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Shum MHH, Lee Y, Tam L, Xia H, Chung OLW, Guo Z, Lam TTY. Binding affinity between coronavirus spike protein and human ACE2 receptor. Comput Struct Biotechnol J 2024; 23:759-770. [PMID: 38304547 PMCID: PMC10831124 DOI: 10.1016/j.csbj.2024.01.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 01/14/2024] [Accepted: 01/15/2024] [Indexed: 02/03/2024] Open
Abstract
Coronaviruses (CoVs) pose a major risk to global public health due to their ability to infect diverse animal species and potential for emergence in humans. The CoV spike protein mediates viral entry into the cell and plays a crucial role in determining the binding affinity to host cell receptors. With particular emphasis on α- and β-coronaviruses that infect humans and domestic animals, current research on CoV receptor use suggests that the exploitation of the angiotensin-converting enzyme 2 (ACE2) receptor poses a significant threat for viral emergence with pandemic potential. This review summarizes the approaches used to study binding interactions between CoV spike proteins and the human ACE2 (hACE2) receptor. Solid-phase enzyme immunoassays and cell binding assays allow qualitative assessment of binding but lack quantitative evaluation of affinity. Surface plasmon resonance, Bio-layer interferometry, and Microscale Thermophoresis on the other hand, provide accurate affinity measurement through equilibrium dissociation constants (KD). In silico modeling predicts affinity through binding structure modeling, protein-protein docking simulations, and binding energy calculations but reveals inconsistent results due to the lack of a standardized approach. Machine learning and deep learning models utilize simulated and experimental protein-protein interaction data to elucidate the critical residues associated with CoV binding affinity to hACE2. Further optimization and standardization of existing approaches for studying binding affinity could aid pandemic preparedness. Specifically, prioritizing surveillance of CoVs that can bind to human receptors stands to mitigate the risk of zoonotic spillover.
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Affiliation(s)
- Marcus Ho-Hin Shum
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong, China
- School of Public Health, The University of Hong Kong, Hong Kong, China
- Laboratory of Data Discovery for Health (D24H), Hong Kong Science Park, Hong Kong, China
| | - Yang Lee
- School of Public Health, The University of Hong Kong, Hong Kong, China
- Centre for Immunology and Infection (C2i), Hong Kong Science Park, Hong Kong, China
| | - Leighton Tam
- School of Public Health, The University of Hong Kong, Hong Kong, China
- Laboratory of Data Discovery for Health (D24H), Hong Kong Science Park, Hong Kong, China
| | - Hui Xia
- Department of Chemistry, South University of Science and Technology of China, China
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Oscar Lung-Wa Chung
- Department of Chemistry, South University of Science and Technology of China, China
| | - Zhihong Guo
- Department of Chemistry, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Tommy Tsan-Yuk Lam
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong, China
- School of Public Health, The University of Hong Kong, Hong Kong, China
- Laboratory of Data Discovery for Health (D24H), Hong Kong Science Park, Hong Kong, China
- Centre for Immunology and Infection (C2i), Hong Kong Science Park, Hong Kong, China
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2
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Jiang Y, Cheng X, Gao M, Yu Y, Dou X, Shen H, Tang M, Zhou S, Peng D. Two mutations on S2 subunit were critical for Vero cell tropism expansion of infectious bronchitis virus HV80. Vet Microbiol 2024; 294:110134. [PMID: 38820725 DOI: 10.1016/j.vetmic.2024.110134] [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: 03/05/2024] [Revised: 05/23/2024] [Accepted: 05/27/2024] [Indexed: 06/02/2024]
Abstract
Infectious bronchitis virus (IBV) restricts cell tropism. Except for the Beaudette strain, other IBVs cannot infect mammalian cell lines. The limited cell tropism of other IBVs has hindered IBV vaccine development and research on the mechanisms of IBV infection. A novel Vero cell-adapted strain, HV80, has been previously reported. In this study, we constructed recombinants expressing the chimeric S glycoprotein, S1 or S2 subunit of strain H120 and demonstrated that mutations on S2 subunit are associated with the strain HV80 Vero cell adaptation. R687P or P687R substitution recombinants were constructed with the genome backbone of strains HV80 or H120. We found that the RRRR690/S motif at the S2' cleavage site is crucial to the Vero cell adaptation of strain HV80. Another six amino acid substitutions in the S2 subunit of the recombinants showed that the Q855H mutation induced syncytium formation. A transient transfection assay demonstrated the S glycoprotein with the PRRR690/S motif at the S2' cleavage site induced low-level cell-cell fusion, while H855Q substitution hindered cell-cell fusion and blocked cleavage event with S20 product. This study provides a basis for the construction of IBV recombinants capable of replicating in Vero cells, thus contributing to the advancement in the development of genetically engineered cell-based IBV vaccines.
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Affiliation(s)
- Yi Jiang
- College of Veterinary Medicine, Yangzhou University, 225009, China; Jiangsu Institute of Poultry Sciences, Yangzhou 225125, China
| | - Xu Cheng
- Jiangsu Institute of Poultry Sciences, Yangzhou 225125, China
| | - Mingyan Gao
- Jiangsu Institute of Poultry Sciences, Yangzhou 225125, China
| | - Yan Yu
- Jiangsu Institute of Poultry Sciences, Yangzhou 225125, China
| | - Xinhong Dou
- Jiangsu Institute of Poultry Sciences, Yangzhou 225125, China; Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
| | - Haiyu Shen
- Jiangsu Institute of Poultry Sciences, Yangzhou 225125, China; Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
| | - Mengjun Tang
- Jiangsu Institute of Poultry Sciences, Yangzhou 225125, China
| | - Sheng Zhou
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao 266109, China.
| | - Daxin Peng
- College of Veterinary Medicine, Yangzhou University, 225009, China; Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China.
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3
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Feinstein P. Rapid Degradation of the Human ACE2 Receptor Upon Binding and Internalization of SARS-Cov-2-Spike-RBD Protein. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.07.583884. [PMID: 38496410 PMCID: PMC10942428 DOI: 10.1101/2024.03.07.583884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
It is widely accepted that the SARS-CoV-2 betacoronavirus infects humans through binding the human Angiotensin Receptor 2 (ACE2) that lines the nasal cavity and lungs, followed by import into a cell utilizing the Transmembrane Protease, Serine 2 (TMPRSS2) cofactor. ACE2 binding is mediated by an approximately 200-residue portion of the SARS-CoV-2 extracellular spike protein, the receptor binding domain (RBD). Robust interactions are shown using a novel cell-based assay between an RBD membrane tethered-GFP fusion protein and the membrane bound ACE2-Cherry fusion protein. Several observations were not predicted including, quick and sustained interactions leading to internalization of RBD fusion protein into the ACE2 cells and rapid downregulation of the ACE2-Cherry fluorescence. Targeted mutation in the RBD disulfide Loop 4 led to a loss of internalization for several variants tested. However, a secreted RBD did not cause ACE2 downregulation of ACE2-Cherry fluorescence. Thus, the membrane associated form of RBD found on the viral coat may have long-term system wide consequences on ACE2 expressing cells.
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Affiliation(s)
- Paul Feinstein
- Department of Biological Sciences, Hunter College, City University of New York, New York, NY 10065
- The Graduate Center Programs in Biochemistry, Biology and CUNY Neuroscience Collaborative, 365 5th Ave, New York, NY 10016
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4
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Feinstein P. Coronavirus Spike-RBD Variants Differentially Bind to the Human ACE2 Receptor. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.07.583944. [PMID: 38496407 PMCID: PMC10942415 DOI: 10.1101/2024.03.07.583944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
The SARS-CoV-2 betacoronavirus infects people through binding the human Angiotensin Receptor 2 (ACE2), followed by import into a cell utilizing the Transmembrane Protease, Serine 2 (TMPRSS2) and Furin cofactors. Analysis of the SARS-CoV-2 extracellular spike protein has suggested critical amino acids necessary for binding within a 197-residue portion, the receptor binding domain (RBD). A cell-based assay between a membrane tethered RBD-GFP fusion protein and the membrane bound ACE2-Cherry fusion protein allowed for mutational intersection of both RBD and ACE2 proteins. Data shows Omicron BA.1 and BA.2 variants have altered dependency on the amino terminus of ACE2 protein and suggests multiple epitopes on both proteins stabilize their interactions at the Nt and internal region of ACE2. In contrast, the H-CoV-NL63 RBD is only dependent on the ACE2 internal region for binding. A peptide inhibitor approach to this internal region thus far have failed to block binding of RBDs to ACE2, suggesting that several binding regions on ACE2 are sufficient to allow functional interactions. In sum, the RBD binding surface of ACE2 appears relatively fluid and amenable to bind a range of novel variants.
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Affiliation(s)
- Paul Feinstein
- Department of Biological Sciences, Hunter College, City University of New York, New York, NY 10065
- The Graduate Center Programs in Biochemistry, Biology and CUNY Neuroscience Collaborative, 365 5th Ave, New York, NY 10016
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5
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Hasani-Sadrabadi MM, Majedi FS, Zarubova J, Thauland TJ, Arumugaswami V, Hsiai TK, Bouchard LS, Butte MJ, Li S. Harnessing Biomaterials to Amplify Immunity in Aged Mice through T Memory Stem Cells. ACS NANO 2024; 18:6908-6926. [PMID: 38381620 DOI: 10.1021/acsnano.3c08559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/23/2024]
Abstract
The durability of a protective immune response generated by a vaccine depends on its ability to induce long-term T cell immunity, which tends to decline in aging populations. The longest protection appears to arise from T memory stem cells (TMSCs) that confer high expandability and effector functions when challenged. Here we engineered artificial antigen presenting cells (aAPC) with optimized size, stiffness and activation signals to induce human and mouse CD8+ TMSCs in vitro. This platform was optimized as a vaccine booster of TMSCs (Vax-T) with prolonged release of small-molecule blockade of the glycogen synthase kinase-3β together with target antigens. By using SARS-CoV-2 antigen as a model, we show that a single injection of Vax-T induces durable antigen-specific CD8+ TMSCs in young and aged mice, and generates humoral responses at a level stronger than or similar to soluble vaccines. This Vax-T approach can boost long-term immunity to fight infectious diseases, cancer, and other diseases.
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Affiliation(s)
| | - Fatemeh S Majedi
- Department of Bioengineering, University of California Los Angeles; Los Angeles, California 90095 United States
| | - Jana Zarubova
- Department of Bioengineering, University of California Los Angeles; Los Angeles, California 90095 United States
| | - Timothy J Thauland
- Department of Pediatrics, Division of Immunology, Allergy, and Rheumatology, University of California Los Angeles, Los Angeles, California 90095 United States
| | - Vaithilingaraja Arumugaswami
- Jonsson Comprehensive Cancer Center, University of California Los Angeles; Los Angeles, California 90095 United States
- Department of Molecular and Medical Pharmacology, University of California Los Angeles; Los Angeles, California 90095 United States
| | - Tzung K Hsiai
- Department of Bioengineering, University of California Los Angeles; Los Angeles, California 90095 United States
| | - Louis-S Bouchard
- Department of Bioengineering, University of California Los Angeles; Los Angeles, California 90095 United States
- Jonsson Comprehensive Cancer Center, University of California Los Angeles; Los Angeles, California 90095 United States
- Department of Chemistry and Biochemistry, University of California Los Angeles; Los Angeles, California 90095 United States
- The Molecular Biology Institute, University of California Los Angeles; Los Angeles, California 90095 United States
| | - Manish J Butte
- Department of Pediatrics, Division of Immunology, Allergy, and Rheumatology, University of California Los Angeles, Los Angeles, California 90095 United States
- Jonsson Comprehensive Cancer Center, University of California Los Angeles; Los Angeles, California 90095 United States
- Department of Microbiology, Immunology, and Molecular Genetics, University of California Los Angeles; Los Angeles, California 90095 United States
| | - Song Li
- Department of Bioengineering, University of California Los Angeles; Los Angeles, California 90095 United States
- Jonsson Comprehensive Cancer Center, University of California Los Angeles; Los Angeles, California 90095 United States
- Department of Medicine, David Geffen School of Medicine, University of California Los Angeles; Los Angeles, California 90095 United States
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California Los Angeles; Los Angeles, California 90095 United States
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6
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Huang L, Zhao F, He M, Fang Y, Ma X, Lu S, Li E, Xiao H, Zhu H, Wang X, Tang S, Yu B, Wang J, Zhao D, Wang C, Li H, Gao Y, Peng X, Shen H. An inoculation site-retained mRNA vaccine induces robust immune responses against SARS-CoV-2 variants. J Control Release 2024; 366:479-493. [PMID: 38184234 DOI: 10.1016/j.jconrel.2024.01.002] [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: 07/30/2023] [Revised: 12/20/2023] [Accepted: 01/01/2024] [Indexed: 01/08/2024]
Abstract
mRNA-based vaccines and therapeutic agents hold great promise in prevention and treatment of human diseases, yet high percentage of systemic adverse effect in clinic remains a big safety concern. One major potential cause is a high level of leakage of the locally inoculated mRNA vaccine nanoparticles into circulation. We have screened and optimized a core-shell structured lipopolyplex (LPP) formulation for mRNA with a tissue-retention property. Upon intramuscular inoculation, the mRNA-encapsulated LPP nanoparticles were preferentially taken up by the phagocytic antigen-presentation cells, and potently promoted dendritic cell maturation. We applied the new formulation to prepare a prophylactic vaccine for SARS-CoV-2, and observed potent humoral and cellular immune responses from the vaccine in both murine models and non-human primates. More importantly, the vaccine demonstrated a benign safety profile in non-human primates, with limited side effects after repeated treatment with high dosages of LPP/mRNA. Taken together, the inoculation site-retained vaccine formulation serves as a promising vehicle for mRNA vaccines and therapeutic agents.
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Affiliation(s)
- Lei Huang
- Stemirna Therapeutics, Shanghai 201206, China; Department of Material Science, Fudan University, Shanghai 200433, China
| | - Fanfan Zhao
- Stemirna Therapeutics, Shanghai 201206, China
| | - Muye He
- Stemirna Therapeutics, Shanghai 201206, China
| | - Yi Fang
- Stemirna Therapeutics, Shanghai 201206, China
| | - Xiaoping Ma
- Stemirna Therapeutics, Shanghai 201206, China
| | - Shuaiyao Lu
- Institute of Medical Biology, Chinese Academy of Medicine Sciences & Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research and Development on Severe Infectious Diseases, Kunming 650118, China
| | - Entao Li
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun 130122, China
| | - Hui Xiao
- Stemirna Therapeutics, Shanghai 201206, China
| | - Hanfei Zhu
- Stemirna Therapeutics, Shanghai 201206, China
| | - Xueli Wang
- Stemirna Therapeutics, Shanghai 201206, China
| | - Siyuan Tang
- Stemirna Therapeutics, Shanghai 201206, China
| | - Bo Yu
- Stemirna Therapeutics, Shanghai 201206, China
| | - Jie Wang
- Stemirna Therapeutics, Shanghai 201206, China
| | - Dong Zhao
- Department of Material Science, Fudan University, Shanghai 200433, China
| | - Chao Wang
- Department of Material Science, Fudan University, Shanghai 200433, China
| | - Hangwen Li
- Stemirna Therapeutics, Shanghai 201206, China.
| | - Yuwei Gao
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun 130122, China.
| | - Xiaozhong Peng
- Institute of Medical Biology, Chinese Academy of Medicine Sciences & Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research and Development on Severe Infectious Diseases, Kunming 650118, China.
| | - Haifa Shen
- Stemirna Therapeutics, Shanghai 201206, China.
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7
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Dénes B, Fuller RN, Kelin W, Levin TR, Gil J, Harewood A, Lőrincz M, Wall NR, Firek AF, Langridge WHR. A CTB-SARS-CoV-2-ACE-2 RBD Mucosal Vaccine Protects Against Coronavirus Infection. Vaccines (Basel) 2023; 11:1865. [PMID: 38140268 PMCID: PMC10747655 DOI: 10.3390/vaccines11121865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 12/08/2023] [Accepted: 12/15/2023] [Indexed: 12/24/2023] Open
Abstract
Mucosal vaccines protect against respiratory virus infection by stimulating the production of IgA antibodies that protect against virus invasion of the mucosal epithelium. In this study, a novel protein subunit mucosal vaccine was constructed for protection against infection by the beta coronavirus SARS-CoV-2. The vaccine was assembled by linking a gene encoding the SARS-CoV-2 virus S1 angiotensin converting enzyme receptor binding domain (ACE-2-RBD) downstream from a DNA fragment encoding the cholera toxin B subunit (CTB), a mucosal adjuvant known to stimulate vaccine immunogenicity. A 42 kDa vaccine fusion protein was identified in homogenates of transformed E. coli BL-21 cells by acrylamide gel electrophoresis and by immunoblotting against anti-CTB and anti-ACE-2-RBD primary antibodies. The chimeric CTB-SARS-CoV-2-ACE-2-RBD vaccine fusion protein was partially purified from clarified bacterial homogenates by nickel affinity column chromatography. Further vaccine purification was accomplished by polyacrylamide gel electrophoresis and electro-elution of the 42 kDa chimeric vaccine protein. Vaccine protection against SARS-CoV-2 infection was assessed by oral, nasal, and parenteral immunization of BALB/c mice with the CTB-SARS-CoV-2-ACE-2-RBD protein. Vaccine-induced SARS-CoV-2 specific antibodies were quantified in immunized mouse serum by ELISA analysis. Serum from immunized mice contained IgG and IgA antibodies that neutralized SARS-CoV-2 infection in Vero E6 cell cultures. In contrast to unimmunized mice, cytological examination of cell necrosis in lung tissues excised from immunized mice revealed no detectable cellular abnormalities. Mouse behavior following vaccine immunization remained normal throughout the duration of the experiments. Together, our data show that a CTB-adjuvant-stimulated CTB-SARS-CoV-2-ACE-2-RBD chimeric mucosal vaccine protein synthesized in bacteria can produce durable and persistent IgA antibodies in mice that neutralize the SARS-CoV-2 subvariant Omicron BA.1.1.
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Affiliation(s)
- Béla Dénes
- Center for Health Disparities and Molecular Medicine, Loma Linda University School of Medicine, Mortensen Hall, Loma Linda, CA 92350, USA; (B.D.); (R.N.F.); (W.K.); (T.R.L.); (J.G.); (A.H.); (N.R.W.); (A.F.F.)
- Department of Microbiology and Infectious Diseases, University of Veterinary Medicine Budapest, 1143 Budapest, Hungary;
- National Laboratory of Infectious Animal Diseases, Antimicrobial Resistance, Veterinary Public Health and Food Chain Safety, University of Veterinary Medicine Budapest, 1078 Budapest, Hungary
| | - Ryan N. Fuller
- Center for Health Disparities and Molecular Medicine, Loma Linda University School of Medicine, Mortensen Hall, Loma Linda, CA 92350, USA; (B.D.); (R.N.F.); (W.K.); (T.R.L.); (J.G.); (A.H.); (N.R.W.); (A.F.F.)
| | - Wayne Kelin
- Center for Health Disparities and Molecular Medicine, Loma Linda University School of Medicine, Mortensen Hall, Loma Linda, CA 92350, USA; (B.D.); (R.N.F.); (W.K.); (T.R.L.); (J.G.); (A.H.); (N.R.W.); (A.F.F.)
| | - Tessa R. Levin
- Center for Health Disparities and Molecular Medicine, Loma Linda University School of Medicine, Mortensen Hall, Loma Linda, CA 92350, USA; (B.D.); (R.N.F.); (W.K.); (T.R.L.); (J.G.); (A.H.); (N.R.W.); (A.F.F.)
| | - Jaipuneet Gil
- Center for Health Disparities and Molecular Medicine, Loma Linda University School of Medicine, Mortensen Hall, Loma Linda, CA 92350, USA; (B.D.); (R.N.F.); (W.K.); (T.R.L.); (J.G.); (A.H.); (N.R.W.); (A.F.F.)
| | - Aaren Harewood
- Center for Health Disparities and Molecular Medicine, Loma Linda University School of Medicine, Mortensen Hall, Loma Linda, CA 92350, USA; (B.D.); (R.N.F.); (W.K.); (T.R.L.); (J.G.); (A.H.); (N.R.W.); (A.F.F.)
- Department of Basic Sciences, Oakwood University, Huntsville, AL 35896, USA
| | - Márta Lőrincz
- Department of Microbiology and Infectious Diseases, University of Veterinary Medicine Budapest, 1143 Budapest, Hungary;
- National Laboratory of Infectious Animal Diseases, Antimicrobial Resistance, Veterinary Public Health and Food Chain Safety, University of Veterinary Medicine Budapest, 1078 Budapest, Hungary
| | - Nathan R. Wall
- Center for Health Disparities and Molecular Medicine, Loma Linda University School of Medicine, Mortensen Hall, Loma Linda, CA 92350, USA; (B.D.); (R.N.F.); (W.K.); (T.R.L.); (J.G.); (A.H.); (N.R.W.); (A.F.F.)
- Division of Biochemistry, Department of Basic Sciences, Loma Linda University School of Medicine, Loma Linda, CA 92350, USA
| | - Anthony F. Firek
- Center for Health Disparities and Molecular Medicine, Loma Linda University School of Medicine, Mortensen Hall, Loma Linda, CA 92350, USA; (B.D.); (R.N.F.); (W.K.); (T.R.L.); (J.G.); (A.H.); (N.R.W.); (A.F.F.)
- Comparative Effectiveness and Clinical Outcomes Research Center (CECORC), Riverside University Health System Medical Center, Moreno Valley, CA 92555, USA
| | - William H. R. Langridge
- Center for Health Disparities and Molecular Medicine, Loma Linda University School of Medicine, Mortensen Hall, Loma Linda, CA 92350, USA; (B.D.); (R.N.F.); (W.K.); (T.R.L.); (J.G.); (A.H.); (N.R.W.); (A.F.F.)
- Division of Biochemistry, Department of Basic Sciences, Loma Linda University School of Medicine, Loma Linda, CA 92350, USA
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Desai PJ. Expression and fusogenic activity of SARS CoV-2 Spike protein displayed in the HSV-1 Virion. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.28.568860. [PMID: 38076893 PMCID: PMC10705244 DOI: 10.1101/2023.11.28.568860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Severe acute respiratory syndrome coronavirus (SARS-CoV) is a zoonotic pathogen that can cause severe respiratory disease in humans. The new SARS-CoV-2 is the cause of the current global pandemic termed coronavirus disease 2019 (COVID-19) that has resulted in many millions of deaths world-wide. The virus is a member of the Betacoronavirus family, its genome is a positive strand RNA molecule that encodes for many genes which are required for virus genome replication as well as for structural proteins that are required for virion assembly and maturation. A key determinant of this virus is the Spike (S) protein embedded in the virion membrane and mediates attachment of the virus to the receptor (ACE2). This protein also is required for cell-cell fusion (syncytia) that is an important pathogenic determinant. We have developed a pseudotyped herpes simplex virus type 1 (HSV-1) recombinant virus expressing S protein in the virion envelop. This virus has also been modified to express a Venus fluorescent protein fusion to VP16, a virion protein of HSV-1. The virus expressing Spike can enter cells and generates large multi-nucleated syncytia which are evident by the Venus fluorescence. The HSV-1 recombinant virus is genetically stable and virus amplification can be easily done by infecting cells. This recombinant virus provides a reproducible platform for Spike function analysis and thus adds to the repertoire of pseudotyped viruses expressing Spike.
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Affiliation(s)
- Prashant J. Desai
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
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9
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Nguyen H, Nguyen HL, Lan PD, Thai NQ, Sikora M, Li MS. Interaction of SARS-CoV-2 with host cells and antibodies: experiment and simulation. Chem Soc Rev 2023; 52:6497-6553. [PMID: 37650302 DOI: 10.1039/d1cs01170g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of the devastating global COVID-19 pandemic announced by WHO in March 2020. Through unprecedented scientific effort, several vaccines, drugs and antibodies have been developed, saving millions of lives, but the fight against COVID-19 continues as immune escape variants of concern such as Delta and Omicron emerge. To develop more effective treatments and to elucidate the side effects caused by vaccines and therapeutic agents, a deeper understanding of the molecular interactions of SARS-CoV-2 with them and human cells is required. With special interest in computational approaches, we will focus on the structure of SARS-CoV-2 and the interaction of its spike protein with human angiotensin-converting enzyme-2 (ACE2) as a prime entry point of the virus into host cells. In addition, other possible viral receptors will be considered. The fusion of viral and human membranes and the interaction of the spike protein with antibodies and nanobodies will be discussed, as well as the effect of SARS-CoV-2 on protein synthesis in host cells.
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Affiliation(s)
- Hung Nguyen
- Institute of Physics, Polish Academy of Sciences, al. Lotnikow 32/46, 02-668 Warsaw, Poland.
| | - Hoang Linh Nguyen
- Institute of Fundamental and Applied Sciences, Duy Tan University, Ho Chi Minh City 700000, Vietnam
- Faculty of Environmental and Natural Sciences, Duy Tan University, Da Nang 550000, Vietnam
| | - Pham Dang Lan
- Life Science Lab, Institute for Computational Science and Technology, Quang Trung Software City, Tan Chanh Hiep Ward, District 12, 729110 Ho Chi Minh City, Vietnam
- Faculty of Physics and Engineering Physics, VNUHCM-University of Science, 227, Nguyen Van Cu Street, District 5, 749000 Ho Chi Minh City, Vietnam
| | - Nguyen Quoc Thai
- Dong Thap University, 783 Pham Huu Lau Street, Ward 6, Cao Lanh City, Dong Thap, Vietnam
| | - Mateusz Sikora
- Malopolska Centre of Biotechnology, Jagiellonian University, Kraków, Poland
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | - Mai Suan Li
- Institute of Physics, Polish Academy of Sciences, al. Lotnikow 32/46, 02-668 Warsaw, Poland.
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10
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Renzi F, Seamann A, Ganguly K, Pandey K, Byrareddy SN, Batra S, Kumar S, Ghersi D. Engineering an ACE2-Derived Fragment as a Decoy for Novel SARS-CoV-2 Virus. ACS Pharmacol Transl Sci 2023; 6:857-867. [PMID: 37325447 PMCID: PMC10262318 DOI: 10.1021/acsptsci.2c00180] [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: 09/05/2022] [Indexed: 06/17/2023]
Abstract
Entry inhibitors are an important resource in the response against emerging pathogens like the novel SARS-CoV-2, which enters human cells via interaction between the surface spike glycoprotein and the cellular membrane receptor angiotensin-converting enzyme 2 (ACE2). Using a combination of comparative structural analyses of the binding surface of the spike to ACE2, docking experiments, and molecular dynamics simulations, we identified a stable fragment of ACE2 that binds to the spike, is soluble, and is not predicted to bind to its physiological ligand angiotensin II. From this fragment we computationally designed and experimentally validated a smaller, stable peptide that disrupts ACE2-spike interaction at nanomolar concentrations, suggesting its potential use as a decoy that could interfere with viral binding by competition.
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Affiliation(s)
- Fabiana Renzi
- Department
of Physics, Università di Roma ”La
Sapienza”, 00185 Rome, Italy
| | - Austin Seamann
- School
of Interdisciplinary Informatics, University
of Nebraska at Omaha, Omaha, Nebraska 68182, USA
| | - Koelina Ganguly
- Department
of Biochemistry & Molecular Biology, University of Nebraska Medical Center, Omaha, Nebraska 68182, USA
| | - Kabita Pandey
- Department
of Pharmacology & Experimental Neuroscience, University of Nebraska Medical Center, Omaha, Nebraska 68182, USA
| | - Siddappa N. Byrareddy
- Department
of Biochemistry & Molecular Biology, University of Nebraska Medical Center, Omaha, Nebraska 68182, USA
- Department
of Pharmacology & Experimental Neuroscience, University of Nebraska Medical Center, Omaha, Nebraska 68182, USA
| | - Surinder Batra
- Department
of Biochemistry & Molecular Biology, University of Nebraska Medical Center, Omaha, Nebraska 68182, USA
| | - Sushil Kumar
- Department
of Biochemistry & Molecular Biology, University of Nebraska Medical Center, Omaha, Nebraska 68182, USA
| | - Dario Ghersi
- School
of Interdisciplinary Informatics, University
of Nebraska at Omaha, Omaha, Nebraska 68182, USA
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11
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Srivastava S, Singh S, Mishra AC, Lohia P, Dwivedi DK. Numerical Study of Titanium Dioxide and MXene Nanomaterial-Based Surface Plasmon Resonance Biosensor for Virus SARS-CoV-2 Detection. PLASMONICS (NORWELL, MASS.) 2023; 18:1-12. [PMID: 37360047 PMCID: PMC10171911 DOI: 10.1007/s11468-023-01874-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 04/28/2023] [Indexed: 06/28/2023]
Abstract
A novel surface plasmon resonance-based biosensor for SARS-CoV-2 virus is proposed in this article. The biosensor is a Kretschmann configuration-based structure that consists of CaF2 prism as base, at which silver (Ag), TiO2, and MXene nanolayers are used to enhance the performance. Theoretically, the performance parameters have been investigated by means of Fresnel equations and transfer matrix method (TMM). The TiO2 nanolayer not only prevents oxidation of Ag layer but also enhances the evanescent field in its vicinity. The sensor provides an ultrahigh angular sensitivity of 346°/RIU for the detection of SARS-CoV-2 virus. Some other performance parameters, including FWHM (full width at half maxima), detection accuracy (DA), limit of detection (LOD), and quality factor (QF) have also been calculated for proposed SPR biosensor with their optimized values 2.907°, 0.3439 deg-1, 1.445 × 10-5, and 118.99 RIU-1, respectively. The obtained results designate that the proposed surface plasmon resonance (SPR) based biosensor has notably enhanced angular sensitivity as compared to previous results reported in the literatures till date. This work may facilitate a significant biological sample sensing device for fast and accurate diagnosis at early stage of SARS-CoV-2 virus.
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Affiliation(s)
- Swati Srivastava
- Photonics and Photovoltaic Research Lab, Department of Physics and Material Science, Madan Mohan Malaviya University of Technology, Gorakhpur, 273010 India
| | - Sachin Singh
- Photonics and Photovoltaic Research Lab, Department of Physics and Material Science, Madan Mohan Malaviya University of Technology, Gorakhpur, 273010 India
| | - Adarsh Chandra Mishra
- Photonics and Photovoltaic Research Lab, Department of Physics and Material Science, Madan Mohan Malaviya University of Technology, Gorakhpur, 273010 India
| | - Pooja Lohia
- Department of Electronics and Communication Engineering, Madan Mohan Malaviya University of Technology, Gorakhpur, 273010 India
| | - D. K. Dwivedi
- Photonics and Photovoltaic Research Lab, Department of Physics and Material Science, Madan Mohan Malaviya University of Technology, Gorakhpur, 273010 India
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12
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Taya SA, Daher MG, Almawgani AHM, Hindi AT, Zyoud SH, Colak I. Detection of Virus SARS-CoV-2 Using a Surface Plasmon Resonance Device Based on BiFeO 3-Graphene Layers. PLASMONICS (NORWELL, MASS.) 2023; 18:1-8. [PMID: 37360049 PMCID: PMC10170057 DOI: 10.1007/s11468-023-01867-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Accepted: 04/24/2023] [Indexed: 06/28/2023]
Abstract
Coronavirus disease (COVID-19) pandemic outbreak is being investigated by severe respirational syndrome coronavirus-2 (SARS-CoV-2) as a global health issue. It is crucial to propose sensitive and rapid coronavirus detectors. Herein, we propose a biosensor based on surface plasmon resonance (SPRE) for the detection of SARS-CoV-2 virus. To achieve improved sensitivity, a BiFeO3 layer is inserted between a metal (Ag) thin film and a graphene layer in the proposed SPRE device so that it has the structure BK7 prism/ Ag/ BiFeO3/ graphene/ analyte. It has been demonstrated that a small variation in the refractive index of the analyte can cause a considerable shift in the resonance angle caused by the remarkable dielectric properties of the BiFeO3 layer, which include a high index of refraction and low loss. The proposed device has shown an extremely high sensitivity of 293 deg/RIU by optimizing the thicknesses of Ag, BiFeO3, and the number of graphene sheets. The proposed SPRE-based sensor is encouraging for use in various sectors of biosensing because of its high sensitivity.
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Affiliation(s)
- Sofyan A. Taya
- Physics Department, Islamic University of Gaza, P.O. Box 108, Gaza, Palestine
| | - Malek G. Daher
- Physics Department, Islamic University of Gaza, P.O. Box 108, Gaza, Palestine
| | - Abdulkarem H. M. Almawgani
- Electrical Engineering Department, College of Engineering, Najran University, Najran, Kingdom of Saudi Arabia
| | - Ayman Taher Hindi
- Electrical Engineering Department, College of Engineering, Najran University, Najran, Kingdom of Saudi Arabia
| | - Samer H. Zyoud
- Department of Mathematics and Sciences, Ajman University, Ajman, United Arab Emirates
| | - Ilhami Colak
- Department of Electrical and Electronics Engineering, Nisantasi University, Istanbul, Turkey
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13
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Castillo G, Mora-Díaz JC, Breuer M, Singh P, Nelli RK, Giménez-Lirola LG. Molecular mechanisms of human coronavirus NL63 infection and replication. Virus Res 2023; 327:199078. [PMID: 36813239 PMCID: PMC9944649 DOI: 10.1016/j.virusres.2023.199078] [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: 12/20/2022] [Revised: 02/16/2023] [Accepted: 02/17/2023] [Indexed: 02/24/2023]
Abstract
Human coronavirus NL63 (HCoV-NL63) is spread globally, causing upper and lower respiratory tract infections mainly in young children. HCoV-NL63 shares a host receptor (ACE2) with severe acute respiratory syndrome coronavirus (SARS-CoV) and SARS-CoV-2 but, unlike them, HCoV-NL63 primarily develops into self-limiting mild to moderate respiratory disease. Although with different efficiency, both HCoV-NL63 and SARS-like CoVs infect ciliated respiratory cells using ACE2 as receptor for binding and cell entry. Working with SARS-like CoVs require access to BSL-3 facilities, while HCoV-NL63 research can be performed at BSL-2 laboratories. Thus, HCoV-NL63 could be used as a safer surrogate for comparative studies on receptor dynamics, infectivity and virus replication, disease mechanism, and potential therapeutic interventions against SARS-like CoVs. This prompted us to review the current knowledge on the infection mechanism and replication of HCoV-NL63. Specifically, after a brief overview on the taxonomy, genomic organization and virus structure, this review compiles the current HCoV-NL63-related research in virus entry and replication mechanism, including virus attachment, endocytosis, genome translation, and replication and transcription. Furthermore, we reviewed cumulative knowledge on the susceptibility of different cells to HCoV-NL63 infection in vitro, which is essential for successful virus isolation and propagation, and contribute to address different scientific questions from basic science to the development and assessment of diagnostic tools, and antiviral therapies. Finally, we discussed different antiviral strategies that have been explored to suppress replication of HCoV-NL63, and other related human coronaviruses, by either targeting the virus or enhancing host antiviral mechanisms.
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Affiliation(s)
- Gino Castillo
- Department of Veterinary Diagnostic and Production Animal Medicine, Veterinary Diagnostic Laboratory, College of Veterinary Medicine, Iowa State University, 1850 Christensen Drive, Ames, IA 50011, USA
| | - Juan Carlos Mora-Díaz
- Department of Veterinary Diagnostic and Production Animal Medicine, Veterinary Diagnostic Laboratory, College of Veterinary Medicine, Iowa State University, 1850 Christensen Drive, Ames, IA 50011, USA
| | - Mary Breuer
- Department of Veterinary Diagnostic and Production Animal Medicine, Veterinary Diagnostic Laboratory, College of Veterinary Medicine, Iowa State University, 1850 Christensen Drive, Ames, IA 50011, USA
| | - Pallavi Singh
- Department of Biological Sciences, Northern Illinois University, DeKalb, IL 60115, USA
| | - Rahul K Nelli
- Department of Veterinary Diagnostic and Production Animal Medicine, Veterinary Diagnostic Laboratory, College of Veterinary Medicine, Iowa State University, 1850 Christensen Drive, Ames, IA 50011, USA
| | - Luis G Giménez-Lirola
- Department of Veterinary Diagnostic and Production Animal Medicine, Veterinary Diagnostic Laboratory, College of Veterinary Medicine, Iowa State University, 1850 Christensen Drive, Ames, IA 50011, USA.
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14
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Akib TBA, Mostufa S, Rana MM, Hossain MB, Islam MR. A performance comparison of heterostructure surface plasmon resonance biosensor for the diagnosis of novel coronavirus SARS-CoV-2. OPTICAL AND QUANTUM ELECTRONICS 2023; 55:448. [PMID: 37008732 PMCID: PMC10039361 DOI: 10.1007/s11082-023-04700-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 02/18/2023] [Indexed: 06/19/2023]
Abstract
This paper presents a performance comparison of heterostructure surface plasmon resonance (SPR) biosensors for the application of Novel Coronavirus SARS-CoV-2 diagnosis. The comparison is performed and compared with the existing literature based on the performance parameters in terms of several prisms such as BaF2, BK7, CaF2, CsF, SF6, and SiO2, several adhesion layers such as TiO2, Chromium, plasmonic metals such as Ag, Au, and two-dimensional (2D) transition metal dichalcogenides materials such as BP, Graphene, PtSe2 MoS2, MoSe2, WS2, WSe2. To study the performance of the heterostructure SPR sensor, the transfer matrix method is applied, and to analyses, the electric field intensity near the graphene-sensing layer contact, the finite-difference time-domain approach is utilized. Numerical results show that the heterostructure comprised of CaF2/TiO2/Ag/BP/Graphene/Sensing-layer has the best sensitivity and detection accuracy. The proposed sensor has an angle shift sensitivity of 390°/refractive index unit (RIU). Furthermore, the sensor achieved a detection accuracy of 0.464, a quality factor of 92.86/RIU, a figure of merit of 87.95, and a combined sensitive factor of 85.28. Furthermore, varied concentrations (0-1000 nM) of biomolecule binding interactions between ligands and analytes have been observed for the prospects of diagnosis of the SARS-CoV-2 virus. Results demonstrate that the proposed sensor is well suited for real-time and label-free detection particularly SARS-CoV-2 virus detection.
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Affiliation(s)
- Tarik Bin Abdul Akib
- Department of Electrical and Electronic Engineering, Rajshahi University of Engineering and Technology, Rajshahi, 6204 Bangladesh
- Department of Electrical and Electronic Engineering, Bangladesh Army University of Engineering and Technology, Rajshahi, 6431 Bangladesh
| | - Shahriar Mostufa
- Department of Electrical and Electronic Engineering, Rajshahi University of Engineering and Technology, Rajshahi, 6204 Bangladesh
| | - Md. Masud Rana
- Department of Electrical and Electronic Engineering, Rajshahi University of Engineering and Technology, Rajshahi, 6204 Bangladesh
| | - Md. Biplob Hossain
- Faculty of Engineering and Information Sciences, University of Wollongong, Wollongong, NSW 2522 Australia
- Department of Electrical and Electronic Engineering, Jashore University of Science and Technology, Jashore, 7408 Bangladesh
| | - Md. Rabiul Islam
- Faculty of Engineering and Information Sciences, University of Wollongong, Wollongong, NSW 2522 Australia
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15
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Cytoplasmic Tail Truncation Stabilizes S1-S2 Association and Enhances S Protein Incorporation into SARS-CoV-2 Pseudovirions. J Virol 2023; 97:e0165022. [PMID: 36790205 PMCID: PMC10062125 DOI: 10.1128/jvi.01650-22] [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: 02/16/2023] Open
Abstract
Truncations of the cytoplasmic tail (CT) of entry proteins of enveloped viruses dramatically increase the infectivity of pseudoviruses (PVs) bearing these proteins. Several mechanisms have been proposed to explain this enhanced entry, including an increase in cell surface expression. However, alternative explanations have also been forwarded, and the underlying mechanisms for the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) S protein remain undetermined. Here, we show that the partial or complete deletion of the CT (residues 19 to 35) does not modify SARS-CoV-2 S protein expression on the cell surface when the S2 subunit is measured, whereas it is significantly increased when the S1 subunit is measured. We also show that the higher level of S1 in these CT-truncated S proteins reflects the decreased dissociation of the S1 subunit from the S2 subunit. In addition, we demonstrate that CT truncation further promotes S protein incorporation into PV particles, as indicated by biochemical analyses and cryo-electron microscopy. Thus, our data show that two distinct mechanisms contribute to the markedly increased infectivity of PVs carrying CT-truncated SARS-CoV-2 S proteins and help clarify the interpretation of the results of studies employing such PVs. IMPORTANCE Various forms of PVs have been used as tools to evaluate vaccine efficacy and study virus entry steps. When PV infectivity is inherently low, such as that of SARS-CoV-2, a CT-truncated version of the viral entry glycoprotein is widely used to enhance PV infectivity, but the mechanism underlying this enhanced PV infectivity has been unclear. Here, our study identified two mechanisms by which the CT truncation of the SARS-CoV-2 S protein dramatically increases PV infectivity: a reduction of S1 shedding and an increase in S protein incorporation into PV particles. An understanding of these mechanisms can clarify the mechanistic bases for the differences observed among various assays employing such PVs.
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16
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Oliveira I, Ferreira I, Jacob B, Cardenas K, Cerni F, Baia-da-Silva D, Arantes E, Monteiro W, Pucca M. Harnessing the Power of Venomous Animal-Derived Toxins against COVID-19. Toxins (Basel) 2023; 15:159. [PMID: 36828473 PMCID: PMC9967918 DOI: 10.3390/toxins15020159] [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: 12/01/2022] [Revised: 01/11/2023] [Accepted: 02/09/2023] [Indexed: 02/17/2023] Open
Abstract
Animal-derived venoms are complex mixtures of toxins triggering important biological effects during envenomings. Although venom-derived toxins are known for their potential of causing harm to victims, toxins can also act as pharmacological agents. During the COVID-19 pandemic, there was observed an increase in in-depth studies on antiviral agents, and since, to date, there has been no completely effective drug against the global disease. This review explores the crosstalk of animal toxins and COVID-19, aiming to map potential therapeutic agents derived from venoms (e.g., bees, snakes, scorpions, etc.) targeting COVID-19.
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Affiliation(s)
- Isadora Oliveira
- Department of BioMolecular Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto 14040-903, SP, Brazil
| | - Isabela Ferreira
- Department of BioMolecular Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto 14040-903, SP, Brazil
| | - Beatriz Jacob
- Department of BioMolecular Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto 14040-903, SP, Brazil
| | - Kiara Cardenas
- Medical School, Federal University of Roraima, Boa Vista 69310-000, RR, Brazil
| | - Felipe Cerni
- Health Sciences Postgraduate Program, Federal University of Roraima, Boa Vista 69310-000, RR, Brazil
| | - Djane Baia-da-Silva
- Institute of Clinical Research Carlos Borborema, Dr. Heitor Vieira Dourado Tropical Medicine Foundation, Manaus 69850-000, AM, Brazil
- Postgraduate Program in Tropical Medicine, School of Health Sciences, Amazonas State University, Manaus 69850-000, AM, Brazil
- Department of Collective Health, Faculty of Medicine, Federal University of Amazonas, Manaus 69077-000, AM, Brazil
- Leônidas and Maria Deane Institute, Fiocruz Amazônia, Manaus 69057-070, AM, Brazil
- Faculty of Pharmacy, Nilton Lins University, Manaus 69058-040, AM, Brazil
| | - Eliane Arantes
- Department of BioMolecular Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto 14040-903, SP, Brazil
| | - Wuelton Monteiro
- Institute of Clinical Research Carlos Borborema, Dr. Heitor Vieira Dourado Tropical Medicine Foundation, Manaus 69850-000, AM, Brazil
- Postgraduate Program in Tropical Medicine, School of Health Sciences, Amazonas State University, Manaus 69850-000, AM, Brazil
| | - Manuela Pucca
- Medical School, Federal University of Roraima, Boa Vista 69310-000, RR, Brazil
- Health Sciences Postgraduate Program, Federal University of Roraima, Boa Vista 69310-000, RR, Brazil
- Postgraduate Program in Tropical Medicine, School of Health Sciences, Amazonas State University, Manaus 69850-000, AM, Brazil
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17
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Khattab ESAEH, Ragab A, Abol-Ftouh MA, Elhenawy AA. Therapeutic strategies for Covid-19 based on molecular docking and dynamic studies to the ACE-2 receptors, Furin, and viral spike proteins. J Biomol Struct Dyn 2022; 40:13291-13309. [PMID: 34647855 PMCID: PMC8544674 DOI: 10.1080/07391102.2021.1989036] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
SARS-CoV-2 is a pandemic virus that caused infections and deaths in many world countries, including the Middle East. The virus-infected human cells by binding via ACE-2 receptor through the Spike protein of the virus with Furin's help causing cell membrane fusion leading to Covid-19-cell entry. No registered drugs or vaccines are triggering this pandemic viral disease yet. Our present work is based on molecular docking and dynamics simulation that performed to spike protein-ACE-2 interface complex, ACE-2 receptor, Spike protein (RBD), and Furin as targets for new small molecules. These drugs target new potential therapies to show their probabilities toward the active sites of mentioned proteins, strongly causing inhibition and/or potential therapy for covid-19. All target proteins were estimated against new target compounds under clinical trials and repurposing drugs currently present. Possibilities of those molecules and potential therapeutics acting on a certain target were predicted. MD simulations over 200 ns with molecular mechanics-generalized Born surface area (MMGBSA) binding energy calculations were performed. The structural and energetic analyses demonstrated the stability of the ligands-MPros complex. Our present work will introduce new visions of some biologically active molecules for further studies in-vitro and in-vivo for Covid-19, repurposing of these molecules should be taking place under clinical works and offering different strategies for drugs repurposing against Covid-19 diseases.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
| | - Ahmed Ragab
- Department of Chemistry, Faculty of Science (Boys), Al-Azhar University, Nasr City, Cairo, Egypt,CONTACT Ahmed Ragab ; Department of Chemistry, Faculty of Science (Boys), Al-Azhar University, Nasr City, Cairo11884, Egypt
| | - Mahmoud A. Abol-Ftouh
- Department of Chemistry, Faculty of Science (Boys), Al-Azhar University, Nasr City, Cairo, Egypt,Mahmoud A. Abol-Ftouh Department of Chemistry, Faculty of Science (Boys), Al-Azhar University, Nasr City, Cairo11884, Egypt
| | - Ahmed A. Elhenawy
- Department of Chemistry, Faculty of Science (Boys), Al-Azhar University, Nasr City, Cairo, Egypt
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18
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Yakoubi A, Dhafer CEB. Advanced Plasmonic Nanoparticle-Based Techniques for the Prevention, Detection, and Treatment of Current COVID-19. PLASMONICS (NORWELL, MASS.) 2022; 18:311-347. [PMID: 36588744 PMCID: PMC9786532 DOI: 10.1007/s11468-022-01754-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 11/20/2022] [Indexed: 06/16/2023]
Abstract
Coronavirus is an ongoing global pandemic caused by severe acute respiratory syndrome coronavirus 2. Coronavirus disease 2019 known as COVID-19 is the worst pandemic since World War II. The outbreak of COVID-19 had a significant repercussion on the health, economy, politics, and environment, making coronavirus-related issues more complicated and becoming one of the most challenging pandemics of the last century with deadly outcomes and a high rate of the reproduction number. There are thousands of different types - or variants - of COVID circulating across the world. Viruses mutate all the time; it emphasizes the critical need for the designing of efficient vaccines to prevent virus infection, early and fast diagnosis, and effective antiviral and protective therapeutics. In this regard, the use of nanotechnology offers new opportunities for the development of novel strategies in terms of prevention, diagnosis, and treatment of COVID-19. This review presents an outline of the platforms developed using plasmonic nanoparticles in the detection, treatment, and prevention of SARS-CoV-2. We select the best strategies in each of these approaches. The properties of metallic plasmon NPs and their relevance in the development of novel point-of-care diagnosis approaches for COVID-19 are highlighted. Also, we discuss the current challenges and the future perspectives looking towards the clinical translation and the commercial aspects of nanotechnology and plasmonic NP-based diagnostic tools and therapy to fight COVID-19 pandemic. The article could be of significance for researchers dedicated to developing suitable plasmonic detection tools and therapy approaches for COVID-19 viruses and future pandemics.
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Affiliation(s)
- Afef Yakoubi
- Laboratory of Hetero-organic Compounds and Nanostructured Materials, Chemistry Department, Faculty of Sciences Bizerte, University of Carthage, LR 18 ES11, 7021 Bizerte, Tunisia
| | - Cyrine El Baher Dhafer
- Chemistry Department College of Science, Jouf University, P.O Box: 2014, Sakaka, Saudi Arabia
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19
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Zolfaghari MA, Ghadiri Moghaddam F, Rajput S, Karimi A, Naghi Vishteh M, Mahmoodpoor A, Dolati S, Yousefi M. SARS-CoV-2 vaccines: A double-edged sword throughout rapid evolution of COVID-19. Cell Biol Int 2022; 46:2009-2017. [PMID: 36047303 PMCID: PMC9539123 DOI: 10.1002/cbin.11903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Revised: 07/12/2022] [Accepted: 08/24/2022] [Indexed: 11/11/2022]
Abstract
After more than 2 years of the coronavirus disease 2019 pandemic caused by severe acute respiratory syndrome coronavirus 2, several questions have remained unanswered that affected our daily lives. Although substantial vaccine development could resist this challenge, emerging new variants in different countries could be considered as potent concerns regarding the adverse effects of reinfection or postvaccination. Precisely, these concerns address some significant and probable outcomes in vaccinated or reinfected models, followed by some virus challenges, such as antibody-dependent enhancement and cytokine storm. Therefore, the importance of evaluating the effectiveness of neutralizing antibodies (nAbs) elicited by vaccination and the rise of new variants must be addressed.
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Affiliation(s)
- Mohammad Ali Zolfaghari
- Student Research CommitteeTabriz University of Medical SciencesTabrizIran
- Department of Molecular Medicine, Faculty of Advanced Medical SciencesTabriz University of Medical SciencesTabrizIran
| | | | - Shabnam Rajput
- Department of Pediatrics, School of MedicineJahrom University of Medical SciencesJahromIran
| | - Abbas Karimi
- Department of Molecular Medicine, Faculty of Advanced Medical SciencesTabriz University of Medical SciencesTabrizIran
- Biotechnology Research CenterTabriz University of Medical SciencesTabrizIran
| | - Mohadeseh Naghi Vishteh
- Department of Genetics and Molecular Biology, School of MedicineIsfahan University of Medical SciencesIsfahanIran
| | - Ata Mahmoodpoor
- Department of AnesthesiologyTabriz University of Medical SciencesTabrizIran
| | - Sanam Dolati
- Physical Medicine and Rehabilitation Research Center, Aging Research InstituteTabriz University of Medical SciencesTabrizIran
| | - Mehdi Yousefi
- Stem Cell Research CenterTabriz University of Medical SciencesTabrizIran
- Department of Immunology, Faculty of MedicineTabriz University of Medical SciencesTabrizIran
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20
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Liu Z, Yang C, Zhang H, Cao G, Wang S, Yin S, Wang Y. SARS-CoV-2 tetrameric RBD protein blocks viral infection and induces potent neutralizing antibody response. Front Immunol 2022; 13:960094. [PMID: 36389744 PMCID: PMC9659643 DOI: 10.3389/fimmu.2022.960094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 10/14/2022] [Indexed: 12/02/2022] Open
Abstract
The pandemic of coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has posed serious threats to global health and economy and calls for the development of safe treatments and effective vaccines. The receptor-binding domain in the spike protein (SRBD) of SARS-CoV-2 is responsible for its binding to angiotensin-converting enzyme 2 (ACE2) receptor. It contains multiple dominant neutralizing epitopes and serves as an important antigen for the development of COVID-19 vaccines. Here, we showed that dimeric SRBD-Fc and tetrameric 2xSRBD-Fc fusion proteins bind ACE2 with different affinity and block SARS-CoV-2 pseudoviral infection. Immunization of mice with SRBD-Fc fusion proteins elicited high titer of RBD-specific antibodies with robust neutralizing activity against pseudoviral infections. As such, our study indicates that the polymeric SRBD-Fc fusion protein can serve as a treatment agent as well as a vaccine for fighting COVID-19.
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21
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Ratnapriya S, Braun AR, Cervera H, Carlson D, Ding S, Paulson C, Mishra N, Sachs JN, Aldrich C, Finzi A, Herschhorn A. Broad Tricyclic Ring Inhibitors Block SARS-CoV-2 Spike Function Required for Viral Entry. ACS Infect Dis 2022; 8:2045-2058. [PMID: 36153947 PMCID: PMC9528568 DOI: 10.1021/acsinfecdis.1c00658] [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: 12/21/2021] [Indexed: 01/29/2023]
Abstract
The entry of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) into host cells requires binding of the viral spike glycoprotein to the angiotensin-converting enzyme 2 (ACE2) receptor, which triggers subsequent conformational changes to facilitate viral and cellular fusion at the plasma membrane or following endocytosis. Here, we experimentally identified selective and broad inhibitors of SARS-CoV-2 entry that share a tricyclic ring (or similar) structure. The inhibitory effect was restricted to early steps during infection and the entry inhibitors interacted with the receptor binding domain of the SARS-CoV-2 spike but did not significantly interfere with receptor (ACE2) binding. Instead, some of these compounds induced conformational changes or affected spike assembly and blocked SARS-CoV-2 spike cell-cell fusion activity. The broad inhibitors define a highly conserved binding pocket that is present on the spikes of SARS-CoV-1, SARS-CoV-2, and all circulating SARS-CoV-2 variants tested and block SARS-CoV spike activity required for mediating viral entry. These compounds provide new insights into the SARS-CoV-2 spike topography, as well as into critical steps on the entry pathway, and can serve as lead candidates for the development of broad-range entry inhibitors against SARS-CoVs.
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Affiliation(s)
- Sneha Ratnapriya
- Division of Infectious Diseases and International Medicine, Department of Medicine, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Anthony R. Braun
- Department of Biomedical Engineering, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Héctor Cervera
- Division of Infectious Diseases and International Medicine, Department of Medicine, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Danielle Carlson
- Division of Infectious Diseases and International Medicine, Department of Medicine, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Shilei Ding
- Centre de Recherche du CHUM, Montreal, QC H2X 0A9, Canada; Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC H2X 0A9, Canada
| | - Carolyn Paulson
- Department of Biomedical Engineering, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Neeraj Mishra
- Department of Medicinal Chemistry, University of Minnesota, 8-101 WDH, 308 Harvard Street SE, Minneapolis, MN, 55455, United States; Center for Drug Design, Academic Health Center, University of Minnesota, Minneapolis, MN, 55455, United States
| | - Jonathan N. Sachs
- Department of Biomedical Engineering, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Courtney Aldrich
- Department of Medicinal Chemistry, University of Minnesota, 8-101 WDH, 308 Harvard Street SE, Minneapolis, MN, 55455, United States; Center for Drug Design, Academic Health Center, University of Minnesota, Minneapolis, MN, 55455, United States
| | - Andrés Finzi
- Centre de Recherche du CHUM, Montreal, QC H2X 0A9, Canada; Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC H2X 0A9, Canada
| | - Alon Herschhorn
- Division of Infectious Diseases and International Medicine, Department of Medicine, University of Minnesota, Minneapolis, Minnesota 55455, USA
- Microbiology, Immunology, and Cancer Biology Graduate Program, University of Minnesota, Minneapolis, Minnesota 55455, USA
- The College of Veterinary Medicine Graduate Program, University of Minnesota, Minneapolis, Minnesota 55455, USA
- Institute for Molecular Virology, University of Minnesota, Minneapolis, Minnesota 55455, USA
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22
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Zhou X, Zhao J, Qiu Y, Jia R. Sequence difference of angiotensin-converting enzyme 2 between nonhuman primates affects its binding-affinity with SARS-CoV-2 S receptor binding domain. BIOSAFETY AND HEALTH 2022; 4:293-298. [PMID: 36105891 PMCID: PMC9461283 DOI: 10.1016/j.bsheal.2022.09.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 09/05/2022] [Accepted: 09/05/2022] [Indexed: 11/24/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused many deaths and contributed to a tremendous public health concern worldwide since 2020. Angiotensin-converting enzyme 2 (ACE2) binds to the SARS-CoV-2 virus as a receptor. The challenge of different nonhuman primate (NHP) species by SARS-CoV-2 virus demonstrated different effects on virus replication and disease pathology. This study characterizes differences between host ACE2 sequences of three NHP species: Macaca mulatta, Macaca fascicularis, and Chlorocebus sabaeus. In addition, the binding affinity between the ACE2 ectodomain and the SARS-CoV-2 S receptor-binding domain (RBD) was analyzed. Variation of ACE2 sequence among NHP species and the binding affinity may account for different susceptibility and responses to SARS-CoV-2 infection.
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Affiliation(s)
- Xiaojun Zhou
- Department of Biosafety, China Biotechnology Co.LTD, Beijing 100025, China
| | - Jingjing Zhao
- Department of Infectious Diseases, Beijing Chaoyang Hospital, Capital Medical University, Beijing 100043, China
| | - Yefeng Qiu
- Laboratory Animal Center, Academy of Military Medical Sciences, Beijing 100071, China,Corresponding authors: Laboratory Animal Center, Academy of Military Medical Sciences, Beijing 100071, China (Y. Qiu); Department of Biosafety, China Biotechnology Co.LTD, Beijing 100025, China (R. Jia)
| | - Rui Jia
- Department of Biosafety, China Biotechnology Co.LTD, Beijing 100025, China,Corresponding authors: Laboratory Animal Center, Academy of Military Medical Sciences, Beijing 100071, China (Y. Qiu); Department of Biosafety, China Biotechnology Co.LTD, Beijing 100025, China (R. Jia)
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23
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Margiana R, Sharma SK, Khan BI, Alameri AA, Opulencia MJC, Hammid AT, Hamza TA, Babakulov SK, Abdelbasset WK, Jawhar ZH. RETRACTED: The pathogenicity of COVID-19 and the role of pentraxin-3: An updated review study. Pathol Res Pract 2022; 238:154128. [PMID: 36137396 PMCID: PMC9476367 DOI: 10.1016/j.prp.2022.154128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Revised: 09/03/2022] [Accepted: 09/13/2022] [Indexed: 01/08/2023]
Abstract
This article has been retracted: please see Elsevier Policy on Article Withdrawal (https://www.elsevier.com/about/policies/article-withdrawal). This article has been retracted at the request of the Editor-in-Chief. In investigating concerns regarding the contributions of the authors to this article, the editors reached out to the authors for an explanation. In addition to the concerns regarding the contribution of each author, the editors discovered suspicious changes in authorship between the original submission and the revised version of this paper. The names of the authors Ameer A Alameri and Zanko Hassan Jawhar were added to the revised version of the article without explanation and without the exceptional approval by the handling Editor, which is contrary to the journal policy on changes to authorship. The authors were unable to provide a reasonable explanation for either of the issues raised. The editor therefore feels that the findings of the manuscript cannot be relied upon and that the article needs to be retracted.
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Affiliation(s)
- Ria Margiana
- Department of Anatomy, Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia; Master's Programme Biomedical Sciences, Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia; Andrology Program, Faculty of Medicine, Universitas Airlangga, Surabaya, Indonesia; Dr. Soetomo General Academic Hospital, Surabaya, Indonesia.
| | - Satish Kumar Sharma
- Department of Pharmacology, Glocal School of Pharmacy, The Glocal University, Saharanpur, India.
| | | | | | | | - Ali Thaeer Hammid
- Computer Engineering Techniques Department, Faculty of Information Technology, Imam Ja'afar Al-Sadiq University, Baghdad, Iraq
| | - Thulfeqar Ahmed Hamza
- Medical laboratory techniques department, Al-Mustaqbal University College, Babylon, Iraq
| | - Sharaf Khamrakulovich Babakulov
- Tashkent State Dental Institute, Makhtumkuli Street 103, Tashkent, 100047, Uzbekistan; Research scholar, Department of Scientific affairs, Samarkand State Medical Institute, Amir Temur Street 18, Samarkand, Uzbekistan
| | - Walid Kamal Abdelbasset
- Department of Health and Rehabilitation Sciences, College of Applied Medical Sciences, Prince Sattam bin Abdulaziz University, Al Kharj, Saudi Arabia; Department of Physical Therapy, Kasr Al-Aini Hospital, Cairo University, Giza, Egypt
| | - Zanko Hassan Jawhar
- Department of Medical Laboratory Science, College of Health Science, Lebanese French University, Kurdistan Region, Iraq
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24
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Therapeutic Approaches in COVID-19 Patients: The Role of the Renin-Angiotensin System. Can Respir J 2022; 2022:8698825. [PMID: 36199292 PMCID: PMC9529525 DOI: 10.1155/2022/8698825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 08/11/2022] [Accepted: 08/27/2022] [Indexed: 12/02/2022] Open
Abstract
Two and a half years after COVID-19 was first reported in China, thousands of people are still dying from the disease every day around the world. The condition is forcing physicians to adopt new treatment strategies while emphasizing continuation of vaccination programs. The renin-angiotensin system plays an important role in the development and progression of COVID-19 patients. Nonetheless, administration of recombinant angiotensin-converting enzyme 2 has been proposed for the treatment of the disease. The catalytic activity of cellular ACE2 (cACE2) and soluble ACE2 (sACE2) prevents angiotensin II and Des-Arg-bradykinin from accumulating in the body. On the other hand, SARS-CoV-2 mainly enters cells via cACE2. Thus, inhibition of ACE2 can prevent viral entry and reduce viral replication in host cells. The benefits of bradykinin inhibitors (BKs) have been reported in some COVID-19 clinical trials. Furthermore, the effects of cyclooxygenase (COX) inhibitors on ACE2 cleavage and prevention of viral entry into host cells have been reported in COVID-19 patients. However, the administration of COX inhibitors can reduce innate immune responses and have the opposite effect. A few studies suggest benefits of low-dose radiation therapy (LDR) in treating acute respiratory distress syndrome in COVID-19 patients. Nonetheless, radiation therapy can stimulate inflammatory pathways, resulting in adverse effects on lung injury in these patients. Overall, progress is being made in treating COVID-19 patients, but questions remain about which drugs will work and when. This review summarizes studies on the effects of a recombinant ACE2, BK and COX inhibitor, and LDR in patients with COVID-19.
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25
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Abstract
The COVID-19 pandemic has caused an unprecedented health crisis and economic burden worldwide. Its etiological agent SARS-CoV-2, a new virus in the coronavirus family, has infected hundreds of millions of people worldwide. SARS-CoV-2 has evolved over the past 2 years to increase its transmissibility as well as to evade the immunity established by previous infection and vaccination. Nevertheless, strong immune responses can be elicited by viral infection and vaccination, which have proved to be protective against the emergence of variants, particularly with respect to hospitalization or severe disease. Here, we review our current understanding of how the virus enters the host cell and how our immune system is able to defend against cell entry and infection. Neutralizing antibodies are a major component of our immune defense and have been extensively studied for SARS-CoV-2 and its variants. Structures of these neutralizing antibodies have provided valuable insights into epitopes that are protective against the original ancestral virus and the variants that have emerged. The molecular characterization of neutralizing epitopes as well as epitope conservation and resistance are important for design of next-generation vaccines and antibody therapeutics.
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Affiliation(s)
- Hejun Liu
- Department of Integrative Structural and Computational BiologyThe Scripps Research InstituteLa JollaCaliforniaUSA
| | - Ian A. Wilson
- Department of Integrative Structural and Computational BiologyThe Scripps Research InstituteLa JollaCaliforniaUSA
- The Skaggs Institute for Chemical BiologyThe Scripps Research InstituteLa JollaCaliforniaUSA
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26
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Rodríguez Y, Cardoze SM, Obineche OW, Melo C, Persaud A, Fernández Romero JA. Small Molecules Targeting SARS-CoV-2 Spike Glycoprotein Receptor-Binding Domain. ACS OMEGA 2022; 7:28779-28789. [PMID: 35991504 PMCID: PMC9380817 DOI: 10.1021/acsomega.2c00844] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 07/06/2022] [Indexed: 06/15/2023]
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused the coronavirus disease 2019 (COVID-19) pandemic. Several variants of SARS-CoV-2 have emerged worldwide. These variants show different transmissibility infectivity due to mutations in the viral spike (S) glycoprotein that interacts with the human angiotensin-converting enzyme 2 (hACE2) receptor and facilitates viral entry into target cells. Despite the effective SARS-CoV-2 vaccines, we still need to identify selective antivirals, and the S glycoprotein is a key target to neutralize the virus. We hypothesize that small molecules could disrupt the interaction of S glycoprotein with hACE2 and inhibit viral entry. We analyzed the S glycoprotein-hACE2 complex structure (PDB: 7DF4) and created models for different viral variants using visual molecular dynamics (VMD) and molecular operating environment (MOE) programs. Moreover, we started the hits search by performing structure-based molecular docking virtual screening of commercially available small molecules against S glycoprotein models using OEDocking FRED-4.0.0.0 software. The FRED-4.0.0.0 Chemguass4 scoring function was used to rank the small molecules based on their affinities. The best candidate compounds were purchased and tested using a standard SARS-CoV-2 pseudotyped cell-based bioassay to investigate their antiviral activity. Three of these compounds, alone or in combination, showed antiviral selectivity. These small molecules may lead to an effective antiviral treatment or serve as probes to better understand the biology of SARS-CoV-2.
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Affiliation(s)
- Yoel Rodríguez
- Department
of Natural Sciences, Hostos Community College
of The City University of New York, 500 Grand Concourse, Bronx, New York, New York 10451, United States
- Department
of Pharmacological Sciences, Icahn School
of Medicine at Mount Sinai, 1425 Madison Avenue, New York, New York 10029, United
States
| | - Scarlet Martínez Cardoze
- Department
of Natural Sciences, Hostos Community College
of The City University of New York, 500 Grand Concourse, Bronx, New York, New York 10451, United States
| | - Onyinyechi W. Obineche
- Department
of Natural Sciences, Hostos Community College
of The City University of New York, 500 Grand Concourse, Bronx, New York, New York 10451, United States
| | - Claudia Melo
- Department
of Science, Borough of Manhattan Community
College of The City University of New York, 199 Chambers St, New York, New York 10007, United States
- Brooklyn
College of The City University of New York, 2900 Bedford Avenue, New
York, New York 11210, United States
| | - Ashanna Persaud
- Department
of Science, Borough of Manhattan Community
College of The City University of New York, 199 Chambers St, New York, New York 10007, United States
| | - José A. Fernández Romero
- Department
of Science, Borough of Manhattan Community
College of The City University of New York, 199 Chambers St, New York, New York 10007, United States
- Center
for Biomedical Research, The Population
Council, 1230 York Avenue, New York, New York 10065, United States
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27
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Lin F, Zhang H, Li L, Yang Y, Zou X, Chen J, Tang X. PEDV: Insights and Advances into Types, Function, Structure, and Receptor Recognition. Viruses 2022; 14:v14081744. [PMID: 36016366 PMCID: PMC9416423 DOI: 10.3390/v14081744] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 08/06/2022] [Accepted: 08/06/2022] [Indexed: 11/16/2022] Open
Abstract
Porcine epidemic diarrhea virus (PEDV) has been endemic in most parts of the world since its emergence in the 1970s. It infects the small intestine and intestinal villous cells, spreads rapidly, and causes infectious intestinal disease characterized by vomiting, diarrhea, and dehydration, leading to high mortality in newborn piglets and causing massive economic losses to the pig industry. The entry of PEDV into cells is mediated by the binding of its spike protein (S protein) to a host cell receptor. Here, we review the structure of PEDV, its strains, and the structure and function of the S protein shared by coronaviruses, and summarize the progress of research on possible host cell receptors since the discovery of PEDV.
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Affiliation(s)
- Feng Lin
- College of Animal Sciences, Jilin University, Changchun 130062, China
| | - Huanyu Zhang
- College of Animal Sciences, Jilin University, Changchun 130062, China
| | - Linquan Li
- College of Animal Sciences, Jilin University, Changchun 130062, China
| | - Yang Yang
- College of Animal Sciences, Jilin University, Changchun 130062, China
| | - Xiaodong Zou
- College of Animal Sciences, Jilin University, Changchun 130062, China
| | - Jiahuan Chen
- College of Animal Sciences, Jilin University, Changchun 130062, China
| | - Xiaochun Tang
- College of Animal Sciences, Jilin University, Changchun 130062, China
- Chongqing Research Institute, Jilin University, Chongqing 401120, China
- Correspondence:
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28
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Kumar A, Ladha A, Choudhury A, Ikbal AMA, Bhattacharjee B, Das T, Gupta G, Sharma C, Sarbajna A, Mandal SC, Choudhury MD, Ali N, Slama P, Rezaei N, Palit P, Tiwari ON. The chimera of S1 and N proteins of SARS-CoV-2: can it be a potential vaccine candidate for COVID-19? Expert Rev Vaccines 2022; 21:1071-1086. [PMID: 35604776 DOI: 10.1080/14760584.2022.2081156] [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: 11/04/2022]
Abstract
INTRODUCTION Coronavirus disease 2019 (COVID-19), caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has emerged as one of the biggest global health issues. Spike protein (S) and nucleoprotein (N), the major immunogenic components of SARS-CoV-2, have been shown to be involved in the attachment and replication of the virus inside the host cell. AREAS COVERED Several investigations have shown that the SARS-CoV-2 nucleoprotein can elicit a cell-mediated immune response capable of regulating viral replication and lowering viral burden. However, the development of an effective vaccine that can stop the transmission of SARS-CoV-2 remains a matter of concern. Literature was retrieved using the keywords COVID-19 vaccine, role of nucleoprotein as vaccine candidate, spike protein, nucleoprotein immune responses against SARS-CoV-2, and chimera vaccine in PubMed, Google Scholar, and Google. EXPERT OPINION We have focussed on the use of chimera protein, consisting of N and S-1 protein components of SARS-CoV-2, as a potential vaccine candidate. This may act as a polyvalent mixed recombinant protein vaccine to elicit a strong T and B cell immune response, which will be capable of neutralizing the wild and mutated variants of SARS-CoV-2, and also restricting its attachment, replication, and budding in the host cell.
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Affiliation(s)
- Amresh Kumar
- Department of Life Sciences and Bioinformatics, Assam University, Silchar, India
| | - Amit Ladha
- Area of Biotechnology and Bioinformatics, NIIT University, Neemrana, India
| | - Ankita Choudhury
- Department of Pharmaceutical Sciences, Allama TR College of Pharmacy, Hospital Rd, Srigouri, India
| | - Abu Md Ashif Ikbal
- Department of Pharmacy, Tripura University (A Central University), Suryamaninagar, Tripura (W), India
| | - Bedanta Bhattacharjee
- Department of Pharmaceutical Sciences, Faculty of Science and Engineering, Dibrugarh University, Dibrugarh, India
| | - Tanmay Das
- Department of Business Administration, Assam University Silchar, India
| | - Gaurav Gupta
- Area of Biotechnology and Bioinformatics, NIIT University, Neemrana, India.,Department of Immunology, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Chhavi Sharma
- Area of Biotechnology and Bioinformatics, NIIT University, Neemrana, India
| | - Adity Sarbajna
- Department of Zoology, Surendranath College, Kolkata, India
| | - Subhash C Mandal
- Department of Pharmaceutical Technology, Jadavpur University, Kolkata, India
| | | | - Nahid Ali
- Division of Immunology, Department of Infectious Diseases, INDIAN INSTITUTE OF CHEMICAL BIOLOGY, Kolkata, India
| | - Petr Slama
- Laboratory of Animal Immunology and Biotechnology, Department of Animal Morphology, Physiology and Genetics, Faculty of AgriSciences, Mendel University in Brno, Zemedelska 1, Brno, Czech Republic
| | - Nima Rezaei
- Research Center for Immunodeficiencies, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran.,Department of Immunology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran.,Network of Immunity in Infection, Malignancy and Autoimmunity (NIIMA), Universal Scientific Education and Research Network (USERN), Stockholm, Sweden
| | - Partha Palit
- Department of Pharmaceutical Sciences Drug Discovery research Laboratory, Assam University, Silchar, India
| | - Onkar Nath Tiwari
- Centre for Conservation and Utilisation of Blue Green Algae (CCUBGA), Division of Microbiology, ICAR-Indian Agricultural Research Institute (IARI), New Delhi, India
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29
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Fan C, Wu Y, Rui X, Yang Y, Ling C, Liu S, Liu S, Wang Y. Animal models for COVID-19: advances, gaps and perspectives. Signal Transduct Target Ther 2022; 7:220. [PMID: 35798699 PMCID: PMC9261903 DOI: 10.1038/s41392-022-01087-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 06/20/2022] [Accepted: 06/27/2022] [Indexed: 01/08/2023] Open
Abstract
COVID-19, caused by SARS-CoV-2, is the most consequential pandemic of this century. Since the outbreak in late 2019, animal models have been playing crucial roles in aiding the rapid development of vaccines/drugs for prevention and therapy, as well as understanding the pathogenesis of SARS-CoV-2 infection and immune responses of hosts. However, the current animal models have some deficits and there is an urgent need for novel models to evaluate the virulence of variants of concerns (VOC), antibody-dependent enhancement (ADE), and various comorbidities of COVID-19. This review summarizes the clinical features of COVID-19 in different populations, and the characteristics of the major animal models of SARS-CoV-2, including those naturally susceptible animals, such as non-human primates, Syrian hamster, ferret, minks, poultry, livestock, and mouse models sensitized by genetically modified, AAV/adenoviral transduced, mouse-adapted strain of SARS-CoV-2, and by engraftment of human tissues or cells. Since understanding the host receptors and proteases is essential for designing advanced genetically modified animal models, successful studies on receptors and proteases are also reviewed. Several improved alternatives for future mouse models are proposed, including the reselection of alternative receptor genes or multiple gene combinations, the use of transgenic or knock-in method, and different strains for establishing the next generation of genetically modified mice.
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Affiliation(s)
- Changfa Fan
- Division of Animal Model Research, Institute for Laboratory Animal Resources, National Institutes for Food and Drug Control (NIFDC), National Rodent Laboratory Animal Resources Center, Beijing, 102629, China
| | - Yong Wu
- Division of Animal Model Research, Institute for Laboratory Animal Resources, National Institutes for Food and Drug Control (NIFDC), National Rodent Laboratory Animal Resources Center, Beijing, 102629, China
| | - Xiong Rui
- Division of Animal Model Research, Institute for Laboratory Animal Resources, National Institutes for Food and Drug Control (NIFDC), National Rodent Laboratory Animal Resources Center, Beijing, 102629, China
- Department of Microbiology & Infectious Disease Center, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100083, China
| | - Yuansong Yang
- Division of Animal Model Research, Institute for Laboratory Animal Resources, National Institutes for Food and Drug Control (NIFDC), National Rodent Laboratory Animal Resources Center, Beijing, 102629, China
| | - Chen Ling
- Division of Animal Model Research, Institute for Laboratory Animal Resources, National Institutes for Food and Drug Control (NIFDC), National Rodent Laboratory Animal Resources Center, Beijing, 102629, China
- College of Life Sciences, Northwest University; Provincial Key Laboratory of Biotechnology of Shaanxi Province, Northwest University, Xi'an, 710069, China
| | - Susu Liu
- Division of Animal Model Research, Institute for Laboratory Animal Resources, National Institutes for Food and Drug Control (NIFDC), National Rodent Laboratory Animal Resources Center, Beijing, 102629, China
| | - Shunan Liu
- Division of Animal Model Research, Institute for Laboratory Animal Resources, National Institutes for Food and Drug Control (NIFDC), National Rodent Laboratory Animal Resources Center, Beijing, 102629, China
| | - Youchun Wang
- Division of HIV/AIDS and Sexually Transmitted Virus Vaccines, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC), Beijing, China.
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30
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Human coronaviruses: origin, host and receptor. J Clin Virol 2022; 155:105246. [PMID: 35930858 PMCID: PMC9301904 DOI: 10.1016/j.jcv.2022.105246] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 07/10/2022] [Accepted: 07/20/2022] [Indexed: 01/02/2023]
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31
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Khanna K, Raymond W, Jin J, Charbit AR, Gitlin I, Tang M, Werts AD, Barrett EG, Cox JM, Birch SM, Martinelli R, Sperber HS, Franz S, Duff T, Hoffmann M, Healy AM, Oscarson S, Pöhlmann S, Pillai SK, Simmons G, Fahy JV. Exploring antiviral and anti-inflammatory effects of thiol drugs in COVID-19. Am J Physiol Lung Cell Mol Physiol 2022; 323:L372-L389. [PMID: 35762590 PMCID: PMC9448286 DOI: 10.1152/ajplung.00136.2022] [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] [Indexed: 12/15/2022] Open
Abstract
The redox status of the cysteine-rich SARS-CoV-2 spike glycoprotein (SARS-2-S) is important for the binding of SARS-2-S to angiotensin-converting enzyme 2 (ACE2), suggesting that drugs with a functional thiol group (“thiol drugs”) may cleave cystines to disrupt SARS-CoV-2 cell entry. In addition, neutrophil-induced oxidative stress is a mechanism of COVID-19 lung injury, and the antioxidant and anti-inflammatory properties of thiol drugs, especially cysteamine, may limit this injury. To first explore the antiviral effects of thiol drugs in COVID-19, we used an ACE-2 binding assay and cell entry assays utilizing reporter pseudoviruses and authentic SARS-CoV-2 viruses. We found that multiple thiol drugs inhibit SARS-2-S binding to ACE2 and virus infection. The most potent drugs were effective in the low millimolar range, and IC50 values followed the order of their cystine cleavage rates and lower thiol pKa values. To determine if thiol drugs have antiviral effects in vivo and to explore any anti-inflammatory effects of thiol drugs in COVID-19, we tested the effects of cysteamine delivered intraperitoneally to hamsters infected with SARS-CoV-2. Cysteamine did not decrease lung viral infection, but it significantly decreased lung neutrophilic inflammation and alveolar hemorrhage. We speculate that the concentration of cysteamine achieved in the lungs with intraperitoneal delivery was insufficient for antiviral effects but sufficient for anti-inflammatory effects. We conclude that thiol drugs decrease SARS-CoV-2 lung inflammation and injury, and we provide rationale for future studies to test if direct (aerosol) delivery of thiol drugs to the airways might also result in antiviral effects.
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Affiliation(s)
- Kritika Khanna
- Cardiovascular Research Institute, University of California San Francisco Medical Center, San Francisco, CA, United States
| | - Wilfred Raymond
- Cardiovascular Research Institute, University of California San Francisco Medical Center, San Francisco, CA, United States
| | - Jing Jin
- Vitalant Research Institute, San Francisco, California, United States
| | - Annabelle R Charbit
- Cardiovascular Research Institute, University of California San Francisco Medical Center, San Francisco, CA, United States
| | - Irina Gitlin
- Cardiovascular Research Institute, University of California San Francisco Medical Center, San Francisco, CA, United States
| | - Monica Tang
- Division of Pulmonary, Critical Care, Allergy and Sleep and the Department of Medicine, University of California San Francisco, San Francisco, California, United States
| | - Adam D Werts
- Lovelace Biomedical Research Institute, Albuquerque, New Mexico, United States
| | - Edward G Barrett
- Lovelace Biomedical Research Institute, Albuquerque, New Mexico, United States
| | - Jason M Cox
- Lovelace Biomedical Research Institute, Albuquerque, New Mexico, United States
| | - Sharla M Birch
- Lovelace Biomedical Research Institute, Albuquerque, New Mexico, United States
| | - Rachel Martinelli
- Vitalant Research Institute, San Francisco, California, United States
| | - Hannah S Sperber
- Vitalant Research Institute, San Francisco, California, United States
| | - Sergej Franz
- Vitalant Research Institute, San Francisco, California, United States
| | - Thomas Duff
- Centre for Synthesis and Chemical Biology, School of Chemistry, University College Dublin, Dublin, Ireland
| | - Markus Hoffmann
- Infection Biology Unit, German Primate Center, Göttingen, Germany.,Faculty of Biology and Psychology, Georg-August-University Göttingen, Göttingen, Germany
| | - Anne Marie Healy
- School of Pharmacy and Pharmaceutical Sciences, Panoz Institute, Trinity College Dublin, Ireland.,SSPC, The Science Foundation Ireland Research Centre for Pharmaceuticals, Trinity College Dublin, Ireland
| | - Stefan Oscarson
- Centre for Synthesis and Chemical Biology, School of Chemistry, University College Dublin, Dublin, Ireland
| | - Stefan Pöhlmann
- Infection Biology Unit, German Primate Center, Göttingen, Germany.,Faculty of Biology and Psychology, Georg-August-University Göttingen, Göttingen, Germany
| | - Satish K Pillai
- Vitalant Research Institute, San Francisco, California, United States.,Department of Laboratory Medicine, University of California San Francisco, San Francisco, California, United States
| | - Graham Simmons
- Vitalant Research Institute, San Francisco, California, United States.,Department of Laboratory Medicine, University of California San Francisco, San Francisco, California, United States
| | - John V Fahy
- Cardiovascular Research Institute, University of California San Francisco Medical Center, San Francisco, CA, United States.,Division of Pulmonary, Critical Care, Allergy and Sleep and the Department of Medicine, University of California San Francisco, San Francisco, California, United States
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32
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Gürer Giray B, Güven Açık G. SARS-CoV-2 and mutation RT-qPCR test positivity correlation with ABO and Rh blood types. J Med Virol 2022; 94:4776-4779. [PMID: 35676713 PMCID: PMC9348292 DOI: 10.1002/jmv.27923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 05/20/2022] [Accepted: 06/07/2022] [Indexed: 11/26/2022]
Abstract
Studies show that there may be a relationship between ABO blood type and SARS‐CoV‐2 transmission. It was aimed to determine by investigating the blood type of patients whose one‐step reverse transcription and real‐time polymerase chain reaction (RT‐qPCR) test were positive for SARS‐CoV‐2. ABO and Rh blood types of individuals whose RT‐qPCR test was positive for SARS‐CoV‐2 were examined and an evaluation was made to identify whether there was a relationship between them or not. The blood type data of 44.928 SARS‐CoV‐2 positive RT‐qPCR test results have been obtained. 17.656 (39.29%) were delta, 8048 (17.91%) were alpha, 800 (1.78%) were beta, and 3000 (6.67%) were omicrons while 15.424 (34.33%) SARS‐CoV‐2 positive mutation was found to be negative. Our study suggests that O and Rh (−) blood types may provide protection against delta, AB and Rh (+) blood types may hinder omicron infection while A and Rh (+) blood types may be more vulnerable to alpha and delta while B and Rh (+) are more sensitive to beta mutation. The molecular mechanism underlying the relationship between blood types and SARS‐CoV‐2 infection needs further molecular studies and multi‐centered studies.
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Affiliation(s)
- Burcu Gürer Giray
- Ankara Provincial Health Directorate Public Health Molecular Diagnosis Laboratory, Ankara, Turkey
| | - Gökçe Güven Açık
- Ankara Provincial Health Directorate Public Health Molecular Diagnosis Laboratory, Ankara, Turkey
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Abduljaleel Z, Shahzad N, Aziz SA, Malik SM. Monoclonal antibody designed for SARS-nCoV-2 spike protein of receptor binding domain on antigenic targeted epitopes for inhibition to prevent viral entry. Mol Divers 2022; 27:695-708. [PMID: 35616802 PMCID: PMC9133318 DOI: 10.1007/s11030-022-10449-x] [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: 02/12/2022] [Accepted: 04/19/2022] [Indexed: 11/25/2022]
Abstract
SARS, or severe acute respiratory syndrome, is caused by a novel coronavirus (COVID-19). This situation has compelled many pharmaceutical R&D companies and public health research sectors to focus their efforts on developing effective therapeutics. SARS-nCoV-2 was chosen as a protein spike to targeted monoclonal antibodies and therapeutics for prevention and treatment. Deep mutational scanning created a monoclonal antibody to characterize the effects of mutations in a variable antibody fragment based on its expression levels, specificity, stability, and affinity for specific antigenic conserved epitopes to the Spike-S-Receptor Binding Domain (RBD). Improved contacts between Fv light and heavy chains and the targeted antigens of RBD could result in a highly potent neutralizing antibody (NAbs) response as well as cross-protection against other SARS-nCoV-2 strains. It undergoes multipoint core mutations that combine enhancing mutations, resulting in increased binding affinity and significantly increased stability between RBD and antibody. In addition, we improved. Structures of variable fragment (Fv) complexed with the RBD of Spike protein were subjected to our established in-silico antibody-engineering platform to obtain enhanced binding affinity to SARS-nCoV-2 and develop ability profiling. We found that the size and three-dimensional shape of epitopes significantly impacted the activity of antibodies produced against the RBD of Spike protein. Overall, because of the conformational changes between RBD and hACE2, it prevents viral entry. As a result of this in-silico study, the designed antibody can be used as a promising therapeutic strategy to treat COVID-19.
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Affiliation(s)
- Zainularifeen Abduljaleel
- Science and Technology Unit, Umm Al-Qura University, P.O. Box 715, Mecca, 21955, Kingdom of Saudi Arabia.
- Department of Medical Genetics, Faculty of Medicine, Umm Al-Qura University, P.O. Box 715, Mecca, 21955, Kingdom of Saudi Arabia.
- The Regional Laboratory, Molecular Diagnostics Unit, Department of Molecular Biology, Ministry of Health (MOH), P.O. Box 6251, Mecca, Saudi Arabia.
| | - Naiyer Shahzad
- Department of Pharmacology and Toxicology, Faculty of Medicine, Umm Al-Qura University, Mecca, Saudi Arabia
| | - Syed A Aziz
- Department of Pathology and Lab Medicine, University of Ottawa, 451 Smyth Road, Ottawa, ON, K1H 8M5, Canada
| | - Shaheer M Malik
- Department of Chemistry, Faculty of Applied Sciences, Umm Al-Qura University, Mecca, Saudi Arabia
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da Costa CHS, de Freitas CAB, Alves CN, Lameira J. Assessment of mutations on RBD in the Spike protein of SARS-CoV-2 Alpha, Delta and Omicron variants. Sci Rep 2022; 12:8540. [PMID: 35595778 PMCID: PMC9121086 DOI: 10.1038/s41598-022-12479-9] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Accepted: 05/03/2022] [Indexed: 12/15/2022] Open
Abstract
The severe acute respiratory syndrome (SARS) coronavirus 2 (CoV-2) variant Omicron spread more rapid than the other variants of SARS-CoV-2 virus. Mutations on the Spike (S) protein receptor-binding domain (RBD) are critical for the antibody resistance and infectivity of the SARS-CoV-2 variants. In this study, we have used accelerated molecular dynamics (aMD) simulations and free energy calculations to present a systematic analysis of the affinity and conformational dynamics along with the interactions that drive the binding between Spike protein RBD and human angiotensin-converting enzyme 2 (ACE2) receptor. We evaluate the impacts of the key mutation that occur in the RBDs Omicron and other variants in the binding with the human ACE2 receptor. The results show that S protein Omicron has stronger binding to the ACE2 than other variants. The evaluation of the decomposition energy per residue shows the mutations N440K, T478K, Q493R and Q498R observed in Spike protein of SARS-CoV-2 provided a stabilization effect for the interaction between the SARS-CoV-2 RBD and ACE2. Overall, the results demonstrate that faster spreading of SARS-CoV-2 Omicron may be correlated with binding affinity of S protein RBD to ACE2 and mutations of uncharged residues to positively charged residues such as Lys and Arg in key positions in the RBD.
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Affiliation(s)
- Clauber Henrique Souza da Costa
- Laboratório de Planejamento e Desenvolvimento de Fármacos, Universidade Federal do Pará, Rua Augusto Correa S/N, Belém, PA, Brazil
| | - Camila Auad Beltrão de Freitas
- Laboratório de Planejamento e Desenvolvimento de Fármacos, Universidade Federal do Pará, Rua Augusto Correa S/N, Belém, PA, Brazil
| | - Cláudio Nahum Alves
- Laboratório de Planejamento e Desenvolvimento de Fármacos, Universidade Federal do Pará, Rua Augusto Correa S/N, Belém, PA, Brazil
| | - Jerônimo Lameira
- Laboratório de Planejamento e Desenvolvimento de Fármacos, Universidade Federal do Pará, Rua Augusto Correa S/N, Belém, PA, Brazil.
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Kashani NR, Azadbakht J, Ehteram H, Kashani HH, Rajabi-Moghadam H, Ahmad E, Nikzad H, Hosseini ES. Molecular and Clinical Investigation of COVID-19: From Pathogenesis and Immune Responses to Novel Diagnosis and Treatment. Front Mol Biosci 2022; 9:770775. [PMID: 35664675 PMCID: PMC9161360 DOI: 10.3389/fmolb.2022.770775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Accepted: 04/04/2022] [Indexed: 01/08/2023] Open
Abstract
The coronavirus-related severe acute respiratory syndrome (SARS-CoV) in 2002/2003, the Middle East respiratory syndrome (MERS-CoV) in 2012/2013, and especially the current 2019/2021 severe acute respiratory syndrome-2 (SARS-CoV-2) negatively affected the national health systems worldwide. Different SARS-CoV-2 variants, including Alpha (B.1.1.7), Beta (B.1.351), Gamma (P.1), Delta (B.1.617.2), and recently Omicron (B.1.1.529), have emerged resulting from the high rate of genetic recombination and S1-RBD/S2 mutation/deletion in the spike protein that has an impact on the virus activity. Furthermore, genetic variability in certain genes involved in the immune system might impact the level of SARS-CoV-2 recognition and immune response against the virus among different populations. Understanding the molecular mechanism and function of SARS-CoV-2 variants and their different epidemiological outcomes is a key step for effective COVID-19 treatment strategies, including antiviral drug development and vaccine designs, which can immunize people with genetic variabilities against various strains of SARS-CoV-2. In this review, we center our focus on the recent and up-to-date knowledge on SARS-CoV-2 (Alpha to Omicron) origin and evolution, structure, genetic diversity, route of transmission, pathogenesis, new diagnostic, and treatment strategies, as well as the psychological and economic impact of COVID-19 pandemic on individuals and their lives around the world.
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Affiliation(s)
- Narjes Riahi Kashani
- Anatomical Sciences Research Center, Institute for Basic Sciences, Kashan University of Medical Sciences, Kashan, Iran
- Gametogenesis Research Center, Kashan University of Medical Sciences, Kashan, Iran
| | - Javid Azadbakht
- Department of Radiology, Faculty of Medicine, Kashan University of Medical Sciences, Kashan, Iran
| | - Hassan Ehteram
- Department of Pathology, School of Medicine, Kashan University of Medical Sciences, Kashan, Iran
| | - Hamed Haddad Kashani
- Anatomical Sciences Research Center, Institute for Basic Sciences, Kashan University of Medical Sciences, Kashan, Iran
- Gametogenesis Research Center, Kashan University of Medical Sciences, Kashan, Iran
| | - Hassan Rajabi-Moghadam
- Department of Cardiovascular Medicine, Kashan University of Medical Sciences, Kashan, Iran
| | - Ejaz Ahmad
- Department of Pathology, Michigan Medicine, University of Michigan, Ann Arbor, MI, United States
| | - Hossein Nikzad
- Anatomical Sciences Research Center, Institute for Basic Sciences, Kashan University of Medical Sciences, Kashan, Iran
- Gametogenesis Research Center, Kashan University of Medical Sciences, Kashan, Iran
| | - Elahe Seyed Hosseini
- Anatomical Sciences Research Center, Institute for Basic Sciences, Kashan University of Medical Sciences, Kashan, Iran
- Gametogenesis Research Center, Kashan University of Medical Sciences, Kashan, Iran
- *Correspondence: Elahe Seyed Hosseini,
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Oral Immunization of Mice with Cell Extracts from Recombinant Lactococcus lactis Expressing SARS-CoV-2 Spike Protein. Curr Microbiol 2022; 79:167. [PMID: 35460453 PMCID: PMC9034443 DOI: 10.1007/s00284-022-02866-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Accepted: 04/05/2022] [Indexed: 12/22/2022]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has spread all over the world and became a pandemic that named coronavirus disease-2019 (COVID-19). At present, several intramuscular vaccines have been successfully developed and mass vaccination has progressed in many countries. The aim of the study is to develop and examine an oral vaccine against COVID-19 with recombinant Lactococcus lactis IL1403, a strain of lactic acid bacteria, expressing SARS-CoV-2 spike (S) protein receptor-binding domain (RBD) S1 subunit as an immunizing antigen. PBS or cell extracts from recombinant L. lactis were orally administered into mice (control VS treatment), and formation of antigen-specific antibodies and changes in the gut microbiome were analyzed. Intracellular antigen was detected, but its secretion was not successful. After immunization, antigen-specific serum IgG and fecal IgA levels were 1.5-fold (P = 0.002) and 1.4-fold (P = 0.016) higher in the immunized mice (treatment) than control, respectively. Gut microbiome profiles were clearly separated between the two groups when analyzed for beta diversity with overall similarity. At the genus level, while Coprococcus (P = 0.036) and unclassified genus of Ruminococcaceae (P = 0.037) in treatment were more abundant than control, rc4-4 (P = 0.013) and Stenotrophomonas (P = 0.021) were less abundant. Our results indicate that cell extract containing SARS-CoV-2 antigen can induce mice to produce antigen-specific antibodies without overall changes in the gut microbiome. This strategy may be useful for the development of other oral viral vaccines.
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Garanina E, Hamza S, Stott-Marshall RJ, Martynova E, Markelova M, Davidyuk Y, Shakirova V, Kaushal N, Baranwal M, Khaertynova IM, Rizvanov A, Foster TL, Khaiboullina S. Antibody and T Cell Immune Responses to SARS-CoV-2 Peptides in COVID-19 Convalescent Patients. Front Microbiol 2022; 13:842232. [PMID: 35509311 PMCID: PMC9058163 DOI: 10.3389/fmicb.2022.842232] [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: 12/23/2021] [Accepted: 01/26/2022] [Indexed: 11/13/2022] Open
Abstract
Identifying immunogenic targets of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is critical to advance diagnostic and disease control strategies. We analyzed humoral (ELISA) and T-cell (ELISpot) immune responses to spike (S) and nucleocapsid (N) SARS-CoV-2 proteins as well as to human endemic coronavirus (eCoV) peptides in serum from convalescent coronavirus disease 2019 (COVID-19) patients from Tatarstan, Russia. We identified multiple SARS-CoV-2 peptides that were reactive with serum antibodies and T cells from convalescent COVID-19. In addition, age and gender associated differences in the reactivity to S and N protein peptides were identified. Moreover, several SARS-CoV-2 peptides tested negatively correlated with disease severity and lung damage. Cross-reactivity to eCoV peptides was analyzed and found to be lower in COVID-19 compared to controls. In this study, we demonstrate the changing pattern of immunogenic peptide reactivity in COVID-19 serum based on age, gender and previous exposure to eCoVs. These data highlight how humoral immune responses and cytotoxic T cell responses to some of these peptides could contribute to SARS-CoV-2 pathogenesis.
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Affiliation(s)
- Ekaterina Garanina
- Intitute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Russia
| | - Shaimaa Hamza
- Intitute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Russia
| | - Robert J. Stott-Marshall
- Faculty of Medicine and Health Sciences, School of Veterinary Medicine and Science, University of Nottingham, Loughborough, United Kingdom
| | - Ekaterina Martynova
- Intitute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Russia
| | - Maria Markelova
- Intitute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Russia
| | - Yuriy Davidyuk
- Intitute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Russia
| | - Venera Shakirova
- Department of Infectious Diseases, Kazan State Medical University, Kazan, Russia
| | - Neha Kaushal
- Department of Biotechnology, Thapar Institute of Engineering and Technology, Patiala, India
| | - Manoj Baranwal
- Department of Biotechnology, Thapar Institute of Engineering and Technology, Patiala, India
| | | | - Albert Rizvanov
- Intitute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Russia
| | - Toshana L. Foster
- Faculty of Medicine and Health Sciences, School of Veterinary Medicine and Science, University of Nottingham, Loughborough, United Kingdom
| | - Svetlana Khaiboullina
- Intitute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Russia
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Lim TS, Choong YS. In silico design of ACE2 mutants for competitive binding of SARS-CoV-2 receptor binding domain with hACE2. PHYSICAL SCIENCES REVIEWS 2022. [DOI: 10.1515/psr-2021-0136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
The receptor binding motif (RBM) within the S-protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been touted as one of the main targets for vaccine/therapeutic development due to its interaction with the human angiotensin II converting enzyme 2 (hACE2) to facilitate virus entry into the host cell. The mechanism of action is based on the disruption of binding between the RBM and the hACE2 to prevent virus uptake for replication. In this work, we applied in silico approaches to design specific competitive binders for SARS-CoV-2 S-protein receptor binding motif (RBM) by using hACE2 peptidase domain (PD) mutants. Online single point mutation servers were utilised to estimate the effect of PD mutation on the binding affinity with RBM. The PD mutants were then modelled and the binding free energy was calculated. Three PD variants were designed with an increased affinity and interaction with SARS-CoV-2-RBM. It is hope that these designs could serve as the initial work for vaccine/drug development and could eventually interfere the preliminary recognition between SARS-CoV-2 and the host cell.
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Affiliation(s)
- Theam Soon Lim
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia , Penang , Malaysia
| | - Yee Siew Choong
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia , Penang , Malaysia
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39
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Szabo MP, Iba M, Nath A, Masliah E, Kim C. Does SARS-CoV-2 affect neurodegenerative disorders? TLR2, a potential receptor for SARS-CoV-2 in the CNS. Exp Mol Med 2022; 54:447-454. [PMID: 35396576 PMCID: PMC8990637 DOI: 10.1038/s12276-022-00755-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 01/13/2022] [Indexed: 12/15/2022] Open
Abstract
The coronavirus (COVID-19) pandemic, caused by severe acute respiratory system coronavirus 2 (SARS-CoV-2), has created significant challenges for scientists seeking to understand the pathogenic mechanisms of SARS-CoV-2 infection and to identify the best therapies for infected patients. Although ACE2 is a known receptor for the virus and has been shown to mediate viral entry into the lungs, accumulating reports highlight the presence of neurological symptoms resulting from infection. As ACE2 expression is low in the central nervous system (CNS), these neurological symptoms are unlikely to be caused by ACE2-virus binding. In this review, we will discuss a proposed interaction between SARS-CoV-2 and Toll-like receptor 2 (TLR2) in the CNS. TLR2 is an innate immune receptor that recognizes exogenous microbial components but has also been shown to interact with multiple viral components, including the envelope (E) protein of SARS-CoV-2. In addition, TLR2 plays an important role in the pathogenesis of neurodegenerative diseases such as Alzheimer's disease (AD) and Parkinson's disease (PD). Based on these observations, we hypothesize that TLR2 may play a critical role in the response to SARS-CoV-2 infiltration in the CNS, thereby resulting in the induction or acceleration of AD and PD pathologies in patients.
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Affiliation(s)
- Marcell P Szabo
- Molecular Neuropathology Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Michiyo Iba
- Molecular Neuropathology Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Avindra Nath
- Section of Infections of the Nervous System, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Eliezer Masliah
- Molecular Neuropathology Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, 20892, USA. .,Division of Neuroscience, National Institute on Aging, National Institutes of Health, Bethesda, MD, 20892, USA.
| | - Changyoun Kim
- Molecular Neuropathology Section, Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, 20892, USA.
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40
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Noorabad Ghahroodi F, Khalili S, Rasaee MJ. Recombinant subunits of SARS‐CoV‐2 spike protein as vaccine candidates to elicit neutralizing antibodies. J Clin Lab Anal 2022; 36:e24328. [PMID: 35349744 PMCID: PMC9102496 DOI: 10.1002/jcla.24328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Revised: 01/24/2022] [Accepted: 02/07/2022] [Indexed: 11/30/2022] Open
Abstract
Objectives The spike protein has been reported as one of the most critical targets for vaccine design strategies against the SARS‐CoV‐2 infection. Hence, we have designed, produced, and evaluated the potential use of three truncated recombinant proteins derived from spike protein as vaccine candidates capable of neutralizing SARS‐CoV‐2 virus. Methods In silico tools were used to design spike‐based subunit recombinant proteins (RBD (P1), fusion peptide (P2), and S1/S2 cleavage site (P3)). These proteins were checked for their ability to be identified by the anti‐SARS‐CoV‐2 antibodies by exposing them to COVID‐19 serum samples. The proteins were also injected into mice and rabbit, and the antibody titers were measured for 390 days to assess their neutralization efficiency. Results The antibodies that existed in the serum of COVID‐19 patients were identified by designed proteins. The anti‐spike antibody titer was increased in the animals injected with recombinant proteins. The VNT results revealed that the produced antibodies could neutralize the cultured live virus. Conclusion Truncated subunit vaccines could also be considered as robust tools for effective vaccination against COVID‐19. Using a combination of in silico, in vitro, and in vivo experiments, it was shown that the injection of spike‐based truncated recombinant proteins could stimulate long‐lasting and neutralizing antibody responses.
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Affiliation(s)
- Faezeh Noorabad Ghahroodi
- 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
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Sheng Y, Vinjamuri A, Alvarez MRS, Xie Y, McGrath M, Chen S, Barboza M, Frieman M, Lebrilla CB. Host Cell Glycocalyx Remodeling Reveals SARS-CoV-2 Spike Protein Glycomic Binding Sites. Front Mol Biosci 2022; 9:799703. [PMID: 35372520 PMCID: PMC8964299 DOI: 10.3389/fmolb.2022.799703] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 01/31/2022] [Indexed: 12/12/2022] Open
Abstract
Glycans on the host cell membrane and viral proteins play critical roles in pathogenesis. Highly glycosylated epithelial cells represent the primary boundary separating embedded host tissues from pathogens within the respiratory and intestinal tracts. SARS-CoV-2, the causative agent for the COVID-19 pandemic, reaches into the respiratory tract. We found purified human milk oligosaccharides (HMOs) inhibited the viral binding on cells. Spike (S) protein receptor binding domain (RBD) binding to host cells were partly blocked by co-incubation with exogenous HMOs, most by 2-6-sialyl-lactose (6′SL), supporting the notion that HMOs can function as decoys in defense against SARS-Cov2. To investigate the effect of host cell glycocalyx on viral adherence, we metabolically modified and confirmed with glycomic methods the cell surface glycome to enrich specific N-glycan types including those containing sialic acids, fucose, mannose, and terminal galactose. Additionally, Immunofluorescence studies demonstrated that the S protein preferentially binds to terminal sialic acids with α-(2,6)-linkages. Furthermore, site-specific glycosylation of S protein RBD and its human receptor ACE2 were characterized using LC-MS/MS. We then performed molecular dynamics calculations on the interaction complex to further explore the interactive complex between ACE2 and the S protein. The results showed that hydrogen bonds mediated the interactions between ACE2 glycans and S protein with desialylated glycans forming significantly fewer hydrogen bonds. These results supported a mechanism where the virus binds initially to glycans on host cells preferring α-(2,6)-sialic acids and finds ACE2 and with the proper orientation infects the cell.
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Affiliation(s)
- Ying Sheng
- Department of Chemistry, University of California, Davis, Davis, CA, United States
- The Biochemistry, Molecular, Cellular and Developmental Biology (BMCDB) Graduate Group, University of California, Davis, Davis, CA, United States
| | - Anita Vinjamuri
- Department of Chemistry, University of California, Davis, Davis, CA, United States
| | | | - Yixuan Xie
- Department of Chemistry, University of California, Davis, Davis, CA, United States
| | - Marisa McGrath
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Siyu Chen
- Department of Chemistry, University of California, Davis, Davis, CA, United States
| | - Mariana Barboza
- Department of Chemistry, University of California, Davis, Davis, CA, United States
- Department of Anatomy, Physiology and Cell Biology, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States
| | - Matthew Frieman
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Carlito B. Lebrilla
- Department of Chemistry, University of California, Davis, Davis, CA, United States
- The Biochemistry, Molecular, Cellular and Developmental Biology (BMCDB) Graduate Group, University of California, Davis, Davis, CA, United States
- *Correspondence: Carlito B. Lebrilla,
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“Anosmia” the mysterious collateral damage of COVID-19. J Neurovirol 2022; 28:189-200. [PMID: 35249186 PMCID: PMC8898086 DOI: 10.1007/s13365-022-01060-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Revised: 10/01/2021] [Accepted: 02/01/2022] [Indexed: 12/24/2022]
Abstract
COVID-19 pandemic spreads worldwide, with more than 100 million positive cases and more than 2 million deaths. From the beginning of the COVID-19 pandemic, several otolaryngologists described many cases of a sudden loss of smell (anosmia) associated with the disease with or without additional symptoms. Anosmia is often the first and sometimes the only sign in the asymptomatic carriers of COVID-19. Still, this disorder is underestimated, and it is not life-threatening. However, it significantly decreases the quality of life. This olfactory dysfunction continues in several cases even after the nasopharyngeal swab was negative. The occurrence of anosmia can be used as a screening tool for COVID-19 patients and can be used to identify these patients to accomplish the isolation and tracking procedures. In this review, we highlighted the possible mechanisms of anosmia in COVID-19 patients, major pathologies and features of anosmia, implications of anosmia in early diagnosis of COVID-19, evaluation of the smell function during COVID-19, and management and treatment options of COVID-19 anosmia.
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43
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Pecetta S, Kratochvil S, Kato Y, Vadivelu K, Rappuoli R. Immunology and Technology of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Vaccines. Pharmacol Rev 2022; 74:313-339. [PMID: 35101964 DOI: 10.1124/pharmrev.120.000285] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
We have experienced an enormous cohesive effort of the scientific community to understand how the immune system reacts to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and how to elicit protective immunity via vaccination. This effort resulted in the development of vaccines in record time with high levels of safety, efficacy, and real-life effectiveness. However, the rapid diffusion of viral variants that escape protective antibodies prompted new studies to understand SARS-CoV-2 vulnerabilities and strategies to guide follow-up actions to increase, and maintain, the protection offered by vaccines. In this review, we report the main findings on human immunity to SARS-CoV-2 after natural infection and vaccination; we dissect the immunogenicity and efficacy of the different vaccination strategies that resulted in products widely used in the population; and we describe the impact of viral variants on vaccine-elicited immunity, summarizing the main discoveries and challenges to stay ahead of SARS-CoV-2 evolution. SIGNIFICANCE STATEMENT: This study reviewed findings on human immunity to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), analyzed the immunogenicity and efficacy of the various vaccines currently used in large vaccination campaigns or candidates in advanced clinical development, and discussed the challenging task to ensure high protective efficacy against the rapidly evolving SARS-CoV-2 virus. This manuscript was completed prior to the emergence of the Omicron variant and to global vaccine boosting efforts.
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Affiliation(s)
- Simone Pecetta
- Research and Development Centre, GSK, Siena, Italy (S.P., K.V., R.R.); Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Cambridge, Massachusetts (S.K.); IconOVir Bio, San Diego, California (Y.K.); and La Jolla Institute for Immunology, La Jolla, California (Y.K.)
| | - Sven Kratochvil
- Research and Development Centre, GSK, Siena, Italy (S.P., K.V., R.R.); Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Cambridge, Massachusetts (S.K.); IconOVir Bio, San Diego, California (Y.K.); and La Jolla Institute for Immunology, La Jolla, California (Y.K.)
| | - Yu Kato
- Research and Development Centre, GSK, Siena, Italy (S.P., K.V., R.R.); Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Cambridge, Massachusetts (S.K.); IconOVir Bio, San Diego, California (Y.K.); and La Jolla Institute for Immunology, La Jolla, California (Y.K.)
| | - Kumaran Vadivelu
- Research and Development Centre, GSK, Siena, Italy (S.P., K.V., R.R.); Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Cambridge, Massachusetts (S.K.); IconOVir Bio, San Diego, California (Y.K.); and La Jolla Institute for Immunology, La Jolla, California (Y.K.)
| | - Rino Rappuoli
- Research and Development Centre, GSK, Siena, Italy (S.P., K.V., R.R.); Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard University, Cambridge, Massachusetts (S.K.); IconOVir Bio, San Diego, California (Y.K.); and La Jolla Institute for Immunology, La Jolla, California (Y.K.)
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Cosar B, Karagulleoglu ZY, Unal S, Ince AT, Uncuoglu DB, Tuncer G, Kilinc BR, Ozkan YE, Ozkoc HC, Demir IN, Eker A, Karagoz F, Simsek SY, Yasar B, Pala M, Demir A, Atak IN, Mendi AH, Bengi VU, Cengiz Seval G, Gunes Altuntas E, Kilic P, Demir-Dora D. SARS-CoV-2 Mutations and their Viral Variants. Cytokine Growth Factor Rev 2022; 63:10-22. [PMID: 34580015 PMCID: PMC8252702 DOI: 10.1016/j.cytogfr.2021.06.001] [Citation(s) in RCA: 81] [Impact Index Per Article: 40.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Revised: 06/10/2021] [Accepted: 06/11/2021] [Indexed: 12/23/2022]
Abstract
Mutations in the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) occur spontaneously during replication. Thousands of mutations have accumulated and continue to since the emergence of the virus. As novel mutations continue appearing at the scene, naturally, new variants are increasingly observed. Since the first occurrence of the SARS-CoV-2 infection, a wide variety of drug compounds affecting the binding sites of the virus have begun to be studied. As the drug and vaccine trials are continuing, it is of utmost importance to take into consideration the SARS-CoV-2 mutations and their respective frequencies since these data could lead the way to multi-drug combinations. The lack of effective therapeutic and preventive strategies against human coronaviruses (hCoVs) necessitates research that is of interest to the clinical applications. The reason why the mutations in glycoprotein S lead to vaccine escape is related to the location of the mutation and the affinity of the protein. At the same time, it can be said that variations should occur in areas such as the receptor-binding domain (RBD), and vaccines and antiviral drugs should be formulated by targeting more than one viral protein. In this review, a literature survey in the scope of the increasing SARS-CoV-2 mutations and the viral variations is conducted. In the light of current knowledge, the various disguises of the mutant SARS-CoV-2 forms and their apparent differences from the original strain are examined as they could possibly aid in finding the most appropriate therapeutic approaches.
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Affiliation(s)
- Begum Cosar
- Başkent University, Faculty of Science and Letters, Department of Molecular Biology and Genetics, Ankara, Turkey
| | - Zeynep Yagmur Karagulleoglu
- Yıldız Technical University, Faculty of Arts and Science, Department of Molecular Biology and Genetics, İstanbul, Turkey
| | - Sinan Unal
- Yıldız Technical University, Faculty of Arts and Science, Department of Molecular Biology and Genetics, İstanbul, Turkey
| | | | - Dilruba Beyza Uncuoglu
- Ankara University, Graduate School of Natural and Applied Sciences, Department of Biology, Ankara, Turkey
| | - Gizem Tuncer
- Hacettepe University, Graduate School of Science and Engineering, General Biology Program, Ankara, Turkey; HücreCELL Biotechnology Development and Commerce, Inc., Ankara, Turkey
| | - Bugrahan Regaip Kilinc
- Kastamonu University, School of Engineering and Architecture, Department of Genetics and Bioengineering, Kastamonu, Turkey; Kastamonu University, School of Engineering and Architecture, Department of Biomedical Engineering, Kastamonu, Turkey
| | - Yunus Emre Ozkan
- Gebze Technical University, Faculty of Science, Department of Molecular Biology and Genetics, Kocaeli, Turkey
| | - Hikmet Ceyda Ozkoc
- Akdeniz University, Faculty of Medicine, Department of Medical Pharmacology, Antalya, Turkey
| | | | - Ali Eker
- Akdeniz University, Faculty of Medicine, Antalya, Turkey
| | | | | | - Bunyamin Yasar
- Alanya Alaaddin Keykubat University, Department of Molecular Medicine, Antalya, Turkey
| | - Mehmetcan Pala
- Sivas Cumhuriyet University, Faculty of Science, Department of Molecular Biology and Genetics, Sivas, Turkey
| | - Aysegul Demir
- Üsküdar University, Faculty of Engineering and Natural Sciences, Department of Molecular Biology and Genetics, İstanbul, Turkey
| | - Irem Naz Atak
- Ankara University, Faculty of Science, Department of Biology, Ankara, Turkey
| | - Aysegul Hanife Mendi
- Gazi University, Faculty of Dentistry, Department of Basic Sciences, Division of Medical Microbiology, Ankara, Turkey
| | - Vahdi Umut Bengi
- Gülhane Training and Research Hospital, Faculty of Dentistry, Department of Periodontology, Ankara, Turkey
| | - Guldane Cengiz Seval
- Ankara University, School of Medicine Department of Hematology, Cebeci, Ankara, Turkey
| | | | - Pelin Kilic
- HücreCELL Biotechnology Development and Commerce, Inc., Ankara, Turkey; Ankara University, Stem Cell Institute, Ankara, Turkey.
| | - Devrim Demir-Dora
- Akdeniz University, Faculty of Medicine, Department of Medical Pharmacology, Antalya, Turkey; Akdeniz University, Health Sciences Institute, Department of Gene and Cell Therapy, Antalya, Turkey; Akdeniz University, Health Sciences Institute, Department of Medical Biotechnology, Antalya, Turkey.
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45
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Wieland E. Immunological Biomarkers in Blood to Monitor the Course and Therapeutic Outcomes of COVID-19. Ther Drug Monit 2022; 44:148-165. [PMID: 34840314 DOI: 10.1097/ftd.0000000000000945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Accepted: 10/29/2021] [Indexed: 11/25/2022]
Abstract
BACKGROUND The COVID-19 pandemic has posed a great challenge to the medical community because little is known about its clinical course, therapeutic options, and laboratory monitoring tools for diagnosis, prognosis, and surveillance. This review focuses on immune biomarkers that can be measured in peripheral blood in a clinical laboratory under routine conditions to monitor the innate immune system response in the acute phase, as well as the adaptive immune response established both after infection and vaccination. METHODS A PubMed search was performed covering January 2020 to June 2021 to extract biomarkers suitable for monitoring the immune response and outcome of COVID-19 and therapeutic interventions, including vaccination. RESULTS To monitor the innate immune response, cytokines such as interleukin-6 or acute phase reactants such as C-reactive protein or procalcitonin can be measured on autoanalyzers complemented by automated white blood cell differential counts. The adaptive immune response can be followed by commercially available enzyme-linked immune spot assays to assess the specific activation of T cells or by monitoring immunoglobulin A (IgA), IgM, and IgG antibodies in serum to follow B-cell activation. As antigens of the SARS-CoV-2 virus, spike and nucleocapsid proteins are particularly suitable and allow differentiation between the immune response after infection or vaccination. CONCLUSIONS Routine immune monitoring of COVID-19 is feasible in clinical laboratories with commercially available instruments and reagents. Strategies such as whether biomarkers reflecting the response of the innate and adaptive immune system can be used to make predictions and assist in individualizing therapeutic interventions or vaccination strategies need to be determined in appropriate clinical trials. Promising preliminary data are already available based on single-center reports and completed or ongoing vaccination trials.
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Grishin AM, Dolgova NV, Landreth S, Fisette O, Pickering IJ, George GN, Falzarano D, Cygler M. Disulfide Bonds Play a Critical Role in the Structure and Function of the Receptor-binding Domain of the SARS-CoV-2 Spike Antigen. J Mol Biol 2022; 434:167357. [PMID: 34780781 PMCID: PMC8588607 DOI: 10.1016/j.jmb.2021.167357] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 10/30/2021] [Accepted: 11/09/2021] [Indexed: 02/07/2023]
Abstract
The current coronavirus pandemic is exerting a tremendously detrimental impact on global health. The Spike proteins of coronaviruses, responsible for cell receptor binding and viral internalization, possess multiple and frequently conserved disulfide bonds raising the question about their role in these proteins. Here, we present a detailed structural and functional investigation of the disulfide bonds of the SARS-CoV-2 Spike receptor-binding domain (RBD). Molecular dynamics simulations of the RBD predict increased flexibility of the surface loops when the four disulfide bonds of the domain are reduced. This flexibility is particularly prominent for the disulfide bond-containing surface loop (residues 456-490) that participates in the formation of the interaction surface with the Spike cell receptor ACE2. In vitro, disulfide bond reducing agents affect the RBD secondary structure, lower its melting temperature from 52 °C to 36-39 °C and decrease its binding affinity to ACE2 by two orders of magnitude at 37 °C. Consistent with these in vitro findings, the reducing agents tris(2-carboxyethyl)phosphine (TCEP) and dithiothreitol (DTT) were able to inhibit viral replication at low millimolar levels in cell-based assays. Our research demonstrates the mechanism by which the disulfide bonds contribute to the molecular structure of the RBD of the Spike protein, allowing the RBD to execute its viral function.
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Affiliation(s)
- Andrey M. Grishin
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, 107 Wiggins Road, Saskatoon, Saskatchewan S7N 5E5, Canada,Corresponding author
| | - Nataliya V. Dolgova
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, 107 Wiggins Road, Saskatoon, Saskatchewan S7N 5E5, Canada,Molecular and Environmental Sciences Group, Department of Geological Sciences, University of Saskatchewan, 114 Science Place, Saskatoon, Saskatchewan S7N 5E2, Canada
| | - Shelby Landreth
- Vaccine and Infectious Disease Organization and Department of Veterinary Microbiology, University of Saskatchewan, 120 Veterinary Road, Saskatoon, Saskatchewan S7N 5E3, Canada
| | - Olivier Fisette
- Research Computing, Information and Communications Technology, University of Saskatchewan, 114 Science Place, Saskatoon, Saskatchewan S7N 5E2, Canada
| | - Ingrid J. Pickering
- Molecular and Environmental Sciences Group, Department of Geological Sciences, University of Saskatchewan, 114 Science Place, Saskatoon, Saskatchewan S7N 5E2, Canada,Department of Chemistry, University of Saskatchewan, 110 Science Place, Saskatoon, Saskatchewan S7N 0X2, Canada
| | - Graham N. George
- Molecular and Environmental Sciences Group, Department of Geological Sciences, University of Saskatchewan, 114 Science Place, Saskatoon, Saskatchewan S7N 5E2, Canada,Department of Chemistry, University of Saskatchewan, 110 Science Place, Saskatoon, Saskatchewan S7N 0X2, Canada
| | - Darryl Falzarano
- Vaccine and Infectious Disease Organization and Department of Veterinary Microbiology, University of Saskatchewan, 120 Veterinary Road, Saskatoon, Saskatchewan S7N 5E3, Canada,Corresponding author
| | - Miroslaw Cygler
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, 107 Wiggins Road, Saskatoon, Saskatchewan S7N 5E5, Canada
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Biswas S, Mahmud S, Mita MA, Afrose S, Hasan MR, Sultana Shimu MS, Saleh MA, Mostafa-Hedeab G, Alqarni M, Obaidullah AJ, Batiha GES. Molecular Docking and Dynamics Studies to Explore Effective Inhibitory Peptides Against the Spike Receptor Binding Domain of SARS-CoV-2. Front Mol Biosci 2022; 8:791642. [PMID: 35187069 PMCID: PMC8851422 DOI: 10.3389/fmolb.2021.791642] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 11/24/2021] [Indexed: 01/15/2023] Open
Abstract
The spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has become a pandemic due to the high transmission and mortality rate of this virus. The world health and economic sectors have been severely affected by this deadly virus, exacerbated by the lack of sufficient efficient vaccines. The design of effective drug candidates and their rapid development is necessary to combat this virus. In this study, we selected 23 antimicrobial peptides from the literature and predicted their structure using PEP-FOLD 3.5. In addition, we docked them to the SARS-CoV-2 spike protein receptor-binding domain (RBD) to study their capability to inhibit the RBD, which plays a significant role in virus binding, fusion and entry into the host cell. We used several docking programs including HDOCK, HPEPDOCK, ClusPro, and HawkDock to calculate the binding energy of the protein-peptide complexes. We identified four peptides with high binding free energy and docking scores. The docking results were further verified by molecular dynamics (MD) simulations to characterize the protein-peptide complexes in terms of their root-mean-square fluctuation (RMSF), root-mean-square deviation (RMSD), radius of gyration (Rg), solvent-accessible surface area (SASA), and hydrogen bond formation. Allergenicity and toxicity predictions suggested that the peptides we identified were non-allergenic and non-toxic. This study suggests that these four antimicrobial peptides could inhibit the RBD of SARS-CoV-2. Future in vitro and in vivo studies are necessary to confirm this.
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Affiliation(s)
- Suvro Biswas
- Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, Bangladesh
| | - Shafi Mahmud
- Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, Bangladesh
- *Correspondence: Shafi Mahmud, ; Md. Abu Saleh,
| | - Mohasana Akter Mita
- Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, Bangladesh
| | - Shamima Afrose
- Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, Bangladesh
| | - Md. Robiul Hasan
- Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, Bangladesh
| | | | - Md. Abu Saleh
- Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, Bangladesh
- *Correspondence: Shafi Mahmud, ; Md. Abu Saleh,
| | - Gomaa Mostafa-Hedeab
- Pharmacology Department and Health Research Unit-medical College, Jouf University, Jouf, Saudi Arabia
- Pharmacology Department, Faculty of Medicine, Beni-Suef University, Beni Suef, Egypt
| | - Mohammed Alqarni
- Department of Pharmaceutical Chemistry, College of Pharmacy, Taif University, Taif, Saudi Arabia
| | - Ahmad J. Obaidullah
- Drug Exploration and Development Chair (DEDC), Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Gaber El-Saber Batiha
- Department of Pharmacology and Therapeutics, Faculty of Veterinary Medicine, Damanhour University, Damanhour, Egypt
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Oluwagbemi OO, Oladipo EK, Dairo EO, Ayeni AE, Irewolede BA, Jimah EM, Oyewole MP, Olawale BM, Adegoke HM, Ogunleye AJ. Computational construction of a glycoprotein multi-epitope subunit vaccine candidate for old and new South-African SARS-CoV-2 virus strains. INFORMATICS IN MEDICINE UNLOCKED 2022; 28:100845. [PMID: 35071728 PMCID: PMC8760845 DOI: 10.1016/j.imu.2022.100845] [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: 10/31/2021] [Revised: 12/28/2021] [Accepted: 01/01/2022] [Indexed: 12/19/2022] Open
Abstract
The discovery of a new SARS-CoV-2 virus strain in South Africa presents a major public health threat, therefore contributing to increased infections and transmission rates during the second wave of the global pandemic. This study lays the groundwork for the development of a novel subunit vaccine candidate from the circulating strains of South African SARS-CoV-2 and provides an understanding of the molecular epidemiological trend of the circulating strains. A total of 475 whole-genome nucleotide sequences from South Africa submitted between December 1, 2020 and February 15, 2021 available at the GISAID database were retrieved based on its size, coverage level and hosts. To obtain the distribution of the clades and lineages of South African SARS-CoV-2 circulating strains, the metadata of the sequence retrieved were subjected to an epidemiological analysis. There was a prediction of the cytotoxic T lymphocytes (CTL), Helper T cells (HTL) and B-cell epitopes. Furthermore, there was allergenicity, antigenicity and toxicity predictions on the epitopes. The analysis of the physicochemical properties of the vaccine construct was performed; the secondary structure, tertiary structure and B-cell 3D conformational structure of the vaccine construct were predicted. Also, molecular binding simulations and dynamics simulations were adopted in the prediction of the vaccine construct's stability and binding affinity with TLRs. Result obtained from the metadata analysis indicated lineage B.1.351 to be in higher circulation among various circulating strains of SARS-CoV-2 in South Africa and GH has the highest number of circulating clades. The construct of the novel vaccine was antigenic, non-allergenic and non-toxic. The Instability index (II) score and aliphatic index were estimated as 41.74 and 78.72 respectively. The computed half-life in mammalian reticulocytes was 4.4 h in vitro, for yeast and in E. coli was >20 h and >10 h in vivo respectively. The grand average of hydropathicity (GRAVY) score is estimated to be -0.129, signifying the hydrophilic nature of the protein. The molecular docking indicates that the vaccine construct has a high binding affinity towards the TLRs with TLR 3 having the highest binding energy (-1203.2 kcal/mol) and TLR 9 with the lowest (-1559.5 kcal/mol). These results show that the vaccine construct is promising and should be evaluated using animal model.
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Affiliation(s)
- Olugbenga Oluseun Oluwagbemi
- Department of Computer Science and Information Technology, Sol Plaatje University, 8301, Kimberley, South Africa
- Department of Mathematical Sciences, Stellenbosch University, 7602, Matieland, South Africa
- National Institute of Theoretical and Computational Sciences (NiTheCS), South Africa
| | - Elijah Kolawole Oladipo
- Department of Microbiology, Laboratory of Molecular Biology, Immunology and Bioinformatics, Adeleke University, Ede, Osun State, Nigeria
- Genomics Unit, Helix Biogen Institute, Ogbomoso, Oyo State, Nigeria
| | - Emmanuel Oluwatobi Dairo
- Department of Virology, College of Medicine, University of Ibadan, Ibadan, Oyo State, Nigeria
- Genomics Unit, Helix Biogen Institute, Ogbomoso, Oyo State, Nigeria
| | - Ayodele Eugene Ayeni
- Genomics Unit, Helix Biogen Institute, Ogbomoso, Oyo State, Nigeria
- Department of Medical Microbiology and Parasitology, Faculty of Basic Medical Sciences, University of Ibadan, Ibadan, Oyo State, Nigeria
| | | | - Esther Moradeyo Jimah
- Department of Medical Microbiology and Parasitology, University of Ilorin, Kwara State, Nigeria
- Genomics Unit, Helix Biogen Institute, Ogbomoso, Oyo State, Nigeria
| | - Moyosoluwa Precious Oyewole
- Department of Biochemistry, Ladoke Akintola University of Technology, Ogbomoso, Oyo State, Nigeria
- Genomics Unit, Helix Biogen Institute, Ogbomoso, Oyo State, Nigeria
| | - Boluwatife Mary Olawale
- Reproduction and Bioinformatics Unit, Department of Physiology, Ladoke Akintola University of Technology, Ogbomoso, Oyo State, Nigeria
- Genomics Unit, Helix Biogen Institute, Ogbomoso, Oyo State, Nigeria
| | | | - Adewale Joseph Ogunleye
- Moscow Institute of Physics and Technology, 141701, Dolgoprudny, Moscow Oblast, Russian Federation
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Abstract
The unprecedented public health and economic impact of the COVID-19 pandemic caused by infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been met with an equally unprecedented scientific response. Much of this response has focused, appropriately, on the mechanisms of SARS-CoV-2 entry into host cells, and in particular the binding of the spike (S) protein to its receptor, angiotensin-converting enzyme 2 (ACE2), and subsequent membrane fusion. This Review provides the structural and cellular foundations for understanding the multistep SARS-CoV-2 entry process, including S protein synthesis, S protein structure, conformational transitions necessary for association of the S protein with ACE2, engagement of the receptor-binding domain of the S protein with ACE2, proteolytic activation of the S protein, endocytosis and membrane fusion. We define the roles of furin-like proteases, transmembrane protease, serine 2 (TMPRSS2) and cathepsin L in these processes, and delineate the features of ACE2 orthologues in reservoir animal species and S protein adaptations that facilitate efficient human transmission. We also examine the utility of vaccines, antibodies and other potential therapeutics targeting SARS-CoV-2 entry mechanisms. Finally, we present key outstanding questions associated with this critical process.
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Affiliation(s)
- Cody B Jackson
- Department of Immunology and Microbiology, Scripps Research, Jupiter, FL, USA
- Charles E. Schmidt College of Medicine, Florida Atlantic University, Boca Raton, FL, USA
| | - Michael Farzan
- Department of Immunology and Microbiology, Scripps Research, Jupiter, FL, USA
| | - Bing Chen
- Division of Molecular Medicine, Boston Children's Hospital, Boston, MA, USA.
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA.
| | - Hyeryun Choe
- Department of Immunology and Microbiology, Scripps Research, Jupiter, FL, USA.
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50
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Implications of testicular ACE2 and the renin-angiotensin system for SARS-CoV-2 on testis function. Nat Rev Urol 2022; 19:116-127. [PMID: 34837081 PMCID: PMC8622117 DOI: 10.1038/s41585-021-00542-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/26/2021] [Indexed: 12/16/2022]
Abstract
Although many studies have focused on SARS-CoV-2 infection in the lungs, comparatively little is known about the potential effects of the virus on male fertility. SARS-CoV-2 infection of target cells requires the presence of furin, angiotensin-converting enzyme 2 (ACE2) receptors, and transmembrane protease serine 2 (TMPRSS2). Thus, cells in the body that express these proteins might be highly susceptible to viral entry and downstream effects. Currently, reports regarding the expression of the viral entry proteins in the testes are conflicting; however, other members of the SARS-CoV family of viruses - such as SARS-CoV - have been suspected to cause testicular dysfunction and/or orchitis. SARS-CoV-2, which displays many similarities to SARS-CoV, could potentially cause similar adverse effects. Commonalities between SARS family members, taken in combination with sparse reports of testicular discomfort and altered hormone levels in patients with SARS-CoV-2, might indicate possible testicular dysfunction. Thus, SARS-CoV-2 infection has the potential for effects on testis somatic and germline cells and experimental approaches might be required to help identify potential short-term and long-term effects of SARS-CoV-2 on male fertility.
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