FMOe:对分子操作环境的碎片分子轨道方法的预处理和可视化包,以及其在联联体和金属蛋白分析中的应用
Hirotomo Moriwaki1, Yusuke Kawashima2, Chiduru Watanabe1,3
1Center for Biosystems Dynamics Research, RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
Journal of chemical information and modeling
|September 5, 2024
概括
一个新的图形用户界面简化了小分子碎片分子轨道 (FMO) 计算的手动碎片. 该工具增强了对药物发现和金属蛋白中的分子识别和相互作用的理解.
科学领域:
- 计算化学计算化学
- 量子化学 是一个量子化学.
- 生物分子建模模型
背景情况:
- 碎片分子轨道 (FMO) 方法对于通过将大型生物分子分成较小的碎片来计算是至关重要的.
- 虽然FMO处理程序可以自动分解蛋白质和核酸,但对于像连接体这样的小分子,需要手动分解.
- 用于FMO计算的手动碎片化可能是复杂和耗时的,阻碍了详细分析.
研究的目的:
- 开发一个用户友好的图形用户界面 (GUI),以简化FMO计算中的手动碎片化.
- 为了使小分子和复杂系统的FMO计算能够有效地进行预处理和可视化.
- 为了促进分子识别研究的深入的断片间相互作用能量 (IFIE) 分析.
主要方法:
- 开发一个图形用户界面 (GUI),作为分子操作环境 (MOE) 的库.
- 对SARS-CoV-2蛋白酶-连接体复合体 (nirmatrelvir) 的手动碎片化和IFIE分析的演示.
- 应用GUI进行碎片化和IFIE分析的结循环,以研究金属协调.
主要成果:
- 该GUI成功地简化了FMO计算的手动碎片化,从而实现了IFIE详细分析.
- 尼马特里尔维尔和SARS-CoV-2 Mpro之间的关键相互作用,包括键和CH/π相互作用,通过连接体碎片化被确定.
- 建立了一种高效准确的Zn2+离子的碎片化方案,该方案由金属蛋白中的histidine残留物协调.
结论:
- 开发的FMOe GUI显著简化了手动的碎片化,允许各种碎片化模式和准确的IFIE分析.
- 该工具为分子识别提供了有价值的见解,特别是用于药物发现和金属蛋白系统中的联结体相互作用.
- 这些发现将有助于分析复杂的系统,包括中型分子和以金属为中心的相互作用.
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