In Silico Approach for Peptide Vaccine Design for CoVID 19

Biswas, Subhamoy; Chatterjee, Shreyans; Dey, Tathagata; Dey, Sumanta; Manna, Sourav; Nandy, Ashesh; Basak, Subhash C.

doi:10.3390/mol2net-06-06787

Cited by 11 publications

(7 citation statements)

References 12 publications

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“…is obtained. For spike glycoprotein of SARS-CoV-2, a preliminary analysis was previously done using this computational model based on a smaller number of sequences (72) as in Biswas et al (2020). But as many as 2812 amino acid sequences (available in the database as on 8 May, 2020) have been considered here and a detailed analysis pertaining to the selection of the most suitable peptide regions have been performed, resulting in a more comprehensive analysis.…”

Section: Further Analysismentioning

confidence: 99%

New Computational Approach for Peptide Vaccine Design Against SARS-COV-2

Biswas

Manna

Nandy

et al. 2021

Int J Pept Res Ther

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The design for vaccines using in silico analysis of genomic data of different viruses has taken many different paths, but lack of any precise computational approach has constrained them to alignment methods and some alignment-free techniques. In this work, a precise computational approach has been established wherein two new mathematical parameters have been suggested to identify the highly conserved and surface-exposed regions which are spread over a large region of the surface protein of the virus so that one can determine possible peptide vaccine candidates from those regions. The first parameter, w, is the sum of the normalized values of the measure of surface accessibility and the normalized measure of conservativeness, and the second parameter is the area of a triangle formed by a mathematical model named 2D Polygon Representation. This method has been, therefore, used to determine possible vaccine targets against SARS-CoV-2 by considering its surfacesituated spike glycoprotein. The results of this model have been verified by a parallel analysis using the older approach of manually estimating the graphs describing the variation of conservativeness and surface-exposure across the protein sequence. Furthermore, the working of the method has been tested by applying it to find out peptide vaccine candidates for Zika and Hendra viruses respectively. A satisfactory consistency of the model results with pre-established results for both the test cases shows that this in silico alignment-free analysis proposed by the model is suitable not only to determine vaccine targets against SARS-CoV-2 but also ready to extend against other viruses.

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Section: Further Analysismentioning

confidence: 99%

New Computational Approach for Peptide Vaccine Design Against SARS-COV-2

Biswas

Manna

Nandy

et al. 2021

Int J Pept Res Ther

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“…As a result of another detailed study conducted with a computer-aided vaccine design (CAVD) approach to develop a series of epitope-based peptide vaccine candidates, 4 possible peptides were presented; (Biswas et al, 2020). Researchers stated that if the peptide sequences are supported by wet laboratory studies, they may be candidates in developing vaccines against COVID-19.…”

Section: Peptide Sequences For Epitope-based Peptide Vaccine Studies Against Sars-cov-2mentioning

confidence: 99%

An insight into the epitope-based peptide vaccine design strategy and studies against COVID-19

et al. 2020

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IntroductionCoronaviruses belonging to the family Coronaviridae from the members of the order Nidovirales are spherical, enveloped, and single-stranded positive RNA viruses within the diameter range of 60-220 nm, which have rodshaped glycoprotein extensions in their outer surfaces and carry a genome size of 26-32 kb (King et al., 2011;Shereen et al., 2020). Among the coronaviruses, which are classified into four subgroups: alpha (α), beta (β), gamma (γ), and delta (δ) (Kin et al., 2015), the strains that currently infect humans are seven; HCoV229E, HCoV-OC43, SARS-CoV, HCoV-NL63, HCoV-HKU1, MERS-CoV, and SARS-CoV-2 (severe acute respiratory syndrome coronavirus) (Nomura et al., 2004).Following the severe acute respiratory syndrome (SARS-CoV) that occurred in China in 2002, MERS-CoV caused endemic in the Middle East countries in 2013 (Brian and Baric, 2005), while SARS-CoV-2 created pandemics in 2020 1 . The SARS-1 WHO has declared COVID-19 as a pandemic. [online] Website: https://www.who.int/dg/speeches/detail/who-director-general-s-opening-remarks-at-the-media-briefing-on-covid-19---11-march-2020 [accessed date 25.05.2020]CoV-2, which caused the COVID-19 pandemic, belongs to the group of betacoronavirus and its clinical manifestations are evaluated in three different stages: i) mild; weakness, fever, dry cough, fatigue, and upper respiratory tract infections, ii) moderate; shortness of breath, severe cough, diarrhea, iii) severe; severe pneumonia, acute lung injury (ALI), and acute respiratory distress syndrome (ARDS), sepsis and septic shock (Cascella et al., 2020). Currently, there is no specific antiviral therapy developed against SARS-CoV-2.Based on previous experiences in SARS-CoV and MERS-CoV outbreaks, some treatment strategies have been developed (Cascella et al., 2020;Mehta et al., 2020;. These strategies include antiviral treatments or combinations of these that have been known to be safe for humans and used in previous viral outbreaks,

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“…[79] Because of various difficulties arising out of treatments by classical vaccines researchers are working on the development of an alternative -the peptide vaccines. [80][81][82][83] The major steps in peptide vaccine design project were: a) Find highly conserved amino acid sequences of important viral proteins like the spike glycoprotein of SARS-CoV-2, b) Test the conserved sequences for their potential immunogenicity using online computational tools, c) Ascertain solvent accessibility of the epitope sequence, and d) Test autoimmune threat potential of the sequences selected by steps a-c above. In the first crucial step of finding highly conserved amino acid sequences mathematical sequence descriptors were used for their selection and clustering.…”

Section: Use Of Alignment-free Sequence Descriptors In Vaccine Designmentioning

confidence: 99%

“…In the first crucial step of finding highly conserved amino acid sequences mathematical sequence descriptors were used for their selection and clustering. [80][81][82][83] My Interaction with Mircea Diudea:…”

Section: Use Of Alignment-free Sequence Descriptors In Vaccine Designmentioning

confidence: 99%

My Tortuous Pathway Through Mathematical Chemistry and QSAR Research With Memories of Some Personal Interactions and Collaborations With Professors Milan Randić and Mircea Diudea

Basak

2020

Croat. Chem. Acta

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In Silico Approach for Peptide Vaccine Design for CoVID 19

Cited by 11 publications

References 12 publications

New Computational Approach for Peptide Vaccine Design Against SARS-COV-2

New Computational Approach for Peptide Vaccine Design Against SARS-COV-2

An insight into the epitope-based peptide vaccine design strategy and studies against COVID-19

My Tortuous Pathway Through Mathematical Chemistry and QSAR Research With Memories of Some Personal Interactions and Collaborations With Professors Milan Randić and Mircea Diudea

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