A web-based platform on COVID-19 to maintain Predicted Diagnostic, Drug and Vaccine candidates

Abstract

A web-based resource CoronaVIR (https://webs.iiitd.edu.in/raghava/coronavir/) has been developed to maintain predicted and existing information on coronavirus SARS-CoV-2. We have integrated multiple modules including “Genomics”, “Diagnosis”, “Immunotherapy” and “Drug Designing” to understand the holistic view of this pandemic medical disaster. Genomics module provides genomic information of different strains of this virus to understand genomic level alterations. The Diagnosis module provides detailed information on currently-in-use diagnostics tests as well as on five novel universal primers-sets predicted using in silico tools. The Immunotherapy module provides information on epitope-based potential vaccine candidates (e.g., LQLPQGTTLPKGFYA, VILLNKHIDAYKTFPPTEPKKDKKKK, EITVATSRTLS, GKGQQQQGQTV, SELVIGAVILR) predicted using state-of-the-art software and resources in the field of immune-informatic. These epitopes have the potential to activate both adaptive (e.g., B-cell, T-cell) and innate (e.g., vaccine adjuvants) immune systems as well suitable for all strains of SARS-CoV-2. Besides, we have also predicted potential candidates for siRNA-based therapy and RNA based vaccine adjuvants. The Drug Designing module maintains information about potential drug targets, tertiary structures, and potential drug molecules. These potential drug molecules were identified from FDA approved drugs using the docking-based approach. We also compiled information from the literature and the Internet on potential drugs, repurposing drugs and monoclonal antibodies. To understand host-virus interaction, we identified cell-penetrating peptides in the virus. In this study, state-of-the-art techniques have been used for predicting the potential candidates for diagnostics and therapeutics.

Next-generation computational tools and resources for coronavirus research: From detection to vaccine discovery

“…CoronaVIR ( https://webs.iiitd.edu.in/raghava/coronavir/ ) [ 59 ] a multi-omics website that contains detailed information about genomic, proteomic, therapeutic, and diagnostic knowledge of novel SARS-CoV-2coronaviruses, that have been manually curated from literature, existing databases and also contain predicted useful information obtained using various computational tools. To provide a holistic platform, four major modules, viz., “Genomics”, “Diagnosis”, “Immunotherapy” and “Drug Designing” have been integrated with CoronaVIR.…”

Potential Challenges for Coronavirus (SARS-CoV-2) Vaccines Under Trial

“…We have enlisted some useful in silico tools in Figure 1 . Various researchers have already identified potential B and T cell epitopes, HLA susceptibility mapping as well as candidate targets by applying a bioinformatic approach ( 64 – 69 ). In the cat and mouse game of a viral pandemic and vaccine development, bioinformatic resources are beneficial and will cut down the chances of failure, a lesson by previous virus endemics.…”

DBCOVP: A database of coronavirus virulent glycoproteins

“…To find putative drug targets and further explore the molecular mechanisms of pathogenicity, sadegh et al, developed a CoronaVirus Explorer (CoVeX, https://exbio.wzw.tum.de/covex/ ) that includes information on drug candidates and experimentally validated virus–human interaction data for both SARS-CoV-2 and SARS-CoV-1 with human interactome [ 34 ]. Apart from the above mentioned web resources, few other platforms are recently made available exclusively focused on coronavirus research like Coronavirus Database V3 ( http://covdb.popgenetics.net/v3/ [ 35 ]), that contains only genomic data; COVID-Profiler ( http://genomics.lshtm.ac.uk/ ), analyses Sars-Cov-2 sequencing and a few immunological data; COVIEdb ( http://biopharm.zju.edu.cn/coviedb/help/ [ 36 ]), holds only some potential B/T cell epitopes for SARS CoV-2, RaTG13-CoV, SARS-CoV and MERS-CoV; CoVIDep ( https://covidep.ust.hk/ [ 37 ]), consists of genetic data for SARS-CoV-2 and immunological data for the 2003 SARS virus, to identify B-cell and T-cell epitopes; CoV3D ( https://cov3d.ibbr.umd.edu/cov3d ), contains structures of SARS-CoV-2, SARS-CoV, and MERS-CoV proteins, without any other structural details; CoronaVIR ( https://webs.iiitd.edu.in/raghava/coronavir/index.html [ 38 ]) contains a few genomic, proteomic, diagnostic and therapeutic knowledge about novel SARS-CoV-2 coronaviruses. Moreover, none of them is specific for the virulence proteins encompassing the spike protein, small envelope protein, membrane protein, and nucleocapsid protein and an in-depth investigation of complete sequence-structural features of these virulence factors across the betacoronavirus family including the newly identified SARS-CoV-2 strains is lacking.…”