Structure-Based Design, Synthesis, and Evaluation of Peptide-Mimetic SARS 3CL Protease Inhibitors

Abstract

The design and evaluation of low molecular weight peptide-based severe acute respiratory syndrome (SARS) chymotrypsin-like protease (3CL) protease inhibitors are described. A substrate-based peptide aldehyde was selected as a starting compound, and optimum side-chain structures were determined, based on a comparison of inhibitory activities with Michael type inhibitors. For the efficient screening of peptide aldehydes containing a specific C-terminal residue, a new approach employing thioacetal to aldehyde conversion mediated by N-bromosuccinimide was devised. Structural optimization was carried out based on X-ray crystallographic analyses of the R188I SARS 3CL protease in a complex with each inhibitor to provide a tetrapeptide aldehyde with an IC(50) value of 98 nM. The resulting compound carried no substrate sequence, except for a P(3) site directed toward the outside of the protease. X-ray crystallography provided insights into the protein-ligand interactions.

Discovery of N-(benzo[1,2,3]triazol-1-yl)-N-(benzyl)acetamido)phenyl) carboxamides as severe acute respiratory syndrome coronavirus (SARS-CoV) 3CLpro inhibitors: Identification of ML300 and noncovalent nanomolar inhibitors with an induced-fit binding

“…Initial reports of 3CLpro inhibitors in the literature focused on peptidomimetics, often four to five residues in length, bearing a reactive “warhead” group, such as an aldehyde, halo-methyl ketone, or Michael acceptor at the terminus with several demonstrating a covalent interaction with the active site Cys-145 residue. 10–16 Until recently, the majority of efforts to develop non-peptidic 3CLpro inhibitors also relied on “warhead” based design strategies (Fig. 1, 1–5 ) 17–21 and a number of these non-peptidic inhibitors achieved sub-micromolar activity.…”

Synthesis of Bioactive Natural Products as Protein Inhibitors

“…43) A substrate-based peptide aldehyde, Ac-ThrSer-Ala-Val-Leu-Gln-H, was selected as the starting compound, and the optimum side chain structure of the potent inhibitor by both peptide aldehyde synthesis methodology with thioacetal and X-ray crystallographic analyses was found to be tetrapeptide aldehyde, Ac-ThrVal-Cha-His-H, which showed the high inhibitory activity, with an IC 50 value of 98 nM toward SARS 3CL-R188I mutant protease. 44 inhibitor, Ac-Thr-Ser-Ala-Val-Leu-Gln-H, at the P1 and P2 sites with the protease appeared to be remarkably effective, and further modification of the small nonpeptide inhibitor is now underway (Fig. 1). A C B Fig.…”

Practical synthesis of peptide C-terminal aldehyde on a solid support

“…On the other hand, acetal linker, 12,13 oxazoline linker, 14,15 threonine-type linker, 16 and semicarbazone linker 17 were developed for the attachment of aldehydes. 20 Herein, we report a practical synthetic route for the preparation of several peptide aldehydes with different amino acids and commercially available linkers on a solid support. In the course of our research regarding cysteine protease inhibitors, 18 we prepared several peptide aldehydes via a thioacetal structure on a solid support since the aldehyde group seems to be effective for the thiol functional group of cysteine protease.…”