A highly potent long-acting small-molecule HIV-1 capsid inhibitor with efficacy in a humanized mouse model

Abstract

People living with HIV (PLWH) have expressed concern about the life-long burden and stigma associated with taking pills daily and can experience medication fatigue that might lead to suboptimal treatment adherence and the emergence of drug-resistant viral variants, thereby limiting future treatment options1,2,3. As such, there is strong interest in long-acting antiretroviral (ARV) agents that can be administered less frequently4. Herein, we report GS-CA1, a new archetypal small-molecule HIV capsid inhibitor with exceptional potency against HIV-2 and all major HIV-1 types, including viral variants resistant to the ARVs currently in clinical use. Mechanism-of-action studies indicate that GS-CA1 binds directly to the HIV-1 capsid and interferes with capsid-mediated nuclear import of viral DNA, HIV particle production and ordered capsid assembly. GS-CA1 selects in vitro for unfit GS-CA1-resistant capsid variants that remain fully susceptible to other classes of ARVs. Its high metabolic stability and low solubility enabled sustained drug release in mice following a single subcutaneous dosing. GS-CA1 showed high antiviral efficacy as a long-acting injectable monotherapy in a humanized mouse model of HIV-1 infection, outperforming long-acting rilpivirine. Collectively, these results demonstrate the potential of ultrapotent capsid inhibitors as new long-acting agents for the treatment of HIV-1 infection.

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Fig. 1: Antiviral properties of GS-CA1.
Fig. 2: GS-CA1 binding to recombinant HIV-1 capsid.
Fig. 3: GS-CA1 mechanisms of action.
Fig. 4: Preclinical PK/PD evaluations of GS-CA1.

Data availability

All data needed to understand and assess the conclusions of this research are available in the main text and supplementary materials. Raw datasets supporting the findings of this study are available from the corresponding author on reasonable request. The availability of GS-CA1 is subject to a material-transfer agreement, which can be requested through the corresponding author. Full uncropped western blots from Extended Data Fig. 7b are available as Source Data.

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Acknowledgements

We are grateful to A. Irrinki for assisting with the FACS portion of the entry studies, and K. Stray for supplying the pLAI-RenLuc vector. We appreciate the expertise provided by J. Wong at the Gladstone Institute Electron Microscopy Core facility, C. Lackman-Smith at Southern Research and C. Verhaeghe at TransCure bioServices as part of the work each performed under contracted research agreements. This study was funded by Gilead Sciences, Inc. The anti-HIV-1 p24 AG3.0 monoclonal antibody was obtained from J. Allan through the NIH AIDS Reagent Program, Division of AIDS, NIAID, NIH.

Author information

T.C. conceived the project, which had leadership from T.C., J.O.L., S.R.Y. and W.C.T. All authors performed some component of the experiments, with input from J.Z., G.A.P., H.Y., T.C., J.O.L., W.I.S. and A.L.B. W.C.T., J.R.Z., S.D.S., K.C., E.Y.H. and J.O.L. contributed to GS-CA1 design or synthesis. S.R.Y., A.M., D.H., G.J.S., S.A., H.Y. and R.R.R. contributed to antiviral and resistance assays. D.J., N.N. and M.H. contributed to protein production. A.N.-M., G.A.P., S.R.Y. and M.H.W. conducted biophysical studies. A.L. performed protease assays. E.S. performed western blot and m.o.i. studies. J.Z., B.L., E.P., D.G. and S.R.Y. contributed to mouse PK and efficacy studies. J.M.P., W.M.M. and A.L.B. supplied ViewHIV data under contract with Gilead as part of a funded research agreement. All authors contributed to data analysis and interpretation. S.R.Y. wrote the manuscript with contributions from A.M., A.N.-M., G.A.P., E.Y.H. and W.M.M. All authors discussed the results and approved the manuscript.

Correspondence to Stephen R. Yant.

Ethics declarations

Competing interests

All authors are current or previous employees of Gilead Sciences (except W.I.S., W.M.M., J.M.P. and A.L.B.) and have received a salary and stock ownership as compensation for their employment. J.O.L., S.D.S., W.C.T. and J.R.Z. are inventors on granted US Patent No. 10,071,985 covering GS-CA1 composition of matter and methods of use.

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Peer review information: Alison Farrell is the primary editor on this article and managed its editorial process and peer review in collaboration with the rest of the editorial team.

Publisher’s note: Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Extended data

Extended Data Fig. 1 GS-CA1 antiviral activity against HIV-2 and SIV.

a, Antiviral activity of GS-CA1 against one HIV-2 and two SIV isolates replicating in human PBMCs. Center line and error bars represent mean ± s.d. values determined 7 d post-infection using a reverse transcriptase (RT) activity readout. Experiment was performed once using triplicate cell cultures. b, Alignment of capsid amino-acid sequences. Dots represent invariant residues. Red arrows highlight HIV-1 residues associated with GS-CA1 resistance.

Extended Data Fig. 2 Infectivity of GS-CA1-selected resistance-associated mutants in MT-2 cells.

WT and mutant single-cycle reporter HIV-1NL4.3 were produced in parallel in HEK293T cells by transient transfection, and the HIV content for each was determined by p24 ELISA using a single serial dilution of each sample and quantified across three samples within the linear range of the assay. MT-2 cells were infected in duplicate with serially-diluted, p24-normalized WT and mutant viruses and developed 3 d later by One-Glo addition. Center line and error bars represent mean ± s.d. infectivity values, expressed as a percentage of the WT virus, obtained from three independent experiments. P values for each mutant (n = 12 replicate cell cultures for Q67Y and Q67H + M66I mutants, 3 replicate cell cultures for all others) relative to WT (n = 18 replicate cell cultures) by unpaired two-tailed Student’s t tests with Welch’s correction are indicated.

Extended Data Fig. 3 GS-CA1 resistance mutations map to a conserved CA subunit interface.

a, Location of the resistance-defined GS-CA1 binding site (highlighted by orange rectangle) within the HIV-1 CA hexamer structure (ref. 13). The resistance-defined GS-CA1-binding subunit is shown in blue and the adjacent CA subunit in silver. b, Location of CA residues associated with GS-CA1 resistance (pink spheres), with CA-binding peptides from cleavage and polyadenylation specificity factor 6 (CPSF6313–327) in yellow and nucleoporin 153 (Nup1531410–1423) in green (ref. 17). CPSF6 Phe321 and Nup153 Phe1417 side chains highlighted in stick mode. c, GS-CA1 binding site conservation. The percent CA conservation is depicted as a heat-map based off >4,400 HIV-1 subtype B sequences.

Extended Data Fig. 4 GS-CA1 inhibits HIV-1 replication after virus entry and reverse transcription.

a, Quantitative BlaM-Vpr reporter assay for HIV-1 entry. PBMCs were infected with BlaM-Vpr/HIV-1 (NL4-3 strain) in the presence of GS-CA1 or the designated control compounds, loaded with CCF2 substrate dye, and CD3+CD4+CD8 T cells containing virus were quantified by flow cytometry to detect CCF2 dye cleavage (indicative of virus entry) after 16 h of incubation. Center line and error bars represent mean ± s.d. values obtained from duplicate cell cultures in each of three independent PBMC donors from a single experiment (n = 3 per group). Significant P values relative to mock-treated HIV-infected samples by unpaired two-tailed Student’s t tests with Welch’s correction are indicated. b, Representative time-of-addition study. MT-2 cells were infected with HIV-1 reporter virus and drugs RPV (93 nM, RT inhibitor), DTG (193 nM, IN inhibitor) and GS-CA1 (30 nM) were added at the indicated time points. Infectivity was measured using a luciferase readout 48 h.p.i. and normalized to mock-treated (DMSO) control. Center line and error bars represent mean ± s.d. values obtained from eight replicate cell cultures per time point and condition from two independent experiments with similar results.

Extended Data Fig. 5 Quantitative analysis of ViewHIV study.

a, Quantitation of total vDNA foci per cell observed in microscopy images. Center line and error bars represent mean ± s.e.m. numbers of vDNA foci per cell 12 h.p.i. Data in panels ac were obtained from two independent transduction experiments, each using an independent CD4+ T cell donor. The total number of images analyzed for each condition in each panel is from left to right: n = 118, n = 26, n = 49, n = 55, n = 44, n = 43, n = 57. Significant P values relative to DMSO by unpaired two-tailed Mann-Whitney U tests are indicated by asterisks. ****P = 6.1 × 10−12. b, Quantitation of nuclear vDNA foci per cell. Center line and error bars represent mean ± s.e.m. numbers of nuclear vDNA foci per cell 12 h.p.i. Significant P values relative to DMSO by unpaired two-tailed Mann–Whitney U tests from left to right were: ****P = 1.7 × 10−11, *P = 0.026, ****P = 6 × 10−14, ****P = 4.8 × 10−9, ****P = 2.8 × 10−12, ****P < 1 × 10−15. c, Percent co-localization of vDNA and CA foci. Center line and error bars represent mean ± s.e.m. percentage of all vDNA foci that co-localized with CA foci at 12 h.p.i. Significant P values relative to DMSO by unpaired two-tailed Mann–Whitney U tests from left to right were: ****P = 1.2 × 10−5, ****P = 1 × 10−8, ****P = 9.5 × 10−12, ****P < 1 × 10−15.

Extended Data Fig. 6 GS-CA1 resistant M66I mutant delays HIV integration.

a, Antiviral activity of GS-CA1 against WT and CA-M66I mutant in MT-2 cells infected with single-cycle reporter HIV-1. Symbols represent mean ± s.d. values obtained from triplicate cell cultures in each of three independent experiments. b, Representative time-of-addition study. MT-2 cells were infected with WT or CA M66I mutant reporter HIV-1 and the drugs efavirenz (EFV, 150 nM, RT inhibitor) and dolutegravir (DTG, 193 nM, IN inhibitor) were added at the indicated times post-infection. Infectivity was measured using a luciferase readout 48 h.p.i. and normalized to mock-treated (DMSO) control. Center line and error bars represent mean ± s.d. values (n = 8 replicate cell cultures per condition) obtained from two independent experiments. Significant P values relative to WT virus by unpaired two-tailed Student’s t test with Welch’s correction are indicated with an asterisk. c, Representative confocal microscopy images of primary human CD4+ T cells infected with WT or CA-M66I mutant HIV-1 for 12, 18, 24 or 36 h in conjunction with the indicated treatments. Nuclei are stained in blue (DAPI) and cells are outlined in white. CA (green), vDNA (red) and merged (yellow) representative images are shown for each condition from two independent donors from a single experiment. Total number of images analyzed for each row from left to right were: (mock) n = 118, n = 92, n = 18, n = 10, n = 19, n = 17, n = 9, n = 6; (1 nM GS-CA1) n = 44, n = 45, n = 16, n = 16, n = 7, n = 12, n = 3, n = 8; (10 nM GS-CA1) n = 43, n = 56, n = 8, n = 5, n = 4, n = 5, n = 6, n = 13. Scale bars, 5 µm.

Extended Data Fig. 7 GS-CA1 reduces intracellular CA precursor polyprotein levels and particle production.

a, Quantitative HIV-1 protease substrate cleavage assay. The effect of GS-CA1 and atazanavir (ATV, protease inhibitor) on the in vitro cleavage activity of recombinant HIV-1 protease was measured against a fluorogenic HIV-1 protease substrate. Symbols represent mean ± s.d. percent substrate cleavage values obtained from five independent experiments performed in duplicate. b, Effect of GS-CA1 on intracellular capsid precursor polyprotein levels. Representative western blots from three independent transfection experiments showing the effect of GS-CA1 on intracellular CA and Gag protein levels. α-tubulin served as a loading control. HEK293T cells producing WT or M66I HIV-1 were incubated ± GS-CA1 for 48 h, cell lysates were prepared and normalized inputs were analyzed by anti-CA and anti-tubulin western blotting. Full uncropped blots are available as Source Data. c, Quantitation of total intracellular p24 levels observed in Western blot images, after normalizing to α-tubulin levels. Center line and error bars represent mean ± s.d. normalized p24 values. For each condition, a single-cell lysate was prepared and analyzed from each of three independent experiments, with similar results. Significant P values relative to matched mock-treated samples by unpaired two-tailed Student’s t tests with Welch’s correction from left to right were: ****P = 2.2 × 10−6, *P = 0.016, *P = 0.038. d, Representative sensorgrams showing binding of GS-CA1 to immobilized recombinant HIV-1 Gag polyprotein. Binding data (black lines) were globally fit (orange lines) to a simple kinetic model and used to calculate mean ± s.d. KD from three independent experiments. Owing to the fast kinetics of this interaction, values for kon and koff could not be determined with sufficient precision. Source Data

Extended Data Fig. 8 GS-CA1 is highly sequestered in mouse but not in human serum.

a, Effect of including 50% serum (mouse or human) in the cell culture medium on the antiviral potency of GS-CA1, RPV and RAL. Center line and error bars represent mean ± s.d. EC50 fold-change values were obtained with or without the indicated serum. Data were obtained from three independent experiments, each performed with three replicate cell cultures per condition. Brackets and numbers highlight potency shift differences between the two sera. Significant P values by unpaired two-tailed Student’s t tests with Welch’s correction are indicated with an asterisk. b, Plasma drug concentrations over time in male C57Bl/6 mice (n = 3 per time point) following seven consecutive daily subcutaneous administrations of either 15 mg per kg (body weight) GS-CA1 or 160 mg per kg (body weight) LA-RPV. Symbols represent mean ± s.d. mouse serum protein binding-adjusted EC95 values for each compound, with mean fold mouse paEC95 values indicated in boxes according to day 14 drug levels.

Supplementary information

Supplementary Information

Supplementary Tables 1–3, Supplementary Figure 1 and Supplementary Methods.

Reporting Summary

Source data

Source Data Extended Data Fig. 7b

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