Binding Kinetics versus Affinities in BRD4 Inhibition
Binding Kinetics versus Affinities in BRD4 Inhibition
复制标题
BRD4 抑制中的结合动力学与亲和力
DOI：
10.1021/acs.jcim.5b00265
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发表时间：
2015-09-01
影响因子：
5.6
通讯作者：
Wu, Ruibo
中科院分区：
文献类型：
--
作者：
Kuang, Ming;Zhou, Jingwei;Wu, Ruibo
溴结构域（BRD）是通过结合乙酰化赖氨酸底物选择性地识别组蛋白作为“阅读器”的蛋白质模块。人BRD 4已成为许多疾病途径的有希望的药物靶标，最近实验发现了几种有效的BRD抑制剂。然而，详细的抑制机制，特别是抑制剂结合动力学尚不清楚。本文采用经典分子动力学（MD）和最先进的密度泛函QM/MM MD模拟方法，揭示了BRD 4中ZA环的动力学特性。然后阐明了结合袋大小与ZA环运动之间的关系。此外，我们的模拟发现，化合物（-）-JQ 1可以合理地容纳在热力学，而它是不可行的结合动力学对BRD 4。它的外消旋（+）-JQ 1被证明对BRD 4既在药物学上合理又在动力学上可实现，这可以解释先前的实验结果，即（+）-JQ 1对BRD 4显示出高抑制作用（IC 50为77 nM），而（-）-JQ 1无活性（>10 μM）。此外，ZA环中的L92/L94/Y 97和BC环中的Asn 140被鉴定为（+）-JQ 1结合/释放动力学中的关键残基。所有这些发现揭示了通过利用BRD的不可忽略的配体结合动力学特征和灵活的ZA环运动，而不仅仅是静态的配体-蛋白质结合亲和力，进一步针对BRD家族的选择性抑制剂设计。
Bromodomains (BRDs) are protein modules that selectively recognize histones as a "reader" by binding to an acetylated lysine substrate. The human BRD4 has emerged as a promising drug target for a number of disease pathways, and several potent BRD inhibitors have been discovered experimentally recently. However, the detailed inhibition mechanism especially for the inhibitor binding kinetics is not clear. Herein, by employing classical molecular dynamics (MD) and state-of-the-art density functional QM/MM MD simulations, the dynamic characteristics of ZA-loop in BRD4 are revealed. And then the correlation between binding pocket size and ZA-loop motion is elucidated. Moreover, our simulations found that the compound (-)-JQ1 could be accommodated reasonably in thermodynamics whereas it is infeasible in binding kinetics against BRD4. Its racemate (+)-JQ1 proved to be both thermodynamically reasonable and kinetically achievable against BRD4, which could explain the previous experimental results that (+)-JQ1 shows a high inhibitory effect toward BRD4 (IC50 is 77 nM) while (-)-JQ1 is inactive (>10 μM). Furthermore, the L92/L94/Y97 in the ZA-loop and Asn140 in the BC-loop are identified to be critical residues in (+)-JQ1 binding/releasing kinetics. All these findings shed light on further selective inhibitor design toward BRD family, by exploiting the non-negligible ligand binding kinetics features and flexible ZA-loop motions of BRD, instead of only the static ligand-protein binding affinity.