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Structures of HIV-1 RT–DNA complexes before and after incorporation of the anti-AIDS drug tenofovir

Nature Structural & Molecular Biology volume 11, pages 469–474 (2004)Cite this article

Abstract

Tenofovir, also known as PMPA, R-9-(2-(phosphonomethoxypropyl)adenine, is a nucleotide reverse transcriptase (RT) inhibitor. We have determined the crystal structures of two related complexes of HIV-1 RT with template primer and tenofovir: (i) a ternary complex at a resolution of 3.0 Å of RT crosslinked to a dideoxy-terminated DNA with tenofovir-diphosphate bound as the incoming substrate; and (ii) a RT–DNA complex at a resolution of 3.1 Å with tenofovir at the 3′ primer terminus. The tenofovir nucleotide in the tenofovir-terminated structure seems to adopt multiple conformations. Some nucleoside reverse transcriptase inhibitors, including 3TC and AZT, have elements ('handles') that project beyond the corresponding elements on normal dNTPs (the 'substrate envelope'). HIV-1 RT resistance mechanisms to AZT and 3TC take advantage of these handles; tenofovir's structure lacks handles that could protrude through the substrate envelope to cause resistance.

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Figure 1: Comparison of the chemical structures of tenofovir, dTMP and the NRTIs 3TCMP and AZTMP.
Figure 2: RT interactions with tenofovir.
Figure 3: Stereo diagram of the relationship between tenofovir-DP in the N site and tenofovir-terminated template primer at the P site.
Figure 4: The active site of the RT(P)–tenofovir complex with tenofovir in two conformations.
Figure 5: Schematic relationship among events involved in chain termination and excision of tenofovir (TFV).

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Acknowledgements

We thank the staffs at Advanced Photon Source BioCARS and CHESS for assistance with synchrotron data collection. We also thank other members of the Arnold lab including D. Sheng, K. Das, D. Oren and J. Birktoft for assistance and helpful discussions. We are grateful for support from US National Institutes of Health grants T32 AI50382 (National Research Service Award postdoctoral fellowship to S.T.), R01 AI27690 (MERIT award to E.A.) and P01 GM56690 (to E.A., S.S.H. and R.A.J.). S.H.H.'s laboratory has been supported by the US National Institute of General Medical Sciences and the US National Cancer Institute.

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Authors and Affiliations

  1. Center for Advanced Biotechnology and Medicine, 679 Hoes Lane, Piscataway, 08854-5638, New Jersey, USA

    Steve Tuske, Stefan G Sarafianos, Arthur D Clark Jr, Jianping Ding & Eddy Arnold

  2. Rutgers University Department of Chemistry and Chemical Biology , 679 Hoes Lane, Piscataway, 08854-5638, New Jersey, USA

    Steve Tuske, Stefan G Sarafianos, Arthur D Clark Jr, Jianping Ding, Gang Wang, Barbara L Gaffney, Roger A Jones & Eddy Arnold

  3. Key Laboratory of Proteomics, Institute of Biology and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Feng-lin Road, Shanghai, 200032, China

    Jianping Ding

  4. Gilead Sciences, Inc., 333 Lakeside Drive, Foster City, 94404, California, USA

    Lisa K Naeger, Kirsten L White, Michael D Miller & Craig S Gibbs

  5. HIV Drug Resistance Program, National Cancer Institute at Frederick Cancer Research and Development Center, Building 539, Frederick, 21702, Maryland, USA

    Paul L Boyer, Patrick Clark & Stephen H Hughes

  6. Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, The National Institutes of Health, Bethesda, 20892-0820, Maryland, USA

    Donald M Jerina

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Correspondence to Eddy Arnold.

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Competing interests

During portions of this study, S.T. and E.A. were paid consultants for Gilead Sciences and L.K.N., K.W., M.D.M. and C.S.G. were employees of Gilead Sciences.

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Tuske, S., Sarafianos, S., Clark, A. et al. Structures of HIV-1 RT–DNA complexes before and after incorporation of the anti-AIDS drug tenofovir. Nat Struct Mol Biol 11, 469–474 (2004). https://doi.org/10.1038/nsmb760

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