101
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Leung-Toung R, Wodzinska J, Li W, Lowrie J, Kukreja R, Desilets D, Karimian K, Tam TF. 1,2,4-thiadiazole: a novel Cathepsin B inhibitor. Bioorg Med Chem 2004; 11:5529-37. [PMID: 14642597 DOI: 10.1016/j.bmc.2003.09.040] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
A novel class of Cathepsin B inhibitors has been developed with a 1,2,4-thiadiazole heterocycle as the thiol trapping pharmacophore. Several compounds with different dipeptide recognition sequence (i.e., P1'-P2'=Leu-Pro-OH or P2-P1=Cbz-Phe-Ala) at the C5 position and with different substituents (i.e., OMe, Ph, or COOH) at the C3 position of the 1,2,4-thiadiazole ring have been synthesized and tested for their inhibitory activities. The substituted thiadiazoles 3a-h inhibit Cat B in a time dependent, irreversible manner. A mechanism based on active-site directed inactivation of the enzyme by disulfide bond formation between the active site cysteine thiol and the sulfur atom of the heterocycle is proposed. Compound 3a (K(i)=2.6 microM, k(i)K(i)=5630 M(-1)s(-1)) with a C3 methoxy moiety and a Leu-Pro-OH dipeptide recognition sequence, is found to be the most potent inhibitor in this series. The enhanced inhibitory potency of 3a is a consequence of its increased enzyme binding affinity (lower K(i)) rather than its increased intrinsic reactivity (higher k(i)). In addition, 3a is inactive against Cathepsin S, is a poor inhibitor of Cathepsin H and is >100-fold more selective for Cat B over papain.
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Affiliation(s)
- Regis Leung-Toung
- Department of Medicinal Chemistry, Apotex Research, Inc, 400 Ormont Drive, Toronto, Ontario, Canada M9L 1N9
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102
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Huang C, Wei P, Fan K, Liu Y, Lai L. 3C-like proteinase from SARS coronavirus catalyzes substrate hydrolysis by a general base mechanism. Biochemistry 2004; 43:4568-74. [PMID: 15078103 DOI: 10.1021/bi036022q] [Citation(s) in RCA: 157] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
SARS 3C-like proteinase has been proposed to be a key enzyme for drug design against SARS. Lack of a suitable assay has been a major hindrance for enzyme kinetic studies and a large-scale inhibitor screen for SARS 3CL proteinase. Since SARS 3CL proteinase belongs to the cysteine protease family (family C3 in clan CB) with a chymotrypsin fold, it is important to understand the catalytic mechanism of SARS 3CL proteinase to determine whether the proteolysis proceeds through a general base catalysis mechanism like chymotrypsin or an ion pair mechanism like papain. We have established a continuous colorimetric assay for SARS 3CL proteinase and applied it to study the enzyme catalytic mechanism. The proposed catalytic residues His41 and Cys145 were confirmed to be critical for catalysis by mutating to Ala, while the Cys145 to Ser mutation resulted in an active enzyme with a 40-fold lower activity. From the pH dependency of catalytic activity, the pK(a)'s for His41 and Cys145 in the wild-type enzyme were estimated to be 6.38 and 8.34, while the pK(a)'s for His41 and Ser145 in the C145S mutant were estimated to be 6.15 and 9.09, respectively. The C145S mutant has a normal isotope effect in D(2)O for general base catalysis, that is, reacts slower in D(2)O, while the wild-type enzyme shows an inverse isotope effect which may come from the lower activation enthalpy. The pK(a) values measured for the active site residues and the activity of the C145S mutant are consistent with a general base catalysis mechanism and cannot be explained by a thiolate-imidazolium ion pair model.
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Affiliation(s)
- Changkang Huang
- State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
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103
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Jain RP, Vederas JC. Structural variations in keto-glutamines for improved inhibition against hepatitis A virus 3C proteinase. Bioorg Med Chem Lett 2004; 14:3655-8. [PMID: 15203137 DOI: 10.1016/j.bmcl.2004.05.021] [Citation(s) in RCA: 107] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2004] [Revised: 05/11/2004] [Accepted: 05/12/2004] [Indexed: 11/23/2022]
Abstract
A series of keto-glutamine tetrapeptide analogs containing a 2-oxo-pyrrolidine ring as a glutamine side chain mimic were synthesized with both R and S configuration at the beta-carbon. Compounds bearing a phthalhydrazide moiety show improved reversible inhibition of HAV 3C proteinase in the low micromolar range.
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Affiliation(s)
- Rajendra P Jain
- Department of Chemistry, University of Alberta, Edmonton, AB, Canada T6G 2G2
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104
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Marcaccini S, Pepino R, Pozo M, Basurto S, Garcı́a-Valverde M, Torroba T. One-pot synthesis of quinolin-2-(1 H )-ones via tandem Ugi–Knoevenagel condensations. Tetrahedron Lett 2004. [DOI: 10.1016/j.tetlet.2004.03.184] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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105
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Ettinger A, Ostroff R, Rhihanek M, Dragovich PS, Zalman LS, Patick AK, Prins TJ, Fuhrman SA, Brown EL, Worland ST, Polisky B. An optical thin film assay incorporating rhinovirus protease inhibitors as detector reagents. Antiviral Res 2004; 61:153-9. [PMID: 15168795 DOI: 10.1016/j.antiviral.2003.09.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2003] [Accepted: 09/09/2003] [Indexed: 11/30/2022]
Abstract
Human rhinoviruses (HRV) are the main cause of the common cold. Viral replication utilizes the activity of the HRV3C protease (3CP) enzyme [Antimicrob. Agents Chemother. 43 (1999) 2444; Antimicrob. Agents Chemother. 44 (2000) 1236]. Therefore, 3CP is an attractive target for antiviral drug development, and a new class of orally bioavailable irreversible 3CP inhibitors has been designed [J. Med. Chem. 45 (2002) 1607]. We have used related inhibitors to develop a rapid test for rhinovirus. The optical immuno assay (OIA) thin film detection technology utilizes an optically coated silicon surface to convert specific molecular binding events into visual color changes by altering the reflective properties of light through molecular thin films. The purpose of this study was to develop a rapid assay for the determination of 3CP combining the Thermo Electron Bio Star OIA technology and the newly designed inhibitor compounds. The advantage of this assay was in its approach, in which therapeutic and diagnostic targets are the same thus allowing patients with detected rhinoviruses to receive optimal treatment. Three different biotinylated inhibitor compounds were synthesized. The length of the spacer between the inhibitor and biotin core was 5, 10, and 15 atoms. These compounds were incorporated into the OIA format for the HRV assay development. A rapid (20 min) OIA test was developed using a 15 atom spacer biotinylated inhibitor (4). Forty different HRV serotypes were studied and thirty three serotypes of these 40 were detected (80%).
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Affiliation(s)
- Anna Ettinger
- Thermo Electron Corp., 331 South 104th Street, Louisville, CO 80027, USA.
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106
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Deaton DN, Kumar S. Cathepsin K Inhibitors: Their Potential as Anti-Osteoporosis Agents. PROGRESS IN MEDICINAL CHEMISTRY 2004; 42:245-375. [PMID: 15003723 DOI: 10.1016/s0079-6468(04)42006-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Affiliation(s)
- David N Deaton
- Medicinal Chemistry Department, GlaxoSmithKline Inc., 5 Moore Drive, Research Triangle Park, NC 27709, USA
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107
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Fan K, Wei P, Feng Q, Chen S, Huang C, Ma L, Lai B, Pei J, Liu Y, Chen J, Lai L. Biosynthesis, purification, and substrate specificity of severe acute respiratory syndrome coronavirus 3C-like proteinase. J Biol Chem 2003; 279:1637-42. [PMID: 14561748 PMCID: PMC7980035 DOI: 10.1074/jbc.m310875200] [Citation(s) in RCA: 249] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The 3C-like proteinase of severe acute respiratory syndrome (SARS) coronavirus has been proposed to be a key target for structural-based drug design against SARS. In order to understand the active form and the substrate specificity of the enzyme, we have cloned, expressed, and purified SARS 3C-like proteinase. Analytic gel filtration shows a mixture of monomer and dimer at a protein concentration of 4 mg/ml and mostly monomer at 0.2 mg/ml, which correspond to the concentration used in the enzyme assays. The linear decrease of the enzymatic-specific activity with the decrease of enzyme concentration revealed that only the dimeric form is active and the dimeric interface could be targeted for structural-based drug design against SARS 3C-like proteinase. By using a high pressure liquid chromatography assay, SARS 3C-like proteinase was shown to cut the 11 peptides covering all of the 11 cleavage sites on the viral polyprotein with different efficiency. The two peptides corresponding to the two self-cleavage sites are the two with highest cleavage efficiency, whereas peptides with non-canonical residues at P2 or P1' positions react slower. The P2 position of the substrates seems to favor large hydrophobic residues. Secondary structure studies for the peptide substrates revealed that substrates with more beta-sheetlike structure tend to react fast. This study provides a basic understanding of the enzyme catalysis and a full substrate specificity spectrum for SARS 3C-like proteinase, which are helpful for structural-based inhibitor design against SARS and other coronavirus.
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Affiliation(s)
- Keqiang Fan
- State Key Laboratory of Structural Chemistry of Stable and Unstable Species, College of Chemistry, Peking University, Beijing 100871, China
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108
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Dragovich PS, Prins TJ, Zhou R, Johnson TO, Hua Y, Luu HT, Sakata SK, Brown EL, Maldonado FC, Tuntland T, Lee CA, Fuhrman SA, Zalman LS, Patick AK, Matthews DA, Wu EY, Guo M, Borer BC, Nayyar NK, Moran T, Chen L, Rejto PA, Rose PW, Guzman MC, Dovalsantos EZ, Lee S, McGee K, Mohajeri M, Liese A, Tao J, Kosa MB, Liu B, Batugo MR, Gleeson JPR, Wu ZP, Liu J, Meador JW, Ferre RA. Structure-based design, synthesis, and biological evaluation of irreversible human rhinovirus 3C protease inhibitors. 8. Pharmacological optimization of orally bioavailable 2-pyridone-containing peptidomimetics. J Med Chem 2003; 46:4572-85. [PMID: 14521419 DOI: 10.1021/jm030166l] [Citation(s) in RCA: 83] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The optimization of the pharmacokinetic performance of various 2-pyridone-containing human rhinovirus (HRV) 3C protease (3CP) inhibitors following oral administration to either beagle dogs or CM-monkeys is described. The molecules described in this work are composed of a 2-pyridone-containing peptidomimetic binding determinant and an alpha,beta-unsaturated ester Michael acceptor moiety which forms an irreversible covalent adduct with the active site cysteine residue of the 3C enzyme. Modification of the ester contained within these compounds is detailed along with alteration of the P(2) substituent present in the peptidomimetic portion of the inhibitors. The pharmacokinetics of several inhibitors in both dogs and monkeys are described (7 h plasma concentrations after oral administration) along with their human plasma stabilities, stabilities in incubations with human, dog, and monkey microsomes and hepatocytes, Caco-2 permeabilities, and aqueous solubilities. Compounds containing an alpha,beta-unsaturated ethyl ester fragment and either an ethyl or propargyl P(2) moiety displayed the most promising combination of 3C enzyme inhibition (k(obs)/[I] 170 000-223 000 M(-1) s(-1)), antiviral activity (EC(50) = 0.047-0.058 microM, mean vs seven HRV serotypes), and pharmacokinetics following oral administration (7 h dog plasma levels = 0.248-0.682 microM; 7 h CM-monkey plasma levels = 0.057-0.896 microM).
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Affiliation(s)
- Peter S Dragovich
- Pfizer Global Research and Development-La Jolla, 10777 Science Center Drive, San Diego, CA 92121-1111, USA.
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109
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Moreno-Vargas AJ, Jiménez-Barbero J, Robina I. Hetaryleneaminopolyols and hetarylenecarbopeptoids: a new type of glyco- and peptidomimetics. Syntheses and studies on solution conformation and dynamics. J Org Chem 2003; 68:4138-50. [PMID: 12762712 DOI: 10.1021/jo026631o] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Ready access to a new class of oligomers has been demonstrated by the synthesis of hetaryleneaminopolyols and hetarylenecarbopeptoids using 3-hydroxymethyl-5-(4-amino-4-deoxy-d-arabinotetritol-1-yl)-2-methylfuran and 5-(4-amino-4-deoxy-d-arabinotetritol-1-yl)-2-methyl-3-furoic acid as novel scaffolds. The conformational behavior of peptidomimetics 22, 23, 25, 26, and 36 have been analyzed by NMR spectroscopy and extensive molecular dynamics simulations. MD simulations using the GB/SA continuum solvent model for water and the MM3 force field provide a population distribution of conformers which satisfactorily agrees with the experimental NMR data for the torsional degrees of freedom of the molecule.
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Affiliation(s)
- Antonio J Moreno-Vargas
- Departamento de Química Orgánica, Facultad de Química, Universidad de Sevilla, Apartado 553, Spain
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110
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Walker MA. Monitor: molecules and profiles. Drug Discov Today 2002. [DOI: 10.1016/s1359-6446(02)02534-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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111
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Powers JC, Asgian JL, Ekici OD, James KE. Irreversible inhibitors of serine, cysteine, and threonine proteases. Chem Rev 2002; 102:4639-750. [PMID: 12475205 DOI: 10.1021/cr010182v] [Citation(s) in RCA: 818] [Impact Index Per Article: 37.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- James C Powers
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, USA.
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