Interactions of conformationally biased north and south 2 '-fluoro-2 ',3 '-dideoxynucleoside 5 '-triphosphates with the active site of HIV-1 reverse transcriptase

Molecular dynamics simulations of a ternary complex of HIV-1 reverse transc riptase (RT), double-stranded DNA, and bound dideoxynucleoside-5'-triphosph ate (RT-DNA-ddNTP), utilizing the ddNTPs ddATP, beta FddATP, and alpha FddA TP, explain the experimentally observed order of potency of these 5'-tripho sphates as inhibitors of RT: ddATP > beta FddATP > alpha FddATP. On the bas is of RT's known preference to bind the incoming dNTP (or ddNTP) with a nor th conformation at the polymerase site, alpha FddATP, which in solution pre fers almost exclusively a north conformation, was predicted to be the most potent inhibitor. However, Tyr115, which appears to function as a steric ga te to preclude the binding of ribonucleoside 5'-triphosphates, prevents the effective binding of alpha FddATP in its preferred north conformation. The south-biased beta FddATP, while able to bind to RT without hindrance by Ty r115, has to pay a high energy penalty to be flipped to the active north co nformation at the polymerase site. Finally, the more flexible and less conf ormationally biased ddATP is able to switch to a north conformation at the RT site with a smaller energy penalty than beta FddATP. These results highl ight the opposite conformational preferences of HIV-1 RT for alpha FddATP a nd beta FddATP and help establish conformational guidelines for optimal bin ding at the polymerase site of this enzyme.