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Shamabadi NS, Bagasra AB, Pawar S, Bagasra O. Potential use of endemic human coronaviruses to stimulate immunity against pathogenic SARS-CoV-2 and its variants. Libyan J Med 2023; 18:2209949. [PMID: 37186902 DOI: 10.1080/19932820.2023.2209949] [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: 05/17/2023] Open
Abstract
While severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes significant morbidity and mortality in humans, there is a wide range of disease outcomes following virus exposures. Some individuals are asymptomatic while others develop complications within a few days after infection that can lead to fatalities in a smaller portion of the population. In the present study, we have analyzed the factors that may influence the outcome of post-SARS-CoV-2 infection. One factor that may influence virus control is pre-existing immunity conferred by an individual's past exposures to endemic coronaviruses (eCOVIDs) which cause the common cold in humans and generally, most children are exposed to one of the four eCOVIDs before 2 years of age. Here, we have carried out protein sequence analyses to show the amino acid homologies between the four eCOVIDs (i.e. OC43, HKU1, 229E, and NL63) as well as examining the cross-reactive immune responses between SARS-CoV-2 and eCOVIDs by epidemiologic analyses. Our results show that the nations where continuous exposures to eCOVIDs are very high due to religious and traditional causes showed significantly lower cases and low mortality rates per 100,000. We hypothesize that in the areas of the globe where Muslims are in majority and due to religious practices are regularly exposed to eCOVIDs they show a significantly lower infection, as well as mortality rate, and that is due to pre-existing cross-immunity against SARS-CoV-2. This is due to cross-reactive antibodies and T-cells that recognize SARS-CoV-2 antigens. We also have reviewed the current literature that has also proposed that human infections with eCOVIDs impart protection against disease caused by subsequent exposure to SARS-CoV-2. We propose that a nasal spray vaccine consisting of selected genes of eCOVIDs would be beneficial against SARS-CoV-2 and other pathogenic coronaviruses.
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Affiliation(s)
| | - Anisah B Bagasra
- Department of Psychology, Kennesaw State University, Kennesaw, GA, USA
| | - Shrikant Pawar
- Department of Computer Science and Biology, Claflin University, SC, USA
| | - Omar Bagasra
- South Carolina Center for Biotechnology, Claflin University, Orangeburg, SC, USA
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2
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Khater I, Nassar A. Seeking antiviral drugs to inhibit SARS-CoV-2 RNA dependent RNA polymerase: A molecular docking analysis. PLoS One 2022; 17:e0268909. [PMID: 35639751 PMCID: PMC9154104 DOI: 10.1371/journal.pone.0268909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 05/10/2022] [Indexed: 11/26/2022] Open
Abstract
COVID-19 outbreak associated with the severe acute respiratory syndrome coronavirus (SARS-CoV-2) raised health concerns across the globe and has been considered highly transmissible between people. In attempts for finding therapeutic treatment for the new disease, this work has focused on examining the polymerase inhibitors against the SARS-CoV-2 nsp12 and co-factors nsp8 and nsp7. Several polymerase inhibitors were examined against PDB ID: 6M71 using computational analysis evaluating the ligand's binding affinity to replicating groove to the active site. The findings of this analysis showed Cytarabine of -5.65 Kcal/mol with the highest binding probability (70%) to replicating groove of 6M71. The complex stability was then examined over 19 ns molecular dynamics simulation suggesting that Cytarabine might be possible potent inhibitor for the SARS-CoV-2 RNA Dependent RNA Polymerase.
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Affiliation(s)
- Ibrahim Khater
- Biophysics Department, Faculty of Science, Cairo University, Giza, Egypt
| | - Aaya Nassar
- Biophysics Department, Faculty of Science, Cairo University, Giza, Egypt
- Department of Clinical Research and Leadership, School of Medicine and Health Sciences, George Washington University, Washington, DC, United States of America
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3
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Nassar A, Ibrahim IM, Amin FG, Magdy M, Elgharib AM, Azzam EB, Nasser F, Yousry K, Shamkh IM, Mahdy SM, Elfiky AA. A Review of Human Coronaviruses' Receptors: The Host-Cell Targets for the Crown Bearing Viruses. Molecules 2021; 26:6455. [PMID: 34770863 PMCID: PMC8587140 DOI: 10.3390/molecules26216455] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 10/20/2021] [Accepted: 10/22/2021] [Indexed: 12/19/2022] Open
Abstract
A novel human coronavirus prompted considerable worry at the end of the year 2019. Now, it represents a significant global health and economic burden. The newly emerged coronavirus disease caused by the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is the primary reason for the COVID-19 global pandemic. According to recent global figures, COVID-19 has caused approximately 243.3 million illnesses and 4.9 million deaths. Several human cell receptors are involved in the virus identification of the host cells and entering them. Hence, understanding how the virus binds to host-cell receptors is crucial for developing antiviral treatments and vaccines. The current work aimed to determine the multiple host-cell receptors that bind with SARS-CoV-2 and other human coronaviruses for the purpose of cell entry. Extensive research is needed using neutralizing antibodies, natural chemicals, and therapeutic peptides to target those host-cell receptors in extremely susceptible individuals. More research is needed to map SARS-CoV-2 cell entry pathways in order to identify potential viral inhibitors.
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Affiliation(s)
- Aaya Nassar
- Biophysics Department, Faculty of Science, Cairo University, Giza 12511, Egypt; (I.M.I.); (F.G.A.); (M.M.); (A.M.E.)
| | - Ibrahim M. Ibrahim
- Biophysics Department, Faculty of Science, Cairo University, Giza 12511, Egypt; (I.M.I.); (F.G.A.); (M.M.); (A.M.E.)
| | - Fatma G. Amin
- Biophysics Department, Faculty of Science, Cairo University, Giza 12511, Egypt; (I.M.I.); (F.G.A.); (M.M.); (A.M.E.)
- Physics Department, Faculty of Science, Alexandria University, Alexandria 21519, Egypt
| | - Merna Magdy
- Biophysics Department, Faculty of Science, Cairo University, Giza 12511, Egypt; (I.M.I.); (F.G.A.); (M.M.); (A.M.E.)
| | - Ahmed M. Elgharib
- Biophysics Department, Faculty of Science, Cairo University, Giza 12511, Egypt; (I.M.I.); (F.G.A.); (M.M.); (A.M.E.)
| | - Eman B. Azzam
- Physics Department, Medical Biophysics Division, Faculty of Science, Helwan University, Cairo 11511, Egypt;
| | - Filopateer Nasser
- Biochemistry Department, Faculty of Science, Cairo University, Giza 12511, Egypt;
| | - Kirllos Yousry
- Faculty of Medicine, Cairo University, Cairo 11511, Egypt;
| | | | - Samah M. Mahdy
- National Museum of Egyptian Civilization, Ain Elsira-Elfustat, Cairo 11511, Egypt;
| | - Abdo A. Elfiky
- Biophysics Department, Faculty of Science, Cairo University, Giza 12511, Egypt; (I.M.I.); (F.G.A.); (M.M.); (A.M.E.)
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4
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Vougogiannopoulou K, Corona A, Tramontano E, Alexis MN, Skaltsounis AL. Natural and Nature-Derived Products Targeting Human Coronaviruses. Molecules 2021; 26:448. [PMID: 33467029 PMCID: PMC7831024 DOI: 10.3390/molecules26020448] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 01/12/2021] [Accepted: 01/13/2021] [Indexed: 01/18/2023] Open
Abstract
The ongoing pandemic of severe acute respiratory syndrome (SARS), caused by the SARS-CoV-2 human coronavirus (HCoV), has brought the international scientific community before a state of emergency that needs to be addressed with intensive research for the discovery of pharmacological agents with antiviral activity. Potential antiviral natural products (NPs) have been discovered from plants of the global biodiversity, including extracts, compounds and categories of compounds with activity against several viruses of the respiratory tract such as HCoVs. However, the scarcity of natural products (NPs) and small-molecules (SMs) used as antiviral agents, especially for HCoVs, is notable. This is a review of 203 publications, which were selected using PubMed/MEDLINE, Web of Science, Scopus, and Google Scholar, evaluates the available literature since the discovery of the first human coronavirus in the 1960s; it summarizes important aspects of structure, function, and therapeutic targeting of HCoVs as well as NPs (19 total plant extracts and 204 isolated or semi-synthesized pure compounds) with anti-HCoV activity targeting viral and non-viral proteins, while focusing on the advances on the discovery of NPs with anti-SARS-CoV-2 activity, and providing a critical perspective.
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Affiliation(s)
- Konstantina Vougogiannopoulou
- Department of Pharmacognosy and Natural Products Chemistry, Faculty of Pharmacy, National and Kapodistrian University of Athens, Panepistimiopolis Zografou, 15771 Athens, Greece;
| | - Angela Corona
- Department of Life and Environmental Sciences, University of Cagliari, Biomedical Section, Laboratory of Molecular Virology, E block, Cittadella Universitaria di Monserrato, SS55409042 Monserrato, Italy; (A.C.); (E.T.)
| | - Enzo Tramontano
- Department of Life and Environmental Sciences, University of Cagliari, Biomedical Section, Laboratory of Molecular Virology, E block, Cittadella Universitaria di Monserrato, SS55409042 Monserrato, Italy; (A.C.); (E.T.)
| | - Michael N. Alexis
- Molecular Endocrinology Team, Inst of Chemical Biology, National Hellenic Research Foundation (NHRF), 48 Vassileos Constantinou Ave., 11635 Athens, Greece;
| | - Alexios-Leandros Skaltsounis
- Department of Pharmacognosy and Natural Products Chemistry, Faculty of Pharmacy, National and Kapodistrian University of Athens, Panepistimiopolis Zografou, 15771 Athens, Greece;
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Balgoma D, Gil-de-Gómez L, Montero O. Lipidomics Issues on Human Positive ssRNA Virus Infection: An Update. Metabolites 2020; 10:E356. [PMID: 32878290 PMCID: PMC7569815 DOI: 10.3390/metabo10090356] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 08/24/2020] [Accepted: 08/27/2020] [Indexed: 12/29/2022] Open
Abstract
The pathogenic mechanisms underlying the Biology and Biochemistry of viral infections are known to depend on the lipid metabolism of infected cells. From a lipidomics viewpoint, there are a variety of mechanisms involving virus infection that encompass virus entry, the disturbance of host cell lipid metabolism, and the role played by diverse lipids in regard to the infection effectiveness. All these aspects have currently been tackled separately as independent issues and focused on the function of proteins. Here, we review the role of cholesterol and other lipids in ssRNA+ infection.
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Affiliation(s)
- David Balgoma
- Analytical Pharmaceutical Chemistry, Department of Medicinal Chemistry, Uppsala University, Husarg. 3, 75123 Uppsala, Sweden;
| | - Luis Gil-de-Gómez
- Center of Childhood Cancer Center, Children’s Hospital of Philadelphia, Colket Translational Research Center, 3501 Civic Center Blvd, Philadelphia, PA 19104, USA;
| | - Olimpio Montero
- Spanish National Research Council (CSIC), Boecillo’s Technological Park Bureau, Av. Francisco Vallés 8, 47151 Boecillo, Spain
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Li Z, Tomlinson AC, Wong AH, Zhou D, Desforges M, Talbot PJ, Benlekbir S, Rubinstein JL, Rini JM. The human coronavirus HCoV-229E S-protein structure and receptor binding. eLife 2019; 8:51230. [PMID: 31650956 PMCID: PMC6970540 DOI: 10.7554/elife.51230] [Citation(s) in RCA: 127] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 10/12/2019] [Indexed: 12/12/2022] Open
Abstract
The coronavirus S-protein mediates receptor binding and fusion of the viral and host cell membranes. In HCoV-229E, its receptor binding domain (RBD) shows extensive sequence variation but how S-protein function is maintained is not understood. Reported are the X-ray crystal structures of Class III-V RBDs in complex with human aminopeptidase N (hAPN), as well as the electron cryomicroscopy structure of the 229E S-protein. The structures show that common core interactions define the specificity for hAPN and that the peripheral RBD sequence variation is accommodated by loop plasticity. The results provide insight into immune evasion and the cross-species transmission of 229E and related coronaviruses. We also find that the 229E S-protein can expose a portion of its helical core to solvent. This is undoubtedly facilitated by hydrophilic subunit interfaces that we show are conserved among coronaviruses. These interfaces likely play a role in the S-protein conformational changes associated with membrane fusion.
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Affiliation(s)
- Zhijie Li
- Department of Molecular Genetics, The University of Toronto, Toronto, Canada
| | | | - Alan Hm Wong
- Department of Biochemistry, The University of Toronto, Toronto, Canada
| | - Dongxia Zhou
- Department of Molecular Genetics, The University of Toronto, Toronto, Canada
| | - Marc Desforges
- Laboratory of Neuroimmunovirology, INRS-Institut Armand-Frappier, Institut National de la Recherche Scientifique, Université du Québec, Laval, Canada
| | - Pierre J Talbot
- Laboratory of Neuroimmunovirology, INRS-Institut Armand-Frappier, Institut National de la Recherche Scientifique, Université du Québec, Laval, Canada
| | - Samir Benlekbir
- Molecular Medicine Program, The Hospital for Sick Children Research Institute, Toronto, Canada
| | - John L Rubinstein
- Department of Biochemistry, The University of Toronto, Toronto, Canada.,Molecular Medicine Program, The Hospital for Sick Children Research Institute, Toronto, Canada.,Department of Medical Biophysics, The University of Toronto, Toronto, Canada
| | - James M Rini
- Department of Molecular Genetics, The University of Toronto, Toronto, Canada.,Department of Biochemistry, The University of Toronto, Toronto, Canada
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Yan L, Meng B, Xiang J, Wilson IA, Yang B. Crystal structure of the post-fusion core of the Human coronavirus 229E spike protein at 1.86 Å resolution. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2018; 74:841-851. [PMID: 30198895 PMCID: PMC6130466 DOI: 10.1107/s2059798318008318] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/07/2018] [Accepted: 06/05/2018] [Indexed: 01/12/2023]
Abstract
Human coronavirus 229E (HCoV‐229E) usually causes mild upper respiratory infections in heathy adults, but may lead to severe complications or mortality in individuals with weakened immune systems. Virus entry of HCoV‐229E is mediated by its spike (S) protein, where the S1 domain facilitates attachment to host cells and the S2 domain is involved in subsequent fusion of the virus and host membranes. During the fusion process, two heptad repeats, HR1 and HR2, in the S2 domain assemble into a six‐helix membrane‐fusion structure termed the fusion core. Here, the complete fusion‐core structure of HCoV‐229E has been determined at 1.86 Å resolution, representing the most complete post‐fusion conformation thus far among published human alphacoronavirus (α‐HCoV) fusion‐core structures. The overall structure of the HCoV‐229E fusion core is similar to those of SARS, MERS and HCoV‐NL63, but the packing of its 3HR1 core differs from those of SARS and MERS in that it contains more noncanonical `x' and `da' layers. Side‐by‐side electrostatic surface comparisons reveal that the electrostatic surface potentials are opposite in α‐HCoVs and β‐HCoVs at certain positions and that the HCoV‐229E surface also appears to be the most hydrophobic among the various HCoVs. In addition to the highly conserved hydrophobic interactions between HR1 and HR2, some polar and electrostatic interactions are also well preserved across different HCoVs. This study adds to the structural profiling of HCoVs to aid in the structure‐based design of pan‐coronavirus small molecules or peptides to inhibit viral fusion.
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Affiliation(s)
- Lei Yan
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 393 Middle Huaxia Road, Shanghai 201210, People's Republic of China
| | - Bing Meng
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 393 Middle Huaxia Road, Shanghai 201210, People's Republic of China
| | - Jiangchao Xiang
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 393 Middle Huaxia Road, Shanghai 201210, People's Republic of China
| | - Ian A Wilson
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 393 Middle Huaxia Road, Shanghai 201210, People's Republic of China
| | - Bei Yang
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 393 Middle Huaxia Road, Shanghai 201210, People's Republic of China
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