Identification of vaccine targets in pathogens and design of a vaccine using computational approaches

Abstract

Antigen identification is an important step in the vaccine development process. Computational approaches including deep learning systems can play an important role in the identification of vaccine targets using genomic and proteomic information. Here, we present a new computational system to discover and analyse novel vaccine targets leading to the design of a multi-epitope subunit vaccine candidate. The system incorporates reverse vaccinology and immuno-informatics tools to screen genomic and proteomic datasets of several pathogens such as Trypanosoma cruzi, Plasmodium falciparum, and Vibrio cholerae to identify potential vaccine candidates (PVC). Further, as a case study, we performed a detailed analysis of the genomic and proteomic dataset of T. cruzi (CL Brenner and Y strain) to shortlist eight proteins as possible vaccine antigen candidates using properties such as secretory/surface-exposed nature, low transmembrane helix (< 2), essentiality, virulence, antigenic, and non-homology with host/gut flora proteins. Subsequently, highly antigenic and immunogenic MHC class I, MHC class II and B cell epitopes were extracted from top-ranking vaccine targets. The designed vaccine construct containing 24 epitopes, 3 adjuvants, and 4 linkers was analysed for its physicochemical properties using different tools, including docking analysis. Immunological simulation studies suggested significant levels of T-helper, T-cytotoxic cells, and IgG1 will be elicited upon administration of such a putative multi-epitope vaccine construct. The vaccine construct is predicted to be soluble, stable, non-allergenic, non-toxic, and to offer cross-protection against related Trypanosoma species and strains. Further, studies are required to validate safety and immunogenicity of the vaccine.

Whole Proteome-Based Therapeutic Targets Annotation and Designing of Multi-Epitope-Based Vaccines against the Gram-Negative XDR-Alcaligenes faecalis Bacterium

“…Protein target annotation is a prerequisite step followed in the process of designing therapeutics [ 56 , 57 ]. This also involves identification of novel targets that can be used in vaccine design approaches [ 58 ].…”

Identification of vaccine targets & design of vaccine against SARS-CoV-2 coronavirus using computational and deep learning-based approaches

“…These attributes of the surface and secretory proteins make them attractive drug & vaccine targets. Retrieval and selection of the outer cellular membrane proteins for the purpose of vaccine design and construction was performed using the state-of-the-art pipeline called VaxELAN ( Rawal et al, 2021 ). The pipeline uses three different tools namely:- CELLO ( Yu, Lin & Hwang, 2004 ), Virus-mPloc tool ( Shen & Chou, 2010 ) and PSORTb ( Yu et al, 2010 ) to determine the location of a given protein.…”

N-acetylmuramoyl-L-alanine amidase : A competent vaccine candidate against IPSID

“…Here, we are using computational tools Vaxi-DL and VaxELAN to analyze a potential vaccine candidate i.e, N-acetylmuramoyl-L-alanine amidase as identified by Vaxign program [4]. VaxELAN which helps a researcher to determine and examine the potential vaccine candidates using their genomic and proteomic information [5,6,8]. Here, we were able to analyze PVC i.e., N-acetylmuramoyl-L-alanine amidase for development of vaccine against IPSID (Immuno proliferative small intestine disease) which was selected as a PVC by vaxign program [4], with the help of Vaxi-DL and VaxELAN [5,6] in terms of adhesion, secretory nature, trans-membrane helices, cleavage sites, MHC-I binding, CTL epitope prediction, essential genes, molecular weight, non-bacterial pathogen, non-homology with human genome, virulence factors, allergenicity, cellular localization and probability of being a PVC.…”

“…VaxELAN which helps a researcher to determine and examine the potential vaccine candidates using their genomic and proteomic information [5,6,8]. Here, we were able to analyze PVC i.e., N-acetylmuramoyl-L-alanine amidase for development of vaccine against IPSID (Immuno proliferative small intestine disease) which was selected as a PVC by vaxign program [4], with the help of Vaxi-DL and VaxELAN [5,6] in terms of adhesion, secretory nature, trans-membrane helices, cleavage sites, MHC-I binding, CTL epitope prediction, essential genes, molecular weight, non-bacterial pathogen, non-homology with human genome, virulence factors, allergenicity, cellular localization and probability of being a PVC. IPSID is a disease emerging from the low socio-economic background areas such as in mediterranean regions and later spread as sporadic cases increased in European and American countries [1].…”