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 6

ZL0580 inhibits Tat transactivation and key factors in HIV transcription elongation.

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ZL0580 inhibits Tat transactivation and key factors in HIV transcription...
(A and B) Western blot measurement of Tat and NF-κB (A) and cellular proteins involved in transcription elongation (B) in WT J-Lat cells 24 hours after treatment. (C) Co-IP analysis for binding of CDK9 to Tat or BRD4 in WT J-Lat cells 24 hours after treatment. Control IgG Co-IP and input CDK9 were used as controls. Total/input CDK9 blots in panels (B and C) represent the same experiment. (D) ELL2 protein expression in WT and BRD4-KO J-Lat cells 24 hours after treatment. (E) ELL2 mRNA expression by qPCR in WT J-Lat cells 24 hours after treatment. (F) Effect of protease inhibition by MG132 on ELL2 protein levels in WT J-Lat cells. Cells were pretreated with proteasome inhibitor MG-132 for 6 hours (bottom) or not treated (top), followed by treatment with PMA or PMA+ZL0580 (10 μM) for 18 hours. ELL2 protein was measured by Western blot. (G) Phosphorylated RNAPII (Ser 2 CTD) in WT (top) and BRD4-KO (bottom) J-Lat cells after different treatments. Loading control GAPDH in panel (D and G) represents the same experiment. (H and I) ChIP-qPCR analysis for recruitment of Tat (H) or BRD4 (I) to HIV 5′ LTR in PMA-activated or unstimulated J-Lat cells 24 hours after treatment. ChIP using control IgG was included for normalization. qPCR was conducted to quantify the precipitated HIV 5′ LTR region. Data were normalized to NC. Error bars (E, H, and I) show SD of qPCR replicate. All experiments were independently conducted at least 3 times. *P < 0.05; **P < 0.005, 1-way ANOVA (H and I). ND, nondetectable.