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. 2023 Jan 4;28(2):514.
doi: 10.3390/molecules28020514.

Discovery of a Novel Trifluoromethyl Diazirine Inhibitor of SARS-CoV-2 Mpro

Andrea Citarella  1 , Davide Moi  2 , Martina Pedrini  1 , Helena Pérez-Peña  1 , Stefano Pieraccini  1 , Claudio Stagno  3 , Nicola Micale  3 , Tanja Schirmeister  4 , Giulia Sibille  5 , Giorgio Gribaudo  5 , Alessandra Silvani  1 , Daniele Passarella  1 , Clelia Giannini  1
Affiliations

Discovery of a Novel Trifluoromethyl Diazirine Inhibitor of SARS-CoV-2 Mpro

Andrea Citarella et al. Molecules. .

Abstract

SARS-CoV-2 Mpro is a chymotrypsin-like cysteine protease playing a relevant role during the replication and infectivity of SARS-CoV-2, the coronavirus responsible for COVID-19. The binding site of Mpro is characterized by the presence of a catalytic Cys145 which carries out the hydrolytic activity of the enzyme. As a consequence, several Mpro inhibitors have been proposed to date in order to fight the COVID-19 pandemic. In our work, we designed, synthesized and biologically evaluated MPD112, a novel inhibitor of SARS-CoV-2 Mpro bearing a trifluoromethyl diazirine moiety. MPD112 displayed in vitro inhibition activity against SARS-CoV-2 Mpro at a low micromolar level (IC50 = 4.1 μM) in a FRET-based assay. Moreover, an inhibition assay against PLpro revealed lack of inhibition, assuring the selectivity of the compound for the Mpro. Furthermore, the target compound MPD112 was docked within the binding site of the enzyme to predict the established intermolecular interactions in silico. MPD112 was subsequently tested on the HCT-8 cell line to evaluate its effect on human cells' viability, displaying good tolerability, demonstrating the promising biological compatibility and activity of a trifluoromethyl diazirine moiety in the design and development of SARS-CoV-2 Mpro binders.

Keywords: COVID-19; SARS-CoV-2; SARS-CoV-2 Mpro; coronavirus; cysteine proteases; diazirines; enzymatic inhibitors.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
Examples of different chemical classes of SARS-CoV-2 Mpro inhibitors. A covalent mechanism of action was observed for Mpro inhibitors bearing electrophilic fragments, such as aldehydes (1), α-ketoamides (2), fluoromethyl ketones (3), and epoxyketones (4). A non-covalent inhibition of Mpro was reported for 5, 6 and 7.
Scheme 1
Scheme 1
Examples of chemical reactivity mechanism of a diazirine moiety via photoactivation.
Figure 2
Figure 2
Design of the SARS-CoV-2 Mpro inhibitor MPD112.
Scheme 2
Scheme 2
Synthesis of MPD112.
Figure 3
Figure 3
Best binding mode of MPD112 obtained by Autodock Vina when bound to the active site of the Mpro of SARS-CoV-2 (PDB: 7NG3) shown in sticks mode (panel A), the protein–ligand interaction profile of the complex (panel B) and its representation in surface mode (panel C).
See this image and copyright information in PMC

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