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Mahnam K, Rajaee SM. A theoretical survey to find potential natural compound for inhibition of binding the RBD domain to ACE2 receptor based on plant antivirals. J Biomol Struct Dyn 2023; 41:14540-14565. [PMID: 36974837 DOI: 10.1080/07391102.2023.2183033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 02/16/2023] [Indexed: 03/29/2023]
Abstract
The spike protein of coronavirus is crucial in binding and arrival of the virus to the human cell via binding to the human ACE2 receptor. In this study, at first 25 antiviral phytochemicals were docked into the RBD domain of spike protein, and then all complexes and free RBD domains were separately subjected to molecular dynamics simulation for 100 ns and MM/PBSA binding free energy calculation. In this phase, four ligands were chosen as hit compounds and a natural compound database (NPASS) was screened based on high similarity with these ligands, and 367 ligands were found. Then the same previous procedure was repeated for these ligands and ADME properties were investigated. Finally, virtual screening and 4400 ns MD simulation and MM/PBSA calculation revealed that new ligands including NPC67959, NPC157855, NPC248793, and NPC216361 can inhibit the RBD domain of spike protein and we propose them as potential drugs for experimental studies.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Karim Mahnam
- Department of Biology, Faculty of Sciences, Shahrekord University, Shahrekord, Iran
- Nanotechnology Research Center, Shahrekord University, Shahrekord, Iran
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Filippatos F, Tatsi EB, Michos A. Immunology of Multisystem Inflammatory Syndrome after COVID-19 in Children: A Review of the Current Evidence. Int J Mol Sci 2023; 24:ijms24065711. [PMID: 36982783 PMCID: PMC10057510 DOI: 10.3390/ijms24065711] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Revised: 03/13/2023] [Accepted: 03/14/2023] [Indexed: 03/19/2023] Open
Abstract
Immune responses following severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in children are still under investigation. Even though coronavirus disease 2019 (COVID-19) is usually mild in the pediatric population, some children exhibit severe clinical manifestations, require hospitalization, or develop the most severe condition: a multisystem inflammatory syndrome in children (MIS-C) associated with SARS-CoV-2 infection. The activated innate, humoral and T-cell-mediated immunological pathways that lead certain pediatric populations to present with MIS-C or remain asymptomatic after SARS-CoV-2 infection are yet to be established. This review focuses on the immunological aspects of MIS-C with respect to innate, humoral, and cellular immunity. In addition, presents the role of the SARS-CoV-2 Spike protein as a superantigen in the pathophysiological mechanisms, discusses the great heterogeneity among the immunological studies in the pediatric population, and highlights possible reasons why some children with a certain genetic background present with MIS-C.
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Felbinger N, Trudil D, Loomis L, Ascione R, Siragusa G, Haba S, Rastogi S, Mucci A, Claycomb M, Snowberger S, Luke B, Francesconi S, Tsang S. Epitope mapping of SARS-CoV-2 spike protein differentiates the antibody binding activity in vaccinated and infected individuals. FRONTIERS IN VIROLOGY 2023. [DOI: 10.3389/fviro.2023.988109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/06/2023]
Abstract
Previous studies have attempted to characterize the antibody response of individuals to the SARS-CoV-2 virus on a linear peptide level by utilizing peptide microarrays. These studies have helped to identify epitopes that have potential to be used for diagnostic tests to identify infected individuals. The immunological responses of individuals who have received the two most popular vaccines available in the US, the Moderna mRNA-1273 or the Pfizer BNT162b2 mRNA vaccines, have not been characterized. We aimed to identify linear peptides of the SARS-CoV-2 spike protein that elicited high IgG or IgA binding activity and to compare the immunoreactivity of infected individuals to those who received both doses of either vaccine by utilizing peptide microarrays. Our results revealed peptide epitopes of significant IgG binding among recently infected individuals. Some of these peptides are located near variable regions of the receptor binding domains as well as the conserved region in the c-terminal of the spike protein implicated in the high infectivity of SARS-CoV-2. Vaccinated individuals lacked a response to these distinct markers despite the overall antibody binding activity being similar.
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Omotuyi O, Olatunji OM, Nash O, Oyinloye B, Soremekun O, Ijagbuji A, Fatumo S. Benzimidazole compound abrogates SARS-COV-2 receptor-binding domain (RBD)/ACE2 interaction In vitro. Microb Pathog 2023; 176:105994. [PMID: 36682669 PMCID: PMC9851952 DOI: 10.1016/j.micpath.2023.105994] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 01/10/2023] [Accepted: 01/13/2023] [Indexed: 01/21/2023]
Abstract
The development of clinically actionable pharmaceuticals against coronavirus disease (COVID-19); an infectious disease caused by the SARS-CoV-2 virus is very important for ending the pandemic. Coronavirus spike glycoprotein (GP)-Receptor Binding Domain (RBD) and its interaction with host receptor angiotensin converting enzyme 2 (ACE2) is one of the most structurally understood but therapeutically untapped aspect of COVID-19 pathogenesis. Binding interface based on previous x-ray structure of RBD/ACE2 were virtually screened to identify fragments with high-binding score from 12,000 chemical building blocks. The hit compound was subjected to fingerprint-based similarity search to identify compounds within the FDA-approved drug library containing the same core scaffold. Identified compounds were then re-docked into of RBD/ACE2. The best ranked compound was validated for RBD/ACE2 inhibition using commercial kit. Molecular dynamics simulation was conducted to provide further insight into the mechanism of inhibition. From the original 12000 chemical building blocks, benzimidazole (BAZ) scaffold was identified. Fingerprint-based similarity search of the FDA-approved drug library for BAZ-containing compounds identified 12 drugs with the benzimidazole-like substructure. When these compounds were re-docked into GP/ACE2 interface, the consensus docking identified bazedoxifene as the hit. In vitro RBD/ACE2 inhibition kinetics showed micromolar IC50 value (1.237 μM) in the presence of bazedoxifene. Molecular dynamics simulation of RBD/ACE2 in the presence BAZ resulted in loss of contact and specific hydrogen-bond interaction required for RBD/ACE2 stability. Taken together, these findings identified benzimidazole scaffold as a building block for developing novel RBD/ACE2 complex inhibitor and provided mechanistic basis for the use of bazedoxifene as a repurposable drug for the treatment of COVID-19 acting at RBD/ACE2 interface.
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Affiliation(s)
- Olaposi Omotuyi
- Institute for Drug Research and Development, S.E. Bogoro Center, Afe Babalola University, Ado-Ekiti, Nigeria; Department of Pharmacology and Toxicology, College of Pharmacy, Afe Babalola University, Ado-Ekiti, Nigeria; Bio-Computing & Drug Research Unit, Mols and Sims, Ado Ekiti, Ekiti State, Nigeria.
| | - Olusina M Olatunji
- Department of Pharmacology and Toxicology, College of Pharmacy, Afe Babalola University, Ado-Ekiti, Nigeria
| | - Oyekanmi Nash
- Center for Genomics Research and Innovation, National Biotechnology Development Agency, Abuja, PMB 5118, Nigeria
| | - Babatunji Oyinloye
- Institute for Drug Research and Development, S.E. Bogoro Center, Afe Babalola University, Ado-Ekiti, Nigeria; Phytomedicine, Biochemical Toxicology and Biotechnology Research Laboratories, Department of Biochemistry, College of Sciences, Afe Babalola University, PMB 5454, Ado-Ekiti, 360001, Nigeria; Biotechnology and Structural Biology (BSB) Group, Department of Biochemistry and Microbiology, University of Zululand, Kwa-Dlangezwa, 3886, South Africa
| | - Opeyemi Soremekun
- The African Computational Genomics (TACG) Research Group, MRC/UVRI, and LSHTM, Entebbe, Uganda
| | - Ayodeji Ijagbuji
- Pharmaceutics International, Inc. Hunt Valley, Maryland, United States
| | - Segun Fatumo
- The African Computational Genomics (TACG) Research Group, MRC/UVRI, and LSHTM, Entebbe, Uganda; H3Africa Bioinformatics Network (H3ABioNet) Node, Centre for Genomics Research and Innovation, NABDA/FMST, Abuja, Nigeria; Department of Non-Communicable Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, UK.
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Behura A, Naik L, Patel S, Das M, Kumar A, Mishra A, Nayak DK, Manna D, Mishra A, Dhiman R. Involvement of epigenetics in affecting host immunity during SARS-CoV-2 infection. Biochim Biophys Acta Mol Basis Dis 2023; 1869:166634. [PMID: 36577469 PMCID: PMC9790847 DOI: 10.1016/j.bbadis.2022.166634] [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: 06/28/2022] [Revised: 10/26/2022] [Accepted: 12/13/2022] [Indexed: 12/27/2022]
Abstract
Coronavirus disease 19 (COVID-19) is caused by a highly contagious RNA virus Severe Acute Respiratory Syndrome coronavirus-2 (SARS-CoV-2), originated in December 2019 in Wuhan, China. Since then, it has become a global public health concern and leads the disease table with the highest mortality rate, highlighting the necessity for a thorough understanding of its biological properties. The intricate interaction between the virus and the host immune system gives rise to diverse implications of COVID-19. RNA viruses are known to hijack the host epigenetic mechanisms of immune cells to regulate antiviral defence. Epigenetics involves processes that alter gene expression without changing the DNA sequence, leading to heritable phenotypic changes. The epigenetic landscape consists of reversible modifications like chromatin remodelling, DNA/RNA methylation, and histone methylation/acetylation that regulates gene expression. The epigenetic machinery contributes to many aspects of SARS-CoV-2 pathogenesis, like global DNA methylation and receptor angiotensin-converting enzyme 2 (ACE2) methylation determines the viral entry inside the host, viral replication, and infection efficiency. Further, it is also reported to epigenetically regulate the expression of different host cytokines affecting antiviral response. The viral proteins of SARS-CoV-2 interact with various host epigenetic enzymes like histone deacetylases (HDACs) and bromodomain-containing proteins to antagonize cellular signalling. The central role of epigenetic factors in SARS-CoV-2 pathogenesis is now exploited as promising biomarkers and therapeutic targets against COVID-19. This review article highlights the ability of SARS-CoV-2 in regulating the host epigenetic landscape during infection leading to immune evasion. It also discusses the ongoing therapeutic approaches to curtail and control the viral outbreak.
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Affiliation(s)
- Assirbad Behura
- Laboratory of Mycobacterial Immunology, Department of Life Science, National Institute of Technology, Rourkela 769008, Odisha, India
| | - Lincoln Naik
- Laboratory of Mycobacterial Immunology, Department of Life Science, National Institute of Technology, Rourkela 769008, Odisha, India
| | - Salina Patel
- Laboratory of Mycobacterial Immunology, Department of Life Science, National Institute of Technology, Rourkela 769008, Odisha, India
| | - Mousumi Das
- Laboratory of Mycobacterial Immunology, Department of Life Science, National Institute of Technology, Rourkela 769008, Odisha, India
| | - Ashish Kumar
- Laboratory of Mycobacterial Immunology, Department of Life Science, National Institute of Technology, Rourkela 769008, Odisha, India
| | - Abtar Mishra
- Laboratory of Mycobacterial Immunology, Department of Life Science, National Institute of Technology, Rourkela 769008, Odisha, India
| | - Dev Kiran Nayak
- Laboratory of Mycobacterial Immunology, Department of Life Science, National Institute of Technology, Rourkela 769008, Odisha, India
| | - Debraj Manna
- Laboratory of Mycobacterial Immunology, Department of Life Science, National Institute of Technology, Rourkela 769008, Odisha, India
| | - Amit Mishra
- Cellular and Molecular Neurobiology Unit, Indian Institute of Technology Jodhpur, Rajasthan 342011, India
| | - Rohan Dhiman
- Laboratory of Mycobacterial Immunology, Department of Life Science, National Institute of Technology, Rourkela 769008, Odisha, India.
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Borkotoky S, Dey D, Hazarika Z. Interactions of angiotensin-converting enzyme-2 (ACE2) and SARS-CoV-2 spike receptor-binding domain (RBD): a structural perspective. Mol Biol Rep 2023; 50:2713-2721. [PMID: 36562937 PMCID: PMC9786537 DOI: 10.1007/s11033-022-08193-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 12/07/2022] [Indexed: 12/24/2022]
Abstract
BACKGROUND Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has caused millions of infections and deaths worldwide since its discovery in late 2019 in Wuhan, China. The receptor-binding domain (RBD) of the SARS-CoV-2 spike protein binds to the human angiotensin-converting enzyme-2 (ACE2) receptor, a critical component of the renin-angiotensin system (RAS) that initiates the viral transmission. Most of the critical mutations found in SARS-CoV-2 are associated with the RBD of the spike protein. These mutations have the potential to reduce the efficacy of vaccines and neutralizing antibodies. METHODS In this review, the structural details of ACE2, RBD and their interactions are discussed. In addition, some critical mutations of RBD and their impact on ACE2-RBD interactions are also discussed. CONCLUSION Preventing the interaction between Spike RBD and ACE2 is considered a viable therapeutic strategy since ACE2 binding by RBD is the first step in virus infection. Because the interactions between the two entities are critical for both viral transmission and therapeutic development, it is essential to understand their interactions in detail.
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Affiliation(s)
- Subhomoi Borkotoky
- Department of Biotechnology, Faculty of Biosciences, Invertis University, Bareilly, Uttar Pradesh, 243123, India.
| | - Debajit Dey
- School of Medicine, University of Maryland Baltimore, Baltimore, MD, 21201, United States of America
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Lung fibrosis: Post-COVID-19 complications and evidences. Int Immunopharmacol 2023; 116:109418. [PMID: 36736220 PMCID: PMC9633631 DOI: 10.1016/j.intimp.2022.109418] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 10/13/2022] [Accepted: 10/31/2022] [Indexed: 11/06/2022]
Abstract
BACKGROUND COVID 19, a lethal viral outbreak that devastated lives and the economy across the globe witnessed non-compensable respiratory illnesses in patients. As been evaluated in reports, patients receiving long-term treatment are more prone to acquire Pulmonary Fibrosis (PF). Repetitive damage and repair of alveolar tissues increase oxidative stress, inflammation and elevated production of fibrotic proteins ultimately disrupting normal lung physiology skewing the balance towards the fibrotic milieu. AIM In the present work, we have discussed several important pathways which are involved in post-COVID PF. Further, we have also highlighted the rationale for the use of antifibrotic agents for post-COVID PF to decrease the burden and improve pulmonary functions in COVID-19 patients. CONCLUSION Based on the available literature and recent incidences, it is crucial to monitor COVID-19 patients over a period of time to rule out the possibility of residual effects. There is a need for concrete evidence to deeply understand the mechanisms responsible for PF in COVID-19 patients.
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Amyloidogenic proteins in the SARS-CoV and SARS-CoV-2 proteomes. Nat Commun 2023; 14:945. [PMID: 36806058 PMCID: PMC9940680 DOI: 10.1038/s41467-023-36234-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 01/20/2023] [Indexed: 02/22/2023] Open
Abstract
The phenomenon of protein aggregation is associated with a wide range of human diseases. Our knowledge of the aggregation behaviour of viral proteins, however, is still rather limited. Here, we investigated this behaviour in the SARS-CoV and SARS-CoV-2 proteomes. An initial analysis using a panel of sequence-based predictors suggested the presence of multiple aggregation-prone regions (APRs) in these proteomes and revealed a strong aggregation propensity in some SARS-CoV-2 proteins. We then studied the in vitro aggregation of predicted aggregation-prone SARS-CoV and SARS-CoV-2 proteins and protein regions, including the signal sequence peptide and fusion peptides 1 and 2 of the spike protein, a peptide from the NSP6 protein, and the ORF10 and NSP11 proteins. Our results show that these peptides and proteins can form amyloid aggregates. We used circular dichroism spectroscopy to reveal the presence of β-sheet rich cores in aggregates and X-ray diffraction and Raman spectroscopy to confirm the formation of amyloid structures. Furthermore, we demonstrated that SARS-CoV-2 NSP11 aggregates are toxic to mammalian cell cultures. These results motivate further studies about the possible role of aggregation of SARS proteins in protein misfolding diseases and other human conditions.
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Du J, Wu G, Chen Q, Yu C, Xu G, Liu A, Wang L. Fingerprinting trimeric SARS-CoV-2 RBD by capillary isoelectric focusing with whole-column imaging detection. Anal Biochem 2023; 663:115034. [PMID: 36586502 PMCID: PMC9794521 DOI: 10.1016/j.ab.2022.115034] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 12/20/2022] [Accepted: 12/27/2022] [Indexed: 12/29/2022]
Abstract
Because the spike (S) protein of the severe acute respiratory syndrome coronavirus (SARS-CoV) is the immunodominant antigen, the S protein and its receptor-binding domain (RBD) are both targets currently to be genetically engineered for designing the broad-spectrum vaccine. In theory, the expressed protein exists as a set of variants that are roughly the same but slightly different, which depends on the protein expression system. The variants can be phenotypically manifested as charge heterogeneity. Here, we attempted to depict the charge heterogeneity of the trimeric SARS-CoV-2 RBD by using capillary isoelectric focusing with whole-column imaging detection (cIEF-WCID). In its nature form, the electropherogram fingerprints of the trimeric RBD were presented under optimized experimental conditions. The peaks of matrix buffers can be fully distinguishable from peaks of trimeric RBD. The isoelectric point (pI) was determined to be within a range of 6.67-9.54 covering the theoretical pI of 9.02. The fingerprints of three batches of trimeric RBDs are completely the same, with the intra-batch and batch-to-batch relative standard deviations (RSDs) of both pI values and area percentage of each peak no more than 1.0%, indicating that the production process is stable and this method can be used to surveillance the batch-to-batch consistency. The fingerprint remained unchanged after incubating at 37 °C for 7 d and oxidizing by 0.015% H2O2. In addition, the fingerprint was destroyed when adjusting the pH value to higher than 10.0 but still stable when the pH was lower than 4.0. In summary, the cIEF-WCID fingerprint can be used for the identification, batch-to-batch consistency evaluation, and stability study of the trimeric SARS-CoV-2 RBD, as part of a quality control strategy during the potential vaccine production.
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Affiliation(s)
- Jialiang Du
- NHC Key Laboratory of Research on Quality and Standardization of Biotech Products, NMPA Key Laboratory for Quality Research and Evaluation of Biological Products, Division of Monoclonal Antibody Products, National Institutes for Food and Drug Control, Beijing, 102629, China
| | - Gang Wu
- NHC Key Laboratory of Research on Quality and Standardization of Biotech Products, NMPA Key Laboratory for Quality Research and Evaluation of Biological Products, Division of Monoclonal Antibody Products, National Institutes for Food and Drug Control, Beijing, 102629, China
| | - Quanyao Chen
- NHC Key Laboratory of Research on Quality and Standardization of Biotech Products, NMPA Key Laboratory for Quality Research and Evaluation of Biological Products, Division of Monoclonal Antibody Products, National Institutes for Food and Drug Control, Beijing, 102629, China,School of Pharmacy, Yantai University, Yantai, 264005, China
| | - Chuanfei Yu
- NHC Key Laboratory of Research on Quality and Standardization of Biotech Products, NMPA Key Laboratory for Quality Research and Evaluation of Biological Products, Division of Monoclonal Antibody Products, National Institutes for Food and Drug Control, Beijing, 102629, China
| | - Gangling Xu
- NHC Key Laboratory of Research on Quality and Standardization of Biotech Products, NMPA Key Laboratory for Quality Research and Evaluation of Biological Products, Division of Monoclonal Antibody Products, National Institutes for Food and Drug Control, Beijing, 102629, China
| | - Anhui Liu
- School of Pharmacy, Yantai University, Yantai, 264005, China
| | - Lan Wang
- NHC Key Laboratory of Research on Quality and Standardization of Biotech Products, NMPA Key Laboratory for Quality Research and Evaluation of Biological Products, Division of Monoclonal Antibody Products, National Institutes for Food and Drug Control, Beijing, 102629, China.
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Ngalamika O, Lidenge SJ, Mukasine MC, Kawimbe M, Kamanzi P, Ngowi JR, Mwaiselage J, Tso FY. SARS-CoV-2-specific T cell and humoral immunity in individuals with and without HIV in an African population: a prospective cohort study. Int J Infect Dis 2023; 127:106-115. [PMID: 36516914 PMCID: PMC9741763 DOI: 10.1016/j.ijid.2022.12.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 11/07/2022] [Accepted: 12/06/2022] [Indexed: 12/14/2022] Open
Abstract
OBJECTIVES To longitudinally compare SARS-CoV-2-specific T cell and humoral immune responses between convalescent individuals who are HIV-positive (HIV+) and HIV-negative (HIV-). METHODS We conducted enzyme-linked immunospots to determine the SARS-CoV-2-specific T cell responses to spike and nucleocapsid, membrane protein, and other open reading frame proteins (NMO), whereas an immunofluorescence assay was used to determine the humoral responses. Participants were sampled at baseline and after 8 weeks of follow-up. RESULTS Individuals who are HIV- had significantly more T cell responses to NMO and spike than individuals who are HIV+ at baseline, P-value = 0.026 and P-value = 0.029, respectively. At follow-up, T cell responses to NMO and spike in individuals who are HIV+ increased to levels comparable with individuals who are HIV-. T cell responses in the HIV- group significantly decreased from baseline levels at the time of follow-up (spike [P-value = 0.011] and NMO [P-value = 0.014]). A significantly higher number of individuals in the HIV+ group had an increase in T cell responses to spike (P-value = 0.01) and NMO (P-value = 0.026) during the follow-up period than the HIV- group. Antispike and antinucleocapsid antibody titers were high (1: 1280) and not significantly different between individuals who were HIV- and HIV+ at baseline. A significant decrease in antinucleocapsid titer was observed in the HIV- (P-value = 0.0001) and the HIV+ (P-value = 0.001) groups at follow-up. SARS-CoV-2 vaccination was more effective in boosting the T cell than antibody responses shortly after infection. CONCLUSION There is an impairment of SARS-CoV-2-specific T cell immunity in individuals who are HIV+ with advanced immunosuppression. SARS-CoV-2-specific T cell immune responses may be delayed in individuals who are HIV+, even in those on antiretroviral therapy. There is no difference in SARS-CoV-2-specific humoral immunity between individuals who are HIV- and HIV+.
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Affiliation(s)
- Owen Ngalamika
- Dermatology and Venereology Division, Department of Medicine, University Teaching Hospital, University of Zambia School of Medicine, Lusaka, Zambia,HHV-8 Molecular Virology Laboratory, University Teaching Hospital, Lusaka, Zambia,Corresponding author: Tel: +260961406928
| | - Salum J. Lidenge
- Ocean Road Cancer Institute, Dar-es-Salam, Tanzania,Muhimbili University of Health and Allied Sciences, Dar-es-Salam, Tanzania
| | | | - Musonda Kawimbe
- HHV-8 Molecular Virology Laboratory, University Teaching Hospital, Lusaka, Zambia
| | - Patrick Kamanzi
- Dermatology and Venereology Division, Department of Medicine, University Teaching Hospital, University of Zambia School of Medicine, Lusaka, Zambia
| | | | - Julius Mwaiselage
- Ocean Road Cancer Institute, Dar-es-Salam, Tanzania,Muhimbili University of Health and Allied Sciences, Dar-es-Salam, Tanzania
| | - For Yue Tso
- Department of Interdisciplinary Oncology, and The Stanley S Scott Cancer Center, Louisiana State University Health Sciences Center, New Orleans, USA
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Jiang F, Liu Y, Xue Y, Cheng P, Wang J, Lian J, Gong W. Developing a multiepitope vaccine for the prevention of SARS-CoV-2 and monkeypox virus co-infection: A reverse vaccinology analysis. Int Immunopharmacol 2023; 115:109728. [PMID: 36652758 PMCID: PMC9832108 DOI: 10.1016/j.intimp.2023.109728] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 01/01/2023] [Accepted: 01/09/2023] [Indexed: 01/13/2023]
Abstract
BACKGROUND Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and monkeypox virus (MPXV) severely threaten human health; however, currently, no vaccine can prevent a co-infection with both viruses. METHODS Five antigens were selected to predict dominant T and B cell epitopes screened for immunogenicity, antigenicity, toxicity, and sensitization. After screening, all antigens joined in the construction of a novel multiepitope vaccine. The physicochemical and immunological characteristics, and secondary and tertiary structures of the vaccine were predicted and analyzed using bio- and immunoinformatics. Finally, codon optimization and cloning in-silico were performed. RESULTS A new multiepitope vaccine, named S7M8, was constructed based on four helper T lymphocyte (HTL) epitopes, six cytotoxic T lymphocyte (CTL) epitopes, five B cell epitopes, as well as Toll-like receptor (TLR) agonists. The antigenicity and immunogenicity scores of the S7M8 vaccine were 0.907374 and 0.6552, respectively. The S7M8 vaccine was comprised of 26.96% α-helices, the optimized Z-value of the tertiary structure was -5.92, and the favored area after majorization in the Ramachandran plot was 84.54%. Molecular docking showed that the S7M8 vaccine could tightly bind to TLR2 (-1100.6 kcal/mol) and TLR4 (-950.3 kcal/mol). In addition, the immune stimulation prediction indicated that the S7M8 vaccine could activate T and B lymphocytes to produce high levels of Th1 cytokines and antibodies. CONCLUSION S7M8 is a promising biomarker with good antigenicity, immunogenicity, non-toxicity, and non-sensitization. The S7M8 vaccine can trigger significantly high levels of Th1 cytokines and antibodies and may be a potentially powerful tool in preventing SARS-CoV-2 and MPXV.
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Affiliation(s)
- Fan Jiang
- Tuberculosis Prevention and Control Key Laboratory/Beijing Key Laboratory of New Techniques of Tuberculosis Diagnosis and Treatment, Senior Department of Tuberculosis, The 8th Medical Center of PLA General Hospital, Beijing, China,The Second Brigade of Cadet, Basic Medical Science Academy of Air Force Medical University, Xi’an, China,Department of Infectious Diseases, Tangdu Hospital, Air Force Medical University, Xi'an, China
| | - Yinping Liu
- Tuberculosis Prevention and Control Key Laboratory/Beijing Key Laboratory of New Techniques of Tuberculosis Diagnosis and Treatment, Senior Department of Tuberculosis, The 8th Medical Center of PLA General Hospital, Beijing, China
| | - Yong Xue
- Tuberculosis Prevention and Control Key Laboratory/Beijing Key Laboratory of New Techniques of Tuberculosis Diagnosis and Treatment, Senior Department of Tuberculosis, The 8th Medical Center of PLA General Hospital, Beijing, China
| | - Peng Cheng
- Tuberculosis Prevention and Control Key Laboratory/Beijing Key Laboratory of New Techniques of Tuberculosis Diagnosis and Treatment, Senior Department of Tuberculosis, The 8th Medical Center of PLA General Hospital, Beijing, China
| | - Jie Wang
- Tuberculosis Prevention and Control Key Laboratory/Beijing Key Laboratory of New Techniques of Tuberculosis Diagnosis and Treatment, Senior Department of Tuberculosis, The 8th Medical Center of PLA General Hospital, Beijing, China
| | - Jianqi Lian
- Department of Infectious Diseases, Tangdu Hospital, Air Force Medical University, Xi'an, China.
| | - Wenping Gong
- Tuberculosis Prevention and Control Key Laboratory/Beijing Key Laboratory of New Techniques of Tuberculosis Diagnosis and Treatment, Senior Department of Tuberculosis, The 8th Medical Center of PLA General Hospital, Beijing, China.
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Baier CJ, Barrantes FJ. Role of cholesterol-recognition motifs in the infectivity of SARS-CoV-2 variants. Colloids Surf B Biointerfaces 2023; 222:113090. [PMID: 36563415 PMCID: PMC9743692 DOI: 10.1016/j.colsurfb.2022.113090] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Revised: 12/02/2022] [Accepted: 12/10/2022] [Indexed: 12/14/2022]
Abstract
The presence of linear amino acid motifs with the capacity to recognize the neutral lipid cholesterol, known as Cholesterol Recognition/interaction Amino acid Consensus sequence (CRAC), and its inverse or mirror image, CARC, has recently been reported in the primary sequence of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike S homotrimeric glycoprotein. These motifs also occur in the two other pathogenic coronaviruses, SARS-CoV, and Middle-East respiratory syndrome CoV (MERS-CoV), most conspicuously in the transmembrane domain, the fusion peptide, the amino-terminal domain, and the receptor binding domain of SARS-CoV-2 S protein. Here we analyze the presence of cholesterol-recognition motifs in these key regions of the spike glycoprotein in the pathogenic CoVs. We disclose the inherent pathophysiological implications of the cholesterol motifs in the virus-host cell interactions and variant infectivity.
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Affiliation(s)
- Carlos Javier Baier
- Laboratorio de Toxicología, Instituto de Ciencias Biológicas y Biomédicas del Sur (INBIOSUR), Universidad Nacional del Sur (UNS), Consejo de Investigaciones Científicas y Técnicas (CONICET), Departamento de Biología, Bioquímica y Farmacia (DBByF), San Juan 670, B8000ICN Bahía Blanca, Argentina,Correspondence to: INBIOSUR-CONICET-UNS, DBByF, San Juan 670, B8000ICN Bahía Blanca, Buenos Aires, Argentina
| | - Francisco J. Barrantes
- Laboratory of Molecular Neurobiology, BIOMED UCA-CONICET, 1600 Av. A. Moreau de Justo, C1107AAZ Buenos Aires, Argentina,Correspondence to: BIOMED UCA-CONICET, Av. Alicia Moreau de Justo 1600, C1107AFF Buenos Aires, Argentina
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63
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Epigenetic Targets and Pathways Linked to SARS-CoV-2 Infection and Pathology. Microorganisms 2023; 11:microorganisms11020341. [PMID: 36838306 PMCID: PMC9967649 DOI: 10.3390/microorganisms11020341] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 01/19/2023] [Accepted: 01/19/2023] [Indexed: 02/03/2023] Open
Abstract
The scale at which the SARS-CoV-2/COVID-19 pandemic has spread remains enormous. Provided the genetic makeup of the virus and humans is readily available, the quest for knowing the mechanism and epidemiology continues to prevail across the entire scientific community. Several aspects, including immunology, molecular biology, and host-pathogen interaction, are continuously being dug into for preparing the human race for future pandemics. The exact reasons for vast differences in symptoms, pathophysiological implications of COVID-infections, and mortality differences remain elusive. Hence, researchers are also looking beyond traditional genomics, proteomics, and transcriptomics approach, especially entrusting the environmental regulation of the genetic landscape of COVID-human interactions. In line with these questions lies a critical process called epigenetics. The epigenetic perturbations in both host and parasites are a matter of great interest to unravel the disparities in COVID-19 mortalities and pathology. This review provides a deeper insight into current research on the epigenetic landscape of SARS-CoV-2 infection in humans and potential targets for augmenting the ongoing investigation. It also explores the potential targets, pathways, and networks associated with the epigenetic regulation of processes involved in SARS-CoV-2 pathology.
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Rodriguez-Aponte SA, Dalvie NC, Wong TY, Johnston RS, Naranjo CA, Bajoria S, Kumru OS, Kaur K, Russ BP, Lee KS, Cyphert HA, Barbier M, Rao HD, Rajurkar MP, Lothe RR, Shaligram US, Batwal S, Chandrasekaran R, Nagar G, Kleanthous H, Biswas S, Bevere JR, Joshi SB, Volkin DB, Damron FH, Love JC. Molecular engineering of a cryptic epitope in Spike RBD improves manufacturability and neutralizing breadth against SARS-CoV-2 variants. Vaccine 2023; 41:1108-1118. [PMID: 36610932 PMCID: PMC9797419 DOI: 10.1016/j.vaccine.2022.12.062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 12/22/2022] [Accepted: 12/25/2022] [Indexed: 12/30/2022]
Abstract
There is a continued need for sarbecovirus vaccines that can be manufactured and distributed in low- and middle-income countries (LMICs). Subunit protein vaccines are manufactured at large scales at low costs, have less stringent temperature requirements for distribution in LMICs, and several candidates have shown protection against SARS-CoV-2. We previously reported an engineered variant of the SARS-CoV-2 Spike protein receptor binding domain antigen (RBD-L452K-F490W; RBD-J) with enhanced manufacturability and immunogenicity compared to the ancestral RBD. Here, we report a second-generation engineered RBD antigen (RBD-J6) with two additional mutations to a hydrophobic cryptic epitope in the RBD core, S383D and L518D, that further improved expression titers and biophysical stability. RBD-J6 retained binding affinity to human convalescent sera and to all tested neutralizing antibodies except antibodies that target the class IV epitope on the RBD core. K18-hACE2 transgenic mice immunized with three doses of a Beta variant of RBD-J6 displayed on a virus-like particle (VLP) generated neutralizing antibodies (nAb) to nine SARS-CoV-2 variants of concern at similar levels as two doses of Comirnaty. The vaccinated mice were also protected from challenge with Alpha or Beta SARS-CoV-2. This engineered antigen could be useful for modular RBD-based subunit vaccines to enhance manufacturability and global access, or for further development of variant-specific or broadly acting booster vaccines.
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Affiliation(s)
- Sergio A Rodriguez-Aponte
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; The Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Neil C Dalvie
- The Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Ting Y Wong
- Department of Microbiology, Immunology, and Cell Biology, West Virginia University, Morgantown, WV 26506, USA; Vaccine Development Center at West Virginia University Health Sciences Center, Morgantown, WV 26506, USA
| | - Ryan S Johnston
- The Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Christopher A Naranjo
- The Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Sakshi Bajoria
- Department of Pharmaceutical Chemistry, Vaccine Analytics and Formulation Center, University of Kansas, Lawrence, KS 66047, USA
| | - Ozan S Kumru
- Department of Pharmaceutical Chemistry, Vaccine Analytics and Formulation Center, University of Kansas, Lawrence, KS 66047, USA
| | - Kawaljit Kaur
- Department of Pharmaceutical Chemistry, Vaccine Analytics and Formulation Center, University of Kansas, Lawrence, KS 66047, USA
| | - Brynnan P Russ
- Department of Microbiology, Immunology, and Cell Biology, West Virginia University, Morgantown, WV 26506, USA; Vaccine Development Center at West Virginia University Health Sciences Center, Morgantown, WV 26506, USA
| | - Katherine S Lee
- Department of Microbiology, Immunology, and Cell Biology, West Virginia University, Morgantown, WV 26506, USA; Vaccine Development Center at West Virginia University Health Sciences Center, Morgantown, WV 26506, USA
| | - Holly A Cyphert
- Department of Biological Sciences, Marshall University, Huntington, WV 26506, USA
| | - Mariette Barbier
- Department of Microbiology, Immunology, and Cell Biology, West Virginia University, Morgantown, WV 26506, USA; Vaccine Development Center at West Virginia University Health Sciences Center, Morgantown, WV 26506, USA
| | - Harish D Rao
- Serum Institute of India Pvt. Ltd., Pune 411028, India
| | | | | | | | | | | | - Gaurav Nagar
- Serum Institute of India Pvt. Ltd., Pune 411028, India
| | | | - Sumi Biswas
- SpyBiotech Limited, Oxford Business Park North, Oxford OX4 2JZ, UK
| | - Justin R Bevere
- Department of Microbiology, Immunology, and Cell Biology, West Virginia University, Morgantown, WV 26506, USA; Vaccine Development Center at West Virginia University Health Sciences Center, Morgantown, WV 26506, USA
| | - Sangeeta B Joshi
- Department of Pharmaceutical Chemistry, Vaccine Analytics and Formulation Center, University of Kansas, Lawrence, KS 66047, USA
| | - David B Volkin
- Department of Pharmaceutical Chemistry, Vaccine Analytics and Formulation Center, University of Kansas, Lawrence, KS 66047, USA
| | - F Heath Damron
- Department of Microbiology, Immunology, and Cell Biology, West Virginia University, Morgantown, WV 26506, USA; Vaccine Development Center at West Virginia University Health Sciences Center, Morgantown, WV 26506, USA
| | - J Christopher Love
- The Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA.
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Padilla-Blanco M, Gucciardi F, Rubio V, Lastra A, Lorenzo T, Ballester B, González-Pastor A, Veses V, Macaluso G, Sheth CC, Pascual-Ortiz M, Maiques E, Rubio-Guerri C, Purpari G, Guercio A. A SARS-CoV-2 full genome sequence of the B.1.1 lineage sheds light on viral evolution in Sicily in late 2020. Front Public Health 2023; 11:1098965. [PMID: 36778569 PMCID: PMC9909176 DOI: 10.3389/fpubh.2023.1098965] [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: 11/15/2022] [Accepted: 01/06/2023] [Indexed: 01/27/2023] Open
Abstract
To investigate the influence of geographic constrains to mobility on SARS-CoV-2 circulation before the advent of vaccination, we recently characterized the occurrence in Sicily of viral lineages in the second pandemic wave (September to December 2020). Our data revealed wide prevalence of the then widespread through Europe B.1.177 variant, although some viral samples could not be classified with the limited Sanger sequencing tools used. A particularly interesting sample could not be fitted to a major variant then circulating in Europe and has been subjected here to full genome sequencing in an attempt to clarify its origin, lineage and relations with the seven full genome sequences deposited for that period in Sicily, hoping to provide clues on viral evolution. The obtained genome is unique (not present in databases). It hosts 20 single-base substitutions relative to the original Wuhan-Hu-1 sequence, 8 of them synonymous and the other 12 encoding 11 amino acid substitutions, all of them already reported one by one. They include four highly prevalent substitutions, NSP12:P323L, S:D614G, and N:R203K/G204R; the much less prevalent S:G181V, ORF3a:G49V and N:R209I changes; and the very rare mutations NSP3:L761I, NSP6:S106F, NSP8:S41F and NSP14:Y447H. GISAID labeled this genome as B.1.1 lineage, a lineage that appeared early on in the pandemic. Phylogenetic analysis also confirmed this lineage diagnosis. Comparison with the seven genome sequences deposited in late 2020 from Sicily revealed branching leading to B.1.177 in one branch and to Alpha in the other branch, and suggested a local origin for the S:G118V mutation.
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Affiliation(s)
- Miguel Padilla-Blanco
- Departamento de Farmacia, Facultad de Ciencias de la Salud, Universidad Cardenal Herrera-CEU (UCH-CEU), CEU Universities, Valencia, Spain
| | - Francesca Gucciardi
- Istituto Zooprofilattico Sperimentale della Sicilia “A. Mirri”, Palermo, Italy
| | - Vicente Rubio
- Department of Genomics and Proteomics, Instituto de Biomedicina de Valencia del Consejo Superior de Investigaciones Científicas (IBV-CSIC) and Centre for Biomedical Network Research on Rare Diseases of the Instituto de Salud Carlos III (CIBERER-ISCIII), CEU Universities, Valencia, Spain
| | - Antonio Lastra
- Istituto Zooprofilattico Sperimentale della Sicilia “A. Mirri”, Palermo, Italy
| | - Teresa Lorenzo
- Departamento de Ciencias Biomédicas, Facultad de Ciencias de la Salud, Universidad Cardenal Herrera-CEU, CEU Universities, Valencia, Spain
| | - Beatriz Ballester
- Departamento de Ciencias Biomédicas, Facultad de Ciencias de la Salud, Universidad Cardenal Herrera-CEU, CEU Universities, Valencia, Spain
| | - Andrea González-Pastor
- Departamento de Medicina, Facultad de Ciencias de la Salud, Universidad Cardenal Herrera-CEU, CEU Universities, Valencia, Spain
| | - Veronica Veses
- Departamento de Ciencias Biomédicas, Facultad de Ciencias de la Salud, Universidad Cardenal Herrera-CEU, CEU Universities, Valencia, Spain
| | - Giusi Macaluso
- Istituto Zooprofilattico Sperimentale della Sicilia “A. Mirri”, Palermo, Italy
| | - Chirag C. Sheth
- Departamento de Medicina, Facultad de Ciencias de la Salud, Universidad Cardenal Herrera-CEU, CEU Universities, Valencia, Spain
| | - Marina Pascual-Ortiz
- Departamento de Ciencias Biomédicas, Facultad de Ciencias de la Salud, Universidad Cardenal Herrera-CEU, CEU Universities, Valencia, Spain
| | - Elisa Maiques
- Departamento de Ciencias Biomédicas, Facultad de Ciencias de la Salud, Universidad Cardenal Herrera-CEU, CEU Universities, Valencia, Spain,*Correspondence: Elisa Maiques ✉
| | - Consuelo Rubio-Guerri
- Departamento de Farmacia, Facultad de Ciencias de la Salud, Universidad Cardenal Herrera-CEU (UCH-CEU), CEU Universities, Valencia, Spain,Consuelo Rubio-Guerri ✉
| | - Giuseppa Purpari
- Istituto Zooprofilattico Sperimentale della Sicilia “A. Mirri”, Palermo, Italy,Giuseppa Purpari ✉
| | - Annalisa Guercio
- Istituto Zooprofilattico Sperimentale della Sicilia “A. Mirri”, Palermo, Italy
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66
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Chrysostomou AC, Aristokleous A, Rodosthenous JH, Christodoulou C, Stathi G, Kostrikis LG. Detection of Circulating SARS-CoV-2 Variants of Concern (VOCs) Using a Multiallelic Spectral Genotyping Assay. Life (Basel) 2023; 13:life13020304. [PMID: 36836661 PMCID: PMC9960118 DOI: 10.3390/life13020304] [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: 12/19/2022] [Revised: 01/17/2023] [Accepted: 01/19/2023] [Indexed: 01/24/2023] Open
Abstract
Throughout the coronavirus disease 2019 (COVID-19) pandemic, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has continuously evolved, resulting in new variants, some of which possess increased infectivity, immune evasion, and virulence. Such variants have been denoted by the World Health Organization as variants of concern (VOC) because they have resulted in an increased number of cases, posing a strong risk to public health. Thus far, five VOCs have been designated, Alpha (B.1.1.7), Beta (B.1.351), Gamma (P.1), Delta (B.1.617.2), and Omicron (B.1.1.529), including their sublineages. Next-generation sequencing (NGS) can produce a significant amount of information facilitating the study of variants; however, NGS is time-consuming and costly and not efficient during outbreaks, when rapid identification of VOCs is urgently needed. In such periods, there is a need for fast and accurate methods, such as real-time reverse transcription PCR in combination with probes, which can be used for monitoring and screening of the population for these variants. Thus, we developed a molecular beacon-based real-time RT-PCR assay according to the principles of spectral genotyping. This assay employs five molecular beacons that target ORF1a:ΔS3675/G3676/F3677, S:ΔH69/V70, S:ΔE156/F157, S:ΔΝ211, S:ins214EPE, and S:ΔL242/A243/L244, deletions and an insertion found in SARS-CoV-2 VOCs. This assay targets deletions/insertions because they inherently provide higher discrimination capacity. Here, the design process of the molecular beacon-based real-time RT-PCR assay for detection and discrimination of SARS-CoV-2 is presented, and experimental testing using SARS-CoV-2 VOC samples from reference strains (cultured virus) and clinical patient samples (nasopharyngeal samples), which have been previously classified using NGS, were evaluated. Based on the results, it was shown that all molecular beacons can be used under the same real-time RT-PCR conditions, consequently improving the time and cost efficiency of the assay. Furthermore, this assay was able to confirm the genotype of each of the tested samples from various VOCs, thereby constituting an accurate and reliable method for VOC detection and discrimination. Overall, this assay is a valuable tool that can be used for screening and monitoring the population for VOCs or other emerging variants, contributing to limiting their spread and protecting public health.
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Affiliation(s)
| | - Antonia Aristokleous
- Department of Biological Sciences, University of Cyprus, Aglantzia, 2109 Nicosia, Cyprus
| | | | | | - Georgia Stathi
- Department of Biological Sciences, University of Cyprus, Aglantzia, 2109 Nicosia, Cyprus
| | - Leondios G. Kostrikis
- Department of Biological Sciences, University of Cyprus, Aglantzia, 2109 Nicosia, Cyprus
- Cyprus Academy of Sciences, Letters, and Arts, 60-68 Phaneromenis Street, 1011 Nicosia, Cyprus
- Correspondence: ; Tel.: +35-72-289-2885
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67
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Najar FZ, Linde E, Murphy CL, Borin VA, Wang H, Haider S, Agarwal PK. Future COVID19 surges prediction based on SARS-CoV-2 mutations surveillance. eLife 2023; 12:82980. [PMID: 36655992 PMCID: PMC9894583 DOI: 10.7554/elife.82980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 01/18/2023] [Indexed: 01/20/2023] Open
Abstract
COVID19 has aptly revealed that airborne viruses such as SARS-CoV-2 with the ability to rapidly mutate combined with high rates of transmission and fatality can cause a deadly worldwide pandemic in a matter of weeks (Plato et al., 2021). Apart from vaccines and post-infection treatment options, strategies for preparedness will be vital in responding to the current and future pandemics. Therefore, there is wide interest in approaches that allow predictions of increase in infections ('surges') before they occur. We describe here real-time genomic surveillance particularly based on mutation analysis, of viral proteins as a methodology for a priori determination of surge in number of infection cases. The full results are available for SARS-CoV-2 at http://pandemics.okstate.edu/covid19/, and are updated daily as new virus sequences become available. This approach is generic and will also be applicable to other pathogens.
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Affiliation(s)
- Fares Z Najar
- High-Performance Computing Center, Oklahoma State UniversityStillwaterUnited States
| | - Evan Linde
- High-Performance Computing Center, Oklahoma State UniversityStillwaterUnited States
| | - Chelsea L Murphy
- High-Performance Computing Center, Oklahoma State UniversityStillwaterUnited States
| | - Veniamin A Borin
- High-Performance Computing Center, Oklahoma State UniversityStillwaterUnited States
- Department of Physiological Sciences, Oklahoma State UniversityStillwaterUnited States
| | - Huan Wang
- University College London School of Pharmacy, Pharmaceutical and Biological ChemistryLondonUnited Kingdom
| | - Shozeb Haider
- University College London School of Pharmacy, Pharmaceutical and Biological ChemistryLondonUnited Kingdom
- University College London Centre for Advanced Research ComputingLondonUnited Kingdom
| | - Pratul K Agarwal
- High-Performance Computing Center, Oklahoma State UniversityStillwaterUnited States
- Department of Physiological Sciences, Oklahoma State UniversityStillwaterUnited States
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Nejat R, Torshizi MF, Najafi DJ. S Protein, ACE2 and Host Cell Proteases in SARS-CoV-2 Cell Entry and Infectivity; Is Soluble ACE2 a Two Blade Sword? A Narrative Review. Vaccines (Basel) 2023; 11:vaccines11020204. [PMID: 36851081 PMCID: PMC9968219 DOI: 10.3390/vaccines11020204] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 01/07/2023] [Accepted: 01/12/2023] [Indexed: 01/19/2023] Open
Abstract
Since the spread of the deadly virus SARS-CoV-2 in late 2019, researchers have restlessly sought to unravel how the virus enters the host cells. Some proteins on each side of the interaction between the virus and the host cells are involved as the major contributors to this process: (1) the nano-machine spike protein on behalf of the virus, (2) angiotensin converting enzyme II, the mono-carboxypeptidase and the key component of renin angiotensin system on behalf of the host cell, (3) some host proteases and proteins exploited by SARS-CoV-2. In this review, the complex process of SARS-CoV-2 entrance into the host cells with the contribution of the involved host proteins as well as the sequential conformational changes in the spike protein tending to increase the probability of complexification of the latter with angiotensin converting enzyme II, the receptor of the virus on the host cells, are discussed. Moreover, the release of the catalytic ectodomain of angiotensin converting enzyme II as its soluble form in the extracellular space and its positive or negative impact on the infectivity of the virus are considered.
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Affiliation(s)
- Reza Nejat
- Department of Anesthesiology and Critical Care Medicine, Laleh Hospital, Tehran 1467684595, Iran
- Correspondence:
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69
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Pereira GC. An Automated Strategy to Handle Antigenic Variability in Immunisation Protocols, Part II: In Vitro Transcribed mRNA Vector Design for Inoculation Against Infectious Agent Variants. Methods Mol Biol 2023; 2575:323-340. [PMID: 36301484 DOI: 10.1007/978-1-0716-2716-7_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
A fully automated strategy to handle antigenic variability in immunisation protocols is here presented. The method comprises of (1) nanopore sequencing of infectious agent variants, with focus on the SARS-CoV-2 and its variants, followed by (2) in-vitro transcribed mRNA vector design for immunotherapy. This chapter introduces the mRNA vector design protocol and Chapter 16 presents the nano-pore sequencing step.
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Pereira GC. Nanotechnology-Driven Delivery Systems in Inoculation Therapies. Methods Mol Biol 2023; 2575:39-57. [PMID: 36301470 DOI: 10.1007/978-1-0716-2716-7_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Nanotechnology and genomics are the newest allies of inoculation design. In recent years, nucleic acids have been targeted as sources of therapeutics to stimulate immune responses, to both fight disease and create memory to trigger further responses to threat. A myriad of promising findings in cancer research and virology has been reported in the current literature. Nanosystems are demonstrating their capabilities as efficient carriers, improving the efficacy of drug delivery, including nucleic acids as therapeutics, at focal sites, in living systems. This chapter approaches major elements involved in the successful use of nanotechnology as delivery platforms to optimise the efficacy of nucleic acids-driven therapeutics, particularly mRNA vectors as coding engines for targeted viral proteins. Latest findings in nanotechnological design are highlighted, key discoveries associated with the success of nanodelivery platforms are presented, and key characteristics of nanodelivery systems in nucleic acids-based vaccine technology are discussed, to illustrate their distinct advantages and disadvantages.
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71
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Almasi F, Mohammadipanah F. Neurological manifestations of SARS-CoV-2 infections: towards quantum dots based management approaches. J Drug Target 2023; 31:51-64. [PMID: 35921123 DOI: 10.1080/1061186x.2022.2110252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Developing numerous nanotechnological designed tools to monitor the existence of SARS-CoV-2, and modifying its interactions address the global needs for efficient remedies required for the management of COVID-19. Herein, through a multidisciplinary outlook encompassing different fields such as the pathophysiology of SARS-CoV-2, analysis of symptoms, and statistics of neurological complications caused by SARS-CoV-2 infection in the central and peripheral nervous systems have been testified. The anosmia (51.1%) and ageusia (45.5%) are reported the most frequent neurological manifestation. Cerebrovascular disease and encephalopathy were mainly related to severe clinical cases. In addition, we focus especially on the various concerned physiological routes, including BBB dysfunction, which transpired due to SARS-CoV-2 infection, direct and indirect effects of the virus on the brain, and also, the plausible mechanisms of viral entry to the nerve system. We also outline the characterisation, and the ongoing pharmaceutical applications of quantum dots as smart nanocarriers crossing the blood-brain barrier and their importance in neurological diseases, mainly SARS-CoV-2 related manifestations Moreover, the market status, six clinical trials recruiting quantum dots, and the challenges limiting the clinical application of QDs are highlighted.
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Affiliation(s)
- Faezeh Almasi
- Pharmaceutical Biotechnology Lab, Department of Microbial Biotechnology, School of Biology and Center of Excellence in Phylogeny of Living Organisms, College of Science, University of Tehran, Tehran, Iran
| | - Fatemeh Mohammadipanah
- Pharmaceutical Biotechnology Lab, Department of Microbial Biotechnology, School of Biology and Center of Excellence in Phylogeny of Living Organisms, College of Science, University of Tehran, Tehran, Iran
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Abstract
Nucleic acids are paving the way for advanced therapeutics. Unveiling the genome enabled a better understanding of unique genotype-phenotype profiling. Methods for engineering and analysis of nucleic acids, from polymerase chain reaction to Cre-Lox recombination, are contributing greatly to biomarkers' discovery, mapping of cellular signaling cascades, and smart design of therapeutics in precision medicine. Investigating the different subtypes of DNA and RNA via sequencing and profiling is empowering the scientific community with valuable information, to be used in advanced therapeutics, tracking epigenetics linked to disease. Recent results from the application of nucleic acids in novel therapeutics and precision medicine are very encouraging, demonstrating great potential to treat cancer, viral infections via inoculation (e.g., SAR-COV-2 mRNA vaccines), along with metabolic and genetic disorders. Limitations posed by challenges in delivery mode are being addressed to enable efficient guided-gene-programmed precision therapies. With the focus on genetic engineering and novel therapeutics, more precisely, in precision medicine, this chapter discusses the advance enabled by knowledge derived from these innovative branches of biotechnology.
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Chrysostomou AC, Vrancken B, Haralambous C, Alexandrou M, Aristokleous A, Christodoulou C, Gregoriou I, Ioannides M, Kalakouta O, Karagiannis C, Koumbaris G, Loizides C, Mendris M, Papastergiou P, Patsalis PC, Pieridou D, Richter J, Schmitt M, Shammas C, Stylianou DC, Themistokleous G, Lemey P, Kostrikis LG. Genomic Epidemiology of the SARS-CoV-2 Epidemic in Cyprus from November 2020 to October 2021: The Passage of Waves of Alpha and Delta Variants of Concern. Viruses 2022; 15:108. [PMID: 36680148 PMCID: PMC9862594 DOI: 10.3390/v15010108] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 12/27/2022] [Accepted: 12/28/2022] [Indexed: 01/03/2023] Open
Abstract
The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in December 2019 resulted in the coronavirus disease 2019 (COVID-19) pandemic, which has had devastating repercussions for public health. Over the course of this pandemic, the virus has continuously been evolving, resulting in new, more infectious variants that have frequently led to surges of new SARS-CoV-2 infections. In the present study, we performed detailed genetic, phylogenetic, phylodynamic and phylogeographic analyses to examine the SARS-CoV-2 epidemic in Cyprus using 2352 SARS-CoV-2 sequences from infected individuals in Cyprus during November 2020 to October 2021. During this period, a total of 61 different lineages and sublineages were identified, with most falling into three groups: B.1.258 & sublineages, Alpha (B.1.1.7 & Q. sublineages), and Delta (B.1.617.2 & AY. sublineages), each encompassing a set of S gene mutations that primarily confer increased transmissibility as well as immune evasion. Specifically, these lineages were coupled with surges of new infections in Cyprus, resulting in the following: the second wave of SARS-CoV-2 infections in Cyprus, comprising B.1.258 & sublineages, during late autumn 2020/beginning of winter 2021; the third wave, comprising Alpha (B.1.1.7 & Q. sublineages), during spring 2021; and the fourth wave, comprising Delta (B.1.617.2 & AY. sublineages) during summer 2021. Additionally, it was identified that these lineages were primarily imported from and exported to the UK, Greece, and Sweden; many other migration links were also identified, including Switzerland, Denmark, Russia, and Germany. Taken together, the results of this study indicate that the SARS-CoV-2 epidemic in Cyprus was characterized by successive introduction of new lineages from a plethora of countries, resulting in the generation of waves of infection. Overall, this study highlights the importance of investigating the spatiotemporal evolution of the SARS-CoV-2 epidemic in the context of Cyprus, as well as the impact of protective measures placed to mitigate transmission of the virus, providing necessary information to safeguard public health.
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Affiliation(s)
| | - Bram Vrancken
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, 3000 Leuven, Belgium
- Spatial Epidemiology Lab (SpELL), Université Libre de Bruxelles, 1050 Bruxelles, Belgium
| | - Christos Haralambous
- Unit for Surveillance and Control of Communicable Diseases, Ministry of Health, Nicosia 1148, Cyprus
| | - Maria Alexandrou
- Microbiology Department, Larnaca General Hospital, Larnaca 6301, Cyprus
| | - Antonia Aristokleous
- Department of Biological Sciences, University of Cyprus, Aglantzia, Nicosia 2109, Cyprus
| | - Christina Christodoulou
- Department of Molecular Virology, Cyprus Institute of Neurology and Genetics, Nicosia 2371, Cyprus
| | - Ioanna Gregoriou
- Unit for Surveillance and Control of Communicable Diseases, Ministry of Health, Nicosia 1148, Cyprus
| | | | - Olga Kalakouta
- Unit for Surveillance and Control of Communicable Diseases, Ministry of Health, Nicosia 1148, Cyprus
| | | | | | | | - Michail Mendris
- Microbiology Department, Limassol General Hospital, Limassol 4131, Cyprus
| | | | - Philippos C. Patsalis
- NIPD Genetics, Nicosia 2409, Cyprus
- Medical School, University of Nicosia, Nicosia 2417, Cyprus
| | - Despo Pieridou
- Microbiology Department, Nicosia General Hospital, Nicosia 2029, Cyprus
| | - Jan Richter
- Department of Molecular Virology, Cyprus Institute of Neurology and Genetics, Nicosia 2371, Cyprus
| | - Markus Schmitt
- Eurofins Genomics Sequencing Europe, 85560 Ebersberg, Germany
| | - Christos Shammas
- S.C.I.N.A Bioanalysis Sciomedical Centre Ltd., Limassol 4040, Cyprus
| | - Dora C. Stylianou
- Department of Biological Sciences, University of Cyprus, Aglantzia, Nicosia 2109, Cyprus
| | | | | | - Philippe Lemey
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, 3000 Leuven, Belgium
| | - Leondios G. Kostrikis
- Department of Biological Sciences, University of Cyprus, Aglantzia, Nicosia 2109, Cyprus
- Cyprus Academy of Sciences, Letters, and Arts, 60-68 Phaneromenis Street, Nicosia 1011, Cyprus
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74
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Mahnam K, Ghobadi Z. Finding a prospective dual-target drug for the treatment of coronavirus disease by theoretical study. J Biomol Struct Dyn 2022; 40:12621-12641. [PMID: 34514953 DOI: 10.1080/07391102.2021.1973910] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Spike protein of coronavirus is a key protein in binding and entrance of virus to the human cell via binding to the receptor-binding domain (RBD) domain of S1 subunit to peptidase domain region of ACE2 receptor. In this study, the possible effect of 24 antiviral drugs on the RBD domain of spike protein was investigated via docking and molecular dynamics simulation for finding a dual-target drug. At first, all drugs were docked to the RBD domain of spike protein, and then all complexes and free RBD domains were separately used for molecular dynamics simulation for 50 ns via amber18 software. The simulation results showed that 10 ligands from 28 ligands were separated from the RBD domain, and among 18 remained ligands, baloxavir marboxil, and danoprevir drugs, besides endonuclease activity and protease inhibitory, can bind to key residues of the RBD domain. Then these drugs have a dual target and should be more effective than current drugs, and experimental studies should be done on baloxavir marboxil and danoprevir as more potential drugs for coronavirus disease Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Karim Mahnam
- Department of Biology, Faculty of Sciences, Shahrekord University, Shahrekord, Iran.,Nanotechnology Research Center, Shahrekord University, Shahrekord, Iran
| | - Zahra Ghobadi
- Department of Biology, Faculty of Sciences, Shahrekord University, Shahrekord, Iran
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75
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Ahmadi K, Shahbazi B, Zakeri AJ, Gouklani H. Characterization of SARS-CoV-2 omicron variants from Iran and evaluation of the effect of mutations on the spike, nucleocapsid, ORF8, and ORF9b proteins function. J Biomol Struct Dyn 2022; 41:11415-11430. [PMID: 36576175 DOI: 10.1080/07391102.2022.2162131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 12/18/2022] [Indexed: 12/29/2022]
Abstract
The SARS-CoV-2 'Omicron' strain, with 15 mutations in the receptor binding domain (RBD), was detected in South Africa and rapidly spread worldwide. SARS-CoV-2 ORF9b protein by binding to the TOM70 receptor and ORF8 protein by binding to MHC-I, IF3 receptors inhibit the host's immune response. In this study, genomics variations were evaluated for 96 samples isolated from Iran from March to July 2022 using the Nextclade web server and informatics tools. We identified the mutations occurring in the SARS-CoV-2 proteins. We also evaluated the effect of mutations on spike protein interaction with the ACE2 receptor, ORF9b protein interaction with the TOM70 receptor, and structural stability of ORF8 and nucleocapsid proteins using docking and molecular dynamics. Results indicated that during March and April 2022, the BA.2 strain was dominant in the south of Iran, while during June 2022, the BA.5 strain was dominant. BF.5 strain had the most divergence among SARS-CoV-2 strains reported from south of Iran. The binding affinity of BA.5 and BF.5 strains spike protein to ACE2 receptor is similar, and compared to BA.2 strain, was stronger. The BF.5 ORF9b K40R mutation causes a better binding affinity of the protein to the TOM70 receptor. Also, mutations that occurred in the ORF8 protein led to instability in the dimer formation of this protein and improved immune response for mutations that occurred in BA.2 strain, while this mutation did not occur in BF.5 strain. The mutations that were detected in nucleocapsid protein CTD and NTD domains caused the stability of these domains.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Khadijeh Ahmadi
- Infectious and Tropical Diseases Research Center, Hormozgan Health Institute, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Behzad Shahbazi
- Molecular Medicine Department, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Abdul-Jabbar Zakeri
- Social Determinants in Health Promotion Research Center, Research Institute for Health, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Hamed Gouklani
- Infectious and Tropical Diseases Research Center, Hormozgan Health Institute, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
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76
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An Immunological Review of SARS-CoV-2 Infection and Vaccine Serology: Innate and Adaptive Responses to mRNA, Adenovirus, Inactivated and Protein Subunit Vaccines. Vaccines (Basel) 2022; 11:vaccines11010051. [PMID: 36679897 PMCID: PMC9865970 DOI: 10.3390/vaccines11010051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 12/16/2022] [Accepted: 12/20/2022] [Indexed: 12/28/2022] Open
Abstract
The coronavirus disease 2019 (COVID-19) pandemic is caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus, which is defined by its positive-sense single-stranded RNA (ssRNA) structure. It is in the order Nidovirales, suborder Coronaviridae, genus Betacoronavirus, and sub-genus Sarbecovirus (lineage B), together with two bat-derived strains with a 96% genomic homology with other bat coronaviruses (BatCoVand RaTG13). Thus far, two Alphacoronavirus strains, HCoV-229E and HCoV-NL63, along with five Betacoronaviruses, HCoV-HKU1, HCoV-OC43, SARS-CoV, MERS-CoV, and SARS-CoV-2, have been recognized as human coronaviruses (HCoVs). SARS-CoV-2 has resulted in more than six million deaths worldwide since late 2019. The appearance of this novel virus is defined by its high and variable transmission rate (RT) and coexisting asymptomatic and symptomatic propagation within and across animal populations, which has a longer-lasting impact. Most current therapeutic methods aim to reduce the severity of COVID-19 hospitalization and virus symptoms, preventing the infection from progressing from acute to chronic in vulnerable populations. Now, pharmacological interventions including vaccines and others exist, with research ongoing. The only ethical approach to developing herd immunity is to develop and provide vaccines and therapeutics that can potentially improve on the innate and adaptive system responses at the same time. Therefore, several vaccines have been developed to provide acquired immunity to SARS-CoV-2 induced COVID-19-disease. The initial evaluations of the COVID-19 vaccines began in around 2020, followed by clinical trials carried out during the pandemic with ongoing population adverse effect monitoring by respective regulatory agencies. Therefore, durability and immunity provided by current vaccines requires further characterization with more extensive available data, as is presented in this paper. When utilized globally, these vaccines may create an unidentified pattern of antibody responses or memory B and T cell responses that need to be further researched, some of which can now be compared within laboratory and population studies here. Several COVID-19 vaccine immunogens have been presented in clinical trials to assess their safety and efficacy, inducing cellular antibody production through cellular B and T cell interactions that protect against infection. This response is defined by virus-specific antibodies (anti-N or anti-S antibodies), with B and T cell characterization undergoing extensive research. In this article, we review four types of contemporary COVID-19 vaccines, comparing their antibody profiles and cellular aspects involved in coronavirus immunology across several population studies.
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77
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Zhou YQ, Wang K, Wang XY, Cui HY, Zhao Y, Zhu P, Chen ZN. SARS-CoV-2 pseudovirus enters the host cells through spike protein-CD147 in an Arf6-dependent manner. Emerg Microbes Infect 2022; 11:1135-1144. [PMID: 35343395 PMCID: PMC9037224 DOI: 10.1080/22221751.2022.2059403] [Citation(s) in RCA: 22] [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: 01/17/2022] [Accepted: 03/25/2022] [Indexed: 12/30/2022]
Abstract
The spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and its variants is threatening public health around the world. Endocytosis functions as an important way for viral infection, and SARS-CoV-2 bears no exception. However, the specific endocytic mechanism of SARS-CoV-2 remains unknown. In this study, we used endocytic inhibitors to evaluate the role of different endocytic routes in SARS-CoV-2 pseudovirus infection and found that the viral infection was associated with caveolar/lipid raft- and cytoskeleton-mediated endocytosis, but independent of the clathrin-mediated endocytosis and macropinocytosis. Meanwhile, the knockdown of CD147 and Rab5a in Vero E6 and Huh-7 cells inhibited SARS-CoV-2 pseudovirus infection, and the co-localization of spike protein, CD147, and Rab5a was observed in pseudovirus-infected Vero E6 cells, which was weakened by CD147 silencing, illustrating that SARS-CoV-2 pseudovirus entered the host cells via CD147-mediated endocytosis. Additionally, Arf6 silencing markedly inhibited pseudovirus infection in Vero E6 and Huh-7 cells, while little change was observed in CD147 knockout-Vero E6 cells. This finding indicated Arf6-mediated CD147 trafficking plays a vital role in SARS-CoV-2 entry. Taken together, our findings provide new insights into the CD147-Arf6 axis in mediating SARS-CoV-2 pseudovirus entry into the host cells, and further suggest that blockade of this pathway seems to be a feasible approach to prevent the SARS-CoV-2 infection clinically.
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Affiliation(s)
- Yun-Qi Zhou
- National Center for International Research of Bio-targeting Theranostics, Guangxi Key Laboratory of Bio-targeting Theranostics, Collaborative Innovation Center for Targeting Tumor Diagnosis and Therapy, Guangxi Talent Highland of Bio-targeting Theranostics, Guangxi Medical University, Nanning, People’s Republic of China
- National Translational Science Center for Molecular Medicine & Department of Cell Biology, Fourth Military Medical University, Xi’an, People’s Republic of China
| | - Ke Wang
- National Translational Science Center for Molecular Medicine & Department of Cell Biology, Fourth Military Medical University, Xi’an, People’s Republic of China
| | - Xue-Yan Wang
- National Center for International Research of Bio-targeting Theranostics, Guangxi Key Laboratory of Bio-targeting Theranostics, Collaborative Innovation Center for Targeting Tumor Diagnosis and Therapy, Guangxi Talent Highland of Bio-targeting Theranostics, Guangxi Medical University, Nanning, People’s Republic of China
- National Translational Science Center for Molecular Medicine & Department of Cell Biology, Fourth Military Medical University, Xi’an, People’s Republic of China
| | - Hong-Yong Cui
- National Translational Science Center for Molecular Medicine & Department of Cell Biology, Fourth Military Medical University, Xi’an, People’s Republic of China
| | - Yongxiang Zhao
- National Center for International Research of Bio-targeting Theranostics, Guangxi Key Laboratory of Bio-targeting Theranostics, Collaborative Innovation Center for Targeting Tumor Diagnosis and Therapy, Guangxi Talent Highland of Bio-targeting Theranostics, Guangxi Medical University, Nanning, People’s Republic of China
| | - Ping Zhu
- Department of Clinical Immunology, Xijing Hospital, Fourth Military Medical University, Xi’an, People’s Republic of China
| | - Zhi-Nan Chen
- National Center for International Research of Bio-targeting Theranostics, Guangxi Key Laboratory of Bio-targeting Theranostics, Collaborative Innovation Center for Targeting Tumor Diagnosis and Therapy, Guangxi Talent Highland of Bio-targeting Theranostics, Guangxi Medical University, Nanning, People’s Republic of China
- National Translational Science Center for Molecular Medicine & Department of Cell Biology, Fourth Military Medical University, Xi’an, People’s Republic of China
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78
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Liu N, Li Y. A Monoclonal Antibody Targeting C-Terminal Domain of Transmissible Gastroenteritis Virus Spike Protein. Monoclon Antib Immunodiagn Immunother 2022; 41:328-332. [PMID: 36525526 DOI: 10.1089/mab.2022.0030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The structure and function of the C-terminus domain (CTD) of porcine transmissible gastroenteritis virus (TGEV) spike protein remain largely unknown, thereby a specific monoclonal antibody (MAb) allows us to fully understand this domain. In this study, we developed a murine MAb against CTD of TGEV spike protein, as evidenced by the results of indirect fluorescent assay, Western blotting, and fluorescence-activated cell sorter. Further study showed that the MAb is able to exclusively recognize a 12-residue peptide (FKNVSDGVIYSV) derived from CTD of TGEV spike protein. This MAb can be used to elucidate the potential function of CTD of TGEV spike in virus attachment and entry, and warrants further intensive investigation.
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Affiliation(s)
- Na Liu
- College of Life Science and Technology, Wuhan University of Bioengineering, Wuhan, China
| | - Yaoming Li
- College of Life Science and Technology, Wuhan University of Bioengineering, Wuhan, China.,Hubei Engineering Research Center of Viral Vector, Applied Biotechnology Research Center, Wuhan University of Bioengineering, Wuhan, China
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79
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Noureldine HA, Maamari J, El Helou MO, Chedid G, Farra A, Husni R, Mokhbat JE. The effect of the BNT162b2 vaccine on antinuclear antibody and antiphospholipid antibody levels. Immunol Res 2022; 70:800-810. [PMID: 35978253 PMCID: PMC9385410 DOI: 10.1007/s12026-022-09309-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 07/20/2022] [Indexed: 11/05/2022]
Abstract
The Food and Drug Administration (FDA) approved the first SARS-CoV-2 mRNA vaccine (Pfizer-BioNTech) in December 2020. New adverse events have emerged since these vaccines have reached market. Although no clear association between messenger ribonucleic acid (mRNA) vaccines and autoimmunity has emerged, the significance of such an association warrants further exploration. After obtaining consent, a standardized survey on baseline characteristics and other relevant variables was conducted on unvaccinated individuals who were scheduled for vaccination and had not previously contracted COVID-19. Blood samples were collected from participants prior to the first dose, prior to the second dose, and 1 month after the second dose. All collected samples were tested for antinuclear antibody (ANA) titers using indirect immunofluorescence microscopy kits, and antiphospholipid (APS) immunoglobulin M (IgM) and immunoglobulin G (IgG) levels using an enzyme-linked immunoassay (ELISA) technique. ANA titers were positive for 9 participants out of 101 (8.9%) in the first pre-vaccination draw. For the second draw, the number of participants testing positive for ANA decreased to 5 (5%). For the last draw, 6 (5.9%) participants tested positive for ANA titers. One participant tested positive for APS IgM at the first pre-vaccination draw, 2 tested positive at the second draw, and 2 at the third draw. As for APS IgG titers, all participants tested negative in the three draws. McNemar's test for two dependent categorical outcomes was conducted on all variables and did not show a statistical significance. The McNemar test of these two composite variables (i.e., ANA/APS, first draw vs. ANA/APS, second and third draws) did not show statistical significance. The 2-sided exact significance of the McNemar test was 1.0. The Friedman test also showed no significance (p = 0.459). No association was found between BNT162b2 vaccine administration and changes in APS and ANA titers. The benefits of the BNT162b2 vaccine significantly outweigh any possible risk of autoimmune dysregulation considering the current evidence.
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Affiliation(s)
- Hussein A Noureldine
- LAU Gilbert and Rose-Marie Chagoury School of Medicine, Lebanese American University, Byblos, Lebanon
| | - Julian Maamari
- LAU Gilbert and Rose-Marie Chagoury School of Medicine, Lebanese American University, Byblos, Lebanon
- Division of Public Health, Infectious Diseases, and Occupational Medicine, Mayo Clinic, Rochester, MN, USA
| | - Mohamad Othman El Helou
- LAU Gilbert and Rose-Marie Chagoury School of Medicine, Lebanese American University, Byblos, Lebanon
- Scholars in Health Research Program, Faculty of Medicine and Faculty of Health Sciences, American University of Beirut, Beirut, Lebanon
| | - Georges Chedid
- LAU Gilbert and Rose-Marie Chagoury School of Medicine, Lebanese American University, Byblos, Lebanon
| | - Anna Farra
- LAU Gilbert and Rose-Marie Chagoury School of Medicine, Lebanese American University, Byblos, Lebanon
- Division of Infectious Diseases, Department of Internal Medicine, Lebanese American University Medical Center - Rizk Hospital, Zahar St, Achrafieh, Beirut, Lebanon
| | - Roula Husni
- LAU Gilbert and Rose-Marie Chagoury School of Medicine, Lebanese American University, Byblos, Lebanon
- Division of Infectious Diseases, Department of Internal Medicine, Lebanese American University Medical Center - Rizk Hospital, Zahar St, Achrafieh, Beirut, Lebanon
| | - Jacques E Mokhbat
- LAU Gilbert and Rose-Marie Chagoury School of Medicine, Lebanese American University, Byblos, Lebanon.
- Division of Infectious Diseases, Department of Internal Medicine, Lebanese American University Medical Center - Rizk Hospital, Zahar St, Achrafieh, Beirut, Lebanon.
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80
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Aloor A, Aradhya R, Venugopal P, Gopalakrishnan Nair B, Suravajhala R. Glycosylation in SARS-CoV-2 variants: A path to infection and recovery. Biochem Pharmacol 2022; 206:115335. [PMID: 36328134 PMCID: PMC9621623 DOI: 10.1016/j.bcp.2022.115335] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 10/25/2022] [Accepted: 10/25/2022] [Indexed: 11/05/2022]
Abstract
Glycan is an essential molecule that controls and drives life in a precise direction. The paucity of research in glycobiology may impede the significance of its role in the pandemic guidelines. The SARS-CoV-2 spike protein is heavily glycosylated, with 22 putative N-glycosylation sites and 17 potential O-glycosylation sites discovered thus far. It is the anchor point to the host cell ACE2 receptor, TMPRSS2, and many other host proteins that can be recognized by their immune system; hence, glycosylation is considered the primary target of vaccine development. Therefore, it is essential to know how this surface glycan plays a role in viral entry, infection, transmission, antigen, antibody responses, and disease progression. Although the vaccines are developed and applied against COVID-19, the proficiency of the immunizations is not accomplished with the current mutant variations. The role of glycosylation in SARS-CoV-2 and its receptor ACE2 with respect to other putative cell glycan receptors and the significance of glycan in host cell immunity in COVID-19 are discussed in this paper. Hence, the molecular signature of the glycan in the coronavirus infection can be incorporated into the mainstream therapeutic process.
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Affiliation(s)
- Arya Aloor
- School of Biotechnology, Amrita Vishwa Vidyapeetham, Amritapuri, Clappana 690525, Kerala, India.
| | - Rajaguru Aradhya
- School of Biotechnology, Amrita Vishwa Vidyapeetham, Amritapuri, Clappana 690525, Kerala, India.
| | - Parvathy Venugopal
- School of Biotechnology, Amrita Vishwa Vidyapeetham, Amritapuri, Clappana 690525, Kerala, India.
| | | | - Renuka Suravajhala
- School of Biotechnology, Amrita Vishwa Vidyapeetham, Amritapuri, Clappana 690525, Kerala, India.
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81
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Parn S, Savsani K, Dakshanamurthy S. SARS-CoV-2 Omicron (BA.1 and BA.2) specific novel CD8+ and CD4+ T cell epitopes targeting spike protein. IMMUNOINFORMATICS (AMSTERDAM, NETHERLANDS) 2022; 8:100020. [PMID: 36337685 PMCID: PMC9624113 DOI: 10.1016/j.immuno.2022.100020] [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] [Indexed: 11/06/2022]
Abstract
The Omicron (BA.1/B.1.1.529) variant of SARS-CoV-2 harbors an alarming 37 mutations on its spike protein, reducing the efficacy of current COVID-19 vaccines. In this study, we identified CD8+ and CD4+ T cell epitopes from SARS-CoV-2 S protein mutants. To identify the highest quality CD8 and CD4 epitopes from the Omicron variant, we selected epitopes with a high binding affinity towards both MHC I and MHC II molecules. We applied other clinical checkpoint predictors, including immunogenicity, antigenicity, allergenicity, instability and toxicity. Subsequently, we found eight Omicron (BA.1/B.1.1.529) specific CD8+ and eleven CD4+ T cell epitopes with a world population coverage of 76.16% and 97.46%, respectively. Additionally, we identified common epitopes across Omicron BA.1 and BA.2 lineages that target mutations critical to SARS-CoV-2 virulence. Further, we identified common epitopes across B.1.1.529 and other circulating SARS-CoV-2 variants, such as B.1.617.2 (Delta). We predicted CD8 epitopes' binding affinity to murine MHC alleles to test the vaccine candidates in preclinical models. The CD8 epitopes were further validated using our previously developed software tool PCOptim. We then modeled the three-dimensional structures of our top CD8 epitopes to investigate the binding interaction between peptide-MHC and peptide-MHC-TCR complexes. Notably, our identified epitopes are targeting the mutations on the RNA-binding domain and the fusion sites of S protein. This could potentially eliminate viral infections and form long-term immune responses compared to relatively short-lived mRNA vaccines and maximize the efficacy of vaccine candidates against the current pandemic and potential future variants.
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Affiliation(s)
- Simone Parn
- University of the District of Columbia, Washington, D.C, USA
| | - Kush Savsani
- Virginia Commonwealth University, Richmond, VA, USA
| | - Sivanesan Dakshanamurthy
- Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington DC 20057 USA
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82
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Valenzuela-Fernández A, Cabrera-Rodriguez R, Ciuffreda L, Perez-Yanes S, Estevez-Herrera J, González-Montelongo R, Alcoba-Florez J, Trujillo-González R, García-Martínez de Artola D, Gil-Campesino H, Díez-Gil O, Lorenzo-Salazar JM, Flores C, Garcia-Luis J. Nanomaterials to combat SARS-CoV-2: Strategies to prevent, diagnose and treat COVID-19. Front Bioeng Biotechnol 2022; 10:1052436. [PMID: 36507266 PMCID: PMC9732709 DOI: 10.3389/fbioe.2022.1052436] [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: 09/23/2022] [Accepted: 11/09/2022] [Indexed: 11/26/2022] Open
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and the associated coronavirus disease 2019 (COVID-19), which severely affect the respiratory system and several organs and tissues, and may lead to death, have shown how science can respond when challenged by a global emergency, offering as a response a myriad of rapid technological developments. Development of vaccines at lightning speed is one of them. SARS-CoV-2 outbreaks have stressed healthcare systems, questioning patients care by using standard non-adapted therapies and diagnostic tools. In this scenario, nanotechnology has offered new tools, techniques and opportunities for prevention, for rapid, accurate and sensitive diagnosis and treatment of COVID-19. In this review, we focus on the nanotechnological applications and nano-based materials (i.e., personal protective equipment) to combat SARS-CoV-2 transmission, infection, organ damage and for the development of new tools for virosurveillance, diagnose and immune protection by mRNA and other nano-based vaccines. All the nano-based developed tools have allowed a historical, unprecedented, real time epidemiological surveillance and diagnosis of SARS-CoV-2 infection, at community and international levels. The nano-based technology has help to predict and detect how this Sarbecovirus is mutating and the severity of the associated COVID-19 disease, thereby assisting the administration and public health services to make decisions and measures for preparedness against the emerging variants of SARS-CoV-2 and severe or lethal COVID-19.
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Affiliation(s)
- Agustín Valenzuela-Fernández
- Laboratorio de Inmunología Celular y Viral, Unidad de Farmacología, Sección de Medicina, Facultad de Ciencias de la Salud, Universidad de La Laguna, San Cristóbal de La Laguna, Spain
| | - Romina Cabrera-Rodriguez
- Laboratorio de Inmunología Celular y Viral, Unidad de Farmacología, Sección de Medicina, Facultad de Ciencias de la Salud, Universidad de La Laguna, San Cristóbal de La Laguna, Spain
| | - Laura Ciuffreda
- Research Unit, Hospital Universitario N. S. de Candelaria, Santa Cruz de Tenerife, Spain
| | - Silvia Perez-Yanes
- Laboratorio de Inmunología Celular y Viral, Unidad de Farmacología, Sección de Medicina, Facultad de Ciencias de la Salud, Universidad de La Laguna, San Cristóbal de La Laguna, Spain
| | - Judith Estevez-Herrera
- Laboratorio de Inmunología Celular y Viral, Unidad de Farmacología, Sección de Medicina, Facultad de Ciencias de la Salud, Universidad de La Laguna, San Cristóbal de La Laguna, Spain
| | | | - Julia Alcoba-Florez
- Servicio de Microbiología, Hospital Universitario N. S. de Candelaria, Santa Cruz de Tenerife, Spain
| | - Rodrigo Trujillo-González
- Laboratorio de Inmunología Celular y Viral, Unidad de Farmacología, Sección de Medicina, Facultad de Ciencias de la Salud, Universidad de La Laguna, San Cristóbal de La Laguna, Spain
- Departamento de Análisis Matemático, Facultad de Ciencias, Universidad de La Laguna, Santa Cruz de Tenerife, Spain
| | | | - Helena Gil-Campesino
- Servicio de Microbiología, Hospital Universitario N. S. de Candelaria, Santa Cruz de Tenerife, Spain
| | - Oscar Díez-Gil
- Servicio de Microbiología, Hospital Universitario N. S. de Candelaria, Santa Cruz de Tenerife, Spain
| | - José M. Lorenzo-Salazar
- Genomics Division, Instituto Tecnológico y de Energías Renovables, Santa Cruz de Tenerife, Spain
| | - Carlos Flores
- Research Unit, Hospital Universitario N. S. de Candelaria, Santa Cruz de Tenerife, Spain
- Genomics Division, Instituto Tecnológico y de Energías Renovables, Santa Cruz de Tenerife, Spain
- CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
- Faculty of Health Sciences, University of Fernando Pessoa Canarias, Las Palmas de Gran Canaria, Spain
| | - Jonay Garcia-Luis
- Laboratorio de Inmunología Celular y Viral, Unidad de Farmacología, Sección de Medicina, Facultad de Ciencias de la Salud, Universidad de La Laguna, San Cristóbal de La Laguna, Spain
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Kubo AL, Rausalu K, Savest N, Žusinaite E, Vasiliev G, Viirsalu M, Plamus T, Krumme A, Merits A, Bondarenko O. Antibacterial and Antiviral Effects of Ag, Cu and Zn Metals, Respective Nanoparticles and Filter Materials Thereof against Coronavirus SARS-CoV-2 and Influenza A Virus. Pharmaceutics 2022; 14:pharmaceutics14122549. [PMID: 36559043 PMCID: PMC9785359 DOI: 10.3390/pharmaceutics14122549] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 11/12/2022] [Accepted: 11/15/2022] [Indexed: 11/23/2022] Open
Abstract
Due to the high prevalence of infectious diseases and their concurrent outbreaks, there is a high interest in developing novel materials with antimicrobial properties. Antibacterial and antiviral properties of a range of metal-based nanoparticles (NPs) are a promising means to fight airborne diseases caused by viruses and bacteria. The aim of this study was to test antimicrobial metals and metal-based nanoparticles efficacy against three viruses, namely influenza A virus (H1N1; A/WSN/1933) and coronaviruses TGEV and SARS-CoV-2; and two bacteria, Escherichia coli and Staphylococcus aureus. The efficacy of ZnO, CuO, and Ag NPs and their respective metal salts, i.e., ZnSO4, CuSO4, and AgNO3, was evaluated in suspensions, and the compounds with the highest antiviral efficacy were chosen for incorporation into fibers of cellulose acetate (CA), using electrospinning to produce filter materials for face masks. Among the tested compounds, CuSO4 demonstrated the highest efficacy against influenza A virus and SARS-CoV-2 (1 h IC50 1.395 mg/L and 0.45 mg/L, respectively), followed by Zn salt and Ag salt. Therefore, Cu compounds were selected for incorporation into CA fibers to produce antiviral and antibacterial filter materials for face masks. CA fibers comprising CuSO4 decreased SARS-CoV-2 titer by 0.38 logarithms and influenza A virus titer by 1.08 logarithms after 5 min of contact; after 1 h of contact, SARS-COV-2 virus was completely inactivated. Developed CuO- and CuSO4-based filter materials also efficiently inactivated the bacteria Escherichia coli and Staphylococcus aureus. The metal NPs and respective metal salts were potent antibacterial and antiviral compounds that were successfully incorporated into the filter materials of face masks. New antibacterial and antiviral materials developed and characterized in this study are crucial in the context of the ongoing SARS-CoV-2 pandemic and beyond.
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Affiliation(s)
- Anna-Liisa Kubo
- Laboratory of Environmental Toxicology, National Institute of Chemical Physics and Biophysics, Akadeemia tee 23, 12618 Tallinn, Estonia
- Nanordica Medical OÜ, Vana-Lõuna 39a-7, 10134 Tallinn, Estonia
| | - Kai Rausalu
- Institute of Technology, University of Tartu, Nooruse 1, 50411 Tartu, Estonia
| | - Natalja Savest
- Laboratory of Polymers and Textile Technology, Department of Materials and Environmental Technology, Tallinn University of Technology, Ehitajate tee 5, 19086 Tallinn, Estonia
| | - Eva Žusinaite
- Institute of Technology, University of Tartu, Nooruse 1, 50411 Tartu, Estonia
| | - Grigory Vasiliev
- Laboratory of Environmental Toxicology, National Institute of Chemical Physics and Biophysics, Akadeemia tee 23, 12618 Tallinn, Estonia
- Nanordica Medical OÜ, Vana-Lõuna 39a-7, 10134 Tallinn, Estonia
| | - Mihkel Viirsalu
- Laboratory of Polymers and Textile Technology, Department of Materials and Environmental Technology, Tallinn University of Technology, Ehitajate tee 5, 19086 Tallinn, Estonia
| | - Tiia Plamus
- Laboratory of Polymers and Textile Technology, Department of Materials and Environmental Technology, Tallinn University of Technology, Ehitajate tee 5, 19086 Tallinn, Estonia
| | - Andres Krumme
- Laboratory of Polymers and Textile Technology, Department of Materials and Environmental Technology, Tallinn University of Technology, Ehitajate tee 5, 19086 Tallinn, Estonia
- Correspondence: (A.K.); (A.M.); (O.B.)
| | - Andres Merits
- Institute of Technology, University of Tartu, Nooruse 1, 50411 Tartu, Estonia
- Correspondence: (A.K.); (A.M.); (O.B.)
| | - Olesja Bondarenko
- Laboratory of Environmental Toxicology, National Institute of Chemical Physics and Biophysics, Akadeemia tee 23, 12618 Tallinn, Estonia
- Nanordica Medical OÜ, Vana-Lõuna 39a-7, 10134 Tallinn, Estonia
- Correspondence: (A.K.); (A.M.); (O.B.)
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84
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Martínez-Murcia A, Garcia-Sirera A, Navarro A, Pérez L. SARS-CoV-2 Variants Identification; A Fast and Affordable Strategy Based on Partial S-Gene Targeted PCR Sequencing. Viruses 2022; 14:v14112588. [PMID: 36423197 PMCID: PMC9696215 DOI: 10.3390/v14112588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 11/11/2022] [Accepted: 11/18/2022] [Indexed: 11/23/2022] Open
Abstract
A considerable number of new SARS-CoV-2 lineages have emerged since the first COVID-19 cases were reported in Wuhan. As a few variants showed higher COVID-19 disease transmissibility and the ability to escape from immune responses, surveillance became relevant at that time. Single-nucleotide mutation PCR-based protocols were not always specific, and consequently, determination of a high number of informative sites was needed for accurate lineage identification. A detailed in silico analysis of SARS-CoV-2 sequences retrieved from GISAID database revealed the S gene 921 bp-fragment, positions 22784-23705 of SARS-CoV-2 reference genome, as the most informative fragment (30 variable sites) to determine relevant SARS-CoV-2 variants. Consequently, a method consisting of the PCR-amplification of this fragment, followed by Sanger's sequencing and a "single-click" informatic program based on a reference database, was developed and validated. PCR-fragments obtained from clinical SARS-CoV-2 samples were compared with homologous variant-sequences and the resulting phylogenetic tree allowed the identification of Alpha, Delta, Omicron, Beta, Gamma, and other variants. The data analysis procedure was automatized and simplified to the point that it did not require specific technical skills. The method is faster and cheaper than current whole-genome sequencing methods; it is available worldwide, and it may help to enhance efficient surveillance in the fight against the COVID-19 pandemic.
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Affiliation(s)
- Antonio Martínez-Murcia
- Department of Microbiology, University Miguel Hernández, 03312 Orihuela, Spain
- Genetic PCR Solutions™, 03300 Orihuela, Spain; (A.G.-S.); (A.N.); (L.P.)
- Correspondence: ; Tel.: +34-965429901
| | | | - Aaron Navarro
- Genetic PCR Solutions™, 03300 Orihuela, Spain; (A.G.-S.); (A.N.); (L.P.)
| | - Laura Pérez
- Genetic PCR Solutions™, 03300 Orihuela, Spain; (A.G.-S.); (A.N.); (L.P.)
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85
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Chen D, Liu X, Chen Y, Lin H. Amyloid peptides with antimicrobial and/or microbial agglutination activity. Appl Microbiol Biotechnol 2022; 106:7711-7720. [PMID: 36322251 PMCID: PMC9628408 DOI: 10.1007/s00253-022-12246-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Revised: 10/11/2022] [Accepted: 10/12/2022] [Indexed: 11/07/2022]
Abstract
Abstract Microbe (including bacteria, fungi, and virus) infection in brains is associated with amyloid fibril deposit and neurodegeneration. Increasing findings suggest that amyloid proteins, like Abeta (Aβ), are important innate immune effectors in preventing infections. In some previous studies, amyloid peptides have been linked to antimicrobial peptides due to their common mechanisms in membrane-disruption ability, while the other mechanisms of bactericidal protein aggregation and protein function knockdown are less discussed. Besides, another important function of amyloid peptides in pathogen agglutination is rarely illustrated. In this review, we summarized and divided the different roles and mechanisms of amyloid peptides against microbes in antimicrobial activity and microbe agglutination activity. Besides, the range of amyloids’ antimicrobial spectrum, the effectiveness of amyloid peptide states (monomers, oligomers, and fibrils), and cytotoxicity are discussed. The good properties of amyloid peptides against microbes might provide implications for the development of novel antimicrobial drug. Key points • Antimicrobial and/or microbial agglutination is a characteristic of amyloid peptides. • Various mechanisms of amyloid peptides against microbes are discovered recently. • Amyloid peptides might be developed into novel antimicrobial drugs. Supplementary information The online version contains supplementary material available at 10.1007/s00253-022-12246-w.
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Affiliation(s)
- Dongru Chen
- Department of Orthodontics, Hospital of Stomatology, Guanghua School of Stomatology, Sun Yat-Sen University, Guangdong Provincial Key Laboratory of Stomatology, Guangzhou, Guangdong, China
| | - Xiangqi Liu
- Department of Oral and Maxillofacial Surgery, Hospital of Stomatology, Guanghua School of Stomatology, Sun Yat-Sen University, Guangdong Provincial Key Laboratory of Stomatology, Guangzhou, Guangdong, China
| | - Yucong Chen
- Department of Preventive Dentistry, Hospital of Stomatology, Guanghua School of Stomatology, Sun Yat-Sen University, Guangdong Provincial Key Laboratory of Stomatology, Guangzhou, Guangdong, China
| | - Huancai Lin
- Department of Preventive Dentistry, Hospital of Stomatology, Guanghua School of Stomatology, Sun Yat-Sen University, Guangdong Provincial Key Laboratory of Stomatology, Guangzhou, Guangdong, China.
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Takahashi W, Mizuno T, Hara K, Ara Y, Hurutani R, Agatsuma T, Fujimori M. Association of Systemic Adverse Reactions and Serum SARS-CoV-2 Spike Protein Antibody Levels after Administration of BNT162b2 mRNA COVID-19 Vaccine. Intern Med 2022; 61:3205-3210. [PMID: 35989281 PMCID: PMC9683821 DOI: 10.2169/internalmedicine.9699-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Objectives The influential factors for anti-severe acute respiratory syndrome coronavirus 2 spike protein antibody (S-ab) levels were assessed after the administration of BNT162b2 mRNA coronavirus disease-2019 (COVID-19) vaccine at short and medium terms. Methods A total of 470 healthcare workers (118 males, mean age 41.0±11.9 years) underwent serum S-ab level measurement at 3 and 8 months after two inoculations of BNT162b2 vaccine given 3 weeks apart, who had no history of COVID-19 were enrolled in this study. The changes and differences after vaccination due to gender and adverse reactions of S-ab were analyzed. Results Systemic adverse reactions incidence (48%) was significantly higher after the second dose than after the first dose (8%). S-ab levels decreased as the age increased (from the 20s to 60s) in both measurements. S-ab level 8 months after the second inoculation [median 476.3 (interquartile range (IQR) 322.4-750.6) U/mL] was significantly lower than that after 3 months [977.5 (637.2-1,409.0) U/mL; p<0.001]. The median decrease rate of S-ab levels in 5 months was 50.3% (IQR 40.3-62.6) and those differences were not observed among all generations. Gender-associated differences in S-ab levels were not observed; however, a significant relationship between higher S-ab levels and the systemic adverse reactions was observed at both measurements. Conclusions The systemic adverse reaction is an independent factor for higher S-ab levels at short and medium terms after BNT162b2 vaccination as demonstrated in our data.
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Affiliation(s)
- Wataru Takahashi
- Department of Clinical Research, National Hospital Organization, Shinshu Ueda Medical Center, Japan
| | - Toshiko Mizuno
- Department of Clinical Research, National Hospital Organization, Shinshu Ueda Medical Center, Japan
| | - Kaori Hara
- Department of Infection Control, National Hospital Organization, Shinshu Ueda Medical Center, Japan
| | - Yoshiaki Ara
- Department of Pharmacy, National Hospital Organization, Shinshu Ueda Medical Center, Japan
| | - Rikiya Hurutani
- Department of Neurology, National Hospital Organization, Shinshu Ueda Medical Center, Japan
| | - Toshihiko Agatsuma
- Department of Infection Control, National Hospital Organization, Shinshu Ueda Medical Center, Japan
| | - Minoru Fujimori
- Department of Breast Surgery, National Hospital Organization, Shinshu Ueda Medical Center, Japan
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Pacheco-Olvera DL, Saint Remy-Hernández S, García-Valeriano MG, Rivera-Hernández T, López-Macías C. Bioinformatic Analysis of B- and T-cell Epitopes from SARS-CoV-2 Structural Proteins and their Potential Cross-reactivity with Emerging Variants and other Human Coronaviruses. Arch Med Res 2022; 53:694-710. [PMID: 36336501 PMCID: PMC9633039 DOI: 10.1016/j.arcmed.2022.10.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 08/23/2022] [Accepted: 10/21/2022] [Indexed: 11/06/2022]
Abstract
BACKGROUND The mutations in SARS-CoV-2 variants of concern (VOC) facilitate the virus' escape from the neutralizing antibodies induced by vaccines. However, the protection from hospitalization and death is not significantly diminished. Both vaccine boosters and infection improve immune responses and provide protection, suggesting that conserved and/or cross-reactive epitopes could be involved. While several important T- and B-cell epitopes have been identified, mainly in the S protein, the M and N proteins and their potential cross-reactive epitopes with other coronaviruses remain largely unexplored. AIMS To identify and map new potential B- and T-cell epitopes within the SARS-CoV-2 S, M and N proteins, as well as cross-reactive epitopes with human coronaviruses. METHODS Different bioinformatics tools were used to: i) Identify new and compile previously-reported B-and T-cell epitopes from SARS-CoV-2 S, M and N proteins; ii) Determine the mutations in S protein from VOC that affect B- and T-cell epitopes, and; iii) Identify cross-reactive epitopes with coronaviruses relevant to human health. RESULTS New, potential B- and T-cell epitopes from S, M and N proteins as well as cross-reactive epitopes with other coronaviruses were found and mapped within the proteins' structures. CONCLUSION Numerous potential B- and T-cell epitopes were found in S, M and N proteins, some of which are conserved between coronaviruses. VOCs present mutations within important epitopes in the S protein; however, a significant number of other epitopes remain unchanged. The epitopes identified here may contribute to augmenting the protective response to SARS-CoV-2 and its variants induced by infection and/or vaccination, and may also be used for the rational design of novel broad-spectrum coronavirus vaccines.
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Affiliation(s)
- Diana Laura Pacheco-Olvera
- Unidad de Investigación Médica en Inmunoquímica, Hospital de Especialidades del Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Ciudad de México, México
| | - Stephanie Saint Remy-Hernández
- Unidad de Investigación Médica en Inmunoquímica, Hospital de Especialidades del Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Ciudad de México, México
| | - María Guadalupe García-Valeriano
- Unidad de Investigación Médica en Inmunoquímica, Hospital de Especialidades del Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Ciudad de México, México
| | - Tania Rivera-Hernández
- Unidad de Investigación Médica en Inmunoquímica, Hospital de Especialidades del Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Ciudad de México, México; Consejo Nacional de Ciencia y Tecnología, Ciudad de México, México
| | - Constantino López-Macías
- Unidad de Investigación Médica en Inmunoquímica, Hospital de Especialidades del Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Ciudad de México, México.
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Shivatare SS, Shivatare VS, Wong CH. Glycoconjugates: Synthesis, Functional Studies, and Therapeutic Developments. Chem Rev 2022; 122:15603-15671. [PMID: 36174107 PMCID: PMC9674437 DOI: 10.1021/acs.chemrev.1c01032] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Glycoconjugates are major constituents of mammalian cells that are formed via covalent conjugation of carbohydrates to other biomolecules like proteins and lipids and often expressed on the cell surfaces. Among the three major classes of glycoconjugates, proteoglycans and glycoproteins contain glycans linked to the protein backbone via amino acid residues such as Asn for N-linked glycans and Ser/Thr for O-linked glycans. In glycolipids, glycans are linked to a lipid component such as glycerol, polyisoprenyl pyrophosphate, fatty acid ester, or sphingolipid. Recently, glycoconjugates have become better structurally defined and biosynthetically understood, especially those associated with human diseases, and are accessible to new drug, diagnostic, and therapeutic developments. This review describes the status and new advances in the biological study and therapeutic applications of natural and synthetic glycoconjugates, including proteoglycans, glycoproteins, and glycolipids. The scope, limitations, and novel methodologies in the synthesis and clinical development of glycoconjugates including vaccines, glyco-remodeled antibodies, glycan-based adjuvants, glycan-specific receptor-mediated drug delivery platforms, etc., and their future prospectus are discussed.
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Affiliation(s)
- Sachin S Shivatare
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Vidya S Shivatare
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Chi-Huey Wong
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
- Genomics Research Center, Academia Sinica, Taipei 115, Taiwan
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Dehghani J, Movafeghi A, Mathieu-Rivet E, Mati-Baouche N, Calbo S, Lerouge P, Bardor M. Microalgae as an Efficient Vehicle for the Production and Targeted Delivery of Therapeutic Glycoproteins against SARS-CoV-2 Variants. Mar Drugs 2022; 20:md20110657. [PMID: 36354980 PMCID: PMC9698596 DOI: 10.3390/md20110657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2022] [Revised: 10/18/2022] [Accepted: 10/20/2022] [Indexed: 11/27/2022] Open
Abstract
Severe acute respiratory syndrome–Coronavirus 2 (SARS-CoV-2) can infect various human organs, including the respiratory, circulatory, nervous, and gastrointestinal ones. The virus is internalized into human cells by binding to the human angiotensin-converting enzyme 2 (ACE2) receptor through its spike protein (S-glycoprotein). As S-glycoprotein is required for the attachment and entry into the human target cells, it is the primary mediator of SARS-CoV-2 infectivity. Currently, this glycoprotein has received considerable attention as a key component for the development of antiviral vaccines or biologics against SARS-CoV-2. Moreover, since the ACE2 receptor constitutes the main entry route for the SARS-CoV-2 virus, its soluble form could be considered as a promising approach for the treatment of coronavirus disease 2019 infection (COVID-19). Both S-glycoprotein and ACE2 are highly glycosylated molecules containing 22 and 7 consensus N-glycosylation sites, respectively. The N-glycan structures attached to these specific sites are required for the folding, conformation, recycling, and biological activity of both glycoproteins. Thus far, recombinant S-glycoprotein and ACE2 have been produced primarily in mammalian cells, which is an expensive process. Therefore, benefiting from a cheaper cell-based biofactory would be a good value added to the development of cost-effective recombinant vaccines and biopharmaceuticals directed against COVID-19. To this end, efficient protein synthesis machinery and the ability to properly impose post-translational modifications make microalgae an eco-friendly platform for the production of pharmaceutical glycoproteins. Notably, several microalgae (e.g., Chlamydomonas reinhardtii, Dunaliella bardawil, and Chlorella species) are already approved by the U.S. Food and Drug Administration (FDA) as safe human food. Because microalgal cells contain a rigid cell wall that could act as a natural encapsulation to protect the recombinant proteins from the aggressive environment of the stomach, this feature could be used for the rapid production and edible targeted delivery of S-glycoprotein and soluble ACE2 for the treatment/inhibition of SARS-CoV-2. Herein, we have reviewed the pathogenesis mechanism of SARS-CoV-2 and then highlighted the potential of microalgae for the treatment/inhibition of COVID-19 infection.
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Affiliation(s)
- Jaber Dehghani
- Université de Rouen Normandie, Laboratoire GlycoMEV UR 4358, SFR Normandie Végétal FED 4277, Innovation Chimie Carnot, F-76000 Rouen, France
| | - Ali Movafeghi
- Department of Plant, Cell and Molecular Biology, Faculty of Natural Sciences, University of Tabriz, Tabriz 5166616471, Iran
| | - Elodie Mathieu-Rivet
- Université de Rouen Normandie, Laboratoire GlycoMEV UR 4358, SFR Normandie Végétal FED 4277, Innovation Chimie Carnot, F-76000 Rouen, France
| | - Narimane Mati-Baouche
- Université de Rouen Normandie, Laboratoire GlycoMEV UR 4358, SFR Normandie Végétal FED 4277, Innovation Chimie Carnot, F-76000 Rouen, France
| | - Sébastien Calbo
- Université de Rouen Normandie, Inserm U1234, F-76000 Rouen, France
| | - Patrice Lerouge
- Université de Rouen Normandie, Laboratoire GlycoMEV UR 4358, SFR Normandie Végétal FED 4277, Innovation Chimie Carnot, F-76000 Rouen, France
| | - Muriel Bardor
- Université de Rouen Normandie, Laboratoire GlycoMEV UR 4358, SFR Normandie Végétal FED 4277, Innovation Chimie Carnot, F-76000 Rouen, France
- Correspondence: ; Tel.: +33-2-35-14-67-51
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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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Aramini B, Masciale V, Samarelli AV, Tonelli R, Cerri S, Clini E, Stella F, Dominici M. Biological effects of COVID-19 on lung cancer: Can we drive our decisions. Front Oncol 2022; 12:1029830. [PMID: 36300087 PMCID: PMC9589049 DOI: 10.3389/fonc.2022.1029830] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Accepted: 09/23/2022] [Indexed: 11/13/2022] Open
Abstract
COVID-19 infection caused by SARS-CoV-2 is considered catastrophic because it affects multiple organs, particularly those of the respiratory tract. Although the consequences of this infection are not fully clear, it causes damage to the lungs, the cardiovascular and nervous systems, and other organs, subsequently inducing organ failure. In particular, the effects of SARS-CoV-2-induced inflammation on cancer cells and the tumor microenvironment need to be investigated. COVID-19 may alter the tumor microenvironment, promoting cancer cell proliferation and dormant cancer cell (DCC) reawakening. DCCs reawakened upon infection with SARS-CoV-2 can populate the premetastatic niche in the lungs and other organs, leading to tumor dissemination. DCC reawakening and consequent neutrophil and monocyte/macrophage activation with an uncontrolled cascade of pro-inflammatory cytokines are the most severe clinical effects of COVID-19. Moreover, neutrophil extracellular traps have been demonstrated to activate the dissemination of premetastatic cells into the lungs. Further studies are warranted to better define the roles of COVID-19 in inflammation as well as in tumor development and tumor cell metastasis; the results of these studies will aid in the development of further targeted therapies, both for cancer prevention and the treatment of patients with COVID-19.
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Affiliation(s)
- Beatrice Aramini
- Division of Thoracic Surgery, Department of Experimental, Diagnostic and Specialty Medicine—DIMES of the Alma Mater Studiorum, University of Bologna, G.B. Morgagni—L. Pierantoni Hospital, Forlì, Italy
- *Correspondence: Beatrice Aramini,
| | - Valentina Masciale
- Division of Oncology, Department of Medical and Surgical Sciences, University of Modena and Reggio Emilia, Modena, Italy
- Laboratory of Cell Therapy, Department of Medical and Surgical Sciences, University Hospital of Modena, University of Modena and Reggio Emilia, Modena, Italy
| | - Anna Valeria Samarelli
- Laboratory of Cell Therapy, Department of Medical and Surgical Sciences, University Hospital of Modena, University of Modena and Reggio Emilia, Modena, Italy
- Respiratory Disease Unit, Department of Medical and Surgical Sciences, University Hospital of Modena, University of Modena and Reggio Emilia, Modena, Italy
| | - Roberto Tonelli
- Respiratory Disease Unit, Department of Medical and Surgical Sciences, University Hospital of Modena, University of Modena and Reggio Emilia, Modena, Italy
| | - Stefania Cerri
- Respiratory Disease Unit, Department of Medical and Surgical Sciences, University Hospital of Modena, University of Modena and Reggio Emilia, Modena, Italy
| | - Enrico Clini
- Respiratory Disease Unit, Department of Medical and Surgical Sciences, University Hospital of Modena, University of Modena and Reggio Emilia, Modena, Italy
| | - Franco Stella
- Division of Thoracic Surgery, Department of Experimental, Diagnostic and Specialty Medicine—DIMES of the Alma Mater Studiorum, University of Bologna, G.B. Morgagni—L. Pierantoni Hospital, Forlì, Italy
| | - Massimo Dominici
- Division of Oncology, Department of Medical and Surgical Sciences, University of Modena and Reggio Emilia, Modena, Italy
- Laboratory of Cell Therapy, Department of Medical and Surgical Sciences, University Hospital of Modena, University of Modena and Reggio Emilia, Modena, Italy
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92
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Zare Marzouni H, Rahbar M, Seddighi N, Nabizadeh M, Meidaninikjeh S, Sabouni N. Antibody Therapy for COVID-19: Categories, Pros, and Cons. Viral Immunol 2022; 35:517-528. [PMID: 36201297 DOI: 10.1089/vim.2021.0160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
COVID-19 is a life-threatening respiratory disease triggered by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). It has been considered a pandemic viral infection since December 2019. The investigation of the effective prophylaxis or therapeutic strategies for emergency management of the current condition has become a priority for medical research centers and pharmaceutical companies. This article provides a comprehensive review of antibody therapy and its different categories with their advantages and disadvantages for COVID-19 over the last few years of the current pandemic. Antibodies can be generated by active immunization, including natural infection with a pathogen and vaccination, or by the passive immunization method such as convalescent plasma therapy (CPT) and antibody synthesis in laboratories. Each of these ways has its characteristics. Arming the immune system with antibodies is the main aim of antiviral therapeutic procedures toward SARS-CoV-2. Collecting and discussing various aspects of available data in this field can give researchers a better perspective for the production of antibody-based products or selection of the most appropriate approach of antibody therapies to improve different cases of COVID-19. Moreover, it can help them control similar viral pandemics that may happen in the future appropriately.
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Affiliation(s)
- Hadi Zare Marzouni
- Qaen School of Nursing and Midwifery, Birjand University of Medical Sciences, Birjand, Iran
| | - Marjan Rahbar
- Department of Food Science and Technology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Nazanin Seddighi
- Qaen School of Nursing and Midwifery, Birjand University of Medical Sciences, Birjand, Iran
| | - Mohsen Nabizadeh
- Department of Biology, Faculty of Basic Sciences, Central Tehran Branch, Islamic Azad University, Tehran, Iran
| | - Sepideh Meidaninikjeh
- Department of Microbiology, Faculty of Biological Sciences, Alzahra University, Tehran, Iran.,Cancer Biomedical Center (CBC) Research Institute, Tehran, Iran
| | - Nasim Sabouni
- Department of Immunology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
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93
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Ao Z, Ouyang MJ, Olukitibi TA, Warner B, Vendramelli R, Truong T, Meilleur C, Zhang M, Kung S, Fowke KR, Kobasa D, Yao X. A Recombinant VSV-Based Bivalent Vaccine Effectively Protects against Both SARS-CoV-2 and Influenza A Virus Infection. J Virol 2022; 96:e0133722. [PMID: 36069551 PMCID: PMC9517730 DOI: 10.1128/jvi.01337-22] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 08/30/2022] [Indexed: 12/03/2022] Open
Abstract
COVID-19 and influenza are both highly contagious respiratory diseases that have been serious threats to global public health. It is necessary to develop a bivalent vaccine to control these two infectious diseases simultaneously. In this study, we generated three attenuated replicating recombinant vesicular stomatitis virus (rVSV)-based vaccine candidates against both SARS-CoV-2 and influenza viruses. These rVSV-based vaccines coexpress SARS-CoV-2 Delta spike protein (SP) bearing the C-terminal 17 amino acid (aa) deletion (SPΔC) and I742A point mutation, or the SPΔC with a deletion of S2 domain, or the RBD domain, and a tandem repeat harboring four copies of the highly conserved influenza M2 ectodomain (M2e) that fused with the Ebola glycoprotein DC-targeting/activation domain. Animal immunization studies have shown that these rVSV bivalent vaccines induced efficient humoral and cellular immune responses against both SARS-CoV-2 SP and influenza M2 protein, including high levels of neutralizing antibodies against SARS-CoV-2 Delta and other variant SP-pseudovirus infections. Importantly, immunization of the rVSV bivalent vaccines effectively protected hamsters or mice against the challenges of SARS-CoV-2 Delta variant and lethal H1N1 and H3N2 influenza viruses and significantly reduced respiratory viral loads. Overall, this study provides convincing evidence for the high efficacy of this bivalent vaccine platform to be used and/or easily adapted to produce new vaccines against new or reemerging SARS-CoV-2 variants and influenza A virus infections. IMPORTANCE Given that both COVID-19 and influenza are preferably transmitted through respiratory droplets during the same seasons, it is highly advantageous to develop a bivalent vaccine that could simultaneously protect against both COVID-19 and influenza. In this study, we generated the attenuated replicating recombinant vesicular stomatitis virus (rVSV)-based vaccine candidates that target both spike protein of SARS-Cov-2 Delta variant and the conserved influenza M2 domain. Importantly, these vaccine candidates effectively protected hamsters or mice against the challenges of SARS-CoV-2 Delta variant and lethal H1N1 and H3N2 influenza viruses and significantly reduced respiratory viral loads.
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Affiliation(s)
- Zhujun Ao
- Laboratory of Molecular Human Retrovirology, University of Manitoba, Winnipeg, Manitoba, Canada
- Department of Medical Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Maggie J. Ouyang
- Laboratory of Molecular Human Retrovirology, University of Manitoba, Winnipeg, Manitoba, Canada
- Department of Medical Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Titus A. Olukitibi
- Laboratory of Molecular Human Retrovirology, University of Manitoba, Winnipeg, Manitoba, Canada
- Department of Medical Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Bryce Warner
- Special Pathogens Program, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Canada
| | - Robert Vendramelli
- Special Pathogens Program, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Canada
| | - Thang Truong
- Special Pathogens Program, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Canada
| | - Courtney Meilleur
- Special Pathogens Program, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Canada
| | - Manli Zhang
- Department of Immunology, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Sam Kung
- Department of Immunology, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Keith R. Fowke
- Department of Medical Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Darwyn Kobasa
- Department of Medical Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
- Special Pathogens Program, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Canada
| | - Xiaojian Yao
- Laboratory of Molecular Human Retrovirology, University of Manitoba, Winnipeg, Manitoba, Canada
- Department of Medical Microbiology, University of Manitoba, Winnipeg, Manitoba, Canada
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94
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Zhao D, Liu L, Liu X, Zhang J, Yin Y, Luan L, Jiang D, Yang X, Li L, Xiong H, Xing D, Zheng Q, Xia N, Tao Y, Li S, Huang H. A potent synthetic nanobody with broad-spectrum activity neutralizes SARS-CoV-2 virus and the Omicron variant BA.1 through a unique binding mode. J Nanobiotechnology 2022; 20:411. [PMID: 36109732 PMCID: PMC9479348 DOI: 10.1186/s12951-022-01619-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 09/05/2022] [Indexed: 12/23/2022] Open
Abstract
The major challenge to controlling the COVID pandemic is the rapid mutation rate of the SARS-CoV-2 virus, leading to the escape of the protection of vaccines and most of the neutralizing antibodies to date. Thus, it is essential to develop neutralizing antibodies with broad-spectrum activity targeting multiple SARS-CoV-2 variants. Here, we report a synthetic nanobody (named C5G2) obtained by phage display and subsequent antibody engineering. C5G2 has a single-digit nanomolar binding affinity to the RBD domain and inhibits its binding to ACE2 with an IC50 of 3.7 nM. Pseudovirus assays indicated that monovalent C5G2 could protect the cells from infection with SARS-CoV-2 wild-type virus and most of the viruses of concern, i.e., Alpha, Beta, Gamma and Omicron variants. Strikingly, C5G2 has the highest potency against Omicron BA.1 among all the variants, with an IC50 of 4.9 ng/mL. The cryo-EM structure of C5G2 in complex with the spike trimer showed that C5G2 binds to RBD mainly through its CDR3 at a conserved region that does not overlap with the ACE2 binding surface. Additionally, C5G2 binds simultaneously to the neighboring NTD domain of the spike trimer through the same CDR3 loop, which may further increase its potency against viral infection. Third, the steric hindrance caused by FR2 of C5G2 could inhibit the binding of ACE2 to RBD as well. Thus, this triple-function nanobody may serve as an effective drug for prophylaxis and therapy against Omicron as well as future variants.
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95
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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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96
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Abstract
The World Health Organisation has reported that the viral disease known as COVID-19, caused by SARS-CoV-2, is the leading cause of death by a single infectious agent. This narrative review examines certain components of the pandemic: its origins, early clinical data, global and UK-focussed epidemiology, vaccination, variants, and long COVID.
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Affiliation(s)
- A. D. Blann
- School of Applied Sciences, University of Huddersfield Queensgate, Huddersfield, United Kingdom
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97
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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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98
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Jiang Y, Zhao T, Zhou X, Xiang Y, Gutierrez‐Castrellon P, Ma X. Inflammatory pathways in COVID-19: Mechanism and therapeutic interventions. MedComm (Beijing) 2022; 3:e154. [PMID: 35923762 PMCID: PMC9340488 DOI: 10.1002/mco2.154] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 06/01/2022] [Accepted: 06/02/2022] [Indexed: 02/05/2023] Open
Abstract
The 2019 coronavirus disease (COVID-19) pandemic has become a global crisis. In the immunopathogenesis of COVID-19, SARS-CoV-2 infection induces an excessive inflammatory response in patients, causing an inflammatory cytokine storm in severe cases. Cytokine storm leads to acute respiratory distress syndrome, pulmonary and other multiorgan failure, which is an important cause of COVID-19 progression and even death. Among them, activation of inflammatory pathways is a major factor in generating cytokine storms and causing dysregulated immune responses, which is closely related to the severity of viral infection. Therefore, elucidation of the inflammatory signaling pathway of SARS-CoV-2 is important in providing otential therapeutic targets and treatment strategies against COVID-19. Here, we discuss the major inflammatory pathways in the pathogenesis of COVID-19, including induction, function, and downstream signaling, as well as existing and potential interventions targeting these cytokines or related signaling pathways. We believe that a comprehensive understanding of the regulatory pathways of COVID-19 immune dysregulation and inflammation will help develop better clinical therapy strategies to effectively control inflammatory diseases, such as COVID-19.
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Affiliation(s)
- Yujie Jiang
- Laboratory of Aging Research and Cancer Drug TargetState Key Laboratory of BiotherapyNational Clinical Research Center for GeriatricsWest China HospitalSichuan UniversityChengduPR China
| | - Tingmei Zhao
- Laboratory of Aging Research and Cancer Drug TargetState Key Laboratory of BiotherapyNational Clinical Research Center for GeriatricsWest China HospitalSichuan UniversityChengduPR China
| | - Xueyan Zhou
- Laboratory of Aging Research and Cancer Drug TargetState Key Laboratory of BiotherapyNational Clinical Research Center for GeriatricsWest China HospitalSichuan UniversityChengduPR China
| | - Yu Xiang
- Department of BiotherapyState Key Laboratory of Biotherapy Cancer CenterWest China HospitalSichuan UniversityChengduPR China
| | - Pedro Gutierrez‐Castrellon
- Center for Translational Research on Health Science Hospital General Dr. Manuel Gea GonzalezMinistry of HealthMexico CityMexico
| | - Xuelei Ma
- Department of BiotherapyState Key Laboratory of Biotherapy Cancer CenterWest China HospitalSichuan UniversityChengduPR China
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99
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Nihal S, Guppy-Coles K, Gholami MD, Punyadeera C, Izake EL. Towards Label-free detection of viral disease agents through their cell surface proteins: Rapid screening SARS-CoV-2 in biological specimens. SLAS DISCOVERY 2022; 27:331-336. [PMID: 35667647 PMCID: PMC9166287 DOI: 10.1016/j.slasd.2022.06.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Revised: 05/27/2022] [Accepted: 06/01/2022] [Indexed: 11/28/2022]
Abstract
Current methods for the screening of viral infections in clinical settings, such as reverse transcription polymerase chain reaction (RT-qPCR) and enzyme-linked immunosorbent assay (ELISA), are expensive, time-consuming, require trained personnel and sophisticated instruments. Therefore, novel sensors that can save time and cost are required specially in remote areas and developing countries that may lack the advanced scientific infrastructure for this task. In this work, we present a sensitive, and highly specific biosensing approach for the detection of harmful viruses that have cysteine residues within the structure of their cell surface proteins. We utilized new method for the rapid screening of SARS-CoV-2 virus in biological fluids through its S1 protein by surface enhanced Raman spectroscopy (SERS). The protein is captured from aqueous solutions and biological specimens using a target-specific extractor substrate. The structure of the purified protein is then modified to convert it into a bio-thiol by breaking the disulfide bonds and freeing up the sulfhydryl (SH) groups of the cysteine residues. The formed biothiol chemisorbs favourably onto a highly sensitive plasmonic sensor and probed by a handheld Raman device in few seconds. The new method was used to screen the S1 protein in aqueous medium, spiked human blood plasma, mucus, and saliva samples down to 150 fg/L. The label-free SERS biosensing method has strong potential for the fingerprint identification many viruses (e.g. the human immunodeficiency virus, the human polyomavirus, the human papilloma virus, the adeno associated viruses, the enteroviruses) through the cysteine residues of their capsid proteins. The new method can be applied at points of care (POC) in remote areas and developing countries lacking sophisticated scientific infrastructure.
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100
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Pipitò L, Rujan R, Reynolds CA, Deganutti G. Molecular dynamics studies reveal structural and functional features of the SARS-CoV-2 spike protein. Bioessays 2022; 44:e2200060. [PMID: 35843871 PMCID: PMC9350306 DOI: 10.1002/bies.202200060] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 06/21/2022] [Accepted: 07/01/2022] [Indexed: 12/23/2022]
Abstract
The SARS-CoV-2 virus is responsible for the COVID-19 pandemic the world experience since 2019. The protein responsible for the first steps of cell invasion, the spike protein, has probably received the most attention in light of its central role during infection. Computational approaches are among the tools employed by the scientific community in the enormous effort to study this new affliction. One of these methods, namely molecular dynamics (MD), has been used to characterize the function of the spike protein at the atomic level and unveil its structural features from a dynamic perspective. In this review, we focus on these main findings, including spike protein flexibility, rare S protein conformational changes, cryptic epitopes, the role of glycans, drug repurposing, and the effect of spike protein variants.
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Affiliation(s)
- Ludovico Pipitò
- Centre for Sport, Exercise and Life Sciences (CSELS)Faculty of Health and Life SciencesCoventry UniversityCoventryUK
| | - Roxana‐Maria Rujan
- Centre for Sport, Exercise and Life Sciences (CSELS)Faculty of Health and Life SciencesCoventry UniversityCoventryUK
| | - Christopher A. Reynolds
- Centre for Sport, Exercise and Life Sciences (CSELS)Faculty of Health and Life SciencesCoventry UniversityCoventryUK
| | - Giuseppe Deganutti
- Centre for Sport, Exercise and Life Sciences (CSELS)Faculty of Health and Life SciencesCoventry UniversityCoventryUK
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