Computational Selectivity Assessment of Protease Inhibitors against SARS-CoV-2

Abstract

The pandemic of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) poses a serious global health threat. Since no specific therapeutics are available, researchers around the world screened compounds to inhibit various molecular targets of SARS-CoV-2 including its main protease (Mpro) essential for viral replication. Due to the high urgency of these discovery efforts, off-target binding, which is one of the major reasons for drug-induced toxicity and safety-related drug attrition, was neglected. Here, we used molecular docking, toxicity profiling, and multiple molecular dynamics (MD) protocols to assess the selectivity of 33 reported non-covalent inhibitors of SARS-CoV-2 Mpro against eight proteases and 16 anti-targets. The panel of proteases included SARS-CoV Mpro, cathepsin G, caspase-3, ubiquitin carboxy-terminal hydrolase L1 (UCHL1), thrombin, factor Xa, chymase, and prostasin. Several of the assessed compounds presented considerable off-target binding towards the panel of proteases, as well as the selected anti-targets. Our results further suggest a high risk of off-target binding to chymase and cathepsin G. Thus, in future discovery projects, experimental selectivity assessment should be directed toward these proteases. A systematic selectivity assessment of SARS-CoV-2 Mpro inhibitors, as we report it, was not previously conducted.

Apixaban, an orally available anticoagulant, inhibits SARS-CoV-2 replication by targeting its major protease in a non-competitive way

“…The FXa and thrombin show considerable similarity to M pro binding site, as judged by the 3D superimposition of their structures with a good correlation (Fig. 1A) and in line with previous literature 22,23 . Thus, we interrogated if the M pro (and as a control papain-like protease, PL pro ) was susceptible to direct inhibitors of FXa (apixaban and rivaroxaban) and thrombin (dabigatran).…”

“…The main protease (M pro ) of SARS-CoV-2 is considered as one of the main targets for drug repurposing, due to its cleavage activity at eleven sites at the viral polyprotein 22 . Curiously, FXa and thrombin share a considerable similarity to SARS-CoV-2 M pro binding site (according to the respective dimensionless scores of 0.71 and 0.74, in a maximum of 1.00).…”

“…Curiously, FXa and thrombin share a considerable similarity to SARS-CoV-2 M pro binding site (according to the respective dimensionless scores of 0.71 and 0.74, in a maximum of 1.00). Compared to SARS-CoV-2 M pro , FXa and thrombin superpose their three-dimensional structures with a minor differences, with respect to Root Mean Square Deviation (RMSD) analysis of just 2.57 and 2.49 Å, respectively 22,23 . Although structural similarities between FXa and thrombin with M pro have been suggested, functional studies to indicate whether M pro could use FXa and thrombin inhibitors or substrates are scarce.…”

“…It is made available under a preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in The copyright holder for this this version posted September 24, 2021. ; https://doi.org/10.1101/2021.09.23.461605 doi: bioRxiv preprint 4 0.74, in a maximum of 1.00). Compared to SARS-CoV-2 M pro , FXa and thrombin superpose their three-dimensional structures with a minor differences, with respect to Root Mean Square Deviation (RMSD) analysis of just 2.57 and 2.49 Å, respectively 22,23 . Although structural similarities between FXa and thrombin with M pro have been suggested, functional studies to indicate whether M pro could use FXa and thrombin inhibitors or substrates are scarce.…”

Screening Anti-inflammatory, Anticoagulant, and Respiratory Agents for SARS-CoV-2 3CL^pro Inhibition from Chemical Fingerprints Through a Deep Learning Approach

“…It has been shown that elevated levels of FXa are related not only to hypercoagulability in patients with severe COVID-19, but also to inflammatory exacerbation and viral infection mechanisms, what positions FXa inhibitors as a potential prophylactic and therapeutic treatment for high-risk patients with COVID-19 45 . Furthermore, considerable active site similarity based on 3D fingerprints and the positioning of catalytic residues was observed between the FXa protease and the 3CL protease 46 , and three FXa inhibitors were screened as potential inhibitors of 3CL pro in an in silico molecular docking of ligand selection 47 .…”