HIV-1 reverse transcriptase connection subdomain mutations involved in resistance to approved non-nucleoside inhibitors.

The human immunodeficiency virus type 1 (HIV-1) reverse transcriptase (RT) is a major target of antiretroviral intervention. Non-nucleoside RT inhibitors (NNRTIs) bind to a hydrophobic pocket located away from the DNA polymerase catalytic site of the RT. Approved NNRTIs are nevirapine, delavirdine, efavirenz, etravirine and rilpivirine. This review describes how these inhibitors affect RT function, the structural basis of NNRTI binding, and the role of specific amino acid substitutions at the NNRTI binding pocket in the acquisition of high-level drug resistance. However, two or more amino acid substitutions are required to achieve >20-fold decreased susceptibility to recently developed NNRTIs such as etravirine or rilpivirine, in phenotypic assays. While genotypic analysis of HIV-1 isolates in infected patients is usually restricted to residues 1-250 of the RT, recent reports indicate that several residues in the connection subdomain of the RT (comprising residues 319-426) could also modulate NNRTI resistance. Examples are Y318F or W, N348I, A376S and T369I or V. Tyr-318 participates in NNRTI binding, but other amino acid substitutions in the connection subdomain may affect resistance through an indirect mechanism. Studies on the effects of N348I and A376S on NNRTI resistance indicate that these changes could affect inhibitor binding by altering the interaction between RT subunits or between the RT and the template-primer. Moreover, those mutations could also modulate RNase H activity not only during DNA strand elongation, but also at the initiation of plus strand DNA synthesis as demonstrated for the N348I mutation.