COVIDrugNet: a network-based web tool to investigate the drugs currently in clinical trial to contrast COVID-19

Abstract

The COVID-19 pandemic poses a huge problem of public health that requires the implementation of all available means to contrast it, and drugs are one of them. In this context, we observed an unmet need of depicting the continuously evolving scenario of the ongoing drug clinical trials through an easy-to-use, freely accessible online tool. Starting from this consideration, we developed COVIDrugNet (http://compmedchem.unibo.it/covidrugnet), a web application that allows users to capture a holistic view and keep up to date on how the clinical drug research is responding to the SARS-CoV-2 infection. Here, we describe the web app and show through some examples how one can explore the whole landscape of medicines in clinical trial for the treatment of COVID-19 and try to probe the consistency of the current approaches with the available biological and pharmacological evidence. We conclude that careful analyses of the COVID-19 drug-target system based on COVIDrugNet can help to understand the biological implications of the proposed drug options, and eventually improve the search for more effective therapies.

Current Therapeutics for COVID-19, What We Know about the Molecular Mechanism and Efficacy of Treatments for This Novel Virus

“…Currently, this database contains 3109 drugs. Lastly, the COVIDrugNet provides a database of ongoing drug research, intending to aid researchers in finding relevant drug trial studies [ 71 ]. Furthermore, this database provides information on drug structure and molecular target(s).…”

“…Furthermore, this database provides information on drug structure and molecular target(s). In addition to these large databases, online drug literature and data platforms, such as LitCovid hub and DrugBank, are currently in existence, also allowing for easier data gathering [ 71 , 72 ]. As the COVID-19 pandemic continues, large databases such as these are a valuable asset, facilitating information sharing and global collaboration, with the goal of using existing knowledge to create newer therapeutic and preventive strategies against the SARS-CoV-2 virus.…”

The R Language: An Engine for Bioinformatics and Data Science

“…To enable researchers lacking these requisites to easily perform their own analysis on omics data, many free web applications have been developed in the last few years, which frequently rely on a newly born R system for generating dynamic web sites: the Shiny R framework, implemented in the homonymous shiny package [ 102 ]. Since R is one of the most popular languages in the world, specifically amongst data scientists, bioinformaticians, and teachers [ 103 ], the development of biology-oriented web sites written through Shiny R has flourished, and contributed the highest number of web tools amongst all programming languages; for example, during the COVID-19 pandemics [ 30 ], providing tools for mutation tracking [ 104 ] and drug–target prediction [ 105 ].…”

Studies on Human-Coronavirus protein-protein interaction network from the perspective of viral adaptation in a novel host

“…This pandemic situation further initiated the discovery of efficient treatments like convalescent plasma therapy (17, 33), the use of monoclonal antibodies (56, 58, 92), the development of vaccines (45, 62, 83) and the repurposing of drugs (20, 41, 51, 82, 91, 98). A huge number of repurposed drugs (293 drugs as of 10 th June 2022) (60) and more than 30 vaccines (https://www.who.int/emergencies/diseases/novel-coronavirus-2019/covid-19-vaccines) were approved globally. However, the challenges had been very tough due to the accumulation of mutations leading to the generation of different SARS-CoV2 variants including the emergence of alpha and beta variants in December 2020 to the omicron in November 2021 (53, 78).…”