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 7

Analysis of chromatin structure in HIV LTR by high-resolution MNase nucleosomal mapping.

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Analysis of chromatin structure in HIV LTR by high-resolution MNase nucl...
(A) Schematic diagram illustrating PCR amplicons at the HIV LTR covering 40–902 nucleotides that correspond to Nuc-0, DNase hypersensitive site 1 (DHS1), Nuc-1, DHS2, and Nuc-2. PCR product sizes are 100 ± 10 bp approximately 30 bp apart from each other. (B) Profile of chromatin structure in the HIV LTR in J-Lat cells after different treatments. Cells were either untreated (NC) or treated with ZL0580 (10 μM) or JQ1 (10 μM) for 24 hours, followed by activation with PMA for 24 hours. Chromatin profile was determined by calculating the ratio (y axis) for the amount of PCR product in the MNase-digested DNA relative to that of the undigested control DNA for each primer pair. The x axis shows corresponding PCR amplicon with bp units with 0 as the start of LTR Nuc-0. The MNase assay was independently repeated twice. Error bars show SD of PCR replicates. ***P < 0.001 denotes statistical comparison among NC, ZL0580, and JQ1 by 1-way ANOVA.