Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Science, Jilin University, 2699 Qianjin Street, Changchun 130012, China.
The Institute of Theoretical Chemistry, College of Chemistry, Jilin University, 2 Liutiao Road, Changchun 130012, China.
Int J Mol Sci. 2023 Jun 29;24(13):10831. doi: 10.3390/ijms241310831.
Bromodomain-Containing Protein 4 (BRD4) can play an important role in gene transcriptional regulation of tumor development and survival by participating in histone modification epigenetic mechanism. Although it has been reported that novel allosteric inhibitors such as ZL0590 have a high affinity with target protein BRD4 and good efficacy, their inhibitory mechanism has not been studied further. The aim of this study was to reveal the inhibition mechanism of allosteric inhibitor ZL0590 on Free-BRD4 and BRD4 binding MS436 (orthosteric inhibitor) by molecular dynamics simulation combined with a Markov model. Our results showed that BRD4-ZL0590 led to α-helices formation of 100-105 compared with Free-BRD4; the combination of MS436 caused residues 30-40 and 95-105 to form α-helices, while the combination of allosteric inhibitors untangled the α-helices formed by the MS436. The results of Markov flux analysis showed that the binding process of inhibitors mainly involved changes in the degree of α-helices at ZA loop. The binding of ZL0590 reduced the distance between ZA loop and BC loop, blocked the conformation at the active site, and inhibited the binding of MS436. After the allosteric inhibitor binding, the MS436 that could normally penetrate into the interior of the pocket was floating on the edge of the active pocket and did not continue to penetrate into the active pocket as expected. In summary, we provide a theoretical basis for the inhibition mechanism of ZL0590 against BRD4, which can be used as a reference for improving the development of drug targets for cancer therapy.
溴结构域蛋白 4（BRD4）可通过参与组蛋白修饰表观遗传机制，在肿瘤发展和存活的基因转录调控中发挥重要作用。虽然已经报道了新型别构抑制剂，如 ZL0590，与靶蛋白 BRD4 具有高亲和力和良好的疗效，但它们的抑制机制尚未进一步研究。本研究旨在通过分子动力学模拟结合马尔可夫模型，揭示别构抑制剂 ZL0590 对游离 BRD4 和 BRD4 结合 MS436（正构抑制剂）的抑制机制。结果表明，BRD4-ZL0590 导致 100-105 位的α-螺旋形成，而游离 BRD4 则没有；MS436 的结合导致 30-40 位和 95-105 位形成α-螺旋，而别构抑制剂的结合则解开了 MS436 形成的α-螺旋。马尔可夫通量分析的结果表明，抑制剂的结合过程主要涉及 ZA 环的α-螺旋程度的变化。ZL0590 的结合降低了 ZA 环与 BC 环之间的距离，阻断了活性部位的构象，抑制了 MS436 的结合。别构抑制剂结合后，原本可以正常穿透口袋内部的 MS436 漂浮在活性口袋的边缘，并没有像预期的那样继续穿透到活性口袋中。综上所述，我们为 ZL0590 抑制 BRD4 的机制提供了理论依据，可为癌症治疗药物靶点的开发提供参考。
