Discovery of C-12 dithiocarbamate andrographolide analogues as inhibitors of SARS-CoV-2 main protease: In vitro and in silico studies

Bodee Nutho; Patcharin Wilasluck; Peerapon Deetanya; Kittikhun Wangkanont; Patcharee Arsakhant; Rungnapha Saeeng; Thanyada Rungrotmongkol

doi:10.1016/j.csbj.2022.05.053

Discovery of C-12 dithiocarbamate andrographolide analogues as inhibitors of SARS-CoV-2 main protease: In vitro and in silico studies

Comput Struct Biotechnol J. 2022 May 30:20:2784-2797. doi: 10.1016/j.csbj.2022.05.053. eCollection 2022.

Authors

Bodee Nutho¹, Patcharin Wilasluck^{2

3}, Peerapon Deetanya^{2

3}, Kittikhun Wangkanont^{2

3}, Patcharee Arsakhant^{4

5}, Rungnapha Saeeng^{4

5}, Thanyada Rungrotmongkol^{6

7}

Affiliations

¹ Department of Pharmacology, Faculty of Science, Mahidol University, Bangkok 10400, Thailand.
² Center of Excellence for Molecular Biology and Genomics of Shrimp, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand.
³ Molecular Crop Research Unit, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand.
⁴ Department of Chemistry and Center for Innovation in Chemistry, Faculty of Science, Burapha University, Chonburi 20131, Thailand.
⁵ The Research Unit in Synthetic Compounds and Synthetic Analogues from Natural Product for Drug Discovery (RSND), Burapha University, Chonburi 20131, Thailand.
⁶ Center of Excellence in Biocatalyst and Sustainable Biotechnology, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand.
⁷ Program in Bioinformatics and Computational Biology, Graduate School, Chulalongkorn University, Bangkok 10330, Thailand.

Abstract

A global crisis of coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has impacted millions of people's lives throughout the world. In parallel to vaccine development, identifying potential antiviral agents against SARS-CoV-2 has become an urgent need to combat COVID-19. One of the most attractive drug targets for discovering anti-SARS-CoV-2 agents is the main protease (M^pro), which plays a pivotal role in the viral life cycle. This study aimed to elucidate a series of twenty-one 12-dithiocarbamate-14-deoxyandrographolide analogues as SARS-CoV-2 M^pro inhibitors using in vitro and in silico studies. These compounds were initially screened for the inhibitory activity toward SARS-CoV-2 M^pro by in vitro enzyme-based assay. We found that compounds 3 k, 3 l, 3 m and 3 t showed promising inhibitory activity against SARS-CoV-2 M^pro with >50% inhibition at 10 μM. Afterward, the binding mode of each compound in the active site of SARS-CoV-2 M^pro was explored by molecular docking. The optimum docked complexes were then chosen and subjected to molecular dynamic (MD) simulations. The MD results suggested that all studied complexes were stable along the simulation time, and most of the compounds could fit well with the SARS-CoV-2 M^pro active site, particularly at S1, S2 and S4 subsites. The per-residue decomposition free energy calculations indicated that the hot-spot residues essential for ligand binding were T25, H41, C44, S46, M49, C145, H163, M165, E166, L167, D187, R188, Q189 and T190. Therefore, the obtained information from the combined experimental and computational techniques could lead to further optimization of more specific and potent andrographolide analogues toward SARS-CoV-2 M^pro.

Keywords: Andrographolide analogues; COVID-19; Drug discovery; Enzyme-based assay; MD simulations; Molecular docking; SARS-CoV-2 main protease.