LOCATIONS OF ANTI-AIDS DRUG-BINDING SITES AND RESISTANCE MUTATIONS INTHE 3-DIMENSIONAL STRUCTURE OF HIV-1 REVERSE-TRANSCRIPTASE - IMPLICATIONS FOR MECHANISMS OF DRUG-INHIBITION AND RESISTANCE

The locations of HIV-1 RT nucleoside and non-nucleoside inhibitor-bind ing sites and inhibitor-resistance mutations are analyzed in the conte xt of the three-dimensional structure of the enzyme and implications f or mechanisms of drug inhibition and resistance are discussed. In orde r to help identify residues that may play a role in inhibitor binding, solvent accessibilities of amino acids that comprise the inhibitor-bi nding sites in the structure of HIV-1 RT complexed with a dsDNA templa te-primer are analyzed. While some mutations that cause resistance to nucleoside analogs, such as AZT, ddI, and ddC, are located near enough to the dNTP-binding site to directly interfere with binding of nucleo side analogs, many are located away from the dNTP-binding site and mor e likely confer resistance by other mechanisms. Many of the latter mut ations are located on the surface of the DNA-binding cleft and may lea d to altered template-primer positioning or conformation, causing a di stortion of the geometry of the polymerase active site and consequent discrimination between normal and altered dNTP substrates. Other nucle oside analog-resistance mutations located on the periphery of the dNTP -binding site may exert their effects via altered interactions with dN TP-binding site residues. The structure of the hydrophobic region in H IV-1 RT that binds non-nucleoside inhibitors, for example, nevirapine and TIBO, has been analyzed in the absence of bound ligand. The pocket that is present when non-nucleoside inhibitors are bound is not obser ved in the inhibitor-free structure of HIV-1 RT with dsDNA. In particu lar it is filled by Tyr181 and Tyr188, suggesting that the pocket is f ormed primarily by rotation of these large aromatic side-chains. Exist ing biochemical data, taken together with the three-dimensional struct ure of HIV-1 RT, makes it possible to propose potential mechanisms of inhibition by non-nucleoside inhibitors. One such mechanism is local d istortion of HIV-1 RT structural elements thought to participate in ca talysis: the beta 9-beta 10 hairpin (which contains polymerase active site residues) and the beta 12-beta 13 hairpin (''primer grip''). An a lternative possibility is restricted mobility of the p66 thumb subdoma in, which is supported by the observation that structural elements of the non-nucleoside inhibitor-binding pocket may act as a ''hinge'' for the thumb. Mutations that have been shown to confer resistance to non -nucleoside inhibitors are observed to cluster around the pocket, sugg esting that most of these resistance mutations lead to direct alterati on of inhibitor binding. A comparison of residues in the non-nucleosid e inhibitor-binding pocket of HIV-1 RT and the corresponding residues in HIV-2 RT can explain the low activity of non-nucleoside compounds a gainst HIV-2 RT.