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.