Investigating novel thiazolyl-indazole derivatives as scaffolds for SARS-CoV-2 MPro inhibitors

Justin Airas; Catherine A Bayas; Abdellah N'Ait Ousidi; Moulay Youssef Ait Itto; Aziz Auhmani; Mohamed Loubidi; M'hamed Esseffar; Julie A Pollock; Carol A Parish

doi:10.1016/j.ejmcr.2022.100034

Investigating novel thiazolyl-indazole derivatives as scaffolds for SARS-CoV-2 M^Pro inhibitors

Eur J Med Chem Rep. 2022 Apr:4:100034. doi: 10.1016/j.ejmcr.2022.100034. Epub 2022 Feb 10.

Authors

Justin Airas¹, Catherine A Bayas¹, Abdellah N'Ait Ousidi², Moulay Youssef Ait Itto², Aziz Auhmani², Mohamed Loubidi², M'hamed Esseffar², Julie A Pollock¹, Carol A Parish¹

Affiliations

¹ Department of Chemistry, University of Richmond, Gottwald Center for the Sciences, Richmond, VA, 23173, USA.
² Département de Chimie, Faculté des Sciences Semlalia, Cadi Ayyad University, BP, 2390, Marrakech, Morocco.

Abstract

COVID-19 is a global pandemic caused by infection with the SARS-CoV-2 virus. Remdesivir, a SARS-CoV-2 RNA polymerase inhibitor, is the only drug to have received widespread approval for treatment of COVID-19. The SARS-CoV-2 main protease enzyme (M^Pro), essential for viral replication and transcription, remains an active target in the search for new treatments. In this study, the ability of novel thiazolyl-indazole derivatives to inhibit M^Pro is evaluated. These compounds were synthesized via the heterocyclization of phenacyl bromide with (R)-carvone, (R)-pulegone and (R)-menthone thiosemicarbazones. The binding affinity and binding interactions of each compound were evaluated through Schrödinger Glide docking, AMBER molecular dynamics simulations, and MM-GBSA free energy estimation, and these results were compared with similar calculations of M^Pro binding various 5-mer substrates (VKLQA, VKLQS, VKLQG) and a previously identified M^Pro tight-binder X77. From these simulations, we can see that binding is driven by residue specific interactions such as π-stacking with His41, and S/π interactions with Met49 and Met165. The compounds were also experimentally evaluated in a M^Pro biochemical assay and the most potent compound containing a phenylthiazole moiety inhibited protease activity with an IC₅₀ of 92.9 μM. This suggests that the phenylthiazole scaffold is a promising candidate for the development of future M^Pro inhibitors.

Keywords: Binding assay; COVID-19; Coronavirus; Drug discovery; Indazole; Inhibitors; MPro; Molecular dynamics; Protease; SARS-CoV-2; Scaffold; Substrate; Thiazolyl; Thiazolyl-indazole.