Structure-guided drug design identifies a BRD4-selective small molecule that suppresses HIV
Qingli Niu, Zhiqing Liu, Edrous Alamer, Xiuzhen Fan, Haiying Chen, Janice Endsley, Benjamin B. Gelman, Bing Tian, Jerome H. Kim, Nelson L. Michael, Merlin L. Robb, Jintanat Ananworanich, Jia Zhou, Haitao Hu
Qingli Niu, Zhiqing Liu, Edrous Alamer, Xiuzhen Fan, Haiying Chen, Janice Endsley, Benjamin B. Gelman, Bing Tian, Jerome H. Kim, Nelson L. Michael, Merlin L. Robb, Jintanat Ananworanich, Jia Zhou, Haitao Hu
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Research Article AIDS/HIV

Structure-guided drug design identifies a BRD4-selective small molecule that suppresses HIV

Abstract

HIV integrates its provirus into the host genome and establishes latent infection. Antiretroviral therapy (ART) can control HIV viremia, but cannot eradicate or cure the virus. Approaches targeting host epigenetic machinery to repress HIV, leading to an aviremic state free of ART, are needed. Bromodomain and extraterminal (BET) family protein BRD4 is an epigenetic reader involved in HIV transcriptional regulation. Using structure-guided drug design, we identified a small molecule (ZL0580) that induced epigenetic suppression of HIV via BRD4. We showed that ZL0580 induced HIV suppression in multiple in vitro and ex vivo cell models. Combination treatment of cells of aviremic HIV-infected individuals with ART and ZL0580 revealed that ZL0580 accelerated HIV suppression during ART and delayed viral rebound after ART cessation. Mechanistically different from the BET/BRD4 pan-inhibitor JQ1, which nonselectively binds to BD1 and BD2 domains of all BET proteins, ZL0580 selectively bound to BD1 domain of BRD4. We further demonstrate that ZL0580 induced HIV suppression by inhibiting Tat transactivation and transcription elongation as well as by inducing repressive chromatin structure at the HIV promoter. Our findings establish a proof of concept for modulation of BRD4 to epigenetically suppress HIV and provide a promising chemical scaffold for the development of probes and/or therapeutic agents for HIV epigenetic silencing.

Authors

Qingli Niu, Zhiqing Liu, Edrous Alamer, Xiuzhen Fan, Haiying Chen, Janice Endsley, Benjamin B. Gelman, Bing Tian, Jerome H. Kim, Nelson L. Michael, Merlin L. Robb, Jintanat Ananworanich, Jia Zhou, Haitao Hu

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Figure 4

Suppressive effect of ZL0580 on HIV in PBMCs of ART-suppressed, aviremic HIV-infected participants.

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Suppressive effect of ZL0580 on HIV in PBMCs of ART-suppressed, aviremic...
(A) PBMCs of aviremic RV254 participants (n = 5) were stimulated with anti-CD3/CD28 and cultured in IL-2–containing medium to induce latent HIV activation and CD4+ T cell expansion. Cells were treated with ART alone, ART+ZL0580 (2.5 μM), or were mock treated (NC). HIV release in supernatants was quantified by the 2-step nested qPCR. Following full HIV suppression, treatments were stopped and viral RNA copies were continuously monitored every 3 days. Data are shown as HIV copies (log10) per 106 PBMCs. (B and C) Quantitative analysis of the effect of ZL0580 on promoting HIV suppression during ART (B) and on viral rebound following ART cessation (C). Comparison of length of time (days) and AUC prior to treatment cessation (B) and after treatment cessation up until first viral rebound (C) between ART and ART+ZL0580 for the 5 PBMCs. AUC for each PBMC was quantified using Prism. (D) HIV production by unactivated RV254 PBMCs (n = 6). PBMCs were directly treated with ZL0580 (2.0 μM) or not treated (NC) on days 0, 3, and 6 (treatment stopped on day 9). HIV production in supernatants was measured once every 3 days as indicated. (E) After day 18, PBMCs were stimulated with PHA to reactivate latent HIV. HIV transcriptional reactivation was measured by quantifying Gag RNA in cells. The data are shown as fold change of ZL0580 treatment relative to NC for each PBMC. (A, D, and E) PCR was conducted in duplicate, and error bars show PCR replicate SD. *P < 0.05; **P < 0.005, (B, C, and E), paired Student’s t test.