HIV-1 reverse transcriptase (RT) polymorphism 172K, suppresses the effect of clinically relevant drug resistance mutations to both nucleoside and nonnucleoside RT inhibitors.

Polymorphisms have been poorly understood effects on drug susceptibility and may affect the outcome of HIV treatment. We have discovered that an HIV-1 reverse transcriptase (RT) polymorphism (RT172K) is present in clinical samples and in widely used laboratory strains (BH10) and profoundly affects HIV-1 susceptibility to both nucleoside (NRTIs) and nonnucleoside RT inhibitors (NNRTIs) when combined with certain mutations. Polymorphism 172K significantly suppressed AZT resistance caused by excision (e.g. thymidine associated mutations, TAMs), not by discrimination mechanism mutations (e.g. Q151M complex). Moreover it attenuated resistance to nevirapine or efavirenz imparted by NNRTI mutations. Although 172K favored RT-DNA binding at an excisable pre-translocation conformation, it decreased excision by TAM-containing RT. 172K affected DNA handling and decreased RT processivity without significantly affecting the kcat/Km for dNTP. Surface plasmon resonance experiments revealed that RT172K decreased DNA binding by increasing the dissociation rate. Hence, the increased AZT susceptibility of RT172K results from its increased dissociation from the chain-terminated DNA and reduced primer unblocking. We solved a high-resolution (2.15 Å) crystal structure of RT mutated at 172 and compared crystal structures of RT172R and RT172K bound to NNRTIs or DNA/dNTP. Our structural analyses highlight differences in the interactions between α-helix E (where 172 resides) and active site β9-strand that involve the YMDD loop and the NNRTI binding pocket. Such changes may increase dissociation of DNA, thus suppressing excision-based NRTI resistance, and also offset the effect of NNRTI resistance mutations thereby restoring NNRTI binding.