Discovery of Zafirlukast as a novel SARS-CoV-2 helicase inhibitor using in silico modelling and a FRET-based assay

• Published in: SAR and QSAR in environmental research 2021-12, Vol.32 (12), p.963-983
• Main Authors: Mehyar, N., Mashhour, A., Islam, I., Alhadrami, H.A., Tolah, A.M., Alghanem, B., Alkhaldi, S., Somaie, B.A., Al Ghobain, M., Alobaida, Y., Alaskar, A.S., Boudjelal, M.
• Format: Article
• Language: English
• Subjects: Animals; Antiviral Agents - pharmacology; Chlorocebus aethiops; COVID-19; COVID-19 - drug therapy; DNA Helicases - antagonists & inhibitors; Fluorescence Resonance Energy Transfer; helicase; Indoles - pharmacology; marketed drugs; Phenylcarbamates - pharmacology; Quantitative Structure-Activity Relationship; repurposing; Sars-Cov-2; SARS-CoV-2 - drug effects; SARS-CoV-2 - enzymology; Sulfonamides - pharmacology; Vero Cells; Virus Replication - drug effects; zafirlukast
• ISSN: 1062-936X; 1029-046X
• DOI: 10.1080/1062936X.2021.1993995

The coronavirus helicase is an essential enzyme required for viral replication/transcription pathways. Structural studies revealed a sulphate moiety that interacts with key residues within the nucleotide-binding site of the helicase. Compounds with a sulphoxide or a sulphone moiety could interfere with these interactions and consequently inhibit the enzyme. The molecular operating environment (MOE) was used to dock 189 sulphoxide and sulphone-containing FDA-approved compounds to the nucleotide-binding site. Zafirlukast, a leukotriene receptor antagonist used to treat chronic asthma, achieved the lowest docking score at −8.75 kcals/mol. The inhibitory effect of the compounds on the SARS-CoV-2 helicase dsDNA unwinding activity was tested by a FRET-based assay. Zafirlukast was the only compound to inhibit the enzyme (IC50 = 16.3 µM). The treatment of Vero E6 cells with 25 µM zafirlukast prior to SARS-CoV-2 infection decreased the cytopathic effects of SARS-CoV-2 significantly. These results suggest that zafirlukast alleviates SARS-CoV-2 pathogenicity by inhibiting the viral helicase and impairing the viral replication/transcription pathway. Zafirlukast could be clinically developed as a new antiviral treatment for SARS-CoV-2 and other coronavirus diseases. This discovery is based on molecular modelling, in vitro inhibition of the SARS-CoV helicase activity and cell-based SARS-CoV-2 viral replication.