We aim to screen out the active components that may have therapeutic effect on coronavirus disease 2019 (COVID-19) from the severe and critical cases' prescriptions in the "Coronavirus Disease 2019 Diagnosis and Treatment Plan (Trial Ninth Edition)" issued by the National Health Commission of the People's Republic of China and explain its mechanism through the interactions with proteins. The ETCM database and SwissADME database were used to screen the active components contained in 25 traditional Chinese medicines in 3 prescriptions, and the PDB database was used to obtain the crystal structures of 4 proteins of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Molecular docking was performed using Autodock Vina and molecular dynamics simulations were performed using GROMACS. Binding energy results showed that 44 active ingredients including xambioona, gancaonin L, cynaroside, and baicalin showed good binding affinity with multiple targets of SARS-CoV-2, while molecular dynamics simulations analysis showed that xambioona bound more tightly to the nucleocapsid protein of SARS-CoV-2 and exerted a potent inhibitory effect. Modern technical methods are used to study the active components of traditional Chinese medicine and show that xambioona is an effective inhibitor of SARS-CoV-2 nucleocapsid protein, which provides a theoretical basis for the development of new anti-SARS-CoV-2 drugs and their treatment methods.
本研究旨在从国家卫生健康委员会发布的《新型冠状病毒肺炎诊疗方案（试行第九版）》重型和危重型药方中筛选可能对新型冠状病毒肺炎（COVID-19）有治疗作用的活性成分，并通过其与严重急性呼吸综合征冠状病毒2（SARS-CoV-2）蛋白的相互作用阐释其作用机制。采用国际ETCM数据库和SwissADME数据库筛选3个药方中25味中药所含有的活性成分，使用PDB数据库获取SARS-CoV-2的4种蛋白质的晶体结构，采用Autodock Vina进行分子对接，使用GROMACS进行分子动力学模拟。分子结合能结果显示夏姆比奥纳、甘草素L、木犀草苷和黄芩苷等44种活性成分与SARS-CoV-2的多个靶点显示出良好的结合亲和力，而分子动力学模拟分析显示夏姆比奥纳与SARS-CoV-2的核衣壳蛋白能够更紧密地结合并发挥有效的抑制作用。本研究采用现代技术方法对中药活性成分进行研究，发现夏姆比奥纳是SARS-CoV-2核衣壳蛋白的有效抑制剂，为开发新型的抗SARS-CoV-2药物及其治疗方法提供科学的理论依据。.
Keywords: COVID-19; Molecular docking; Molecular dynamics simulations; Traditional Chinese medicines; Virtual screening; Xambioona.