在生物系统中模拟分子光开关的热异构
Amirhossein Bakhtiiari1, Gustavo J Costa1, Ruibin Liang1
1Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409, United States.
分子光开关,如光静止剂 (PST),使光控制药物治疗成为可能. 精确模拟它们在生物环境中的热异构,特别是使用明确溶剂,是预测药物性能和设计新型光调节药物的关键.
科学领域:
- 计算化学的计算化学
- 生物物理学的生物物理.
- 药物发现 药物发现 药物发现
背景情况:
- 分子光开关提供了对生物分子功能的精确控制,是光调节疗法的候选者.
- 量化热异构化速率对于优化光开关药物活性至关重要,但蛋白质结合效应尚不清楚.
- 模拟对于理解这些效应至关重要,但在描述复杂的电子结构和相互作用时面临着挑战.
研究的目的:
- 通过使用多尺度模拟,描述光静态素 (PST) 的热异构,潜在的癌症疗法.
- 调查蛋白质结合和明确溶剂环境对PST异构化动学的影响.
- 开发和验证一种计算方法,用于预测生物系统中的光开关行为.
主要方法:
- 采用了多尺度模拟,将初始多参考电子结构理论与量子力学/分子力学 (QM/MM) 结合起来.
- 利用增强的采样技术来确定真空,溶液和结合管的PST的cis-to-trans自由能量概况.
- 基准计算与高级ab initio方法进行比较,并探索了竞争的异构化途径.
主要成果:
- 显式溶剂处理对于准确预测PST热半衰期的实验顺序至关重要,其性能优于真空和隐式溶剂模型.
- 通过与极性残留物的结合,发现蛋白质结合会扰乱自由能量屏障.
- 新的计算方法有效地处理了PST在整个构造采样过程中的多引用特征.
结论:
- 在明确的分子环境中,初始的多参考自由能量计算对于准确预测生物系统中的光开关热半衰期至关重要.
- 该研究提供了基准数据和指导,用于选择光开关异构化研究的计算方法.
- 了解替代剂对热半衰期的影响需要考虑有效的药物设计的明确溶剂和蛋白质相互作用.
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