{"title":"刺突蛋白与ACE2的硅结合亲和力和S基因的相对进化距离可能是快速获得SARS-CoV-2初始风险的潜在因素","authors":"Aki Sugano , Junon Murakami , Haruyuki Kataguchi , Mika Ohta , Yoshiaki Someya , Shigemi Kimura , Akira Kanno , Yoshimasa Maniwa , Toshihide Tabata , Kazuyuki Tobe , Yutaka Takaoka","doi":"10.1016/j.mran.2023.100278","DOIUrl":null,"url":null,"abstract":"<div><h3>Objectives</h3><p>In this research, we aimed to find potential factors which are rapidly obtained for the risk of the coming new variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), when their genetic substitutions were detected in late 2022.</p></div><div><h3>Methods</h3><p>We first performed molecular docking simulation<span> analyses of the spike proteins with human angiotensin-converting enzyme 2 (ACE2) by using ZDOCK program to determine the binding affinities to human cells of three new variants of SARS-CoV-2: Omicron BQ.1, XBB, and XBB.1.5. We then investigated the three variants to determine the relative evolutionary distance of the spike protein gene (S gene) from the Wuhan, Omicron BA.1, and Omicron BA.4/5 variants.</span></p></div><div><h3>Results</h3><p>The results indicated that Omicron BQ.1. had a highest binding affinity but had the shortest evolutionary distance from BA.4/5. The XBB variant had a lower binding affinity and long evolutionary distances from all the three variants. However, the XBB.1.5 variant had the highest binding affinity of the spike protein with ACE2 and the longest evolutionary distance of the S gene.</p></div><div><h3>Conclusion</h3><p>This result suggested that <em>in silico</em> binding affinity of the spike protein with ACE2 and the relative evolutionary distance of S gene may be potential factors for the risk of SARS-CoV-2 variants based on the comparison of infectivity of BQ.1, XBB, and XBB.1.5.</p></div>","PeriodicalId":48593,"journal":{"name":"Microbial Risk Analysis","volume":"25 ","pages":"Article 100278"},"PeriodicalIF":3.0000,"publicationDate":"2023-09-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":"{\"title\":\"In silico binding affinity of the spike protein with ACE2 and the relative evolutionary distance of S gene may be potential factors rapidly obtained for the initial risk of SARS-CoV-2\",\"authors\":\"Aki Sugano , Junon Murakami , Haruyuki Kataguchi , Mika Ohta , Yoshiaki Someya , Shigemi Kimura , Akira Kanno , Yoshimasa Maniwa , Toshihide Tabata , Kazuyuki Tobe , Yutaka Takaoka\",\"doi\":\"10.1016/j.mran.2023.100278\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<div><h3>Objectives</h3><p>In this research, we aimed to find potential factors which are rapidly obtained for the risk of the coming new variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), when their genetic substitutions were detected in late 2022.</p></div><div><h3>Methods</h3><p>We first performed molecular docking simulation<span> analyses of the spike proteins with human angiotensin-converting enzyme 2 (ACE2) by using ZDOCK program to determine the binding affinities to human cells of three new variants of SARS-CoV-2: Omicron BQ.1, XBB, and XBB.1.5. We then investigated the three variants to determine the relative evolutionary distance of the spike protein gene (S gene) from the Wuhan, Omicron BA.1, and Omicron BA.4/5 variants.</span></p></div><div><h3>Results</h3><p>The results indicated that Omicron BQ.1. had a highest binding affinity but had the shortest evolutionary distance from BA.4/5. The XBB variant had a lower binding affinity and long evolutionary distances from all the three variants. However, the XBB.1.5 variant had the highest binding affinity of the spike protein with ACE2 and the longest evolutionary distance of the S gene.</p></div><div><h3>Conclusion</h3><p>This result suggested that <em>in silico</em> binding affinity of the spike protein with ACE2 and the relative evolutionary distance of S gene may be potential factors for the risk of SARS-CoV-2 variants based on the comparison of infectivity of BQ.1, XBB, and XBB.1.5.</p></div>\",\"PeriodicalId\":48593,\"journal\":{\"name\":\"Microbial Risk Analysis\",\"volume\":\"25 \",\"pages\":\"Article 100278\"},\"PeriodicalIF\":3.0000,\"publicationDate\":\"2023-09-24\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Microbial Risk Analysis\",\"FirstCategoryId\":\"93\",\"ListUrlMain\":\"https://www.sciencedirect.com/science/article/pii/S2352352223000336\",\"RegionNum\":4,\"RegionCategory\":\"环境科学与生态学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q2\",\"JCRName\":\"ENVIRONMENTAL SCIENCES\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Microbial Risk Analysis","FirstCategoryId":"93","ListUrlMain":"https://www.sciencedirect.com/science/article/pii/S2352352223000336","RegionNum":4,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q2","JCRName":"ENVIRONMENTAL SCIENCES","Score":null,"Total":0}
In silico binding affinity of the spike protein with ACE2 and the relative evolutionary distance of S gene may be potential factors rapidly obtained for the initial risk of SARS-CoV-2
Objectives
In this research, we aimed to find potential factors which are rapidly obtained for the risk of the coming new variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), when their genetic substitutions were detected in late 2022.
Methods
We first performed molecular docking simulation analyses of the spike proteins with human angiotensin-converting enzyme 2 (ACE2) by using ZDOCK program to determine the binding affinities to human cells of three new variants of SARS-CoV-2: Omicron BQ.1, XBB, and XBB.1.5. We then investigated the three variants to determine the relative evolutionary distance of the spike protein gene (S gene) from the Wuhan, Omicron BA.1, and Omicron BA.4/5 variants.
Results
The results indicated that Omicron BQ.1. had a highest binding affinity but had the shortest evolutionary distance from BA.4/5. The XBB variant had a lower binding affinity and long evolutionary distances from all the three variants. However, the XBB.1.5 variant had the highest binding affinity of the spike protein with ACE2 and the longest evolutionary distance of the S gene.
Conclusion
This result suggested that in silico binding affinity of the spike protein with ACE2 and the relative evolutionary distance of S gene may be potential factors for the risk of SARS-CoV-2 variants based on the comparison of infectivity of BQ.1, XBB, and XBB.1.5.
期刊介绍：
The journal Microbial Risk Analysis accepts articles dealing with the study of risk analysis applied to microbial hazards. Manuscripts should at least cover any of the components of risk assessment (risk characterization, exposure assessment, etc.), risk management and/or risk communication in any microbiology field (clinical, environmental, food, veterinary, etc.). This journal also accepts article dealing with predictive microbiology, quantitative microbial ecology, mathematical modeling, risk studies applied to microbial ecology, quantitative microbiology for epidemiological studies, statistical methods applied to microbiology, and laws and regulatory policies aimed at lessening the risk of microbial hazards. Work focusing on risk studies of viruses, parasites, microbial toxins, antimicrobial resistant organisms, genetically modified organisms (GMOs), and recombinant DNA products are also acceptable.
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