Mining Genomes for New Drugs

The June 16, 2009, BMC Bioinformatics includes Automated Genome Mining for Natural Products by Michael HT Li and colleagues at the University of Michigan. This article describes a program called NP.search, which one of the authors—David H. Sherman—describes by saying:

This software tool mines microbial genomes for clusters of secondary metabolite biosynthetic genes, decodes the enzymatic machinery, and translates this information into predicted 2- or 3-D natural product chemical structures.

So rather than screening organisms—in wet labs—for what they make and what might be useful, this program—open-source code, written in C++—can search a microorganism’s genome for what it can make, and then build structural models of the natural products. Eventually, such models could be tested computationally against disease targets. So far, though, some fine tuning remains. For example, the authors wrote:

Currently, the best predicted structure of the molecule differs significantly in many cases from the actual molecule because of non-functional domains and unrecognized post-tailoring modifications.

Still, this approach could enhance the future approach to drug discovery by making it possible to “screen” far more compounds—doing so more quickly and economically.

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