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Letter

AutoDocking Dinucleotides to the HIV-1 Integrase Core Domain: Exploring Possible Binding Sites for Viral and Genomic DNA

Supporting Info

Alexander L. Perryman*^† and J. Andrew McCammon^†^‡

Howard Hughes Medical Institute, Department of Chemistry & Biochemistry, and Department of Pharmacology, University of California at San Diego, La Jolla, California 92093-0365

J. Med. Chem., 2002, 45 (26), pp 5624–5627

DOI: 10.1021/jm025554m

Publication Date (Web): November 14, 2002

To whom correspondence should be addressed. Phone: 858-534-2798. FaxL 858-534-0006. E-mail: aperryma@mccammon.ucsd.edu.

†

Howard Hughes Medical Institute and Department of Pharmacology.

‡

Department of Chemistry & Biochemistry.

Abstract

To understand the binding of both viral and human DNA to HIV-1 integrase, fully flexible dinucleotides were docked onto the core domain of integrase. AutoDocking did identify sites on integrase where favorable interactions with nucleotides can occur, and those sites were in agreement with recently published protein fingerprinting data. By analyzing the phosphates of the docked dinucleotides, we developed a model indicating where the viral cDNA and human DNA bind to the integrase core domain.

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