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Bioinformatics Advance Access published online on September 5, 2007
Bioinformatics, doi:10.1093/bioinformatics/btm424
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© The Author (2007). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Identification of potential HIV-1 targets of minocycline

Ekachai Jenwitheesuk 1,2 and Ram Samudrala 2,*

1National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, 113 Thailand Science Park, Pahonyothin Road, Klong 1, Klongluang, Pathumtani 12120, Thailand
2Department of Microbiology, University of Washington School of Medicine, Seattle, WA 98195, US

*To whom correspondence should be addressed. Ram Samudrala, E-mail: ram{at}compbio.washington.edu


  Abstract

Summary: Minocycline, a broad spectrum antibiotic, has been discovered to have inhibitory activity against HIV-1 in vitro, but the targets inhibited are unknown. We used a docking with dynamics protocol developed by us to predict the binding affinities of minocycline against seven active sites of five HIV-1 proteins to putatively identify the potential target(s) of minocycline. The results indicate that minocycline has the highest predicted binding affinity against HIV-1 integrase

Contact: ram{at}compbio.washington.edu

Associate Editor: Prof. Dmitrij Frishman

Received on June 5, 2007; revised on July 28, 2007; accepted on August 14, 2007

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