NONNUCLEOSIDE RT INHIBITORS GIVE HIV-1 RT A CROOKED BACK. Yu Hsiou1, Jianping Ding1, Kalyan Das1, Stephen H. Hughes2, and Edward Arnold1* 1Center for Advanced Biotechnology and Medicine (CABM) and Rutgers University Chemistry Department, 679 Hoes Lane, Piscataway, NJ 08854-5638, USA; 2ABL-Basic Research Program, NCI-Frederick Cancer Research and Development Center, P.O. Box B, Frederick, MD 21702-1201, USA
The combined structural, biological, and genetic information on HIV-1 reverse transcriptase (RT) has enhanced our understanding of the mechanisms of polymerization and inhibition. Crystal structures of HIV-1 RT, either unliganded or complexed with different nonnucleoside RT inhibitors (NNRTI) or a double-stranded DNA, have been reported. There are significant differences between different HIV-1 RT structures; this serves to illustrate the high flexibility of this enzyme.
Comparison of various RT structures with or without bound ligand or substrate reveals that the p66 thumb subdomain can occupied at least three different positions that depend on whether RT interacts with or without substrate or various ligands. In contrast to the "thumb down" position found in the unliganded form, when HIV-1 RT binds a DNA substrate the p66 thumb is rotated open at the thumb's "knuckle", which is near residues Trp239 and Val317. This knuckle movement of the p66 thumb affects only the position of the p66 thumb, not other subdomains. The binding of an NNRTI, however, induces a hinge-like movement at the base of the p66 thumb subdomain, between the [[beta]]6-[[beta]]10-[[beta]]9 and [[beta]]12-[[beta]]13-[[beta]]14 ("primer grip") sheets. Associated with this hinge-like movement, the p66 thumb subdomain is further extended to a wide open position. The p66 connection subdomain, RNase H domain, and the subdomains in the p51 subunit are displaced by this hinge-like movement as well.
The polymerase active site is composed of structural elements from both protein and nucleic acid. NNRTI binding to HIV-1 RT leads to altered positions of both the p66 thumb and the primer grip, which consequently would alter the position of template-primer relative to both the polymerase and the RNase H active sites. Those conformational changes could account for the inhibition activity of NNRTIs, and explain the alteration of cleavage specificity of RNase H by NNRTI binding.