D-101 Structural Basis of Inhibition and Resistance Mechanism to EFdA, a highly potent NRTI

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4′-ethynyl-2-fluoro-2′-deoxyadenosine (EFdA) is the most potent nucleoside analog inhibitor of HIV reverse transcriptase (RT). It is stable and well tolerated in clinical trials (MK-8591), having the potential for once-weekly oral dosing (Hazuda, CROI 2016). EFdA retains a 3′-OH, yet acts as a chain-terminator by diminishing translocation from the pre-translocation Nucleotide-binding site (N-site) to the post-translocation Primer-binding site (P-site). To understand the high potency and unusual inhibition mechanism of EFdA we solved crystal structures representing intermediates of EFdA blocking DNA synthesis. Two of these show EFdA bound at the N- and P-sites, providing molecular insights of EFdA inhibition as an immediate or delayed chain terminator. The structures show that EFdA blocks RT translocation through favorable interactions of its 4′-ethynyl (4′-E) at a conserved hydrophobic pocket at the N-site, and unfavorable interactions of 4′-E at the P-site, leading to localized primer distortion. Passages of HIV in presence of a 4′-E NRTI selected RT resistance mutations. The primary mutation, M184V, conferred 7-fold resistance to EFdA. Secondary substitutions T165R and I142V increased resistance to 22-fold. Importantly, the mutations reduced replication capacity. To identify the resistance mechanism we solved structures of M184V/T165R/I142V, M184V/T165R, and M184V in complex with DNA and EFdA-triphosphate (TP). Replacement of the flexible Met side-chain with a rigid b-branched Val in M184V, mildly decreased EFdA-TP binding, leading to resistance through steric hindrance. T165R in α-helix E blocked contacts of R165 with Q182, enabling interactions with 184 of the YMDD loop, which in turn binds incoming dNTP and EFdA-TP. Hence, M184V and T165R confer EFdA resistance by decreasing its incorporation. In contrast, I142V helps unblock EFdA-terminated primers. Hence, unlike with other NRTIs, multiple resistance mechanisms are needed for only a 22-fold resistance to EFdA, making it a promising antiviral.

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