing potential Grant and Contracts opportunities.



Facilities/Equipment Description

Sapient Discovery operates out of their 7200 Sq. Ft. facility in San Diego, CA which includes: (1) 2,000 sq. ft. for computational chemistry, bioinformatics, and space for the computers and peripherals and (2) 3,200 sq. ft. of laboratory space for cell and molecular biology, protein production and crystallography.

Sapient Discovery conducts all of its structure-based design and screening activities using distributed processing over a supecomputer network consisting of an IBM 128 processor Linux Cluster, 12 SGI 02 machines, 2 SGI Origin 200 machines, 1 SGI Origin 2000 and 6 SGI Octanes.  All machines are networked for effective distributed and parallel computing.  The computing facility is equipped with 750 gigabytes of disk space and several peripherals and a large portfolio of proprietary and commercial software for use in molecular modeling, bioinformatics, and drug design.


© 2006-2012 Sapient Discovery