Multi-target direct-acting SARS-CoV-2 antivirals against the nucleotide-binding pockets of virus-specific proteins

Ruchi Rani; Siwen Long; Akshay Pareek; Preeti Dhaka; Ankur Singh; Pravindra Kumar; Gerald McInerney; Shailly Tomar

doi:10.1016/j.virol.2022.08.008

Multi-target direct-acting SARS-CoV-2 antivirals against the nucleotide-binding pockets of virus-specific proteins

Virology. 2022 Dec:577:1-15. doi: 10.1016/j.virol.2022.08.008. Epub 2022 Oct 7.

Authors

Ruchi Rani¹, Siwen Long², Akshay Pareek¹, Preeti Dhaka¹, Ankur Singh¹, Pravindra Kumar¹, Gerald McInerney², Shailly Tomar³

Affiliations

¹ Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, India.
² Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, SE-17177 Stockholm, Sweden.
³ Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, India. Electronic address: shailly.tomar@bt.iitr.ac.in.

Abstract

The nucleotide-binding pockets (NBPs) in virus-specific proteins have proven to be the most successful antiviral targets for several viral diseases. Functionally important NBPs are found in various structural and non-structural proteins of SARS-CoV-2. In this study, the first successful multi-targeting attempt to identify effective antivirals has been made against NBPs in nsp12, nsp13, nsp14, nsp15, nsp16, and nucleocapsid (N) proteins of SARS-CoV-2. A structure-based drug repurposing in silico screening approach with ADME analysis identified small molecules targeting NBPs in SARS-CoV-2 proteins. Further, isothermal titration calorimetry (ITC) experiments validated the binding of top hit molecules to the purified N-protein. Importantly, cell-based antiviral assays revealed antiviral potency for INCB28060, darglitazone, and columbianadin with EC₅₀ values 15.71 μM, 5.36 μM, and 22.52 μM, respectively. These effective antivirals targeting multiple proteins are envisioned to direct the development of antiviral therapy against SARS-CoV-2 and its emerging variants.

Keywords: Antivirals; Drug repurposing; In silico; Nucleotide-binding pocket; SARS-CoV-2.