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

The discovery of the first infectious variant in Wuhan, China, in December 2019, has posed concerns over global health due to the spread of COVID-19 and subsequent variants. While the majority of patients experience flu-like symptoms such as cold and fever, a small percentage, particularly those with compromised immune systems, progress from mild illness to fatality. COVID-19 is caused by a RNA virus known as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Our approach involved utilizing immunoinformatic to identify vaccine candidates with multiple epitopes and ligand-binding regions in reported SARS-CoV-2 variants. Through analysis of the spike glycoprotein, we identified dominant epitopes for T-cells and B-cells, resulting in a vaccine construct containing two helper T-cell epitopes, six cytotoxic T-cell epitopes, and four linear B-cell epitopes. Prior to conjugation with adjuvants and linkers, all epitopes were evaluated for antigenicity, toxicity, and allergenicity. Additionally, we assessed the vaccine Toll-Like Receptors complex (2, 3, and 4). The vaccine construct demonstrated antigenicity, non-toxicity, and non-allergenicity, thereby enabling the host to generate antibodies with favorable physicochemical characteristics. Furthermore, the 3D structure of the B-cell construct exhibited a ProSA-web z-score plot with a value of -1.71, indicating the reliability of the designed structure. The Ramachandran plot analysis revealed that 99.6% of the amino acid residues in the vaccine subunit were located in the high favored observation region, further establishing its strong candidacy as a vaccination option.

Bioinformatics analysis of structural protein to approach a vaccine candidate against Vibrio cholerae infection.

The bacteria Vibrio cholerae causes cholera, an acute diarrheal infection that can lead to dehydration and even death. Over 100,000 people die each year as a result of epidemic diseases; vaccination has emerged as a successful strategy for combating cholera. This study uses bioinformatics tools to create a multi-epitope vaccine against cholera infection using five structural polyproteins from the V. cholerae (CTB, TCPA, TCPF, OMPU, and OMPW). The antigenic retrieved protein sequence were analyzed using BCPred and IEDB bioinformatics tools to predict B cell and T cell epitopes, respectively, which were then linked with flexible linkers together with an adjuvant to boost it immunogenicity. The construct has a theoretical PI of 6.09, a molecular weight of 53.85 kDa, and an estimated half-life for mammalian reticulocytes in vitro of 4.4 h. These results demonstrate the construct's longevity. The vaccine design was docked against the human toll-like receptor (TLR) to evaluate compatibility and effectiveness; also other additional post-vaccination assessments were carried out on the designed vaccine. Through in silico cloning, its expression was determined. The results show that it has a CAI value of 0.1 and GC contents of 58.97% which established the adequate expression and downstream processing of the vaccine construct, and our research demonstrated that the multi-epitope subunit vaccine exhibits antigenic characteristics. Additionally, we carried out an in silico immunological simulation to examine the immune reaction to an injection. Our results strongly suggest that the vaccine candidate on further validation would induce immune response against the V. cholerae infection.

Immunoinformatics design of multi-epitope peptide for the diagnosis of Schistosoma haematobium infection.

Schistosoma haematobium has been identified as a significant cause of urogenital disease, as well as a risk factor for bladder cancer and HIV/AIDS. The parasites are obtained trans-dermally by swimming or wading in contaminated freshwater, and they are also transmitted to humans by freshwater snails. The organisms infect the vasculature of the gastrointestinal or genitourinary tracts. Worms live in blood vessels and lay eggs that become embedded in the bladder wall, causing chronic immune-mediated disease and squamous cell carcinoma growth. The primary goal of this research is to predict and design a novel synthetic protein containing multiple immunodominant B cell epitopes using three schistosome proteins: XP-012801068.2, XP-012801892.2, and XP-012793835.2 softwares were used to analyze the proteins' primary, secondary, and tertiary structures (BepiPred, BcPred).The B cell construct was then evaluated using I-TASSER server, and physicochemical properties, as well as homology modeling of the 3 D structure of the protein, was obtained. In silico analyses revealed regions with high immunogenicity. For XP-012801068.2, three epitopes are found between residues 292-334, 3-22, and 314-333; for XP-012801892.2, three epitopes are found in the residues 184-236, 81-100, and 329-348 for XP-012793835.2, four epitopes are found in the residues 185-222, 469-512, 649-713, and 338-357. The construct's has an average length of 308 bp, instability index of 49.96, theoretical PI of 4.2 and a C score -1.59. Furthermore, these parameters analyzed reveals that the constructed multi-epitope peptide has the potential to provide a theoretical basis for the development of a Schistosoma haematobium diagnostic kit.Communicated by Ramaswamy H. Sarma.