Novelin silicotools for designing peptide-based subunit vaccines and immunotherapeutics

Abstract

The conventional approach for designing vaccine against a particular disease involves stimulation of the immune system using the whole pathogen responsible for the disease. In the post-genomic era, a major challenge is to identify antigenic regions or epitopes that can stimulate different arms of the immune system. In the past two decades, numerous methods and databases have been developed for designing vaccine or immunotherapy against various pathogen-causing diseases. This review describes various computational resources important for designing subunit vaccines or epitope-based immunotherapy. First, different immunological databases are described that maintain epitopes, antigens and vaccine targets. This is followed by in silico tools used for predicting linear and conformational B-cell epitopes required for activating humoral immunity. Finally, information on T-cell epitope prediction methods is provided that includes indirect methods like prediction of Major Histocompatibility Complex and transporter-associated protein binders. Different studies for validating the predicted epitopes are also examined critically. This review enlists novel in silico resources and tools available for predicting humoral and cell-mediated immune potential. These predicted epitopes could be used for designing epitope-based vaccines or immunotherapy as they may activate the adaptive immunity. Authors emphasized the need to develop tools for the prediction of adjuvants to activate innate and adaptive immune system simultaneously. In addition, attention has also been given to novel prediction methods to predict general therapeutic properties of peptides like half-life, cytotoxicity and immune toxicity.

PEPlife: A Repository of the Half-life of Peptides

“…Peptides containing various therapeutic properties have been discovered67891011121314151617181920 and their number is increasing with time21. Owing to their applicability, a number of bioinformatics platforms have been developed to assist peptide therapeutics22232425262728. According to a recent report, 128 peptides are in the clinical pipeline.…”

Peptides: A New Therapeutic Approach

“…Therefore, keeping the above facts in mind, THPdb was developed, which is a comprehensive resource of all US-FDA approved protein and peptide therapeutics along with their corresponding drug variants available in the market. It is anticipated that the information available in the THPdb is very helpful to the researchers working in he field of peptide and protein-based drug discovery [28].…”

Prediction of Antitubercular Peptides From Sequence Information Using Ensemble Classifier and Hybrid Features

“…Therefore, to assist them, a number of in silico tools to predict and design various kind of therapeutic peptide such as cell-penetrating, tumor-hoping, anti-microbial, anti-bacterial, anti-fungal, vaccine, immunotherapy, etc. has been developed in recent years (Lata et al, 2007; Sharma et al, 2013; Dhanda et al, 2017; Agrawal et al, 2018; Kumar et al, 2018; Usmani et al, 2018a). Mycobacterium , neither Gram-positive nor Gram-negative, has unusual waxy coating (primarily of mycolic acid) on the cell surface, being dissimilar to other bacteria (Bhat et al, 2017; Squeglia et al, 2018; Velayati et al, 2018).…”