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摘要
分子动力学模拟是一种运用牛顿定律来评估水、离子、小分子、高分子或更复杂系统变化的计算机计算方法。例如,对于全部病毒,重塑生物环境的行为,包括水分子和类脂膜。尤其是结构变化如那些依赖于温度和溶液或者溶剂结构,在研究配体蛋白或者蛋白-蛋白复合物的认知模式中是非常重要的,在这个意义上,分子动力学是非常有用的因为这些变化可以用这个方法来造模。此外,药物设计的分子动力学模拟为设计与靶点具有更高亲和性的新颖结构的腔结构提供了见解。同时,药物设计分子动力学模拟的使用有助于改善靶点的三维结构,为了获得一个更好的结合构成样本以及与更好的结构优势更依赖性的亲和力价值,因为与传统对接过程,它们包含了一些具有结构变化的生物条件。 本文分析了药物设计中分子动力学模拟的概念和应用,因为分子结构变化被肯定,并且这些帮助鉴定报道中蛋白位点的热点和破译结构细节,这与消除那些来自分子动力学结构特征条件的人工结构位点。此外能够更好的获得蛋白配体认知自由能值,这些值在实验过程中由于分子动力学模拟方法的稳固性可以被证实。
关键词: 药物设计;分子动力学模拟;蛋白变化;药物发现;连接研究;几种蛋白构型的采样
Current Medicinal Chemistry
Title:Current Tools and Methods in Molecular Dynamics (MD) Simulations for Drug Design
Volume: 23 Issue: 34
Author(s): Maricarmen Hernández-Rodríguez, Martha C. Rosales-Hernández, Jessica E. Mendieta-Wejebe, Marlet Martínez-Archundia and José Correa Basurto
Affiliation:
关键词: 药物设计;分子动力学模拟;蛋白变化;药物发现;连接研究;几种蛋白构型的采样
摘要: Molecular Dynamics (MD) simulations is a computational method that employs Newton’s laws to evaluate the motions of water, ions, small molecules, and macromolecules or more complex systems, for example, whole viruses, to reproduce the behavior of the biological environment, including water molecules and lipid membranes. Specifically, structural motions, such as those that are dependent of the temperature and solute/ solvent are very important to study the recognition pattern of ligandprotein or protein-protein complexes, in that sense, MD simulations are very useful because these motions can be modeled using this methodology. Furthermore, MD simulations for drug design provide insights into the structural cavities required to design novel structures with higher affinity to the target. Also, the employment of MD simulations to drug design can help to refine the three-dimensional (3D) structure of targets in order to obtain a better sampling of the binding poses and more reliable affinity values with better structural advantages, because they incorporate some biological conditions that include structural motions compared to traditional docking procedures.
This work analyzes the concepts and applicability of MD simulations for drug design because molecular structural motions are considered, and these help to identify hot spots, decipher structural details in the reported protein sites, as well as to eliminate sites that could be structural artifacts which could be originated from the structural characterization conditions from MD. Moreover, better free energy values for protein ligand recognition can also be obtained, and these can be validated under experimental procedures due to the robustness of the MD simulation methods.
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Maricarmen Hernández-Rodríguez, Martha C. Rosales-Hernández, Jessica E. Mendieta-Wejebe, Marlet Martínez-Archundia and José Correa Basurto , Current Tools and Methods in Molecular Dynamics (MD) Simulations for Drug Design, Current Medicinal Chemistry 2016; 23 (34) . https://dx.doi.org/10.2174/0929867323666160530144742
DOI https://dx.doi.org/10.2174/0929867323666160530144742 |
Print ISSN 0929-8673 |
Publisher Name Bentham Science Publisher |
Online ISSN 1875-533X |
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