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HIV-1 reverse transcriptase complex with DNA and nevirapine reveals non-nucleoside inhibition mechanism

Nature Structural & Molecular Biology volume 19, pages 253–259 (2012)Cite this article

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Abstract

Combinations of nucleoside and non-nucleoside inhibitors (NNRTIs) of HIV-1 reverse transcriptase (RT) are widely used in anti-AIDS therapies. Five NNRTIs, including nevirapine, are clinical drugs; however, the molecular mechanism of inhibition by NNRTIs is not clear. We determined the crystal structures of RT–DNA–nevirapine, RT–DNA, and RT–DNA–AZT-triphosphate complexes at 2.85-, 2.70- and 2.80-Å resolution, respectively. The RT–DNA complex in the crystal could bind nevirapine or AZT-triphosphate but not both. Binding of nevirapine led to opening of the NNRTI-binding pocket. The pocket formation caused shifting of the 3′ end of the DNA primer by ~5.5 Å away from its polymerase active site position. Nucleic acid interactions with fingers and palm subdomains were reduced, the dNTP-binding pocket was distorted and the thumb opened up. The structures elucidate complementary roles of nucleoside and non-nucleoside inhibitors in inhibiting RT.

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Figure 1: Polymerase domain of HIV-1 RT in complex with DNA.
Figure 2: Effects of nevirapine on polymerase active site conformation and dNTP-binding.
Figure 3: Impact of nevirapine binding on thumb, fingers and DNA.
Figure 4: A molecular mechanism of non-nucleoside inhibition and impact of DNA binding on resistance to non-nucleoside drugs.

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Acknowledgements

We acknowledge the staff members at the Cornell High Energy Synchrotron Source (CHESS) and Brookhaven National Laboratory (BNL) for their generous allocation of data collection time. We thank A. Clark, S. Hughes and S. Tuske for advice, and we thank S. Sarafianos and A. Shatkin for helpful comments on the manuscript. We are grateful to the US National Institutes of Health for R21 Award AI 087201 to K.D. and R37 MERIT Award AI 27690 to E.A.

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Authors and Affiliations

  1. Department of Chemistry and Chemical Biology, Center for Advanced Biotechnology and Medicine, Rutgers University, Piscataway, New Jersey, USA

    Kalyan Das, Sergio E Martinez, Joseph D Bauman & Eddy Arnold

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  1. Kalyan Das
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  2. Sergio E Martinez
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  3. Joseph D Bauman
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Contributions

K.D. and E.A. designed the project, S.E.M. conducted the experiments, K.D. carried out structural studies and analyses, and J.D.B. cloned and expressed the protein. K.D., S.E.M. and E.A. wrote the paper.

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Correspondence to Kalyan Das or Eddy Arnold.

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The authors declare no competing financial interests.

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–4 and Supplementary Table 1 (PDF 492 kb)

Supplementary Movie 1

Morphing between RT–DNA and nevirapine-ternary structures illustrates the structural changes in the polymerase domain of HIV-1 RT upon nevirapine (green space filling) binding. The primer grip on b12-b13-b14 (magenta) sheet is displaced by ~4 Å, fingers and thumb subdomains are repositioned, and the nucleic acid is shifted out of the polymerase active site. The nonnucleoside-binding pocket residues Tyr181, Tyr188, and Trp229 (cyan) are rearranged/repositioned upon nevirapine binding. The polymerase active-side residue Asp186 is rearranged to accommodate the primer terminal 3'-azido group (blue) in RT–DNA and AZTTP-ternary structures. (MOV 4824 kb)

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Das, K., Martinez, S., Bauman, J. et al. HIV-1 reverse transcriptase complex with DNA and nevirapine reveals non-nucleoside inhibition mechanism. Nat Struct Mol Biol 19, 253–259 (2012). https://doi.org/10.1038/nsmb.2223

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