Non-covalent SARS-CoV-2 Mpro inhibitors developed from in silico screen hits

Abstract

Mpro, the main protease of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is essential for the viral life cycle. Accordingly, several groups have performed in silico screens to identify Mpro inhibitors that might be used to treat SARS-CoV-2 infections. We selected more than five hundred compounds from the top-ranking hits of two very large in silico screens for on-demand synthesis. We then examined whether these compounds could bind to Mpro and inhibit its protease activity. Two interesting chemotypes were identified, which were further evaluated by characterizing an additional five hundred synthesis on-demand analogues. The compounds of the first chemotype denatured Mpro and were considered not useful for further development. The compounds of the second chemotype bound to and enhanced the melting temperature of Mpro. The most active compound from this chemotype inhibited Mpro in vitro with an IC50 value of 1 μM and suppressed replication of the SARS-CoV-2 virus in tissue culture cells. Its mode of binding to Mpro was determined by X-ray crystallography, revealing that it is a non-covalent inhibitor. We propose that the inhibitors described here could form the basis for medicinal chemistry efforts that could lead to the development of clinically relevant inhibitors.

Structure basis for inhibition of SARS-CoV-2 by the feline drug GC376

“…In addition to GC376, non-covalent SARS-COV-2 M pro inhibitors have also been developed [ 11 ]. To verify the effectiveness of GC376, we tested the inhibitory activity of GC376 for SARS-CoV-2 M pro , with the 50% inhibition concentration (IC 50 ) of 1.5 μM (Fig.…”

When Virtual Screening Yields Inactive Drugs: Dealing with False Theoretical Friends

“…The binding to M pro was determined by using the protocol for protein expression, purification, and activity assay described elsewhere [23] . In that approach, the interaction of the selected molecules was assessed by using differential scanning fluorimetry.…”

“…This is a critical step, though still not enough for deciding the final candidates to be tested on a wet lab. A more recent study by Halazonetis and co‐workers further refines these abovementioned ultra‐large screens by imposing general requisites such as drug‐likeness and chemical diversity [23] . These additional criteria lead to 207 compounds from Gorgulla collection [14] .…”

Oral antiviral treatments for COVID-19: opportunities and challenges

“…Furthermore, PL pro of SARS-CoV has de-ubiquitinating and interferon antagonism effects and subsequently prevents activation of interferon-regulatory factor 3 and inhibits the nuclear factor-j-light-chain-enhancer of activated B cells pathway [ 104 ]. Therefore, the inhibition of these two proteases is expected to suppress replication and translation of the SARS-CoV-2 and was suggested as a promising antiviral drug target [ 105 , 106 ]. For instance, using a combination of lopinavir and ritonavir can decrease the virus load in COVID-19 patients [ 107 ].…”