Abstract
Coronavirus disease 2019 (COVID-19) is caused by a novel virus named Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2). This virus induced a large number of deaths and millions of confirmed cases worldwide, creating a serious danger to public health. However, there are no specific therapies or drugs available for COVID-19 treatment. While new drug discovery is a long process, repurposing available drugs for COVID-19 can help recognize treatments with known clinical profiles. Computational drug repurposing methods can reduce the cost, time, and risk of drug toxicity. In this work, we build a graph as a COVID-19 related biological network. This network is related to virus targets or their associated biological processes. We select essential proteins in the constructed biological network that lead to a major disruption in the network. Our method from these essential proteins chooses 93 proteins related to COVID-19 pathology. Then, we propose multiple informative features based on drug–target and protein−protein interaction information. Through these informative features, we find five appropriate clusters of drugs that contain some candidates as potential COVID-19 treatments. To evaluate our results, we provide statistical and clinical evidence for our candidate drugs. From our proposed candidate drugs, 80% of them were studied in other studies and clinical trials.
Highlights
The pandemic situation for Coronavirus disease 2019 (COVID-19) causes more than 197 million infections and more than 4.2 million deaths in more than 200 countries worldwide and this number is increasing rapidly
We focused on finding the most effective essential proteins related to COVID-19
It is noticeable that not every essential protein is an appropriate candidate as an essential protein for COVID-19 pathology
Summary
The pandemic situation for Coronavirus disease 2019 (COVID-19) causes more than 197 million infections and more than 4.2 million deaths in more than 200 countries worldwide (until the end of July 2021) and this number is increasing rapidly. To design antiviral drugs, a complete understanding of the interaction between human proteins and viral is crucial [5] It is worth mentioning, in drug repurposing to fight the virus, targeting just virus proteins is not the proper approach. Host-directed treatments propose significant strategies [6] These methods select human proteins as the main carriers for the virus to enter and control human cells. In host-directed treatments, it is important to find proteins that are essential for the maintenance and persistence of the disease that is caused by a virus in the human cells. When these proteins are targeted as drug targets, the replication mechanism of the virus collapses. Gordon et al [14] proposed a map from human proteins with
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