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利用高性能计算加速 COVID-19 药物研发。

Accelerating COVID-19 Drug Discovery with High-Performance Computing.

机构信息

In Silico Research and Development, Evotec UK Ltd., Abingdon, UK.

出版信息

Methods Mol Biol. 2024;2716:405-411. doi: 10.1007/978-1-0716-3449-3_19.

Abstract

The recent COVID-19 pandemic has served as a timely reminder that the existing drug discovery is a laborious, expensive, and slow process. Never has there been such global demand for a therapeutic treatment to be identified as a matter of such urgency. Unfortunately, this is a scenario likely to repeat itself in future, so it is of interest to explore ways in which to accelerate drug discovery at pandemic speed. Computational methods naturally lend themselves to this because they can be performed rapidly if sufficient computational resources are available. Recently, high-performance computing (HPC) technologies have led to remarkable achievements in computational drug discovery and yielded a series of new platforms, algorithms, and workflows. The application of artificial intelligence (AI) and machine learning (ML) approaches is also a promising and relatively new avenue to revolutionize the drug design process and therefore reduce costs. In this review, I describe how molecular dynamics simulations (MD) were successfully integrated with ML and adapted to HPC to form a powerful tool to study inhibitors for four of the COVID-19 target proteins. The emphasis of this review is on the strategy that was used with an explanation of each of the steps in the accelerated drug discovery workflow. For specific technical details, the reader is directed to the relevant research publications.

摘要

最近的 COVID-19 大流行及时提醒人们,现有的药物发现是一个艰苦、昂贵和缓慢的过程。从未有过如此全球性的需求,需要如此紧急地确定一种治疗方法。不幸的是,这种情况很可能在未来再次发生,因此,探索如何以大流行的速度加速药物发现是很有意义的。计算方法自然适合这种情况,因为如果有足够的计算资源,它们可以快速执行。最近,高性能计算 (HPC) 技术在计算药物发现方面取得了显著成就,并产生了一系列新的平台、算法和工作流程。人工智能 (AI) 和机器学习 (ML) 方法的应用也是一个很有前途的、相对较新的途径,可以彻底改变药物设计过程,从而降低成本。在这篇综述中,我描述了如何成功地将分子动力学模拟 (MD) 与机器学习集成,并适应高性能计算,形成一种强大的工具来研究四种 COVID-19 靶蛋白的抑制剂。本综述的重点是所使用的策略,并解释了加速药物发现工作流程中的每一步。有关具体技术细节,读者可参考相关研究出版物。

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