Dolutegravir Interactions with HIV-1 Integrase-DNA: Structural Rationale for Drug Resistance and Dissociation Kinetics

Abstract

Signature HIV-1 integrase mutations associated with clinical raltegravir resistance involve 1 of 3 primary genetic pathways, Y143C/R, Q148H/K/R and N155H, the latter 2 of which confer cross-resistance to elvitegravir. In accord with clinical findings, in vitro drug resistance profiling studies with wild-type and site-directed integrase mutant viruses have shown significant fold increases in raltegravir and elvitegravir resistance for the specified viral mutants relative to wild-type HIV-1. Dolutegravir, in contrast, has demonstrated clinical efficacy in subjects failing raltegravir therapy due to integrase mutations at Y143, Q148 or N155, which is consistent with its distinct in vitro resistance profile as dolutegravir’s antiviral activity against these viral mutants is equivalent to its activity against wild-type HIV-1. Kinetic studies of inhibitor dissociation from wild-type and mutant integrase-viral DNA complexes have shown that dolutegravir also has a distinct off-rate profile with dissociative half-lives substantially longer than those of raltegravir and elvitegravir, suggesting that dolutegravir’s prolonged binding may be an important contributing factor to its distinct resistance profile. To provide a structural rationale for these observations, we constructed several molecular models of wild-type and clinically relevant mutant HIV-1 integrase enzymes in complex with viral DNA and dolutegravir, raltegravir or elvitegravir. Here, we discuss our structural models and the posited effects that the integrase mutations and the structural and electronic properties of the integrase inhibitors may have on the catalytic pocket and inhibitor binding and, consequently, on antiviral potency in vitro and in the clinic.

Effects of Raltegravir or Elvitegravir Resistance Signature Mutations on the Barrier to Dolutegravir Resistance In Vitro

“…DTG was designed to maintain activity against many INSTI-resistant mutants with single or multiple substitutions (20,(31)(32)(33)(34)(35), and this is consistent with biochemical and structural observations (36,37). Studies showed that the dissociation half-life of DTG from IN/ substrate-DNA/INSTI triple complex in the presence of the amino acid substitutions Q148H, Q148K, or Q148R and N155H significantly reduced the dissociation half-life from that of wildtype IN but was still similar to that of RAL to wild-type IN.…”

“…In vitro virology studies and the biochemical study suggest that the binding of DTG to the IN-substrate-DNA complex is less affected by the IN active site surrounding amino acid substitutions than by RAL and EVG. The HIV-1 IN/substrate-DNA/ INSTI docking model suggested that the interaction of DTG with the 3=-terminal two nucleotides of substrate DNA and strong binding ability to the metal ions, along with the streamlined DTG architecture, might be a likely explanation for the distinct resistance profile of DTG (36).…”

Impact of HIV-1 Integrase L74F and V75I Mutations in a Clinical Isolate on Resistance to Second-Generation Integrase Strand Transfer Inhibitors

“…INSTIs such as DTG efficiently chelate two divalent metal ions that are coordinated by the catalytic carboxylates of HIV-1 IN (DDE motif D64-D116-E152) (4,28,29). Molecular modeling studies have shown that the N155H mutation deforms the ␣4 helix and widens the bottom of the catalytic pocket between residues D64 and E152.…”

“…Molecular modeling studies have shown that the N155H mutation deforms the ␣4 helix and widens the bottom of the catalytic pocket between residues D64 and E152. Given the proximity of N155 to D64 in the wild-type HIV-1 IN, it is possible that this mutation may also affect the position of the active site divalent metals (28). Binding of DTG to the prototype foamy virus (PFV) N224H mutant (equivalent to HIV-1 N155H) was reported to affect electrostatic interactions between H224 and the phosphate of the 3= nucleotide (29,30).…”

Multifunctional facets of retrovirus integrase

“…In contrast, DTG has a high genetic barrier and to date significant resistant IN mutants have been nearly absent in treatmentnaïve patients [81,84,85] . The higher genetic barrier of DTG in patients may be due to its longer dissociative half-life from the HIV IN-DNA complex suggesting that DTG extended binding may be a significant factor for prevention of drug-resistance [86] ; also shown to be a factor in producing kinetically stabilized RSV SC ( Figure 9). HIV carrying the rare signature IN R263K mutation (others are H51Y and E138K) observed with DTG apparently cannot co-exist in combination with many of the above classical IN resistance mutations [87] .…”