The design, synthesis, X-ray crystal structure, molecular modeling, and biological evaluation of a series of new generation SARS-CoV PLpro inhibitors are described. A new lead compound 3 (6577871) was identified via high-throughput screening of a diverse chemical library. Subsequently, we carried out lead optimization and structure-activity studies to provide a series of improved inhibitors that show potent PLpro inhibition and antiviral activity against SARS-CoV infected Vero E6 cells. Interestingly, the (S)-Me inhibitor 15h (enzyme IC50 = 0.56 μM; antiviral EC50 = 9.1 μM) and the corresponding (R)-Me 15g (IC50 = 0.32 μM; antiviral EC50 = 9.1 μM) are the most potent compounds in this series, with nearly equivalent enzymatic inhibition and antiviral activity. A protein-ligand X-ray structure of 15g-bound SARS-CoV PLpro and a corresponding model of 15h docked to PLpro provide intriguing molecular insight into the ligand-binding site interactions.

We describe here the design, synthesis, molecular modeling, and biological evaluation of a series of small molecule, nonpeptide inhibitors of SARS-CoV PLpro. Our initial lead compound was identified via high-throughput screening of a diverse chemical library. We subsequently carried out structure-activity relationship studies, and optimized the lead structure to potent inhibitors that have shown antiviral activity against SARS-CoV infected Vero E6 cells. Based upon the X-ray crystal structure of one of the potent inhibitors 24-bound to SARS-CoV PLpro, a drug-design template was created. Our structure-based modification led to the design of a more potent inhibitor, 2 (enzyme IC50 = 0.46 μM; antiviral EC50 = 12.5 μM). Interestingly, its methylamine derivative 49 displayed good enzyme inhibitory potency (IC50 = 1.3 μM) and most potent SARS antiviral activity (EC50 = 2.5 μM) in the series. We have carried out computational docking studies and generated a predictive 3D-QSAR model for SARS-CoV PLpro inhibitors.

Design, synthesis and biological evaluation of a series of 5-chloropyridine ester-derived severe acute respiratory syndrome-coronavirus chymotrypsin-like protease inhibitors is described. Position of the carboxylate functionality is critical to potency. Inhibitor 10 with a 5-chloropyridinyl ester at position 4 of the indole ring is the most potent inhibitor with a SARS 3Clpro IC 50 value of 30 nM and antiviral EC 50 value of 6.9 μM. Molecular Docking studies have provided possible binding modes of these inhibitors.© 2008 Elsevier Ltd. All rights reserved. Publisher's Disclaimer: This is a PDF file of an unedited manuscript that has been accepted for publication. As a service to our customers we are providing this early version of the manuscript. The manuscript will undergo copyediting, typesetting, and review of the resulting proof before it is published in its final citable form. Please note that during the production process errors may be discovered which could affect the content, and all legal disclaimers that apply to the journal pertain. 4 While SARS is contained in the world and no more cases have been reported since April 2004, there is expectation that this epidemic will strike again in an even more severe form. Furthermore, the nature of its unpredictable outbreak is a potential threat to the global economy and public heath. To date, no effective therapy exists for this viral illness. NIH Public AccessThe SARS coronavirus is a positive-strand RNA virus. The 5′ two-thirds of the genome encodes two overlapping polyproteins, pp1a and pp1ab, which are processed to generate the viral replication complex. During viral replication, the replicase polyprotein undergoes extensive processing by two viral proteases namely, chymotrypsin-like protease (3CLpro) and papainlike protease (PLpro). 5,6 Because of their essential roles in viral replication, both proteases are recognized as attractive targets for development of anti-SARS therapeutics. 7 The structure and activity of active sites of both SARS-CoV 3CLpro and SARS-CoV PLpro have been elucidated. Thus far, inhibitor design efforts are mostly limited to SARS-CoV 3CLpro and numerous covalent and noncovalent inhibitors have been reported. 7 In our continuing interest in the design and development of SARS-CoV 3CLpro inhibitors, we recently reported structurebased design of a number of potent peptidomimetic SARS-CoV 3CLpro inhibitors (1 and 2). The SARS-CoV 3CLpro active site contains a catalytic dyad where a cysteine residue acts as a nucleophile and a histidine residue acts as the general acid base. 9 The inhibitors bind to SARS-CoV-3CLpro through covalent bonding with the active site cysteine 145 residue. These inhibitors contain peptidomimetic scaffolds and lacked adequate potency, particularly antiviral activity suitable for drug-development. Recently, Wong and co-workers reported a new class of potent small molecule benzotriazole ester-based 3CLpro inhibitors. Compound 3 is the most potent inhibitor among the benzotriazole esters. 10 The mode of acti...