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Ramos-Llorca A, Decraecker L, Cacheux VMY, Zeiburlina I, De bruyn M, Battut L, Moreno-Cinos C, Ceradini D, Espinosa E, Dietrich G, Berg M, De Meester I, Van Der Veken P, Boeckxstaens G, Lambeir AM, Denadai-Souza A, Augustyns K. Chemically diverse activity-based probes with unexpected inhibitory mechanisms targeting trypsin-like serine proteases. Front Chem 2023; 10:1089959. [PMID: 36688031 PMCID: PMC9849758 DOI: 10.3389/fchem.2022.1089959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 12/19/2022] [Indexed: 01/07/2023] Open
Abstract
Activity-based probes (ABP) are molecules that bind covalently to the active form of an enzyme family, making them an attractive tool for target and biomarker identification and drug discovery. The present study describes the synthesis and biochemical characterization of novel activity-based probes targeting trypsin-like serine proteases. We developed an extensive library of activity-based probes with "clickable" affinity tags and a diaryl phosphonate warhead. A wide diversity was achieved by including natural amino acid analogs as well as basic polar residues as side chains. A detailed enzymatic characterization was performed in a panel of trypsin-like serine proteases. Their inhibitory potencies and kinetic profile were examined, and their IC50 values, mechanism of inhibition, and kinetic constants were determined. The activity-based probes with a benzyl guanidine side chain showed the highest inhibitory effects in the panel. Surprisingly, some of the high-affinity probes presented a reversible inhibitory mechanism. On the other hand, probes with different side chains exhibited the expected irreversible mechanism. For the first time, we demonstrate that not only irreversible probes but also reversible probes can tightly label recombinant proteases and proteases released from human mast cells. Even under denaturing SDS-PAGE conditions, reversible slow-tight-binding probes can label proteases due to the formation of high-affinity complexes and slow dissociation rates. This unexpected finding will transform the view on the required irreversible nature of activity-based probes. The diversity of this library of activity-based probes combined with a detailed enzyme kinetic characterization will advance their applications in proteomic studies and drug discovery.
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Affiliation(s)
- Alba Ramos-Llorca
- Laboratory of Medicinal Chemistry, Department of Pharmaceutical Sciences, Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, University of Antwerp, Antwerp, Belgium
| | - Lisse Decraecker
- Laboratory for Intestinal Neuroimmune Interactions, Translational Research Center for Gastrointestinal Disorders, Department of Chronic Diseases, Metabolism and Ageing, KU Leuven, Leuven, Belgium
| | - Valérie M. Y. Cacheux
- Laboratory of Medicinal Chemistry, Department of Pharmaceutical Sciences, Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, University of Antwerp, Antwerp, Belgium
| | - Irena Zeiburlina
- Laboratory for Intestinal Neuroimmune Interactions, Translational Research Center for Gastrointestinal Disorders, Department of Chronic Diseases, Metabolism and Ageing, KU Leuven, Leuven, Belgium
| | - Michelle De bruyn
- Laboratory of Medical Biochemistry, Department of Pharmaceutical Sciences, Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, University of Antwerp, Antwerp, Belgium
| | - Louise Battut
- IRSD, Université de Toulouse, INSERM, INRA, ENVT, UPS, Toulouse, France
| | - Carlos Moreno-Cinos
- Laboratory of Medicinal Chemistry, Department of Pharmaceutical Sciences, Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, University of Antwerp, Antwerp, Belgium
| | | | - Eric Espinosa
- IRSD, Université de Toulouse, INSERM, INRA, ENVT, UPS, Toulouse, France
| | - Gilles Dietrich
- IRSD, Université de Toulouse, INSERM, INRA, ENVT, UPS, Toulouse, France
| | - Maya Berg
- Laboratory of Medicinal Chemistry, Department of Pharmaceutical Sciences, Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, University of Antwerp, Antwerp, Belgium
| | - Ingrid De Meester
- Laboratory of Medical Biochemistry, Department of Pharmaceutical Sciences, Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, University of Antwerp, Antwerp, Belgium
| | - Pieter Van Der Veken
- Laboratory of Medicinal Chemistry, Department of Pharmaceutical Sciences, Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, University of Antwerp, Antwerp, Belgium
| | - Guy Boeckxstaens
- Laboratory for Intestinal Neuroimmune Interactions, Translational Research Center for Gastrointestinal Disorders, Department of Chronic Diseases, Metabolism and Ageing, KU Leuven, Leuven, Belgium
| | - Anne-Marie Lambeir
- Laboratory of Medical Biochemistry, Department of Pharmaceutical Sciences, Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, University of Antwerp, Antwerp, Belgium
| | - Alexandre Denadai-Souza
- Laboratory for Intestinal Neuroimmune Interactions, Translational Research Center for Gastrointestinal Disorders, Department of Chronic Diseases, Metabolism and Ageing, KU Leuven, Leuven, Belgium
| | - Koen Augustyns
- Laboratory of Medicinal Chemistry, Department of Pharmaceutical Sciences, Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, University of Antwerp, Antwerp, Belgium
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Kumar G, Narayan R, Kapoor S. Chemical Tools for Illumination of Tuberculosis Biology, Virulence Mechanisms, and Diagnosis. J Med Chem 2020; 63:15308-15332. [PMID: 33307693 DOI: 10.1021/acs.jmedchem.0c01337] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Tuberculosis (TB) remains one of the deadliest infectious diseases and begs the scientific community to up the ante for research and exploration of completely novel therapeutic avenues. Chemical biology-inspired design of tunable chemical tools has aided in clinical diagnosis, facilitated discovery of therapeutics, and begun to enable investigation of virulence mechanisms at the host-pathogen interface of Mycobacterium tuberculosis. This Perspective highlights chemical tools specific to mycobacterial proteins and the cell lipid envelope that have furnished rapid and selective diagnostic strategies and provided unprecedented insights into the function of the mycobacterial proteome and lipidome. We discuss chemical tools that have enabled elucidating otherwise intractable biological processes by leveraging the unique lipid and metabolite repertoire of mycobacterial species. Some of these probes represent exciting starting points with the potential to illuminate poorly understood aspects of mycobacterial pathogenesis, particularly the host membrane-pathogen interactions.
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Affiliation(s)
- Gautam Kumar
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400 076, Maharashtra, India
| | - Rishikesh Narayan
- School of Chemical and Materials Sciences, Indian Institute of Technology Goa, Ponda 403 401, Goa, India
| | - Shobhna Kapoor
- Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400 076, Maharashtra, India.,Wadhwani Research Center for Bioengineering, Indian Institute of Technology Bombay, Mumbai 400 076, Maharashtra, India
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Marto J, Ruivo E, Lucas SD, Gonçalves LM, Simões S, Gouveia LF, Felix R, Moreira R, Ribeiro HM, Almeida AJ. Starch nanocapsules containing a novel neutrophil elastase inhibitor with improved pharmaceutical performance. Eur J Pharm Biopharm 2018; 127:1-11. [PMID: 29409864 DOI: 10.1016/j.ejpb.2018.01.011] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Revised: 01/07/2018] [Accepted: 01/17/2018] [Indexed: 12/22/2022]
Abstract
Psoriasis and atopic dermatitis patients show an excessive amount of elastase in peripheral blood neutrophils due to an imbalance between this proteolytic enzyme and its endogenous inhibitors, the search for new human neutrophil elastase (HNE) inhibitors are required. The HNE is an attractive therapeutic target and inhibitors with new molecular architectures have been extensively investigated. In this context a promising novel synthetic human neutrophil elastase inhibitor (ER143) was associated to a starch-based nanoparticulate system (StNC) with improved pharmaceutical performance, using a quality by design approach to support product development and optimization. The resulting formulation was characterized in terms of and in vitro release, permeation and retention studies in newborn pig skin, using Franz diffusion cells revealing the StNC have the ability to control the drug release rate and contribute to a high skin retention and/or permeation profiles. The anti-inflammatory activity accessed in vivo using the croton oil-induced ear inflammation model in mice showed that erythema and edema were attenuated in 98% following local application. These observations suggest the association of ER143 to the StNC promotes a deeper skin penetration and retention, also confirming StNC as a potential topical delivery system.
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Affiliation(s)
- J Marto
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Portugal
| | - E Ruivo
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Portugal
| | - S D Lucas
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Portugal
| | - L M Gonçalves
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Portugal
| | - S Simões
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Portugal
| | - L F Gouveia
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Portugal
| | - R Felix
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Portugal
| | - R Moreira
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Portugal.
| | - H M Ribeiro
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Portugal
| | - A J Almeida
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Portugal.
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Jones LH, Neubert H. Clinical chemoproteomics-Opportunities and obstacles. Sci Transl Med 2017; 9:9/386/eaaf7951. [PMID: 28424333 DOI: 10.1126/scitranslmed.aaf7951] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Accepted: 03/06/2017] [Indexed: 12/19/2022]
Abstract
Chemoproteomics is the large-scale study of proteins using chemical methods. Although chemoproteomic techniques are becoming commonplace in preclinical research, few examples have found clinical utility. We explore the prospects for advancing chemoproteomics into the clinical setting to understand drug-target interactions and to identify new therapeutically relevant targets.
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Affiliation(s)
- Lyn H Jones
- Medicine Design, Pfizer, 610 Main Street, Cambridge, MA 02139, USA.
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Ruivo EFP, Gonçalves LM, Carvalho LAR, Guedes RC, Hofbauer S, Brito JA, Archer M, Moreira R, Lucas SD. Clickable 4-Oxo-β-lactam-Based Selective Probing for Human Neutrophil Elastase Related Proteomes. ChemMedChem 2016; 11:2037-42. [DOI: 10.1002/cmdc.201600258] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Revised: 06/28/2016] [Indexed: 01/09/2023]
Affiliation(s)
- Eduardo F. P. Ruivo
- Research Institute for Medicines (iMed.ULisboa); Faculty of Pharmacy; Universidade de Lisboa; Av. Prof. Gama Pinto 1649-003 Lisbon Portugal
| | - Lídia M. Gonçalves
- Research Institute for Medicines (iMed.ULisboa); Faculty of Pharmacy; Universidade de Lisboa; Av. Prof. Gama Pinto 1649-003 Lisbon Portugal
| | - Luís A. R. Carvalho
- Research Institute for Medicines (iMed.ULisboa); Faculty of Pharmacy; Universidade de Lisboa; Av. Prof. Gama Pinto 1649-003 Lisbon Portugal
| | - Rita C. Guedes
- Research Institute for Medicines (iMed.ULisboa); Faculty of Pharmacy; Universidade de Lisboa; Av. Prof. Gama Pinto 1649-003 Lisbon Portugal
| | - Stefan Hofbauer
- Instituto de Tecnologia Química e Biológica-António Xavier; Universidade Nova de Lisboa; Avenida da República 2780-157 Oeiras Portugal
- Department for Structural and Computational Biology; Max F. Perutz Laboratories; University of Vienna; 1030 Vienna Austria
| | - José A. Brito
- Instituto de Tecnologia Química e Biológica-António Xavier; Universidade Nova de Lisboa; Avenida da República 2780-157 Oeiras Portugal
| | - Margarida Archer
- Instituto de Tecnologia Química e Biológica-António Xavier; Universidade Nova de Lisboa; Avenida da República 2780-157 Oeiras Portugal
| | - Rui Moreira
- Research Institute for Medicines (iMed.ULisboa); Faculty of Pharmacy; Universidade de Lisboa; Av. Prof. Gama Pinto 1649-003 Lisbon Portugal
| | - Susana D. Lucas
- Research Institute for Medicines (iMed.ULisboa); Faculty of Pharmacy; Universidade de Lisboa; Av. Prof. Gama Pinto 1649-003 Lisbon Portugal
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Chen B, Ge SS, Zhao YC, Chen C, Yang S. Activity-based protein profiling: an efficient approach to study serine hydrolases and their inhibitors in mammals and microbes. RSC Adv 2016. [DOI: 10.1039/c6ra20006k] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
This review focuses on the identification of serine hydrolases and their inhibitors in mammals and microbes with activity-based protein profiling (ABPP).
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Affiliation(s)
- Biao Chen
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering
- Key Laboratory of Green Pesticide and Agricultural Bioengineering
- Ministry of Education
- Center for R&D of Fine Chemicals of Guizhou University
- Guiyang
| | - Sha-Sha Ge
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering
- Key Laboratory of Green Pesticide and Agricultural Bioengineering
- Ministry of Education
- Center for R&D of Fine Chemicals of Guizhou University
- Guiyang
| | - Yuan-Chao Zhao
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering
- Key Laboratory of Green Pesticide and Agricultural Bioengineering
- Ministry of Education
- Center for R&D of Fine Chemicals of Guizhou University
- Guiyang
| | - Chong Chen
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering
- Key Laboratory of Green Pesticide and Agricultural Bioengineering
- Ministry of Education
- Center for R&D of Fine Chemicals of Guizhou University
- Guiyang
| | - Song Yang
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering
- Key Laboratory of Green Pesticide and Agricultural Bioengineering
- Ministry of Education
- Center for R&D of Fine Chemicals of Guizhou University
- Guiyang
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