Structural Basis of the Allosteric Inhibitor Interaction on the HIV-1 Reverse Transcriptase RNase H Domain

• Published in: Chemical biology & drug design 2012-11, Vol.80 (5), p.706-716
• Main Authors: Christen, Martin T., Menon, Lakshmi, Myshakina, Nataliya S., Ahn, Jinwoo, Parniak, Michael A., Ishima, Rieko
• Format: Article
• Language: English
• Subjects: acylhydrazone; Allosteric Site; dimer; enzyme; HIV; HIV Infections - drug therapy; HIV Infections - enzymology; HIV Reverse Transcriptase - antagonists & inhibitors; HIV Reverse Transcriptase - chemistry; HIV Reverse Transcriptase - metabolism; HIV-1 - drug effects; HIV-1 - enzymology; Humans; Hydrazones - chemistry; Hydrazones - pharmacology; inhibitor; Magnesium - metabolism; molecular docking; Molecular Dynamics Simulation; NMR; protein; Protein Binding; Protein Multimerization; Protein Structure, Tertiary; reverse transcriptase; Reverse Transcriptase Inhibitors - chemistry; Reverse Transcriptase Inhibitors - pharmacology; ribonuclease H; Ribonuclease H - antagonists & inhibitors; Ribonuclease H - chemistry; Ribonuclease H - metabolism
• ISSN: 1747-0277; 1747-0285
• DOI: 10.1111/cbdd.12010

HIV‐1 reverse transcriptase (RT) has been an attractive target for the development of antiretroviral agents. Although this enzyme is bi‐functional, having both DNA polymerase and ribonuclease H (RNH) activities, there is no clinically approved inhibitor of the RNH activity. Here, we characterize the structural basis and molecular interaction of an allosteric site inhibitor, BHMP07, with the wild‐type (WT) RNH fragment. Solution NMR experiments for inhibitor titration on WT RNH showed relatively wide chemical shift perturbations, suggesting a long‐range conformational effect on the inhibitor interaction. Comparisons of the inhibitor‐induced NMR chemical shift changes of RNH with those of RNH dimer, in the presence and absence of Mg2+, were performed to determine and verify the interaction site. The NMR results, with assistance of molecular docking, indicate that BHMP07 preferentially binds to a site that is located between the RNH active site and the region encompassing helices B and D (the ‘substrate‐handle region’). The interaction site is consistent with the previous proposed site, identified using a chimeric RNH (p15‐EC) [Gong et al. (2011) Chem Biol Drug Des 77, 39–47], but with slight differences that reflect the characteristics of the amino acid sequences in p15‐EC compared to the WT RNH. Currently, there is no clinically approved inhibitor of the RNH activity in HIV‐1 reverse transcriptase (RT). Little structural information about the interactions between RT RNH and inhibitors is available. Here, we identify an allosteric interaction site for an acylhydrazone inhibitor, BHMP07, on the HIV‐1 RNH fragment.