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Anzai I, Fujita J, Ono C, Kosaka Y, Miyamoto Y, Shichinohe S, Takada K, Torii S, Taguwa S, Suzuki K, Makino F, Kajita T, Inoue T, Namba K, Watanabe T, Matsuura Y. Characterization of a neutralizing antibody that recognizes a loop region adjacent to the receptor-binding interface of the SARS-CoV-2 spike receptor-binding domain. Microbiol Spectr 2024; 12:e0365523. [PMID: 38415660 DOI: 10.1128/spectrum.03655-23] [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: 10/11/2023] [Accepted: 02/12/2024] [Indexed: 02/29/2024] Open
Abstract
Although the global crisis caused by the coronavirus disease 2019 (COVID-19) pandemic is over, the global epidemic of the disease continues. Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), the cause of COVID-19, initiates infection via the binding of the receptor-binding domain (RBD) of its spike protein to the human angiotensin-converting enzyme II (ACE2) receptor, and this interaction has been the primary target for the development of COVID-19 therapeutics. Here, we identified neutralizing antibodies against SARS-CoV-2 by screening mouse monoclonal antibodies and characterized an antibody, CSW1-1805, that targets a narrow region at the RBD ridge of the spike protein. CSW1-1805 neutralized several variants in vitro and completely protected mice from SARS-CoV-2 infection. Cryo-EM and biochemical analyses revealed that this antibody recognizes the loop region adjacent to the ACE2-binding interface with the RBD in both a receptor-inaccessible "down" state and a receptor-accessible "up" state and could stabilize the RBD conformation in the up-state. CSW1-1805 also showed different binding orientations and complementarity determining region properties compared to other RBD ridge-targeting antibodies with similar binding epitopes. It is important to continuously characterize neutralizing antibodies to address new variants that continue to emerge. Our characterization of this antibody that recognizes the RBD ridge of the spike protein will aid in the development of future neutralizing antibodies.IMPORTANCESARS-CoV-2 cell entry is initiated by the interaction of the viral spike protein with the host cell receptor. Therefore, mechanistic findings regarding receptor recognition by the spike protein help uncover the molecular mechanism of SARS-CoV-2 infection and guide neutralizing antibody development. Here, we characterized a SARS-CoV-2 neutralizing antibody that recognizes an epitope, a loop region adjacent to the receptor-binding interface, that may be involved in the conformational transition of the receptor-binding domain (RBD) of the spike protein from a receptor-inaccessible "down" state into a receptor-accessible "up" state, and also stabilizes the RBD in the up-state. Our mechanistic findings provide new insights into SARS-CoV-2 receptor recognition and guidance for neutralizing antibody development.
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Grants
- JP16H06429, JP16K21723, JP16H06432 Ministry of Education, Culture, Sports, Science and Technology (MEXT)
- JP16H06429, JP16K21723, JP16H06434 Ministry of Education, Culture, Sports, Science and Technology (MEXT)
- JP22H02521 MEXT | Japan Society for the Promotion of Science (JSPS)
- JP21K15042 MEXT | Japan Society for the Promotion of Science (JSPS)
- JP21H02736 MEXT | Japan Society for the Promotion of Science (JSPS)
- JP25K000013 MEXT | Japan Society for the Promotion of Science (JSPS)
- JP20K22630 MEXT | Japan Society for the Promotion of Science (JSPS)
- JP223fa627002, JP22am0401030, JP23fk0108659, JP20jk0210021, JP22gm1610010, JP19fk0108113 Japan Agency for Medical Research and Development (AMED)
- JP223fa627002 Japan Agency for Medical Research and Development (AMED)
- JP19fk0108113, JP20fk0108281, JP20pc0101047 Japan Agency for Medical Research and Development (AMED)
- JP20fk0108401, JP21fk0108493 Japan Agency for Medical Research and Development (AMED)
- JP21am0101117, JP17pc0101020 Japan Agency for Medical Research and Development (AMED)
- JPMJOP1861 MEXT | Japan Science and Technology Agency (JST)
- JPMJMS2025 MEXT | Japan Science and Technology Agency (JST)
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Affiliation(s)
- Itsuki Anzai
- Department of Molecular Virology, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan
- Center for Infectious Disease Education and Research (CiDER), Osaka University, Suita, Osaka, Japan
| | - Junso Fujita
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka, Japan
- JEOL YOKOGUSHI Research Alliance Laboratories, Osaka University, Suita, Osaka, Japan
- Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka, Japan
| | - Chikako Ono
- Center for Infectious Disease Education and Research (CiDER), Osaka University, Suita, Osaka, Japan
- Laboratory of Virus Control, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan
| | | | | | - Shintaro Shichinohe
- Department of Molecular Virology, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan
| | - Kosuke Takada
- Department of Molecular Virology, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan
| | - Shiho Torii
- Laboratory of Virus Control, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan
| | - Shuhei Taguwa
- Center for Infectious Disease Education and Research (CiDER), Osaka University, Suita, Osaka, Japan
- Laboratory of Virus Control, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan
- Center for Advanced Modalities and DDS, Osaka University, Suita, Osaka, Japan
| | - Koichiro Suzuki
- The Research Foundation for Microbial Diseases of Osaka University (BIKEN), Suita, Osaka, Japan
| | - Fumiaki Makino
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka, Japan
- JEOL YOKOGUSHI Research Alliance Laboratories, Osaka University, Suita, Osaka, Japan
- JEOL Ltd., Akishima, Tokyo, Japan
| | | | - Tsuyoshi Inoue
- Graduate School of Pharmaceutical Sciences, Osaka University, Suita, Osaka, Japan
| | - Keiichi Namba
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka, Japan
- JEOL YOKOGUSHI Research Alliance Laboratories, Osaka University, Suita, Osaka, Japan
- RIKEN Center for Biosystems Dynamics Research and Spring-8 Center, Suita, Osaka, Japan
| | - Tokiko Watanabe
- Department of Molecular Virology, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan
- Center for Infectious Disease Education and Research (CiDER), Osaka University, Suita, Osaka, Japan
- Center for Advanced Modalities and DDS, Osaka University, Suita, Osaka, Japan
| | - Yoshiharu Matsuura
- Center for Infectious Disease Education and Research (CiDER), Osaka University, Suita, Osaka, Japan
- Laboratory of Virus Control, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan
- Center for Advanced Modalities and DDS, Osaka University, Suita, Osaka, Japan
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2
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Tu T, Rathnayaka T, Kato T, Mizutani K, Saotome T, Noguchi K, Kidokoro SI, Kuroda Y. Design and Escherichia coli Expression of a Natively Folded Multi-Disulfide Bonded Influenza H1N1-PR8 Receptor-Binding Domain (RBD). Int J Mol Sci 2024; 25:3943. [PMID: 38612753 PMCID: PMC11012049 DOI: 10.3390/ijms25073943] [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: 01/29/2024] [Revised: 03/22/2024] [Accepted: 03/29/2024] [Indexed: 04/14/2024] Open
Abstract
Refolding multi-disulfide bonded proteins expressed in E. coli into their native structure is challenging. Nevertheless, because of its cost-effectiveness, handiness, and versatility, the E. coli expression of viral envelope proteins, such as the RBD (Receptor-Binding Domain) of the influenza Hemagglutinin protein, could significantly advance research on viral infections. Here, we show that H1N1-PR8-RBD (27 kDa, containing four cysteines forming two disulfide bonds) expressed in E. coli and was purified with nickel affinity chromatography, and reversed-phase HPLC was successfully refolded into its native structure, as assessed with several biophysical and biochemical techniques. Analytical ultracentrifugation indicated that H1N1-PR8-RBD was monomeric with a hydrodynamic radius of 2.5 nm. Thermal denaturation, monitored with DSC and CD at a wavelength of 222 nm, was cooperative with a midpoint temperature around 55 °C, strongly indicating a natively folded protein. In addition, the 15N-HSQC NMR spectrum exhibited several 1H-15N resonances indicative of a beta-sheeted protein. Our results indicate that a significant amount (40 mg/L) of pure and native H1N1-PR8-RBD can be produced using an E. coli expression system with our refolding procedure, offering potential insights into the molecular characterization of influenza virus infection.
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Affiliation(s)
- Thao Tu
- Department of Biotechnology and Life Science, Faculty of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Nakamachi, Koganei-shi 184-8588, Tokyo, Japan; (T.T.); (T.R.)
| | - Tharangani Rathnayaka
- Department of Biotechnology and Life Science, Faculty of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Nakamachi, Koganei-shi 184-8588, Tokyo, Japan; (T.T.); (T.R.)
| | - Toshiyo Kato
- NMR Group, Smart-Core-Facility Promotion Organization, Tokyo University of Agriculture and Technology, 2-24-16 Nakamachi, Koganei-shi 184-8588, Tokyo, Japan; (T.K.); (K.N.)
| | - Kenji Mizutani
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro, Yokohama 230-0045, Kanagawa, Japan;
| | - Tomonori Saotome
- Department of Materials Science and Bioengineering, Nagaoka University of Technology, 1603-1 Kamitomioka-cho, Nagaoka-shi 940-2188, Niigata, Japan; (T.S.); (S.-i.K.)
| | - Keiichi Noguchi
- NMR Group, Smart-Core-Facility Promotion Organization, Tokyo University of Agriculture and Technology, 2-24-16 Nakamachi, Koganei-shi 184-8588, Tokyo, Japan; (T.K.); (K.N.)
| | - Shun-ichi Kidokoro
- Department of Materials Science and Bioengineering, Nagaoka University of Technology, 1603-1 Kamitomioka-cho, Nagaoka-shi 940-2188, Niigata, Japan; (T.S.); (S.-i.K.)
| | - Yutaka Kuroda
- Department of Biotechnology and Life Science, Faculty of Engineering, Tokyo University of Agriculture and Technology, 2-24-16 Nakamachi, Koganei-shi 184-8588, Tokyo, Japan; (T.T.); (T.R.)
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3
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Das T, Luo S, Tang H, Fang J, Mao Y, Yen HH, Dash S, Shajahan A, Pepi L, Huang S, Jones VS, Xie S, Huang GF, Lu J, Anderson B, Zhang B, Azadi P, Huang RP. N-glycosylation of the SARS-CoV-2 spike protein at Asn331 and Asn343 is involved in spike-ACE2 binding, virus entry, and regulation of IL-6. Microbiol Immunol 2024. [PMID: 38444370 DOI: 10.1111/1348-0421.13121] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 12/06/2023] [Accepted: 02/12/2024] [Indexed: 03/07/2024]
Abstract
The coronavirus disease 2019 (COVID-19) pandemic is an ongoing global public health crisis. The causative agent, the SARS-CoV-2 virus, enters host cells via molecular interactions between the viral spike protein and the host cell ACE2 surface protein. The SARS-CoV-2 spike protein is extensively decorated with up to 66 N-linked glycans. Glycosylation of viral proteins is known to function in immune evasion strategies but may also function in the molecular events of viral entry into host cells. Here, we show that N-glycosylation at Asn331 and Asn343 of SARS-CoV-2 spike protein is required for it to bind to ACE2 and for the entry of pseudovirus harboring the SARS-CoV-2 spike protein into cells. Interestingly, high-content glycan binding screening data have shown that N-glycosylation of Asn331 and Asn343 of the RBD is important for binding to the specific glycan molecule G4GN (Galβ-1,4 GlcNAc), which is critical for spike-RBD-ACE2 binding. Furthermore, IL-6 was identified through antibody array analysis of conditioned media of the corresponding pseudovirus assay. Mutation of N-glycosylation of Asn331 and Asn343 sites of the spike receptor-binding domain (RBD) significantly reduced the transcriptional upregulation of pro-inflammatory signaling molecule IL-6. In addition, IL-6 levels correlated with spike protein levels in COVID-19 patients' serum. These findings establish the importance of RBD glycosylation in SARS-CoV-2 pathogenesis, which can be exploited for the development of novel therapeutics for COVID-19.
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Affiliation(s)
- Tuhin Das
- RayBiotech Life Inc., Peachtree Corners, Georgia, USA
| | - Shuhong Luo
- RayBiotech Life Inc., Peachtree Corners, Georgia, USA
- RayBiotech Guangzhou Co. Ltd. Guangzhou, Guangzhou, China
| | - Hao Tang
- RayBiotech Life Inc., Peachtree Corners, Georgia, USA
- RayBiotech Guangzhou Co. Ltd. Guangzhou, Guangzhou, China
| | - Jianmin Fang
- RayBiotech Life Inc., Peachtree Corners, Georgia, USA
- RayBiotech Guangzhou Co. Ltd. Guangzhou, Guangzhou, China
| | - Yinging Mao
- RayBiotech Life Inc., Peachtree Corners, Georgia, USA
| | - Haw-Han Yen
- RayBiotech Life Inc., Peachtree Corners, Georgia, USA
| | - Sabyasachi Dash
- Department of Pathology, Center for Vascular Biology, Weill Cornell Medicine, New York, New York, USA
| | - Asif Shajahan
- Vaccine Research Center, Gaithersburg, Maryland, USA
| | - Lauren Pepi
- Vaccine Research Center, Gaithersburg, Maryland, USA
| | - Steven Huang
- RayBiotech Life Inc., Peachtree Corners, Georgia, USA
| | | | - Shehuo Xie
- RayBiotech Guangzhou Co. Ltd. Guangzhou, Guangzhou, China
| | | | - Jinqiao Lu
- RayBiotech Life Inc., Peachtree Corners, Georgia, USA
| | | | - Benyue Zhang
- RayBiotech Life Inc., Peachtree Corners, Georgia, USA
| | - Parastoo Azadi
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia, USA
| | - Ruo-Pan Huang
- RayBiotech Life Inc., Peachtree Corners, Georgia, USA
- RayBiotech Guangzhou Co. Ltd. Guangzhou, Guangzhou, China
- South China Biochip Research Center, Guangzhou, China
- Affiliated Cancer Hospital & Institute of Guangzhou Medical University, Guangzhou Medical University, Guangzhou, China
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4
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Zheng L, Wang H, Liu X, Xu C, Tian M, Shi G, Bai C, Li Z, Wang J, Liu S. A panel of multivalent nanobodies broadly neutralizing Omicron subvariants and recombinant. J Med Virol 2024; 96:e29528. [PMID: 38501378 DOI: 10.1002/jmv.29528] [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: 12/19/2023] [Revised: 02/05/2024] [Accepted: 03/02/2024] [Indexed: 03/20/2024]
Abstract
The emerging Omicron subvariants have a remarkable ability to spread and escape nearly all current monoclonal antibody (mAb) treatments. Although the virulence of SARS-CoV-2 has now diminished, it remains a significant threat to public health due to its high transmissibility and susceptibility to mutation. Therefore, it is urgent to develop broad-acting and potent therapeutics targeting current and emerging Omicron variants. Here, we identified a panel of Omicron BA.1 spike receptor-binding domain (RBD)-targeted nanobodies (Nbs) from a naive alpaca VHH library. This panel of Nbs exhibited high binding affinity to the spike RBD of wild-type, Alpha B.1.1.7, Beta B.1.351, Delta plus, Omicron BA.1, and BA.2. Through multivalent Nb construction, we obtained a subpanel of ultrapotent neutralizing Nbs against Omicron BA.1, BA.2, BF.7 and even emerging XBB.1.5, and XBB.1.16 pseudoviruses. Protein structure prediction and docking analysis showed that Nb trimer 2F2E5 targets two independent RBD epitopes, thus minimizing viral escape. Taken together, we obtained a panel of broad and ultrapotent neutralizing Nbs against Omicron BA.1, Omicron BA.2, BF.7, XBB.1.5, and XBB.1.16. These multivalent Nbs hold great promise for the treatment against SARS-CoV-2 infection and could possess a superwide neutralizing breadth against novel omicron mutants or recombinants.
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Affiliation(s)
- Liuhai Zheng
- Department of Critical Medicine, School of Medicine, Shenzhen People's Hospital, First Affiliated Hospital of Southern University of Science and Technology, Second Clinical Medical College of Jinan University, Shenzhen, Guangdong, China
- NMPA Key Laboratory for Research and Evaluation of Drug Metabolism & Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, China
| | - Huifang Wang
- Department of Critical Medicine, School of Medicine, Shenzhen People's Hospital, First Affiliated Hospital of Southern University of Science and Technology, Second Clinical Medical College of Jinan University, Shenzhen, Guangdong, China
| | - Xueyan Liu
- Department of Critical Medicine, School of Medicine, Shenzhen People's Hospital, First Affiliated Hospital of Southern University of Science and Technology, Second Clinical Medical College of Jinan University, Shenzhen, Guangdong, China
| | - Chengchao Xu
- Department of Critical Medicine, School of Medicine, Shenzhen People's Hospital, First Affiliated Hospital of Southern University of Science and Technology, Second Clinical Medical College of Jinan University, Shenzhen, Guangdong, China
- College of Integrative Medicine, Laboratory of Pathophysiology, Key Laboratory of Integrative Medicine on Chronic Diseases, Fujian University of Traditional Chinese Medicine, Fuzhou, China
- State Key Laboratory for Quality Assurance and Sustainable Use of Dao-di Herbs, Artemisinin Research Center, and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Mingxiong Tian
- School of Medicine, Zhongda Hospital, Southeast University, Nanjing, China
| | - Guangwei Shi
- NMPA Key Laboratory for Research and Evaluation of Drug Metabolism & Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, China
| | - Chongzhi Bai
- Central Laboratory, Shanxi Province Hospital of Traditional Chinese Medicine, Taiyuan, China
| | - Zhijie Li
- Department of Critical Medicine, School of Medicine, Shenzhen People's Hospital, First Affiliated Hospital of Southern University of Science and Technology, Second Clinical Medical College of Jinan University, Shenzhen, Guangdong, China
| | - Jigang Wang
- Department of Critical Medicine, School of Medicine, Shenzhen People's Hospital, First Affiliated Hospital of Southern University of Science and Technology, Second Clinical Medical College of Jinan University, Shenzhen, Guangdong, China
- NMPA Key Laboratory for Research and Evaluation of Drug Metabolism & Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, China
- State Key Laboratory for Quality Assurance and Sustainable Use of Dao-di Herbs, Artemisinin Research Center, and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
- Department of Oncology, the Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan, China
- State Key Laboratory of Antiviral Drugs, School of Pharmacy, Henan University, Kaifeng, Henan, China
| | - Shuwen Liu
- NMPA Key Laboratory for Research and Evaluation of Drug Metabolism & Guangdong Provincial Key Laboratory of New Drug Screening, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, China
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Kim JW, Lee JH, Kim HJ, Heo K, Lee Y, Jang HJ, Lee HY, Park JW, Cho YB, Shin HG, Yang HR, Lee HE, Song JY, Lee S. Empowering SARS-CoV-2 variant neutralization with a bifunctional antibody engineered with tandem heptad repeat 2 peptides. J Med Virol 2024; 96:e29506. [PMID: 38445718 DOI: 10.1002/jmv.29506] [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: 11/17/2023] [Revised: 01/28/2024] [Accepted: 02/23/2024] [Indexed: 03/07/2024]
Abstract
With the global pandemic and the continuous mutations of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the need for effective and broadly neutralizing treatments has become increasingly urgent. This study introduces a novel strategy that targets two aspects simultaneously, using bifunctional antibodies to inhibit both the attachment of SARS-CoV-2 to host cell membranes and viral fusion. We developed pioneering IgG4-(HR2)4 bifunctional antibodies by creating immunoglobulin G4-based and phage display-derived human monoclonal antibodies (mAbs) that specifically bind to the SARS-CoV-2 receptor-binding domain, engineered with four heptad repeat 2 (HR2) peptides. Our in vitro experiments demonstrate the superior neutralization efficacy of these engineered antibodies against various SARS-CoV-2 variants, ranging from original SARS-CoV-2 strain to the recently emerged Omicron variants, as well as SARS-CoV, outperforming the parental mAb. Notably, intravenous monotherapy with the bifunctional antibody neutralizes a SARS-CoV-2 variant in a murine model without causing significant toxicity. In summary, this study unveils the significant potential of HR2 peptide-driven bifunctional antibodies as a potent and versatile strategy for mitigating SARS-CoV-2 infections. This approach offers a promising avenue for rapid development and management in the face of the continuously evolving SARS-CoV-2 variants, holding substantial promise for pandemic control.
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Affiliation(s)
- Ji Woong Kim
- Department of Biopharmaceutical Chemistry, Kookmin University, Seoul, Republic of Korea
| | - Ji Hyun Lee
- Department of Biopharmaceutical Chemistry, Kookmin University, Seoul, Republic of Korea
| | - Hyun Jung Kim
- Department of Biopharmaceutical Chemistry, Kookmin University, Seoul, Republic of Korea
| | - Kyun Heo
- Department of Biopharmaceutical Chemistry, Kookmin University, Seoul, Republic of Korea
- Department of Chemistry, Kookmin University, Seoul, Republic of Korea
- Antibody Research Institute, Kookmin University, Seoul, Republic of Korea
| | - Yoonwoo Lee
- Department of Nuclear Medicine, Seoul National University Bundang Hospital, Seoul, Republic of Korea
| | - Hui Jeong Jang
- Department of Nuclear Medicine, Seoul National University Bundang Hospital, Seoul, Republic of Korea
| | - Ho-Young Lee
- Department of Nuclear Medicine, Seoul National University Bundang Hospital, Seoul, Republic of Korea
| | - Jun Won Park
- Division of Biomedical Convergence, Kangwon National University, Chuncheon, Republic of Korea
| | - Yea Bin Cho
- Department of Biopharmaceutical Chemistry, Kookmin University, Seoul, Republic of Korea
| | - Ha Gyeong Shin
- Department of Biopharmaceutical Chemistry, Kookmin University, Seoul, Republic of Korea
| | - Ha Rim Yang
- Department of Biopharmaceutical Chemistry, Kookmin University, Seoul, Republic of Korea
| | - Hee Eon Lee
- Department of Biopharmaceutical Chemistry, Kookmin University, Seoul, Republic of Korea
| | - Jin Young Song
- Department of Biopharmaceutical Chemistry, Kookmin University, Seoul, Republic of Korea
| | - Sukmook Lee
- Department of Biopharmaceutical Chemistry, Kookmin University, Seoul, Republic of Korea
- Department of Chemistry, Kookmin University, Seoul, Republic of Korea
- Antibody Research Institute, Kookmin University, Seoul, Republic of Korea
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Zhang T, Zheng N, Wang Z, Xu X. Structure-based design of oligomeric receptor-binding domain (RBD) recombinant proteins as potent vaccine candidates against SARS-CoV-2. Hum Vaccin Immunother 2023; 19:2174755. [PMID: 36846890 PMCID: PMC10026890 DOI: 10.1080/21645515.2023.2174755] [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] [Indexed: 03/01/2023] Open
Abstract
The receptor-binding domain (RBD) of SARS-CoV-2 S protein is proved to be the major target of neutralizing antibodies. However, on the S protein, only a portion of epitopes in RBD can be effectively displayed with dynamic changes in spatial conformations. Using RBD fragment as antigen can better expose the neutralizing epitopes, but the immunogenicity of RBD monomer is suboptimal. Multimeric display of RBD molecules is a feasible strategy to optimize RBD-based vaccines. In this study, RBD single-chain dimer derived from Wuhan-Hu-1 was fused with a trimerization motif, and a cysteine was also introduced at the C-terminus. The resultant recombinant protein 2RBDpLC was expressed in Sf9 cells using a baculovirus expression system. Reducing/non-reducing PAGE, size-exclusion chromatography and in silico structure prediction indicated that 2RBDpLC polymerized and possibly formed RBD dodecamers through trimerization motif and intermolecular disulfide bonds. In mice, 2RBDpLC induced higher levels of RBD-specific and neutralizing antibody responses than RBD dimer, RBD trimer and prefusion-stabilized S protein (S2P). In addition, cross-neutralizing antibodies against Delta and Omicron VOC were also detected in the immune sera. Our results demonstrate that 2RBDpLC is a promising vaccine candidate, and the method of constructing dodecamers may be an effective strategy for designing RBD-based vaccines.
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Affiliation(s)
- Ting Zhang
- Department of Biophysics and Structural Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China
| | - Ningchen Zheng
- Department of Biophysics and Structural Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China
| | - Zhirong Wang
- Department of Biophysics and Structural Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China
| | - Xuemei Xu
- Department of Biophysics and Structural Biology, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing, China
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Hu C, Guo T, Zou Y, Gao J, Gao Y, Niu M, Xia Y, Shen X, Li J. Discovery of dual S-RBD/NRP1-targeting peptides: structure-based virtual screening, synthesis, biological evaluation, and molecular dynamics simulation studies. J Enzyme Inhib Med Chem 2023; 38:2212327. [PMID: 37194732 DOI: 10.1080/14756366.2023.2212327] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/18/2023] Open
Abstract
Both receptor-binding domain in spike protein (S-RBD) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and human neuropilin-1 (NRP1) are important in the virus entry, and their concomitant inhibition may become a potential strategy against the SARS-CoV-2 infection. Herein, five novel dual S-RBD/NRP1-targeting peptides with nanomolar binding affinities were identified by structure-based virtual screening. Particularly, RN-4 was found to be the most promising peptide targeting S-RBD (Kd = 7.4 ± 0.5 nM) and NRP1-BD (the b1 domain of NRP1) (Kd = 16.1 ± 1.1 nM) proteins. Further evidence in the pseudovirus infection assay showed that RN-4 can significantly inhibit the SARS-CoV-2 pseudovirus entry into 293 T cells (EC50 = 0.39 ± 0.09 μM) without detectable side effects. These results suggest that RN-4, a novel dual S-RBD/NRP1-targeting agent, holds potential as an effective therapeutic to combat the SARS-CoV-2 infection.
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Affiliation(s)
- Chunfang Hu
- Institute of Clinical Medicine, The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou, China
| | - Ting Guo
- Institute of Clinical Medicine, Taizhou People's Hospital Affiliated to Nanjing University of Traditional Chinese Medicine, Taizhou, China
| | - Yunting Zou
- Department of Pharmaceutical Analysis, China Pharmaceutical University, Nanjing, China
| | - Junyi Gao
- Institute of Clinical Medicine, The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou, China
| | - Yi Gao
- Institute of Clinical Medicine, The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou, China
| | - Miaomiao Niu
- Department of Pharmaceutical Analysis, China Pharmaceutical University, Nanjing, China
| | - Yang Xia
- Institute of Clinical Medicine, The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou, China
| | - Xiaozhou Shen
- Institute of Clinical Medicine, The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou, China
| | - Jindong Li
- Institute of Clinical Medicine, The Affiliated Taizhou People's Hospital of Nanjing Medical University, Taizhou, China
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8
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Ye G, Pan R, Bu F, Zheng J, Mendoza A, Wen W, Du L, Spiller B, Wadzinski BE, Liu B, Perlman S, Li F. Discovery of Nanosota-2, -3, and -4 as super potent and broad-spectrum therapeutic nanobody candidates against COVID-19. J Virol 2023; 97:e0144823. [PMID: 37855638 PMCID: PMC10688364 DOI: 10.1128/jvi.01448-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [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: 09/15/2023] [Accepted: 09/18/2023] [Indexed: 10/20/2023] Open
Abstract
IMPORTANCE The COVID-19 pandemic exposed limitations of conventional antibodies as therapeutics, including high cost, limited potency, ineffectiveness against new viral variants, and primary reliance on injection-only delivery. Nanobodies are single-domain antibodies with therapeutic potentials. We discovered three anti-SARS-CoV-2 nanobodies, named Nanosota-2, -3, and -4, from an immunized alpaca. Nanosota-2 is super potent against prototypic SARS-CoV-2, Nanosota-3 is highly potent against the omicron variant, and Nanosota-4 is effective against both SARS-CoV-1 and SARS-CoV-2. In addition to their super potency and combined broad antiviral spectrum, these nanobodies are cost-effective, can be easily adapted to new viral variants through phage display, and can potentially be administered as inhalers. The Nanosota series are powerful therapeutic candidates to combat circulating SARS-CoV-2 and prepare for possible future coronavirus pandemics.
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Affiliation(s)
- Gang Ye
- Department of Pharmacology, University of Minnesota Medical School, Minneapolis, Minnesota, USA
- Center for Coronavirus Research, University of Minnesota, Minneapolis, Minnesota, USA
| | - Ruangang Pan
- Department of Microbiology and Immunology, University of Iowa, Iowa City, Iowa, USA
| | - Fan Bu
- Department of Pharmacology, University of Minnesota Medical School, Minneapolis, Minnesota, USA
- Center for Coronavirus Research, University of Minnesota, Minneapolis, Minnesota, USA
- Hormel Institute, University of Minnesota, Austin, Minnesota, USA
| | - Jian Zheng
- Department of Microbiology and Immunology, University of Iowa, Iowa City, Iowa, USA
| | - Alise Mendoza
- Department of Pharmacology, University of Minnesota Medical School, Minneapolis, Minnesota, USA
- Center for Coronavirus Research, University of Minnesota, Minneapolis, Minnesota, USA
| | - Wei Wen
- Department of Pharmacology, University of Minnesota Medical School, Minneapolis, Minnesota, USA
- Center for Coronavirus Research, University of Minnesota, Minneapolis, Minnesota, USA
| | - Lanying Du
- Institute for Biomedical Sciences, Georgia State University, Atlanta, Georgia, USA
| | - Benjamin Spiller
- Department of Pharmacology, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Brian E. Wadzinski
- Department of Pharmacology, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Bin Liu
- Hormel Institute, University of Minnesota, Austin, Minnesota, USA
| | - Stanley Perlman
- Department of Microbiology and Immunology, University of Iowa, Iowa City, Iowa, USA
| | - Fang Li
- Department of Pharmacology, University of Minnesota Medical School, Minneapolis, Minnesota, USA
- Center for Coronavirus Research, University of Minnesota, Minneapolis, Minnesota, USA
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9
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Wu Y, Shi J, He X, Lu J, Gao X, Zhu X, Chen X, Zhang M, Fang L, Zhang J, Yuan Z, Xiao G, Zhou P, Pan X. Protection of the receptor binding domain (RBD) dimer against SARS-CoV-2 and its variants. J Virol 2023; 97:e0127923. [PMID: 37843372 PMCID: PMC10688353 DOI: 10.1128/jvi.01279-23] [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: 08/18/2023] [Accepted: 09/16/2023] [Indexed: 10/17/2023] Open
Abstract
IMPORTANCE Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants achieved immune escape and became less virulent and easily transmissible through rapid mutation in the spike protein, thus the efficacy of vaccines on the market or in development continues to be challenged. Updating the vaccine, exploring compromise vaccination strategies, and evaluating the efficacy of candidate vaccines for the emerging variants in a timely manner are important to combat complex and volatile SARS-CoV-2. This study reports that vaccines prepared from the dimeric receptor-binding domain (RBD) recombinant protein, which can be quickly produced using a mature and stable process platform, had both good immunogenicity and protection in vivo and could completely protect rodents from lethal challenge by SARS-CoV-2 and its variants, including the emerging Omicron XBB.1.16, highlighting the value of dimeric recombinant vaccines in the post-COVID-19 era.
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Affiliation(s)
- Yan Wu
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Jian Shi
- Wuhan YZY Biopharma Co., Ltd., Wuhan, China
| | - Xiaoxue He
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Jia Lu
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
- University of the Chinese Academy of Sciences, Beijing, China
| | - Xiao Gao
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
- University of the Chinese Academy of Sciences, Beijing, China
| | - Xuerui Zhu
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Xinlan Chen
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
- University of the Chinese Academy of Sciences, Beijing, China
| | - Man Zhang
- Wuhan YZY Biopharma Co., Ltd., Wuhan, China
| | | | - Jing Zhang
- Wuhan YZY Biopharma Co., Ltd., Wuhan, China
| | - Zhiming Yuan
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
- University of the Chinese Academy of Sciences, Beijing, China
- Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Gengfu Xiao
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
- University of the Chinese Academy of Sciences, Beijing, China
- Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | | | - Xiaoyan Pan
- State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
- University of the Chinese Academy of Sciences, Beijing, China
- Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
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10
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Koseki T, Teramachi M, Koga M, Ko MSH, Amano T, Yu H, Amano M, Leyder E, Badiola M, Ray P, Kim J, Ko AC, Achour A, Weng NP, Imai T, Yoshida H, Taniuchi S, Shintani A, Fujigaki H, Kondo M, Doi Y. A Phase I/II Clinical Trial of Intradermal, Controllable Self-Replicating Ribonucleic Acid Vaccine EXG-5003 against SARS-CoV-2. Vaccines (Basel) 2023; 11:1767. [PMID: 38140172 PMCID: PMC10747308 DOI: 10.3390/vaccines11121767] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 11/11/2023] [Accepted: 11/22/2023] [Indexed: 12/24/2023] Open
Abstract
mRNA vaccines against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have played a key role in reducing morbidity and mortality from coronavirus disease 2019 (COVID-19). We conducted a double-blind, placebo-controlled phase I/II trial to evaluate the safety, tolerability, and immunogenicity of EXG-5003, a two-dose, controllable self-replicating RNA vaccine against SARS-CoV-2. EXG-5003 encodes the receptor binding domain (RBD) of SARS-CoV-2 and was administered intradermally without lipid nanoparticles (LNPs). The participants were followed for 12 months. Forty healthy participants were enrolled in Cohort 1 (5 µg per dose, n = 16; placebo, n = 4) and Cohort 2 (25 µg per dose, n = 16; placebo, n = 4). No safety concerns were observed with EXG-5003 administration. SARS-CoV-2 RBD antibody titers and neutralizing antibody titers were not elevated in either cohort. Elicitation of antigen-specific cellular immunity was observed in the EXG-5003 recipients in Cohort 2. At the 12-month follow-up, participants who had received an approved mRNA vaccine (BNT162b2 or mRNA-1273) >1 month after receiving the second dose of EXG-5003 showed higher cellular responses compared with equivalently vaccinated participants in the placebo group. The findings suggest a priming effect of EXG-5003 on the long-term cellular immunity of approved SARS-CoV-2 mRNA vaccines.
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Affiliation(s)
- Takenao Koseki
- Department of Pharmacotherapeutics and Informatics, School of Medicine, Fujita Health University, Toyoake 470-1192, Japan;
| | - Mayumi Teramachi
- Center for Clinical Trial and Research Support, School of Medicine, Fujita Health University, Toyoake 470-1192, Japan; (M.T.); (M.K.)
| | - Minako Koga
- KM Pharmaceutical Consulting, Washington, DC 20006, USA;
| | - Minoru S. H. Ko
- Elixirgen Therapeutics, Inc., Baltimore, MD 21205, USA; (M.S.H.K.); (T.A.); (H.Y.); (M.A.); (E.L.); (M.B.); (P.R.); (J.K.); (A.C.K.)
| | - Tomokazu Amano
- Elixirgen Therapeutics, Inc., Baltimore, MD 21205, USA; (M.S.H.K.); (T.A.); (H.Y.); (M.A.); (E.L.); (M.B.); (P.R.); (J.K.); (A.C.K.)
| | - Hong Yu
- Elixirgen Therapeutics, Inc., Baltimore, MD 21205, USA; (M.S.H.K.); (T.A.); (H.Y.); (M.A.); (E.L.); (M.B.); (P.R.); (J.K.); (A.C.K.)
| | - Misa Amano
- Elixirgen Therapeutics, Inc., Baltimore, MD 21205, USA; (M.S.H.K.); (T.A.); (H.Y.); (M.A.); (E.L.); (M.B.); (P.R.); (J.K.); (A.C.K.)
| | - Erica Leyder
- Elixirgen Therapeutics, Inc., Baltimore, MD 21205, USA; (M.S.H.K.); (T.A.); (H.Y.); (M.A.); (E.L.); (M.B.); (P.R.); (J.K.); (A.C.K.)
| | - Maria Badiola
- Elixirgen Therapeutics, Inc., Baltimore, MD 21205, USA; (M.S.H.K.); (T.A.); (H.Y.); (M.A.); (E.L.); (M.B.); (P.R.); (J.K.); (A.C.K.)
| | - Priyanka Ray
- Elixirgen Therapeutics, Inc., Baltimore, MD 21205, USA; (M.S.H.K.); (T.A.); (H.Y.); (M.A.); (E.L.); (M.B.); (P.R.); (J.K.); (A.C.K.)
| | - Jiyoung Kim
- Elixirgen Therapeutics, Inc., Baltimore, MD 21205, USA; (M.S.H.K.); (T.A.); (H.Y.); (M.A.); (E.L.); (M.B.); (P.R.); (J.K.); (A.C.K.)
| | - Akihiro C. Ko
- Elixirgen Therapeutics, Inc., Baltimore, MD 21205, USA; (M.S.H.K.); (T.A.); (H.Y.); (M.A.); (E.L.); (M.B.); (P.R.); (J.K.); (A.C.K.)
| | - Achouak Achour
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, MD 20892, USA; (A.A.); (N.-p.W.)
| | - Nan-ping Weng
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, MD 20892, USA; (A.A.); (N.-p.W.)
| | - Takumi Imai
- Department of Medical Statistics, Graduate School of Medicine, Osaka Metropolitan University, Osaka 545-8585, Japan; (T.I.); (H.Y.); (S.T.); (A.S.)
| | - Hisako Yoshida
- Department of Medical Statistics, Graduate School of Medicine, Osaka Metropolitan University, Osaka 545-8585, Japan; (T.I.); (H.Y.); (S.T.); (A.S.)
| | - Satsuki Taniuchi
- Department of Medical Statistics, Graduate School of Medicine, Osaka Metropolitan University, Osaka 545-8585, Japan; (T.I.); (H.Y.); (S.T.); (A.S.)
| | - Ayumi Shintani
- Department of Medical Statistics, Graduate School of Medicine, Osaka Metropolitan University, Osaka 545-8585, Japan; (T.I.); (H.Y.); (S.T.); (A.S.)
| | - Hidetsugu Fujigaki
- Department of Advanced Diagnostic System Development, Graduate School of Health Sciences, Fujita Health University, Toyoake 470-1192, Japan
| | - Masashi Kondo
- Center for Clinical Trial and Research Support, School of Medicine, Fujita Health University, Toyoake 470-1192, Japan; (M.T.); (M.K.)
- Department of Respiratory Medicine, School of Medicine, Fujita Health University, Toyoake 470-1192, Japan
| | - Yohei Doi
- Departments of Microbiology and Infectious Diseases, School of Medicine, Fujita Health University, Toyoake 470-1192, Japan
- Center for Infectious Disease Research, Fujita Health University, Toyoake 470-1192, Japan
- Division of Infectious Diseases, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
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11
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Geng Q, Wan Y, Hsueh FC, Shang J, Ye G, Bu F, Herbst M, Wilkens R, Liu B, Li F. Lys417 acts as a molecular switch that regulates the conformation of SARS-CoV-2 spike protein. eLife 2023; 12:e74060. [PMID: 37991488 PMCID: PMC10695562 DOI: 10.7554/elife.74060] [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: 09/20/2021] [Accepted: 11/21/2023] [Indexed: 11/23/2023] Open
Abstract
SARS-CoV-2 spike protein plays a key role in mediating viral entry and inducing host immune responses. It can adopt either an open or closed conformation based on the position of its receptor-binding domain (RBD). It is yet unclear what causes these conformational changes or how they influence the spike's functions. Here, we show that Lys417 in the RBD plays dual roles in the spike's structure: it stabilizes the closed conformation of the trimeric spike by mediating inter-spike-subunit interactions; it also directly interacts with ACE2 receptor. Hence, a K417V mutation has opposing effects on the spike's function: it opens up the spike for better ACE2 binding while weakening the RBD's direct binding to ACE2. The net outcomes of this mutation are to allow the spike to bind ACE2 with higher probability and mediate viral entry more efficiently, but become more exposed to neutralizing antibodies. Given that residue 417 has been a viral mutational hotspot, SARS-CoV-2 may have been evolving to strike a balance between infection potency and immune evasion, contributing to its pandemic spread.
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Affiliation(s)
- Qibin Geng
- Department of Pharmacology, University of Minnesota Medical SchoolMinneapolisUnited States
- Center for Coronavirus Research, University of MinnesotaMinneapolisUnited States
| | - Yushun Wan
- Department of Pharmacology, University of Minnesota Medical SchoolMinneapolisUnited States
- Center for Coronavirus Research, University of MinnesotaMinneapolisUnited States
| | - Fu-Chun Hsueh
- Department of Pharmacology, University of Minnesota Medical SchoolMinneapolisUnited States
- Center for Coronavirus Research, University of MinnesotaMinneapolisUnited States
| | - Jian Shang
- Department of Pharmacology, University of Minnesota Medical SchoolMinneapolisUnited States
- Center for Coronavirus Research, University of MinnesotaMinneapolisUnited States
| | - Gang Ye
- Department of Pharmacology, University of Minnesota Medical SchoolMinneapolisUnited States
- Center for Coronavirus Research, University of MinnesotaMinneapolisUnited States
| | - Fan Bu
- Department of Pharmacology, University of Minnesota Medical SchoolMinneapolisUnited States
- Center for Coronavirus Research, University of MinnesotaMinneapolisUnited States
| | - Morgan Herbst
- Department of Pharmacology, University of Minnesota Medical SchoolMinneapolisUnited States
- Center for Coronavirus Research, University of MinnesotaMinneapolisUnited States
| | - Rowan Wilkens
- Department of Pharmacology, University of Minnesota Medical SchoolMinneapolisUnited States
- Center for Coronavirus Research, University of MinnesotaMinneapolisUnited States
| | - Bin Liu
- Hormel Institute, University of MinnesotaAustinUnited States
| | - Fang Li
- Department of Pharmacology, University of Minnesota Medical SchoolMinneapolisUnited States
- Center for Coronavirus Research, University of MinnesotaMinneapolisUnited States
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12
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Boumaiza M, Chaabene A, Akrouti I, Ben Zakour M, Askri H, Salhi S, Ben Hamouda W, Marzouki S, Benabdessalem C, Ben Ahmed M, Trabelsi K, Rourou S. Development of an Optimized Process for Functional Recombinant SARS-CoV-2 Spike S1 Receptor-Binding Domain Protein Produced in the Baculovirus Expression Vector System. Trop Med Infect Dis 2023; 8:501. [PMID: 37999620 PMCID: PMC10674791 DOI: 10.3390/tropicalmed8110501] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 10/05/2023] [Accepted: 10/07/2023] [Indexed: 11/25/2023] Open
Abstract
To map the spread of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) and evaluate immune response variations against this virus, it is essential to set up efficient serological tests locally. The SARS-CoV-2 immunogenic proteins were very expensive and not affordable for lower- middle-income countries (LMICs). For this purpose, the commonly used antigen, receptor-binding domain (RBD) of spike S1 protein (S1RBD), was produced using the baculovirus expression vector system (BEVS). In the current study, the expression of S1RBD was monitored using Western blot under different culture conditions. Different parameters were studied: the multiplicity of infection (MOI), cell density at infection, and harvest time. Hence, optimal conditions for efficient S1RBD production were identified: MOI 3; cell density at infection 2-3 × 106 cells/mL; and time post-infection (tPI or harvest time) of 72 h and 72-96 h, successively, for expression in shake flasks and a 7L bioreactor. A high production yield of S1RBD varying between 4 mg and 70 mg per liter of crude cell culture supernatant was achieved, respectively, in the shake flasks and 7L bioreactor. Moreover, the produced S1RBD showed an excellent antigenicity potential against COVID-19 (Wuhan strain) patient sera evaluated by Western blot. Thus, additional serological assays, such as in-house ELISA and seroprevalence studies based on the purified S1RDB, were developed.
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Affiliation(s)
- Mohamed Boumaiza
- Laboratory of Molecular Microbiology, Vaccinology and Biotechnology Development, Group of Biotechnology Development, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis 1002, Tunisia
| | - Ameni Chaabene
- Laboratory of Molecular Microbiology, Vaccinology and Biotechnology Development, Group of Biotechnology Development, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis 1002, Tunisia
| | - Ines Akrouti
- Laboratory of Molecular Microbiology, Vaccinology and Biotechnology Development, Group of Biotechnology Development, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis 1002, Tunisia
| | - Meriem Ben Zakour
- Laboratory of Molecular Microbiology, Vaccinology and Biotechnology Development, Group of Biotechnology Development, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis 1002, Tunisia
| | - Hana Askri
- Laboratory of Molecular Microbiology, Vaccinology and Biotechnology Development, Group of Biotechnology Development, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis 1002, Tunisia
| | - Said Salhi
- Laboratory of Molecular Microbiology, Vaccinology and Biotechnology Development, Group of Biotechnology Development, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis 1002, Tunisia
| | - Wafa Ben Hamouda
- Laboratory of Transmission, Control and Immunobiology of Infections (LTCII), LR11IPT-02, Institut Pasteur de Tunis, Université Tunis El Manar, 13, Place Pasteur. BP. 74, Tunis 1002, Tunisia
| | - Soumaya Marzouki
- Laboratory of Transmission, Control and Immunobiology of Infections (LTCII), LR11IPT-02, Institut Pasteur de Tunis, Université Tunis El Manar, 13, Place Pasteur. BP. 74, Tunis 1002, Tunisia
| | - Chaouki Benabdessalem
- Laboratory of Transmission, Control and Immunobiology of Infections (LTCII), LR11IPT-02, Institut Pasteur de Tunis, Université Tunis El Manar, 13, Place Pasteur. BP. 74, Tunis 1002, Tunisia
| | - Melika Ben Ahmed
- Laboratory of Transmission, Control and Immunobiology of Infections (LTCII), LR11IPT-02, Institut Pasteur de Tunis, Université Tunis El Manar, 13, Place Pasteur. BP. 74, Tunis 1002, Tunisia
| | - Khaled Trabelsi
- Laboratory of Molecular Microbiology, Vaccinology and Biotechnology Development, Group of Biotechnology Development, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis 1002, Tunisia
| | - Samia Rourou
- Laboratory of Molecular Microbiology, Vaccinology and Biotechnology Development, Group of Biotechnology Development, Institut Pasteur de Tunis, Université Tunis El Manar, Tunis 1002, Tunisia
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13
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Martinez DR, Schäfer A, Gavitt TD, Mallory ML, Lee E, Catanzaro NJ, Chen H, Gully K, Scobey T, Korategere P, Brown A, Smith L, Parks R, Barr M, Newman A, Bowman C, Powers JM, Soderblom EJ, Mansouri K, Edwards RJ, Baric RS, Haynes BF, Saunders KO. Vaccine-mediated protection against Merbecovirus and Sarbecovirus challenge in mice. Cell Rep 2023; 42:113248. [PMID: 37858337 PMCID: PMC10842144 DOI: 10.1016/j.celrep.2023.113248] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [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: 05/02/2023] [Revised: 08/30/2023] [Accepted: 09/26/2023] [Indexed: 10/21/2023] Open
Abstract
The emergence of three highly pathogenic human coronaviruses-severe acute respiratory syndrome coronavirus (SARS-CoV) in 2003, Middle Eastern respiratory syndrome (MERS)-CoV in 2012, and SARS-CoV-2 in 2019-underlines the need to develop broadly active vaccines against the Merbecovirus and Sarbecovirus betacoronavirus subgenera. While SARS-CoV-2 vaccines protect against severe COVID-19, they do not protect against other sarbecoviruses or merbecoviruses. Here, we vaccinate mice with a trivalent sortase-conjugate nanoparticle (scNP) vaccine containing the SARS-CoV-2, RsSHC014, and MERS-CoV receptor-binding domains (RBDs), which elicited live-virus neutralizing antibody responses. The trivalent RBD scNP elicited serum neutralizing antibodies against bat zoonotic Wuhan Institute of Virology-1 (WIV-1)-CoV, SARS-CoV, SARS-CoV-2 BA.1, SARS-CoV-2 XBB.1.5, and MERS-CoV live viruses. The monovalent SARS-CoV-2 RBD scNP vaccine only protected against Sarbecovirus challenge, whereas the trivalent RBD scNP vaccine protected against both Merbecovirus and Sarbecovirus challenge in highly pathogenic and lethal mouse models. This study demonstrates proof of concept for a single pan-sarbecovirus/pan-merbecovirus vaccine that protects against three highly pathogenic human coronaviruses spanning two betacoronavirus subgenera.
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Affiliation(s)
- David R Martinez
- Department of Immunobiology, Yale School of Medicine, New Haven, CT 06510, USA; Yale Center for Infection and Immunity, Yale School of Medicine, New Haven, CT 06510, USA.
| | - Alexandra Schäfer
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Tyler D Gavitt
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Michael L Mallory
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Esther Lee
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Nicholas J Catanzaro
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Haiyan Chen
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Kendra Gully
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Trevor Scobey
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Pooja Korategere
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Alecia Brown
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Lena Smith
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Robert Parks
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Maggie Barr
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Amanda Newman
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Cindy Bowman
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - John M Powers
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Erik J Soderblom
- Proteomics and Metabolomics Core Facility, Duke University School of Medicine, Durham, NC 27710, USA
| | - Katayoun Mansouri
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Robert J Edwards
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Ralph S Baric
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
| | - Barton F Haynes
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA.
| | - Kevin O Saunders
- Duke Human Vaccine Institute, Duke University School of Medicine, Durham, NC 27710, USA.
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14
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Kim JW, Kim HJ, Heo K, Lee Y, Jang HJ, Lee HY, Park JW, Cho YB, Lee JH, Shin HG, Yang HR, Choi HL, Shim HB, Lee S. A novel bispecific antibody dual-targeting approach for enhanced neutralization against fast-evolving SARS-CoV-2 variants. Front Immunol 2023; 14:1271508. [PMID: 37822941 PMCID: PMC10562541 DOI: 10.3389/fimmu.2023.1271508] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 09/11/2023] [Indexed: 10/13/2023] Open
Abstract
Introduction The emergence of new severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants has caused unprecedented health and socioeconomic crises, necessitating the immediate development of highly effective neutralizing antibodies. Despite recent advancements in anti-SARS-CoV-2 receptor-binding domain (RBD)-specific monoclonal antibodies (mAbs) derived from convalescent patient samples, their efficacy against emerging variants has been limited. In this study, we present a novel dual-targeting strategy using bispecific antibodies (bsAbs) that specifically recognize both the SARS-CoV-2 RBD and fusion peptide (FP), crucial domains for viral attachment to the host cell membrane and fusion in SARS-CoV-2 infection. Methods Using phage display technology, we rapidly isolated FP-specific mAbs from an established human recombinant antibody library, identifying K107.1 with a nanomolar affinity for SARS-CoV-2 FP. Furthermore, we generated K203.A, a new bsAb built in immunoglobulin G4-(single-chain variable fragment)2 forms and demonstrating a high manufacturing yield and nanomolar affinity to both the RBD and FP, by fusing K102.1, our previously reported RBD-specific mAb, with K107.1. Results Our comprehensive in vitro functional analyses revealed that the K203.A bsAb significantly outperformed the parental RBD-specific mAb in terms of neutralization efficacy against SARS-CoV-2 variants. Furthermore, intravenous monotherapy with K203.A demonstrated potent in vivo neutralizing activity without significant in vivo toxicity in a mouse model infected with a SARS-CoV-2 variant. Conclusion These findings present a novel bsAb dual-targeting strategy, directed at SARS-CoV-2 RBD and FP, as an effective approach for rapid development and management against continuously evolving SARS-CoV-2 variants.
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Affiliation(s)
- Ji Woong Kim
- Department of Chemistry, Kookmin University, Seoul, Republic of Korea
| | - Hyun Jung Kim
- Department of Biopharmaceutical Chemistry, Kookmin University, Seoul, Republic of Korea
| | - Kyun Heo
- Department of Chemistry, Kookmin University, Seoul, Republic of Korea
- Department of Biopharmaceutical Chemistry, Kookmin University, Seoul, Republic of Korea
- Antibody Research Institute, Kookmin University, Seoul, Republic of Korea
| | - Yoonwoo Lee
- Department of Nuclear Medicine, Seoul National University Bundang Hospital, Seoul, Republic of Korea
| | - Hui Jeong Jang
- Department of Nuclear Medicine, Seoul National University Bundang Hospital, Seoul, Republic of Korea
| | - Ho-Young Lee
- Department of Nuclear Medicine, Seoul National University Bundang Hospital, Seoul, Republic of Korea
| | - Jun Won Park
- Division of Biomedical Convergence, Kangwon National University, Chuncheon, Republic of Korea
| | - Yea Bin Cho
- Department of Chemistry, Kookmin University, Seoul, Republic of Korea
| | - Ji Hyun Lee
- Department of Biopharmaceutical Chemistry, Kookmin University, Seoul, Republic of Korea
| | - Ha Gyeong Shin
- Department of Biopharmaceutical Chemistry, Kookmin University, Seoul, Republic of Korea
| | - Ha Rim Yang
- Department of Biopharmaceutical Chemistry, Kookmin University, Seoul, Republic of Korea
| | - Hye Lim Choi
- Department of Biopharmaceutical Chemistry, Kookmin University, Seoul, Republic of Korea
| | - Hyun Bo Shim
- Department of Life Sciences, Ewha Womans University, Seoul, Republic of Korea
| | - Sukmook Lee
- Department of Chemistry, Kookmin University, Seoul, Republic of Korea
- Department of Biopharmaceutical Chemistry, Kookmin University, Seoul, Republic of Korea
- Antibody Research Institute, Kookmin University, Seoul, Republic of Korea
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15
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Burgos G, Ambuludí A, Morales-Jadán D, Garcia-Bereguiain MA, Muslin C, Armijos-Jaramillo V. A tool for the cheap and rapid screening of SARS-CoV-2 variants of concern (VoCs) by Sanger sequencing. Microbiol Spectr 2023; 11:e0506422. [PMID: 37676038 PMCID: PMC10586709 DOI: 10.1128/spectrum.05064-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 07/05/2023] [Indexed: 09/08/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an emerging virus that, since March 2020, has been responsible for a global and ongoing pandemic. Its rapid spread over the past nearly 3 years has caused novel variants to arise. To monitor the circulation and emergence of SARS-CoV-2 variants, surveillance systems based on nucleotide mutations are required. In this regard, we searched in the spike, ORF8, and nucleocapsid genes to detect variable sites among SARS-CoV-2 variants. We describe polymorphic genetic regions that enable us to differentiate between the Alpha, Beta, Gamma, Delta, and Omicron variants of concern (VoCs). We found 21 relevant mutations, 13 of which are unique for Omicron lineages BA.1/BA.1.1, BA.2, BA.3, BA.4, and BA.5. This genetic profile enables the discrimination between VoCs using only four reverse transcription PCR fragments and Sanger sequencing, offering a cheaper and faster alternative to whole-genome sequencing for SARS-CoV-2 surveillance. IMPORTANCE Our work describes a new (Sanger sequencing-based) screening methodology for SARS-CoV-2, performing PCR amplifications of a few target regions to detect diagnostic mutations between virus variants. Using the methodology developed in this work, we were able to discriminate between the following VoCs: Alpha, Beta, Gamma, Delta, and Omicron (BA.1/BA.1.1, BA.2, BA.3, BA.4, and BA.5). This becomes important, especially in low-income countries where current methodologies like next-generation sequencing have prohibitive costs. Furthermore, rapid detection would allow sanitary authorities to take rapid measures to limit the spread of the virus and therefore reduce the probability of new virus dispersion. With this methodological approach, 13 previously unreported diagnostic mutations among several Omicron lineages were found.
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Affiliation(s)
- Germán Burgos
- Facultad de Medicina, Universidad de Las Américas (UDLA), Quito, Ecuador
- One Health Research Group, Faculty of Health Sciences, Universidad de Las Américas (UDLA), Quito, Ecuador
| | - Andrés Ambuludí
- Carrera de Ingeniería en Biotecnología, Facultad de Ingenierías y Ciencias Aplicadas, Universidad de Las Américas (UDLA), Quito, Ecuador
| | - USFQ SARS-CoV-2 Consortium
- Instituto de Microbiología, Colegio de Ciencias Biológicas y Ambientales (COCIBA), Universidad San Francisco de Quito (USFQ), Cumbaya, Ecuador
| | - Diana Morales-Jadán
- One Health Research Group, Faculty of Health Sciences, Universidad de Las Américas (UDLA), Quito, Ecuador
| | | | - Claire Muslin
- One Health Research Group, Faculty of Health Sciences, Universidad de Las Américas (UDLA), Quito, Ecuador
| | - Vinicio Armijos-Jaramillo
- Carrera de Ingeniería en Biotecnología, Facultad de Ingenierías y Ciencias Aplicadas, Universidad de Las Américas (UDLA), Quito, Ecuador
- Grupo de Bio-Quimioinformática, Universidad de Las Américas (UDLA), Quito, Ecuador
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16
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Matveev AL, Pyankov OV, Khlusevich YA, Tyazhelkova OV, Emelyanova LA, Timofeeva AM, Shipovalov AV, Chechushkov AV, Zaitseva NS, Kudrov GA, Yusubalieva GM, Yussubaliyeva SM, Zhukova OA, Tikunov AY, Baklaushev VP, Sedykh SE, Lifshits GI, Tikunova NV. Novel B-Cell Epitopes of Non-Neutralizing Antibodies in the Receptor-Binding Domain of the SARS-CoV-2 S-Protein with Different Effects on the Severity of COVID-19. Biochemistry (Mosc) 2023; 88:1205-1214. [PMID: 37770389 DOI: 10.1134/s000629792309002x] [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] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 08/14/2023] [Accepted: 08/18/2023] [Indexed: 09/30/2023]
Abstract
Antibodies against the receptor-binding domain of the SARS-CoV-2 spike protein (RBD S-protein) contribute significantly to the humoral immune response during coronavirus infection (COVID-19) and after vaccination. The main focus of the studies of the RBD epitope composition is usually concentrated on the epitopes recognized by the virus-neutralizing antibodies. The role of antibodies that bind to RBD but do not neutralize SARS-CoV-2 remains unclear. In this study, immunochemical properties of the two mouse monoclonal antibodies (mAbs), RS17 and S11, against the RBD were examined. Both mAbs exhibited high affinity to RBD, but they did not neutralize the virus. The epitopes of these mAbs were mapped using phage display: the epitope recognized by the mAb RS17 is located at the N-terminal site of RBD (348-SVYAVNRKRIS-358); the mAb S11 epitope is inside the receptor-binding motif of RBD (452-YRLFRKSN-459). Three groups of sera were tested for presence of antibodies competing with the non-neutralizing mAbs S11 and RS17: (i) sera from the vaccinated healthy volunteers without history of COVID-19; (ii) sera from the persons who had a mild form of COVID-19; (iii) sera from the persons who had severe COVID-19. Antibodies competing with the mAb S11 were found in each group of sera with equal frequency, whereas presence of the antibodies competing with the mAb RS17 in the sera was significantly more frequent in the group of sera obtained from the patients recovered from severe COVID-19 indicating that such antibodies are associated with the severity of COVID-19. In conclusion, despite the clear significance of anti-RBD antibodies in the effective immune response against SARS-CoV-2, it is important to analyze their virus-neutralizing activity and to confirm absence of the antibody-mediated enhancement of infection by the anti-RBD antibodies.
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Affiliation(s)
- Andrey L Matveev
- Federal State Public Scientific Institution "Institute of Chemical Biology and Fundamental Medicine", Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia.
| | - Oleg V Pyankov
- State Research Center of Virology and Biotechnology "VECTOR", Federal Service for the Oversight of Consumer Protection and Welfare, Koltsovo, 630559, Novosibirsk Region, Russia
| | - Yana A Khlusevich
- Federal State Public Scientific Institution "Institute of Chemical Biology and Fundamental Medicine", Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia
| | - Olga V Tyazhelkova
- Federal State Public Scientific Institution "Institute of Chemical Biology and Fundamental Medicine", Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia
| | - Ljudmila A Emelyanova
- Federal State Public Scientific Institution "Institute of Chemical Biology and Fundamental Medicine", Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia
| | - Anna M Timofeeva
- Federal State Public Scientific Institution "Institute of Chemical Biology and Fundamental Medicine", Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia
| | - Andrey V Shipovalov
- State Research Center of Virology and Biotechnology "VECTOR", Federal Service for the Oversight of Consumer Protection and Welfare, Koltsovo, 630559, Novosibirsk Region, Russia
| | - Anton V Chechushkov
- Federal State Public Scientific Institution "Institute of Chemical Biology and Fundamental Medicine", Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia
| | | | - Gleb A Kudrov
- State Research Center of Virology and Biotechnology "VECTOR", Federal Service for the Oversight of Consumer Protection and Welfare, Koltsovo, 630559, Novosibirsk Region, Russia
| | - Gaukhar M Yusubalieva
- Federal Research and Clinical Center of Specialized Medical Care and Medical Technologies FMBA of Russia, Moscow, 115682, Russia
- Federal Center of Brain Research and Neurotechnologies, FMBA of Russia, Moscow, 117513, Russia
| | | | - Oxana A Zhukova
- Federal Research and Clinical Center of Specialized Medical Care and Medical Technologies FMBA of Russia, Moscow, 115682, Russia
| | - Artem Yu Tikunov
- Federal State Public Scientific Institution "Institute of Chemical Biology and Fundamental Medicine", Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia
| | - Vladimir P Baklaushev
- Federal Research and Clinical Center of Specialized Medical Care and Medical Technologies FMBA of Russia, Moscow, 115682, Russia
- Pulmonology Research Institute FMBA of Russia, Moscow, 115682, Russia
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991, Russia
| | | | - Galina I Lifshits
- Federal State Public Scientific Institution "Institute of Chemical Biology and Fundamental Medicine", Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia
| | - Nina V Tikunova
- Federal State Public Scientific Institution "Institute of Chemical Biology and Fundamental Medicine", Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia
- Novosibirsk State University, Novosibirsk, 630090, Russia
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17
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Mohammadzadeh Hosseini Moghri SAH, Ranjbar M, Hassannia H, Khakdan F. In silico analysis of the conserved surface-exposed epitopes to design novel multiepitope peptide vaccine for all variants of the SARS-CoV-2. J Biomol Struct Dyn 2023; 41:7603-7615. [PMID: 36124826 DOI: 10.1080/07391102.2022.2123395] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 09/04/2022] [Indexed: 10/14/2022]
Abstract
Recently the prevalence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has become a pervasive threat to generic health. The SARS-CoV-2 spike (S) glycoprotein plays a fundamental role in binds and fusion to the angiotensin-converting enzyme 2 (ACE2). The multi-epitope peptide vaccines would be able to elicit both long-lasting humoral and cellular immune responses, resulting the eliminating SARS-CoV-2 infections as asymptomatic patients are in large numbers. Recently, the omicron variant of the SARS-CoV-2 became a variant of concern that contained just 15-point mutations in the receptor-binding domain of the spike protein. In order to eliminate new evidence on coronavirus variants of concern detected through epidemic intelligence, the conserved epitopes of the receptor-binding domain (RBD) and spike cleavage site is the most probable target for vaccine development to inducing binds and fusion inhibitors neutralizing antibodies respectively. In this study, we utilized bioinformatics tools for identifying and analyzing the spike (S) glycoprotein sequence, e.g. the prediction of the potential linear B-cell epitopes, B-cell multi‑epitope design, secondary and tertiary structures, physicochemical properties, solubility, antigenicity, allergenicity, the molecular docking and molecular dynamics simulation for the promising vaccine candidate against all variant of concern of SARS-CoV-2. Among the epitopes of the RBD region are surface-exposed epitopes SVYAWNRKRISNCV and ATRFASVYAWNRKR as the conserved sequences in all variants of concern can be a good candidate to induce an immune response.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
| | - Mojtaba Ranjbar
- Microbial Biotechnology Department, Faculty of Biotechnology, Amol University of Special Modern Technologies, Amol, Islamic Republic of Iran
| | - Hadi Hassannia
- Immunogenetic Research Center, Faculty of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
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18
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Hua RH, Zhang SJ, Niu B, Ge JY, Lan T, Bu ZG. A Novel Conserved Linear Neutralizing Epitope on the Receptor-Binding Domain of the SARS-CoV-2 Spike Protein. Microbiol Spectr 2023; 11:e0119023. [PMID: 37306579 PMCID: PMC10433833 DOI: 10.1128/spectrum.01190-23] [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: 03/20/2023] [Accepted: 05/23/2023] [Indexed: 06/13/2023] Open
Abstract
The continuous emergence of new variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has made it challenging to develop broad-spectrum prophylactic vaccines and therapeutic antibodies. Here, we have identified a broad-spectrum neutralizing antibody and its highly conserved epitope in the receptor-binding domain (RBD) of the spike protein (S) S1 subunit of SARS-CoV-2. First, nine monoclonal antibodies (MAbs) against the RBD or S1 were generated; of these, one RBD-specific MAb, 22.9-1, was selected for its broad RBD-binding abilities and neutralizing activities against SARS-CoV-2 variants. An epitope of 22.9-1 was fine-mapped with overlapping and truncated peptide fusion proteins. The core sequence of the epitope, 405D(N)EVR(S)QIAPGQ414, was identified on the internal surface of the up-state RBD. The epitope was conserved in nearly all variants of concern of SARS-CoV-2. MAb 22.9-1 and its novel epitope could be beneficial for research on broad-spectrum prophylactic vaccines and therapeutic antibody drugs. IMPORTANCE The continuous emergence of new variants of SARS-CoV-2 has caused great challenge in vaccine design and therapeutic antibody development. In this study, we selected a broad-spectrum neutralizing mouse monoclonal antibody which recognized a conserved linear B-cell epitope located on the internal surface of RBD. This MAb could neutralize all variants until now. The epitope was conserved in all variants. This work provides new insights in developing broad-spectrum prophylactic vaccines and therapeutic antibodies.
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Affiliation(s)
- Rong-Hong Hua
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin, China
| | - Shu-Jian Zhang
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin, China
| | - Bei Niu
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin, China
| | - Jin-Ying Ge
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin, China
| | - Ting Lan
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin, China
| | - Zhi-Gao Bu
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin, China
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19
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Sharma T, Gerstman B, Chapagain P. Distinctive Features of the XBB.1.5 and XBB.1.16 Spike Protein Receptor-Binding Domains and Their Roles in Conformational Changes and Angiotensin-Converting Enzyme 2 Binding. Int J Mol Sci 2023; 24:12586. [PMID: 37628766 PMCID: PMC10454900 DOI: 10.3390/ijms241612586] [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: 07/10/2023] [Revised: 08/03/2023] [Accepted: 08/07/2023] [Indexed: 08/27/2023] Open
Abstract
The emergence and the high transmissibility of the XBB.1.5 and XBB.1.16 subvariants of the SARS-CoV-2 omicron has reignited concerns over the potential impact on vaccine efficacy for these and future variants. We investigated the roles of the XBB.1.5 and XBB.1.16 mutations on the structure of the spike protein's receptor-binding domain (RBD) and its interactions with the host cell receptor ACE2. To bind to ACE2, the RBD must transition from the closed-form to the open-form configuration. We found that the XBB variants have less stable closed-form structures that may make the transition to the open-form easier. We found that the mutations enhance the RBD-ACE2 interactions in XBB.1.16 compared to XBB.1.5. We observed significant structural changes in the loop and motif regions of the RBD, altering well-known antibody-binding sites and potentially rendering primary RBD-specific antibodies ineffective. Our findings elucidate how subtle structural changes and interactions contribute to the subvariants' fitness over their predecessors.
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Affiliation(s)
- Tej Sharma
- Department of Physics, Florida International University, Miami, FL 33199, USA
| | - Bernard Gerstman
- Department of Physics, Florida International University, Miami, FL 33199, USA
- Biomolecular Sciences Institute, Florida International University, Miami, FL 33199, USA
| | - Prem Chapagain
- Department of Physics, Florida International University, Miami, FL 33199, USA
- Biomolecular Sciences Institute, Florida International University, Miami, FL 33199, USA
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20
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Xiao L, Yu W, Shen L, Yan W, Qi J, Hu T. Mucosal SARS-CoV-2 Nanoparticle Vaccine Based on Mucosal Adjuvants and Its Immune Effectiveness by Intranasal Administration. ACS Appl Mater Interfaces 2023. [PMID: 37466148 DOI: 10.1021/acsami.3c05456] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/20/2023]
Abstract
SARS-CoV-2 is a respiratory virus that causes significant threats to human health. Mucosal immunity provides a first-line defense to prevent the infection of SARS-CoV-2 in the respiratory tract. Because most SARS-CoV-2 vaccines could not stimulate mucosal immunity in the respiratory tract, appropriate mucosal adjuvants or delivery systems are needed for mucosal vaccine development. Mannan, polyarginine, and 2',3'-cGAMP are three mucosal adjuvants that could stimulate mucosal immunity. In the present study, the three adjuvants were assembled with a receptor-binding domain (RBD) by electrostatic interaction to generate a nanoparticle vaccine (RBD-MP-cG). RBD-MP-cG elicited mucosal IgA and IgG response in bronchoalveolar lavage and nasal lavage by intranasal administration. It induced a robust RBD-specific antibody response, high levels of protective neutralizing antibody, and ACE2-blocking activity in the mouse sera. It stimulated the splenic secretion of high levels of Th1-, Th2-, and Th17-type cytokines. Thus, RBD-MP-cG elicited strong mucosal immunity and systematic immunity by intranasal administration. RBD-MP-cG was expected to act as a safe, effective, and easily produced mucosal nanoparticle vaccine to combat the infection of SARS-CoV-2.
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Affiliation(s)
- Lucheng Xiao
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, 1 Bei-Er-Jie Street, Haidian District, Beijing 100190, China
- University of Chinese Academy of Sciences, 19 Yuquan Road, Shijingshan District, Beijing 100049, China
| | - Weili Yu
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, 1 Bei-Er-Jie Street, Haidian District, Beijing 100190, China
| | - Lijuan Shen
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, 1 Bei-Er-Jie Street, Haidian District, Beijing 100190, China
| | - Wenying Yan
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, 1 Bei-Er-Jie Street, Haidian District, Beijing 100190, China
- University of Chinese Academy of Sciences, 19 Yuquan Road, Shijingshan District, Beijing 100049, China
| | - Jinming Qi
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, 1 Bei-Er-Jie Street, Haidian District, Beijing 100190, China
| | - Tao Hu
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, 1 Bei-Er-Jie Street, Haidian District, Beijing 100190, China
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21
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Zhao Q, Wang X, Zhang Z, Liu X, Wang P, Cao J, Liang Q, Qu J, Zhou M. Serum neutralization of SARS-CoV-2 Omicron BA.2, BA.2.75, BA.2.76, BA.5, BF.7, BQ.1.1 and XBB.1.5 in individuals receiving Evusheld. J Med Virol 2023; 95:e28932. [PMID: 37403923 DOI: 10.1002/jmv.28932] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2023] [Revised: 06/07/2023] [Accepted: 06/19/2023] [Indexed: 07/06/2023]
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant is undergoing continuous evolution and convergent mutation. These new subvariants are raising concerns that they may evade neutralizing monoclonal antibodies (mAbs). We investigated the serum neutralization efficacy of Evusheld (cilgavimab and tixagevimab) against SARS-CoV-2 Omicron BA.2, BA.2.75, BA.2.76, BA.5, BF.7, BQ.1.1, and XBB.1.5. A total of 90 serum samples from healthy individuals were collected in Shanghai. Anti-RBD antibodies were measured and symptoms of infection with COVID-19 were compared among those individuals. The neutralizing activity of serum against Omicron variants was analyzed by pseudovirus neutralization assays in 22 samples. Evusheld retained neutralizing activity against BA.2, BA.2.75, and BA.5, albeit with somewhat reduced titers. However, the neutralizing activity of Evusheld against BA.2.76, BF.7, BQ.1.1, and XBB.1.5 significantly decreased, with XBB.1.5 showing the greatest escape activity among the subvariants. We also observed that Evusheld recipients displayed elevated antibody levels in their serum, which efficiently neutralized the original variant, and exhibited different characteristics of infection than those who did not receive Evusheld. The mAb has partial neutralization activity against Omicron sublineages. However, the increasing doses of mAb and a larger size of population should be further investigated.
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Affiliation(s)
- Qianqian Zhao
- Department of Pulmonary and Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Institute of Respiratory Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xin Wang
- Center for Immune-Related Diseases at Shanghai Institute of Immunology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Department of Immunology and Microbiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ze Zhang
- Department of Pulmonary and Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Institute of Respiratory Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xuefei Liu
- Department of Pulmonary and Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Institute of Respiratory Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ping Wang
- Department of Pulmonary and Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Institute of Respiratory Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jin Cao
- Department of Pulmonary and Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Institute of Respiratory Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Qiming Liang
- Center for Immune-Related Diseases at Shanghai Institute of Immunology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Department of Immunology and Microbiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jieming Qu
- Department of Pulmonary and Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Institute of Respiratory Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Min Zhou
- Department of Pulmonary and Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Institute of Respiratory Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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22
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Ishimaru H, Nishimura M, Tjan LH, Sutandhio S, Marini MI, Effendi GB, Shigematsu H, Kato K, Hasegawa N, Aoki K, Kurahashi Y, Furukawa K, Shinohara M, Nakamura T, Arii J, Nagano T, Nakamura S, Sano S, Iwata S, Okamura S, Mori Y. Identification and Analysis of Monoclonal Antibodies with Neutralizing Activity against Diverse SARS-CoV-2 Variants. J Virol 2023; 97:e0028623. [PMID: 37191569 PMCID: PMC10308935 DOI: 10.1128/jvi.00286-23] [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: 02/22/2023] [Accepted: 04/11/2023] [Indexed: 05/17/2023] Open
Abstract
We identified neutralizing monoclonal antibodies against severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) variants (including Omicron variants BA.5 and BA.2.75) from individuals who received two doses of mRNA vaccination after they had been infected with the D614G virus. We named them MO1, MO2, and MO3. Among them, MO1 showed particularly high neutralizing activity against authentic variants: D614G, Delta, BA.1, BA.1.1, BA.2, BA.2.75, and BA.5. Furthermore, MO1 suppressed BA.5 infection in hamsters. A structural analysis revealed that MO1 binds to the conserved epitope of seven variants, including Omicron variants BA.5 and BA.2.75, in the receptor-binding domain of the spike protein. MO1 targets an epitope conserved among Omicron variants BA.1, BA.2, and BA.5 in a unique binding mode. Our findings confirm that D614G-derived vaccination can induce neutralizing antibodies that recognize the epitopes conserved among the SARS-CoV-2 variants. IMPORTANCE Omicron variants of SARS-CoV-2 acquired escape ability from host immunity and authorized antibody therapeutics and thereby have been spreading worldwide. We reported that patients infected with an early SARS-CoV-2 variant, D614G, and who received subsequent two-dose mRNA vaccination have high neutralizing antibody titer against Omicron lineages. It was speculated that the patients have neutralizing antibodies broadly effective against SARS-CoV-2 variants by targeting common epitopes. Here, we explored human monoclonal antibodies from B cells of the patients. One of the monoclonal antibodies, named MO1, showed high potency against broad SARS-CoV-2 variants including BA.2.75 and BA.5 variants. The results prove that monoclonal antibodies that have common neutralizing epitopes among several Omicrons were produced in patients infected with D614G and who received mRNA vaccination.
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Affiliation(s)
- Hanako Ishimaru
- Division of Clinical Virology, Center for Infectious Diseases, Kobe University Graduate School of Medicine, Kobe, Hyogo, Japan
| | - Mitsuhiro Nishimura
- Division of Clinical Virology, Center for Infectious Diseases, Kobe University Graduate School of Medicine, Kobe, Hyogo, Japan
| | - Lidya Handayani Tjan
- Division of Clinical Virology, Center for Infectious Diseases, Kobe University Graduate School of Medicine, Kobe, Hyogo, Japan
| | - Silvia Sutandhio
- Division of Clinical Virology, Center for Infectious Diseases, Kobe University Graduate School of Medicine, Kobe, Hyogo, Japan
| | - Maria Istiqomah Marini
- Division of Clinical Virology, Center for Infectious Diseases, Kobe University Graduate School of Medicine, Kobe, Hyogo, Japan
| | - Gema Barlian Effendi
- Division of Clinical Virology, Center for Infectious Diseases, Kobe University Graduate School of Medicine, Kobe, Hyogo, Japan
| | - Hideki Shigematsu
- Structural Biology Division, Japan Synchrotron Radiation Research Institute SPring-8, Hyogo, Japan
| | - Koji Kato
- Structural Biology Division, Japan Synchrotron Radiation Research Institute SPring-8, Hyogo, Japan
| | - Natsumi Hasegawa
- Division of Clinical Virology, Center for Infectious Diseases, Kobe University Graduate School of Medicine, Kobe, Hyogo, Japan
| | - Kaito Aoki
- Division of Clinical Virology, Center for Infectious Diseases, Kobe University Graduate School of Medicine, Kobe, Hyogo, Japan
| | - Yukiya Kurahashi
- Division of Clinical Virology, Center for Infectious Diseases, Kobe University Graduate School of Medicine, Kobe, Hyogo, Japan
| | - Koichi Furukawa
- Division of Clinical Virology, Center for Infectious Diseases, Kobe University Graduate School of Medicine, Kobe, Hyogo, Japan
| | - Mai Shinohara
- Division of Clinical Virology, Center for Infectious Diseases, Kobe University Graduate School of Medicine, Kobe, Hyogo, Japan
| | - Tomoka Nakamura
- Division of Clinical Virology, Center for Infectious Diseases, Kobe University Graduate School of Medicine, Kobe, Hyogo, Japan
| | - Jun Arii
- Division of Clinical Virology, Center for Infectious Diseases, Kobe University Graduate School of Medicine, Kobe, Hyogo, Japan
| | - Tatsuya Nagano
- Division of Respiratory Medicine, Department of Internal Medicine, Kobe University Graduate School of Medicine, Kobe, Hyogo, Japan
| | - Sachiko Nakamura
- Division of General Internal Medicine, Hyogo Prefectural Kakogawa Medical Center, Kakogawa, Hyogo, Japan
| | - Shigeru Sano
- Acute Care Medical Center, Hyogo Prefectural Kakogawa Medical Center, Kakogawa, Hyogo, Japan
| | - Sachiyo Iwata
- Division of Cardiovascular Medicine, Hyogo Prefectural Kakogawa Medical Center, Kakogawa, Hyogo, Japan
| | - Shinya Okamura
- The Research Foundation for Microbial Diseases of Osaka University, Suita, Osaka, Japan
| | - Yasuko Mori
- Division of Clinical Virology, Center for Infectious Diseases, Kobe University Graduate School of Medicine, Kobe, Hyogo, Japan
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23
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Gonzalez-Hernandez M, Kaiser FK, Steffen I, Ciurkiewicz M, van Amerongen G, Tchelet R, Emalfarb M, Saloheimo M, Wiebe MG, Vitikainen M, Albulescu IC, Bosch BJ, Baumgärtner W, Haagmans BL, Osterhaus ADME. Preclinical immunogenicity and protective efficacy of a SARS-CoV-2 RBD-based vaccine produced with the thermophilic filamentous fungal expression system Thermothelomyces heterothallica C1. Front Immunol 2023; 14:1204834. [PMID: 37359531 PMCID: PMC10289020 DOI: 10.3389/fimmu.2023.1204834] [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] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 05/22/2023] [Indexed: 06/28/2023] Open
Abstract
Introduction The emergency use of vaccines has been the most efficient way to control the coronavirus disease 19 (COVID-19) pandemic. However, the emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern has reduced the efficacy of currently used vaccines. The receptor-binding domain (RBD) of the SARS-CoV-2 spike (S) protein is the main target for virus neutralizing (VN) antibodies. Methods A SARS-CoV-2 RBD vaccine candidate was produced in the Thermothelomyces heterothallica (formerly, Myceliophthora thermophila) C1 protein expression system and coupled to a nanoparticle. Immunogenicity and efficacy of this vaccine candidate was tested using the Syrian golden hamster (Mesocricetus auratus) infection model. Results One dose of 10-μg RBD vaccine based on SARS-CoV-2 Wuhan strain, coupled to a nanoparticle in combination with aluminum hydroxide as adjuvant, efficiently induced VN antibodies and reduced viral load and lung damage upon SARS-CoV-2 challenge infection. The VN antibodies neutralized SARS-CoV-2 variants of concern: D614G, Alpha, Beta, Gamma, and Delta. Discussion Our results support the use of the Thermothelomyces heterothallica C1 protein expression system to produce recombinant vaccines against SARS-CoV-2 and other virus infections to help overcome limitations associated with the use of mammalian expression system.
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Affiliation(s)
- Mariana Gonzalez-Hernandez
- Research Center for Emerging Infections and Zoonoses, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
| | - Franziska Karola Kaiser
- Research Center for Emerging Infections and Zoonoses, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
| | - Imke Steffen
- Research Center for Emerging Infections and Zoonoses, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
- Institute for Biochemistry, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
| | - Malgorzata Ciurkiewicz
- Department of Pathology, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
| | | | - Ronen Tchelet
- Dyadic International, Inc., Jupiter, FL, United States
| | - Mark Emalfarb
- Dyadic International, Inc., Jupiter, FL, United States
| | | | | | | | - Irina C. Albulescu
- Virology Section, Infectious Diseases and Immunology Division, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
| | - Berend-Jan Bosch
- Virology Section, Infectious Diseases and Immunology Division, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
| | - Wolfgang Baumgärtner
- Department of Pathology, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
| | - Bart L. Haagmans
- Department of Viroscience, Erasmus Medical Center, Rotterdam, Netherlands
| | - Albert D. M. E. Osterhaus
- Research Center for Emerging Infections and Zoonoses, University of Veterinary Medicine Hannover, Foundation, Hannover, Germany
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24
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Saba-Mayoral A, Rosa C, Sobrino-Mengual G, Armario-Najera V, Christou P, Capell T. Production of the SARS-CoV-2 receptor-binding domain in stably transformed rice plants for developing country applications. Plant Biotechnol J 2023; 21:1094-1096. [PMID: 36740598 DOI: 10.1111/pbi.14023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Revised: 12/20/2022] [Accepted: 01/25/2023] [Indexed: 05/27/2023]
Affiliation(s)
- Andrea Saba-Mayoral
- Applied Plant Biotechnology Group, Department of Plant Production and Forestry Science, University of Lleida-Agrotecnio CERCA Center, Lleida, Spain
| | - Claudia Rosa
- Applied Plant Biotechnology Group, Department of Plant Production and Forestry Science, University of Lleida-Agrotecnio CERCA Center, Lleida, Spain
| | - Guillermo Sobrino-Mengual
- Applied Plant Biotechnology Group, Department of Plant Production and Forestry Science, University of Lleida-Agrotecnio CERCA Center, Lleida, Spain
| | - Victoria Armario-Najera
- Applied Plant Biotechnology Group, Department of Plant Production and Forestry Science, University of Lleida-Agrotecnio CERCA Center, Lleida, Spain
| | - Paul Christou
- Applied Plant Biotechnology Group, Department of Plant Production and Forestry Science, University of Lleida-Agrotecnio CERCA Center, Lleida, Spain
- ICREA, Catalan Institute for Research and Advanced Studies, Barcelona, Spain
| | - Teresa Capell
- Applied Plant Biotechnology Group, Department of Plant Production and Forestry Science, University of Lleida-Agrotecnio CERCA Center, Lleida, Spain
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25
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Volosnikova EA, Merkuleva IA, Esina TI, Shcherbakov DN, Borgoyakova MB, Isaeva AA, Nesmeyanova VS, Volkova NV, Belenkaya SV, Zaykovskaya AV, Pyankov OV, Starostina EV, Zadorozhny AM, Zaitsev BN, Karpenko LI, Ilyichev AA, Danilenko ED. SARS-CoV-2 RBD Conjugated to Polyglucin, Spermidine, and dsRNA Elicits a Strong Immune Response in Mice. Vaccines (Basel) 2023; 11:vaccines11040808. [PMID: 37112720 PMCID: PMC10146165 DOI: 10.3390/vaccines11040808] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Revised: 03/31/2023] [Accepted: 04/04/2023] [Indexed: 04/29/2023] Open
Abstract
Despite the rapid development and approval of several COVID vaccines based on the full-length spike protein, there is a need for safe, potent, and high-volume vaccines. Considering the predominance of the production of neutralizing antibodies targeting the receptor-binding domain (RBD) of S-protein after natural infection or vaccination, it makes sense to choose RBD as a vaccine immunogen. However, due to its small size, RBD exhibits relatively poor immunogenicity. Searching for novel adjuvants for RBD-based vaccine formulations is considered a good strategy for enhancing its immunogenicity. Herein, we assess the immunogenicity of severe acute respiratory syndrome coronavirus 2 RBD conjugated to a polyglucin:spermidine complex (PGS) and dsRNA (RBD-PGS + dsRNA) in a mouse model. BALB/c mice were immunized intramuscularly twice, with a 2-week interval, with 50 µg of RBD, RBD with Al(OH)3, or conjugated RBD. A comparative analysis of serum RBD-specific IgG and neutralizing antibody titers showed that PGS, PGS + dsRNA, and Al(OH)3 enhanced the specific humoral response in animals. There was no significant difference between the groups immunized with RBD-PGS + dsRNA and RBD with Al(OH)3. Additionally, the study of the T-cell response in animals showed that, unlike adjuvants, the RBD-PGS + dsRNA conjugate stimulates the production of specific CD4+ and CD8+ T cells in animals.
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Affiliation(s)
- Ekaterina A Volosnikova
- State Research Center of Virology and Biotechnology VECTOR, Rospotrebnadzor, 630559 Koltsovo, Russia
| | - Iuliia A Merkuleva
- State Research Center of Virology and Biotechnology VECTOR, Rospotrebnadzor, 630559 Koltsovo, Russia
| | - Tatiana I Esina
- State Research Center of Virology and Biotechnology VECTOR, Rospotrebnadzor, 630559 Koltsovo, Russia
| | - Dmitry N Shcherbakov
- State Research Center of Virology and Biotechnology VECTOR, Rospotrebnadzor, 630559 Koltsovo, Russia
| | - Mariya B Borgoyakova
- State Research Center of Virology and Biotechnology VECTOR, Rospotrebnadzor, 630559 Koltsovo, Russia
| | - Anastasiya A Isaeva
- State Research Center of Virology and Biotechnology VECTOR, Rospotrebnadzor, 630559 Koltsovo, Russia
| | - Valentina S Nesmeyanova
- State Research Center of Virology and Biotechnology VECTOR, Rospotrebnadzor, 630559 Koltsovo, Russia
| | - Natalia V Volkova
- State Research Center of Virology and Biotechnology VECTOR, Rospotrebnadzor, 630559 Koltsovo, Russia
| | - Svetlana V Belenkaya
- State Research Center of Virology and Biotechnology VECTOR, Rospotrebnadzor, 630559 Koltsovo, Russia
| | - Anna V Zaykovskaya
- State Research Center of Virology and Biotechnology VECTOR, Rospotrebnadzor, 630559 Koltsovo, Russia
| | - Oleg V Pyankov
- State Research Center of Virology and Biotechnology VECTOR, Rospotrebnadzor, 630559 Koltsovo, Russia
| | - Ekaterina V Starostina
- State Research Center of Virology and Biotechnology VECTOR, Rospotrebnadzor, 630559 Koltsovo, Russia
| | - Alexey M Zadorozhny
- State Research Center of Virology and Biotechnology VECTOR, Rospotrebnadzor, 630559 Koltsovo, Russia
| | - Boris N Zaitsev
- State Research Center of Virology and Biotechnology VECTOR, Rospotrebnadzor, 630559 Koltsovo, Russia
| | - Larisa I Karpenko
- State Research Center of Virology and Biotechnology VECTOR, Rospotrebnadzor, 630559 Koltsovo, Russia
| | - Alexander A Ilyichev
- State Research Center of Virology and Biotechnology VECTOR, Rospotrebnadzor, 630559 Koltsovo, Russia
| | - Elena D Danilenko
- State Research Center of Virology and Biotechnology VECTOR, Rospotrebnadzor, 630559 Koltsovo, Russia
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26
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Mohammadzadeh Hosseini Moghri SAH, Ranjbar M, Hassannia H, Khakdan F. Comparison and monitoring of antibody response in convalescent and healthy vaccinated individuals against RBD and PCS of SARS-CoV-2 spike protein. J Biomol Struct Dyn 2023; 41:14224-14231. [PMID: 36961201 DOI: 10.1080/07391102.2023.2193981] [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: 10/20/2022] [Accepted: 02/06/2023] [Indexed: 03/25/2023]
Abstract
The prevalence of SARS-CoV-2 as a global health threat has called for population-wide vaccination to curb COVID-19. Hence, the World Health Organization (WHO) has approved several platforms of SARS-CoV-2 vaccines for emergency use. Therefore, a more comprehensive study on the immune response induced by vaccines in diverse individuals is still required. Here, we expressed a local variant of SARS-CoV-2 receptor-binding domain (RBD) and protease cleavage site (PCS), playing a vital role in binding and fusion in Rosetta (DE3). We then characterized it through SDS-PAGE analysis and western blotting. Moreover, we compared and monitored ChAdOx1 nCoV-19 vaccination-induced antibody response in convalescent and healthy vaccinated individuals after the first and second vaccine doses through serologic assay against RBD and PCS, which have not yet been compared. We investigated a cohort of 100 sera samples; based on our parameters, 25 serum samples were selected as convalescent samples and 25 serum samples as healthy samples for comparison. These findings demonstrate that most of the convalescent sera show more reactivity with PCS (80%) than with RBD (56%). Interestingly, IgG antibody response against PCS was more significant in both pre- and post-vaccination in convalescent individuals than in healthy individuals. Indeed, anti-RBD antibody titers were most significant in pre-vaccination and post-first vaccination in convalescent individuals than in healthy individuals and not in pre-vaccination and post-second vaccination. Besides monitoring IgG antibody response against COVID-19, these findings could shed light on the progress, assessment, and efficacy evaluation of SARS-CoV-2 vaccines.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
| | - Mojtaba Ranjbar
- Department of Microbial Biotechnology, Faculty of Biotechnology, Amol University of Special Modern Technologies, Amol, Iran
| | - Hadi Hassannia
- Immunogenetic Research Center, Faculty of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
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27
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Shi J, Zhao Y, Peng M, Zhu S, Wu Y, Ji R, Shen C. Screening of Efficient Adjuvants for the RBD-Based Subunit Vaccine of SARS-CoV-2. Vaccines (Basel) 2023; 11:vaccines11040713. [PMID: 37112625 PMCID: PMC10147067 DOI: 10.3390/vaccines11040713] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 03/12/2023] [Accepted: 03/17/2023] [Indexed: 04/29/2023] Open
Abstract
The variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are more transmissible, with a reduced sensitivity to vaccines targeting the original virus strain. Therefore, developing an effective vaccine against both the original SARS-CoV-2 strain and its variants is an urgent need. It is known that the receptor-binding domain (RBD) in the S protein of SARS-CoV-2 is an important vaccine target, but subunit vaccines usually have lower immunogenicity and efficacy. Thus, selecting appropriate adjuvants to enhance the immunogenicity of protein-based subunit vaccine antigens is necessary. Here, an RBD-Fc subunit vaccine of SARS-CoV-2 has been generated, followed by vaccination in B6 mice, and four adjuvant regimens were investigated, including aluminum salts (Alum) + 3-O-desacyl-4'-monophosphoryl lipid A (MPL), AddaVax, QS21 + MPL, and Imiquimod. The adjuvant potency was evaluated by comparing the elicited polyclonal antibodies titers with measuring binding to RBD and S protein in ELISA and Western blot analysis, and also the cross-neutralizing antibodies titers using a pseudovirus infection assay of hACE2-expressing 293T cells, with pseudoviruses expressing the S protein of the SARS-CoV-2 original strain and Delta strain. The presence of QS21 + MPL adjuvant induced stronger polyclonal antibody response and neutralization potency blocking the original strain and Delta strain, as compared with the non-adjuvant RBD-Fc group and other adjuvant groups. Meanwhile, Imiquimod even had a negative effect in inducing specific antibodies and cross-neutralizing antibody production as an adjuvant.
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Affiliation(s)
- Juan Shi
- Department of Microbiology and Immunology, Medical School of Southeast University, Nanjing 210009, China
| | - Yu Zhao
- Department of Microbiology and Immunology, Medical School of Southeast University, Nanjing 210009, China
| | - Min Peng
- Department of Microbiology and Immunology, Medical School of Southeast University, Nanjing 210009, China
| | - Suyue Zhu
- Department of Microbiology and Immunology, Medical School of Southeast University, Nanjing 210009, China
| | - Yandan Wu
- Department of Microbiology and Immunology, Medical School of Southeast University, Nanjing 210009, China
| | - Ruixue Ji
- Department of Microbiology and Immunology, Medical School of Southeast University, Nanjing 210009, China
| | - Chuanlai Shen
- Department of Microbiology and Immunology, Medical School of Southeast University, Nanjing 210009, China
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28
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Pushan SS, Samantaray M, Rajagopalan M, Ramaswamy A. Evolution of Indian Influenza A (H1N1) Hemagglutinin Strains: A Comparative Analysis of the Pandemic Californian HA Strain. Front Mol Biosci 2023; 10:1111869. [PMID: 37006623 PMCID: PMC10061220 DOI: 10.3389/fmolb.2023.1111869] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 02/20/2023] [Indexed: 03/18/2023] Open
Abstract
The need for a vaccine/inhibitor design has become inevitable concerning the emerging epidemic and pandemic viral infections, and the recent outbreak of the influenza A (H1N1) virus is one such example. From 2009 to 2018, India faced severe fatalities due to the outbreak of the influenza A (H1N1) virus. In this study, the potential features of reported Indian H1N1 strains are analyzed in comparison with their evolutionarily closest pandemic strain, A/California/04/2009. The focus is laid on one of its surface proteins, hemagglutinin (HA), which imparts a significant role in attacking the host cell surface and its entry. The extensive analysis performed, in comparison with the A/California/04/2009 strain, revealed significant point mutations in all Indian strains reported from 2009 to 2018. Due to these mutations, all Indian strains disclosed altered features at the sequence and structural levels, which are further presumed to be associated with their functional diversity as well. The mutations observed with the 2018 HA sequence such as S91R, S181T, S200P, I312V, K319T, I419M, and E523D might improve the fitness of the virus in a new host and environment. The higher fitness and decreased sequence similarity of mutated strains may compromise therapeutic efficacy. In particular, the mutations observed commonly, such as serine-to-threonine, alanine-to-threonine, and lysine-to-glutamine at various regions, alter the physico-chemical features of receptor-binding domains, N-glycosylation, and epitope-binding sites when compared with the reference strain. Such mutations render diversity among all Indian strains, and the structural and functional characterization of these strains becomes inevitable. In this study, we observed that mutational drift results in the alteration of the receptor-binding domain, the generation of new variant N-glycosylation along with novel epitope-binding sites, and modifications at the structural level. Eventually, the pressing need to develop potentially distinct next-generation therapeutic inhibitors against the HA strains of the Indian influenza A (H1N1) virus is also highlighted here.
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Affiliation(s)
- Shilpa Sri Pushan
- Department of Bioinformatics, Pondicherry University, Puducherry, India
| | - Mahesh Samantaray
- Department of Bioinformatics, Pondicherry University, Puducherry, India
| | - Muthukumaran Rajagopalan
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology Kanpur, Kanpur, India
| | - Amutha Ramaswamy
- Department of Bioinformatics, Pondicherry University, Puducherry, India
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29
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Yadav MK, Ahmad S, Raza K, Kumar S, Eswaran M, Pasha Km M. Predictive modeling and therapeutic repurposing of natural compounds against the receptor-binding domain of SARS-CoV-2. J Biomol Struct Dyn 2023; 41:1527-1539. [PMID: 34974820 DOI: 10.1080/07391102.2021.2021993] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is a member of the Coronaviridae family, causing major destructions to human life directly and indirectly to the economic crisis around the world. Although there is significant reporting on the whole genome sequences and updated data for the different receptors are widely analyzed and screened to find a proper medication. Only a few bioassay experiments were completed against SARS-CoV-2 spike protein. We collected the compounds dataset from the PubChem Bioassay database having 1786 compounds and split it into the ratio of 80-20% for model training and testing purposes, respectively. Initially, we have created 11 models and validated them using a fivefold validation strategy. The hybrid consensus model shows a predictive accuracy of 95.5% for training and 94% for the test dataset. The model was applied to screen a virtual chemical library of Natural products of 2598 compounds. Our consensus model has successfully identified 75 compounds with an accuracy range of 70-100% as active compounds against SARS-CoV-2 RBD protein. The output of ML data (75 compounds) was taken for the molecular docking and dynamics simulation studies. In the complete analysis, the Epirubicin and Daunorubicin have shown the docking score of -9.937 and -9.812, respectively, and performed well in the molecular dynamics simulation studies. Also, Pirarubicin, an analogue of anthracycline, has widely been used due to its lower cardiotoxicity. It shows the docking score of -9.658, which also performed well during the complete analysis. Hence, after the following comprehensive pipeline-based study, these drugs can be further tested in vivo for further human utilization.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Manoj Kumar Yadav
- Department of Bioinformatics, SRM University, Sonepat, Haryana, India
| | - Shaban Ahmad
- Department of Bioinformatics, SRM University, Sonepat, Haryana, India
| | - Khalid Raza
- Department of Computer Science, Jamia Millia Islamia, New Delhi, India
| | - Sunil Kumar
- ICAR-Indian Agricultural Statistical Research Institute, New Delhi, India
| | - Murugesh Eswaran
- Plant Molecular Biology Division, International Center for Genetic Engineering and Biotechnology, New Delhi, India
| | - Mussuvir Pasha Km
- Department of Studies and Research in chemistry, Vijayanagara Sri Krishnadevaraya University, Ballari, India
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30
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Lim K, Nishide G, Sajidah ES, Yamano T, Qiu Y, Yoshida T, Kobayashi A, Hazawa M, Ando T, Hanayama R, Wong RW. Nanoscopic Assessment of Anti-SARS-CoV-2 Spike Neutralizing Antibody Using High-Speed AFM. Nano Lett 2023; 23:619-628. [PMID: 36641798 PMCID: PMC9881159 DOI: 10.1021/acs.nanolett.2c04270] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 12/20/2022] [Indexed: 06/17/2023]
Abstract
Anti-spike neutralizing antibodies (S NAbs) have been developed for prevention and treatment against COVID-19. The nanoscopic characterization of the dynamic interaction between spike proteins and S NAbs remains difficult. By using high-speed atomic force microscopy (HS-AFM), we elucidate the molecular property of an S NAb and its interaction with spike proteins. The S NAb appeared as monomers with a Y conformation at low density and formed hexameric oligomers at high density. The dynamic S NAb-spike protein interaction at RBD induces neither RBD opening nor S1 subunit shedding. Furthermore, the interaction was stable at endosomal pH. These findings indicated that the S NAb could have a negligible risk of antibody-dependent enhancement. Dynamic movement of spike proteins on small extracellular vesicles (S sEV) resembled that on SARS-CoV-2. The sensitivity of variant S sEVs to S NAb could be evaluated using HS-AFM. Altogether, we demonstrate a nanoscopic assessment platform for evaluating the binding property of S NAbs.
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Affiliation(s)
- Keesiang Lim
- WPI-Nano
Life Science Institute, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan
| | - Goro Nishide
- Division
of Nano Life Science in the Graduate School of Frontier Science Initiative,
WISE Program for Nano-Precision Medicine, Science and Technology, Kanazawa University, Kanazawa, Ishikawa 920-1192, Japan
| | - Elma Sakinatus Sajidah
- Division
of Nano Life Science in the Graduate School of Frontier Science Initiative, Kanazawa University, Kanazawa Ishikawa 920-1192, Japan
| | - Tomoyoshi Yamano
- WPI-Nano
Life Science Institute, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan
- Department
of Immunology, Kanazawa University Graduate
School of Medical Sciences, 13-1 Takara-machi, Kanazawa, Ishikawa 920-8640, Japan
| | - Yujia Qiu
- Division
of Nano Life Science in the Graduate School of Frontier Science Initiative, Kanazawa University, Kanazawa Ishikawa 920-1192, Japan
| | - Takeshi Yoshida
- Department
of Immunology, Kanazawa University Graduate
School of Medical Sciences, 13-1 Takara-machi, Kanazawa, Ishikawa 920-8640, Japan
| | - Akiko Kobayashi
- Cell-Bionomics
Research Unit, Institute for Frontier Science Initiative (INFINITI), Kanazawa University,
Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan
| | - Masaharu Hazawa
- WPI-Nano
Life Science Institute, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan
- Cell-Bionomics
Research Unit, Institute for Frontier Science Initiative (INFINITI), Kanazawa University,
Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan
| | - Toshio Ando
- WPI-Nano
Life Science Institute, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan
| | - Rikinari Hanayama
- WPI-Nano
Life Science Institute, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan
- Department
of Immunology, Kanazawa University Graduate
School of Medical Sciences, 13-1 Takara-machi, Kanazawa, Ishikawa 920-8640, Japan
| | - Richard W. Wong
- WPI-Nano
Life Science Institute, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan
- Cell-Bionomics
Research Unit, Institute for Frontier Science Initiative (INFINITI), Kanazawa University,
Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan
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31
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Lee DB, Kim H, Jeong JH, Jang US, Jang Y, Roh S, Jeon H, Kim EJ, Han SY, Maeng JY, Magez S, Radwanska M, Mun JY, Jun HS, Lee G, Song MS, Lee HR, Chung MS, Baek YH, Kim KH. Mosaic RBD nanoparticles induce intergenus cross-reactive antibodies and protect against SARS-CoV-2 challenge. Proc Natl Acad Sci U S A 2023; 120:e2208425120. [PMID: 36669119 DOI: 10.1073/pnas.2208425120] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [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: 01/22/2023] Open
Abstract
Recurrent spillovers of α- and β-coronaviruses (CoV) such as severe acute respiratory syndrome (SARS)-CoV, Middle East respiratory syndrome-CoV, SARS-CoV-2, and possibly human CoV have caused serious morbidity and mortality worldwide. In this study, six receptor-binding domains (RBDs) derived from α- and β-CoV that are considered to have originated from animals and cross-infected humans were linked to a heterotrimeric scaffold, proliferating cell nuclear antigen (PCNA) subunits, PCNA1, PCNA2, and PCNA3. They assemble to create a stable mosaic multivalent nanoparticle, 6RBD-np, displaying a ring-shaped disk with six protruding antigens, like jewels in a crown. Prime-boost immunizations with 6RBD-np in mice induced significantly high Ab titers against RBD antigens derived from α- and β-CoV and increased interferon (IFN-γ) production, with full protection against the SARS-CoV-2 wild type and Delta challenges. The mosaic 6RBD-np has the potential to induce intergenus cross-reactivity and to be developed as a pan-CoV vaccine against future CoV spillovers.
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Romanenko YO, Silkina MV, Kartseva AS, Marin MA, Shkuratova MA, Makarova MA, Ryabko AK, Konyshkova DA, Zeninskaya NA, Khlyntseva AE, Shemyakin IG, Firstova VV. Characterization of the C6D7-RBD Human Monoclonal Antibody Specific to the SARS-CoV-2 S Protein Receptor-Binding Domain. Acta Naturae 2023; 15:81-86. [PMID: 37153507 PMCID: PMC10154778 DOI: 10.32607/actanaturae.11849] [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] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 02/20/2023] [Indexed: 05/09/2023] Open
Abstract
The new coronavirus infection COVID-19 is an acute viral disease that affects primarily the upper respiratory tract. The etiological agent of COVID-19 is the SARS-CoV-2 RNA virus (Coronaviridae family, Betacoronavirus genus, Sarbecovirus subgenus). We have developed a high-affinity human monoclonal antibody, called C6D7-RBD, which is specific to the S protein receptor-binding domain (RBD) from the SARS-CoV-2 Wuhan-Hu-1 strain and exhibits virus-neutralizing activity in a test with recombinant antigens: angiotensin-converting enzyme 2 (ACE2) and RBD.
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Affiliation(s)
- Ya. O. Romanenko
- Federal Budget Institution of Science State Research Center for Applied Microbiology and Biotechnology, Obolensk, Moscow region, 142279 Russian Federation
| | - M. V. Silkina
- Federal Budget Institution of Science State Research Center for Applied Microbiology and Biotechnology, Obolensk, Moscow region, 142279 Russian Federation
| | - A. S. Kartseva
- Federal Budget Institution of Science State Research Center for Applied Microbiology and Biotechnology, Obolensk, Moscow region, 142279 Russian Federation
| | - M. A. Marin
- Federal Budget Institution of Science State Research Center for Applied Microbiology and Biotechnology, Obolensk, Moscow region, 142279 Russian Federation
| | - M. A. Shkuratova
- Federal Budget Institution of Science State Research Center for Applied Microbiology and Biotechnology, Obolensk, Moscow region, 142279 Russian Federation
| | - M. A. Makarova
- Federal Budget Institution of Science State Research Center for Applied Microbiology and Biotechnology, Obolensk, Moscow region, 142279 Russian Federation
| | - A. K. Ryabko
- Federal Budget Institution of Science State Research Center for Applied Microbiology and Biotechnology, Obolensk, Moscow region, 142279 Russian Federation
| | - D. A. Konyshkova
- Federal Budget Institution of Science State Research Center for Applied Microbiology and Biotechnology, Obolensk, Moscow region, 142279 Russian Federation
| | - N. A. Zeninskaya
- Federal Budget Institution of Science State Research Center for Applied Microbiology and Biotechnology, Obolensk, Moscow region, 142279 Russian Federation
| | - A. E. Khlyntseva
- Federal Budget Institution of Science State Research Center for Applied Microbiology and Biotechnology, Obolensk, Moscow region, 142279 Russian Federation
| | - I. G. Shemyakin
- Federal Budget Institution of Science State Research Center for Applied Microbiology and Biotechnology, Obolensk, Moscow region, 142279 Russian Federation
| | - V. V. Firstova
- Federal Budget Institution of Science State Research Center for Applied Microbiology and Biotechnology, Obolensk, Moscow region, 142279 Russian Federation
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Abstract
INTRODUCTION The Coronavirus Disease 2019 (COVID-19) pandemic has caused devastating human and economic costs. Vaccination is an important step in controlling the pandemic. Severe acute respiratory coronavirus-2 (SARS-CoV-2), the causative agent of COVID-19, infects cells by binding a cellular receptor through the receptor-binding domain (RBD) within the S1 subunit of the spike (S) protein. Viral entry and membrane fusion are mediated by the S2 subunit. AREAS COVERED SARS-CoV-2 S protein, particularly RBD, serves as an important target for vaccines. Here we review the structure and function of SARS-CoV-2 S protein and its RBD, summarize current COVID-19 vaccines targeting the RBD, and outline potential strategies for improving RBD-based vaccines. Overall, this review provides important information that will facilitate rational design and development of safer and more effective COVID-19 vaccines. EXPERT OPINION The S protein of SARS-CoV-2 harbors numerous mutations, mostly in the RBD, resulting in multiple variant strains. Although many COVID-19 vaccines targeting the RBD of original virus strain (and previous variants) can prevent infection of these strains, their ability against recent dominant variants, particularly Omicron and its offspring, is significantly reduced. Collective efforts are needed to develop effective broad-spectrum vaccines to control current and future variants that have pandemic potential.
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Affiliation(s)
- Xiaoqing Guan
- Institute for Biomedical Sciences, Georgia State University, Atlanta, GA, USA
| | - Yang Yang
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, USA
| | - Lanying Du
- Institute for Biomedical Sciences, Georgia State University, Atlanta, GA, USA
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Abstract
Spike (S) glycoproteins mediate the coronavirus entry into the host cell. The S1 subunit of S-proteins contains the receptor-binding domain (RBD) that is able to recognize different host receptors, highlighting its remarkable capacity to adapt to their hosts along the viral evolution. While RBD in spike proteins is determinant for the virus-receptor interaction, the active residues lie at the receptor-binding motif (RBM), a region located in RBD that plays a fundamental role binding the outer surface of their receptors. Here, we address the hypothesis that SARS-CoV and SARS-CoV-2 strains able to use angiotensin-converting enzyme 2 (ACE2) proteins have adapted their RBM along the viral evolution to explore specific conformational topology driven by the residues YGF to infect host cells. We also speculate that this YGF-based mechanism can act as a protein signature located at the RBM to distinguish coronaviruses able to use ACE2 as a cell entry receptor.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Patrícia P. D. Carvalho
- Departamento de Física, FFCLRP, Universidade de São Paulo, Ribeirão Preto, SP, Brazil,CONTACT Patrícia P. D. Carvalho ;
| | - Nelson A. Alves
- Departamento de Física, FFCLRP, Universidade de São Paulo, Ribeirão Preto, SP, Brazil,Nelson Alves
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Gupta D, Kumar M, Sharma P, Mohan T, Prakash A, Kumari R, Kaur P. Effect of Double Mutation (L452R and E484Q) on the Binding Affinity of Monoclonal Antibodies (mAbs) against the RBD-A Target for Vaccine Development. Vaccines (Basel) 2022; 11. [PMID: 36679867 DOI: 10.3390/vaccines11010023] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 12/17/2022] [Accepted: 12/20/2022] [Indexed: 12/24/2022] Open
Abstract
The COVID-19 pandemic, caused by SARS-CoV-2, emerges as a global health problem, as the viral genome is evolving rapidly to form several variants. Advancement and progress in the development of effective vaccines and neutralizing monoclonal antibodies are promising to combat viral infections. In the current scenario, several lineages containing "co-mutations" in the receptor-binding domain (RBD) region of the spike (S) protein are imposing new challenges. Co-occurrence of some co-mutations includes delta (L452R/T478K), kappa (L452R/E484Q), and a common mutation in both beta and gamma variants (E484K/N501Y). The effect of co-mutants (L452R/E484Q) on human angiotensin-converting enzyme 2 (hACE2) binding has already been elucidated. Here, for the first time, we investigated the role of these RBD co-mutations (L452R/E484Q) on the binding affinity of mAbs by adopting molecular dynamics (MD) simulation and free-energy binding estimation. The results obtained from our study suggest that the structural and dynamic changes introduced by these co-mutations reduce the binding affinity of the viral S protein to monoclonal antibodies (mAbs). The structural changes imposed by L452R create a charged patch near the interfacial surface that alters the affinity towards mAbs. In E484Q mutation, polar negatively charged E484 helps in the formation of electrostatic interaction, while the neutrally charged Q residue affects the interaction by forming repulsive forces. MD simulations along with molecular mechanics-generalized Born surface area (MMGBSA) studies revealed that the REGN 10933, BD-368-2, and S2M11 complexes have reduced binding affinity towards the double-mutant RBD. This indicates that their mutant (MT) structures have a stronger ability to escape from most antibodies than the wild type (WT). However, EY6A Ab showed higher affinity towards the double MT-RBD complex as compared to the WT. However, no significant effect of the per-residue contribution of double-mutated residues was observed, as this mAb does not interact with the region harboring L452 and E484 residues.
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36
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Yamamoto Y, Nakano Y, Murae M, Shimizu Y, Sakai S, Ogawa M, Mizukami T, Inoue T, Onodera T, Takahashi Y, Wakita T, Fukasawa M, Miyazaki S, Noguchi K. Direct Inhibition of SARS-CoV-2 Spike Protein by Peracetic Acid. Int J Mol Sci 2022; 24. [PMID: 36613459 DOI: 10.3390/ijms24010020] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 12/16/2022] [Accepted: 12/16/2022] [Indexed: 12/24/2022] Open
Abstract
Peracetic acid (PAA) disinfectants are effective against a wide range of pathogenic microorganisms, including bacteria, fungi, and viruses. Several studies have shown the efficacy of PAA against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2); however, its efficacy in SARS-CoV-2 variants and the molecular mechanism of action of PAA against SARS-CoV-2 have not been investigated. SARS-CoV-2 infection depends on the recognition and binding of the cell receptor angiotensin-converting enzyme 2 (ACE2) via the receptor-binding domain (RBD) of the spike protein. Here, we demonstrated that PAA effectively suppressed pseudotyped virus infection in the Wuhan type and variants, including Delta and Omicron. Similarly, PAA reduced the authentic viral load of SARS-CoV-2. Computational analysis suggested that the hydroxyl radicals produced by PAA cleave the disulfide bridges in the RBD. Additionally, the PAA treatment decreased the abundance of the Wuhan- and variant-type spike proteins. Enzyme-linked immunosorbent assay showed direct inhibition of RBD-ACE2 interactions by PAA. In conclusion, the PAA treatment suppressed SARS-CoV-2 infection, which was dependent on the inhibition of the interaction between the spike RBD and ACE2 by inducing spike protein destabilization. Our findings provide evidence of a potent disinfection strategy against SARS-CoV-2.
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Hu Q, Zhao Y, Shaabani N, Lyu X, Powers C, Sun H, Cruz V, Stegman K, Xu J, Fossier A, Huang Y, Ho G, Kao Y, Wang Z, Wang Z, Hu Y, Zheng Y, Kyaw L, Zuluaga C, Wang H, Pei H, Allen R, Xie H, Ji H, Chen R. Chimeric mRNA-based COVID-19 vaccine induces protective immunity against Omicron and Delta variants. Mol Ther Nucleic Acids 2022; 30:465-476. [PMID: 36345542 PMCID: PMC9628198 DOI: 10.1016/j.omtn.2022.10.021] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 10/31/2022] [Indexed: 11/05/2022]
Abstract
The emerging SARS-CoV-2 variants of concern (VOCs) exhibit enhanced transmission and immune escape, reducing the effectiveness of currently approved mRNA vaccines. To achieve wider coverage of VOCs, we first constructed a cohort of mRNAs harboring a furin cleavage mutation in the spike (S) protein of predominant VOCs, including Alpha (B.1.1.7), Beta (B.1.351), Gamma (P.1), and Delta (B.1.617.2). The mutation abolished the cleavage between the S1 and S2 subunits. Systematic evaluation in vaccinated mice discovered that individual VOC mRNAs elicited strong neutralizing activity in a VOC-specific manner. In particular, the neutralizing antibodies (nAb) produced by immunization with Beta-Furin and Washington (WA)-Furin mRNAs showed potent cross-reactivity with other VOCs. However, neither mRNA elicited strong neutralizing activity against the Omicron variant. Hence, we further developed an Omicron-specific mRNA vaccine that restored protection against the original Omicron variant and some sublineages. Finally, to broaden the protection spectrum of the new Omicron mRNA vaccine, we engineered an mRNA-based chimeric immunogen by introducing the receptor-binding domain of Delta variant into the entire S antigen of Omicron. The resultant chimeric mRNA induced potent and broadly nAbs against Omicron and Delta, which paves the way to developing new vaccine candidates to target emerging variants in the future.
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Affiliation(s)
- Qidong Hu
- Sorrento Therapeutics Inc., 4955 Directors Place, San Diego, CA 92121, USA
| | - Ying Zhao
- Sorrento Therapeutics Inc., 4955 Directors Place, San Diego, CA 92121, USA
| | - Namir Shaabani
- Sorrento Therapeutics Inc., 4955 Directors Place, San Diego, CA 92121, USA
| | - Xiaoxuan Lyu
- Sorrento Therapeutics Inc., 4955 Directors Place, San Diego, CA 92121, USA
| | - Colin Powers
- Sorrento Therapeutics Inc., 4955 Directors Place, San Diego, CA 92121, USA
| | - Haotian Sun
- Sorrento Therapeutics Inc., 4955 Directors Place, San Diego, CA 92121, USA
| | - Vincent Cruz
- Sorrento Therapeutics Inc., 4955 Directors Place, San Diego, CA 92121, USA
| | - Karen Stegman
- Sorrento Therapeutics Inc., 4955 Directors Place, San Diego, CA 92121, USA
| | - Jia Xu
- Sorrento Therapeutics Inc., 4955 Directors Place, San Diego, CA 92121, USA
| | - Amber Fossier
- Sorrento Therapeutics Inc., 4955 Directors Place, San Diego, CA 92121, USA
| | - Yu Huang
- Sorrento Therapeutics Inc., 4955 Directors Place, San Diego, CA 92121, USA
| | - Giang Ho
- Sorrento Therapeutics Inc., 4955 Directors Place, San Diego, CA 92121, USA
| | - Yi Kao
- Sorrento Therapeutics Inc., 4955 Directors Place, San Diego, CA 92121, USA
| | - Zhihao Wang
- Sorrento Therapeutics Inc., 4955 Directors Place, San Diego, CA 92121, USA
| | - Zhenping Wang
- Sorrento Therapeutics Inc., 4955 Directors Place, San Diego, CA 92121, USA
| | - Yue Hu
- Sorrento Therapeutics Inc., 4955 Directors Place, San Diego, CA 92121, USA
| | - Yi Zheng
- Sorrento Therapeutics Inc., 4955 Directors Place, San Diego, CA 92121, USA
| | - Lilian Kyaw
- Sorrento Therapeutics Inc., 4955 Directors Place, San Diego, CA 92121, USA
| | - Cipriano Zuluaga
- Sorrento Therapeutics Inc., 4955 Directors Place, San Diego, CA 92121, USA
| | - Hua Wang
- Sorrento Therapeutics Inc., 4955 Directors Place, San Diego, CA 92121, USA
| | - Hong Pei
- Sorrento Therapeutics Inc., 4955 Directors Place, San Diego, CA 92121, USA
| | - Robert Allen
- Sorrento Therapeutics Inc., 4955 Directors Place, San Diego, CA 92121, USA
| | - Hui Xie
- Sorrento Therapeutics Inc., 4955 Directors Place, San Diego, CA 92121, USA
| | - Henry Ji
- Sorrento Therapeutics Inc., 4955 Directors Place, San Diego, CA 92121, USA
| | - Runqiang Chen
- Sorrento Therapeutics Inc., 4955 Directors Place, San Diego, CA 92121, USA
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38
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Mamchur AA, Stanishneva-Konovalova TB, Mokrushina YA, Abrikosova VA, Guo Y, Zhang H, Terekhov SS, Smirnov IV, Yaroshevich IA. Conformational Dynamics of the Receptor-Binding Domain of the SARS-CoV-2 Spike Protein. Biomedicines 2022; 10. [PMID: 36551988 DOI: 10.3390/biomedicines10123233] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 11/22/2022] [Accepted: 12/06/2022] [Indexed: 12/15/2022] Open
Abstract
Variants of SARS-CoV-2 keep emerging and causing new waves of COVID-19 around the world. Effective new approaches in drug development are based on the binding of agents, such as neutralizing monoclonal antibodies to a receptor-binding domain (RBD) of SARS-CoV-2 spike protein. However, mutations in RBD may lower the affinity of previously developed antibodies. Therefore, rapid analysis of new variants and selection of a binding partner with high affinity is of great therapeutic importance. Here, we explore a computational approach based on molecular dynamics simulations and conformational clusterization techniques for the wild-type and omicron variants of RBD. Biochemical experiments support the hypothesis of the presence of several conformational states within the RBD assembly. The development of such an approach will facilitate the selection of neutralization drugs with higher affinity based on the primary structure of the target antigen.
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39
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Rombel‐Bryzek A, Miller A, Witkowska D. Thermodynamic analysis of the interactions between human ACE2 and spike RBD of Betacoronaviruses (SARS-CoV-1 and SARS-CoV-2). FEBS Open Bio 2022; 13:174-184. [PMID: 36416453 PMCID: PMC9808565 DOI: 10.1002/2211-5463.13525] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 11/11/2022] [Accepted: 11/22/2022] [Indexed: 11/24/2022] Open
Abstract
There are many scientific reports on the interaction of the SARS-CoV-2 virus S protein (and its RBD) with the human ACE2 receptor protein. However, there are no reliable data on how this interaction differs from the interaction of the receptor binding domain of SARS-CoV-1 with ACE2, in terms of binding strength and changes in reaction enthalpy and entropy. Our studies have revealed these differences and the impact of zinc ions on this interaction. Intriguingly, the binding affinity of both RBDs (of SARS-CoV-1 and of SARS-CoV-2) to the ACE2 receptor protein is almost identical; however, there are some differences in the entropic and enthalpic contributions to these interactions.
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40
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Bauer G, Struck F, Staschik E, Maile J, Wochinz‐Richter K, Motz M, Soutschek E. Differential avidity determination of IgG directed towards the receptor-binding domain (RBD) of SARS-CoV-2 wild-type and its variants in one assay: Rational tool for the assessment of protective immunity. J Med Virol 2022; 94:5294-5303. [PMID: 35851961 PMCID: PMC9349558 DOI: 10.1002/jmv.28006] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 07/02/2022] [Accepted: 07/14/2022] [Indexed: 12/15/2022]
Abstract
The avidity (binding strength) of IgG directed towards the receptor-binding domain (RBD) of spike protein has been recognized as a central marker in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) serology. It seems to be linked to increased infection-neutralization potential and therefore might indicate protective immunity. Using a prototype line assay based on the established recomLine SARS-CoV-2 assay, supplemented with RBD of the delta and the omicron variant, differential avidity determination of IgG directed towards RBD of wild-type (WT) SARS-CoV-2 and distinct variants was possible within one assay. Our data confirm that natural SARS-CoV-2 infection or one vaccination step lead to low avidity IgG, whereas further vaccination steps gradually increase avidity to high values. High avidity is not reached by infection alone. After infection with WT SARS-CoV-2 or vaccination based on mRNA WT, the avidity of cross-reacting IgG directed towards RBD of the delta variant only showed marginal differences compared to IgG directed towards RBD WT. In contrast, the avidity of IgG cross-reacting with RBD of the omicron variant was always much lower than for IgG RBD WT, except after the third vaccination step. Therefore, parallel avidity testing of RBD WT and omicron seems to be mandatory for a significant assessment of protective immunity towards SARS-CoV-2.
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Affiliation(s)
- Georg Bauer
- Institute of Virology, Medical CenterUniversity of FreiburgFreiburgGermany,Faculty of MedicineUniversity of FreiburgFreiburgGermany
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41
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Bhadane R, Salo-Ahen OMH. High-Throughput Molecular Dynamics-Based Alchemical Free Energy Calculations for Predicting the Binding Free Energy Change Associated with the Selected Omicron Mutations in the Spike Receptor-Binding Domain of SARS-CoV-2. Biomedicines 2022; 10:2779. [PMID: 36359299 PMCID: PMC9687918 DOI: 10.3390/biomedicines10112779] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 10/17/2022] [Accepted: 10/25/2022] [Indexed: 11/10/2023] Open
Abstract
The ongoing pandemic caused by SARS-CoV-2 has gone through various phases. Since the initial outbreak, the virus has mutated several times, with some lineages showing even stronger infectivity and faster spread than the original virus. Among all the variants, omicron is currently classified as a variant of concern (VOC) by the World Health Organization, as the previously circulating variants have been replaced by it. In this work, we have focused on the mutations observed in omicron sub lineages BA.1, BA.2, BA.4 and BA.5, particularly at the receptor-binding domain (RBD) of the spike protein that is responsible for the interactions with the host ACE2 receptor and binding of antibodies. Studying such mutations is particularly important for understanding the viral infectivity, spread of the disease and for tracking the escape routes of this virus from antibodies. Molecular dynamics (MD) based alchemical free energy calculations have been shown to be very accurate in predicting the free energy change, due to a mutation that could have a deleterious or a stabilizing effect on either the protein itself or its binding affinity to another protein. Here, we investigated the significance of five spike RBD mutations on the stability of the spike protein binding to ACE2 by free energy calculations using high throughput MD simulations. For comparison, we also used conventional MD simulations combined with a Molecular Mechanics-Generalized Born Surface Area (MM-GBSA) based approach, and compared our results with the available experimental data. Overall, the alchemical free energy calculations performed far better than the MM-GBSA approach in predicting the individual impact of the mutations. When considering the experimental variation, the alchemical free energy method was able to produce a relatively accurate prediction for N501Y, the mutant that has previously been reported to increase the binding affinity to hACE2. On the other hand, the other individual mutations seem not to have a significant effect on the spike RBD binding affinity towards hACE2.
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Affiliation(s)
- Rajendra Bhadane
- Structural Bioinformatics Laboratory, Faculty of Science and Engineering, Biochemistry, Åbo Akademi University, FI-20520 Turku, Finland
- Pharmaceutical Sciences Laboratory, Faculty of Science and Engineering, Pharmacy, Åbo Akademi University, FI-20520 Turku, Finland
| | - Outi M. H. Salo-Ahen
- Structural Bioinformatics Laboratory, Faculty of Science and Engineering, Biochemistry, Åbo Akademi University, FI-20520 Turku, Finland
- Pharmaceutical Sciences Laboratory, Faculty of Science and Engineering, Pharmacy, Åbo Akademi University, FI-20520 Turku, Finland
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Ovchynnykova O, Kapusta K, Sizochenko N, Sukhyy KM, Kolodziejczyk W, Hill GA, Saloni J. Homology Modeling and Molecular Dynamics-Driven Search for Natural Inhibitors That Universally Target Receptor-Binding Domain of Spike Glycoprotein in SARS-CoV-2 Variants. Molecules 2022; 27:7336. [PMID: 36364158 PMCID: PMC9657887 DOI: 10.3390/molecules27217336] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 10/16/2022] [Accepted: 10/20/2022] [Indexed: 11/24/2022] Open
Abstract
The rapid spread of SARS-CoV-2 required immediate actions to control the transmission of the virus and minimize its impact on humanity. An extensive mutation rate of this viral genome contributes to the virus' ability to quickly adapt to environmental changes, impacts transmissibility and antigenicity, and may facilitate immune escape. Therefore, it is of great interest for researchers working in vaccine development and drug design to consider the impact of mutations on virus-drug interactions. Here, we propose a multitarget drug discovery pipeline for identifying potential drug candidates which can efficiently inhibit the Receptor Binding Domain (RBD) of spike glycoproteins from different variants of SARS-CoV-2. Eight homology models of RBDs for selected variants were created and validated using reference crystal structures. We then investigated interactions between host receptor ACE2 and RBDs from nine variants of SARS-CoV-2. It led us to conclude that efficient multi-variant targeting drugs should be capable of blocking residues Q(R)493 and N487 in RBDs. Using methods of molecular docking, molecular mechanics, and molecular dynamics, we identified three lead compounds (hesperidin, narirutin, and neohesperidin) suitable for multitarget SARS-CoV-2 inhibition. These compounds are flavanone glycosides found in citrus fruits - an active ingredient of Traditional Chinese Medicines. The developed pipeline can be further used to (1) model mutants for which crystal structures are not yet available and (2) scan a more extensive library of compounds against other mutated viral proteins.
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Affiliation(s)
- Olha Ovchynnykova
- Department of Fuel, Polymer, and Polygraphic Materials Technologies, Ukrainian State University of Chemical Technology, 49005 Dnipro, Ukraine
| | - Karina Kapusta
- Department of Chemistry and Physics, Tougaloo College, Tougaloo, MS 39174, USA
| | - Natalia Sizochenko
- The Ronin Institute for Independent Scholarship, Montclair, NJ 07043, USA
| | - Kostyantyn M. Sukhyy
- Department of Fuel, Polymer, and Polygraphic Materials Technologies, Ukrainian State University of Chemical Technology, 49005 Dnipro, Ukraine
| | - Wojciech Kolodziejczyk
- Interdisciplinary Center for Nanotoxicity, Department of Chemistry, Physics and Atmospheric Sciences, Jackson State University, Jackson, MS 39217, USA
| | - Glake A. Hill
- Interdisciplinary Center for Nanotoxicity, Department of Chemistry, Physics and Atmospheric Sciences, Jackson State University, Jackson, MS 39217, USA
| | - Julia Saloni
- Interdisciplinary Center for Nanotoxicity, Department of Chemistry, Physics and Atmospheric Sciences, Jackson State University, Jackson, MS 39217, USA
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43
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Tian R, Widel M, Imanian B. The Light Chain Domain and Especially the C-Terminus of Receptor-Binding Domain of the Botulinum Neurotoxin (BoNT) Are the Hotspots for Amino Acid Variability and Toxin Type Diversity. Genes (Basel) 2022; 13. [PMID: 36292800 DOI: 10.3390/genes13101915] [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] [Received: 09/26/2022] [Revised: 10/17/2022] [Accepted: 10/18/2022] [Indexed: 01/15/2023] Open
Abstract
Botulinum neurotoxins (BoNT) are the most potent toxins in the world. They are produced by a few dozens of strains within several clostridial species. The toxin that they produce can cause botulism, a flaccid paralysis in humans and other animals. With seven established serologically different types and over 40 subtypes, BoNTs are among the most diverse known toxins. The toxin, its structure, its function and its physiological effects on the neural cell and animal hosts along with its diversity have been the subjects of numerous studies. However, many gaps remain in our knowledge about the BoNT toxin and the species that produce them. One of these gaps involves the distribution and extent of variability along the full length of the gene and the protein as well as its domains and subdomains. In this study, we performed an extensive analysis of all of the available 143 unique BoNT-encoding genes and their products, and we investigated their diversity and evolution. Our results indicate that while the nucleotide variability is almost uniformly distributed along the entire length of the gene, the amino acid variability is not. We found that most of the differences were concentrated along the protein's light chain (LC) domain and especially, the C-terminus of the receptor-binding domain (HCC). These two regions of the protein are thus identified as the main source of the toxin type differentiation, and consequently, this toxin's versatility to bind different receptors and their isoforms and act upon different substrates, thus infecting different hosts.
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Xu Z, Zou Y, Gao X, Niu MM, Li J, Xue L, Jiang S. Dual-targeting cyclic peptides of receptor-binding domain (RBD) and main protease (Mpro) as potential drug leads for the treatment of SARS-CoV-2 infection. Front Pharmacol 2022; 13:1041331. [PMID: 36339564 PMCID: PMC9627161 DOI: 10.3389/fphar.2022.1041331] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Accepted: 10/10/2022] [Indexed: 12/01/2023] Open
Abstract
The receptor-binding domain (RBD) and the main protease (Mpro) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) play a crucial role in the entry and replication of viral particles, and co-targeting both of them could be an attractive approach for the treatment of SARS-CoV-2 infection by setting up a "double lock" in the viral lifecycle. However, few dual RBD/Mpro-targeting agents have been reported. Here, four novel RBD/Mpro dual-targeting peptides, termed as MRs 1-4, were discovered by an integrated virtual screening scheme combining molecular docking-based screening and molecular dynamics simulation. All of them possessed nanomolar binding affinities to both RBD and Mpro ranging from 14.4 to 39.2 nM and 22.5-40.4 nM, respectively. Further pseudovirus infection assay revealed that the four selected peptides showed >50% inhibition against SARS-CoV-2 pseudovirus at a concentration of 5 µM without significant cytotoxicity to host cells. This study leads to the identification of a class of dual RBD/Mpro-targeting agents, which may be developed as potential and effective SARS-CoV-2 therapeutics.
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Affiliation(s)
- Zhen Xu
- Institute of Clinical Medicine, The Affiliated Taizhou People’s Hospital of Nanjing Medical University, Taizhou, China
| | - Yunting Zou
- Department of Pharmaceutical Analysis, China Pharmaceutical University, Nanjing, China
| | - Xi Gao
- Institute of Clinical Medicine, The Affiliated Taizhou People’s Hospital of Nanjing Medical University, Taizhou, China
| | - Miao-Miao Niu
- Department of Pharmaceutical Analysis, China Pharmaceutical University, Nanjing, China
| | - Jindong Li
- Department of Pharmacy, The Affiliated Taizhou People’s Hospital of Nanjing Medical University, Taizhou, China
| | - Lu Xue
- Institute of Clinical Medicine, The Affiliated Taizhou People’s Hospital of Nanjing Medical University, Taizhou, China
| | - Su Jiang
- Institute of Clinical Medicine, The Affiliated Taizhou People’s Hospital of Nanjing Medical University, Taizhou, China
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Khorattanakulchai N, Manopwisedjaroen S, Rattanapisit K, Panapitakkul C, Kemthong T, Suttisan N, Srisutthisamphan K, Malaivijitnond S, Thitithanyanont A, Jongkaewwattana A, Shanmugaraj B, Phoolcharoen W. Receptor binding domain proteins of SARS-CoV-2 variants produced in Nicotiana benthamiana elicit neutralizing antibodies against variants of concern. J Med Virol 2022; 94:4265-4276. [PMID: 35615895 PMCID: PMC9348024 DOI: 10.1002/jmv.27881] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Revised: 05/23/2022] [Accepted: 05/23/2022] [Indexed: 11/15/2022]
Abstract
The constantly emerging severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) variants of concerns (VOCs) with mutations in the receptor-binding domain (RBD) spread rapidly and has become a severe public health problem worldwide. Effective vaccines and optimized booster vaccination strategies are thus highly required. Here, the gene encoding six different RBD (Alpha, Beta, Gamma, Kappa, Delta, and Epsilon variants) along with the Fc fragment of human IgG1 (RBD-Fc) was cloned into plant expression vector and produced in Nicotiana benthamiana by transient expression. Further, the immunogenicity of plant-produced variant RBD-Fc fusion proteins were tested in cynomolgus monkeys. Each group of cynomolgus monkeys was immunized three times intramuscularly with variant RBD-Fc vaccines at Day 0, 21, 42, and neutralizing antibody responses were evaluated against ancestral (Wuhan), Alpha, Beta, Gamma, and Delta variants. The results showed that three doses of the RBD-Fc vaccine significantly enhanced the immune response against all tested SARS-CoV-2 variants. In particular, the vaccines based on Delta and Epsilon mutant RBD elicit broadly neutralizing antibodies against ancestral (Wuhan), Alpha, and Delta SARS-CoV-2 variants whereas Beta and Gamma RBD-Fc vaccines elicit neutralizing antibodies against their respective SARS-CoV-2 strains. The Delta and Epsilon RBD-Fc based vaccines displayed cross-reactive immunogenicity and might be applied as a booster vaccine to induce broadly neutralizing antibodies. These proof-of-concept results will be helpful for the development of plant-derived RBD-Fc-based vaccines against SARS-CoV-2 and its variants.
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Affiliation(s)
- Narach Khorattanakulchai
- Center of Excellence in Plant‐produced PharmaceuticalsChulalongkorn UniversityBangkokThailand
- Department of Pharmacognosy and Pharmaceutical Botany, Faculty of Pharmaceutical SciencesChulalongkorn UniversityBangkokThailand
| | | | | | - Chalisa Panapitakkul
- Center of Excellence in Plant‐produced PharmaceuticalsChulalongkorn UniversityBangkokThailand
- Department of Pharmacognosy and Pharmaceutical Botany, Faculty of Pharmaceutical SciencesChulalongkorn UniversityBangkokThailand
| | - Taratorn Kemthong
- National Primate Research Center of ThailandChulalongkorn UniversitySaraburiThailand
| | - Nutchanat Suttisan
- National Primate Research Center of ThailandChulalongkorn UniversitySaraburiThailand
| | - Kanjana Srisutthisamphan
- Virology and Cell Technology Laboratory, National Center for Genetic Engineering and Biotechnology (BIOTEC)National Science and Technology Development AgencyPathumthaniThailand
| | | | | | - Anan Jongkaewwattana
- Virology and Cell Technology Laboratory, National Center for Genetic Engineering and Biotechnology (BIOTEC)National Science and Technology Development AgencyPathumthaniThailand
| | | | - Waranyoo Phoolcharoen
- Center of Excellence in Plant‐produced PharmaceuticalsChulalongkorn UniversityBangkokThailand
- Department of Pharmacognosy and Pharmaceutical Botany, Faculty of Pharmaceutical SciencesChulalongkorn UniversityBangkokThailand
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Magnus CL, Hiergeist A, Schuster P, Rohrhofer A, Medenbach J, Gessner A, Peterhoff D, Schmidt B. Targeted escape of SARS-CoV-2 in vitro from monoclonal antibody S309, the precursor of sotrovimab. Front Immunol 2022; 13:966236. [PMID: 36090991 PMCID: PMC9449809 DOI: 10.3389/fimmu.2022.966236] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 08/03/2022] [Indexed: 12/01/2022] Open
Abstract
Class 1 and 2 monoclonal antibodies inhibit SARS-CoV-2 entry by blocking the interaction of the viral receptor-binding domain with angiotensin-converting enzyme 2 (ACE2), while class 3 antibodies target a highly conserved epitope outside the ACE2 binding site. We aimed to investigate the plasticity of the spike protein by propagating wild-type SARS-CoV-2 in the presence of class 3 antibody S309. After 12 weeks, we obtained a viral strain that was completely resistant to inhibition by S309, due to successively evolving amino acid exchanges R346S and P337L located in the paratope of S309. The antibody lost affinity to receptor-binding domains carrying P337L or both amino acid exchanges, while ACE2 binding was not affected. The resistant strain replicated efficiently in human CaCo-2 cells and was more susceptible to inhibition of fusion than the original strain. Overall, SARS-CoV-2 escaped inhibition by class 3 antibody S309 through a slow, but targeted evolution enabling immune escape and altering cell entry. This immune-driven enhancement of infectivity and pathogenicity could play an important role in the future evolution of SARS-CoV-2, which is under increasing immunological pressure from vaccination and previous infections.
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Affiliation(s)
- Clara Luzia Magnus
- Institute of Clinical Microbiology and Hygiene, University Hospital Regensburg, Regensburg, Germany
| | - Andreas Hiergeist
- Institute of Clinical Microbiology and Hygiene, University Hospital Regensburg, Regensburg, Germany
| | - Philipp Schuster
- Institute of Medical Microbiology and Hygiene, University of Regensburg, Regensburg, Germany
| | - Anette Rohrhofer
- Institute of Clinical Microbiology and Hygiene, University Hospital Regensburg, Regensburg, Germany
| | - Jan Medenbach
- Biochemistry I, Faculty of Biology and Pre-Clinical Medicine, University of Regensburg, Regensburg, Germany
| | - André Gessner
- Institute of Clinical Microbiology and Hygiene, University Hospital Regensburg, Regensburg, Germany
- Institute of Medical Microbiology and Hygiene, University of Regensburg, Regensburg, Germany
| | - David Peterhoff
- Institute of Clinical Microbiology and Hygiene, University Hospital Regensburg, Regensburg, Germany
- Institute of Medical Microbiology and Hygiene, University of Regensburg, Regensburg, Germany
| | - Barbara Schmidt
- Institute of Clinical Microbiology and Hygiene, University Hospital Regensburg, Regensburg, Germany
- Institute of Medical Microbiology and Hygiene, University of Regensburg, Regensburg, Germany
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Abstract
In 1977, the world witnessed both the eradication of smallpox and the beginning of the modern age of genomics. Over the following half-century, 7 epidemic viruses of international concern galvanized virologists across the globe and led to increasingly extensive virus genome sequencing. These sequencing efforts exerted over periods of rapid adaptation of viruses to new hosts, in particular, humans provide insight into the molecular mechanisms underpinning virus evolution. Investment in virus genome sequencing was dramatically increased by the unprecedented support for phylogenomic analyses during the COVID-19 pandemic. In this review, we attempt to piece together comprehensive molecular histories of the adaptation of variola virus, HIV-1 M, SARS, H1N1-SIV, MERS, Ebola, Zika, and SARS-CoV-2 to the human host. Disruption of genes involved in virus-host interaction in animal hosts, recombination including genome segment reassortment, and adaptive mutations leading to amino acid replacements in virus proteins involved in host receptor binding and membrane fusion are identified as the key factors in the evolution of epidemic viruses.
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Affiliation(s)
- Nash D Rochman
- National Center for Biotechnology InformationNational Library of MedicineBethesdaMDUSA
| | - Yuri I Wolf
- National Center for Biotechnology InformationNational Library of MedicineBethesdaMDUSA
| | - Eugene V Koonin
- National Center for Biotechnology InformationNational Library of MedicineBethesdaMDUSA
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Li Y, Zheng P, Liu T, Shi C, Wang B, Xu Y, Jin T. Structural Requirements and Plasticity of Receptor-Binding Domain in Human Coronavirus Spike. Front Mol Biosci 2022; 9:930931. [PMID: 35903152 PMCID: PMC9315343 DOI: 10.3389/fmolb.2022.930931] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 06/06/2022] [Indexed: 11/22/2022] Open
Abstract
The most recent human coronaviruses including severe acute respiratory syndrome coronavirus-2 causing severe respiratory tract infection and high pathogenicity bring significant global public health concerns. Infections are initiated by recognizing host cell receptors by coronavirus spike protein S1 subunit, and then S2 mediates membrane fusion. However, human coronavirus spikes undergo frequent mutation, which may result in diverse pathogenesis and infectivity. In this review, we summarize some of these recent structural and mutational characteristics of RBD of human coronavirus spike protein and their interaction with specific human cell receptors and analyze the structural requirements and plasticity of RBD. Stability of spike protein, affinity toward receptor, virus fitness, and infectivity are the factors controlling the viral tropisms. Thus, understanding the molecular details of RBDs and their mutations is critical in deciphering virus evolution. Structural information of spike and receptors of human coronaviruses not only reveals the molecular mechanism of host–microbe interaction and pathogenesis but also helps develop effective drug to control these infectious pathogens and cope with the future emerging coronavirus outbreaks.
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Affiliation(s)
- Yajuan Li
- Department of Clinical Laboratory, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Peiyi Zheng
- Laboratory of Structural Immunology, CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Tingting Liu
- Department of Clinical Laboratory, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Cuixiao Shi
- Department of Clinical Laboratory, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Bo Wang
- Department of Clinical Laboratory, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Yuanhong Xu
- Department of Clinical Laboratory, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Tengchuan Jin
- Laboratory of Structural Immunology, CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
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Bolkhovitina EL, Vavilova JD, Bogorodskiy AO, Zagryadskaya YA, Okhrimenko IS, Sapozhnikov AM, Borshchevskiy VI, Shevchenko MA. Short-Term Effect of SARS-CoV-2 Spike Protein Receptor-Binding Domain-Specific Antibody Induction on Neutrophil-Mediated Immune Response in Mice. Int J Mol Sci 2022; 23:8234. [PMID: 35897803 DOI: 10.3390/ijms23158234] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [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] [Received: 06/30/2022] [Revised: 07/23/2022] [Accepted: 07/24/2022] [Indexed: 02/04/2023] Open
Abstract
Vaccination protects against COVID-19 via the spike protein receptor-binding domain (RBD)-specific antibody formation, but it also affects the innate immunity. The effects of specific antibody induction on neutrophils that can cause severe respiratory inflammation are important, though not completely investigated. In the present study, using a mouse model mimicking SARS-CoV-2 virus particle inhalation, we investigated neutrophil phenotype and activity alterations in the presence of RBD-specific antibodies. Mice were immunized with RBD and a week after a strong antibody response establishment received 100 nm particles in the RBD solution. Control mice received injections of a phosphate buffer instead of RBD. We show that the application of 100 nm particles in the RBD solution elevates neutrophil recruitment to the blood and the airways of RBD-immunized mice rather than in control mice. Analysis of bone marrow cells of mice with induced RBD-specific antibodies revealed the increased population of CXCR2+CD101+ neutrophils. These neutrophils did not demonstrate an enhanced ability of neutrophil extracellular traps (NETs) formation compared to the neutrophils from control mice. Thus, the induction of RBD-specific antibodies stimulates the activation of mature neutrophils that react to RBD-coated particles without triggering excessive inflammation.
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Aoki A, Adachi H, Mori Y, Ito M, Sato K, Okuda K, Sakakibara T, Okamoto Y, Jinno H. Discrimination of SARS-CoV-2 Omicron Sublineages BA.1 and BA.2 Using a High-Resolution Melting-Based Assay: a Pilot Study. Microbiol Spectr 2022;:e0136722. [PMID: 35861527 DOI: 10.1128/spectrum.01367-22] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [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: 12/04/2022] Open
Abstract
The Omicron variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has spread worldwide. As of March 2022, Omicron variant BA.2 is rapidly replacing variant BA.1. As variant BA.2 may cause more severe disease than variant BA.1, variant BA.2 requires continuous monitoring. The current study aimed to develop a novel high-resolution melting (HRM) assay for variants BA.1 and BA.2 and to determine the sensitivity and specificity of our method using clinical samples. Here, we focused on the mutational spectra at three regions in the spike receptor-binding domain (RBD; R408, G446/L452, and S477/T478) for the variant-selective HRM analysis. Each variant was identified based on the mutational spectra as follows: no mutations (Alpha variant); L452R and T478K (Delta variant); G446S and S477N/T478K (Omicron variant BA.1); and R408S and S477N/T478K (Omicron variant BA.2). Upon analysis of mutation-coding RNA fragments, the melting curves of the wild-type fragments were distinct from those of the mutant fragments. The sensitivity and specificity of this method were determined as 100% and more than 97.5%, respectively, based on 128 clinical samples (40 Alpha, 40 Delta, 40 Omicron variant BA.1/BA.1.1, and 8 Omicron variant BA.2). These results suggest that this HRM-based assay is a promising screening method for monitoring the transmission of Omicron variants BA.1 and BA.2. IMPORTANCE This study seeks to apply a novel high-resolution melting (HRM) assay to identify and discriminate BA.1 and BA.2 sublineages of the SARS-CoV-2 Omicron variant. Variant BA.2 may cause more severe disease than variant BA.1, meaning that identifying this variant is an important step toward improving the care of patients suffering from COVID-19. However, screening for these variants remains difficult, as current methods mostly rely on next-generation sequencing, which is significantly costlier and more time-consuming than other methods. We believe that our study makes a significant contribution to the literature because we show that this method was 100% sensitive and over 97.5% specific in our confirmation of 128 clinical samples.
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