1
|
Guenthoer J, Garrett ME, Lilly M, Depierreux DM, Ruiz F, Chi M, Stoddard CI, Chohan V, Yaffe ZA, Sung K, Ralph D, Chu HY, Matsen FA, Overbaugh J. The S2 subunit of spike encodes diverse targets for functional antibody responses to SARS-CoV-2. PLoS Pathog 2024; 20:e1012383. [PMID: 39093891 PMCID: PMC11324185 DOI: 10.1371/journal.ppat.1012383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 08/14/2024] [Accepted: 07/01/2024] [Indexed: 08/04/2024] Open
Abstract
The SARS-CoV-2 virus responsible for the COVID-19 global pandemic has exhibited a striking capacity for viral evolution that drives continued evasion from vaccine and infection-induced immune responses. Mutations in the receptor binding domain of the S1 subunit of the spike glycoprotein have led to considerable escape from antibody responses, reducing the efficacy of vaccines and monoclonal antibody (mAb) therapies. Therefore, there is a need to interrogate more constrained regions of spike, such as the S2 subdomain. Here, we present a collection of S2 mAbs from two SARS-CoV-2 convalescent individuals that target multiple regions in S2, including regions outside of those commonly reported. One of the S2 mAbs, C20.119, which bound to a highly conserved epitope in the fusion peptide, was able to broadly neutralize across SARS-CoV-2 variants, SARS-CoV-1, and closely related zoonotic sarbecoviruses. The majority of the mAbs were non-neutralizing; however, many of them could mediate antibody-dependent cellular cytotoxicity (ADCC) at levels similar to the S1-targeting mAb S309 that was previously authorized for treatment of SARS-CoV-2 infections. Several of the mAbs with ADCC function also bound to spike trimers from other human coronaviruses (HCoVs), such as MERS-CoV and HCoV-HKU1. Our findings suggest S2 mAbs can target diverse epitopes in S2, including functional mAbs with HCoV and sarbecovirus breadth that likely target functionally constrained regions of spike. These mAbs could be developed for potential future pandemics, while also providing insight into ideal epitopes for eliciting a broad HCoV response.
Collapse
Affiliation(s)
- Jamie Guenthoer
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
| | - Meghan E. Garrett
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
| | - Michelle Lilly
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
| | - Delphine M. Depierreux
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
| | - Felicitas Ruiz
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
| | - Margaret Chi
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
| | - Caitlin I. Stoddard
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
| | - Vrasha Chohan
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
| | - Zak A. Yaffe
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
| | - Kevin Sung
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
| | - Duncan Ralph
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
| | - Helen Y. Chu
- Division of Allergy and Infectious Diseases, University of Washington, Seattle, Washington, United States of America
| | - Frederick A. Matsen
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
- Howard Hughes Medical Institute, Seattle, Washington, United States of America
| | - Julie Overbaugh
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, Washington, United States of America
| |
Collapse
|
2
|
Das R, Sinnarasan VSP, Paul D, Venkatesan A. A Machine Learning Approach to Identify Potential miRNA-Gene Regulatory Network Contributing to the Pathogenesis of SARS-CoV-2 Infection. Biochem Genet 2024; 62:987-1006. [PMID: 37515735 DOI: 10.1007/s10528-023-10458-x] [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: 01/04/2023] [Accepted: 07/14/2023] [Indexed: 07/31/2023]
Abstract
Worldwide, many lives have been lost in the recent outbreak of coronavirus disease. The pathogen responsible for this disease takes advantage of the host machinery to replicate itself and, in turn, causes pathogenesis in humans. Human miRNAs are seen to have a major role in the pathogenesis and progression of viral diseases. Hence, an in-silico approach has been used in this study to uncover the role of miRNAs and their target genes in coronavirus disease pathogenesis. This study attempts to perform the miRNA seq data analysis to identify the potential differentially expressed miRNAs. Considering only the experimentally proven interaction databases TarBase, miRTarBase, and miRecords, the target genes of the miRNAs have been identified from the mirNET analytics platform. The identified hub genes were subjected to gene ontology and pathway enrichment analysis using EnrichR. It is found that a total of 9 miRNAs are deregulated, out of which 2 were upregulated (hsa-mir-3614-5p and hsa-mir-3614-3p) and 7 were downregulated (hsa-mir-17-5p, hsa-mir-106a-5p, hsa-mir-17-3p, hsa-mir-181d-5p, hsa-mir-93-3p, hsa-mir-28-5p, and hsa-mir-100-5p). These miRNAs help us to classify the diseased and healthy control patients accurately. Moreover, it is also found that crucial target genes (UBC and UBB) of 4 signature miRNAs interact with viral replicase polyprotein 1ab of SARS-Coronavirus. As a result, it is noted that the virus hijacks key immune pathways like various cancer and virus infection pathways and molecular functions such as ubiquitin ligase binding and transcription corepressor and coregulator binding.
Collapse
Affiliation(s)
- Rajesh Das
- Department of Bioinformatics, Pondicherry University, RV Nagar, Kalapet, Puducherry, 605014, India
| | | | - Dahrii Paul
- Department of Bioinformatics, Pondicherry University, RV Nagar, Kalapet, Puducherry, 605014, India
| | - Amouda Venkatesan
- Department of Bioinformatics, Pondicherry University, RV Nagar, Kalapet, Puducherry, 605014, India.
| |
Collapse
|
3
|
Chiyyeadu A, Asgedom G, Bruhn M, Rocha C, Schlegel TU, Neumann T, Galla M, Vollmer Barbosa P, Hoffmann M, Ehrhardt K, Ha TC, Morgan M, Schoeder CT, Pöhlmann S, Kalinke U, Schambach A. A tetravalent bispecific antibody outperforms the combination of its parental antibodies and neutralizes diverse SARS-CoV-2 variants. Clin Immunol 2024; 260:109902. [PMID: 38218210 DOI: 10.1016/j.clim.2024.109902] [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: 10/11/2023] [Revised: 12/21/2023] [Accepted: 01/09/2024] [Indexed: 01/15/2024]
Abstract
The devastating impact of COVID-19 on global health shows the need to increase our pandemic preparedness. Recombinant therapeutic antibodies were successfully used to treat and protect at-risk patients from COVID-19. However, the currently circulating Omicron subvariants of SARS-CoV-2 are largely resistant to therapeutic antibodies, and novel approaches to generate broadly neutralizing antibodies are urgently needed. Here, we describe a tetravalent bispecific antibody, A7A9 TVB, which actively neutralized many SARS-CoV-2 variants of concern, including early Omicron subvariants. Interestingly, A7A9 TVB neutralized more variants at lower concentration as compared to the combination of its parental monoclonal antibodies, A7K and A9L. A7A9 also reduced the viral load of authentic Omicron BA.1 virus in infected pseudostratified primary human nasal epithelial cells. Overall, A7A9 displayed the characteristics of a potent broadly neutralizing antibody, which may be suitable for prophylactic and therapeutic applications in the clinics, thus highlighting the usefulness of an effective antibody-designing approach.
Collapse
Affiliation(s)
- Abhishek Chiyyeadu
- Institute of Experimental Hematology, Hannover Medical School, 30625 Hannover, Germany; REBIRTH Research Center for Translational Regenerative Medicine, Hannover Medical School, 30625 Hannover, Germany
| | - Girmay Asgedom
- Institute of Experimental Hematology, Hannover Medical School, 30625 Hannover, Germany
| | - Matthias Bruhn
- Institute for Experimental Infection Research, TWINCORE, Center for Experimental and Clinical Infection Research, a joint venture between the Helmholtz Centre for Infection Research and the Hannover Medical School, 30625 Hannover, Germany
| | - Cheila Rocha
- German Primate Center, Leibniz Institute for Primate Research, 37077 Göttingen, Germany; Faculty of Biology and Psychology, Georg-August-University Göttingen, 37073 Göttingen, Germany
| | - Tom U Schlegel
- Institute for Drug Discovery, Faculty of Medicine, Leipzig University, 04103 Leipzig, Germany
| | - Thomas Neumann
- Institute of Experimental Hematology, Hannover Medical School, 30625 Hannover, Germany
| | - Melanie Galla
- Institute of Experimental Hematology, Hannover Medical School, 30625 Hannover, Germany; REBIRTH Research Center for Translational Regenerative Medicine, Hannover Medical School, 30625 Hannover, Germany
| | - Philippe Vollmer Barbosa
- Institute of Experimental Hematology, Hannover Medical School, 30625 Hannover, Germany; REBIRTH Research Center for Translational Regenerative Medicine, Hannover Medical School, 30625 Hannover, Germany; Fraunhofer Institute for Toxicology and Experimental Medicine, Hannover Medical School, 30625 Hannover, Germany
| | - Markus Hoffmann
- German Primate Center, Leibniz Institute for Primate Research, 37077 Göttingen, Germany; Faculty of Biology and Psychology, Georg-August-University Göttingen, 37073 Göttingen, Germany
| | - Katrin Ehrhardt
- Institute of Experimental Hematology, Hannover Medical School, 30625 Hannover, Germany
| | - Teng-Cheong Ha
- Institute of Experimental Hematology, Hannover Medical School, 30625 Hannover, Germany; REBIRTH Research Center for Translational Regenerative Medicine, Hannover Medical School, 30625 Hannover, Germany
| | - Michael Morgan
- Institute of Experimental Hematology, Hannover Medical School, 30625 Hannover, Germany; REBIRTH Research Center for Translational Regenerative Medicine, Hannover Medical School, 30625 Hannover, Germany
| | - Clara T Schoeder
- Institute for Drug Discovery, Faculty of Medicine, Leipzig University, 04103 Leipzig, Germany
| | - Stefan Pöhlmann
- German Primate Center, Leibniz Institute for Primate Research, 37077 Göttingen, Germany; Faculty of Biology and Psychology, Georg-August-University Göttingen, 37073 Göttingen, Germany
| | - Ulrich Kalinke
- Institute for Experimental Infection Research, TWINCORE, Center for Experimental and Clinical Infection Research, a joint venture between the Helmholtz Centre for Infection Research and the Hannover Medical School, 30625 Hannover, Germany; Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, 30625 Hannover, Germany
| | - Axel Schambach
- Institute of Experimental Hematology, Hannover Medical School, 30625 Hannover, Germany; REBIRTH Research Center for Translational Regenerative Medicine, Hannover Medical School, 30625 Hannover, Germany; Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, United States of America.
| |
Collapse
|
4
|
He Q, Hu D, Zheng F, Chen W, Hu K, Liu J, Yao C, Li H, Wei Y. Investigating the Nexus of NLRP3 Inflammasomes and COVID-19 Pathogenesis: Unraveling Molecular Triggers and Therapeutic Strategies. Viruses 2024; 16:213. [PMID: 38399989 PMCID: PMC10892947 DOI: 10.3390/v16020213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 01/25/2024] [Accepted: 01/27/2024] [Indexed: 02/25/2024] Open
Abstract
The coronavirus disease 2019 (COVID-19) global pandemic, caused by severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2), has been marked by severe cases demonstrating a "cytokine storm", an upsurge of pro-inflammatory cytokines in the bloodstream. NLRP3 inflammasomes, integral to the innate immune system, are speculated to be activated by SARS-CoV-2 within host cells. This review investigates the potential correlation between NLRP3 inflammasomes and COVID-19, exploring the cellular and molecular mechanisms through which SARS-CoV-2 triggers their activation. Furthermore, promising strategies targeting NLRP3 inflammasomes are proposed to mitigate the excessive inflammatory response provoked by SARS-CoV-2 infection. By synthesizing existing studies, this paper offers insights into NLRP3 as a therapeutic target, elucidating the interplay between COVID-19 and its pathophysiology. It serves as a valuable reference for future clinical approaches in addressing COVID-19 by targeting NLRP3, thus providing potential avenues for therapeutic intervention.
Collapse
Affiliation(s)
- Qun He
- Sino-German Biomedical Center, National “111” Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei University of Technology, Wuhan 430068, China; (Q.H.); (F.Z.); (W.C.); (K.H.); (J.L.); (C.Y.); (H.L.)
| | - Da Hu
- Sinopharm Animal Health Corporation Ltd., Wuhan 430075, China;
| | - Fuqiang Zheng
- Sino-German Biomedical Center, National “111” Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei University of Technology, Wuhan 430068, China; (Q.H.); (F.Z.); (W.C.); (K.H.); (J.L.); (C.Y.); (H.L.)
| | - Wenxuan Chen
- Sino-German Biomedical Center, National “111” Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei University of Technology, Wuhan 430068, China; (Q.H.); (F.Z.); (W.C.); (K.H.); (J.L.); (C.Y.); (H.L.)
| | - Kanghong Hu
- Sino-German Biomedical Center, National “111” Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei University of Technology, Wuhan 430068, China; (Q.H.); (F.Z.); (W.C.); (K.H.); (J.L.); (C.Y.); (H.L.)
| | - Jinbiao Liu
- Sino-German Biomedical Center, National “111” Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei University of Technology, Wuhan 430068, China; (Q.H.); (F.Z.); (W.C.); (K.H.); (J.L.); (C.Y.); (H.L.)
| | - Chenguang Yao
- Sino-German Biomedical Center, National “111” Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei University of Technology, Wuhan 430068, China; (Q.H.); (F.Z.); (W.C.); (K.H.); (J.L.); (C.Y.); (H.L.)
| | - Hanluo Li
- Sino-German Biomedical Center, National “111” Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei University of Technology, Wuhan 430068, China; (Q.H.); (F.Z.); (W.C.); (K.H.); (J.L.); (C.Y.); (H.L.)
| | - Yanhong Wei
- Sino-German Biomedical Center, National “111” Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering (Ministry of Education), Hubei University of Technology, Wuhan 430068, China; (Q.H.); (F.Z.); (W.C.); (K.H.); (J.L.); (C.Y.); (H.L.)
| |
Collapse
|
5
|
Groß-Albenhausen E, Weier A, Velten M, Heider T, Chunder R, Kuerten S. Immune monitoring of SARS-CoV-2-specific T cell and B cell responses in patients with multiple sclerosis treated with ocrelizumab. Front Immunol 2023; 14:1254128. [PMID: 37841269 PMCID: PMC10569464 DOI: 10.3389/fimmu.2023.1254128] [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: 07/06/2023] [Accepted: 08/30/2023] [Indexed: 10/17/2023] Open
Abstract
Introduction Since the development of the coronavirus disease (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2), there has been significant interest in determining the effectiveness of SARS-CoV-2 vaccines in patients under immunomodulatory or immunosuppressive therapies. The aim of this study was to evaluate the impact of ocrelizumab, a monoclonal anti-CD20 antibody, on SARS-CoV-2-specific T cell and B cell responses in patients with relapsing-remitting multiple sclerosis (RRMS). Methods To this end, peripheral blood mononuclear cells (PBMCs) were isolated from n = 23 patients with RRMS. Of these patients, n = 17 were tested before (time point t0) and one month after (time point t1) their first dose of ocrelizumab. In addition, we studied n = 9 RRMS patients that got infected with SARS-CoV-2 over the course of ocrelizumab therapy (time point t2). PBMCs were also isolated from n = 19 age- and gender-matched healthy controls (HCs) after vaccination or infection with SARS-CoV-2, respectively. Interferon-γ (IFN-γ)/interleukin-2 (IL-2) and granzyme B (GzB)/perforin (PFN) double-color enzyme-linked immunospot (ELISPOT) assays or single-color ELISPOT assays were performed to measure SARS-CoV-2 antigen-specific T cell and B cell responses. Anti-viral antibody titers were quantified in the serum by chemiluminescence immunoassay. Results Our data indicate a significant difference in the SARS-CoV-2 specific IFN-γ (P = 0.0119) and PFN (P = 0.0005) secreting T cell compartment in the MS cohort at t0 compared to HCs. Following the first dose of ocrelizumab treatment, a significant decrease in the number of SARS-CoV-2 spike protein-specific B cells was observed (P = 0.0012). Infection with SARS-CoV-2 in MS patients under ocrelizumab therapy did not significantly alter their existing immune response against the virus. Kaplan-Meier survival analysis suggested that the spike S1 protein-specific immunoglobulin (Ig)G response might be a key parameter for predicting the probability of (re)infection with SARS-CoV-2. Discussion Our results call for a critical discussion regarding appropriate vaccination intervals and potential biomarkers for the prediction of (re)infection with SARS-CoV-2 in patients with MS receiving ocrelizumab. Unique identifier DRKS00029110; URL: http://apps.who.int/trialsearch/.
Collapse
Affiliation(s)
- Elina Groß-Albenhausen
- Institute of Neuroanatomy, Faculty of Medicine, University of Bonn and University Hospital Bonn, Bonn, Germany
| | - Alicia Weier
- Institute of Neuroanatomy, Faculty of Medicine, University of Bonn and University Hospital Bonn, Bonn, Germany
| | - Markus Velten
- Department of Anesthesiology and Intensive Care Medicine, University Medical Center Bonn, Bonn, Germany
| | - Thorsten Heider
- Clinic for Neurology, Klinikum St. Marien Amberg, Amberg, Germany
| | - Rittika Chunder
- Institute of Neuroanatomy, Faculty of Medicine, University of Bonn and University Hospital Bonn, Bonn, Germany
| | - Stefanie Kuerten
- Institute of Neuroanatomy, Faculty of Medicine, University of Bonn and University Hospital Bonn, Bonn, Germany
| |
Collapse
|
6
|
Bykova A, Saura A, Glazko GV, Roche-Lima A, Yurchenko V, Rogozin IB. The 29-nucleotide deletion in SARS-CoV: truncated versions of ORF8 are under purifying selection. BMC Genomics 2023; 24:387. [PMID: 37430204 DOI: 10.1186/s12864-023-09482-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 06/23/2023] [Indexed: 07/12/2023] Open
Abstract
BACKGROUND Accessory proteins have diverse roles in coronavirus pathobiology. One of them in SARS-CoV (the causative agent of the severe acute respiratory syndrome outbreak in 2002-2003) is encoded by the open reading frame 8 (ORF8). Among the most dramatic genomic changes observed in SARS-CoV isolated from patients during the peak of the pandemic in 2003 was the acquisition of a characteristic 29-nucleotide deletion in ORF8. This deletion cause splitting of ORF8 into two smaller ORFs, namely ORF8a and ORF8b. Functional consequences of this event are not entirely clear. RESULTS Here, we performed evolutionary analyses of ORF8a and ORF8b genes and documented that in both cases the frequency of synonymous mutations was greater than that of nonsynonymous ones. These results suggest that ORF8a and ORF8b are under purifying selection, thus proteins translated from these ORFs are likely to be functionally important. Comparisons with several other SARS-CoV genes revealed that another accessory gene, ORF7a, has a similar ratio of nonsynonymous to synonymous mutations suggesting that ORF8a, ORF8b, and ORF7a are under similar selection pressure. CONCLUSIONS Our results for SARS-CoV echo the known excess of deletions in the ORF7a-ORF7b-ORF8 complex of accessory genes in SARS-CoV-2. A high frequency of deletions in this gene complex might reflect recurrent searches in "functional space" of various accessory protein combinations that may eventually produce more advantageous configurations of accessory proteins similar to the fixed deletion in the SARS-CoV ORF8 gene.
Collapse
Affiliation(s)
- Anastassia Bykova
- Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava, 710 00, Czech Republic
| | - Andreu Saura
- Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava, 710 00, Czech Republic
| | - Galina V Glazko
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, USA
| | - Abiel Roche-Lima
- Center for Collaborative Research in Health Disparities-RCMI Program, Medical Sciences Campus, University of Puerto Rico, San Juan, PR, 00936, USA
| | - Vyacheslav Yurchenko
- Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava, 710 00, Czech Republic.
| | - Igor B Rogozin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, USA.
| |
Collapse
|
7
|
Popovic M, Martin JH, Head RJ. COVID infection in 4 steps: Thermodynamic considerations reveal how viral mucosal diffusion, target receptor affinity and furin cleavage act in concert to drive the nature and degree of infection in human COVID-19 disease. Heliyon 2023; 9:e17174. [PMID: 37325453 PMCID: PMC10259165 DOI: 10.1016/j.heliyon.2023.e17174] [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: 11/13/2022] [Revised: 06/04/2023] [Accepted: 06/09/2023] [Indexed: 06/17/2023] Open
Abstract
We have developed a mechanistic model of SARS-CoV-2 and SARS-CoV infection, exploring the relationship between the viral diffusion in the mucosa and viral affinity for the angiotensin converting enzyme 2 (ACE2) target. Utilising the structural similarity of SARS-CoV and SARS-CoV-2 and a shared viral target receptor (ACE2), but a dramatic difference in upper or lower respiratory tract infectivity, we were able to generate insights into the linkage of mucosal diffusion and target receptor affinity in determining the pathophysiological pathways of these two viruses. Our analysis reveals that for SARS-CoV-2 the higher affinity of ACE2 binding, the faster and more complete the mucosal diffusion in its transport from the upper airway to the region of the ACE2 target on the epithelium. This diffusional process is essential for the presentation of this virus to the furin catalysed highly efficient entry and infection process in the upper respiratory tract epithelial cells. A failure of SARS-CoV to follow this path is associated with lower respiratory tract infection and decreased infectivity. Thus, our analysis supports the view that through tropism SARS-CoV-2 has evolved a highly efficient membrane entry process that can act in concert with a high binding affinity of this virus and its variants for its ACE2 which in turn promotes enhanced movement of the virus from airway to epithelium. In this way ongoing mutations yielding higher affinities of SARS-CoV-2 for the ACE2 target becomes the basis for higher upper respiratory tract infectivity and greater viral spread. It is concluded that SARS-CoV-2 is constrained in the extent of its activities by the fundamental laws of physics and thermodynamics. Laws that describe diffusion and molecular binding. Moreover it can be speculated that the very earliest contact of this virus with the human mucosa defines the pathogenesis of this infection.
Collapse
Affiliation(s)
- Marko Popovic
- Institute of Chemistry, Technology and Metallurgy, University of Belgrade, Njegoševa 12, 11000 Belgrade, Serbia
| | - Jennifer H Martin
- Centre for Drug Repurposing and Medicines Research, University of Newcastle and Hunter Medical Research Institute, Newcastle 2305, Australia
| | - Richard J Head
- Drug Discovery and Development, Clinical and Health Sciences, University of South Australia, Adelaide, South Australia, Australia
| |
Collapse
|
8
|
Salarifar A, Khalili S, Rasaee MJ. Recombinant highly antigenic truncated fusion-based protein as a diagnostic antigen for anti-SARS-CoV-2 nucleocapsid antibody ELISA. Protein Expr Purif 2023; 203:106200. [PMID: 36379348 PMCID: PMC9653556 DOI: 10.1016/j.pep.2022.106200] [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: 08/01/2022] [Revised: 11/07/2022] [Accepted: 11/08/2022] [Indexed: 11/14/2022]
Abstract
Among the main structural protein of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), nucleocapsid phosphoprotein (NP) exhibits high immunogenicity and is the most abundant viral protein produced and shed during infection. Detection of antibodies against NP may help assess the number of individuals exposed to SARS-COV-2 or vaccinated against it. Based on these findings and other structural and antigenic evaluations, we designed a recombinant truncated fusion NP-based protein for application in an immunoassay for detecting immunoglobulins in patients who have recovered from COVID-19. In this research, we aligned the NPs from SARS-CoV and SARS-CoV-2 and selected highly antigenic parts of the SARS-CoV-2 sequences based on in-silico studies. The protein was expressed under optimum conditions in the bacterial host BL21 and purified by nickel immobilized metal affinity chromatography. Moreover, the purity level was assessed by SDS-PAGE and Western blotting whereas the folding of the protein was evaluated by circular dichroism. Ultimately, we used the purified recombinant protein in ELISA development in which 42 samples from convalescent patients were compared with 20 samples of the past 2019 patients who had attended laboratories for various clinical check-ups. The sensitivity and specificity were determined as 71% and 90%, respectively, in the optimum cut-off point measured by the receiver operating characteristic curve.
Collapse
Affiliation(s)
- Abbasali Salarifar
- Department of Clinical Biochemistry, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Saeed Khalili
- Department of Biology Sciences, Shahid Rajaee Teacher Training University, Tehran, Iran
| | - Mohammad Javad Rasaee
- Department of Clinical Biochemistry, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran.
| |
Collapse
|
9
|
Navish AA, Uthayakumar R. A comparative study on structural proteins of viruses that belong to the identical family. THE EUROPEAN PHYSICAL JOURNAL. SPECIAL TOPICS 2023; 232:1-10. [PMID: 36846473 PMCID: PMC9936937 DOI: 10.1140/epjs/s11734-023-00791-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 01/25/2023] [Indexed: 06/18/2023]
Abstract
Recent studies have focused on the similarity between SARS Cov-2 and various viruses from the Coronaviridae family (such as MERS Cov, SARS Cov and Bat Cov RaTG13) to uncover the mystery of SARS Cov-2. Specifically, some studies identified that the SARS Cov-2 is closely related to Bat Cov RaTG13 (a SARS-related coronavirus found in bats) rather than the other viruses in that family. These studies are mainly focusing on the biological techniques to show the similarity between the SARS Cov-2 and other viruses. Examining proteins is not easy for common researchers unless for biologists. To rectify this flaw, we have to convert the protein to one of the known formats, which are easy to understand. Consequently, this study uses viral structural proteins to analyse the relationship between SARS Cov-2 and the rest of the coronavirus with the help of mathematical and statistical parameters and explores the various graph representations of MERS Cov, SARS Cov, Bat Cov RaTG13 and SARS Cov-2 structural proteins, such as zig-zag curve, Protein Contact Map ( PCM ) and Chaos Game Representation ( CGR ). Though these graph interpretations are visually similar, a slight variation between the graphs reflects their structural and functional differences. Thus, we use an elegant parameter known as the fractal dimension to observe their minor changes. According to the nature of the graph, we employ different types of fractal dimensions, namely mass dimension and box dimension. Furthermore, we perform the similarity tests with normalized cross-correlation and cosine similarity to assess the comparability of the PCM and CGR graphs. The acquired C C n values are near the sequence identity between SARS Cov-2 and MERS Cov, SARS Cov, Bat Cov RaTG13.
Collapse
Affiliation(s)
- A. A. Navish
- Department of Mathematics, The Gandhigram Rural Institute-Deemed to be University, Gandhigram, Dindigul, 624 302 Tamil Nadu India
| | - R. Uthayakumar
- Department of Mathematics, The Gandhigram Rural Institute-Deemed to be University, Gandhigram, Dindigul, 624 302 Tamil Nadu India
| |
Collapse
|
10
|
Deletions across the SARS-CoV-2 Genome: Molecular Mechanisms and Putative Functional Consequences of Deletions in Accessory Genes. Microorganisms 2023; 11:microorganisms11010229. [PMID: 36677521 PMCID: PMC9862619 DOI: 10.3390/microorganisms11010229] [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: 12/21/2022] [Revised: 01/13/2023] [Accepted: 01/13/2023] [Indexed: 01/18/2023] Open
Abstract
The analysis of deletions may reveal evolutionary trends and provide new insight into the surprising variability and rapidly spreading capability that SARS-CoV-2 has shown since its emergence. To understand the factors governing genomic stability, it is important to define the molecular mechanisms of deletions in the viral genome. In this work, we performed a statistical analysis of deletions. Specifically, we analyzed correlations between deletions in the SARS-CoV-2 genome and repetitive elements and documented a significant association of deletions with runs of identical (poly-) nucleotides and direct repeats. Our analyses of deletions in the accessory genes of SARS-CoV-2 suggested that there may be a hypervariability in ORF7A and ORF8 that is not associated with repetitive elements. Such recurrent search in a "sequence space" of accessory genes (that might be driven by natural selection) did not yet cause increased viability of the SARS-CoV-2 variants. However, deletions in the accessory genes may ultimately produce new variants that are more successful compared to the viral strains with the conventional architecture of the SARS-CoV-2 accessory genes.
Collapse
|
11
|
Impaired VEGF-A-Mediated Neurovascular Crosstalk Induced by SARS-CoV-2 Spike Protein: A Potential Hypothesis Explaining Long COVID-19 Symptoms and COVID-19 Vaccine Side Effects? Microorganisms 2022; 10:microorganisms10122452. [PMID: 36557705 PMCID: PMC9784975 DOI: 10.3390/microorganisms10122452] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 12/03/2022] [Accepted: 12/10/2022] [Indexed: 12/14/2022] Open
Abstract
Long coronavirus disease-19 (COVID-19) is a newly discovered syndrome characterized by multiple organ manifestations that persist for weeks to months, following the recovery from acute disease. Occasionally, neurological and cardiovascular side effects mimicking long COVID-19 have been reported in recipients of COVID-19 vaccines. Hypothetically, the clinical similarity could be due to a shared pathogenic role of the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) spike (S) protein produced by the virus or used for immunization. The S protein can bind to neuropilin (NRP)-1, which normally functions as a coreceptor for the vascular endothelial growth factor (VEGF)-A. By antagonizing the docking of VEGF-A to NRP-1, the S protein could disrupt physiological pathways involved in angiogenesis and nociception. One consequence could be the increase in unbound forms of VEGF-A that could bind to other receptors. SARS-CoV-2-infected individuals may exhibit increased plasma levels of VEGF-A during both acute illness and convalescence, which could be responsible for diffuse microvascular and neurological damage. A few studies suggest that serum VEGF-A may also be a potential biomarker for long COVID-19, whereas evidence for COVID-19 vaccines is lacking and merits further investigation.
Collapse
|
12
|
Lin C, Wang W, Li M, Lin Y, Yang Z, Urbina AN, Assavalapsakul W, Thitithanyanont A, Chen K, Kuo C, Lin Y, Hsiao H, Lin K, Lin S, Chen Y, Yu M, Su L, Wang S. Boosting the detection performance of severe acute respiratory syndrome coronavirus 2 test through a sensitive optical biosensor with new superior antibody. Bioeng Transl Med 2022; 8:e10410. [PMID: 36248235 PMCID: PMC9538096 DOI: 10.1002/btm2.10410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 08/29/2022] [Accepted: 08/30/2022] [Indexed: 11/15/2022] Open
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus emerged in late 2019 leading to the COVID-19 disease pandemic that triggered socioeconomic turmoil worldwide. A precise, prompt, and affordable diagnostic assay is essential for the detection of SARS-CoV-2 as well as its variants. Antibody against SARS-CoV-2 spike (S) protein was reported as a suitable strategy for therapy and diagnosis of COVID-19. We, therefore, developed a quick and precise phase-sensitive surface plasmon resonance (PS-SPR) biosensor integrated with a novel generated anti-S monoclonal antibody (S-mAb). Our results indicated that the newly generated S-mAb could detect the original SARS-CoV-2 strain along with its variants. In addition, a SARS-CoV-2 pseudovirus, which could be processed in BSL-2 facility was generated for evaluation of sensitivity and specificity of the assays including PS-SPR, homemade target-captured ELISA, spike rapid antigen test (SRAT), and quantitative reverse transcription polymerase chain reaction (qRT-PCR). Experimentally, PS-SPR exerted high sensitivity to detect SARS-CoV-2 pseudovirus at 589 copies/ml, with 7-fold and 70-fold increase in sensitivity when compared with the two conventional immunoassays, including homemade target-captured ELISA (4 × 103 copies/ml) and SRAT (4 × 104 copies/ml), using the identical antibody. Moreover, the PS-SPR was applied in the measurement of mimic clinical samples containing the SARS-CoV-2 pseudovirus mixed with nasal mucosa. The detection limit of PS-SPR is calculated to be 1725 copies/ml, which has higher accuracy than homemade target-captured ELISA (4 × 104 copies/ml) and SRAT (4 × 105 copies/ml) and is comparable with qRT-PCR (1250 copies/ml). Finally, the ability of PS-SPR to detect SARS-CoV-2 in real clinical specimens was further demonstrated, and the assay time was less than 10 min. Taken together, our results indicate that this novel S-mAb integrated into PS-SPR biosensor demonstrates high sensitivity and is time-saving in SARS-CoV-2 virus detection. This study suggests that incorporation of a high specific recognizer in SPR biosensor is an alternative strategy that could be applied in developing other emerging or re-emerging pathogenic detection platforms.
Collapse
Affiliation(s)
- Chih‐Yen Lin
- Department of Medical Laboratory Science and BiotechnologyKaohsiung Medical UniversityKaohsiungTaiwan
- Center for Tropical Medicine and Infectious Disease ResearchKaohsiung Medical UniversityKaohsiungTaiwan
| | - Wen‐Hung Wang
- Center for Tropical Medicine and Infectious Disease ResearchKaohsiung Medical UniversityKaohsiungTaiwan
- School of Medicine, College of MedicineNational Sun Yat‐Sen UniversityKaohsiungTaiwan
- Division of Infection Disease, Department of Internal MedicineKaohsiung Medical University HospitalKaohsiungTaiwan
| | - Meng‐Chi Li
- Thin Film Technology CenterNational Central UniversityTaoyuanTaiwan
- Optical Sciences CenterNational Central UniversityTaoyuanTaiwan
| | - Yu‐Ting Lin
- Department of Medical Laboratory Science and BiotechnologyKaohsiung Medical UniversityKaohsiungTaiwan
- Center for Tropical Medicine and Infectious Disease ResearchKaohsiung Medical UniversityKaohsiungTaiwan
| | - Zih‐Syuan Yang
- Department of Medical Laboratory Science and BiotechnologyKaohsiung Medical UniversityKaohsiungTaiwan
- Center for Tropical Medicine and Infectious Disease ResearchKaohsiung Medical UniversityKaohsiungTaiwan
| | - Aspiro Nayim Urbina
- Center for Tropical Medicine and Infectious Disease ResearchKaohsiung Medical UniversityKaohsiungTaiwan
| | | | | | - Kai‐Ren Chen
- Department of Optics and PhotonicsNational Central UniversityTaoyuanTaiwan
| | - Chien‐Cheng Kuo
- Thin Film Technology CenterNational Central UniversityTaoyuanTaiwan
- Department of Optics and PhotonicsNational Central UniversityTaoyuanTaiwan
| | | | - Hui‐Hua Hsiao
- Division of Hematology and Oncology, Department of Internal MedicineKaohsiung Medical University HospitalKaohsiungTaiwan
| | - Kun‐Der Lin
- Division of Endocrinology and MetabolismKaohsiung Medical University Hospital, Kaohsiung Medical UniversityKaohsiungTaiwan
| | - Shang‐Yi Lin
- Division of Infection Disease, Department of Internal MedicineKaohsiung Medical University HospitalKaohsiungTaiwan
- Department of Laboratory MedicineKaohsiung Medical University HospitalKaohsiungTaiwan
| | - Yen‐Hsu Chen
- Center for Tropical Medicine and Infectious Disease ResearchKaohsiung Medical UniversityKaohsiungTaiwan
- School of Medicine, College of MedicineNational Sun Yat‐Sen UniversityKaohsiungTaiwan
- Division of Infection Disease, Department of Internal MedicineKaohsiung Medical University HospitalKaohsiungTaiwan
| | - Ming‐Lung Yu
- School of Medicine, College of MedicineNational Sun Yat‐Sen UniversityKaohsiungTaiwan
- Hepatobiliary Section, Department of Internal Medicine, and Hepatitis CenterKaohsiung Medical University HospitalKaohsiungTaiwan
| | - Li‐Chen Su
- General Education CenterMing Chi University of TechnologyNew Taipei CityTaiwan
- Organic Electronics Research CenterMing Chi University of TechnologyNew Taipei CityTaiwan
| | - Sheng‐Fan Wang
- Department of Medical Laboratory Science and BiotechnologyKaohsiung Medical UniversityKaohsiungTaiwan
- Center for Tropical Medicine and Infectious Disease ResearchKaohsiung Medical UniversityKaohsiungTaiwan
- Department of Medical ResearchKaohsiung Medical University HospitalKaohsiungTaiwan
| |
Collapse
|
13
|
Manan A, Pirzada RH, Haseeb M, Choi S. Toll-like Receptor Mediation in SARS-CoV-2: A Therapeutic Approach. Int J Mol Sci 2022; 23:10716. [PMID: 36142620 PMCID: PMC9502216 DOI: 10.3390/ijms231810716] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Revised: 09/10/2022] [Accepted: 09/10/2022] [Indexed: 01/18/2023] Open
Abstract
The innate immune system facilitates defense mechanisms against pathogen invasion and cell damage. Toll-like receptors (TLRs) assist in the activation of the innate immune system by binding to pathogenic ligands. This leads to the generation of intracellular signaling cascades including the biosynthesis of molecular mediators. TLRs on cell membranes are adept at recognizing viral components. Viruses can modulate the innate immune response with the help of proteins and RNAs that downregulate or upregulate the expression of various TLRs. In the case of COVID-19, molecular modulators such as type 1 interferons interfere with signaling pathways in the host cells, leading to an inflammatory response. Coronaviruses are responsible for an enhanced immune signature of inflammatory chemokines and cytokines. TLRs have been employed as therapeutic agents in viral infections as numerous antiviral Food and Drug Administration-approved drugs are TLR agonists. This review highlights the therapeutic approaches associated with SARS-CoV-2 and the TLRs involved in COVID-19 infection.
Collapse
Affiliation(s)
- Abdul Manan
- Department of Molecular Science and Technology, Ajou University, Suwon 16499, Korea
| | | | - Muhammad Haseeb
- Department of Molecular Science and Technology, Ajou University, Suwon 16499, Korea
- S&K Therapeutics, Ajou University Campus Plaza 418, 199 Worldcup-ro, Yeongtong-gu, Suwon 16502, Korea
| | - Sangdun Choi
- Department of Molecular Science and Technology, Ajou University, Suwon 16499, Korea
- S&K Therapeutics, Ajou University Campus Plaza 418, 199 Worldcup-ro, Yeongtong-gu, Suwon 16502, Korea
| |
Collapse
|
14
|
Shim JE, Kim YJ, Choe JH, Lee TG, You EA. Single-Nanoparticle-Based Digital SERS Sensing Platform for the Accurate Quantitative Detection of SARS-CoV-2. ACS APPLIED MATERIALS & INTERFACES 2022; 14:38459-38470. [PMID: 35951983 PMCID: PMC9396967 DOI: 10.1021/acsami.2c07497] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 08/01/2022] [Indexed: 06/15/2023]
Abstract
To prevent the ongoing spread of the highly infectious severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), accurate and early detection based on a rapid, ultrasensitive, and highly reliable sensing method is crucially important. Here, we present a bumpy core-shell surface-enhanced Raman spectroscopy (SERS) nanoprobe-based sensing platform with single-nanoparticle (SNP)-based digital SERS analysis. The tailorable bumpy core-shell SERS nanoprobe with an internal self-assembled monolayer of 4-nitrobenzenethiol Raman reporters, synthesized using HEPES biological buffer, generates a strong, uniform, and reproducible SERS signal with an SNP-level sensitive and narrowly distributed enhancement factor (2.1 × 108 to 2.2 × 109). We also propose an SNP-based digital SERS analysis method that provides direct visualization of SNP detection at ultralow concentrations and reliable quantification over a wide range of concentrations. The bumpy core-shell SERS nanoprobe-based sensing platform with SNP-based digital SERS analysis achieves the ultrasensitive and quantitative detection of the SARS-CoV-2 spike protein with a limit of detection of 7.1 × 10-16 M over a wide dynamic range from 3.7 × 10-15 to 3.7 × 10-8 M, far outperforming the conventional enzyme-linked immunosorbent assay method for the target protein. Furthermore, it can detect mutated spike proteins from the SARS-CoV-2 variants, representing the key mutations of Alpha, Beta, Gamma, Delta, and Omicron variants. Therefore, this sensing platform can be effectively and efficiently used for the accurate and early detection of SARS-CoV-2 and be adapted for the ultrasensitive and reliable detection of other highly infectious diseases.
Collapse
Affiliation(s)
- Jae-Eul Shim
- Nanobiosensor
Team, Korea Research Institute of Standards
and Science, Daejeon 34113, Republic of Korea
| | - Young Jun Kim
- Nanobiosensor
Team, Korea Research Institute of Standards
and Science, Daejeon 34113, Republic of Korea
| | - Jong-Ho Choe
- Department
of Physics, Korea University, Seoul 02841, Republic of Korea
| | - Tae Geol Lee
- Nanobiosensor
Team, Korea Research Institute of Standards
and Science, Daejeon 34113, Republic of Korea
| | - Eun-Ah You
- Nanobiosensor
Team, Korea Research Institute of Standards
and Science, Daejeon 34113, Republic of Korea
| |
Collapse
|
15
|
Consecutive deletions in a unique Uruguayan SARS-CoV-2 lineage evidence the genetic variability potential of accessory genes. PLoS One 2022; 17:e0263563. [PMID: 35176063 PMCID: PMC8853529 DOI: 10.1371/journal.pone.0263563] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 01/24/2022] [Indexed: 11/19/2022] Open
Abstract
Deletions frequently occur in the six accessory genes of SARS-CoV-2, but most genomes with deletions are sporadic and have limited spreading capability. Here, we analyze deletions in the ORF7a of the N.7 lineage, a unique Uruguayan clade from the Brazilian B.1.1.33 lineage. Thirteen samples collected during the early SARS-CoV-2 wave in Uruguay had deletions in the ORF7a. Complete genomes were obtained by Illumina next-generation sequencing, and deletions were confirmed by Sanger sequencing and capillary electrophoresis. The N.7 lineage includes several individuals with a 12-nucleotide deletion that removes four amino acids of the ORF7a. Notably, four individuals underwent an additional 68-nucleotide novel deletion that locates 44 nucleotides downstream in the terminal region of the same ORF7a. The simultaneous occurrence of the 12 and 68-nucleotide deletions fuses the ORF7a and ORF7b, two contiguous accessory genes that encode transmembrane proteins with immune-modulation activity. The fused ORF retains the signal peptide and the complete Ig-like fold of the 7a protein and the transmembrane domain of the 7b protein, suggesting that the fused protein plays similar functions to original proteins in a single format. Our findings evidence the remarkable dynamics of SARS-CoV-2 and the possibility that single and consecutive deletions occur in accessory genes and promote changes in the genomic organization that help the virus explore genetic variations and select for new, higher fit changes.
Collapse
|
16
|
Toft-Bertelsen TL, Jeppesen MG, Tzortzini E, Xue K, Giller K, Becker S, Mujezinovic A, Bentzen BH, B Andreas L, Kolocouris A, Kledal TN, Rosenkilde MM. Amantadine has potential for the treatment of COVID-19 because it inhibits known and novel ion channels encoded by SARS-CoV-2. Commun Biol 2021; 4:1347. [PMID: 34853399 PMCID: PMC8636635 DOI: 10.1038/s42003-021-02866-9] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 11/02/2021] [Indexed: 12/16/2022] Open
Abstract
The dire need for COVID-19 treatments has inspired strategies of repurposing approved drugs. Amantadine has been suggested as a candidate, and cellular as well as clinical studies have indicated beneficial effects of this drug. We demonstrate that amantadine and hexamethylene-amiloride (HMA), but not rimantadine, block the ion channel activity of Protein E from SARS-CoV-2, a conserved viroporin among coronaviruses. These findings agree with their binding to Protein E as evaluated by solution NMR and molecular dynamics simulations. Moreover, we identify two novel viroporins of SARS-CoV-2; ORF7b and ORF10, by showing ion channel activity in a X. laevis oocyte expression system. Notably, amantadine also blocks the ion channel activity of ORF10, thereby providing two ion channel targets in SARS-CoV-2 for amantadine treatment in COVID-19 patients. A screen of known viroporin inhibitors on Protein E, ORF7b, ORF10 and Protein 3a from SARS-CoV-2 revealed inhibition of Protein E and ORF7b by emodin and xanthene, the latter also blocking Protein 3a. This illustrates a general potential of well-known ion channel blockers against SARS-CoV-2 and specifically a dual molecular basis for the promising effects of amantadine in COVID-19 treatment. We therefore propose amantadine as a novel, cheap, readily available and effective way to treat COVID-19.
Collapse
Affiliation(s)
- Trine Lisberg Toft-Bertelsen
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Neuroscience, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Mads Gravers Jeppesen
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Synklino ApS, Charlottenlund, Denmark
| | - Eva Tzortzini
- Laboratory of Medicinal Chemistry, Section of Pharmaceutical Chemistry, Department of Pharmacy, National and Kapodistrian University of Athens, Panepistimioupolis-Zografou, Athens, Greece
| | - Kai Xue
- Department of NMR-based structural biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Karin Giller
- Department of NMR-based structural biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Stefan Becker
- Department of NMR-based structural biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Amer Mujezinovic
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Bo Hjorth Bentzen
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Loren B Andreas
- Department of NMR-based structural biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Antonios Kolocouris
- Laboratory of Medicinal Chemistry, Section of Pharmaceutical Chemistry, Department of Pharmacy, National and Kapodistrian University of Athens, Panepistimioupolis-Zografou, Athens, Greece
| | | | - Mette Marie Rosenkilde
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.
| |
Collapse
|