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Mazzocato Y, Perin S, Morales-Sanfrutos J, Romanyuk Z, Pluda S, Acquasaliente L, Borsato G, De Filippis V, Scarso A, Angelini A. A novel genetically-encoded bicyclic peptide inhibitor of human urokinase-type plasminogen activator with better cross-reactivity toward the murine orthologue. Bioorg Med Chem 2023; 95:117499. [PMID: 37879145 DOI: 10.1016/j.bmc.2023.117499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Revised: 08/30/2023] [Accepted: 10/10/2023] [Indexed: 10/27/2023]
Abstract
The inhibition of human urokinase-type plasminogen activator (huPA), a serine protease that plays an important role in pericellular proteolysis, is a promising strategy to decrease the invasive and metastatic activity of tumour cells. However, the generation of selective small molecule huPA inhibitors has proven to be challenging due to the high structural similarity of huPA to other paralogue serine proteases. Efforts to generate more specific therapies have led to the development of cyclic peptide-based inhibitors with much higher selectivity against huPA. While this latter property is desired, the sparing of the orthologue murine poses difficulties for the testing of the inhibitor in preclinical mouse model. In this work, we have applied a Darwinian evolution-based approach to identify phage-encoded bicyclic peptide inhibitors of huPA with better cross-reactivity towards murine uPA (muPA). The best selected bicyclic peptide (UK132) inhibited huPA and muPA with Ki values of 0.33 and 12.58 µM, respectively. The inhibition appears to be specific for uPA, as UK132 only weakly inhibits a panel of structurally similar serine proteases. Removal or substitution of the second loop with one not evolved in vitro led to monocyclic and bicyclic peptide analogues with lower potency than UK132. Moreover, swapping of 1,3,5-tris-(bromomethyl)-benzene with different small molecules not used in the phage selection, resulted in an 80-fold reduction of potency, revealing the important structural role of the branched cyclization linker. Further substitution of an arginine in UK132 to a lysine resulted in a bicyclic peptide UK140 with enhanced inhibitory potency against both huPA (Ki = 0.20 µM) and murine orthologue (Ki = 2.79 µM). By combining good specificity, nanomolar affinity and a low molecular mass, the bicyclic peptide inhibitor developed in this work may provide a novel human and murine cross-reactive lead for the development of a potent and selective anti-metastatic therapy.
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Affiliation(s)
- Ylenia Mazzocato
- Department of Molecular Sciences and Nanosystems, Ca' Foscari University of Venice, Via Torino 155, 30172 Venice, Italy
| | - Stefano Perin
- Department of Molecular Sciences and Nanosystems, Ca' Foscari University of Venice, Via Torino 155, 30172 Venice, Italy
| | - Julia Morales-Sanfrutos
- Proteomics Unit, Spanish National Cancer Research Centre (CNIO), C. de Melchor Fernández Almagro 3, 28029 Madrid, Spain
| | - Zhanna Romanyuk
- Department of Molecular Sciences and Nanosystems, Ca' Foscari University of Venice, Via Torino 155, 30172 Venice, Italy
| | - Stefano Pluda
- Department of Molecular Sciences and Nanosystems, Ca' Foscari University of Venice, Via Torino 155, 30172 Venice, Italy; Fidia Farmaceutici S.p.A., Via Ponte della Fabbrica 3/A, Abano Terme 35031, Italy
| | - Laura Acquasaliente
- Department of Pharmaceutical and Pharmacological Sciences, School of Medicine, University of Padova, Via Marzolo 5, 35131 Padova, Italy
| | - Giuseppe Borsato
- Department of Molecular Sciences and Nanosystems, Ca' Foscari University of Venice, Via Torino 155, 30172 Venice, Italy
| | - Vincenzo De Filippis
- Department of Pharmaceutical and Pharmacological Sciences, School of Medicine, University of Padova, Via Marzolo 5, 35131 Padova, Italy
| | - Alessandro Scarso
- Department of Molecular Sciences and Nanosystems, Ca' Foscari University of Venice, Via Torino 155, 30172 Venice, Italy
| | - Alessandro Angelini
- Department of Molecular Sciences and Nanosystems, Ca' Foscari University of Venice, Via Torino 155, 30172 Venice, Italy; European Centre for Living Technology (ECLT), Ca' Bottacin, Dorsoduro 3911, Calle Crosera, 30123 Venice, Italy.
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2
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Wehrhan L, Leppkes J, Dimos N, Loll B, Koksch B, Keller BG. Water Network in the Binding Pocket of Fluorinated BPTI-Trypsin Complexes─Insights from Simulation and Experiment. J Phys Chem B 2022; 126:9985-9999. [PMID: 36409613 DOI: 10.1021/acs.jpcb.2c05496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Structural waters in the S1 binding pocket of β-trypsin are critical for the stabilization of the complex of β-trypsin with its inhibitor bovine pancreatic trypsin inhibitor (BPTI). The inhibitor strength of BPTI can be modulated by replacing the critical lysine residue at the P1 position by non-natural amino acids. We study BPTI variants in which the critical Lys15 in BPTI has been replaced by α-aminobutyric acid (Abu) and its fluorinated derivatives monofluoroethylglycine (MfeGly), difluoroethylglycine (DfeGly), and trifluoroethylglycine (TfeGly). We investigate the hypothesis that additional water molecules in the binding pocket can form specific noncovalent interactions with the fluorinated side chains and thereby act as an extension of the inhibitors. We report potentials of mean force (PMF) of the unbinding process for all four complexes and enzyme activity inhibition assays. Additionally, we report the protein crystal structure of the Lys15MfeGly-BPTI-β-trypsin complex (pdb: 7PH1). Both experimental and computational data show a stepwise increase in inhibitor strength with increasing fluorination of the Abu side chain. The PMF additionally shows a minimum for the encounter complex and an intermediate state just before the bound state. In the bound state, the computational analysis of the structure and dynamics of the water molecules in the S1 pocket shows a highly dynamic network of water molecules that does not indicate a rigidification or stabilizing trend in regard to energetic properties that could explain the increase in inhibitor strength. The analysis of the energy and the entropy of the water molecules in the S1 binding pocket using grid inhomogeneous solvation theory confirms this result. Overall, fluorination systematically changes the binding affinity, but the effect cannot be explained by a persistent water network in the binding pocket. Other effects, such as the hydrophobicity of fluorinated amino acids and the stability of the encounter complex as well as the additional minimum in the potential of mean force in the bound state, likely influence the affinity more directly.
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Affiliation(s)
- Leon Wehrhan
- Department of Biology, Chemistry, and Pharmacy, Freie Universität Berlin, Institute of Chemistry and Biochemistry, Arnimallee 22, Berlin14195, Germany
| | - Jakob Leppkes
- Department of Biology, Chemistry, and Pharmacy, Freie Universität Berlin, Institute of Chemistry and Biochemistry, Arnimallee 20, Berlin14195, Germany
| | - Nicole Dimos
- Department of Biology, Chemistry, and Pharmacy, Freie Universität Berlin, Institute of Chemistry and Biochemistry, Takustr. 6, Berlin14195, Germany
| | - Bernhard Loll
- Department of Biology, Chemistry, and Pharmacy, Freie Universität Berlin, Institute of Chemistry and Biochemistry, Takustr. 6, Berlin14195, Germany
| | - Beate Koksch
- Department of Biology, Chemistry, and Pharmacy, Freie Universität Berlin, Institute of Chemistry and Biochemistry, Arnimallee 20, Berlin14195, Germany
| | - Bettina G Keller
- Department of Biology, Chemistry, and Pharmacy, Freie Universität Berlin, Institute of Chemistry and Biochemistry, Arnimallee 22, Berlin14195, Germany
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3
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Urokinase plasminogen activator as an anti-metastasis target: inhibitor design principles, recent amiloride derivatives, and issues with human/mouse species selectivity. Biophys Rev 2022; 14:277-301. [PMID: 35340592 PMCID: PMC8921380 DOI: 10.1007/s12551-021-00921-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Accepted: 11/18/2021] [Indexed: 01/09/2023] Open
Abstract
The urokinase plasminogen activator (uPA) is a widely studied anticancer drug target with multiple classes of inhibitors reported to date. Many of these inhibitors contain amidine or guanidine groups, while others lacking these groups show improved oral bioavailability. Most of the X-ray co-crystal structures of small molecule uPA inhibitors show a key salt bridge with the side chain carboxylate of Asp189 in the S1 pocket of uPA. This review summarises the different classes of uPA inhibitors, their binding interactions and experimentally measured inhibitory potencies and highlights species selectivity issues with attention to recently described 6-substituted amiloride and 5‑N,N-(hexamethylene)amiloride (HMA) derivatives.
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4
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S El Salamouni N, Buckley BJ, Jiang L, Huang M, Ranson M, Kelso MJ, Yu H. Disruption of Water Networks is the Cause of Human/Mouse Species Selectivity in Urokinase Plasminogen Activator (uPA) Inhibitors Derived from Hexamethylene Amiloride (HMA). J Med Chem 2021; 65:1933-1945. [PMID: 34898192 DOI: 10.1021/acs.jmedchem.1c01423] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The urokinase plasminogen activator (uPA) plays a critical role in tumor cell invasion and migration and is a promising antimetastasis target. 6-Substituted analogues of 5-N,N-(hexamethylene)amiloride (HMA) are potent and selective uPA inhibitors that lack the diuretic and antikaliuretic properties of the parent drug amiloride. However, the compounds display pronounced selectivity for human over mouse uPA, thus confounding interpretation of data from human xenograft mouse models of cancer. Here, computational and experimental findings reveal that residue 99 is a key contributor to the observed species selectivity, whereby enthalpically unfavorable expulsion of a water molecule by the 5-N,N-hexamethylene ring occurs when residue 99 is Tyr (as in mouse uPA). Analogue 7 lacking the 5-N,N-hexamethylene ring maintained similar water networks when bound to human and mouse uPA and displayed reduced selectivity, thus supporting this conclusion. The study will guide further optimization of dual-potent human/mouse uPA inhibitors from the amiloride class as antimetastasis drugs.
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Affiliation(s)
- Nehad S El Salamouni
- School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW 2522, Australia.,Molecular Horizons, University of Wollongong, Wollongong, NSW 2522, Australia.,Illawarra Health and Medical Research Institute, Wollongong, NSW 2522, Australia
| | - Benjamin J Buckley
- School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW 2522, Australia.,Molecular Horizons, University of Wollongong, Wollongong, NSW 2522, Australia.,Illawarra Health and Medical Research Institute, Wollongong, NSW 2522, Australia.,CONCERT-Translational Cancer Research Centre, Sydney, NSW 2750, Australia
| | - Longguang Jiang
- National Joint Biomedical Engineering Research Centre on Photodynamic Technologies, Fuzhou University, Fujian 350116, China
| | - Mingdong Huang
- National Joint Biomedical Engineering Research Centre on Photodynamic Technologies, Fuzhou University, Fujian 350116, China
| | - Marie Ranson
- School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW 2522, Australia.,Molecular Horizons, University of Wollongong, Wollongong, NSW 2522, Australia.,Illawarra Health and Medical Research Institute, Wollongong, NSW 2522, Australia.,CONCERT-Translational Cancer Research Centre, Sydney, NSW 2750, Australia
| | - Michael J Kelso
- School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW 2522, Australia.,Molecular Horizons, University of Wollongong, Wollongong, NSW 2522, Australia.,Illawarra Health and Medical Research Institute, Wollongong, NSW 2522, Australia
| | - Haibo Yu
- School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW 2522, Australia.,Molecular Horizons, University of Wollongong, Wollongong, NSW 2522, Australia.,Illawarra Health and Medical Research Institute, Wollongong, NSW 2522, Australia
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5
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A facile approach towards amidinophenylalanine derivatives as building blocks for the synthesis of non-natural peptides and peptidomimetics. Tetrahedron Lett 2021. [DOI: 10.1016/j.tetlet.2021.153342] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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6
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Lorthiois E, Roache J, Barnes-Seeman D, Altmann E, Hassiepen U, Turner G, Duvadie R, Hornak V, Karki RG, Schiering N, Weihofen WA, Perruccio F, Calhoun A, Fazal T, Dedic D, Durand C, Dussauge S, Fettis K, Tritsch F, Dentel C, Druet A, Liu D, Kirman L, Lachal J, Namoto K, Bevan D, Mo R, Monnet G, Muller L, Zessis R, Huang X, Lindsley L, Currie T, Chiu YH, Fridrich C, Delgado P, Wang S, Hollis-Symynkywicz M, Berghausen J, Williams E, Liu H, Liang G, Kim H, Hoffmann P, Hein A, Ramage P, D’Arcy A, Harlfinger S, Renatus M, Ruedisser S, Feldman D, Elliott J, Sedrani R, Maibaum J, Adams CM. Structure-Based Design and Preclinical Characterization of Selective and Orally Bioavailable Factor XIa Inhibitors: Demonstrating the Power of an Integrated S1 Protease Family Approach. J Med Chem 2020; 63:8088-8113. [DOI: 10.1021/acs.jmedchem.0c00279] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Edwige Lorthiois
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | - James Roache
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts 02139, United States
| | - David Barnes-Seeman
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts 02139, United States
| | - Eva Altmann
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | - Ulrich Hassiepen
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | - Gordon Turner
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts 02139, United States
| | - Rohit Duvadie
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts 02139, United States
| | - Viktor Hornak
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts 02139, United States
| | - Rajeshri G. Karki
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts 02139, United States
| | - Nikolaus Schiering
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | - Wilhelm A. Weihofen
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts 02139, United States
| | - Francesca Perruccio
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | - Amy Calhoun
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts 02139, United States
| | - Tanzina Fazal
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts 02139, United States
| | - Darija Dedic
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | - Corinne Durand
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | - Solene Dussauge
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | - Kamal Fettis
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | - Fabien Tritsch
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | - Celine Dentel
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | - Adelaide Druet
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | - Donglei Liu
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts 02139, United States
| | - Louise Kirman
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts 02139, United States
| | - Julie Lachal
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | - Kenji Namoto
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | - Douglas Bevan
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts 02139, United States
| | - Rose Mo
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts 02139, United States
| | - Gabriela Monnet
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | - Lionel Muller
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | - Richard Zessis
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts 02139, United States
| | - Xueming Huang
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts 02139, United States
| | - Loren Lindsley
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts 02139, United States
| | - Treeve Currie
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts 02139, United States
| | - Yu-Hsin Chiu
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts 02139, United States
| | - Cary Fridrich
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts 02139, United States
| | - Peter Delgado
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts 02139, United States
| | - Shuangxi Wang
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts 02139, United States
| | | | - Joerg Berghausen
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | - Eric Williams
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts 02139, United States
| | - Hong Liu
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts 02139, United States
| | - Guiqing Liang
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts 02139, United States
| | - Hyungchul Kim
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts 02139, United States
| | - Peter Hoffmann
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts 02139, United States
| | - Andreas Hein
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | - Paul Ramage
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | - Allan D’Arcy
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | - Stefanie Harlfinger
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | - Martin Renatus
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | - Simon Ruedisser
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | - David Feldman
- Novartis Institutes for BioMedical Research, East Hanover, New Jersey 07396, United States
| | - Jason Elliott
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts 02139, United States
| | - Richard Sedrani
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | - Juergen Maibaum
- Novartis Institutes for BioMedical Research, Novartis Campus, CH-4056 Basel, Switzerland
| | - Christopher M. Adams
- Novartis Institutes for BioMedical Research, Cambridge, Massachusetts 02139, United States
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7
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Kaur N, Verma Y, Grewal P, Ahlawat N, Bhardwaj P, Jangid NK. Palladium acetate assisted synthesis of five-membered N-polyheterocycles. SYNTHETIC COMMUN 2020. [DOI: 10.1080/00397911.2020.1723640] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- Navjeet Kaur
- Department of Chemistry, Banasthali Vidyapith, Jaipur, India
| | - Yamini Verma
- Department of Chemistry, Banasthali Vidyapith, Jaipur, India
| | - Pooja Grewal
- Department of Chemistry, Banasthali Vidyapith, Jaipur, India
| | - Neha Ahlawat
- Department of Chemistry, Banasthali Vidyapith, Jaipur, India
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8
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Ngo K, Collins-Kautz C, Gerstenecker S, Wagner B, Heine A, Klebe G. Protein-Induced Change in Ligand Protonation during Trypsin and Thrombin Binding: Hint on Differences in Selectivity Determinants of Both Proteins? J Med Chem 2020; 63:3274-3289. [DOI: 10.1021/acs.jmedchem.9b02061] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Khang Ngo
- Institute of Pharmaceutical Chemistry, Philipps-University Marburg, Marbacher Weg 6, 35032 Marburg, Germany
| | - Chelsey Collins-Kautz
- Institute of Pharmaceutical Chemistry, Philipps-University Marburg, Marbacher Weg 6, 35032 Marburg, Germany
| | - Stefan Gerstenecker
- Institute of Pharmaceutical Chemistry, Philipps-University Marburg, Marbacher Weg 6, 35032 Marburg, Germany
| | - Björn Wagner
- Pharma Research Non-Clinical Safety, F. Hoffmann-La Roche AG, 4070 Basel, Switzerland
| | - Andreas Heine
- Institute of Pharmaceutical Chemistry, Philipps-University Marburg, Marbacher Weg 6, 35032 Marburg, Germany
| | - Gerhard Klebe
- Institute of Pharmaceutical Chemistry, Philipps-University Marburg, Marbacher Weg 6, 35032 Marburg, Germany
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9
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Huang B, Yang C, Zhou J, Xia W. Electrochemically generated N-iodoaminium species as key intermediates for selective methyl sulphonylimination of tertiary amines. Chem Commun (Camb) 2020; 56:5010-5013. [DOI: 10.1039/c9cc09869k] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This study presents a straightforward protocol for approaching N-sulphonylamidines via an electricity-driven, iodine-mediated cross dehydrogenative condensation (CDC) between sulphonamides and tertiary amines.
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Affiliation(s)
- Binbin Huang
- State Key Lab of Urban Water Resource and Environment
- School of Science, Harbin Institute of Technology (Shenzhen)
- Shenzhen 518055
- China
| | - Chao Yang
- State Key Lab of Urban Water Resource and Environment
- School of Science, Harbin Institute of Technology (Shenzhen)
- Shenzhen 518055
- China
| | - Jia Zhou
- State Key Lab of Urban Water Resource and Environment
- School of Science, Harbin Institute of Technology (Shenzhen)
- Shenzhen 518055
- China
| | - Wujiong Xia
- State Key Lab of Urban Water Resource and Environment
- School of Science, Harbin Institute of Technology (Shenzhen)
- Shenzhen 518055
- China
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10
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Chen J, Long W, Zhao Y, Li H, Zheng Y, Lian P, Wan X. In Situ Generation of Oxazole Ylide and Interception with Sulfonamide: Construction of Amidines Using Two Diazo Molecules. CHINESE J CHEM 2018. [DOI: 10.1002/cjoc.201800208] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Jijun Chen
- Key Laboratory of Organic Synthesis of Jiangsu Province, College of Chemistry, Chemical Engineering and Materials Science; Soochow University; Suzhou Jiangsu 215123 China
| | - Wenhao Long
- Key Laboratory of Organic Synthesis of Jiangsu Province, College of Chemistry, Chemical Engineering and Materials Science; Soochow University; Suzhou Jiangsu 215123 China
| | - Yanwei Zhao
- Key Laboratory of Organic Synthesis of Jiangsu Province, College of Chemistry, Chemical Engineering and Materials Science; Soochow University; Suzhou Jiangsu 215123 China
| | - Haiyan Li
- Key Laboratory of Organic Synthesis of Jiangsu Province, College of Chemistry, Chemical Engineering and Materials Science; Soochow University; Suzhou Jiangsu 215123 China
| | - Yonggao Zheng
- Key Laboratory of Organic Synthesis of Jiangsu Province, College of Chemistry, Chemical Engineering and Materials Science; Soochow University; Suzhou Jiangsu 215123 China
| | - Pengcheng Lian
- Key Laboratory of Organic Synthesis of Jiangsu Province, College of Chemistry, Chemical Engineering and Materials Science; Soochow University; Suzhou Jiangsu 215123 China
| | - Xiaobing Wan
- Key Laboratory of Organic Synthesis of Jiangsu Province, College of Chemistry, Chemical Engineering and Materials Science; Soochow University; Suzhou Jiangsu 215123 China
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11
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Gerasyuto AI, Arnold MA, Wang J, Chen G, Zhang X, Smith S, Woll MG, Baird J, Zhang N, Almstead NG, Narasimhan J, Peddi S, Dumble M, Sheedy J, Weetall M, Branstrom AA, Prasad JVN, Karp GM. Discovery and Optimization of Indolyl-Containing 4-Hydroxy-2-Pyridone Type II DNA Topoisomerase Inhibitors Active against Multidrug Resistant Gram-negative Bacteria. J Med Chem 2018; 61:4456-4475. [PMID: 29727185 PMCID: PMC5991783 DOI: 10.1021/acs.jmedchem.8b00114] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
There exists an urgent medical need to identify new chemical entities (NCEs) targeting multidrug resistant (MDR) bacterial infections, particularly those caused by Gram-negative pathogens. 4-Hydroxy-2-pyridones represent a novel class of nonfluoroquinolone inhibitors of bacterial type II topoisomerases active against MDR Gram-negative bacteria. Herein, we report on the discovery and structure-activity relationships of a series of fused indolyl-containing 4-hydroxy-2-pyridones with improved in vitro antibacterial activity against fluoroquinolone resistant strains. Compounds 6o and 6v are representative of this class, targeting both bacterial DNA gyrase and topoisomerase IV (Topo IV). In an abbreviated susceptibility screen, compounds 6o and 6v showed improved MIC90 values against Escherichia coli (0.5-1 μg/mL) and Acinetobacter baumannii (8-16 μg/mL) compared to the precursor compounds. In a murine septicemia model, both compounds showed complete protection in mice infected with a lethal dose of E. coli.
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Affiliation(s)
- Aleksey I Gerasyuto
- PTC Therapeutics, Inc. , 100 Corporate Court , South Plainfield , New Jersey 07080 , United States
| | - Michael A Arnold
- PTC Therapeutics, Inc. , 100 Corporate Court , South Plainfield , New Jersey 07080 , United States
| | - Jiashi Wang
- PTC Therapeutics, Inc. , 100 Corporate Court , South Plainfield , New Jersey 07080 , United States
| | - Guangming Chen
- PTC Therapeutics, Inc. , 100 Corporate Court , South Plainfield , New Jersey 07080 , United States
| | - Xiaoyan Zhang
- PTC Therapeutics, Inc. , 100 Corporate Court , South Plainfield , New Jersey 07080 , United States
| | - Sean Smith
- PTC Therapeutics, Inc. , 100 Corporate Court , South Plainfield , New Jersey 07080 , United States
| | - Matthew G Woll
- PTC Therapeutics, Inc. , 100 Corporate Court , South Plainfield , New Jersey 07080 , United States
| | - John Baird
- PTC Therapeutics, Inc. , 100 Corporate Court , South Plainfield , New Jersey 07080 , United States
| | - Nanjing Zhang
- PTC Therapeutics, Inc. , 100 Corporate Court , South Plainfield , New Jersey 07080 , United States
| | - Neil G Almstead
- PTC Therapeutics, Inc. , 100 Corporate Court , South Plainfield , New Jersey 07080 , United States
| | - Jana Narasimhan
- PTC Therapeutics, Inc. , 100 Corporate Court , South Plainfield , New Jersey 07080 , United States
| | - Srinivasa Peddi
- PTC Therapeutics, Inc. , 100 Corporate Court , South Plainfield , New Jersey 07080 , United States
| | - Melissa Dumble
- PTC Therapeutics, Inc. , 100 Corporate Court , South Plainfield , New Jersey 07080 , United States
| | - Josephine Sheedy
- PTC Therapeutics, Inc. , 100 Corporate Court , South Plainfield , New Jersey 07080 , United States
| | - Marla Weetall
- PTC Therapeutics, Inc. , 100 Corporate Court , South Plainfield , New Jersey 07080 , United States
| | - Arthur A Branstrom
- PTC Therapeutics, Inc. , 100 Corporate Court , South Plainfield , New Jersey 07080 , United States
| | - J V N Prasad
- PTC Therapeutics, Inc. , 100 Corporate Court , South Plainfield , New Jersey 07080 , United States
| | - Gary M Karp
- PTC Therapeutics, Inc. , 100 Corporate Court , South Plainfield , New Jersey 07080 , United States
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12
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Solis-Calero C, Zanatta G, Pessoa CDÓ, Carvalho HF, Freire VN. Explaining urokinase type plasminogen activator inhibition by amino-5-hydroxybenzimidazole and two naphthamidine-based compounds through quantum biochemistry. Phys Chem Chem Phys 2018; 20:22818-22830. [DOI: 10.1039/c8cp04315a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Urokinase plasminogen activator (uPA) is a biomarker and therapeutic target for several cancer types whose inhibition has been shown to slow tumor growth and metastasis.
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Affiliation(s)
- Christian Solis-Calero
- Department of Structural and Functional Biology
- State University of Campinas
- 13083-863 Campinas
- Brazil
| | - Geancarlo Zanatta
- Department of Physics
- Federal University of Ceará
- 60455-760 Fortaleza
- Brazil
| | - Claudia do Ó Pessoa
- Department of Physiology and Pharmacology
- Federal University of Ceará
- 60430-270 Fortaleza
- Brazil
| | - Hernandes F. Carvalho
- Department of Structural and Functional Biology
- State University of Campinas
- 13083-863 Campinas
- Brazil
| | - Valder N. Freire
- Department of Physics
- Federal University of Ceará
- 60455-760 Fortaleza
- Brazil
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13
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Xu P, Andreasen PA, Huang M. Structural Principles in the Development of Cyclic Peptidic Enzyme Inhibitors. Int J Biol Sci 2017; 13:1222-1233. [PMID: 29104489 PMCID: PMC5666521 DOI: 10.7150/ijbs.21597] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Accepted: 08/28/2017] [Indexed: 01/23/2023] Open
Abstract
This review summarizes our studies in the development of small cyclic peptides for specifically modulating enzyme activity. Serine proteases share highly similar active sites but perform diverse physiological and pathological functions. From a phage-display peptide library, we isolated two mono-cyclic peptides, upain-1 (CSWRGLENHRMC) and mupain-1 (CPAYSRYLDC), which inhibit the activity of human and murine urokinase-type plasminogen activators (huPA and muPA) with Ki values in the micromolar or sub-micromolar range, respectively. The following affinity maturations significantly enhanced the potencies of the two peptides, 10-fold and >250-fold for upain-1 and mupain-1, respectively. The most potent muPA inhibitor has a potency (Ki = 2 nM) and specificity comparable to mono-clonal antibodies. Furthermore, we also found an unusual feature of mupain-1 that its inhibitory potency can be enhanced by increasing the flexibility, which challenges the traditional viewpoint that higher rigidity leading to higher affinity. Moreover, by changing a few key residues, we converted mupain-1 from a uPA inhibitor to inhibitors of other serine proteases, including plasma kallikrein (PK) and coagulation factor XIa (fXIa). PK and fXIa inhibitors showed Ki values in the low nanomolar range and high specificity. Our studies demonstrate the versatility of small cyclic peptides to engineer inhibitory potency against serine proteases and to provide a new strategy for generating peptide inhibitors of serine proteases.
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Affiliation(s)
- Peng Xu
- State Key Laboratory of Structural Chemistry and Danish-Chinese Centre for Proteases and Cancer, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, Fujian, 350002, P.R. China
| | - Peter A Andreasen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, 8000, Denmark
| | - Mingdong Huang
- State Key Laboratory of Structural Chemistry and Danish-Chinese Centre for Proteases and Cancer, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, Fujian, 350002, P.R. China.,College of Chemistry, Fuzhou University, Fuzhou, Fujian, 350116, P.R. China
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14
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Solís-Calero C, Carvalho HF. KLK14 interactions with HAI-1 and HAI-2 serine protease inhibitors: A molecular dynamics and relative free-energy calculations study. Cell Biol Int 2017; 41:1246-1264. [PMID: 28817220 DOI: 10.1002/cbin.10839] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Accepted: 08/12/2017] [Indexed: 01/13/2023]
Abstract
Kallikrein 14 (KLK14) is a serine protease linked to several pathologies including prostate cancer and positively correlates with Gleason score. Though KLK14 functioning in cancer is poorly understood, it has been implicated in HGF/Met signaling, given that KLK14 proteolytically inhibits HGF activator-inhibitor 1 (HAI-1), which strongly inhibits pro-HGF activators, thereby contributing to tumor progression. In this work, KLK14 binding to either hepatocyte growth factor activator inhibitor type-1 (HAI-1) or type-2 (HAI-2) was essayed using homology modeling, molecular dynamic simulations and free-energy calculations through MM/PBSA and MM/GBSA. KLK14 was successfully modeled. Calculated free energies suggested higher binding affinity for the KLK14/HAI-1 interaction than for KLK14/HAI-2. This difference in binding affinity is largely explained by the higher stability of the hydrogen-bond networks in KLK14/HAI-1 along the simulation trajectory. A key arginine residue in both HAI-1 and HAI-2 is responsible for their interaction with the S1 pocket in KLK14. Additionally, MM/GBSA free-energy decomposition postulates that KLK14 Asp174 and Trp196 are hotspots for binding HAI-1 and HAI-2.
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Affiliation(s)
- Christian Solís-Calero
- Department of Structural and Functional Biology, State University of Campinas, Campinas, São Paulo, Brazil
| | - Hernandes F Carvalho
- Department of Structural and Functional Biology, State University of Campinas, Campinas, São Paulo, Brazil
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15
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Chow SY, Odell LR. Synthesis of N-Sulfonyl Amidines and Acyl Sulfonyl Ureas from Sulfonyl Azides, Carbon Monoxide, and Amides. J Org Chem 2017; 82:2515-2522. [DOI: 10.1021/acs.joc.6b02894] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Shiao Y. Chow
- Organic Pharmaceutical Chemistry, Department
of Medicinal Chemistry, Uppsala Biomedical Center, Uppsala University, P.O. Box 574, SE-751 23 Uppsala, Sweden
| | - Luke R. Odell
- Organic Pharmaceutical Chemistry, Department
of Medicinal Chemistry, Uppsala Biomedical Center, Uppsala University, P.O. Box 574, SE-751 23 Uppsala, Sweden
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16
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Gopal SM, Klumpers F, Herrmann C, Schäfer LV. Solvent effects on ligand binding to a serine protease. Phys Chem Chem Phys 2017; 19:10753-10766. [DOI: 10.1039/c6cp07899k] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
ITC experiments and MD simulations reveal the mechanism behind enthalpy/entropy compensation upon trypsin-benzamidine binding at different solvation conditions.
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Affiliation(s)
- Srinivasa M. Gopal
- Center for Theoretical Chemistry
- Faculty of Chemistry and Biochemistry
- Ruhr-University Bochum
- D-44780 Bochum
- Germany
| | - Fabian Klumpers
- Physical Chemistry I
- Faculty of Chemistry and Biochemistry
- Ruhr-University Bochum
- D-44780 Bochum
- Germany
| | - Christian Herrmann
- Physical Chemistry I
- Faculty of Chemistry and Biochemistry
- Ruhr-University Bochum
- D-44780 Bochum
- Germany
| | - Lars V. Schäfer
- Center for Theoretical Chemistry
- Faculty of Chemistry and Biochemistry
- Ruhr-University Bochum
- D-44780 Bochum
- Germany
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17
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Subedi M, Minn I, Chen J, Kim Y, Ok K, Jung YW, Pomper MG, Byun Y. Design, synthesis and biological evaluation of PSMA/hepsin-targeted heterobivalent ligands. Eur J Med Chem 2016; 118:208-218. [PMID: 27128184 DOI: 10.1016/j.ejmech.2016.04.033] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Revised: 03/14/2016] [Accepted: 04/12/2016] [Indexed: 01/08/2023]
Abstract
Cell surface biomarkers such as prostate-specific membrane antigen (PSMA) and hepsin have received considerable attention as targets for imaging prostate cancer (PCa) due to their high cell surface expression in such tumors and easy access for imaging probes. Novel amidine-containing indole analogs (13-21) as hepsin inhibitors were designed and synthesized. These compounds showed in vitro inhibitory activity against hepsin with IC50 values from 5.9 to 70 μM. Based on the SAR of amidine-derived analogs, the novel heterobivalent compound 30, targeting both hepsin and PSMA, was synthesized by linking compound 18 with Lys-urea-Glu, the key scaffold for the specific binding to PSMA, followed by the conjugation of the optical dye SulfoCy7. Compound 30 exhibited inhibitory activities against PSMA and hepsin, with IC50 values of 28 nM and 2.8 μM, respectively. In vitro cell uptake and preliminary in vivo optical imaging studies of 30 showed selective binding and retention in both PSMA and hepsin high-expressing PC3/ML-PSMA-HPN cells as compared with low-expressing PC3/ML cells.
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Affiliation(s)
- Milan Subedi
- College of Pharmacy, Korea University, 2511 Sejong-ro, Jochiwon-eup, Sejong 339-700, South Korea
| | - Il Minn
- Department of Radiology, Johns Hopkins Medical Institution, 1550 Orleans street, Baltimore 21287, MD, USA
| | - Jianbo Chen
- College of Pharmacy, Korea University, 2511 Sejong-ro, Jochiwon-eup, Sejong 339-700, South Korea
| | - YunHye Kim
- College of Pharmacy, Korea University, 2511 Sejong-ro, Jochiwon-eup, Sejong 339-700, South Korea
| | - Kiwon Ok
- College of Pharmacy, Korea University, 2511 Sejong-ro, Jochiwon-eup, Sejong 339-700, South Korea
| | - Yong Woo Jung
- College of Pharmacy, Korea University, 2511 Sejong-ro, Jochiwon-eup, Sejong 339-700, South Korea
| | - Martin G Pomper
- Department of Radiology, Johns Hopkins Medical Institution, 1550 Orleans street, Baltimore 21287, MD, USA
| | - Youngjoo Byun
- College of Pharmacy, Korea University, 2511 Sejong-ro, Jochiwon-eup, Sejong 339-700, South Korea.,Department of Radiology, Johns Hopkins Medical Institution, 1550 Orleans street, Baltimore 21287, MD, USA.,Biomedical Research Center, Korea University Guro Hospital, 148 Gurodong-ro, Guro-gu, Seoul 152-703, South Korea
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18
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Selection of High-Affinity Peptidic Serine Protease Inhibitors with Increased Binding Entropy from a Back-Flip Library of Peptide-Protease Fusions. J Mol Biol 2015; 427:3110-22. [PMID: 26281711 DOI: 10.1016/j.jmb.2015.08.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2015] [Revised: 07/19/2015] [Accepted: 08/07/2015] [Indexed: 11/21/2022]
Abstract
We have developed a new concept for designing peptidic protein modulators, by recombinantly fusing the peptidic modulator, with randomized residues, directly to the target protein via a linker and screening for internal modulation of the activity of the protein. We tested the feasibility of the concept by fusing a 10-residue-long, disulfide-bond-constrained inhibitory peptide, randomized in selected positions, to the catalytic domain of the serine protease murine urokinase-type plasminogen activator. High-affinity inhibitory peptide variants were identified as those that conferred to the fusion protease the lowest activity for substrate hydrolysis. The usefulness of the strategy was demonstrated by the selection of peptidic inhibitors of murine urokinase-type plasminogen activator with a low nanomolar affinity. The high affinity could not have been predicted by rational considerations, as the high affinity was associated with a loss of polar interactions and an increased binding entropy.
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19
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Kaczmarek JZ, Skottrup PD. Selection and characterization of camelid nanobodies towards urokinase-type plasminogen activator. Mol Immunol 2015; 65:384-90. [DOI: 10.1016/j.molimm.2015.02.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2014] [Revised: 02/04/2015] [Accepted: 02/09/2015] [Indexed: 01/17/2023]
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20
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Noël S, Hoegy F, Rivault F, Rognan D, Schalk IJ, Mislin GLA. Synthesis and biological properties of thiazole-analogues of pyochelin, a siderophore of Pseudomonas aeruginosa. Bioorg Med Chem Lett 2014; 24:132-5. [PMID: 24332092 DOI: 10.1016/j.bmcl.2013.11.054] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2013] [Revised: 11/22/2013] [Accepted: 11/23/2013] [Indexed: 11/29/2022]
Abstract
Pyochelin is a siderophore common to all strains of Pseudomonas aeruginosa utilized by this Gram-negative bacterium to acquire iron(III). FptA is the outer membrane transporter responsible of ferric-pyochelin uptake in P. aeruginosa. We describe in this Letter the synthesis and the biological properties ((55)Fe uptake, binding to FptA) of several thiazole analogues of pyochelin. Among them we report in this Letter the two first pyochelin analogues able to bind FptA without promoting any iron uptake in P. aeruginosa.
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Affiliation(s)
- Sabrina Noël
- Team 'Transports Membranaires Bactériens', UMR 7242 CNRS-Université de Strasbourg, 300 Boulevard Sébastien Brant, BP 10413, F-67412 Illkirch-Graffenstaden Cedex, France
| | - Françoise Hoegy
- Team 'Transports Membranaires Bactériens', UMR 7242 CNRS-Université de Strasbourg, 300 Boulevard Sébastien Brant, BP 10413, F-67412 Illkirch-Graffenstaden Cedex, France
| | - Freddy Rivault
- Team 'Transports Membranaires Bactériens', UMR 7242 CNRS-Université de Strasbourg, 300 Boulevard Sébastien Brant, BP 10413, F-67412 Illkirch-Graffenstaden Cedex, France
| | - Didier Rognan
- Team 'Chémogénomique Structurale' Laboratoire d'Innovation Thérapeutique (LIT), UMR 7200 CNRS-Université de Strasbourg, Faculté de Pharmacie, 74 route du Rhin, 67400 Illkirch-Graffenstaden, France
| | - Isabelle J Schalk
- Team 'Transports Membranaires Bactériens', UMR 7242 CNRS-Université de Strasbourg, 300 Boulevard Sébastien Brant, BP 10413, F-67412 Illkirch-Graffenstaden Cedex, France
| | - Gaëtan L A Mislin
- Team 'Transports Membranaires Bactériens', UMR 7242 CNRS-Université de Strasbourg, 300 Boulevard Sébastien Brant, BP 10413, F-67412 Illkirch-Graffenstaden Cedex, France.
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21
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Xu XH, Taniguchi M, Azuma A, Liu GK, Tokunaga E, Shibata N. Remote Anionic Fries Rearrangement of Sulfonates: Regioselective Synthesis of Indole Triflones. Org Lett 2013; 15:686-9. [DOI: 10.1021/ol3035559] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Xiu-Hua Xu
- Department of Frontier Materials, Graduate School of Engineering, Nagoya Institute of Technology, Gokiso, Showa-ku, Nagoya, 466-8555, Japan
| | - Misaki Taniguchi
- Department of Frontier Materials, Graduate School of Engineering, Nagoya Institute of Technology, Gokiso, Showa-ku, Nagoya, 466-8555, Japan
| | - Ayaka Azuma
- Department of Frontier Materials, Graduate School of Engineering, Nagoya Institute of Technology, Gokiso, Showa-ku, Nagoya, 466-8555, Japan
| | - Guo Kai Liu
- Department of Frontier Materials, Graduate School of Engineering, Nagoya Institute of Technology, Gokiso, Showa-ku, Nagoya, 466-8555, Japan
| | - Etsuko Tokunaga
- Department of Frontier Materials, Graduate School of Engineering, Nagoya Institute of Technology, Gokiso, Showa-ku, Nagoya, 466-8555, Japan
| | - Norio Shibata
- Department of Frontier Materials, Graduate School of Engineering, Nagoya Institute of Technology, Gokiso, Showa-ku, Nagoya, 466-8555, Japan
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22
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Venkatraj M, Messagie J, Joossens J, Lambeir AM, Haemers A, Van der Veken P, Augustyns K. Synthesis and evaluation of non-basic inhibitors of urokinase-type plasminogen activator (uPA). Bioorg Med Chem 2012; 20:1557-68. [DOI: 10.1016/j.bmc.2011.12.040] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2011] [Revised: 12/15/2011] [Accepted: 12/17/2011] [Indexed: 11/16/2022]
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23
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Tumor suppressor function of Liver kinase B1 (Lkb1) is linked to regulation of epithelial integrity. Proc Natl Acad Sci U S A 2012; 109:E388-97. [PMID: 22308451 DOI: 10.1073/pnas.1120421109] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Although loss of epithelial integrity is a hallmark of advanced cancer, it remains poorly understood whether genetic alterations corrupting this integrity causally facilitate tumorigenesis. We show that conditional deletion of tumor suppressor gene Lkb1 (Par-4) in the mammary gland compromises epithelial integrity manifested by mislocalization of cell polarity markers, lateralization of tight junctions, deterioration of desmosomes and basement membrane (BM), and hyperbranching of the mammary ductal tree. We identify the desmosomal BM remodelling serine protease Hepsin as a key factor mediating Lkb1 loss-induced structural alterations in mammary epithelium and BM fragmentation. Although loss of Lkb1 alone does not promote mammary tumorigenesis, combination of Lkb1 deficiency with oncogenic c-Myc leads to dramatic acceleration in tumor formation. The results coupling Lkb1 loss-mediated epithelial integrity defects to mislocalization of serine protease Hepsin and to oncogenic synergy with c-Myc imply that Lkb1 loss facilitates oncogenic proliferation by releasing epithelial cells from structural BM boundaries.
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24
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Massey AP, Harley WR, Pasupuleti N, Gorin FA, Nantz MH. 2-Amidino analogs of glycine-amiloride conjugates: inhibitors of urokinase-type plasminogen activator. Bioorg Med Chem Lett 2012; 22:2635-9. [PMID: 22366654 DOI: 10.1016/j.bmcl.2011.12.123] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2011] [Revised: 12/23/2011] [Accepted: 12/27/2011] [Indexed: 10/14/2022]
Abstract
The relative non-toxicity of the diuretic amiloride, coupled with its selective inhibition of the protease urokinase plasminogen activator (uPA), makes this compound class attractive for structure-activity studies. Herein we substituted the C(2)-acylguanidine of C(5)-glycyl-amiloride with amidine and amidoxime groups. The data show the importance of maintaining C(5)-hydrophobicity. The C(5)-benzylglycine analogs containing either C(2)-acylguanidine or amidine inhibited uPA with an IC(50) ranging from 3 to 7 μM and were cytotoxic to human U87 malignant glioma cells.
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Affiliation(s)
- Archna P Massey
- Department of Chemistry, University of Louisville, Louisville, KY 40292, USA
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25
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Mikulskis P, Genheden S, Rydberg P, Sandberg L, Olsen L, Ryde U. Binding affinities in the SAMPL3 trypsin and host-guest blind tests estimated with the MM/PBSA and LIE methods. J Comput Aided Mol Des 2011; 26:527-41. [PMID: 22198518 DOI: 10.1007/s10822-011-9524-z] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2011] [Accepted: 12/08/2011] [Indexed: 11/28/2022]
Abstract
We have estimated affinities for the binding of 34 ligands to trypsin and nine guest molecules to three different hosts in the SAMPL3 blind challenge, using the MM/PBSA, MM/GBSA, LIE, continuum LIE, and Glide score methods. For the trypsin challenge, none of the methods were able to accurately predict the experimental results. For the MM/GB(PB)SA and LIE methods, the rankings were essentially random and the mean absolute deviations were much worse than a null hypothesis giving the same affinity to all ligand. Glide scoring gave a Kendall's τ index better than random, but the ranking is still only mediocre, τ = 0.2. However, the range of affinities is small and most of the pairs of ligands have an experimental affinity difference that is not statistically significant. Removing those pairs improves the ranking metric to 0.4-1.0 for all methods except CLIE. Half of the trypsin ligands were non-binders according to the binding assay. The LIE methods could not separate the inactive ligands from the active ones better than a random guess, whereas MM/GBSA and MM/PBSA were slightly better than random (area under the receiver-operating-characteristic curve, AUC = 0.65-0.68), and Glide scoring was even better (AUC = 0.79). For the first host, MM/GBSA and MM/PBSA reproduce the experimental ranking fairly good, with τ = 0.6 and 0.5, respectively, whereas the Glide scoring was considerably worse, with a τ = 0.4, highlighting that the success of the methods is system-dependent.
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Affiliation(s)
- Paulius Mikulskis
- Department of Theoretical Chemistry, Lund University, Chemical Centre, P.O. Box 124, 221 00 Lund, Sweden
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26
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Genheden S, Mikulskis P, Hu L, Kongsted J, Söderhjelm P, Ryde U. Accurate Predictions of Nonpolar Solvation Free Energies Require Explicit Consideration of Binding-Site Hydration. J Am Chem Soc 2011; 133:13081-92. [DOI: 10.1021/ja202972m] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Samuel Genheden
- Department of Theoretical Chemistry, Lund University, Chemical Centre, P.O. Box 124, SE-221 00 Lund, Sweden
| | - Paulius Mikulskis
- Department of Theoretical Chemistry, Lund University, Chemical Centre, P.O. Box 124, SE-221 00 Lund, Sweden
| | - LiHong Hu
- Department of Theoretical Chemistry, Lund University, Chemical Centre, P.O. Box 124, SE-221 00 Lund, Sweden
- School of Computer Science and Information Technology, Northeast Normal University, Changchun, 130024, People's Republic of China
| | - Jacob Kongsted
- Department of Physics and Chemistry, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
| | - Pär Söderhjelm
- Department of Chemistry and Applied Biosciences—Computational Science, ETH Zürich, Via Giuseppe Buffi 13, CH-6900 Lugano, Switzerland
| | - Ulf Ryde
- Department of Theoretical Chemistry, Lund University, Chemical Centre, P.O. Box 124, SE-221 00 Lund, Sweden
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27
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Barillari C, Duncan AL, Westwood IM, Blagg J, van Montfort RLM. Analysis of water patterns in protein kinase binding sites. Proteins 2011; 79:2109-21. [PMID: 21557316 DOI: 10.1002/prot.23032] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2010] [Revised: 03/02/2011] [Accepted: 03/03/2011] [Indexed: 11/10/2022]
Abstract
Deregulation of protein kinases is associated with numerous diseases, making them important targets for drug discovery. The majority of drugs target the catalytic site of these proteins, but due to the high level of similarity within the ATP binding sites of protein kinases, it is often difficult to achieve the required pharmacological selectivity. In this study, we describe the identification and subsequent analysis of water patterns in the ATP binding sites of 171 protein kinase structures, comprising 19 different kinases from various branches of the kinome, and demonstrate that structurally similar binding sites often have significantly different water patterns. We show that the observed variations in water patterns of different, but structurally similar kinases can be exploited in the structure-based design of potent and selective kinase inhibitors.
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Affiliation(s)
- Caterina Barillari
- Section of Cancer Therapeutics, The Institute of Cancer Research, Haddow Laboratories, Sutton, Surrey SM2 5NG, United Kingdom
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28
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Chen L, Petrelli R, Gao G, Wilson DJ, McLean GT, Jayaram HN, Sham YY, Pankiewicz KW. Dual inhibitors of inosine monophosphate dehydrogenase and histone deacetylase based on a cinnamic hydroxamic acid core structure. Bioorg Med Chem 2010; 18:5950-64. [PMID: 20650640 DOI: 10.1016/j.bmc.2010.06.081] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2010] [Revised: 06/19/2010] [Accepted: 06/23/2010] [Indexed: 11/17/2022]
Abstract
Small molecules that act on multiple biological targets have been proposed to combat the drug resistance commonly observed for cancer chemotherapy. By combining the structural features of known inhibitors of inosine monophosphate dehydrogense (IMPDH) and histone deacetylase (HDAC), dual inhibitors of IMPDH and HDAC based on the scaffold of cinnamic hydroxamic acid (CHA) have been designed, synthesized, and evaluated in biological assays. Key features, including the linker length, linker functionality, substitution position, and interacting groups, have been explored. Their individual contribution to the inhibitory activities against human IMPDH1 and IMPDH2 as well as HDAC has been assessed.
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Affiliation(s)
- Liqiang Chen
- Center for Drug Design, Academic Health Center, University of Minnesota, Minneapolis, MN 55455, USA.
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29
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LXXLL peptide mimetics as inhibitors of the interaction of vitamin D receptor with coactivators. Bioorg Med Chem Lett 2010; 20:1712-7. [DOI: 10.1016/j.bmcl.2010.01.079] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2009] [Revised: 01/07/2010] [Accepted: 01/08/2010] [Indexed: 11/24/2022]
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30
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Henrich S, Feierberg I, Wang T, Blomberg N, Wade RC. Comparative binding energy analysis for binding affinity and target selectivity prediction. Proteins 2009; 78:135-53. [DOI: 10.1002/prot.22579] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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31
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Bakunova SM, Bakunov SA, Patrick DA, Kumar EVKS, Ohemeng KA, Bridges AS, Wenzler T, Barszcz T, Jones SK, Werbovetz KA, Brun R, Tidwell RR. Structure-activity study of pentamidine analogues as antiprotozoal agents. J Med Chem 2009; 52:2016-35. [PMID: 19267462 DOI: 10.1021/jm801547t] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Diamidine 1 (pentamidine) and 65 analogues (2-66) have been tested for in vitro antiprotozoal activities against Trypanosoma brucei rhodesiense, Plasmodium falciparum, and Leishmania donovani, and for cytotoxicity against mammalian cells. Dications 32, 64, and 66 exhibited antitrypanosomal potencies equal or greater than melarsoprol (IC(50) = 4 nM). Nine congeners (2-4, 12, 27, 30, and 64-66) were more active against P. falciparum than artemisinin (IC(50) = 6 nM). Eight compounds (12, 32, 33, 44, 59, 62, 64, and 66) exhibited equal or better antileishmanial activities than 1 (IC(50) = 1.8 microM). Several congeners were more active than 1 in vivo, curing at least 2/4 infected animals in the acute mouse model of trypanosomiasis. The diimidazoline 66 was the most promising compound in the series, showing excellent in vitro activities and high selectivities against T. b. rhodesiense, P. falciparum, and L. donovani combined with high antitrypanosomal efficacy in vivo.
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Affiliation(s)
- Svetlana M Bakunova
- Department of Pathology and Laboratory Medicine, School of Medicine, The University of North Carolina, Chapel Hill, North Carolina 27599, USA
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Wu E, Han K, Zhang J. Selectivity of Neutral/Weakly Basic P1 Group Inhibitors of Thrombin and Trypsin by a Molecular Dynamics Study. Chemistry 2008; 14:8704-14. [DOI: 10.1002/chem.200800277] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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A cyclic peptidylic inhibitor of murine urokinase-type plasminogen activator: changing species specificity by substitution of a single residue. Biochem J 2008; 412:447-57. [PMID: 18318660 DOI: 10.1042/bj20071646] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
uPA (urokinase-type plasminogen activator) is a potential therapeutic target in a variety of pathological conditions, including cancer. In order to find new principles for inhibiting uPA in murine cancer models, we screened a phage-displayed peptide library with murine uPA as bait. We thereby isolated several murine uPA-binding peptide sequences, the predominant of which was the disulfide-bridged constrained sequence CPAYSRYLDC, which we will refer to as mupain-1. A chemically synthesized peptide corresponding to this sequence was found to be a competitive inhibitor of murine uPA, inhibiting its activity towards a low-molecular-mass chromogenic substrate as well as towards its natural substrate plasminogen. The K(i) value for inhibition as well as the K(D) value for binding were approx. 400 nM. Among a variety of other murine and human serine proteases, including trypsin, mupain-1 was found to be highly selective for murine uPA and did not even measurably inhibit human uPA. The cyclic structure of mupain-1 was indispensable for binding. Alanine scanning mutagenesis identified Arg(6) of mupain-1 as the P1 residue and indicated an extended binding interaction including the P5, P3, P2, P1 and P1' residues of mupain-1 and the specificity pocket, the catalytic triad and amino acids 41, 99 and 192 located in and around the active site of murine uPA. Exchanging His(99) of human uPA by a tyrosine residue, the corresponding residue in murine uPA, conferred mupain-1 susceptibility on to the latter. Peptide-derived inhibitors, such as mupain-1, may provide novel mechanistic information about enzyme-inhibitor interactions, provide alternative methodologies for designing effective protease inhibitors, and be used for target validation in murine model systems.
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Frederickson M, Callaghan O, Chessari G, Congreve M, Cowan SR, Matthews JE, McMenamin R, Smith DM, Vinković M, Wallis NG. Fragment-Based Discovery of Mexiletine Derivatives as Orally Bioavailable Inhibitors of Urokinase-Type Plasminogen Activator. J Med Chem 2007; 51:183-6. [DOI: 10.1021/jm701359z] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Martyn Frederickson
- Astex Therapeutics Ltd, 436 Cambridge Science Park, Milton Road, Cambridge, CB4 0QA, United Kingdom
| | - Owen Callaghan
- Astex Therapeutics Ltd, 436 Cambridge Science Park, Milton Road, Cambridge, CB4 0QA, United Kingdom
| | - Gianni Chessari
- Astex Therapeutics Ltd, 436 Cambridge Science Park, Milton Road, Cambridge, CB4 0QA, United Kingdom
| | - Miles Congreve
- Astex Therapeutics Ltd, 436 Cambridge Science Park, Milton Road, Cambridge, CB4 0QA, United Kingdom
| | - Suzanna R. Cowan
- Astex Therapeutics Ltd, 436 Cambridge Science Park, Milton Road, Cambridge, CB4 0QA, United Kingdom
| | - Julia E. Matthews
- Astex Therapeutics Ltd, 436 Cambridge Science Park, Milton Road, Cambridge, CB4 0QA, United Kingdom
| | - Rachel McMenamin
- Astex Therapeutics Ltd, 436 Cambridge Science Park, Milton Road, Cambridge, CB4 0QA, United Kingdom
| | - Donna-Michelle Smith
- Astex Therapeutics Ltd, 436 Cambridge Science Park, Milton Road, Cambridge, CB4 0QA, United Kingdom
| | - Mladen Vinković
- Astex Therapeutics Ltd, 436 Cambridge Science Park, Milton Road, Cambridge, CB4 0QA, United Kingdom
| | - Nicola G. Wallis
- Astex Therapeutics Ltd, 436 Cambridge Science Park, Milton Road, Cambridge, CB4 0QA, United Kingdom
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35
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Joossens J, Ali OM, El-Sayed I, Surpateanu G, Van der Veken P, Lambeir AM, Setyono-Han B, Foekens JA, Schneider A, Schmalix W, Haemers A, Augustyns K. Small, potent, and selective diaryl phosphonate inhibitors for urokinase-type plasminogen activator with in vivo antimetastatic properties. J Med Chem 2007; 50:6638-46. [PMID: 18052026 DOI: 10.1021/jm700962j] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
A set of small nonpeptidic diaryl phosphonate inhibitors was prepared. Some of these inhibitors show potent and highly selective irreversible uPA inhibition. The biochemical and modeling data prove that the combination of a benzylguanidine moiety with a diaryl phosphonate ester results in optimized molecules for derivatizing the serine alcohol in the uPA active site. Selected compounds show significant antimetastatic effects in the BN-472 rat mammary carcinoma model. We report in this paper a preclinical proof of concept that selective, irreversible uPA inhibitors could be valuable in antimetastatic therapy.
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Affiliation(s)
- Jurgen Joossens
- Laboratory of Medicinal Chemistry, University of Antwerp, Universiteitsplein 1, B-2610 Antwerp, Belgium
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36
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Zhao G, Yuan C, Wind T, Huang Z, Andreasen PA, Huang M. Structural basis of specificity of a peptidyl urokinase inhibitor, upain-1. J Struct Biol 2007; 160:1-10. [PMID: 17692534 DOI: 10.1016/j.jsb.2007.06.003] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2007] [Revised: 05/16/2007] [Accepted: 06/07/2007] [Indexed: 11/17/2022]
Abstract
Urokinase-type plasminogen activator (uPA) plays a crucial role in the regulation of plasminogen activation, tumor cell adhesion and migration. The inhibition of uPA activity is a promising mechanism for anti-cancer therapy. A cyclic peptidyl inhibitor, upain-1, CSWRGLENHRMC, was identified recently as a competitive and highly specific uPA inhibitor. We determined the crystal structure of uPA in complex with upain-1 at 2.15 A. The structure reveals that the cyclic peptide adopts a rigid conformation stabilized by a disulfide bond (residues 1-12) and three tight beta turns (residues 3-6, 6-9, 9-12). The Glu7 residue of upain-1 forms hydrogen bonds with the main chain nitrogen atoms of residues 4, 5, and 6 of upain-1, and is also critical for maintaining the active conformation of upain-1. The Arg4 of upain-1 is inserted into the uPA's specific S1 pocket. The Ser2 residue of upain-1 locates close to the S1beta pocket of uPA. The Gly5 and Glu7 residues of upain-1 occupy the S2 pocket and the oxyanion hole of uPA, respectively. Furthermore, the Asn8 residue of upain-1 binds to the 37- and 60-loops of uPA and renders the specificity of upain-1 for uPA. Based on this structure, a new pharmacophore for the design of highly specific uPA inhibitors was proposed.
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Affiliation(s)
- Gengxiang Zhao
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, 155 Yang Qiao Xi Lu, Fuzhou, Fujian 350002, China
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37
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Ye B, Arnaiz DO, Chou YL, Griedel BD, Karanjawala R, Lee W, Morrissey MM, Sacchi KL, Sakata ST, Shaw KJ, Wu SC, Zhao Z, Adler M, Cheeseman S, Dole WP, Ewing J, Fitch R, Lentz D, Liang A, Light D, Morser J, Post J, Rumennik G, Subramanyam B, Sullivan ME, Vergona R, Walters J, Wang YX, White KA, Whitlow M, Kochanny MJ. Thiophene-anthranilamides as highly potent and orally available factor Xa inhibitors. J Med Chem 2007; 50:2967-80. [PMID: 17536795 DOI: 10.1021/jm070125f] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
There remains a high unmet medical need for a safe oral therapy for thrombotic disorders. The serine protease factor Xa (fXa), with its central role in the coagulation cascade, is among the more promising targets for anticoagulant therapy and has been the subject of intensive drug discovery efforts. Investigation of a hit from high-throughput screening identified a series of thiophene-substituted anthranilamides as potent nonamidine fXa inhibitors. Lead optimization by incorporation of hydrophilic groups led to the discovery of compounds with picomolar inhibitory potency and micromolar in vitro anticoagulant activity. Based on their high potency, selectivity, oral pharmacokinetics, and efficacy in a rat venous stasis model of thrombosis, compounds ZK 814048 (10b), ZK 810388 (13a), and ZK 813039 (17m) were advanced into development.
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Affiliation(s)
- Bin Ye
- Berlex Biosciences, Post Office Box 4099, Richmond, California 94804-0099, USA.
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38
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Barillari C, Taylor J, Viner R, Essex JW. Classification of water molecules in protein binding sites. J Am Chem Soc 2007; 129:2577-87. [PMID: 17288418 DOI: 10.1021/ja066980q] [Citation(s) in RCA: 223] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Water molecules play a crucial role in mediating the interaction between a ligand and a macromolecular receptor. An understanding of the nature and role of each water molecule in the active site of a protein could greatly increase the efficiency of rational drug design approaches: if the propensity of a water molecule for displacement can be determined, then synthetic effort may be most profitably applied to the design of specific ligands with the displacement of this water molecule in mind. In this paper, a thermodynamic analysis of water molecules in the binding sites of six proteins, each complexed with a number of inhibitors, is presented. Two classes of water molecules were identified: those conserved and not displaced by any of the ligands, and those that are displaced by some ligands. The absolute binding free energies of 54 water molecules were calculated using the double decoupling method, with replica exchange thermodynamic integration in Monte Carlo simulations. It was found that conserved water molecules are on average more tightly bound than displaced water molecules. In addition, Bayesian statistics is used to calculate the probability that a particular water molecule may be displaced by an appropriately designed ligand, given the calculated binding free energy of the water molecule. This approach therefore allows the numerical assessment of whether or not a given water molecule should be targeted for displacement as part of a rational drug design strategy.
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Affiliation(s)
- Caterina Barillari
- School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, U.K
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39
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Kochanny MJ, Adler M, Ewing J, Griedel BD, Ho E, Karanjawala R, Lee W, Lentz D, Liang AM, Morrissey MM, Phillips GB, Post J, Sacchi KL, Sakata ST, Subramanyam B, Vergona R, Walters J, White KA, Whitlow M, Ye B, Zhao Z, Shaw KJ. Substituted thiophene-anthranilamides as potent inhibitors of human factor Xa. Bioorg Med Chem 2006; 15:2127-46. [PMID: 17227710 DOI: 10.1016/j.bmc.2006.12.019] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2006] [Revised: 11/30/2006] [Accepted: 12/11/2006] [Indexed: 11/22/2022]
Abstract
A series of thiophene-containing non-amidine factor Xa inhibitors is described. Simple methyl-substituted thiophene analogs were relatively weak inhibitors. However, introduction of hydrophilic substituents at C-4 or C-5 of the thiophene afforded inhibitors with low nanomolar potency. Optimization of the thiophene substituent at C-4 afforded subnanomolar inhibitors with improved in vitro anticoagulant activity. Incorporating basic amine substituents on the thiophene increased hydrophilicity and improved anticoagulant activity. The pharmacokinetic profile of one inhibitor was evaluated in dogs, and the X-ray crystal structure of this compound bound to factor Xa provides insight into the observed SAR for binding to factor Xa.
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40
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Schweizer E, Hoffmann-Röder A, Schärer K, Olsen JA, Fäh C, Seiler P, Obst-Sander U, Wagner B, Kansy M, Diederich F. A fluorine scan at the catalytic center of thrombin: C--F, C--OH, and C--OMe bioisosterism and fluorine effects on pKa and log D values. ChemMedChem 2006; 1:611-21. [PMID: 16892401 DOI: 10.1002/cmdc.200600015] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
A series of 16 tricyclic thrombin inhibitors was prepared by using the 1,3-dipolar cycloaddition of azomethine ylides derived from 3- or 4-hydroxyproline and 4-bromobenzaldehyde, with N-(4-fluorobenzyl)maleimide as the key step. The terminal pyrrolidine ring of the inhibitors was systematically substituted to explore the potential bioisosteric behavior of C-F, C-OH, and C-OMe residues pointing into the environment of the catalytic center of a serine protease. X-ray crystal structure analyses revealed a distinct puckering preference of this ring. Substitution by F, HO, and MeO has a strong effect on the basicity of the adjacent pyrrolidine nitrogen center which originates from two sigma-inductive pathways between this center and the electronegative O and F atoms. gem-Difluorination decreases the pKa value of this tertiary amine center to <2, making the conjugated ammonium ion a moderately strong acid. Unexpectedly, F substitution next to the nitrogen center reduced the lipophilicity of the ligands, as revealed by measurements of the logarithmic partition coefficient log D. The biological assays showed that all compounds are thrombin inhibitors with activities between Ki=0.08 and 2.17 microM. Bioisosteric behavior of F, HO, and MeO substituents was observed. Their electronegative F and O atoms undergo energetically similar polar interactions with positively polarized centers, such as the N atom of His 57 which is hydrogen bonded to the catalytic Ser 195. However, for energetically similar polar interactions of C-F, C-OH, and C-OMe to occur, sufficient space is necessary for the accommodation of the Me group of the C-OMe residue, and a H-bond acceptor must be present to prevent unfavorable desolvation of the C-OH residue.
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Affiliation(s)
- Eliane Schweizer
- Laboratorium für Organische Chemie, ETH Zürich, Hönggerberg, HCI, 8093 Zürich, Switzerland
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41
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Hoffmann-Röder A, Schweizer E, Egger J, Seiler P, Obst-Sander U, Wagner B, Kansy M, Banner DW, Diederich F. Mapping the Fluorophilicity of a Hydrophobic Pocket: Synthesis and Biological Evaluation of Tricyclic Thrombin Inhibitors Directing Fluorinated Alkyl Groups into the P Pocket. ChemMedChem 2006; 1:1205-15. [PMID: 17001711 DOI: 10.1002/cmdc.200600124] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
In the completion of our fluorine scan of tricyclic inhibitors to map the fluorophilicity/fluorophobicity of the thrombin active site, a series of 11 new ligands featuring alkyl, alkenyl, and fluoroalkyl groups was prepared to explore fluorine effects on binding into the hydrophobic proximal (P) pocket, lined by Tyr 60A and Trp 60D, His 57, and Leu 99. The synthesis of the tricyclic scaffolds was based on the 1,3-dipolar cycloaddition of azomethine ylides, derived from L-proline and 4-bromobenzaldehyde, with N-(4-fluorobenzyl)maleimide. Introduction of alkyl, alkenyl, and partially fluorinated alkyl residues was achieved upon substitution of a sulfonyl group by mixed Mg/Zn organometallics followed by oxidation/deoxyfluorination, as well as oxidation/reduction/deoxyfluorination sequences. In contrast, the incorporation of perfluoroalkyl groups required a stereoselective nucleophilic addition reaction at the "upper" carbonyl group of the tricycles, thereby yielding scaffolds with an additional OH, F, or OMe group, respectively. All newly prepared inhibitors showed potent biological activity, with inhibitory constants (K(i) values) in the range of 0.008-0.163 microM. The X-ray crystal structure of a protein-ligand complex revealed the exact positioning of a difluoromethyl substituent in the tight P pocket. Fluorophilic characteristics are attributed to this hydrophobic pocket, although the potency of the inhibitors was found to be modulated by steric rather than electronic factors.
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Affiliation(s)
- Anja Hoffmann-Röder
- Institut für Organische Chemie, Johannes Gutenberg-Universität, Duesbergweg 10-14, 55128 Mainz, Germany
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42
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Joossens J, Van der Veken P, Surpateanu G, Lambeir AM, El-Sayed I, Ali OM, Augustyns K, Haemers A. Diphenyl Phosphonate Inhibitors for the Urokinase-Type Plasminogen Activator: Optimization of the P4 Position. J Med Chem 2006; 49:5785-93. [PMID: 16970403 DOI: 10.1021/jm060622g] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
This paper describes the structure-activity relationship in a series of tripeptidyl diphenyl phosphonate irreversible urokinase plasminogen activator (uPA) inhibitors, originally derived from an arginyltripeptide. uPA is considered an interesting target in anticancer drug design. The selectivity of these inhibitors for uPA is enhanced by the optimization of the P4 position. The most interesting compound shows an IC(50) of 5 nM, with a selectivity index of more than 3000 toward other Arg/Lys-specific proteases such as tissue-type plasminogen activator, plasmin, factor Xa, and thrombin. A synthetic strategy for the preparation of small libraries of diphenyl phosphonate analogues of capped tripeptides is described. It is shown that uPA is irreversibly inhibited, and interactions with the active site were modeled. Finally, a diparacetamol phosphonate analogue was developed to circumvent the release of cytotoxic phenol.
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Affiliation(s)
- Jurgen Joossens
- Laboratory of Medicinal Chemistry, University of Antwerp, Universiteitsplein 1, BE-2610 Antwerp, Belgium
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43
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Berg V, Sellstedt M, Hedenström M, Pinkner JS, Hultgren SJ, Almqvist F. Design, synthesis and evaluation of peptidomimetics based on substituted bicyclic 2-pyridones-targeting virulence of uropathogenic E. coli. Bioorg Med Chem 2006; 14:7563-81. [PMID: 16904898 DOI: 10.1016/j.bmc.2006.07.017] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2006] [Accepted: 07/03/2006] [Indexed: 10/24/2022]
Abstract
Substituted bicyclic 2-pyridones, termed pilicides, are dipeptide mimetics that prevent pilus assembly in uropathogenic Escherichia coli. Here, we apply rational design to produce four classes of extended peptidomimetics based on two bioactive 2-pyridones. The key intermediate in the synthesis was an amino-functionalised 2-pyridone scaffold, which could be obtained via a mild and selective nitration and subsequent reduction. Procedures were then developed to further derivatize this amino-substituted core and a total of 24 extended peptidomimetics were synthesised and evaluated for chaperone affinity and in vivo antivirulence activity in P pili producing E. coli. Enhanced affinities for the target protein were observed within the generated set of compounds, while the ability to prevent pilus assembly in vivo was significantly decreased compared to the parent lead compounds. The results suggest that the limited in vivo potencies of the analogues are either uptake/distribution related or due to loss in binding specificity.
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Affiliation(s)
- Veronica Berg
- Organic Chemistry, Department of Chemistry, Umeå University, SE-90187 Umeå, Sweden
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44
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Heynekamp JJ, Hunsaker LA, Vander Jagt TA, Deck LM, Vander Jagt DL. Uncharged isocoumarin-based inhibitors of urokinase-type plasminogen activator. BMC CHEMICAL BIOLOGY 2006; 6:1. [PMID: 16466576 PMCID: PMC1479381 DOI: 10.1186/1472-6769-6-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/24/2005] [Accepted: 02/08/2006] [Indexed: 11/10/2022]
Abstract
Background Urokinase-type plasminogen activator (uPA) plays a major role in extracellular proteolytic events associated with tumor cell growth, migration and angiogenesis. Consequently, uPA is an attractive target for the development of small molecule active site inhibitors. Most of the recent drug development programs aimed at nonpeptidic inhibitors targeted at uPA have focused on arginino mimetics containing amidine or guanidine functional groups attached to aromatic or heterocyclic scaffolds. There is a general problem of limited bioavailability of these charged inhibitors. In the present study, uPA inhibitors were designed on an isocoumarin scaffold containing uncharged substituents. Results 4-Chloro-3-alkoxyisocoumarins were synthesized in which the 3-alkoxy group contained a terminal bromine; these were compared with similar inhibitors that contained a charged terminal functional group. Additional variations included functional groups attached to the seven position of the isocoumarin scaffold. N- [3-(3-Bromopropoxy)-4-chloro-1-oxo-1H-isochromen-7-yl]benzamide was identified as an uncharged lead inhibitor of uPA, Ki = 0.034 μM. Molecular modeling of human uPA with these uncharged inhibitors suggests that the bromine occupies the same position as positively charged arginino mimetic groups. Conclusion This study demonstrates that potent uncharged inhibitors of uPA can be developed based upon the isocoumarin scaffold. A tethered bromine in the three position and an aromatic group in the seven position are important contributors to binding. Although the aim was to develop compounds that act as mechanism-based inactivators, these inhibitors are competitive reversible inhibitors.
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Affiliation(s)
| | - Lucy A Hunsaker
- Department of Biochemistry and Molecular Biology, University of New Mexico School of Medicine, Albuquerque, NM, USA
| | - Thomas A Vander Jagt
- Department of Biochemistry and Molecular Biology, University of New Mexico School of Medicine, Albuquerque, NM, USA
| | - Lorraine M Deck
- Department of Chemistry, University of New Mexico, Albuquerque, NM, USA
| | - David L Vander Jagt
- Department of Biochemistry and Molecular Biology, University of New Mexico School of Medicine, Albuquerque, NM, USA
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Bhongade BA, Gadad AK. Insight into the Structural Requirements of Urokinase-Type Plasminogen Activator Inhibitors Based on 3D QSAR CoMFA/CoMSIA Models. J Med Chem 2005; 49:475-89. [PMID: 16420035 DOI: 10.1021/jm050149r] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Urokinase-type plasminogen activator (uPA), a trypsin-like serine protease, has been implicated in large number of malignancies, tumor cell invasion, angiogenesis and metastasis; hence, the potent and selective inhibitors of uPA may therefore be therapeutically useful drugs for treatment of various forms of cancer. A three-dimensional quantitative structure-activity relationship (3D QSAR) study was performed on five different chemical series reported as selective uPA inhibitors employing comparative molecular field analysis (CoMFA)/comparative molecular similarity indices analysis (CoMSIA) techniques to investigate the structural requirements for substrates and derive a predictive model that may be used for the design of novel uPA inhibitors. ClogP has been used as an additional descriptor in the CoMFA analysis to study the effects of lipophilic parameters on activity. Inclusion of ClogP did not improve the models significantly and exhibited comparable correlation coefficients with CoMFA steric and electrostatic models. 3D QSAR models were derived for 2-pyridinylguanidines (training set N = 25, test set N = 8), 4-aminoarylguanidines and 4-aminoarylbenzamidines (training set N = 29, test set N = 8), thiophene-2-carboxamindines (training set N = 64, test set N = 19), 2-naphthamidines (training set N = 32, test set N = 8), and 1-isoquinolinylguanidines (training set N = 29, test set N = 7). The CoMFA models with steric and electrostatic fields exhibited r(2)(cv) 0.452-0.722, r(2)(ncv) 0.812-0.986, r(2)(pred) 0.597-0.870, whereas CoMFA ClogP models showed r(2)(cv) 0.420-0.707, r(2)(ncv) 0.849-0.957, r(2)(pred) 0.600-0.870. The CoMSIA models displayed r(2)(cv) 0.663-0.729, r(2)(ncv) 0.909-0.998, r(2)(pred) 0.554-0.855. 3D contour maps generated from these models were analyzed individually, which provides the regions in space where interactive fields may influence the activity. The superimposition of contour maps on the active site of serine proteases additionally helps in understanding the structural requirements of these inhibitors. Further, the predictive ability of 3D QSAR models was affirmed by predicting the activity of novel 2-naphthamidines. 3D QSAR models developed may be used in designing and predicting the uPA inhibitory activity of novel molecules.
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Affiliation(s)
- Bhoomendra A Bhongade
- Department of Medicinal Chemistry, College of Pharmacy, J. N. Medical College, Belgaum 590 010, Karnataka, India
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46
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Hansen M, Wind T, Blouse GE, Christensen A, Petersen HH, Kjelgaard S, Mathiasen L, Holtet TL, Andreasen PA. A Urokinase-type Plasminogen Activator-inhibiting Cyclic Peptide with an Unusual P2 Residue and an Extended Protease Binding Surface Demonstrates New Modalities for Enzyme Inhibition. J Biol Chem 2005; 280:38424-37. [PMID: 16141208 DOI: 10.1074/jbc.m505933200] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
To find new principles for inhibiting serine proteases, we screened phage-displayed random peptide repertoires with urokinase-type plasminogen activator (uPA) as the target. The most frequent of the isolated phage clones contained the disulfide bridge-constrained sequence CSWRGLENHRMC, which we designated upain-1. When expressed recombinantly with a protein fusion partner, upain-1 inhibited the enzymatic activity of uPA competitively with a temperature and pH-dependent K(i), which at 25 degrees C and pH 7.4 was approximately 500 nm. At the same conditions, the equilibrium dissociation constant K(D), monitored by displacement of p-aminobenzamidine from the specificity pocket of uPA, was approximately 400 nm. By an inhibitory screen against other serine proteases, including trypsin, upain-1 was found to be highly selective for uPA. The cyclical structure of upain-1 was indispensable for uPA binding. Alanine-scanning mutagenesis identified Arg(4) of upain-1 as the P(1) residue and indicated an extended binding interaction including the specificity pocket and the 37-, 60-, and 97-loops of uPA and the P(1), P(2), P(3)', P(4)', and the P(5)' residues of upain-1. Substitution with alanine of the P(2) residue, Trp(3), converted upain-1 into a distinct, although poor, uPA substrate. Upain-1 represents a new type of uPA inhibitor that achieves selectivity by targeting uPA-specific surface loops. Most likely, the inhibitory activity depends on its cyclical structure and the unusual P(2) residue preventing the scissile bond from assuming a tetrahedral geometry and thus from undergoing hydrolysis. Peptide-derived inhibitors such as upain-1 may provide novel mechanistic information about enzyme-inhibitor interactions and alternative methodologies for designing effective protease inhibitors.
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Affiliation(s)
- Martin Hansen
- Department of Molecular Biology, University of Aarhus, Gustav Wied's Vej 10C, 8000 Aarhus C, Denmark
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Tang J, Yu CL, Williams SR, Springman E, Jeffery D, Sprengeler PA, Estevez A, Sampang J, Shrader W, Spencer J, Young W, McGrath M, Katz BA. Expression, crystallization, and three-dimensional structure of the catalytic domain of human plasma kallikrein. J Biol Chem 2005; 280:41077-89. [PMID: 16199530 DOI: 10.1074/jbc.m506766200] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Plasma kallikrein is a serine protease that has many important functions, including modulation of blood pressure, complement activation, and mediation and maintenance of inflammatory responses. Although plasma kallikrein has been purified for 40 years, its structure has not been elucidated. In this report, we described two systems (Pichia pastoris and baculovirus/Sf9 cells) for expression of the protease domain of plasma kallikrein, along with the purification and high resolution crystal structures of the two recombinant forms. In the Pichia pastoris system, the protease domain was expressed as a heterogeneously glycosylated zymogen that was activated by limited trypsin digestion and treated with endoglycosidase H deglycosidase to reduce heterogeneity from the glycosylation. The resulting protein was chromatographically resolved into four components, one of which was crystallized. In the baculovirus/Sf9 system, homogeneous, crystallizable, and nonglycosylated protein was expressed after mutagenizing three asparagines (the glycosylation sites) to glutamates. When assayed against the peptide substrates, pefachrome-PK and oxidized insulin B chain, both forms of the protease domain were found to have catalytic activity similar to that of the full-length protein. Crystallization and x-ray crystal structure determination of both forms have yielded the first three-dimensional views of the catalytic domain of plasma kallikrein. The structures, determined at 1.85 A for the endoglycosidase H-deglycosylated protease domain produced from P. pastoris and at 1.40 A for the mutagenically deglycosylated form produced from Sf9 cells, show that the protease domain adopts a typical chymotrypsin-like serine protease conformation. The structural information provides insights into the biochemical and enzymatic properties of plasma kallikrein and paves the way for structure-based design of protease inhibitors that are selective either for or against plasma kallikrein.
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Affiliation(s)
- Jie Tang
- Department of Structural Chemistry, Celera Genomics, South San Francisco, California 94080, USA
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Jensen CM, Lindsay KB, Andreasen P, Skrydstrup T. Synthesis of a Hydroxyethylene Isostere of the Tripeptide Arg-Gly-Leu via a Convergent Acyl-like Radical Addition Strategy. J Org Chem 2005; 70:7512-9. [PMID: 16149778 DOI: 10.1021/jo0505775] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
[reaction: see text] A hydroxyethylene isostere of the tripeptide Arg-Gly-Leu, representing an important fragment of a novel cyclic-peptide-based uPA inhibitor, was synthesized in few steps employing as the key step a samarium diiodide promoted coupling of either the 4-thiopyridyl ester of N(alpha)-Fmoc- or N(alpha)-Cbz-protected L-ornithine with the N-acryloyl derivative of L-leucine methyl ester. Epimerization under the coupling conditions at the chiral center in the alpha-position to the ketone was demonstrated not to take place. A stereoselective reduction of the Cbz-protected aminoketone obtained from this radical reaction was promoted by the same single-electron reducing agent in the presence of methanol providing the syn-amino alcohol with a diastereoselectivity of 85:15. With the use of lithium tri-tert-butoxyaluminum hydride in methanol, the corresponding anti-isomer was obtained almost exclusively. Subsequent elaboration of the ornithine moiety in the anti-isomer by introduction of the guanidine group followed by hydrolysis of the C-terminal ester bond and protection of the alcohol as its tert-butyldimethylsilyl ether provided the desired tripeptide mimic. The long reaction times required for the radical addition reactions with N(delta)-Boc-L-ornithine (up to 5 days) led to a short study where a series of 4-thiopyridyl esters of Cbz-protected amino acids were reacted with two acrylates. Whereas N(delta)-Boc-L-ornithine, alanine, phenylalanine, proline, and leucine all provided the aminoketone in 43-79% yield, valine only afforded traces of the coupling product.
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Affiliation(s)
- Christina M Jensen
- Department of Chemistry, University of Aarhus, Langelandsgade 140, 8000 Aarhus C, Denmark
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Bhongade BA, Gouripur VV, Gadad AK. 3D-QSAR CoMFA studies on trypsin-like serine protease inhibitors: a comparative selectivity analysis. Bioorg Med Chem 2005; 13:2773-82. [PMID: 15781388 DOI: 10.1016/j.bmc.2005.02.027] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2005] [Revised: 02/14/2005] [Accepted: 02/15/2005] [Indexed: 11/28/2022]
Abstract
A series of indole/benzoimidazole-5-carboxamidines have been reported to inhibit various trypsin-like serine proteases viz. uPA, tPA, factor Xa, thrombin, plasmin, and trypsin, which are involved in various types of pathophysiological conditions such as cancer progression, thrombosis etc. Inhibition of these protease enzymes may serve as therapeutic agents in various types of cancer as well serve as anticoagulant or antithrombotic agents. The dual inhibitory action may result in poor clinical candidates. 3D-QSAR models were generated for indole/benzoimidazole-5-carboxamidines using the CoMFA technique to study their selectivity trends toward various trypsin-like serine proteases. Molecular superimposition was carried out on the template structure using atom-based RMS fit method. The CoMFA models were established from the training set of 25-29 molecules and validated by predicting the activities of seven-eight test set molecules. The CoMFA models generated using steric and electrostatic fields for tPA, fXa, thrombin, plasmin, and trypsin inhibition exhibited better statistical significance than the CoMFA models generated using ClogP as an additional descriptor. Thus, the validated CoMFA models with steric and electrostatic fields were used to generate 3D contour maps, which may provide possible modification of molecules for better selectivity/activity. The present 3D-QSAR studies emphasize the selectivity trends of indole/benzoimidazole-5-carboxamidines, which may be obliging in designing novel selective serine protease inhibitors of therapeutic interest.
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Affiliation(s)
- Bhoomendra A Bhongade
- Department of Medicinal Chemistry, College of Pharmacy, J. N. Medical College, Belgaum 590 010, Karnataka, India
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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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