Conserved interactions required for in vitro inhibition of the main protease of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)

Abstract

The COVID-19 pandemic caused by the SARS-CoV-2 requires a fast development of antiviral drugs. SARS-CoV-2 viral main protease (Mpro, also called 3C-like protease, 3CLpro) is a potential target for drug design. Crystal and co-crystal structures of the SARS-CoV-2 Mpro have been solved, enabling the rational design of inhibitory compounds. In this study we analyzed the available SARS-CoV-2 and the highly similar SARS-CoV-1 crystal structures. We identified within the active site of the Mpro, in addition to the inhibitory ligands’ interaction with the catalytic C145, two key H-bond interactions with the conserved H163 and E166 residues. Both H-bond interactions are present in almost all co-crystals and are likely to occur also during the viral polypeptide cleavage process as suggested from docking of the Mpro cleavage recognition sequence. We screened in silico a library of 6,900 FDA-approved drugs (ChEMBL) and filtered using these key interactions and selected 29 non-covalent compounds predicted to bind to the protease. Additional screen, using DOCKovalent was carried out on DrugBank library (11,414 experimental and approved drugs) and resulted in 6 covalent compounds. The selected compounds from both screens were tested in vitro by a protease activity inhibition assay. Two compounds showed activity at the 50μM concentration range. Our analysis and findings can facilitate and focus the development of highly potent inhibitors against SARS-CoV-2 infection.

Engineering of 2D nanomaterials to trap and kill SARS-CoV-2: a new insight from multi-microsecond atomistic simulations

“…To characterize more inhibitory potentials of proposed 2D nanomaterials against SARS-CoV-2, we set additional coarse-grained long time-scale simulations to elucidate their impact on SARS-CoV-2 M pro . Up to date, researchers have investigated various inhibitors against the M pro , such as peptide-inhibitors [57,95,96], previously FDAapproved drugs [97,98], and herbal components [99]. Our observations from the previous section confirmed that 2D engineered nanomaterials are competent in blocking spike protein.…”

Engineering of 2D Materials To Trap And Kill SARS-CoV-2: A New Insight From Multi-Microsecond Atomistic Simulations

“…To characterize more inhibitory potentials of proposed 2D materials against SARS-CoV-2, we set additional coarse-grained long time-scale simulations to elucidate their impact on SARS-CoV-2 M pro . Up to date, researchers have investigated various inhibitors against the M pro , such as peptide-inhibitors [98-100], previously FDA-approved drugs [101,102], and herbal components [103]. Our observations from the previous section con rmed that 2D engineered nanosheets are competent in blocking spike protein.…”

Ugonin J Acts as a SARS-CoV-2 3C-like Protease Inhibitor and Exhibits Anti-inflammatory Properties

“…Specifically, the IC 50 value of UJ against SARS-CoV-2 3CLpro was about 0.94 µM. In molecular modeling, UJ interacted with several core and consensus anchor residues in the active site of SARS-CoV-2 3CLpro (Shitrit et al, 2020;Pathak et al, 2021) (i.e., H163, M165 and E166, G143 and C145, Q189, and P168 in subsites S1, S1′, S2, and S4, respectively) via hydrogen bonding and/or van der Waals interactions, thereby blocking the peptide substrate from accessing the active site. In contrast, the core and consensus residues that Lu, Kae, and Ikae interacted with were M165 and E166, H41, M49 and Q189, and P168 in subsites S1, S2, and S4, respectively, via primarily van der Waals forces.…”

“…In contrast, the core and consensus residues that Lu, Kae, and Ikae interacted with were M165 and E166, H41, M49 and Q189, and P168 in subsites S1, S2, and S4, respectively, via primarily van der Waals forces. In particular, forming hydrogen bonding with H163 and E166 has been regarded as an important feature for potent inhibition of the viral polypeptide cleavage process of SARS-CoV-2 3CLpro (Shitrit et al, 2020).…”