Optimization of Triarylpyridinone Inhibitors of the Main Protease of SARS-CoV-2 to Low-Nanomolar Antiviral Potency

Abstract

Non-covalent inhibitors of the main protease (M pro ) of SARS-CoV-2 having a pyridinone core were previously reported with IC 50 values as low as 0.018 μM for inhibition of enzymatic activity and EC 50 values as low as 0.8 μM for inhibition of viral replication in Vero E6 cells. The series has now been further advanced by consideration of placement of substituted five-membered-ring heterocycles in the S4 pocket of M pro and N-methylation of a uracil ring. Free energy perturbation calculations provided guidance on the choice of the heterocycles, and protein crystallography confirmed the desired S4 placement. Here we report inhibitors with EC 50 values as low as 0.080 μM, while remdesivir yields values of 0.5–2 μM in side-by-side testing with infectious SARS-CoV-2. A key factor in the improvement is enhanced cell permeability, as reflected in PAMPA measurements. Compounds 19 and 21 are particularly promising as potential therapies for COVID-19, featuring IC 50 values of 0.044–0.061 μM, EC 50 values of ca. 0.1 μM, good aqueous solubility, and no cytotoxicity.

A Review of the Current Landscape of SARS-CoV-2 Main Protease Inhibitors: Have We Hit the Bullseye Yet?

“…This prediction was confirmed by Jorgensen and coworkers, although perampanel showed only an approximate IC 50 of 100–250 μM [ 43 ]. The same authors also optimized this compound and synthesized several derivative compounds [ 44 , 45 , 46 ]. Some of these perampanel derivatives have IC 50 values in the low nanomolar range and are some of the most potent non-covalent SARS-CoV-2 M-pro inhibitors found to date.…”

“…This compound also inhibited in vitro human TMPRSS2 and furin enzymes, which are required for viral entry [ 101 ]. Compounds with the CAS number 2603242-35-7, 2603242-41-5, 2679814-93-6, 2679814-92-5, 2679814-91-4, 2679814-96-9, 2603242-04-0 are perampanel derivatives that can inhibit the SARS-CoV-2 M-pro in vitro, with IC 50 values between 0.128 and 0.018 μM [ 44 , 46 ]. The most potent compounds in this set, 2603242-35-7 and 2603242-41-5, showed antiviral activity in a viral plaque assay but lacked antiviral activity in a 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay [ 44 ] ( Table 3 ).…”

Pyrido[1,2-e]purine: Design and Synthesis of Appropriate Inhibitory Candidates against the Main Protease of COVID-19

“… 5 − 7 Therefore, two separate diverse potent inhibitors of 3CL pro , including both peptidomimetic inhibitors and nonpeptidic inhibitors, have been reported to overcome the rapid spread of the COVID-19 pandemic. 8 − 12 …”

Computationally driven discovery of SARS-CoV-2 Mproinhibitors: from design to experimental validation

“…Many studies have been devoted to the design of new M pro inhibitors 3,5,[15][16][17][18][19][20][21][22][23][24][25] through joint computational and experimental approaches. In particular, a recent study by the Jorgensen group highlighted the usefulness of relative binding free energy (RBFE) computations as part of the drug design process.…”