Design of a peptide-based vaccine from late stage specific immunogenic cross-reactive antigens of PE/PPE proteins of Mycobacterium tuberculosis

Since decades now, Tuberculosis (TB) is among the leading cause of death globally. Innovative and extensive research strategies are necessary to lower TB incidence and achieve the End TB Strategy milestone. Epitope-based vaccine designing and development provides a promising solution with high efficacy and effectiveness. Mining of less studied genes of Mycobacterium tuberculosis (Mtb) is crucial for recognizing potential antigenic peptide epitopes which can mount protective immune response in host. Many proteins from ESX associated Proline-Glutamate (PE)/ Proline-Proline-Glutamate (PPE) family are virulence factors and alter host mediated immune response against the pathogen. In the present study, we have targeted 34 late stage expressing (being expressed at 90 days) PE/PPE proteins of Mtb for prediction and identification of promiscuous, immunogenic and cross-reactive CD4⁺ T cell specific epitopes. We found a total of 149 promiscuous and cross-reactive epitopes out of which 42 were antigenic as well. Further, we shortlisted top 10 Promiscuous, Cross-reactive CD4⁺ T cell specific, Antigenic Peptide Epitopes (PCAPEs) which were characterized to be non-allergenic and pro-inflammatory cytokine inducing in nature. These epitopes also showed strong binding affinity for CD8⁺ T cell restricted Major Histo-compatibility Complex (MHC) class I alleles. Additionally, these PCAPEs showed wide population coverage of 99.6% globally for both MHC class I and class II alleles. Molecular docking studies were conducted to confirm the affinity of these shortlisted peptides for widely occurring MHC alleles. Additionally, we performed codon adaptation and in silico cloning of the recombinant vaccine construct incorporating EsxA (ESAT-6) as an adjuvant and the 10 selected PCAPEs joined by linkers. The recombinant vaccine construct showed strong affinity for Toll-like receptor2 (TLR2) immune receptor in docking studies. In silico prediction based study using C-ImmSim server shows significant population of Th1 type immune cells with memory cells lasting for months in response to our vaccine administration. Since, majority of TB vaccines under clinical trials are antigens expressed at early stages; a combinatorial approach inclusive of peptide epitopes derived from proteins being expressed at all stages could be a promising strategy to design and develop effective TB vaccine. Synthesis and experimental validation of this multi-epitopic recombinant TB vaccine construct may result in an effective vaccine to confer protection against Mtb.

Prediction and identification of T cell epitopes of COVID-19 with balanced cytokine response for the development of peptide based vaccines

Recent outbreak of 2019 novel Corona virus poses serious challenge for the global health system. In lieu of paucity of experimental data, tools and the very basic understanding of host immune responses against SARS-CoV-2, well thought effective measures are needed to control COVID-19 pandemic. We have identified specific overlapping antigenic peptide epitopes (OAPE) within the 4 structural proteins of SARS-CoV-2 predictive of triggering robust CD4 and CD8 T cell responses in host using bio-informatics tools (NetMHC4.0, IEDB, and Vaxijen2.0). We speculate an early release of pro-inflammatory cytokines for protection and later release of anti-inflammatory cytokines for prevention of immunopathology in designing a vaccine for Covid-19. Therefore, the selected immunogenic OAPE were subjected to in silico tools (IL-6-Pred, IFNepitope and PIP-EL) for analyzing their pro-inflammatory response. The OAPEs found to be pro-inflammatory in nature were further subjected to prediction servers (IL-4-Pred, IL-10-Pred, Pre-AIP) to characterize them as inducers of anti-inflammatory response as well. We finally filtered out 12 OAPE which had affinity for both CD4 and CD8 T cells as well as were inducers of pro-inflammatory and anti-inflammatory cytokines. On confirmation of OAPE binding affinity for respective T cell specific MHC allele using docking studies (pepATTRACT, Hex8.0 and Discovery studio) they were found to be have more immunogenic potential than the 3 negative control peptides (NCPs) included in the study. Additionally, we constructed CTxB-adjuvanated multi-epitopic vaccine inclusive of the 12 OAPEs which was non-toxic, non-allergenic and capable of inducing both pro-inflammatory and anti-inflammatory cytokines. A successful in silico cloning and docking of modeled subunit vaccine construct with toll like receptor-2 (TLR-2) confirmed the high efficacy of our multi-epitopic vaccine which can through a balanced interplay of cytokines help in creating a steady-state immune equilibrium. In silico immune simulation studies with the vaccine using C-ImmSim server also showed higher percentage of T cells along with production of pro-inflammatory as well as some anti-inflammatory cytokines. Experimental validation of this prediction based study on Peripheral Blood Mononuclear Cells (PBMCs) of un-infected individuals, patients and recovered individuals will facilitate production of high priority effective SARS -CoV-2 vaccine candidate.

Supplementary Information

The online version contains supplementary material available at 10.1007/s40203-021-00098-7.