Structure Based Affinity Maturation and Characterizing of SARS-CoV Antibody CR3022 against SARS-CoV-2 by Computational and Experimental Approaches
The COVID-19 epidemic is raging around the world. Neutralizing antibodies are powerful tools for the prevention and treatment of SARS-CoV-2 infection. Antibody CR3022, a SARS-CoV neutralizing antibody, was found to cross-react with SARS-CoV-2, but its affinity was lower than that of its binding with...
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| Language: | English |
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MDPI AG
2022-01-01
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| Series: | Viruses |
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| Online Access: | https://www.mdpi.com/1999-4915/14/2/186 |
| _version_ | 1797476090081443840 |
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| author | Wei Yu Nan Zhong Xin Li Jiayi Ren Yueming Wang Chengming Li Gui Yao Rui Zhu Xiaoli Wang Zhenxing Jia Changwen Wu Rongfeng Chen Weihong Zheng Huaxin Liao Xiaomin Wu Xiaohui Yuan |
| author_facet | Wei Yu Nan Zhong Xin Li Jiayi Ren Yueming Wang Chengming Li Gui Yao Rui Zhu Xiaoli Wang Zhenxing Jia Changwen Wu Rongfeng Chen Weihong Zheng Huaxin Liao Xiaomin Wu Xiaohui Yuan |
| author_sort | Wei Yu |
| collection | DOAJ |
| description | The COVID-19 epidemic is raging around the world. Neutralizing antibodies are powerful tools for the prevention and treatment of SARS-CoV-2 infection. Antibody CR3022, a SARS-CoV neutralizing antibody, was found to cross-react with SARS-CoV-2, but its affinity was lower than that of its binding with SARS-CoV, which greatly limited the further development of CR3022 against SARS-CoV-2. Therefore, it is necessary to improve its affinity to SARS-CoV-2 in vitro. In this study, the structure-based molecular simulations were utilized to virtually mutate the possible key residues in the complementarity-determining regions (CDRs) of the CR3022 antibody. According to the criteria of mutation energy, the mutation sites that have the potential to impact the antibody affinity were then selected. Then optimized CR3022 mutants with the enhanced affinity were further identified and verified by enzyme-linked immunosorbent assay (ELISA), surface plasma resonance (SPR) and autoimmune reactivity experiments. Finally, molecular dynamics (MD) simulation and binding free energy calculation (MM/PBSA) were performed on the wild-type CR3022 and its two double-site mutants to understand in more detail the contribution of these sites to the higher affinity. It was found that the binding affinity of the CR3022 antibody could be significantly enhanced more than ten times after the introduction of the S103F/Y mutation in HCDR–3 and the S33R mutation in LCDR–1. The additional hydrogen-bonding, hydrophobic interactions, as well as salt-bridges formed between the modified double-site mutated antibody and SARS-CoV-2 RBD were identified. The computational and experimental results clearly demonstrated that the affinity of the modified antibody has been greatly enhanced. This study indicates that CR3022 as a neutralizing antibody recognizing the conserved region of RBD against SARS-CoV with cross-reactivity with SARS-CoV-2, a different member in a large family of coronaviruses, could be improved by the computational and experimental approaches which provided insights for developing antibody drugs against SARS-CoV-2. |
| first_indexed | 2024-03-09T20:53:02Z |
| format | Article |
| id | doaj.art-e73170e884b54f9e9c6308650f702675 |
| institution | Directory Open Access Journal |
| issn | 1999-4915 |
| language | English |
| last_indexed | 2024-03-09T20:53:02Z |
| publishDate | 2022-01-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Viruses |
| spelling | doaj.art-e73170e884b54f9e9c6308650f7026752023-11-23T22:28:56ZengMDPI AGViruses1999-49152022-01-0114218610.3390/v14020186Structure Based Affinity Maturation and Characterizing of SARS-CoV Antibody CR3022 against SARS-CoV-2 by Computational and Experimental ApproachesWei Yu0Nan Zhong1Xin Li2Jiayi Ren3Yueming Wang4Chengming Li5Gui Yao6Rui Zhu7Xiaoli Wang8Zhenxing Jia9Changwen Wu10Rongfeng Chen11Weihong Zheng12Huaxin Liao13Xiaomin Wu14Xiaohui Yuan15Institute of Biomedicine, Jinan University, Guangzhou 510632, ChinaInstitute of Biomedicine, Jinan University, Guangzhou 510632, ChinaInstitute of Biomedicine, Jinan University, Guangzhou 510632, ChinaInstitute of Biomedicine, Jinan University, Guangzhou 510632, ChinaInstitute of Biomedicine, Jinan University, Guangzhou 510632, ChinaInstitute of Biomedicine, Jinan University, Guangzhou 510632, ChinaAnhui Province Key Laboratory of Pollutant Sensitive Materials and Environmental Remediation, College of Life Sciences, Huaibei Normal University, Huaibei 235000, ChinaAnhui Province Key Laboratory of Pollutant Sensitive Materials and Environmental Remediation, College of Life Sciences, Huaibei Normal University, Huaibei 235000, ChinaZhuhai Trinomab Biotechnology Co., Ltd., Zhuhai 519040, ChinaZhuhai Trinomab Biotechnology Co., Ltd., Zhuhai 519040, ChinaZhuhai Trinomab Biotechnology Co., Ltd., Zhuhai 519040, ChinaZhuhai Trinomab Biotechnology Co., Ltd., Zhuhai 519040, ChinaZhuhai Trinomab Biotechnology Co., Ltd., Zhuhai 519040, ChinaInstitute of Biomedicine, Jinan University, Guangzhou 510632, ChinaAnhui Province Key Laboratory of Pollutant Sensitive Materials and Environmental Remediation, College of Life Sciences, Huaibei Normal University, Huaibei 235000, ChinaInstitute of Biomedicine, Jinan University, Guangzhou 510632, ChinaThe COVID-19 epidemic is raging around the world. Neutralizing antibodies are powerful tools for the prevention and treatment of SARS-CoV-2 infection. Antibody CR3022, a SARS-CoV neutralizing antibody, was found to cross-react with SARS-CoV-2, but its affinity was lower than that of its binding with SARS-CoV, which greatly limited the further development of CR3022 against SARS-CoV-2. Therefore, it is necessary to improve its affinity to SARS-CoV-2 in vitro. In this study, the structure-based molecular simulations were utilized to virtually mutate the possible key residues in the complementarity-determining regions (CDRs) of the CR3022 antibody. According to the criteria of mutation energy, the mutation sites that have the potential to impact the antibody affinity were then selected. Then optimized CR3022 mutants with the enhanced affinity were further identified and verified by enzyme-linked immunosorbent assay (ELISA), surface plasma resonance (SPR) and autoimmune reactivity experiments. Finally, molecular dynamics (MD) simulation and binding free energy calculation (MM/PBSA) were performed on the wild-type CR3022 and its two double-site mutants to understand in more detail the contribution of these sites to the higher affinity. It was found that the binding affinity of the CR3022 antibody could be significantly enhanced more than ten times after the introduction of the S103F/Y mutation in HCDR–3 and the S33R mutation in LCDR–1. The additional hydrogen-bonding, hydrophobic interactions, as well as salt-bridges formed between the modified double-site mutated antibody and SARS-CoV-2 RBD were identified. The computational and experimental results clearly demonstrated that the affinity of the modified antibody has been greatly enhanced. This study indicates that CR3022 as a neutralizing antibody recognizing the conserved region of RBD against SARS-CoV with cross-reactivity with SARS-CoV-2, a different member in a large family of coronaviruses, could be improved by the computational and experimental approaches which provided insights for developing antibody drugs against SARS-CoV-2.https://www.mdpi.com/1999-4915/14/2/186COVID-19SARS-CoV-2receptor-binding domain (RBD)CR3022molecular dynamics (MD) simulation |
| spellingShingle | Wei Yu Nan Zhong Xin Li Jiayi Ren Yueming Wang Chengming Li Gui Yao Rui Zhu Xiaoli Wang Zhenxing Jia Changwen Wu Rongfeng Chen Weihong Zheng Huaxin Liao Xiaomin Wu Xiaohui Yuan Structure Based Affinity Maturation and Characterizing of SARS-CoV Antibody CR3022 against SARS-CoV-2 by Computational and Experimental Approaches Viruses COVID-19 SARS-CoV-2 receptor-binding domain (RBD) CR3022 molecular dynamics (MD) simulation |
| title | Structure Based Affinity Maturation and Characterizing of SARS-CoV Antibody CR3022 against SARS-CoV-2 by Computational and Experimental Approaches |
| title_full | Structure Based Affinity Maturation and Characterizing of SARS-CoV Antibody CR3022 against SARS-CoV-2 by Computational and Experimental Approaches |
| title_fullStr | Structure Based Affinity Maturation and Characterizing of SARS-CoV Antibody CR3022 against SARS-CoV-2 by Computational and Experimental Approaches |
| title_full_unstemmed | Structure Based Affinity Maturation and Characterizing of SARS-CoV Antibody CR3022 against SARS-CoV-2 by Computational and Experimental Approaches |
| title_short | Structure Based Affinity Maturation and Characterizing of SARS-CoV Antibody CR3022 against SARS-CoV-2 by Computational and Experimental Approaches |
| title_sort | structure based affinity maturation and characterizing of sars cov antibody cr3022 against sars cov 2 by computational and experimental approaches |
| topic | COVID-19 SARS-CoV-2 receptor-binding domain (RBD) CR3022 molecular dynamics (MD) simulation |
| url | https://www.mdpi.com/1999-4915/14/2/186 |
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