Immunoinformatics Patterns and Characteristic of Epitope-Based Peptide Vaccine candidates against COVID-19

Vaccination as defined by the WHO is “the administration of agent-specific, but safe, antigenic components that in vaccinated individuals can induce protective immunity against the corresponding infectious agent”. Regardless of their debated history, the standard vaccine approaches have been unsuccessful in providing vaccines for numerous infectious organisms. In the recent three decades, an enormous amount of immunological data was retrieved from clinical studies due to the advancement in human genome sequencing. These data are being deposited in databases and numerous scientific literature. The development of several bioinformatics tools to analyze this rapidly increasing immunological databank has given rise to the field of immunoinformatics. This approach allows the selection of immunogenic residues from the pathogen genomes. The ideal residues could be industrialized as vaccine candidates to provide protective immune responses in the hosts. This methodology will significantly decrease the time and cost needed for the vaccine development. This review focus on published articles that proposed as vaccine candidates through immunoinformatics analysis. The reviewed Published immunoinformatics studies provided vaccine peptide candidates against SARS-COV-2, which is based on functional and non functional immunogenic proteins like open reading frame , spike protein, envelope protein and membranous protein .All of which are designed by unique strategies like reverse vaccinology . Spike protein was the most common used target with different suggeststed B and T cell peptides due to the difference in methodology between the findings.

Download Full-text

Epitope order Matters in multi-epitope-based peptide (MEBP) vaccine design: An in silico study

10.1101/2021.06.29.450372 ◽

2021 ◽

Author(s):

Muthu Raj Salaikumaran ◽

Prasanna Sudharson Kasamuthu ◽

V L S Prasad Burra

Keyword(s):

In Silico ◽

Experimental Validation ◽

Vaccine Development ◽

Experimental Testing ◽

Peptide Vaccine ◽

Vaccine Design ◽

Vaccine Candidates ◽

Vaccine Potency ◽

Experimental Protocols ◽

The Many

With different countries facing multiple waves, with some SARS-CoV-2 variants more deadly and virulent, the COVID-19 pandemic is becoming more dangerous by the day and the world is facing an even more dreadful extended pandemic with exponential positive cases and increasing death rates. There is an urgent need for more efficient and faster methods of vaccine development against SARS-CoV-2. Compared to experimental protocols, the opportunities to innovate are very high in immunoinformatics/in silico approaches especially with the recent adoption of structural bioinformatics in peptide vaccine design. In recent times, multi-epitope-based peptide vaccine candidates (MEBPVCs) have shown extraordinarily high humoral and cellular responses to immunization. Most of the publications claim that respective reported MEBPVC(s) assembled using a set of in silico predicted epitopes, to be the computationally validated potent vaccine candidate(s) ready for experimental validation. However, in this article, for a given set of predicted epitopes, it is shown that the published MEBPVC is one among the many possible variants and there is high likelihood of finding more potent MEBPVCs than the published candidate. To test the same, a methodology is developed where novel MEBP variants are derived by changing the epitope order of the published MEBPVC. Further, to overcome the limitations of current qualitative methods of assessment of MEBPVC, to enable quantitative comparison, ranking, and the discovery of more potent MEBPVCs, novel predictors, Percent Epitope Accessibility (PEA), Receptor specific MEBP vaccine potency(RMVP), MEBP vaccine potency(MVP) are introduced. The MEBP variants indeed showed varied MVP scores indicating varied immunogenicity. When the MEBP variants were ranked in descending order of their MVP scores, the published MEBPVC had the least MVP score. Further, the MEBP variants with IDs, SPVC_387 and SPVC_206, had the highest MVP scores indicating these variants to be more potent MEBPVCs than the published MEBPVC and hence should be prioritized for experimental testing and validation. Through this method, more vaccine candidates will be available for experimental validation and testing. This study also opens the opportunity to develop new software tools for designing more potent MEBPVCs in less time. The computationally validated top-ranked MEBPVCs must be experimentally tested, validated, and verified. The differences and deviations between experimental results and computational predictions provide an opportunity for improving and developing more efficient algorithms and reliable scoring schemes and software.

Download Full-text

Protective Immunity against SARS Subunit Vaccine Candidates Based on Spike Protein: Lessons for Coronavirus Vaccine Development

Journal of Immunology Research ◽

10.1155/2020/7201752 ◽

2020 ◽

Vol 2020 ◽

pp. 1-11

Author(s):

Atin Khalaj-Hedayati

Keyword(s):

Neutralizing Antibodies ◽

Protective Immunity ◽

Subunit Vaccine ◽

Vaccine Development ◽

Spike Protein ◽

Effective Vaccine ◽

Universal Vaccine ◽

Health Security ◽

Vaccine Candidates ◽

Novel Coronavirus

The recent outbreak of the novel coronavirus disease, COVID-19, has highlighted the threat that highly pathogenic coronaviruses have on global health security and the imminent need to design an effective vaccine for prevention purposes. Although several attempts have been made to develop vaccines against human coronavirus infections since the emergence of Severe Acute Respiratory Syndrome coronavirus (SARS-CoV) in 2003, there is no available licensed vaccine yet. A better understanding of previous coronavirus vaccine studies may help to design a vaccine for the newly emerged virus, SARS-CoV-2, that may also cover other pathogenic coronaviruses as a potentially universal vaccine. In general, coronavirus spike protein is the major antigen for the vaccine design as it can induce neutralizing antibodies and protective immunity. By considering the high genetic similarity between SARS-CoV and SARS-CoV-2, here, protective immunity against SARS-CoV spike subunit vaccine candidates in animal models has been reviewed to gain advances that can facilitate coronavirus vaccine development in the near future.

Download Full-text

Characterization of a Novel Orthomyxo-like Virus Causing Mass Die-Offs of Tilapia

mBio ◽

10.1128/mbio.00431-16 ◽

2016 ◽

Vol 7 (2) ◽

Cited By ~ 96

Author(s):

Eran Bacharach ◽

Nischay Mishra ◽

Thomas Briese ◽

Michael C. Zody ◽

Japhette Esther Kembou Tsofack ◽

...

Keyword(s):

Vaccine Development ◽

Infectious Agent ◽

Farmed Fish ◽

Reading Frame ◽

Complementary Sequences ◽

Influenza C Virus ◽

Negative Sense ◽

Global Food

ABSTRACTTilapia are an important global food source due to their omnivorous diet, tolerance for high-density aquaculture, and relative disease resistance. Since 2009, tilapia aquaculture has been threatened by mass die-offs in farmed fish in Israel and Ecuador. Here we report evidence implicating a novel orthomyxo-like virus in these outbreaks. The tilapia lake virus (TiLV) has a 10-segment, negative-sense RNA genome. The largest segment, segment 1, contains an open reading frame with weak sequence homology to the influenza C virus PB1 subunit. The other nine segments showed no homology to other viruses but have conserved, complementary sequences at their 5′ and 3′ termini, consistent with the genome organization found in other orthomyxoviruses.In situhybridization indicates TiLV replication and transcription at sites of pathology in the liver and central nervous system of tilapia with disease.IMPORTANCEThe economic impact of worldwide trade in tilapia is estimated at $7.5 billion U.S. dollars (USD) annually. The infectious agent implicated in mass tilapia die-offs in two continents poses a threat to the global tilapia industry, which not only provides inexpensive dietary protein but also is a major employer in the developing world. Here we report characterization of the causative agent as a novel orthomyxo-like virus, tilapia lake virus (TiLV). We also describe complete genomic and protein sequences that will facilitate TiLV detection and containment and enable vaccine development.

Download Full-text

Identification of Immunogenic and Virulence-Associated Campylobacter jejuni Proteins

Clinical and Vaccine Immunology ◽

10.1128/cvi.05161-11 ◽

2011 ◽

Vol 19 (2) ◽

pp. 113-119 ◽

Cited By ~ 13

Author(s):

Lene N. Nielsen ◽

Thomas A. Luijkx ◽

Christina S. Vegge ◽

Christina Kofoed Johnsen ◽

Piet Nuijten ◽

...

Keyword(s):

Campylobacter Jejuni ◽

Epithelial Cell Line ◽

Expression Library ◽

Content Type ◽

Reading Frame ◽

Vaccine Candidates ◽

Host Interaction ◽

Strain Bl21 ◽

Immunogenic Proteins ◽

Expression Strain

ABSTRACTWith the aim of identifying proteins important for host interaction and virulence, we have screened an expression library of NCTC 11168Campylobacter jejunigenes for highly immunogenic proteins. A commercialC. jejuniopen reading frame (ORF) library consisting of more than 1,600 genes was transformed into theEscherichia coliexpression strain BL21(DE3), resulting in 2,304 clones. This library was subsequently screened for immunogenic proteins using antibodies raised in rabbit against a clinical isolate ofC. jejuni; this resulted in 52 highly reactive clones representing 25 different genes after sequencing. Selected candidate genes were inactivated inC. jejuniNCTC 11168, and the virulence was examined using INT 407 epithelial cell line and motility, biofilm, autoagglutination, and serum resistance assays. These investigations revealedC. jejuniantigen 0034c (Cj0034c) to be a novel virulence factor and support the usefulness of the method. Further, several antigens were tested as vaccine candidates in two mouse models, in which Cj0034c, Cj0404, and Cj0525c resulted in a reduction of invasion in spleen and liver after challenge.

Download Full-text

Selecting soluble/foldable protein domains through single-gene or genomic ORF filtering: structure of the head domain of Burkholderia pseudomallei antigen BPSL2063

Acta Crystallographica Section D Biological Crystallography ◽

10.1107/s1399004715015680 ◽

2015 ◽

Vol 71 (11) ◽

pp. 2227-2235 ◽

Cited By ~ 7

Author(s):

Louise J. Gourlay ◽

Clelia Peano ◽

Cecilia Deantonio ◽

Lucia Perletti ◽

Alessandro Pietrelli ◽

...

Keyword(s):

Burkholderia Pseudomallei ◽

Vaccine Development ◽

Single Gene ◽

Soluble Form ◽

Protein Antigens ◽

Reading Frame ◽

X Ray Crystallography ◽

Conserved Domain ◽

Structural Vaccinology ◽

Selection Of

The 1.8 Å resolution crystal structure of a conserved domain of the potential Burkholderia pseudomallei antigen and trimeric autotransporter BPSL2063 is presented as a structural vaccinology target for melioidosis vaccine development. Since BPSL2063 (1090 amino acids) hosts only one conserved domain, and the expression/purification of the full-length protein proved to be problematic, a domain-filtering library was generated using β-lactamase as a reporter gene to select further BPSL2063 domains. As a result, two domains (D1 and D2) were identified and produced in soluble form in Escherichia coli. Furthermore, as a general tool, a genomic open reading frame-filtering library from the B. pseudomallei genome was also constructed to facilitate the selection of domain boundaries from the entire ORFeome. Such an approach allowed the selection of three potential protein antigens that were also produced in soluble form. The results imply the further development of ORF-filtering methods as a tool in protein-based research to improve the selection and production of soluble proteins or domains for downstream applications such as X-ray crystallography.

Download Full-text

Evolution of SARS-CoV-2 virus and assessment of the effectiveness of COVID-19 vaccine

F1000Research ◽

10.12688/f1000research.28215.1 ◽

2021 ◽

Vol 10 ◽

pp. 28

Author(s):

Veljko Veljkovic ◽

Vladimir Perovic ◽

Isabelle Chambers ◽

Slobodan Paessler

Keyword(s):

Viral Replication ◽

Reference Strain ◽

Vaccine Development ◽

Spike Protein ◽

Effective Vaccine ◽

Vaccine Candidates ◽

Proof Reading

A safe and effective vaccine is urgently needed to bring the current SARS-CoV-2 pandemic under control. The spike protein (SP) of SARS-CoV-2 represents the principal target for most vaccines currently under development. Despite the presence of a CoV proof-reading function in viral replication, SP protein from SARS-CoV still extensively mutates, which might have an impact on current and future vaccine development. Here, we present analysis of more than 1600 SP unique variants suggesting that vaccine candidates based on the Wuhan-Hu-1 reference strain would be effective against most of currently circulated SARS-CoV-2 viruses, but that further monitoring of the evolution of this virus is important for identification of other mutations, which could affect the effectiveness of vaccines.

Download Full-text

Immunogenicity of trimeric autotransporter adhesins and their potential as vaccine targets

Medical Microbiology and Immunology ◽

10.1007/s00430-019-00649-y ◽

2019 ◽

Vol 209 (3) ◽

pp. 243-263

Author(s):

Arno Thibau ◽

Alexander A. Dichter ◽

Diana J. Vaca ◽

Dirk Linke ◽

Adrian Goldman ◽

...

Keyword(s):

Vaccine Development ◽

Outer Membrane Proteins ◽

Host Cells ◽

Vaccine Candidates ◽

Bacterial Surface ◽

Major Interest ◽

Vaccine Antigens ◽

A Subunit ◽

Extracellular Environment ◽

Selection Of

AbstractThe current problem of increasing antibiotic resistance and the resurgence of numerous infections indicate the need for novel vaccination strategies more than ever. In vaccine development, the search for and the selection of adequate vaccine antigens is the first important step. In recent years, bacterial outer membrane proteins have become of major interest, as they are the main proteins interacting with the extracellular environment. Trimeric autotransporter adhesins (TAAs) are important virulence factors in many Gram-negative bacteria, are localised on the bacterial surface, and mediate the first adherence to host cells in the course of infection. One example is the Neisseria adhesin A (NadA), which is currently used as a subunit in a licensed vaccine against Neisseria meningitidis. Other TAAs that seem promising vaccine candidates are the Acinetobacter trimeric autotransporter (Ata), the Haemophilus influenzae adhesin (Hia), and TAAs of the genus Bartonella. Here, we review the suitability of various TAAs as vaccine candidates.

Download Full-text

SARS-CoV-2 Preimmune IgM Epitopes

10.21203/rs.3.rs-21020/v1 ◽

2020 ◽

Author(s):

Velizar Shivarov ◽

Peter Petrov ◽

Anastas Pashov

Keyword(s):

Fast Track ◽

Vaccine Development ◽

Open Reading Frame ◽

Spike Protein ◽

Reading Frame

Abstract While studying the human public IgM igome as represented by a library of 224087 linear mimotopes, three exact matches to peptides in the proteins of SARS-CoV-2 were found: two in the open reading frame 1ab and one in the spike protein. Joining the efforts to fast track SARS-CoV-2 vaccine development, here we describe briefly these potential epitopes in comparison to mimotopes representing peptides of SARS-CoV , HCoV 229E and OC43.

Download Full-text

Viral Vectors for COVID-19 Vaccine Development

Viruses ◽

10.3390/v13020317 ◽

2021 ◽

Vol 13 (2) ◽

pp. 317

Author(s):

Kenneth Lundstrom

Keyword(s):

Immune Responses ◽

Viral Vectors ◽

Vaccine Development ◽

Rna Virus ◽

Influenza Viruses ◽

Spike Protein ◽

Vaccine Candidates ◽

Vaccinia Viruses ◽

Simian Adenovirus ◽

The Uk

Vaccine development against SARS-CoV-2 has been fierce due to the devastating COVID-19 pandemic and has included all potential approaches for providing the global community with safe and efficient vaccine candidates in the shortest possible timeframe. Viral vectors have played a central role especially using adenovirus-based vectors. Additionally, other viral vectors based on vaccinia viruses, measles viruses, rhabdoviruses, influenza viruses and lentiviruses have been subjected to vaccine development. Self-amplifying RNA virus vectors have been utilized for lipid nanoparticle-based delivery of RNA as COVID-19 vaccines. Several adenovirus-based vaccine candidates have elicited strong immune responses in immunized animals and protection against challenges in mice and primates has been achieved. Moreover, adenovirus-based vaccine candidates have been subjected to phase I to III clinical trials. Recently, the simian adenovirus-based ChAdOx1 vector expressing the SARS-CoV-2 S spike protein was approved for use in humans in the UK.

Download Full-text

COMBINATORIAL POLYNOMIALLY COMPUTABLE CHARACTERISTICS OF SUBSTITUTIONS AND THEIR PROPERTIES

Computational nanotechnology ◽

10.33693/2313-223x-2020-7-2-34-41 ◽

2020 ◽

Vol 7 (2) ◽

pp. 34-41

Author(s):

VLADIMIR NIKONOV ◽

◽

ANTON ZOBOV ◽

Keyword(s):

Mathematical Expectation ◽

Point Of View ◽

Small Range ◽

Computational Point ◽

Wide Range ◽

Bijective Function ◽

The Difference ◽

Element Base ◽

Selection Of

The construction and selection of a suitable bijective function, that is, substitution, is now becoming an important applied task, particularly for building block encryption systems. Many articles have suggested using different approaches to determining the quality of substitution, but most of them are highly computationally complex. The solution of this problem will significantly expand the range of methods for constructing and analyzing scheme in information protection systems. The purpose of research is to find easily measurable characteristics of substitutions, allowing to evaluate their quality, and also measures of the proximity of a particular substitutions to a random one, or its distance from it. For this purpose, several characteristics were proposed in this work: difference and polynomial, and their mathematical expectation was found, as well as variance for the difference characteristic. This allows us to make a conclusion about its quality by comparing the result of calculating the characteristic for a particular substitution with the calculated mathematical expectation. From a computational point of view, the thesises of the article are of exceptional interest due to the simplicity of the algorithm for quantifying the quality of bijective function substitutions. By its nature, the operation of calculating the difference characteristic carries out a simple summation of integer terms in a fixed and small range. Such an operation, both in the modern and in the prospective element base, is embedded in the logic of a wide range of functional elements, especially when implementing computational actions in the optical range, or on other carriers related to the field of nanotechnology.

Download Full-text