Inhibitors of HIV-1 Reverse Transcriptase-Associated Ribonuclease H Activity

Abstract

HIV-1 enzyme reverse transcriptase (RT) is a major target for antiviral drug development, with over half of current FDA-approved therapeutics against HIV infection targeting the DNA polymerase activity of this enzyme. HIV-1 RT is a multifunctional enzyme that has RNA and DNA dependent polymerase activity, along with ribonuclease H (RNase H) activity. The latter is responsible for degradation of the viral genomic RNA template during first strand DNA synthesis to allow completion of reverse transcription and the viral dsDNA. While the RNase H activity of RT has been shown to be essential for virus infectivity, all currently used drugs directed at RT inhibit the polymerase activity of the enzyme; none target RNase H. In the last decade, the increasing prevalence of HIV variants resistant to clinically used antiretrovirals has stimulated the search for inhibitors directed at stages of HIV replication different than those targeted by current drugs. HIV RNase H is one such novel target and, over the past few years, significant progress has been made in identifying and characterizing new RNase H inhibitor pharmacophores. In this review we focus mainly on the most potent low micromolar potency compounds, as these provide logical bases for further development. We also discuss why HIV RNase H has been a difficult target for antiretroviral drug development.

Keywords: HIV-1; reverse transcription; ribonuclease H (RNase H); ribonuclease H inhibitor (RNHI).

Figure 1

Structure of HIV-1 p66/p51 heterodimeric reverse transcriptase in complex with nucleic acid. The subdomains of the p66 subunit are depicted in different colors; the p51 subunit is depicted in gray. The red ball and stick residues in the RNase H domain denote the active site carboxylate amino acids. The figure is derived from PDB file 1RTD and was drawn using UCSF Chimera software [6].

Figure 2

Structure of the RNase H domain of HIV-1 RT. Active site catalytic residues are depicted in stick form and the active site Mg²⁺cations are shown as spheres. The figure is derived from PDB file 3K2P and was drawn using UCSF Chimera software [6].

Figure 3

Schematic of the two-metal mechanism of RNase H hydrolysis. The active site metals are indicated as A and B. details are provided in the text. The figure was adapted from [14].

Figure 4

Schematic of the stages of reverse transcription. Stages where RT-RNase H functions are indicated by “RNase H” and a dashed line denoting RNA hydrolysis. Details are in the text.

Figure 5

Modes of RT RNase H cleavages. The DNA strand of the nucleic acid duplex is black and the RNA strand is red. Details are provided in the text. Figure adapted from [14].

Figure 6

Binding of the N-hydroxy naphthyridinone inhibitor MK1 to the RT RNase H active site. The figure is derived from PDB file 3LP0 and was drawn using UCSF Chimera software [6]. Dashed lines indicate interactions with the metal cations.