准确的基于物理的预测RNA和DNA向质的结合性亲和关系
Ara M Abramyan1, Anna Bochicchio2, Chuanjie Wu3
1Schrödinger Incorporated, San Diego, California 92121, United States.
Journal of chemical information and modeling
|January 30, 2025
概括
自由能量扰动 (FEP) 方法准确地预测了对核酸的联体结合亲缘关系. 这种使用FEP+和OPLS4的计算方法有助于发现针对DNA和RNA的抗癌,抗病毒和抗菌剂的药物.
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:
- 预测连接体-核酸结合亲和力对于开发向DNA和RNA的药物至关重要.
- 目前的计算方法难以准确地预测核酸目标的亲和力.
- 自由能量扰动 (FEP) 是一种可靠的方法来预测蛋白质 - 连接体结合亲和力.
研究的目的:
- 系统地评估FEP的准确性,使用FEP+和OPLS4,用于预测配体与DNA/RNA系统的相对结合自由能量.
- 为了确定FEP对核酸向配体的适用性和可靠性.
- 评估FEP在指导药物发现工作方面的潜力.
主要方法:
- 用OPLS4力场在FEP+软件中实现的应用FEP.
- 在100多个具有多种结合方式的配体上进行了测试,与各种DNA/RNA系统相互作用.
- 在所有预测中使用一致的模拟协议.
主要成果:
- 超过一半的FEP+预测在实验值1kcal/mol以内.
- 报告了 <1.4 kcal/mol. 的双向根-平方平均误差的组合平均值.
- 在实验分离常数的一个日志单位内达到准确性.
结论:
- FEP+显示出足够的准确性来预测与核酸相对结合的自由能量.
- 在针对RNA和DNA的药物发现计划中,FEP+方法可以有效指导序列优化.
- 这项研究验证了FEP作为基于核酸的药物开发的强大计算工具.
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