Newswise — Scientists at Sanford-Burnham Medical Research Institute (Sanford-Burnham) are collaborating with scientists and software developers at MEDIT SA in France to use and enhance a new software platform built around a computer program called MED-SuMo. This platform searches protein structure databases to find compounds that bind to a particular target, and then helps optimize these “hits” to design new drugs.
“We believe that this collaboration with MEDIT significantly enhances our ability to perform structure-based drug design,” said Nicholas Cosford, Ph.D. associate professor in the Apoptosis and Cell Death Research Program in Sanford-Burnham’s Cancer Center and leader of the collaborative team. “MEDIT’s MED-SuMo software offers unique capabilities that will complement drug discovery platforms already being used in the Conrad Prebys Center for Chemical Genomics [CPCCG] at Sanford-Burnham.”
Here’s how the MEDIT technology works: Sanford-Burnham researchers select a protein they wish to target. Let’s say that this protein, Protein X, normally tells cells to divide, but when it malfunctions, it causes unchecked cell division that leads to a tumor. In an effort to uncover new anti-cancer drugs, scientists want to find compounds that bind to the deviant Protein X and turn it off. Normally, it might take months or years of work and a stroke of luck to find the one needle-in-a-haystack compound that binds and inhibits Protein X without interfering with other proteins.
Dr. Cosford and his team are taking a more targeted approach to drug design with MEDIT’s software platform. MED-SuMo takes a 3D model of Protein X and breaks it down into pieces. Then the software digs through a publically available database containing more than 60,000 proteins with known structures to find “hits” – pieces that structurally resemble parts of Protein X, but are already known to bind certain compounds. MED-SuMo superimposes the matching hits on the structure of Protein X, allowing researchers to see a 3D image of the interaction. Chemical fragments bound to the hits will bind to Protein X in a similar fashion, forming the initial building blocks for a new drug.
Once MED-SuMo puts these pieces together, MEDIT technology takes drug design several steps further. Another program, called MED-Ligand, can optimize multiple hits by finding ways they could be combined to form a single hybrid drug compound that binds Protein X better and more selectively. The system can even screen out any combinations that couldn’t realistically be generated by chemists in the laboratory, as well as those that might harm other proteins or cause toxicity in humans.
“We’re using MEDIT’s software to look for highly effective drugs,” explained Peter Teriete, Ph.D., post-doctoral researcher in Dr. Cosford’s group. “The great thing about using MED-SuMo at Sanford-Burnham is that we’re also surrounded by drug discovery experts. So if I find something that looks good on the computer, I can work with chemists and assay developers to synthesize the compound in the lab and test it to determine whether or not it has the potential to become a new drug.”
The collaboration goes both ways – Dr. Teriete and others benefit from the software and MEDIT SA’s engineers benefit from their feedback on what works, what could work better, and what additional features would be helpful. Their ideas and experiences will enrich future versions of the MEDIT technology platform, making it an even more powerful tool for drug discovery.
“This agreement with Sanford-Burnham, a leading scientific institution in the U.S., is a great opportunity for our company,” said Stephane Richard, Ph.D., vice president of business development at MEDIT SA. “The collaborative nature of the deal and the involvement of our technology in a number of structure-based drug design efforts will allow researchers at Sanford-Burnham to capitalize on our scientists’ expertise in this field.”
For more information about Sanford-Burnham research, visit http://beaker.sanfordburnham.org.
About Sanford-Burnham Medical Research Institute Sanford-Burnham Medical Research Institute is dedicated to discovering the fundamental molecular causes of disease and devising the innovative therapies of tomorrow. Sanford-Burnham, with operations in California and Florida, is one of the fastest-growing research institutes in the country. The Institute ranks among the top independent research institutions nationally for NIH grant funding and among the top organizations worldwide for its research impact. From 1999 – 2009, Sanford-Burnham ranked #1 worldwide among all types of organizations in the fields of biology and biochemistry for the impact of its research publications, defined by citations per publication, according to the Institute for Scientific Information. According to government statistics, Sanford-Burnham ranks #2 nationally among all organizations in capital efficiency of generating patents, defined by the number of patents issued per grant dollars awarded.
Sanford-Burnham utilizes a unique, collaborative approach to medical research and has established major research programs in cancer, neurodegeneration, diabetes, and infectious, inflammatory, and childhood diseases. The Institute is especially known for its world-class capabilities in stem cell research and drug discovery technologies. Sanford-Burnham is a nonprofit public benefit corporation. For more information, please visit www.sanfordburnham.org.
About Sanford-Burnham’s Conrad Prebys Center for Chemical Genomics (CPCCG)The Conrad Prebys Center for Chemical Genomics (CPCCG) at Sanford-Burnham uses robotic technology to screen chemical compounds by the millions to find the few that could potentially be developed into new medicines. CPCCG is one of four Comprehensive Centers chosen nationally to be a part of the NIH’s Molecular Libraries Probe Program (MLP), which established the Molecular Libraries Probe Production Centers Network (MLPCN). The goal is to produce small molecule probes that enable research into health and disease on the cellular level for the public good. For more information, please visit http://www.sanfordburnham.org/cpccg/about_cpccg.aspx.
About MEDIT SAMEDIT SA is a privately held software editor company incorporated in 2003 and operating in the Saclay Scientipole area, France. In the process of expending its activities in the USA, MEDIT SA recently opened an office in San Diego, California.
MEDIT SA efforts are focused on mining exclusively structural experimental data from the Protein Data Bank (PDB) as the guideline for target characterization and/or Structure Based Drug Design (SBDD). Our core technology is a new high speed, accurate and innovative chemogenomic solution offered to crystallographers, molecular modelers and medicinal chemists for allosteric site detection, functional annotation, binding site characterization, selectivity assessment, target druggability, off target identification, drug repurposing , scaffold hopping, bioisosterism replacement, fragment binding prediction, fragment-based lead generation. For more information, please visit www.medit-pharma.com.
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