Background: Concerns about the development of the high viral resistance to 3TC have prompted the studies of the molecular mechanism of resistance. The crystal structure of M184V Reverse Transcriptase (RT) was recently reported to have only minimal conformational changes in the polymerase active site, indicating that the resistance can occur only after incorporation of the DNA template-primer and/or the NRTI triphosphate because they are in close contact with the bulky side chain of Val184. In this study, the different modes of interaction of Val184 with 3TC triphosphate and NRTI triphosphates which are active against M184V RT such as 2’,3’-unsaturated (d4) nucleosides and heterosubstituted 2’,3’-dideoxynucleosides (dioxolane, dOTC) were modeled by energy minimization studies of RT complexed with various NRTI triphosphates.

Methods: Triphosphates of 3TC, d4T, abacavir, D-2’-F-d4C, D-5-F-d4C, D-dioxolane T, D-dioxolane 5-FC and (-)-dOTC were docked into the active site of wild-type (WT) RT, and the resulting complexes were energy-minimized. The minimized structures of WT RT-NRTI triphosphate complexes were then changed to the corresponding M184V RT complexes by the point mutation at codon 184. The effect of mutation to the binding of NRTI triphosphates to mutant RT was investigated before and after minimization.

Results: The bulky side chain of Val184 can adjust its conformation to prevent the steric hindrance with primer strand, which can be found in binding modes of natural substrate (dNTP). However, in 3TC triphosphate-RT complex, the unnatural L-configured oxathiolane sugar moiety of 3TC is too close to Val184 to allow any conformational adjustment of Val184 resulting in the repositioning of the primer strand out of the binding site. The d4 nucleosides are located far away from Val184 due to the p-p interaction with nearby Tyr115 and the heterosubstituted 2’,3’-dideoxynucleosides do not experience any steric hindrance with the bulky side chain of Val184, but maintain the favorable binding modes through the interaction of 3’-oxygen with active site residues such as Arg72 or Tyr115.

Conclusion: It is apparent that the mutation M184V imposes steric hindrance to the incoming nucleoside triphosphates as well as the nearby primer chain. Therefore, for a nucleoside triphosphate-RT complex to be active against M184V RT, the NRTI triphosphates should be able to interact with active site residues to maintain their sugar moieties far away from the bulky side chain of Val184.