Identification of CD4+ T-cell epitope and investigation of HLA distribution for the immunogenic proteins of Burkholderia pseudomallei using in silico approaches - A key vaccine development strategy for melioidosis

Designing multi-epitope vaccine against human cytomegalovirus integrating pan-genome and reverse vaccinology pipelines

Human cytomegalovirus (HCMV) is accountable for high morbidity in neonates and immunosuppressed individuals. Due to the high genetic variability of HCMV, current prophylactic measures are insufficient. In this study, we employed a pan-genome and reverse vaccinology approach to screen the target for efficient vaccine candidates. Four proteins, envelope glycoprotein M, UL41A, US23, and US28, were shortlisted based on cellular localization, high solubility, antigenicity, and immunogenicity. A total of 29 B-cell and 44 T-cell highly immunogenic and antigenic epitopes with high global population coverage were finalized using immunoinformatics tools and algorithms. Further, the epitopes that were overlapping among the finalized B-cell and T-cell epitopes were linked with suitable linkers to form various combinations of multi-epitopic vaccine constructs. Among 16 vaccine constructs, Vc12 was selected based on physicochemical and structural properties. The docking and molecular simulations of VC12 were performed, which showed its high binding affinity (-23.35 kcal/mol) towards TLR4 due to intermolecular hydrogen bonds, salt bridges, and hydrophobic interactions, and there were only minimal fluctuations. Furthermore, Vc12 eliciting a good response was checked for its expression in Escherichia coli through in silico cloning and codon optimization, suggesting it to be a potent vaccine candidate.

Integrating pan-genome and reverse vaccinology to design multi-epitope vaccine against Herpes simplex virus type-1

Herpes simplex virus type-1 (HSV-1), the etiological agent of sporadic encephalitis and recurring oral (sometimes genital) infections in humans, affects millions each year. The evolving viral genome reduces susceptibility to existing antivirals and, thus, necessitates new therapeutic strategies. Immunoinformatics strategies have shown promise in designing novel vaccine candidates in the absence of a clinically licensed vaccine to prevent HSV-1. However, to encourage clinical translation, the HSV-1 pan-genome was integrated with the reverse-vaccinology pipeline for rigorous screening of universal vaccine candidates. Viral targets were screened from 104 available complete genomes. Among 364 proteins, envelope glycoprotein D being an outer membrane protein with a high antigenicity score (> 0.4) and solubility (> 0.6) was selected for epitope screening. A total of 17 T-cell and 4 B-cell epitopes with highly antigenic, immunogenic, non-toxic properties and high global population coverage were identified. Furthermore, 8 vaccine constructs were designed using different combinations of epitopes and suitable linkers. VC-8 was identified as the most potential vaccine candidate regarding chemical and structural stability. Molecular docking revealed high interactive affinity (low binding energy: - 56.25 kcal/mol) of VC-8 with the target elicited by firm intermolecular H-bonds, salt-bridges, and hydrophobic interactions, which was validated with simulations. Compatibility of the vaccine candidate to be expressed in pET-29(a) + plasmid was established by in silico cloning studies. Immune simulations confirmed the potential of VC-8 to trigger robust B-cell, T-cell, cytokine, and antibody-mediated responses, thereby suggesting a promising candidate for the future of HSV-1 prevention.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-024-04022-6.

Multi-Epitope Vaccine for Monkeypox Using Pan-Genome and Reverse Vaccinology Approaches

Outbreaks of monkeypox virus infections have imposed major health concerns worldwide, with high morbidity threats to children and immunocompromised adults. Although repurposed drugs and vaccines are being used to curb the disease, the evolving traits of the virus, exhibiting considerable genetic dynamicity, challenge the limits of a targeted treatment. A pan-genome-based reverse vaccinology approach can provide fast and efficient solutions to resolve persistent inconveniences in experimental vaccine design during an outbreak-exigency. The approach encompassed screening of available monkeypox whole genomes (n = 910) to identify viral targets. From 102 screened viral targets, viral proteins L5L, A28, and L5 were finalized based on their location, solubility, and antigenicity. The potential T-cell and B-cell epitopes were extracted from the proteins using immunoinformatics tools and algorithms. Multiple vaccine constructs were designed by combining the epitopes. Based on immunological properties, chemical stability, and structural quality, a novel multi-epitopic vaccine construct, V4, was finalized. Flexible-docking and coarse-dynamics simulation portrayed that the V4 had high binding affinity towards human HLA-proteins (binding energy < -15.0 kcal/mol) with low conformational fluctuations (<1 Å). Thus, the vaccine construct (V4) may act as an efficient vaccine to induce immunity against monkeypox, which encourages experimental validation and similar approaches against emerging viral infections.

In-silico strategies to combat COVID-19: A comprehensive review

The novel coronavirus SARS-CoV-2 since its emergence at Wuhan, China in December 2019 has been creating global health turmoil despite extensive containment measures and has resulted in the present pandemic COVID-19. Although the virus and its interaction with the host have been thoroughly characterized, effective treatment regimens beyond symptom-based care and repurposed therapeutics could not be identified. Various countries have successfully developed vaccines to curb the disease-transmission and prevent future outbreaks. Vaccination-drives are being conducted on a war-footing, but the process is time-consuming, especially in the densely populated regions of the world. Bioinformaticians and computational biologists have been playing an efficient role in this state of emergency to escalate clinical research and therapeutic development. However, there are not many reviews available in the literature concerning COVID-19 and its management. Hence, we have focused on designing a comprehensive review on in-silico approaches concerning COVID-19 to discuss the relevant bioinformatics and computational resources, tools, patterns of research, outcomes generated so far and their future implications to efficiently model data based on epidemiology; identify drug targets to design new drugs; predict epitopes for vaccine design and conceptualize diagnostic models. Artificial intelligence/machine learning can be employed to accelerate the research programs encompassing all the above urgent needs to counter COVID-19 and similar outbreaks.

Immunoinformatics and molecular dynamics studies to predict T-cell-specific epitopes of four Klebsiella pneumoniae fimbriae antigens

Klebsiella pneumoniae (K. pneumoniae) is a causative agent of severe infections in humans. There is no publically available vaccine for K. pneumoniae infections yet. Here, using comprehensive immunoinformatics methods, T-cell-specific epitopes of four type 1 fimbriae antigens of K. pneumoniae were predicted and evaluated as potential vaccine candidates. Both CD8+ (class I) and CD4+ (class II) T-cell-specific epitopes were predicted and the epitopes similar to human proteome were excluded. Subsequently, the windows of class-II epitopes containing class-I epitopes were determined. The immunogenicity, IFN-γ production and population coverage were also estimated. Using the 3D structure of HLA and epitopes, molecular docking was carried out. Two best epitopes were selected for molecular dynamics studies. Our prediction and analyses resulted in the several dominant epitopes for each antigen. The docking results showed that all selected epitopes can bind to their restricted HLA molecules with high affinity. The molecular dynamics results indicated the stability of system with minimum possible deviation, suggesting the selected epitopes can be promising candidates for stably binding to HLA molecules. Altogether, our results suggest that the selected T-cell-specific epitopes of K. pneumoniae fimbriae antigens, particularly the two epitopes confirmed by molecular dynamics, can be applied for vaccine development. However, the in vitro and in vivo studies are required to authenticate the results of the present study.Communicated by Ramaswamy H. Sarma.

Infection with Burkholderia pseudomallei - immune correlates of survival in acute melioidosis

Melioidosis, caused by Burkholderia pseudomallei, is a potentially lethal infection with no licensed vaccine. There is little understanding of why some exposed individuals have no symptoms, while others rapidly progress to sepsis and death, or why diabetes confers increased susceptibility. We prospectively recruited a cohort of 183 acute melioidosis patients and 21 control subjects from Northeast Thailand and studied immune parameters in the context of survival status and the presence or absence of diabetes. HLA-B*46 (one of the commonest HLA class I alleles in SE Asia) and HLA-C*01 were associated with an increased risk of death (odds ratio 2.8 and 3.1 respectively). Transcriptomic analysis during acute infection in diabetics indicated the importance of interplay between immune pathways including those involved in antigen presentation, chemotaxis, innate and adaptive immunity and their regulation. Survival was associated with enhanced T cell immunity to nine of fifteen immunodominant antigens analysed including AhpC (BPSL2096), BopE (BPSS1525), PilO (BPSS1599), ATP binding protein (BPSS1385) and an uncharacterised protein (BPSL2520). T cell immunity to GroEL (BPSL2697) was specifically impaired in diabetic individuals. This characterization of immunity associated with survival during acute infection offers insights into correlates of protection and a foundation for design of an effective multivalent vaccine.