A New Lead for Nonpeptidic Active-Site-Directed Inhibitors of the Severe Acute Respiratory Syndrome Coronavirus Main Protease Discovered by a Combination of Screening and Docking Methods

• Published in: Journal of medicinal chemistry 2005-11, Vol.48 (22), p.6832-6842
• Main Authors: Kaeppler, Ulrich, Stiefl, Nikolaus, Schiller, Markus, Vicik, Radim, Breuning, Alexander, Schmitz, Werner, Rupprecht, Daniel, Schmuck, Carsten, Baumann, Knut, Ziebuhr, John, Schirmeister, Tanja
• Format: Article
• Language: English
• Subjects: Amides - chemical synthesis; Amides - chemistry; Amides - pharmacology; Antibiotics. Antiinfectious agents. Antiparasitic agents; Antiviral agents; Binding Sites; Biological and medical sciences; Chromatography, High Pressure Liquid; Cysteine Endopeptidases; Endopeptidases - chemistry; Ethacrynic Acid - analogs & derivatives; Ethacrynic Acid - chemical synthesis; Ethacrynic Acid - chemistry; Medical sciences; Models, Molecular; Pharmacology. Drug treatments; Protease Inhibitors - chemical synthesis; Protease Inhibitors - chemistry; SARS coronavirus; SARS Virus - enzymology; Structure-Activity Relationship; Viral Proteins - antagonists & inhibitors; Viral Proteins - chemistry
• ISSN: 0022-2623; 1520-4804
• DOI: 10.1021/jm0501782

The coronavirus main protease, Mpro, is considered to be a major target for drugs suitable for combating coronavirus infections including severe acute respiratory syndrome (SARS). An HPLC-based screening of electrophilic compounds that was performed to identify potential Mpro inhibitors revealed etacrynic acid tert-butylamide (6a) as an effective nonpeptidic inhibitor. Docking studies suggested a binding mode in which the phenyl ring acts as a spacer bridging the inhibitor's activated double bond and its hydrophobic tert-butyl moiety. The latter is supposed to fit into the S4 pocket of the target protease. Furthermore, these studies revealed etacrynic acid amide (6b) as a promising lead for nonpeptidic active-site-directed Mpro inhibitors. In a fluorimetric enzyme assay using a novel fluorescence resonance energy transfer (FRET) pair labeled substrate, compound 6b showed a K i value of 35.3 μM. Since the novel lead compound does not target the S1‘, S1, and S2 subsites of the enzyme's substrate-binding pockets, there is room for improvement that underlines the lead character of compound 6b.