1
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Kolodziejczyk-Czepas J, Czepas J. Plant-Derived Compounds and Extracts as Modulators of Plasmin Activity-A Review. Molecules 2023; 28:molecules28041677. [PMID: 36838662 PMCID: PMC9965408 DOI: 10.3390/molecules28041677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 02/03/2023] [Accepted: 02/08/2023] [Indexed: 02/12/2023] Open
Abstract
Functionality of the fibrinolytic system is based on activity of its central enzyme, plasmin, responsible for the removal of fibrin clots. Besides the hemostasis, fibrinolytic proteins are also involved in many other physiological and pathological processes, including immune response, extracellular matrix degradation, cell migration, and tissue remodeling. Both the impaired and enhanced activity of fibrinolytic proteins may result in serious physiological consequences: prothrombotic state or excessive bleeding, respectively. However, current medicine offers very few options for treating fibrinolytic disorders, particularly in the case of plasmin inhibition. Although numerous attempts have been undertaken to identify natural or to develop engineered fibrinolytic system modulators, structural similarities within serine proteases of the hemostatic system and pleiotropic activity of fibrinolytic proteins constitute a serious problem in discovering anti- or profibrinolytic agents that could precisely affect the target molecules and reduce the risk of side effects. Therefore, this review aims to present a current knowledge of various classes of natural inhibitors and stimulators of the fibrinolytic system being well-defined low-molecular plant secondary metabolites or constituents of plant extracts as well as plant peptides. This work also discusses obstacles caused by low specificity of most of natural compounds and, hence, outlines recent trends in studies aimed at finding more efficient modulators of plasmin activity, including investigation of modifications of natural pharmacophore templates.
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Affiliation(s)
- Joanna Kolodziejczyk-Czepas
- Department of General Biochemistry, Faculty of Biology and Environmental Protection, University of Lodz, 90-236 Lodz, Poland
- Correspondence:
| | - Jan Czepas
- Department of Oncobiology and Epigenetics, Faculty of Biology and Environmental Protection, University of Lodz, 90-236 Lodz, Poland
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2
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Ferguson TEG, Reihill JA, Martin SL, Walker B. Novel inhibitors and activity-based probes targeting serine proteases. Front Chem 2022; 10:1006618. [PMID: 36247662 PMCID: PMC9555310 DOI: 10.3389/fchem.2022.1006618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 08/18/2022] [Indexed: 11/13/2022] Open
Abstract
Serine proteases play varied and manifold roles in important biological, physiological, and pathological processes. These include viral, bacterial, and parasitic infection, allergic sensitization, tumor invasion, and metastasis. The use of activity-based profiling has been foundational in pinpointing the precise roles of serine proteases across this myriad of processes. A broad range of serine protease-targeted activity-based probe (ABP) chemotypes have been developed and we have recently introduced biotinylated and "clickable" peptides containing P1 N-alkyl glycine arginine N-hydroxy succinimidyl (NHS) carbamates as ABPs for detection/profiling of trypsin-like serine proteases. This present study provides synthetic details for the preparation of additional examples of this ABP chemotype, which function as potent irreversible inhibitors of their respective target serine protease. We describe their use for the activity-based profiling of a broad range of serine proteases including trypsin, the trypsin-like protease plasmin, chymotrypsin, cathepsin G, and neutrophil elastase (NE), including the profiling of the latter protease in clinical samples obtained from patients with cystic fibrosis.
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Affiliation(s)
| | | | | | - Brian Walker
- Biomolecular Sciences Research Group, School of Pharmacy, Queen’s University Belfast, Belfast, United Kingdom
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3
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Exploration of Active Site-Directed Plasmin Inhibitors: Beyond Tranexamic Acid. Processes (Basel) 2021. [DOI: 10.3390/pr9020329] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Plasmin (Plm), a trypsin-like serine protease, is responsible for fibrinolysis pathway and pathologic events, such as angiogenesis, tumor invasion, and metastasis, and alters the expression of cytokines. A growing body of data indicates that a Plm inhibitor is a potential candidate as an anti-inflammatory and anti-cancer agent. A class of active site-directed plasmin inhibitors containing tranexamic acid residue has been designed. As evidenced by docking studies, the inhibitor binds to the active site not to the lysine binding site (LBS) in plasmin, thus preventing plasmin from digesting the substrate. Further optimization of the series, concerning both activity and selectivity, led to the second generation of inhibitors. This review focuses on the Plm inhibitory activity-structure relationship of Plm inhibitors with the goal of realizing their design and clinical application.
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4
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Vadivel K, Zaiss AK, Kumar Y, Fabian FM, Ismail AEA, Arbing MA, Buchholz WG, Velander WH, Bajaj SP. Enhanced Antifibrinolytic Efficacy of a Plasmin-Specific Kunitz-Inhibitor (60-Residue Y11T/L17R with C-Terminal IEK) of Human Tissue Factor Pathway Inhibitor Type-2 Domain1. J Clin Med 2020; 9:E3684. [PMID: 33212896 PMCID: PMC7698382 DOI: 10.3390/jcm9113684] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Accepted: 10/21/2020] [Indexed: 12/13/2022] Open
Abstract
Current antifibrinolytic agents reduce blood loss by inhibiting plasmin active sites (e.g., aprotinin) or by preventing plasminogen/tissue plasminogen activator (tPA) binding to fibrin clots (e.g., ε-aminocaproic acid and tranexamic acid); however, they have adverse side effects. Here, we expressed 60-residue (NH2NAE…IEKCOOH) Kunitz domain1 (KD1) mutants of human tissue factor pathway inhibitor type-2 that inhibit plasmin as well as plasminogen activation. A single (KD1-L17R-KCOOH) and a double mutant (KD1-Y11T/L17R- KCOOH) were expressed in Escherichia coli as His-tagged constructs, each with enterokinase cleavage sites. KD1-Y11T/L17R-KCOOH was also expressed in Pichia pastoris. KD1-Y11T/L17R-KCOOH inhibited plasmin comparably to aprotinin and bound to the kringle domains of plasminogen/plasmin and tPA with Kd of ~50 nM and ~35 nM, respectively. Importantly, compared to aprotinin, KD1-L17R-KCOOH and KD1-Y11T/L17R-KCOOH did not inhibit kallikrein. Moreover, the antifibrinolytic potential of KD1-Y11T/L17R-KCOOH was better than that of KD1-L17R-KCOOH and similar to that of aprotinin in plasma clot-lysis assays. In thromboelastography experiments, KD1-Y11T/L17R-KCOOH was shown to inhibit fibrinolysis in a dose dependent manner and was comparable to aprotinin at a higher concentration. Further, KD1-Y11T/L17R-KCOOH did not induce cytotoxicity in primary human endothelial cells or fibroblasts. We conclude that KD1-Y11T/L17R-KCOOH is comparable to aprotinin, the most potent known inhibitor of plasmin and can be produced in large amounts using Pichia.
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Affiliation(s)
- Kanagasabai Vadivel
- Department of Orthopedic Surgery, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA; (K.V.); (A.K.Z.); (Y.K.)
| | - Anne K. Zaiss
- Department of Orthopedic Surgery, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA; (K.V.); (A.K.Z.); (Y.K.)
| | - Yogesh Kumar
- Department of Orthopedic Surgery, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA; (K.V.); (A.K.Z.); (Y.K.)
| | - Frank M. Fabian
- Department of Chemical and Biomolecular Engineering, University of Nebraska, Lincoln, NE 68588, USA; (F.M.F.); (A.E.A.I.); (W.G.B.); (W.H.V.)
- Chemistry Department, Walla Walla University, College Place, WA 99324, USA
| | - Ayman E. A. Ismail
- Department of Chemical and Biomolecular Engineering, University of Nebraska, Lincoln, NE 68588, USA; (F.M.F.); (A.E.A.I.); (W.G.B.); (W.H.V.)
| | - Mark A. Arbing
- Protein Expression Technology Center, UCLA-DOE Institute, University of California, Los Angeles, CA 90095, USA;
| | - Wallace G. Buchholz
- Department of Chemical and Biomolecular Engineering, University of Nebraska, Lincoln, NE 68588, USA; (F.M.F.); (A.E.A.I.); (W.G.B.); (W.H.V.)
| | - William H. Velander
- Department of Chemical and Biomolecular Engineering, University of Nebraska, Lincoln, NE 68588, USA; (F.M.F.); (A.E.A.I.); (W.G.B.); (W.H.V.)
| | - S. Paul Bajaj
- Department of Orthopedic Surgery, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA; (K.V.); (A.K.Z.); (Y.K.)
- Molecular Biology Institute, University of California, Los Angeles, CA 90095, USA
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5
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Qi E, Wang D, Li Y, Li G, Su Z. Revealing favorable and unfavorable residues in cooperative positions in protease cleavage sites. Biochem Biophys Res Commun 2019; 519:714-720. [PMID: 31543345 DOI: 10.1016/j.bbrc.2019.09.056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Accepted: 09/14/2019] [Indexed: 11/17/2022]
Abstract
Proteases play critical roles in a wide variety of fundamental biological functions, and numerous protease inhibitors have been developed to treat various diseases including cancer. A wide range of experimental and computational methods have been developed to investigate the specificity and catalytic mechanisms of proteases. However, these methods only focused on the preferences of a single position around a cleavage site in a substrate, rarely on the compositionality of the subsites. We present new methods to quantify the specificity of proteases by considering the combinatorial patterns of amino acid residuals of cleavage sites in substrates. By incorporating the preference at positions, we modeled three types of favorable combinations of residues in cleavage sites. Moreover, by constructing a relationship weight matrix of residues between two positions, we can easily identify unfavorable combinations of residues at the positions. Applying these methods to a set of known cleavage sites of proteases, we revealed numerous favorable and unfavorable residues in cooperative positions in the protease cleavage sites. The results can help understand the specificity and catalytic mechanisms of proteases. To our knowledge, this is the first study that quantifies unfavorable combinations of amino acids between two sites. Furthermore, this method is not limited to the study of proteases and cleavage sites, and can be generalized to uncover the relationships of residues at meaningful sites in other proteins.
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Affiliation(s)
- Enfeng Qi
- School of Mathematics, Shandong University, Jinan, 250100, China; School of Mathematics and Statistics, Guangxi Normal University, Guilin, 541000, China
| | - Dongyu Wang
- The State Key Laboratory of Microbial Technology, Shandong University, Jinan, 250100, China
| | - Yang Li
- School of Mathematics, Shandong University, Jinan, 250100, China
| | - Guojun Li
- School of Mathematics, Shandong University, Jinan, 250100, China.
| | - Zhengchang Su
- Department of Bioinformatics and Genomics, The University of North Carolina at Charlotte, Charlotte, 28223, USA.
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6
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Steinmetzer T, Pilgram O, Wenzel BM, Wiedemeyer SJA. Fibrinolysis Inhibitors: Potential Drugs for the Treatment and Prevention of Bleeding. J Med Chem 2019; 63:1445-1472. [PMID: 31658420 DOI: 10.1021/acs.jmedchem.9b01060] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Hyperfibrinolytic situations can lead to life-threatening bleeding, especially during cardiac surgery. The approved antifibrinolytic agents such as tranexamic acid, ε-aminocaproic acid, 4-aminomethylbenzoic acid, and aprotinin were developed in the 1960s without the structural insight of their respective targets. Crystal structures of the main antifibrinolytic targets, the lysine binding sites on plasminogen's kringle domains, and plasmin's serine protease domain greatly contributed to the structure-based drug design of novel inhibitor classes. Two series of ligands targeting the lysine binding sites have been recently described, which are more potent than the most-widely used antifibrinolytic agent, tranexamic acid. Furthermore, four types of promising active site inhibitors of plasmin have been developed: tranexamic acid conjugates targeting the S1 pocket and primed sites, substrate-analogue linear homopiperidylalanine-containing 4-amidinobenzylamide derivatives, macrocyclic inhibitors addressing nonprimed binding regions, and bicyclic 14-mer SFTI-1 analogues blocking both, primed and nonprimed binding sites of plasmin. Furthermore, several allosteric plasmin inhibitors based on heparin mimetics have been developed.
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Affiliation(s)
- Torsten Steinmetzer
- Department of Pharmacy, Institute of Pharmaceutical Chemistry , Philipps University Marburg , Marbacher Weg 6 , D-35032 Marburg , Germany
| | - Oliver Pilgram
- Department of Pharmacy, Institute of Pharmaceutical Chemistry , Philipps University Marburg , Marbacher Weg 6 , D-35032 Marburg , Germany
| | - Benjamin M Wenzel
- Department of Pharmacy, Institute of Pharmaceutical Chemistry , Philipps University Marburg , Marbacher Weg 6 , D-35032 Marburg , Germany
| | - Simon J A Wiedemeyer
- Department of Pharmacy, Institute of Pharmaceutical Chemistry , Philipps University Marburg , Marbacher Weg 6 , D-35032 Marburg , Germany
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7
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Goettig P, Brandstetter H, Magdolen V. Surface loops of trypsin-like serine proteases as determinants of function. Biochimie 2019; 166:52-76. [PMID: 31505212 PMCID: PMC7615277 DOI: 10.1016/j.biochi.2019.09.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 09/06/2019] [Indexed: 02/07/2023]
Abstract
Trypsin and chymotrypsin-like serine proteases from family S1 (clan PA) constitute the largest protease group in humans and more generally in vertebrates. The prototypes chymotrypsin, trypsin and elastase represent simple digestive proteases in the gut, where they cleave nearly any protein. Multidomain trypsin-like proteases are key players in the tightly controlled blood coagulation and complement systems, as well as related proteases that are secreted from diverse immune cells. Some serine proteases are expressed in nearly all tissues and fluids of the human body, such as the human kallikreins and kallikrein-related peptidases with specialization for often unique substrates and accurate timing of activity. HtrA and membrane-anchored serine proteases fulfill important physiological tasks with emerging roles in cancer. The high diversity of all family members, which share the tandem β-barrel architecture of the chymotrypsin-fold in the catalytic domain, is conferred by the large differences of eight surface loops, surrounding the active site. The length of these loops alters with insertions and deletions, resulting in remarkably different three-dimensional arrangements. In addition, metal binding sites for Na+, Ca2+ and Zn2+ serve as regulatory elements, as do N-glycosylation sites. Depending on the individual tasks of the protease, the surface loops determine substrate specificity, control the turnover and allow regulation of activation, activity and degradation by other proteins, which are often serine proteases themselves. Most intriguingly, in some serine proteases, the surface loops interact as allosteric network, partially tuned by protein co-factors. Knowledge of these subtle and complicated molecular motions may allow nowadays for new and specific pharmaceutical or medical approaches.
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Affiliation(s)
- Peter Goettig
- Division of Structural Biology, Department of Biosciences, University of Salzburg, Billrothstrasse 11, 5020, Salzburg, Austria.
| | - Hans Brandstetter
- Division of Structural Biology, Department of Biosciences, University of Salzburg, Billrothstrasse 11, 5020, Salzburg, Austria
| | - Viktor Magdolen
- Clinical Research Unit, Department of Obstetrics and Gynecology, School of Medicine, Technical University of Munich, Ismaninger Strasse 22, 81675, München, Germany
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8
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Magnen M, Elsässer BM, Zbodakova O, Kasparek P, Gueugnon F, Petit-Courty A, Sedlacek R, Goettig P, Courty Y. Kallikrein-related peptidase 5 and seasonal influenza viruses, limitations of the experimental models for activating proteases. Biol Chem 2019; 399:1053-1064. [PMID: 29883316 DOI: 10.1515/hsz-2017-0340] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Accepted: 04/15/2018] [Indexed: 11/15/2022]
Abstract
Every year, influenza A virus (IAV) affects and kills many people worldwide. The viral hemagglutinin (HA) is a critical actor in influenza virus infectivity which needs to be cleaved by host serine proteases to exert its activity. KLK5 has been identified as an activating protease in humans with a preference for the H3N2 IAV subtype. We investigated the origin of this preference using influenza A/Puerto Rico/8/34 (PR8, H1N1) and A/Scotland/20/74 (Scotland, H3N2) viruses. Pretreatment of noninfectious virions with human KLK5 increased infectivity of Scotland IAV in MDCK cells and triggered influenza pneumonia in mice. These effects were not observed with the PR8 IAV. Molecular modeling and in vitro enzymatic studies of peptide substrates and recombinant HAs revealed that the sequences around the cleavage site do not represent the sole determinant of the KLK5 preference for the H3N2 subtype. Using mouse Klk5 and Klk5-deficient mice, we demonstrated in vitro and in vivo that the mouse ortholog protease is not an IAV activating enzyme. This may be explained by unfavorable interactions between H3 HA and mKlk5. Our data highlight the limitations of some approaches used to identify IAV-activating proteases.
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Affiliation(s)
- Mélia Magnen
- INSERM U1100, Centre d'Etude des Pathologies Respiratoires, Faculté de Médecine, F-37032 Tours, France.,Université de Tours, F-37032 Tours, France
| | | | - Olga Zbodakova
- Laboratory of Transgenic Models of Diseases, Division BIOCEV, Institute of Molecular Genetics, CZ-25250 Vestec, Czech Republic
| | - Petr Kasparek
- Laboratory of Transgenic Models of Diseases, Division BIOCEV, Institute of Molecular Genetics, CZ-25250 Vestec, Czech Republic
| | - Fabien Gueugnon
- INSERM U1100, Centre d'Etude des Pathologies Respiratoires, Faculté de Médecine, F-37032 Tours, France.,Université de Tours, F-37032 Tours, France
| | - Agnès Petit-Courty
- INSERM U1100, Centre d'Etude des Pathologies Respiratoires, Faculté de Médecine, F-37032 Tours, France.,Université de Tours, F-37032 Tours, France
| | - Radislav Sedlacek
- Laboratory of Transgenic Models of Diseases, Division BIOCEV, Institute of Molecular Genetics, CZ-25250 Vestec, Czech Republic
| | - Peter Goettig
- Department of Biosciences, University of Salzburg, A-5020 Salzburg, Austria
| | - Yves Courty
- INSERM U1100, Centre d'Etude des Pathologies Respiratoires, Faculté de Médecine, F-37032 Tours, France.,Université de Tours, F-37032 Tours, France
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9
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Swedberg JE, Wu G, Mahatmanto T, Durek T, Caradoc-Davies TT, Whisstock JC, Law RHP, Craik DJ. Highly Potent and Selective Plasmin Inhibitors Based on the Sunflower Trypsin Inhibitor-1 Scaffold Attenuate Fibrinolysis in Plasma. J Med Chem 2018; 62:552-560. [DOI: 10.1021/acs.jmedchem.8b01139] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Joakim E. Swedberg
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Guojie Wu
- ARC Centre of Excellence in Advanced Molecular Imaging, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Tunjung Mahatmanto
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Thomas Durek
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | | | - James C. Whisstock
- ARC Centre of Excellence in Advanced Molecular Imaging, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Ruby H. P. Law
- ARC Centre of Excellence in Advanced Molecular Imaging, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - David J. Craik
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
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10
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Li CY, de Veer SJ, Law RHP, Whisstock JC, Craik DJ, Swedberg JE. Characterising the Subsite Specificity of Urokinase-Type Plasminogen Activator and Tissue-Type Plasminogen Activator using a Sequence-Defined Peptide Aldehyde Library. Chembiochem 2018; 20:46-50. [PMID: 30225958 DOI: 10.1002/cbic.201800395] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 09/05/2018] [Indexed: 01/08/2023]
Abstract
Urokinase-type plasminogen activator (uPA) and tissue-type plasminogen activator (tPA) are two serine proteases that contribute to initiating fibrinolysis by activating plasminogen. uPA is also an important tumour-associated protease due to its role in extracellular matrix remodelling. Overexpression of uPA has been identified in several different cancers and uPA inhibition has been reported as a promising therapeutic strategy. Although several peptide-based uPA inhibitors have been developed, the extent to which uPA tolerates different tetrapeptide sequences that span the P1-P4 positions remains to be thoroughly explored. In this study, we screened a sequence-defined peptide aldehyde library against uPA and tPA. Preferred sequences from the library screen yielded potent inhibitors for uPA, led by Ac-GTAR-H (Ki =18 nm), but not for tPA. Additionally, synthetic peptide substrates corresponding to preferred inhibitor sequences were cleaved with high catalytic efficiency by uPA but not by tPA. These findings provide new insights into the binding specificity of uPA and tPA and the relative activity of tetrapeptide inhibitors and substrates against these enzymes.
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Affiliation(s)
- Choi Yi Li
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Simon J de Veer
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Ruby H P Law
- Department of Biochemistry and Molecular Biology, Biomedical Discovery Institute, Monash University, Melbourne, VIC, 3800, Australia
| | - James C Whisstock
- Department of Biochemistry and Molecular Biology, Biomedical Discovery Institute, Monash University, Melbourne, VIC, 3800, Australia
| | - David J Craik
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Joakim E Swedberg
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
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11
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Xu P, Huang M. Small Peptides as Modulators of Serine Proteases. Curr Med Chem 2018; 27:3686-3705. [PMID: 30332941 DOI: 10.2174/0929867325666181016163630] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Revised: 09/26/2018] [Accepted: 10/09/2018] [Indexed: 02/08/2023]
Abstract
Serine proteases play critical roles in many physiological and pathological processes, and are proven diagnostic and therapeutic targets in a number of clinical indications. Suppression of the aberrant proteolytic activities of these proteases has been clinically used for the treatments of relevant diseases. Polypeptides with 10-20 residues are of great interests as medicinal modulators of serine proteases, because these peptides demonstrate the characteristics of both small molecule drugs and macromolecular drugs. In this review, we summarized the recent development of peptide-based inhibitors against serine proteases with potent inhibitory and high specificity comparable to monoclonal antibodies. In addition, we also discussed the strategies of enhancing plasma half-life and bioavailability of peptides in vivo, which is the main hurdle that limits the clinical translation of peptide-based drugs. This review advocates new avenue for the development of effective serine protease inhibitors and highlights the prospect of the medicinal use of these inhibitors.
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Affiliation(s)
- Peng Xu
- College of Biological Science and Engineering, Fuzhou University, Fuzhou, Fujian 350116, China
| | - Mingdong Huang
- College of Chemistry, Fuzhou University, Fuzhou, Fujian 350116, China
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12
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Böttcher-Friebertshäuser E, Garten W, Klenk HD. The Antiviral Potential of Host Protease Inhibitors. ACTIVATION OF VIRUSES BY HOST PROTEASES 2018. [PMCID: PMC7122247 DOI: 10.1007/978-3-319-75474-1_11] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The replication of numerous pathogenic viruses depends on host proteases, which therefore emerged as potential antiviral drug targets. In some cases, e.g., for influenza viruses, their function during the viral propagation cycle is relatively well understood, where they cleave and activate viral surface glycoproteins. For other viruses, e.g., Ebola virus, the function of host proteases during replication is still not clear. Host proteases may also contribute to the pathogenicity of virus infection by activating proinflammatory cytokines. For some coronaviruses, human proteases can also serve in a nonproteolytical fashion simply as receptors for virus entry. However, blocking of such protein-protein contacts is challenging, because receptor surfaces are often flat and difficult to address with small molecules. In contrast, many proteases possess well-defined binding pockets. Therefore, they can be considered as well-druggable targets, especially, if they are extracellularly active. The number of their experimental crystal structures is steadily increasing, which is an important prerequisite for a rational structure-based inhibitor design using computational chemistry tools in combination with classical medicinal chemistry approaches. Moreover, host proteases can be considered as stable targets, and their inhibition should prevent rapid resistance developments, which is often observed when addressing viral proteins. Otherwise, the inhibition of host proteases can also affect normal physiological processes leading to a higher probability of side effects and a narrow therapeutic window. Therefore, they should be preferably used in combination therapies with additional antiviral drugs. This strategy should provide a stronger antiviral efficacy, allow to use lower drug doses, and minimize side effects. Despite numerous experimental findings on their antiviral activity, no small-molecule inhibitors of host proteases have been approved for the treatment of virus infections, so far.
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Affiliation(s)
| | - Wolfgang Garten
- Institut für Virologie, Philipps Universität, Marburg, Germany
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13
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Roslin S, Dahl K, Nordeman P. Reaction of 11
C-benzoyl chlorides with metalloid reagents: 11
C-labeling of benzyl alcohols, benzaldehydes, and phenyl ketones from [11
C]CO. J Labelled Comp Radiopharm 2018; 61:447-454. [DOI: 10.1002/jlcr.3609] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2017] [Revised: 01/14/2018] [Accepted: 01/16/2018] [Indexed: 11/07/2022]
Affiliation(s)
- Sara Roslin
- Organic Pharmaceutical Chemistry, Department of Medicinal Chemistry; Uppsala University; Uppsala Sweden
| | - Kenneth Dahl
- Division of Nuclear Medicine and Molecular Imaging, Massachusetts General Hospital, and Department of Radiology; Harvard Medical School; Boston MA USA
| | - Patrik Nordeman
- Organic Pharmaceutical Chemistry, Department of Medicinal Chemistry; Uppsala University; Uppsala Sweden
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14
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Soualmia F, El Amri C. Serine protease inhibitors to treat inflammation: a patent review (2011-2016). Expert Opin Ther Pat 2017; 28:93-110. [PMID: 29171765 DOI: 10.1080/13543776.2018.1406478] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
INTRODUCTION Inflammation is a physiological part of the complex biological response of tissues to counteract various harmful signals. This process involves diverse actors such as immune cells, blood vessels, and nerves as sources of mediators for inflammation control. Among them serine proteases are key elements in both physiological and pathological inflammation. AREAS COVERED Serine protease inhibitors to treat inflammatory diseases are being actively investigated by various industrial and academic institutions. The present review covers patent literature on serine protease inhibitors for the therapy of inflammatory diseases patented between 2011 and 2016. EXPERT OPINION Serine proteases regulating inflammation are versatile enzymes, usually involved in proinflammatory cytokine production and activation of immune cells. Their dysregulation during inflammation can have devastating consequences, promoting various diseases including skin and lung inflammation, neuroinflammation, and inflammatory arthritis. Several serine proteases were selected for their contribution to inflammatory diseases and significant efforts that are spread to develop inhibitors. Strategies developed for inhibitor identification consist on either peptide-based inhibitor derived from endogenous protein inhibitors or small-organic molecules. It is also worth noting that among the recent patents on serine protease inhibitors related to inflammation a significant number are related to retinal vascular dysfunction and skin diseases.
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Affiliation(s)
- Feryel Soualmia
- a B2A, Biological Adaptation and Ageing, Integrated Cellular Ageing and Inflammation, Molecular & Functional Enzymology , Sorbonne Universités , UPMC Univ Paris 06, UMR 8256 , Paris , France
| | - Chahrazade El Amri
- a B2A, Biological Adaptation and Ageing, Integrated Cellular Ageing and Inflammation, Molecular & Functional Enzymology , Sorbonne Universités , UPMC Univ Paris 06, UMR 8256 , Paris , France
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15
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Swedberg JE, Li CY, de Veer SJ, Wang CK, Craik DJ. Design of Potent and Selective Cathepsin G Inhibitors Based on the Sunflower Trypsin Inhibitor-1 Scaffold. J Med Chem 2017; 60:658-667. [PMID: 28045523 DOI: 10.1021/acs.jmedchem.6b01509] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Neutrophils are directly responsible for destroying invading pathogens via reactive oxygen species, antimicrobial peptides, and neutrophil serine proteases (NSPs). Imbalance between NSP activity and endogenous protease inhibitors is associated with chronic inflammatory disorders, and engineered inhibitors of NSPs are a potential therapeutic pathway. In this study we characterized the extended substrate specificity (P4-P1) of the NSP cathepsin G using a peptide substrate library. Substituting preferred cathepsin G substrate sequences into sunflower trypsin inhibitor-1 (SFTI-1) produced a potent cathepsin G inhibitor (Ki = 0.89 nM). Cathepsin G's P2' preference was determined by screening against a P2' diverse SFTI-based library, and the most preferred residue at P2' was combined in SFTI-1 with a preferred substrate sequence (P4-P2) and a nonproteinogenic P1 residue (4-guanidyl-l-phenylalanine) to produce a potent (Ki = 1.6 nM) and the most selective (≥360-fold) engineered cathepsin G inhibitor reported to date. This compound is a promising lead for further development of cathepsin G inhibitors targeting chronic inflammatory disorders.
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Affiliation(s)
- Joakim E Swedberg
- Institute for Molecular Bioscience, The University of Queensland , Brisbane, QLD 4072, Australia
| | - Choi Yi Li
- Institute for Molecular Bioscience, The University of Queensland , Brisbane, QLD 4072, Australia
| | - Simon J de Veer
- Institute for Molecular Bioscience, The University of Queensland , Brisbane, QLD 4072, Australia
| | - Conan K Wang
- Institute for Molecular Bioscience, The University of Queensland , Brisbane, QLD 4072, Australia
| | - David J Craik
- Institute for Molecular Bioscience, The University of Queensland , Brisbane, QLD 4072, Australia
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16
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de Veer SJ, Swedberg JE, Brattsand M, Clements JA, Harris JM. Exploring the active site binding specificity of kallikrein-related peptidase 5 (KLK5) guides the design of new peptide substrates and inhibitors. Biol Chem 2016; 397:1237-1249. [DOI: 10.1515/hsz-2016-0112] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Accepted: 02/16/2016] [Indexed: 12/24/2022]
Abstract
Abstract
Kallikrein-related peptidase 5 (KLK5) is a promising therapeutic target in several skin diseases, including Netherton syndrome, and is emerging as a potential target in various cancers. In this study, we used a sparse matrix library of 125 individually synthesized peptide substrates to characterize the binding specificity of KLK5. The sequences most favored by KLK5 were GRSR, YRSR and GRNR, and we identified sequence-specific interactions involving the peptide N-terminus by analyzing kinetic constants (kcat and KM) and performing molecular dynamics simulations. KLK5 inhibitors were subsequently engineered by substituting substrate sequences into the binding loop (P1, P2 and P4 residues) of sunflower trypsin inhibitor-1 (SFTI-1). These inhibitors were effective against KLK5 but showed limited selectivity, and performing a further substitution at P2′ led to the design of a new variant that displayed improved activity against KLK5 (Ki=4.2±0.2 nm), weak activity against KLK7 and 12-fold selectivity over KLK14. Collectively, these findings provide new insight into the design of highly favored binding sequences for KLK5 and reveal several opportunities for modulating inhibitor selectivity over closely related proteases that will be useful for future studies aiming to develop therapeutic molecules targeting KLK5.
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17
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Vadivel K, Kumar Y, Ogueli GI, Ponnuraj SM, Wongkongkathep P, Loo JA, Bajaj MS, Bajaj SP. S2'-subsite variations between human and mouse enzymes (plasmin, factor XIa, kallikrein) elucidate inhibition differences by tissue factor pathway inhibitor -2 domain1-wild-type, Leu17Arg-mutant and aprotinin. J Thromb Haemost 2016; 14:2509-2523. [PMID: 27797450 PMCID: PMC5504414 DOI: 10.1111/jth.13538] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Indexed: 12/20/2022]
Abstract
Essentials Current antifibrinolytics - aminocaproic acid and tranexamic acid-can cause seizures or renal injury. KD1L17R -KT , aprotinin and tranexamic acid were tested in a modified mouse tail-amputation model. S2'-subsite variations between human and mouse factor XIa result in vastly different inhibition profiles. KD1L17R -KT reduces blood loss and D-dimer levels in mouse with unobserved seizures or renal injury. SUMMARY Background Using tissue factor pathway inhibitor (TFPI)-2 Kunitz domain1 (KD1), we obtained a bifunctional antifibrinolytic molecule (KD1L17R -KT ) with C-terminal lysine (kringle domain binding) and P2'-residue arginine (improved specificity towards plasmin). KD1L17R -KT strongly inhibited human plasmin (hPm), with no inhibition of human kallikrein (hKLK) or factor XIa (hXIa). Furthermore, KD1L17R -KT reduced blood loss comparable to aprotinin in a mouse liver-laceration model of organ hemorrhage. However, effectiveness of these antifibrinolytic agents in a model of hemorrhage mimicking extremity trauma and their inhibition efficiencies for mouse enzymes (mPm, mKLK or mXIa) remain to be determined. Objective To determine potential differences in inhibition constants of various antifibrinolytic agents against mouse and human enzymes and test their effectiveness in a modified mouse tail-amputation hemorrhage model. Methods/Results Unexpectedly, mXIa was inhibited with ~ 17-fold increased affinity by aprotinin (Ki ~ 20 nm) and with measurable affinity for KD1L17R -KT (Ki ~ 3 μm); in contrast, KD1WT -VT inhibited hXIa or mXIa with similar affinity. Compared with hPm, mPm had ~ 3-fold reduced affinity, whereas species specificity for hKLK and mKLK was comparable for each inhibitor. S2'-subsite variations largely accounted for the observed differences. KD1L17R -KT and aprotinin were more effective than KD1WT -VT or tranexamic acid in inhibiting tPA-induced mouse plasma clot lysis. Further, KD1L17R -KT was more effective than KD1WT -VT and was comparable to aprotinin and tranexamic acid in reducing blood loss and D-dimer levels in the mouse tail-amputation model. Conclusions Inhibitor potencies differ between antifibrinolytic agents against human and mouse enzymes. KD1L17R -KT is effective in reducing blood loss in a tail-amputation model that mimics extremity injury.
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Affiliation(s)
- K Vadivel
- Department of Orthopaedic Surgery, University of California, Los Angeles, CA, USA
| | - Y Kumar
- Department of Orthopaedic Surgery, University of California, Los Angeles, CA, USA
| | - G I Ogueli
- Department of Orthopaedic Surgery, University of California, Los Angeles, CA, USA
| | - S M Ponnuraj
- Department of Orthopaedic Surgery, University of California, Los Angeles, CA, USA
| | - P Wongkongkathep
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, USA
| | - J A Loo
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, USA
- Molecular Biology Institute, University of California, Los Angeles, CA, USA
| | - M S Bajaj
- Division of Pulmonology and Critical Care, Department of Medicine, University of California, Los Angeles, CA, USA
| | - S P Bajaj
- Department of Orthopaedic Surgery, University of California, Los Angeles, CA, USA
- Molecular Biology Institute, University of California, Los Angeles, CA, USA
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18
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Mahatmanto T. Review seed biopharmaceutical cyclic peptides: From discovery to applications. Biopolymers 2016; 104:804-14. [PMID: 26385189 DOI: 10.1002/bip.22741] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Revised: 08/17/2015] [Accepted: 09/16/2015] [Indexed: 02/02/2023]
Abstract
Mini-proteins (or peptides) with disulfide bond/s and a cyclic backbone offer exciting opportunities for applications in medicine, as these ribosomally synthesized and posttranslationally modified peptides are exceptionally stable and amenable to grafting epitopes with desirable activities. Here I discuss important aspects of the discovery and applications of disulfide-bonded cyclic peptides from seeds, i.e., the trypsin inhibitor cyclotides and the preproalbumin with sunflower trypsin inhibitor-derived peptides, focusing on bioanalytical methods for and insights generated from their discovery as well as their potential use as engineering scaffolds for peptide-based drug design. The recent discovery of their precursors and processing enzymes could potentially enable in planta production of designer disulfide-bonded cyclic peptides, preferably in edible seeds, and address the demand for new biopharmaceutical peptides in a cost-effective manner.
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Affiliation(s)
- Tunjung Mahatmanto
- Department of Agricultural Product Technology, Faculty of Agricultural Technology, Brawijaya University, Malang, East Java, 65145, Indonesia
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19
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Swedberg JE, Mahatmanto T, Abdul Ghani H, de Veer SJ, Schroeder CI, Harris JM, Craik DJ. Substrate-Guided Design of Selective FXIIa Inhibitors Based on the Plant-Derived Momordica cochinchinensis Trypsin Inhibitor-II (MCoTI-II) Scaffold. J Med Chem 2016; 59:7287-92. [DOI: 10.1021/acs.jmedchem.6b00557] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Joakim E. Swedberg
- Institute
for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Tunjung Mahatmanto
- Institute
for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Hafiza Abdul Ghani
- Institute
for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Simon J. de Veer
- Institute
of Health and Biomedical Innovation, Queensland University of Technology, Brisbane Queensland 4059, Australia
| | - Christina I. Schroeder
- Institute
for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Jonathan M. Harris
- Institute
of Health and Biomedical Innovation, Queensland University of Technology, Brisbane Queensland 4059, Australia
| | - David J. Craik
- Institute
for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
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20
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Hinkes S, Wuttke A, Saupe SM, Ivanova T, Wagner S, Knörlein A, Heine A, Klebe G, Steinmetzer T. Optimization of Cyclic Plasmin Inhibitors: From Benzamidines to Benzylamines. J Med Chem 2016; 59:6370-86. [DOI: 10.1021/acs.jmedchem.6b00606] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Stefan Hinkes
- Department of Pharmacy, Institute
of Pharmaceutical Chemistry, Philipps University Marburg, Marbacher Weg
6, D-35032 Marburg, Germany
| | - André Wuttke
- Department of Pharmacy, Institute
of Pharmaceutical Chemistry, Philipps University Marburg, Marbacher Weg
6, D-35032 Marburg, Germany
| | - Sebastian M. Saupe
- Department of Pharmacy, Institute
of Pharmaceutical Chemistry, Philipps University Marburg, Marbacher Weg
6, D-35032 Marburg, Germany
| | - Teodora Ivanova
- Department of Pharmacy, Institute
of Pharmaceutical Chemistry, Philipps University Marburg, Marbacher Weg
6, D-35032 Marburg, Germany
| | - Sebastian Wagner
- Department of Pharmacy, Institute
of Pharmaceutical Chemistry, Philipps University Marburg, Marbacher Weg
6, D-35032 Marburg, Germany
| | - Anna Knörlein
- Department of Pharmacy, Institute
of Pharmaceutical Chemistry, Philipps University Marburg, Marbacher Weg
6, D-35032 Marburg, Germany
| | - Andreas Heine
- Department of Pharmacy, Institute
of Pharmaceutical Chemistry, Philipps University Marburg, Marbacher Weg
6, D-35032 Marburg, Germany
| | - Gerhard Klebe
- Department of Pharmacy, Institute
of Pharmaceutical Chemistry, Philipps University Marburg, Marbacher Weg
6, D-35032 Marburg, Germany
| | - Torsten Steinmetzer
- Department of Pharmacy, Institute
of Pharmaceutical Chemistry, Philipps University Marburg, Marbacher Weg
6, D-35032 Marburg, Germany
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21
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de Veer SJ, Ukolova SS, Munro CA, Swedberg JE, Buckle AM, Harris JM. Mechanism-based selection of a potent kallikrein-related peptidase 7 inhibitor from a versatile library based on the sunflower trypsin inhibitor SFTI-1. Biopolymers 2016; 100:510-8. [PMID: 24078181 DOI: 10.1002/bip.22231] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2012] [Revised: 03/01/2013] [Accepted: 03/02/2013] [Indexed: 02/06/2023]
Abstract
Potent and specific enzyme inhibition is a key goal in the development of therapeutic inhibitors targeting proteolytic activity. The backbone-cyclized peptide, Sunflower Trypsin Inhibitor (SFTI-1) affords a scaffold that can be engineered to achieve both these aims. SFTI-1's mechanism of inhibition is unusual in that it shows fast-on/slow-off kinetics driven by cleavage and religation of a scissile bond. This phenomenon was used to select a nanomolar inhibitor of kallikrein-related peptidase 7 (KLK7) from a versatile library of SFTI variants with diversity tailored to exploit distinctive surfaces present in the active site of serine proteases. Inhibitor selection was achieved through the use of size exclusion chromatography to separate protease/inhibitor complexes from unbound inhibitors followed by inhibitor identification according to molecular mass ascertained by mass spectrometry. This approach identified a single dominant inhibitor species with molecular weight of 1562.4 Da, which is consistent with the SFTI variant SFTI-WCTF. Once synthesized individually this inhibitor showed an IC50 of 173.9 ± 7.6 nM against chromogenic substrates and could block protein proteolysis. Molecular modeling analysis suggested that selection of SFTI-WCTF was driven by specific aromatic interactions and stabilized by an enhanced internal hydrogen bonding network. This approach provides a robust and rapid route to inhibitor selection and design.
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Affiliation(s)
- Simon J de Veer
- Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Queensland, 4059, Australia
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22
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de Veer SJ, Wang CK, Harris JM, Craik DJ, Swedberg JE. Improving the Selectivity of Engineered Protease Inhibitors: Optimizing the P2 Prime Residue Using a Versatile Cyclic Peptide Library. J Med Chem 2015; 58:8257-68. [PMID: 26393374 DOI: 10.1021/acs.jmedchem.5b01148] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Standard mechanism inhibitors are attractive design templates for engineering reversible serine protease inhibitors. When optimizing interactions between the inhibitor and target protease, many studies focus on the nonprimed segment of the inhibitor's binding loop (encompassing the contact β-strand). However, there are currently few methods for screening residues on the primed segment. Here, we designed a synthetic inhibitor library (based on sunflower trypsin inhibitor-1) for characterizing the P2' specificity of various serine proteases. Screening the library against 13 different proteases revealed unique P2' preferences for trypsin, chymotrypsin, matriptase, plasmin, thrombin, four kallikrein-related peptidases, and several clotting factors. Using this information to modify existing engineered inhibitors yielded new variants that showed considerably improved selectivity, reaching up to 7000-fold selectivity over certain off-target proteases. Our study demonstrates the importance of the P2' residue in standard mechanism inhibition and unveils a new approach for screening P2' substitutions that will benefit future inhibitor engineering studies.
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Affiliation(s)
- Simon J de Veer
- Institute of Health and Biomedical Innovation, Queensland University of Technology , Brisbane, Queensland QLD 4059, Australia
| | - Conan K Wang
- Institute for Molecular Bioscience, The University of Queensland , 306 Carmody Road, Building 80, Queensland Bioscience Presinct, Brisbane, Queensland, QLD 4072, Australia
| | - Jonathan M Harris
- Institute of Health and Biomedical Innovation, Queensland University of Technology , Brisbane, Queensland QLD 4059, Australia
| | - David J Craik
- Institute for Molecular Bioscience, The University of Queensland , 306 Carmody Road, Building 80, Queensland Bioscience Presinct, Brisbane, Queensland, QLD 4072, Australia
| | - Joakim E Swedberg
- Institute for Molecular Bioscience, The University of Queensland , 306 Carmody Road, Building 80, Queensland Bioscience Presinct, Brisbane, Queensland, QLD 4072, Australia
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23
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Teno N, Gohda K, Wanaka K, Tsuda Y, Akagawa M, Akiduki E, Araki M, Masuda A, Otsubo T, Yamashita Y. Novel type of plasmin inhibitors: Providing insight into P4 moiety and alternative scaffold to pyrrolopyrimidine. Bioorg Med Chem 2015; 23:3696-704. [DOI: 10.1016/j.bmc.2015.04.013] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Revised: 04/01/2015] [Accepted: 04/02/2015] [Indexed: 10/23/2022]
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24
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Plasmin regulation through allosteric, sulfated, small molecules. Molecules 2015; 20:608-24. [PMID: 25569517 PMCID: PMC6272155 DOI: 10.3390/molecules20010608] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Accepted: 12/26/2014] [Indexed: 01/16/2023] Open
Abstract
Plasmin, a key serine protease, plays a major role in clot lysis and extracellular matrix remodeling. Heparin, a natural polydisperse sulfated glycosaminoglycan, is known to allosterically modulate plasmin activity. No small allosteric inhibitor of plasmin has been discovered to date. We screened an in-house library of 55 sulfated, small glycosaminoglycan mimetics based on nine distinct scaffolds and varying number and positions of sulfate groups to discover several promising hits. Of these, a pentasulfated flavonoid-quinazolinone dimer 32 was found to be the most potent sulfated small inhibitor of plasmin (IC50 = 45 μM, efficacy = 100%). Michaelis-Menten kinetic studies revealed an allosteric inhibition of plasmin by these inhibitors. Studies also indicated that the most potent inhibitors are selective for plasmin over thrombin and factor Xa, two serine proteases in coagulation cascade. Interestingly, different inhibitors exhibited different levels of efficacy (40%–100%), an observation alluding to the unique advantage offered by an allosteric process. Overall, our work presents the first small, synthetic allosteric plasmin inhibitors for further rational design.
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25
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Al-Horani RA, Desai UR. Recent advances on plasmin inhibitors for the treatment of fibrinolysis-related disorders. Med Res Rev 2014; 34:1168-1216. [PMID: 24659483 PMCID: PMC8788159 DOI: 10.1002/med.21315] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/07/2023]
Abstract
Growing evidence suggests that plasmin is involved in a number of physiological processes in addition to its key role in fibrin cleavage. Plasmin inhibition is critical in preventing adverse consequences arising from plasmin overactivity, e.g., blood loss that may follow cardiac surgery. Aprotinin was widely used as an antifibrinolytic drug before its discontinuation in 2008. Tranexamic acid and ε-aminocaproic acid, two small molecule plasmin inhibitors, are currently used in the clinic. Several molecules have been designed utilizing covalent, but reversible, chemistry relying on reactive cyclohexanones, nitrile warheads, and reactive aldehyde peptidomimetics. Other major classes of plasmin inhibitors include the cyclic peptidomimetics and polypeptides of the Kunitz and Kazal-type. Allosteric inhibitors of plasmin have also been designed including small molecule lysine analogs that bind to plasmin's kringle domain(s) and sulfated glycosaminoglycan mimetics that bind to plasmin's catalytic domain. Plasmin inhibitors have also been explored for resolving other disease states including cell metastasis, cell proliferation, angiogenesis, and embryo implantation. This review highlights functional and structural aspects of plasmin inhibitors with the goal of advancing their design.
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Affiliation(s)
- Rami A Al-Horani
- Department of Medicinal Chemistry and Institute for Structural Biology and Drug Discovery, Virginia Commonwealth University, Richmond, Virginia
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26
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Teno N, Gohda K, Wanaka K, Tsuda Y, Sueda T, Yamashita Y, Otsubo T. Pyrrolopyrimidine-inhibitors with hydantoin moiety as spacer can explore P4/S4 interaction on plasmin. Bioorg Med Chem 2014; 22:2339-52. [DOI: 10.1016/j.bmc.2014.02.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2013] [Revised: 01/30/2014] [Accepted: 02/03/2014] [Indexed: 11/29/2022]
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27
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Saupe SM, Leubner S, Betz M, Klebe G, Steinmetzer T. Development of New Cyclic Plasmin Inhibitors with Excellent Potency and Selectivity. J Med Chem 2013; 56:820-31. [DOI: 10.1021/jm3012917] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Sebastian M. Saupe
- Department
of Pharmacy, Institute of Pharmaceutical
Chemistry, Philipps University Marburg,
Marbacher Weg 6, D-35032 Marburg, Germany
| | - Stephanie Leubner
- Department
of Pharmacy, Institute of Pharmaceutical
Chemistry, Philipps University Marburg,
Marbacher Weg 6, D-35032 Marburg, Germany
| | - Michael Betz
- Department
of Pharmacy, Institute of Pharmaceutical
Chemistry, Philipps University Marburg,
Marbacher Weg 6, D-35032 Marburg, Germany
| | - Gerhard Klebe
- Department
of Pharmacy, Institute of Pharmaceutical
Chemistry, Philipps University Marburg,
Marbacher Weg 6, D-35032 Marburg, Germany
| | - Torsten Steinmetzer
- Department
of Pharmacy, Institute of Pharmaceutical
Chemistry, Philipps University Marburg,
Marbacher Weg 6, D-35032 Marburg, Germany
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28
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Teno N, Otsubo T, Gohda K, Wanaka K, Sueda T, Ikeda K, Hijikata-Okunomiya A, Tsuda Y. Synthesis and evaluation of tripeptidic plasmin inhibitors with nitrile as warhead. J Pept Sci 2012; 18:620-5. [DOI: 10.1002/psc.2442] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2012] [Revised: 07/05/2012] [Accepted: 07/16/2012] [Indexed: 11/06/2022]
Affiliation(s)
- Naoki Teno
- Hiroshima International University; Faculty of Pharmaceutical Sciences; 5-1-1, Hirokoshingai, Kure Hiroshima 737-0112 Japan
| | - Tadamune Otsubo
- Hiroshima International University; Faculty of Pharmaceutical Sciences; 5-1-1, Hirokoshingai, Kure Hiroshima 737-0112 Japan
| | - Keigo Gohda
- Computer-aided Molecular Modeling Research Center, Kansai (CAMM-Kansai); 5-1-7, Ohmichidori, Nagata-ku Kobe 653-0833 Japan
| | - Keiko Wanaka
- Kobe Research Projects on Thrombosis and Haemostasis; 3-15-18, Asahigaoka, Tarumi-ku Kobe 655-0033 Japan
| | - Takuya Sueda
- Hiroshima International University; Faculty of Pharmaceutical Sciences; 5-1-1, Hirokoshingai, Kure Hiroshima 737-0112 Japan
| | - Kiyoshi Ikeda
- Hiroshima International University; Faculty of Pharmaceutical Sciences; 5-1-1, Hirokoshingai, Kure Hiroshima 737-0112 Japan
| | - Akiko Hijikata-Okunomiya
- Kobe International University; Faculty of Rehabilitation; 9-1-6, Koyocho-naka, Higashinada-ku Kobe 658-0032 Japan
| | - Yuko Tsuda
- Kobe Gakuin University; Faculty of Pharmaceutical Sciences; 1-1-3, Minatojima, Chuo-ku Kobe 650-8586 Japan
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29
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de Veer SJ, Swedberg JE, Parker EA, Harris JM. Non-combinatorial library screening reveals subsite cooperativity and identifies new high-efficiency substrates for kallikrein-related peptidase 14. Biol Chem 2012; 393:331-41. [PMID: 22505516 DOI: 10.1515/bc-2011-250] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2011] [Accepted: 12/05/2011] [Indexed: 11/15/2022]
Abstract
An array of substrates link the tryptic serine protease, kallikrein-related peptidase 14 (KLK14), to physiological functions including desquamation and activation of signaling molecules associated with inflammation and cancer. Recognition of protease cleavage sequences is driven by complementarity between exposed substrate motifs and the physicochemical signature of an enzyme's active site cleft. However, conventional substrate screening methods have generated conflicting subsite profiles for KLK14. This study utilizes a recently developed screening technique, the sparse matrix library, to identify five novel high-efficiency sequences for KLK14. The optimal sequence, YASR, was cleaved with higher efficiency (k(cat)/K(m)=3.81 ± 0.4 × 10(6) M(-1) s(-1)) than favored substrates from positional scanning and phage display by 2- and 10-fold, respectively. Binding site cooperativity was prominent among preferred sequences, which enabled optimal interaction at all subsites as indicated by predictive modeling of KLK14/substrate complexes. These simulations constitute the first molecular dynamics analysis of KLK14 and offer a structural rationale for the divergent subsite preferences evident between KLK14 and closely related KLKs, KLK4 and KLK5. Collectively, these findings highlight the importance of binding site cooperativity in protease substrate recognition, which has implications for discovery of optimal substrates and engineering highly effective protease inhibitors.
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Affiliation(s)
- Simon J de Veer
- Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Australia
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30
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Craik DJ, Swedberg JE, Mylne JS, Cemazar M. Cyclotides as a basis for drug design. Expert Opin Drug Discov 2012; 7:179-94. [PMID: 22468950 DOI: 10.1517/17460441.2012.661554] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
INTRODUCTION Cyclotides are plant-made defence proteins with a head-to-tail cyclic backbone combined with a conserved, six cystine knot. They have a range of biological activities, including uterotonic and anti-HIV activity, which have attracted attention to their potential pharmaceutical applications. Furthermore, their unique structures and high stability make them appealing as peptide-based templates for drug design applications. Methods have been developed for their production, including solid phase peptide synthesis as well as recombinant methods. AREAS COVERED This article reviews the recent literature associated with therapeutic applications of naturally occurring and synthetically modified cyclotides. It includes applications of cyclotides and cyclotide-like molecules as peptide-based drug leads and diagnostic agents. EXPERT OPINION The ultra-stable cyclotides are promising templates for drug development applications and are currently being assessed for the potential breadth of their applications. For synthetic versions of cyclotides to enter human clinical trials further studies to examine their biopharmaceutical properties and toxicities are required. However, several promising proof-of-concept studies have established that pharmaceutically relevant bioactive peptide sequences can be grafted into cyclotide frameworks and thereby stabilised, while maintaining biological activity. These studies include examples directed at cancer, cardiovascular disease and infectious diseases. Solid phase peptide synthesis has been the preferred approach for making pharmaceutically modified cyclotides so far, but promising progress is being made in biological approaches to cyclotide production.
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Affiliation(s)
- David J Craik
- The University of Queensland, Institute for Molecular Bioscience, Brisbane, Australia.
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Saupe SM, Steinmetzer T. A New Strategy for the Development of Highly Potent and Selective Plasmin Inhibitors. J Med Chem 2012; 55:1171-80. [DOI: 10.1021/jm2011996] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Sebastian M. Saupe
- Department of Pharmacy,
Institute of Pharmaceutical
Chemistry, Philipps University Marburg,
Marbacher Weg 6, D-35032 Marburg, Germany
| | - Torsten Steinmetzer
- Department of Pharmacy,
Institute of Pharmaceutical
Chemistry, Philipps University Marburg,
Marbacher Weg 6, D-35032 Marburg, Germany
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Swedberg JE, Harris JM. Natural and engineered plasmin inhibitors: applications and design strategies. Chembiochem 2012; 13:336-48. [PMID: 22238174 DOI: 10.1002/cbic.201100673] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2011] [Indexed: 12/17/2022]
Abstract
The serine protease plasmin is ubiquitously expressed throughout the human body in the form of the zymogen plasminogen. Conversion to active plasmin occurs through enzymatic cleavage by plasminogen activators. The plasminogen activator/plasmin system has a well-established function in the removal of intravascular fibrin deposition through fibrinolysis and the inhibition of plasmin activity; this has found widespread clinical use in reducing perioperative bleeding. Increasing evidence also suggests diverse, although currently less defined, roles for plasmin in a number of physiological and pathological processes relating to extracellular matrix degradation, cell migration and tissue remodelling. In particular, dysregulation of plasmin has been linked to cancer invasion/metastasis and various chronic inflammatory conditions; this has prompted efforts to develop inhibitors of this protease. Although a number of plasmin inhibitors exist, they commonly suffer from poor potency and/or specificity of inhibition that either results in reduced efficacy or prevents clinical use. Consequently, there is a need for further development of high-affinity plasmin inhibitors that maintain selectivity over other serine proteases. This review summarises clearly defined and potential applications for plasmin inhibition. The properties of naturally occurring and engineered plasmin inhibitors are discussed in the context of current knowledge regarding plasmin structure, specificity and function. This includes design strategies to obtain the potency and specificity of inhibition in addition to controlled temporal and spatial distribution tailored for the intended use.
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Affiliation(s)
- Joakim E Swedberg
- Institute for Molecular Bioscience, The University of Queensland, Brisbane QLD 4072 (Australia)
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