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1.
PLoS One ; 16(11): e0258645, 2021.
Article in English | MEDLINE | ID: covidwho-1518355

ABSTRACT

All approved coronavirus disease 2019 (COVID-19) vaccines in current use are safe, effective, and reduce the risk of severe illness. Although data on the immunological presentation of patients with COVID-19 is limited, increasing experimental evidence supports the significant contribution of B and T cells towards the resolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. Despite the availability of several COVID-19 vaccines with high efficacy, more effective vaccines are still needed to protect against the new variants of SARS-CoV-2. Employing a comprehensive immunoinformatic prediction algorithm and leveraging the genetic closeness with SARS-CoV, we have predicted potential immune epitopes in the structural proteins of SARS-CoV-2. The S and N proteins of SARS-CoV-2 and SARS-CoVs are main targets of antibody detection and have motivated us to design four multi-epitope vaccines which were based on our predicted B- and T-cell epitopes of SARS-CoV-2 structural proteins. The cardinal epitopes selected for the vaccine constructs are predicted to possess antigenic, non-allergenic, and cytokine-inducing properties. Additionally, some of the predicted epitopes have been experimentally validated in published papers. Furthermore, we used the C-ImmSim server to predict effective immune responses induced by the epitope-based vaccines. Taken together, the immune epitopes predicted in this study provide a platform for future experimental validations which may facilitate the development of effective vaccine candidates and epitope-based serological diagnostic assays.


Subject(s)
Computational Biology , Epitope Mapping , SARS-CoV-2/immunology , Viral Structural Proteins/immunology , Amino Acid Sequence , COVID-19 Vaccines/chemistry , COVID-19 Vaccines/immunology , Databases as Topic , Epitopes, B-Lymphocyte/chemistry , Epitopes, B-Lymphocyte/immunology , Epitopes, T-Lymphocyte/chemistry , Epitopes, T-Lymphocyte/immunology , Histocompatibility Antigens Class I/metabolism , Humans , Models, Molecular , Protein Conformation , Reproducibility of Results , Viral Structural Proteins/chemistry
2.
Viruses ; 13(11)2021 10 27.
Article in English | MEDLINE | ID: covidwho-1488757

ABSTRACT

The current COVID-19 pandemic has highlighted the need for the research community to develop a better understanding of viruses, in particular their modes of infection and replicative lifecycles, to aid in the development of novel vaccines and much needed anti-viral therapeutics. Several viruses express proteins capable of forming pores in host cellular membranes, termed "Viroporins". They are a family of small hydrophobic proteins, with at least one amphipathic domain, which characteristically form oligomeric structures with central hydrophilic domains. Consequently, they can facilitate the transport of ions through the hydrophilic core. Viroporins localise to host membranes such as the endoplasmic reticulum and regulate ion homeostasis creating a favourable environment for viral infection. Viroporins also contribute to viral immune evasion via several mechanisms. Given that viroporins are often essential for virion assembly and egress, and as their structural features tend to be evolutionarily conserved, they are attractive targets for anti-viral therapeutics. This review discusses the current knowledge of several viroporins, namely Influenza A virus (IAV) M2, Human Immunodeficiency Virus (HIV)-1 Viral protein U (Vpu), Hepatitis C Virus (HCV) p7, Human Papillomavirus (HPV)-16 E5, Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV) Open Reading Frame (ORF)3a and Polyomavirus agnoprotein. We highlight the intricate but broad immunomodulatory effects of these viroporins and discuss the current antiviral therapies that target them; continually highlighting the need for future investigations to focus on novel therapeutics in the treatment of existing and future emergent viruses.


Subject(s)
Immunomodulation , Ion Channels/metabolism , Viroporin Proteins/metabolism , Virus Diseases/drug therapy , Viruses/metabolism , Antiviral Agents/pharmacology , Antiviral Agents/therapeutic use , Autophagy , Host-Pathogen Interactions , Human Immunodeficiency Virus Proteins/chemistry , Human Immunodeficiency Virus Proteins/metabolism , Immune Evasion , Inflammasomes/immunology , Oncogene Proteins, Viral/chemistry , Oncogene Proteins, Viral/metabolism , Viral Matrix Proteins/chemistry , Viral Matrix Proteins/metabolism , Viral Proteins/chemistry , Viral Proteins/metabolism , Viral Regulatory and Accessory Proteins/chemistry , Viral Regulatory and Accessory Proteins/metabolism , Viral Structural Proteins/chemistry , Viral Structural Proteins/metabolism , Viroporin Proteins/chemistry , Virus Diseases/immunology , Virus Diseases/virology , Viruses/drug effects , Viruses/immunology , Viruses/pathogenicity
3.
Hum Gene Ther ; 32(11-12): 541-562, 2021 06.
Article in English | MEDLINE | ID: covidwho-1216585

ABSTRACT

Severe acute respiratory syndrome (SARS) is a newly emerging infectious disease (COVID-19) caused by the novel coronavirus SARS-coronavirus 2 (CoV-2). To combat the devastating spread of SARS-CoV-2, extraordinary efforts from numerous laboratories have focused on the development of effective and safe vaccines. Traditional live-attenuated or inactivated viral vaccines are not recommended for immunocompromised patients as the attenuated virus can still cause disease via phenotypic or genotypic reversion. Subunit vaccines require repeated dosing and adjuvant use to be effective, and DNA vaccines exhibit lower immune responses. mRNA vaccines can be highly unstable under physiological conditions. On the contrary, naturally antigenic viral vectors with well-characterized structure and safety profile serve as among the most effective gene carriers to provoke immune response via heterologous gene transfer. Viral vector-based vaccines induce both an effective cellular immune response and a humoral immune response owing to their natural adjuvant properties via transduction of immune cells. Consequently, viral vectored vaccines carrying the SARS-CoV-2 spike protein have recently been generated and successfully used to activate cytotoxic T cells and develop a neutralizing antibody response. Recent progress in SARS-CoV-2 vaccines, with an emphasis on gene therapy viral vector-based vaccine development, is discussed in this review.


Subject(s)
COVID-19 Vaccines/pharmacology , Genetic Vectors , Vaccines, Attenuated/pharmacology , Vaccines, Synthetic/pharmacology , Viral Structural Proteins/chemistry , Adenoviridae/genetics , Genetic Therapy/methods , Genetic Vectors/chemistry , Genetic Vectors/genetics , Humans , Lentivirus/genetics , SARS-CoV-2/genetics , Vaccines, DNA/pharmacology , Viral Structural Proteins/genetics , Viral Structural Proteins/metabolism
4.
J Med Virol ; 93(5): 2790-2798, 2021 May.
Article in English | MEDLINE | ID: covidwho-1196503

ABSTRACT

Coronavirus disease-2019 (COVID-19), the ongoing pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a major threat to the entire human race. It is reported that SARS-CoV-2 seems to have relatively low pathogenicity and higher transmissibility than previously outbroke SARS-CoV. To explore the reason of the increased transmissibility of SARS-CoV-2 compared with SARS-CoV, we have performed a comparative analysis on the structural proteins (spike, envelope, membrane, and nucleoprotein) of two viruses. Our analysis revealed that extensive substitutions of hydrophobic to polar and charged amino acids in spike glycoproteins of SARS-CoV2 creates an intrinsically disordered region (IDR) at the beginning of membrane-fusion subunit and intrinsically disordered residues in fusion peptide. IDR provides a potential site for proteolysis by furin and enriched disordered residues facilitate prompt fusion of the SARS-CoV2 with host membrane by recruiting molecular recognition features. Here, we have hypothesized that mutation-driven accumulation of intrinsically disordered residues in spike glycoproteins play dual role in enhancing viral transmissibility than previous SARS-coronavirus. These analyses may help in epidemic surveillance and preventive measures against COVID-19.


Subject(s)
COVID-19/epidemiology , Disease Outbreaks , Membrane Fusion/genetics , SARS-CoV-2/genetics , Spike Glycoprotein, Coronavirus/genetics , Amino Acid Sequence , COVID-19/transmission , COVID-19/virology , Humans , Mutation , Protein Subunits , SARS Virus/genetics , SARS-CoV-2/metabolism , Spike Glycoprotein, Coronavirus/chemistry , Spike Glycoprotein, Coronavirus/metabolism , Viral Structural Proteins/chemistry , Viral Structural Proteins/genetics , Viral Structural Proteins/metabolism , Virus Internalization
5.
Cells ; 10(4)2021 04 06.
Article in English | MEDLINE | ID: covidwho-1178117

ABSTRACT

Coronavirus belongs to the family of Coronaviridae, comprising single-stranded, positive-sense RNA genome (+ ssRNA) of around 26 to 32 kilobases, and has been known to cause infection to a myriad of mammalian hosts, such as humans, cats, bats, civets, dogs, and camels with varied consequences in terms of death and debilitation. Strikingly, novel coronavirus (2019-nCoV), later renamed as severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), and found to be the causative agent of coronavirus disease-19 (COVID-19), shows 88% of sequence identity with bat-SL-CoVZC45 and bat-SL-CoVZXC21, 79% with SARS-CoV and 50% with MERS-CoV, respectively. Despite key amino acid residual variability, there is an incredible structural similarity between the receptor binding domain (RBD) of spike protein (S) of SARS-CoV-2 and SARS-CoV. During infection, spike protein of SARS-CoV-2 compared to SARS-CoV displays 10-20 times greater affinity for its cognate host cell receptor, angiotensin-converting enzyme 2 (ACE2), leading proteolytic cleavage of S protein by transmembrane protease serine 2 (TMPRSS2). Following cellular entry, the ORF-1a and ORF-1ab, located downstream to 5' end of + ssRNA genome, undergo translation, thereby forming two large polyproteins, pp1a and pp1ab. These polyproteins, following protease-induced cleavage and molecular assembly, form functional viral RNA polymerase, also referred to as replicase. Thereafter, uninterrupted orchestrated replication-transcription molecular events lead to the synthesis of multiple nested sets of subgenomic mRNAs (sgRNAs), which are finally translated to several structural and accessory proteins participating in structure formation and various molecular functions of virus, respectively. These multiple structural proteins assemble and encapsulate genomic RNA (gRNA), resulting in numerous viral progenies, which eventually exit the host cell, and spread infection to rest of the body. In this review, we primarily focus on genomic organization, structural and non-structural protein components, and potential prospective molecular targets for development of therapeutic drugs, convalescent plasm therapy, and a myriad of potential vaccines to tackle SARS-CoV-2 infection.


Subject(s)
COVID-19/therapy , COVID-19/virology , Drug Discovery , SARS-CoV-2/physiology , Viral Nonstructural Proteins/metabolism , Viral Structural Proteins/metabolism , Animals , Antibodies, Neutralizing/pharmacology , Antibodies, Neutralizing/therapeutic use , COVID-19/drug therapy , COVID-19/metabolism , Drug Design , Humans , Immunization, Passive , Molecular Targeted Therapy , SARS-CoV-2/drug effects , SARS-CoV-2/genetics , Viral Nonstructural Proteins/chemistry , Viral Nonstructural Proteins/genetics , Viral Structural Proteins/chemistry , Viral Structural Proteins/genetics , Virus Internalization/drug effects , Virus Replication/drug effects
6.
Genome ; 64(7): 665-678, 2021 Jul.
Article in English | MEDLINE | ID: covidwho-1166573

ABSTRACT

SARS-CoV-2 is mutating and creating divergent variants across the world. An in-depth investigation of the amino acid substitutions in the genomic signature of SARS-CoV-2 proteins is highly essential for understanding its host adaptation and infection biology. A total of 9587 SARS-CoV-2 structural protein sequences collected from 49 different countries are used to characterize protein-wise variants, substitution patterns (type and location), and major substitution changes. The majority of the substitutions are distinct, mostly in a particular location, and lead to a change in an amino acid's biochemical properties. In terms of mutational changes, envelope (E) and membrane (M) proteins are relatively more stable than nucleocapsid (N) and spike (S) proteins. Several co-occurrence substitutions are observed, particularly in S and N proteins. Substitution specific to active sub-domains reveals that heptapeptide repeat, fusion peptides, transmembrane in S protein, and N-terminal and C-terminal domains in the N protein are remarkably mutated. We also observe a few deleterious mutations in the above domains. The overall study on non-synonymous mutation in structural proteins of SARS-CoV-2 at the start of the pandemic indicates a diversity amongst virus sequences.


Subject(s)
SARS-CoV-2/chemistry , Viral Structural Proteins/chemistry , Viral Structural Proteins/genetics , Amino Acid Substitution , Amino Acids/chemistry , Coronavirus Envelope Proteins/chemistry , Coronavirus Envelope Proteins/genetics , Coronavirus Nucleocapsid Proteins/chemistry , Coronavirus Nucleocapsid Proteins/genetics , Humans , Mutation , Mutation Rate , Phosphoproteins/chemistry , Phosphoproteins/genetics , SARS-CoV-2/genetics , SARS-CoV-2/isolation & purification , Spike Glycoprotein, Coronavirus/chemistry , Spike Glycoprotein, Coronavirus/genetics , Viral Matrix Proteins/chemistry , Viral Matrix Proteins/genetics
7.
Int J Mol Sci ; 22(5)2021 Mar 05.
Article in English | MEDLINE | ID: covidwho-1129735

ABSTRACT

We observed substantial differences in predicted Major Histocompatibility Complex II (MHCII) epitope presentation of SARS-CoV-2 proteins for different populations but only minor differences in predicted MHCI epitope presentation. A comparison of this predicted epitope MHC-coverage revealed for the early phase of infection spread (till day 15 after reaching 128 observed infection cases) highly significant negative correlations with the case fatality rate. Specifically, this was observed in different populations for MHC class II presentation of the viral spike protein (p-value: 0.0733 for linear regression), the envelope protein (p-value: 0.023), and the membrane protein (p-value: 0.00053), indicating that the high case fatality rates of COVID-19 observed in some countries seem to be related with poor MHC class II presentation and hence weak adaptive immune response against these viral envelope proteins. Our results highlight the general importance of the SARS-CoV-2 structural proteins in immunological control in early infection spread looking at a global census in various countries and taking case fatality rate into account. Other factors such as health system and control measures become more important after the early spread. Our study should encourage further studies on MHCII alleles as potential risk factors in COVID-19 including assessment of local populations and specific allele distributions.


Subject(s)
COVID-19/mortality , Histocompatibility Antigens Class II/genetics , Histocompatibility Antigens Class II/immunology , SARS-CoV-2/chemistry , Viral Structural Proteins/chemistry , Adaptive Immunity , Alleles , COVID-19/immunology , COVID-19/transmission , Computational Biology/methods , Correlation of Data , Epitopes, B-Lymphocyte/genetics , Epitopes, B-Lymphocyte/immunology , Epitopes, T-Lymphocyte/genetics , Epitopes, T-Lymphocyte/immunology , HLA Antigens/genetics , Histocompatibility Antigens Class I/genetics , Histocompatibility Antigens Class I/immunology , Humans , Mortality , SARS-CoV-2/immunology , Viral Structural Proteins/immunology
8.
PLoS One ; 16(2): e0247396, 2021.
Article in English | MEDLINE | ID: covidwho-1090539

ABSTRACT

Among various delivery systems for vaccine and drug delivery, cell-penetrating peptides (CPPs) have been known as a potent delivery system because of their capability to penetrate cell membranes and deliver some types of cargoes into cells. Several CPPs were found in the proteome of viruses such as Tat originated from human immunodeficiency virus-1 (HIV-1), and VP22 derived from herpes simplex virus-1 (HSV-1). In the current study, a wide-range of CPPs was identified in the proteome of SARS-CoV-2, a new member of coronaviruses family, using in silico analyses. These CPPs may play a main role for high penetration of virus into cells and infection of host. At first, we submitted the proteome of SARS-CoV-2 to CellPPD web server that resulted in a huge number of CPPs with ten residues in length. Afterward, we submitted the predicted CPPs to C2Pred web server for evaluation of the probability of each peptide. Then, the uptake efficiency of each peptide was investigated using CPPred-RF and MLCPP web servers. Next, the physicochemical properties of the predicted CPPs including net charge, theoretical isoelectric point (pI), amphipathicity, molecular weight, and water solubility were calculated using protparam and pepcalc tools. In addition, the probability of membrane binding potential and cellular localization of each CPP were estimated by Boman index using APD3 web server, D factor, and TMHMM web server. On the other hand, the immunogenicity, toxicity, allergenicity, hemolytic potency, and half-life of CPPs were predicted using various web servers. Finally, the tertiary structure and the helical wheel projection of some CPPs were predicted by PEP-FOLD3 and Heliquest web servers, respectively. These CPPs were divided into: a) CPP containing tumor homing motif (RGD) and/or tumor penetrating motif (RXXR); b) CPP with the highest Boman index; c) CPP with high half-life (~100 hour) in mammalian cells, and d) CPP with +5.00 net charge. Based on the results, we found a large number of novel CPPs with various features. Some of these CPPs possess tumor-specific motifs which can be evaluated in cancer therapy. Furthermore, the novel and potent CPPs derived from SARS-CoV-2 may be used alone or conjugated to some sequences such as nuclear localization sequence (NLS) for vaccine and drug delivery.


Subject(s)
COVID-19 Vaccines/chemistry , Cell-Penetrating Peptides/chemistry , Computational Biology , Computer Simulation , Drug Delivery Systems , Proteome , SARS-CoV-2/chemistry , Animals , COVID-19 , COVID-19 Vaccines/genetics , COVID-19 Vaccines/metabolism , Cell-Penetrating Peptides/genetics , Cell-Penetrating Peptides/metabolism , HIV-1/chemistry , HIV-1/genetics , Herpesvirus 1, Human/chemistry , Herpesvirus 1, Human/genetics , Humans , SARS-CoV-2/genetics , SARS-CoV-2/metabolism , Viral Structural Proteins/chemistry , Viral Structural Proteins/genetics , tat Gene Products, Human Immunodeficiency Virus/chemistry , tat Gene Products, Human Immunodeficiency Virus/genetics
9.
Emerg Microbes Infect ; 9(1): 2653-2662, 2020 Dec.
Article in English | MEDLINE | ID: covidwho-977352

ABSTRACT

In the face of COVID-19 pandemic caused by the newly emerged SARS-CoV-2, an inactivated, Vero cell-based, whole virion vaccine candidate has been developed and entered into phase III clinical trials within six months. Biochemical and immunogenic characterization of structural proteins and their post-translational modifications in virions, the end-products of the vaccine candidate, would be essential for the quality control and process development of vaccine products and for studying the immunogenicity and pathogenesis of SARS-CoV-2. By using a panel of rabbit antisera against virions and five structural proteins together with a convalescent serum, the spike (S) glycoprotein was shown to be N-linked glycosylated, PNGase F-sensitive, endoglycosidase H-resistant and cleaved by Furin-like proteases into S1 and S2 subunits. The full-length S and S1/S2 subunits could form homodimers/trimers. The membrane (M) protein was partially N-linked glycosylated; the accessory protein 3a existed in three different forms, indicative of cleavage and dimerization. Furthermore, analysis of the antigenicity of these proteins and their post-translationally modified forms demonstrated that S protein induced the strongest antibody response in both convalescent and immunized animal sera. Interestingly, immunization with the inactivated vaccine did not elicit antibody response against the S2 subunit, whereas strong antibody response against both S1 and S2 subunits was detected in the convalescent serum. Moreover, vaccination stimulated stronger antibody response against S multimers than did the natural infection. This study revealed that the native S glycoprotein stimulated neutralizing antibodies, while bacterially-expressed S fragments did not. The study on S modifications would facilitate design of S-based anti-SARS-CoV-2 vaccines.


Subject(s)
COVID-19 Vaccines , Protein Processing, Post-Translational , SARS-CoV-2/isolation & purification , Viral Structural Proteins , Virion , Animals , Antigens, Viral/analysis , Antigens, Viral/metabolism , COVID-19 Vaccines/chemistry , COVID-19 Vaccines/immunology , Cattle , Chlorocebus aethiops , Humans , Rabbits , SARS-CoV-2/immunology , Vaccines, Inactivated/chemistry , Vaccines, Inactivated/immunology , Vero Cells , Viral Structural Proteins/chemistry , Viral Structural Proteins/immunology , Viral Structural Proteins/isolation & purification , Virion/chemistry , Virion/immunology , Virion/isolation & purification
10.
Biochem Soc Trans ; 48(6): 2625-2641, 2020 12 18.
Article in English | MEDLINE | ID: covidwho-952199

ABSTRACT

The race to identify a successful treatment for COVID19 will be defined by fundamental research into the replication cycle of the SARS-CoV-2 virus. This has identified five distinct stages from which numerous vaccination and clinical trials have emerged alongside an innumerable number of drug discovery studies currently in development for disease intervention. Informing every step of the viral replication cycle has been an unprecedented 'call-to-arms' by the global structural biology community. Of the 20 main SARS-CoV-2 proteins, 13 have been resolved structurally for SARS-CoV-2 with most having a related SARS-CoV and MERS-CoV structural homologue totalling some 300 structures currently available in public repositories. Herein, we review the contribution of structural studies to our understanding of the virus and their role in structure-based development of therapeutics.


Subject(s)
Antiviral Agents/chemistry , Antiviral Agents/therapeutic use , COVID-19/therapy , Drug Discovery/methods , SARS-CoV-2 , Antiviral Agents/chemical synthesis , COVID-19/drug therapy , COVID-19/immunology , Drug Development/methods , Genome, Viral , Humans , Models, Molecular , Protein Structural Elements , SARS-CoV-2/chemistry , SARS-CoV-2/drug effects , SARS-CoV-2/immunology , SARS-CoV-2/physiology , Spike Glycoprotein, Coronavirus/chemistry , Spike Glycoprotein, Coronavirus/physiology , Structure-Activity Relationship , Viral Structural Proteins/chemistry , Viral Structural Proteins/physiology , Virus Replication/drug effects , Virus Replication/physiology
11.
J Mol Biol ; 433(2): 166725, 2021 01 22.
Article in English | MEDLINE | ID: covidwho-947287

ABSTRACT

The unprecedented scale of the ongoing COVID-19 pandemic has catalyzed an intense effort of the global scientific community to unravel different aspects of the disease in a short time. One of the crucial aspects of these developments is the determination of more than three hundred experimental structures of SARS-CoV-2 proteins in the last few months. These include structures of viral non-structural, structural, and accessory proteins and their complexes determined by either X-ray diffraction or cryo-electron microscopy. These structures elucidate the intricate working of different components of the viral machinery at the atomic level during different steps of the viral life cycle, including attachment to the host cell, viral genome replication and transcription, and genome packaging and assembly of the virion. Some of these proteins are also potential targets for drug development against the disease. In this review, we discuss important structural features of different SARS-CoV-2 proteins with their function, and their potential as a target for therapeutic interventions.


Subject(s)
COVID-19/virology , SARS-CoV-2/chemistry , SARS-CoV-2/genetics , Viral Proteins/chemistry , Coronavirus 3C Proteases/chemistry , Coronavirus 3C Proteases/genetics , Cryoelectron Microscopy , Genome, Viral , Humans , Life Cycle Stages/genetics , Models, Molecular , Protein Conformation , Viral Nonstructural Proteins/chemistry , Viral Nonstructural Proteins/genetics , Viral Proteins/genetics , Viral Regulatory and Accessory Proteins/chemistry , Viral Regulatory and Accessory Proteins/genetics , Viral Structural Proteins/chemistry , Viral Structural Proteins/genetics , Virus Replication
12.
Molecules ; 25(23)2020 Nov 25.
Article in English | MEDLINE | ID: covidwho-945888

ABSTRACT

A serious pandemic has been caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The interaction between spike surface viral protein (Sgp) and the angiotensin-converting enzyme 2 (ACE2) cellular receptor is essential to understand the SARS-CoV-2 infectivity and pathogenicity. Currently, no drugs are available to treat the infection caused by this coronavirus and the use of antimicrobial peptides (AMPs) may be a promising alternative therapeutic strategy to control SARS-CoV-2. In this study, we investigated the in silico interaction of AMPs with viral structural proteins and host cell receptors. We screened the antimicrobial peptide database (APD3) and selected 15 peptides based on their physicochemical and antiviral properties. The interactions of AMPs with Sgp and ACE2 were performed by docking analysis. The results revealed that two amphibian AMPs, caerin 1.6 and caerin 1.10, had the highest affinity for Sgp proteins while interaction with the ACE2 receptor was reduced. The effective AMPs interacted particularly with Arg995 located in the S2 subunits of Sgp, which is key subunit that plays an essential role in viral fusion and entry into the host cell through ACE2. Given these computational findings, new potentially effective AMPs with antiviral properties for SARS-CoV-2 were identified, but they need experimental validation for their therapeutic effectiveness.


Subject(s)
Angiotensin-Converting Enzyme 2/chemistry , COVID-19/drug therapy , SARS-CoV-2/chemistry , Spike Glycoprotein, Coronavirus/chemistry , Amphibian Proteins/chemistry , Amphibian Proteins/therapeutic use , Angiotensin-Converting Enzyme 2/genetics , Angiotensin-Converting Enzyme 2/therapeutic use , Antimicrobial Cationic Peptides/chemistry , Antimicrobial Cationic Peptides/therapeutic use , Antiviral Agents/chemistry , Antiviral Agents/therapeutic use , Binding Sites/genetics , COVID-19/genetics , COVID-19/virology , Computer Simulation , Humans , Pandemics , Pore Forming Cytotoxic Proteins/chemistry , Pore Forming Cytotoxic Proteins/therapeutic use , Protein Binding/genetics , SARS-CoV-2/pathogenicity , Spike Glycoprotein, Coronavirus/therapeutic use , Viral Structural Proteins/chemistry , Viral Structural Proteins/genetics , Viral Structural Proteins/therapeutic use
13.
Sci Rep ; 10(1): 18995, 2020 11 04.
Article in English | MEDLINE | ID: covidwho-910353

ABSTRACT

The current pandemic is caused by the SARS-CoV-2 virus and large progress in understanding the pathology of the virus has been made since its emergence in late 2019. Several reports indicate short lasting immunity against endemic coronaviruses, which contrasts studies showing that biobanked venous blood contains T cells reactive to SARS-CoV-2 S-protein even before the outbreak in Wuhan. This suggests a preformed T cell memory towards structural proteins in individuals not exposed to SARS-CoV-2. Given the similarity of SARS-CoV-2 to other members of the Coronaviridae family, the endemic coronaviruses appear likely candidates to generate this T cell memory. However, given the apparent poor immunological memory created by the endemic coronaviruses, immunity against other common pathogens might offer an alternative explanation. Here, we utilize a combination of epitope prediction and similarity to common human pathogens to identify potential sources of the SARS-CoV-2 T cell memory. Although beta-coronaviruses are the most likely candidates to explain the pre-existing SARS-CoV-2 reactive T cells in uninfected individuals, the SARS-CoV-2 epitopes with the highest similarity to those from beta-coronaviruses are confined to replication associated proteins-not the host interacting S-protein. Thus, our study suggests that the observed SARS-CoV-2 pre-formed immunity to structural proteins is not driven by near-identical epitopes.


Subject(s)
Coronavirus Infections/immunology , Epitopes/immunology , Immunologic Memory , Pneumonia, Viral/immunology , T-Lymphocytes/immunology , Viral Structural Proteins/immunology , Antigens, Viral/chemistry , Antigens, Viral/immunology , Betacoronavirus/immunology , COVID-19 , Epitopes/chemistry , Humans , Pandemics , SARS-CoV-2 , Viral Structural Proteins/chemistry
14.
Bioorg Chem ; 104: 104326, 2020 11.
Article in English | MEDLINE | ID: covidwho-848891

ABSTRACT

SARS-CoV-2 (COVID-19) epidemic has created an unprecedented medical and economic crisis all over the world. SARS-CoV-2 is found to have more contagious character as compared to MERS-CoV and is spreading in a very fast manner all around the globe. It has affected over 31 million people all over the world till date. This virus shares around 80% of genome similarity with SARS-CoV. In this perspective, we have explored three major targets namely; SARS-CoV-2 spike (S) protein, RNA dependent RNA polymerase, and 3CL or Mpro Protease for the inhibition of SARS-CoV-2. These targets have attracted attention of the medicinal chemists working on computer-aided drug design in developing new small molecules that might inhibit these targets for combating COVID-19 disease. Moreover, we have compared the similarity of these target proteins with earlier reported coronavirus (SARS-CoV). We have observed that both the coronaviruses share around 80% similarity in their amino acid sequence. The key amino acid interactions which can play a crucial role in designing new small molecule inhibitors against COVID-19 have been reported in this perspective. Authors believe that this study will help the medicinal chemists to understand the key amino acids essential for interactions at the active site of target proteins in SARS-CoV-2, based on their similarity with earlier reported viruses. In this review, we have also described the lead molecules under various clinical trials for their efficacy against COVID-19.


Subject(s)
Antiviral Agents/metabolism , SARS Virus/chemistry , SARS-CoV-2/chemistry , Viral Nonstructural Proteins/metabolism , Viral Structural Proteins/metabolism , Amino Acid Sequence , Animals , Antiviral Agents/therapeutic use , Binding Sites , COVID-19/drug therapy , COVID-19/epidemiology , COVID-19/virology , Drug Repositioning , Humans , Protein Binding , SARS-CoV-2/drug effects , Viral Nonstructural Proteins/chemistry , Viral Structural Proteins/chemistry
15.
Infect Genet Evol ; 85: 104517, 2020 11.
Article in English | MEDLINE | ID: covidwho-737519

ABSTRACT

The present study aimed to predict a novel chimeric vaccine by simultaneously targeting four major structural proteins via the establishment of ancestral relationship among different strains of coronaviruses. Conserved regions from the homologous protein sets of spike glycoprotein, membrane protein, envelope protein and nucleocapsid protein were identified through multiple sequence alignment. The phylogeny analyses of whole genome stated that four proteins reflected the close ancestral relation of SARS-CoV-2 to SARS-COV-1 and bat coronavirus. Numerous immunogenic epitopes (both T cell and B cell) were generated from the common fragments which were further ranked on the basis of antigenicity, transmembrane topology, conservancy level, toxicity and allergenicity pattern and population coverage analysis. Top putative epitopes were combined with appropriate adjuvants and linkers to construct a novel multiepitope subunit vaccine against COVID-19. The designed constructs were characterized based on physicochemical properties, allergenicity, antigenicity and solubility which revealed the superiority of construct V3 in terms safety and efficacy. Essential molecular dynamics and normal mode analysis confirmed minimal deformability of the refined model at molecular level. In addition, disulfide engineering was investigated to accelerate the stability of the protein. Molecular docking study ensured high binding affinity between construct V3 and HLA cells, as well as with different host receptors. Microbial expression and translational efficacy of the constructs were checked using pET28a(+) vector of E. coli strain K12. However, the in vivo and in vitro validation of suggested vaccine molecule might be ensured with wet lab trials using model animals for the implementation of the presented data.


Subject(s)
Epitopes, B-Lymphocyte/genetics , Epitopes, T-Lymphocyte/genetics , SARS-CoV-2/classification , Vaccines, Subunit/genetics , Viral Structural Proteins/genetics , Epitopes, B-Lymphocyte/immunology , Epitopes, T-Lymphocyte/immunology , Escherichia coli/genetics , Escherichia coli/growth & development , Evolution, Molecular , Genome, Viral , Humans , Models, Molecular , Molecular Docking Simulation , Molecular Dynamics Simulation , Phylogeny , Protein Conformation , SARS-CoV-2/genetics , SARS-CoV-2/immunology , Vaccines, Subunit/chemistry , Vaccines, Subunit/metabolism , Viral Structural Proteins/chemistry , Viral Structural Proteins/immunology , Viral Vaccines/chemistry , Viral Vaccines/genetics , Viral Vaccines/metabolism
16.
Infect Genet Evol ; 85: 104497, 2020 11.
Article in English | MEDLINE | ID: covidwho-704005

ABSTRACT

COVID-19 pandemic is rapidly advancing among human population. Development of new interventions including therapeutics and vaccines against SARS-CoV-2 will require time and validation before it could be made available for public use. Keeping in view of the emergent and evolving situation the motive is to repurpose and test the immediate efficacy of available drugs and therapeutics against COVID-19. Through this article we propose and discuss the possibility of repurposing the available nuclease resistant RNA aptamer against the nucleocapsid protein of SARS-CoV as a potential therapeutic agent for COVID-19.


Subject(s)
Antiviral Agents/pharmacology , Aptamers, Nucleotide/pharmacology , SARS-CoV-2/metabolism , Viral Structural Proteins/antagonists & inhibitors , Amino Acid Sequence , Antiviral Agents/chemistry , Antiviral Agents/therapeutic use , Aptamers, Nucleotide/chemistry , Aptamers, Nucleotide/therapeutic use , Coronavirus Nucleocapsid Proteins/antagonists & inhibitors , Coronavirus Nucleocapsid Proteins/chemistry , Drug Repositioning , Humans , Models, Molecular , Molecular Conformation , SARS-CoV-2/drug effects , Spike Glycoprotein, Coronavirus/antagonists & inhibitors , Spike Glycoprotein, Coronavirus/chemistry , Viral Structural Proteins/chemistry
17.
Med Sci (Paris) ; 36(6-7): 633-641, 2020.
Article in French | MEDLINE | ID: covidwho-611702

ABSTRACT

Coronavirus is a large family of viruses that infect mammals and birds. Coronaviruses are known to cross barrier species and infect new ones. In the past twenty years, we witnessed the emergence of three different coronaviruses, the latest one being the SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) responsible for the COVID-19 (covid disease 19) pandemic. Coronaviruses are enveloped virus with a long positive sense RNA genome. Like all viruses, they hijack the cellular machinery to replicate and produce new virions. There is no approved vaccine or specific antiviral molecule against coronaviruses but with the urgency to treat COVID-19, several candidate therapies are currently investigated.


TITLE: Les coronavirus, ennemis incertains. ABSTRACT: Les coronavirus sont une famille de virus qui infectent un grand nombre de mammifères et d'oiseaux. Cette famille de virus est connue pour sa capacité à franchir les barrières d'espèces et à en infecter de nouvelles. La pandémie actuelle de COVID-19 (coronavirus disease 19) est la conséquence de la troisième émergence de coronavirus, la plus récente, dans la population humaine depuis le début du siècle, celle du SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2). Les coronavirus sont des virus enveloppés à ARN simple brin de polarité positive, qui, comme tous les virus, exploitent la machinerie cellulaire pour se multiplier. À ce jour, il n'existe aucun vaccin ni traitement antiviral spécifique pour lutter contre les coronavirus, mais plusieurs pistes thérapeutiques sont explorées pour traiter le COVID-19.


Subject(s)
Betacoronavirus , Coronavirus Infections/epidemiology , Coronavirus Infections/virology , Virus Physiological Phenomena , Animals , Betacoronavirus/classification , Betacoronavirus/physiology , Betacoronavirus/ultrastructure , COVID-19 , Coronavirus Infections/drug therapy , Epidemics , Humans , Middle East Respiratory Syndrome Coronavirus , Pandemics , Pneumonia, Viral/epidemiology , Pneumonia, Viral/virology , SARS Virus , SARS-CoV-2 , Severe Acute Respiratory Syndrome/epidemiology , Severe Acute Respiratory Syndrome/virology , Viral Structural Proteins/chemistry , Zoonoses/epidemiology , Zoonoses/virology
18.
Genomics ; 112(5): 3226-3237, 2020 09.
Article in English | MEDLINE | ID: covidwho-597640

ABSTRACT

A global emergency due to the COVID-19 pandemic demands various studies related to genes and genomes of the SARS-CoV2. Among other important proteins, the role of accessory proteins are of immense importance in replication, regulation of infections of the coronavirus in the hosts. The largest accessory protein in the SARS-CoV2 genome is ORF3a which modulates the host response to the virus infection and consequently it plays an important role in pathogenesis. In this study, an attempt is made to decipher the conservation of nucleotides, dimers, codons and amino acids in the ORF3a genes across thirty-two genomes of Indian patients. ORF3a gene possesses single and double point mutations in Indian SARS-CoV2 genomes suggesting the change of SARS-CoV2's virulence property in Indian patients. We find that the parental origin of the ORF3a gene over the genomes of SARS-CoV2 and Pangolin-CoV is same from the phylogenetic analysis based on conservation of nucleotides and so on. This study highlights the accumulation of mutation on ORF3a in Indian SARS-CoV2 genomes which may provide the designing therapeutic approach against SARS-CoV2.


Subject(s)
Betacoronavirus/genetics , Conserved Sequence , Coronavirus Infections/virology , Mutation , Pneumonia, Viral/virology , Viral Regulatory and Accessory Proteins/genetics , Animals , Base Sequence , Biological Evolution , COVID-19 , Chiroptera/virology , Coronavirus Infections/veterinary , Eutheria/virology , Genome, Viral , Genomics , Humans , India , Pandemics , Phylogeny , SARS-CoV-2 , Viral Regulatory and Accessory Proteins/chemistry , Viral Structural Proteins/chemistry , Viral Structural Proteins/genetics , Viroporin Proteins
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