Identification of SARS-CoV-2 virus-induced metabolic pathways reveals possible drug repurposing strategies

Scientists identified proteins and metabolic pathways induced by the SARS-CoV-2 virus and examined the functioning of the pathways in the presence of clinically approved drugs. This analysis identified 200 drugs that are predicted to target pathways induced by SARS-CoV-2 infection, of which 40 are already in clinical trials against COVID-19 disease. Using artificial neural network analysis, these 200 drugs were classified into nine different pathways within two comprehensive mechanisms of action: virus replication (126) and immune response (74). Two drugs (proguanil and sulfasalazine) have been shown to inhibit SARS-CoV-2 virus replication in cellular assays.

To determine the mechanism of development of COVID-19 disease that occurs due to SARS-CoV-2 virus infection, the scientists undertook a comprehensive analysis of protein pathways essential in the development of COVID-19 disease, using a computational approach to integrate data and build protein networks.
Within the protein-protein interaction networks, proteins that are central within the metabolic pathway are desirable as targets for drugs because they can have a greater impact on the functionality of the entire pathway. Several different algorithms have been applied to identify key proteins and pathways within COVID-19 disease. After essential proteins were identified, 1917 approved drugs were collected from publicly available databases [ChEMBL and DrugBank]. Virtual screening identified 200 drugs that target key proteins of the SARS-CoV-2 virus-induced protein network.
Researchers then attempted to identify exactly which protein within the SARS-CoV-2 virus-induced protein network targets each of the 200 drugs. It was found that out of a total of 1573 proteins targeted by these 200 drugs, most (66%) of them are targeted by one drug, while 30 proteins (0.19%) are targeted by at least eight or more drugs. These 30 proteins were then shown to be associated with the synthesis of nicotinamide adenine dinucleotide phosphate (NADP +) and nitric oxide (NO). Because NO is important for the life cycle of the virus and because NADP + affects NO production, this provides insight into the potential mechanism by which these drugs can affect viral infection.

In the next phase of research, cellular assays have shown that five drugs (ademetionine, alogliptin, flucytosine, proguanil, and sulfasalazine) have good safety profiles. To assess whether these five drugs were able to reduce SARS-CoV-2 virus infection, an initial screening was performed using the Vero E6 monkey cell line. It was observed that two of the five drugs, proguanil and sulfasalazine, showed significant antiviral effects without noticeable cytotoxicity. These two drugs were then tested using the human Calu-3 cell line (along with Vero E6 cells). Treatment of Vero E6 and Calu-3 cells with proguanil and sulfasalazine showed strong anti-SARS-CoV-2 effects. It has also been shown that the effective concentration of sulfasalazine is comparable to the maximum plasma concentrations routinely administered in patients with rheumatoid arthritis or inflammatory bowel disease.

To further investigate the effect of these two drugs on the SARS-CoV-2 virus, the activity of recently identified intracellular pathways directly related to SARS-CoV-2 infection and cytokine production was examined. Proguanil or sulfasalazine treatment significantly reduced the phosphorylation of MAPKAPK2 (p-MK2 and T334), an important component of the p38 / mitogen-activated protein kinase (MAPK) signaling pathway, activated by SARS-CoV-2 infection and stimulate the cytokine response. Aleksandra Maršavelski,
Specijalist za računalnu biokemiju

For more information see the paper published on June 30, 2021 in Science Advances


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