1
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Jangra J, Bajad NG, Singh R, Kumar A, Singh SK. Identification of novel potential cathepsin-B inhibitors through pharmacophore-based virtual screening, molecular docking, and dynamics simulation studies for the treatment of Alzheimer's disease. Mol Divers 2024:10.1007/s11030-024-10821-z. [PMID: 38517648 DOI: 10.1007/s11030-024-10821-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 02/03/2024] [Indexed: 03/24/2024]
Abstract
Cathepsin B is a cysteine protease lysosomal enzyme involved in several physiological functions. Overexpression of the enzyme enhances its proteolytic activity and causes the breakdown of amyloid precursor protein (APP) into neurotoxic amyloid β (Aβ), a characteristic hallmark of Alzheimer's disease (AD). Therefore, inhibition of the enzyme is a crucial therapeutic aspect for treating the disease. Combined structure and ligand-based drug design strategies were employed in the current study to identify the novel potential cathepsin B inhibitors. Five different pharmacophore models were developed and used for the screening of the ZINC-15 database. The obtained hits were analyzed for the presence of duplicates, interfering PAINS moieties, and structural similarities based on Tanimoto's coefficient. The molecular docking study was performed to screen hits with better target binding affinity. The top seven hits were selected and were further evaluated based on their predicted ADME properties. The resulting best hits, ZINC827855702, ZINC123282431, and ZINC95386847, were finally subjected to molecular dynamics simulation studies to determine the stability of the protein-ligand complex during the run. ZINC123282431 was obtained as the virtual lead compound for cathepsin B inhibition and may be a promising novel anti-Alzheimer agent.
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Affiliation(s)
- Jatin Jangra
- Pharmaceutical Chemistry Research Laboratory-I, Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi, 221005, India
| | - Nilesh Gajanan Bajad
- Pharmaceutical Chemistry Research Laboratory-I, Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi, 221005, India
| | - Ravi Singh
- Pharmaceutical Chemistry Research Laboratory-I, Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi, 221005, India
| | - Ashok Kumar
- Pharmaceutical Chemistry Research Laboratory-I, Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi, 221005, India
| | - Sushil Kumar Singh
- Pharmaceutical Chemistry Research Laboratory-I, Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi, 221005, India.
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2
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Nicolau I, Hădade ND, Matache M, Funeriu DP. Synthetic Approaches of Epoxysuccinate Chemical Probes. Chembiochem 2023; 24:e202300157. [PMID: 37096389 DOI: 10.1002/cbic.202300157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Revised: 04/21/2023] [Accepted: 04/23/2023] [Indexed: 04/26/2023]
Abstract
Synthetic chemical probes are powerful tools for investigating biological processes. They are particularly useful for proteomic studies such as activity-based protein profiling (ABPP). These chemical methods initially used mimics of natural substrates. As the techniques gained prominence, more and more elaborate chemical probes with increased specificity towards given enzyme/protein families and amenability to various reaction conditions were used. Among the chemical probes, peptidyl-epoxysuccinates represent one of the first types of compounds used to investigate the activity of the cysteine protease papain-like family of enzymes. Structurally derived from the natural substrate, a wide body of inhibitors and activity- or affinity-based probes bearing the electrophilic oxirane unit for covalent labeling of active enzymes now exists. Herein, we review the literature regarding the synthetic approaches to epoxysuccinate-based chemical probes together with their reported applications, from biological chemistry and inhibition studies to supramolecular chemistry and the formation of protein arrays.
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Affiliation(s)
- Ioana Nicolau
- University of Bucharest, Faculty of Chemistry, Department of Organic Chemistry, Biochemistry and Catalysis, Research Centre of Applied Organic Chemistry, 90 Panduri Street, 050663, Bucharest, Romania
| | - Niculina D Hădade
- Babes-Bolyai University, Faculty of Chemistry and Chemical Engineering, Supramolecular and Organometallic Chemistry Centre, 11 Arany Janos Street, 400028, Cluj-Napoca, Romania
| | - Mihaela Matache
- University of Bucharest, Faculty of Chemistry, Department of Organic Chemistry, Biochemistry and Catalysis, Research Centre of Applied Organic Chemistry, 90 Panduri Street, 050663, Bucharest, Romania
| | - Daniel P Funeriu
- University of Bucharest, Faculty of Chemistry, Department of Organic Chemistry, Biochemistry and Catalysis, Research Centre of Applied Organic Chemistry, 90 Panduri Street, 050663, Bucharest, Romania
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3
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Barthels F, Barthels U, Schwickert M, Schirmeister T. FINDUS: An Open-Source 3D Printable Liquid-Handling Workstation for Laboratory Automation in Life Sciences. SLAS Technol 2019; 25:190-199. [PMID: 31540570 DOI: 10.1177/2472630319877374] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
3D-printed laboratory devices can enable ambitious research purposes even at a low-budget level. To follow this trend, here we describe the construction, calibration, and usage of the FINDUS (Fully Integrable Noncommercial Dispensing Utility System). We report the successful 3D printing and assembly of a liquid-handling workstation for less than $400. Using this setup, we achieve reliable and flexible liquid-dispensing automation with relative pipetting errors of less than 0.3%. We show our system is well suited for several showcase applications from both the biology and chemistry fields. In support of the open-source spirit, we make all 3D models, assembly instructions, and source code available for free download, rebuild, and modification.
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Affiliation(s)
- Fabian Barthels
- Institute of Pharmacy and Biochemistry, Johannes Gutenberg University Mainz, Mainz, Germany
| | - Ulrich Barthels
- Institute of Pharmacy and Biochemistry, Johannes Gutenberg University Mainz, Mainz, Germany
| | - Marvin Schwickert
- Institute of Pharmacy and Biochemistry, Johannes Gutenberg University Mainz, Mainz, Germany
| | - Tanja Schirmeister
- Institute of Pharmacy and Biochemistry, Johannes Gutenberg University Mainz, Mainz, Germany
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4
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Singha M, Roy S, Moirangthem R, Das AK, Basak A. Naphthalimide-Based Template for Inhibitor Screening via Cross-Linking and In-Gel Fluorescence: A Case Study against HCA II. ACS OMEGA 2019; 4:11914-11920. [PMID: 31460302 PMCID: PMC6681978 DOI: 10.1021/acsomega.9b01044] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 06/26/2019] [Indexed: 06/10/2023]
Abstract
We describe a rapid electrophoresis-based method for profiling of carbonic anhydrase inhibitors. In addition to the pharmacophore moiety intended for reversible interaction with a target enzyme, a fluorescent template with a built-in azide group for photoaffinity labeling is also included as a part of the inhibitor design. Following incubation and irradiation, gel electrophoresis with visualization under UV allows assessment of the efficiency of cross-linking. The relative efficiency of cross-linking of various probes can be regarded as a reflection of their inhibition potencies, an assumption supported by the trend in their IC50/K i values. The method has the advantage of being applicable to impure enzyme preparations and also can be used to screen several inhibitors including their promiscuity in parallel in a short time as has been currently demonstrated with HCA II.
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Affiliation(s)
- Monisha Singha
- Department
of Chemistry, School of Bioscience, and Department of Biotechnology Indian Institute of Technology Kharagpur, Kharagpur 721302, India
| | - Sayantani Roy
- Department
of Chemistry, School of Bioscience, and Department of Biotechnology Indian Institute of Technology Kharagpur, Kharagpur 721302, India
| | - Ravina Moirangthem
- Department
of Chemistry, School of Bioscience, and Department of Biotechnology Indian Institute of Technology Kharagpur, Kharagpur 721302, India
| | - Amit K. Das
- Department
of Chemistry, School of Bioscience, and Department of Biotechnology Indian Institute of Technology Kharagpur, Kharagpur 721302, India
| | - Amit Basak
- Department
of Chemistry, School of Bioscience, and Department of Biotechnology Indian Institute of Technology Kharagpur, Kharagpur 721302, India
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5
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Cathepsin B: Active site mapping with peptidic substrates and inhibitors. Bioorg Med Chem 2018; 27:1-15. [PMID: 30473362 DOI: 10.1016/j.bmc.2018.10.017] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 10/16/2018] [Accepted: 10/18/2018] [Indexed: 12/11/2022]
Abstract
The potential of papain-like cysteine proteases, such as cathepsin B, as drug discovery targets for systemic human diseases has prevailed over the past years. The development of potent and selective low-molecular cathepsin B inhibitors relies on the detailed expertise on preferred amino acid and inhibitor residues interacting with the corresponding specificity pockets of cathepsin B. Such knowledge might be obtained by mapping the active site of the protease with combinatorial libraries of peptidic substrates and peptidomimetic inhibitors. This review, for the first time, summarizes a wide spectrum of active site mapping approaches. It considers relevant X-ray crystallographic data and discloses propensities towards favorable protein-ligand interactions in case of the therapeutically relevant protease cathepsin B.
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6
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Shi MW, Stewart SG, Sobolev AN, Dittrich B, Schirmeister T, Luger P, Hesse M, Chen Y, Spackman PR, Spackman MA, Grabowsky S. Approaching an experimental electron density model of the biologically active
trans
‐epoxysuccinyl amide group—Substituent effects vs. crystal packing. J PHYS ORG CHEM 2017. [DOI: 10.1002/poc.3683] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Ming W. Shi
- School of Chemistry and Biochemistry The University of Western Australia Perth WA Australia
| | - Scott G. Stewart
- School of Chemistry and Biochemistry The University of Western Australia Perth WA Australia
| | - Alexandre N. Sobolev
- School of Chemistry and Biochemistry The University of Western Australia Perth WA Australia
| | - Birger Dittrich
- Anorganische Chemie und Strukturchemie Heinrich‐Heine‐Universität Düsseldorf Düsseldorf Germany
| | - Tanja Schirmeister
- Institut für Pharmazie und Biochemie Johannes‐Gutenberg‐Universität Mainz Mainz Germany
| | - Peter Luger
- Institut für Chemie und Biochemie, Anorganische Chemie Freie Universität Berlin Berlin Germany
| | - Malte Hesse
- Fachbereich 2—Biologie/Chemie, Institut für Anorganische Chemie und Kristallographie Universität Bremen Bremen Germany
| | - Yu‐Sheng Chen
- ChemMatCARS The University of Chicago Argonne IL USA
| | - Peter R. Spackman
- School of Chemistry and Biochemistry The University of Western Australia Perth WA Australia
| | - Mark A. Spackman
- School of Chemistry and Biochemistry The University of Western Australia Perth WA Australia
| | - Simon Grabowsky
- School of Chemistry and Biochemistry The University of Western Australia Perth WA Australia
- Fachbereich 2—Biologie/Chemie, Institut für Anorganische Chemie und Kristallographie Universität Bremen Bremen Germany
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7
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Schmitz J, Li T, Bartz U, Gütschow M. Cathepsin B Inhibitors: Combining Dipeptide Nitriles with an Occluding Loop Recognition Element by Click Chemistry. ACS Med Chem Lett 2016; 7:211-6. [PMID: 26985300 DOI: 10.1021/acsmedchemlett.5b00474] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Accepted: 12/27/2015] [Indexed: 12/21/2022] Open
Abstract
An active site mapping of human cathepsin B with dipeptide nitrile inhibitors was performed for a combinatorial approach by introducing several points of diversity and stepwise optimizing the inhibitor structure. To address the occluding loop of cathepsin B by a carboxylate moiety, click chemistry to generate linker-connected molecules was applied. Inhibitor 17 exhibited K i values of 41.3 nM, 27.3 nM, or 19.2 nM, depending on the substrate and pH of the assay. Kinetic data were discussed with respect to the conformational selection and induced fit models.
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Affiliation(s)
- Janina Schmitz
- Pharmaceutical Institute, Pharmaceutical
Chemistry I, University of Bonn, An der Immenburg 4, D-53121 Bonn, Germany
- Department of Natural Sciences, University of Applied Sciences Bonn-Rhein-Sieg, von-Liebig-Strasse 20, D-53359 Rheinbach, Germany
| | - Tianwei Li
- Pharmaceutical Institute, Pharmaceutical
Chemistry I, University of Bonn, An der Immenburg 4, D-53121 Bonn, Germany
| | - Ulrike Bartz
- Department of Natural Sciences, University of Applied Sciences Bonn-Rhein-Sieg, von-Liebig-Strasse 20, D-53359 Rheinbach, Germany
| | - Michael Gütschow
- Pharmaceutical Institute, Pharmaceutical
Chemistry I, University of Bonn, An der Immenburg 4, D-53121 Bonn, Germany
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8
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Radzey H, Rethmeier M, Klimpel D, Grundhuber M, Sommerhoff CP, Schaschke N. E-64c-hydrazide: a lead structure for the development of irreversible cathepsin C inhibitors. ChemMedChem 2013; 8:1314-21. [PMID: 23780739 DOI: 10.1002/cmdc.201300093] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2013] [Indexed: 12/18/2022]
Abstract
Cathepsin C is a papain-like cysteine protease with dipeptidyl aminopeptidase activity that is thought to activate various granule-associated serine proteases. Its exopeptidase activity is structurally explained by the so-called exclusion domain, which blocks the active-site cleft beyond the S2 site and, with its Asp 1 residue, provides an anchoring point for the N terminus of peptide and protein substrates. Here, the hydrazide of (2S,3S)-trans-epoxysuccinyl-L-leucylamido-3-methylbutane (E-64c) (k2/Ki =140±5 M(-1) s(-1)) is demonstrated to be a lead structure for the development of irreversible cathepsin C inhibitors. The distal amino group of the hydrazide moiety addresses the acidic Asp 1 residue at the entrance of the S2 pocket by hydrogen bonding while also occupying the flat hydrophobic S1'-S2' area with its leucine-isoamylamide moiety. Furthermore, structure-activity relationship studies revealed that functionalization of this distal amino group with alkyl residues can be used to occupy the conserved hydrophobic S2 pocket. In particular, the n-butyl derivative was identified as the most potent inhibitor of the series (k2/Ki =56 000±1700 M(-1) s(-1)).
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Affiliation(s)
- Hanna Radzey
- Fakultät für Chemie, Universität Bielefeld, Universitätsstr. 25, 33615 Bielefeld, Germany
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9
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Dana D, Davalos AR, De S, Rathod P, Gamage RK, Huestis J, Afzal N, Zavlanov Y, Paroly SS, Rotenberg SA, Subramaniam G, Mark KJ, Chang EJ, Kumar S. Development of cell-active non-peptidyl inhibitors of cysteine cathepsins. Bioorg Med Chem 2013; 21:2975-87. [PMID: 23623677 DOI: 10.1016/j.bmc.2013.03.062] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2013] [Revised: 03/15/2013] [Accepted: 03/23/2013] [Indexed: 11/26/2022]
Abstract
Cysteine cathepsins are an important class of enzymes that coordinate a variety of important cellular processes, and are implicated in various types of human diseases. However, small molecule inhibitors that are cell-permeable and non-peptidyl in nature are scarcely available. Herein the synthesis and development of sulfonyloxiranes as covalent inhibitors of cysteine cathepsins are reported. From a library of compounds, compound 5 is identified as a selective inhibitor of cysteine cathepsins. Live cell imaging and immunocytochemistry of metastatic human breast carcinoma MDA-MB-231 cells document the efficacy of compound 5 in inhibiting cysteine cathepsin activity in living cells. A cell-motility assay demonstrates that compound 5 is effective in mitigating the cell-migratory potential of highly metastatic breast carcinoma MDA-MB-231 cells.
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Affiliation(s)
- Dibyendu Dana
- Department of Chemistry and Biochemistry, Queens College and the Graduate Center of The City University of New York, Queens, NY 11367-1597, USA
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10
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Biniossek ML, Nägler DK, Becker-Pauly C, Schilling O. Proteomic identification of protease cleavage sites characterizes prime and non-prime specificity of cysteine cathepsins B, L, and S. J Proteome Res 2011; 10:5363-73. [PMID: 21967108 DOI: 10.1021/pr200621z] [Citation(s) in RCA: 135] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Cysteine cathepsins mediate proteome homeostasis and have pivotal functions in diseases such as cancer. To better understand substrate recognition by cathepsins B, L, and S, we applied proteomic identification of protease cleavage sites (PICS) for simultaneous profiling of prime and non-prime specificity. PICS profiling of cathepsin B endopeptidase specificity highlights strong selectivity for glycine in P3' due to an occluding loop blocking access to the primed subsites. In P1', cathepsin B has a partial preference for phenylalanine, which is not found for cathepsins L and S. Occurrence of P1' phenylalanine often coincides with aromatic residues in P2. For cathepsin L, PICS identifies 845 cleavage sites, representing the most comprehensive PICS profile to date. Cathepsin L specificity is dominated by the canonical preference for aromatic residues in P2 with limited contribution of prime-site selectivity determinants. Profiling of cathepsins B and L with a shorter incubation time (4 h instead of 16 h) did not reveal time-dependency of individual specificity determinants. Cathepsin S specificity was profiled at pH 6.0 and 7.5. The PICS profiles at both pH values display a high degree of similarity. Cathepsin S specificity is primarily guided by aliphatic residues in P2 with limited importance of prime-site residues.
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Affiliation(s)
- Martin L Biniossek
- Institute for Molecular Medicine and Cell Research, University of Freiburg, Germany
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11
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Cysteine cathepsins: from structure, function and regulation to new frontiers. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2011; 1824:68-88. [PMID: 22024571 PMCID: PMC7105208 DOI: 10.1016/j.bbapap.2011.10.002] [Citation(s) in RCA: 852] [Impact Index Per Article: 65.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/16/2011] [Revised: 10/03/2011] [Accepted: 10/04/2011] [Indexed: 02/06/2023]
Abstract
It is more than 50 years since the lysosome was discovered. Since then its hydrolytic machinery, including proteases and other hydrolases, has been fairly well identified and characterized. Among these are the cysteine cathepsins, members of the family of papain-like cysteine proteases. They have unique reactive-site properties and an uneven tissue-specific expression pattern. In living organisms their activity is a delicate balance of expression, targeting, zymogen activation, inhibition by protein inhibitors and degradation. The specificity of their substrate binding sites, small-molecule inhibitor repertoire and crystal structures are providing new tools for research and development. Their unique reactive-site properties have made it possible to confine the targets simply by the use of appropriate reactive groups. The epoxysuccinyls still dominate the field, but now nitriles seem to be the most appropriate “warhead”. The view of cysteine cathepsins as lysosomal proteases is changing as there is now clear evidence of their localization in other cellular compartments. Besides being involved in protein turnover, they build an important part of the endosomal antigen presentation. Together with the growing number of non-endosomal roles of cysteine cathepsins is growing also the knowledge of their involvement in diseases such as cancer and rheumatoid arthritis, among others. Finally, cysteine cathepsins are important regulators and signaling molecules of an unimaginable number of biological processes. The current challenge is to identify their endogenous substrates, in order to gain an insight into the mechanisms of substrate degradation and processing. In this review, some of the remarkable advances that have taken place in the past decade are presented. This article is part of a Special Issue entitled: Proteolysis 50 years after the discovery of lysosome.
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12
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Löser R, Gütschow M. Dipeptide-derived nitriles containing additional electrophilic sites: potentially irreversible inhibitors of cysteine proteases. J Enzyme Inhib Med Chem 2010; 24:1245-52. [PMID: 19912058 DOI: 10.3109/14756360902797328] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Heterocyclic and open-chain dipeptide-derived nitriles have been synthesized, containing an additional electrophilic center enabling the subsequent covalent modification of the thioimidate nitrogen formed in situ at the active site of the enzyme. The inhibitory potential of these nitriles against the cysteine proteases papain and cathepsins L, S, and K was determined. The open-chain dipeptide nitriles 8 and 10 acted as moderate reversible inhibitors, but no evidence for an irreversible inhibition of these enzymes was discernable.
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Affiliation(s)
- Reik Löser
- Pharmazeutisches Institut, Pharmazeutische Chemie I, Rheinische Friedrich-Wilhelms-Universität, Bonn, Germany.
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13
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Ovat A, Muindi F, Fagan C, Brouner M, Hansell E, Dvořák J, Sojka D, Kopáček P, McKerrow JH, Caffrey CR, Powers JC. Aza-Peptidyl Michael Acceptor and Epoxide Inhibitors—Potent and Selective Inhibitors of Schistosoma mansoni and Ixodes ricinus Legumains (Asparaginyl Endopeptidases). J Med Chem 2009; 52:7192-210. [DOI: 10.1021/jm900849h] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Asli Ovat
- School of Chemistry and Biochemistry, and the Petit Institute for Bioscience and Bioengineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0400
| | - Fanuel Muindi
- School of Chemistry and Biochemistry, and the Petit Institute for Bioscience and Bioengineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0400
| | - Crystal Fagan
- School of Chemistry and Biochemistry, and the Petit Institute for Bioscience and Bioengineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0400
| | - Michelle Brouner
- School of Chemistry and Biochemistry, and the Petit Institute for Bioscience and Bioengineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0400
| | - Elizabeth Hansell
- Sandler Center for Basic Research in Parasitic Diseases, California Institute for Quantitative Biosciences, University of California, San Francisco, California 94158
| | - Jan Dvořák
- Sandler Center for Basic Research in Parasitic Diseases, California Institute for Quantitative Biosciences, University of California, San Francisco, California 94158
| | - Daniel Sojka
- Institute of Parasitology, Biology Centre of the Academy of Sciences of the Czech Republic, České Budějovice, CZ-370 05, Czech Republic
| | - Petr Kopáček
- Institute of Parasitology, Biology Centre of the Academy of Sciences of the Czech Republic, České Budějovice, CZ-370 05, Czech Republic
| | - James H. McKerrow
- Sandler Center for Basic Research in Parasitic Diseases, California Institute for Quantitative Biosciences, University of California, San Francisco, California 94158
| | - Conor R. Caffrey
- Sandler Center for Basic Research in Parasitic Diseases, California Institute for Quantitative Biosciences, University of California, San Francisco, California 94158
| | - James C. Powers
- School of Chemistry and Biochemistry, and the Petit Institute for Bioscience and Bioengineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0400
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14
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Mladenovic M, Ansorg K, Fink RF, Thiel W, Schirmeister T, Engels B. Atomistic insights into the inhibition of cysteine proteases: first QM/MM calculations clarifying the stereoselectivity of epoxide-based inhibitors. J Phys Chem B 2008; 112:11798-808. [PMID: 18712902 DOI: 10.1021/jp803895f] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Due to their important role in many diseases, cysteine proteases represent new promising drug targets. An important class of cysteine-protease inhibitors is derived from the naturally occurring compound E64, possessing an epoxysuccinyl moiety as warhead. Experimental studies show stereoselectivity concerning the inhibition potency, e.g., a trans-configured epoxide ring is essential for inhibition, and furthermore, in most cases, the ( S, S)-configured inhibitors have a higher inhibition potency than their ( R, R)-counterparts. However, the underlying effects are not fully understood. In this work, such effects are investigated by classical molecular dynamics simulations and combined quantum mechanics/molecular modeling (QM/MM) calculations for the E64c-cathepsin B complex. Our computations reveal that the hydrogen bonding network between the enzyme and the E64c (or its derivatives) determines the stereoselectivity of the subsequent ring opening reaction by governing the distance between the attacking thiolate and the attacked C2 atom of the epoxide ring. For the ( S, S)-configuration, a strong network can be realized which enables a close contact between the reacting centers, so that the irreversible step becomes very efficient. The ( R, S)-configuration ( cis-configuration) can only form networks in which the two reacting centers are so far away from each other that the irreversible step can hardly happen. The ( R, R)-configuration is in between, less optimal than the ( S, S)-configuration but much better than the ( R, S)-configuration. Exceptions where the ( R, R)-configurations shows higher potency than the ( S, S) ones are also explained.
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Affiliation(s)
- Milena Mladenovic
- Institut fur Organische Chemie, Universitat Wurzburg, Am Hubland, Wurzburg, Germany
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15
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Sadaghiani AM, Verhelst SHL, Gocheva V, Hill K, Majerova E, Stinson S, Joyce JA, Bogyo M. Design, Synthesis, and Evaluation of In Vivo Potency and Selectivity of Epoxysuccinyl-Based Inhibitors of Papain-Family Cysteine Proteases. ACTA ACUST UNITED AC 2007; 14:499-511. [PMID: 17524981 DOI: 10.1016/j.chembiol.2007.03.010] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2006] [Revised: 02/16/2007] [Accepted: 03/13/2007] [Indexed: 10/23/2022]
Abstract
The papain-family cathepsins are cysteine proteases that are emerging as promising therapeutic targets for a number of human disease conditions ranging from osteoporosis to cancer. Relatively few selective inhibitors for this family exist, and the in vivo selectivity of most existing compounds is unclear. We present here the synthesis of focused libraries of epoxysuccinyl-based inhibitors and their screening in crude tissue extracts. We identified a number of potent inhibitors that display selectivity for endogenous cathepsin targets both in vitro and in vivo. Importantly, the selectivity patterns observed in crude extracts were generally retained in vivo, as assessed by active-site labeling of tissues from treated animals. Overall, this study identifies several important compound classes and highlights the use of activity-based probes to assess pharmacodynamic properties of small-molecule inhibitors in vivo.
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16
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Geraghty P, Rogan MP, Greene CM, Boxio RMM, Poiriert T, O'Mahony M, Belaaouaj A, O'Neill SJ, Taggart CC, McElvaney NG. Neutrophil Elastase Up-Regulates Cathepsin B and Matrix Metalloprotease-2 Expression. THE JOURNAL OF IMMUNOLOGY 2007; 178:5871-8. [PMID: 17442971 DOI: 10.4049/jimmunol.178.9.5871] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Neutrophil elastase (NE) activity is increased in many diseases. Other families of proteases, including cathepsins and matrix metalloproteases (MMPs), are also present at elevated levels in similar disease conditions. We postulated that NE could induce expression of cathepsins and MMPs in human macrophages. NE exposure resulted in macrophages, producing significantly greater amounts of cathepsin B and latent and active MMP-2. Cathepsin B and MMP-2 activities were decreased in Pseudomonas-infected NE knockout mice compared with wild-type littermates. We also demonstrate that NE can activate NF-kappaB in macrophages, and inhibition of NF-kappaB resulted in a reduction of NE-induced cathepsin B and MMP-2. Also, inhibition of TLR-4 or transfection of macrophages with dominant-negative IL-1R-associated kinase-1 resulted in a reduction of NE-induced cathepsin B and MMP-2. This study describes for the first time a novel hierarchy among proteases whereby a serine protease up-regulates expression of MMPs and cathepsins. This has important implications for therapeutic intervention in protease-mediated diseases.
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Affiliation(s)
- Patrick Geraghty
- Pulmonary Research Division, Royal College of Surgeons in Ireland, Beaumont Hospital, Dublin, Ireland
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17
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Cuerrier D, Moldoveanu T, Campbell RL, Kelly J, Yoruk B, Verhelst SHL, Greenbaum D, Bogyo M, Davies PL. Development of Calpain-specific Inactivators by Screening of Positional Scanning Epoxide Libraries. J Biol Chem 2007; 282:9600-9611. [PMID: 17218315 DOI: 10.1074/jbc.m610372200] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Calpains are calcium-dependent proteases that are required for numerous intracellular processes but also play an important role in the development of pathologies such as ischemic injury and neurodegeneration. Many current small molecule calpain inhibitors also inhibit other cysteine proteases, including cathepsins, and need improved selectivity. The specificity of inhibition of several calpains and papain was profiled using synthetic positional scanning libraries of epoxide-based compounds that target the active-site cysteine. These peptidomimetic libraries probe the P4, P3, and P2 positions, display (S,S)- or (R,R)-epoxide stereochemistries, and incorporate both natural and non-natural amino acids. To facilitate library screening, an SDS-PAGE assay that measures the extent of hydrolysis of an inactive recombinant m-calpain was developed. Individual epoxide inhibitors were synthesized guided by calpain-specific preferences observed from the profiles and tested for inhibition against calpain. The most potent compounds were assayed for specificity against cathepsins B, L, and K. Several compounds demonstrated high inhibition specificity for calpains over cathepsins. The best of these inhibitors, WRH(R,R), irreversibly inactivates m- and mu-calpain rapidly (k(2)/K(i) = 131,000 and 16,500 m(-1) s(-1), respectively) but behaves exclusively as a reversible and less potent inhibitor toward the cathepsins. X-ray crystallography of the proteolytic core of rat mu-calpain inactivated by the epoxide compounds WR gamma-cyano-alpha-aminobutyric acid (S,S) and WR allylglycine (R,R) reveals that the stereochemistry of the epoxide influences positioning and orientation of the P2 residue, facilitating alternate interactions within the S2 pocket. Moreover, the WR gamma-cyano-alpha-aminobutyric acid (S,S)-complexed structure defines a novel hydrogen-bonding site within the S2 pocket of calpains.
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Affiliation(s)
- Dominic Cuerrier
- Department of Biochemistry, Queen's University, Kingston, Ontario K7L 3N6, Canada
| | - Tudor Moldoveanu
- Department of Biochemistry, Queen's University, Kingston, Ontario K7L 3N6, Canada
| | - Robert L Campbell
- Department of Biochemistry, Queen's University, Kingston, Ontario K7L 3N6, Canada
| | - Jacqueline Kelly
- Department of Biochemistry, Queen's University, Kingston, Ontario K7L 3N6, Canada
| | - Bilge Yoruk
- Department of Biochemistry, Queen's University, Kingston, Ontario K7L 3N6, Canada
| | - Steven H L Verhelst
- Department of Pathology, Stanford University School of Medicine, Stanford, Califorina 94305
| | - Doron Greenbaum
- Department of Pathology, Stanford University School of Medicine, Stanford, Califorina 94305
| | - Matthew Bogyo
- Department of Pathology, Stanford University School of Medicine, Stanford, Califorina 94305
| | - Peter L Davies
- Department of Biochemistry, Queen's University, Kingston, Ontario K7L 3N6, Canada; Protein Function Discovery Group, Queen's University, Kingston, Ontario K7L 3N6, Canada.
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18
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19
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Watanabe D, Yamamoto A, Tomoo K, Matsumoto K, Murata M, Kitamura K, Ishida T. Quantitative evaluation of each catalytic subsite of cathepsin B for inhibitory activity based on inhibitory activity-binding mode relationship of epoxysuccinyl inhibitors by X-ray crystal structure analyses of complexes. J Mol Biol 2006; 362:979-93. [PMID: 16950396 DOI: 10.1016/j.jmb.2006.07.070] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2006] [Revised: 07/17/2006] [Accepted: 07/26/2006] [Indexed: 10/24/2022]
Abstract
To quantitatively estimate the inhibitory effect of each substrate-binding subsite of cathepsin B (CB), a series of epoxysuccinyl derivatives with different functional groups bound to both carbon atoms of the epoxy ring were synthesized, and the relationship between their inhibitory activities and binding modes at CB subsites was evaluated by the X-ray crystal structure analyses of eight complexes. With the common reaction in which the epoxy ring of inhibitor was opened to form a covalent bond with the SgammaH group of the active center Cys29, the observed binding modes of the substituents of inhibitors at the binding subsites of CB enabled the quantitative assessment of the inhibitory effect of each subsite. Although the single blockage of S1' or S2' subsite exerts only the inhibitory effect of IC50 = approximately 24 microM (k2 = approximately 1250 M(-1) s(-1)) or approximately 15 microM (k2 = approximately 1800 M(-1) s(-1)), respectively, the synchronous block of both subsites leads to IC50 = approximately 23 nM (k2 = 153,000 - 185,000 M(-1) s(-1)), under the condition that (i) the inhibitor possesses a P1' hydrophobic residue such as Ile and a P2' hydrophobic residue such as Ala, Ile or Pro, and (ii) the C-terminal carboxyl group of a P2' residue is able to form paired hydrogen bonds with the imidazole NH of His110 and the imidazole N of His111 of CB. The inhibitor of a Pn' > or = 3' substituent was not potentiated by collision with the occluding loop. On the other hand, it was suggested that the inhibitory effects of Sn subsites are independent of those of Sn' subsites, and the simultaneous blockage of the funnel-like arrangement of S2 and S3 subsites leads to the inhibition of IC50 = approximately 40 nM (k2 = approximately 66,600 M(-1) s(-1)) regardless of the lack of Pn' substituents. Here we present a systematic X-ray structure-based evaluation of structure-inhibitory activity relationship of each binding subsite of CB, and the results provide the structural basis for designing a more potent CB-specific inhibitor.
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Affiliation(s)
- Daiya Watanabe
- Department of Physical Chemistry, Osaka University of Pharmaceutical Sciences, 4-20-1 Nasahara,Takatsuki, Osaka 569-1094, Japan
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20
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Verhelst SHL, Bogyo M. Solid-phase synthesis of double-headed epoxysuccinyl activity-based probes for selective targeting of papain family cysteine proteases. Chembiochem 2006; 6:824-7. [PMID: 15776409 DOI: 10.1002/cbic.200400377] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Steven H L Verhelst
- Department of Pathology, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA 94305, USA
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21
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22
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Štern I, Schaschke N, Moroder L, Turk D. Crystal structure of NS-134 in complex with bovine cathepsin B: a two-headed epoxysuccinyl inhibitor extends along the entire active-site cleft. Biochem J 2004; 381:511-7. [PMID: 15084146 PMCID: PMC1133859 DOI: 10.1042/bj20040237] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2004] [Revised: 04/05/2004] [Accepted: 04/15/2004] [Indexed: 11/17/2022]
Abstract
The crystal structure of the inhibitor NS-134 in complex with bovine cathepsin B reveals that functional groups attached to both sides of the epoxysuccinyl reactive group bind to the part of active-site cleft as predicted. The -Leu-Pro-OH side binds to the primed binding sites interacting with the His110 and His111 residues with its C-terminal carboxy group, whereas the -Leu-Gly-Meu (-Leu-Gly-Gly-OMe) part (Meu, methoxycarbonylmethyl) binds along the non-primed binding sites. Comparison with the propeptide structures of cathepsins revealed that the binding of the latter part is least similar to the procathepsin B structure; this result, together with the two-residue shift in positioning of the Leu-Gly-Gly part, suggests that the propeptide structures of the cognate enzymes may not be the best starting point for the design of reverse binding inhibitors.
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Affiliation(s)
- Igor Štern
- *Department of Biochemistry and Molecular Biology, Josef Stefan Institute, Jamova 39, SI-1000 Ljubljana, Slovenia
| | - Norbert Schaschke
- †Max-Planck-Institut für Biochemie, Am Klopferspitz 18A, D-82152 Martinsried, Germany
| | - Luis Moroder
- †Max-Planck-Institut für Biochemie, Am Klopferspitz 18A, D-82152 Martinsried, Germany
| | - Dušan Turk
- *Department of Biochemistry and Molecular Biology, Josef Stefan Institute, Jamova 39, SI-1000 Ljubljana, Slovenia
- To whom correspondence should be addressed (e-mail )
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23
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Kam CM, Götz MG, Koot G, McGuire M, Thiele D, Hudig D, Powers JC. Design and evaluation of inhibitors for dipeptidyl peptidase I (Cathepsin C). Arch Biochem Biophys 2004; 427:123-34. [PMID: 15196986 DOI: 10.1016/j.abb.2004.04.011] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2004] [Revised: 04/20/2004] [Indexed: 12/20/2022]
Abstract
Dipeptidyl peptidase I (DPPI, cathepsin C) is a lysosomal cysteine protease that can activate zymogens of several different serine proteases by one step or sequential removal of dipeptides from the N-termini of the pro-protease protein substrates. To find DPPI inhibitors more suitable for cellular applications than diazomethyl ketones, we synthesized three types of inhibitors: dipeptide acyloxymethyl ketones, fluoromethyl ketones, and vinyl sulfones (VS). The acyloxymethyl ketones inhibited DPPI slowly and are moderate inhibitors of cellular DPPI. The fluoromethyl ketones were potent, but the inhibited DPPI regained activity quickly. The dipeptide vinyl sulfones were effective inhibitors for DPPI, but they also inhibited cathepsins B, H, and L weakly. The best inhibitor, Ala-Hph-VS-Ph, had a k2/K(I) of 2,000,000M(-1)s(-1). The vinyl sulfones also inhibited intracellular DPPI, and for this application the more stable inhibitors exhibit better potency. We conclude that vinyl sulfones are promising inhibitors to study the intracellular functions of DPPI.
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Affiliation(s)
- Chih-Min Kam
- School of Chemistry and Biochemistry and the Petit Institute for Bioscience and Bioengineering, Georgia Institute of Technology, Atlanta, GA 30332-0400, USA
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24
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James KE, Asgian JL, Li ZZ, Ekici OD, Rubin JR, Mikolajczyk J, Salvesen GS, Powers JC. Design, Synthesis, and Evaluation of Aza-Peptide Epoxides as Selective and Potent Inhibitors of Caspases-1, -3, -6, and -8. J Med Chem 2004; 47:1553-74. [PMID: 14998341 DOI: 10.1021/jm0305016] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Aza-peptide epoxides, a novel class of irreversible protease inhibitors, are specific for the clan CD cysteine proteases. Aza-peptide epoxides with an aza-Asp residue at P1 are excellent irreversible inhibitors of caspases-1, -3, -6, and -8 with second-order inhibition rates up to 1 910 000 M(-1) s(-1). In general, the order of reactivity of aza-peptide epoxides is S,S > R,R > trans > cis. Interestingly, some of the R,R epoxides while being less potent are actually more selective than the S,S epoxides. Our aza-peptide epoxides designed for caspases are stable, potent, and specific inhibitors, as they show little to no inhibition of other proteases such as the aspartyl proteases porcine pepsin, human cathepsin D, plasmepsin 2 from P. falciparum, HIV-1 protease, and the secreted aspartic proteinase 2 (SAP-2) from Candida albicans; the serine proteases granzyme B and alpha-chymotrypsin; and the cysteine proteases cathepsin B and papain (clan CA), and legumain (clan CD).
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Affiliation(s)
- Karen Ellis James
- School of Chemistry and Biochemistry and the Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, USA
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25
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James KE, Götz MG, Caffrey CR, Hansell E, Carter W, Barrett AJ, McKerrow JH, Powers JC. Aza-Peptide Epoxides: Potent and Selective Inhibitors of Schistosoma mansoni and Pig Kidney Legumains (Asparaginyl Endopeptidases). Biol Chem 2003; 384:1613-8. [PMID: 14719804 DOI: 10.1515/bc.2003.179] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
Aza-peptide epoxides are a new class of irreversible
cysteine protease inhibitors. Derivatives containing a
P1 aza-asparagine residue are specific for Schistosoma
mansoni and pig kidney legumains, which are clan
CD cysteine proteases. The inhibitors have secondorder
rate constants of up to 104 M-1s -1 with pig kidney
legumain and IC50 values as low as 45 nM with S.
mansoni legumain. The most potent epoxides contain
an ester moiety with S,S stereochemistry attached to
the epoxide. Interestingly, amide and amino acid derivatives
of the epoxysuccinate moiety were not inhibitors
of legumain, while disubstituted amide derivatives
are quite potent. The inhibitors have little or no
inhibitory activity with other proteases such as caspases,
chymotrypsin, papain, cathepsin B, granzyme
B, and various aspartyl proteases.
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Affiliation(s)
- Karen Ellis James
- School of Chemistry and Biochemistry, and the Petit Institute for Bioscience and Bioengineering, Georgia Institute of Technology, Atlanta, GA 30332-0400, USA
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26
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Rozman-Pungercar J, Kopitar-Jerala N, Bogyo M, Turk D, Vasiljeva O, Stefe I, Vandenabeele P, Brömme D, Puizdar V, Fonović M, Trstenjak-Prebanda M, Dolenc I, Turk V, Turk B. Inhibition of papain-like cysteine proteases and legumain by caspase-specific inhibitors: when reaction mechanism is more important than specificity. Cell Death Differ 2003; 10:881-8. [PMID: 12867995 DOI: 10.1038/sj.cdd.4401247] [Citation(s) in RCA: 159] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
We report here that a number of commonly used small peptide caspase inhibitors consisting of a caspase recognition sequence linked to chloromethylketone, fluoromethylketone or aldehyde reactive group efficiently inhibit other cysteine proteases than caspases. The in vitro studies included cathepsins B, H, L, S, K, F, V, X and C, papain and legumain. Z-DEVD-cmk was shown to be the preferred irreversible inhibitor of most of the cathepsins in vitro, followed by Z-DEVD-fmk, Ac-YVAD-cmk, Z-YVAD-fmk and Z-VAD-fmk. Inactivation of legumain by all the inhibitors investigated was moderate, whereas cathepsins H and C were poorly inhibited or not inhibited at all. Inhibition by aldehydes was not very potent. All the three fluoromethylketones efficiently inhibited cathepsins in Jurkat and human embryonic kidney 293 cells at concentrations of 100 microM. Furthermore, they completely inhibited cathepsins B and X activity in tissue extracts at concentrations as low as 1 microM. These results suggest that data based on the use of these inhibitors should be taken with caution and that other proteases may be implicated in the processes previously ascribed solely to caspases.
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Affiliation(s)
- J Rozman-Pungercar
- Department of Biochemistry and Molecular Biology, J. Stefan Institute, Jamova 39, SI-1000 Ljubljana, Slovenia
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27
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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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28
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Asgian JL, James KE, Li ZZ, Carter W, Barrett AJ, Mikolajczyk J, Salvesen GS, Powers JC. Aza-peptide epoxides: a new class of inhibitors selective for clan CD cysteine proteases. J Med Chem 2002; 45:4958-60. [PMID: 12408706 DOI: 10.1021/jm025581c] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Aza-peptide epoxides, a new class of irreversible protease inhibitors, are specific for the clan CD cysteine proteases. The inhibitors have second-order rate constants up to 10(5) M(-1) s(-1), with the most potent epoxides having the S,S stereochemistry. The aza-Asn derivatives are effective legumain inhibitors, while the aza-Asp epoxides were specific for caspases. The inhibitors have little or no inhibition with other proteases such as chymotrypsin, papain, or cathepsin B.
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Affiliation(s)
- Juliana L Asgian
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta 30332-0400, USA
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29
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Greenbaum DC, Arnold WD, Lu F, Hayrapetian L, Baruch A, Krumrine J, Toba S, Chehade K, Brömme D, Kuntz ID, Bogyo M. Small molecule affinity fingerprinting. A tool for enzyme family subclassification, target identification, and inhibitor design. CHEMISTRY & BIOLOGY 2002; 9:1085-94. [PMID: 12401493 DOI: 10.1016/s1074-5521(02)00238-7] [Citation(s) in RCA: 140] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Classifying proteins into functionally distinct families based only on primary sequence information remains a difficult task. We describe here a method to generate a large data set of small molecule affinity fingerprints for a group of closely related enzymes, the papain family of cysteine proteases. Binding data was generated for a library of inhibitors based on the ability of each compound to block active-site labeling of the target proteases by a covalent activity based probe (ABP). Clustering algorithms were used to automatically classify a reference group of proteases into subfamilies based on their small molecule affinity fingerprints. This approach was also used to identify cysteine protease targets modified by the ABP in complex proteomes by direct comparison of target affinity fingerprints with those of the reference library of proteases. Finally, experimental data were used to guide the development of a computational method that predicts small molecule inhibitors based on reported crystal structures. This method could ultimately be used with large enzyme families to aid in the design of selective inhibitors of targets based on limited structural/function information.
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Affiliation(s)
- Doron C Greenbaum
- Department of Pharmaceutical Chemistry, San Francisco, CA 94143, USA
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30
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Cathers BE, Barrett C, Palmer JT, Rydzewski RM. pH Dependence of inhibitors targeting the occluding loop of cathepsin B. Bioorg Chem 2002; 30:264-75. [PMID: 12392705 DOI: 10.1016/s0045-2068(02)00009-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Potent and selective cathepsin B inhibitors have previously been synthesized based upon the natural product cysteine protease inhibitor E-64. X-ray crystal data indicates that these compounds interact through their free carboxylate with the positively charged histidine residues located on the prime-side of the active site within the occluding loop of cathepsin B. Herein, we examine the pH dependence of two prime-side-binding compounds. In each case there is a dramatic decrease in k(inact)/K(I) as the pH is raised from 4 to 7.8 corresponding to a single ionization of pK(a) 4.4. These results suggest that targeting of the occluding loop of cathepsin B may be a poor inhibitor design strategy if the enzyme environment has a pH greater than 5.5. However, this type of inhibitor may be a useful tool to help elucidate the role and the environment of cathepsin B in invading tumors.
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Affiliation(s)
- Brian E Cathers
- Axys Pharmaceuticals Inc, 180 Kimball Way, South San Francisco, CA 94080, USA.
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31
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Huang L, Lee A, Ellman JA. Identification of potent and selective mechanism-based inhibitors of the cysteine protease cruzain using solid-phase parallel synthesis. J Med Chem 2002; 45:676-84. [PMID: 11806719 DOI: 10.1021/jm010333m] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Targeted libraries of ketone-based cysteine protease inhibitors were synthesized and screened against cruzain, a cysteine protease implicated in Chagas' disease. A number of single digit nanomolar, low molecular weight inhibitors were identified and optimized for solubility and potency. Specifically, the best inhibitors identified have K(i) values of 0.9-10 nM and molecular weights between 499 and 609 Da. The most effective inhibitor was also found to be greater than 1000-fold selective for cruzain relative to cathepsin B and 100-fold selective for cruzain relative to cathepsin L.
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Affiliation(s)
- Lily Huang
- Department of Chemistry, University of California, Berkeley, California 94720, USA
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32
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Greenbaum D, Baruch A, Hayrapetian L, Darula Z, Burlingame A, Medzihradszky KF, Bogyo M. Chemical approaches for functionally probing the proteome. Mol Cell Proteomics 2002; 1:60-8. [PMID: 12096141 DOI: 10.1074/mcp.t100003-mcp200] [Citation(s) in RCA: 244] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
With the availability of complete genome sequences, emphasis has shifted toward the understanding of protein function. We have developed a functional proteomic methodology that makes use of chemically reactive fluorescent probes to profile and identify enzymes in complex mixtures by virtue of their catalytic activity. This methodology allows a comparison of changes in activity of multiple enzymes under a variety of conditions using a single two-dimensional separation. The probes can also be used to localize active enzymes in intact cells using fluorescence microscopy. Furthermore, the probes enable screens for selective small molecule inhibitors of each enzyme family member within crude lysates or intact cells. Ultimately, this technology allows the rapid identification of potential drug targets and small molecule lead compounds targeted to them.
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Affiliation(s)
- Doron Greenbaum
- Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94143, USA
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33
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Design, Synthesis and Evaluation of d-Homophenylalanyl Epoxysuccinate Inhibitors of the Trypanosomal Cysteine Protease Cruzain. Tetrahedron 2000. [DOI: 10.1016/s0040-4020(00)00882-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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34
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Schaschke N, Assfalg-Machleidt I, Lassleben T, Sommerhoff CP, Moroder L, Machleidt W. Epoxysuccinyl peptide-derived affinity labels for cathepsin B. FEBS Lett 2000; 482:91-6. [PMID: 11018529 DOI: 10.1016/s0014-5793(00)02047-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Extracellular cysteine proteases, in particular cathepsin B, have been implicated in a variety of pathological processes. Selectively targeting labels of this enzyme are important tools to gain more detailed understanding of its specific roles. Starting from our recently developed irreversible epoxysuccinyl-based inhibitor (R-Gly-Gly-Leu-(2S,3S)-tEps-Leu-Pro-OH, R=OMe), we have synthesized two affinity labels, R=NH-(CH(2))(6)-NH-rhodamine B and R=NH-(CH(2))(6)-NH-biotin. Using MCF-7 cells, the labeled inhibitors were shown to be virtually non-cell-permeant. Moreover, affinity blot analysis with the biotinylated inhibitor allowed a highly sensitive and selective non-radioactive detection of active cathepsin B.
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Affiliation(s)
- N Schaschke
- Max-Planck-Institut für Biochemie, Martinsried, Germany
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35
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Schirmeister T, Peric M. Aziridinyl peptides as inhibitors of cysteine proteases: effect of a free carboxylic acid function on inhibition. Bioorg Med Chem 2000; 8:1281-91. [PMID: 10896108 DOI: 10.1016/s0968-0896(00)00058-4] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Peptides containing aziridine-2,3-dicarboxylate (Azi) as electrophilic building block are evaluated as inhibitors of the cysteine proteases papain, cathepsin B, cathepsin L and clostripain. The influence of a free carboxylic acid as functional group at different positions of the inhibitor molecule on inhibition is analyzed. Structure-activity relationships and binding mode hypotheses are discussed. In contrast to the bacterial enzyme clostripain, the papain like mammalian proteases (cathepsins) are irreversibly inactivated by aziridinyl peptides. N-Unsubstituted aziridines are much more potent inhibitors of papain and cathepsins if they contain the free carboxylic acid attached to the aziridine ring (HOAzi-Leu-ProOBzl). Two free carboxylic acid functions at the aziridine ring are necessary for good inhibition of these enzymes by N-acylated aziridinyl peptides (BOC-Phe-Azi(OH)2). Chimeric bispeptidyl derivatives are selective CB inhibitors if the free acid is located at the C-terminus of the peptide (BOC-Phe-(EtO)Azi-Leu-ProOH). Clostripain is only inhibited by aziridinyl peptide esters.
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Affiliation(s)
- T Schirmeister
- Department of Pharmaceutical Chemistry, Pharmaceutical Institute, Albert-Ludwigs-University of Freiburg, Germany.
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Guncar G, Klemencic I, Turk B, Turk V, Karaoglanovic-Carmona A, Juliano L, Turk D. Crystal structure of cathepsin X: a flip-flop of the ring of His23 allows carboxy-monopeptidase and carboxy-dipeptidase activity of the protease. Structure 2000; 8:305-13. [PMID: 10745011 DOI: 10.1016/s0969-2126(00)00108-8] [Citation(s) in RCA: 62] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
BACKGROUND Cathepsin X is a widespread, abundantly expressed papain-like mammalian lysosomal cysteine protease. It exhibits carboxy-monopeptidase as well as carboxy-dipeptidase activity and shares a similar activity profile with cathepsin B. The latter has been implicated in normal physiological events as well as in various pathological states such as rheumatoid arthritis, Alzheimer's disease and cancer progression. Thus the question is raised as to which of the two enzyme activities has actually been monitored. RESULTS The crystal structure of human cathepsin X has been determined at 2.67 A resolution. The structure shares the common features of a papain-like enzyme fold, but with a unique active site. The most pronounced feature of the cathepsin X structure is the mini-loop that includes a short three-residue insertion protruding into the active site of the protease. The residue Tyr27 on one side of the loop forms the surface of the S1 substrate-binding site, and His23 on the other side modulates both carboxy-monopeptidase as well as carboxy-dipeptidase activity of the enzyme by binding the C-terminal carboxyl group of a substrate in two different sidechain conformations. CONCLUSIONS The structure of cathepsin X exhibits a binding surface that will assist in the design of specific inhibitors of cathepsin X as well as of cathepsin B and thereby help to clarify the physiological roles of both proteases.
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Affiliation(s)
- G Guncar
- Department of Biochemistry and Molecular Biology, Jozef Stefan Institute, Ljubljana, 1000, Slovenia
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Schaschke N, Assfalg-Machleidt I, Machleidt W, Moroder L. Substrate/propeptide-derived endo-epoxysuccinyl peptides as highly potent and selective cathepsin B inhibitors. FEBS Lett 1998; 421:80-2. [PMID: 9462845 DOI: 10.1016/s0014-5793(97)01538-x] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Based on recent information about the anti-substrate binding mode of the propeptide portion of procathepsin B and the well established substrate-like binding of epoxysuccinyl-dipeptide carboxylates to the S' subsites of cathepsin B a new endo-trans-epoxysuccinyl peptide was synthesized that contains the dipeptide moiety Leu-Pro-OH for the P1'-P2' substrate positions and the tripeptide moiety Leu-Gly-Gly-OMe (sequence portion 46-48 of the propeptide) for the P2-P4 positions in anti-substrate orientation. With an unequivocal (2S,3S) configuration this new trans-epoxysuccinyl peptide derivative was found to inhibit cathepsin B with an apparent second-order rate constant of 1,520,000 M(-1) s(-1) which represents so far the most potent inhibitor among E-64-derived compounds. Conversely, the (2R,3R) diastereomer exhibited a significantly lower inhibition potency. This observation fully agrees with our previous findings that inhibitor/enzyme interactions at the S subsites are favored by the (2S,3S) and reverse interactions at the S' subsites by the (2R,3R) configuration of the trans-epoxysuccinyl moiety.
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Affiliation(s)
- N Schaschke
- Max-Planck-Institut für Biochemie, Martinsried, Germany
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