Mechanisms of HIV-1 Integrase Resistance to Dolutegravir and Potent Inhibition of Drug Resistant Variants

Abstract

HIV-1 infection depends on the integration of viral DNA into host chromatin. Integration is mediated by the viral enzyme integrase and is blocked by integrase strand transfer inhibitors (INSTIs), first-line antiretroviral therapeutics widely used in the clinic. Resistance to even the best INSTIs is a problem and the mechanisms of resistance are poorly understood. Here, we analyze combinations of the INSTI-resistant mutations E138K, G140A/S, and Q148H/K/R, which confer resistance to INSTIs. The investigational drug 4d more effectively inhibited the mutants compared with the approved drug Dolutegravir (DTG). We present 11 new cryo-EM structures of drug resistant HIV-1 intasomes bound to DTG or 4d, with better than 3 A resolution. These structures, complemented with free energy simulations, explain the mechanisms of DTG resistance involving E138K+G140A/S+Q148H/K/R and show why 4d maintains potency better than DTG. These data establish a foundation for further development of INSTIs that potently inhibit resistant forms in integrase.

Kinetic co-evolutionary models predict the temporal emergence of HIV resistance mutations under drug selection pressure

“…The fast mutation N155H arises in combination with numerous other background DRMs, but Q148H is most commonly found in combination with G140S. Indeed, our prediction confirms the numerous literature reports (78-80) for the significant contribution of G140S to the adaptive frequency of Q148H. The N155H mutants emerge first, and are eventually replaced by Q148H and Y143R mutants (81), usually in combination with G140S (82) which explains the decrease in N155H frequency (downward black solid arrow in Fig.…”

“…In contrast, the slow-arising mutation Q148H is well-known for its detrimental effect on enzyme activity. The mechanism of resistance for Q148H can be explained by the introduction of an electropositive moiety underneath the two Mg 2+ metal ions, weakening metal chelation and leading to INSTI displacement (57, 58). Importantly, Q148H also significantly compromises enzyme activity, because the Mg 2+ ions are also directly involved in catalysis.…”

“…5. The extent of the known molecular envelope for different bound drugs is shown as a red mesh; The molecular envelope is created using UCSF Chimera (58) and using the PDBs: PIs: DRV (PDB: 4Q1X) SQV (PDB: 3S56), NFV (PDB: 3EKX), DRV (PDB: 3D20), LPV (PDB: 2QHC), TPV (PDB: 4NJU); NRTIs: FTC (PDB: 6UIR), AZT (PDB: 3KLG); NNRTIs: RPV (PDB: 3BGR), DOR (PDB: 7Z2G), EFV (PDB: 1IKW), ETR (PDB: 3MEC), NVP (PDB: 4PWD); INSTIs: DTG (8FNZ), BIC (6PUW).…”

Oligomeric HIV-1 Integrase Structures Reveal Functional Plasticity for Intasome Assembly and RNA Binding

“…Prior lentiviral intasome structures have revealed a diversity of oligomeric IN species ranging from tetramer to hexadecamer [8][9][10]12,13,17 , and recent results suggested that functional IN tetramerization is essential for lentiviral intasome assembly 9 . However, owing to the propensity of HIV-1 IN to aggregate in vitro, and to challenges with biochemical intasome assembly, structures of HIV-1 intasomes containing fully resolved flanking subunits have remained elusive.…”

“…arise from sixteen copies of viral IN 11 . However, all HIV-1 intasome structures resolved to date 8,[12][13][14] lack key IN flanking subunits that assemble on the intasome periphery, and atomic models constitute only ~40% of the total protein mass. These limitations can be attributed to the dynamic nature of HIV-1 IN 15,16 (also observed with simian immunodeficiency virus IN 17 ), characteristics that confer significant challenges to structural biology attempts.…”