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Mezhibovsky E, Hoang SH, Szeto S, Roopchand DE. In silico analysis of dietary polyphenols and their gut microbial metabolites suggest inhibition of SARS-CoV-2 infection, replication, and host inflammatory mediators. J Biomol Struct Dyn 2023; 41:14339-14357. [PMID: 36803516 PMCID: PMC10439978 DOI: 10.1080/07391102.2023.2180669] [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: 08/09/2022] [Accepted: 02/09/2023] [Indexed: 02/22/2023]
Abstract
The outcome of SARS-CoV-2 infection ranges from asymptomatic to severe COVID-19 and death resulting from an exaggerated immune response termed cytokine storm. Epidemiological data have associated consumption of a high-quality plant-based diet with decreased incidence and severity of COVID-19. Dietary polyphenols and their microbial metabolites (MMs) have anti-viral and anti-inflammatory activities. Autodock Vina and Yasara were used in molecular docking and dynamics studies to investigate potential interactions of 7 parent polyphenols (PPs) and 11 MMs with the α- and Omicron variants of the SARS-CoV-2 spike glycoprotein (SGP), papain-like pro-tease (PLpro) and 3 chymotrypsin-like protease (3CLpro), as well as host inflammatory mediators including complement component 5a (C5a), C5a receptor (C5aR), and C-C chemokine receptor type 5 (CCR5). PPs and MMs interacted to varying degrees with residues on target viral and host inflammatory proteins showing potential as competitive inhibitors. Based on these in silico findings, PPs and MMs may inhibit SARS-CoV-2 infection, replication, and/or modulate host immunity in the gut or periphery. Such inhibition may explain why people that consume a high-quality plant-based diet have less incidence and severity of COVID-19.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Esther Mezhibovsky
- Department of Food Science, Rutgers University, NJ Institute for Food, Nutrition and Health (Rutgers Center for Lipid Research and Center for Nutrition, Microbiome, and Health), 61 Dudley Rd., New Brunswick, NJ 08901 USA
- Department of Nutritional Sciences Graduate Program, Rutgers University
| | - Skyler H. Hoang
- Department of Food Science, Rutgers University, NJ Institute for Food, Nutrition and Health (Rutgers Center for Lipid Research and Center for Nutrition, Microbiome, and Health), 61 Dudley Rd., New Brunswick, NJ 08901 USA
| | - Samantha Szeto
- Department of Food Science, Rutgers University, NJ Institute for Food, Nutrition and Health (Rutgers Center for Lipid Research and Center for Nutrition, Microbiome, and Health), 61 Dudley Rd., New Brunswick, NJ 08901 USA
| | - Diana E. Roopchand
- Department of Food Science, Rutgers University, NJ Institute for Food, Nutrition and Health (Rutgers Center for Lipid Research and Center for Nutrition, Microbiome, and Health), 61 Dudley Rd., New Brunswick, NJ 08901 USA
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Hatta MHM, Matmin J, Malek NANN, Kamisan FH, Badruzzaman A, Batumalaie K, Ling Lee S, Abdul Wahab R. COVID‐19: Prevention, Detection, and Treatment by Using Carbon Nanotubes‐Based Materials. ChemistrySelect 2023. [DOI: 10.1002/slct.202204615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
Affiliation(s)
- Mohd Hayrie Mohd Hatta
- Centre for Research and Development Asia Metropolitan University 81750 Johor Bahru Johor Malaysia
| | - Juan Matmin
- Department of Chemistry Faculty of Science Universiti Teknologi Malaysia 81310 UTM Johor Bahru Johor Malaysia
- Centre for Sustainable Nanomaterials Ibnu Sina Institute for Scientific and Industrial Research Universiti Teknologi Malaysia 81310 UTM Johor Bahru Johor Malaysia
| | - Nik Ahmad Nizam Nik Malek
- Centre for Sustainable Nanomaterials Ibnu Sina Institute for Scientific and Industrial Research Universiti Teknologi Malaysia 81310 UTM Johor Bahru Johor Malaysia
- Department of Biosciences, Faculty of Science Universiti Teknologi Malaysia 81310 UTM Johor Bahru Johor Malaysia
| | - Farah Hidayah Kamisan
- Department of Biomedical Sciences Faculty of Health Sciences Asia Metropolitan University 81750 Johor Bahru Johor Malaysia
| | - Aishah Badruzzaman
- Centre for Foundation, Language and General Studies Asia Metropolitan University 81750 Johor Bahru Johor Malaysia
| | - Kalaivani Batumalaie
- Department of Biomedical Sciences Faculty of Health Sciences Asia Metropolitan University 81750 Johor Bahru Johor Malaysia
| | - Siew Ling Lee
- Department of Chemistry Faculty of Science Universiti Teknologi Malaysia 81310 UTM Johor Bahru Johor Malaysia
- Centre for Sustainable Nanomaterials Ibnu Sina Institute for Scientific and Industrial Research Universiti Teknologi Malaysia 81310 UTM Johor Bahru Johor Malaysia
| | - Roswanira Abdul Wahab
- Department of Chemistry Faculty of Science Universiti Teknologi Malaysia 81310 UTM Johor Bahru Johor Malaysia
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53
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Experimental and clinical data analysis for identification of COVID-19 resistant ACE2 mutations. Sci Rep 2023; 13:2351. [PMID: 36759535 PMCID: PMC9910265 DOI: 10.1038/s41598-022-20773-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 09/19/2022] [Indexed: 02/11/2023] Open
Abstract
The high magnitude zoonotic event has caused by Severe Acute Respitarory Syndrome CoronaVirus-2 (SARS-CoV-2) is Coronavirus Disease-2019 (COVID-19) epidemics. This disease has high rate of spreading than mortality in humans. The human receptor, Angiotensin-Converting Enzyme 2 (ACE2), is the leading target site for viral Spike-protein (S-protein) that function as binding ligands and are responsible for their entry in humans. The patients infected with COVID-19 with comorbidities, particularly cancer patients, have a severe effect or high mortality rate because of the suppressed immune system. Nevertheless, there might be a chance wherein cancer patients cannot be infected with SARS-CoV-2 because of mutations in the ACE2, which may be resistant to the spillover between species. This study aimed to determine the mutations in the sequence of the human ACE2 protein and its dissociation with SARS-CoV-2 that might be rejecting viral transmission. The in silico approaches were performed to identify the impact of SARS-CoV-2 S-protein with ACE2 mutations, validated experimentally, occurred in the patient, and reported in cell lines. The identified changes significantly affect SARS-CoV-2 S-protein interaction with ACE2, demonstrating the reduction in the binding affinity compared to SARS-CoV. The data presented in this study suggest ACE2 mutants have a higher and lower affinity with SARS-Cov-2 S-protein to the wild-type human ACE2 receptor. This study would likely be used to report SARS-CoV-2 resistant ACE2 mutations and can be used to design active peptide development to inactivate the viral spread of SARS-CoV-2 in humans.
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Barreiro A, Prenafeta A, Bech-Sabat G, Roca M, Perozo Mur E, March R, González-González L, Madrenas L, Corominas J, Fernández A, Moros A, Cañete M, Molas M, Pentinat-Pelegrin T, Panosa C, Moreno A, Puigvert Molas E, Pol Vilarrassa E, Palmada J, Garriga C, Prat Cabañas T, Iglesias-Fernández J, Vergara-Alert J, Lorca-Oró C, Roca N, Fernández-Bastit L, Rodon J, Pérez M, Segalés J, Pradenas E, Marfil S, Trinité B, Ortiz R, Clotet B, Blanco J, Díaz Pedroza J, Ampudia Carrasco R, Rosales Salgado Y, Loubat-Casanovas J, Capdevila Larripa S, Prado JG, Barretina J, Sisteré-Oró M, Cebollada Rica P, Meyerhans A, Ferrer L. Preclinical evaluation of a COVID-19 vaccine candidate based on a recombinant RBD fusion heterodimer of SARS-CoV-2. iScience 2023; 26:106126. [PMID: 36748086 PMCID: PMC9893798 DOI: 10.1016/j.isci.2023.106126] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 12/22/2022] [Accepted: 01/28/2023] [Indexed: 02/05/2023] Open
Abstract
Current COVID-19 vaccines have been associated with a decline in infection rates, prevention of severe disease, and a decrease in mortality rates. However, SARS-CoV-2 variants are continuously evolving, and development of new accessible COVID-19 vaccines is essential to mitigate the pandemic. Here, we present data on preclinical studies in mice of a receptor-binding domain (RBD)-based recombinant protein vaccine (PHH-1V) consisting of an RBD fusion heterodimer comprising the B.1.351 and B.1.1.7 SARS-CoV-2 variants formulated in SQBA adjuvant, an oil-in-water emulsion. A prime-boost immunisation with PHH-1V in BALB/c and K18-hACE2 mice induced a CD4+ and CD8+ T cell response and RBD-binding antibodies with neutralizing activity against several variants, and also showed a good tolerability profile. Significantly, RBD fusion heterodimer vaccination conferred 100% efficacy, preventing mortality in SARS-CoV-2 infected K18-hACE2 mice, but also reducing Beta, Delta and Omicron infection in lower respiratory airways. These findings demonstrate the feasibility of this recombinant vaccine strategy.
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Affiliation(s)
- Antonio Barreiro
- HIPRA, Avda. La Selva, 135, Amer, 17170 Girona, Spain,Corresponding author
| | - Antoni Prenafeta
- HIPRA, Avda. La Selva, 135, Amer, 17170 Girona, Spain,Corresponding author
| | | | - Mercè Roca
- HIPRA, Avda. La Selva, 135, Amer, 17170 Girona, Spain
| | | | - Ricard March
- HIPRA, Avda. La Selva, 135, Amer, 17170 Girona, Spain
| | | | - Laia Madrenas
- HIPRA, Avda. La Selva, 135, Amer, 17170 Girona, Spain
| | | | | | | | - Manuel Cañete
- HIPRA, Avda. La Selva, 135, Amer, 17170 Girona, Spain
| | - Mercè Molas
- HIPRA, Avda. La Selva, 135, Amer, 17170 Girona, Spain
| | | | - Clara Panosa
- HIPRA, Avda. La Selva, 135, Amer, 17170 Girona, Spain
| | | | | | | | - Jordi Palmada
- HIPRA, Avda. La Selva, 135, Amer, 17170 Girona, Spain
| | - Carme Garriga
- HIPRA, Avda. La Selva, 135, Amer, 17170 Girona, Spain
| | | | | | - Júlia Vergara-Alert
- Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Centre de Recerca en Sanitat Animal (CReSA, IRTA-UAB), Campus de la UAB, 08193 Cerdanyola del Vallès, Spain
| | - Cristina Lorca-Oró
- Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Centre de Recerca en Sanitat Animal (CReSA, IRTA-UAB), Campus de la UAB, 08193 Cerdanyola del Vallès, Spain
| | - Núria Roca
- Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Centre de Recerca en Sanitat Animal (CReSA, IRTA-UAB), Campus de la UAB, 08193 Cerdanyola del Vallès, Spain
| | - Leira Fernández-Bastit
- Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Centre de Recerca en Sanitat Animal (CReSA, IRTA-UAB), Campus de la UAB, 08193 Cerdanyola del Vallès, Spain
| | - Jordi Rodon
- Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Centre de Recerca en Sanitat Animal (CReSA, IRTA-UAB), Campus de la UAB, 08193 Cerdanyola del Vallès, Spain
| | - Mònica Pérez
- Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Centre de Recerca en Sanitat Animal (CReSA, IRTA-UAB), Campus de la UAB, 08193 Cerdanyola del Vallès, Spain
| | - Joaquim Segalés
- Universitat Autònoma de Barcelona, CReSA (IRTA-UAB), Campus de la UAB, 08193 Cerdanyola del Vallès, Spain,Departament de Sanitat i Anatomia Animals, Facultat de Veterinària, UAB, 08193 Cerdanyola del Vallès, Spain
| | - Edwards Pradenas
- IrsiCaixa. AIDS Research Institute, Germans Trias i Pujol Research Institute (IGTP), Can Ruti Campus, UAB, 08916 Badalona, Spain
| | - Silvia Marfil
- IrsiCaixa. AIDS Research Institute, Germans Trias i Pujol Research Institute (IGTP), Can Ruti Campus, UAB, 08916 Badalona, Spain
| | - Benjamin Trinité
- IrsiCaixa. AIDS Research Institute, Germans Trias i Pujol Research Institute (IGTP), Can Ruti Campus, UAB, 08916 Badalona, Spain
| | - Raquel Ortiz
- IrsiCaixa. AIDS Research Institute, Germans Trias i Pujol Research Institute (IGTP), Can Ruti Campus, UAB, 08916 Badalona, Spain
| | - Bonaventura Clotet
- IrsiCaixa. AIDS Research Institute, Germans Trias i Pujol Research Institute (IGTP), Can Ruti Campus, UAB, 08916 Badalona, Spain,University of Vic–Central University of Catalonia (UVic-UCC), Vic, 08500 Catalonia, Spain
| | - Julià Blanco
- IrsiCaixa. AIDS Research Institute, Germans Trias i Pujol Research Institute (IGTP), Can Ruti Campus, UAB, 08916 Badalona, Spain,University of Vic–Central University of Catalonia (UVic-UCC), Vic, 08500 Catalonia, Spain
| | - Jorge Díaz Pedroza
- Comparative Medicine and Bioimage Centre of Catalonia, Germans Trias i Pujol Research Institute (CMCiB-IGTP), 08916 Badalona, Spain
| | - Rosa Ampudia Carrasco
- Comparative Medicine and Bioimage Centre of Catalonia, Germans Trias i Pujol Research Institute (CMCiB-IGTP), 08916 Badalona, Spain
| | - Yaiza Rosales Salgado
- Comparative Medicine and Bioimage Centre of Catalonia, Germans Trias i Pujol Research Institute (CMCiB-IGTP), 08916 Badalona, Spain
| | - Jordina Loubat-Casanovas
- Comparative Medicine and Bioimage Centre of Catalonia, Germans Trias i Pujol Research Institute (CMCiB-IGTP), 08916 Badalona, Spain
| | - Sara Capdevila Larripa
- Comparative Medicine and Bioimage Centre of Catalonia, Germans Trias i Pujol Research Institute (CMCiB-IGTP), 08916 Badalona, Spain
| | - Julia Garcia Prado
- IrsiCaixa. AIDS Research Institute, Germans Trias i Pujol Research Institute (IGTP), Can Ruti Campus, UAB, 08916 Badalona, Spain,Comparative Medicine and Bioimage Centre of Catalonia, Germans Trias i Pujol Research Institute (CMCiB-IGTP), 08916 Badalona, Spain
| | - Jordi Barretina
- Comparative Medicine and Bioimage Centre of Catalonia, Germans Trias i Pujol Research Institute (CMCiB-IGTP), 08916 Badalona, Spain
| | - Marta Sisteré-Oró
- Infection Biology Laboratory, Department of Experimental and Health Sciences (DCEXS), Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Paula Cebollada Rica
- Infection Biology Laboratory, Department of Experimental and Health Sciences (DCEXS), Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Andreas Meyerhans
- Infection Biology Laboratory, Department of Experimental and Health Sciences (DCEXS), Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain,Catalan Institution for Research and Advanced Studies (ICREA), Pg. Lluís Companys 23, 08010 Barcelona, Spain
| | - Laura Ferrer
- HIPRA, Avda. La Selva, 135, Amer, 17170 Girona, Spain
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Liu Y, Sulaiman HF, Johnson BR, Ma R, Gao Y, Fernando H, Amarasekara A, Ashley-Oyewole A, Fan H, Ingram HN, Briggs JM. QM/MM study of N501 involved intermolecular interaction between SARS-CoV-2 receptor binding domain and antibody of human origin. Comput Biol Chem 2023; 102:107810. [PMID: 36610304 PMCID: PMC9811887 DOI: 10.1016/j.compbiolchem.2023.107810] [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: 11/25/2022] [Revised: 01/02/2023] [Accepted: 01/03/2023] [Indexed: 01/06/2023]
Abstract
Intermolecular interaction between key residue N501 of the epitope on SARS-CoV-2 RBD and screening antibody B38 was studied using the QM/MM and QM approach. The QM/MM optimized geometry shows that angle X-H---Y is 165° for O-H---O between mAb light chain S30 and RBD N501. High level MP2 calculations indicated the interaction between RBD N501 and S30 of B38 Fab light chain provide a relatively strong attractive force of - 3.32 kcal/mol, whereas the hydrogen bond between RBD Q498 and S30 was quantified as 0.10 kcal/mol. The decrease in ESP partial charge on hydrogen atom of hydroxyl group on S30 drops from 0.38 a.u. to 0.31 a.u., exhibiting the sharing of 0.07 a.u. from the lone pair electron oxygen of N501 due to hydrogen bond formation. The NBO occupancy of hydrogen atom also decreases from 25.79 % to 22.93 % in the hydroxyl H-O NBO bond of S30. However, the minor change of NBO hybridization of hydroxyl oxygen of S30 from sp3.00 to sp3.05 implies the rigidity of hydrogen bond tetrahedral geometry in the relative dynamic protein complex. The O-H---O angle is 165° which is close but not exactly linear. The structural requirement for sp3 hybridization of oxygen for hydroxyl group on S30 and dimension of protein likely prevent O-H---O from adopting linear geometry. The hydrogen bond strengths were also calculated using a variety of DFT methods, and the result of - 3.33 kcal/mol from the M06L method is the closest to that of the MP2 calculation. Results of this work may aid in the COVID-19 vaccine and drug screening.
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Affiliation(s)
- Yuemin Liu
- Department of Chemistry, Prairie View A&M University, Prairie View, TX 77446, the United States of America,Department of Chemistry, Rice University, Houston, TX 77005, the United States of America,Corresponding author at: Department of Chemistry, Prairie View A&M University, Prairie View, TX 77446, the United States of America
| | - Hana F. Sulaiman
- Department of Chemistry, Prairie View A&M University, Prairie View, TX 77446, the United States of America
| | - Bruce R. Johnson
- Department of Chemistry, Rice University, Houston, TX 77005, the United States of America
| | - Rulong Ma
- Department of Biology and Biochemistry, University of Houston, Houston, TX 77004, the United States of America
| | - Yunxiang Gao
- Department of Chemistry, Prairie View A&M University, Prairie View, TX 77446, the United States of America
| | - Harshica Fernando
- Department of Chemistry, Prairie View A&M University, Prairie View, TX 77446, the United States of America
| | - Ananda Amarasekara
- Department of Chemistry, Prairie View A&M University, Prairie View, TX 77446, the United States of America
| | - Andrea Ashley-Oyewole
- Department of Chemistry, Prairie View A&M University, Prairie View, TX 77446, the United States of America
| | - Huajun Fan
- College of Chemical Engineering, Sichuan University Science and Engineering, Zigong, Sichuan 643000, PR China
| | - Heaven N. Ingram
- Department of Chemistry, Prairie View A&M University, Prairie View, TX 77446, the United States of America
| | - James M. Briggs
- Department of Biology and Biochemistry, University of Houston, Houston, TX 77004, the United States of America
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Bhattacharya M, Chatterjee S, Sharma AR, Lee SS, Chakraborty C. Delta variant (B.1.617.2) of SARS-CoV-2: current understanding of infection, transmission, immune escape, and mutational landscape. Folia Microbiol (Praha) 2023; 68:17-28. [PMID: 35962276 PMCID: PMC9374302 DOI: 10.1007/s12223-022-01001-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 08/07/2022] [Indexed: 12/01/2022]
Abstract
The Delta variant is one of the alarming variants of the SARS-CoV-2 virus that have been immensely detrimental and a significant cause of the prolonged pandemic (B.1.617.2). During the SARS-CoV-2 pandemic from December 2020 to October 2021, the Delta variant showed global dominance, and afterwards, the Omicron variant showed global dominance. Delta shows high infectivity rate which accounted for nearly 70% of the cases after December 2020. This review discusses the additional attributes that make the Delta variant so infectious and transmissible. The study also focuses on the significant mutations, namely the L452R and T478K present on the receptor-binding domain of spike (S)-glycoprotein, which confers specific alterations to the Delta variant. Considerably, we have also highlighted other notable factors such as the immune escape, infectivity and re-infectivity, vaccine escape, Ro number, S-glycoprotein stability, cleavage pattern, and its binding affinity with the host cell receptor protein. We have also emphasized clinical manifestations, symptomatology, morbidity, and mortality for the Delta variant compared with other significant SARS-CoV-2 variants. This review will help the researchers to get an elucidative view of the Delta variant to adopt some practical strategies to minimize the escalating spread of the SARS-CoV-2 Delta variant.
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Affiliation(s)
- Manojit Bhattacharya
- Department of Zoology, Fakir Mohan University, Vyasa Vihar, Balasore-756020, Odisha, India
| | - Srijan Chatterjee
- Department of Biotechnology, School of Life Science and Biotechnology, Adamas University, Kolkata, West Bengal, 700126, India
| | - Ashish Ranjan Sharma
- Institute for Skeletal Aging & Orthopaedic Surgery, Hallym University-Chuncheon Sacred Heart Hospital, Chuncheon-si, 24252, Gangwon-do, Republic of Korea
| | - Sang-Soo Lee
- Institute for Skeletal Aging & Orthopaedic Surgery, Hallym University-Chuncheon Sacred Heart Hospital, Chuncheon-si, 24252, Gangwon-do, Republic of Korea
| | - Chiranjib Chakraborty
- Department of Biotechnology, School of Life Science and Biotechnology, Adamas University, Kolkata, West Bengal, 700126, India.
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57
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Alyahyawi HE, Alharbi RA, Alatawi SK, Ahmed WAM, Almalki SSR. Assessment of the Prevalence and Incidence of COVID-19 in Saudi Arabia. J Multidiscip Healthc 2023; 16:227-236. [PMID: 36718380 PMCID: PMC9883987 DOI: 10.2147/jmdh.s394038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 01/18/2023] [Indexed: 01/25/2023] Open
Abstract
The global pandemic of coronavirus disease 2019 (COVID 19) is reported to have started in Wuhan City, Hebei Province, China. It has spread rapidly all over the world, including Saudi Arabia, having a severe health emergency. This new virus was named as the 2019 novel coronavirus (2019-nCoV), and now severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) based on previous practice and phylogenetic and taxonomic investigations. SARS-CoV-2 belongs to the family of Coronaviridae, Betacoronavirus, Sarbecovirus subgenus, genome β. Throughout the COVID 19 pandemic, several strains of SARS-CoV-2 have been recognized around the world. The SARS-CoV-2 variants have caused significant morbidity and mortality worldwide and in Saudi Arabia as well. The rate at which COVID-19 spread across borders and affected countries has highlighted the significance of health care systems to nations and global operations. This review focuses on the origin, epidemiology, pathophysiology, transmission, and the impact of this disease, while highlighting the knowledge about SARS-CoV-2 variants.
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Affiliation(s)
- Hanan E Alyahyawi
- Department of Laboratory Medicine, Faculty of Applied Medical Sciences, Albaha University, Al Bahah, Saudi Arabia
| | - Raed A Alharbi
- Department of Laboratory Medicine, Faculty of Applied Medical Sciences, Albaha University, Al Bahah, Saudi Arabia
| | - Saleha Keder Alatawi
- Department of Optometry, Faculty of Applied Medical Sciences, Albaha University, Al Bahah, Saudi Arabia
| | - Waled A M Ahmed
- Department of Nursing, Faculty of Applied Medical Sciences, Albaha University, Al Bahah, Saudi Arabia
| | - Shaia S R Almalki
- Department of Laboratory Medicine, Faculty of Applied Medical Sciences, Albaha University, Al Bahah, Saudi Arabia,Correspondence: Shaia SR Almalki, Department of Laboratory Medicine, Faculty of Applied Medical Sciences, Albaha University, Al Bahah, Saudi Arabia, Tel +966- 556556714, Email
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58
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Mahmoudvand S, Esmaeili Gouvarchin Ghaleh H, Jalilian FA, Farzanehpour M, Dorostkar R. Design of a multi-epitope-based vaccine consisted of immunodominant epitopes of structural proteins of SARS-CoV-2 using immunoinformatics approach. Biotechnol Appl Biochem 2023:10.1002/bab.2431. [PMID: 36577011 PMCID: PMC9880719 DOI: 10.1002/bab.2431] [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: 02/25/2022] [Accepted: 12/11/2022] [Indexed: 12/29/2022]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has shown rapid global spread and has resulted in a significant death toll worldwide. In this study, we aimed to design a multi-epitope vaccine against SARS-CoV-2 based on structural proteins S, M, N, and E. We identified B- and T-cell epitopes and then the antigenicity, toxicity, allergenicity, and similarity of predicted epitopes were analyzed. T-cell epitopes were docked with corresponding HLA alleles. Consequently, the selected T- and B-cell epitopes were included in the final construct. All selected epitopes were connected with different linkers and flagellin and pan-HLA DR binding epitopes (PADRE) as an adjuvant were used in the vaccine construct. Furthermore, molecular docking was used to evaluate the complex between the final vaccine construct and two alleles, HLA-A*02:01 and HLA-DRB1*01:01. Finally, codons were optimized for in silico cloning into pET28a(+) vector using SnapGene. The final vaccine construct comprised 11 CTL, HTL, and B-cell epitopes corresponding to 394 amino acid residues. In silico evaluation showed that the designed vaccine might potentially promote an immune response. Further in vivo preclinical and clinical testing is required to determine the safety and efficacy of the designed vaccine.
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Affiliation(s)
- Shahab Mahmoudvand
- Applied Virology Research CenterBaqiyatallah University of Medical SciencesTehranIran
| | | | - Farid Azizi Jalilian
- Department of Medical VirologyFaculty of MedicineHamadan University of Medical SciencesHamadanIran
| | - Mahdieh Farzanehpour
- Applied Virology Research CenterBaqiyatallah University of Medical SciencesTehranIran
| | - Ruhollah Dorostkar
- Applied Virology Research CenterBaqiyatallah University of Medical SciencesTehranIran
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59
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Zhou J, Liu Z, Zhang G, Xu W, Xing L, Lu L, Wang Q, Jiang S. Development of variant-proof severe acute respiratory syndrome coronavirus 2, pan-sarbecovirus, and pan-β-coronavirus vaccines. J Med Virol 2023; 95:e28172. [PMID: 36161303 PMCID: PMC9538210 DOI: 10.1002/jmv.28172] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 09/19/2022] [Accepted: 09/20/2022] [Indexed: 01/11/2023]
Abstract
The newly emerged severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants with high transmission rates and striking immune evasion have posed a serious challenge to the application of current first-generation SARS-CoV-2 vaccines. Other sarbecoviruses, such as SARS-CoV and SARS-related coronaviruses (SARSr-CoVs), have the potential to cause outbreaks in the future. These facts call for the development of variant-proof SARS-CoV-2, pan-sarbecovirus or pan-β-CoV vaccines. Several novel vaccine platforms have been used to develop vaccines with broad-spectrum neutralizing antibody responses and protective immunity to combat the current SARS-CoV-2 and its variants, other sarbecoviruses, as well as other β-CoVs, in the future. In this review, we discussed the major target antigens and protective efficacy of current SARS-CoV-2 vaccines and summarized recent advances in broad-spectrum vaccines against sarbecoviruses and β-CoVs.
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Affiliation(s)
- Jie Zhou
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS)Shanghai Institute of Infectious Disease and Biosecurity, School of Basic Medical SciencesFudan UniversityShanghaiChina
| | - Zezhong Liu
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS)Shanghai Institute of Infectious Disease and Biosecurity, School of Basic Medical SciencesFudan UniversityShanghaiChina
- Department of Pharmacology, School of PharmacyFudan UniversityShanghaiChina
| | - Guangxu Zhang
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS)Shanghai Institute of Infectious Disease and Biosecurity, School of Basic Medical SciencesFudan UniversityShanghaiChina
| | - Wei Xu
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS)Shanghai Institute of Infectious Disease and Biosecurity, School of Basic Medical SciencesFudan UniversityShanghaiChina
| | - Lixiao Xing
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS)Shanghai Institute of Infectious Disease and Biosecurity, School of Basic Medical SciencesFudan UniversityShanghaiChina
| | - Lu Lu
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS)Shanghai Institute of Infectious Disease and Biosecurity, School of Basic Medical SciencesFudan UniversityShanghaiChina
| | - Qian Wang
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS)Shanghai Institute of Infectious Disease and Biosecurity, School of Basic Medical SciencesFudan UniversityShanghaiChina
| | - Shibo Jiang
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS)Shanghai Institute of Infectious Disease and Biosecurity, School of Basic Medical SciencesFudan UniversityShanghaiChina
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60
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Klüpfel J, Paßreiter S, Rumpf M, Christa C, Holthoff HP, Ungerer M, Lohse M, Knolle P, Protzer U, Elsner M, Seidel M. Automated detection of neutralizing SARS-CoV-2 antibodies in minutes using a competitive chemiluminescence immunoassay. Anal Bioanal Chem 2023; 415:391-404. [PMID: 36346456 PMCID: PMC9643999 DOI: 10.1007/s00216-022-04416-6] [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: 08/11/2022] [Revised: 10/13/2022] [Accepted: 10/31/2022] [Indexed: 11/09/2022]
Abstract
The SARS-CoV-2 pandemic has shown the importance of rapid and comprehensive diagnostic tools. While there are numerous rapid antigen tests available, rapid serological assays for the detection of neutralizing antibodies are and will be needed to determine not only the amount of antibodies formed after infection or vaccination but also their neutralizing potential, preventing the cell entry of SARS-CoV-2. Current active-virus neutralization assays require biosafety level 3 facilities, while virus-free surrogate assays are more versatile in applications, but still take typically several hours until results are available. To overcome these disadvantages, we developed a competitive chemiluminescence immunoassay that enables the detection of neutralizing SARS-CoV-2 antibodies within 7 min. The neutralizing antibodies bind to the viral receptor binding domain (RBD) and inhibit the binding to the human angiotensin-converting enzyme 2 (ACE2) receptor. This competitive binding inhibition test was characterized with a set of 80 samples, which could all be classified correctly. The assay results favorably compare to those obtained with a more time-intensive ELISA-based neutralization test and a commercial surrogate neutralization assay. Our test could further be used to detect individuals with a high total IgG antibody titer, but only a low neutralizing titer, as well as for monitoring neutralizing antibodies after vaccinations. This effective performance in SARS-CoV-2 seromonitoring delineates the potential for the test to be adapted to other diseases in the future.
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Affiliation(s)
- Julia Klüpfel
- Institute of Water Chemistry, Chair of Analytical Chemistry and Water Chemistry, Technical University of Munich, Lichtenbergstr. 4, 85748 Garching, Germany
| | - Sandra Paßreiter
- Institute of Water Chemistry, Chair of Analytical Chemistry and Water Chemistry, Technical University of Munich, Lichtenbergstr. 4, 85748 Garching, Germany
| | - Melina Rumpf
- Institute of Water Chemistry, Chair of Analytical Chemistry and Water Chemistry, Technical University of Munich, Lichtenbergstr. 4, 85748 Garching, Germany
| | - Catharina Christa
- Institute of Virology, Technical University of Munich/Helmholtz Zentrum München, Trogerstr. 30, 81675 Munich, Germany
| | | | - Martin Ungerer
- ISAR Bioscience GmbH, Semmelweisstr. 5, 82152 Planegg, Germany
| | - Martin Lohse
- ISAR Bioscience GmbH, Semmelweisstr. 5, 82152 Planegg, Germany
| | - Percy Knolle
- Institute of Molecular Immunology/Experimental Oncology, Technical University of Munich, Ismaningerstr. 22, 81675 Munich, Germany
| | - Ulrike Protzer
- Institute of Virology, Technical University of Munich/Helmholtz Zentrum München, Trogerstr. 30, 81675 Munich, Germany ,German Center for Infection Research (DZIF), 81675 Munich, Germany
| | - Martin Elsner
- Institute of Water Chemistry, Chair of Analytical Chemistry and Water Chemistry, Technical University of Munich, Lichtenbergstr. 4, 85748 Garching, Germany
| | - Michael Seidel
- Institute of Water Chemistry, Chair of Analytical Chemistry and Water Chemistry, Technical University of Munich, Lichtenbergstr. 4, 85748 Garching, Germany
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61
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In Silico Analysis of Bacteriocins from Lactic Acid Bacteria Against SARS-CoV-2. Probiotics Antimicrob Proteins 2023; 15:17-29. [PMID: 34837166 PMCID: PMC8626284 DOI: 10.1007/s12602-021-09879-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/11/2021] [Indexed: 01/18/2023]
Abstract
The COVID-19 pandemic caused by a novel coronavirus (SARS-CoV-2) is a serious health concern in the twenty-first century for scientists, health workers, and all humans. The absence of specific biotherapeutics requires new strategies to prevent the spread and prophylaxis of the novel virus and its variants. The SARS-CoV-2 virus shows pathogenesis by entering the host cells via spike protein and Angiotensin-Converting Enzyme 2 receptor protein. Thus, the present study aims to compute the binding energies between a wide range of bacteriocins with receptor-binding domain (RBD) on spike proteins of wild type (WT) and beta variant (lineage B.1.351). Molecular docking analyses were performed to evaluate binding energies. Upon achieving the best bio-peptides with the highest docking scores, further molecular dynamics (MD) simulations were performed to validate the structure and interaction stability. Protein-protein docking of the chosen 22 biopeptides with WT-RBD showed docking scores lower than -7.9 kcal/mol. Pediocin PA-1 and salivaricin P showed the lowest (best) docking scores of - 12 kcal/mol. Pediocin PA-1, salivaricin B, and salivaricin P showed a remarkable increase in the double mutant's predicted binding affinity with -13.8 kcal/mol, -13.0 kcal/mol, and -12.5 kcal/mol, respectively. Also, a better predicted binding affinity of pediocin PA-1 and salivaricin B against triple mutant was observed compared to the WT. Thus, pediocin PA-1 binds stronger to mutants of the RBD, particularly to double and triple mutants. Salivaricin B showed a better predicted binding affinity towards triple mutant compared to WT, showing that it might be another bacteriocin with potential activity against the SARS-CoV-2 beta variant. Overall, pediocin PA-1, salivaricin P, and salivaricin B are the most promising candidates for inhibiting SARS-CoV-2 (including lineage B.1.351) entrance into the human cells. These bacteriocins derived from lactic acid bacteria hold promising potential for paving an alternative way for treatment and prophylaxis of WT and beta variants.
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62
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Carvalho PPD, Alves NA. Featuring ACE2 binding SARS-CoV and SARS-CoV-2 through a conserved evolutionary pattern of amino acid residues. J Biomol Struct Dyn 2022; 40:11719-11728. [PMID: 34486937 PMCID: PMC8425439 DOI: 10.1080/07391102.2021.1965028] [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] [Indexed: 12/24/2022]
Abstract
Spike (S) glycoproteins mediate the coronavirus entry into the host cell. The S1 subunit of S-proteins contains the receptor-binding domain (RBD) that is able to recognize different host receptors, highlighting its remarkable capacity to adapt to their hosts along the viral evolution. While RBD in spike proteins is determinant for the virus-receptor interaction, the active residues lie at the receptor-binding motif (RBM), a region located in RBD that plays a fundamental role binding the outer surface of their receptors. Here, we address the hypothesis that SARS-CoV and SARS-CoV-2 strains able to use angiotensin-converting enzyme 2 (ACE2) proteins have adapted their RBM along the viral evolution to explore specific conformational topology driven by the residues YGF to infect host cells. We also speculate that this YGF-based mechanism can act as a protein signature located at the RBM to distinguish coronaviruses able to use ACE2 as a cell entry receptor.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Patrícia P. D. Carvalho
- Departamento de Física, FFCLRP, Universidade de São Paulo, Ribeirão Preto, SP, Brazil,CONTACT Patrícia P. D. Carvalho ;
| | - Nelson A. Alves
- Departamento de Física, FFCLRP, Universidade de São Paulo, Ribeirão Preto, SP, Brazil,Nelson Alves
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63
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Elssaig EH, Alnour TM, Ullah MF, Ahmed-Abakur EH. Omicron SARS-CoV-2 Variants in an In Silico Genomic Comparison Study with the Original Wuhan Strain and WHO-Recognized Variants of Concern. Pol J Microbiol 2022; 71:577-587. [PMID: 36537060 PMCID: PMC9944972 DOI: 10.33073/pjm-2022-053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Accepted: 11/12/2022] [Indexed: 12/24/2022] Open
Abstract
This study aimed to determine the genetic alterations in the Omicron variants compared to other variants of concern (VOCs) to trace the evolutionary genetics of the SARS-CoV-2 variants responsible for the multiple COVID-19 waves globally. The present study is an in silico analysis determining the evolution of selected 11 VOCs compared to the original Wuhan strain. The variants included six Omicrons and one variant of Alpha, Beta, Delta, Gamma, and Mu. The pairwise alignment with the local alignment search tool of NCBI Nucleotide-BLAST and NCBI Protein-BLAST were used to determine the nucleotide base changes and corresponding amino acid changes in proteins, respectively. The genomic analysis revealed 210 nucleotide changes; most of these changes (127/210, 60.5%) were non-synonymous mutations that occurred mainly in the S gene (52/127, 40.1%). The remaining 10.5% (22/210) and 1.9% (4/210) of the mutations were frameshift deletions and frameshift insertions, respectively. The frameshift insertion (Ins22194T T22195G) led to frameshift deletion (Δ211N). Only four mutations (C241T, C3037T, C14408T, and A23403G) were shared among all the VOCs. The nucleotide changes among Omicron variants resulted in 61 amino acid changes, while the nucleotide changes in other VOCs showed 11 amino acid changes. The present study showed that most mutations (38/61, 62.3%) among Omicron variants occurred in the S gene; and 34.2% of them (13/38) occurred in the receptor-binding domain. The present study confirmed that most of mutations developed by Omicron variants occurred in the vaccine target gene (S gene).
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Affiliation(s)
- Elmutuz H. Elssaig
- Department of Medical Laboratory Technology (FAMS), University of Tabuk, TabukSaudi Arabia,Prince Fahd Bin Sultan Chair for Biomedical Research, University of Tabuk, Tabuk, Saudi Arabia,Faculty of Medical Laboratory Science, Department of Microbiology and Immunology, Alzaiem Alazhari University, Khartoum Bahry, Sudan
| | - Tarig M.S. Alnour
- Department of Medical Laboratory Technology (FAMS), University of Tabuk, TabukSaudi Arabia,Prince Fahd Bin Sultan Chair for Biomedical Research, University of Tabuk, Tabuk, Saudi Arabia,Faculty of Medical Laboratory Science, Department of Microbiology and Immunology, Alzaiem Alazhari University, Khartoum Bahry, Sudan, T.M.S. Alnour, Department of Medical Laboratory Technology (FAMS), University of Tabuk, Saudi Arabia; Prince Fahd Bin Sultan Chair for Biomedical Research, University of Tabuk, Tabuk, Saudi Arabia; Faculty of Medical Laboratory Science, Department of Microbiology and Immunology, Alzaiem Alazhari University, Khartoum Bahry, Sudan;
| | - Mohammad Fahad Ullah
- Department of Medical Laboratory Technology (FAMS), University of Tabuk, TabukSaudi Arabia,Prince Fahd Bin Sultan Chair for Biomedical Research, University of Tabuk, Tabuk, Saudi Arabia
| | - Eltayib H. Ahmed-Abakur
- Department of Medical Laboratory Technology (FAMS), University of Tabuk, TabukSaudi Arabia,Prince Fahd Bin Sultan Chair for Biomedical Research, University of Tabuk, Tabuk, Saudi Arabia,Faculty of Medical Laboratory Science, Department of Microbiology and Immunology, Alzaiem Alazhari University, Khartoum Bahry, Sudan
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64
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Fryer HA, Hartley GE, Edwards ES, O'Hehir RE, van Zelm MC. Humoral immunity and B-cell memory in response to SARS-CoV-2 infection and vaccination. Biochem Soc Trans 2022; 50:1643-1658. [PMID: 36421662 PMCID: PMC9788580 DOI: 10.1042/bst20220415] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 11/08/2022] [Accepted: 11/09/2022] [Indexed: 01/15/2024]
Abstract
Natural infection with SARS-CoV-2 induces a robust circulating memory B cell (Bmem) population, which remains stable in number at least 8 months post-infection despite the contraction of antibody levels after 1 month. Multiple vaccines have been developed to combat the virus. These include two new formulations, mRNA and adenoviral vector vaccines, which have varying efficacy rates, potentially related to their distinct capacities to induce humoral immune responses. The mRNA vaccines BNT162b2 (Pfizer-BioNTech) and mRNA-1273 (Moderna) elicit significantly higher serum IgG and neutralizing antibody levels than the adenoviral vector ChAdOx1 (AstraZeneca) and Ad26.COV2.S (Janssen) vaccines. However, all vaccines induce Spike- and RBD-specific Bmem, which are vital in providing long-lasting protection in the form of rapid recall responses to subsequent infections. Past and current SARS-CoV-2 variants of concern (VoC) have shown the capacity to escape antibody neutralization to varying degrees. A booster dose with an mRNA vaccine following primary vaccination restores antibody levels and improves the capacity of these antibodies and Bmem to bind viral variants, including the current VoC Omicron. Future experimental research will be essential to evaluate the durability of protection against VoC provided by each vaccine and to identify immune markers of protection to enable prognostication of people who are at risk of severe complications from COVID-19.
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Affiliation(s)
- Holly A. Fryer
- Allergy and Clinical Immunology Laboratory, Department of Immunology and Pathology, Central Clinical School, Monash University, Melbourne, VIC, Australia
| | - Gemma E. Hartley
- Allergy and Clinical Immunology Laboratory, Department of Immunology and Pathology, Central Clinical School, Monash University, Melbourne, VIC, Australia
| | - Emily S.J. Edwards
- Allergy and Clinical Immunology Laboratory, Department of Immunology and Pathology, Central Clinical School, Monash University, Melbourne, VIC, Australia
| | - Robyn E. O'Hehir
- Allergy and Clinical Immunology Laboratory, Department of Immunology and Pathology, Central Clinical School, Monash University, Melbourne, VIC, Australia
- Allergy, Asthma and Clinical Immunology Service, Alfred Hospital, Melbourne, VIC, Australia
| | - Menno C. van Zelm
- Allergy and Clinical Immunology Laboratory, Department of Immunology and Pathology, Central Clinical School, Monash University, Melbourne, VIC, Australia
- Allergy, Asthma and Clinical Immunology Service, Alfred Hospital, Melbourne, VIC, Australia
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65
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Fiaz N, Zahoor I, Saima S, Basheer A. Genomic landscape of alpha-variant of SARS-CoV-2 circulated in Pakistan. PLoS One 2022; 17:e0276171. [PMID: 36512569 PMCID: PMC9746927 DOI: 10.1371/journal.pone.0276171] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 09/27/2022] [Indexed: 12/14/2022] Open
Abstract
In this study, we investigated the genomic variability of alpha-VOC of SARS-CoV-2 in Pakistan, in context of the global population of this variant. A set of 461 whole-genome sequences of Pakistani samples of alpha-variant, retrieved from GISAID, were aligned in MAFFT and used as an input to the Coronapp web-application. Phylogenetic tree was constructed through maximum-likelihood method by downloading the 100 whole-genome sequences of alpha-variant for each of the 12 countries having the largest number of Pakistani diasporas. We detected 1725 mutations, which were further categorized into 899 missense mutations, 654 silent mutations, 52 mutations in non-coding regions, 25 in-frame deletions, 01 in-frame insertion, 51 frameshift deletions, 21 frameshift insertions, 21 stop-gained variants, and 1 stop-gained deletion. We found NSP3 and Spike as the most variable proteins with 355 and 233 mutations respectively. However, some characteristic mutations like Δ144(S), G204R(N), and T1001I, I2230T, del3675-3677(ORF1ab) were missing in the Pakistani population of alpha-variant. Likewise, R1518K(NSP3), P83L(NSP9), and A52V, H164Y(NSP13) were found for the first time in this study. Interestingly, Y145 deletion(S) had 99% prevalence in Pakistan but globally it was just 4.2% prevalent. Likewise, R68S substitution (ORF3a), F120 frameshift deletion, L120 insertion, L118V substitution (ORF8), and N280Y(NSP2) had 20.4%, 14.3%, 14.8%, 9.1%, 13.9% prevalence locally but globally they were just 0.1%, 0.2%, 0.04%, 1.5%, and 2.4% prevalent respectively. The phylogeny analysis revealed that majority of Pakistani samples were grouped together in the same clusters with Italian, and Spanish samples suggesting the transmission of alpha-variant to Pakistan from these western European countries.
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Affiliation(s)
- Nazia Fiaz
- Genetic and Genomic Laboratory, Department of Animal Breeding and Genetics, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Imran Zahoor
- Genetic and Genomic Laboratory, Department of Animal Breeding and Genetics, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Saima Saima
- Department of Animal Nutrition, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Atia Basheer
- Genetic and Genomic Laboratory, Department of Animal Breeding and Genetics, University of Veterinary and Animal Sciences, Lahore, Pakistan
- * E-mail:
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66
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Thermophilic Filamentous Fungus C1-Cell-Cloned SARS-CoV-2-Spike-RBD-Subunit-Vaccine Adjuvanted with Aldydrogel ®85 Protects K18-hACE2 Mice against Lethal Virus Challenge. Vaccines (Basel) 2022; 10:vaccines10122119. [PMID: 36560529 PMCID: PMC9783968 DOI: 10.3390/vaccines10122119] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 11/30/2022] [Accepted: 11/30/2022] [Indexed: 12/14/2022] Open
Abstract
SARS-CoV-2 is evolving with increased transmission, host range, pathogenicity, and virulence. The original and mutant viruses escape host innate (Interferon) immunity and adaptive (Antibody) immunity, emphasizing unmet needs for high-yield, commercial-scale manufacturing to produce inexpensive vaccines/boosters for global/equitable distribution. We developed DYAI-100A85, a SARS-CoV-2 spike receptor binding domain (RBD) subunit antigen vaccine expressed in genetically modified thermophilic filamentous fungus, Thermothelomyces heterothallica C1, and secreted at high levels into fermentation medium. The RBD-C-tag antigen strongly binds ACE2 receptors in vitro. Alhydrogel®'85'-adjuvanted RDB-C-tag-based vaccine candidate (DYAI-100A85) demonstrates strong immunogenicity, and antiviral efficacy, including in vivo protection against lethal intranasal SARS-CoV-2 (D614G) challenge in human ACE2-transgenic mice. No loss of body weight or adverse events occurred. DYAI-100A85 also demonstrates excellent safety profile in repeat-dose GLP toxicity study. In summary, subcutaneous prime/boost DYAI-100A85 inoculation induces high titers of RBD-specific neutralizing antibodies and protection of hACE2-transgenic mice against lethal challenge with SARS-CoV-2. Given its demonstrated safety, efficacy, and low production cost, vaccine candidate DYAI-100 received regulatory approval to initiate a Phase 1 clinical trial to demonstrate its safety and efficacy in humans.
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67
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Zolfaghari MA, Ghadiri Moghaddam F, Rajput S, Karimi A, Naghi Vishteh M, Mahmoodpoor A, Dolati S, Yousefi M. SARS-CoV-2 vaccines: A double-edged sword throughout rapid evolution of COVID-19. Cell Biol Int 2022; 46:2009-2017. [PMID: 36047303 PMCID: PMC9539123 DOI: 10.1002/cbin.11903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Revised: 07/12/2022] [Accepted: 08/24/2022] [Indexed: 11/11/2022]
Abstract
After more than 2 years of the coronavirus disease 2019 pandemic caused by severe acute respiratory syndrome coronavirus 2, several questions have remained unanswered that affected our daily lives. Although substantial vaccine development could resist this challenge, emerging new variants in different countries could be considered as potent concerns regarding the adverse effects of reinfection or postvaccination. Precisely, these concerns address some significant and probable outcomes in vaccinated or reinfected models, followed by some virus challenges, such as antibody-dependent enhancement and cytokine storm. Therefore, the importance of evaluating the effectiveness of neutralizing antibodies (nAbs) elicited by vaccination and the rise of new variants must be addressed.
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Affiliation(s)
- Mohammad Ali Zolfaghari
- Student Research CommitteeTabriz University of Medical SciencesTabrizIran
- Department of Molecular Medicine, Faculty of Advanced Medical SciencesTabriz University of Medical SciencesTabrizIran
| | | | - Shabnam Rajput
- Department of Pediatrics, School of MedicineJahrom University of Medical SciencesJahromIran
| | - Abbas Karimi
- Department of Molecular Medicine, Faculty of Advanced Medical SciencesTabriz University of Medical SciencesTabrizIran
- Biotechnology Research CenterTabriz University of Medical SciencesTabrizIran
| | - Mohadeseh Naghi Vishteh
- Department of Genetics and Molecular Biology, School of MedicineIsfahan University of Medical SciencesIsfahanIran
| | - Ata Mahmoodpoor
- Department of AnesthesiologyTabriz University of Medical SciencesTabrizIran
| | - Sanam Dolati
- Physical Medicine and Rehabilitation Research Center, Aging Research InstituteTabriz University of Medical SciencesTabrizIran
| | - Mehdi Yousefi
- Stem Cell Research CenterTabriz University of Medical SciencesTabrizIran
- Department of Immunology, Faculty of MedicineTabriz University of Medical SciencesTabrizIran
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68
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Rothenberger S, Hurdiss DL, Walser M, Malvezzi F, Mayor J, Ryter S, Moreno H, Liechti N, Bosshart A, Iss C, Calabro V, Cornelius A, Hospodarsch T, Neculcea A, Looser T, Schlegel A, Fontaine S, Villemagne D, Paladino M, Schiegg D, Mangold S, Reichen C, Radom F, Kaufmann Y, Schaible D, Schlegel I, Zitt C, Sigrist G, Straumann M, Wolter J, Comby M, Sacarcelik F, Drulyte I, Lyoo H, Wang C, Li W, Du W, Binz HK, Herrup R, Lusvarghi S, Neerukonda SN, Vassell R, Wang W, Adler JM, Eschke K, Nascimento M, Abdelgawad A, Gruber AD, Bushe J, Kershaw O, Knutson CG, Balavenkatraman KK, Ramanathan K, Wyler E, Teixeira Alves LG, Lewis S, Watson R, Haeuptle MA, Zürcher A, Dawson KM, Steiner D, Weiss CD, Amstutz P, van Kuppeveld FJM, Stumpp MT, Bosch BJ, Engler O, Trimpert J. The trispecific DARPin ensovibep inhibits diverse SARS-CoV-2 variants. Nat Biotechnol 2022; 40:1845-1854. [PMID: 35864170 PMCID: PMC9750863 DOI: 10.1038/s41587-022-01382-3] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 06/02/2022] [Indexed: 01/14/2023]
Abstract
The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants with potential resistance to existing drugs emphasizes the need for new therapeutic modalities with broad variant activity. Here we show that ensovibep, a trispecific DARPin (designed ankyrin repeat protein) clinical candidate, can engage the three units of the spike protein trimer of SARS-CoV-2 and inhibit ACE2 binding with high potency, as revealed by cryo-electron microscopy analysis. The cooperative binding together with the complementarity of the three DARPin modules enable ensovibep to inhibit frequent SARS-CoV-2 variants, including Omicron sublineages BA.1 and BA.2. In Roborovski dwarf hamsters infected with SARS-CoV-2, ensovibep reduced fatality similarly to a standard-of-care monoclonal antibody (mAb) cocktail. When used as a single agent in viral passaging experiments in vitro, ensovibep reduced the emergence of escape mutations in a similar fashion to the same mAb cocktail. These results support further clinical evaluation of ensovibep as a broad variant alternative to existing targeted therapies for Coronavirus Disease 2019 (COVID-19).
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Affiliation(s)
- Sylvia Rothenberger
- Spiez Laboratory, Austrasse, Spiez, Switzerland
- Institute of Microbiology, University Hospital Center and University of Lausanne, Lausanne, Switzerland
| | - Daniel L Hurdiss
- Department Biomolecular Health Sciences, Division Infectious Diseases & Immunology - Virology section, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
- Cryo-Electron Microscopy, Bijvoet Center for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, Netherlands
| | - Marcel Walser
- Molecular Partners AG, Zurich-Schlieren, Switzerland
| | | | - Jennifer Mayor
- Spiez Laboratory, Austrasse, Spiez, Switzerland
- Institute of Microbiology, University Hospital Center and University of Lausanne, Lausanne, Switzerland
| | - Sarah Ryter
- Spiez Laboratory, Austrasse, Spiez, Switzerland
| | - Hector Moreno
- Institute of Microbiology, University Hospital Center and University of Lausanne, Lausanne, Switzerland
| | | | | | - Chloé Iss
- Molecular Partners AG, Zurich-Schlieren, Switzerland
| | | | | | | | | | - Thamar Looser
- Molecular Partners AG, Zurich-Schlieren, Switzerland
| | - Anja Schlegel
- Molecular Partners AG, Zurich-Schlieren, Switzerland
| | | | | | | | | | | | | | - Filip Radom
- Molecular Partners AG, Zurich-Schlieren, Switzerland
| | | | | | - Iris Schlegel
- Molecular Partners AG, Zurich-Schlieren, Switzerland
| | - Christof Zitt
- Molecular Partners AG, Zurich-Schlieren, Switzerland
| | | | | | - Julia Wolter
- Molecular Partners AG, Zurich-Schlieren, Switzerland
| | - Marco Comby
- Molecular Partners AG, Zurich-Schlieren, Switzerland
| | | | - Ieva Drulyte
- Materials and Structural Analysis, Thermo Fisher Scientific, Eindhoven, Netherlands
| | - Heyrhyoung Lyoo
- Department Biomolecular Health Sciences, Division Infectious Diseases & Immunology - Virology section, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
| | - Chunyan Wang
- Department Biomolecular Health Sciences, Division Infectious Diseases & Immunology - Virology section, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
| | - Wentao Li
- Department Biomolecular Health Sciences, Division Infectious Diseases & Immunology - Virology section, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
| | - Wenjuan Du
- Department Biomolecular Health Sciences, Division Infectious Diseases & Immunology - Virology section, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
| | | | - Rachel Herrup
- Laboratory of Immunoregulation, Division of Viral Products, Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, MD, USA
| | - Sabrina Lusvarghi
- Laboratory of Immunoregulation, Division of Viral Products, Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, MD, USA
| | - Sabari Nath Neerukonda
- Laboratory of Immunoregulation, Division of Viral Products, Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, MD, USA
| | - Russell Vassell
- Laboratory of Immunoregulation, Division of Viral Products, Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, MD, USA
| | - Wei Wang
- Laboratory of Immunoregulation, Division of Viral Products, Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, MD, USA
| | - Julia M Adler
- Freie Universität Berlin, Institut für Virologie, Berlin, Germany
| | - Kathrin Eschke
- Freie Universität Berlin, Institut für Virologie, Berlin, Germany
| | | | - Azza Abdelgawad
- Freie Universität Berlin, Institut für Virologie, Berlin, Germany
| | - Achim D Gruber
- Freie Universität Berlin, Institut für Tierpathologie, Berlin, Germany
| | - Judith Bushe
- Freie Universität Berlin, Institut für Tierpathologie, Berlin, Germany
| | - Olivia Kershaw
- Freie Universität Berlin, Institut für Tierpathologie, Berlin, Germany
| | - Charles G Knutson
- Novartis Institutes for BioMedical Research, PK Sciences, Cambridge, MA, USA
| | | | | | - Emanuel Wyler
- Max-Delbrück-Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
| | | | - Seth Lewis
- Molecular Partners AG, Zurich-Schlieren, Switzerland
| | | | | | | | | | | | - Carol D Weiss
- Laboratory of Immunoregulation, Division of Viral Products, Center for Biologics Evaluation and Research, US Food and Drug Administration, Silver Spring, MD, USA
| | | | - Frank J M van Kuppeveld
- Department Biomolecular Health Sciences, Division Infectious Diseases & Immunology - Virology section, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
| | | | - Berend-Jan Bosch
- Department Biomolecular Health Sciences, Division Infectious Diseases & Immunology - Virology section, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
| | | | - Jakob Trimpert
- Freie Universität Berlin, Institut für Virologie, Berlin, Germany
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69
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Rodriguez JA, Gonzalez J, Arboleda-Bustos CE, Mendoza N, Martinez C, Pinzon A. Computational modeling of the effect of five mutations on the structure of the ACE2 receptor and their correlation with infectivity and virulence of some emerged variants of SARS-CoV-2 suggests mechanisms of binding affinity dysregulation. Chem Biol Interact 2022; 368:110244. [PMID: 36336003 PMCID: PMC9630301 DOI: 10.1016/j.cbi.2022.110244] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 10/11/2022] [Accepted: 10/24/2022] [Indexed: 11/06/2022]
Abstract
Interactions between the human angiotensin-converting enzyme 2 (ACE2) and the RBD region of the SARS-CoV-2 Spike protein are critical for virus entry into the host cell. The objective of this work was to identify some of the most relevant SARS-CoV-2 Spike variants that emerged during the pandemic and evaluate their binding affinity with human variants of ACE2 since some ACE2 variants can enhance or reduce the affinity of the interaction between the ACE2 and S proteins. However, no information has been sought to extrapolate to different variants of SARS-CoV-2. Therefore, to understand the impact on the affinity of the interaction between ACE2 protein variants and SARS-CoV-2 protein S variants, molecular docking was used in this study to predict the effects of five mutations of ACE2 when they interact with Alpha, Beta, Delta, Omicron variants and a hypothetical variant, which present mutations in the RBD region of the SARS-CoV-2 Spike protein. Our results suggest that these variants could alter the interaction of the Spike and the human ACE2 protein, losing or creating new inter-protein contacts, enhancing viral fitness by improving binding affinity, and leading to an increase in infectivity, virulence, and transmission. This investigation highlighted that the S19P mutation of ACE2 decreases the binding affinity between the ACE2 and Spike proteins in the presence of the Beta variant and the wild-type variant of SARS-CoV-2 isolated in Wuhan-2019. The R115Q mutation of ACE2 lowers the binding affinity of these two proteins in the presence of the Beta and Delta variants. Similarly, the K26R mutation lowers the affinity of the interaction between the ACE2 and Spike proteins in the presence of the Alpha variant. This decrease in binding affinity is probably due to the lack of interaction between some of the key residues of the interaction complex between the ACE2 protein and the RBD region of the SARS-CoV-2 Spike protein. Therefore, ACE2 mutations appear in the presence of these variants, they could suggest an intrinsic resistance to COVID-19 disease. On the other hand, our results suggested that the K26R, M332L, and K341R mutations of ACE2 expressively showed the affinity between the ACE2 and Spike proteins in the Alpha, Beta, and Delta variants. Consequently, these ACE2 mutations in the presence of the Alpha, Beta, and delta variants of SARS-CoV-2 could be more infectious and virulent in human cells compared to the SARS-CoV-2 isolated in Wuhan-2019 and it could have a negative prognosis of the disease. Finally, the Omicron variant in interaction with ACE2 WT, S19P, R115Q, M332L, and K341R mutations of ACE2 showed a significant decrease in binding affinity. This could be consistent that the Omicron variant causes less severe symptoms than previous variants. On the other hand, our results suggested Omicron in the complex with K26R, the binding affinity is increased between ACE2/RBD, which could indicate a negative prognosis of the disease in people with these allelic conditions.
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Affiliation(s)
- J A Rodriguez
- Bioinformatics and Systems Biology Laboratory (GIBBS). Instituto de Genética, Universidad Nacional de Colombia, Colombia.
| | - J Gonzalez
- Departamento de Nutrición y Bioquímica. Pontificia Universidad Javeriana Bogotá, Colombia
| | - C E Arboleda-Bustos
- Neurosciences Group. Instituto de Genética, Universidad Nacional de Colombia, Colombia
| | - N Mendoza
- Bioinformatics and Systems Biology Laboratory (GIBBS). Instituto de Genética, Universidad Nacional de Colombia, Colombia
| | - C Martinez
- Neurosciences Group. Instituto de Genética, Universidad Nacional de Colombia, Colombia
| | - A Pinzon
- Bioinformatics and Systems Biology Laboratory (GIBBS). Instituto de Genética, Universidad Nacional de Colombia, Colombia
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70
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McCann N, Castellino FJ. Cell Entry and Unusual Replication of SARS-CoV-2. Curr Drug Targets 2022; 23:1539-1554. [PMID: 36239725 DOI: 10.2174/1389450124666221014102927] [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: 06/17/2022] [Revised: 09/13/2022] [Accepted: 09/19/2022] [Indexed: 01/25/2023]
Abstract
BACKGROUND SARS-CoV-2 is the causative virus for the CoVID-19 pandemic that has frequently mutated to continue to infect and resist available vaccines. Emerging new variants of the virus have complicated notions of immunity conferred by vaccines versus immunity that results from infection. While we continue to progress from epidemic to endemic as a result of this collective immunity, the pandemic remains a morbid and mortal problem. OBJECTIVE The SARS-CoV-2 virus has a very complex manner of replication. The spike protein, one of the four structural proteins of the encapsulated virus, is central to the ability of the virus to penetrate cells to replicate. The objective of this review is to summarize these complex features of viral replication. METHODS A review of the recent literature was performed on the biology of SARS-CoV-2 infection from published work from PubMed and works reported to preprint servers, e.g., bioRxiv and medRxiv. RESULTS AND CONCLUSION The complex molecular and cellular biology involved in SARS-CoV-2 replication and the origination of >30 proteins from a single open reading frame (ORF) have been summarized, as well as the structural biology of spike protein, a critical factor in the cellular entry of the virus, which is a necessary feature for it to replicate and cause disease.
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Affiliation(s)
- Nathan McCann
- Department of Chemistry and Biochemistry and W.M. Keck Center for Transgene Research, University of Notre Dame, Notre Dame, IN 46530, USA
| | - Francis J Castellino
- Department of Chemistry and Biochemistry and W.M. Keck Center for Transgene Research, University of Notre Dame, Notre Dame, IN 46530, USA
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71
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Acosta‐Gutiérrez S, Buckley J, Battaglia G. The Role of Host Cell Glycans on Virus Infectivity: The SARS-CoV-2 Case. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 10:e2201853. [PMID: 36417571 PMCID: PMC9811451 DOI: 10.1002/advs.202201853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 10/03/2022] [Indexed: 06/16/2023]
Abstract
Glycans are ubiquitously expressed sugars, coating the cell and protein surfaces. They are found on many proteins as either short and branched chains or long chains sticking out from special membrane proteins, known as proteoglycans. This sugar cushion, the glycocalyx, modulates specific interactions and protects the cell. Here it is shown that both the expression of proteoglycans and the glycans expressed on the surface of both the host and virus proteins have a critical role in modulating viral attachment to the cell. A mathematical model using SARS-Cov-2 as an archetypical virus to study the glycan role during infection is proposed. It is shown that this occurs via a tug-of-war of forces. On one side, the multivalent molecular recognition that viral proteins have toward specific host glycans and receptors. On the other side, the glycan steric repulsion that a virus must overcome to approach such specific receptors. By balancing both interactions, viral tropism can be predicted. In other words, the authors can map out the cells susceptible to virus infection in terms of receptors and proteoglycans compositions.
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Affiliation(s)
- Silvia Acosta‐Gutiérrez
- Institute for the Physics of Living SystemsUniversity College LondonLondonCentral LondonUK
- Institute of Structural and Molecular BiologyUniversity College LondonLondonCentral LondonUK
- Department of ChemistryUniversity College London20 Gordon StLondonCentral LondonWC1H 0AJUK
| | - Joseph Buckley
- Institute for the Physics of Living SystemsUniversity College LondonLondonCentral LondonUK
- Institute of Structural and Molecular BiologyUniversity College LondonLondonCentral LondonUK
- Department of ChemistryUniversity College London20 Gordon StLondonCentral LondonWC1H 0AJUK
| | - Giuseppe Battaglia
- Institute for the Physics of Living SystemsUniversity College LondonLondonCentral LondonUK
- Institute of Structural and Molecular BiologyUniversity College LondonLondonCentral LondonUK
- Department of ChemistryUniversity College London20 Gordon StLondonCentral LondonWC1H 0AJUK
- Institute for Bioengineering of Catalunya (IBEC)The Barcelona Institute of Science and TechnologyBarcelonaBarcelona08028Spain
- Catalan Institution for Research and Advances Studies (ICREA)BarcelonaSpain
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72
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Chan KC, Song Y, Xu Z, Shang C, Zhou R. SARS-CoV-2 Delta Variant: Interplay between Individual Mutations and Their Allosteric Synergy. Biomolecules 2022; 12:biom12121742. [PMID: 36551170 PMCID: PMC9775976 DOI: 10.3390/biom12121742] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 11/17/2022] [Accepted: 11/20/2022] [Indexed: 11/25/2022] Open
Abstract
Since its first appearance in April 2021, B.1.617.2, also termed variant Delta, catalyzed one major worldwide wave dominating the second year of coronavirus disease 2019 (COVID-19) pandemic. Despite its quick disappearance worldwide, the strong virulence caused by a few point mutations remains an unsolved problem largely. Along with the other two sublineages, the Delta variant harbors an accumulation of Spike protein mutations, including the previously identified L452R, E484Q, and the newly emerged T478K on its receptor binding domain (RBD). We used molecular dynamics (MD) simulations, in combination with free energy perturbation (FEP) calculations, to examine the effects of two combinative mutation sets, L452R + E484Q and L452R + T478K. Our dynamic trajectories reveal an enhancement in binding affinity between mutated RBD and the common receptor protein angiotensin converting enzyme 2 (ACE2) through a net increase in the buried molecular surface area of the binary complex. This enhanced binding, mediated through Gln493, sets the same stage for all three sublineages due to the presence of L452R mutation. The other mutation component, E484Q or T478K, was found to impact the RBD-ACE2 binding and help the variant to evade several monoclonal antibodies (mAbs) in a distinct manner. Especially for L452R + T478K, synergies between mutations are mediated through a complex residual and water interaction network and further enhance its binding to ACE2. Taking together, this study demonstrates that new variants of SARS-CoV-2 accomplish both "attack" (infection) and "defense" (antibody neutralization escape) with the same "polished sword" (mutated Spike RBD).
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Affiliation(s)
- Kevin C. Chan
- Institute of Quantitative Biology, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
- Shanghai Institute for Advanced Study, Zhejiang University, 799 Dangui Road, Shanghai 201203, China
| | - Yi Song
- Institute of Quantitative Biology, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Zheng Xu
- BirenTech Research, Shanghai 201112, China
| | - Chun Shang
- Institute of Quantitative Biology, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Ruhong Zhou
- Institute of Quantitative Biology, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
- Shanghai Institute for Advanced Study, Zhejiang University, 799 Dangui Road, Shanghai 201203, China
- Department of Chemistry, Columbia University, New York, NY 10027, USA
- The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310058, China
- Correspondence:
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73
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Hu X, Cui J, Chen J, Du S, Wang X, Zhang Y, Qian J, Chen H, Wei F, Cai Q, Jia J, Wu J. Identification of hACE2-interacting sites in SARS-CoV-2 spike receptor binding domain for antiviral drugs screening. Virus Res 2022; 321:198915. [PMID: 36084746 PMCID: PMC9446661 DOI: 10.1016/j.virusres.2022.198915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 09/01/2022] [Accepted: 09/05/2022] [Indexed: 12/24/2022]
Abstract
The key structure of the interface between the spike protein of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) and human angiotensin-converting enzyme 2 (hACE2) acts as an essential switch for cell entry by the virus and drugs targets. However, this is largely unknown. Here, we tested three peptides of spike receptor binding domain (RBD) and found that peptide 391-465 aa is the major hACE2-interacting sites in SARS-CoV-2 spike RBD. We then identified essential amino acid residues (403R, 449Y, 454R) of peptide 391-465 aa that were critical for the interaction between the RBD and hACE2. Additionally, a pseudotyped virus containing SARS-CoV-2 spike with individual mutation (R454G, Y449F, R403G, N439I, or N440I) was determined to have very low infectivity compared with the pseudotyped virus containing the wildtype (WT) spike from reference strain Wuhan 1, respectively. Furthermore, we showed the key amino acids had the potential to drug screening. For example, molecular docking (Docking) and infection assay showed that Cephalosporin derivatives can bind with the key amino acids to efficiently block infection of the pseudoviruses with wild type spike or new variants. Moreover, Cefixime inhibited live SARS-CoV-2 infection. These results also provide a novel model for drug screening and support further clinical evaluation and development of Cephalosporin derivatives as novel, safe, and cost-effective drugs for prevention/treatment of SARS-CoV-2.
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Affiliation(s)
- Xiaopeng Hu
- Renji Hospital, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Bio-X Institutes, School of Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jiahua Cui
- School of Chemistry and Chemical Engineering, Shanghai Jiaotong University, China
| | - Jun Chen
- Key Laboratory of Microbial Metabolism, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, College of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Shujuan Du
- MOE & MOH Key Laboratory of Medical Molecular Virology, School of Basic Medicine, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Xinyu Wang
- MOE & MOH Key Laboratory of Medical Molecular Virology, School of Basic Medicine, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Yabin Zhang
- Renji Hospital, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Bio-X Institutes, School of Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jiajun Qian
- School of Chemistry and Chemical Engineering, Shanghai Jiaotong University, China
| | - Haifeng Chen
- Key Laboratory of Microbial Metabolism, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, College of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Fang Wei
- Sheng Yushou Center of Cell Biology and Immunology, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiaotong University, Shanghai 200032, China,Corresponding authors
| | - Qiliang Cai
- MOE & MOH Key Laboratory of Medical Molecular Virology, School of Basic Medicine, Shanghai Medical College, Fudan University, Shanghai 200032, China,Corresponding authors
| | - Jinping Jia
- School of Chemistry and Chemical Engineering, Shanghai Jiaotong University, China,Corresponding authors
| | - Ji Wu
- Renji Hospital, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Bio-X Institutes, School of Medicine, Shanghai Jiao Tong University, Shanghai 200240, China,Corresponding authors
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74
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Yang F, Yan S, Zhu L, Wang FX, Liu F, Cheng L, Yao H, Wu N, Lu R, Wu H. Evaluation of panel of neutralising murine monoclonal antibodies and a humanised bispecific antibody against influenza A(H1N1)pdm09 virus infection in a mouse model. Antiviral Res 2022; 208:105462. [DOI: 10.1016/j.antiviral.2022.105462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Revised: 11/01/2022] [Accepted: 11/06/2022] [Indexed: 11/15/2022]
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75
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Du J, Yao N, Ma X, Wang H, Li Q, Feng Z. Infrared spectra of the SARS-CoV-2 spike receptor-binding domain: Molecular dynamics simulations. Chem Phys Lett 2022; 810:140176. [DOI: 10.1016/j.cplett.2022.140176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2022] [Revised: 10/24/2022] [Accepted: 11/01/2022] [Indexed: 11/06/2022]
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76
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Sekhon SS, Shin W, Kim SY, Jeong D, Choi W, Choi B, Min J, Ahn J, Kim Y. Cyclophilin A-mediated mitigation of coronavirus SARS-CoV-2. Bioeng Transl Med 2022; 8:e10436. [PMID: 36712291 PMCID: PMC9874840 DOI: 10.1002/btm2.10436] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 09/26/2022] [Accepted: 10/10/2022] [Indexed: 02/01/2023] Open
Abstract
Human cyclophilin A (hCypA) is important for the replication of multiple coronaviruses (CoVs), and cyclosporine A inhibitors can suppress CoVs. The emergence of rapidly spreading severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants has sparked concerns that mutations affect the binding ability of the spike (S) protein to the angiotensin-converting enzyme 2 (ACE2) cell receptor, affecting the severity of coronavirus disease (COVID-19). Far-western blotting and surface plasmon resonance (SPR) results revealed that hCypA interacts strongly with the viral SARS-CoV-2 receptor-binding domain (RBD), with a binding affinity of 6.85 × 10-8 M. The molecular interaction between hCypA and the viral protein interface was shown using three-dimensional structural analysis, which revealed the blocking of key residues on the RBD interface by hCypA. The RBD facilitates binding to the ACE2 receptor. The hCypA-S protein complex suppressed the binding of RBD to the ACE2 receptor, which a required event for CoV entry into the host cell. The reliability of this postulated blocking mechanism of the hCypA-SARS-CoV2 RBD complex with ACE was confirmed by SPR and molecular interaction lateral flow (MILF) strip assay, which offers the immunochromatographic signal read-outs. The emergence of new SARS-CoV-2 variants with key mutations in RBD had a negligible effect on the binding of the RBD variants to hCypA, indicating an effective mitigation strategy for SARS-CoV-2 variants. The MILF strip assay results also highlight the neutralizing effect of hCypA by effectively blocking RBD (wild type and its variants) from binding ACE2. Given the importance of hCypA in viral entry regulation, it has the potential to be used as a target for antiviral therapy.
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Affiliation(s)
| | - Woo‐Ri Shin
- Department of MicrobiologyChungbuk National UniversitySeowon‐GuCheongjuSouth Korea
| | - Sang Yong Kim
- Department of Food Science and BiotechnologyShin Ansan UniversityDanwon‐Gu, AnsanRepublic of Korea
| | - Dong‐Seok Jeong
- SEJONGBIOHeungdeok‐gu, Cheongju‐siChungcheongbuk‐doRepublic of Korea
| | - Wooil Choi
- Graduate School of Semiconductor and Chemical EngineeringJeonbuk National UniversityJeonjuKorea
| | | | - Jiho Min
- Graduate School of Semiconductor and Chemical EngineeringJeonbuk National UniversityJeonjuKorea
| | - Ji‐Young Ahn
- Department of MicrobiologyChungbuk National UniversitySeowon‐GuCheongjuSouth Korea
| | - Yang‐Hoon Kim
- Department of MicrobiologyChungbuk National UniversitySeowon‐GuCheongjuSouth Korea
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77
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Jain M, Patil N, Gor D, Sharma MK, Goel N, Kaushik P. Proteomic Approach for Comparative Analysis of the Spike Protein of SARS-CoV-2 Omicron (B.1.1.529) Variant and Other Pango Lineages. Proteomes 2022; 10:34. [PMID: 36278694 PMCID: PMC9624331 DOI: 10.3390/proteomes10040034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 10/11/2022] [Accepted: 10/13/2022] [Indexed: 11/24/2022] Open
Abstract
The novel SARS-CoV-2 variant, Omicron (B.1.1.529), is being testified, and the WHO has characterized Omicron as a variant of concern due to its higher transmissibility and very contagious behavior, immunization breakthrough cases. Here, the comparative proteomic study has been conducted on spike-protein, hACE2 of five lineages (α, β, δ, γ and Omicron. The docking was performed on spike protein- hACE-2 protein using HADDOCK, and PRODIGY was used to analyze the binding energy affinity using a reduced Haddock score. Followed by superimposition in different variant-based protein structures and calculated the esteem root mean square deviation (RMSD). This study reveals that Omicron was seen generating a monophyletic clade. Further, as α variant is the principal advanced strain after Wuhan SARS-CoV-2, and that is the reason it was showing the least likeness rate with the Omicron and connoting Omicron has developed of late with the extreme number of mutations. α variant has shown the highest binding affinity with hACE2, followed by β strain, and followed with γ. Omicron showed a penultimate binding relationship, while the δ variant was seen as having the least binding affinity. This proteomic basis in silico analysis of variable spike proteins of variants will impart light on the development of vaccines and the identification of mutations occurring in the upcoming variants.
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Affiliation(s)
- Mukul Jain
- Parul Institute of Applied Sciences, Parul University, Vadodara 391760, Gujarat, India; (N.P.); (D.G.)
- Lab 209—Cell & Developmental Biology, Centre of Research for Development, Parul University, Vadodara 391760, Gujarat, India
| | - Nil Patil
- Parul Institute of Applied Sciences, Parul University, Vadodara 391760, Gujarat, India; (N.P.); (D.G.)
- Lab 209—Cell & Developmental Biology, Centre of Research for Development, Parul University, Vadodara 391760, Gujarat, India
| | - Darshil Gor
- Parul Institute of Applied Sciences, Parul University, Vadodara 391760, Gujarat, India; (N.P.); (D.G.)
| | - Mohit Kumar Sharma
- School of Molecular Medicine, Medical University of Warsaw, ul. Żwirki i Wigury 61, 02-091 Warsaw, Poland;
- Malopolska Center of Biotechnology, 30-387 Krakow, Poland
| | - Neha Goel
- Institute of Biomedicine, University of Turku, 20500 Turku, Finland;
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78
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Taft JM, Weber CR, Gao B, Ehling RA, Han J, Frei L, Metcalfe SW, Overath MD, Yermanos A, Kelton W, Reddy ST. Deep mutational learning predicts ACE2 binding and antibody escape to combinatorial mutations in the SARS-CoV-2 receptor-binding domain. Cell 2022; 185:4008-4022.e14. [PMID: 36150393 PMCID: PMC9428596 DOI: 10.1016/j.cell.2022.08.024] [Citation(s) in RCA: 45] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 06/22/2022] [Accepted: 08/25/2022] [Indexed: 01/26/2023]
Abstract
The continual evolution of SARS-CoV-2 and the emergence of variants that show resistance to vaccines and neutralizing antibodies threaten to prolong the COVID-19 pandemic. Selection and emergence of SARS-CoV-2 variants are driven in part by mutations within the viral spike protein and in particular the ACE2 receptor-binding domain (RBD), a primary target site for neutralizing antibodies. Here, we develop deep mutational learning (DML), a machine-learning-guided protein engineering technology, which is used to investigate a massive sequence space of combinatorial mutations, representing billions of RBD variants, by accurately predicting their impact on ACE2 binding and antibody escape. A highly diverse landscape of possible SARS-CoV-2 variants is identified that could emerge from a multitude of evolutionary trajectories. DML may be used for predictive profiling on current and prospective variants, including highly mutated variants such as Omicron, thus guiding the development of therapeutic antibody treatments and vaccines for COVID-19.
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Affiliation(s)
- Joseph M Taft
- Department of Biosystems Science and Engineering, ETH Zurich, Basel 4058, Switzerland; Botnar Research Centre for Child Health, Basel 4058, Switzerland
| | - Cédric R Weber
- Alloy Therapeutics (Switzerland) AG, Basel 4058, Switzerland
| | - Beichen Gao
- Department of Biosystems Science and Engineering, ETH Zurich, Basel 4058, Switzerland; Botnar Research Centre for Child Health, Basel 4058, Switzerland
| | - Roy A Ehling
- Department of Biosystems Science and Engineering, ETH Zurich, Basel 4058, Switzerland
| | - Jiami Han
- Department of Biosystems Science and Engineering, ETH Zurich, Basel 4058, Switzerland; Botnar Research Centre for Child Health, Basel 4058, Switzerland
| | - Lester Frei
- Department of Biosystems Science and Engineering, ETH Zurich, Basel 4058, Switzerland; Botnar Research Centre for Child Health, Basel 4058, Switzerland
| | - Sean W Metcalfe
- Department of Biosystems Science and Engineering, ETH Zurich, Basel 4058, Switzerland
| | - Max D Overath
- Department of Biosystems Science and Engineering, ETH Zurich, Basel 4058, Switzerland
| | - Alexander Yermanos
- Department of Biosystems Science and Engineering, ETH Zurich, Basel 4058, Switzerland; Botnar Research Centre for Child Health, Basel 4058, Switzerland; Department of Biology, Institute of Microbiology and Immunology, ETH Zurich, Zurich 8093, Switzerland; Department of Pathology and Immunology, University of Geneva, Geneva 1211, Switzerland
| | - William Kelton
- Te Huataki Waiora School of Health, University of Waikato, Hamilton 3240, New Zealand
| | - Sai T Reddy
- Department of Biosystems Science and Engineering, ETH Zurich, Basel 4058, Switzerland; Botnar Research Centre for Child Health, Basel 4058, Switzerland.
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79
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Wozney AJ, Smith MA, Abdrabbo M, Birch CM, Cicigoi KA, Dolan CC, Gerzema AEL, Hansen A, Henseler EJ, LaBerge B, Leavens CM, Le CN, Lindquist AC, Ludwig RK, O'Reilly MG, Reynolds JH, Sherman BA, Sillman HW, Smith MA, Snortheim MJ, Svaren LM, Vanderpas EC, Voon A, Wackett MJ, Weiss MM, Hati S, Bhattacharyya S. Evolution of Stronger SARS-CoV-2 Variants as Revealed Through the Lens of Molecular Dynamics Simulations. Protein J 2022; 41:444-456. [PMID: 35913554 PMCID: PMC9340756 DOI: 10.1007/s10930-022-10065-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/27/2022] [Indexed: 12/03/2022]
Abstract
Using molecular dynamics simulations, the protein-protein interactions of the receptor-binding domain of the wild-type and seven variants of the severe acute respiratory syndrome coronavirus 2 spike protein and the peptidase domain of human angiotensin-converting enzyme 2 were investigated. These variants are alpha, beta, gamma, delta, eta, kappa, and omicron. Using 100 ns simulation data, the residue interaction networks at the protein-protein interface were identified. Also, the impact of mutations on essential protein dynamics, backbone flexibility, and interaction energy of the simulated protein-protein complexes were studied. The protein-protein interface for the wild-type, delta, and omicron variants contained several stronger interactions, while the alpha, beta, gamma, eta, and kappa variants exhibited an opposite scenario as evident from the analysis of the inter-residue interaction distances and pair-wise interaction energies. The study reveals that two distinct residue networks at the central and right contact regions forge stronger binding affinity between the protein partners. The study provides a molecular-level insight into how enhanced transmissibility and infectivity by delta and omicron variants are most likely tied to a handful of interacting residues at the binding interface, which could potentially be utilized for future antibody constructs and structure-based antiviral drug design.
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Affiliation(s)
- Alec J Wozney
- Department of Chemistry and Biochemistry, University of Wisconsin-Eau Claire, 101 Roosevelt Avenue, Eau Claire, WI, 54701, USA
| | - Macey A Smith
- Department of Chemistry and Biochemistry, University of Wisconsin-Eau Claire, 101 Roosevelt Avenue, Eau Claire, WI, 54701, USA
| | - Mobeen Abdrabbo
- Department of Chemistry and Biochemistry, University of Wisconsin-Eau Claire, 101 Roosevelt Avenue, Eau Claire, WI, 54701, USA
| | - Cole M Birch
- Department of Chemistry and Biochemistry, University of Wisconsin-Eau Claire, 101 Roosevelt Avenue, Eau Claire, WI, 54701, USA
| | - Kelsey A Cicigoi
- Department of Chemistry and Biochemistry, University of Wisconsin-Eau Claire, 101 Roosevelt Avenue, Eau Claire, WI, 54701, USA
| | - Connor C Dolan
- Department of Chemistry and Biochemistry, University of Wisconsin-Eau Claire, 101 Roosevelt Avenue, Eau Claire, WI, 54701, USA
| | - Audrey E L Gerzema
- Department of Chemistry and Biochemistry, University of Wisconsin-Eau Claire, 101 Roosevelt Avenue, Eau Claire, WI, 54701, USA
| | - Abby Hansen
- Department of Chemistry and Biochemistry, University of Wisconsin-Eau Claire, 101 Roosevelt Avenue, Eau Claire, WI, 54701, USA
| | - Ethan J Henseler
- Department of Chemistry and Biochemistry, University of Wisconsin-Eau Claire, 101 Roosevelt Avenue, Eau Claire, WI, 54701, USA
| | - Ben LaBerge
- Department of Chemistry and Biochemistry, University of Wisconsin-Eau Claire, 101 Roosevelt Avenue, Eau Claire, WI, 54701, USA
| | - Caterra M Leavens
- Department of Chemistry and Biochemistry, University of Wisconsin-Eau Claire, 101 Roosevelt Avenue, Eau Claire, WI, 54701, USA
| | - Christine N Le
- Department of Chemistry and Biochemistry, University of Wisconsin-Eau Claire, 101 Roosevelt Avenue, Eau Claire, WI, 54701, USA
| | - Allison C Lindquist
- Department of Chemistry and Biochemistry, University of Wisconsin-Eau Claire, 101 Roosevelt Avenue, Eau Claire, WI, 54701, USA
| | - Rikaela K Ludwig
- Department of Chemistry and Biochemistry, University of Wisconsin-Eau Claire, 101 Roosevelt Avenue, Eau Claire, WI, 54701, USA
| | - Maggie G O'Reilly
- Department of Chemistry and Biochemistry, University of Wisconsin-Eau Claire, 101 Roosevelt Avenue, Eau Claire, WI, 54701, USA
| | - Jacob H Reynolds
- Department of Chemistry and Biochemistry, University of Wisconsin-Eau Claire, 101 Roosevelt Avenue, Eau Claire, WI, 54701, USA
| | - Brandon A Sherman
- Department of Chemistry and Biochemistry, University of Wisconsin-Eau Claire, 101 Roosevelt Avenue, Eau Claire, WI, 54701, USA
| | - Hunter W Sillman
- Department of Chemistry and Biochemistry, University of Wisconsin-Eau Claire, 101 Roosevelt Avenue, Eau Claire, WI, 54701, USA
| | - Michael A Smith
- Department of Chemistry and Biochemistry, University of Wisconsin-Eau Claire, 101 Roosevelt Avenue, Eau Claire, WI, 54701, USA
| | - Marissa J Snortheim
- Department of Chemistry and Biochemistry, University of Wisconsin-Eau Claire, 101 Roosevelt Avenue, Eau Claire, WI, 54701, USA
| | - Levi M Svaren
- Department of Chemistry and Biochemistry, University of Wisconsin-Eau Claire, 101 Roosevelt Avenue, Eau Claire, WI, 54701, USA
| | - Emily C Vanderpas
- Department of Chemistry and Biochemistry, University of Wisconsin-Eau Claire, 101 Roosevelt Avenue, Eau Claire, WI, 54701, USA
| | - Aidan Voon
- Department of Chemistry and Biochemistry, University of Wisconsin-Eau Claire, 101 Roosevelt Avenue, Eau Claire, WI, 54701, USA
| | - Miles J Wackett
- Department of Chemistry and Biochemistry, University of Wisconsin-Eau Claire, 101 Roosevelt Avenue, Eau Claire, WI, 54701, USA
| | - Moriah M Weiss
- Department of Chemistry and Biochemistry, University of Wisconsin-Eau Claire, 101 Roosevelt Avenue, Eau Claire, WI, 54701, USA
| | - Sanchita Hati
- Department of Chemistry and Biochemistry, University of Wisconsin-Eau Claire, 101 Roosevelt Avenue, Eau Claire, WI, 54701, USA.
| | - Sudeep Bhattacharyya
- Department of Chemistry and Biochemistry, University of Wisconsin-Eau Claire, 101 Roosevelt Avenue, Eau Claire, WI, 54701, USA.
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da-Costa-Rodrigues B, Cheohen C, Sciammarella F, Pierre-Bonetti-Pozzobon A, Ribeiro L, Nepomuceno-Silva JL, Medeiros M, Mury F, Monteiro-de-Barros C, Lazoski C, Leal-da-Silva M, Tanuri A, Nunes-da-Fonseca R. SARS-CoV-2 Spatiotemporal Genomic and Molecular Analysis of the First Wave of the COVID-19 Pandemic in Macaé, the Brazilian Capital of Oil. Int J Mol Sci 2022; 23:ijms231911497. [PMID: 36232806 PMCID: PMC9569756 DOI: 10.3390/ijms231911497] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 09/23/2022] [Accepted: 09/25/2022] [Indexed: 11/25/2022] Open
Abstract
The SARS-CoV-2 virus infection led to millions of deaths during the COVID-19 pandemic. Hundreds of workers from several other Brazilian cities, as well as from other countries, arrive daily in Macaé to work in the oil supply chain, making this city a putative hotspot for the introduction of new viral lineages. In this study, we performed a genomic survey of SARS-CoV-2 samples from Macaé during the first outbreak of COVID-19, combined with clinical data and a molecular integrative analysis. First, phylogenomic analyses showed a high occurrence of viral introduction events and the establishment of local transmissions in Macaé, including the ingression and spread of the B.1.1.28 lineage in the municipality from June to August 2020. Second, SARS-CoV-2 mutations were identified in patients with distinct levels of COVID-19 severity. Third, molecular interactions of the mutated spike protein from three B.1.1.33 local samples and human ACE2 showed higher interactions than that of the wild-type spike protein from the ancestral virus. Altogether, these results elucidate the SARS-CoV-2 genomic profile in a strategic Brazilian city and further explore the functional aspects of SARS-CoV-2 with a characterization of emerging viral mutations associated with clinical data and the potential targets for drug development against SARS-CoV-2.
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Affiliation(s)
- Bruno da-Costa-Rodrigues
- Instituto de Biodiversidade e Sustentabilidade-NUPEM, Universidade Federal do Rio de Janeiro (UFRJ), Av. São José do Barreto 764, Macaé 27965-550, Brazil
- Programa de Ciências Morfológicas, Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro 21941-170, Brazil
- Correspondence: (B.d.-C.-R.); (R.N.-d.-F.)
| | - Caio Cheohen
- Instituto de Biodiversidade e Sustentabilidade-NUPEM, Universidade Federal do Rio de Janeiro (UFRJ), Av. São José do Barreto 764, Macaé 27965-550, Brazil
| | - Felipe Sciammarella
- Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro 21941-902, Brazil
| | - Allan Pierre-Bonetti-Pozzobon
- Instituto de Biodiversidade e Sustentabilidade-NUPEM, Universidade Federal do Rio de Janeiro (UFRJ), Av. São José do Barreto 764, Macaé 27965-550, Brazil
| | - Lupis Ribeiro
- Instituto de Biodiversidade e Sustentabilidade-NUPEM, Universidade Federal do Rio de Janeiro (UFRJ), Av. São José do Barreto 764, Macaé 27965-550, Brazil
| | - José Luciano Nepomuceno-Silva
- Instituto de Biodiversidade e Sustentabilidade-NUPEM, Universidade Federal do Rio de Janeiro (UFRJ), Av. São José do Barreto 764, Macaé 27965-550, Brazil
| | - Marcio Medeiros
- Instituto de Biodiversidade e Sustentabilidade-NUPEM, Universidade Federal do Rio de Janeiro (UFRJ), Av. São José do Barreto 764, Macaé 27965-550, Brazil
| | - Flávia Mury
- Instituto de Biodiversidade e Sustentabilidade-NUPEM, Universidade Federal do Rio de Janeiro (UFRJ), Av. São José do Barreto 764, Macaé 27965-550, Brazil
| | - Cintia Monteiro-de-Barros
- Instituto de Biodiversidade e Sustentabilidade-NUPEM, Universidade Federal do Rio de Janeiro (UFRJ), Av. São José do Barreto 764, Macaé 27965-550, Brazil
| | - Cristiano Lazoski
- Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro 21941-902, Brazil
| | - Manuela Leal-da-Silva
- Instituto de Biodiversidade e Sustentabilidade-NUPEM, Universidade Federal do Rio de Janeiro (UFRJ), Av. São José do Barreto 764, Macaé 27965-550, Brazil
| | - Amilcar Tanuri
- Instituto de Biologia, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro 21941-902, Brazil
| | - Rodrigo Nunes-da-Fonseca
- Instituto de Biodiversidade e Sustentabilidade-NUPEM, Universidade Federal do Rio de Janeiro (UFRJ), Av. São José do Barreto 764, Macaé 27965-550, Brazil
- Programa de Ciências Morfológicas, Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro 21941-170, Brazil
- Correspondence: (B.d.-C.-R.); (R.N.-d.-F.)
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81
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Lai HTT, Nguyen LH, Phan AD, Kranjc A, Nguyen TT, Nguyen-Manh D. A comparative study of receptor interactions between SARS-CoV and SARS-CoV-2 from molecular modeling. J Mol Model 2022; 28:305. [PMID: 36074206 PMCID: PMC9453729 DOI: 10.1007/s00894-022-05231-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 07/16/2022] [Indexed: 11/26/2022]
Abstract
The pandemic of COVID-19 severe acute respiratory syndrome, which was fatal for millions of people worldwide, triggered the race to understand in detail the molecular mechanisms of this disease. In this work, the differences of interactions between the SARS-CoV/SARS-CoV-2 Receptor binding domain (RBD) and the human Angiotensin Converting Enzyme 2 (ACE2) receptor were studied using in silico tools. Our results show that SARS-CoV-2 RBD is more stable and forms more interactions with ACE2 than SARS-CoV. At its interface, three stable binding patterns are observed and named red-K31, green-K353 and blue-M82 according to the central ACE2 binding residue. In SARS-CoV instead, only the first two binding patches are persistently formed during the MD simulation. Our MM/GBSA calculations indicate the binding free energy difference of about 2.5 kcal/mol between SARS-CoV-2 and SARS-CoV which is compatible with the experiments. The binding free energy decomposition points out that SARS-CoV-2 RBD-ACE2 interactions of the red-K31 ([Formula: see text]) and blue-M82 ([Formula: see text]) patterns contribute more to the binding affinity than in SARS-CoV ([Formula: see text] for red-K31), while the contribution of the green-K353 pattern is very similar in the two strains ([Formula: see text] and [Formula: see text] for SARS-CoV-2 and SARS-CoV, respectively). Five groups of mutations draw our attention at the RBD-ACE2 binding interface, among them, the mutation -PPA469-471/GVEG482-485 has the most important and favorable impact on SARS-CoV-2 binding to the ACE2 receptor. These results, highlighting the molecular differences in the binding between the two viruses, contribute to the common knowledge about the new corona virus and to the development of appropriate antiviral treatments, addressing the necessity of ongoing pandemics.
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Affiliation(s)
- Hien T. T. Lai
- Key Laboratory for Multiscale Simulation of Complex Systems, VNU University of Science, Vietnam National University, 334 Nguyen Trai street, Hanoi, 11416 Vietnam
| | - Ly H. Nguyen
- Key Laboratory for Multiscale Simulation of Complex Systems, VNU University of Science, Vietnam National University, 334 Nguyen Trai street, Hanoi, 11416 Vietnam
| | - Anh D. Phan
- Faculty of Materials Science and Engineering, Phenikaa Institute for Advanced Study, Phenikaa University, Hanoi, 12116 Vietnam
| | - Agata Kranjc
- Institute of Neuroscience and Medicine (INM-9)/ Institute for Advanced Simulation (IAS-5), Forschungszentrum Jülich, Jülich, 52428 Germany
- Laboratoire de Biochimie Théorique, UPR 9080 CNRS, Université de Paris, 13 rue Pierre et Marie Curie, F-75005 Paris, France
- Institut de Biologie Physico-Chimique-Fondation Edmond de Rotschild, SL Research University, 75005 Paris, France
| | - Toan T. Nguyen
- Key Laboratory for Multiscale Simulation of Complex Systems, VNU University of Science, Vietnam National University, 334 Nguyen Trai street, Hanoi, 11416 Vietnam
| | - Duc Nguyen-Manh
- CCFE, United Kingdom Atomic Energy Authority, OX14 3DB Abingdon, UK
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82
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Khan SA, Khan A, Zia K, Shawish I, Barakat A, Ul-Haq Z. Cheminformatics-Based Discovery of Potential Chemical Probe Inhibitors of Omicron Spike Protein. Int J Mol Sci 2022; 23:ijms231810315. [PMID: 36142242 PMCID: PMC9498999 DOI: 10.3390/ijms231810315] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 09/01/2022] [Accepted: 09/03/2022] [Indexed: 11/16/2022] Open
Abstract
During the past two decades, the world has witnessed the emergence of various SARS-CoV-2 variants with distinct mutational profiles influencing the global health, economy, and clinical aspects of the COVID-19 pandemic. These variants or mutants have raised major concerns regarding the protection provided by neutralizing monoclonal antibodies and vaccination, rates of virus transmission, and/or the risk of reinfection. The newly emerged Omicron, a genetically distinct lineage of SARS-CoV-2, continues its spread in the face of rising vaccine-induced immunity while maintaining its replication fitness. Efforts have been made to improve the therapeutic interventions and the FDA has issued Emergency Use Authorization for a few monoclonal antibodies and drug treatments for COVID-19. However, the current situation of rapidly spreading Omicron and its lineages demands the need for effective therapeutic interventions to reduce the COVID-19 pandemic. Several experimental studies have indicated that the FDA-approved monoclonal antibodies are less effective than antiviral drugs against the Omicron variant. Thus, in this study, we aim to identify antiviral compounds against the Spike protein of Omicron, which binds to the human angiotensin-converting enzyme 2 (ACE2) receptor and facilitates virus invasion. Initially, docking-based virtual screening of the in-house database was performed to extract the potential hit compounds against the Spike protein. The obtained hits were optimized by DFT calculations to determine the electronic properties and molecular reactivity of the compounds. Further, MD simulation studies were carried out to evaluate the dynamics of protein–ligand interactions at an atomistic level in a time-dependent manner. Collectively, five compounds (AKS-01, AKS-02, AKS-03, AKS-04, and AKS-05) with diverse scaffolds were identified as potential hits against the Spike protein of Omicron. Our study paves the way for further in vitro and in vivo studies.
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Affiliation(s)
- Salman Ali Khan
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan
| | - Alamgir Khan
- H.E.J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan
| | - Komal Zia
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan
| | - Ihab Shawish
- Department of Math and Sciences, College of Humanities and Sciences, Prince Sultan University, P.O. Box 66833, Riyadh 11586, Saudi Arabia
| | - Assem Barakat
- Department of Chemistry, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia
- Correspondence: (A.B.); (Z.U.-H.)
| | - Zaheer Ul-Haq
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan
- H.E.J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan
- Correspondence: (A.B.); (Z.U.-H.)
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Maghsood F, Amiri MM, Zarnani AH, Salimi V, Kardar GA, Khoshnoodi J, Mobini M, Ahmadi Zare H, Ghaderi A, Jeddi-Tehrani M, Schmidt S, Laumond G, Moog C, Shokri F. Epitope mapping of severe acute respiratory syndrome coronavirus 2 neutralizing receptor binding domain-specific monoclonal antibodies. Front Med (Lausanne) 2022; 9:973036. [PMID: 36148457 PMCID: PMC9485472 DOI: 10.3389/fmed.2022.973036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Accepted: 08/16/2022] [Indexed: 11/13/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of the outbreak led to the coronavirus disease 2019 (COVID-19) pandemic. Receptor binding domain (RBD) of spike (S) protein of SARS-CoV-2 is considered as a major target for immunotherapy and vaccine design. Here, we generated and characterized a panel of anti-RBD monoclonal antibodies (MAbs) isolated from eukaryotic recombinant RBD-immunized mice by hybridoma technology. Epitope mapping was performed using a panel of 20-mer overlapping peptides spanning the entire sequence of the RBD protein from wild-type (WT) Wuhan strain by enzyme-linked immunosorbent assay (ELISA). Several hybridomas showed reactivity toward restricted RBD peptide pools by Pepscan analysis, with more focus on peptides encompassing aa 76-110 and 136-155. However, our MAbs with potent neutralizing activity which block SARS-CoV-2 spike pseudovirus as well as the WT virus entry into angiotensin-converting enzyme-2 (ACE2) expressing HEK293T cells showed no reactivity against these peptides. These findings, largely supported by the Western blotting results suggest that the neutralizing MAbs recognize mainly conformational epitopes. Moreover, our neutralizing MAbs recognized the variants of concern (VOC) currently in circulation, including alpha, beta, gamma, and delta by ELISA, and neutralized alpha and omicron variants at different levels by conventional virus neutralization test (CVNT). While the neutralization of MAbs to the alpha variant showed no substantial difference as compared with the WT virus, their neutralizing activity was lower on omicron variant, suggesting the refractory effect of mutations in emerging variants against this group of neutralizing MAbs. Also, the binding reactivity of our MAbs to delta variant showed a modest decline by ELISA, implying that our MAbs are insensitive to the substitutions in the RBD of delta variant. Our data provide important information for understanding the immunogenicity of RBD, and the potential application of the novel neutralizing MAbs for passive immunotherapy of SARS-CoV-2 infection.
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Affiliation(s)
- Faezeh Maghsood
- Department of Immunology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Mohammad Mehdi Amiri
- Department of Immunology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Amir-Hassan Zarnani
- Department of Immunology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Vahid Salimi
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Gholam Ali Kardar
- Immunology, Asthma and Allergy Research Institute, Children’s Medical Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Jalal Khoshnoodi
- Department of Immunology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Maryam Mobini
- Department of Immunology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Hengameh Ahmadi Zare
- Department of Immunology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Abbas Ghaderi
- Shiraz Institute for Cancer Research, School of Medicine, Shiraz University of Medical Science, Shiraz, Iran
| | - Mahmood Jeddi-Tehrani
- Monoclonal Antibody Research Center, Avicenna Research Institute, Academic Center for Education, Culture and Research (ACECR), Tehran, Iran
| | - Sylvie Schmidt
- Laboratoire d’ImmunoRhumatologie Moléculaire, Institut National de la Santé et de la Recherche Médicale (INSERM) UMR_S 1109, Institut Thématique Interdisciplinaire (ITI) de Médecine de Précision de Strasbourg, Transplantex NG, Faculté de Médecine, Fédération Hospitalo-Universitaire OMICARE, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Strasbourg, France
| | - Géraldine Laumond
- Laboratoire d’ImmunoRhumatologie Moléculaire, Institut National de la Santé et de la Recherche Médicale (INSERM) UMR_S 1109, Institut Thématique Interdisciplinaire (ITI) de Médecine de Précision de Strasbourg, Transplantex NG, Faculté de Médecine, Fédération Hospitalo-Universitaire OMICARE, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Strasbourg, France
| | - Christiane Moog
- Laboratoire d’ImmunoRhumatologie Moléculaire, Institut National de la Santé et de la Recherche Médicale (INSERM) UMR_S 1109, Institut Thématique Interdisciplinaire (ITI) de Médecine de Précision de Strasbourg, Transplantex NG, Faculté de Médecine, Fédération Hospitalo-Universitaire OMICARE, Fédération de Médecine Translationnelle de Strasbourg (FMTS), Strasbourg, France
| | - Fazel Shokri
- Department of Immunology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
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Erausquin E, Glaser F, Fernández-Recio J, López-Sagaseta J. Structural bases for the higher adherence to ACE2 conferred by the SARS-CoV-2 spike Q498Y substitution. Acta Crystallogr D Struct Biol 2022; 78:1156-1170. [PMID: 36048155 PMCID: PMC9435600 DOI: 10.1107/s2059798322007677] [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: 02/25/2022] [Accepted: 07/28/2022] [Indexed: 11/18/2022] Open
Abstract
A remarkable number of SARS‐CoV‐2 variants and other as yet unmonitored lineages harbor amino‐acid substitutions with the potential to modulate the interface between the spike receptor‐binding domain (RBD) and its receptor ACE2. The naturally occurring Q498Y substitution, which is present in currently circulating SARS‐CoV‐2 variants, has drawn the attention of several investigations. While computational predictions and in vitro binding studies suggest that Q498Y increases the binding affinity of the spike protein for ACE2, experimental in vivo models of infection have shown that a triple mutant carrying the Q498Y replacement is fatal in mice. To accurately characterize the binding kinetics of the RBD Q498Y–ACE2 interaction, biolayer interferometry analyses were performed. A significant enhancement of the RBD–ACE2 binding affinity relative to a reference SARS‐CoV‐2 variant of concern carrying three simultaneous replacements was observed. In addition, the RBD Q498Y mutant bound to ACE2 was crystallized. Compared with the structure of its wild‐type counterpart, the RBD Q498Y–ACE2 complex reveals the conservation of major hydrogen‐bond interactions and a more populated, nonpolar set of contacts mediated by the bulky side chain of Tyr498 that collectively lead to this increase in binding affinity. In summary, these studies contribute to a deeper understanding of the impact of a relevant mutation present in currently circulating SARS‐CoV‐2 variants which might lead to stronger host–pathogen interactions.
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85
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Banerjee S, Wang X, Du S, Zhu C, Jia Y, Wang Y, Cai Q. Comprehensive role of SARS-CoV-2 spike glycoprotein in regulating host signaling pathway. J Med Virol 2022; 94:4071-4087. [PMID: 35488404 PMCID: PMC9348444 DOI: 10.1002/jmv.27820] [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: 03/26/2022] [Revised: 04/21/2022] [Accepted: 04/27/2022] [Indexed: 11/06/2022]
Abstract
Since the outbreak of coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, global public health and the economy have suffered unprecedented damage. Based on the increasing related literature, the characteristics and pathogenic mechanisms of the virus, and epidemiological and clinical features of the disease are being rapidly discovered. The spike glycoprotein (S protein), as a key antigen of SARS-CoV-2 for developing vaccines, antibodies, and drug targets, has been shown to play an important role in viral entry, tissue tropism, and pathogenesis. In this review, we summarize the molecular mechanisms of interaction between S protein and host factors, especially receptor-mediated viral modulation of host signaling pathways, and highlight the progression of potential therapeutic targets, prophylactic and therapeutic agents for prevention and treatment of SARS-CoV-2 infection.
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Affiliation(s)
- Shuvomoy Banerjee
- Department of Biotechnology and BioengineeringKoba Institutional AreaGandhinagarGujaratIndia
| | - Xinyu Wang
- MOE&NHC&CAMS Key Laboratory of Medical Molecular Virology, Shanghai Institute of Infections Disease and Biosecurity, & School of Basic Medical Science, Shanghai Medical CollegeFudan UniversityShanghaiChina
| | - Shujuan Du
- MOE&NHC&CAMS Key Laboratory of Medical Molecular Virology, Shanghai Institute of Infections Disease and Biosecurity, & School of Basic Medical Science, Shanghai Medical CollegeFudan UniversityShanghaiChina
| | - Caixia Zhu
- MOE&NHC&CAMS Key Laboratory of Medical Molecular Virology, Shanghai Institute of Infections Disease and Biosecurity, & School of Basic Medical Science, Shanghai Medical CollegeFudan UniversityShanghaiChina
| | - Yuping Jia
- Shandong Academy of Pharmaceutical SciencesJinanChina
| | - Yuyan Wang
- MOE&NHC&CAMS Key Laboratory of Medical Molecular Virology, Shanghai Institute of Infections Disease and Biosecurity, & School of Basic Medical Science, Shanghai Medical CollegeFudan UniversityShanghaiChina
| | - Qiliang Cai
- MOE&NHC&CAMS Key Laboratory of Medical Molecular Virology, Shanghai Institute of Infections Disease and Biosecurity, & School of Basic Medical Science, Shanghai Medical CollegeFudan UniversityShanghaiChina
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86
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Candido KL, Eich CR, de Fariña LO, Kadowaki MK, da Conceição Silva JL, Maller A, Simão RDCG. Spike protein of SARS-CoV-2 variants: a brief review and practical implications. Braz J Microbiol 2022; 53:1133-1157. [PMID: 35397075 PMCID: PMC8994061 DOI: 10.1007/s42770-022-00743-z] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Accepted: 03/21/2022] [Indexed: 12/24/2022] Open
Abstract
The scientific community has been alarmed by the possible immunological evasion, higher infectivity, and severity of disease caused by the newest variants of SARS-CoV-2. The spike protein has an important role in the cellular invasion of viruses and is the target of several vaccines and therapeutic resources, such as monoclonal antibodies. In addition, some of the most relevant mutations in the different variants are on the spike (S) protein gene sequence that leads to structural alterations in the predicted protein, thus causing concern about the protection mediated by vaccines against these new strains. The present review highlights the most recent knowledge about COVID-19 and vaccines, emphasizing the different spike protein structures of SARS-CoV-2 and updating the reader about the emerging viral variants and their classifications, the more common viral mutations described and their distribution in Brazil. It also compiles a table with the most recent knowledge about all of the Omicron spike mutations.
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Affiliation(s)
- Kattlyn Laryssa Candido
- Present Address: Laboratório de Bioquímica Molecular (LaBioqMol), Centro de Ciências Médicas e Farmacêuticas, Unioeste, Cascavel, PR Brazil
| | - Caio Ricardo Eich
- Present Address: Laboratório de Bioquímica Molecular (LaBioqMol), Centro de Ciências Médicas e Farmacêuticas, Unioeste, Cascavel, PR Brazil
| | - Luciana Oliveira de Fariña
- Present Address: Laboratório de Bioquímica Molecular (LaBioqMol), Centro de Ciências Médicas e Farmacêuticas, Unioeste, Cascavel, PR Brazil
| | - Marina Kimiko Kadowaki
- Present Address: Laboratório de Bioquímica Molecular (LaBioqMol), Centro de Ciências Médicas e Farmacêuticas, Unioeste, Cascavel, PR Brazil
| | - José Luis da Conceição Silva
- Present Address: Laboratório de Bioquímica Molecular (LaBioqMol), Centro de Ciências Médicas e Farmacêuticas, Unioeste, Cascavel, PR Brazil
| | - Alexandre Maller
- Present Address: Laboratório de Bioquímica Molecular (LaBioqMol), Centro de Ciências Médicas e Farmacêuticas, Unioeste, Cascavel, PR Brazil
| | - Rita de Cássia Garcia Simão
- Present Address: Laboratório de Bioquímica Molecular (LaBioqMol), Centro de Ciências Médicas e Farmacêuticas, Unioeste, Cascavel, PR Brazil
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87
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Yang HC, Wang JH, Yang CT, Lin YC, Hsieh HN, Chen PW, Liao HC, Chen CH, Liao JC. Subtyping of major SARS-CoV-2 variants reveals different transmission dynamics based on 10 million genomes. PNAS NEXUS 2022; 1:pgac181. [PMID: 36714842 PMCID: PMC9802201 DOI: 10.1093/pnasnexus/pgac181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 08/30/2022] [Indexed: 02/01/2023]
Abstract
SARS-CoV-2 continues to evolve, causing waves of the pandemic. Up to May 2022, 10 million genome sequences have accumulated, which are classified into five major variants of concern. With the growing number of sequenced genomes, analysis of the big dataset has become increasingly challenging. Here we developed systematic approaches based on sets of correlated single nucleotide variations (SNVs) for comprehensive subtyping and pattern recognition of transmission dynamics. The approach outperformed single-SNV and spike-centric scans. Moreover, the derived subtypes elucidate the relationship of signature SNVs and transmission dynamics. We found that different subtypes of the same variant, including Delta and Omicron exhibited distinct temporal trajectories. For example, some Delta and Omicron subtypes did not spread rapidly, while others did. We identified sets of characteristic SNVs that appeared to enhance transmission or decrease efficacy of antibodies for some subtypes. We also identified a set of SNVs that appeared to suppress transmission or increase viral sensitivity to antibodies. For the Omicron variant, the dominant type in the world, we identified the subtypes with enhanced and suppressed transmission in an analysis of eight million genomes as of March 2022 and further confirmed the findings in a later analysis of ten million genomes as of May 2022. While the "enhancer" SNVs exhibited an enriched presence on the spike protein, the "suppressor" SNVs are mainly elsewhere. Disruption of the SNV correlation largely destroyed the enhancer-suppressor phenomena. These results suggest the importance of fine subtyping of variants, and point to potential complex interactions among SNVs.
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Affiliation(s)
| | | | | | | | - Han-Ni Hsieh
- Institute of Statistical Science, Academia Sinica, Academia Rd, Nangang District Taipei 115, Taiwan
| | - Po-Wen Chen
- Institute of Statistical Science, Academia Sinica, Academia Rd, Nangang District Taipei 115, Taiwan
| | - Hsiao-Chi Liao
- Institute of Statistical Science, Academia Sinica, Academia Rd, Nangang District Taipei 115, Taiwan
| | - Chun-houh Chen
- Institute of Statistical Science, Academia Sinica, Academia Rd, Nangang District Taipei 115, Taiwan
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88
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Ghotloo S, Maghsood F, Golsaz‐Shirazi F, Amiri MM, Moog C, Shokri F. Epitope mapping of neutralising anti-SARS-CoV-2 monoclonal antibodies: Implications for immunotherapy and vaccine design. Rev Med Virol 2022; 32:e2347. [PMID: 35394093 PMCID: PMC9111153 DOI: 10.1002/rmv.2347] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 03/08/2022] [Accepted: 03/15/2022] [Indexed: 12/12/2022]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of the coronavirus disease 2019 (COVID-19) pandemic. This disease has currently affected more than 346 million people and resulted in more than 5.5 million deaths in many countries. Neutralising monoclonal antibodies (MAbs) against the SARS-CoV-2 virus could serve as prophylactic/therapeutic agents in COVID-19 infection by providing passive protection against the virus in individuals. Until now, no Food and Drug Administration/European Medicines Agency-approved neutralising MAb against SARS-CoV-2 virus exists in the market, though a number of MAbs have been authorised for emergency use. Therefore, there is an urgent need for development of efficient anti-SARS-CoV-2 neutralising MAbs for use in the clinic. Moreover, neutralising anti-SARS-CoV-2 MAbs could be used as beneficial tools for designing epitope-based vaccines against the virus. Given that the target epitope of a MAb is a crucial feature influencing its neutralising potency, target epitopes of neutralising anti-SARS-CoV-2 MAbs already reported in the literature and reactivity of these MAbs with SARS-CoV-2 variants are reviewed herein.
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Affiliation(s)
- Somayeh Ghotloo
- Department of Medical Laboratory SciencesSchool of Allied Medical SciencesKashan University of Medical SciencesKashanIran
| | - Faezeh Maghsood
- Department of ImmunologySchool of Public HealthTehran University of Medical SciencesTehranIran
| | - Forough Golsaz‐Shirazi
- Department of ImmunologySchool of Public HealthTehran University of Medical SciencesTehranIran
| | - Mohammad Mehdi Amiri
- Department of ImmunologySchool of Public HealthTehran University of Medical SciencesTehranIran
| | - Christiane Moog
- Laboratoire d’ImmunoRhumatologie MoléculaireInstitut national de la santé et de la recherche médicale (INSERM) UMR_S 1109Institut thématique interdisciplinaire (ITI) de Médecine de Précision de StrasbourgTransplantex NGFaculté de MédecineFédération Hospitalo‐Universitaire OMICAREFédération de Médecine Translationnelle de Strasbourg (FMTS)Université de StrasbourgStrasbourgFrance
| | - Fazel Shokri
- Department of ImmunologySchool of Public HealthTehran University of Medical SciencesTehranIran
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89
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Hattori T, Saito T, Okuya K, Takahashi Y, Miyamoto H, Kajihara M, Igarashi M, Takada A. Human ACE2 Genetic Polymorphism Affecting SARS-CoV and SARS-CoV-2 Entry into Cells. Microbiol Spectr 2022; 10:e0087022. [PMID: 35862965 PMCID: PMC9430119 DOI: 10.1128/spectrum.00870-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 06/27/2022] [Indexed: 11/29/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus (SARS-CoV) and SARS-CoV-2 have a single envelope glycoprotein (S protein) that binds to human angiotensin-converting enzyme 2 (ACE2) on the host cell membrane. Previous mutational scanning studies have suggested that some substitutions corresponding to single nucleotide variants (SNVs) in human ACE2 affect the binding affinity to the receptor binding domain (RBD) of the SARS-CoV-2 S protein. However, the importance of these substitutions in actual virus infection is still unclear. In this study, we investigated the effects of the reported ACE2 SNV substitutions on the entry of SARS-CoV and SARS-CoV-2 into cells, using vesicular stomatitis Indiana virus (VSIV) pseudotyped with S proteins of these coronaviruses (CoVs). HEK293T cells transfected with plasmids expressing ACE2 having each SNV substitution were infected with the pseudotyped VSIVs and relative infectivities were determined compared to the cells expressing wild-type ACE2. We found that some of the SNV substitutions positively or negatively affected the infectivities of the pseudotyped viruses. Particularly, the H505R substitution significantly enhanced the infection with the pseudotyped VSIVs, including those having the substitutions found in the S protein RBD of SARS-CoV-2 variants of concern. Our findings suggest that human ACE2 SNVs may potentially affect cell susceptibilities to SARS-CoV and SARS-CoV-2. IMPORTANCE SARS-CoV and SARS-CoV-2 are known to cause severe pneumonia in humans. The S protein of these CoVs binds to the ACE2 molecule on the plasma membrane and mediates virus entry into cells. The interaction between the S protein and ACE2 is thought to be important for host susceptibility to these CoVs. Although previous studies suggested that some SNV substitutions in ACE2 might affect the binding to the S protein, it remains elusive whether these SNV substitutions actually alter the efficiency of the entry of SARS CoVs into cells. We analyzed the impact of the ACE2 SNVs on the cellular entry of SARS CoVs using pseudotyped VSIVs having the S protein on the viral surface. We found that some of the SNV substitutions positively or negatively affected the infectivities of the viruses. Our data support the notion that genetic polymorphisms of ACE2 may potentially influence cell susceptibilities to SARS CoVs.
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Affiliation(s)
- Takanari Hattori
- Division of Global Epidemiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Takeshi Saito
- Division of Global Epidemiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Kosuke Okuya
- Division of Global Epidemiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Yuji Takahashi
- Division of Global Epidemiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Hiroko Miyamoto
- Division of Global Epidemiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Masahiro Kajihara
- Division of Global Epidemiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Manabu Igarashi
- Division of Global Epidemiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
- International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Ayato Takada
- Division of Global Epidemiology, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
- International Collaboration Unit, International Institute for Zoonosis Control, Hokkaido University, Sapporo, Japan
- Department of Disease Control, School of Veterinary Medicine, University of Zambia, Lusaka, Zambia
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90
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Wu J, Zhang J, Zhang HX. Computational Design of Miniprotein Inhibitors Targeting SARS-CoV-2 Spike Protein. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:10690-10703. [PMID: 35984970 PMCID: PMC9437664 DOI: 10.1021/acs.langmuir.2c01699] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 07/31/2022] [Indexed: 05/16/2023]
Abstract
The ongoing pandemic of COVID-19 caused by SARS-CoV-2 has become a global health problem. There is an urgent need to develop therapeutic drugs, effective therapies, and vaccines to prevent the spread of the virus. The virus first enters the host cell through the interaction between the receptor binding domain (RBD) of spike protein and the peptidase domain (PD) of the angiotensin-converting enzyme 2 (ACE2). Therefore, blocking the binding of RBD and ACE2 is a promising strategy to inhibit the invasion and infection of the virus in the host cell. In the study, we designed several miniprotein inhibitors against SARS-CoV-2 by single/double/triple-point mutant, based on the initial inhibitor LCB3. Molecular dynamics (MD) simulations and trajectory analysis were performed for an in-depth analysis of the structural stability, essential protein motions, and per-residue energy decomposition involved in the interaction of inhibitors with the RBD. The results showed that the inhibitors have adapted the protein RBD in the binding interface, thereby forming stable complexes. These inhibitors display low binding free energy in the MM/PBSA calculations, substantiating their strong interaction with RBD. Moreover, the binding affinity of the best miniprotein inhibitor, H6Y-M7L-L17F mutant, to RBD was ∼45 980 times (ΔG = RT ln Ki) higher than that of the initial inhibitor LCB3. Following H6Y-M7L-L17F mutant, the inhibitors with strong binding activity are successively H6Y-L17F, L17F, H6Y, and F30Y mutants. Our research proves that the miniprotein inhibitors can maintain their secondary structure and have a highly stable blocking (binding) effect on SARS-CoV-2. This study proposes novel miniprotein mutant inhibitors with enhanced binding to spike protein and provides potential guidance for the rational design of new SARS-CoV-2 spike protein inhibitors.
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Affiliation(s)
- Jianhua Wu
- Institute
of Theoretical Chemistry, College of Chemistry, Jilin University, Changchun 130023, Jilin, People’s Republic of China
| | - Jilong Zhang
- Institute
of Theoretical Chemistry, College of Chemistry, Jilin University, Changchun 130023, Jilin, People’s Republic of China
| | - Hong-Xing Zhang
- Institute
of Theoretical Chemistry, College of Chemistry, Jilin University, Changchun 130023, Jilin, People’s Republic of China
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91
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Bonifacio MA, Laterza R, Vinella A, Schirinzi A, Defilippis M, Di Serio F, Ostuni A, Fasanella A, Mariggiò MA. Correlation between In Vitro Neutralization Assay and Serological Tests for Protective Antibodies Detection. Int J Mol Sci 2022; 23:ijms23179566. [PMID: 36076960 PMCID: PMC9455156 DOI: 10.3390/ijms23179566] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 08/20/2022] [Accepted: 08/21/2022] [Indexed: 11/21/2022] Open
Abstract
Serological assays are useful in investigating the development of humoral immunity against SARS-CoV-2 in the context of epidemiological studies focusing on the spread of protective immunity. The plaque reduction neutralization test (PRNT) is the gold standard method to assess the titer of protective antibodies in serum samples. However, to provide a result, the PRNT requires several days, skilled operators, and biosafety level 3 laboratories. Therefore, alternative methods are being assessed to establish a relationship between their outcomes and PRNT results. In this work, four different immunoassays (Roche Elecsys® Anti SARS-CoV-2 S, Snibe MAGLUMI® SARS-CoV-2 S-RBD IgG, Snibe MAGLUMI® 2019-nCoV IgG, and EUROIMMUN® SARS-CoV-2 NeutraLISA assays, respectively) have been performed on individuals healed after SARS-CoV-2 infection. The correlation between each assay and the reference method has been explored through linear regression modeling, as well as through the calculation of Pearson’s and Spearman’s coefficients. Furthermore, the ability of serological tests to discriminate samples with high titers of neutralizing antibodies (>160) has been assessed by ROC curve analyses, Cohen’s Kappa coefficient, and positive predictive agreement. The EUROIMMUN® NeutraLISA assay displayed the best correlation with PRNT results (Pearson and Spearman coefficients equal to 0.660 and 0.784, respectively), as well as the ROC curve with the highest accuracy, sensitivity, and specificity (0.857, 0.889, and 0.829, respectively).
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Affiliation(s)
- Maria Addolorata Bonifacio
- Department of Biomedical Sciences and Human Oncology, University of Bari Aldo Moro Medical School, 70124 Bari, Italy
| | - Riccardo Laterza
- Department of Biomedical Sciences and Human Oncology, University of Bari Aldo Moro Medical School, 70124 Bari, Italy
| | - Angela Vinella
- Department of Biomedical Sciences and Human Oncology, University of Bari Aldo Moro Medical School, 70124 Bari, Italy
| | - Annalisa Schirinzi
- Clinical Pathology Unit, University of Bari Aldo Moro, 70124 Bari, Italy
| | - Mariangela Defilippis
- Immunohematology and Transfusion Medicine Service, Azienda Ospedaliero-Universitaria Consorziale Policlinico di Bari, University of Bari “Aldo Moro”, 70124 Bari, Italy
| | - Francesca Di Serio
- Clinical Pathology Unit, University of Bari Aldo Moro, 70124 Bari, Italy
| | - Angelo Ostuni
- Immunohematology and Transfusion Medicine Service, Azienda Ospedaliero-Universitaria Consorziale Policlinico di Bari, University of Bari “Aldo Moro”, 70124 Bari, Italy
| | - Antonio Fasanella
- Istituto Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, 71121 Foggia, Italy
| | - Maria Addolorata Mariggiò
- Department of Biomedical Sciences and Human Oncology, University of Bari Aldo Moro Medical School, 70124 Bari, Italy
- Correspondence:
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92
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Abstract
Despite effective spike-based vaccines and monoclonal antibodies, the SARS-CoV-2 pandemic continues more than two and a half years post-onset. Relentless investigation has outlined a causative dynamic between host-derived antibodies and reciprocal viral subversion. Integration of this paradigm into the architecture of next generation antiviral strategies, predicated on a foundational understanding of the virology and immunology of SARS-CoV-2, will be critical for success. This review aims to serve as a primer on the immunity endowed by antibodies targeting SARS-CoV-2 spike protein through a structural perspective. We begin by introducing the structure and function of spike, polyclonal immunity to SARS-CoV-2 spike, and the emergence of major SARS-CoV-2 variants that evade immunity. The remainder of the article comprises an in-depth dissection of all major epitopes on SARS-CoV-2 spike in molecular detail, with emphasis on the origins, neutralizing potency, mechanisms of action, cross-reactivity, and variant resistance of representative monoclonal antibodies to each epitope.
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Affiliation(s)
- John M Errico
- Department of Pathology & Immunology, Washington University School of Medicine, St Louis, MO, United States
| | - Lucas J Adams
- Department of Pathology & Immunology, Washington University School of Medicine, St Louis, MO, United States
| | - Daved H Fremont
- Department of Pathology & Immunology, Washington University School of Medicine, St Louis, MO, United States; Department of Molecular Microbiology, Washington University School of Medicine, St Louis, MO, United States; Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St Louis, MO, United States.
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93
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Yokoyama K, Lam T, Santariello J, Ichiki A. Nano-size dependent protein corona formation by SARS-CoV-2 Omicron spike protein over gold nano-colloid and reversible aggregation. Colloids Surf A Physicochem Eng Asp 2022; 647:128967. [PMID: 35466287 PMCID: PMC9012667 DOI: 10.1016/j.colsurfa.2022.128967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 03/28/2022] [Accepted: 04/09/2022] [Indexed: 11/24/2022]
Abstract
The adsorption process of SARS-CoV-2 Omicron spike protein to the nano-gold colloid surfaces was examined by monitoring the surface plasmon resonance (SPR) band shift of gold-nano particles ranging between diameters of d = 10–100 nm. The externally changed pH between 3 and 11 at 24.5 ± 0.4 °C initiated a reversible formation of the gold colloid aggregates, where formation/deformation of the aggregates were monitored by red/blue shift of the peak of the SPR band. There was no sign of reversible aggregation for d = 10, 15, and 20 nm gold colloids. A clear undulation of the peak shift corresponding to pH hopping between pH ~3 and ~11 was confirmed for colloidal d > 30 nm. This degree of the reversibility was compared to previously reported SARS-CoV-2 Alpha spike protein coated gold colloids. It was concluded that Omicron spike protein possesses a similar low affinity for gold nano particle d < 20 nm and possesses the higher affinity to the gold nanoparticles of d > 30 nm. However, the Omicron spike protein conformation was presumed to be more denatured compared to the SARS-CoV-2 Alpha spike protein. Our finding suggested Omicron spike protein was more acid labile/flexible.
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Affiliation(s)
- Kazushige Yokoyama
- Department of Chemistry, The State University of New York Geneseo College, Geneseo, NY, USA
| | - Theresa Lam
- Department of Chemistry, The State University of New York Geneseo College, Geneseo, NY, USA
| | - Jack Santariello
- Department of Chemistry, The State University of New York Geneseo College, Geneseo, NY, USA
| | - Akane Ichiki
- Department of Chemistry, The State University of New York Geneseo College, Geneseo, NY, USA
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94
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Sharif N, Alzahrani KJ, Ahmed SN, Khan A, Banjer HJ, Alzahrani FM, Parvez AK, Dey SK. Genomic surveillance, evolution and global transmission of SARS-CoV-2 during 2019-2022. PLoS One 2022; 17:e0271074. [PMID: 35913920 PMCID: PMC9342790 DOI: 10.1371/journal.pone.0271074] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 06/23/2022] [Indexed: 12/19/2022] Open
Abstract
In spite of the availability of vaccine, the health burden associated with the COVID-19 pandemic continues to increase. An estimated 5 million people have died with SARS-CoV-2 infection. Analysis of evolution and genomic diversity can provide sufficient information to reduce the health burden of the pandemic. This study focused to conduct worldwide genomic surveillance. About 7.6 million genomic data were analyzed during 2019 to 2022. Multiple sequence alignment was conducted by using maximum likelihood method. Clade GK (52%) was the most predominant followed by GRY (12%), GRA (11%), GR (8%), GH (7%), G (6%), GV (3%), and O (1%), respectively. VOC Delta (66%) was the most prevalent variant followed by VOC Alpha (18%), VOC Omicron (13%), VOC Gamma (2%) and VOC Beta (1%), respectively. The frequency of point mutations including E484K, N501Y, N439K, and L452R at spike protein has increased 10%-92%. Evolutionary rate of the variants was 23.7 substitution per site per year. Substitution mutations E484K and N501Y had significant correlation with cases (r = .45, r = .23), fatalities (r = .15, r = .44) and growth rate R0 (r = .28, r = .54). This study will help to understand the genomic diversity, evolution and the impact of the variants on the outcome of the COVID-19 pandemic.
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Affiliation(s)
- Nadim Sharif
- Department of Microbiology, Jahangirnagar University, Savar, Dhaka, Bangladesh
| | - Khalid J. Alzahrani
- Department of Clinical Laboratories Sciences, College of Applied Medical Sciences, Taif University, Taif, Saudi Arabia
| | - Shamsun Nahar Ahmed
- Department of Microbiology, Jahangirnagar University, Savar, Dhaka, Bangladesh
| | - Afsana Khan
- Department of Statistics, Jahangirnagar University, Savar, Dhaka, Bangladesh
| | - Hamsa Jameel Banjer
- Department of Clinical Laboratories Sciences, College of Applied Medical Sciences, Taif University, Taif, Saudi Arabia
| | - Fuad M. Alzahrani
- Department of Clinical Laboratories Sciences, College of Applied Medical Sciences, Taif University, Taif, Saudi Arabia
| | | | - Shuvra Kanti Dey
- Department of Microbiology, Jahangirnagar University, Savar, Dhaka, Bangladesh
- * E-mail:
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95
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Mahmanzar M, Houseini ST, Rahimian K, Namini AM, Gholamzad A, Tokhanbigli S, Sisakht MM, Farhadi A, Kuehu DL, Deng Y. The First Geographic Identification by Country of Sustainable Mutations of SARS-COV2 Sequence Samples: Worldwide Natural Selection Trends. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2022.07.18.500565. [PMID: 35898341 PMCID: PMC9327626 DOI: 10.1101/2022.07.18.500565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The high mutation rates of RNA viruses, coupled with short generation times and large population sizes, allow viruses to evolve rapidly and adapt to the host environment. The rapidity of viral mutation also causes problems in developing successful vaccines and antiviral drugs. With the spread of SARS-CoV-2 worldwide, thousands of mutations have been identified, some of which have relatively high incidences, but their potential impacts on virus characteristics remain unknown. The present study analyzed mutation patterns, SARS-CoV-2 AASs retrieved from the GISAID database containing 10,500,000 samples. Python 3.8.0 programming language was utilized to pre-process FASTA data, align to the reference sequence, and analyze the sequences. Upon completion, all mutations discovered were categorized based on geographical regions and dates. The most stable mutations were found in nsp1(8% S135R), nsp12(99.3% P323L), nsp16 (1.2% R216C), envelope (30.6% T9I), spike (97.6% D614G), and Orf8 (3.5% S24L), and were identified in the United States on April 3, 2020, and England, Gibraltar, and, New Zealand, on January 1, 2020, respectively. The study of mutations is the key to improving understanding of the function of the SARS-CoV-2, and recent information on mutations helps provide strategic planning for the prevention and treatment of this disease. Viral mutation studies could improve the development of vaccines, antiviral drugs, and diagnostic assays designed with high accuracy, specifically useful during pandemics. This knowledge helps to be one step ahead of new emergence variants.
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Affiliation(s)
- Mohammadamin Mahmanzar
- Department of Quantitative Health Sciences, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, HI 96813, USA
| | - Seyed Taleb Houseini
- Department of Biology, Faculty of Basic Sciences, Qaemshahr Branch, Islamic Azad University, Mazandaran, Iran
| | - Karim Rahimian
- Bioinformatics and Computational Omics Lab (BioCOOL), Department of Biophysics. Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Arsham Mikaeili Namini
- Department of Animal Biology, Faculty of Biological Sciences, Kharazmi University, Tehran, Iran
| | - Amir Gholamzad
- Department of Laboratory Medicine, Faculty of Paramedical Sciences, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Samaneh Tokhanbigli
- Department of Molecular and Cellular Sciences, Faculty of Advanced Sciences and Technology, pharmaceutical Sciences Branch, Islamic Azad University, Tehran, Iran (IAUPS)
| | - Mahsa Mollapour Sisakht
- Department of Biochemistry, Erasmus University Medical Center, P.O. Box 2040, 3000 CA Rotterdam, The Netherlands
| | - Amin Farhadi
- Department of Biology, Payame Noor University, Tehran, Iran
| | - Donna Lee Kuehu
- Department of Quantitative Health Sciences, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, HI 96813, USA
| | - Youping Deng
- Department of Quantitative Health Sciences, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, HI 96813, USA
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96
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Silwal AP, Thennakoon SKS, Arya SP, Postema RM, Jahan R, Phuoc CMT, Tan X. DNA aptamers inhibit SARS-CoV-2 spike-protein binding to hACE2 by an RBD- independent or dependent approach. Theranostics 2022; 12:5522-5536. [PMID: 35910791 PMCID: PMC9330529 DOI: 10.7150/thno.74428] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 06/23/2022] [Indexed: 11/12/2022] Open
Abstract
Objective: Nobody knows when the COVID-19 pandemic will end or when and where the next coronavirus will outbreak. Therefore, it is still necessary to develop SARS-CoV-2 inhibitors for different variants or even the new coronavirus. Since SARS-CoV-2 uses its surface spike-protein to recognize hACE2, mediating its entry into cells, ligands that can specifically recognize the spike-protein have the potential to prevent infection. Methods: We have recently discovered DNA aptamers against the S2-domain of the WT spike-protein by exploiting the selection process called SELEX. After optimization, among all candidates, the aptamer S2A2C1 has the shortest sequence and the best binding affinity toward the S2-protein. More importantly, the S2A2C1 aptamer does not bind to the RBD of the spike-protein, but it efficiently blocks the spike-protein/hACE2 interaction, suggesting an RBD-independent inhibition approach. To further improve its performance, we conjugated the S2A2C1 aptamer with a reported anti-RBD aptamer, S1B6C3, using various linkers and constructed hetero-bivalent fusion aptamers. Binding affinities of mono and fusion aptamers against the spike-proteins were measured. The inhibition efficacies of mono and fusion aptamers to prevent the hACE2/spike-protein interaction were determined using ELISA. Results: Anti-spike-protein aptamers, including S2A2C1 and S1B6C3-A5-S2A2C1, maintained high binding affinity toward the WT, Delta, and Omicron spike-proteins and high inhibition efficacies to prevent them from binding to hACE2, rendering them well-suited as diagnostic and therapeutic molecular tools to target SARS-CoV-2 and its variants. Conclusions: Overall, we discovered the anti-S2 aptamer, S2A2C1, which inhibits the hACE2/spike-protein interaction via an RBD-independent approach. The anti-S2 and anti-RBD aptamers were conjugated to obtain the fusion aptamer, S1B6C3-A5-S2A2C1, which recognizes the spike-protein by an RBD-dependent approach. Our strategies, which discovered aptamer inhibitors targeting the highly conserved S2-protein, as well as the design of fusion aptamers, can be used to target new coronaviruses as they emerge.
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Affiliation(s)
| | | | | | | | | | | | - Xiaohong Tan
- Department of Chemistry and Center for Photochemical Sciences, Bowling Green State University, Bowling Green, Ohio 43403, United States
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97
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Bandaru R, Rout SR, Kamble OS, Samal SK, Gorain B, Sahebkar A, Ahmed FJ, Kesharwani P, Dandela R. Clinical progress of therapeutics and vaccines: Rising hope against COVID-19 treatment. Process Biochem 2022; 118:154-170. [PMID: 35437418 PMCID: PMC9008982 DOI: 10.1016/j.procbio.2022.04.011] [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] [Received: 07/30/2021] [Revised: 03/11/2022] [Accepted: 04/08/2022] [Indexed: 02/07/2023]
Abstract
Cases of deaths due to COVID-19 (COrona VIrus Disease-19) infection are increasing gradually worldwide. Immense research is ongoing to control this pandemic condition. Continual research outcomes are indicating that therapeutic and prophylactic agents are the possible hope to prevent the pandemic from spreading and to combat this increasing death count. Experience gained from previous coronavirus infections (eg., SARS (Severe Acute Respiratory Syndrome), MERS (Middle Ease Respiratory Syndrome), accumulated clinical knowledge during this pandemic, and research helped to identify a few therapeutic agents for emergency treatment of COVID-19. Thereby, monoclonal antibodies, antivirals, broad-spectrum antimicrobials, immunomodulators, and supplements are being suggested for treatment depending on the stage of the disease. These recommended treatments are authorized under medical supervision in emergency conditions only. Urgent need to control the pandemic condition had resulted in various approaches of repurposing the existing drugs, However, poorly designed clinical trials and associated outcomes do not provide enough evidence to fully approve treatments against COVID-19. So far, World Health Organization (WHO) authorized three vaccines as prophylactic against SARS-CoV-2. Here, we discussed about various therapeutic agents, their clinical trials, and limitations of trials for the management of COVID-19. Further, we have also spotlighted different vaccines in research in combating COVID-19.
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Affiliation(s)
- Ravi Bandaru
- Department of Industrial and Engineering Chemistry, Institute of Chemical Technology, Indian oil Odisha Campus, Samantpuri, Bhubaneswar 751013, India
| | - Smruti Rekha Rout
- Department of Industrial and Engineering Chemistry, Institute of Chemical Technology, Indian oil Odisha Campus, Samantpuri, Bhubaneswar 751013, India
| | - Omkar S Kamble
- Department of Industrial and Engineering Chemistry, Institute of Chemical Technology, Indian oil Odisha Campus, Samantpuri, Bhubaneswar 751013, India
| | - Sangram K Samal
- Laboratory of Biomaterials and Regenerative Medicine for Advanced Therapies, Indian Council of Medical Research-Regional Medical Research Center, Bhubaneswar 751023, India
| | - Bapi Gorain
- Department of Pharmaceutical Sciences and Technology, Birla Institute of Technology, Mesra, Ranchi 835215, India
| | - Amirhossein Sahebkar
- Biotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
- Applied Biomedical Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Farhan J Ahmed
- Department of Pharmaceutics, School of Pharmaceutical Education and Research, Jamia Hamdard 110062, New Delhi, India
| | - Prashant Kesharwani
- Department of Pharmaceutics, School of Pharmaceutical Education and Research, Jamia Hamdard 110062, New Delhi, India
| | - Rambabu Dandela
- Department of Industrial and Engineering Chemistry, Institute of Chemical Technology, Indian oil Odisha Campus, Samantpuri, Bhubaneswar 751013, India
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98
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Liu JZ, Lyu HC, Fu YJ, Cui Q. Amomum tsao-ko essential oil, a novel anti-COVID-19 Omicron spike protein natural products: A computational study. ARAB J CHEM 2022; 15:103916. [PMID: 35462797 PMCID: PMC9014638 DOI: 10.1016/j.arabjc.2022.103916] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 04/10/2022] [Indexed: 12/20/2022] Open
Abstract
Since the outbreak of COVID-19, this virus has been constantly mutating. The latest mutant Omicron has been identified as VOC by WHO. The main reason for its concern is the mutation of 46 amino acids in spike protein, which has brought the global epidemic prevention into another difficulty. Herbal aromatic plant Amomum tsao-ko was excavated from formula 1 and 2 for the treatment of COVID-19 in China, and its active components were extracted and identified. Molecular dynamics simulation and Fpocket were applied to find the key sites on RBDOmicron, and molecular docking was also used to reveal the interaction between A. tsao-ko essential oil (AEO) and RBDOmicron. The AEO components were analyzed and identified by GC/Q-TOF MS. There were 20 kinds of AEO with a relative area percentage of more than 1%, and they were related to the three active centres of RBDOmicron. In this study, virtual screening was used to mine the essential oil components of medicinal plants, and it was found that the components could interact with the spike protein RBD in aerosol to block the interaction of RBD and hACE2, thus cutting off the transmission route and protecting the host. This study has certain guiding significance in the modernization of Traditional Chinese medicine and the prevention of COVID-19.
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Affiliation(s)
- Ju-Zhao Liu
- College of Pharmaceutical Science, Zhejiang Chinese Medical University, Hangzhou 311402, PR China
| | - Hong-Chang Lyu
- School of Modern Post (School of Automation), Beijing University of Posts and Telecommunications, Beijing 100876, PR China
| | - Yu-Jie Fu
- College of Forestry, Beijing Forestry University, No. 35, Tsinghua East Road, Haidian District, Beijing 100083, PR China
| | - Qi Cui
- College of Pharmaceutical Science, Zhejiang Chinese Medical University, Hangzhou 311402, PR China
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99
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Yi C, Sun X, Ling Z, Sun B. Jigsaw puzzle of SARS-CoV-2 RBD evolution and immune escape. Cell Mol Immunol 2022; 19:848-851. [PMID: 35676326 PMCID: PMC9174622 DOI: 10.1038/s41423-022-00884-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 05/10/2022] [Indexed: 11/09/2022] Open
Affiliation(s)
- Chunyan Yi
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 200031, China
| | - Xiaoyu Sun
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 200031, China
| | - Zhiyang Ling
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 200031, China.
| | - Bing Sun
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, 200031, China.
- School of Life Science and Technology, ShanghaiTech University, 100 Haike Road, Shanghai, 201210, China.
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100
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Neutralization mechanism of a human antibody with pan-coronavirus reactivity including SARS-CoV-2. Nat Microbiol 2022; 7:1063-1074. [PMID: 35773398 DOI: 10.1038/s41564-022-01155-3] [Citation(s) in RCA: 70] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Accepted: 05/20/2022] [Indexed: 12/23/2022]
Abstract
Frequent outbreaks of coronaviruses underscore the need for antivirals and vaccines that can counter a broad range of coronavirus types. We isolated a human antibody named 76E1 from a COVID-19 convalescent patient, and report that it has broad-range neutralizing activity against multiple α- and β-coronaviruses, including the SARS-CoV-2 variants. 76E1 also binds its epitope in peptides from γ- and δ-coronaviruses. 76E1 cross-protects against SARS-CoV-2 and HCoV-OC43 infection in both prophylactic and therapeutic murine animal models. Structural and functional studies revealed that 76E1 targets a unique epitope within the spike protein that comprises the highly conserved S2' site and the fusion peptide. The epitope that 76E1 binds is partially buried in the structure of the SARS-CoV-2 spike trimer in the prefusion state, but is exposed when the spike protein binds to ACE2. This observation suggests that 76E1 binds to the epitope at an intermediate state of the spike trimer during the transition from the prefusion to the postfusion state, thereby blocking membrane fusion and viral entry. We hope that the identification of this crucial epitope, which can be recognized by 76E1, will guide epitope-based design of next-generation pan-coronavirus vaccines and antivirals.
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