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Wang R, Han Y, Zhang R, Zhu J, Nan X, Liu Y, Yang Z, Zhou B, Yu J, Lin Z, Li J, Chen P, Wang Y, Li Y, Liu D, Shi X, Wang X, Zhang Q, Yang YR, Li T, Zhang L. Dissecting the intricacies of human antibody responses to SARS-CoV-1 and SARS-CoV-2 infection. Immunity 2023; 56:2635-2649.e6. [PMID: 37924813 DOI: 10.1016/j.immuni.2023.10.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 08/25/2023] [Accepted: 10/11/2023] [Indexed: 11/06/2023]
Abstract
The 2003 severe acute respiratory syndrome coronavirus (SARS-CoV-1) causes more severe disease than SARS-CoV-2, which is responsible for COVID-19. However, our understanding of antibody response to SARS-CoV-1 infection remains incomplete. Herein, we studied the antibody responses in 25 SARS-CoV-1 convalescent patients. Plasma neutralization was higher and lasted longer in SARS-CoV-1 patients than in severe SARS-CoV-2 patients. Among 77 monoclonal antibodies (mAbs) isolated, 60 targeted the receptor-binding domain (RBD) and formed 7 groups (RBD-1 to RBD-7) based on their distinct binding and structural profiles. Notably, RBD-7 antibodies bound to a unique RBD region interfaced with the N-terminal domain of the neighboring protomer (NTD proximal) and were more prevalent in SARS-CoV-1 patients. Broadly neutralizing antibodies for SARS-CoV-1, SARS-CoV-2, and bat and pangolin coronaviruses were also identified. These results provide further insights into the antibody response to SARS-CoV-1 and inform the design of more effective strategies against diverse human and animal coronaviruses.
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Affiliation(s)
- Ruoke Wang
- Comprehensive AIDS Research Center, Center for Global Health and Infectious Diseases Research, NexVac Research Center, Center for Infectious Diseases Research, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Joint Center for Life Sciences, Beijing 100084, China
| | - Yang Han
- Department of Infectious Diseases, Peking Union Medical College Hospital, Beijing 100730, China; State Key Laboratory for Complex, Severe, and Rare Diseases, Peking Union Medical College Hospital, Beijing 100005, China
| | - Rui Zhang
- Comprehensive AIDS Research Center, Center for Global Health and Infectious Diseases Research, NexVac Research Center, Center for Infectious Diseases Research, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Jiayi Zhu
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, National Center for Nanoscience and Technology of China, CAS, Beijing 100190, China
| | - Xuanyu Nan
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, National Center for Nanoscience and Technology of China, CAS, Beijing 100190, China
| | - Yaping Liu
- Comprehensive AIDS Research Center, Center for Global Health and Infectious Diseases Research, NexVac Research Center, Center for Infectious Diseases Research, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Ziqing Yang
- Comprehensive AIDS Research Center, Center for Global Health and Infectious Diseases Research, NexVac Research Center, Center for Infectious Diseases Research, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Bini Zhou
- Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Jinfang Yu
- The Ministry of Education Key Laboratory of Protein Science, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Collaborative Innovation Center for Biotherapy, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Zichun Lin
- The Ministry of Education Key Laboratory of Protein Science, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Collaborative Innovation Center for Biotherapy, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Jinqian Li
- Comprehensive AIDS Research Center, Center for Global Health and Infectious Diseases Research, NexVac Research Center, Center for Infectious Diseases Research, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Peng Chen
- Comprehensive AIDS Research Center, Center for Global Health and Infectious Diseases Research, NexVac Research Center, Center for Infectious Diseases Research, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Yangjunqi Wang
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, National Center for Nanoscience and Technology of China, CAS, Beijing 100190, China
| | - Yujie Li
- Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Dongsheng Liu
- Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Xuanling Shi
- Comprehensive AIDS Research Center, Center for Global Health and Infectious Diseases Research, NexVac Research Center, Center for Infectious Diseases Research, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Xinquan Wang
- The Ministry of Education Key Laboratory of Protein Science, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Collaborative Innovation Center for Biotherapy, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Qi Zhang
- Comprehensive AIDS Research Center, Center for Global Health and Infectious Diseases Research, NexVac Research Center, Center for Infectious Diseases Research, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China
| | - Yuhe R Yang
- CAS Key Laboratory of Nanosystem and Hierarchical Fabrication, National Center for Nanoscience and Technology of China, CAS, Beijing 100190, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Taisheng Li
- Department of Infectious Diseases, Peking Union Medical College Hospital, Beijing 100730, China; State Key Laboratory for Complex, Severe, and Rare Diseases, Peking Union Medical College Hospital, Beijing 100005, China.
| | - Linqi Zhang
- Comprehensive AIDS Research Center, Center for Global Health and Infectious Diseases Research, NexVac Research Center, Center for Infectious Diseases Research, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China; Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China; Institute of Biomedical Health Technology and Engineering, Shenzhen Bay Laboratory, Shenzhen 518132, China.
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Garg N, Kunamneni AS, Garg P, Sharma S, Sharma D, Kunamneni A. Antiviral Drugs and Vaccines for Omicron Variant: A Focused Review. THE CANADIAN JOURNAL OF INFECTIOUS DISEASES & MEDICAL MICROBIOLOGY = JOURNAL CANADIEN DES MALADIES INFECTIEUSES ET DE LA MICROBIOLOGIE MEDICALE 2023; 2023:6695533. [PMID: 37719798 PMCID: PMC10504046 DOI: 10.1155/2023/6695533] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 08/14/2023] [Accepted: 08/31/2023] [Indexed: 09/19/2023]
Abstract
The Omicron variant of concern (VOC) replaced the delta variant rapidly and became the predominant strain due to more mutations in spike protein and receptor-binding domain (RBD) enhancing its infectivity and binding affinity. The severity of the illness is less than that of the delta variant. Omicron is nonsusceptible to REGEN-COV™ and bamlanivimab with etesevimab. Drugs that are effective against the Omicron variant are oral antiviral drugs such as Paxlovid (nirmatrelvir/ritonavir), remdesivir, sotrovimab, and molnupiravir. The potency of sotrovimab is reduced to 3-fold against Omicron, and 8-fold reduction in potency with sotrovimab is found in a particular variant of Omicron with a R346K substitution in spike protein. There are neither clinical trials comparing the efficacy of these 4 therapies with each other nor any data on a combination of two or more therapies. The current recommendation for mild-moderate, nonhospitalized patients who are at a high risk of disease progression is to use Paxlovid as the first-line option. If Paxlovid is not available or cannot be administered due to drug interactions, then the next best choice is sotrovimab. The third choice is remdesivir if sotrovimab is also not available and molnupiravir is to be given if the other three options are not available or cannot be administered. For prevention, 2130 (cilgavimab) in combination with COV2-2196 (tixagevimab) has been effective against BA.2 only. LY-CoV1404 (bebtelovimab) is recently authorized as it is effective against all sublineages of the Omicron variant. Regarding vaccine efficacy (VE), the 3-dose VE with mRNA vaccines at 14-60 days was found to be 71.6%, and after 60 days, it is 47.4%. There is a 34-38-fold reduction of neutralizing activity with prebooster sera and a 19-fold reduction with booster sera for the Omicron variant. This probably explains the reason for worldwide breakthrough infections with the Omicron variant with waning immunity. The neutralizing antibody response against Omicron elicited by the bivalent vaccine is superior to that of the ancestral Wuhan strain, without any safety concerns. For future advances, the ribosome display technology can be applied for the generation of human single-chain fragment variable (scFv) antibodies from B cells of recovered patients against Omicron and other Coronavirus variants as they are easier and faster to produce and have high affinity and high specificity.
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Affiliation(s)
- Nidhi Garg
- Division of Infectious Diseases, Department of Internal Medicine, Mayo Clinic, Jacksonville, Florida, USA
| | | | - Pankaj Garg
- Department of Chemistry, GLA University, Mathura, India
| | - Sandeep Sharma
- Department of Medical Laboratory Science, Lovely Professional University, Phagwara, Punjab 144411, India
| | - Divakar Sharma
- Department of Microbiology, Lady Hardinge Medical College, New Delhi 110001, India
| | - Adinarayana Kunamneni
- Division of Infectious Diseases, Department of Internal Medicine, Mayo Clinic, Jacksonville, Florida, USA
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Lorenzo MM, Marín-López A, Chiem K, Jimenez-Cabello L, Ullah I, Utrilla-Trigo S, Calvo-Pinilla E, Lorenzo G, Moreno S, Ye C, Park JG, Matía A, Brun A, Sánchez-Puig JM, Nogales A, Mothes W, Uchil PD, Kumar P, Ortego J, Fikrig E, Martinez-Sobrido L, Blasco R. Vaccinia Virus Strain MVA Expressing a Prefusion-Stabilized SARS-CoV-2 Spike Glycoprotein Induces Robust Protection and Prevents Brain Infection in Mouse and Hamster Models. Vaccines (Basel) 2023; 11:1006. [PMID: 37243110 PMCID: PMC10220993 DOI: 10.3390/vaccines11051006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 05/11/2023] [Accepted: 05/15/2023] [Indexed: 05/28/2023] Open
Abstract
The COVID-19 pandemic has underscored the importance of swift responses and the necessity of dependable technologies for vaccine development. Our team previously developed a fast cloning system for the modified vaccinia virus Ankara (MVA) vaccine platform. In this study, we reported on the construction and preclinical testing of a recombinant MVA vaccine obtained using this system. We obtained recombinant MVA expressing the unmodified full-length SARS-CoV-2 spike (S) protein containing the D614G amino-acid substitution (MVA-Sdg) and a version expressing a modified S protein containing amino-acid substitutions designed to stabilize the protein a in a pre-fusion conformation (MVA-Spf). S protein expressed by MVA-Sdg was found to be expressed and was correctly processed and transported to the cell surface, where it efficiently produced cell-cell fusion. Version Spf, however, was not proteolytically processed, and despite being transported to the plasma membrane, it failed to induce cell-cell fusion. We assessed both vaccine candidates in prime-boost regimens in the susceptible transgenic K18-human angiotensin-converting enzyme 2 (K18-hACE2) in mice and in golden Syrian hamsters. Robust immunity and protection from disease was induced with either vaccine in both animal models. Remarkably, the MVA-Spf vaccine candidate produced higher levels of antibodies, a stronger T cell response, and a higher degree of protection from challenge. In addition, the level of SARS-CoV-2 in the brain of MVA-Spf inoculated mice was decreased to undetectable levels. Those results add to our current experience and range of vaccine vectors and technologies for developing a safe and effective COVID-19 vaccine.
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Affiliation(s)
- María M. Lorenzo
- Departamento de Biotecnología, INIA CSIC, Carretera La Coruña km 7.5, E-28040 Madrid, Spain; (M.M.L.); (S.M.); (A.M.); (J.M.S.-P.)
| | - Alejandro Marín-López
- Department of Internal Medicine, Yale School of Medicine, New Haven, CT 06519, USA; (A.M.-L.); (I.U.); (E.F.)
| | - Kevin Chiem
- Texas Biomedical Research Institute, San Antonio, TX 78227, USA; (K.C.); (C.Y.); (J.-G.P.); (P.K.)
| | - Luis Jimenez-Cabello
- Centro de Investigación en Sanidad Animal, INIA CSIC, Carretera Valdeolmos a El Casar, Valdeolmos, E-28130 Madrid, Spain; (L.J.-C.); (S.U.-T.); (E.C.-P.); (G.L.); (A.B.); (A.N.); (J.O.)
| | - Irfan Ullah
- Department of Internal Medicine, Yale School of Medicine, New Haven, CT 06519, USA; (A.M.-L.); (I.U.); (E.F.)
| | - Sergio Utrilla-Trigo
- Centro de Investigación en Sanidad Animal, INIA CSIC, Carretera Valdeolmos a El Casar, Valdeolmos, E-28130 Madrid, Spain; (L.J.-C.); (S.U.-T.); (E.C.-P.); (G.L.); (A.B.); (A.N.); (J.O.)
| | - Eva Calvo-Pinilla
- Centro de Investigación en Sanidad Animal, INIA CSIC, Carretera Valdeolmos a El Casar, Valdeolmos, E-28130 Madrid, Spain; (L.J.-C.); (S.U.-T.); (E.C.-P.); (G.L.); (A.B.); (A.N.); (J.O.)
| | - Gema Lorenzo
- Centro de Investigación en Sanidad Animal, INIA CSIC, Carretera Valdeolmos a El Casar, Valdeolmos, E-28130 Madrid, Spain; (L.J.-C.); (S.U.-T.); (E.C.-P.); (G.L.); (A.B.); (A.N.); (J.O.)
| | - Sandra Moreno
- Departamento de Biotecnología, INIA CSIC, Carretera La Coruña km 7.5, E-28040 Madrid, Spain; (M.M.L.); (S.M.); (A.M.); (J.M.S.-P.)
- Centro de Investigación en Sanidad Animal, INIA CSIC, Carretera Valdeolmos a El Casar, Valdeolmos, E-28130 Madrid, Spain; (L.J.-C.); (S.U.-T.); (E.C.-P.); (G.L.); (A.B.); (A.N.); (J.O.)
| | - Chengjin Ye
- Texas Biomedical Research Institute, San Antonio, TX 78227, USA; (K.C.); (C.Y.); (J.-G.P.); (P.K.)
| | - Jun-Gyu Park
- Texas Biomedical Research Institute, San Antonio, TX 78227, USA; (K.C.); (C.Y.); (J.-G.P.); (P.K.)
| | - Alejandro Matía
- Departamento de Biotecnología, INIA CSIC, Carretera La Coruña km 7.5, E-28040 Madrid, Spain; (M.M.L.); (S.M.); (A.M.); (J.M.S.-P.)
| | - Alejandro Brun
- Centro de Investigación en Sanidad Animal, INIA CSIC, Carretera Valdeolmos a El Casar, Valdeolmos, E-28130 Madrid, Spain; (L.J.-C.); (S.U.-T.); (E.C.-P.); (G.L.); (A.B.); (A.N.); (J.O.)
| | - Juana M. Sánchez-Puig
- Departamento de Biotecnología, INIA CSIC, Carretera La Coruña km 7.5, E-28040 Madrid, Spain; (M.M.L.); (S.M.); (A.M.); (J.M.S.-P.)
| | - Aitor Nogales
- Centro de Investigación en Sanidad Animal, INIA CSIC, Carretera Valdeolmos a El Casar, Valdeolmos, E-28130 Madrid, Spain; (L.J.-C.); (S.U.-T.); (E.C.-P.); (G.L.); (A.B.); (A.N.); (J.O.)
| | - Walther Mothes
- Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, CT 06510, USA; (W.M.); (P.D.U.)
| | - Pradeep D. Uchil
- Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, CT 06510, USA; (W.M.); (P.D.U.)
| | - Priti Kumar
- Texas Biomedical Research Institute, San Antonio, TX 78227, USA; (K.C.); (C.Y.); (J.-G.P.); (P.K.)
| | - Javier Ortego
- Centro de Investigación en Sanidad Animal, INIA CSIC, Carretera Valdeolmos a El Casar, Valdeolmos, E-28130 Madrid, Spain; (L.J.-C.); (S.U.-T.); (E.C.-P.); (G.L.); (A.B.); (A.N.); (J.O.)
| | - Erol Fikrig
- Department of Internal Medicine, Yale School of Medicine, New Haven, CT 06519, USA; (A.M.-L.); (I.U.); (E.F.)
| | - Luis Martinez-Sobrido
- Texas Biomedical Research Institute, San Antonio, TX 78227, USA; (K.C.); (C.Y.); (J.-G.P.); (P.K.)
| | - Rafael Blasco
- Departamento de Biotecnología, INIA CSIC, Carretera La Coruña km 7.5, E-28040 Madrid, Spain; (M.M.L.); (S.M.); (A.M.); (J.M.S.-P.)
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4
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Shen J, Fan J, Zhao Y, Jiang D, Niu Z, Zhang Z, Cao G. Innate and adaptive immunity to SARS-CoV-2 and predisposing factors. Front Immunol 2023; 14:1159326. [PMID: 37228604 PMCID: PMC10203583 DOI: 10.3389/fimmu.2023.1159326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Accepted: 04/27/2023] [Indexed: 05/27/2023] Open
Abstract
The coronavirus disease 2019 (COVID-19) pandemic, caused by severe acute respiratory syndrome coronavirus (SARS-CoV-2), has affected all countries worldwide. Although some symptoms are relatively mild, others are still associated with severe and even fatal clinical outcomes. Innate and adaptive immunity are important for the control of SARS-CoV-2 infections, whereas a comprehensive characterization of the innate and adaptive immune response to COVID-19 is still lacking and the mechanisms underlying immune pathogenesis and host predisposing factors are still a matter of scientific debate. Here, the specific functions and kinetics of innate and adaptive immunity involved in SARS-CoV-2 recognition and resultant pathogenesis are discussed, as well as their immune memory for vaccinations, viral-mediated immune evasion, and the current and future immunotherapeutic agents. We also highlight host factors that contribute to infection, which may deepen the understanding of viral pathogenesis and help identify targeted therapies that attenuate severe disease and infection.
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Affiliation(s)
- Jiaying Shen
- Tongji University School of Medicine, Tongji University, Shanghai, China
| | - Junyan Fan
- Department of Epidemiology, Shanghai Key Laboratory of Medical Bioprotection, Key Laboratory of Biological Defense, Ministry of Education, Second Military Medical University, Shanghai, China
| | - Yue Zhao
- Department of Epidemiology, Shanghai Key Laboratory of Medical Bioprotection, Key Laboratory of Biological Defense, Ministry of Education, Second Military Medical University, Shanghai, China
| | - Doming Jiang
- Tongji University School of Medicine, Tongji University, Shanghai, China
| | - Zheyun Niu
- Tongji University School of Medicine, Tongji University, Shanghai, China
| | - Zihan Zhang
- Tongji University School of Medicine, Tongji University, Shanghai, China
| | - Guangwen Cao
- Tongji University School of Medicine, Tongji University, Shanghai, China
- Department of Epidemiology, Shanghai Key Laboratory of Medical Bioprotection, Key Laboratory of Biological Defense, Ministry of Education, Second Military Medical University, Shanghai, China
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Yu K, Liu B, Yu H, Sun C, Wang X, Li G, Dong M, Wang Y, Zhang J, Xu N, Liu W. A neutralizing bispecific single-chain antibody against SARS-CoV-2 Omicron variant produced based on CR3022. Front Cell Infect Microbiol 2023; 13:1155293. [PMID: 37207187 PMCID: PMC10189128 DOI: 10.3389/fcimb.2023.1155293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 04/21/2023] [Indexed: 05/21/2023] Open
Abstract
Introduction The constantly mutating SARS-CoV-2 has been infected an increasing number of people, hence the safe and efficacious treatment are urgently needed to combat the COVID-19 pandemic. Currently, neutralizing antibodies (Nabs), targeting the receptor-binding domain (RBD) of the SARS-CoV-2 spike protein are potentially effective therapeutics against COVID-19. As a new form of antibody, bispecific single chain antibodies (BscAbs) can be easily expressed in E. coli and exhibits broad-spectrum antiviral activity. Methods In this study, we constructed two BscAbs 16-29, 16-3022 and three single chain variable fragments (scFv) S1-16, S2-29 and S3022 as a comparison to explore their antiviral activity against SARS-CoV-2. The affinity of the five antibodies was characterized by ELISA and SPR and the neutralizing activity of them was analyzed using pseudovirus or authentic virus neutralization assay. Bioinformatics and competitive ELISA methods were used to identify different epitopes on RBD. Results Our results revealed the potent neutralizing activity of two BscAbs 16-29 and 16-3022 against SARS-CoV-2 original strain and Omicron variant infection. In addition, we also found that SARS-CoV RBD-targeted scFv S3022 could play a synergistic role with other SARS-CoV-2 RBD-targeted antibodies to enhance neutralizing activity in the form of a BscAb or in cocktail therapies. Discussion This innovative approach offers a promising avenue for the development of subsequent antibody therapies against SARSCoV-2. Combining the advantages of cocktails and single-molecule strategies, BscAb therapy has the potential to be developed as an effective immunotherapeutic for clinical use to mitigate the ongoing pandemic.
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Affiliation(s)
- Kaikai Yu
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Science, Changchun, Jilin, China
| | - Bin Liu
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Haotian Yu
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Science, Changchun, Jilin, China
| | - Chengbiao Sun
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Science, Changchun, Jilin, China
| | - Xuefeng Wang
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Science, Changchun, Jilin, China
| | - Guorui Li
- College of Life Sciences and Food Engineering, Inner Mongolia Minzu University, Tongliao, China
| | - Mingxin Dong
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Science, Changchun, Jilin, China
| | - Yan Wang
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Science, Changchun, Jilin, China
| | - Jianxu Zhang
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Science, Changchun, Jilin, China
| | - Na Xu
- Academic Affairs Office, Jilin Medical University, Jilin, Jilin, China
| | - Wensen Liu
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Science, Changchun, Jilin, China
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6
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Ceja-Gálvez HR, Renteria-Flores FI, Nicoletti F, Hernández-Bello J, Macedo-Ojeda G, Muñoz-Valle JF. Severe COVID-19: Drugs and Clinical Trials. J Clin Med 2023; 12:jcm12082893. [PMID: 37109231 PMCID: PMC10142549 DOI: 10.3390/jcm12082893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 04/08/2023] [Accepted: 04/14/2023] [Indexed: 04/29/2023] Open
Abstract
By January of 2023, the COVID-19 pandemic had led to a reported total of 6,700,883 deaths and 662,631,114 cases worldwide. To date, there have been no effective therapies or standardized treatment schemes for this disease; therefore, the search for effective prophylactic and therapeutic strategies is a primary goal that must be addressed. This review aims to provide an analysis of the most efficient and promising therapies and drugs for the prevention and treatment of severe COVID-19, comparing their degree of success, scope, and limitations, with the aim of providing support to health professionals in choosing the best pharmacological approach. An investigation of the most promising and effective treatments against COVID-19 that are currently available was carried out by employing search terms including "Convalescent plasma therapy in COVID-19" or "Viral polymerase inhibitors" and "COVID-19" in the Clinicaltrials.gov and PubMed databases. From the current perspective and with the information available from the various clinical trials assessing the efficacy of different therapeutic options, we conclude that it is necessary to standardize certain variables-such as the viral clearance time, biomarkers associated with severity, hospital stay, requirement of invasive mechanical ventilation, and mortality rate-in order to facilitate verification of the efficacy of such treatments and to better assess the repeatability of the most effective and promising results.
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Affiliation(s)
- Hazael Ramiro Ceja-Gálvez
- Institute of Research in Biomedical Sciences, University Center of Health Sciences (CUCS), University of Guadalajara, Guadalajara 44340, Jalisco, Mexico
| | - Francisco Israel Renteria-Flores
- Institute of Research in Biomedical Sciences, University Center of Health Sciences (CUCS), University of Guadalajara, Guadalajara 44340, Jalisco, Mexico
| | - Ferdinando Nicoletti
- Department of Biomedical and Biotechnological Sciences, University of Catania, 95123 Catania, Italy
| | - Jorge Hernández-Bello
- Institute of Research in Biomedical Sciences, University Center of Health Sciences (CUCS), University of Guadalajara, Guadalajara 44340, Jalisco, Mexico
| | - Gabriela Macedo-Ojeda
- Institute of Research in Biomedical Sciences, University Center of Health Sciences (CUCS), University of Guadalajara, Guadalajara 44340, Jalisco, Mexico
| | - José Francisco Muñoz-Valle
- Institute of Research in Biomedical Sciences, University Center of Health Sciences (CUCS), University of Guadalajara, Guadalajara 44340, Jalisco, Mexico
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7
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Kim CM, Kim DM, Bang MS, Seo JW, Kim DY, Yun NR, Lim SC, Lee JH, Sohn EJ, Kang H, Min K, Choi BH, Lee S. Efficacy of Plant-Made Human Recombinant ACE2 against COVID-19 in a Golden Syrian Hamster Model. Viruses 2023; 15:v15040964. [PMID: 37112944 PMCID: PMC10146983 DOI: 10.3390/v15040964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 03/31/2023] [Accepted: 04/10/2023] [Indexed: 04/29/2023] Open
Abstract
Coronavirus disease 2019 (COVID-19) is a novel infectious respiratory disease caused by SARS-CoV-2. We evaluated the efficacy of a plant-based human recombinant angiotensin-converting enzyme 2 (hrACE2) and hrACE2-foldon (hrACE2-Fd) protein against COVID-19. In addition, we analyzed the antiviral activity of hrACE2 and hrACE2-Fd against SARS-CoV-2 using real-time reverse-transcription PCR and plaque assays. The therapeutic efficacy was detected using the Golden Syrian hamster model infected with SARS-CoV-2. Both hrACE2 and hrACE2-Fd inhibited SARS-CoV-2 by 50% at concentrations below the maximum plasma concentration, with EC50 of 5.8 μg/mL and 6.2 μg/mL, respectively. The hrACE2 and hrACE2-Fd injection groups showed a tendency for decreased viral titers in nasal turbinate tissues on day 3 after virus inoculation; however, this decrease was not detectable in lung tissues. Histopathological examination on day 9 after virus inoculation showed continued inflammation in the SARS-CoV-2 infection group, whereas decreased inflammation was observed in both the hrACE2 and hrACE2-Fd injection groups. No significant changes were observed at other time points. In conclusion, the potential therapeutic efficacy of plant-based proteins, hrACE2 and hrACE2-Fd, against COVID-19 was confirmed in a SARS-CoV-2-inoculated Golden Syrian hamster model. Further preclinical studies on primates and humans are necessary to obtain additional evidence and determine the effectiveness of these therapies.
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Affiliation(s)
- Choon-Mee Kim
- Premedical Science, Chosun University College of Medicine, Gwangju 61452, Republic of Korea
| | - Dong-Min Kim
- Department of Internal Medicine, Chosun University College of Medicine, Gwangju 61452, Republic of Korea
| | - Mi-Seon Bang
- Department of Internal Medicine, Chosun University College of Medicine, Gwangju 61452, Republic of Korea
| | - Jun-Won Seo
- Department of Internal Medicine, Chosun University College of Medicine, Gwangju 61452, Republic of Korea
| | - Da-Young Kim
- Department of Internal Medicine, Chosun University College of Medicine, Gwangju 61452, Republic of Korea
| | - Na-Ra Yun
- Department of Internal Medicine, Chosun University College of Medicine, Gwangju 61452, Republic of Korea
| | - Sung-Chul Lim
- Department of Pathology, Chosun University College of Medicine, Gwangju 61452, Republic of Korea
| | - Ju-Hyung Lee
- Department of Preventive Medicine, Jeonbuk National University Medical School, Jeonju 54907, Republic of Korea
| | - Eun-Ju Sohn
- BioApplications Inc., Pohang Techno Park Complex, 394 Jigok-ro Nam-gu, Pohang 37668, Republic of Korea
| | - Hyangju Kang
- BioApplications Inc., Pohang Techno Park Complex, 394 Jigok-ro Nam-gu, Pohang 37668, Republic of Korea
| | - Kyungmin Min
- BioApplications Inc., Pohang Techno Park Complex, 394 Jigok-ro Nam-gu, Pohang 37668, Republic of Korea
| | - Bo-Hwa Choi
- BioApplications Inc., Pohang Techno Park Complex, 394 Jigok-ro Nam-gu, Pohang 37668, Republic of Korea
| | - Sangmin Lee
- BioApplications Inc., Pohang Techno Park Complex, 394 Jigok-ro Nam-gu, Pohang 37668, Republic of Korea
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8
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Hernandez NE, Jankowski W, Frick R, Kelow SP, Lubin JH, Simhadri V, Adolf-Bryfogle J, Khare SD, Dunbrack RL, Gray JJ, Sauna ZE. Computational design of nanomolar-binding antibodies specific to multiple SARS-CoV-2 variants by engineering a specificity switch of antibody 80R using RosettaAntibodyDesign (RAbD) results in potential generalizable therapeutic antibodies for novel SARS-CoV-2 virus. Heliyon 2023; 9:e15032. [PMID: 37035348 PMCID: PMC10069166 DOI: 10.1016/j.heliyon.2023.e15032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 03/22/2023] [Accepted: 03/24/2023] [Indexed: 04/05/2023] Open
Abstract
The human infectious disease COVID-19 caused by the SARS-CoV-2 virus has become a major threat to global public health. Developing a vaccine is the preferred prophylactic response to epidemics and pandemics. However, for individuals who have contracted the disease, the rapid design of antibodies that can target the SARS-CoV-2 virus fulfils a critical need. Further, discovering antibodies that bind multiple variants of SARS-CoV-2 can aid in the development of rapid antigen tests (RATs) which are critical for the identification and isolation of individuals currently carrying COVID-19. Here we provide a proof-of-concept study for the computational design of high-affinity antibodies that bind to multiple variants of the SARS-CoV-2 spike protein using RosettaAntibodyDesign (RAbD). Well characterized antibodies that bind with high affinity to the SARS-CoV-1 (but not SARS-CoV-2) spike protein were used as templates and re-designed to bind the SARS-CoV-2 spike protein with high affinity, resulting in a specificity switch. A panel of designed antibodies were experimentally validated. One design bound to a broad range of variants of concern including the Omicron, Delta, Wuhan, and South African spike protein variants.
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Affiliation(s)
- Nancy E. Hernandez
- Hemostasis Branch 1, Division of Hemostasis, Office of Plasma Protein Therapeutics, Office of Therapeutic Products, Center for Biologics Evaluation and Research U.S. FDA, Silver Spring, MD, USA
| | - Wojciech Jankowski
- Hemostasis Branch 1, Division of Hemostasis, Office of Plasma Protein Therapeutics, Office of Therapeutic Products, Center for Biologics Evaluation and Research U.S. FDA, Silver Spring, MD, USA
| | - Rahel Frick
- Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Simon P. Kelow
- Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, PA, USA
- Dept. of Biochemistry and Molecular Biophysics, University of Pennsylvania, Philadelphia, PA, USA
| | - Joseph H. Lubin
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ USA
| | - Vijaya Simhadri
- Hemostasis Branch 1, Division of Hemostasis, Office of Plasma Protein Therapeutics, Office of Therapeutic Products, Center for Biologics Evaluation and Research U.S. FDA, Silver Spring, MD, USA
| | | | - Sagar D. Khare
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ USA
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - Roland L. Dunbrack
- Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Jeffrey J. Gray
- Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA
- Program in Molecular Biophysics, Johns Hopkins University, Baltimore, MD, USA
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, MD, USA
- Institute for Nanobiotechnology, Johns Hopkins University, Baltimore, MD, USA
| | - Zuben E. Sauna
- Hemostasis Branch 1, Division of Hemostasis, Office of Plasma Protein Therapeutics, Office of Therapeutic Products, Center for Biologics Evaluation and Research U.S. FDA, Silver Spring, MD, USA
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9
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Enhancing neutralizing antibodies against receptor binding domain of SARS-CoV-2 by a safe natural adjuvant system. Virus Res 2023; 326:199047. [PMID: 36693449 PMCID: PMC9867563 DOI: 10.1016/j.virusres.2023.199047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 01/09/2023] [Accepted: 01/15/2023] [Indexed: 01/22/2023]
Abstract
The receptor binding domain (RBD) plays a pivotal role in the viral entry as it enables the engagement of severe acute respiratory syndrome 2 (SARS-CoV-2) with the human angiotensin-converting enzyme 2 (ACE2) receptor for host cell entry. RBD is the major target for developing viral inhibitors and vaccines. Expression of recombinant RBD in E.coli is highly scalable with a low-cost procedure despite its high expression level compared to expression in mammalian and yeast cells. Using an alternative natural adjuvant system instead of alum adjuvant, increased immunogenicity of RBD antigen in serological assay including direct ELISA and surrogate Virus Neutralization Test (sVNT) was demonstrated with high levels of IgGs and neutralizing antibodies in mice sera immunized with RBD:AlSa (Alum and Sodium alginate) formulation. The sVNT is a simple and fast test that can be used instead of the conventional virus neutralization test requiring live virus and BSL3 laboratory to detect total neutralizing antibodies against RBD. Additionally, results showed a safety profile for sodium alginate which supported using it as an alternative natural adjuvant.
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10
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He S, Wang J, Chen H, Qian Z, Hu K, Shi B, Wang J. A Competitive Panning Method Reveals an Anti-SARS-CoV-2 Nanobody Specific for an RBD-ACE2 Binding Site. Vaccines (Basel) 2023; 11:vaccines11020371. [PMID: 36851249 PMCID: PMC9964001 DOI: 10.3390/vaccines11020371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 01/18/2023] [Accepted: 01/21/2023] [Indexed: 02/09/2023] Open
Abstract
Most neutralizing antibodies neutralize the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by directly blocking the interactions between the spike glycoprotein receptor-binding domain (RBD) and its receptor, human angiotensin-converting enzyme 2 (ACE2). Here, we report a novel nanobody (Nb) identified by an RBD-ACE2 competitive panning method that could specifically bind to the RBD of SARS-CoV-2 with a high affinity (EC50 = 0.03 nM) and successfully block the binding between the RBD and ACE2 recombinant protein. A structural simulation of the RBD-VHH complex also supports a mechanism of the Nb to block the interaction between the RBD and ACE2. A pseudovirus assay of the Nb showed it could neutralize the WT pseudovirus with high potency (IC50 = 0.026 μg/mL). Furthermore, we measured its binding to phages displaying RBDs of different SARS-CoV-2 variants and found that it could bind to recombinant phages displaying the RBD of beta and delta variants. This study also provides a method of phage library competitive panning, which could be useful for directly screening high-affinity antibodies targeting important functional regions.
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Affiliation(s)
- Siqi He
- School of Life Sciences, Beijing University of Chinese Medicine, Beijing 100029, China
| | - Jiali Wang
- School of Life Sciences, Beijing University of Chinese Medicine, Beijing 100029, China
| | - Hanyi Chen
- School of Life Sciences, Beijing University of Chinese Medicine, Beijing 100029, China
| | - Zhaohui Qian
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Keping Hu
- The Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
- Andes Antibody Technology Hengshui LL Company, Hengshui 053000, China
| | - Bingjie Shi
- School of Life Sciences, Beijing University of Chinese Medicine, Beijing 100029, China
| | - Jianxun Wang
- School of Life Sciences, Beijing University of Chinese Medicine, Beijing 100029, China
- Shenzhen Research Institute, Beijing University of Chinese Medicine, Shenzhen 518118, China
- Correspondence: ; Tel.: +86-10-5291-2186
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11
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Boorla VS, Chowdhury R, Ramasubramanian R, Ameglio B, Frick R, Gray JJ, Maranas CD. De novo design and Rosetta-based assessment of high-affinity antibody variable regions (Fv) against the SARS-CoV-2 spike receptor binding domain (RBD). Proteins 2023; 91:196-208. [PMID: 36111441 PMCID: PMC9538105 DOI: 10.1002/prot.26422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 08/17/2022] [Accepted: 09/06/2022] [Indexed: 01/11/2023]
Abstract
The continued emergence of new SARS-CoV-2 variants has accentuated the growing need for fast and reliable methods for the design of potentially neutralizing antibodies (Abs) to counter immune evasion by the virus. Here, we report on the de novo computational design of high-affinity Ab variable regions (Fv) through the recombination of VDJ genes targeting the most solvent-exposed hACE2-binding residues of the SARS-CoV-2 spike receptor binding domain (RBD) protein using the software tool OptMAVEn-2.0. Subsequently, we carried out computational affinity maturation of the designed variable regions through amino acid substitutions for improved binding with the target epitope. Immunogenicity of designs was restricted by preferring designs that match sequences from a 9-mer library of "human Abs" based on a human string content score. We generated 106 different antibody designs and reported in detail on the top five that trade-off the greatest computational binding affinity for the RBD with human string content scores. We further describe computational evaluation of the top five designs produced by OptMAVEn-2.0 using a Rosetta-based approach. We used Rosetta SnugDock for local docking of the designs to evaluate their potential to bind the spike RBD and performed "forward folding" with DeepAb to assess their potential to fold into the designed structures. Ultimately, our results identified one designed Ab variable region, P1.D1, as a particularly promising candidate for experimental testing. This effort puts forth a computational workflow for the de novo design and evaluation of Abs that can quickly be adapted to target spike epitopes of emerging SARS-CoV-2 variants or other antigenic targets.
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Affiliation(s)
- Veda Sheersh Boorla
- Department of Chemical Engineering, The Pennsylvania State University, University Park. PA 16802
| | - Ratul Chowdhury
- Department of Chemical Engineering, The Pennsylvania State University, University Park. PA 16802
| | | | - Brandon Ameglio
- Program in Molecular Biophysics, Johns Hopkins University, Baltimore, MD, USA
| | - Rahel Frick
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Jeffrey J. Gray
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Costas D. Maranas
- Department of Chemical Engineering, The Pennsylvania State University, University Park. PA 16802,Corresponding author:
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12
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Chang MR, Ke H, Losada Miguéns L, Coherd C, Nguyen K, Kamkaew M, Johnson R, Storm N, Honko A, Zhu Q, Griffiths A, Marasco WA. The variable conversion of neutralizing anti-SARS-CoV-2 single-chain antibodies to IgG provides insight into RBD epitope accessibility. Protein Eng Des Sel 2023; 36:gzad008. [PMID: 37561410 PMCID: PMC10505556 DOI: 10.1093/protein/gzad008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 06/29/2023] [Accepted: 06/30/2023] [Indexed: 08/11/2023] Open
Abstract
Monoclonal antibody (mAb) therapies have rapidly become a powerful class of therapeutics with applications covering a diverse range of clinical indications. Though most widely used for the treatment of cancer, mAbs are also playing an increasing role in the defense of viral infections, most recently with palivizumab for prevention and treatment of severe RSV infections in neonatal and pediatric populations. In addition, during the COVID-19 pandemic, mAbs provided a bridge to the rollout of vaccines; however, their continued role as a therapeutic option for those at greatest risk of severe disease has become limited due to the emergence of neutralization resistant Omicron variants. Although there are many techniques for the identification of mAbs, including single B cell cloning and immunization of genetically engineered mice, the low cost, rapid throughput and technological simplicity of antibody phage display has led to its widespread adoption in mAb discovery efforts. Here we used our 27-billion-member naïve single-chain antibody (scFv) phage library to identify a panel of neutralizing anti-SARS-CoV-2 scFvs targeting diverse epitopes on the receptor binding domain (RBD). Although typically a routine process, we found that upon conversion to IgG, a number of our most potent clones failed to maintain their neutralization potency. Kinetic measurements confirmed similar affinity to the RBD; however, mechanistic studies provide evidence that the loss of neutralization is a result of structural limitations likely arising from initial choice of panning antigen. Thus this work highlights a risk of scFv-phage panning to mAb conversion and the importance of initial antigen selection.
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Affiliation(s)
- Matthew R Chang
- Department of Cancer Immunology & Virology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Hanzhong Ke
- Department of Cancer Immunology & Virology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Laura Losada Miguéns
- Department of Cancer Immunology & Virology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Christian Coherd
- Department of Cancer Immunology & Virology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Katrina Nguyen
- Department of Cancer Immunology & Virology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Maliwan Kamkaew
- Department of Cancer Immunology & Virology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Rebecca Johnson
- Department of Virology, Immunology, and Microbiology and National Emerging Infectious Diseases Laboratories, Boston University School of Medicine, Boston, MA 02118, USA
| | - Nadia Storm
- Department of Virology, Immunology, and Microbiology and National Emerging Infectious Diseases Laboratories, Boston University School of Medicine, Boston, MA 02118, USA
| | - Anna Honko
- Department of Virology, Immunology, and Microbiology and National Emerging Infectious Diseases Laboratories, Boston University School of Medicine, Boston, MA 02118, USA
| | - Quan Zhu
- Department of Cancer Immunology & Virology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Anthony Griffiths
- Department of Virology, Immunology, and Microbiology and National Emerging Infectious Diseases Laboratories, Boston University School of Medicine, Boston, MA 02118, USA
| | - Wayne A Marasco
- Department of Cancer Immunology & Virology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
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13
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Abebe EC, Dejenie TA. Protective roles and protective mechanisms of neutralizing antibodies against SARS-CoV-2 infection and their potential clinical implications. Front Immunol 2023; 14:1055457. [PMID: 36742320 PMCID: PMC9892939 DOI: 10.3389/fimmu.2023.1055457] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 01/03/2023] [Indexed: 01/20/2023] Open
Abstract
Neutralizing antibodies (NAbs) are central players in the humoral immunity that defends the body from SARS-CoV-2 infection by blocking viral entry into host cells and neutralizing their biological effects. Even though NAbs primarily work by neutralizing viral antigens, on some occasions, they may also combat the SARS-CoV-2 virus escaping neutralization by employing several effector mechanisms in collaboration with immune cells like natural killer (NK) cells and phagocytes. Besides their prophylactic and therapeutic roles, antibodies can be used for COVID-19 diagnosis, severity evaluation, and prognosis assessment in clinical practice. Furthermore, the measurement of NAbs could have key implications in determining individual or herd immunity against SARS-CoV-2, vaccine effectiveness, and duration of the humoral protective response, as well as aiding in the selection of suitable individuals who can donate convalescent plasma to treat infected people. Despite all these clinical applications of NAbs, using them in clinical settings can present some challenges. This review discusses the protective functions, possible protective mechanisms against SARS-CoV-2, and potential clinical applications of NAbs in COVID-19. This article also highlights the possible challenges and solutions associated with COVID-19 antibody-based prophylaxis, therapy, and vaccination.
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Affiliation(s)
- Endeshaw Chekol Abebe
- Department of Medical Biochemistry, College of Health Sciences, Debre Tabor University, Debre Tabor, Ethiopia
| | - Tadesse Asmamaw Dejenie
- Department of Medical Biochemistry, College of Medicine and Health Sciences, University of Gondar, Gondar, Ethiopia
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14
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Qin R, An C, Chen W. Physical-Chemical Regulation of Membrane Receptors Dynamics in Viral Invasion and Immune Defense. J Mol Biol 2023; 435:167800. [PMID: 36007627 PMCID: PMC9394170 DOI: 10.1016/j.jmb.2022.167800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 08/13/2022] [Accepted: 08/18/2022] [Indexed: 02/04/2023]
Abstract
Mechanical cues dynamically regulate membrane receptors functions to trigger various physiological and pathological processes from viral invasion to immune defense. These cues mainly include various types of dynamic mechanical forces and the spatial confinement of plasma membrane. However, the molecular mechanisms of how they couple with biochemical cues in regulating membrane receptors functions still remain mysterious. Here, we review recent advances in methodologies of single-molecule biomechanical techniques and in novel biomechanical regulatory mechanisms of critical ligand recognition of viral and immune receptors including SARS-CoV-2 spike protein, T cell receptor (TCR) and other co-stimulatory immune receptors. Furthermore, we provide our perspectives of the general principle of how force-dependent kinetics determine the dynamic functions of membrane receptors and of biomechanical-mechanism-driven SARS-CoV-2 neutralizing antibody design and TCR engineering for T-cell-based therapies.
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Affiliation(s)
- Rui Qin
- Department of Cell Biology and Department of Cardiology of the Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Chenyi An
- Department of Cell Biology and Department of Cardiology of the Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou 310058, China; School of Biology and Engineering, Guizhou Medical University, Guiyang, China
| | - Wei Chen
- Department of Cell Biology and Department of Cardiology of the Second Affiliated Hospital, Zhejiang University School of Medicine, Zhejiang University, Hangzhou 310058, China; Liangzhu Laboratory, Zhejiang University Medical Center, 1369 West Wenyi Road, Hangzhou 311121, China; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the MOE Frontier Science Center for Brain Science & Brain-Machine Integration, State Key Laboratory for Modern Optical Instrumentation Key Laboratory for Biomedical Engineering of the Ministry of Education, College of Biomedical Engineering and Instrument Science, Zhejiang University, Hangzhou 310058, Zhejiang, China.
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15
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Lioznov D, Amosova I, Sheetikov SA, Zornikova KV, Serdyuk Y, Efimov GA, Tsyferov M, Khmelevskii M, Afanasiev A, Khomyakova N, Zubkov D, Tikhonov A, Zhu T, Barreto L, Dzutseva V. Immunogenicity and safety of a recombinant adenovirus type-5 COVID-19 vaccine in adults: Data from a randomised, double-blind, placebo-controlled, single-dose, phase 3 trial in Russia. PLoS One 2023; 18:e0278878. [PMID: 36888640 PMCID: PMC9994755 DOI: 10.1371/journal.pone.0278878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 10/28/2022] [Indexed: 03/09/2023] Open
Abstract
BACKGROUND To determine the immunogenicity, efficacy, reactogenicity, and safety of a single dose of recombinant adenovirus type-5 vectored COVID-19 vaccine (Ad5-nCoV, 5 × 1010 viral particles per 0.5 mL dose), we conducted a single-dose, randomised, double-blind, placebo-controlled, parallel group (3:1 Ad5-nCoV:placebo), phase 3 trial (Prometheus). METHODS From 11-September-2020 to 05-May-2021, across six sites in the Russian Federation, 496 participants were injected with either placebo or Ad5-nCoV expressing the full-length spike (S) protein from the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). RESULTS Seroconversion (the primary endpoint) rates of 78.5% (95% CI: 73.9; 82.6) against receptor binding domain (RBD), 90.6% (95% CI: 87.2; 93.4) against S protein and 59.0% (95% CI: 53.3; 64.6) seroconversion of neutralising antibodies against SARS-CoV-2 at 28 days post-vaccination were observed. Geometric mean titres (GMTs) were also elevated for antibodies against the RBD (405 [95% CI: 366; 449]) and S protein (677 [95% CI: 608; 753]) compared to the GMT of neutralising antibodies against SARS-CoV-2 (16.7 [95% CI: 15.3; 18.3]). Using an IFN-γ ELISpot assay after stimulating the cells with recombinant S protein ectodomain we showed that the Ad5-nCoV vaccine induced the most robust cellular immune response on Days 14 and 28. Up to Day 28, the primary and all secondary endpoints of the Ad5-nCoV vaccine were statistically significant compared with the placebo (р<0.001). Systemic reactions were reported in 113 of 496 (22.8%) participants (Ad5-nCoV, 26.9%; Placebo, 10.5%), and local reactions were reported in 108 (21.8%) participants (Ad5-nCoV, 28.5%; Placebo, 1.6%). These were generally mild and resolved within 7 days after vaccination. Of the six serious adverse events reported, none of the events were vaccine related. There were no deaths or premature withdrawals. CONCLUSION A single-dose of Ad5-nCoV vaccine induced a marked specific humoral and cellular immune response with a favourable safety profile. TRIAL REGISTRATION Trial registration: ClinicalTrials.gov: NCT04540419.
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Affiliation(s)
- Dmitry Lioznov
- Smorodintsev Research Institute of Influenza, St Petersburg, Russia
- Department of Infectious Diseases and Epidemiology, First Pavlov State Medical University, St. Petersburg, Russia
| | - Irina Amosova
- Smorodintsev Research Institute of Influenza, St Petersburg, Russia
| | | | | | - Yana Serdyuk
- National Research Center for Hematology, Moscow, Russia
| | | | | | | | | | | | | | | | - Tao Zhu
- CanSino Biologics Inc., Tianjin, China
| | | | - Vitalina Dzutseva
- NPO Petrovax Pharm LLC, Moscow, Russia
- Novosibirsk State University, Medical School, Novosibirsk, Russia
- * E-mail:
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16
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Jamal QMS. Antiviral Potential of Plants against COVID-19 during Outbreaks-An Update. Int J Mol Sci 2022; 23:13564. [PMID: 36362351 PMCID: PMC9655040 DOI: 10.3390/ijms232113564] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 10/06/2022] [Accepted: 11/02/2022] [Indexed: 12/01/2023] Open
Abstract
Several human diseases are caused by viruses, including cancer, Type I diabetes, Alzheimer's disease, and hepatocellular carcinoma. In the past, people have suffered greatly from viral diseases such as polio, mumps, measles, dengue fever, SARS, MERS, AIDS, chikungunya fever, encephalitis, and influenza. Recently, COVID-19 has become a pandemic in most parts of the world. Although vaccines are available to fight the infection, their safety and clinical trial data are still questionable. Social distancing, isolation, the use of sanitizer, and personal productive strategies have been implemented to prevent the spread of the virus. Moreover, the search for a potential therapeutic molecule is ongoing. Based on experiences with outbreaks of SARS and MERS, many research studies reveal the potential of medicinal herbs/plants or chemical compounds extracted from them to counteract the effects of these viral diseases. COVID-19's current status includes a decrease in infection rates as a result of large-scale vaccination program implementation by several countries. But it is still very close and needs to boost people's natural immunity in a cost-effective way through phytomedicines because many underdeveloped countries do not have their own vaccination facilities. In this article, phytomedicines as plant parts or plant-derived metabolites that can affect the entry of a virus or its infectiousness inside hosts are described. Finally, it is concluded that the therapeutic potential of medicinal plants must be analyzed and evaluated entirely in the control of COVID-19 in cases of uncontrollable SARS infection.
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Affiliation(s)
- Qazi Mohammad Sajid Jamal
- Department of Health Informatics, College of Public Health and Health Informatics, Qassim University, Al Bukayriyah 52741, Saudi Arabia
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17
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Plant Molecular Pharming and Plant-Derived Compounds towards Generation of Vaccines and Therapeutics against Coronaviruses. Vaccines (Basel) 2022; 10:vaccines10111805. [DOI: 10.3390/vaccines10111805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 10/14/2022] [Accepted: 10/19/2022] [Indexed: 11/17/2022] Open
Abstract
The current century has witnessed infections of pandemic proportions caused by Coronaviruses (CoV) including severe acute respiratory syndrome-related CoV (SARS-CoV), Middle East respiratory syndrome-related CoV (MERS-CoV) and the recently identified SARS-CoV2. Significantly, the SARS-CoV2 outbreak, declared a pandemic in early 2020, has wreaked devastation and imposed intense pressure on medical establishments world-wide in a short time period by spreading at a rapid pace, resulting in high morbidity and mortality. Therefore, there is a compelling need to combat and contain the CoV infections. The current review addresses the unique features of the molecular virology of major Coronaviruses that may be tractable towards antiviral targeting and design of novel preventative and therapeutic intervention strategies. Plant-derived vaccines, in particular oral vaccines, afford safer, effectual and low-cost avenues to develop antivirals and fast response vaccines, requiring minimal infrastructure and trained personnel for vaccine administration in developing countries. This review article discusses recent developments in the generation of plant-based vaccines, therapeutic/drug molecules, monoclonal antibodies and phytochemicals to preclude and combat infections caused by SARS-CoV, MERS-CoV and SARS-CoV-2 viruses. Efficacious plant-derived antivirals could contribute significantly to combating emerging and re-emerging pathogenic CoV infections and help stem the tide of any future pandemics.
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18
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Chang MR, Tomasovic L, Kuzmina NA, Ronk AJ, Byrne PO, Johnson R, Storm N, Olmedillas E, Hou YJ, Schäfer A, Leist SR, Tse LV, Ke H, Coherd C, Nguyen K, Kamkaew M, Honko A, Zhu Q, Alter G, Saphire EO, McLellan JS, Griffiths A, Baric RS, Bukreyev A, Marasco WA. IgG-like bispecific antibodies with potent and synergistic neutralization against circulating SARS-CoV-2 variants of concern. Nat Commun 2022; 13:5814. [PMID: 36192374 PMCID: PMC9528872 DOI: 10.1038/s41467-022-33030-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Accepted: 08/26/2022] [Indexed: 11/25/2022] Open
Abstract
Monoclonal antibodies are a promising approach to treat COVID-19, however the emergence of SARS-CoV-2 variants has challenged the efficacy and future of these therapies. Antibody cocktails are being employed to mitigate these challenges, but neutralization escape remains a major challenge and alternative strategies are needed. Here we present two anti-SARS-CoV-2 spike binding antibodies, one Class 1 and one Class 4, selected from our non-immune human single-chain variable fragment (scFv) phage library, that are engineered into four, fully-human IgG-like bispecific antibodies (BsAb). Prophylaxis of hACE2 mice and post-infection treatment of golden hamsters demonstrates the efficacy of the monospecific antibodies against the original Wuhan strain, while promising in vitro results with the BsAbs demonstrate enhanced binding and distinct synergistic effects on neutralizing activity against circulating variants of concern. In particular, one BsAb engineered in a tandem scFv-Fc configuration shows synergistic neutralization activity against several variants of concern including B.1.617.2. This work provides evidence that synergistic neutralization can be achieved using a BsAb scaffold, and serves as a foundation for the future development of broadly reactive BsAbs against emerging variants of concern. COVID-19 can be treated with monoclonal antibodies against SARS-CoV-2, but emerging new variants might show resistance towards existing therapy. Here authors show that anti-SARS-CoV-2 spike human single-chain antibody fragments could gain neutralizing activity against variants of concern upon engineering into a human bispecific antibody.
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Affiliation(s)
- Matthew R Chang
- Department of Cancer Immunology & Virology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Luke Tomasovic
- Department of Cancer Immunology & Virology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Natalia A Kuzmina
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, 77555, USA.,Galveston National Laboratory, Galveston, TX, 77555, USA.,Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - Adam J Ronk
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, 77555, USA.,Galveston National Laboratory, Galveston, TX, 77555, USA.,Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - Patrick O Byrne
- Department of Molecular Biosciences, University of Texas, Austin, TX, 78712, USA
| | - Rebecca Johnson
- Department of Microbiology and National Emerging Infectious Diseases Laboratories, Boston University, School of Medicine, Boston, MA, 02118, USA
| | - Nadia Storm
- Department of Microbiology and National Emerging Infectious Diseases Laboratories, Boston University, School of Medicine, Boston, MA, 02118, USA
| | | | - Yixuan J Hou
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Alexandra Schäfer
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Sarah R Leist
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Longping V Tse
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Hanzhong Ke
- Department of Cancer Immunology & Virology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.,Department of Medicine, Harvard Medical School, Boston, MA, 02115, USA
| | - Christian Coherd
- Department of Cancer Immunology & Virology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Katrina Nguyen
- Department of Cancer Immunology & Virology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Maliwan Kamkaew
- Department of Cancer Immunology & Virology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Anna Honko
- Department of Microbiology and National Emerging Infectious Diseases Laboratories, Boston University, School of Medicine, Boston, MA, 02118, USA
| | - Quan Zhu
- Department of Cancer Immunology & Virology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.,Department of Medicine, Harvard Medical School, Boston, MA, 02115, USA
| | - Galit Alter
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, 02139, USA
| | | | - Jason S McLellan
- Department of Molecular Biosciences, University of Texas, Austin, TX, 78712, USA
| | - Anthony Griffiths
- Department of Microbiology and National Emerging Infectious Diseases Laboratories, Boston University, School of Medicine, Boston, MA, 02118, USA
| | - Ralph S Baric
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Alexander Bukreyev
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, 77555, USA.,Galveston National Laboratory, Galveston, TX, 77555, USA.,Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - Wayne A Marasco
- Department of Cancer Immunology & Virology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA. .,Department of Medicine, Harvard Medical School, Boston, MA, 02115, USA.
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19
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Dickey TH, Tang WK, Butler B, Ouahes T, Orr-Gonzalez S, Salinas ND, Lambert LE, Tolia NH. Design of the SARS-CoV-2 RBD vaccine antigen improves neutralizing antibody response. SCIENCE ADVANCES 2022; 8:eabq8276. [PMID: 36103542 PMCID: PMC9473567 DOI: 10.1126/sciadv.abq8276] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 07/27/2022] [Indexed: 06/01/2023]
Abstract
The receptor binding domain (RBD) of the SARS-CoV-2 spike protein is the primary target of neutralizing antibodies and is a component of almost all current vaccines. Here, RBD immunogens were created with stabilizing amino acid changes that improve the neutralizing antibody response, as well as characteristics for production, storage, and distribution. A computational design and in vitro screening platform identified three improved immunogens, each with approximately nine amino acid changes relative to the native RBD sequence, and four key changes conserved between immunogens. The changes are adaptable to all vaccine platforms and compatible with mutations in emerging variants of concern. The immunogens elicit higher levels of neutralizing antibodies than native RBD, focus the immune response to structured neutralizing epitopes, and have increased production yields and thermostability. Incorporating these variant-independent amino acid changes in next-generation COVID vaccines may enhance the neutralizing antibody response and lead to longer duration and broader protection.
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Affiliation(s)
- Thayne H. Dickey
- Laboratory of Malaria Immunology and Vaccinology, National Institute of Allergy and Infectious Diseases, National Institutes of Health (NIH), Bethesda, MD, USA
| | - Wai Kwan Tang
- Laboratory of Malaria Immunology and Vaccinology, National Institute of Allergy and Infectious Diseases, National Institutes of Health (NIH), Bethesda, MD, USA
| | - Brandi Butler
- Laboratory of Malaria Immunology and Vaccinology, National Institute of Allergy and Infectious Diseases, National Institutes of Health (NIH), Bethesda, MD, USA
| | - Tarik Ouahes
- Laboratory of Malaria Immunology and Vaccinology, National Institute of Allergy and Infectious Diseases, National Institutes of Health (NIH), Bethesda, MD, USA
| | - Sachy Orr-Gonzalez
- Laboratory of Malaria Immunology and Vaccinology, National Institute of Allergy and Infectious Diseases, National Institutes of Health (NIH), Bethesda, MD, USA
| | - Nichole D. Salinas
- Laboratory of Malaria Immunology and Vaccinology, National Institute of Allergy and Infectious Diseases, National Institutes of Health (NIH), Bethesda, MD, USA
| | - Lynn E. Lambert
- Laboratory of Malaria Immunology and Vaccinology, National Institute of Allergy and Infectious Diseases, National Institutes of Health (NIH), Bethesda, MD, USA
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20
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Rodríguez Y, Cardoze SM, Obineche OW, Melo C, Persaud A, Fernández Romero JA. Small Molecules Targeting SARS-CoV-2 Spike Glycoprotein Receptor-Binding Domain. ACS OMEGA 2022; 7:28779-28789. [PMID: 35991504 PMCID: PMC9380817 DOI: 10.1021/acsomega.2c00844] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 07/06/2022] [Indexed: 06/15/2023]
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused the coronavirus disease 2019 (COVID-19) pandemic. Several variants of SARS-CoV-2 have emerged worldwide. These variants show different transmissibility infectivity due to mutations in the viral spike (S) glycoprotein that interacts with the human angiotensin-converting enzyme 2 (hACE2) receptor and facilitates viral entry into target cells. Despite the effective SARS-CoV-2 vaccines, we still need to identify selective antivirals, and the S glycoprotein is a key target to neutralize the virus. We hypothesize that small molecules could disrupt the interaction of S glycoprotein with hACE2 and inhibit viral entry. We analyzed the S glycoprotein-hACE2 complex structure (PDB: 7DF4) and created models for different viral variants using visual molecular dynamics (VMD) and molecular operating environment (MOE) programs. Moreover, we started the hits search by performing structure-based molecular docking virtual screening of commercially available small molecules against S glycoprotein models using OEDocking FRED-4.0.0.0 software. The FRED-4.0.0.0 Chemguass4 scoring function was used to rank the small molecules based on their affinities. The best candidate compounds were purchased and tested using a standard SARS-CoV-2 pseudotyped cell-based bioassay to investigate their antiviral activity. Three of these compounds, alone or in combination, showed antiviral selectivity. These small molecules may lead to an effective antiviral treatment or serve as probes to better understand the biology of SARS-CoV-2.
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Affiliation(s)
- Yoel Rodríguez
- Department
of Natural Sciences, Hostos Community College
of The City University of New York, 500 Grand Concourse, Bronx, New York, New York 10451, United States
- Department
of Pharmacological Sciences, Icahn School
of Medicine at Mount Sinai, 1425 Madison Avenue, New York, New York 10029, United
States
| | - Scarlet Martínez Cardoze
- Department
of Natural Sciences, Hostos Community College
of The City University of New York, 500 Grand Concourse, Bronx, New York, New York 10451, United States
| | - Onyinyechi W. Obineche
- Department
of Natural Sciences, Hostos Community College
of The City University of New York, 500 Grand Concourse, Bronx, New York, New York 10451, United States
| | - Claudia Melo
- Department
of Science, Borough of Manhattan Community
College of The City University of New York, 199 Chambers St, New York, New York 10007, United States
- Brooklyn
College of The City University of New York, 2900 Bedford Avenue, New
York, New York 11210, United States
| | - Ashanna Persaud
- Department
of Science, Borough of Manhattan Community
College of The City University of New York, 199 Chambers St, New York, New York 10007, United States
| | - José A. Fernández Romero
- Department
of Science, Borough of Manhattan Community
College of The City University of New York, 199 Chambers St, New York, New York 10007, United States
- Center
for Biomedical Research, The Population
Council, 1230 York Avenue, New York, New York 10065, United States
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21
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Dutta S, Panthi B, Chandra A. All-Atom Simulations of Human ACE2-Spike Protein RBD Complexes for SARS-CoV-2 and Some of its Variants: Nature of Interactions and Free Energy Diagrams for Dissociation of the Protein Complexes. J Phys Chem B 2022; 126:5375-5389. [PMID: 35833966 PMCID: PMC9328126 DOI: 10.1021/acs.jpcb.2c00833] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Revised: 06/25/2022] [Indexed: 12/18/2022]
Abstract
The spike protein of SARS-CoV-2 is known to interact with the human ACE2 protein via its receptor binding domain (RBD). We have investigated the molecular nature of this interprotein interaction and the associated free energy diagrams for the unbinding of the two proteins for SARS-CoV-2 and some of its known variants through all-atom simulations. The present work involves generation and analysis of 2.5 μs of unbiased and 4.2 μs of biased molecular dynamics trajectories in total for five explicitly solvated RBD-ACE2 systems at full atomic level. First, we have made a comparative analysis of the details of residue-wise specific interactions of the spike protein with ACE2 for SARS-CoV-1 and SARS-CoV-2. It is found that the average numbers of both direct interprotein and water-bridged hydrogen bonds between the RBD and ACE2 are higher for SARS-CoV-2 than SARS-CoV-1. These higher hydrogen bonded interactions are further aided by enhanced nonspecific electrostatic attractions between the two protein surfaces for SARS-CoV-2. The free energy calculations reveal that there is an increase in the free energy barrier by ∼1.5 kcal/mol for the unbinding of RBD from ACE2 for SARS-CoV-2 compared to that for SARS-CoV-1. Subsequently, we considered the RBDs of three variants of SARS-CoV-2, namely N501Y, E484Q/L452R, and N440K. The free energy barrier of protein unbinding for the N501Y variant is found to be ∼4 kcal/mol higher than the wild type SARS-CoV-2 which can be attributed to additional specific interactions involving Tyr501 of RBD and Lys353 and Tyr42 of ACE2 and also enhanced nonspecific electrostatic interaction between the protein surfaces. For the other two mutant variants of E484Q/L452R and N440K, the free energy barrier for protein unbinding increases by ∼2 and ∼1 kcal/mol, respectively, compared with the wild type SARS-CoV-2, which can be attributed to an increase in the number of interprotein hydrogen bonds for the former and also to enhanced positive electrostatic potential on the RBD surfaces for both of the variants. The successive breaking of interprotein hydrogen bonds along the free energy pathway of the unbinding process is also found out for all five systems studied here.
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Affiliation(s)
- Saheb Dutta
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, Uttar Pradesh 208016, India
| | - Bhavana Panthi
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, Uttar Pradesh 208016, India
| | - Amalendu Chandra
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, Uttar Pradesh 208016, India
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22
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Tsukahara N, Murakami A, Motohashi M, Nakayama H, Kondo Y, Ito Y, Azuma T, Kishimoto H. An alpaca single-domain antibody (VHH) phage display library constructed by CDR shuffling provided high-affinity VHHs against desired protein antigens. Int Immunol 2022; 34:421-434. [PMID: 35689594 DOI: 10.1093/intimm/dxac022] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 06/08/2022] [Indexed: 11/13/2022] Open
Abstract
Antigen-combining sites of the camelid heavy-chain antibody variable domain (VHH) are constructed by three complementarity-determining regions (CDR1, CDR2 and CDR3). We prepared cDNA using mRNA extracted from peripheral lymphocytes of alpacas that had been non-immunized or immunized with human serum albumin (HSA). The VHH gene fragments encoding the amino-terminal half-containing CDR1 as well as CDR2 and the carboxy-terminal half-containing CDR3 were amplified independently by PCR, and then full-length VHH gene fragments were generated by overlap extension PCR and cloned into the phagemid vector. This protocol, referred to as CDR shuffling, allowed us to construct an alpaca VHH phage display library possessing repertoires different from those naturally occurring in animals. We asked, first, whether this library was able to provide the functional VHH fragments against HSA, an immunized antigen, and obtained 29 anti-HSA VHH clones, 41% possessed KD values of lower than 10-8 M, 5 of which had KD values of 10-10 M. We also obtained VHH clones against non-immunized protein antigens such as cardiac troponin T and I, Ebola virus glycoprotein 1 and human immunoglobulin G by biopanning. We compared the amino acid sequences and affinities and found that 43% of VHHs had KD values of less than 10-8 M, although those having KD values of 10-10 M were unavailable. These results suggested that the CDR-shuffled VHH phage display library could potentially provide VHHs against non-immunized protein antigens with similar levels of affinities to those against immunized antigens.
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Affiliation(s)
- Narutoshi Tsukahara
- Department of Immunology & Parasitology, Graduate School of Medicine, University of the Ryukyus, Uehara, Nishihara, Nakagami, Okinawa, Japan.,RePHAGEN Co., Ltd., Suzaki, Uruma, Okinawa, Japan
| | - Akikazu Murakami
- RePHAGEN Co., Ltd., Suzaki, Uruma, Okinawa, Japan.,Department of Oral Microbiology, Graduate School of Biomedical Sciences, Tokushima University, Kuramoto, Tokushima, Tokushima, Japan
| | - Maiko Motohashi
- Department of Immunology & Parasitology, Graduate School of Medicine, University of the Ryukyus, Uehara, Nishihara, Nakagami, Okinawa, Japan
| | | | | | - Yuji Ito
- Graduate School of Science and Engineering, Kagoshima University, Korimoto, Kagoshima, Kagoshima, Japan
| | - Takachika Azuma
- Antibody Engineering Research Center Co., Ltd., Yamazaki, Noda, Chiba, Japan
| | - Hidehiro Kishimoto
- Department of Immunology & Parasitology, Graduate School of Medicine, University of the Ryukyus, Uehara, Nishihara, Nakagami, Okinawa, Japan
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23
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Shukla SK, Patra S, Das TR, Kumar D, Mishra A, Tiwari A. Progress in COVID research and developments during pandemic. VIEW 2022; 3:20210020. [PMID: 35941909 PMCID: PMC9350081 DOI: 10.1002/viw.20210020] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 04/09/2022] [Accepted: 06/14/2022] [Indexed: 11/25/2022] Open
Abstract
The pandemic respiratory disease COVID-19 has spread over the globe within a small span of time. Generally, there are two important points are being highlighted and considered towards the successful diagnosis and treatment process. The first point includes the reduction of the rate of infections and the next one is the decrease of the death rate. The major threat to public health globally progresses due to the absence of effective medication and widely accepted immunization for the COVID-19. Whereas, understanding of host susceptibility, clinical features, adaptation of COVID-19 to new environments, asymptomatic infection is difficult and challenging. Therefore, a rapid and an exact determination of pathogenic viruses play an important role in deciding treatments and preventing pandemic to save the people's lives. It is urgent to fix a standardized diagnostic approach for detecting the COVID-19. Here, this systematic review describes all the current approaches using for screening and diagnosing the COVID-19 infectious patient. The renaissance in pathogen due to host adaptability and new region, facing creates several obstacles in diagnosis, drug, and vaccine development process. The study shows that adaptation of accurate and affordable diagnostic tools based on candidate biomarkers using sensor and digital medicine technology can deliver effective diagnosis services at the mass level. Better prospects of public health management rely on diagnosis with high specificity and cost-effective manner along with multidisciplinary research, specific policy, and technology adaptation. The proposed healthcare model with defined road map represents effective prognosis system.
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Affiliation(s)
- Sudheesh K. Shukla
- Institute of Advanced MaterialsIAAMGammalkilsvägen 18Ulrika59053Sweden
- VBRI Innovation Centre7/16 Kalkaji ExtnNew Delhi110019India
| | - Santanu Patra
- Institute of Advanced MaterialsIAAMGammalkilsvägen 18Ulrika59053Sweden
- VBRI Innovation Centre7/16 Kalkaji ExtnNew Delhi110019India
| | - Trupti R. Das
- CIPET, Institute of Petrochemicals Technology (IPT)‐BhubaneswarPatiaBhubaneswarIndia
| | - Dharmesh Kumar
- VBRI Innovation Centre7/16 Kalkaji ExtnNew Delhi110019India
| | - Anshuman Mishra
- Institute of Advanced MaterialsIAAMGammalkilsvägen 18Ulrika59053Sweden
| | - Ashutosh Tiwari
- Institute of Advanced MaterialsIAAMGammalkilsvägen 18Ulrika59053Sweden
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24
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Krut' VG, Chuvpilo SA, Astrakhantseva IV, Kozlovskaya LI, Efimov GA, Kruglov AA, Drutskaya MS, Nedospasov SA. Will Peptides Help to Stop COVID-19? BIOCHEMISTRY (MOSCOW) 2022; 87:590-604. [PMID: 36154880 PMCID: PMC9282900 DOI: 10.1134/s0006297922070021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Peptides are widely used for the diagnostics, prevention, and therapy of certain human diseases. How useful can they be for the disease caused by the SARS-CoV-2 coronavirus? In this review, we discuss the possibility of using synthetic and recombinant peptides and polypeptides for prevention of COVID-19 via blocking the interaction between the virus and its main receptor ACE2, as well as components of antiviral vaccines, in particular, against new emerging virus variants.
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Affiliation(s)
- Viktoriya G Krut'
- Sirius University of Science and Technology, Federal Territory Sirius, Krasnodar Krai, 354340, Russia
| | - Sergei A Chuvpilo
- Sirius University of Science and Technology, Federal Territory Sirius, Krasnodar Krai, 354340, Russia
| | - Irina V Astrakhantseva
- Sirius University of Science and Technology, Federal Territory Sirius, Krasnodar Krai, 354340, Russia
| | - Liubov I Kozlovskaya
- Chumakov Federal Scientific Center for Research and Development of Immunobiological Products, Russian Academy of Sciences, Moscow, 108819, Russia
- Institute of Translational Medicine and Biotechnology, Sechenov Moscow State Medical University, Moscow, 119991, Russia
| | - Grigory A Efimov
- National Medical Research Center of Hematology, Ministry of Health of the Russian Federation, Moscow, 125167, Russia
| | - Andrei A Kruglov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119234, Russia
- Faculty of Biology, Lomonosov Moscow State University, Moscow, 119234, Russia
- German Rheumatism Research Center (DRFZ), Leibniz Institute, Berlin, 10117, Germany
| | - Marina S Drutskaya
- Sirius University of Science and Technology, Federal Territory Sirius, Krasnodar Krai, 354340, Russia
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991, Russia
| | - Sergei A Nedospasov
- Sirius University of Science and Technology, Federal Territory Sirius, Krasnodar Krai, 354340, Russia.
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119234, Russia
- Faculty of Biology, Lomonosov Moscow State University, Moscow, 119234, Russia
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991, Russia
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25
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de Oliveira CF, Neto WFF, da Silva CP, Ribeiro ACS, Martins LC, de Sousa AW, Freitas MNO, Chiang JO, Silva FA, dos Santos EB, Medeiros DBA, Pinheiro GS, Brandão GF, Carvalho VL, Azevedo RSS, Vasconcelos PFC, Costa IB, Costa IB, dos Santos MC, Soares LS, Bedran RLS, Ferreira JL, Amarilla AA, Modhiran N, McMillan CLD, Freney ME, Muller DA, Watterson D, Casseb LMN, Henriques DF. Absence of Anti-RBD Antibodies in SARS-CoV-2 Infected or Naive Individuals Prior to Vaccination with CoronaVac Leads to Short Protection of Only Four Months Duration. Vaccines (Basel) 2022; 10:vaccines10050690. [PMID: 35632447 PMCID: PMC9147084 DOI: 10.3390/vaccines10050690] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 03/22/2022] [Accepted: 04/01/2022] [Indexed: 02/06/2023] Open
Abstract
The COVID-19 pandemic is the biggest public health threat facing the world today. Multiple vaccines have been approved; however, the emergence of viral variants such as the recent Omicron raises the possibility of booster doses to achieve adequate protection. In Brazil, the CoronaVac (Sinovac, Beijing, China) vaccine was used; however, it is important to assess the immune response to this vaccine over time. This study aimed to monitor the anti-SARS-CoV-2 antibody responses in those immunized with CoronaVac and SARS-CoV-2 infected individuals. Samples were collected between August 2020 and August 2021. Within the vaccinated cohort, some individuals had a history of infection by SARS-CoV-2 prior to immunization, while others did not. We analyzed RBD-specific and neutralizing-antibodies. Anti-RBD antibodies were detected in both cohorts, with a peak between 45–90 days post infection or vaccination, followed by a steady decline over time. In those with a previous history of COVID-19, a higher, longer, more persistent response was observed. This trend was mirrored in the neutralization assays, where infection, followed by immunization, resulted in higher, longer lasting responses which were conditioned on the presence of levels of RBD antibodies right before the vaccination. This supports the necessity of booster doses of CoronaVac in due course to prevent serious disease.
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Affiliation(s)
- Camille F. de Oliveira
- Department of Arbovirology and Hemorrhagic Fevers, Evandro Chagas Institute, Ananindeua 67030-000, PA, Brazil; (C.F.d.O.); (W.F.F.N.); (C.P.d.S.); (A.C.S.R.); (L.C.M.); (A.W.d.S.); (M.N.O.F.); (J.O.C.); (F.A.S.); (E.B.d.S.); (D.B.A.M.); (G.S.P.); (G.F.B.); (V.L.C.); (R.S.S.A.); (L.M.N.C.)
| | - Walter F. F. Neto
- Department of Arbovirology and Hemorrhagic Fevers, Evandro Chagas Institute, Ananindeua 67030-000, PA, Brazil; (C.F.d.O.); (W.F.F.N.); (C.P.d.S.); (A.C.S.R.); (L.C.M.); (A.W.d.S.); (M.N.O.F.); (J.O.C.); (F.A.S.); (E.B.d.S.); (D.B.A.M.); (G.S.P.); (G.F.B.); (V.L.C.); (R.S.S.A.); (L.M.N.C.)
| | - Carla P. da Silva
- Department of Arbovirology and Hemorrhagic Fevers, Evandro Chagas Institute, Ananindeua 67030-000, PA, Brazil; (C.F.d.O.); (W.F.F.N.); (C.P.d.S.); (A.C.S.R.); (L.C.M.); (A.W.d.S.); (M.N.O.F.); (J.O.C.); (F.A.S.); (E.B.d.S.); (D.B.A.M.); (G.S.P.); (G.F.B.); (V.L.C.); (R.S.S.A.); (L.M.N.C.)
| | - Ana Claudia S. Ribeiro
- Department of Arbovirology and Hemorrhagic Fevers, Evandro Chagas Institute, Ananindeua 67030-000, PA, Brazil; (C.F.d.O.); (W.F.F.N.); (C.P.d.S.); (A.C.S.R.); (L.C.M.); (A.W.d.S.); (M.N.O.F.); (J.O.C.); (F.A.S.); (E.B.d.S.); (D.B.A.M.); (G.S.P.); (G.F.B.); (V.L.C.); (R.S.S.A.); (L.M.N.C.)
| | - Lívia C. Martins
- Department of Arbovirology and Hemorrhagic Fevers, Evandro Chagas Institute, Ananindeua 67030-000, PA, Brazil; (C.F.d.O.); (W.F.F.N.); (C.P.d.S.); (A.C.S.R.); (L.C.M.); (A.W.d.S.); (M.N.O.F.); (J.O.C.); (F.A.S.); (E.B.d.S.); (D.B.A.M.); (G.S.P.); (G.F.B.); (V.L.C.); (R.S.S.A.); (L.M.N.C.)
| | - Alana W. de Sousa
- Department of Arbovirology and Hemorrhagic Fevers, Evandro Chagas Institute, Ananindeua 67030-000, PA, Brazil; (C.F.d.O.); (W.F.F.N.); (C.P.d.S.); (A.C.S.R.); (L.C.M.); (A.W.d.S.); (M.N.O.F.); (J.O.C.); (F.A.S.); (E.B.d.S.); (D.B.A.M.); (G.S.P.); (G.F.B.); (V.L.C.); (R.S.S.A.); (L.M.N.C.)
| | - Maria N. O. Freitas
- Department of Arbovirology and Hemorrhagic Fevers, Evandro Chagas Institute, Ananindeua 67030-000, PA, Brazil; (C.F.d.O.); (W.F.F.N.); (C.P.d.S.); (A.C.S.R.); (L.C.M.); (A.W.d.S.); (M.N.O.F.); (J.O.C.); (F.A.S.); (E.B.d.S.); (D.B.A.M.); (G.S.P.); (G.F.B.); (V.L.C.); (R.S.S.A.); (L.M.N.C.)
| | - Jannifer O. Chiang
- Department of Arbovirology and Hemorrhagic Fevers, Evandro Chagas Institute, Ananindeua 67030-000, PA, Brazil; (C.F.d.O.); (W.F.F.N.); (C.P.d.S.); (A.C.S.R.); (L.C.M.); (A.W.d.S.); (M.N.O.F.); (J.O.C.); (F.A.S.); (E.B.d.S.); (D.B.A.M.); (G.S.P.); (G.F.B.); (V.L.C.); (R.S.S.A.); (L.M.N.C.)
| | - Franko A. Silva
- Department of Arbovirology and Hemorrhagic Fevers, Evandro Chagas Institute, Ananindeua 67030-000, PA, Brazil; (C.F.d.O.); (W.F.F.N.); (C.P.d.S.); (A.C.S.R.); (L.C.M.); (A.W.d.S.); (M.N.O.F.); (J.O.C.); (F.A.S.); (E.B.d.S.); (D.B.A.M.); (G.S.P.); (G.F.B.); (V.L.C.); (R.S.S.A.); (L.M.N.C.)
| | - Eder B. dos Santos
- Department of Arbovirology and Hemorrhagic Fevers, Evandro Chagas Institute, Ananindeua 67030-000, PA, Brazil; (C.F.d.O.); (W.F.F.N.); (C.P.d.S.); (A.C.S.R.); (L.C.M.); (A.W.d.S.); (M.N.O.F.); (J.O.C.); (F.A.S.); (E.B.d.S.); (D.B.A.M.); (G.S.P.); (G.F.B.); (V.L.C.); (R.S.S.A.); (L.M.N.C.)
| | - Daniele B. A. Medeiros
- Department of Arbovirology and Hemorrhagic Fevers, Evandro Chagas Institute, Ananindeua 67030-000, PA, Brazil; (C.F.d.O.); (W.F.F.N.); (C.P.d.S.); (A.C.S.R.); (L.C.M.); (A.W.d.S.); (M.N.O.F.); (J.O.C.); (F.A.S.); (E.B.d.S.); (D.B.A.M.); (G.S.P.); (G.F.B.); (V.L.C.); (R.S.S.A.); (L.M.N.C.)
| | - Gleiciane S. Pinheiro
- Department of Arbovirology and Hemorrhagic Fevers, Evandro Chagas Institute, Ananindeua 67030-000, PA, Brazil; (C.F.d.O.); (W.F.F.N.); (C.P.d.S.); (A.C.S.R.); (L.C.M.); (A.W.d.S.); (M.N.O.F.); (J.O.C.); (F.A.S.); (E.B.d.S.); (D.B.A.M.); (G.S.P.); (G.F.B.); (V.L.C.); (R.S.S.A.); (L.M.N.C.)
| | - Gleiciane F. Brandão
- Department of Arbovirology and Hemorrhagic Fevers, Evandro Chagas Institute, Ananindeua 67030-000, PA, Brazil; (C.F.d.O.); (W.F.F.N.); (C.P.d.S.); (A.C.S.R.); (L.C.M.); (A.W.d.S.); (M.N.O.F.); (J.O.C.); (F.A.S.); (E.B.d.S.); (D.B.A.M.); (G.S.P.); (G.F.B.); (V.L.C.); (R.S.S.A.); (L.M.N.C.)
| | - Valéria L. Carvalho
- Department of Arbovirology and Hemorrhagic Fevers, Evandro Chagas Institute, Ananindeua 67030-000, PA, Brazil; (C.F.d.O.); (W.F.F.N.); (C.P.d.S.); (A.C.S.R.); (L.C.M.); (A.W.d.S.); (M.N.O.F.); (J.O.C.); (F.A.S.); (E.B.d.S.); (D.B.A.M.); (G.S.P.); (G.F.B.); (V.L.C.); (R.S.S.A.); (L.M.N.C.)
| | - Raimunda S. S. Azevedo
- Department of Arbovirology and Hemorrhagic Fevers, Evandro Chagas Institute, Ananindeua 67030-000, PA, Brazil; (C.F.d.O.); (W.F.F.N.); (C.P.d.S.); (A.C.S.R.); (L.C.M.); (A.W.d.S.); (M.N.O.F.); (J.O.C.); (F.A.S.); (E.B.d.S.); (D.B.A.M.); (G.S.P.); (G.F.B.); (V.L.C.); (R.S.S.A.); (L.M.N.C.)
| | - Pedro F. C. Vasconcelos
- Department of Biological and Health Sciences, University of Pará State, Belém 66087-670, PA, Brazil;
| | - Igor B. Costa
- Department of Virology, Evandro Chagas Institute, Ananindeua 67030-000, PA, Brazil; (I.B.C.); (I.B.C.); (M.C.d.S.); (L.S.S.); (R.L.S.B.); (J.L.F.)
| | - Iran B. Costa
- Department of Virology, Evandro Chagas Institute, Ananindeua 67030-000, PA, Brazil; (I.B.C.); (I.B.C.); (M.C.d.S.); (L.S.S.); (R.L.S.B.); (J.L.F.)
| | - Mirleide C. dos Santos
- Department of Virology, Evandro Chagas Institute, Ananindeua 67030-000, PA, Brazil; (I.B.C.); (I.B.C.); (M.C.d.S.); (L.S.S.); (R.L.S.B.); (J.L.F.)
| | - Luana S. Soares
- Department of Virology, Evandro Chagas Institute, Ananindeua 67030-000, PA, Brazil; (I.B.C.); (I.B.C.); (M.C.d.S.); (L.S.S.); (R.L.S.B.); (J.L.F.)
| | - Rayssa L. S. Bedran
- Department of Virology, Evandro Chagas Institute, Ananindeua 67030-000, PA, Brazil; (I.B.C.); (I.B.C.); (M.C.d.S.); (L.S.S.); (R.L.S.B.); (J.L.F.)
| | - James L. Ferreira
- Department of Virology, Evandro Chagas Institute, Ananindeua 67030-000, PA, Brazil; (I.B.C.); (I.B.C.); (M.C.d.S.); (L.S.S.); (R.L.S.B.); (J.L.F.)
| | - Alberto A. Amarilla
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD 4072, Australia; (A.A.A.); (N.M.); (C.L.D.M.); (M.E.F.); (D.A.M.); (D.W.)
| | - Naphak Modhiran
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD 4072, Australia; (A.A.A.); (N.M.); (C.L.D.M.); (M.E.F.); (D.A.M.); (D.W.)
| | - Christopher L. D. McMillan
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD 4072, Australia; (A.A.A.); (N.M.); (C.L.D.M.); (M.E.F.); (D.A.M.); (D.W.)
| | - Morgan E. Freney
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD 4072, Australia; (A.A.A.); (N.M.); (C.L.D.M.); (M.E.F.); (D.A.M.); (D.W.)
| | - David A. Muller
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD 4072, Australia; (A.A.A.); (N.M.); (C.L.D.M.); (M.E.F.); (D.A.M.); (D.W.)
- Australian Infectious Disease Research Centre, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Daniel Watterson
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD 4072, Australia; (A.A.A.); (N.M.); (C.L.D.M.); (M.E.F.); (D.A.M.); (D.W.)
- Australian Infectious Disease Research Centre, The University of Queensland, St Lucia, QLD 4072, Australia
- The Australian Institute for Biotechnology and Nanotechnology, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Lívia M. N. Casseb
- Department of Arbovirology and Hemorrhagic Fevers, Evandro Chagas Institute, Ananindeua 67030-000, PA, Brazil; (C.F.d.O.); (W.F.F.N.); (C.P.d.S.); (A.C.S.R.); (L.C.M.); (A.W.d.S.); (M.N.O.F.); (J.O.C.); (F.A.S.); (E.B.d.S.); (D.B.A.M.); (G.S.P.); (G.F.B.); (V.L.C.); (R.S.S.A.); (L.M.N.C.)
| | - Daniele F. Henriques
- Department of Arbovirology and Hemorrhagic Fevers, Evandro Chagas Institute, Ananindeua 67030-000, PA, Brazil; (C.F.d.O.); (W.F.F.N.); (C.P.d.S.); (A.C.S.R.); (L.C.M.); (A.W.d.S.); (M.N.O.F.); (J.O.C.); (F.A.S.); (E.B.d.S.); (D.B.A.M.); (G.S.P.); (G.F.B.); (V.L.C.); (R.S.S.A.); (L.M.N.C.)
- Correspondence:
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Hurlburt NK, Homad LJ, Sinha I, Jennewein MF, MacCamy AJ, Wan YH, Boonyaratanakornkit J, Sholukh AM, Jackson AM, Zhou P, Burton DR, Andrabi R, Ozorowski G, Ward AB, Stamatatos L, Pancera M, McGuire AT. Structural definition of a pan-sarbecovirus neutralizing epitope on the spike S2 subunit. Commun Biol 2022; 5:342. [PMID: 35411021 PMCID: PMC9001700 DOI: 10.1038/s42003-022-03262-7] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 03/11/2022] [Indexed: 12/11/2022] Open
Abstract
Three betacoronaviruses have crossed the species barrier and established human-to-human transmission causing significant morbidity and mortality in the past 20 years. The most current and widespread of these is SARS-CoV-2. The identification of CoVs with zoonotic potential in animal reservoirs suggests that additional outbreaks could occur. Monoclonal antibodies targeting conserved neutralizing epitopes on diverse CoVs can form the basis for prophylaxis and therapeutic treatments and enable the design of vaccines aimed at providing pan-CoV protection. We previously identified a neutralizing monoclonal antibody, CV3-25 that binds to the SARS-CoV-2 spike, neutralizes the SARS-CoV-2 Beta variant comparably to the ancestral Wuhan Hu-1 strain, cross neutralizes SARS-CoV-1 and binds to recombinant proteins derived from the spike-ectodomains of HCoV-OC43 and HCoV-HKU1. Here, we show that the neutralizing activity of CV3-25 is maintained against the Alpha, Delta, Gamma and Omicron variants of concern as well as a SARS-CoV-like bat coronavirus with zoonotic potential by binding to a conserved linear peptide in the stem-helix region. Negative stain electron microscopy and a 1.74 Å crystal structure of a CV3-25/peptide complex demonstrates that CV3-25 binds to the base of the stem helix at the HR2 boundary to an epitope that is distinct from other stem-helix directed neutralizing mAbs.
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Affiliation(s)
- Nicholas K Hurlburt
- Fred Hutchinson Cancer Research Center, Vaccine and Infectious Disease Division, Seattle, WA, USA
| | - Leah J Homad
- Fred Hutchinson Cancer Research Center, Vaccine and Infectious Disease Division, Seattle, WA, USA
| | - Irika Sinha
- Fred Hutchinson Cancer Research Center, Vaccine and Infectious Disease Division, Seattle, WA, USA
| | - Madeleine F Jennewein
- Fred Hutchinson Cancer Research Center, Vaccine and Infectious Disease Division, Seattle, WA, USA
| | - Anna J MacCamy
- Fred Hutchinson Cancer Research Center, Vaccine and Infectious Disease Division, Seattle, WA, USA
| | - Yu-Hsin Wan
- Fred Hutchinson Cancer Research Center, Vaccine and Infectious Disease Division, Seattle, WA, USA
| | - Jim Boonyaratanakornkit
- Fred Hutchinson Cancer Research Center, Vaccine and Infectious Disease Division, Seattle, WA, USA
| | - Anton M Sholukh
- Fred Hutchinson Cancer Research Center, Vaccine and Infectious Disease Division, Seattle, WA, USA
| | - Abigail M Jackson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Panpan Zhou
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Dennis R Burton
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Raiees Andrabi
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Gabriel Ozorowski
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Andrew B Ward
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Leonidas Stamatatos
- Fred Hutchinson Cancer Research Center, Vaccine and Infectious Disease Division, Seattle, WA, USA.
- Department of Global Health, University of Washington, Seattle, WA, USA.
| | - Marie Pancera
- Fred Hutchinson Cancer Research Center, Vaccine and Infectious Disease Division, Seattle, WA, USA.
- Vaccine Research Center, NAID, NIH, Bethesda, MD, USA.
| | - Andrew T McGuire
- Fred Hutchinson Cancer Research Center, Vaccine and Infectious Disease Division, Seattle, WA, USA.
- Department of Global Health, University of Washington, Seattle, WA, USA.
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA.
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27
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Xiang R, Wang Y, Wang L, Deng X, Huo S, Jiang S, Yu F. Neutralizing monoclonal antibodies against highly pathogenic coronaviruses. Curr Opin Virol 2022; 53:101199. [PMID: 35038651 PMCID: PMC8716168 DOI: 10.1016/j.coviro.2021.12.015] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Revised: 12/17/2021] [Accepted: 12/24/2021] [Indexed: 12/15/2022]
Abstract
The pandemic of Coronavirus Disease 2019 (COVID-19) caused by severe acute respiratory syndrome 2 coronavirus (SARS-CoV-2) is a continuing worldwide threat to human health and social economy. Historically, SARS-CoV-2 follows SARS and MERS as the third coronavirus spreading across borders and continents, but far more dangerous with long-lasting symptomatic consequences. The current situation is strong evidence that coronaviruses will continue to be pathogens of consequence in the future, thus calling for the development of neutralizing antibody-based prophylactics and therapeutics for prevention and treatment of COVID-19 and other human coronavirus diseases. This review summarized the progresses of developing neutralizing monoclonal antibodies against infection of SARS-CoV-2, SARS-CoV, and MERS-CoV, and discussed their potential applications in prevention and treatment of COVID-19 and other human coronavirus diseases.
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Affiliation(s)
- Rong Xiang
- College of Life Sciences, Hebei Agricultural University, Baoding, China
| | - Yang Wang
- College of Life Sciences, Hebei Agricultural University, Baoding, China
| | - Lili Wang
- Research Center of Chinese Jujube, Hebei Agricultural University, Baoding, China
| | - Xiaoqian Deng
- College of Life Sciences, Hebei Agricultural University, Baoding, China
| | - Shanshan Huo
- College of Life Sciences, Hebei Agricultural University, Baoding, China; Hebei Key Laboratory of Analysis and Control of Zoonotic Pathogenic Microorganism, Baoding, China.
| | - Shibo Jiang
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, China.
| | - Fei Yu
- College of Life Sciences, Hebei Agricultural University, Baoding, China; Hebei Key Laboratory of Analysis and Control of Zoonotic Pathogenic Microorganism, Baoding, China.
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28
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Ranjan P, Neha, Devi C, Jain G, Mallick CB, Das P. Impact of B.1.617 and RBD SARS-CoV-2 variants on vaccine efficacy: An in-silico approach. Indian J Med Microbiol 2022; 40:413-419. [PMID: 35370005 PMCID: PMC8971047 DOI: 10.1016/j.ijmmb.2022.03.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 03/18/2022] [Accepted: 03/22/2022] [Indexed: 12/05/2022]
Abstract
Purpose The existing panels of COVID-19 vaccines are based on the spike protein of an earlier SARS-CoV-2 strain that emerged in Wuhan, China. However, the evolving nature of SARS-CoV-2 has resulted in the emergence of new variants, thereby posing a greater challenge in the management of the disease. India faced a deadlier second wave of infections very recently, and genomic surveillance revealed that the B.1.617 variant and its sublineages are responsible for the majority of the cases. Hence, it's crucial to determine if the current vaccines available can be effective against these variants. Methods To address this, we performed molecular dynamics (MD) simulation on B.1.617 along with K417G variants and other RBD variants. We studied structural alteration of the spike protein and factors affecting antibody neutralization and immune escape via In silico docking. Results We found that in seven of the 12 variants studied, there was a structural alteration in the RBD region, further affecting its stability and function. Docking analysis of RBD variants and wild-type strains revealed that these variants have a higher affinity for the ACE2 (angiotensin 2 altered enzymes) receptor. Molecular interaction with CR3022 antibody revealed that binding affinity was less in comparison to wild type, with B.1.617 showing the least binding affinity. Conclusions The results of the extensive simulations provide novel mechanistic insights into the conformational dynamics and improve our understanding of the enhanced properties of these variants in terms of infectivity, transmissibility, neutralization potential, virulence, and host-viral replication fitness.
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Neutralizing Monoclonal Antibodies Inhibit SARS-CoV-2 Infection through Blocking Membrane Fusion. Microbiol Spectr 2022; 10:e0181421. [PMID: 35293796 PMCID: PMC9045258 DOI: 10.1128/spectrum.01814-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Most of SARS-CoV-2 neutralizing antibodies (nAbs) targeted the receptor binding domain (RBD) of the SARS-CoV-2 spike (S) protein. However, mutations at RBD sequences found in the emerging SARS-CoV-2 variants greatly reduced the effectiveness of nAbs. Here we showed that four nAbs, S2-4D, S2-5D, S2-8D, and S2-4A, which recognized a conserved epitope in the S2 subunit of the S protein, can inhibit SARS-CoV-2 infection through blocking the S protein-mediated membrane fusion. Notably, these four nAbs exhibited broadly neutralizing activity against SARS-CoV-2 Alpha, Gamma, Delta, and Epsilon variants. Antisera collected from mice immunized with the identified epitope peptides of these four nAbs also exhibited potent virus neutralizing activity. Discovery of the S2-specific nAbs and their unique antigenic epitopes paves a new path for development of COVID-19 therapeutics and vaccines. IMPORTANCE The spike (S) protein on the surface of SARS-CoV-2 mediates receptor binding and virus-host cell membrane fusion during virus entry. Many neutralizing antibodies (nAbs), which targeted the receptor binding domain (RBD) of S protein, lost the neutralizing activity against the newly emerging SARS-CoV-2 variants with sequence mutations at the RBD. In contrast, the nAb against the highly conserved S2 subunit, which plays the key role in virus–host cell membrane fusion, was poorly discovered. We showed that four S2-specific nAbs, S2-4D, S2-5D, S2-8D, and S2-4A, inhibited SARS-CoV-2 infection through blocking the S protein-mediated membrane fusion. These nAbs exhibited broadly neutralizing activity against Alpha, Gamma, Delta, and Epsilon variants. Antisera induced by the identified epitope peptides also possessed potent neutralizing activity. This work not only unveiled the S2-specific nAbs but also discovered an immunodominant epitope in the S2 subunit that can be rationally designed as the broad-spectrum vaccine against the SARS-like coronaviruses.
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Govind Kumar V, Ogden DS, Isu UH, Polasa A, Losey J, Moradi M. Prefusion spike protein conformational changes are slower in SARS-CoV-2 than in SARS-CoV-1. J Biol Chem 2022; 298:101814. [PMID: 35278433 PMCID: PMC8907130 DOI: 10.1016/j.jbc.2022.101814] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 03/04/2022] [Accepted: 03/06/2022] [Indexed: 01/01/2023] Open
Abstract
Within the last 2 decades, severe acute respiratory syndrome coronaviruses 1 and 2 (SARS-CoV-1 and SARS-CoV-2) have caused two major outbreaks; yet, for reasons not fully understood, the coronavirus disease 2019 pandemic caused by SARS-CoV-2 has been significantly more widespread than the 2003 SARS epidemic caused by SARS-CoV-1, despite striking similarities between these two viruses. The SARS-CoV-1 and SARS-CoV-2 spike proteins, both of which bind to host cell angiotensin-converting enzyme 2, have been implied to be a potential source of their differential transmissibility. However, the mechanistic details of prefusion spike protein binding to angiotensin-converting enzyme 2 remain elusive at the molecular level. Here, we performed an extensive set of equilibrium and nonequilibrium microsecond-level all-atom molecular dynamics simulations of SARS-CoV-1 and SARS-CoV-2 prefusion spike proteins to determine their differential dynamic behavior. Our results indicate that the active form of the SARS-CoV-2 spike protein is more stable than that of SARS-CoV-1 and the energy barrier associated with the activation is higher in SARS-CoV-2. These results suggest that not only the receptor-binding domain but also other domains such as the N-terminal domain could play a crucial role in the differential binding behavior of SARS-CoV-1 and SARS-CoV-2 spike proteins.
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Affiliation(s)
- Vivek Govind Kumar
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas, USA
| | - Dylan S Ogden
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas, USA
| | - Ugochi H Isu
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas, USA
| | - Adithya Polasa
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas, USA
| | - James Losey
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas, USA
| | - Mahmoud Moradi
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas, USA.
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Dutta SK, Sengupta S, Tripathi A. In silico and in vitro evaluation of silibinin: a promising anti-Chikungunya agent. In Vitro Cell Dev Biol Anim 2022; 58:255-267. [PMID: 35381943 DOI: 10.1007/s11626-022-00666-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 03/16/2022] [Indexed: 11/29/2022]
Abstract
Chikungunya virus (CHIKV) infection and subsequent high patient morbidity is a global threat. The present study aimed to identify the potent antiviral agent against Chikungunya virus, with minimum in vitro cytotoxicity. CHIKV nsP4 3D structure was determined using the I-TASSER server followed by its refinement and pocket determination. Furthermore, high-throughput molecular docking was employed to identify candidate CHIKV nsP4 inhibitors in a library containing 214 compounds. The top ranked compound was evaluated further with various assays, including cytotoxicity, antiviral activity, time of drug addition, viral entry attachment, and microneutralization assays. High-throughput computational screening indicated silibinin to have the best interaction with CHIKV nsP4 protein, immature and mature glycoproteins with highest negative free binding energy, - 5.24 to - 5.86 kcal/mol, and the lowest inhibitory constant, 50.47 to 143.2 µM. Further in vitro analysis demonstrated silibinin could exhibit statistically significant (p < 0.05) dose-dependent anti-CHIKV activity within 12.5-100-µM concentrations with CC50 as 50.90 µM. In total, 50 µM silibinin interfered with both CHIKV attachment (75%) and entry (82%) to Vero cells. Time of addition assay revealed silibinin interfered with late phase of the CHIKV replication cycle. Microneutralization assay revealed that silibinin could inhibit clearing of 50% Vero cell monolayer caused by CHIKV-induced CPE at a minimum dose of 25 µM. These data indicated silibinin to be a promising candidate drug against CHIKV infection.
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Affiliation(s)
- Sudip Kumar Dutta
- Department of Biochemistry and Medical Biotechnology, Calcutta School of Tropical Medicine, 108, C.R. Avenue, Kolkata, 700073, West Bengal, India
| | - Siddhartha Sengupta
- Department of Biochemistry and Medical Biotechnology, Calcutta School of Tropical Medicine, 108, C.R. Avenue, Kolkata, 700073, West Bengal, India
| | - Anusri Tripathi
- Department of Biochemistry and Medical Biotechnology, Calcutta School of Tropical Medicine, 108, C.R. Avenue, Kolkata, 700073, West Bengal, India.
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32
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Functional Reconstitution of the MERS CoV Receptor Binding Motif. Mol Immunol 2022; 145:3-16. [PMID: 35272105 PMCID: PMC8894742 DOI: 10.1016/j.molimm.2022.03.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 02/14/2022] [Accepted: 03/01/2022] [Indexed: 01/19/2023]
Abstract
In the early 1960’s the first human coronaviruses (designated 229E and OC43) were identified as etiologic agents of the common cold, to be followed by the subsequent isolation of three more human coronaviruses similarly associated with cold-like diseases. In contrast to these “mild” coronaviruses, over the last 20 years there have been three independent events of emergence of pandemic severe and acute life-threatening respiratory diseases caused by three novel beta-coronaviruses, SARS CoV, MERS CoV and most recently SARS CoV2. Whereas the first SARS CoV appeared in November 2002 and spontaneously disappeared by the summer of 2003, MERS CoV has continued persistently to spill over to humans via an intermediary camel vector, causing tens of cases annually. Although human-to-human transmission is rare, the fatality rate of MERS CoV disease is remarkably higher than 30%. COVID-19 however, is fortunately much less fatal, despite that its etiologic agent, SARS CoV2, is tremendously infectious, particularly with the recent evolution of the Omicron variants of concern (BA.1 and BA.2). Of note, MERS CoV prevalence in camel populations in Africa and the Middle East is extremely high. Moreover, MERS CoV and SARS CoV2 co-exist in the Middle East and especially in Saudi Arabia and the UAE, where sporadic incidences of co-infection have already been reported. Co-infection, either due to reverse spill-over of SARS CoV2 to camels or in double infected humans could lead to recombination between the two viruses, rendering either SARS CoV2 more lethal or MERS CoV more transmittable. In an attempt to prepare for what could develop into a catastrophic event, we have focused on developing a novel epitope-based immunogen for MERS CoV. Implementing combinatorial phage-display conformer libraries, the Receptor Binding Motif (RBM) of the MERS CoV Spike protein has been successfully reconstituted and shown to be recognized by a panel of seven neutralizing monoclonal antibodies.
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Ge S, Wu R, Zhou T, Liu X, Zhu J, Zhang X. Specific anti-SARS-CoV-2 S1 IgY-scFv is a promising tool for recognition of the virus. AMB Express 2022; 12:18. [PMID: 35150368 PMCID: PMC8840941 DOI: 10.1186/s13568-022-01355-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 01/26/2022] [Indexed: 11/10/2022] Open
Abstract
As severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues to spread globally, a series of vaccines, antibodies and drugs have been developed to combat coronavirus disease 2019 (COVID-19). High specific antibodies are powerful tool for the development of immunoassay and providing passive immunotherapy against SARS-CoV-2 and expected with large scale production. SARS-CoV-2 S1 protein was expressed in E. coli BL21 and purified by immobilized metal affinity chromatography, as antigen used to immunize hens, the specific IgY antibodies were extracted form egg yolk by PEG-6000 precipitation, and the titer of anti-S1 IgY antibody reached 1:10,000. IgY single chain variable fragment antibody (IgY-scFv) was generated by using phage display technology and the IgY-scFv showed high binding sensitivity and capacity to S1 protein of SARS-CoV-2, and the minimum detectable antigen S1 protein concentration was 6 ng/µL. The docking study showed that the multiple epitopes on the IgY-scFv interacted with multiple residues on SARS-CoV-2 S1 RBD to form hydrogen bonds. This preliminary study suggests that IgY and IgY-scFv are suitable candidates for the development of immunoassay and passive immunotherapy for COVID-19 to humans and animals.
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Advances in Targeting ACE2 for Developing COVID-19 Therapeutics. Ann Biomed Eng 2022; 50:1734-1749. [PMID: 36261668 PMCID: PMC9581451 DOI: 10.1007/s10439-022-03094-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 09/29/2022] [Indexed: 01/01/2023]
Abstract
Since the onset of the coronavirus pandemic in December 2019, the SARS-CoV-2 virus has accounted for over 6.3 million lives resulting in the demand to develop novel therapeutic approaches to target and treat SARS-CoV-2. Improved understanding of viral entry and infection mechanisms has led to identifying different target receptors to mitigate infection in the host. Researchers have been working on identifying and targeting potential therapeutic target receptors utilizing different candidate drugs. Angiotensin-converting enzyme-2 (ACE2) has been known to perform critical functions in maintaining healthy cardiorespiratory function. However, ACE2 also functions as the binding site for the spike protein of SARS-CoV-2, allowing the virus to enter the cells and ensue infection. Therefore, drugs targeting ACE2 receptors can be considered as therapeutic candidates. Strategies targeting the level of ACE2 expression have been investigated and compared to other potential therapeutic targets, such as TMPRSS2, RdRp, and DPP4. This mini review discusses the key therapeutic approaches that target the ACE2 receptor, which is critical to the cellular entry and propagation of the novel SARS-CoV-2. In addition, we summarize the main advantages of ACE2 targeting against alternative approaches for the treatment of COVID-19.
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Lan Q, Xia S, Lu L. Coronavirus Entry Inhibitors. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1366:101-121. [DOI: 10.1007/978-981-16-8702-0_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Hashemi B, Akram FA, Amirazad H, Dadashpour M, Sheervalilou M, Nasrabadi D, Ahmadi M, Sheervalilou R, Ameri Shah Reza M, Ghazi F, Roshangar L. Emerging importance of nanotechnology-based approaches to control the COVID-19 pandemic; focus on nanomedicine iterance in diagnosis and treatment of COVID-19 patients. J Drug Deliv Sci Technol 2022; 67:102967. [PMID: 34777586 PMCID: PMC8576597 DOI: 10.1016/j.jddst.2021.102967] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 11/03/2021] [Accepted: 11/03/2021] [Indexed: 02/06/2023]
Abstract
The ongoing outbreak of the newly emerged coronavirus disease 2019, which has tremendously concerned global health safety, is the result of infection with severe acute respiratory syndrome of coronavirus 2 with high morbidity and mortality. Because of the coronavirus has no specific treatment, so it is necessary to early detection and produce antiviral agents and efficacious vaccines in order to prevent the contagion of coronavirus. Due to the unique properties of nanomaterials, nanotechnology appears to be a highly relevant discipline in this global emergency, providing expansive chemical functionalization to develop advanced biomedical tools. Fascinatingly, nanomedicine as a hopeful approach for the treatment and diagnosis of diseases, could efficiently help success the fight among coronavirus and host cells. In this review, we will critically discuss how nanomedicine can play an indispensable role in creating useful treatments and diagnostics for coronavirus.
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Affiliation(s)
- Behnam Hashemi
- Stem Cell Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Firouzi-Amandi Akram
- Department of Immunology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Halimeh Amirazad
- Department of Medical Biotechnology, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mehdi Dadashpour
- Department of Biotechnology, Faculty of Medicine, Semnan University of Medical Sciences, Semnan, Iran
- Biotechnology Research Center, Semnan University of Medical Sciences, Semnan, Iran
| | - Milad Sheervalilou
- Infectious and Tropical Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Davood Nasrabadi
- Department of Biotechnology, Faculty of Medicine, Semnan University of Medical Sciences, Semnan, Iran
- Biotechnology Research Center, Semnan University of Medical Sciences, Semnan, Iran
| | - Majid Ahmadi
- Stem Cell Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | | | | | - Farhood Ghazi
- Stem Cell Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Leila Roshangar
- Stem Cell Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
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Tristán-Flores FE, Casique-Aguirre D, Pliego-Arreaga R, Cervantes-Montelongo JA, García-Gutierrez P, Acosta-García G, Silva-Martínez GA. Identification of potential inhibitors of SARS-CoV-2 S protein-ACE2 interaction by in silico drug repurposing. F1000Res 2021; 10. [PMID: 34900223 PMCID: PMC8630554 DOI: 10.12688/f1000research.52168.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/01/2021] [Indexed: 11/28/2022] Open
Abstract
Background: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a new coronavirus discovered that appeared in Wuhan, China, in December 2019, causes COVID-19 disease which have resulted in cases similar to SARS-atypical pneumonia. Worldwide, around 116 million cases and 2.57 million deaths are reported with new cases and increasing mortality every day. To date, there is no specific commercial treatment to control the infection. Repurpose drugs targeting the angiotensin-converting enzyme 2 (ACE2) receptor represents an alternative strategy to block the binding of SARS-CoV-2 protein S and forestall virus adhesion, internalization, and replication in the host cell. Methods: We performed a rigid molecular docking using the receptor binding domain of the S1 subunit of S protein (RBD
S1)-ACE2 (PDB ID: 6VW1) interaction site and 1,283 drugs FDA approved. The docking score, frequency of the drug in receptor site, and interactions at the binding site residues were used as analyzing criteria. Results: This research yielded 40 drugs identified as a potential inhibitor of RBD
S1-ACE2 interaction. Among the inhibitors, compounds such as ipratropium, formoterol, and fexofenadine can be found. Specialists employ these drugs as therapies to treat chronic obstructive pulmonary disease, asthma and virtually any respiratory infection. Conclusions: Our results will serve as the basis for
in vitro and
in vivo studies to evaluate the potential use of those drugs to generate affordable and convenient therapies to treat COVID-19.
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Affiliation(s)
| | - Diana Casique-Aguirre
- Escuela Nacional de Ciencias Biológicas (ENCB), Instituto Politécnico Nacional (IPN), CDMX, CDMX, 11340, Mexico
| | | | | | | | - Gerardo Acosta-García
- Ingeniería Bioquímica, Tecnológico Nacional de México en Celaya, Celaya, Guanajuato, 38010, Mexico
| | - Guillermo A Silva-Martínez
- Ingeniería Bioquímica, Tecnológico Nacional de México en Celaya, Celaya, Guanajuato, 38010, Mexico.,Ingeniería Bioquímica, Cátedras CONACYT-Tecnológico Nacional de México en Celaya, Celaya, Guanajuato, 38010, Mexico
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Mabrouk MT, Chiem K, Rujas E, Huang WC, Jahagirdar D, Quinn B, Surendran Nair M, Nissly RH, Cavener VS, Boyle NR, Sornberger TA, Kuchipudi SV, Ortega J, Julien JP, Martinez-Sobrido L, Lovell J. Lyophilized, thermostable Spike or RBD immunogenic liposomes induce protective immunity against SARS-CoV-2 in mice. SCIENCE ADVANCES 2021; 7:eabj1476. [PMID: 34851667 PMCID: PMC8635435 DOI: 10.1126/sciadv.abj1476] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 10/12/2021] [Indexed: 05/22/2023]
Abstract
The COVID-19 pandemic has spurred interest in potent and thermostable SARS-CoV-2 vaccines. Here, we assess low-dose immunization with lyophilized nanoparticles decorated with recombinant SARS-CoV-2 antigens. The SARS-CoV-2 Spike glycoprotein or its receptor-binding domain (RBD; mouse vaccine dose, 0.1 μg) was displayed on liposomes incorporating a particle-inducing lipid, cobalt porphyrin-phospholipid (dose, 0.4 μg), along with monophosphoryl lipid A (dose, 0.16 μg) and QS-21 (dose, 0.16 μg). Following optimization of lyophilization conditions, Spike or RBD-decorated liposomes were effectively reconstituted and maintained conformational capacity for binding human angiotensin-converting enzyme 2 (hACE2) for at least a week when stored at 60°C in lyophilized but not liquid format. Prime-boost intramuscular vaccination of hACE2-transgenic mice with the reconstituted vaccine formulations induced effective antibody responses that inhibited RBD binding to hACE2 and neutralized pseudotyped and live SARS-CoV-2. Two days following viral challenge, immunized transgenic mice cleared the virus and were fully protected from lethal disease.
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Affiliation(s)
- Moustafa T. Mabrouk
- Department of Biomedical Engineering, University at Buffalo, State University of New York, Buffalo, NY 14260, USA
| | - Kevin Chiem
- Texas Biomedical Research Institute, San Antonio, TX 78227, USA
| | - Edurne Rujas
- Program in Molecular Medicine, The Hospital for Sick Children Research Institute, Toronto, ON, Canada
- Biofisika Institute (CSIC, UPV/EHU) and Department of Biochemistry and Molecular Biology, University of the Basque Country (UPV/EHU), Bilbao, Spain
| | - Wei-Chiao Huang
- Department of Biomedical Engineering, University at Buffalo, State University of New York, Buffalo, NY 14260, USA
| | - Dushyant Jahagirdar
- Department of Anatomy and Cell Biology, McGill University, Montreal, Quebec H3A 0C7, Canada
| | - Breandan Quinn
- Department of Biomedical Engineering, University at Buffalo, State University of New York, Buffalo, NY 14260, USA
| | - Meera Surendran Nair
- Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, PA 16802, USA
| | - Ruth H. Nissly
- Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, PA 16802, USA
| | - Victoria S. Cavener
- Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, PA 16802, USA
| | - Nina R. Boyle
- Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, PA 16802, USA
| | - Ty A. Sornberger
- Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, PA 16802, USA
| | - Suresh V. Kuchipudi
- Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, Pennsylvania State University, University Park, PA 16802, USA
| | - Joaquin Ortega
- Department of Anatomy and Cell Biology, McGill University, Montreal, Quebec H3A 0C7, Canada
| | - Jean-Philippe Julien
- Program in Molecular Medicine, The Hospital for Sick Children Research Institute, Toronto, ON, Canada
- Departments of Biochemistry and Immunology, University of Toronto, Toronto, ON M5S 1A8, Canada
| | | | - Jonathan Lovell
- Department of Biomedical Engineering, University at Buffalo, State University of New York, Buffalo, NY 14260, USA
- Corresponding author.
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Dastar S, Gharesouran J, Mortazavi D, Hosseinzadeh H, Kian SJ, Taheri M, Ghafouri-Fard S, Jamali E, Rezazadeh M. COVID-19 pandemic: Insights into genetic susceptibility to SARS-CoV-2 and host genes implications on virus spread, disease severity and outcomes. Hum Antibodies 2021; 30:1-14. [PMID: 34864654 DOI: 10.3233/hab-211506] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
The outbreak of the newly emerging severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) all over the world has caused global public health emergencies, international concern and economic crises. The systemic SARS-CoV-2 disease (COVID-19) can lead to death through causing unrestrained cytokines-storm and subsequent pulmonary shutdown among the elderly and patients with pre-existing comorbidities. Additionally, in comparison with poor nations without primary health care services, in developed countries with advanced healthcare system we can witness higher number of infections per one million people. In this review, we summarize the latest studies on genes associated with SARS-CoV-2 pathogenesis and propose possible mechanisms of the virus replication cycle and its triggered signaling pathways to encourage researchers to investigate genetic and immune profiles of the disease and try strategies for its treatment. Our review shows that immune response in people with different genetic background might vary as African and then Asian populations have lowest number of affected cases compared with European and American nations. Considering SARS-CoV-2 pathogenesis, we put forward some potentially important genetic gateways to COVID-19 infection including genes involved in the entry and replication of SARS-CoV-2 and the regulation of host immune response which might represent explanation for its spread, severity, and morality. Finally, we suggest that genetic alterations within these gateways could be critical factors in influencing geographical discrepancies of the virus, so it is essential to fully study them and design appropriated and reliable therapeutic agents against COVID-19.
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Affiliation(s)
- Saba Dastar
- Division of Cancer Genetics, Department of Basic Oncology, Oncology Institute, Istanbul University, Fatih, Istanbul, Turkey
| | - Jalal Gharesouran
- Department of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Deniz Mortazavi
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Hassan Hosseinzadeh
- Department of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Seyed Jalal Kian
- Department of Virology, Iran University of Medical Sciences, School of Medicine, Tehran, Iran
| | - Mohammad Taheri
- Skull Base Research Center, Loghman Hakim Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Soudeh Ghafouri-Fard
- Department of Medical Genetics, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Elena Jamali
- Department of Pathology, Loghman Hakim Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Maryam Rezazadeh
- Department of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
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Immunoinformatics mapping of potential epitopes in SARS-CoV-2 structural proteins. PLoS One 2021; 16:e0258645. [PMID: 34780495 PMCID: PMC8592446 DOI: 10.1371/journal.pone.0258645] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 10/01/2021] [Indexed: 01/03/2023] Open
Abstract
All approved coronavirus disease 2019 (COVID-19) vaccines in current use are safe, effective, and reduce the risk of severe illness. Although data on the immunological presentation of patients with COVID-19 is limited, increasing experimental evidence supports the significant contribution of B and T cells towards the resolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. Despite the availability of several COVID-19 vaccines with high efficacy, more effective vaccines are still needed to protect against the new variants of SARS-CoV-2. Employing a comprehensive immunoinformatic prediction algorithm and leveraging the genetic closeness with SARS-CoV, we have predicted potential immune epitopes in the structural proteins of SARS-CoV-2. The S and N proteins of SARS-CoV-2 and SARS-CoVs are main targets of antibody detection and have motivated us to design four multi-epitope vaccines which were based on our predicted B- and T-cell epitopes of SARS-CoV-2 structural proteins. The cardinal epitopes selected for the vaccine constructs are predicted to possess antigenic, non-allergenic, and cytokine-inducing properties. Additionally, some of the predicted epitopes have been experimentally validated in published papers. Furthermore, we used the C-ImmSim server to predict effective immune responses induced by the epitope-based vaccines. Taken together, the immune epitopes predicted in this study provide a platform for future experimental validations which may facilitate the development of effective vaccine candidates and epitope-based serological diagnostic assays.
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Parmar MS. TMPRSS2: An Equally Important Protease as ACE2 in the Pathogenicity of SARS-CoV-2 Infection. Mayo Clin Proc 2021; 96:2748-2752. [PMID: 34736607 PMCID: PMC8279956 DOI: 10.1016/j.mayocp.2021.07.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 04/10/2021] [Accepted: 07/09/2021] [Indexed: 01/09/2023]
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Qiao L, Chen M, Li S, Hu J, Gong C, Zhang Z, Cao X. A peptide-based subunit candidate vaccine against SARS-CoV-2 delivered by biodegradable mesoporous silica nanoparticles induced high humoral and cellular immunity in mice. Biomater Sci 2021; 9:7287-7296. [PMID: 34612299 DOI: 10.1039/d1bm01060c] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Development of a rapidly scalable vaccine is still an urgent task to halt the spread of COVID-19. We have demonstrated biodegradable mesoporous silica nanoparticles (BMSNs) as a good drug delivery carrier for tumor therapy. In this study, seven linear B cell epitopes and three CD8+ T cell epitopes were screened from the spike (S) glycoprotein of SARS-CoV-2 by computer-based immunoinformatic approaches for vaccine design. A nanoparticle-based candidate vaccine (B/T@BMSNs) against SARS-CoV-2 was rapidly prepared by encapsulating these ten epitope peptides within BMSNs, respectively. BMSNs with potential biodegradability, proved to possess excellent safety in vitro and in vivo, could efficiently deliver epitope peptides into the cytoplasm of RAW264.7 cells. Strong Th1-biased humoral and cellular immunity were induced by B/T@BMSNs in mice and all the 10 selected epitopes were identified as effective antigen epitopes, which could induce robust peptide-specific immune response. The elicited functional antibody could bind to the recombinant S protein and block the binding of the S protein to the ACE-2 receptor. These results demonstrate the potential of a nanoparticles vaccine platform based on BMSNs to rapidly develop peptide-based subunit vaccine candidates against SARS-CoV-2.
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Affiliation(s)
- Lei Qiao
- Central Laboratory of Affiliated Hospital of China University of Mining and Technology, Xuzhou 221116, P. R. China
| | - Minmin Chen
- School of Materials and Physics, China University of Mining and Technology, Xuzhou 221116, P. R. China.
| | - Suyan Li
- Central Laboratory of Affiliated Hospital of China University of Mining and Technology, Xuzhou 221116, P. R. China
| | - Jinxia Hu
- School of Materials and Physics, China University of Mining and Technology, Xuzhou 221116, P. R. China.
| | - Chaoju Gong
- Central Laboratory of Affiliated Hospital of China University of Mining and Technology, Xuzhou 221116, P. R. China
| | - Zhuoqi Zhang
- School of International Education, Xuzhou Medical University, Xuzhou 221004, P. R. China.
| | - Xichuan Cao
- School of Materials and Physics, China University of Mining and Technology, Xuzhou 221116, P. R. China.
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Kandikattu HK, Yadavalli CS, Venkateshaiah SU, Mishra A. Vaccine efficacy in mutant SARS-CoV-2 variants. INTERNATIONAL JOURNAL OF CELL BIOLOGY AND PHYSIOLOGY 2021; 4:1-12. [PMID: 34790972 PMCID: PMC8594908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Many aspects of the SARS-CoV-2 virus remain poorly understood, including its rapid mutation and its effects on populations of different ages. The present literature of review is focused on the effectiveness of current available vaccines in view of immerging several SARS-CoV-2 variants. The most dangerous and infectious SARS-CoV-2 strain, B117, was recently discovered in the United Kingdom, and another new variant, 501.V2, was discovered in South Africa. In countries such as the United States, Japan, India, and Brazil, the variant B117 spread far more quickly than the original strain. The new SARS-CoV-2 mutations have made producing a universal and effective vaccine more difficult. SARS-CoV-2's S protein, which aids in receptor identification and membrane fusion, is a primary target for vaccine development using its mRNA or inactivated virus. Currently, in the interval of few days new more infectious SARS-CoV-2 mutant is detected, started from SARS-CoV-2 Alpha (B.1.1.7), beta (B.1.351), delta (B.1.617.2), delta plus, gamma (P.1) and now variant lamda. The variant detected first in Peru and spread almost 27 countries including UK that accounts for 82% of new infections. These mutant variants are posing new challenge even to the fully vaccinated individuals and a challenge for the public health. Thus, a need to review current treatment vaccination guideline and strategy as early as possible. Reporting all new SARS-CoV-2 variants and their effectiveness in response to several available vaccines, we would like to draw the attention of health care provider, and all developed countries health care agencies including WHO to frame new guidelines for vaccination and immediate intervention to control the development of new SARS-CoV-2 variants from the third world countries by providing vaccines to the poor countries as early as possible.
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Williams A, Branscome H, Khatkar P, Mensah GA, Al Sharif S, Pinto DO, DeMarino C, Kashanchi F. A comprehensive review of COVID-19 biology, diagnostics, therapeutics, and disease impacting the central nervous system. J Neurovirol 2021; 27:667-690. [PMID: 34581996 PMCID: PMC8477646 DOI: 10.1007/s13365-021-00998-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 05/17/2021] [Accepted: 07/01/2021] [Indexed: 01/08/2023]
Abstract
The ongoing COVID-19 pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is a highly transmissible disease. SARS-CoV-2 is estimated to have infected over 153 million people and to have caused over 3.2 million global deaths since its emergence in December 2019. SARS-CoV-2 is the seventh coronavirus known to infect humans, and like other coronaviruses, SARS-CoV-2 infection is characterized by a variety of symptoms including general flu-like symptoms such as a fever, sore throat, fatigue, and shortness of breath. Severe cases often display signs of pneumonia, lymphopenia, acute kidney injury, cardiac injury, cytokine storms, lung damage, acute respiratory distress syndrome (ARDS), multiple organ failure, sepsis, and death. There is evidence that around 30% of COVID-19 cases have central nervous system (CNS) or peripheral nervous system (PNS) symptoms along with or in the absence of the previously mentioned symptoms. In cases of CNS/PNS impairments, patients display dizziness, ataxia, seizure, nerve pain, and loss of taste and/or smell. This review highlights the neurological implications of SARS-CoV-2 and provides a comprehensive summary of the research done on SARS-CoV-2 pathology, diagnosis, therapeutics, and vaccines up to May 5.
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Affiliation(s)
- Anastasia Williams
- Laboratory of Molecular Virology, School of Systems Biology, George Mason University, Manassas, VA, USA
| | - Heather Branscome
- Laboratory of Molecular Virology, School of Systems Biology, George Mason University, Manassas, VA, USA
- American Type Culture Collection (ATCC), Manassas, VA, USA
| | - Pooja Khatkar
- Laboratory of Molecular Virology, School of Systems Biology, George Mason University, Manassas, VA, USA
| | - Gifty A Mensah
- Laboratory of Molecular Virology, School of Systems Biology, George Mason University, Manassas, VA, USA
| | - Sarah Al Sharif
- Laboratory of Molecular Virology, School of Systems Biology, George Mason University, Manassas, VA, USA
| | - Daniel O Pinto
- Laboratory of Molecular Virology, School of Systems Biology, George Mason University, Manassas, VA, USA
- Immunology Core, Malaria Biologics Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Catherine DeMarino
- Laboratory of Molecular Virology, School of Systems Biology, George Mason University, Manassas, VA, USA
| | - Fatah Kashanchi
- Laboratory of Molecular Virology, School of Systems Biology, George Mason University, Manassas, VA, USA.
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Miersch S, Li Z, Saberianfar R, Ustav M, Brett Case J, Blazer L, Chen C, Ye W, Pavlenco A, Gorelik M, Garcia Perez J, Subramania S, Singh S, Ploder L, Ganaie S, Chen RE, Leung DW, Pandolfi PP, Novelli G, Matusali G, Colavita F, Capobianchi MR, Jain S, Gupta JB, Amarasinghe GK, Diamond MS, Rini J, Sidhu SS. Tetravalent SARS-CoV-2 Neutralizing Antibodies Show Enhanced Potency and Resistance to Escape Mutations. J Mol Biol 2021; 433:167177. [PMID: 34329642 PMCID: PMC8316672 DOI: 10.1016/j.jmb.2021.167177] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 07/17/2021] [Accepted: 07/21/2021] [Indexed: 12/16/2022]
Abstract
Neutralizing antibodies (nAbs) hold promise as therapeutics against COVID-19. Here, we describe protein engineering and modular design principles that have led to the development of synthetic bivalent and tetravalent nAbs against SARS-CoV-2. The best nAb targets the host receptor binding site of the viral S-protein and tetravalent versions block entry with a potency exceeding bivalent nAbs by an order of magnitude. Structural studies show that both the bivalent and tetravalent nAbs can make multivalent interactions with a single S-protein trimer, consistent with the avidity and potency of these molecules. Significantly, we show that the tetravalent nAbs show increased tolerance to potential virus escape mutants and an emerging variant of concern. Bivalent and tetravalent nAbs can be produced at large-scale and are as stable and specific as approved antibody drugs. Our results provide a general framework for enhancing antiviral therapies against COVID-19 and related viral threats, and our strategy can be applied to virtually any antibody drug.
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Affiliation(s)
- Shane Miersch
- The Donnelly Centre, University of Toronto, Toronto, Canada
| | - Zhijie Li
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | | | | | - James Brett Case
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Levi Blazer
- The Donnelly Centre, University of Toronto, Toronto, Canada
| | - Chao Chen
- The Donnelly Centre, University of Toronto, Toronto, Canada
| | - Wei Ye
- The Donnelly Centre, University of Toronto, Toronto, Canada
| | | | - Maryna Gorelik
- The Donnelly Centre, University of Toronto, Toronto, Canada
| | | | | | - Serena Singh
- The Donnelly Centre, University of Toronto, Toronto, Canada
| | - Lynda Ploder
- The Donnelly Centre, University of Toronto, Toronto, Canada
| | - Safder Ganaie
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Rita E Chen
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Daisy W Leung
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Pier Paolo Pandolfi
- Renown Institute for Cancer, Nevada System of Higher Education, Reno, NV, USA; Department of Molecular Biotechnologies & Health Sciences, Molecular Biotechnology Center, University of Turin, Italy
| | - Giuseppe Novelli
- Department of Biomedicine and Prevention, Tor Vergata University of Rome, 00133 Rome, Italy
| | - Giulia Matusali
- Laboratory of Virology, National Institute for Infectious Diseases "L. Spallanzani" IRCCS, Rome, Italy
| | - Francesca Colavita
- Laboratory of Virology, National Institute for Infectious Diseases "L. Spallanzani" IRCCS, Rome, Italy
| | - Maria R Capobianchi
- Laboratory of Virology, National Institute for Infectious Diseases "L. Spallanzani" IRCCS, Rome, Italy
| | | | - J B Gupta
- Virna Therapeutics, West Roxbury, MA, USA
| | - Gaya K Amarasinghe
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - Michael S Diamond
- Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA; Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA; Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
| | - James Rini
- Department of Molecular Genetics, University of Toronto, Toronto, Canada; Department of Biochemistry, University of Toronto, Toronto, Canada.
| | - Sachdev S Sidhu
- The Donnelly Centre, University of Toronto, Toronto, Canada.
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Khan AA, Alahmari AA, Almuzaini Y, Alamri F, Alsofayan YM, Aburas A, Al-Muhsen S, Van Kerkhove M, Yezli S, Ciottone GR, Assiri AM, Jokhdar HA. Potential Cross-Reactive Immunity to COVID-19 Infection in Individuals With Laboratory-Confirmed MERS-CoV Infection: A National Retrospective Cohort Study From Saudi Arabia. Front Immunol 2021; 12:727989. [PMID: 34603300 PMCID: PMC8484965 DOI: 10.3389/fimmu.2021.727989] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2021] [Accepted: 08/17/2021] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND A growing number of experiments have suggested potential cross-reactive immunity between severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) and previous human coronaviruses. We conducted the present retrospective cohort study to investigate the relationship between previous Middle East respiratory syndrome-coronavirus (MERS-CoV) infection and the risk of SARS-CoV-2 infection as well as the relationship between previous MERS-CoV and COVID-19-related hospitalization and mortality. METHODS Starting in March 2020, we prospectively followed two groups of individuals who tested negative for COVID-19 infection. The first group had a previously confirmed MERS-CoV infection, which was compared to a control group of MERS-negative individuals. The studied cohort was then followed until November 2020 to track evidence of contracting COVID-19 infection. FINDINGS A total of 82 (24%) MERS-positive and 260 (31%) MERS-negative individuals had COVID-19 infection. Patients in the MERS-positive group had a lower risk of COVID-19 infection than those in the MERS-negative group (Risk ratio [RR] 0.696, 95% confidence interval [CI] 0.522-0.929; p =0.014). The risk of COVID-19-related hospitalization in the MERS-positive group was significantly higher (RR 4.036, 95% CI 1.705-9.555; p =0.002). The case fatality rate (CFR) from COVID-19 was 4.9% in the MERS-positive group and 1.2% in the MERS-negative group (p =0.038). The MERS-positive group had a higher risk of death than the MERS-negative group (RR 6.222, 95% CI 1.342-28.839; p =0.019). However, the risk of mortality was similar between the two groups when death was adjusted for age (p =0.068) and age and sex (p =0.057). After controlling for all the independent variables, only healthcare worker occupation and >1 comorbidity were independent predictors of SARS-CoV-2 infection. INTERPRETATION Individuals with previous MERS-CoV infection can exhibit a cross-reactive immune response to SARS-CoV-2 infection. Our study demonstrated that patients with MERS-CoV infection had higher risks of COVID-19-related hospitalization and death than MERS-negative individuals.
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Affiliation(s)
- Anas A. Khan
- Department of Emergency Medicine, College of Medicine, King Saud University, Riyadh, Saudi Arabia
- Global Center of Mass Gatherings Medicine, Ministry of Health, Riyadh, Saudi Arabia
| | - Ahmed A. Alahmari
- Global Center of Mass Gatherings Medicine, Ministry of Health, Riyadh, Saudi Arabia
| | - Yasir Almuzaini
- Global Center of Mass Gatherings Medicine, Ministry of Health, Riyadh, Saudi Arabia
| | - Fahad Alamri
- Global Center of Mass Gatherings Medicine, Ministry of Health, Riyadh, Saudi Arabia
| | | | - Alhanouf Aburas
- Global Center of Mass Gatherings Medicine, Ministry of Health, Riyadh, Saudi Arabia
| | - Saleh Al-Muhsen
- Immunology Research Laboratory, Department of Pediatrics, College of Medicine, King Saud University Medical City, King Saud University, Riyadh, Saudi Arabia
| | - Maria Van Kerkhove
- Infectious Hazards Management, Health Emergencies Programme, World Health Organization, Geneva, Switzerland
| | - Saber Yezli
- Global Center of Mass Gatherings Medicine, Ministry of Health, Riyadh, Saudi Arabia
| | - Gregory R. Ciottone
- Department of Emergency Medicine, Harvard Medical School, Boston, MA, United States
| | | | - Hani A. Jokhdar
- Deputyship of Public Health, Ministry of Health, Riyadh, Saudi Arabia
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47
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Güler G, Özdemir H, Omar D, Akdoğan G. Coronavirus disease 2019 (COVID-19): Biophysical and biochemical aspects of SARS-CoV-2 and general characteristics. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2021; 164:3-18. [PMID: 34033836 PMCID: PMC8142027 DOI: 10.1016/j.pbiomolbio.2021.05.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 05/07/2021] [Accepted: 05/18/2021] [Indexed: 01/08/2023]
Abstract
The coronavirus disease (COVID-19) arises from the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) which is an enveloped RNA virus. COVID-19 has rapidly spread throughout the world by infecting more than 143 million people and causing 3.04 million deaths worldwide by 22 April 2021, confirmed by the World Health Organization. It caused great concern and pandemic all over the world, therewithal there has not been found any specific and efficient treatment yet. In the current review, we aimed to define the biophysical and biochemical aspects of SARS-CoV-2, including renin-angiotensin-system, cytokine storms, receptor binding, protein structural and functional features, molecular interactions, and conformational changes that take place during viral attachment and entering into human cells. It was also aimed to highlight the general hallmarks of COVID-19, including treatment strategies, diagnosis and even prevention. Thus, this review will serve as an updated comprehensive body of information and discussion on COVID-19 and will help the molecular scientists, biophysicists, clinicians, as well as medical engineers. Thereby, further understanding of COVID-19 will provide novel insights and advances in development of therapeutic potentials and vaccine alternatives as well as in detection of specific targets for diagnosis.
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Affiliation(s)
- Günnur Güler
- Department of Biomedical Engineering, Izmir University of Economics, 35330 Izmir, Turkey.
| | - Helin Özdemir
- Faculty of Medicine, Izmir University of Economics, 35330 Izmir, Turkey
| | - Dilara Omar
- Faculty of Medicine, Izmir University of Economics, 35330 Izmir, Turkey
| | - Gül Akdoğan
- Faculty of Medicine, Izmir University of Economics, 35330 Izmir, Turkey
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Kayode AJ, Banji-Onisile FO, Olaniran AO, Okoh AI. An Overview of the Pathogenesis, Transmission, Diagnosis, and Management of Endemic Human Coronaviruses: A Reflection on the Past and Present Episodes and Possible Future Outbreaks. Pathogens 2021; 10:1108. [PMID: 34578140 PMCID: PMC8470645 DOI: 10.3390/pathogens10091108] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 06/22/2021] [Accepted: 06/29/2021] [Indexed: 01/08/2023] Open
Abstract
The outbreak of the 2019 coronavirus pandemic caught the world by surprise in late 2019 and has held it hostage for months with an increasing number of infections and deaths. Although coronavirus was first discovered in the 1960s and was known to cause respiratory infection in humans, no information was available about the epidemic pattern of the virus until the past two decades. This review addresses the pathogenesis, transmission dynamics, diagnosis, management strategies, the pattern of the past and present events, and the possibility of future outbreaks of the endemic human coronaviruses. Several studies have described bats as presumptive natural reservoirs of coronaviruses. In essence, the identification of a diverse group of similar SARS coronaviruses in bats suggests the possibility of a future epidemic due to severe acute respiratory syndrome (SARS-like) coronaviruses originating from different reservoir hosts. The study also identified a lack of vaccines to prevent human coronavirus infections in humans in the past, however, the recent breakthrough in vaccine discovery and approval for emergency use for the treatment of Severe Acute Respiratory Syndrome Coronavirus 2 is commendable. The high rates of genomic substitution and recombination due to errors in RNA replication and the potential for independent species crossing suggest the chances of an entirely new strain evolving. Therefore, rapid research efforts should be deployed for vaccination to combat the COVID-19 pandemic and prevent a possible future outbreak. More sensitization and enlightenment on the need to adopt good personal hygiene practices, social distancing, and scientific evaluation of existing medications with promising antiviral effects against SARS-CoV-2 is required. In addition, intensive investigations to unravel and validate the possible reservoirs, the intermediate host, as well as insight into the ability of the virus to break the species barrier are needed to prevent future viral spillover and possible outbreaks.
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Affiliation(s)
- Adeoye J. Kayode
- Applied and Environmental Microbiology Research Group (AEMREG), Department of Biochemistry and Microbiology, University of Fort Hare, Private Bag X1314, Alice 5700, South Africa; or
- Wastewater Coronavirus Surveillance Laboratory, SAMRC Microbial Water Quality Monitoring Center, University of Fort Hare, Private Bag X1314, Alice 5700, South Africa
| | - Folasade O. Banji-Onisile
- Department of Microbiology, School of Life Sciences, College of Agriculture, Engineering and Science, University of KwaZulu-Natal, Durban 4000, South Africa; (F.O.B.-O.); (A.O.O.)
| | - Ademola O. Olaniran
- Department of Microbiology, School of Life Sciences, College of Agriculture, Engineering and Science, University of KwaZulu-Natal, Durban 4000, South Africa; (F.O.B.-O.); (A.O.O.)
| | - Anthony I. Okoh
- Applied and Environmental Microbiology Research Group (AEMREG), Department of Biochemistry and Microbiology, University of Fort Hare, Private Bag X1314, Alice 5700, South Africa; or
- Wastewater Coronavirus Surveillance Laboratory, SAMRC Microbial Water Quality Monitoring Center, University of Fort Hare, Private Bag X1314, Alice 5700, South Africa
- Department of Environmental Health Sciences, College Health Sciences, University of Sharjah, Sharjah 555588, United Arab Emirates
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49
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Shanmugaraj B, Siriwattananon K, Malla A, Phoolcharoen W. Potential for Developing Plant-Derived Candidate Vaccines and Biologics against Emerging Coronavirus Infections. Pathogens 2021; 10:1051. [PMID: 34451516 PMCID: PMC8400130 DOI: 10.3390/pathogens10081051] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 08/13/2021] [Accepted: 08/17/2021] [Indexed: 01/03/2023] Open
Abstract
The emerging human coronavirus infections in the 21st century remain a major public health crisis causing worldwide impact and challenging the global health care system. The virus is circulating in several zoonotic hosts and continuously evolving, causing occasional outbreaks due to spill-over events occurring between animals and humans. Hence, the development of effective vaccines or therapeutic interventions is the current global priority in order to reduce disease severity, frequent outbreaks, and to prevent future infections. Vaccine development for newly emerging pathogens takes a long time, which hinders rapid immunization programs. The concept of plant-based pharmaceuticals can be readily applied to meet the recombinant protein demand by means of transient expression. Plants are evolved as an expression platform, and they bring a combination of unique interests in terms of rapid scalability, flexibility, and economy for industrial-scale production of effective vaccines, diagnostic reagents, and other biopharmaceuticals. Plants offer safe biologics to fulfill emergency demands, especially during pandemic situations or outbreaks caused by emerging strains. This review highlights the features of a plant expression platform for producing recombinant biopharmaceuticals to combat coronavirus infections with emphasis on COVID-19 vaccine and biologics development.
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Affiliation(s)
| | - Konlavat Siriwattananon
- Research Unit for Plant-Produced Pharmaceuticals, Chulalongkorn University, Bangkok 10330, Thailand;
- Department of Pharmacognosy and Pharmaceutical Botany, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok 10330, Thailand
| | - Ashwini Malla
- Baiya Phytopharm Co., Ltd., Bangkok 10250, Thailand; (B.S.); (A.M.)
| | - Waranyoo Phoolcharoen
- Baiya Phytopharm Co., Ltd., Bangkok 10250, Thailand; (B.S.); (A.M.)
- Research Unit for Plant-Produced Pharmaceuticals, Chulalongkorn University, Bangkok 10330, Thailand;
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50
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Li JF, He L, Deng YQ, Qi SH, Chen YH, Zhang XL, Hu SX, Fan RW, Zhao GY, Qin CF. Generation and Characterization of a Nanobody Against SARS-CoV. Virol Sin 2021; 36:1484-1491. [PMID: 34403037 PMCID: PMC8369142 DOI: 10.1007/s12250-021-00436-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Accepted: 05/06/2021] [Indexed: 01/09/2023] Open
Abstract
The sudden emergence of severe acute respiratory syndrome coronavirus (SARS-CoV) has caused global panic in 2003, and the risk of SARS-CoV outbreak still exists. However, no specific antiviral drug or vaccine is available; thus, the development of therapeutic antibodies against SARS-CoV is needed. In this study, a nanobody phage-displayed library was constructed from peripheral blood mononuclear cells of alpacas immunized with the recombinant receptor-binding domain (RBD) of SARS-CoV. Four positive clones were selected after four rounds of bio-panning and subjected to recombinant expression in E. coli. Further biological identification demonstrated that one of the nanobodies, S14, showed high affinity to SARS-CoV RBD and potent neutralization activity at the picomole level against SARS-CoV pseudovirus. A competitive inhibition assay showed that S14 blocked the binding of SARS-CoV RBD to either soluble or cell-expressed angiotensin-converting enzyme 2 (ACE2). In summary, we developed a novel nanobody targeting SARS-CoV RBD, which might be useful for the development of therapeutics against SARS.
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Affiliation(s)
- Jiang-Fan Li
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences (AMMS), Beijing, 100071, China
| | - Lei He
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences (AMMS), Beijing, 100071, China
| | - Yong-Qiang Deng
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences (AMMS), Beijing, 100071, China
| | - Shu-Hui Qi
- College of Veterinary Medicine, Shanxi Agriculture University, Jinzhong, 030801, China
| | - Yue-Hong Chen
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences (AMMS), Beijing, 100071, China
| | - Xiao-Lu Zhang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences (AMMS), Beijing, 100071, China
| | - Shi-Xiong Hu
- College of Veterinary Medicine, Shanxi Agriculture University, Jinzhong, 030801, China
| | - Rui-Wen Fan
- College of Veterinary Medicine, Shanxi Agriculture University, Jinzhong, 030801, China
| | - Guang-Yu Zhao
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences (AMMS), Beijing, 100071, China.
| | - Cheng-Feng Qin
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Academy of Military Medical Sciences (AMMS), Beijing, 100071, China.
- Research Unit of Discovery and Tracing of Natural Focus Diseases, Chinese Academy of Medical Sciences, Beijing, 100071, China.
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