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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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2
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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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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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4
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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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6
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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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7
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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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Breuning A, Vicik R, Schirmeister T. An improved synthesis of aziridine-2,3-dicarboxylates via azido alcohols—epimerization studies. ACTA ACUST UNITED AC 2003. [DOI: 10.1016/j.tetasy.2003.09.015] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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9
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Yasothornsrikul S, Greenbaum D, Medzihradszky KF, Toneff T, Bundey R, Miller R, Schilling B, Petermann I, Dehnert J, Logvinova A, Goldsmith P, Neveu JM, Lane WS, Gibson B, Reinheckel T, Peters C, Bogyo M, Hook V. Cathepsin L in secretory vesicles functions as a prohormone-processing enzyme for production of the enkephalin peptide neurotransmitter. Proc Natl Acad Sci U S A 2003; 100:9590-5. [PMID: 12869695 PMCID: PMC170962 DOI: 10.1073/pnas.1531542100] [Citation(s) in RCA: 174] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Multistep proteolytic mechanisms are essential for converting proprotein precursors into active peptide neurotransmitters and hormones. Cysteine proteases have been implicated in the processing of proenkephalin and other neuropeptide precursors. Although the papain family of cysteine proteases has been considered the primary proteases of the lysosomal degradation pathway, more recent studies indicate that functions of these enzymes are linked to specific biological processes. However, few protein substrates have been described for members of this family. We show here that secretory vesicle cathepsin L is the responsible cysteine protease of chromaffin granules for converting proenkephalin to the active enkephalin peptide neurotransmitter. The cysteine protease activity was identified as cathepsin L by affinity labeling with an activity-based probe for cysteine proteases followed by mass spectrometry for peptide sequencing. Production of [Met]enkephalin by cathepsin L occurred by proteolytic processing at dibasic and monobasic prohormone-processing sites. Cellular studies showed the colocalization of cathepsin L with [Met]enkephalin in secretory vesicles of neuroendocrine chromaffin cells by immunofluorescent confocal and immunoelectron microscopy. Functional localization of cathepsin L to the regulated secretory pathway was demonstrated by its cosecretion with [Met]enkephalin. Finally, in cathepsin L gene knockout mice, [Met]enkephalin levels in brain were reduced significantly; this occurred with an increase in the relative amounts of enkephalin precursor. These findings indicate a previously uncharacterized biological role for secretory vesicle cathepsin L in the production of [Met]enkephalin, an endogenous peptide neurotransmitter.
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10
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Medzihradszky K. Josef Rudinger Memorial Lecture 2002. The chemistry of the opioid receptor binding sites. J Pept Sci 2003; 9:333-53. [PMID: 12846480 DOI: 10.1002/psc.469] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Since the discovery of the opioid receptors and their endogenous ligands an immense research work has been devoted to the exploration of their specificity, the mechanism of ligand binding and ligand-receptor interactions. One of the main goals has been the location and characterization of the binding sites. The present review compiles the results achieved in this field in the last quarter of a century, and puts some questions concerning the success of these efforts.
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Affiliation(s)
- Kálmán Medzihradszky
- Research Group of Peptide Chemistry, Hungarian Academy of Sciences, Budapest, Hungary.
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11
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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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12
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Nakagomi K, Takatsu K, Takagi S, Ebisu H, Sadakane Y, Fujii N, Akizawa T, Tanimura T, Hatanaka Y. Isolation of cathepsin B inhibitory peptides, Cabin-A1 and -A2, from a tryptic and chymotryptic hydrolysate of human serum albumin. Peptides 2002; 23:1567-71. [PMID: 12217416 DOI: 10.1016/s0196-9781(02)00098-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Two novel peptides that inhibit cathepsin B were isolated from a tryptic and chymotryptic hydrolysate of human serum albumin, and designated as Cabin-A1 and -A2. Cabin-A1 and -A2 were purified by reversed-phase HPLC and identified as Ser-Leu-His-Thr-Leu-Phe and Phe-Gln-Asn-Ala-Leu, respectively. These peptides correspond to f(65-70) and f(403-407) of human serum albumin. Human albutensin A (Ala-Phe-Lys-Ala-Trp-Ala-Val-Ala-Arg), which corresponds to f(210-218), was also isolated as a potent cathepsin B inhibitor. Synthetic Cabin-A1, -A2, and human albutensin A showed dose-dependent inhibition of cathepsin B, with K(i) values of 2.4, 290, and 3.8 microM, respectively.
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Affiliation(s)
- Kazuya Nakagomi
- Faculty of Pharmaceutical Sciences, Toyama Medical and Pharmaceutical University, 2630 Sugitani, Toyama, Japan.
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13
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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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14
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Nakagomi K, Fujimura A, Maeda H, Sadakane Y, Fujii N, Akizawa T, Tanimura T, Hatanaka Y. Isolation of novel peptides, cabin-1, -2, -3, and -4, that inhibit cathepsin B from a thermolysin digest of human plasma. Biol Pharm Bull 2002; 25:564-8. [PMID: 12033493 DOI: 10.1248/bpb.25.564] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Four novel peptides that inhibit cathepsin B, designated as Cabin-1, -2, -3, and -4, were isolated from a thermolysin digest of human plasma. After gel filtration and cation-exchange chromatography, the peptide mixture was purified by reverse-phase HPLC to isolate Cabin-1, -2, -3, and 4, with the amino acid sequences LGPVTQE, VLQSSGLYS, VVSVLT, and LVYDAY, respectively. These peptides correspond to f(64-70) of human apolipoprotein A-I for Cabin-1, f(56-64) and f(185-190) of the human immunoglobulin G gamma chain for Cabin-2 and -3, and f(66-71) of human transferrin for Cabin-4. Synthetic Cabin-1, -2, -3, and -4 showed dose-dependent inhibition of cathepsin B. Their IC50 values were 450, 500, 20, and 5.0 micromol/l, respectively. Lineweaver-Burk plots suggested that Cabin-3 is a noncompetitive inhibitor, while Cabin-4 is a competitive inhibitor. Among the N- and C-terminal deletion peptides of Cabin-2 and -4, Cabin-2(1-8), VLQSSGLY, was found to have the most potent inhibitory activity, with an IC50 of 3.8 micromol/l.
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Affiliation(s)
- Kazuya Nakagomi
- Faculty of Pharmaceutical Sciences, Toyama Medical and Pharmaceutical University, Japan.
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Schirmeister T. (S)-Thiirancarboxylic acid as a reactive building block for a new class of cysteine protease inhibitors. Bioorg Med Chem Lett 2000; 10:2647-51. [PMID: 11128643 DOI: 10.1016/s0960-894x(00)00549-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
For (S)-thiirancarboxylic acid a second-order rate constant of k2nd = 222 M(-1) min(-1) for the irreversible inhibition of papain was determined. The ethyl and methyl ester do not inhibit the enzyme time-dependently. An improved synthesis of enantiomerically pure thiirancarboxylic acid is described. It is shown that thiirancarboxylates can be substrates for serine proteases (alpha-chymotrypsin) and esterases (pig liver esterase) and even for metallo proteases (thermolysin).
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Affiliation(s)
- T Schirmeister
- Institute for Pharmacy and Food Chemistry, University of Würzburg, Germany.
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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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Abstract
Mammalian cysteine proteases of the papain superfamily are interesting targets for the development of new drugs against diseases connected to abnormal degradation of muscle or bone proteins. The high nucleophilicity of the active site of these proteases as well as the characteristics of the well-known epoxysuccinic acid derived cysteine protease inhibitors provided a basis for the design of new types of selective and irreversible inhibitors for these enzymes. We designed and synthesized a novel class of peptidic cysteine protease inhibitors containing aziridine-2,3-dicarboxylic acid as electrophilic amino acid. Three types of aziridinyl peptides that differ in the position of the aziridine building block within the peptide chain have been synthesized and tested as inhibitors of several cysteine proteases. Remarkable differences could be observed between the three types of inhibitors concerning their activity, stereospecificity, pH dependency of inhibition, and selectivity between different cysteine proteases, respectively, indicating that different binding modes of the three types of inhibitors in respect to their orientation in the S and S' binding sites of the enzymes may be present.
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Affiliation(s)
- T Schirmeister
- Department of Pharmaceutical Chemistry, Albert-Ludwigs University of Freiburg, Germany
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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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Nagao Y, Sano S, Morimoto K, Kakegawa H, Takatani T, Shiro M, Katunuma N. Synthesis of a new class of cathepsin B inhibitors exploiting a unique reaction cascade. Tetrahedron Lett 2000. [DOI: 10.1016/s0040-4039(00)00177-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Bogyo M, Verhelst S, Bellingard-Dubouchaud V, Toba S, Greenbaum D. Selective targeting of lysosomal cysteine proteases with radiolabeled electrophilic substrate analogs. CHEMISTRY & BIOLOGY 2000; 7:27-38. [PMID: 10662686 DOI: 10.1016/s1074-5521(00)00061-2] [Citation(s) in RCA: 179] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
BACKGROUND The lysosomal cysteine proteases of the papain family are some of the best studied proteolytic enzymes. Small-molecule inhibitors and fluorogenic substrate mimics have been used to probe the physiological roles of these proteases. A high degree of homology between family members and overlap in substrate specificity have made elucidating individual protease function, expression and activity difficult. RESULTS Using peptide vinyl sulfones and epoxide as templates, we have generated probes that can be tagged with radioactive iodine. The resulting compounds covalently label various cathepsins and several unidentified polypeptides likely to be proteases. MB-074 was found to be a highly selective probe of cathepsin B activity. Probes that labeled several cathepsins were used to examine the specificity and cell permeability of the CA-074 family of inhibitors. Although CA-074 reportedly acts in vivo, we find it is unable to penetrate cells. Esterifying CA-074 resulted in a cell-permeable inhibitor with dramatically reduced activity and specificity for cathepsin B. The probes were also used to monitor protease activity in primary human tumor tissue and cells derived from human placenta. CONCLUSIONS We have generated a highly selective cathepsin B probe and several less specific reagents for the study of cathepsin biology. The reagents have several advantages over commonly used fluorogenic substrates, allowing inhibitor targets to be identified in a pool of total cellular enzymes. We have used the probes to show that cathepsin activity is regulated in tumor tissues and during differentiation of placental-derived cytotrophoblasts to invasive cells required for establishing blood circulation in a developing embryo.
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Affiliation(s)
- M Bogyo
- Departments of Biochemistry and Biophysics, University of California, San Francisco, CA 94143, USA.
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Schirmeister T. New peptidic cysteine protease inhibitors derived from the electrophilic alpha-amino acid aziridine-2,3-dicarboxylic acid. J Med Chem 1999; 42:560-72. [PMID: 10052963 DOI: 10.1021/jm981061z] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Three different types of peptides containing aziridine-2, 3-dicarboxylic acid (Azi) as an electrophilic alpha-amino acid at different positions within the peptide chain (type I, N-acylated aziridines with Azi as C-terminal amino acid; type II, N-unsubstituted aziridines with Azi as N-terminal amino acid; type III, N-acylated bispeptidyl derivatives of Azi) have been synthesized and tested as inhibitors of the cysteine proteases papain, cathepsins B, L, and H, and calpains I and II, as well as against several serine proteases, one aspartate, and one metalloprotease. All aziridinyl peptides are specific cysteine protease inhibitors. Papain and cathepsins B and L are inhibited irreversibly, whereas cathepsin H and calpains are inhibited in a non-time-dependent manner. Some compounds turned out to be substrates for serine proteases and for the metalloprotease thermolysin. Remarkable differences can be observed between the three different types of inhibitors concerning stereospecificity, pH dependency of inhibition, selectivity between different cysteine proteases, and the importance of a free carboxylic acid function at the aziridine ring for inhibition. Above all type II inhibitors, aza analogues of the well-known epoxysuccinyl peptides, are potent cysteine protease inhibitors. With the exception of BOC-Leu-Gly-(S, S+R,R)-Azi-(OEt)2 (28a+b), a highly selective and potent cathepsin L inhibitor, N-acylated aziridines of type I are weaker inhibitors than type II or type III compounds. The observed results can be explained by different binding modes of the three types of inhibitors with respect to their orientation in the S- and S'-binding sites of the enzymes. Furthermore, the presence of a protonated aziridine N modifies the binding mode of type II inhibitors.
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Affiliation(s)
- T Schirmeister
- Department of Pharmaceutical Chemistry, Pharmaceutical Institute, Albert-Ludwigs-University of Freiburg, Hermann-Herder-Strasse 9, D-79104 Freiburg, Germany
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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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Schaschke N, Assfalg-Machleidt I, Machleidt W, Turk D, Moroder L. E-64 analogues as inhibitors of cathepsin B. On the role of the absolute configuration of the epoxysuccinyl group. Bioorg Med Chem 1997; 5:1789-97. [PMID: 9354234 DOI: 10.1016/s0968-0896(97)00105-3] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
A series of trans-epoxysuccinyl-peptide derivatives based on the natural inhibitor E-64 were synthesized in the (2R,3R) and (2S,3S) configuration in order to analyze the role of the stereochemistry of this residue in dictating inhibitory potency and selectivity for cysteine proteases. We confirmed that binding of E-64 like trans-epoxysuccinyl compounds is remarkably favored by the (2S,3S) configuration, but we also found that CA030-type compounds are stronger inhibitors in the (2R,3R) configuration than the related diastereomers. Consequently, the structural requirements for exploiting both the S and S' subsites are not additive and a structure-based design of bis-peptidyl derivatives of trans-epoxysuccinic acid to increase selective inhibition becomes even more difficult. Additional contrasting effects were observed for the pH optima required in the electrostatic interactions at the S and S' subsites.
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Affiliation(s)
- N Schaschke
- Max-Planck-Institut für Biochemie, Martinsried, Germany
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25
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Albeck A, Kliper S. Mechanism of cysteine protease inactivation by peptidyl epoxides. Biochem J 1997; 322 ( Pt 3):879-84. [PMID: 9148764 PMCID: PMC1218270 DOI: 10.1042/bj3220879] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Peptidyl epoxides are time- and concentration-dependent selective cysteine protease inhibitors. The lack of recovery of enzymic activity and the retention of 1 molar equivalent of radioactive inhibitor associated with the enzyme on dialysis, shown in this study, indicate that they form a covalent irreversible equimolar complex with the enzyme. It is also shown that the peptidyl epoxide inhibitors alkylate the active-site thiol. This alkylation only occurs when the enzyme is in its native conformation, as the denatured enzyme does not undergo alkylation by the inhibitor to any appreciable extent. Finally, the inactivation process is compared with a model reaction between a peptidyl epoxide and a protected cysteine in neutral and basic aqueous media. The inactivation of cathepsin B by Cbz-Phe-(O-benzyl)-Thr-epoxide is accelerated by 5.5 orders of magnitude relative to the rate of the model reaction at pH 10.0 and 25 degrees C, and estimated to be at least 10(8) times faster than the model reaction at pH 7.0. These results, in conjunction with the selectivity exhibited by peptidyl epoxides at all levels, point to a mechanism-based inhibition, and may have mechanistic implications regarding the catalysis carried out by cysteine proteases.
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Affiliation(s)
- A Albeck
- Department of Chemistry, Bar Ilan University, Ramat Gan 52900, Israel
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26
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Affiliation(s)
- Hans-Hartwig Otto
- Department of Pharmaceutical Chemistry, University of Freiburg, Hermann-Herder-Str. 9, D-79104 Freiburg i.Br., Germany
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27
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Chen Y, Plouffe C, Ménard R, Storer AC. Delineating functionally important regions and residues in the cathepsin B propeptide for inhibitory activity. FEBS Lett 1996; 393:24-6. [PMID: 8804416 DOI: 10.1016/0014-5793(96)00847-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Synthetic peptides derived from the proregion of rat cathepsin B were used to identify functionally important regions and residues for cathepsin B inhibition. Successive 5 amino acid deletions of a 56 amino acid propeptide from both the N- and C-termini has allowed the identification of two regions important for inhibitory activity: the NTTWQ (residues 21p-25p) and CGTVL (42p-46p) regions. Alanine scanning of residues within these two regions indicates that Trp-24p and Cys-42p contribute strongly to inhibition, their replacement by Ala resulting in 160- and 140-fold increases in Ki, respectively.
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Affiliation(s)
- Y Chen
- Biotechnology Research Institute, National Research Council of Canada, Montreal, Quebec, Canada
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29
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Brömme D, Klaus JL, Okamoto K, Rasnick D, Palmer JT. Peptidyl vinyl sulphones: a new class of potent and selective cysteine protease inhibitors: S2P2 specificity of human cathepsin O2 in comparison with cathepsins S and L. Biochem J 1996; 315 ( Pt 1):85-9. [PMID: 8670136 PMCID: PMC1217200 DOI: 10.1042/bj3150085] [Citation(s) in RCA: 122] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Peptidyl vinyl sulphones are a novel class of extremely potent and specific cysteine protease inhibitors. They are highly active against the therapeutically important cathepsins O2, S and L. The highest kinact/K1 values exceed 10(7)M(-1) x s(-1) for cathepsin S and 10(5)M(-1) x s(-1) for cathepsins O2 and L. To study the primary specificity site of the novel human cathepsin O2 and the effectiveness of this novel class of inhibitors, a series of peptidyl vinyl sulphones with variations in the P2 residue was synthesized. Leucine in the P2 position was proven to be the most effective residue for cathepsin O2 and also for cathepsins S and L. Cathepsins O2 and S share a decreased accessibility towards P2 hydrophobic non-branched residues such as aminohexanoic acid (norleucine), methionine and oxidized methionine, but are distinguished by their different affinity towards phenylalanine in the P2 position. In contrast, cathepsin S accepts a broader range of hydrophobic residues in its S2 subsite than cathepsins O2 and L. The primary specificity-determining subsite pocket S2 in cathepsin O2 appears to be spatially more restricted than those of cathepsins S and L.
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Affiliation(s)
- D Brömme
- Khepri Pharmaceuticals, Inc., San Francisco, CA 94080, U.S.A
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30
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S-pegylthiopapain, a versatile intermediate for the preparation of the fully active form of the cysteine proteinase archetype. J Chromatogr A 1996. [DOI: 10.1016/0021-9673(95)00910-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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31
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32
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Meara JP, Rich DH. Measurement of individual rate constants of irreversible inhibition of a cysteine proteinase by an epoxysuccinyl inhibitor. Bioorg Med Chem Lett 1995. [DOI: 10.1016/0960-894x(95)00396-b] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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33
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Design of a new selective cysteine protease inactivator and its mechanistic implications. Bioorg Med Chem Lett 1995. [DOI: 10.1016/0960-894x(95)00312-h] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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34
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Andruszkiewicz R, Milewski S, Borowski E. Amide and ester derivatives of N3-trans-epoxysuccinoyl-L-2,3-diaminopropanoic acid: inhibitors of glucosamine-6-phosphate synthase. JOURNAL OF ENZYME INHIBITION 1995; 9:123-33. [PMID: 8583250 DOI: 10.3109/14756369509042812] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Several analogs 5, 6, 7, 8, 10 and 11 of the C-terminal fragment of a peptide antibiotic Sch 37137 were designed and tested as inhibitors of glucosamine-6-phosphate synthase from Saccharomyces cerevisiae. From IC50 values and kinetic parameters of inhibition of glucosamine-6-phosphate synthase by compounds 5-11 it has been found that the inhibitory potency of these compounds follows the order: 6 > 5 > 8 > 9 > 7, 10, 11. This suggests that an inhibitor with a primary amido group binds better to the active site of the enzyme than other inhibitors. The order of reactivity of compounds 5-11 may be attributed to a steric inability of the inhibitor to fit into the active site of the enzyme and also indicates the importance of the chirality of trans-epoxysuccinic acid on the inhibitory properties of the synthesized compounds.
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Affiliation(s)
- R Andruszkiewicz
- Department of Pharmaceutical Technology and Biochemistry, Technical University of Gdańsk, Poland
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35
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Brömme D, Bonneau PR, Lachance P, Storer AC. Engineering the S2 subsite specificity of human cathepsin S to a cathepsin L- and cathepsin B-like specificity. J Biol Chem 1994. [DOI: 10.1016/s0021-9258(18)43803-3] [Citation(s) in RCA: 67] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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36
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Gour-Salin BJ, Lachance P, Magny MC, Plouffe C, Ménard R, Storer AC. E64 [trans-epoxysuccinyl-L-leucylamido-(4-guanidino)butane] analogues as inhibitors of cysteine proteinases: investigation of S2 subsite interactions. Biochem J 1994; 299 ( Pt 2):389-92. [PMID: 8172599 PMCID: PMC1138284 DOI: 10.1042/bj2990389] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
A number of epoxysuccinyl amino acid benzyl esters (HO-Eps-AA-OBzl) and benzyl amides (HO-Eps-AA-NHBzl) (where AA represents amino acid) were synthesized as analogues of E64, a naturally occurring inhibitor of cysteine proteinases. These inhibitors were designed to evaluate if selectivity for cathepsin B could be achieved by varying the amino acid on the basis of known substrate specificity. Contrary to the situation with substrates, it was found that variation of the amino acid in the E64 analogues does not lead to major changes in the kinetic parameter kinac./Ki and that the specificity of these analogues does not parallel that observed for substrates. This is particularly true in the case of the benzyl ester derivatives where the deviation from substrate-like behaviour is more important than with the benzyl amide derivatives. The results suggest that the amide proton of the benzyl amide group in HO-Eps-AA-NHBzl interacts in the S2 subsite in both cathepsin B and papain and contributes to increase the potency of these inhibitors. The kinetic data also suggest that differences in the orientation of the C alpha-C beta bond of the side chain in the S2 subsite of the enzyme might explain the differences between substrate and E64 analogue specificities. This hypothesis is supported by the fact that the order of inactivation rates with chloromethane inhibitors (which are believed to be good models of enzyme-substrate interactions) is indeed very similar to that observed with the corresponding amidomethylcoumarin substrates. In conclusion, the information available from S2-P2 interactions with substrates cannot be used to enhance the selectivity of the E64 analogues in a rational manner.
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Affiliation(s)
- B J Gour-Salin
- Biotechnology Research Institute, Montreal, Quebec, Canada
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37
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Korn A, Rudolph-Böhner S, Moroder L. A convenient synthesis of optically pure (2R, 3R)-2, 3- Epoxysuccinyl - dipeptides. Tetrahedron 1994. [DOI: 10.1016/s0040-4020(01)85561-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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38
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Brömme D, Demuth HU. N,O-diacyl hydroxamates as selective and irreversible inhibitors of cysteine proteinases. Methods Enzymol 1994; 244:671-85. [PMID: 7845243 DOI: 10.1016/0076-6879(94)44050-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- D Brömme
- Khepri Pharmaceuticals, Inc., South San Francisco, California 94080
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39
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Ménard R, Carmona E, Plouffe C, Brömme D, Konishi Y, Lefebvre J, Storer AC. The specificity of the S1' subsite of cysteine proteases. FEBS Lett 1993; 328:107-10. [PMID: 8344413 DOI: 10.1016/0014-5793(93)80975-z] [Citation(s) in RCA: 71] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
The specificity of the S1' subsite of the cysteine proteases cathepsin B, L, S and papain has been investigated using a series of intramolecularly quenched fluorogenic substrates (Dansyl-Phe-Arg-AA-Trp-Ala) where the P1' amino acid (AA) has been varied. Taken individually, each enzyme displays a relatively broad S1' subsite specificity and this subsite cannot be considered as a primary site of specificity. Notable differences do exist however between the various proteases. Cathepsin B prefers large hydrophobic residues in the P1' position of a substrate while cathepsin L has an opposite trend, favoring amino acids with small (Ala, Ser) or long but non-branched (Asn, Gln, Lys) side chains. Cathepsin S and papain display a somewhat broader S1' subsite specificity.
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Affiliation(s)
- R Ménard
- Biotechnology Research Institute, National Research Council of Canada, Montréal, Québec
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40
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Chapter 20. Proteinases in Inflammation. ANNUAL REPORTS IN MEDICINAL CHEMISTRY 1993. [DOI: 10.1016/s0065-7743(08)60890-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register]
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