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Champions informatics Structural Bioinformatics

March 7, 2002

Structural Bioinformatics Inc.
Edward T. Maggio, Ph.D.
Chairman and CEO

Modeling 3-D Structure Drives Small Molecule Design

What is the history of your organization’s involvement in life sciences?
: Over the last four years, SBI has been involved in developing large-scale computational proteomics and proteomics-driven drug discovery solutions to accelerate the drug discovery process. Computational proteomics is the large-scale generation and use of 3-D protein structure. Our immediate predecessor company, ImmunoPharmaceutics Inc. (IPI), was successful in developing a number of novel drug-lead molecules against a variety of targets. This led to being acquired by Texas Biotechnology Corp. One of our molecules, an endothelin subtype A receptor antagonist, has now been brought into Phase 3 clinical trials by Texas Biotechnology under the name sitaxsentan.

What is your vision for the development of the life sciences market?
: Broad availability of protein structural information, coupled with advanced computational techniques for predicting drug shapes from the dynamic trajectories of protein molecules, have allowed SBI to create a true “high-bandwidth” drug discovery capability applicable to the thousands of new drug targets emerging from the Human Genome Project and similar sequencing efforts for the genomes of many infectious disease agents. So SBI’s first mission is to play a significant role in the discovery of new drugs designed against many new drug targets both for our pharmaceutical company collaborators as well as for our own company.

Secondly, structure is fundamentally enabling for rational experimental design across all life science disciplines. So a second SBI mission is to facilitate significant improvements in efficiency and cost-effectiveness in many aspects of life sciences research. We do this by making 3-D protein structure abundantly available to life scientists, not only in the pharmaceutical industry but throughout the entire life sciences research field, through our ProMax™ and our Variome™ 3-D protein structure databases.

What products and services does your company provide to the life sciences market?
: At SBI, we have developed the capability to computationally generate protein structures comparable in quality to X-ray crystallographic structures but at a fraction of the cost and time. In addition, we have developed technologies that allow us to extract drug shape information from the dynamic trajectories calculated for these modeled protein structures using virtual constructs that we call DynaPharm® templates.

Additionally, we have developed two large-scale 3-D protein structural databases. The first is called ProMax, which is a drug target database. The ProMax database contains more than 6,000 proprietary structures covering more than 460 protein fold families. The second, called the Variome database, is actually a collection of individual modules built around single targets. So, for example, our Variome HIV protease and HIV reverse transcriptase modules each contain more than 50,000 unique protein structures derived from more than 30,000 infected individuals. The Variome databases provide pharmacogenomic insights early on in the drug discovery process to allow scientists to design drugs that work with the largest possible fraction of the patient population.

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