Design and Synthesis of Peptidomimetic Severe Acute Respiratory Syndrome Chymotrypsin-like Protease Inhibitors

Ghosh, Arun K.; Xi, Kai; Ratia, Kiira; Santarsiero, Bernard D.; Fu, Wentao; Harcourt, Brian H.; Rota, Paul A.; Baker, Susan C.; Johnson, Michael E.; Mesecar, Andrew D.

doi:10.1021/jm050548m

Cited by 122 publications

(127 citation statements)

References 20 publications

Supporting

Mentioning

124

Contrasting

Unclassified

Order By: Relevance

“…A few non-covalent, competitive inhibitors 10 and peptidic, covalent inhibitors have been visualized in SARS 3CL pro crystal structures. 7,8,[11][12][13] The covalent inhibitors studied to date carry either a halomethyl ketone, an epoxide or a 1,4 Michael acceptor function as the reactive "warheads". Such functionalities permanently inactivate the viral peptidase via the formation of a nonhydrolysable covalent linkage to Cys145 as the result of the nucleophilic attack by its S γ atom.…”

Section: Introductionmentioning

confidence: 99%

A Mechanistic View of Enzyme Inhibition and Peptide Hydrolysis in the Active Site of the SARS-CoV 3C-like Peptidase

Jiang

Niu

Cherney

et al. 2007

Journal of Molecular Biology

View full text Add to dashboard Cite

The 3C-like main peptidase 3CL pro is a viral polyprotein processing enzyme essential for the viability of the Severe Acute Respiratory Syndrome coronavirus (SARS-CoV). While it is generalized that 3CL pro and the structurally related 3C pro viral peptidases cleave their substrates via a mechanism similar to that underlying the peptide hydrolysis by chymotrypsin-like serine proteinases (CLSPs), some of the hypothesized key intermediates have not been structurally characterized. Here, we present three crystal structures of SARS 3CL pro in complex with each of two members of a new class of peptide-based phthalhydrazide inhibitors. Both inhibitors form an unusual thiiranium ring with the nucleophilic sulfur atom of Cys145, trapping the enzyme's catalytic residues in configurations similar to the intermediate states proposed to exist during the hydrolysis of native substrates. Most significantly, our crystallographic data are consistent with a scenario in which a water molecule, possibly via indirect coordination from the carbonyl oxygen of Thr26, has initiated nucleophilic attack on the enzyme-bound inhibitor. Our data suggest that this structure resembles that of the proposed tetrahedral intermediate during the deacylation step of normal peptidyl cleavage.

show abstract

Section: Introductionmentioning

confidence: 99%

A Mechanistic View of Enzyme Inhibition and Peptide Hydrolysis in the Active Site of the SARS-CoV 3C-like Peptidase

Jiang

Niu

Cherney

et al. 2007

Journal of Molecular Biology

View full text Add to dashboard Cite

show abstract

“…Although successful containment measures halted the spread of the virus, the possibility of future outbreaks of both SARS-CoV and related viruses warrants a continued search for new, effective antivirals. Replication of the SARS-CoV genome is mediated by nonstructural proteins (nsps [1][2][3][4][5][6][7][8][9][10][11][12][13][14][15][16]) that assemble to generate the multifunctional, membrane-associated replicase complex. The nsps are encoded in two ORFs (ORF1a and ORF1b) encompassing Ͼ20 kb of the 5Ј-most region of the RNA genome.…”

mentioning

confidence: 99%

Severe acute respiratory syndrome coronavirus papain-like protease: Structure of a viral deubiquitinating enzyme

Ratia

Saikatendu²,

Santarsiero

et al. 2006

Proc. Natl. Acad. Sci. U.S.A.

Self Cite

385

531

View full text Add to dashboard Cite

Replication of severe acute respiratory syndrome (SARS) coronavirus (SARS-CoV) requires proteolytic processing of the replicase polyprotein by two viral cysteine proteases, a chymotrypsin-like protease (3CLpro) and a papain-like protease (PLpro). These proteases are important targets for development of antiviral drugs that would inhibit viral replication and reduce mortality associated with outbreaks of SARS-CoV. In this work, we describe the 1.85-Å crystal structure of the catalytic core of SARS-CoV PLpro and show that the overall architecture adopts a fold closely resembling that of known deubiquitinating enzymes. Key features, however, distinguish PLpro from characterized deubiquitinating enzymes, including an intact zinc-binding motif, an unobstructed catalytically competent active site, and the presence of an intriguing, ubiquitinlike N-terminal domain. To gain insight into the active-site recognition of the C-terminal tail of ubiquitin and the related LXGG motif, we propose a model of PLpro in complex with ubiquitinaldehyde that reveals well defined sites within the catalytic cleft that help to account for strict substrate-recognition motifs.membrane-associated protease ͉ ubiquitin-like domain

show abstract

“…Data were indexed with HKL2000 and scaled and merged with SCALEPACK (Otwinowski and Minor, 1997). 20 The structure was determined via molecular replacement using the coordinates 2ALV from the PDB (Ghosh et al, 2005) 11 and refined with REFMAC from the CCP4 suite (Collaborative, 1994). R-factors were minimized by an additional 4-5% by using 10 cycles of TLS refinement on 19 segments.…”

mentioning

confidence: 99%

Structure-based design, synthesis, and biological evaluation of peptidomimetic SARS-CoV 3CLpro inhibitors

Ghosh

Grum-Tokars

et al. 2007

Bioorganic & Medicinal Chemistry Letters

Self Cite

View full text Add to dashboard Cite

Structure-based design, synthesis and biological evaluation of a series of peptidomimetic severe acute respiratory syndrome-coronavirus chymotrypsin-like protease inhibitors is described. These inhibitors were designed and synthesized based upon our X-ray crystal structure of inhibitor 1 bound to SARS-CoV 3CLpro. Incorporation of Boc-Ser as the P4-ligand resulted in enhanced SARS-CoV 3CLpro inhibitory activity. Structural analysis of inhibitor-bound X-ray structure revealed high binding affinity towards the enzyme. Keywordsdesign; synthesis; SARS 3CLpro; inhibitor; X-ray structure Severe acute respiratory syndrome (SARS), a contagious and fatal respiratory illness was first reported in Guangdong province, China in November 2002. 1 It's rapid and unexpected spread to other Asian countries, North America and Europe alarmed both the public and the World Health Organization. SARS is caused by a novel coronavirus, SARS-CoV. 2,3 Its emergence affected more than 8000 individuals and caused more than 800 deaths within a few months. 4 This signifies just how rapidly contagious illness can spread in a more mobile and highly interconnected world in the 21 st century. Remarkably, the world has witnessed how concerted international cooperation allowed health experts to identify the novel etiologic agent and contain the SARS epidemic just months after its emergence. Currently, there is no known SARS transmission anywhere in the world. At the same time, there is no guarantee that this outbreak will not strike again in an even more severe form. Thus far, no effective therapy exists for this viral infection.The SARS-CoV is a positive-strand RNA virus whose genome sequence reveals only moderate relation to other known coronaviruses. 5 During viral replication, viral replicase polyproteins undergo extensive processing by two viral proteases, namely chymotrypsin-like protease Correspondence to: Arun K. Ghosh. 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. (3CLpro) and papain-like protease (PLpro) to generate a functional viral replication complex. 6,7 Therefore, both SARS-CoV 3CLpro and SARS-CoV PLpro are recognized as logical targets for therapeutic intervention against SARS-CoV and related interactions. 8 NIH Public AccessThe structure and activity of the SARS-CoV 3CLpro have been investigated. 9 The enzyme active site contains a catalytic dyad where a cysteine residue acts as a nucleophile and a histidine residue acts as the general acid base. SARS-CoV 3CLpro is functionally analogous to the main picornaviral protease 3Cpro and there have been significant drug-design efforts agai...

show abstract

Design and Synthesis of Peptidomimetic Severe Acute Respiratory Syndrome Chymotrypsin-like Protease Inhibitors

Cited by 122 publications

References 20 publications

A Mechanistic View of Enzyme Inhibition and Peptide Hydrolysis in the Active Site of the SARS-CoV 3C-like Peptidase

A Mechanistic View of Enzyme Inhibition and Peptide Hydrolysis in the Active Site of the SARS-CoV 3C-like Peptidase

Severe acute respiratory syndrome coronavirus papain-like protease: Structure of a viral deubiquitinating enzyme

Structure-based design, synthesis, and biological evaluation of peptidomimetic SARS-CoV 3CLpro inhibitors

Contact Info

Product

Resources

About