Structural Implications of Genotypic Variations in HIV-1 Integrase From Diverse Subtypes

Abstract

Human immunodeficiency virus type 1 (HIV-1) integrase (IN) integrates viral DNA into the host genome using its 3'-end processing and strand-transfer activities. Due to the importance of HIV-1 IN, it is targeted by the newest class of approved drugs known as integrase strand transfer inhibitors (INSTIs). INSTIs are efficient in maintaining low viral load; however, as with other approved antivirals, resistance mutations emerge in patients receiving INSTI-containing therapy. As INSTIs are becoming increasingly accessible worldwide, it is important to understand the mechanism(s) of INSTI susceptibility. There is strong evidence suggesting differences in the patterns and mechanisms of drug resistance between HIV-1 subtype B, which dominates in United States, Western Europe and Australia, and non-B infections that are most prevalent in countries of Africa and Asia. IN polymorphisms and other genetic differences among diverse subtypes are likely responsible for these different patterns, but lack of a full-length high-resolution structure of HIV-1 IN has been a roadblock in understanding the molecular mechanisms of INSTI resistance and the impact of polymorphisms on therapy outcome. A recently reported full-length medium-resolution cryoEM structure of HIV-1 IN provides insights into understanding the mechanism of integrase function and the impact of genetic variation on the effectiveness of INSTIs. Here we use molecular modeling to explore the structural impact of IN polymorphisms on the IN reaction mechanism and INSTI susceptibility.

Keywords: HIV-1 integrase; HIV-1 subtypes; drug-resistance; polymorphism; strand transfer inhibitor.

FIGURE 1

Prevalence of PMs in IN genes from diverse subtypes – Panel A shows the quantitative distribution (frequency in percentage) of naturally occurring polymorphisms in HIV-1C (in blue) and A-like (A1/A2, 01_AE, and 02_AG, in shades of gray) which are statistically significantly different compared to HIV-1B (shown in red). Panel B shows the positions of PMs in the context of IN domains. The active site residues (D64, D116, and E152) are marked as red dots.

FIGURE 2

Structure of HIV-1B intasome – This figure shows the structure of the HIV-1 synaptic stable complex (SSC) intasome as determined using cryoEM (PDB file 5U1C). This structure represents the complex after the strand transfer reaction. The integrated viral DNA is rendered as ladders in magenta and gray colors, whereas the host DNA is colored light green and orange. Two IN molecules that directly bind to DNA are shown as ribbons in cyan and maroon. These IN molecules are referred to as inner INs. The other two IN molecules that bind to inner INs are rendered as ribbons in medium blue and wheat colors. These IN subunits are called outer IN molecules.

FIGURE 3

Locations and interactions of NTD PMs – Panels A–C show PMs and their interactions in the NTD. The M50I PM belongs to the linker region and is shown in panel D. The interactions (hydrogen bonding and/or ion-pairs) are shown as dotted lines. In this and following figures, the amino acid residues are shown in ball-and-stick representation and colored as green carbons for HIV-1B and gray carbons in non-B HIV-1. The other atoms are colored as red (oxygen), blue (nitrogen) and yellow (sulfur). The DNA is shown as sticks. The viral DNA is colored with magenta and gray carbons, and target DNA is colored with green and orange carbons. For reference purposes, we have included the zinc-binding motif in panel A.

FIGURE 4

Topological positions of IN PMs near the active site of CCD – Panels a, b, and c show the positions of V72I, L74M and F100Y/L101I, respectively. As a reference point, D64 and metal ion at the active site are also shown.

FIGURE 5

Interactions of PMs in CCD and CTD domains – Panels a and b show the position and interactions of T124A and D167E PMs of the CCD. Panels c and d show the interactions of V201I and R269K PMs of the CTD. Panels d and e show the positions of K269R and A265V PMs, respectively.

FIGURE 6

The conformation and sequence of DNA used in the cryoEM structure of IN – Panel A shows the viral (gray and magenta) DNA and target (green and orange) DNA. The base-paired region is shown in the middle of this panel. The T–T mismatch in this and in panels B and C is shown with yellow carbons. The overall DNA conformation is shown in panel B. This DNA conformation represents the structure after the strand transfer reaction. Panel C shows an enlarged segment from panel B.