抑制剂与BRD4和BRD9的结合机制通过多个独立分子动力学模拟和深度学习来解码
Jian Wang1, Wanchun Yang1, Lu Zhao1
1School of Science, Shandong Jiaotong University, Jinan 250357, China.
Molecules (Basel, Switzerland)
|April 27, 2024
概括
odomain 4 和 9 (BRD4 和 BRD9) 抑制剂对 BRD9 的结合比 BRD4 强,主要是通过范德瓦尔斯力. 本研究确定了开发向疗法的关键结合点.
科学领域:
- 生物化学 生物化学
- 计算化学的计算化学
- 药物发现 药物发现 药物发现
背景情况:
- odomain 4 (BRD4) 和odomain 9 (BRD9) 是各种疾病的关键药物标.
- 了解抑制剂与这些原体的相互作用是治疗开发的关键.
研究的目的:
- 研究三种抑制剂 (H1B,JQ1,TVU) 对BRD4和BRD9.9的结合方式和亲缘关系.
- 确定关键的相互作用部位和控制抑制剂结合的作用力.
- 为设计选择性BRD家族抑制剂提供理论见解.
主要方法:
- 分子动力学 (MD) 模拟来分析蛋白质动力学.
- 深度学习 (DL) 用于从MD轨迹中识别功能域.
- 具有约束力的自由能量计算 (MM-GBSA) 用于量化具有约束力的亲和关系.
- 基于残留的自由能量估计,以确定热点.
主要成果:
- 深度学习识别了像BC-loop和ZA-loop这样的功能域.
- 抑制剂结合显著改变了BRD4和BRD9.9的结构灵活性和动态.
- 与BRD4.4相比,H1B,JQ1和TVU对BRD9的结合更强烈.
- 范德瓦尔斯相互作用是抑制剂结合中的主要力量.
- 确定了BRD4和BRD9的关键残留热点.
结论:
- 这项研究提供了详细的分子理解与BRD4和BRD9.9的抑制剂相互作用.
- 结合 afinities 和相互作用机制被阐明,有利于BRD9.
- 已识别的热点为开发选择性BRD抑制剂提供了有价值的目标.
- 这项研究支持合理设计针对BRD家族的新疗法.
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