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Clinical targeting of HIV capsid protein with a long-acting small molecule

Abstract

Oral antiretroviral agents provide life-saving treatments for millions of people living with HIV, and can prevent new infections via pre-exposure prophylaxis1,2,3,4,5. However, some people living with HIV who are heavily treatment-experienced have limited or no treatment options, owing to multidrug resistance6. In addition, suboptimal adherence to oral daily regimens can negatively affect the outcome of treatment—which contributes to virologic failure, resistance generation and viral transmission—as well as of pre-exposure prophylaxis, leading to new infections1,2,4,7,8,9. Long-acting agents from new antiretroviral classes can provide much-needed treatment options for people living with HIV who are heavily treatment-experienced, and additionally can improve adherence10. Here we describe GS-6207, a small molecule that disrupts the functions of HIV capsid protein and is amenable to long-acting therapy owing to its high potency, low in vivo systemic clearance and slow release kinetics from the subcutaneous injection site. Drawing on X-ray crystallographic information, we designed GS-6207 to bind tightly at a conserved interface between capsid protein monomers, where it interferes with capsid-protein-mediated interactions between proteins that are essential for multiple phases of the viral replication cycle. GS-6207 exhibits antiviral activity at picomolar concentrations against all subtypes of HIV-1 that we tested, and shows high synergy and no cross-resistance with approved antiretroviral drugs. In phase-1 clinical studies, monotherapy with a single subcutaneous dose of GS-6207 (450 mg) resulted in a mean log10-transformed reduction of plasma viral load of 2.2 after 9 days, and showed sustained plasma exposure at antivirally active concentrations for more than 6 months. These results provide clinical validation for therapies that target the functions of HIV capsid protein, and demonstrate the potential of GS-6207 as a long-acting agent to treat or prevent infection with HIV.

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Fig. 1: GS-6207 is a potent CA-targeting inhibitor of HIV replication.
Fig. 2: GS-6207 inhibits multiple CA-dependent steps of HIV-1 replication.
Fig. 3: Resistance to GS-6207 maps to CA.
Fig. 4: Clinical testing of GS-6207 in humans.

Data availability

All data to understand and assess the conclusions of this research are available in the Article and Supplementary Information. Raw gel source data for Fig. 2f are available in Supplementary Fig. 1. Small-molecule X-ray crystallographic coordinates and structure factor files have been deposited in the Protein Data Bank (PDB) with accession number 6V2F. Study GS-US-200-4072 was registered with ClinicalTrials.gov, NCT03739866. The datasets generated during and/or analysed during the current study are available from the corresponding author on reasonable request.

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Acknowledgements

We thank D. Cowfer, K. Brendza, G. Czerwieniec, M. Tsiang, K. Wang, G. Lane, M. Kenney, M. Ceo, S. Kazerani, T. Lane, L. Meng, T. Rainey, A. Vandehey, A. Wagner, M. O’Keefe, J. Yoon, S. Neville, W. Lew, B. Ross, Q. Wang, J. Cha, M. Tran and K. Nguyen for their support and contributions, and all the people who participated in the phase-I clinical trials, including the study participants, their families, and the principal investigators and their staff.

Author information

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Authors

Contributions

T.C. conceived the project. D.J., M.H. and N.N. conducted protein purifications, and X.L. and R.S. oversaw the analysis. S.R.Y., N.P., T.Z.C., D.K. and L.L designed, conducted and analysed small-molecule library screens. T.C., J.O.L., S.R.Y., R.L.H., W.C.T., M.S.R. and A.E.C. provided project leadership. J.O.L., W.C.T., S.D.S., C.-H.C., E.C., G.B., J.R.Z., J. Li, M.G., P.M., Q.L., Q.W., R.L.H., R.D.S., S.D.S., S.E.L. and S.B. were responsible for the design, synthesis, characterization and scaling-up of small molecules. A.N.-M. conducted and analysed in vitro CA assembly assays. S.R.Y. and A.N.-M. conducted and analysed virion morphology by electron microscopy. G.J.S., S.A. and H.Y. designed, conducted and analysed high-throughput antiviral measurements. G.J.S, S.A., A.M. and Y.X. conducted cell-based assays for cytotoxicity. G.J.S. conducted and analysed in vitro drug combination studies. A.M. and R.R.R. conducted and analysed in vitro antiviral testing against HIV mutants with resistance to existing agents. A.G.V. and R.L.A. conducted protein crystallization studies, J.R.S. collected and analysed X-ray crystallographic data, and T.C.A. prepared the refinement table. C.E.C. and E.Y.H. conducted structural modelling studies to guide small-molecule development. G.A.P., M.H.W., S.A.L., S.C. and L.L. conducted and analysed biosensor binding studies. S.R.Y. A.M., E.S. and L.K.T. conducted and analysed cell-based mechanism-of-action studies. A.L. conducted and analysed biochemical protease assays. A.M., D.H., R.A.B. and S.R.Y. conducted resistance selection assays and characterized emergent HIV-1 CA variants. J.Z., B.L. and J.M. designed and executed preclinical pharmacokinetics and metabolism studies, and summarized results. A.E.C. oversaw all anatomical pathology examinations and analyses of preclinical animal species. W.R., S. Sellers and A.C. designed and tested drug formulations. A.C. and S.A.W. oversaw GS-6207 chemistry, manufacture and control for clinical studies. M.S.R., R.H., R.B. and D.M.B. designed and supervised the clinical studies, and G.I.S., P.J.R., G.E.C., C.K.M. and E.S.D conducted them. R.B., J. Ling, Y.-P. L., N.M. and C.C. conducted and coordinated clinical sample and statistical analyses. W.I.S. provided project guidance during the early discovery phase, and S. Swaminathan and W.E.L. provided long-term project oversight. S.R.Y., M.S.R., J.O.L. and T.C. wrote the manuscript, with input from all authors.

Corresponding author

Correspondence to Stephen R. Yant.

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Competing interests

All authors are current or previous employees of Gilead Sciences (except for G.I.S., P.J.R., G.E.C., C.K.M., W.I.S. and E.S.D.) and received salary and stock ownership as compensation for their employment. M.G., J.O.L., W.R., R.D.S., S.D.S., W.C.T. and J.R.Z. are inventors on granted US patent no. 10,071,985B2 covering GS-6207 composition of matter and methods of use. G.I.S. receives research support from Gilead Sciences, Janssen Pharmaceutica, GlaxoSmithKline, Abbvie and Cepheid, and is on the speaker’s bureau and advisory board for Janssen, ViiV Healthcare and Merck. G.E.C. receives grants (investigator research payments) from Gilead Sciences, ViiV Healthcare, Merck and Janssen Pharmaceutica. C.K.M. receives research support from Gilead Sciences, Merck, ViiV Healthcare and Janssen Pharmaceutica, is on the speaker’s bureau for Gilead Sciences, Merck and Insmed, and is on an advisory board for Gilead Sciences. E.S.D. receives research support from Gilead Sciences, Merck and ViiV Healthcare, and has served as a consultant for Gilead Sciences.

Additional information

Peer review information Nature thanks Daniel R. Kuritzkes, Kevan Shokat and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.

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Extended data figures and tables

Extended Data Table 1 Cytotoxicity of GS-6207 in human cell lines and primary cells
Extended Data Table 2 In vitro combination studies with GS-6207
Extended Data Table 3 GS-6207 activity against HIV-1 isolates that are resistant to existing antiretroviral inhibitors
Extended Data Table 4 Data collection and refinement statistics (molecular replacement)
Extended Data Table 5 Biosensor surface-plasmon-resonance assays of GS-6207 binding to recombinant CA
Extended Data Table 6 Resistance profile of HIV-1 CA mutants identified in viruses selected by GS-6207
Extended Data Table 7 Baseline characteristics and clinical adverse events in healthy participants (that affected >1 participant overall) in study GS-US-200-4070
Extended Data Table 8 Baseline characteristics and clinical serious adverse events (that affected any participant) and adverse events (that affected >1 participant overall) in participants living with HIV in study GS-US-200-4072
Extended Data Table 9 Clinical pharmacokinetic parameters in healthy volunteers and participants living with HIV
Extended Data Table 10 Plasma HIV-1 RNA levels and genotype in participants living with HIV (GS-US-200-4072)

Supplementary information

Supplementary Information

This file contains Supplementary Figures 1-5 and the Chemistry Experimental details.

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Link, J.O., Rhee, M.S., Tse, W.C. et al. Clinical targeting of HIV capsid protein with a long-acting small molecule. Nature 584, 614–618 (2020). https://doi.org/10.1038/s41586-020-2443-1

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