Inhibition of the 3CL Protease and SARS-CoV-2 Replication by Dalcetrapib

Abstract

The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) 3CL protease is a promising target for inhibition of viral replication by interaction with a cysteine residue (Cys145) at its catalytic site. Dalcetrapib exerts its lipid-modulating effect by binding covalently to cysteine 13 of a cholesteryl ester transfer protein. Because 12 free cysteine residues are present in the 3CL protease, we investigated the potential of dalcetrapib to inhibit 3CL protease activity and SARS-CoV-2 replication. Molecular docking investigations suggested that dalcetrapib-thiol binds to the catalytic site of the 3CL protease with a delta G value of −8.5 kcal/mol. Dalcetrapib inhibited both 3CL protease activity in vitro and viral replication in Vero E6 cells with IC 50 values of 14.4 ± 3.3 μM and an EC 50 of 17.5 ± 3.5 μM (mean ± SD). Near-complete inhibition of protease activity persisted despite 1000-fold dilution after ultrafiltration with a nominal dalcetrapib-thiol concentration of approximately 100 times below the IC 50 of 14.4 μM, suggesting stable protease–drug interaction. The inhibitory effect of dalcetrapib on the SARS-CoV-2 3CL protease and viral replication warrants its clinical evaluation for the treatment of COVID-19.

Computational investigation of benzalacetophenone derivatives against SARS-CoV-2 as potential multi-target bioactive compounds

“…In addition, Cys145 – His41 are the two catalytic dyad residues of 3CL pro to play an important role in the cleavage of SARS-CoV-2 polyproteins [ 58 ]. In addition, other research groups also reported the potential role of targeting Cys145 to design novel antivirals against 3CL pro [ 59 , 60 ]. Interestingly, we observed conserved binding site interactions ( Thr25, Met49, and Met165 ) in both these compounds during the 150 ns MD simulation.…”

In Vitro Selection of Remdesivir-Resistant SARS-CoV-2 Demonstrates High Barrier to Resistance

“…A control virus was passaged concomitantly in the absence of drug during all the selection procedure. At specified RDV concentrations, EC 50 values were determined by a plaque reduction assay ( 10 ), and the Nsp12 genotype was determined by PCR amplification followed by Sanger sequencing. In addition, complete sequences of viral genomes at selected passages were determined using a published SARS-CoV-2 protocol ( 11 ) and MinION flowcells on a GridION X5 sequencer (Oxford Nanopore Technologies).…”

Molecular interactions and inhibition of the SARS‐CoV‐2 main protease by a thiadiazolidinone derivative

“…In subsequent simulations, we observed that these hydrogen bonds were not stable and that CCG‐50014 instead formed new hydrogen bonds and stacking interactions with the residues H41, M49, E166, and Q189. While a limited work has gone into investigating covalent inhibitors that may form disulfide bonds with the catalytic cysteine residue, 64 other studies have focused on several potential covalent inhibitors 65 , 66 , 67 , 68 , 69 , 70 , 71 which may modify the catalytic cysteine residue of M Pro via a C‐S bond. The covalent inhibitors investigated in these studies formed interactions with the residues N142, G143, H164, E166, P168, and Q189, the residues that we also observed to interact with CCG‐50014 in our work.…”