HIV Protease: Historical Perspective and Current Research

Abstract

The retroviral protease of human immunodeficiency virus (HIV) is an excellent target for antiviral inhibitors for treating HIV/AIDS. Despite the efficacy of therapy, current efforts to control the disease are undermined by the growing threat posed by drug resistance. This review covers the historical background of studies on the structure and function of HIV protease, the subsequent development of antiviral inhibitors, and recent studies on drug-resistant protease variants. We highlight the important contributions of Dr. Stephen Oroszlan to fundamental knowledge about the function of the HIV protease and other retroviral proteases. These studies, along with those of his colleagues, laid the foundations for the design of clinical inhibitors of HIV protease. The drug-resistant protease variants also provide an excellent model for investigating the molecular mechanisms and evolution of resistance.

Keywords: HIV/AIDS; antiretroviral inhibitors; drug resistance; protease structures; retroviral proteases.

Figure 1

(A) The HIV-1 Gag-Pol polyprotein precursor is processed by PR during maturation to release individual structural proteins MA, CA, and NC, and enzymes PR, RT, and IN. (B) PR hydrolyzes the peptide bond, indicated by an arrow in the listed cleavage site sequences of Gag-Pol. (C) The dimer of mature PR (grey ribbons) exists in an open conformation in the absence of substrate or inhibitor. The conserved catalytic triplet of residues Asp-Thr-Gly is shown in red, the conserved triplet of Gly-Arg-Asn in the alpha helix is in green, and the Gly-rich ends of the flexible flaps are in purple. (D) The PR dimer (blue ribbons) bound to the peptide analog of the sp1/NC cleavage site (cyan sticks) has closed conformation flaps.

Figure 2

(a) Substrate peptide in the binding cavity of HIV-1 PR. P3 to P3’ amino acids are shown for a peptide analog of the sp1/NC cleavage site, T-I-Nle-Nle-Q-R, where Nle is norleucine, an analog of methionine, and non-hydrolyzable CH₂-NH replaces the peptide bond between P1 and P1’. Each side chain of the peptide binds in pockets or subsites S3–S3’ (curved lines) in the PR dimer. PR residues contributing to the subsites are indicated. Residues that vary in different retroviral PRs are shown in red; (b) hydrogen bond interactions between PR (grey bonds) and the sp1/NC substrate analog (cyan bonds) are shown in an orientation approximately perpendicular to (a). Water molecules in the binding site are shown as red spheres. Hydrogen bond interactions are indicated as dotted lines. Red dotted lines show conserved interactions between main chain C=O and NH groups of PR and main chain groups of substrate analog. Black dotted lines indicate non-conserved hydrogen bonds.

Figure 3

(a) Chemical structures of clinical inhibitor saquinavir (approved in 1995), clinical inhibitor darunavir (approved in 2006), and investigational inhibitor GRL142, colored to show differences from darunavir; (b) hydrogen bond interactions between PR (grey bonds) and inhibitors darunavir (top in green bonds) and GRL142 (bottom in magenta bonds). A key water molecule is shown as a red sphere. Hydrogen bonds are shown as dotted lines. Red dotted lines indicate interactions similar to those observed for peptide analogs (see Figure 2b). Green dotted lines indicate halide interactions. Black dotted lines indicate non-conserved hydrogen bonds.

Figure 4

Drug-resistant mutations (DRMs) mapped on the structure of the HIV PR dimer (grey ribbons) in complex with darunavir (green sticks). Major DRMs are numbered red spheres, and minor or accessory mutations are blue spheres. Major DRMs are listed on the right.

Figure 5

(a) Sites of DRMs (spheres) mapped on the PR dimer (grey ribbons). PR20 and PRS17 show different sets of mutations. Mutations only in PR20 are pink, mutations only in PRS17 are light blue, mutations common to PR20 and PRS17 are purple, and other DRMs are grey; (b) different flap conformations are observed for PR20 (pink ribbons) and PRS17 (light blue ribbons) dimers in the absence of inhibitors. PR20 has one flap in an extended open conformation and one flap protruding into the active site. PRS17 has a more symmetrical arrangement with two open flaps.