Search

There has been progressive improvement in immunoinformatics approaches for epitope-based peptide design. Computational-based immune-informatics approaches were applied to identify the epitopes of SARS-CoV-2 to develop vaccines. The accessibility of the SARS-CoV-2 protein surface was analyzed, and hexa-peptide sequences (KTPKYK) were observed having a maximum score of 8.254, located between amino acids 97 and 102, whereas the FSVLAC at amino acids 112 to 117 showed the lowest score of 0.114. The surface flexibility of the target protein ranged from 0.864 to 1.099 having amino acid ranges of 159 to 165 and 118 to 124, respectively, harboring the FCYMHHM and YNGSPSG heptapeptide sequences. The surface flexibility was predicted, and a 0.864 score was observed from amino acids 159 to 165 with the hepta-peptide (FCYMHHM) sequence. Moreover, the highest score of 1.099 was observed between amino acids 118 and 124 against YNGSPSG. B-cell epitopes and cytotoxic T-lymphocyte (CTL) epitopes were also identified against SARS-CoV-2. In molecular docking analyses, -0.54 to -26.21 kcal/mol global energy was observed against the selected CTL epitopes, exhibiting binding solid energies of -3.33 to -26.36 kcal/mol. Based on optimization, eight epitopes (SEDMLNPNY, GSVGFNIDY, LLEDEFTPF, DYDCVSFCY, GTDLEGNFY, QTFSVLACY, TVNVLAWLY, and TANPKTPKY) showed reliable findings. The study calculated the associated HLA alleles with MHC-I and MHC-II and found that MHC-I epitopes had higher population coverage (0.9019% and 0.5639%) than MHC-II epitopes, which ranged from 58.49% to 34.71% in Italy and China, respectively. The CTL epitopes were docked with antigenic sites and analyzed with MHC-I HLA protein. In addition, virtual screening was conducted using the ZINC database library, which contained 3,447 compounds. The 10 top-ranked scrutinized molecules (ZINC222731806, ZINC077293241, ZINC014880001, ZINC003830427, ZINC030731133, ZINC003932831, ZINC003816514, ZINC004245650, ZINC000057255, and ZINC011592639) exhibited the least binding energy (-8.8 to -7.5 kcal/mol). The molecular dynamics (MD) and immune simulation data suggest that these epitopes could be used to design an effective SARS-CoV-2 vaccine in the form of a peptide-based vaccine. Our identified CTL epitopes have the potential to inhibit SARS-CoV-2 replication. [ABSTRACT FROM AUTHOR]

Copyright of Shipin Kexue/ Food Science is the property of Food Science Editorial Department and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Since the outbreak of severe acute respiratory syndrome‐coronavirus 2 (SARS‐CoV‐2) in December 2019 in China, there has been an upsurge in the number of deaths and infected individuals throughout the world, thereby leading to the World Health Organization declaration of a pandemic. Since no specific therapy is currently available for the same, the present study was aimed to explore the SARS‐CoV‐2 genome for the identification of immunogenic regions using immunoinformatics approach. A series of computational tools were applied in a systematic way to identify the epitopes that could be utilized in vaccine development. The screened‐out epitopes were passed through several immune filters, such as promiscuousity, conservancy, antigenicity, nonallergenicity, population coverage, nonhomologous to human proteins, and affinity with human leukocyte antigen alleles, to screen out the best possible ones. Further, a construct comprising 11 CD4, 12 CD8, 3 B cell, and 3 interferon‐γ epitopes, along with an adjuvant β‐defensin, was designed in silico, resulting in the formation of a multiepitope vaccine. The in silico immune simulation and population coverage analysis of the vaccine sequence showed its capacity to elicit cellular, humoral, and innate immune cells and to cover up a worldwide population of more than 97%. Further, the interaction analysis of the vaccine construct with Toll‐like receptor 3 (immune receptor) was carried out by docking and dynamics simulations, revealing high affinity, constancy, and pliability between the two. The overall findings suggest that the vaccine may be highly effective, and is therefore required to be tested in the lab settings to evaluate its efficacy. [ABSTRACT FROM AUTHOR]

The widespread of coronavirus (COVID-19) is a new global health crisis that poses a threat to the world. The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) originated in bats and was discovered first in Wuhan, Hubei province, China in December 2019. Immunoinformatics and bioinformatics tools were employed for the construction of a multi-epitope subunit vaccine to prevent the diseases. The antigenicity, toxicity and allergenicity of all epitopes used in the construction of the vaccine were predicted and then conjugated with adjuvants and linkers. Vaccine Toll-Like Receptors (2, 3, 4, 8 and 9) complex was also evaluated. The vaccine construct was antigenic, non-toxic and non-allergic, which indicates the vaccines ability to induce antibodies in the host, making it an effective vaccine candidate. [ABSTRACT FROM AUTHOR]

Last December, a novel coronavirus emerged in Wuhan city, China. Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) causes a high intense acute respiratory syndrome with elevation mortality. Nucleocapsid phosphoprotein (NP) is one of the most structural proteins of the virus. NP possesses active immunogenicity for T-cell response. Because NP considered as a potential vaccine target, our study goal was to identify the cytotoxic T-cell (CTL) and B-cell epitopes inside NP peptides. Methods. We used a series of popular immunoinformatics and algorithm tools such as FASTA-NCBI, CLUSTAL-OMGA, T-COFFEE, SWISS-MODEL, CTLPred and its branches. Results. Homology modeling and alignment of SARS-CoV-2 NP showed high conserved residues compared with related sequences. Different types of the major histocompatibility complex (MHC) alleles were identified, specifically human leukocyte antigens (HLA-A) affinity for NP. We also demonstrate six B-cell epitopes with a high score above the threshold. Conclusions. We recorded high binder HLA-A*02:01 alleles matched between the novel coronavirus SARS-CoV-2 NP and the Bat coronavirus SARS-Bat-CoV NP. Identification of CTL response and B-cell predictions will be helpful in reverse immunogenetic approaches, hence in the strategy process of the plausible design of the vaccine. [ABSTRACT FROM AUTHOR]

Background: Alpha-papillomavirus 9 (α-9) is a member of the human papillomavirus (HPV) α genus, causing 75% invasive cervical cancers worldwide. The purpose of this study was to provide data for effective treatment of HPV-induced cervical lesions in Taizhou by analysing the genetic variation and antigenic epitopes of α-9 HPV E6 and E7., Methods: Cervical exfoliated cells were collected for HPV genotyping. Positive samples of the α-9 HPV single type were selected for E6 and E7 gene sequencing. The obtained nucleotide sequences were translated into amino acid sequences (protein primary structure) using MEGA X, and positive selection sites of the amino acid sequences were evaluated using PAML. The secondary and tertiary structures of the E6 and E7 proteins were predicted using PSIPred, SWISS-MODEL, and PyMol. Potential T/B-cell epitopes were predicted by Industrial Engineering Database (IEDB)., Results: From 2012 to 2023, α-9 HPV accounted for 75.0% (7815/10423) of high-risk HPV-positive samples in Taizhou, both alone and in combination with other types. Among these, single-type-positive samples of α-9 HPV were selected, and the entire E6 and E7 genes were sequenced, including 298 HPV16, 149 HPV31, 185 HPV33, 123 HPV35, 325 HPV52, and 199 HPV58 samples. Compared with reference sequences, 34, 12, 10, 2, 17, and 17 nonsynonymous nucleotide mutations were detected in HPV16, 31, 33, 35, 52, and 58, respectively. Among all nonsynonymous nucleotide mutations, 19 positive selection sites were selected, which may have evolutionary significance in rendering α-9 HPV adaptive to its environment. Immunoinformatics predicted 57 potential linear and 59 conformational B-cell epitopes, many of which are also predicted as CTL epitopes., Conclusion: The present study provides almost comprehensive data on the genetic variations, phylogenetics, positive selection sites, and antigenic epitopes of α-9 HPV E6 and E7 in Taizhou, China, which will be helpful for local HPV therapeutic vaccine development., (© 2024. The Author(s).)

Recently, a novel coronavirus (SARS-CoV-2) appeared which is conscientious for the current outbreak in China and rapidly spread worldwide. Unluckily, there is no approved vaccine found against SARS-CoV- 2. Therefore, there is an urgent need for designing a suitable peptide vaccine constituent against the SARS-CoV-2. In this study, we characterized the spike glycoprotein of SARS-CoV-2 to obtain immunogenic epitopes. In addition, we used 58 SARS-CoV-2 isolates were retrieved from the Global Initiative on Sharing All Influenza Data (GISAID) and National Center for Biotechnology Information (NCBI), then aligned to obtain the conserved region of SARS-CoV-2 spike glycoprotein. The interaction between the conserved region with ACE2 receptor, a SARS-CoV-2 receptor on the host cell, has been evaluated through molecular docking approach. The B-cell epitope was identified using the immune epitope database (IEDB) web server. Interestingly, we recommend Pep_4 ADHQPQTFVNTELH as a epitope-based peptide vaccine candidate to deal with the SARS-CoV-2 outbreak. Pep_4 has a high level of immunogenicity and does not trigger autoimmune mechanisms. Pep_4 is capable of forming BCR/ Fab molecular complexes with the lowest binding energy for activation of transduction signal the direct B-cell immune response. However, further study is suggested for confirmation (in vitro and in vivo). [ABSTRACT FROM AUTHOR]

The 2019 novel coronavirus (2019‐nCoV) outbreak has caused a large number of deaths with thousands of confirmed cases worldwide, especially in East Asia. This study took an immunoinformatics approach to identify significant cytotoxic T lymphocyte (CTL) and B cell epitopes in the 2019‐nCoV surface glycoprotein. Also, interactions between identified CTL epitopes and their corresponding major histocompatibility complex (MHC) class I supertype representatives prevalent in China were studied by molecular dynamics simulations. We identified five CTL epitopes, three sequential B cell epitopes and five discontinuous B cell epitopes in the viral surface glycoprotein. Also, during simulations, the CTL epitopes were observed to be binding MHC class I peptide‐binding grooves via multiple contacts, with continuous hydrogen bonds and salt bridge anchors, indicating their potential in generating immune responses. Some of these identified epitopes can be potential candidates for the development of 2019‐nCoV vaccines. Highlights: Five CTL epitopes and eight B cell epitopes were computationally identified.Epitope‐MHC‐I complexes were studied by molecular dynamics simulation.Persistent H‐bonds and salt bridges were observed between epitopes and MHC‐I.The identified epitopes can be a promising foundation for vaccine development. [ABSTRACT FROM AUTHOR]