University of California, San Diego researchers have devised a way to cut the time it takes to determine the structure of peptides derived from natural compounds from six months or a year to as little as one day. This advance may assist drug discovery researchers – who need to know as much as possible as quickly as possible about the natural products with antibiotic, antiviral, and other pharmacologically interesting properties that they are probing. The findings were presented atRECOMB 2008 (Research in Computational Molecular Biology).
A new tool in the search of “the next cyclosporine” takes peptide rings of unknown compounds and determines their molecular structure using a combination of mass spectrometry and bioinformatics.
The Jacobs School computer science algorithms glue the overlapping pieces together until they have reassembled a series of possible original ring structures.
According to the researchers, it is currently difficult, time consuming and costly to determine the molecular structure of a class of natural compounds called nonribosomal peptides (NRPs) that are intensely studied for their drug potential. To address this issue, UCSD researchers developed a quick, automated and inexpensive way to determine the structure of NRPs through an innovative collaboration between mass spectrometry experts at the UCSD Skaggs School of Pharmacy and Pharmaceutical Sciences and bioinformatics experts and computer scientists from UCSD’s Jacobs School of Engineering.
If you imagine the structure of an NRP as a cyclic string of beads, then the new algorithms both decipher the mass of each bead based on the mass spectrometry and determine the order of the beads within the ring – crucial pieces of information for uncovering both the structure of the molecule and its pharmacological activities.
Release date: March 31, 2008
Source: University of California, San Diego
Filed Under: Drug Discovery