Virtual screening for natural product inhibitors of HIV-1 integrase

Julius Woodie


Since there is no human homolog of this enzyme, HIV-1 integrase (IN) represents a rational and important target for treating HIV infection and preventing AIDS. Hence, The 3D structure of full-length HIV-1 IN, either separately or in complex with its inhibitors, has been lacking.To more rationally design potent HIV-1 IN inhibitors, we have previously constructed a model of the full-length HIV-1 IN tetramer and a model of the protein-viral DNA complex. In this paper, the pharmacophore model of INSTIs was used as a 3D query to screen the Traditional Chinese Medicine Database (TCMD). The hit compounds were further filtered by Lipinski’s Rule of Five and docking study to refine the retrieved hits. Finally, 9 suitable ligands with similar structures belonging to the thioglycosides were selected. Subsequent molecular dynamics simulation showed that these compounds had interactions with HIV-1 IN binding site and their possible function as IN inhibitors was discussed.


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