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New drugs faster from natural compounds: A UC San Diego breakthrough
Date:7/13/2009

armacologically important biological compounds that remain virtually untouched by computational research. As a result, it is currently one of the most painfully slow processes, it is a real bottleneck that we have now removed," said Pavel Pevzner, a computer science professor at UC San Diego's Jacobs School of Engineering and the corresponding author on the Nature Methods paper.

Researchers can now separate known compounds from those that are unknown.

"If I collect 1,000 ocean compounds, why waste time with compounds that are already known or patented?" added Nuno Bandeira, co-lead author on the paper, director of UC San Diego's Center for Computational Mass Spectrometry (CCMS) and a researcher at the UC San Diego division of Calit2, the California Institute of Telecommunications and Information Technology.

"Our algorithms can tell natural product researchers what their compounds are. Manual annotations should be something of the past," said Julio Ng, a co-lead author on the Nature Methods paper and a doctoral student in Bioinformatics at UC San Diego.

"Compound 879," for example, is a cyclic NRP discussed in the Nature Methods paper that was thought to be novel when it was isolated. A lengthy and expensive patenting process, however, uncovered that compound 879 had already been described as an antibiotic and named neoviridogrisen. The new UC San Diego algorithms would have quickly identified this fact. These algorithms make sense of the flood of tiny peptide fragments that are generated by machines called mass spectrometers that blast nonribosomal peptides apart and determine their sizes.

Two complementary processes are used to glean insights from data generated from the mass spectrometers that break the cyclic peptides into smaller and smaller linear pieces.

First, the authors present new algorithms that computers use to piece these peptide fragments back together in order to determine th
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Contact: Daniel Kane
dbkane@ucsd.edu
858-534-3262
University of California - San Diego
Source:Eurekalert  

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