Chang Chun-Chun, Hsu Hao-Jen, Wu Tien-Yuan, Liou Je-Wen
Department of Laboratory Medicine, Hualien Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, Hualien, Taiwan.
Department of Laboratory Medicine and Biotechnology, Tzu Chi University, Hualien, Taiwan.
Tzu Chi Med J. 2022 Mar 28;34(3):276-286. doi: 10.4103/tcmj.tcmj_318_21. eCollection 2022 Jul-Sep.
Coronavirus disease 2019 (COVID-19) pandemic is currently the most serious public health threat faced by mankind. Thus, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which causes COVID-19, is being intensively investigated. Several vaccines are now available for clinical use. However, owing to the highly mutated nature of RNA viruses, the SARS-CoV-2 is changing at a rapid speed. Breakthrough infections by SARS-CoV-2 variants have been seen in vaccinated individuals. As a result, effective therapeutics for treating COVID-19 patients is urgently required. With the advance of computer technology, computational methods have become increasingly powerful in the biomedical research and pharmaceutical drug discovery. The applications of these techniques have largely reduced the costs and simplified processes of pharmaceutical drug developments. Intensive and extensive studies on SARS-CoV-2 proteins have been carried out and three-dimensional structures of the major SARS-CoV-2 proteins have been resolved and deposited in the Protein Data Bank. These structures provide the foundations for drug discovery and design using the structure-based computations, such as molecular docking and molecular dynamics simulations. In this review, introduction to the applications of computational methods in the discovery and design of novel drugs and repurposing of existing drugs for the treatments of COVID-19 is given. The examples of computer-aided investigations and screening of COVID-19 effective therapeutic compounds, functional peptides, as well as effective molecules from the herb medicines are discussed.
2019年冠状病毒病（COVID-19）大流行是目前人类面临的最严重的公共卫生威胁。因此，引发COVID-19的严重急性呼吸综合征冠状病毒2（SARS-CoV-2）正在接受深入研究。目前有几种疫苗可供临床使用。然而，由于RNA病毒具有高度变异的特性，SARS-CoV-2正在迅速发生变化。在接种疫苗的个体中已出现SARS-CoV-2变体的突破性感染。因此，迫切需要用于治疗COVID-19患者的有效疗法。随着计算机技术的进步，计算方法在生物医学研究和药物研发中变得越来越强大。这些技术的应用在很大程度上降低了药物研发的成本并简化了流程。对SARS-CoV-2蛋白进行了深入广泛的研究，主要SARS-CoV-2蛋白的三维结构已得到解析并存入蛋白质数据库。这些结构为使用基于结构的计算方法（如分子对接和分子动力学模拟）进行药物发现和设计奠定了基础。在这篇综述中，介绍了计算方法在发现和设计新型药物以及将现有药物重新用于治疗COVID-19方面的应用。讨论了计算机辅助研究和筛选COVID-19有效治疗化合物、功能肽以及草药有效分子的实例。
