STRUCTURE AND MECHANISM OF ACTION OF NONNUCLEOSIDE INHIBITORS OF HIV-1 REVERSE-TRANSCRIPTASE - STRATEGIES TO COMBAT DRUG-RESISTANCE

In the past few years, drug research has focused on three HIV-1 enzyme s, reverse transcriptase (RT), protease, and integrase. In the case of RT, a number of potent inhibitors have been discovered. These can be classified into two distinct groups, nucleoside analogs and nonnucleos ide inhibitors; however, mutations in RT have allowed the virus to dev elop resistance to all of the known drugs. In order to better understa nd the interactions between amino acid residues in the protein and non nucleoside inhibitors, a computer model of the nonnucleoside inhibitor binding pocket of RT has been developed, using a subset of amino acid residues surrounding the pocket. The results of molecular mechanics m inimizations of three RT/nonnucleoside inhibitor complexes showed that the resultant total energies of complexation (binding energies) corre lated with EC50 values if and only if the calculations were carried ou t using coordinates from the cognate complex while allowing for adjust ments of the protein relative to the inhibitor. If a model was constru cted using only the crystal data of one particular RT/inhibitor comple x (RT/8-Cl TIBO), the calculations did not correctly order the other i nhibitors, The difficulty in devising such a ''generic'' model nonnucl eoside binding site in HIV-1 RT is likely due to the inherent flexibil ity of the enzyme. A comparison of the structure(s) of HIV-1 RT in com plexes with different nonnucleoside inhibitors shows that the enzyme r eadily adapts to the shape of each inhibitor upon complexation. In con trast to the side-chain residues of HIV protease, the amino acid resid ues surrounding the binding pocket in RT adopt geometries that are uni que to each bound inhibitor, adopting positions that make tight van de r Waals contacts. Accompanying these changes at the site where the inh ibitor binds are alterations in the geometry of the nearby polymerase active site. These changes can be conveniently monitored by measuring the increase in the distance between residue G231 in the RT primer gri p region and aspartyl residues (D110, D185, and D186) in the polymeras e active site. The magnitude of the change in this distance correlates inversely with inhibitor EC50, suggesting a possible mechanism of act ion of the drugs. Calculations using a site where various amino acids residues were changed to simulate mutations in RT that induce resistan ce to the nonnucleoside inhibitors revealed that a combination of less favorable inhibitor-protein interactions and slight geometry changes in the polymerase active site are responsible for the decreased effect iveness of the inhibitors against mutant RTs. The modeling results are discussed with regard to both the mechanism of inhibition as well as application of these insights to strategies for the design of better n onnucleoside inhibitors. Published by Elsevier Science B.V.