P.M. Afladhanti, M.D. Romadhan, H. A. Hamzah, S. Putri, Ellen Callista Angelica Angelica
{"title":"银杏二叶化合物作为SARS-CoV-2潜在抑制剂的分子对接研究","authors":"P.M. Afladhanti, M.D. Romadhan, H. A. Hamzah, S. Putri, Ellen Callista Angelica Angelica","doi":"10.32734/scripta.v4i1.8399","DOIUrl":null,"url":null,"abstract":"COVID-19 pandemic caused by SARS-CoV-2 is a challenge for researchers to find effective drugs for this disease. Previous research had identified the role of Mpro, TMPRSS2, RdRp, and ACE2 which were useful as promising drug targets to inhibit SARS-CoV-2. This study aims to identify the potential compounds derived from Ginkgo biloba as potential SARS-CoV-2 inhibitors using a molecular docking study. A total of twenty-one compounds of Ginkgo biloba and comparative drugs were used in this study. The materials were downloaded from rcsb for protein targets and pubchem for comparative drugs and compounds. In this study, Lipinski rule of five using Swiss ADME web tool was used. Moreover, toxicity analysis using admetSAR 2.0 online test also used to predict toxicological profile of compounds. Dockings were carried out on Mpro, TMPRSS2, RdRp, and ACE2 protein targets by AutodockTools 1.5.6 and Autodock Vina. The visualization of molecular interaction was carried out by Discovery Studio v16. Nine compounds met the criteria as drug-like components and were safe. Docking results showed that ginkgolide-C and bilobetin showed strong molecular interactions to all protein targets compared to the comparative drugs and other compounds. In RdRp, ginkgolide-C showed the highest binding energy with -12.7 kcal/mol. Moreover, in TMPRSS2, ACE2 and Mpro, bilobetin also showed the highest binding energy with -12.7, -9.7 and -10 kcal/mol, respectively. Ginkgolide-C and bilobetin have the potential to be developed as SARS-CoV-2 inhibitors. Therefore, in vitro and in vivo investigations are needed to bring these compounds to the clinical setting.","PeriodicalId":365874,"journal":{"name":"SCRIPTA SCORE Scientific Medical Journal","volume":null,"pages":null},"PeriodicalIF":0.0000,"publicationDate":"2022-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":"{\"title\":\"Molecular Docking Study of Gingkgo biloba Compounds as Potential Inhibitors of SARS-CoV-2\",\"authors\":\"P.M. Afladhanti, M.D. Romadhan, H. A. Hamzah, S. Putri, Ellen Callista Angelica Angelica\",\"doi\":\"10.32734/scripta.v4i1.8399\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"COVID-19 pandemic caused by SARS-CoV-2 is a challenge for researchers to find effective drugs for this disease. Previous research had identified the role of Mpro, TMPRSS2, RdRp, and ACE2 which were useful as promising drug targets to inhibit SARS-CoV-2. This study aims to identify the potential compounds derived from Ginkgo biloba as potential SARS-CoV-2 inhibitors using a molecular docking study. A total of twenty-one compounds of Ginkgo biloba and comparative drugs were used in this study. The materials were downloaded from rcsb for protein targets and pubchem for comparative drugs and compounds. In this study, Lipinski rule of five using Swiss ADME web tool was used. Moreover, toxicity analysis using admetSAR 2.0 online test also used to predict toxicological profile of compounds. Dockings were carried out on Mpro, TMPRSS2, RdRp, and ACE2 protein targets by AutodockTools 1.5.6 and Autodock Vina. The visualization of molecular interaction was carried out by Discovery Studio v16. Nine compounds met the criteria as drug-like components and were safe. Docking results showed that ginkgolide-C and bilobetin showed strong molecular interactions to all protein targets compared to the comparative drugs and other compounds. In RdRp, ginkgolide-C showed the highest binding energy with -12.7 kcal/mol. Moreover, in TMPRSS2, ACE2 and Mpro, bilobetin also showed the highest binding energy with -12.7, -9.7 and -10 kcal/mol, respectively. Ginkgolide-C and bilobetin have the potential to be developed as SARS-CoV-2 inhibitors. Therefore, in vitro and in vivo investigations are needed to bring these compounds to the clinical setting.\",\"PeriodicalId\":365874,\"journal\":{\"name\":\"SCRIPTA SCORE Scientific Medical Journal\",\"volume\":null,\"pages\":null},\"PeriodicalIF\":0.0000,\"publicationDate\":\"2022-09-01\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"SCRIPTA SCORE Scientific Medical Journal\",\"FirstCategoryId\":\"1085\",\"ListUrlMain\":\"https://doi.org/10.32734/scripta.v4i1.8399\",\"RegionNum\":0,\"RegionCategory\":null,\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"\",\"JCRName\":\"\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"SCRIPTA SCORE Scientific Medical Journal","FirstCategoryId":"1085","ListUrlMain":"https://doi.org/10.32734/scripta.v4i1.8399","RegionNum":0,"RegionCategory":null,"ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"","JCRName":"","Score":null,"Total":0}
引用次数: 0
摘要
由SARS-CoV-2引起的COVID-19大流行是研究人员寻找有效药物的挑战。先前的研究已经确定了Mpro、TMPRSS2、RdRp和ACE2的作用,它们是抑制SARS-CoV-2的有希望的药物靶点。本研究旨在通过分子对接研究,鉴定从银杏中提取的潜在化合物作为潜在的SARS-CoV-2抑制剂。本研究共使用了21个银杏化合物及其比较药物。蛋白质靶点的材料从rcsb下载,比较药物和化合物的材料从pubchem下载。本研究采用瑞士ADME网络工具,采用Lipinski五法则。此外,使用admetSAR 2.0在线测试进行毒性分析也用于预测化合物的毒理学特征。利用AutodockTools 1.5.6和Autodock Vina对Mpro、TMPRSS2、RdRp和ACE2蛋白靶点进行对接。分子相互作用的可视化由Discovery Studio v16进行。其中9种化合物符合药物样成分标准且安全。对接结果显示,银杏内酯- c和bilobtin相对于对照药物和其他化合物,对所有蛋白靶点都表现出较强的分子相互作用。在RdRp中,银杏内酯c的结合能最高,为-12.7 kcal/mol。此外,在TMPRSS2、ACE2和Mpro中,bilobetin的结合能最高,分别为-12.7、-9.7和-10 kcal/mol。银杏内酯- c和胆素有潜力被开发为SARS-CoV-2抑制剂。因此,体外和体内的研究需要将这些化合物带到临床环境。
Molecular Docking Study of Gingkgo biloba Compounds as Potential Inhibitors of SARS-CoV-2
COVID-19 pandemic caused by SARS-CoV-2 is a challenge for researchers to find effective drugs for this disease. Previous research had identified the role of Mpro, TMPRSS2, RdRp, and ACE2 which were useful as promising drug targets to inhibit SARS-CoV-2. This study aims to identify the potential compounds derived from Ginkgo biloba as potential SARS-CoV-2 inhibitors using a molecular docking study. A total of twenty-one compounds of Ginkgo biloba and comparative drugs were used in this study. The materials were downloaded from rcsb for protein targets and pubchem for comparative drugs and compounds. In this study, Lipinski rule of five using Swiss ADME web tool was used. Moreover, toxicity analysis using admetSAR 2.0 online test also used to predict toxicological profile of compounds. Dockings were carried out on Mpro, TMPRSS2, RdRp, and ACE2 protein targets by AutodockTools 1.5.6 and Autodock Vina. The visualization of molecular interaction was carried out by Discovery Studio v16. Nine compounds met the criteria as drug-like components and were safe. Docking results showed that ginkgolide-C and bilobetin showed strong molecular interactions to all protein targets compared to the comparative drugs and other compounds. In RdRp, ginkgolide-C showed the highest binding energy with -12.7 kcal/mol. Moreover, in TMPRSS2, ACE2 and Mpro, bilobetin also showed the highest binding energy with -12.7, -9.7 and -10 kcal/mol, respectively. Ginkgolide-C and bilobetin have the potential to be developed as SARS-CoV-2 inhibitors. Therefore, in vitro and in vivo investigations are needed to bring these compounds to the clinical setting.