新设计的微小蛋白抑制SARS-CoV-2主要蛋白酶的酶活性。

IF 5.3 2区化学 Q1 CHEMISTRY, MEDICINAL

Journal of Chemical Information and Modeling Pub Date : 2025-10-08 DOI:10.1021/acs.jcim.5c01708

Tayná E Lima,Emerson G Moreira,Danilo F Coêlho,Carlos H B Cruz,Rafael Dhalia,Bruno H S Leite,Lícya S Xavier,Marta Perez Illana,Gabriel L Wallau,Isabelle F T Viana,Roberto D Lins

{"title":"新设计的微小蛋白抑制SARS-CoV-2主要蛋白酶的酶活性。","authors":"Tayná E Lima,Emerson G Moreira,Danilo F Coêlho,Carlos H B Cruz,Rafael Dhalia,Bruno H S Leite,Lícya S Xavier,Marta Perez Illana,Gabriel L Wallau,Isabelle F T Viana,Roberto D Lins","doi":"10.1021/acs.jcim.5c01708","DOIUrl":null,"url":null,"abstract":"Targeting viral proteases is a well-established antiviral strategy and a promising approach that has been actively explored against SARS-CoV-2. The SARS-CoV-2 main protease (Mpro) is essential for viral replication and functions as a homodimer, making its dimerization interface an attractive therapeutic target. In this study, we report the rational design of HB3-Core25, a miniprotein computationally engineered to disrupt Mpro dimerization and inhibit its catalytic activity. In vitro production followed by biophysical characterization showed that HB3-Core25 folds into a compact trimeric helical bundle, exhibiting high solubility and thermal stability. Biophysical assays confirmed binding to Mpro with a dissociation constant (KD) of 0.567 μM and the lowest IC50 reported to date for the dimer interface. Functional assays further demonstrated inhibition of Mpro catalytic activity, with 51.1%. These findings highlight HB3-Core25 as a stable inhibitor of Mpro activity by interfering with its dimerization, offering a complementary strategy to classical active-site inhibition in antiviral drug development.","PeriodicalId":44,"journal":{"name":"Journal of Chemical Information and Modeling ","volume":"18 1","pages":""},"PeriodicalIF":5.3000,"publicationDate":"2025-10-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":"{\"title\":\"De Novo-Designed Miniprotein Inhibits the Enzymatic Activity of the SARS-CoV-2 Main Protease.\",\"authors\":\"Tayná E Lima,Emerson G Moreira,Danilo F Coêlho,Carlos H B Cruz,Rafael Dhalia,Bruno H S Leite,Lícya S Xavier,Marta Perez Illana,Gabriel L Wallau,Isabelle F T Viana,Roberto D Lins\",\"doi\":\"10.1021/acs.jcim.5c01708\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"Targeting viral proteases is a well-established antiviral strategy and a promising approach that has been actively explored against SARS-CoV-2. The SARS-CoV-2 main protease (Mpro) is essential for viral replication and functions as a homodimer, making its dimerization interface an attractive therapeutic target. In this study, we report the rational design of HB3-Core25, a miniprotein computationally engineered to disrupt Mpro dimerization and inhibit its catalytic activity. In vitro production followed by biophysical characterization showed that HB3-Core25 folds into a compact trimeric helical bundle, exhibiting high solubility and thermal stability. Biophysical assays confirmed binding to Mpro with a dissociation constant (KD) of 0.567 μM and the lowest IC50 reported to date for the dimer interface. Functional assays further demonstrated inhibition of Mpro catalytic activity, with 51.1%. These findings highlight HB3-Core25 as a stable inhibitor of Mpro activity by interfering with its dimerization, offering a complementary strategy to classical active-site inhibition in antiviral drug development.\",\"PeriodicalId\":44,\"journal\":{\"name\":\"Journal of Chemical Information and Modeling \",\"volume\":\"18 1\",\"pages\":\"\"},\"PeriodicalIF\":5.3000,\"publicationDate\":\"2025-10-08\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Journal of Chemical Information and Modeling \",\"FirstCategoryId\":\"92\",\"ListUrlMain\":\"https://doi.org/10.1021/acs.jcim.5c01708\",\"RegionNum\":2,\"RegionCategory\":\"化学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q1\",\"JCRName\":\"CHEMISTRY, MEDICINAL\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Journal of Chemical Information and Modeling ","FirstCategoryId":"92","ListUrlMain":"https://doi.org/10.1021/acs.jcim.5c01708","RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q1","JCRName":"CHEMISTRY, MEDICINAL","Score":null,"Total":0}

引用次数: 0

摘要

靶向病毒蛋白酶是一种成熟的抗病毒策略，也是一种积极探索的有前景的抗病毒方法。SARS-CoV-2主蛋白酶（Mpro）对病毒复制至关重要，并具有同型二聚体的功能，使其二聚界面成为一个有吸引力的治疗靶点。在这项研究中，我们报道了HB3-Core25的合理设计，HB3-Core25是一种计算工程化的微型蛋白，可以破坏Mpro二聚化并抑制其催化活性。体外生产和生物物理表征表明，HB3-Core25折叠成紧凑的三聚体螺旋束，具有高溶解度和热稳定性。生物物理实验证实与Mpro结合的解离常数（KD）为0.567 μM，是迄今为止报道的最低的二聚体界面IC50。功能分析进一步表明，Mpro的催化活性抑制率为51.1%。这些发现强调HB3-Core25是一种稳定的Mpro活性抑制剂，通过干扰其二聚化，为抗病毒药物开发中的经典活性位点抑制提供了一种补充策略。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

查看原文本刊更多论文

De Novo-Designed Miniprotein Inhibits the Enzymatic Activity of the SARS-CoV-2 Main Protease.

Targeting viral proteases is a well-established antiviral strategy and a promising approach that has been actively explored against SARS-CoV-2. The SARS-CoV-2 main protease (Mpro) is essential for viral replication and functions as a homodimer, making its dimerization interface an attractive therapeutic target. In this study, we report the rational design of HB3-Core25, a miniprotein computationally engineered to disrupt Mpro dimerization and inhibit its catalytic activity. In vitro production followed by biophysical characterization showed that HB3-Core25 folds into a compact trimeric helical bundle, exhibiting high solubility and thermal stability. Biophysical assays confirmed binding to Mpro with a dissociation constant (KD) of 0.567 μM and the lowest IC50 reported to date for the dimer interface. Functional assays further demonstrated inhibition of Mpro catalytic activity, with 51.1%. These findings highlight HB3-Core25 as a stable inhibitor of Mpro activity by interfering with its dimerization, offering a complementary strategy to classical active-site inhibition in antiviral drug development.

求助全文

通过发布文献求助，成功后即可免费获取论文全文。去求助

来源期刊

Journal of Chemical Information and Modeling 化学-化学综合

CiteScore

9.80

自引率

10.70%

发文量

529

审稿时长

1.4 months

期刊介绍： The Journal of Chemical Information and Modeling publishes papers reporting new methodology and/or important applications in the fields of chemical informatics and molecular modeling. Specific topics include the representation and computer-based searching of chemical databases, molecular modeling, computer-aided molecular design of new materials, catalysts, or ligands, development of new computational methods or efficient algorithms for chemical software, and biopharmaceutical chemistry including analyses of biological activity and other issues related to drug discovery. Astute chemists, computer scientists, and information specialists look to this monthly’s insightful research studies, programming innovations, and software reviews to keep current with advances in this integral, multidisciplinary field. As a subscriber you’ll stay abreast of database search systems, use of graph theory in chemical problems, substructure search systems, pattern recognition and clustering, analysis of chemical and physical data, molecular modeling, graphics and natural language interfaces, bibliometric and citation analysis, and synthesis design and reactions databases.