Abstract
Human immunodeficiency virus (HIV) encodes four essential enzymes: protease, integrase, reverse transcriptase (RT)-associated DNA polymerase, and RT-associated ribonuclease H (RNase H). Current clinically approved anti-AIDS drugs target all HIV enzymatic activities except RNase H, which has proven to be a very difficult target for HIV drug discovery. Our high-throughput screening activities identified the dihydroxycoumarin compound F3284-8495 as a specific inhibitor of RT RNase H, with low micromolar potency in vitro. Optimization of inhibitory potency can be facilitated by structural information about inhibitor–target binding. Here, we report the crystal structure of F3284-8495 bound to the active site of an isolated RNase H domain of HIV-1 RT at a resolution limit of 1.71Å. From predictions based on this structure, compounds were obtained that showed improved inhibitory activity. Computational analysis suggested structural alterations that could provide additional interactions with RT and thus improve inhibitory potency. These studies established proof of concept that F3284-8495 could be used as a favorable chemical scaffold for development of HIV RNase H inhibitors.
[Display omitted]
•Both the DNA polymerase and RNase H activities of RT are vital for HIV viability.•Only the DNA polymerase activity of this enzyme has been targeted by anti-AIDS drugs.•F3284-8495 is a micromolar inhibitor of HIV RNase H that is chemically modifiable.•A 1.71-Å crystal structure is presented of F3284-8495 bound to the RNase H active site and analysis of more active analogs.•Our analysis establishes proof of concept that the F3284-8495 scaffold can be the basis for development of more potent HIV RNase H inhibitors.