Identification of Generalized Peptide Regions for Designing Vaccine Effective for All Significant Mutated Strains of SARS-CoV-2

2021 ◽  
Vol 24 ◽  
Author(s):  
Subhamoy Biswas ◽  
Smarajit Manna ◽  
Tathagata Dey ◽  
Shreyans Chatterjee ◽  
Sumanta Dey
Keyword(s):  
Comparative Study ◽  
Zika Virus ◽  
Peptide Vaccine ◽  
Vaccine Design ◽  
Current Approach ◽  
Polar Plot ◽  
Vaccine Candidates ◽  
The Future ◽  
Potential Vaccine ◽  
The Comparative Study

Background: Coronavirus disease 2019 (COVID-19) caused by SARS-CoV-2 has become a worldwide pandemic and created an utmost crisis across the globe. To mitigate the crisis, the design of vaccines is a crucial solution. The frequent mutation of the virus demands generalized vaccine candidates, which would be effective for all mutated strains at present and for the strains that would evolve due to further new mutations in the virus. Objective: The objective of this study is to identify more frequently occurring mutated variants of SARS-CoV-2 and to suggest peptide vaccine candidates effective in common against the viral strains considered. Method: In this study, we have identified all currently prevailing mutated strains of SARS-CoV-2 through 2D Polar plot and Quotient Radius〖(q〗_R) characterization descriptor. Then, by considering the top eight mutation strains, which are significant due to their frequency of occurrence, peptide regions suitable for vaccine design have been identified with the help of a mathematical model – 2D Polygon Representation, followed by the evaluation of epitope potential and ensuring that there is no case of any autoimmune threat. Lastly, in order to verify whether this entire approach is applicable for vaccine design against any other virus in general, we have made a comparative study between the peptide vaccine candidates prescribed for the Zika virus using the current approach and a list of potential vaccine candidates for the same already established in the past. Results: We have finally suggested three generalized peptide regions which would be suitable as sustainable peptide vaccine candidates against SARS-CoV-2 irrespective of its currently prevailing strains as well any other variant of the same that may appear in the future. We also observed that during the comparative study using the case of E protein of Zika virus, the peptide regions suggested using the new approach matched with the already established results. Conclusion: The study, therefore, illustrates an approach that would help in developing peptide vaccine against SARS-CoV-2 by suggesting those peptide regions which can be targeted irrespective of any mutated form of this virus. The consistency with which this entire approach was also able to figure out similar vaccine candidates for Zika virus with utmost accuracy proves that this protocol can be extended for peptide vaccine design against any other virus in the future.

scholarly journals Immunoinformatics Approach for Epitope-Based Peptide Vaccine Design and Active Site Prediction against Polyprotein of Emerging Oropouche Virus

2018 ◽  
Vol 2018 ◽  
pp. 1-22 ◽  
Author(s):  
Utpal Kumar Adhikari ◽  
Mourad Tayebi ◽  
M. Mizanur Rahman
Keyword(s):  
T Cell ◽  
Ligand Binding ◽  
B Cell ◽  
Peptide Vaccine ◽  
Vaccine Design ◽  
Binding Interaction ◽  
B Cell Epitopes ◽  
Vaccine Candidates ◽  
Binding Pockets ◽  
Potential Vaccine

Oropouche virus (OROV) is an emerging pathogen which causes Oropouche fever and meningitis in humans. Several outbreaks of OROV in South America, especially in Brazil, have changed its status as an emerging disease, but no vaccine or specific drug target is available yet. Our approach was to identify the epitope-based vaccine candidates as well as the ligand-binding pockets through the use of immunoinformatics. In this report, we identified both T-cell and B-cell epitopes of the most antigenic OROV polyprotein with the potential to induce both humoral and cell-mediated immunity. Eighteen highly antigenic and immunogenic CD8+ T-cell epitopes were identified, including three 100% conserved epitopes (TSSWGCEEY, CSMCGLIHY, and LAIDTGCLY) as the potential vaccine candidates. The selected epitopes showed 95.77% coverage for the mixed Brazilian population. The docking simulation ensured the binding interaction with high affinity. A total of five highly conserved and nontoxic linear B-cell epitopes “NQKIDLSQL,” “HPLSTSQIGDRC,” “SHCNLEFTAITADKIMSL,” “PEKIPAKEGWLTFSKEHTSSW,” and “HHYKPTKNLPHVVPRYH” were selected as potential vaccine candidates. The predicted eight conformational B-cell epitopes represent the accessibility for the entered virus. In the posttherapeutic strategy, ten ligand-binding pockets were identified for effective inhibitor design against emerging OROV infection. Collectively, this research provides novel candidates for epitope-based peptide vaccine design against OROV.

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

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.

scholarly journals Óscar Pérez (1981-2018): chronicle of a death foretold

Contratexto ◽  
2020 ◽  
pp. 67-80
Author(s):  
Allan Deneuville
Keyword(s):  
Comparative Study ◽  
User Generated Content ◽  
Life And Death ◽  
The Future ◽  
The Comparative Study

In this article, we propose the comparative study of two works that use videos of Venezuelan political opponent Óscar Pérez who was killed during a military raid. Romain Champalaune’s film (The Life and Death of Óscar Pérez) and the website of the British collective Forensic Architecture question us about the future of user-generated content and the place of the artist and the researcher in the society of hyper-production of texts and documents. After introducing the Perez case and presenting the works, we analyze the regime of proof and the idea of truth and the archive in the era of algorithmic governmentalities. Finally, we study how investigation and the collection of user-generated content allow for a shift in our power regimes through the implementation of counter-narration to that of the powers that be.

Identification of epitope-based peptide vaccine candidates against enterotoxigenic Escherichia coli: a comparative genomics and immunoinformatics approach

2016 ◽  
Vol 12 (3) ◽  
pp. 890-901 ◽  
Author(s):  
Kusum Mehla ◽  
Jayashree Ramana
Keyword(s):  
Escherichia Coli ◽  
Comparative Genomics ◽  
Peptide Vaccine ◽  
Enterotoxigenic Escherichia Coli ◽  
Vaccine Candidates ◽  
Integrated Omics ◽  
Potential Vaccine

In the present study, we have employed integrated omics approach to identify potential vaccine candidates against ETEC.

scholarly journals Computer-Assisted and Data Driven Approaches for Surveillance, Drug Discovery, and Vaccine Design for the Zika Virus

2019 ◽  
Vol 12 (4) ◽  
pp. 157 ◽  
Author(s):  
Subhash C. Basak ◽  
Subhabrata Majumdar ◽  
Ashesh Nandy ◽  
Proyasha Roy ◽  
Tathagata Dutta ◽  
...  
Keyword(s):  
Public Health ◽  
Zika Virus ◽  
Human Life ◽  
Peptide Vaccine ◽  
Vaccine Design ◽  
New Drugs ◽  
Computer Assisted ◽  
Global Public Health ◽  
Emerging Pathogens ◽  
Therapeutic Molecules

Human life has been at the edge of catastrophe for millennia due diseases which emerge and reemerge at random. The recent outbreak of the Zika virus (ZIKV) is one such menace that shook the global public health community abruptly. Modern technologies, including computational tools as well as experimental approaches, need to be harnessed fast and effectively in a coordinated manner in order to properly address such challenges. In this paper, based on our earlier research, we have proposed a four-pronged approach to tackle the emerging pathogens like ZIKV: (a) Epidemiological modelling of spread mechanisms of ZIKV; (b) assessment of the public health risk of newly emerging strains of the pathogens by comparing them with existing strains/pathogens using fast computational sequence comparison methods; (c) implementation of vaccine design methods in order to produce a set of probable peptide vaccine candidates for quick synthesis/production and testing in the laboratory; and (d) designing of novel therapeutic molecules and their laboratory testing as well as validation of new drugs or repurposing of drugs for use against ZIKV. For each of these stages, we provide an extensive review of the technical challenges and current state-of-the-art. Further, we outline the future areas of research and discuss how they can work together to proactively combat ZIKV or future emerging pathogens.

scholarly journals ON THE SYSTEM OF THE PARTICIPLES IN BULGARIAN AND GREEK

2020 ◽  
pp. 42-52
Author(s):  
Desislava YORDANOVA-PETROVA
Keyword(s):  
Comparative Analysis ◽  
Comparative Study ◽  
System Level ◽  
Field Of Study ◽  
The Past ◽  
Different Types ◽  
The Future ◽  
Similarities And Differences ◽  
The Comparative Study

This paper is devoted to the participle system in Bulgarian and Greek, presenting in a comparative plan the formation, meanings, functions and use of the different types of participles in the two languages. The paper focuses on the similarities and differences in the different types of participles, giving information about the frequency of their use in both languages. The traditional types of active and passive participles are considered separately. However, for some of the types of participles there are different opinions whether they should be included in the participle systems of the two studied languages, the article presents the relevant views and arguments of researchers. Such are, for example, the past imperfect active participle and the present passive participle in the Bulgarian language, as well as the present active participle and the aorist active participle in Greek. The present study is the first attempt to present the participle system in Bulgarian and Greek, with the comparison made at the system level in both languages. Apart from the theoretical plan, the conclusions formulated as a result of the comparative study of the participle systems of the two languages would be useful in practice in the assimilation of certain types of Greek participles by Bulgarians learning Greek. In the future, the field of study could be expanded into the comparative analysis of the participle system in Bulgarian and Greek at the level of speech (for example, on the basis of a translation corpus).

GPS Satellite Advancements and its Future

2020 ◽  
Vol 07 (01) ◽  
pp. 1-4
Author(s):  
Gopal Kochhar ◽  
Keyword(s):  
Comparative Study ◽  
Global Positioning System ◽  
Positioning System ◽  
Tracking Systems ◽  
Gps Satellites ◽  
Global Positioning ◽  
The Future ◽  
The Comparative Study

This paper gives an brief introduction of global positioning system, its generations, the future and progressions that are attained by the GPS and tracking systems. The latest usage and the comparative study of the GPS satellites that are launched and are operational till date.

Sign in / Sign up

Export Citation Format

Share Document