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Zhang X, Wu J, Luo Y, Wang Y, Wu Y, Xu X, Zhang Y, Kong R, Chi Y, Sun Y, Chen S, He Q, Zhu F, Zhou Z. CovEpiAb: a comprehensive database and analysis resource for immune epitopes and antibodies of human coronaviruses. Brief Bioinform 2024; 25:bbae183. [PMID: 38653491 PMCID: PMC11036340 DOI: 10.1093/bib/bbae183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 02/24/2024] [Accepted: 04/08/2024] [Indexed: 04/25/2024] Open
Abstract
Coronaviruses have threatened humans repeatedly, especially COVID-19 caused by SARS-CoV-2, which has posed a substantial threat to global public health. SARS-CoV-2 continuously evolves through random mutation, resulting in a significant decrease in the efficacy of existing vaccines and neutralizing antibody drugs. It is critical to assess immune escape caused by viral mutations and develop broad-spectrum vaccines and neutralizing antibodies targeting conserved epitopes. Thus, we constructed CovEpiAb, a comprehensive database and analysis resource of human coronavirus (HCoVs) immune epitopes and antibodies. CovEpiAb contains information on over 60 000 experimentally validated epitopes and over 12 000 antibodies for HCoVs and SARS-CoV-2 variants. The database is unique in (1) classifying and annotating cross-reactive epitopes from different viruses and variants; (2) providing molecular and experimental interaction profiles of antibodies, including structure-based binding sites and around 70 000 data on binding affinity and neutralizing activity; (3) providing virological characteristics of current and past circulating SARS-CoV-2 variants and in vitro activity of various therapeutics; and (4) offering site-level annotations of key functional features, including antibody binding, immunological epitopes, SARS-CoV-2 mutations and conservation across HCoVs. In addition, we developed an integrated pipeline for epitope prediction named COVEP, which is available from the webpage of CovEpiAb. CovEpiAb is freely accessible at https://pgx.zju.edu.cn/covepiab/.
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Affiliation(s)
- Xue Zhang
- National Key Laboratory of Advanced Drug Delivery and Release Systems & Zhejiang Provincial Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - JingCheng Wu
- National Key Laboratory of Advanced Drug Delivery and Release Systems & Zhejiang Provincial Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yuanyuan Luo
- National Key Laboratory of Advanced Drug Delivery and Release Systems & Zhejiang Provincial Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yilin Wang
- National Key Laboratory of Advanced Drug Delivery and Release Systems & Zhejiang Provincial Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yujie Wu
- National Key Laboratory of Advanced Drug Delivery and Release Systems & Zhejiang Provincial Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Xiaobin Xu
- National Key Laboratory of Advanced Drug Delivery and Release Systems & Zhejiang Provincial Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yufang Zhang
- National Key Laboratory of Advanced Drug Delivery and Release Systems & Zhejiang Provincial Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Ruiying Kong
- National Key Laboratory of Advanced Drug Delivery and Release Systems & Zhejiang Provincial Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Ying Chi
- Alibaba-Zhejiang University Joint Research Center of Future Digital Healthcare, Hangzhou 310058, China
- ZJU-UoE Institute, Zhejiang University, Haining 314400, China
| | - Yisheng Sun
- Key Lab of Vaccine, Prevention and Control of Infectious Disease of Zhejiang Province, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou 310015, China
| | - Shuqing Chen
- National Key Laboratory of Advanced Drug Delivery and Release Systems & Zhejiang Provincial Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Qiaojun He
- National Key Laboratory of Advanced Drug Delivery and Release Systems & Zhejiang Provincial Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
- Zhejiang University Innovation Institute for Artificial Intelligence in Medicine, Engineering Research Center of Innovative Anticancer Drugs, Ministry of Education, Hangzhou 310018, China
| | - Feng Zhu
- National Key Laboratory of Advanced Drug Delivery and Release Systems & Zhejiang Provincial Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
- Zhejiang University Innovation Institute for Artificial Intelligence in Medicine, Engineering Research Center of Innovative Anticancer Drugs, Ministry of Education, Hangzhou 310018, China
- Alibaba-Zhejiang University Joint Research Center of Future Digital Healthcare, Hangzhou 310058, China
| | - Zhan Zhou
- National Key Laboratory of Advanced Drug Delivery and Release Systems & Zhejiang Provincial Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
- Zhejiang University Innovation Institute for Artificial Intelligence in Medicine, Engineering Research Center of Innovative Anticancer Drugs, Ministry of Education, Hangzhou 310018, China
- Alibaba-Zhejiang University Joint Research Center of Future Digital Healthcare, Hangzhou 310058, China
- The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu 322000, China
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Li J, Wang Y, Rajpoot S, Lavrijsen M, Pan Q, Li P, Baig MS. Investigating theobromine as a potential anti-human coronaviral agent. Microbiol Immunol 2023; 67:404-412. [PMID: 37415325 DOI: 10.1111/1348-0421.13086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 05/08/2023] [Accepted: 06/08/2023] [Indexed: 07/08/2023]
Abstract
Coronaviruses (CoVs) have long been known to infect humans, mainly alpha-CoV and beta-CoV. The vaccines developed for SARS-CoV-2 are likely not effective against other coronavirus species, whereas the risk of the emergence of new strains that may cause the next epidemic/pandemic is high. The development of antiviral drugs that are effective across different CoVs represents a viable strategy for improving pandemic preparedness. In this study, we aim to identify pan-coronaviral agents by targeting the conserved main protease (Mpro). For drug screening, the catalytic dyad of four human CoVs (HCoVs: SARS-CoV-2, and seasonal CoV NL63, OC43, and 229E) was targeted by molecular docking. The identified leading candidate theobromine, a xanthine derivative, was further tested in cell culture models of coronavirus infection. Theobromine binds strongly with the catalytic dyad (His41 and Cys144/145) of SARS-CoV-2 and HCoV-NL63 Mpro, mildly with HCoV-OC43, but not with HCoV-229E. However, theobromine only shows dose-dependent inhibition in Calu3 cells inoculated with SARS-CoV-2, but not in cells inoculated with seasonal CoVs. Theobromine exerts antiviral activity against coronavirus infections potentially through targeting Mpro. However, the antiviral potency is distinct among different CoVs.
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Affiliation(s)
- Jiajing Li
- Department of Gastroenterology & Hepatology, Erasmus MC-University Medical Center, Rotterdam, The Netherlands
| | - Yining Wang
- Department of Gastroenterology & Hepatology, Erasmus MC-University Medical Center, Rotterdam, The Netherlands
| | - Sajjan Rajpoot
- Department of Biosciences & Biomedical Engineering (BSBE), Indian Institute of Technology Indore (IITI), Indore, India
| | - Marla Lavrijsen
- Department of Gastroenterology & Hepatology, Erasmus MC-University Medical Center, Rotterdam, The Netherlands
| | - Qiuwei Pan
- Department of Gastroenterology & Hepatology, Erasmus MC-University Medical Center, Rotterdam, The Netherlands
| | - Pengfei Li
- Department of Gastroenterology & Hepatology, Erasmus MC-University Medical Center, Rotterdam, The Netherlands
| | - Mirza S Baig
- Department of Biosciences & Biomedical Engineering (BSBE), Indian Institute of Technology Indore (IITI), Indore, India
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Wang Y, Rajpoot S, Li P, Lavrijsen M, Ma Z, Hirani N, Saqib U, Pan Q, Baig MS. Repurposing dyphylline as a pan-coronavirus antiviral therapy. Future Med Chem 2022. [PMID: 35387498 DOI: 10.4155/fmc-2021-0311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Background: In the last two decades, the world has witnessed the emergence of zoonotic corona viruses (CoVs), which cause mild to severe respiratory diseases in humans. Human coronaviruses (HCoVs), mainly from the alpha-CoV and beta-CoV genera, have evolved to be highly pathogenic, such as SARS-CoV-2 causing the COVID-19 pandemic. These coronaviruses carry functional enzymes necessary for the virus life cycle, which represent attractive antiviral targets. Methods & Results: We aimed to therapeutically target the main protease (Mpro) of HCoV-NL63 and HCoV-229E (from alpha-CoV genus) and HCoV-OC43 and SARS-CoV-2 (from beta-CoV genus). Through virtual screening, we identified an FDA-approved drug dyphylline, a xanthine derivate, that binds to the catalytic dyad residues; histidine and cystine of the Mpro structures. Importantly, dyphylline dose-dependently inhibited the viral replication in cell culture models infected with the viruses. Conclusion: Our findings support the repurposing of dyphylline as a pan-coronavirus antiviral agent.
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Wang J, Li D, Zhou Q, Wiltse A, Zand MS. Antibody Mediated Immunity to SARS-CoV-2 and Human Coronaviruses: Multiplex Beads Assay and Volumetric Absorptive Microsampling to Generate Immune Repertoire Cartography. Front Immunol 2021; 12:696370. [PMID: 34386006 PMCID: PMC8353270 DOI: 10.3389/fimmu.2021.696370] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Accepted: 06/21/2021] [Indexed: 12/20/2022] Open
Abstract
The COVID-19 pandemic is caused by SARS-CoV-2, a novel zoonotic coronavirus. Emerging evidence indicates that preexisting humoral immunity against other seasonal human coronaviruses (HCoVs) plays a critical role in the specific antibody response to SARS-CoV-2. However, current work to assess the effects of preexisting and cross-reactive anti-HCoVs antibodies has been limited. To address this issue, we have adapted our previously reported multiplex assay to simultaneously and quantitatively measure anti-HCoV antibodies. The full mPlex-CoV panel covers the spike (S) and nucleocapsid (N) proteins of three highly pathogenic HCoVs (SARS-CoV-1, SARS-CoV-2, MERS) and four human seasonal strains (OC43, HKU1, NL63, 229E). Combining this assay with volumetric absorptive microsampling (VAMS), we measured the anti-HCoV IgG, IgA, and IgM antibodies in fingerstick blood samples. The results demonstrate that the mPlex-CoV assay has high specificity and sensitivity. It can detect strain-specific anti-HCoV antibodies down to 0.1 ng/ml with 4 log assay range and with low intra- and inter-assay coefficients of variation (%CV). We also estimate multiple strain HCoVs IgG, IgA and IgM concentration in VAMS samples in three categories of subjects: pre-COVID-19 (n=21), post-COVID-19 convalescents (n=19), and COVID-19 vaccine recipients (n=14). Using metric multidimensional scaling (MDS) analysis, HCoVs IgG concentrations in fingerstick blood samples were well separated between the pre-COVID-19, post-COVID-19 convalescents, and COVID-19 vaccine recipients. In addition, we demonstrate how multi-dimensional scaling analysis can be used to visualize IgG mediated antibody immunity against multiple human coronaviruses. We conclude that the combination of VAMS and the mPlex-Cov assay is well suited to performing remote study sample collection under pandemic conditions to monitor HCoVs antibody responses in population studies.
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Affiliation(s)
- Jiong Wang
- Department of Medicine, Division of Nephrology, University of Rochester Medical Center, Rochester, NY, United States
| | - Dongmei Li
- Clinical and Translational Science Institute, University of Rochester Medical Center, Rochester, NY, United States
| | - Qian Zhou
- Department of Medicine, Division of Nephrology, University of Rochester Medical Center, Rochester, NY, United States
| | - Alexander Wiltse
- Department of Medicine, Division of Nephrology, University of Rochester Medical Center, Rochester, NY, United States
| | - Martin S Zand
- Department of Medicine, Division of Nephrology, University of Rochester Medical Center, Rochester, NY, United States.,Clinical and Translational Science Institute, University of Rochester Medical Center, Rochester, NY, United States
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