In silico identification of cytotoxic T lymphocyte epitopes encoded by RD5 region of Mycobacterium tuberculosis

Zhao, Junwei; Yan, Min; Shi, Guang; Zhang, Shulin; Ming, Liang

doi:10.3855/jidc.7207

Cited by 5 publications

(2 citation statements)

References 24 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The MHC-1 binding peptides, Proteasomal C-terminal cleavages and Transporter Associated with Antigen Processing (TAP) transport efficiency were the three major components that the prediction was based. The threshold value used for the Epitopes identification during the CTL Epitopes prediction was 0.75 while the weights on C-terminal cleavage and TAP transport efficiency used during the prediction were 0.15 and 0.05 respectively [ 17 ].…”

Section: Methodsmentioning

confidence: 99%

Exploration of surface glycoprotein to design multi-epitope vaccine for the prevention of Covid-19

Oladipo

Ajayi

Ariyo

et al. 2020

Informatics in Medicine Unlocked

View full text Add to dashboard Cite

Stimulation and generation of T and B cell mediated long-term immune response is essential for the curbing of a deadly virus such as SAR-CoV-2. Immunoinformatics approach in vaccine design takes advantage of antigenic and non-allergenic epitopes present on the spike glycoprotein of SARS-CoV-2 to elicit immune responses. T cells and B cells epitopes were predicted, and the selected residues were subjected to allergenicity, antigenicity and toxicity screening which were linked by appropriate linkers to form a multi-epitope subunit vaccine. The physiochemical properties of the vaccine construct was analyzed and the molecular weight, molecular formula, theoretical isoelectric point value, half-life, solubility score, instability index, aliphatic index and GRAVY were predicted. The vaccine structure was constructed, refined, validated, and disulfide engineered to get the best model. Molecular binding simulation and molecular dynamics simulation were carried out to predict the stability and binding affinity of the vaccine construct with TLRs. Codon acclimatization and in silico cloning were performed to confirm the vaccine expression and potency. Results obtained indicated that this novel vaccine candidate is non-toxic, capable of initiating the immunogenic response and will not induce an allergic reaction. The highest binding energy was observed in TLR 4 (-1398.1) and the least is TLR 2 (-1479. 6). The steady rise in Th (helper) cell population with memory development was noticed and IFN-g was provoked after simulation. At this point, the vaccine candidate awaits animal trial to validate its efficacy and safety for use in the prevention of the novel COVID-19 infections.

show abstract

Section: Methodsmentioning

confidence: 99%

Exploration of surface glycoprotein to design multi-epitope vaccine for the prevention of Covid-19

Oladipo

Ajayi

Ariyo

et al. 2020

Informatics in Medicine Unlocked

View full text Add to dashboard Cite

show abstract

“…For the 12 most commonly occurring HLA class I alleles in humans, such as A1, A2, A3, A24, A26, B7, B8, B27, B39, B44, B58, and B62, the NetCTL 1.2 service predicts 9-mer CTL epitopes ( http://www.cbs.dtu.dk/services/NetCTL/ ). The weights on C-terminal cleavage and TAP transport efficiency were 0.15 and 0.05, respectively, during the CTL Epitopes prediction, while the threshold value for Epitopes identification was 0.75 [ 7 ]. The NetMHCIIpan 3.2 service was used to predict MHC class-II restricted CD4+ HTL epitopes.…”

Section: Methodsmentioning

confidence: 99%

In silico multi-epitope Bunyumwera virus vaccine to target virus nucleocapsid N protein

Nelluri

Ammulu

Durga

et al. 2022

Journal of Genetic Engineering and Biotechnology

View full text Add to dashboard Cite

Background Bunyumwera virus can cause 82% mortality in humans currently with no vaccine or drugs for treatment. We described an in silico multi-epitope vaccine targeting Bunyumwera virus nucleocapsid N-protein and predicted B and T cell epitopes for immunogenicity, allergenicity, toxicity, and conservancy. For creating the most potent immunological response possible, docking epitopes with HLA alleles are chosen to screen them. The 3D vaccination was docked with the Toll-like receptor-8 using molecular dynamic simulations. To ensure production efficiency, the vaccine sequence was further cloned in silico in a plasmid pIB2 vector. For efficacy and safety, results must be supported in vitro and in vivo. Results The vaccine was cloned to enable expression and translation in a plasmid vector pIB2. It was expected to be antigenic, non-allergenic, and have a high binding affinity with TLR-8 in silico cloning. This multi-epitope vaccination may stimulate both innate and adaptive immunity. Conclusion The vaccine developed in this work was based on the nucleocapsid N-protein of the Bunyumwera virus and was created using a reverse vaccinology method. Further experimental validation is required to assess the vaccine’s therapeutic effectiveness and immunogenicity.

show abstract

Proteome based analysis of circulating SARS-CoV-2 variants: approach to a universal vaccine candidate

Oladipo,

Ojo,

Olufemi

et al. 2023

Genes Genom

View full text Add to dashboard Cite

In silico identification of cytotoxic T lymphocyte epitopes encoded by RD5 region of Mycobacterium tuberculosis

Cited by 5 publications

References 24 publications

Exploration of surface glycoprotein to design multi-epitope vaccine for the prevention of Covid-19

Exploration of surface glycoprotein to design multi-epitope vaccine for the prevention of Covid-19

In silico multi-epitope Bunyumwera virus vaccine to target virus nucleocapsid N protein

Proteome based analysis of circulating SARS-CoV-2 variants: approach to a universal vaccine candidate

Contact Info

Product

Resources

About