In silico design of multi-epitope-based peptide vaccine against SARS-CoV-2 using its spike protein. 2022

Debarghya Mitra, and Janmejay Pandey, and Alok Jain, and Shiv Swaroop
Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, Ajmer, Rajasthan, India.

SARS-CoV-2 has been efficient in ensuring that many countries are brought to a standstill. With repercussions ranging from rampant mortality, fear, paranoia, and economic recession, the virus has brought together countries to look at possible therapeutic countermeasures. With prophylactic interventions possibly months away from being particularly effective, a slew of measures and possibilities concerning the design of vaccines are being worked upon. We attempted a structure-based approach utilizing a combination of epitope prediction servers and Molecular dynamic (MD) simulations to develop a multi-epitope-based subunit vaccine that involves the two subunits of the spike glycoprotein of SARS-CoV-2 (S1 and S2) coupled with a substantially effective chimeric adjuvant to create stable vaccine constructs. The designed constructs were evaluated based on their docking with Toll-Like Receptor (TLR) 4. Our findings provide an epitope-based peptide fragment that can be a potential candidate for the development of a vaccine against SARS-CoV-2. Recent experimental studies based on determining immunodominant regions across the spike glycoprotein of SARS-CoV-2 indicate the presence of the predicted epitopes included in this study.Communicated by Ramaswamy H. Sarma.

UI MeSH Term Description Entries
D006801 Humans Members of the species Homo sapiens. Homo sapiens,Man (Taxonomy),Human,Man, Modern,Modern Man
D000086382 COVID-19 A viral disorder generally characterized by high FEVER; COUGH; DYSPNEA; CHILLS; PERSISTENT TREMOR; MUSCLE PAIN; HEADACHE; SORE THROAT; a new loss of taste and/or smell (see AGEUSIA and ANOSMIA) and other symptoms of a VIRAL PNEUMONIA. In severe cases, a myriad of coagulopathy associated symptoms often correlating with COVID-19 severity is seen (e.g., BLOOD COAGULATION; THROMBOSIS; ACUTE RESPIRATORY DISTRESS SYNDROME; SEIZURES; HEART ATTACK; STROKE; multiple CEREBRAL INFARCTIONS; KIDNEY FAILURE; catastrophic ANTIPHOSPHOLIPID ANTIBODY SYNDROME and/or DISSEMINATED INTRAVASCULAR COAGULATION). In younger patients, rare inflammatory syndromes are sometimes associated with COVID-19 (e.g., atypical KAWASAKI SYNDROME; TOXIC SHOCK SYNDROME; pediatric multisystem inflammatory disease; and CYTOKINE STORM SYNDROME). A coronavirus, SARS-CoV-2, in the genus BETACORONAVIRUS is the causative agent. 2019 Novel Coronavirus Disease,2019 Novel Coronavirus Infection,2019-nCoV Disease,2019-nCoV Infection,COVID-19 Pandemic,COVID-19 Pandemics,COVID-19 Virus Disease,COVID-19 Virus Infection,Coronavirus Disease 2019,Coronavirus Disease-19,SARS Coronavirus 2 Infection,SARS-CoV-2 Infection,Severe Acute Respiratory Syndrome Coronavirus 2 Infection,COVID19,2019 nCoV Disease,2019 nCoV Infection,2019-nCoV Diseases,2019-nCoV Infections,COVID 19,COVID 19 Pandemic,COVID 19 Virus Disease,COVID 19 Virus Infection,COVID-19 Virus Diseases,COVID-19 Virus Infections,Coronavirus Disease 19,Disease 2019, Coronavirus,Disease, 2019-nCoV,Disease, COVID-19 Virus,Infection, 2019-nCoV,Infection, COVID-19 Virus,Infection, SARS-CoV-2,Pandemic, COVID-19,SARS CoV 2 Infection,SARS-CoV-2 Infections,Virus Disease, COVID-19,Virus Infection, COVID-19
D000086402 SARS-CoV-2 A species of BETACORONAVIRUS causing atypical respiratory disease (COVID-19) in humans. The organism was first identified in 2019 in Wuhan, China. The natural host is the Chinese intermediate horseshoe bat, RHINOLOPHUS affinis. 2019 Novel Coronavirus,COVID-19 Virus,COVID19 Virus,Coronavirus Disease 2019 Virus,SARS Coronavirus 2,SARS-CoV-2 Virus,Severe Acute Respiratory Syndrome Coronavirus 2,Wuhan Coronavirus,Wuhan Seafood Market Pneumonia Virus,2019-nCoV,2019 Novel Coronaviruses,COVID 19 Virus,COVID-19 Viruses,COVID19 Viruses,Coronavirus 2, SARS,Coronavirus, 2019 Novel,Coronavirus, Wuhan,Novel Coronavirus, 2019,SARS CoV 2 Virus,SARS-CoV-2 Viruses,Virus, COVID-19,Virus, COVID19,Virus, SARS-CoV-2,Viruses, COVID19
D000086663 COVID-19 Vaccines Vaccines or candidate vaccines containing SARS-CoV-2 component antigens, genetic materials, or inactivated SARS-CoV-2 virus, and designed to prevent COVID-19. 2019 Novel Coronavirus Vaccine,2019 Novel Coronavirus Vaccines,2019-nCoV Vaccine,2019-nCoV Vaccines,COVID 19 Vaccine,COVID-19 Vaccine,COVID-19 Virus Vaccine,COVID-19 Virus Vaccines,COVID19 Vaccine,COVID19 Vaccines,COVID19 Virus Vaccine,COVID19 Virus Vaccines,Coronavirus Disease 2019 Vaccine,Coronavirus Disease 2019 Vaccines,Coronavirus Disease 2019 Virus Vaccine,Coronavirus Disease 2019 Virus Vaccines,Coronavirus Disease-19 Vaccine,Coronavirus Disease-19 Vaccines,SARS Coronavirus 2 Vaccines,SARS-CoV-2 Vaccine,SARS-CoV-2 Vaccines,SARS2 Vaccine,SARS2 Vaccines,2019 nCoV Vaccine,2019 nCoV Vaccines,COVID 19 Vaccines,COVID 19 Virus Vaccine,COVID 19 Virus Vaccines,Coronavirus Disease 19 Vaccine,Coronavirus Disease 19 Vaccines,SARS CoV 2 Vaccine,SARS CoV 2 Vaccines,Vaccine, 2019-nCoV,Vaccine, COVID 19,Vaccine, COVID-19,Vaccine, COVID-19 Virus,Vaccine, COVID19,Vaccine, COVID19 Virus,Vaccine, Coronavirus Disease-19,Vaccine, SARS-CoV-2,Vaccine, SARS2,Vaccines, 2019-nCoV,Vaccines, COVID-19,Vaccines, COVID-19 Virus,Vaccines, COVID19,Vaccines, COVID19 Virus,Vaccines, Coronavirus Disease-19,Vaccines, SARS-CoV-2,Vaccines, SARS2,Virus Vaccine, COVID-19,Virus Vaccine, COVID19,Virus Vaccines, COVID-19,Virus Vaccines, COVID19
D062105 Molecular Docking Simulation A computer simulation technique that is used to model the interaction between two molecules. Typically the docking simulation measures the interactions of a small molecule or ligand with a part of a larger molecule such as a protein. Molecular Docking,Molecular Docking Simulations,Molecular Docking Analysis,Analysis, Molecular Docking,Docking Analysis, Molecular,Docking Simulation, Molecular,Docking, Molecular,Molecular Docking Analyses,Molecular Dockings,Simulation, Molecular Docking
D018984 Epitopes, T-Lymphocyte Antigenic determinants recognized and bound by the T-cell receptor. Epitopes recognized by the T-cell receptor are often located in the inner, unexposed side of the antigen, and become accessible to the T-cell receptors after proteolytic processing of the antigen. T-Cell Epitopes,T-Lymphocyte Epitopes,T-Cell Epitope,T-Lymphocyte Epitope,Epitope, T-Cell,Epitope, T-Lymphocyte,Epitopes, T Lymphocyte,Epitopes, T-Cell,T Cell Epitope,T Cell Epitopes,T Lymphocyte Epitope,T Lymphocyte Epitopes
D018985 Epitopes, B-Lymphocyte Antigenic determinants recognized and bound by the B-cell receptor. Epitopes recognized by the B-cell receptor are located on the surface of the antigen. B-Cell Epitopes,B-Lymphocyte Epitopes,B-Cell Epitope,B-Lymphocyte Epitope,B Cell Epitope,B Cell Epitopes,B Lymphocyte Epitope,B Lymphocyte Epitopes,Epitope, B-Cell,Epitope, B-Lymphocyte,Epitopes, B Lymphocyte,Epitopes, B-Cell
D022223 Vaccines, Subunit Vaccines consisting of one or more antigens that stimulate a strong immune response. They are purified from microorganisms or produced by recombinant DNA techniques, or they can be chemically synthesized peptides. Subunit Vaccine,Subunit Vaccines,Vaccine, Subunit
D064370 Spike Glycoprotein, Coronavirus A class I viral fusion protein that forms the characteristic spikes, or peplomers, found on the viral surface that mediate virus attachment, fusion, and entry into the host cell. During virus maturation, it is cleaved into two subunits: S1, which binds to receptors in the host cell, and S2, which mediates membrane fusion. Spike Glycoprotein, Bovine Coronavirus,Spike Glycoproteins, Coronavirus,E2 Spike Glycoprotein, Coronavirus,Glycoprotein S, Coronavirus,Spike Glycoprotein S1, Coronavirus,Spike Protein S2, Coronavirus,Spike Protein, Coronavirus,Coronavirus Spike Glycoprotein,Coronavirus Spike Protein

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