评估基于遗传算法的对接协议,用于预测氨酸寡糖化合物对蛋白质的结合几何
Samuel G Holmes1,2, Umesh R Desai1,2
1Department of Medicinal Chemistry, School of Pharmacy, Virginia Commonwealth University, Richmond, VA 23298, USA.
Biomolecules
|November 25, 2023
概括
我们开发了一种半刚性对接协议,用于糖氨基糖 (GAG) 和蛋白质相互作用. 这种方法可以准确地预测GAG蛋白结合的姿势,特别是在更长的链上,从而改善了药物发现工作.
科学领域:
- 生物化学 生物化学
- 计算生物学 计算生物学
- 结构生物学 结构生物学
背景情况:
- 由于GAG的灵活性和复杂的结合,糖氨基甘 (GAG) 与蛋白质的分子对接是具有挑战性的.
- 现有的刚性或灵活的对接方法在准确建模GAG-蛋白相互作用方面存在局限性.
研究的目的:
- 开发和评估一个半刚性对接 (SRD) 协议,以改进GAG-蛋白质复合体建模.
- 为了比较不同长度的氨酸/硫酸氨酸 (Hp/HS) 链的刚性,半刚性和柔性对接协议的性能.
主要方法:
- 在18个Hp/HS蛋白共同复合体上使用了基于遗传算法的对接.
- 刚性,半刚性和灵活的对接协议在GAG链上进行了测试,从分糖酸到分糖酸.
- 开发了一种新的计算参数,以区分选择性与非选择性GAG蛋白结合.
主要成果:
- 与灵活的协议相比,半刚性对接协议显示了较长的Hp/HS链 (5-10 mers) 的本地姿势的优越复述.
- 半刚性方法为较短的Hp/HS链 (2-4 mers) 提供了更好的预测.
- 当晶体结构信息无法获得时,SRD协议是有利的,并有助于识别可用药物的目标.
结论:
- 开发的半刚性对接协议为建模GAG-蛋白相互作用提供了更准确的方法.
- 这种方法与新的计算参数相结合,可促进药物样GAG序列和潜在治疗点的高通量查.
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