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Grams RJ, Santos WL, Scorei IR, Abad-García A, Rosenblum CA, Bita A, Cerecetto H, Viñas C, Soriano-Ursúa MA. The Rise of Boron-Containing Compounds: Advancements in Synthesis, Medicinal Chemistry, and Emerging Pharmacology. Chem Rev 2024; 124:2441-2511. [PMID: 38382032 DOI: 10.1021/acs.chemrev.3c00663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2024]
Abstract
Boron-containing compounds (BCC) have emerged as important pharmacophores. To date, five BCC drugs (including boronic acids and boroles) have been approved by the FDA for the treatment of cancer, infections, and atopic dermatitis, while some natural BCC are included in dietary supplements. Boron's Lewis acidity facilitates a mechanism of action via formation of reversible covalent bonds within the active site of target proteins. Boron has also been employed in the development of fluorophores, such as BODIPY for imaging, and in carboranes that are potential neutron capture therapy agents as well as novel agents in diagnostics and therapy. The utility of natural and synthetic BCC has become multifaceted, and the breadth of their applications continues to expand. This review covers the many uses and targets of boron in medicinal chemistry.
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Affiliation(s)
- R Justin Grams
- Department of Chemistry and Virginia Tech Center for Drug Discovery, Virginia Tech, 900 West Campus Drive, Blacksburg, Virginia 24061, United States
| | - Webster L Santos
- Department of Chemistry and Virginia Tech Center for Drug Discovery, Virginia Tech, 900 West Campus Drive, Blacksburg, Virginia 24061, United States
| | | | - Antonio Abad-García
- Academia de Fisiología y Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina del Instituto Politécnico Nacional, Plan de San Luis y Díaz Mirón s/n, 11340 Mexico City, Mexico
| | - Carol Ann Rosenblum
- Department of Chemistry and Virginia Tech Center for Drug Discovery, Virginia Tech, 900 West Campus Drive, Blacksburg, Virginia 24061, United States
| | - Andrei Bita
- Department of Pharmacognosy & Phytotherapy, Faculty of Pharmacy, University of Medicine and Pharmacy of Craiova, 2 Petru Rareş Street, 200349 Craiova, Romania
| | - Hugo Cerecetto
- Centro de Investigaciones Nucleares, Facultad de Ciencias, Universidad de la República, Mataojo 2055, 11400 Montevideo, Uruguay
| | - Clara Viñas
- Institut de Ciència de Materials de Barcelona (ICMAB-CSIC), Campus UAB, 08193 Bellaterra, Spain
| | - Marvin A Soriano-Ursúa
- Academia de Fisiología y Sección de Estudios de Posgrado e Investigación, Escuela Superior de Medicina del Instituto Politécnico Nacional, Plan de San Luis y Díaz Mirón s/n, 11340 Mexico City, Mexico
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2
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Giardina SF, Werner DS, Pingle M, Feinberg PB, Foreman KW, Bergstrom DE, Arnold LD, Barany F. Novel, Self-Assembling Dimeric Inhibitors of Human β Tryptase. J Med Chem 2020; 63:3004-3027. [PMID: 32057241 DOI: 10.1021/acs.jmedchem.9b01689] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
β-Tryptase, a homotetrameric serine protease, has four identical active sites facing a central pore, presenting an optimized setting for the rational design of bivalent inhibitors that bridge two adjacent sites. Using diol, hydroxymethyl phenols or benzoyl methyl hydroxamates, and boronic acid chemistries to reversibly join two [3-(1-acylpiperidin-4-yl)phenyl]methanamine core ligands, we have successfully produced a series of self-assembling heterodimeric inhibitors. These heterodimeric tryptase inhibitors demonstrate superior activity compared to monomeric modes of inhibition. X-ray crystallography validated the dimeric mechanism of inhibition, and compounds demonstrated high selectivity against related proteases, good target engagement, and tryptase inhibition in HMC1 xenograft models. Screening 3872 possible combinations from 44 boronic acid and 88 diol derivatives revealed several combinations that produced nanomolar inhibition, and seven unique pairs produced greater than 100-fold improvement in potency over monomeric inhibition. These heterodimeric tryptase inhibitors demonstrate the power of target-driven combinatorial chemistry to deliver bivalent drugs in a small molecule form.
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Affiliation(s)
- Sarah F Giardina
- Department of Microbiology and Immunology, Weill Cornell Medicine, 1300 York Avenue, Box 62, New York, New York 10065, United States
| | - Douglas S Werner
- Coferon, Inc., 25 Health Sciences Drive, Mailbox 123, Stony Brook, New York 11790, United States
| | - Maneesh Pingle
- Department of Microbiology and Immunology, Weill Cornell Medicine, 1300 York Avenue, Box 62, New York, New York 10065, United States.,Coferon, Inc., 25 Health Sciences Drive, Mailbox 123, Stony Brook, New York 11790, United States
| | - Philip B Feinberg
- Department of Microbiology and Immunology, Weill Cornell Medicine, 1300 York Avenue, Box 62, New York, New York 10065, United States
| | - Kenneth W Foreman
- Coferon, Inc., 25 Health Sciences Drive, Mailbox 123, Stony Brook, New York 11790, United States
| | - Donald E Bergstrom
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, 575 Stadium Mall, West Lafa-yette, Indiana 47907, United States
| | - Lee D Arnold
- Coferon, Inc., 25 Health Sciences Drive, Mailbox 123, Stony Brook, New York 11790, United States
| | - Francis Barany
- Department of Microbiology and Immunology, Weill Cornell Medicine, 1300 York Avenue, Box 62, New York, New York 10065, United States
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3
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Pejler G. The emerging role of mast cell proteases in asthma. Eur Respir J 2019; 54:13993003.00685-2019. [PMID: 31371445 DOI: 10.1183/13993003.00685-2019] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Accepted: 07/23/2019] [Indexed: 12/31/2022]
Abstract
It is now well established that mast cells (MCs) play a crucial role in asthma. This is supported by multiple lines of evidence, including both clinical studies and studies on MC-deficient mice. However, there is still only limited knowledge of the exact effector mechanism(s) by which MCs influence asthma pathology. MCs contain large amounts of secretory granules, which are filled with a variety of bioactive compounds including histamine, cytokines, lysosomal hydrolases, serglycin proteoglycans and a number of MC-restricted proteases. When MCs are activated, e.g. in response to IgE receptor cross-linking, the contents of their granules are released to the exterior and can cause a massive inflammatory reaction. The MC-restricted proteases include tryptases, chymases and carboxypeptidase A3, and these are expressed and stored at remarkably high levels. There is now emerging evidence supporting a prominent role of these enzymes in the pathology of asthma. Interestingly, however, the role of the MC-restricted proteases is multifaceted, encompassing both protective and detrimental activities. Here, the current knowledge of how the MC-restricted proteases impact on asthma is reviewed.
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Affiliation(s)
- Gunnar Pejler
- Dept of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden .,Dept of Anatomy, Physiology and Biochemistry, Swedish University of Agricultural Sciences, Uppsala, Sweden
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4
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Compain P. Multivalent Effect in Glycosidase Inhibition: The End of the Beginning. CHEM REC 2019; 20:10-22. [PMID: 30993894 DOI: 10.1002/tcr.201900004] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 03/15/2019] [Indexed: 12/21/2022]
Abstract
Glycosidases are ubiquitous enzymes involved in a diversity of key biological processes such as energy uptake or cell wall degradation. The design of specific glycosidase inhibitors has been therefore the subject of intense research efforts in academia and pharmaceutical industry. However, until recently, the study of the impact of multivalency on glycosidase inhibition was almost completely neglected. The following account will review our ten year journey on the design of multivalent glycomimetics within our research group, from the discovery of the first strong multivalent effect in glycosidase inhibition to the high-resolution crystal structures of Jack bean α-mannosidase in complex with the multimeric inhibitor displaying the largest binding enhancements reported so far.
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Affiliation(s)
- Philippe Compain
- Laboratoire d'Innovation Moléculaire et Applications (LIMA), Univ. de Strasbourg, Univ. de Haute-Alsace, CNRS (UMR 7042), Equipe de Synthèse Organique et Molécules Bioactives (SYBIO), ECPM, 25 Rue Becquerel, 67000, Strasbourg, France
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5
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Dal Corso A, Catalano M, Schmid A, Scheuermann J, Neri D. Affinity Enhancement of Protein Ligands by Reversible Covalent Modification of Neighboring Lysine Residues. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201811650] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Alberto Dal Corso
- Department of Chemistry and Applied Biosciences Swiss Federal Institute of Technology (ETH Zürich) Vladimir-Prelog-Weg 4 8093 Zurich Switzerland
| | - Marco Catalano
- Department of Chemistry and Applied Biosciences Swiss Federal Institute of Technology (ETH Zürich) Vladimir-Prelog-Weg 4 8093 Zurich Switzerland
| | - Anja Schmid
- Department of Chemistry and Applied Biosciences Swiss Federal Institute of Technology (ETH Zürich) Vladimir-Prelog-Weg 4 8093 Zurich Switzerland
| | - Jörg Scheuermann
- Department of Chemistry and Applied Biosciences Swiss Federal Institute of Technology (ETH Zürich) Vladimir-Prelog-Weg 4 8093 Zurich Switzerland
| | - Dario Neri
- Department of Chemistry and Applied Biosciences Swiss Federal Institute of Technology (ETH Zürich) Vladimir-Prelog-Weg 4 8093 Zurich Switzerland
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6
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Dal Corso A, Catalano M, Schmid A, Scheuermann J, Neri D. Affinity Enhancement of Protein Ligands by Reversible Covalent Modification of Neighboring Lysine Residues. Angew Chem Int Ed Engl 2018; 57:17178-17182. [DOI: 10.1002/anie.201811650] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Indexed: 01/18/2023]
Affiliation(s)
- Alberto Dal Corso
- Department of Chemistry and Applied Biosciences Swiss Federal Institute of Technology (ETH Zürich) Vladimir-Prelog-Weg 4 8093 Zurich Switzerland
| | - Marco Catalano
- Department of Chemistry and Applied Biosciences Swiss Federal Institute of Technology (ETH Zürich) Vladimir-Prelog-Weg 4 8093 Zurich Switzerland
| | - Anja Schmid
- Department of Chemistry and Applied Biosciences Swiss Federal Institute of Technology (ETH Zürich) Vladimir-Prelog-Weg 4 8093 Zurich Switzerland
| | - Jörg Scheuermann
- Department of Chemistry and Applied Biosciences Swiss Federal Institute of Technology (ETH Zürich) Vladimir-Prelog-Weg 4 8093 Zurich Switzerland
| | - Dario Neri
- Department of Chemistry and Applied Biosciences Swiss Federal Institute of Technology (ETH Zürich) Vladimir-Prelog-Weg 4 8093 Zurich Switzerland
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7
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Anderson E, Stavenhagen K, Kolarich D, Sommerhoff CP, Maurer M, Metz M. Human Mast Cell Tryptase Is a Potential Treatment for Snakebite Envenoming Across Multiple Snake Species. Front Immunol 2018; 9:1532. [PMID: 30038613 PMCID: PMC6047305 DOI: 10.3389/fimmu.2018.01532] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Accepted: 06/20/2018] [Indexed: 12/16/2022] Open
Abstract
Snake envenoming is a serious and neglected public health crisis that is responsible for as many as 125,000 deaths per year, which is one of the reasons the World Health Organization has recently reinstated snakebite envenoming to its list of category A neglected tropical diseases. Here, we investigated the ability of human mast cell proteases to detoxify six venoms from a spectrum of phylogenetically distinct snakes. To this end, we developed a zebrafish model to assess effects on the toxicity of the venoms and characterized the degradation of venom proteins by mass spectrometry. All snake venoms tested were detoxified by degradation of various venom proteins by the mast cell protease tryptase β, and not by other proteases. Our data show that recombinant human tryptase β degrades and detoxifies a phylogenetically wide range of venoms, indicating that recombinant human tryptase could possibly be developed as a universal antidote to venomous snakebites.
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Affiliation(s)
- Elizabeth Anderson
- Department of Dermatology and Allergy, Charité – Universitätsmedizin Berlin, Berlin, Germany
| | - Kathrin Stavenhagen
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Potsdam, Germany
| | - Daniel Kolarich
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Potsdam, Germany
| | - Christian P. Sommerhoff
- Institute of Laboratory Medicine, University Hospital, Ludwig-Maximilians-University, Munich, Germany
| | - Marcus Maurer
- Department of Dermatology and Allergy, Charité – Universitätsmedizin Berlin, Berlin, Germany
| | - Martin Metz
- Department of Dermatology and Allergy, Charité – Universitätsmedizin Berlin, Berlin, Germany
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8
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Lepage ML, Schneider JP, Bodlenner A, Meli A, De Riccardis F, Schmitt M, Tarnus C, Nguyen-Huynh NT, Francois YN, Leize-Wagner E, Birck C, Cousido-Siah A, Podjarny A, Izzo I, Compain P. Iminosugar-Cyclopeptoid Conjugates Raise Multivalent Effect in Glycosidase Inhibition at Unprecedented High Levels. Chemistry 2016; 22:5151-5. [DOI: 10.1002/chem.201600338] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Indexed: 12/20/2022]
Affiliation(s)
- Mathieu L. Lepage
- Laboratoire de Synthèse Organique et Molécules Bioactives Université de Strasbourg et CNRS (UMR 7509); Ecole Européenne de Chimie, Polymères et Matériaux; 25 rue Becquerel 67087 Strasbourg France
| | - Jérémy P. Schneider
- Laboratoire de Synthèse Organique et Molécules Bioactives Université de Strasbourg et CNRS (UMR 7509); Ecole Européenne de Chimie, Polymères et Matériaux; 25 rue Becquerel 67087 Strasbourg France
| | - Anne Bodlenner
- Laboratoire de Synthèse Organique et Molécules Bioactives Université de Strasbourg et CNRS (UMR 7509); Ecole Européenne de Chimie, Polymères et Matériaux; 25 rue Becquerel 67087 Strasbourg France
| | - Alessandra Meli
- Department of Chemistry and Biology; University of Salerno; Via Giovanni Paolo II,132 84084 Fisciano, Salerno Italy
| | - Francesco De Riccardis
- Department of Chemistry and Biology; University of Salerno; Via Giovanni Paolo II,132 84084 Fisciano, Salerno Italy
| | - Marjorie Schmitt
- Université de Haute Alsace; Laboratoire de Chimie Organique et Bioorganique (EA4466), ENSCMu; 3, rue Alfred Werner 68093 Mulhouse Cedex France
| | - Céline Tarnus
- Université de Haute Alsace; Laboratoire de Chimie Organique et Bioorganique (EA4466), ENSCMu; 3, rue Alfred Werner 68093 Mulhouse Cedex France
| | - Nha-Thi Nguyen-Huynh
- Laboratoire de Spectrométrie de Masse des Interactions et des Systèmes; UMR CNRS 7140; Université de Strasbourg; 67008 Strasbourg France
| | - Yannis-Nicolas Francois
- Laboratoire de Spectrométrie de Masse des Interactions et des Systèmes; UMR CNRS 7140; Université de Strasbourg; 67008 Strasbourg France
| | - Emmanuelle Leize-Wagner
- Laboratoire de Spectrométrie de Masse des Interactions et des Systèmes; UMR CNRS 7140; Université de Strasbourg; 67008 Strasbourg France
| | - Catherine Birck
- Structural Biology Platform, CBI-IGBMC; 1 rue Laurent Fries 67404 Illkirch France
| | - Alexandra Cousido-Siah
- Department of Integrative Biology; Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS, INSERM, UdS; 1 rue Laurent Fries 67404 Illkirch CEDEX France
| | - Alberto Podjarny
- Department of Integrative Biology; Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS, INSERM, UdS; 1 rue Laurent Fries 67404 Illkirch CEDEX France
| | - Irene Izzo
- Department of Chemistry and Biology; University of Salerno; Via Giovanni Paolo II,132 84084 Fisciano, Salerno Italy
| | - Philippe Compain
- Laboratoire de Synthèse Organique et Molécules Bioactives Université de Strasbourg et CNRS (UMR 7509); Ecole Européenne de Chimie, Polymères et Matériaux; 25 rue Becquerel 67087 Strasbourg France
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9
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Datta A, Kundu P, Bhunia A. Designing potent antimicrobial peptides by disulphide linked dimerization and N-terminal lipidation to increase antimicrobial activity and membrane perturbation: Structural insights into lipopolysaccharide binding. J Colloid Interface Sci 2016; 461:335-345. [DOI: 10.1016/j.jcis.2015.09.036] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2015] [Revised: 09/14/2015] [Accepted: 09/14/2015] [Indexed: 11/25/2022]
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10
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Böcker S, Laaf D, Elling L. Galectin Binding to Neo-Glycoproteins: LacDiNAc Conjugated BSA as Ligand for Human Galectin-3. Biomolecules 2015. [PMID: 26213980 PMCID: PMC4598770 DOI: 10.3390/biom5031671] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Carbohydrate-lectin interactions are relatively weak. As they play an important role in biological recognition processes, multivalent glycan ligands are designed to enhance binding affinity and inhibitory potency. We here report on novel neo-glycoproteins based on bovine serum albumin as scaffold for multivalent presentation of ligands for galectins. We prepared two kinds of tetrasaccharides (N-acetyllactosamine and N,N-diacetyllactosamine terminated) by multi-step chemo-enzymatic synthesis utilizing recombinant glycosyltransferases. Subsequent conjugation of these glycans to lysine groups of bovine serum albumin via squaric acid diethyl ester yielded a set of 22 different neo-glycoproteins with tuned ligand density. The neo-glycoproteins were analyzed by biochemical and chromatographic methods proving various modification degrees. The neo-glycoproteins were used for binding and inhibition studies with human galectin-3 showing high affinity. Binding strength and inhibition potency are closely related to modification density and show binding enhancement by multivalent ligand presentation. At galectin-3 concentrations comparable to serum levels of cancer patients, we detect the highest avidities. Selectivity of N,N-diacetyllactosamine terminated structures towards galectin-3 in comparison to galectin-1 is demonstrated. Moreover, we also see strong inhibitory potency of our scaffolds towards galectin-3 binding. These novel neo-glycoproteins may therefore serve as selective and strong galectin-3 ligands in cancer related biomedical research.
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Affiliation(s)
- Sophia Böcker
- Laboratory for Biomaterials, Institute for Biotechnology and Helmholtz-Institute for Biomedical Engineering, RWTH Aachen University, Pauwelsstr. 20, 52074 Aachen, Germany.
| | - Dominic Laaf
- Laboratory for Biomaterials, Institute for Biotechnology and Helmholtz-Institute for Biomedical Engineering, RWTH Aachen University, Pauwelsstr. 20, 52074 Aachen, Germany.
| | - Lothar Elling
- Laboratory for Biomaterials, Institute for Biotechnology and Helmholtz-Institute for Biomedical Engineering, RWTH Aachen University, Pauwelsstr. 20, 52074 Aachen, Germany.
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11
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Liese S, Netz RR. Influence of length and flexibility of spacers on the binding affinity of divalent ligands. Beilstein J Org Chem 2015; 11:804-16. [PMID: 26124882 PMCID: PMC4464470 DOI: 10.3762/bjoc.11.90] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Accepted: 04/29/2015] [Indexed: 11/23/2022] Open
Abstract
We present a quantitative model for the binding of divalent ligand–receptor systems. We study the influence of length and flexibility of the spacers on the overall binding affinity and derive general rules for the optimal ligand design. To this end, we first compare different polymeric models and determine the probability to simultaneously bind to two neighboring receptor binding pockets. In a second step the binding affinity of divalent ligands in terms of the IC50 value is derived. We find that a divalent ligand has the potential to bind more efficiently than its monovalent counterpart only, if the monovalent dissociation constant is lower than a critical value. This critical monovalent dissociation constant depends on the ligand-spacer length and flexibility as well as on the size of the receptor. Regarding the optimal ligand-spacer length and flexibility, we find that the average spacer length should be equal or slightly smaller than the distance between the receptor binding pockets and that the end-to-end spacer length fluctuations should be in the same range as the size of a receptor binding pocket.
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Affiliation(s)
- Susanne Liese
- Fachbereich für Physik, Freie Universität Berlin, 14195 Berlin, Germany
| | - Roland R Netz
- Fachbereich für Physik, Freie Universität Berlin, 14195 Berlin, Germany
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12
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Kanfar N, Bartolami E, Zelli R, Marra A, Winum JY, Ulrich S, Dumy P. Emerging trends in enzyme inhibition by multivalent nanoconstructs. Org Biomol Chem 2015; 13:9894-906. [DOI: 10.1039/c5ob01405k] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
This review highlights the recent implementation of multivalent nanoconstructs in enzyme inhibition and discusses the emerging trends in their design and identification.
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Affiliation(s)
- Nasreddine Kanfar
- Institut des Biomolécules Max Mousseron (IBMM)
- UMR 5247 CNRS
- Université Montpellier
- ENSCM
- Ecole Nationale Supérieure de Chimie de Montpellier
| | - Eline Bartolami
- Institut des Biomolécules Max Mousseron (IBMM)
- UMR 5247 CNRS
- Université Montpellier
- ENSCM
- Ecole Nationale Supérieure de Chimie de Montpellier
| | - Renaud Zelli
- Institut des Biomolécules Max Mousseron (IBMM)
- UMR 5247 CNRS
- Université Montpellier
- ENSCM
- Ecole Nationale Supérieure de Chimie de Montpellier
| | - Alberto Marra
- Institut des Biomolécules Max Mousseron (IBMM)
- UMR 5247 CNRS
- Université Montpellier
- ENSCM
- Ecole Nationale Supérieure de Chimie de Montpellier
| | - Jean-Yves Winum
- Institut des Biomolécules Max Mousseron (IBMM)
- UMR 5247 CNRS
- Université Montpellier
- ENSCM
- Ecole Nationale Supérieure de Chimie de Montpellier
| | - Sébastien Ulrich
- Institut des Biomolécules Max Mousseron (IBMM)
- UMR 5247 CNRS
- Université Montpellier
- ENSCM
- Ecole Nationale Supérieure de Chimie de Montpellier
| | - Pascal Dumy
- Institut des Biomolécules Max Mousseron (IBMM)
- UMR 5247 CNRS
- Université Montpellier
- ENSCM
- Ecole Nationale Supérieure de Chimie de Montpellier
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13
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Gouin SG. Multivalent Inhibitors for Carbohydrate-Processing Enzymes: Beyond the “Lock-and-Key” Concept. Chemistry 2014; 20:11616-28. [DOI: 10.1002/chem.201402537] [Citation(s) in RCA: 93] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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14
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Valdés JJ, Schwarz A, Cabeza de Vaca I, Calvo E, Pedra JHF, Guallar V, Kotsyfakis M. Tryptogalinin is a tick Kunitz serine protease inhibitor with a unique intrinsic disorder. PLoS One 2013; 8:e62562. [PMID: 23658744 PMCID: PMC3643938 DOI: 10.1371/journal.pone.0062562] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2013] [Accepted: 03/22/2013] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND A salivary proteome-transcriptome project on the hard tick Ixodes scapularis revealed that Kunitz peptides are the most abundant salivary proteins. Ticks use Kunitz peptides (among other salivary proteins) to combat host defense mechanisms and to obtain a blood meal. Most of these Kunitz peptides, however, remain functionally uncharacterized, thus limiting our knowledge about their biochemical interactions. RESULTS We discovered an unusual cysteine motif in a Kunitz peptide. This peptide inhibits several serine proteases with high affinity and was named tryptogalinin due to its high affinity for β-tryptase. Compared with other functionally described peptides from the Acari subclass, we showed that tryptogalinin is phylogenetically related to a Kunitz peptide from Rhipicephalus appendiculatus, also reported to have a high affinity for β-tryptase. Using homology-based modeling (and other protein prediction programs) we were able to model and explain the multifaceted function of tryptogalinin. The N-terminus of the modeled tryptogalinin is detached from the rest of the peptide and exhibits intrinsic disorder allowing an increased flexibility for its high affinity with its inhibiting partners (i.e., serine proteases). CONCLUSIONS By incorporating experimental and computational methods our data not only describes the function of a Kunitz peptide from Ixodes scapularis, but also allows us to hypothesize about the molecular basis of this function at the atomic level.
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Affiliation(s)
- James J Valdés
- Institute of Parasitology, Biology Centre of the Academy of Sciences of the Czech Republic, České Budějovice, Czech Republic.
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15
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Jiang QQ, Bartsch L, Sicking W, Wich PR, Heider D, Hoffmann D, Schmuck C. A new approach to inhibit human β-tryptase by protein surface binding of four-armed peptide ligands with two different sets of arms. Org Biomol Chem 2013; 11:1631-9. [DOI: 10.1039/c3ob27302d] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
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16
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Scheibe C, Bujotzek A, Dernedde J, Weber M, Seitz O. DNA-programmed spatial screening of carbohydrate–lectin interactions. Chem Sci 2011. [DOI: 10.1039/c0sc00565g] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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17
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Multivalent Antimicrobial Peptides as Therapeutics: Design Principles and Structural Diversities. Int J Pept Res Ther 2010; 16:199-213. [PMID: 20835389 PMCID: PMC2931633 DOI: 10.1007/s10989-010-9230-z] [Citation(s) in RCA: 79] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/17/2010] [Indexed: 01/15/2023]
Abstract
This review highlights the design principles, progress and advantages attributed to the structural diversity associated with both natural and synthetic multivalent antimicrobial peptides (AMPs). Natural homo- or hetero-dimers of AMPs linked by intermolecular disulfide bonds existed in the animal kingdom, but the multivalency strategy has been adopted to create synthetic branched or polymeric AMPs that do not exist in nature. The multivalent strategy for the design of multivalent AMPs provides advantages to overcome the challenges faced in clinical applications of AMPs, such as: stability, efficiency, toxicity, maintenance of activity in high salt concentrations and under physiological conditions, and importantly overcoming bacterial resistance which is currently a leading health problem in the world. The multivalency strategy is valuable for moving multivalent AMPs toward clinical applications.
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Scheuermann J, Neri D. DNA-encoded chemical libraries: a tool for drug discovery and for chemical biology. Chembiochem 2010; 11:931-7. [PMID: 20391457 DOI: 10.1002/cbic.201000066] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Jörg Scheuermann
- ETH Zürich, Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, Wolfgang-Pauli-Strasse 10, 8093 Zürich, Switzerland.
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19
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Ting SRS, Chen G, Stenzel MH. Synthesis of glycopolymers and their multivalent recognitions with lectins. Polym Chem 2010. [DOI: 10.1039/c0py00141d] [Citation(s) in RCA: 321] [Impact Index Per Article: 22.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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20
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Sommerhoff CP, Avrutina O, Schmoldt HU, Gabrijelcic-Geiger D, Diederichsen U, Kolmar H. Engineered cystine knot miniproteins as potent inhibitors of human mast cell tryptase beta. J Mol Biol 2009; 395:167-75. [PMID: 19852971 DOI: 10.1016/j.jmb.2009.10.028] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2009] [Revised: 10/12/2009] [Accepted: 10/15/2009] [Indexed: 11/16/2022]
Abstract
Here we report the design, chemical and recombinant synthesis, and functional properties of a series of novel inhibitors of human mast cell tryptase beta, a protease of considerable interest as a therapeutic target for the treatment of allergic asthma and inflammatory disorders. These inhibitors are derived from a linear variant of the cyclic cystine knot miniprotein MCoTI-II, originally isolated from the seeds of Momordica cochinchinensis. A synthetic cyclic miniprotein that bears additional positive charge in the loop connecting the N- and C-termini inhibits all monomers of the tryptase beta tetramer with an overall equilibrium dissociation constant K(i) of 1 nM and thus is one of the most potent proteinaceous inhibitors of tryptase beta described to date. These cystine knot miniproteins may therefore become valuable scaffolds for the design of a new generation of tryptase inhibitors.
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Affiliation(s)
- Christian P Sommerhoff
- Division of Clinical Chemistry and Clinical Biochemistry, Surgical Department, Ludwig-Maximilians-University Munich, Nussbaumstrasse 20, D-80336 Munich, Germany
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Schiemann F, Brandt E, Gross R, Lindner B, Mittelstädt J, Sommerhoff CP, Schulmistrat J, Petersen F. The cathelicidin LL-37 activates human mast cells and is degraded by mast cell tryptase: counter-regulation by CXCL4. THE JOURNAL OF IMMUNOLOGY 2009; 183:2223-31. [PMID: 19625657 DOI: 10.4049/jimmunol.0803587] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The cathelicidin LL-37 represents a potent antimicrobial and cell-stimulating agent, most abundantly expressed in peripheral organs such as lung and skin during inflammation. Because mast cells (MC) overtake prominent immunomodulatory roles in these organs, we wondered whether interactions exist between MC and LL-37. In this study, we show for the first time to our knowledge that physiological concentrations of LL-37 induce degranulation in purified human lung MC. Intriguingly, as a consequence LL-37 rapidly undergoes limited cleavage by a released protease. The enzyme was identified as beta-tryptase by inhibitor studies and by comparison to the recombinant protease. Examining the resulting LL-37 fragments for their functional activity, we found that none of the typical capacities of intact LL-37, i.e., MC degranulation, bactericidal activity, and neutralization of LPS, were retained. Conversely, we found that another inflammatory protein, the platelet-derived chemokine CXCL4, protects LL-37 from cleavage by beta-tryptase. Interestingly, CXCL4 did not act as a direct enzyme inhibitor, but destabilized active tetrameric beta-tryptase by antagonizing the heparin component required for the integrity of the tetramer. Altogether our results suggest that interaction of LL-37 and MC initiates an effective feedback loop to limit cathelicidin activity during inflammation, whereas CXCL4 may represent a physiological counter-regulator of beta-tryptase activity.
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Affiliation(s)
- Florian Schiemann
- Department of Immunology and Cell Biology, Research Center Borstel, Borstel, Germany.
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22
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Cecioni S, Argintaru OA, Docsa T, Gergely P, Praly JP, Vidal S. Probing multivalency for the inhibition of an enzyme: glycogen phosphorylase as a case study. NEW J CHEM 2009. [DOI: 10.1039/b812540f] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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23
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Pieters RJ. Maximising multivalency effects in protein–carbohydrate interactions. Org Biomol Chem 2009; 7:2013-25. [DOI: 10.1039/b901828j] [Citation(s) in RCA: 288] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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24
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Palmer HS, Kelso EB, Lockhart JC, Sommerhoff CP, Plevin R, Goh FG, Ferrell WR. Protease-activated receptor 2 mediates the proinflammatory effects of synovial mast cells. ACTA ACUST UNITED AC 2007; 56:3532-40. [DOI: 10.1002/art.22936] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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25
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Abstract
In 1960, a trypsin-like activity was found in mast cells [Glenner GG & Cohen LA (1960) Nature 185, 846-847] and this activity is now commonly referred to as 'tryptase'. Over the years, much knowledge about mast cell tryptase has been gathered, and a recent (18 January 2006) PubMed search for the keywords 'tryptase + mast cell*' retrieved 1661 articles. However, still very little is known about its true biological function. For example, the true physiological substrate(s) for mast cell tryptase has not been identified, and the potential role of tryptase in mast cell-related disease is not understood. Mast cell tryptase has several unique features, with perhaps the most remarkable being its organization into a tetrameric state with all of the active sites oriented towards a narrow central pore and its consequent complete resistance towards endogenous macromolecular protease inhibitors. Much effort has been invested to elucidate these properties of tryptase. In this review we summarize the current knowledge of mast cell tryptase, including novel insights into its possible biological functions and mechanisms of regulation.
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Affiliation(s)
- Jenny Hallgren
- Department of Molecular Biosciences, The Biomedical Centre, Swedish University of Agricultural Sciences, Uppsala, Sweden.
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26
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Lee Y, Sampson NS. Romping the cellular landscape: linear scaffolds for molecular recognition. Curr Opin Struct Biol 2006; 16:544-50. [PMID: 16781140 DOI: 10.1016/j.sbi.2006.05.015] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2006] [Revised: 05/03/2006] [Accepted: 05/30/2006] [Indexed: 11/25/2022]
Abstract
Multivalent molecules with a precise array of recognition elements that interact with specific cell types are important for characterizing the topology of molecules on a cell surface. Applications ranging from the control of cellular signaling to drug delivery and tissue imaging rely on these surface-mapping molecules. Linear polymers provide a molecular scaffold that is advantageous for these types of applications and their synthesis can be amenable to the introduction of different recognition elements. Recently, advances have been made in the development of synthetic approaches for preparing linear polymeric substrates with highly controlled lengths and recognition element spacing.
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Affiliation(s)
- Younjoo Lee
- Department of Chemistry, Stony Brook University, Stony Brook, NY 11794-3400, USA
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27
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Rohr KB, Selwood T, Marquardt U, Huber R, Schechter NM, Bode W, Than ME. X-ray structures of free and leupeptin-complexed human alphaI-tryptase mutants: indication for an alpha-->beta-tryptase transition. J Mol Biol 2005; 357:195-209. [PMID: 16414069 DOI: 10.1016/j.jmb.2005.12.037] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2005] [Revised: 12/07/2005] [Accepted: 12/08/2005] [Indexed: 11/20/2022]
Abstract
Tryptases alpha and beta are trypsin-like serine proteinases expressed in large amounts by mast cells. Beta-tryptase is a tetramer that has enzymatic activity, but requires heparin binding to maintain functional and structural stability, whereas alpha-tryptase has little, if any, enzymatic activity but is a stable tetramer in the absence of heparin. As shown previously, these differences can be mainly attributed to the different conformations of the 214-220 segment. Interestingly, the replacement of Asp216 by Gly, which is present in beta-tryptase, results in enzymatically active but less stable alpha-tryptase mutants. We have solved the crystal structures of both the single (D216G) and the double (K192Q/D216G) mutant forms of recombinant human alphaI-tryptase in complex with the peptide inhibitor leupeptin, as well as the structure of the non-inhibited single mutant. The inhibited mutants exhibited an open functional substrate binding site, while in the absence of an inhibitor, the open (beta-tryptase-like) and the closed (alpha-tryptase-like) conformations were present simultaneously. This shows that both forms are in a two-state equilibrium, which is influenced by the residues in the vicinity of the active site and by inhibitor/substrate binding. Novel insights regarding the observed stability differences as well as a potential proteolytic activity of wild-type alpha-tryptase, which may possess a cryptic active site, are discussed.
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Affiliation(s)
- Kerstin B Rohr
- Max-Planck-Institut für Biochemie, Abteilung Strukturforschung, Am Klopferspitz 18, 82152 Martinsried, Germany
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28
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Handl HL, Vagner J, Han H, Mash E, Hruby VJ, Gillies RJ. Hitting multiple targets with multimeric ligands. Expert Opin Ther Targets 2005; 8:565-86. [PMID: 15584863 DOI: 10.1517/14728222.8.6.565] [Citation(s) in RCA: 93] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Multimeric ligands consist of multiple monomeric ligands attached to a single backbone molecule, creating a multimer that can bind to multiple receptors or targets simultaneously. Numerous examples of multimeric binding exist within nature. Due to the multiple and simultaneous binding events, multimeric ligands bind with an increased affinity compared to their corresponding monomers. Multimeric ligands may provide opportunities in the field of drug discovery by providing enhanced selectivity and affinity of binding interactions, thus providing molecular-based targeted therapies. However, gaps in our knowledge currently exist regarding the quantitative measures for important design characteristics, such as flexibility, length and orientation of the inter-ligand linkers, receptor density and ligand sequence. In this review, multimeric ligand binding in two separate phases is examined. The prerecruitment phase describes the binding of one ligand of a multimer to its corresponding receptor, an event similar to monomeric ligand binding. This results in transient increases in the local concentration of the other ligands, leading to apparent cooperativity. The postrecruitment phase only occurs once all receptors have been aligned and bound by their corresponding ligand. This phase is analogous to DNA-DNA interactions in that the stability of the complex is derived from physical orientation. Multiple factors influence the kinetics and thermodynamics of multimeric binding, and these are discussed.
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Affiliation(s)
- Heather L Handl
- Arizona Cancer Center, Department of Biochemistry and Molecular Biophysics, 1515 N. Campbell Avenue, Tucson, AZ 85724-5024, USA
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29
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Ilies MA, Supuran CT, Scozzafava A. Therapeutic applications of serine protease inhibitors. Expert Opin Ther Pat 2005. [DOI: 10.1517/13543776.12.8.1181] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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30
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Abstract
Monosaccharides and amino acids are fundamental building blocks in the assembly of nature's polymers. They have different structural aspects and, to a significant extent, different functional groups. Oligomerization gives rise to oligosaccharides and peptides, respectively. While carbohydrates and peptides can be found conjoined in nature, e.g., in glycopeptides, the aim of this review is the radical redesign of peptide structures using carbohydrates, particularly monosaccharides and cyclic oligosaccharides, to produce novel peptides, peptidomimetics, and abiotic proteins. These hybrid molecules, chimeras, have properties arising largely from the combination of structural characteristics of carbohydrates with the functional group diversity of peptides. This field includes de novo designed synthetic glycopeptides, sugar (carbohydrate) amino acids, carbohydrate scaffolds for nonpeptidal peptidomimetics of cyclic peptides, cyclodextrin functionalized peptides, and carboproteins, i.e., carbohydrate-based proteinmimetics. These successful applications demonstrate the general utility of carbohydrates in peptide and protein architecture.
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Affiliation(s)
- Knud J Jensen
- Department of Natural Sciences, Section for Bioorganic Chemistry, KVL, 1871 Frederiksberg C, Denmark.
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31
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Schaschke N, Gabrijelcic-Geiger D, Dominik A, Sommerhoff CP. Affinity Chromatography of Tryptases: Design, Synthesis and Characterization of a Novel Matrix-Bound Bivalent Inhibitor. Chembiochem 2004; 6:95-103. [PMID: 15593113 DOI: 10.1002/cbic.200400217] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
beta-Tryptases are mast cell-derived serine proteases that are enzymatically active in the form of an oligomer consisting of four subunits each with trypsin-like activity. The active-site clefts, which are directed toward the central pore of the tetramer, form spatial arrays of four negatively charged S1 binding pockets. Therefore, dibasic inhibitors of appropriate geometry can bind in a bivalent fashion to neighboring subunits. We have recently identified a potent bivalent inhibitor (K(i)=18 nM), based on the bifunctional scaffold cyclo-(-D-Asp-L-Asp-) and the arginine mimetic dl-3-aminomethyl-phenylalanine methyl ester as a ligand for S1 pockets that takes advantage of the this unique tetrameric geometry. To generate an affinity matrix, the bivalent ligand was modified and immobilized on a Sepharose matrix by use of the PEG derivative Jeffamine ED 900 as spacer. This matrix selectively recognizes and binds beta-tryptase from crude protein mixtures and thus is useful as a geometry-driven means of isolating and purifying human mast cell tryptases.
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Affiliation(s)
- Norbert Schaschke
- Max-Planck-Institut für Biochemie, Am Klopferspitz 18a, 82152 Martinsried, Germany.
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32
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Zhang Z, Liu J, Verlinde CLMJ, Hol WGJ, Fan E. Large cyclic peptides as cores of multivalent ligands: application to inhibitors of receptor binding by cholera toxin. J Org Chem 2004; 69:7737-40. [PMID: 15498005 DOI: 10.1021/jo0489770] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Large cyclic decapeptides (up to 50-atom ring) were synthesized efficiently on the solid phase with allyl-ester protection of the carboxyl terminus during elongation. Pentavalent ligands, in a "core-linker-finger" modular setup, were assembled by using these cyclic peptide cores to demonstrate large affinity gains for inhibition of surface receptor binding by the cholera toxin B pentamer. The results suggest that the peptide cores retain expanded conformation in solution so that shorter flexible linkers are needed for larger peptide cores to achieve the best inhibitory results.
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Affiliation(s)
- Zhongsheng Zhang
- Biomolecular Structure Center, Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
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33
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Scarpi D, McBride JD, Leatherbarrow RJ. Inhibition of human β-tryptase by Bowman–Birk inhibitor derived peptides: creation of a new tri-functional inhibitor. Bioorg Med Chem 2004; 12:6045-52. [PMID: 15519150 DOI: 10.1016/j.bmc.2004.09.015] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2004] [Accepted: 09/10/2004] [Indexed: 10/26/2022]
Abstract
Bowman-Birk inhibitor proteins (BBIs), which are potent inhibitors of chymotrypsin-like proteases, do not inhibit human beta-tryptase despite this protein having a chymotrypsin-like fold. We have reported previously that, in contrast, BBI-derived peptides (whose sequences incorporate the solvent exposed reactive site loop motif) are able to inhibit human beta-tryptase. This is due to their small size, which allows them to access the restricted active site(s) of tryptase, which has an unusual tetrameric arrangement with four active sites flanking a central pore. In this paper, we have examined the possibility of creating additional interactions within this pore by adding extensions to the BBI-peptide motif. We have taken the core disulfide-bridged sequence SCTKSIPPQCY and examined a series of extensions, at both the C- and N-termini, that bear a second positively charged Lys residue at their end. The aim was to construct inhibitors that could make additional interactions in tryptase by spanning the gap between adjacent active sites in the enzyme, producing a double-headed inhibitor; a positively charged group was used as the dominant specificity of this enzyme is for a positively charged P1 residue. Both N- and C-terminal extensions are found to produce inhibitors of much increased potency, with a strong dependence of potency on chain length. Moreover, it was found that the C- and N-terminal extensions were able to synergise, with their combination on the same peptide producing an even better inhibitor with a potency 10(4)-fold greater than the original sequence. We suggest that the C- and N-terminal extensions are picking up interactions with separate additional sites on the tryptase, making the doubly extended BBI peptide a tri-functional tryptase inhibitor.
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Affiliation(s)
- Dina Scarpi
- Department of Chemistry, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
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34
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Vaz RJ, Gao Z, Pribish J, Chen X, Levell J, Davis L, Albert E, Brollo M, Ugolini A, Cramer DM, Cairns J, Sides K, Liu F, Kwong J, Kang J, Rebello S, Elliot M, Lim H, Chellaraj V, Singleton RW, Li Y. Design of bivalent ligands using hydrogen bond linkers: synthesis and evaluation of inhibitors for human β-tryptase. Bioorg Med Chem Lett 2004; 14:6053-6. [PMID: 15546728 DOI: 10.1016/j.bmcl.2004.09.065] [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: 09/09/2004] [Revised: 09/23/2004] [Accepted: 09/23/2004] [Indexed: 11/24/2022]
Abstract
We exploit the concept of using hydrogen bonds to link multiple ligands for maintaining simultaneous interactions with polyvalent binding sites. This approach is demonstrated by the syntheses and evaluation of pseudo-bivalent ligands as potent inhibitors of human beta-tryptase.
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Affiliation(s)
- Roy J Vaz
- Aventis Pharmaceuticals, 1041 Route 202/206 N, Bridgewater, NJ 088707, USA
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Selwood T, Elrod KC, Schechter NM. Potent bivalent inhibition of human tryptase-beta by a synthetic inhibitor. Biol Chem 2004; 384:1605-11. [PMID: 14719803 DOI: 10.1515/bc.2003.178] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Human tryptase-beta (HTbeta) is a unique serine protease exhibiting a frame-like tetramer structure with four active sites directed toward a central pore. Potent inhibition of HTbeta has been attained using CRA-2059. This compound has two phenylguanidinium head groups connected via a linker capable of spanning between two active sites. The properties of the CRA-2059:HTbeta interaction were defined in this study. Tight-binding reversible inhibition was observed with an inhibition constant (Ki) of 620 pM, an association rate constant of 7x10(7) M(-1) s(-1) and a relatively slow dissociation rate constant of 0.04 s(-1). Bivalent inhibition was demonstrated by displacement of p-aminobenzamidine from the primary specificity pocket with a stoichiometry, [CRA-2059]0/[HTbeta]0, of 0.5. The potency of the bivalent interaction was illustrated by CRA-2059 inhibition of HTbeta, 24% or 53% inhibited by pre-incubation with an irreversible inhibitor. Two interactions were observed consistent with mono- and bi-valent binding; the Ki value for bivalent inhibition was at least 10(4)-fold lower than that for monovalent inhibition. Comparison of the affinities of CRA-2059 and phenylguanidine for HTbeta finds an approximate doubling of the free energy change upon bivalent binding. This doubling suggests that the linker portion minimally hinders the binding of CRA-2059 to HTbeta. The potency of CRA-2059 is thus attributable to effective bivalent binding.
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Affiliation(s)
- Trevor Selwood
- University of Pennsylvania, Department of Dermatology, Philadelphia, PA 19104, USA
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36
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Zhang Z, Fan E. Modular synthesis and study of multivalent carbohydrate ligands with long and flexible linkers. Methods Enzymol 2003; 362:209-18. [PMID: 12968365 DOI: 10.1016/s0076-6879(03)01014-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Affiliation(s)
- Zhongsheng Zhang
- Departments of Biochemistry and Biological Structure, University of Washington, Biomolecular Structure Center, Seattle, Washington 98195, USA
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van Ameijde J, Liskamp RMJ. Synthesis of novel trivalent amino acid glycoconjugates based on the cyclotriveratrylene ('CTV') scaffold. Org Biomol Chem 2003; 1:2661-9. [PMID: 12948190 DOI: 10.1039/b303795a] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The convenient synthesis of novel trivalent amino acid glycoconjugates based on cyclotriveratrylene ('CTV') is described. These constructs consist of the CTV scaffold, three oligoethylene glycol spacers of variable length connected to a glyco amino acid residue which can also be varied. The resulting library of trivalent glycoconjugates can be used for studying multivalent interactions.
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Affiliation(s)
- Jeroen van Ameijde
- Department of Medicinal Chemistry, Utrecht Institute for Pharmaceutical Sciences, Utrecht University, PO Box 80082, 3508 TB Utrecht, The Netherlands
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38
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39
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Zhang Z, Merritt EA, Ahn M, Roach C, Hou Z, Verlinde CLMJ, Hol WGJ, Fan E. Solution and crystallographic studies of branched multivalent ligands that inhibit the receptor-binding of cholera toxin. J Am Chem Soc 2002; 124:12991-8. [PMID: 12405825 DOI: 10.1021/ja027584k] [Citation(s) in RCA: 105] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The structure-based design of multivalent ligands offers an attractive strategy toward high affinity protein inhibitors. The spatial arrangement of the receptor-binding sites of cholera toxin, the causative agent of the severe diarrheal disease cholera and a member of the AB(5) bacterial toxin family, provides the opportunity of designing branched multivalent ligands with 5-fold symmetry. Our modular synthesis enabled the construction of a family of complex ligands with five flexible arms each ending with a bivalent ligand. The largest of these ligands has a molecular weight of 10.6 kDa. These ligands are capable of simultaneously binding to two toxin B pentamer molecules with high affinity, thus blocking the receptor-binding process of cholera toxin. A more than million-fold improvement over the monovalent ligand in inhibitory power was achieved with the best branched decavalent ligand. This is better than the improvement observed earlier for the corresponding nonbranched pentavalent ligand. Dynamic light scattering studies demonstrate the formation of concentration-dependent unique 1:1 and 1:2 ligand/toxin complexes in solution with no sign of nonspecific aggregation. This is in complete agreement with a crystal structure of the branched multivalent ligand/toxin B pentamer complex solved at 1.45 A resolution that shows the specific 1:2 ligand/toxin complex formation in the solid state. These results reiterate the power of the structure-based design of multivalent protein ligands as a general strategy for achieving high affinity and potent inhibition.
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Affiliation(s)
- Zhongsheng Zhang
- Biomolecular Structure Center and Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
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40
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Riley AM, Morris SA, Nerou EP, Correa V, Potter BVL, Taylor CW. Interactions of inositol 1,4,5-trisphosphate (IP(3)) receptors with synthetic poly(ethylene glycol)-linked dimers of IP(3) suggest close spacing of the IP(3)-binding sites. J Biol Chem 2002; 277:40290-5. [PMID: 12183463 DOI: 10.1074/jbc.m206925200] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The distances between the inositol 1,4,5-trisphosphate (IP(3))-binding sites of tetrameric IP(3) receptors were probed using dimers of IP(3) linked by poly(ethylene glycol) (PEG) molecules of differing lengths (1-8 nm). Each of the dimers potently stimulated (45)Ca(2+) release from permeabilized cells expressing predominantly type 1 (SH-SY5Y cells) or type 2 (hepatocytes) IP(3) receptors. The shortest dimers, with PEG linkers of an effective length of 1.5 nm or less, were the most potent, being 3-4-fold more potent than IP(3). In radioligand binding experiments using cerebellar membranes, the shortest dimers bound with highest affinity, although the longest dimer (8 nm) also bound with almost 4-fold greater affinity than IP(3). The affinity of monomeric IP(3) with only the PEG attached was 2-fold weaker than IP(3), confirming that the increased affinity of the dimers requires the presence of both IP(3) motifs. The increased affinity of the long dimer probably results from the linked IP(3) molecules binding to sites on different receptors, because the dimer bound with greater affinity than IP(3) to cerebellar membranes, where receptors are densely packed, but with the same affinity as IP(3) to purified receptors. IP(3) and the IP(3) dimers, irrespective of their length, bound with similar affinity to a monomeric IP(3)-binding domain of the type 1 IP(3) receptor expressed in bacteria. Short dimers therefore bind with increased affinity only when the receptor is tetrameric. We conclude that the four IP(3)-binding sites of an IP(3) receptor may be separated by as little as 1.5 nm and are therefore likely to be placed centrally in this large (25 x 25 nm) structure, consistent with previous work indicating a close association between the central pore and the IP(3)-binding sites of the IP(3) receptor.
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Affiliation(s)
- Andrew M Riley
- Department of Pharmacology, University of Cambridge, Tennis Court Road, Cambridge CB2 1PD, United Kingdom
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41
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Murray CW, Verdonk ML. The consequences of translational and rotational entropy lost by small molecules on binding to proteins. J Comput Aided Mol Des 2002; 16:741-53. [PMID: 12650591 DOI: 10.1023/a:1022446720849] [Citation(s) in RCA: 142] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
When a small molecule binds to a protein, it loses a significant amount of rigid body translational and rotational entropy. Estimates of the associated energy barrier vary widely in the literature yet accurate estimates are important in the interpretation of results from fragment-based drug discovery techniques. This paper describes an analysis that allows the estimation of the rigid body entropy barrier from the increase in binding affinities that results when two fragments of known affinity and known binding mode are joined together. The paper reviews the relatively rare number of examples where good quality data is available. From the analysis of this data, we estimate that the barrier to binding, due to the loss of rigid-body entropy, is 15-20 kJ/mol, i.e. around 3 orders of magnitude in affinity at 298 K. This large barrier explains why it is comparatively rare to observe multiple fragments binding to non-overlapping adjacent sites in enzymes. The barrier is also consistent with medicinal chemistry experience where small changes in the critical binding regions of ligands are often poorly tolerated by enzymes.
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Affiliation(s)
- Christopher W Murray
- Astex Technology Ltd, 250 Cambridge Science Park, Milton Road, Cambridge, CB4 0WE, UK.
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Marquardt U, Zettl F, Huber R, Bode W, Sommerhoff C. The crystal structure of human alpha1-tryptase reveals a blocked substrate-binding region. J Mol Biol 2002; 321:491-502. [PMID: 12162961 DOI: 10.1016/s0022-2836(02)00625-3] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Human mast cell tryptases represent a subfamily of trypsin-like serine proteinases implicated in asthma. Unlike beta-tryptases, alpha-tryptases apparently are proteolytically inactive. We have solved the 2.2A crystal structure of mature human alpha1-tryptase. It reveals a frame-like tetrameric architecture that, surprisingly, does not require heparin-binding for stability. In marked contrast to beta2-tryptase, the Ser214-Gly219 segment, which normally provides the template for substrate binding, is kinked in alpha-tryptase, thereby blocking its non-primed subsites. This so far unobserved subsite distortion is incompatible with productive substrate binding and processing. alpha-Tryptase apparently is trapped in this off-conformation by repulsions and attractions of the Asp216 side-chain. However, proteolytic activity could be generated by an induced-fit mechanism.
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Affiliation(s)
- Ulf Marquardt
- Max-Planck-Institut für Biochemie, Abteilung Strukturforschung, Am Klopferspitz 18a, D-82152 Martinsried bei, München, Germany
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Schaschke N, Dominik A, Matschiner G, Sommerhoff CP. Bivalent inhibition of beta-tryptase: distance scan of neighboring subunits by dibasic inhibitors. Bioorg Med Chem Lett 2002; 12:985-8. [PMID: 11959009 DOI: 10.1016/s0960-894x(02)00063-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Based on bifunctional diketopiperazines as templates and m-aminomethyl-phenylalanine as arginine mimetic, we have synthesized a new class of structurally related dibasic tryptase inhibitors with systematically increasing spacer length. These compounds were used to scan the distance between the active sites of two neighboring subunits of the beta-tryptase tetramer. The K(i)-values obtained are a function of the distance between the terminal amino groups and indicate optimal binding of inhibitors with 29-31 bonds between the amino groups. These experimental data are in full agreement with predictions derived from a novel modeling program that allows the docking of bivalent ligands.
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