COVID-19 Vaccine: Designing the peptide-based vaccine
Our researchers are using advanced immunoinformatics and data analytics techniques to develop computational pipelines for designing peptide-based vaccine candidates for SARS-CoV-2.
Although a number of vaccines have been rolled-out for SARS-CoV-2, but due to intrinsic nature of viruses in mutating and evolving over time, continues efforts are needed to develop superior vaccine candidates.
Here at the Northern Ireland Centre for Stratified Medicine (NICSM) the Shukla Lab led by Dr Priyank Shukla is collaborating with researchers at Medical University of South Carolina (USA), CSIR-Institute of Himalayan Bioresource Technology (India), University of Cambridge (UK), and Coalition for Epidemic Preparedness Innovations (Norway) for develop computational pipelines for designing peptide-based vaccine candidates for SARS-CoV-2.
The first version of this computational analysis pipeline known as PVPredPip (Peptide-based Vaccine Prediction Pipeline) has been recently published in Briefings in Bioinformatics journal and all the code has been made available at the Github public repository. PVPredPip predicted four potential vaccine candidates which have the capability to initiate both antibody and cell-mediated immune responses, are non-allergenic, do not trigger autoimmunity, show 99.82% of global population coverage based on the genotypic frequencies of HLA binding alleles for both MHC class-I and class-II, and are unique for SARS-CoV-2 isolated from human as a host species.
The team is working closely with other colleagues at NICSM and School of Computing Engineering and Intelligent Systems and making use of Northern Ireland High Performance Computing (NI-HPC) service Kelvin2 to perform molecular docking and molecular dynamics simulation experiments, followed by binding free energy calculations with molecular mechanics Poisson–Boltzmann surface area, essential dynamics analysis and free energy landscape analysis for studying the binding and interaction of designed peptide based vaccine candidates with HLA molecules.
The Ulster University has filed a UK-wide patent application (No. 2002598.6) and Dr Shukla was recently successful in securing funding from Invest NI PoC Stage-1 program to work towards the commercialisation aspects of this work. The team is currently working towards designing a universal peptide-based vaccine candidate which can be effective against all the mutated strains of SARS-CoV-2.
Immuno-informatics analysis predicts B and T cell consensus epitopes for designing peptide vaccine against SARS-CoV-2 with 99.82% global population coverage