In Silico Analysis of Antiviral Activity and Pharmacokinetic Prediction of Brazilein Sappan Wood (Caesalpinia sappan L.) Against SARS-CoV-2 Spike Glycoproteins

Dwi Krihariyani, E. Haryanto, Retno Sasongkowati
{"title":"In Silico Analysis of Antiviral Activity and Pharmacokinetic Prediction of Brazilein Sappan Wood (Caesalpinia sappan L.) Against SARS-CoV-2 Spike Glycoproteins","authors":"Dwi Krihariyani, E. Haryanto, Retno Sasongkowati","doi":"10.33086/IJMLST.V3I1.1854","DOIUrl":null,"url":null,"abstract":"Brazilein is one of the secondary sappan wood metabolites which can be used empirically as an antivirus. The SARS-CoV-2 spike (S) glycoproteins play significant roles in attaching and entering the virus into the host cell. This study aims to predict the antiviral activity and pharmacokinetic properties of brazilein of the sappan wood against the in-silico SARS-CoV-2 S glycoproteins with vitamin C as the reference compound. Molegro Virtual Docker 5.5 was used to predict antiviral activity by docking process. SARS-CoV-2 S glycoprotein with NAG ligand available in Protein Data Bank (PDB) (PDB ID: 7C01) was the receptor used. The pkCSM online tool was used to predict the pharmacokinetic properties and toxicity of brazilein. Data were analyzed on the target receptors by comparing the docking bond energies between NAG, brazilein, and vitamin C. The smaller the ligands’ bond energy to the target receptor, the more stable the bonds are. The bond energy of NAG, brazilein, and vitamin C was -59.2864 kcal/mol, -65.8911 kcal/mol, and -53.9093 kcal/mol, respectively. These results suggested that brazilein has a greater capacity as an antivirus compared to NAG and vitamin C. In silico test using the pkCSM online tool demonstrated that brazilein had strong pharmacokinetic properties and relatively low toxicity.","PeriodicalId":158539,"journal":{"name":"Indonesian Journal of Medical Laboratory Science and Technology","volume":"1 1","pages":"0"},"PeriodicalIF":0.0000,"publicationDate":"2021-04-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Indonesian Journal of Medical Laboratory Science and Technology","FirstCategoryId":"1085","ListUrlMain":"https://doi.org/10.33086/IJMLST.V3I1.1854","RegionNum":0,"RegionCategory":null,"ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"","JCRName":"","Score":null,"Total":0}
引用次数: 0

Abstract

Brazilein is one of the secondary sappan wood metabolites which can be used empirically as an antivirus. The SARS-CoV-2 spike (S) glycoproteins play significant roles in attaching and entering the virus into the host cell. This study aims to predict the antiviral activity and pharmacokinetic properties of brazilein of the sappan wood against the in-silico SARS-CoV-2 S glycoproteins with vitamin C as the reference compound. Molegro Virtual Docker 5.5 was used to predict antiviral activity by docking process. SARS-CoV-2 S glycoprotein with NAG ligand available in Protein Data Bank (PDB) (PDB ID: 7C01) was the receptor used. The pkCSM online tool was used to predict the pharmacokinetic properties and toxicity of brazilein. Data were analyzed on the target receptors by comparing the docking bond energies between NAG, brazilein, and vitamin C. The smaller the ligands’ bond energy to the target receptor, the more stable the bonds are. The bond energy of NAG, brazilein, and vitamin C was -59.2864 kcal/mol, -65.8911 kcal/mol, and -53.9093 kcal/mol, respectively. These results suggested that brazilein has a greater capacity as an antivirus compared to NAG and vitamin C. In silico test using the pkCSM online tool demonstrated that brazilein had strong pharmacokinetic properties and relatively low toxicity.
巴西杉木抗病毒活性的计算机分析及药动学预测抗SARS-CoV-2刺突糖蛋白
巴西蓝素是巴西木次生代谢物之一,可作为抗虫药。SARS-CoV-2刺突(S)糖蛋白在病毒附着和进入宿主细胞中发挥重要作用。本研究旨在以维生素C为参比化合物,预测柚木巴西蛋白对硅化sars - cov - 2s糖蛋白的抗病毒活性和药动学特性。采用Molegro Virtual Docker 5.5通过对接过程预测抗病毒活性。受体为可在蛋白质数据库(PDB)中找到的带有NAG配体的sars - cov - 2s糖蛋白(PDB ID: 7C01)。利用pkCSM在线工具预测巴西豆素的药动学性质和毒性。通过比较NAG、巴西蛋白和维生素c三者之间的对接键能对靶受体进行数据分析。配体与靶受体的对接键能越小,其结合越稳定。NAG、巴西蛋白和维生素C的键能分别为-59.2864 kcal/mol、-65.8911 kcal/mol和-53.9093 kcal/mol。这些结果表明,与NAG和维生素c相比,巴西豆素具有更强的抗病毒能力。使用pkCSM在线工具进行的硅测试表明,巴西豆素具有较强的药代动力学特性和相对较低的毒性。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
求助全文
约1分钟内获得全文 求助全文
来源期刊
自引率
0.00%
发文量
0
×
引用
GB/T 7714-2015
复制
MLA
复制
APA
复制
导出至
BibTeX EndNote RefMan NoteFirst NoteExpress
×
提示
您的信息不完整,为了账户安全,请先补充。
现在去补充
×
提示
您因"违规操作"
具体请查看互助需知
我知道了
×
提示
确定
请完成安全验证×
copy
已复制链接
快去分享给好友吧!
我知道了
右上角分享
点击右上角分享
0
联系我们:info@booksci.cn Book学术提供免费学术资源搜索服务,方便国内外学者检索中英文文献。致力于提供最便捷和优质的服务体验。 Copyright © 2023 布克学术 All rights reserved.
京ICP备2023020795号-1
ghs 京公网安备 11010802042870号
Book学术文献互助
Book学术文献互助群
群 号:481959085
Book学术官方微信