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使用高斯加速分子动力学模拟,探索N234和N343链接到SARS CoV 2尖端蛋白口袋可访问性的N234和N343糖的影响

Ronny L Cheng¹, James Peter L Lim¹, Myrnel A Fortuna¹

¹Institute of Chemistry, University of the Philippines Diliman, Quezon City, 1101, Philippines.

Scientific reports

|February 27, 2025

概括

在SARS-CoV-2病毒中,尖蛋白是最常见的.

科学领域:

结构生物学是结构生物学.
病毒学病毒学
计算生物物理学的计算生物物理.

背景情况:

与N234和N343相关的甘氨酸稳定了SARS-CoV-2尖端蛋白的受体结合域 (RBDs) 进行HACE2相互作用.
对HACE2结合对这些甘氨酸的影响以及随后的可药性口袋可访问性尚未得到充分了解.

研究的目的:

为了研究 hACE2 结合对 SARS-CoV-2 尖端蛋白 N234 和 N343 甘氨酸的作用.
分析这些甘氨酸变化如何影响潜在药物标口袋的可访问性.

主要方法:

用高斯加速分子动力学 (GaMD) 模拟用于无HAC2和HAC2结合的尖端蛋白状态.
生物物理分析的重点是位于RBD子单元下方的三个特定可用药物口袋的可访问性.

主要成果:

与N234结合的甘氨酸屏蔽相邻的口袋组件; hACE2结合改变了可访问性.
由于在绑定时增加了NTD-RBD联系,Pocket A的可访问性降低了.
由于暴露的残留物,B口袋在绑定状态下显示了增加的可访问性,而C口袋的可访问性因N234屏蔽而减少.

结论:

尽管有绑定诱导的可访问性变化,但分析的口袋仍然可以访问连接体.
这些口袋代表了开发抑制SARS-CoV-2进入的抗病毒药物的可行目标.

关键词:

生物物理分析分析在 COVID-19 疫情中,斯加速分子动力学葡萄糖基酶化是指葡萄糖基酶化的过程.在SARS-CoV-2病毒中,尖蛋白是最常见的.

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