Hit Expansion of a Noncovalent SARS-CoV-2 Main Protease Inhibitor

Abstract

Inhibition of the SARS-CoV-2 main protease (M pro ) is a major focus of drug discovery efforts against COVID-19. Here we report a hit expansion of non-covalent inhibitors of M pro . Starting from a recently discovered scaffold (The COVID Moonshot Consortium. Open Science Discovery of Oral Non-Covalent SARS-CoV-2 Main Protease Inhibitor Therapeutics. bioRxiv 2020.10.29.339317) represented by an isoquinoline series, we searched a database of over a billion compounds using a cheminformatics molecular fingerprinting approach. We identified and tested 48 compounds in enzyme inhibition assays, of which 21 exhibited inhibitory activity above 50% at 20 μM. Among these, four compounds with IC 50 values around 1 μM were found. Interestingly, despite the large search space, the isoquinolone motif was conserved in each of these four strongest binders. Roomtemperature X-ray structures of co-crystallized protein−inhibitor complexes were determined up to 1.9 Å resolution for two of these compounds as well as one of the stronger inhibitors in the original isoquinoline series, revealing essential interactions with the binding site and water molecules. Molecular dynamics simulations and quantum chemical calculations further elucidate the binding interactions as well as electrostatic effects on ligand binding. The results help explain the strength of this new non-covalent scaffold for M pro inhibition and inform lead optimization efforts for this series, while demonstrating the effectiveness of a high-throughput computational approach to expanding a pharmacophore library.

The SARS‐CoV‐2 main protease (Mpro): Structure, function, and emerging therapies for COVID‐19

“…Six compounds presented inhibitory effects against 3CL pro both in vitro and in HEK293T cells, and Z1759961356 hindered viral replication in Vero E6 cells with an EC 50 value of 8.52 μM. Four isoquinolone‐based compounds from a database were reported as SARS‐CoV‐2 3CL pro inhibitors with IC 50 values of approximately 1 μM 137 …”

“…Four isoquinolone-based compounds from a database were reported as SARS-CoV-2 3CL pro inhibitors with IC 50 values of approximately 1 μM. 137 In fact, some inhibitors have a potential impact on several 3CL pro s due to the high conservation of this protease among CoVs. 138 For example, ML188 inhibited the 3CL pro of SARS-CoV, SARS-CoV-2, and porcine epidemic diarrhea virus, making it a promising broad-spectrum antiviral agent.…”

On drug discovery against infectious diseases and academic medicinal chemistry contributions

“…And this was only achieved following many iterations of structure-based design, synthesis and assays of analogues [78,81,82]. Also of concern, a subsequent virtual hit expansion/ligandbased screening starting with the isoquinoline-bearing inhibitors such as 6 and using the Ukrainian REAL database which contains 1.37 billion of compounds, actually failed to go beyond this chemical motif [83]. In any case, what would have been the results of all these computer-based endeavors had the hits 4 and 5, which led to compounds 6 and 7, not been reported [79,80] in 2013?…”

Different Aspects of Emetine’s Capabilities as a Highly Potent SARS-CoV-2 Inhibitor against COVID-19

“… 3 , 4 In structural evaluations to find anti-COVID-19 agents, quinoline and isoquinoline scaffolds are among the most important platforms that have been repeatedly observed in the structure of potent SARS-CoV-2 inhibitors. 5 , 6 Emetine, which itself has two isoquinoline-like moieties, is the main pharmacologically active alkaloid in ipecac root that was previously used in traditional medicine and clinics as an expectorant, emetic, and anti-amoebic agent, and it has been approved by competent authorities such as the U.S. Food and Drug Administration (FDA) for clinical usages. In addition to the mentioned drug effects, studies reported some other important biological activities for this compound, such as inhibition of protein synthesis 7 , 8 and anti-cancer effects.…”

“…Today, naturally occurring compounds are receiving increasing attention for the treatment of diseases (such as COVID-19) because they offer a diversity of biological activities and low toxicity. , In structural evaluations to find anti-COVID-19 agents, quinoline and isoquinoline scaffolds are among the most important platforms that have been repeatedly observed in the structure of potent SARS-CoV-2 inhibitors. , Emetine, which itself has two isoquinoline-like moieties, is the main pharmacologically active alkaloid in ipecac root that was previously used in traditional medicine and clinics as an expectorant, emetic, and anti-amoebic agent, and it has been approved by competent authorities such as the U.S. Food and Drug Administration (FDA) for clinical usages. In addition to the mentioned drug effects, studies reported some other important biological activities for this compound, such as inhibition of protein synthesis , and anti-cancer effects. − This compound also has excellent broad-spectrum antiviral effects against a wide range of RNA and DNA viruses at a non-cytotoxic concentration, without causing drug resistance .…”