AEGiS-AIDSWeekly: HIV/AIDS Drug Screening: Protease inhibitors identified by chemical taxonomy-based search engine

Important note: Information in this article was accurate in August 2006. The state of the art may have changed since the publication date.

HIV/AIDS Drug Screening: Protease inhibitors identified by chemical taxonomy-based search engine

AIDSWEEKLY Plus; Monday, August 7, 2006
Staff Medical Writers

NewsRx -- A chemical taxonomy-based search engine is used to identify antiretroviral agents. According to recent research from the United States, “A novel technique to annotate, query, and analyze chemical compounds has been developed and is illustrated by using the inhibitor data on HIV protease-inhibitor complexes. In this method, all chemical compounds are annotated in terms of standard chemical structural fragments.

“These standard fragments are defined by using criteria, such as chemical classification; structural, chemical, or functional groups; and commercial, scientific or common names, or synonyms. These fragments are then organized into a data tree based on their chemical substructures.“

“Search engines have been developed to use this data tree to enable query on inhibitors of HIV protease (http://xpdb.nist. gov/hivsdb/hivsdb.html). These search engines use a new novel technique, Chemical Block Layered Alignment of Substructure Technique (Chem-BILAST) to search on the fragments of an inhibitor to look for its chemical structural neighbors.

“This novel technique to annotate and query compounds lays the foundation for the use of the Semantic Web concept on chemical compounds to allow end users to group, sort, and search structural neighbors accurately and efficiently,“ researchers said.

“During annotation,“ reported M.D. Prasanna and colleagues at the National Institute of Standards & Technology in Gaithersburg, “it enables the attachment of 'meaning' (i.e., semantics) to data in a manner that far exceeds the current practice of associating 'metadata' with data by creating a knowledge base (or ontology) associated with compounds.“

The authors concluded, “Intended users of the technique are the research community and pharmaceutical industry, for which it will provide a new tool to better identify novel chemical structural neighbors to aid drug discovery.“

Prasanna and colleagues published their study in Proteins - Structure Function and Bioinformatics (Chemical compound navigator: A Web-based chem-BLAST, chemical taxonomy-based search engine for browsing compounds. Proteins. 2006 Jun 1;63(4):907-17).

For additional information, contact T.N. Bhat, NIST, Biochemistry Science Division 831, 100 Bur Dr., Gaithersburg, MD 20899, USA.

Publisher contact information for the journal Proteins - Structure Function and Bioinformatics is: Wiley-Liss, Division John Wiley & Sons Inc., 111 River St., Hoboken, NJ 07030, USA.

Keywords: Gaithersburg, Maryland, United States, HIV/AIDS, Chemical Knowledge Base, Drug Discovery, Protease Inhibitor, Taxonomy-Based Search Engine.

This article was prepared by AIDS Weekly editors from staff and other reports.

Reference

Prasanna MD, Vondrasek J, Wlodawer A, et al., “Chemical compound navigator: a web-based chem-BLAST, chemical taxonomy-based search engine for browsing compounds”, Proteins. 2006 Jun 1;63(4):907-17.

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