Identifying SARS-CoV-2 Antiviral Compounds by Screening for Small Molecule Inhibitors of Nsp13 Helicase

Abstract

The coronavirus disease 2019 (COVID-19) pandemic, which is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a global public health challenge. While the efficacy of vaccines against emerging and future virus variants remains unclear, there is a need for therapeutics. Repurposing existing drugs represents a promising and potentially rapid opportunity to find novel antivirals against SARS-CoV-2. The virus encodes at least nine enzymatic activities that are potential drug targets. Here we have expressed, purified and developed enzymatic assays for SARS-CoV-2 nsp13 helicase, a viral replication protein that is essential for the coronavirus life cycle. We screened a custom chemical library of over 5000 previously characterised pharmaceuticals for nsp13 inhibitors using a FRET-based high-throughput screening (HTS) approach. From this, we have identified FPA-124 and several suramin-related compounds as novel inhibitors of nsp13 helicase activity in vitro. We describe the efficacy of these drugs using assays we developed to monitor SARS-CoV-2 growth in Vero E6 cells.

Suramin action in African trypanosomes involves a RuvB-like DNA helicase

“…However, the fact that the mutation of RuvBL1 significantly lowered the susceptibility to suramin, strongly suggests that the DNA helicase is a major target of suramin in T. brucei. Further, this hypothesis is in agreement with the published findings that (i) suramin inhibits DNA helicases from Dengue virus (Basavannacharya, 2014), hepatitis C virus (Mukherjee, 2012), and SARS-CoV2 virus (Zeng, 2021); and (ii) exposure of bloodstream-form T.…”

“…However, the fact that the mutation of RuvBL1 significantly lowered the susceptibility to suramin, strongly suggests that the DNA helicase is a major target of suramin in T. brucei . Further, this hypothesis is in agreement with the published findings that (i) suramin inhibits DNA helicases from Dengue virus (Basavannacharya, 2014), hepatitis C virus (Mukherjee, 2012), and SARS-CoV2 virus (Zeng, 2021); and (ii) exposure of bloodstream-form T. brucei to suramin caused a cytokinesis phenotype (Thomas, 2018) similar to the one observed upon RNAi-mediated down-regulation of RuvBL1. Functional assays to corroborate a direct interaction between T. brucei RuvBL1 helicase and suramin will be challenging, requiring the presence of RuvBL2 and possibly further proteins of the complex, or even a DNA substrate.…”