1
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Feral A, Martin AR, Desfoux A, Amblard M, Vezenkov LL. Covalent-reversible peptide-based protease inhibitors. Design, synthesis, and clinical success stories. Amino Acids 2023; 55:1775-1800. [PMID: 37330416 DOI: 10.1007/s00726-023-03286-1] [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: 03/30/2023] [Accepted: 05/22/2023] [Indexed: 06/19/2023]
Abstract
Dysregulated human peptidases are implicated in a large variety of diseases such as cancer, hypertension, and neurodegeneration. Viral proteases for their part are crucial for the pathogens' maturation and assembly. Several decades of research were devoted to exploring these precious therapeutic targets, often addressing them with synthetic substrate-based inhibitors to elucidate their biological roles and develop medications. The rational design of peptide-based inhibitors offered a rapid pathway to obtain a variety of research tools and drug candidates. Non-covalent modifiers were historically the first choice for protease inhibition due to their reversible enzyme binding mode and thus presumably safer profile. However, in recent years, covalent-irreversible inhibitors are having a resurgence with dramatic increase of their related publications, preclinical and clinical trials, and FDA-approved drugs. Depending on the context, covalent modifiers could provide more effective and selective drug candidates, hence requiring lower doses, thereby limiting off-target effects. Additionally, such molecules seem more suitable to tackle the crucial issue of cancer and viral drug resistances. At the frontier of reversible and irreversible based inhibitors, a new drug class, the covalent-reversible peptide-based inhibitors, has emerged with the FDA approval of Bortezomib in 2003, shortly followed by 4 other listings to date. The highlight in the field is the breathtakingly fast development of the first oral COVID-19 medication, Nirmatrelvir. Covalent-reversible inhibitors can hipothetically provide the safety of the reversible modifiers combined with the high potency and specificity of their irreversible counterparts. Herein, we will present the main groups of covalent-reversible peptide-based inhibitors, focusing on their design, synthesis, and successful drug development programs.
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Affiliation(s)
- Anthony Feral
- IBMM, University Montpellier, CNRS, ENSCM, Montpellier, France
| | | | | | - Muriel Amblard
- IBMM, University Montpellier, CNRS, ENSCM, Montpellier, France
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2
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Solania A, González-Páez GE, Wolan DW. Selective and Rapid Cell-Permeable Inhibitor of Human Caspase-3. ACS Chem Biol 2019; 14:2463-2470. [PMID: 31334631 DOI: 10.1021/acschembio.9b00564] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Individual roles and overlapping functionalities of 12 human caspases during apoptosis and other cellular processes remain poorly resolved primarily due to a lack of chemical tools. Here we present a new selective caspase-3 inhibitor, termed Ac-ATS010-KE, with rapid and irreversible binding kinetics. Relative to previously designed caspase-3-selective molecules that have tremendously abated inhibitory rates and thus limited use in biological settings, the improved kinetics of Ac-ATS010-KE permits its use in a cell-based capacity. We demonstrate that Ac-ATS010-KE prevents apoptosis with comparable efficacy to the general caspase inhibitor Ac-DEVD-KE and surprisingly does so without side-chain methylation. This observation is in contrast to the well-established peptide modification strategy typically employed for improving cellular permeability. Ac-ATS010-KE protects against extrinsic apoptosis, which demonstrates the utility of a thiophene carboxylate leaving group in biological settings, challenges the requisite neutralization of free carboxylic acids to improve cell permeability, and provides a tool-like compound to interrogate the role of caspase-3 in a variety of cellular processes.
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Affiliation(s)
- Angelo Solania
- Departments of Molecular Medicine and Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Gonzalo E. González-Páez
- Departments of Molecular Medicine and Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Dennis W. Wolan
- Departments of Molecular Medicine and Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
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3
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Xu F, Si XJ, Song YY, Wang XD, Liu CS, Geng PF, Du M. Palladium-Catalyzed C–N Bond Cleavage of 2H-Azirines for the Synthesis of Functionalized α-Amido Ketones. J Org Chem 2019; 84:2200-2208. [DOI: 10.1021/acs.joc.8b03193] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Fen Xu
- College of Material and Chemical Engineering, Zhengzhou University of Light Industry, Zhengzhou 450002, China
| | - Xiao-Ju Si
- College of Material and Chemical Engineering, Zhengzhou University of Light Industry, Zhengzhou 450002, China
| | - Yuan-Yuan Song
- College of Material and Chemical Engineering, Zhengzhou University of Light Industry, Zhengzhou 450002, China
| | - Xing-Dong Wang
- College of Material and Chemical Engineering, Zhengzhou University of Light Industry, Zhengzhou 450002, China
| | - Chun-Sen Liu
- College of Material and Chemical Engineering, Zhengzhou University of Light Industry, Zhengzhou 450002, China
| | - Peng-Fei Geng
- College of Material and Chemical Engineering, Zhengzhou University of Light Industry, Zhengzhou 450002, China
| | - Miao Du
- College of Material and Chemical Engineering, Zhengzhou University of Light Industry, Zhengzhou 450002, China
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4
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Kim Y, Pak HK, Rhee YH, Park J. Catalytic transformation of esters of 1,2-azido alcohols into α-amido ketones. Chem Commun (Camb) 2016; 52:6549-52. [DOI: 10.1039/c6cc02063a] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The esters of 1,2-azido alcohols were transformed into α-amido ketones without external oxidants through the Ru-catalyzed formation of N–H imines with the liberation of N2 followed by intramolecular migration of the acyl moiety.
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Affiliation(s)
- Yongjin Kim
- Department of Chemistry
- POSTECH (Pohang University of Science and Technology)
- Pohang 790-784
- Korea
| | - Han Kyu Pak
- Department of Chemistry
- POSTECH (Pohang University of Science and Technology)
- Pohang 790-784
- Korea
| | - Young Ho Rhee
- Department of Chemistry
- POSTECH (Pohang University of Science and Technology)
- Pohang 790-784
- Korea
| | - Jaiwook Park
- Department of Chemistry
- POSTECH (Pohang University of Science and Technology)
- Pohang 790-784
- Korea
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5
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Lv Y, Li Y, Xiong T, Lu Y, Liu Q, Zhang Q. nBu4NI-Catalyzed oxidative imidation of ketones with imides: synthesis of α-amino ketones. Chem Commun (Camb) 2014; 50:2367-9. [DOI: 10.1039/c3cc48887j] [Citation(s) in RCA: 91] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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6
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DiRocco DA, Rovis T. Catalytic asymmetric cross-aza-benzoin reactions of aliphatic aldehydes with N-Boc-protected imines. Angew Chem Int Ed Engl 2012; 51:5904-6. [PMID: 22566184 DOI: 10.1002/anie.201202442] [Citation(s) in RCA: 110] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2012] [Indexed: 11/05/2022]
Affiliation(s)
- Daniel A DiRocco
- Department of Chemistry, Colorado State University, Fort Collins, CO 80526, USA
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7
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DiRocco DA, Rovis T. Catalytic Asymmetric Cross-Aza-Benzoin Reactions of Aliphatic Aldehydes withN-Boc-Protected Imines. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201202442] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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8
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Roiban GD, Matache M, Hădade ND, Funeriu DP. A general solid phase method for the synthesis of sequence independent peptidyl-fluoromethyl ketones. Org Biomol Chem 2012; 10:4516-23. [PMID: 22543859 DOI: 10.1039/c2ob25096a] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We present here a new, general, solid phase strategy for the synthesis of sequence independent peptidyl-fluoromethyl ketones using standard Fmoc peptide chemistry. Our method is based on the synthesis of bifunctional linkers which allows the incorporation of amino acid fluoromethyl ketone unit at the C-terminal end of peptide sequences. Application of this approach for the synthesis of activity based probes for SENPs is also described.
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Affiliation(s)
- Gheorghe-Doru Roiban
- Department of Chemistry, Marie Curie Excellence Team, Technical University München, 4 Lichtenberg str. 85748, Garching, Germany
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9
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Lazny R, Nodzewska A, Zabicka B. Asymmetric solid-phase alkylation of ketones immobilized via SAMP hydrazone analogue linkers. JOURNAL OF COMBINATORIAL CHEMISTRY 2008; 10:986-91. [PMID: 18950231 DOI: 10.1021/cc8001298] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The preparation and application of new solid supports with chiral linkers, analogues of SAMP hydrazine on solid-phase, are described. The supports were used for immobilization of ketones (diethylketone, cyclohexanone, 4- tert-butylcyclohexanone), and diastereoselective alkylation of formed chiral ketone hydrazones. The enantiomeric purities of cleaved alpha-alkylated chiral ketones ranged from 10 to 73%. The use of chiral lithium amides for metalation of hydrazones of t-butylcyclohexanone increased the enantiomeric excess of the alkylated product by 25-47%.
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Affiliation(s)
- Ryszard Lazny
- Institute of Chemistry, University of Bialystok, ul. Hurtowa 1, 15-399 Bialystok, Poland.
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10
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Jung N, Wiehn M, Bräse S. Multifunctional Linkers for Combinatorial Solid Phase Synthesis. Top Curr Chem (Cham) 2007. [DOI: 10.1007/128_2007_118] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
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11
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Sexton KB, Witte MD, Blum G, Bogyo M. Design of cell-permeable, fluorescent activity-based probes for the lysosomal cysteine protease asparaginyl endopeptidase (AEP)/legumain. Bioorg Med Chem Lett 2006; 17:649-53. [PMID: 17189693 PMCID: PMC1832115 DOI: 10.1016/j.bmcl.2006.10.100] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2006] [Revised: 10/31/2006] [Accepted: 10/31/2006] [Indexed: 11/24/2022]
Abstract
Asparaginyl endopeptidase (AEP), also known as legumain, is a cysteine protease that has been ascribed roles in antigen presentation yet its exact role in human biology remains poorly understood. We report here, the use of a positional scanning combinatorial library of peptide AOMKs containing a P1 aspartic acid to probe the P2, P3, and P4 subsite specificity of endogenous legumain. Using inhibitor specificity profiles of cathepsin B and legumain, we designed fluorescent ABPs that are highly selective, cell-permeable reagents for monitoring legumain activity in complex proteomes.
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Affiliation(s)
- Kelly B Sexton
- Department of Pathology, Stanford University School of Medicine, 300 Pasteur Dr., Stanford, CA 940305, USA
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12
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Weik S, Luksch T, Evers A, Böttcher J, Sotriffer CA, Hasilik A, Löffler HG, Klebe G, Rademann J. The potential of P1 site alterations in peptidomimetic protease inhibitors as suggested by virtual screening and explored by the use of C-C-coupling reagents. ChemMedChem 2006; 1:445-57. [PMID: 16892380 DOI: 10.1002/cmdc.200500027] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
A synthetic concept is presented that allows the construction of peptide isostere libraries through polymer-supported C-acylation reactions. A phosphorane linker reagent is used as a carbanion equivalent; by employing MSNT as a coupling reagent, the C-acylation can be conducted without racemization. Diastereoselective reduction was effected with L-selectride. The reagent linker allows the preparation of a norstatine library with full variation of the isosteric positions including the P1 side chain that addresses the protease S1 pocket. Therefore, the concept was employed to investigate the P1 site specificity of peptide isostere inhibitors systematically. The S1 pocket of several aspartic proteases including plasmepsin II and cathepsin D was modeled and docked with approximately 500 amino acid side chains. Inspired by this virtual screen, a P1 site mutation library was designed, synthesized, and screened against three aspartic proteases (plasmepsin II, HIV protease, and cathepsin D). The potency of norstatine inhibitors was found to depend strongly on the P1 substituent. Large, hydrophobic residues such as biphenyl, 4-bromophenyl, and 4-nitrophenyl enhanced the inhibitory activity (IC50) by up to 70-fold against plasmepsin II. In addition, P1 variation introduced significant selectivity, as up to 9-fold greater activity was found against plasmepsin II relative to human cathepsin D. The active P1 site residues did not fit into the crystal structure; however, molecular dynamics simulation suggested a possible alternative binding mode.
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Affiliation(s)
- Steffen Weik
- Leibniz Institute for Molecular Pharmacology (FMP), and Free University Berlin, Takustrasse 3, 14195 Berlin, Germany
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13
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Berger AB, Witte MD, Denault JB, Sadaghiani AM, Sexton KMB, Salvesen GS, Bogyo M. Identification of Early Intermediates of Caspase Activation Using Selective Inhibitors and Activity-Based Probes. Mol Cell 2006; 23:509-21. [PMID: 16916639 DOI: 10.1016/j.molcel.2006.06.021] [Citation(s) in RCA: 103] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2006] [Revised: 06/05/2006] [Accepted: 06/13/2006] [Indexed: 12/28/2022]
Abstract
Caspases are cysteine proteases that are key effectors in apoptotic cell death. Currently, there is a lack of tools that can be used to monitor the regulation of specific caspases in the context of distinct apoptotic programs. We describe the development of highly selective inhibitors and active site probes and their applications to directly monitor executioner (caspase-3 and -7) and initiator (caspase-8 and -9) caspase activity. Specifically, these reagents were used to dissect the kinetics of caspase activation upon stimulation of apoptosis in cell-free extracts and intact cells. These studies identified a full-length caspase-7 intermediate that becomes catalytically activated early in the pathway and whose further processing is mediated by mature executioner caspases rather than initiator caspases. This form also shows distinct inhibitor sensitivity compared to processed caspase-7. Our data suggest that caspase-7 activation proceeds through a previously uncharacterized intermediate that is formed without cleavage of the intact zymogen.
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Affiliation(s)
- Alicia B Berger
- Department of Pathology, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, California 94305, USA
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14
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Vázquez J, Albericio F. A convenient semicarbazide resin for the solid-phase synthesis of peptide ketones and aldehydes. Tetrahedron Lett 2006. [DOI: 10.1016/j.tetlet.2005.12.101] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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15
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Lazny R, Nodzewska A, Sienkiewicz M, Wolosewicz K. Strategy for the synthesis of polymeric supports with hydrazone linkers for solid-phase alkylation of ketones and aldehydes. ACTA ACUST UNITED AC 2006; 7:109-16. [PMID: 15638489 DOI: 10.1021/cc049874y] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A new approach to polymeric supports useful for the immobilization of aldehydes and ketones via hydrazone linkers is reported. The new strategy gives supports with better properties and is effective for the synthesis of all supports previously used for the alkylation of ketones anchored as hydrazones. In contrast to other approaches, the new strategy also provided a polymer with an economical C2 spacer linker. The supports were used for immobilization of ketones 3-pentanone, acetone, N-benzylpiperidone, and aldehydes hexanal and 3-phenylpropanal in the form of their hydrazones. The polymer-supported hydrazones were subjected to alpha-alkylation (LDA/RX) followed by acidic, reductive, or oxidative cleavage/workup procedures to provide alpha-alkylated aldehydes or ketones as well as corresponding primary amines, alcohols, nitriles or acids.
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Affiliation(s)
- Ryszard Lazny
- Institute of Chemistry, University of Bialystok, Al. Pilsudskiego 11/4, 15-443 Bialystok, Poland.
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16
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A new and direct approach to functionalized biaryl α-ketophosphonic acids via aqueous Suzuki coupling on solid support. Tetrahedron Lett 2006. [DOI: 10.1016/j.tetlet.2005.10.122] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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17
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Kato D, Boatright KM, Berger AB, Nazif T, Blum G, Ryan C, Chehade KAH, Salvesen GS, Bogyo M. Activity-based probes that target diverse cysteine protease families. Nat Chem Biol 2005; 1:33-8. [PMID: 16407991 DOI: 10.1038/nchembio707] [Citation(s) in RCA: 284] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2005] [Accepted: 04/19/2005] [Indexed: 11/09/2022]
Abstract
Proteases are one of the largest and best-characterized families of enzymes in the human proteome. Unfortunately, the understanding of protease function in the context of complex proteolytic cascades remains in its infancy. One major reason for this gap in understanding is the lack of technologies that allow direct assessment of protease activity. We report here an optimized solid-phase synthesis protocol that allows rapid generation of activity-based probes (ABPs) targeting a range of cysteine protease families. These reagents selectively form covalent bonds with the active-site thiol of a cysteine protease, allowing direct biochemical profiling of protease activities in complex proteomes. We present a number of probes containing either a single amino acid or an extended peptide sequence that target caspases, legumains, gingipains and cathepsins. Biochemical studies using these reagents highlight their overall utility and provide insight into the biochemical functions of members of these protease families.
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Affiliation(s)
- Daisuke Kato
- Department of Pathology, Stanford University School of Medicine, 300 Pasteur Dr., Stanford, California, USA
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18
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Lai JYQ, Langston S, Adams R, Beevers RE, Boyce R, Burckhardt S, Cobb J, Ferguson Y, Figueroa E, Grimster N, Henry AH, Khan N, Jenkins K, Jones MW, Judkins R, Major J, Masood A, Nally J, Payne H, Payne L, Raphy G, Raynham T, Reader J, Reader V, Reid A, Ruprah P, Shaw M, Sore H, Stirling M, Talbot A, Taylor J, Thompson S, Wada H, Walker D. Preparation of kinase-biased compounds in the search for lead inhibitors of kinase targets. Med Res Rev 2005; 25:310-30. [PMID: 15593285 DOI: 10.1002/med.20026] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
This work describes the preparation of approximately 13,000 compounds for rapid identification of hits in high-throughput screening (HTS). These compounds were designed as potential serine/threonine or tyrosine kinase inhibitors. The library consists of various scaffolds, e.g., purines, oxindoles, and imidazoles, whereby each core scaffold generally includes the hydrogen bond acceptor/donor properties known to be important for kinase binding. Several of these are based upon literature kinase templates, or adaptations of them to provide novelty. The routes to their preparation are outlined. A variety of automation techniques were used to prepare >500 compounds per scaffold. Where applicable, scavenger resins were employed to remove excess reagents and when necessary, preparative high performance liquid chromatography (HPLC) was used for purification. These compounds were screened against an 'in-house' kinase panel. The success rate in HTS was significantly higher than the corporate compound collection.
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Affiliation(s)
- Justine Y Q Lai
- Millennium Pharmaceuticals R&D Limited, Granta Park, Great Abington, Cambridge CB1 6ET, United Kingdom
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19
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Grimm EL, Roy B, Aspiotis R, Bayly CI, Nicholson DW, Rasper DM, Renaud J, Roy S, Tam J, Tawa P, Vaillancourt JP, Xanthoudakis S, Zamboni RJ. Solid phase synthesis of selective caspase-3 peptide inhibitors. Bioorg Med Chem 2004; 12:845-51. [PMID: 14980595 DOI: 10.1016/j.bmc.2004.01.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2003] [Revised: 12/23/2003] [Accepted: 01/10/2004] [Indexed: 01/15/2023]
Abstract
A robust method for the solid phase synthesis of a series of selective caspase-3 peptide inhibitors is described. The inhibitors can be obtained after cleavage from the solid support without further purification.
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Affiliation(s)
- Erich L Grimm
- Merck Frosst Centre for Therapeutic Research, Merck Frosst Canada & Co. PO Box 1005, Pointe-Claire-Dorval, Québec, Canada H9R 4P8.
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20
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Arkin MR, Wells JA. Small-molecule inhibitors of protein-protein interactions: progressing towards the dream. Nat Rev Drug Discov 2004; 3:301-17. [PMID: 15060526 DOI: 10.1038/nrd1343] [Citation(s) in RCA: 1212] [Impact Index Per Article: 60.6] [Reference Citation Analysis] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Michelle R Arkin
- Sunesis Pharmaceuticals, 341 Oyster Point Boulevard, South San Francisco, California 94080, USA.
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21
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Oh BH, Nakamura I, Yamamoto Y. Palladium-Catalyzed Ring-Opening Reaction of Methyleneaziridines with Carboxylic Acids: Synthesis of α-Amidoketones. J Org Chem 2004; 69:2856-8. [PMID: 15074939 DOI: 10.1021/jo035739g] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In the presence of palladium catalysts, the reaction of methyleneaziridines 1 with carboxylic acids 2proceeded smoothly to give the corresponding alpha-amidoketones 3 in good to high yields.
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Affiliation(s)
- Byoung Ho Oh
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-8578, Japan
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22
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Han Y, Giroux A, Grimm EL, Aspiotis R, Francoeur S, Bayly CI, Mckay DJ, Roy S, Xanthoudakis S, Vaillancourt JP, Rasper DM, Tam J, Tawa P, Thornberry NA, Paterson EP, Garcia-Calvo M, Becker JW, Rotonda J, Nicholson DW, Zamboni RJ. Discovery of novel aspartyl ketone dipeptides as potent and selective caspase-3 inhibitors. Bioorg Med Chem Lett 2004; 14:805-8. [PMID: 14741294 DOI: 10.1016/j.bmcl.2003.10.064] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
The discovery of a series of potent, selective and reversible dipeptidyl caspase-3 inhibitors are reported. The iterative discovery process of using combinatorial chemistry, parallel synthesis, moleculare modelling and structural biology will be discussed.
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Affiliation(s)
- Yongxin Han
- Department of Medicinal Chemistry, Merck Frosst Centre for Therapeutic Research, Merck Frosst Canada & Co, PO Box 1005, Pointe-Claire-Dorval, Québec, Canada H9R 4P8.
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23
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Abstract
Solid-phase synthesis of biomolecules, of which peptides are the principal example, is well established. However, synthetic peptides containing modifications at the carboxy termini are often desired because of their potential therapeutic properties. As a result, there is a necessity for effective solid-phase strategies for the preparation of peptides with C-terminal end groups other than the usual carboxylic acid and carboxamide functionalities. The present article primarily reviews literature reports on methods for solid-phase synthesis of C-terminal modified peptides. In addition, general information about biological activities and/or synthetic applications of each individual class of peptide is also provided.
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Affiliation(s)
- Jordi Alsina
- Department of Chemistry, Indiana University-Purdue University Indianapolis, 402 North Blackford Street, Indianapolis, IN 46202, USA.
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24
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Mikolajczyk J, Boatright KM, Stennicke HR, Nazif T, Potempa J, Bogyo M, Salvesen GS. Sequential autolytic processing activates the zymogen of Arg-gingipain. J Biol Chem 2003; 278:10458-64. [PMID: 12533545 DOI: 10.1074/jbc.m210564200] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Most proteases are synthesized as inactive precursors to protect the synthetic machinery of the cell and allow timing of activation. The mechanisms used to render latency are varied but tend to be conserved within protease families. Proteases belonging to the caspase family have a unique mechanism mediated by transitions of two surface loops, and on the basis of conservation of mechanism one would expect this to be preserved by caspase relatives. We have been able to express the full-length precursor of the Arg-specific caspase relative from the bacterium Porphyromonas gingivalis, Arg-gingipain-B, and we show that it contains N- and C-terminal extensions that render a low amount of latency, meaning that the zymogen is substantially active. Three sequential autolytic processing steps at the N and C terminus are required for full activity, and the N-propeptide may serve as an intramolecular chaperone rather than an inhibitory peptide. Each step in activation requires the previous step, and an affinity probe reveals that incremental activity enhancements are achieved in a stepwise manner.
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Abstract
In both solution and the solid phase, a variety of ketone oxime anions have been treated with 4-substituted-2-fluorobenzonitriles to give the corresponding nucleophilic aromatic substitution aryloxime adducts. Under aqueous acidic conditions, these adducts underwent cyclization to give the corresponding ketones. Suzuki and amide coupling reactions were also successfully performed on two resin-bound oximes followed by subsequent cyclorelease to give ketone product in good yields and purities. [reaction--see text]
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Affiliation(s)
- Salvatore D Lepore
- Eli Lilly and Company, Lilly Corporate Center, Indianapolis, IN 46285, USA.
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26
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Huang L, Brinen LS, Ellman JA. Crystal structures of reversible ketone-Based inhibitors of the cysteine protease cruzain. Bioorg Med Chem 2003; 11:21-9. [PMID: 12467703 DOI: 10.1016/s0968-0896(02)00427-3] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The crystal structures of two hydroxymethyl ketone inhibitors complexed to the cysteine protease cruzain have been determined at 1.1 and 1.2 A resolution, respectively. These high resolution crystal structures provide the first structures of non-covalent inhibitors bound to cruzain. A series of compounds were prepared and tested based upon the structures providing further insight into the key binding interactions.
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Affiliation(s)
- Lily Huang
- Center for New Directions in Organic Synthesis, Department of Chemistry, University of California, Berkeley 94720, USA
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27
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Parallel synthesis of 1,2,4-trisubstituted imidazoles via N-alkyl-N-(β-keto)amides using a carbazate linker. Tetrahedron Lett 2002. [DOI: 10.1016/s0040-4039(02)01810-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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28
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Tice CM, Michelotti EL, Mata EG, Nicolàs E, Garcia J, Albericio F. Solid phase synthesis of α-acylamino-α,α-disubstituted ketones. Tetrahedron Lett 2002. [DOI: 10.1016/s0040-4039(02)01803-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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29
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Abstract
Tens of thousands of proteins have been identified as a result of recent large scale genomic and proteomic efforts. With this large influx of new proteins, the formidable task of elucidating their function begins. However, this task becomes more manageable if proteins are divided into families based upon sequence homology, thereby allowing tools for their systematic study to be developed based upon their common structural and mechanistic characteristics. Combinatorial chemistry is ideally suited for the systematic study of protein families because a large amount of diversity can be readily displayed about a common scaffold designed to target a given protein family. Targeted combinatorial libraries have been particularly effective for the study of a ubiquitous family of proteins, the proteases. Substrate-specificity profiles of many proteases have been determined by using combinatorial libraries of appropriately labeled peptides. This specificity information been utilized to identify the physiological protein substrates of these enzymes and has facilitated inhibitor design efforts. Furthermore, combinatorial libraries of small molecules prepared with mechanism-based scaffolds have resulted in the identification of potent, small-molecule inhibitors of numerous proteases. Cell-permeable small-molecule inhibitors identified by these methods have served as powerful chemical tools to study protease function in vitro and in vivo and have served as leads for the development of therapeutic agents.
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Affiliation(s)
- Dustin J Maly
- Department of Chemistry, University of California, Berkeley, CA 94720-1460, USA
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30
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Ellman JA. Combinatorial methods to engineer small molecules for functional genomics. ERNST SCHERING RESEARCH FOUNDATION WORKSHOP 2001:183-204. [PMID: 11077609 DOI: 10.1007/978-3-662-04042-3_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- J A Ellman
- Department of Chemistry, University of California, Berkely 94720-1460, USA
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31
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32
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Abstract
Nowadays it is rare to find an issue of a major chemistry journal without at least one article on solid-phase synthesis. This is hardly surprising: the technique promises an end to arduous work-up procedures and the ability to facilitate the creation of vast libraries of compounds using combinatorial techniques. No longer is the technique only of interest to those involved in peptide synthesis: an enormous variety of product classes have now been prepared on and isolated from the solid phase. It is the "linker" which is the focus of this article. The linker's ultimate function is to release a product from the support into solution: it does this, without exception, with a chemical change to the product at the former linkage site. Some linkers, apparently, are "traceless". But what, in fact, is "tracelessness"? Twenty years ago, in a climate where cleavage of a linker resulted in formation of a polar carboxylic acid as the vestige of the support, the concept was attractive. Today the chemist is faced with a myriad of novel linkers which have the ability to release products bearing most major functionalities at the former linkage site and we will argue here that the term "traceless", although currently in widespread use, is meaningless. Instead, we propose a new categorization of linkers based on the functionality they release upon cleavage, and suggest a nomenclature to underpin this categorization. We anticipate that the article will also serve to highlight areas of linker technology in need of further research.
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Affiliation(s)
- Alex C. Comely
- Department of Chemistry King's College, London, Strand London, WC2R 2LS (UK)
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33
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Terrett N. Combinatorial chemistry. Drug Discov Today 2000; 5:211-212. [PMID: 10790266 DOI: 10.1016/s1359-6446(00)01490-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- N Terrett
- Discovery Chemistry, Pfizer Central Research, Sandwich, Kent, UK
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