Structure of HIV-2 reverse transcriptase at 2.35-A resolution and the mechanism of resistance to non-nucleoside inhibitors

Abstract

The HIV-2 serotype of HIV is a cause of disease in parts of the West African population, and there is evidence for its spread to Europe and Asia. HIV-2 reverse transcriptase (RT) demonstrates an intrinsic resistance to non-nucleoside RT inhibitors (NNRTIs), one of two classes of anti-AIDS drugs that target the viral RT. We report the crystal structure of HIV-2 RT to 2.35 A resolution, which reveals molecular details of the resistance to NNRTIs. HIV-2 RT has a similar overall fold to HIV-1 RT but has structural differences within the "NNRTI pocket" at both conserved and nonconserved residues. The structure points to the role of sequence differences that can give rise to unfavorable inhibitor contacts or destabilization of part of the binding pocket at positions 101, 106, 138, 181, 188, and 190. We also present evidence that the conformation of Ile-181 compared with the HIV-1 Tyr-181 could be a significant contributory factor to this inherent drug resistance of HIV-2 to NNRTIs. The availability of a refined structure of HIV-2 RT will provide a stimulus for the structure-based design of novel non-nucleoside inhibitors that could be used against HIV-2 infection.

Fig 1.

(A) 2|F_o| − |F_c| electron density map contoured at 1 σ showing residues from 400 to 406 in p68 of HIV-2 RT. (B) Ribbon diagram showing the overall fold of HIV-2 RT overlapped with unliganded HIV-1 RT (1hmv); the HIV-1 RT is shown in gray, and the domains of HIV-2 RT are colored as follows: fingers, blue; palm, green; thumb, orange; connection, red; and RNase H, purple. (C) Ribbon diagram showing the overall fold of HIV-2 RT overlapped with the HIV-1 RT/nevirapine complex (1rtv); the color scheme is as in B.

Fig 2.

(A) Stereo diagram comparing the NNRTI site of an unliganded HIV-1 RT and the corresponding region of HIV-2 RT. The HIV-1 RT is colored in gray, and the main chain and side chains of HIV-2 RT are shown in green and orange, respectively. (B) Stereo diagram showing part of the HIV-2 RT p55 subunit containing the Ile-181 and Leu-188 side chains (blue and green) overlapped with the corresponding region of the p66 subunit in the nevirapine-bound HIV-1 RT (orange and red). Nevirapine is drawn as ball-and-sticks and colored by atoms. (C) Stereo diagram showing a cavity located at the junction of the p68 palm, p68 connection, and p55 fingers domains (ribbon and coils colored in green, red, and blue, respectively). Side chains of the residues lining the cavity, a bound glycerol and a sulfate are shown in ball-and-stick representation, and are colored by atoms, with carbon atoms in cyan for the side chains and black for the glycerol. Water molecules in the cavity are shown as small red spheres. Larger red spheres label the Cα position of the three catalytic Asp residues at the polymerase active site. Nevirapine colored in gray is shown to mark the NNRTI site in HIV-1 RT. The dashed yellow sticks indicate the four H-bonds from the glycerol to the carbonyl oxygen of Gly-99, the main-chain nitrogen of Ala-101, and a water molecule.

Fig 3.

Comparison of the structure around residues 181 and 188 of the p55 subunit in HIV-2 RT with that of p51 subunit in HIV-1 RT. The main chains are shown as ribbons and coils, and side chains as ball-and-stick representations, with HIV-1 RT colored orange and red, and HIV-2 RT blue and green.