沃罗诺伊 entropy作为一个连接体分子描述蛋白质-连接体相互作用的分子描述器
Sergey Shityakov1, Aleksandr S Aglikov1, Ekaterina V Skorb1
1Infochemistry Scientific Center (ISC), ITMO University, 9 Lomonosova St., St. Petersburg 191002, Russia.
ACS omega
|December 11, 2023
概括
较少排序的配体表现出更高的受体亲和力. 沃罗诺伊 (VE) 与与SARS-CoV-2主要蛋白酶结合的连接体有很强的相关性,与香农 (SE) 不同.
科学领域:
- 计算化学是一种计算化学.
- 分子建模分子建模
- 药物发现 药物发现
背景情况:
- 了解配体受体相互作用对于药物开发至关重要.
- 分子复杂性和空间布局影响结合亲和力.
- 之前的研究探索了各种分子描述器来预测结合.
研究的目的:
- 调查连接体的Voronoi (VE) 与它们与SARS-CoV-2主蛋白酶的结合亲和力之间的相关性.
- 测试假设,少排序的连接体具有更高的分子流动性,从而增加受体附着概率.
- 为了比较VE的预测能力与Shannon (SE) 对于配体-受体结合.
主要方法:
- 使用基于SMILES的2D图表计算了1144个连接体的Voronoi (VE).
- 从BindingDB数据库中获取了SARS-CoV-2主要蛋白酶的联体亲和数据 (IC50).
- 分析了 VE,SE 和 IC50 值之间的相关性.
主要成果:
- 在 VE 和 IC50 (IC50 = -275 * S + 613 nM) 之间发现了强烈的相关性,这表明连接体复杂性会影响亲和力.
- VE分布遵循高斯式模式 (0.4 ≤ S ≤ 1.66).
- 香农 (SE) 与结合亲和力没有显著的相关性 (p值>0.05).
结论:
- 通过Voronoi度测量的连接物分子复杂性,是与SARS-CoV-2主要蛋白酶结合亲和力的重要预测因素.
- 原子的空间排列,被 VE 捕获,对于分子运动和有效的结合至关重要.
- 沃罗诺伊是药物发现和优化的描述符.
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