A comprehensive analysis of amino-peptidase N1 protein (APN) from Anopheles culicifacies for epitope design using Immuno-informatics models

Jakhar, Renu; Kumar, Pawan; Sehrawat, Neelam; Gakhar, S. K.

doi:10.6026/97320630015600

Cited by 6 publications

(7 citation statements)

References 42 publications

(39 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Other epitopes, that is, 46 EAAAKMLNPNYED 58 and 89 GGSDEFTP 96 were also screened with a good PI score (0.77). The obtained Protrusion score confirms that the designed subunit vaccine is assessable to the surface and immunogenic in nature 43 (Figure 2).…”

Section: Resultssupporting

confidence: 73%

See 1 more Smart Citation

3CL hydrolase‐based multiepitope peptide vaccine against SARS‐CoV‐2 using immunoinformatics

Jakhar

Kaushik

Gakhar

2020

Journal of Medical Virology

Self Cite

View full text Add to dashboard Cite

The present study provides the first multiepitope vaccine construct using the 3CL hydrolase protein of SARS‐CoV‐2. The coronavirus 3CL hydrolase (Mpro) enzyme is essential for proteolytic maturation of the virus. This study was based on immunoinformatics and structural vaccinology strategies. The design of the multiepitope vaccine was built using helper T‐cell and cytotoxic T‐cell epitopes from the 3CL hydrolase protein along with an adjuvant to enhance immune response; these are joined to each other by short peptide linkers. The vaccine also carries potential B‐cell linear epitope regions, B‐cell discontinuous epitopes, and interferon‐γ‐inducing epitopes. Epitopes of the constructed multiepitope vaccine were found to be antigenic, nonallergic, nontoxic, and covering large human populations worldwide. The vaccine construct was modeled, validated, and refined by different programs to achieve a high‐quality three‐dimensional structure. The resulting high‐quality model was applied for conformational B‐cell epitope selection and docking analyses with toll‐like receptor‐3 for understanding the capability of the vaccine to elicit an immune response. In silico cloning and codon adaptation were also performed with the pET‐19b plasmid vector. The designed multiepitope peptide vaccine may prompt the development of a vaccine to control SARS‐CoV‐2 infection.

show abstract

Section: Resultssupporting

confidence: 73%

“…The conformational epitopes were predicted by using a three‐dimensional (3D) structure of the 3CL hydrolase protein of SARS‐CoV‐2. ElliPro gives a score to each output epitope, which is the Protrusion Index (PI) value averaged over each epitope residue 43 . Some ellipsoids approximated the tertiary structure of the protein.…”

Section: Resultsmentioning

confidence: 99%

3CL hydrolase‐based multiepitope peptide vaccine against SARS‐CoV‐2 using immunoinformatics

Jakhar

Kaushik

Gakhar

2020

Journal of Medical Virology

Self Cite

View full text Add to dashboard Cite

show abstract

“…Whereas in the case of C. perfringens endo-beta-N-acetylglucosaminidase, SagA protein, phospholipase C, translation elongation factor, acetyl-CoA acetyltransferase, fructose-bisphosphate aldolase and ornithine carbamoyl transferase were reported as immunogenic proteins and the recombinant ornithine carbamoyl transferase extended the death time of mice challenged with C. perfringens (Sengupta et al 2010 ). Phosphoglycerate kinase was successfully expressed by prokaryotic expression system and the recombinant protein showed favorable immunogenicity in mice (He et al 2013 ) Peptidase protein had been known as immunogenic protein in anopheles culicifacies or gambiae for epitope design using immuno-informatics models (Jakhar et al 2019 ). Metallopeptidase was identified as immunogenic proteins in various cancer including breast cancer (Chantada-Vázquez et al 2020 ).…”

Section: Resultsmentioning

confidence: 99%

Immunoproteomic analysis of Clostridium botulinum type B secretome for identification of immunogenic proteins against botulism

et al. 2021

View full text Add to dashboard Cite

Objectives To identify immunogenic proteins of C. botulinum type B secretome by immunoproteomic analysis. Results In the present study, an attempt was made to elucidate the vaccine candidates/diagnostic molecules against botulism using immuno proteomic approach. C. botulinum type B secretome was elucidated when it was grown in TPGY as well as CMM media. Predominant 51 proteins were identified in both the media using 2-DE and mass spectrometry analysis. 2D gels (CMM & TPGY) were probed with respected proteins mice antiserum and obtained 17 and 10 immunogenic proteins in TPGY as well as CMM media respectively. Hypothetical protein CLOSPO_00563, ornithine carbamoyl transferase, FlaA, molecular chaperone GroEL and secreted protease proteins were found as the common immuno dominant proteins in both media. Polyclonal Antibodies raised against C. botulinum types A and E showed cross-reactivity with secretome C. botulinum type B at the lowest dilution (1:1000) but did not show cross reactivity with highest dilution (1:30,000) with C. botulinum type B secretome. Polyclonal antibodies against C. botulinum type F secretome did not show cross reactivity with C. botulinum type B secretome. Conclusions Identified immunogenic proteins can be used as vaccine candidates and diagnostic markers for the infant and wound botulism but common immunogenic proteins may be the best vaccine candidate molecule for development of vaccine as well as diagnostic system against the infant and wound botulism. Supplementary Information The online version contains supplementary material available at 10.1007/s10529-021-03091-4.

show abstract

“…In this study, we aimed to determine the highly potential immunogenic epitopes for B and T indicates that 76% of protein residues lie within ellipsoid and the remaining 24% residues lie outside. PI score and solvent accessibility are directly proportional to each other if the PI score is higher; maximum is the solvent accessibility of the residues [50]. Thus, this epitope enables direct interactions with an immune receptor, which could be the putative vaccine candidates.…”

Section: Discussionmentioning

confidence: 99%

“…The conformational B-cell epitopes were also obtained in five chains of envelope protein by using ElliPro. ElliPro gives the score to each output epitope, which is Protrusion Index (PI) value averaged over each epitope residue [50]. Some ellipsoids approximated the tertiary structure of the protein.…”

Section: Prediction Of Conformational and Linear B-cell Epitopementioning

confidence: 99%

An Immunoinformatics Study to Predict Epitopes in the Envelope Protein of SARS-COV-2

Jakhar

Gakhar

2020

Preprint

Self Cite

View full text Add to dashboard Cite

COVID-19 is a new viral emergent human disease caused by a novel strain of Coronavirus.This virus has caused a huge problem in the world as millions of the people are affected with this disease in the entire world. We aimed to design a peptide vaccine for COVID-19 particularly for the envelope protein using computational methods to predict epitopes inducing the immune system and can be used later to create a new peptide vaccine that could replace conventional vaccines. A total of available 370 sequences of SARS-CoV-2 were retrieved from NCBI for bioinformatics analysis using Immune Epitope Data Base (IEDB) to predict B and T cells epitopes. Then we docked the best predicted CTL epitopes with HLA alleles. CTL cell epitopes namely interacted with MHC class I alleles and we suggested them to become universal peptides based vaccine against COVID-19. Potentially continuous B cell epitopes were predicted using tools from IEDB. The Allergenicity of predicted epitopes was analyzed by AllerTOP tool and the coverage was determined throughout the worlds. We found these CTL epitopes to be T helper epitopes also. The B cell epitope, SRVKNL and T cell epitope, FLAFVVFLL were suggested to become a universal candidate for peptide-based vaccine against COVID-19. We hope to confirm our findings by adding complementary steps of both in vitro and in vivo studies to support this new universal predicted candidate.

show abstract

A comprehensive analysis of amino-peptidase N1 protein (APN) from Anopheles culicifacies for epitope design using Immuno-informatics models

Cited by 6 publications

References 42 publications

3CL hydrolase‐based multiepitope peptide vaccine against SARS‐CoV‐2 using immunoinformatics

3CL hydrolase‐based multiepitope peptide vaccine against SARS‐CoV‐2 using immunoinformatics

Immunoproteomic analysis of Clostridium botulinum type B secretome for identification of immunogenic proteins against botulism

An Immunoinformatics Study to Predict Epitopes in the Envelope Protein of SARS-COV-2

Contact Info

Product

Resources

About