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Müller P, Meta M, Meidner JL, Schwickert M, Meyr J, Schwickert K, Kersten C, Zimmer C, Hammerschmidt SJ, Frey A, Lahu A, de la Hoz-Rodríguez S, Agost-Beltrán L, Rodríguez S, Diemer K, Neumann W, Gonzàlez FV, Engels B, Schirmeister T. Investigation of the Compatibility between Warheads and Peptidomimetic Sequences of Protease Inhibitors-A Comprehensive Reactivity and Selectivity Study. Int J Mol Sci 2023; 24:ijms24087226. [PMID: 37108388 PMCID: PMC10138721 DOI: 10.3390/ijms24087226] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 04/06/2023] [Accepted: 04/10/2023] [Indexed: 04/29/2023] Open
Abstract
Covalent peptidomimetic protease inhibitors have gained a lot of attention in drug development in recent years. They are designed to covalently bind the catalytically active amino acids through electrophilic groups called warheads. Covalent inhibition has an advantage in terms of pharmacodynamic properties but can also bear toxicity risks due to non-selective off-target protein binding. Therefore, the right combination of a reactive warhead with a well-suited peptidomimetic sequence is of great importance. Herein, the selectivities of well-known warheads combined with peptidomimetic sequences suited for five different proteases were investigated, highlighting the impact of both structure parts (warhead and peptidomimetic sequence) for affinity and selectivity. Molecular docking gave insights into the predicted binding modes of the inhibitors inside the binding pockets of the different enzymes. Moreover, the warheads were investigated by NMR and LC-MS reactivity assays against serine/threonine and cysteine nucleophile models, as well as by quantum mechanics simulations.
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Affiliation(s)
- Patrick Müller
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University Mainz, Staudinger Weg 5, D-55128 Mainz, Germany
| | - Mergim Meta
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University Mainz, Staudinger Weg 5, D-55128 Mainz, Germany
| | - Jan Laurenz Meidner
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University Mainz, Staudinger Weg 5, D-55128 Mainz, Germany
| | - Marvin Schwickert
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University Mainz, Staudinger Weg 5, D-55128 Mainz, Germany
| | - Jessica Meyr
- Institute of Physical and Theoretical Chemistry, Julius-Maximilians-University of Wuerzburg, Emil-Fischer-Straße 42 Süd, D-97074 Wuerzburg, Germany
| | - Kevin Schwickert
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University Mainz, Staudinger Weg 5, D-55128 Mainz, Germany
| | - Christian Kersten
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University Mainz, Staudinger Weg 5, D-55128 Mainz, Germany
| | - Collin Zimmer
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University Mainz, Staudinger Weg 5, D-55128 Mainz, Germany
| | - Stefan Josef Hammerschmidt
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University Mainz, Staudinger Weg 5, D-55128 Mainz, Germany
| | - Ariane Frey
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University Mainz, Staudinger Weg 5, D-55128 Mainz, Germany
| | - Albin Lahu
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University Mainz, Staudinger Weg 5, D-55128 Mainz, Germany
| | | | - Laura Agost-Beltrán
- Departament de Química Inorgànica i Orgànica, Universitat Jaume I, 12080 Castelló de la Pana, Spain
| | - Santiago Rodríguez
- Departament de Química Inorgànica i Orgànica, Universitat Jaume I, 12080 Castelló de la Pana, Spain
| | - Kira Diemer
- Institute of Physical and Theoretical Chemistry, Julius-Maximilians-University of Wuerzburg, Emil-Fischer-Straße 42 Süd, D-97074 Wuerzburg, Germany
| | - Wilhelm Neumann
- Institute of Physical and Theoretical Chemistry, Julius-Maximilians-University of Wuerzburg, Emil-Fischer-Straße 42 Süd, D-97074 Wuerzburg, Germany
| | - Florenci V Gonzàlez
- Departament de Química Inorgànica i Orgànica, Universitat Jaume I, 12080 Castelló de la Pana, Spain
| | - Bernd Engels
- Institute of Physical and Theoretical Chemistry, Julius-Maximilians-University of Wuerzburg, Emil-Fischer-Straße 42 Süd, D-97074 Wuerzburg, Germany
| | - Tanja Schirmeister
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University Mainz, Staudinger Weg 5, D-55128 Mainz, Germany
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Yazdian F, Ramezanpour S, Ayatollahi SA, Ghodrati A, Mahmoudzadeh K. An efficient multicomponent synthesis of fused pyrido-dipyrimidines containing tranexamic acid under green conditions. MONATSHEFTE FUR CHEMIE 2023. [DOI: 10.1007/s00706-022-03027-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
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3
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Peptidomimetic inhibitors of TMPRSS2 block SARS-CoV-2 infection in cell culture. Commun Biol 2022; 5:681. [PMID: 35804152 PMCID: PMC9270327 DOI: 10.1038/s42003-022-03613-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 06/21/2022] [Indexed: 12/02/2022] Open
Abstract
The transmembrane serine protease 2 (TMPRSS2) primes the SARS-CoV-2 Spike (S) protein for host cell entry and represents a promising target for COVID-19 therapy. Here we describe the in silico development and in vitro characterization of peptidomimetic TMPRSS2 inhibitors. Molecular docking studies identified peptidomimetic binders of the TMPRSS2 catalytic site, which were synthesized and coupled to an electrophilic serine trap. The compounds inhibit TMPRSS2 while demonstrating good off-target selectivity against selected coagulation proteases. Lead candidates are stable in blood serum and plasma for at least ten days. Finally, we show that selected peptidomimetics inhibit SARS-CoV-2 Spike-driven pseudovirus entry and authentic SARS-CoV-2 infection with comparable efficacy as camostat mesylate. The peptidomimetic TMPRSS2 inhibitors also prevent entry of recent SARS-CoV-2 variants of concern Delta and Omicron BA.1. In sum, our study reports antivirally active and stable TMPRSS2 inhibitors with prospects for further preclinical and clinical development as antiviral agents against SARS-CoV-2 and other TMPRSS2-dependent viruses. This study describes the development and characterization of peptidomimetic inhibitors of TMPRSS2, which primes the Spike protein of SARS-CoV-2. The inhibitors are shown to prevent SARS-CoV-2 infection in cells as efficiently as camostat mesylate.
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Knaff PM, Müller P, Kersten C, Wettstein L, Münch J, Landfester K, Mailänder V. Structure-Based Design of High-Affinity and Selective Peptidomimetic Hepsin Inhibitors. Biomacromolecules 2022; 23:2236-2242. [PMID: 35593713 DOI: 10.1021/acs.biomac.1c01011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In many solid tumors, increased upregulation of transmembrane serine proteases (TTSPs) leads to an overactivation of growth factors, which promotes tumor progression. Here, we have used a combinatorial methodology to develop high-affinity tetrapeptidic inhibitors. A previous virtual screening of 8000 peptide combinations against the crystal structure of the TTSP hepsin identified a series of recognition sequences, customized for the non-prime substrate binding (P) sites of this serine protease. A combination of the top recognition sequences with an electrophilic warhead resulted in highly potent inhibitors with good selectivity against coagulation proteases factor Xa and thrombin. Structure-activity relationships of two selected compounds were further elucidated by investigation of their stability in biological fluids as well as the influence of the warhead and truncated inhibitors on the inhibitory potency. Overall, this methodology yielded compounds as selective inhibitors for potential cancer drug development, where hepsin is overexpressed.
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Affiliation(s)
- Philip Maximilian Knaff
- Max Planck Institute for Polymer Research, Ackermannweg 10, Mainz 55128, Germany.,Dermatology Clinic of the University Medicine of the Johannes Gutenberg University Mainz, Langenbeckstraße 1, Mainz 55131, Germany
| | - Patrick Müller
- Institute for Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University Mainz, Staudingerweg 5, Mainz 55128, Germany
| | - Christian Kersten
- Institute for Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University Mainz, Staudingerweg 5, Mainz 55128, Germany
| | - Lukas Wettstein
- Institute of Molecular Virology, Ulm University Medical Center, Ulm 89081, Germany
| | - Jan Münch
- Institute of Molecular Virology, Ulm University Medical Center, Ulm 89081, Germany
| | - Katharina Landfester
- Max Planck Institute for Polymer Research, Ackermannweg 10, Mainz 55128, Germany
| | - Volker Mailänder
- Max Planck Institute for Polymer Research, Ackermannweg 10, Mainz 55128, Germany.,Dermatology Clinic of the University Medicine of the Johannes Gutenberg University Mainz, Langenbeckstraße 1, Mainz 55131, Germany
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5
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Wang N, Lin JY, Luo SH, Zhou YJ, Yang K, Chen RH, Yang GX, Wang ZY. Furanonyl amino acid derivatives as hemostatic drugs: design, synthesis and hemostasis performance. Amino Acids 2022; 54:989-999. [PMID: 35305164 DOI: 10.1007/s00726-022-03155-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Accepted: 03/07/2022] [Indexed: 11/01/2022]
Abstract
Using 3,4-dihalo-2(5H)-furanones and easily available hemostatic drugs, such as tranexamic acid (TA), 4-aminomethylbenzoic acid (ABA), aminocaproic acid (AA) as starting materials, serial multi-functional molecules 2(5H)-furanonyl amino acids are designed by the combination of different pharmacophores, and successfully synthesized by a transition metal-free Michael addition-elimination reaction. The reaction is carried out under mild conditions with ethanol-dichloromethane as solvent and only stirring at room temperature for 24 h, and the yield can be up to 91%. All products are well characterized by infrared spectroscopy (IR), nuclear magnetic resonance (NMR), high-resolution mass spectra (HRMS). Ten typical target compounds among them are selected out for the experiments of hemostasis performance by the evaluation of in vitro clot formation model and liver hemorrhage model. The test results show that, their hemostasis effect is better than the original drugs. Especially the target compound G, a TA derivative from 5-borneoloxy-3,4-dibromo-2(5H)-furanone, has the best hemostasis effect among all the tested compounds. These obtained target molecules are expected to be used as multi-functional hemostatic drugs.
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Affiliation(s)
- Neng Wang
- School of Chemistry, Key Laboratory of Theoretical Chemistry of Environment, Ministry of Education, South China Normal University, Guangzhou, 510006, People's Republic of China.,School of Chemistry, Guangzhou Key Laboratory of Analytical Chemistry for Biomedicine, South China Normal University, Guangzhou, 510006, People's Republic of China.,School of Chemistry, GDMPA Key Laboratory for Process Control and Quality Evaluation of Chiral Pharmaceuticals, South China Normal University, Guangzhou, 510006, People's Republic of China
| | - Jian-Yun Lin
- School of Chemistry, Key Laboratory of Theoretical Chemistry of Environment, Ministry of Education, South China Normal University, Guangzhou, 510006, People's Republic of China.,School of Chemistry, Guangzhou Key Laboratory of Analytical Chemistry for Biomedicine, South China Normal University, Guangzhou, 510006, People's Republic of China.,School of Chemistry, GDMPA Key Laboratory for Process Control and Quality Evaluation of Chiral Pharmaceuticals, South China Normal University, Guangzhou, 510006, People's Republic of China
| | - Shi-He Luo
- School of Chemistry, Key Laboratory of Theoretical Chemistry of Environment, Ministry of Education, South China Normal University, Guangzhou, 510006, People's Republic of China. .,Key Laboratory of Functional Molecular Engineering of Guangdong Province, School of Chemistry and Chemical Engineering, South China University of Technology, 381 Wushan Road, Guangzhou, 510640, People's Republic of China. .,School of Chemistry, Guangzhou Key Laboratory of Analytical Chemistry for Biomedicine, South China Normal University, Guangzhou, 510006, People's Republic of China. .,School of Chemistry, GDMPA Key Laboratory for Process Control and Quality Evaluation of Chiral Pharmaceuticals, South China Normal University, Guangzhou, 510006, People's Republic of China.
| | - Yong-Jun Zhou
- School of Chemistry, Key Laboratory of Theoretical Chemistry of Environment, Ministry of Education, South China Normal University, Guangzhou, 510006, People's Republic of China.,School of Chemistry, Guangzhou Key Laboratory of Analytical Chemistry for Biomedicine, South China Normal University, Guangzhou, 510006, People's Republic of China.,School of Chemistry, GDMPA Key Laboratory for Process Control and Quality Evaluation of Chiral Pharmaceuticals, South China Normal University, Guangzhou, 510006, People's Republic of China
| | - Kai Yang
- School of Chemistry, Key Laboratory of Theoretical Chemistry of Environment, Ministry of Education, South China Normal University, Guangzhou, 510006, People's Republic of China. .,College of Pharmacy, Gannan Medical University, Ganzhou, 341000, People's Republic of China. .,School of Chemistry, Guangzhou Key Laboratory of Analytical Chemistry for Biomedicine, South China Normal University, Guangzhou, 510006, People's Republic of China. .,School of Chemistry, GDMPA Key Laboratory for Process Control and Quality Evaluation of Chiral Pharmaceuticals, South China Normal University, Guangzhou, 510006, People's Republic of China.
| | - Ren-Hong Chen
- Guangdong Food and Drug Vocational College, Guangzhou, 510520, People's Republic of China.
| | - Guo-Xian Yang
- School of Chemistry, Key Laboratory of Theoretical Chemistry of Environment, Ministry of Education, South China Normal University, Guangzhou, 510006, People's Republic of China.,School of Chemistry, Guangzhou Key Laboratory of Analytical Chemistry for Biomedicine, South China Normal University, Guangzhou, 510006, People's Republic of China.,School of Chemistry, GDMPA Key Laboratory for Process Control and Quality Evaluation of Chiral Pharmaceuticals, South China Normal University, Guangzhou, 510006, People's Republic of China
| | - Zhao-Yang Wang
- School of Chemistry, Key Laboratory of Theoretical Chemistry of Environment, Ministry of Education, South China Normal University, Guangzhou, 510006, People's Republic of China. .,Key Laboratory of Functional Molecular Engineering of Guangdong Province, School of Chemistry and Chemical Engineering, South China University of Technology, 381 Wushan Road, Guangzhou, 510640, People's Republic of China. .,School of Chemistry, Guangzhou Key Laboratory of Analytical Chemistry for Biomedicine, South China Normal University, Guangzhou, 510006, People's Republic of China. .,School of Chemistry, GDMPA Key Laboratory for Process Control and Quality Evaluation of Chiral Pharmaceuticals, South China Normal University, Guangzhou, 510006, People's Republic of China.
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6
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Recent progress on inhibitors of the type II transmembrane serine proteases, hepsin, matriptase and matriptase-2. Future Med Chem 2019; 11:743-769. [DOI: 10.4155/fmc-2018-0446] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Members of the type II transmembrane serine proteases (TTSP) family play a vital role in cell growth and development but many are also implicated in disease. Two of the well-studied TTSPs, matriptase and hepsin proteolytically process multiple protein substrates such as the inactive single-chain zymogens pro-HGF and pro-macrophage stimulating protein into the active heterodimeric forms, HGF and macrophage stimulating protein. These two proteases also have many other substrates which are associated with cancer and tumor progression. Another related TTSP, matriptase-2 is expressed in the liver and functions by regulating iron homoeostasis through the cleavage of hemojuvelin and thus is implicated in iron overload diseases. In the present review, we will discuss inhibitor design strategy and Structure activity relationships of TTSP inhibitors, which have been reported in the literature.
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7
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Mohajeri M, Kovanen PT, Bianconi V, Pirro M, Cicero AFG, Sahebkar A. Mast cell tryptase - Marker and maker of cardiovascular diseases. Pharmacol Ther 2019; 199:91-110. [PMID: 30877022 DOI: 10.1016/j.pharmthera.2019.03.008] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 03/01/2019] [Indexed: 12/14/2022]
Abstract
Mast cells are tissue-resident cells, which have been proposed to participate in various inflammatory diseases, among them the cardiovascular diseases (CVDs). For mast cells to be able to contribute to an inflammatory process, they need to be activated to exocytose their cytoplasmic secretory granules. The granules contain a vast array of highly bioactive effector molecules, the neutral protease tryptase being the most abundant protein among them. The released tryptase may act locally in the inflamed cardiac or vascular tissue, so contributing directly to the pathogenesis of CVDs. Moreover, a fraction of the released tryptase reaches the systemic circulation, thereby serving as a biomarker of mast cell activation. Actually, increased levels of circulating tryptase have been found to associate with CVDs. Here we review the biological relevance of the circulating tryptase as a biomarker of mast cell activity in CVDs, with special emphasis on the relationship between activation of mast cells in their tissue microenvironments and the pathophysiological pathways of CVDs. Based on the available in vitro and in vivo studies, we highlight the potential molecular mechanisms by which tryptase may contribute to the pathogenesis of CVDs. Finally, the synthetic and natural inhibitors of tryptase are reviewed for their potential utility as therapeutic agents in CVDs.
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Affiliation(s)
- Mohammad Mohajeri
- Department of Medical Biotechnology, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | | | - Vanessa Bianconi
- Unit of Internal Medicine, Department of Medicine, University of Perugia, Perugia, Italy
| | - Matteo Pirro
- Unit of Internal Medicine, Department of Medicine, University of Perugia, Perugia, Italy
| | - Arrigo F G Cicero
- Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy
| | - Amirhossein Sahebkar
- Biotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran; Neurogenic Inflammation Research Center, Mashhad University of Medical Sciences, Mashhad, Iran; School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran.
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8
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He W, Zhao A, Zou J, Luo X, Lin X, Wang L, Lin C. Synthesis, in vitro coagulation activities and molecular docking studies on three L-histidine amide derivatives. Chem Res Chin Univ 2018. [DOI: 10.1007/s40242-018-7184-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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9
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Konnert L, Lamaty F, Martinez J, Colacino E. Recent Advances in the Synthesis of Hydantoins: The State of the Art of a Valuable Scaffold. Chem Rev 2017. [PMID: 28644621 DOI: 10.1021/acs.chemrev.7b00067] [Citation(s) in RCA: 117] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The review highlights the hydantoin syntheses presented from the point of view of the preparation methods. Novel synthetic routes to various hydantoin structures, the advances brought to the classical methods in the aim of producing more sustainable and environmentally friendly procedures for the preparation of these biomolecules, and a critical comparison of the different synthetic approaches developed in the last twelve years are also described. The review is composed of 95 schemes, 8 figures and 528 references for the last 12 years and includes the description of the hydantoin-based marketed drugs and clinical candidates.
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Affiliation(s)
- Laure Konnert
- Université de Montpellier, Institut des Biomolécules Max Mousseron UMR 5247 CNRS - Universités Montpellier - ENSCM , Place E. Bataillon, Campus Triolet, cc 1703, 34095 Montpellier, France
| | - Frédéric Lamaty
- Université de Montpellier, Institut des Biomolécules Max Mousseron UMR 5247 CNRS - Universités Montpellier - ENSCM , Place E. Bataillon, Campus Triolet, cc 1703, 34095 Montpellier, France
| | - Jean Martinez
- Université de Montpellier, Institut des Biomolécules Max Mousseron UMR 5247 CNRS - Universités Montpellier - ENSCM , Place E. Bataillon, Campus Triolet, cc 1703, 34095 Montpellier, France
| | - Evelina Colacino
- Université de Montpellier, Institut des Biomolécules Max Mousseron UMR 5247 CNRS - Universités Montpellier - ENSCM , Place E. Bataillon, Campus Triolet, cc 1703, 34095 Montpellier, France
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10
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Abstract
INTRODUCTION Tryptase is one of the main serine-proteinases located in the secretory granules of mast cells, and is released through degranulation, which is involved in the pathogenesis of allergic inflammatory disease, cardiovascular diseases, lung fibrosis and tumor. Therefore, inhibitors targeting tryptase may represent a new direction for the treatment of allergic inflammatory disease and other diseases. Areas covered: In this article, we discussed the history and development of tryptase inhibitors and described a variety of tryptase inhibitors via their structures and biological importance in clinical studies and drug development for tryptase-related diseases. Expert opinion: Initial tryptase inhibitors based on indole structure as the hydrophobic substituent on a benzylamine-piperidine template have low specificity and poor bioavailability. Therefore, designing new and specific inhibitors targeting tryptase should be involved in future clinical studies. Modifications toward indoles with varying N-substitution, introducing an amide bond, and growing the chain length contribute to an increase in the specific selectivity and potency of tryptase inhibitors. Tryptase has become the research hotspot to explore many related diseases. Therefore, there has been growing appreciation for the potential importance of the tryptase inhibitors as a target for treating these diseases.
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Affiliation(s)
- Wei-Wei Ni
- a Research Division of Clinical Pharmacology , the First Affiliated Hospital of Nanjing Medical University , Nanjing , Jiangsu , China
| | - Meng-Da Cao
- a Research Division of Clinical Pharmacology , the First Affiliated Hospital of Nanjing Medical University , Nanjing , Jiangsu , China
| | - Wen Huang
- a Research Division of Clinical Pharmacology , the First Affiliated Hospital of Nanjing Medical University , Nanjing , Jiangsu , China
| | - Ling Meng
- a Research Division of Clinical Pharmacology , the First Affiliated Hospital of Nanjing Medical University , Nanjing , Jiangsu , China
| | - Ji-Fu Wei
- a Research Division of Clinical Pharmacology , the First Affiliated Hospital of Nanjing Medical University , Nanjing , Jiangsu , China
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11
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Modulating the selectivity of matriptase-2 inhibitors with unnatural amino acids. Eur J Med Chem 2017; 129:110-123. [DOI: 10.1016/j.ejmech.2017.02.006] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Revised: 01/19/2017] [Accepted: 02/05/2017] [Indexed: 12/12/2022]
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12
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Han Z, Harris PKW, Karmakar P, Kim T, Owusu BY, Wildman SA, Klampfer L, Janetka JW. α-Ketobenzothiazole Serine Protease Inhibitors of Aberrant HGF/c-MET and MSP/RON Kinase Pathway Signaling in Cancer. ChemMedChem 2016; 11:585-99. [PMID: 26889658 DOI: 10.1002/cmdc.201500600] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Indexed: 12/20/2022]
Abstract
Upregulation of the HGF and MSP growth-factor processing serine endopeptidases HGFA, matriptase and hepsin is correlated with increased metastasis in multiple tumor types driven by c-MET or RON kinase signaling. We rationally designed P1' α-ketobenzothiazole mechanism-based inhibitors of these proteases. Structure-activity studies are presented, which resulted in the identification of potent inhibitors with differential selectivity. The tetrapeptide inhibitors span the P1-P1' substrate cleavage site via a P1' amide linker off the benzothiazole, occupying the S3' pocket. Optimized inhibitors display sub-nanomolar enzyme inhibition against one, two, or all three of HGFA, matriptase, and hepsin. Several compounds also have good selectivity against the related trypsin-like proteases, thrombin and Factor Xa. Finally, we show that inhibitors block the fibroblast (HGF)-mediated migration of invasive DU145 prostate cancer cells. In addition to prostate cancer, breast, colon, lung, pancreas, gliomas, and multiple myeloma tumors all depend on HGF and MSP for tumor survival and progression. Therefore, these unique inhibitors have potential as new therapeutics for a diverse set of tumor types.
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Affiliation(s)
- Zhenfu Han
- Department of Biochemistry and Molecular Biophysics, Alvin J. Siteman Cancer Center, Washington University School of Medicine, 660 S. Euclid Ave., Saint Louis, MO, 63110, USA
| | - Peter K W Harris
- Department of Biochemistry and Molecular Biophysics, Alvin J. Siteman Cancer Center, Washington University School of Medicine, 660 S. Euclid Ave., Saint Louis, MO, 63110, USA
| | - Partha Karmakar
- Department of Biochemistry and Molecular Biophysics, Alvin J. Siteman Cancer Center, Washington University School of Medicine, 660 S. Euclid Ave., Saint Louis, MO, 63110, USA
| | - Tommy Kim
- Department of Biochemistry and Molecular Biophysics, Alvin J. Siteman Cancer Center, Washington University School of Medicine, 660 S. Euclid Ave., Saint Louis, MO, 63110, USA
| | - Ben Y Owusu
- Department of Oncology, Southern Research Institute, 2000 9th Ave., Birmingham, AL, 35205, USA
| | - Scott A Wildman
- Department of Biochemistry and Molecular Biophysics, Alvin J. Siteman Cancer Center, Washington University School of Medicine, 660 S. Euclid Ave., Saint Louis, MO, 63110, USA.,Carbone Cancer Center, School of Medicine and Public Health, University of Wisconsin, Madison, WI, 53792, USA
| | - Lidija Klampfer
- Department of Oncology, Southern Research Institute, 2000 9th Ave., Birmingham, AL, 35205, USA
| | - James W Janetka
- Department of Biochemistry and Molecular Biophysics, Alvin J. Siteman Cancer Center, Washington University School of Medicine, 660 S. Euclid Ave., Saint Louis, MO, 63110, USA.
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Janssen FJ, Baggelaar MP, Hummel JJA, Overkleeft HS, Cravatt BF, Boger DL, van der Stelt M. Comprehensive Analysis of Structure-Activity Relationships of α-Ketoheterocycles as sn-1-Diacylglycerol Lipase α Inhibitors. J Med Chem 2015; 58:9742-53. [PMID: 26584396 PMCID: PMC4690813 DOI: 10.1021/acs.jmedchem.5b01627] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Diacylglycerol lipase α (DAGLα) is responsible for the formation of the endocannabinoid 2-arachidonoylglycerol (2-AG) in the central nervous system. DAGLα inhibitors are required to study the physiological role of 2-AG. Previously, we identified the α-ketoheterocycles as potent and highly selective DAGLα inhibitors. Here, we present the first comprehensive structure-activity relationship study of α-ketoheterocycles as DAGLα inhibitors. Our findings indicate that the active site of DAGLα is remarkably sensitive to the type of heterocyclic scaffold with oxazolo-4N-pyridines as the most active framework. We uncovered a fundamental substituent effect in which electron-withdrawing meta-oxazole substituents increased inhibitor potency. (C6-C9)-acyl chains with a distal phenyl group proved to be the most potent inhibitors. The integrated SAR data was consistent with the proposed binding pose in a DAGLα homology model. Altogether, our results may guide the design of future DAGLα inhibitors as leads for molecular therapies to treat neuroinflammation, obesity, and related metabolic disorders.
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Affiliation(s)
- Freek J. Janssen
- Department of Molecular Physiology, Leiden Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA Leiden, Netherlands
| | - Marc P. Baggelaar
- Department of Molecular Physiology, Leiden Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA Leiden, Netherlands
| | - Jessica J. A. Hummel
- Department of Molecular Physiology, Leiden Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA Leiden, Netherlands
| | - Herman S. Overkleeft
- Department of Bio-Organic Synthesis, Leiden Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA Leiden, Netherlands
| | - Benjamin F. Cravatt
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Dale L. Boger
- Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Mario van der Stelt
- Department of Molecular Physiology, Leiden Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA Leiden, Netherlands
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14
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Pramanik N, Sarkar S, Roy D, Debnath S, Ghosh S, Khamarui S, Maiti DK. Synthesis and diverse general oxidative cyclization catalysis of high-valent MoVIO2(HL) to ubiquitous heterocycles and their chiral analogues with high selectivity. RSC Adv 2015. [DOI: 10.1039/c5ra21825j] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The first synthesis and diverse oxidative cyclization catalysis properties of high-valent MoVI–triazole are demonstrated towards highly selective construction of benzimidazoles, benzothiazoles, isoxazolines, isoxazoles and their chiral analogues.
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Affiliation(s)
| | - Satinath Sarkar
- Department of Chemistry
- University of Calcutta
- Kolkata-700009
- India
| | - Dipanwita Roy
- Department of Chemistry
- University of Calcutta
- Kolkata-700009
- India
| | - Sudipto Debnath
- Department of Chemistry
- University of Calcutta
- Kolkata-700009
- India
| | - Sukla Ghosh
- Department of Chemistry
- University of Calcutta
- Kolkata-700009
- India
| | - Saikat Khamarui
- Department of Chemistry
- University of Calcutta
- Kolkata-700009
- India
| | - Dilip K. Maiti
- Department of Chemistry
- University of Calcutta
- Kolkata-700009
- India
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15
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Duchêne D, Colombo E, Désilets A, Boudreault PL, Leduc R, Marsault E, Najmanovich R. Analysis of Subpocket Selectivity and Identification of Potent Selective Inhibitors for Matriptase and Matriptase-2. J Med Chem 2014; 57:10198-204. [DOI: 10.1021/jm5015633] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Dominic Duchêne
- Departments of Biochemistry and ‡Pharmacology, Faculty of Medicine and Health
Sciences, Université de Sherbrooke, 3001 12e Avenue Nord, Sherbrooke, Quebec J1H 5N4, Canada
| | - Eloïc Colombo
- Departments of Biochemistry and ‡Pharmacology, Faculty of Medicine and Health
Sciences, Université de Sherbrooke, 3001 12e Avenue Nord, Sherbrooke, Quebec J1H 5N4, Canada
| | - Antoine Désilets
- Departments of Biochemistry and ‡Pharmacology, Faculty of Medicine and Health
Sciences, Université de Sherbrooke, 3001 12e Avenue Nord, Sherbrooke, Quebec J1H 5N4, Canada
| | - Pierre-Luc Boudreault
- Departments of Biochemistry and ‡Pharmacology, Faculty of Medicine and Health
Sciences, Université de Sherbrooke, 3001 12e Avenue Nord, Sherbrooke, Quebec J1H 5N4, Canada
| | - Richard Leduc
- Departments of Biochemistry and ‡Pharmacology, Faculty of Medicine and Health
Sciences, Université de Sherbrooke, 3001 12e Avenue Nord, Sherbrooke, Quebec J1H 5N4, Canada
| | - Eric Marsault
- Departments of Biochemistry and ‡Pharmacology, Faculty of Medicine and Health
Sciences, Université de Sherbrooke, 3001 12e Avenue Nord, Sherbrooke, Quebec J1H 5N4, Canada
| | - Rafael Najmanovich
- Departments of Biochemistry and ‡Pharmacology, Faculty of Medicine and Health
Sciences, Université de Sherbrooke, 3001 12e Avenue Nord, Sherbrooke, Quebec J1H 5N4, Canada
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16
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Kokotos G, Feuerherm AJ, Barbayianni E, Shah I, Sæther M, Magrioti V, Nguyen T, Constantinou-Kokotou V, Dennis EA, Johansen B. Inhibition of group IVA cytosolic phospholipase A2 by thiazolyl ketones in vitro, ex vivo, and in vivo. J Med Chem 2014; 57:7523-35. [PMID: 25152071 DOI: 10.1021/jm500192s] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Group IVA cytosolic phospholipase A2 (GIVA cPLA2) is the rate-limiting provider of pro-inflammatory mediators in many tissues and is thus an attractive target for the development of novel anti-inflammatory agents. In this work, we present the synthesis of new thiazolyl ketones and the study of their activities in vitro, in cells, and in vivo. Within this series of compounds, methyl 2-(2-(4-octylphenoxy)acetyl)thiazole-4-carboxylate (GK470) was found to be the most potent inhibitor of GIVA cPLA2, exhibiting an XI(50) value of 0.011 mole fraction in a mixed micelle assay and an IC50 of 300 nM in a vesicle assay. In a cellular assay using SW982 fibroblast-like synoviocytes, it suppressed the release of arachidonic acid with an IC50 value of 0.6 μM. In a prophylactic collagen-induced arthritis model, it exhibited an anti-inflammatory effect comparable to the reference drug methotrexate, whereas in a therapeutic model, it showed results comparable to those of the reference drug Enbrel. In both models, it significantly reduced plasma PGE2 levels.
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Affiliation(s)
- George Kokotos
- Laboratory of Organic Chemistry, Department of Chemistry, University of Athens, Panepistimiopolis , Athens 15771, Greece
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17
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Shokhen M, Hirsch M, Khazanov N, Ozeri R, Perlman N, Traube T, Vijayakumar S, Albeck A. From Catalytic Mechanism to Rational Design of Reversible Covalent Inhibitors of Serine and Cysteine Hydrolases. Isr J Chem 2014. [DOI: 10.1002/ijch.201300144] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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18
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Traube T, Shokhen M, Albeck A. A new method for filtering of reactive "warheads" of transition-state analog protease inhibitors. Eur J Med Chem 2014; 77:134-8. [PMID: 24631732 DOI: 10.1016/j.ejmech.2014.02.059] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2014] [Accepted: 02/27/2014] [Indexed: 10/25/2022]
Abstract
In light of the major contribution of the reactive warhead to the binding energy trend in reversible covalent transition-state analog inhibitors of serine and cysteine hydrolases, would it be possible to rationally design and quickly filter such warheads, especially for large-scale screening? The previously defined W1 and W2 covalent descriptors quantitatively account for the energetic effect of the covalent bonds reorganization, accompanying enzyme-inhibitor covalent binding. The quantum mechanically calculated W1 and W2 reflect the warhead binding energy by modeling of the enzyme-inhibitor reaction core. Here, we demonstrate the use of these descriptors for warhead filtering, and examine its scope and limitations. The W1 and W2 descriptors provide a tool for rational design of various warheads as universal building blocks of real inhibitors without the requirement of 3D structural information about the target enzyme or QSAR studies. These warheads could then be used as hit structural templates in the subsequent optimization of inhibitors recognition sites.
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Affiliation(s)
- Tamar Traube
- The Julius Spokojny Bioorganic Chemistry Laboratory, Department of Chemistry, Bar Ilan University, Ramat Gan 52900, Israel
| | - Michael Shokhen
- The Julius Spokojny Bioorganic Chemistry Laboratory, Department of Chemistry, Bar Ilan University, Ramat Gan 52900, Israel.
| | - Amnon Albeck
- The Julius Spokojny Bioorganic Chemistry Laboratory, Department of Chemistry, Bar Ilan University, Ramat Gan 52900, Israel.
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19
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Meanwell NA. The Influence of Bioisosteres in Drug Design: Tactical Applications to Address Developability Problems. TACTICS IN CONTEMPORARY DRUG DESIGN 2014; 9. [PMCID: PMC7416817 DOI: 10.1007/7355_2013_29] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The application of bioisosteres in drug discovery is a well-established design concept that has demonstrated utility as an approach to solving a range of problems that affect candidate optimization, progression, and durability. In this chapter, the application of isosteric substitution is explored in a fashion that focuses on the development of practical solutions to problems that are encountered in typical optimization campaigns. The role of bioisosteres to affect intrinsic potency and selectivity, influence conformation, solve problems associated with drug developability, including P-glycoprotein recognition, modulating basicity, solubility, and lipophilicity, and to address issues associated with metabolism and toxicity is used as the underlying theme to capture a spectrum of creative applications of structural emulation in the design of drug candidates.
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20
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Traube T, Shokhen M, Albeck A. Application of EMBM to Structure-Based Design of Warheads for Protease Inhibitors. Mol Inform 2014; 33:36-42. [PMID: 27485197 DOI: 10.1002/minf.201300099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2013] [Accepted: 08/27/2013] [Indexed: 11/06/2022]
Abstract
Most CADD tools handle non-covalent enzyme inhibitors, despite the growing interest of the pharma industry in covalent inhibitors. We have recently introduced an enzyme mechanism-based method, EMBM, as a computational tool for binding trend analysis and prediction of chemical sites (CS) of reversible covalent enzyme inhibitors. In the current study we demonstrate the utility of EMBM to structure-based applications. In this mode, the energy of the enzyme-inhibitor covalent bond is accounted for by the W1 and W2 covalent descriptors we have developed, whereas the non-covalent interactions between the inhibitor CS and the enzyme active site can be estimated directly on the 3D structure of the enzyme-inhibitor complex.
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Affiliation(s)
- Tamar Traube
- The Julius Spokojny Bioorganic Chemistry Laboratory, Department of Chemistry, Bar Ilan University, Ramat Gan 52900, Israel tel.: 972-3-5318862, fax: 972-3-7384053
| | - Michael Shokhen
- The Julius Spokojny Bioorganic Chemistry Laboratory, Department of Chemistry, Bar Ilan University, Ramat Gan 52900, Israel tel.: 972-3-5318862, fax: 972-3-7384053.
| | - Amnon Albeck
- The Julius Spokojny Bioorganic Chemistry Laboratory, Department of Chemistry, Bar Ilan University, Ramat Gan 52900, Israel tel.: 972-3-5318862, fax: 972-3-7384053.
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21
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Bauer MR, Ibrahim TM, Vogel SM, Boeckler FM. Evaluation and Optimization of Virtual Screening Workflows with DEKOIS 2.0 – A Public Library of Challenging Docking Benchmark Sets. J Chem Inf Model 2013; 53:1447-62. [DOI: 10.1021/ci400115b] [Citation(s) in RCA: 94] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Matthias R. Bauer
- Laboratory
for Molecular Design and Pharmaceutical
Biophysics, Department of Pharmaceutical and
Medicinal Chemistry, Institute of Pharmacy, Eberhard Karls University Tuebingen, Auf der Morgenstelle
8, 72076 Tuebingen, Germany
| | - Tamer M. Ibrahim
- Laboratory
for Molecular Design and Pharmaceutical
Biophysics, Department of Pharmaceutical and
Medicinal Chemistry, Institute of Pharmacy, Eberhard Karls University Tuebingen, Auf der Morgenstelle
8, 72076 Tuebingen, Germany
| | - Simon M. Vogel
- Laboratory
for Molecular Design and Pharmaceutical
Biophysics, Department of Pharmaceutical and
Medicinal Chemistry, Institute of Pharmacy, Eberhard Karls University Tuebingen, Auf der Morgenstelle
8, 72076 Tuebingen, Germany
| | - Frank M. Boeckler
- Laboratory
for Molecular Design and Pharmaceutical
Biophysics, Department of Pharmaceutical and
Medicinal Chemistry, Institute of Pharmacy, Eberhard Karls University Tuebingen, Auf der Morgenstelle
8, 72076 Tuebingen, Germany
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22
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Fittler H, Avrutina O, Glotzbach B, Empting M, Kolmar H. Combinatorial tuning of peptidic drug candidates: high-affinity matriptase inhibitors through incremental structure-guided optimization. Org Biomol Chem 2013; 11:1848-57. [DOI: 10.1039/c3ob27469a] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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23
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Guha R. Exploring uncharted territories: predicting activity cliffs in structure-activity landscapes. J Chem Inf Model 2012; 52:2181-91. [PMID: 22873578 PMCID: PMC3448951 DOI: 10.1021/ci300047k] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The notion of activity cliffs is an intuitive approach to characterizing structural features that play a key role in modulating biological activity of a molecule. A variety of methods have been described to quantitatively characterize activity cliffs, such as SALI and SARI. However, these methods are primarily retrospective in nature; highlighting cliffs that are already present in the data set. The current study focuses on employing a pairwise characterization of a data set to train a model to predict whether a new molecule will exhibit an activity cliff with one or more members of the data set. The approach is based on predicting a value for pairs of objects rather than the individual objects themselves (and thus allows for robust models even for small structure-activity relationship data sets). We extracted structure-activity data for several ChEMBL assays and developed random forest models to predict SALI values, from pairwise combinations of molecular descriptors. The models exhibited reasonable RMSE's though, surprisingly, performance on the more significant cliffs tended to be better than on the lesser ones. While the models do not exhibit very high levels of accuracy, our results indicate that they are able to prioritize molecules in terms of their ability to activity cliffs, thus serving as a tool to prospectively identify activity cliffs.
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Affiliation(s)
- Rajarshi Guha
- NIH Center for Advancing Translational Sciences, 9800 Medical Center Drive, Rockville, Maryland 20850, USA
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24
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Colombo É, Désilets A, Duchêne D, Chagnon F, Najmanovich R, Leduc R, Marsault E. Design and synthesis of potent, selective inhibitors of matriptase. ACS Med Chem Lett 2012; 3:530-4. [PMID: 24900505 DOI: 10.1021/ml3000534] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2012] [Accepted: 04/11/2012] [Indexed: 02/02/2023] Open
Abstract
Matriptase is a member of the type II transmembrane serine protease family. Several studies have reported deregulated matriptase expression in several types of epithelial cancers, suggesting that matriptase constitutes a potential target for cancer therapy. We report herein a new series of slow, tight-binding inhibitors of matriptase, which mimic the P1-P4 substrate recognition sequence of the enzyme. Preliminary structure-activity relationships indicate that this benzothiazole-containing RQAR-peptidomimetic is a very potent inhibitor and possesses a good selectivity for matriptase versus other serine proteases. A molecular model was generated to elucidate the key contacts between inhibitor 1 and matriptase.
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Affiliation(s)
- Éloïc Colombo
- Department
of Pharmacology and ‡Department of Biochemistry, Faculty of Medicine and
Health Sciences, Université de Sherbrooke, 3001 12e Avenue Nord, Sherbrooke PQ, J1H5N4, Canada
| | - Antoine Désilets
- Department
of Pharmacology and ‡Department of Biochemistry, Faculty of Medicine and
Health Sciences, Université de Sherbrooke, 3001 12e Avenue Nord, Sherbrooke PQ, J1H5N4, Canada
| | - Dominic Duchêne
- Department
of Pharmacology and ‡Department of Biochemistry, Faculty of Medicine and
Health Sciences, Université de Sherbrooke, 3001 12e Avenue Nord, Sherbrooke PQ, J1H5N4, Canada
| | - Félix Chagnon
- Department
of Pharmacology and ‡Department of Biochemistry, Faculty of Medicine and
Health Sciences, Université de Sherbrooke, 3001 12e Avenue Nord, Sherbrooke PQ, J1H5N4, Canada
| | - Rafael Najmanovich
- Department
of Pharmacology and ‡Department of Biochemistry, Faculty of Medicine and
Health Sciences, Université de Sherbrooke, 3001 12e Avenue Nord, Sherbrooke PQ, J1H5N4, Canada
| | - Richard Leduc
- Department
of Pharmacology and ‡Department of Biochemistry, Faculty of Medicine and
Health Sciences, Université de Sherbrooke, 3001 12e Avenue Nord, Sherbrooke PQ, J1H5N4, Canada
| | - Eric Marsault
- Department
of Pharmacology and ‡Department of Biochemistry, Faculty of Medicine and
Health Sciences, Université de Sherbrooke, 3001 12e Avenue Nord, Sherbrooke PQ, J1H5N4, Canada
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25
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Frankowski KJ, Hedrick MP, Gosalia P, Li K, Shi S, Whipple D, Ghosh P, Prisinzano TE, Schoenen FJ, Su Y, Vasile S, Sergienko E, Gray W, Hariharan S, Milan L, Heynen-Genel S, Mangravita-Novo A, Vicchiarelli M, Smith LH, Streicher JM, Caron MG, Barak LS, Bohn LM, Chung TDY, Aubé J. Discovery of Small Molecule Kappa Opioid Receptor Agonist and Antagonist Chemotypes through a HTS and Hit Refinement Strategy. ACS Chem Neurosci 2012; 3:221-236. [PMID: 22737280 DOI: 10.1021/cn200128x] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Herein we present the outcome of a high throughput screening (HTS) campaign-based strategy for the rapid identification and optimization of selective and general chemotypes for both kappa (κ) opioid receptor (KOR) activation and inhibition. In this program, we have developed potent antagonists (IC(50) < 120 nM) or agonists of high binding affinity (K(i) < 3 nM). In contrast to many important KOR ligands, the compounds presented here are highly modular, readily synthesized and, in most cases, achiral. The four new chemotypes hold promise for further development into chemical tools for studying the KOR or as potential therapeutic lead candidates.
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Affiliation(s)
- Kevin J. Frankowski
- University of Kansas Specialized
Chemistry Center, University of Kansas,
Lawrence, Kansas 66047, United States
| | - Michael P. Hedrick
- Conrad Prebys Center for Chemical Genomics at Sanford-Burnham Medical Research Institute, La Jolla, California 92037, United States
| | - Palak Gosalia
- Conrad Prebys Center for Chemical Genomics at Sanford-Burnham Medical Research Institute, La Jolla, California 92037, United States
| | - Kelin Li
- University of Kansas Specialized
Chemistry Center, University of Kansas,
Lawrence, Kansas 66047, United States
| | - Shenghua Shi
- Conrad Prebys Center for Chemical Genomics at Sanford-Burnham Medical Research Institute, La Jolla, California 92037, United States
| | - David Whipple
- University of Kansas Specialized
Chemistry Center, University of Kansas,
Lawrence, Kansas 66047, United States
| | - Partha Ghosh
- University of Kansas Specialized
Chemistry Center, University of Kansas,
Lawrence, Kansas 66047, United States
| | - Thomas E. Prisinzano
- University of Kansas Specialized
Chemistry Center, University of Kansas,
Lawrence, Kansas 66047, United States
| | - Frank J. Schoenen
- University of Kansas Specialized
Chemistry Center, University of Kansas,
Lawrence, Kansas 66047, United States
| | - Ying Su
- Conrad Prebys Center for Chemical Genomics at Sanford-Burnham Medical Research Institute, La Jolla, California 92037, United States
| | - S. Vasile
- Conrad Prebys Center for Chemical Genomics at Sanford-Burnham Medical Research Institute, La Jolla, California 92037, United States
| | - Eduard Sergienko
- Conrad Prebys Center for Chemical Genomics at Sanford-Burnham Medical Research Institute, La Jolla, California 92037, United States
| | - Wilson Gray
- Conrad Prebys Center for Chemical Genomics at Sanford-Burnham Medical Research Institute, La Jolla, California 92037, United States
| | - Santosh Hariharan
- Conrad Prebys Center for Chemical Genomics at Sanford-Burnham Medical Research Institute, La Jolla, California 92037, United States
| | - Loribelle Milan
- Conrad Prebys Center for Chemical Genomics at Sanford-Burnham Medical Research Institute, La Jolla, California 92037, United States
| | - Susanne Heynen-Genel
- Conrad Prebys Center for Chemical Genomics at Sanford-Burnham Medical Research Institute, La Jolla, California 92037, United States
| | - Arianna Mangravita-Novo
- Conrad Prebys Center for Chemical Genomics at Sanford-Burnham Medical Research Institute at Lake Nona, Orlando, Florida 32827, United States
| | - Michael Vicchiarelli
- Conrad Prebys Center for Chemical Genomics at Sanford-Burnham Medical Research Institute at Lake Nona, Orlando, Florida 32827, United States
| | - Layton H. Smith
- Conrad Prebys Center for Chemical Genomics at Sanford-Burnham Medical Research Institute at Lake Nona, Orlando, Florida 32827, United States
| | - John M. Streicher
- Department of Molecular
Therapeutics, The Scripps Research Institute, Jupiter, Florida 33458,
United States
| | - Marc G. Caron
- Department of Cell Biology, Duke University, Durham, North Carolina 27710, United
States
| | - Lawrence S. Barak
- Department of Cell Biology, Duke University, Durham, North Carolina 27710, United
States
| | - Laura M. Bohn
- Department of Molecular
Therapeutics, The Scripps Research Institute, Jupiter, Florida 33458,
United States
| | - Thomas D. Y. Chung
- Conrad Prebys Center for Chemical Genomics at Sanford-Burnham Medical Research Institute, La Jolla, California 92037, United States
| | - Jeffrey Aubé
- University of Kansas Specialized
Chemistry Center, University of Kansas,
Lawrence, Kansas 66047, United States
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26
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DOGS: reaction-driven de novo design of bioactive compounds. PLoS Comput Biol 2012; 8:e1002380. [PMID: 22359493 PMCID: PMC3280956 DOI: 10.1371/journal.pcbi.1002380] [Citation(s) in RCA: 164] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2011] [Accepted: 12/21/2011] [Indexed: 11/19/2022] Open
Abstract
We present a computational method for the reaction-based de novo design of drug-like molecules. The software DOGS (Design of Genuine Structures) features a ligand-based strategy for automated ‘in silico’ assembly of potentially novel bioactive compounds. The quality of the designed compounds is assessed by a graph kernel method measuring their similarity to known bioactive reference ligands in terms of structural and pharmacophoric features. We implemented a deterministic compound construction procedure that explicitly considers compound synthesizability, based on a compilation of 25'144 readily available synthetic building blocks and 58 established reaction principles. This enables the software to suggest a synthesis route for each designed compound. Two prospective case studies are presented together with details on the algorithm and its implementation. De novo designed ligand candidates for the human histamine H4 receptor and γ-secretase were synthesized as suggested by the software. The computational approach proved to be suitable for scaffold-hopping from known ligands to novel chemotypes, and for generating bioactive molecules with drug-like properties. The computer program DOGS aims at the automated generation of new bioactive compounds. Only a single known reference compound is required to have the computer come up with suggestions for potentially isofunctional molecules. A specific feature of the algorithm is its capability to propose a synthesis plan for each designed compound, based on a large set of readily available molecular building blocks and established reaction protocols. The de novo design software provides rapid access to tool compounds and starting points for the development of a lead candidate structure. The manuscript gives a detailed description of the algorithm. Theoretical analysis and prospective case studies demonstrate its ability to propose bioactive, plausible and chemically accessible compounds.
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27
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van Berkel SS, van der Lee B, van Delft FL, Wagenvoord R, Hemker HC, Rutjes FPJT. Fluorogenic peptide-based substrates for monitoring thrombin activity. ChemMedChem 2012; 7:606-17. [PMID: 22294421 DOI: 10.1002/cmdc.201100560] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2011] [Revised: 01/02/2012] [Indexed: 11/11/2022]
Abstract
The synthesis of a series of peptides containing C-terminal 7-amino-4-methylcoumarin (AMC) for use in the thrombin generation test (TGT) is described. The lead structure in this project was H-Gly-Gly-Arg-AMC, of which the water solubility and kinetic parameters (K(M) and k(cat)) are greatly improved over those of the substrate in current use in the TGT: Cbz-Gly-Gly-Arg-AMC. A series of N-terminally substituted Gly-Gly-Arg-AMC derivatives were synthesized, as well as implementation of structural changes at either the P(2) or P(3) position of the peptide backbone. Furthermore, two substrates were synthesized that have structural similarities to the chromogenic thrombin substrate SQ68 or that contain a 1,2,3-triazole moiety in the peptide chain, mimicking an amide bond. To determine the applicability of newly synthesized fluorogenic substrates for monitoring continuous thrombin generation, the K(M) and k(cat) values of the conversion of these fluorogenic substrates by thrombin (FIIa) and factor Xa (FXa) were quantified. An initial selection was made on basis of these data, and suitable substrates were further evaluated as substrates in the thrombin generation assay. Assessment of the acquired data showed that several substrates, including the SQ68 derivative Et-malonate-Gly-Arg-AMC and N-functionalized Gly-Gly-Arg-AMC derivatives, are suitable candidates for replacement of the substrate currently in use.
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Affiliation(s)
- Sander S van Berkel
- Radboud University Nijmegen, Institute for Molecules and Materials, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
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28
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Pejchal V, Stepankova S, Padelkova Z, Imramovsky A, Jampilek J. 1,3-substituted imidazolidine-2,4,5-triones: synthesis and inhibition of cholinergic enzymes. Molecules 2011; 16:7565-82. [PMID: 21894089 PMCID: PMC6264296 DOI: 10.3390/molecules16097565] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2011] [Revised: 08/30/2011] [Accepted: 08/31/2011] [Indexed: 11/20/2022] Open
Abstract
A series of novel and highly active acetylcholinesterase and butyrylcholinesterase inhibitors derived from substituted benzothiazoles containing an imidazolidine-2,4,5-trione moiety were synthesized and characterized. The molecular structure of 1-(2,6-diisopropyl-phenyl)-3-[(1R)-1-(6-fluoro-1,3-benzothiazol-2-yl)ethyl]-imidazolidine-2,4,5-trione (3g) was determined by single-crystal X-ray diffraction. Both optical isomers are present as two independent molecules in the triclinic crystal system. The lipophilicity of the compounds was determined as the partition coefficient log K(ow) using the traditional shake-flask method. The in vitro inhibitory activity on acetylcholinesterase from electric eel and butyrylcholinesterase isolated from equine serum was determined. The inhibitory activity on acetylcholinesterase was significantly higher than that of the standard drug rivastigmine. The discussed compounds are also promising inhibitors of butyrylcholinesterase, as some of the prepared compounds inhibit butyrylcholinesterase better than the internal standards rivastigmine and galanthamine. The highest inhibitory activity (IC₅₀ = 1.66 μmol/L) corresponds to the compound 1-(4-isopropylphenyl)-3-[(R)-1-(6-fluorobenzo[d]thiazol-2-yl)ethyl]imidazolidine-2,4,5-trione (3d). For all the studied compounds, the relationships between the lipophilicity and the chemical structure as well as their structure-activity relationships are discussed.
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Affiliation(s)
- Vladimir Pejchal
- Institute of Organic Chemistry and Technology, Faculty of Chemical Technology, University of Pardubice, Studentska 573, 532 10 Pardubice, Czech Republic
| | - Sarka Stepankova
- Department of Biological and Biochemical Sciences, Faculty of Chemical Technology, University of Pardubice, Studentska 573, Pardubice 53210, Czech Republic
| | - Zdenka Padelkova
- Department of General and Inorganic Chemistry, Faculty of Chemical Technology, University of Pardubice, Studentska 573, 532 10 Pardubice, Czech Republic
| | - Ales Imramovsky
- Institute of Organic Chemistry and Technology, Faculty of Chemical Technology, University of Pardubice, Studentska 573, 532 10 Pardubice, Czech Republic
| | - Josef Jampilek
- Department of Chemical Drugs, Faculty of Pharmacy, University of Veterinary and Pharmaceutical Sciences, Palackeho 1/3, 612 42 Brno, Czech Republic
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29
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Storgaard M, Henriksen ST, Zaragoza F, Peschke B, Tanner D. Design, synthesis and biological activity of novel peptidyl benzyl ketone FVIIa inhibitors. Bioorg Med Chem Lett 2011; 21:3918-22. [DOI: 10.1016/j.bmcl.2011.05.025] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2011] [Revised: 05/09/2011] [Accepted: 05/09/2011] [Indexed: 11/25/2022]
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30
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Shokhen M, Traube T, Vijayakumar S, Hirsch M, Uritsky N, Albeck A. Differentiating serine and cysteine protease mechanisms by new covalent QSAR descriptors. Chembiochem 2011; 12:1023-6. [PMID: 21438106 PMCID: PMC3088911 DOI: 10.1002/cbic.201000459] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2010] [Indexed: 11/11/2022]
Affiliation(s)
- Michael Shokhen
- Dr. M. Shokhen, T. Traube, Dr. S. Vijayakumar, M. Hirsch, N. Uritsky, Dr. A. Albeck The Julius Spokojny Bioorganic Chemistry Laboratory Department of Chemistry, Bar Ilan University Ramat Gan 52900, Israel
| | - Tamar Traube
- Dr. M. Shokhen, T. Traube, Dr. S. Vijayakumar, M. Hirsch, N. Uritsky, Dr. A. Albeck The Julius Spokojny Bioorganic Chemistry Laboratory Department of Chemistry, Bar Ilan University Ramat Gan 52900, Israel
| | - Subramaniam Vijayakumar
- Dr. M. Shokhen, T. Traube, Dr. S. Vijayakumar, M. Hirsch, N. Uritsky, Dr. A. Albeck The Julius Spokojny Bioorganic Chemistry Laboratory Department of Chemistry, Bar Ilan University Ramat Gan 52900, Israel
| | - Michal Hirsch
- Dr. M. Shokhen, T. Traube, Dr. S. Vijayakumar, M. Hirsch, N. Uritsky, Dr. A. Albeck The Julius Spokojny Bioorganic Chemistry Laboratory Department of Chemistry, Bar Ilan University Ramat Gan 52900, Israel
| | - Neta Uritsky
- Dr. M. Shokhen, T. Traube, Dr. S. Vijayakumar, M. Hirsch, N. Uritsky, Dr. A. Albeck The Julius Spokojny Bioorganic Chemistry Laboratory Department of Chemistry, Bar Ilan University Ramat Gan 52900, Israel
| | - Amnon Albeck
- Dr. M. Shokhen, T. Traube, Dr. S. Vijayakumar, M. Hirsch, N. Uritsky, Dr. A. Albeck The Julius Spokojny Bioorganic Chemistry Laboratory Department of Chemistry, Bar Ilan University Ramat Gan 52900, Israel
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31
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Meanwell NA. Synopsis of Some Recent Tactical Application of Bioisosteres in Drug Design. J Med Chem 2011; 54:2529-91. [DOI: 10.1021/jm1013693] [Citation(s) in RCA: 1876] [Impact Index Per Article: 144.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Nicholas A. Meanwell
- Department of Medicinal Chemistry, Bristol-Myers Squibb Pharmaceutical Research and Development, 5 Research Parkway, Wallingford, Connecticut 06492, United States
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32
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Steert K, Berg M, Mottram JC, Westrop GD, Coombs GH, Cos P, Maes L, Joossens J, Van der Veken P, Haemers A, Augustyns K. α-ketoheterocycles as inhibitors of Leishmania mexicana cysteine protease CPB. ChemMedChem 2011; 5:1734-48. [PMID: 20799311 DOI: 10.1002/cmdc.201000265] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Cysteine proteases of the papain superfamily are present in nearly all eukaryotes and also play pivotal roles in the biology of parasites. Inhibition of cysteine proteases is emerging as an important strategy to combat parasitic diseases such as sleeping sickness, Chagas disease, and leishmaniasis. Inspired by the in vivo antiparasitic activity of the vinylsulfone-based cysteine protease inhibitors, a series of α-ketoheterocycles were developed as reversible inhibitors of a recombinant L. mexicana cysteine protease, CPB2.8. Three isoxazoles and especially one oxadiazole compound are potent reversible inhibitors of CPB2.8; however, in vitro whole-organism screening against a panel of protozoan parasites did not fully correlate with the observed inhibition of the cysteine protease.
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Affiliation(s)
- Koen Steert
- Department of Medicinal Chemistry, University of Antwerp, Universiteitsplein 1, 2610 Antwerp, Belgium
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El-Dahshan A, Nazir S, Ahsanullah, Ansari FL, Rademann J. Peptide-Heterocycle Chimera: New Classes of More Drug-Like Peptidomimetics by Ligations of Peptide-Bis(electrophiles) with Various Bis(nucleophiles). European J Org Chem 2010. [DOI: 10.1002/ejoc.201001206] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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34
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Traube T, Vijayakumar S, Hirsch M, Uritsky N, Shokhen M, Albeck A. EMBM - a new enzyme mechanism-based method for rational design of chemical sites of covalent inhibitors. J Chem Inf Model 2010; 50:2256-65. [PMID: 21090595 DOI: 10.1021/ci100330y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
We introduce an enzyme mechanism-based method (EMBM) aimed at rational design of chemical sites (CS) of reaction coordinate analog inhibitors. The energy of valence reorganization of CS, caused by the formation of the enzyme-inhibitor covalent complex, is accounted for by new covalent descriptors W1 and W2. We considered CS fragments with a carbonyl reactivity center, like in native protease substrates. The W1 and W2 descriptors are calculated quantum mechanically on small molecular clusters simulating the reaction core of the formed covalent tetrahedral complex, anionic TC(O-) or neutral TC(OH). The modeling on a reaction core allows generation of various CS and corresponding TC(O-) and TC(OH) as universal building blocks of real inhibitors and their covalent complexes with serine or cysteine hydrolases. Moreover, the approach avoids the need for 3D structure of the target enzyme, so EMBM may be used for ligand-based design. We have built a chemical site of inhibitors (CSI) databank with pairs of W1 and W2 descriptors precalculated for both CH₃O(-) and CH₃S(-) nucleophiles for every collected CS fragment. We demonstrated that contribution of a CS fragment to the binding affinity of an inhibitor depends on both its covalent reorganization during the chemical transformation and its noncovalent interactions in the enzyme active site. Consequently, prediction of inhibitors binding trend can be done only by accounting for all of these factors, using W1 and W2 in combination with noncovalent QSAR descriptors.
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Affiliation(s)
- Tamar Traube
- The Julius Spokojny Bioorganic Chemistry Laboratory, Department of Chemistry, Bar Ilan University, Ramat Gan 52900, Israel
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35
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El-Dahshan A, Ahsanullah, Rademann J. Efficient access to peptidyl ketones and peptidyl diketones via C-alkylations and C-acylations of polymer-supported phosphorus ylides followed by hydrolytic and/or oxidative cleavage. Biopolymers 2010; 94:220-8. [DOI: 10.1002/bip.21378] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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36
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Lu T, Markotan T, Ballentine SK, Giardino EC, Spurlino J, Brown K, Maryanoff BE, Tomczuk BE, Damiano BP, Shukla U, End D, Andrade-Gordon P, Bone RF, Player MR. Discovery and Clinical Evaluation of 1-{N-[2-(Amidinoaminooxy)ethyl]amino}carbonylmethyl-6-methyl-3-[2,2-difluoro-2-phenylethylamino]pyrazinone (RWJ-671818), a Thrombin Inhibitor with an Oxyguanidine P1 Motif. J Med Chem 2010; 53:1843-56. [DOI: 10.1021/jm901802n] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Tianbao Lu
- Johnson & Johnson Pharmaceutical Research and Development, Welsh and McKean Roads, Spring House, Pennsylvania 19477-0776
| | - Thomas Markotan
- Johnson & Johnson Pharmaceutical Research and Development, Welsh and McKean Roads, Spring House, Pennsylvania 19477-0776
| | - Shelley K. Ballentine
- Johnson & Johnson Pharmaceutical Research and Development, Welsh and McKean Roads, Spring House, Pennsylvania 19477-0776
| | - Edward C. Giardino
- Johnson & Johnson Pharmaceutical Research and Development, Welsh and McKean Roads, Spring House, Pennsylvania 19477-0776
| | - John Spurlino
- Johnson & Johnson Pharmaceutical Research and Development, Welsh and McKean Roads, Spring House, Pennsylvania 19477-0776
| | - Kathryn Brown
- Johnson & Johnson Pharmaceutical Research and Development, Welsh and McKean Roads, Spring House, Pennsylvania 19477-0776
| | - Bruce E. Maryanoff
- Johnson & Johnson Pharmaceutical Research and Development, Welsh and McKean Roads, Spring House, Pennsylvania 19477-0776
| | - Bruce E. Tomczuk
- Johnson & Johnson Pharmaceutical Research and Development, Welsh and McKean Roads, Spring House, Pennsylvania 19477-0776
| | - Bruce P. Damiano
- Johnson & Johnson Pharmaceutical Research and Development, Welsh and McKean Roads, Spring House, Pennsylvania 19477-0776
| | - Umesh Shukla
- Johnson & Johnson Pharmaceutical Research and Development, Welsh and McKean Roads, Spring House, Pennsylvania 19477-0776
| | - David End
- Johnson & Johnson Pharmaceutical Research and Development, Welsh and McKean Roads, Spring House, Pennsylvania 19477-0776
| | - Patricia Andrade-Gordon
- Johnson & Johnson Pharmaceutical Research and Development, Welsh and McKean Roads, Spring House, Pennsylvania 19477-0776
| | - Roger F. Bone
- Johnson & Johnson Pharmaceutical Research and Development, Welsh and McKean Roads, Spring House, Pennsylvania 19477-0776
| | - Mark R. Player
- Johnson & Johnson Pharmaceutical Research and Development, Welsh and McKean Roads, Spring House, Pennsylvania 19477-0776
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37
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Berg M, Van der Veken P, Joossens J, Muthusamy V, Breugelmans M, Moss CX, Rudolf J, Cos P, Coombs GH, Maes L, Haemers A, Mottram JC, Augustyns K. Design and evaluation of Trypanosoma brucei metacaspase inhibitors. Bioorg Med Chem Lett 2010; 20:2001-6. [PMID: 20167486 DOI: 10.1016/j.bmcl.2010.01.099] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2009] [Revised: 01/14/2010] [Accepted: 01/16/2010] [Indexed: 02/01/2023]
Abstract
Metacaspase (MCA) is an important enzyme in Trypanosoma brucei, absent from humans and differing significantly from the orthologous human caspases. Therefore MCA constitutes a new attractive drug target for antiparasitic chemotherapeutics, which needs further characterization to support the discovery of innovative drug candidates. A first series of inhibitors has been prepared on the basis of known substrate specificity and the predicted catalytic mechanism of the enzyme. In this Letter we present the first inhibitors of TbMCA2 with low micromolar enzymatic and antiparasitic activity in vitro combined with low cytotoxicity.
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Affiliation(s)
- Maya Berg
- Laboratory of Medicinal Chemistry, University of Antwerp, Antwerp, Belgium
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38
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Liebeskind L, Yang H, Li H. A Copper‐Catalyzed, pH‐Neutral Construction of High‐Enantiopurity Peptidyl Ketones from PeptidicS‐Acylthiosalicylamides in Air at Room Temperature. Angew Chem Int Ed Engl 2009. [DOI: 10.1002/ange.200804524] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Lanny S. Liebeskind
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, GA 30322 (USA), Fax: (+1) 404‐727‐6604
| | - Hao Yang
- Abbott Laboratories, GPRD, Process R&D, R450‐NCR13‐323A, 1401 Sheridan Road, North Chicago, IL 60064 (USA)
| | - Hao Li
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, GA 30322 (USA), Fax: (+1) 404‐727‐6604
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39
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Liebeskind LS, Yang H, Li H. A copper-catalyzed, pH-neutral construction of high-enantiopurity peptidyl ketones from peptidic s-acylthiosalicylamides in air at room temperature. Angew Chem Int Ed Engl 2009; 48:1417-21. [PMID: 19145620 PMCID: PMC2790066 DOI: 10.1002/anie.200804524] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
A copper-catalyzed transformation of peptidic thiol esters and boronic acids gives peptidyl ketones and takes place in DMF or DMF/H(2)O at room temperature in air (see scheme). This aerobic reaction only occurs at a thiol ester group capable of coordinating to Cu through its appendage on the sulfur center and is not hampered by racemization of the reactants or products.
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Affiliation(s)
- Lanny S Liebeskind
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, GA 30322, USA.
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40
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Tully DC, Vidal A, Chatterjee AK, Williams JA, Roberts MJ, Petrassi HM, Spraggon G, Bursulaya B, Pacoma R, Shipway A, Schumacher AM, Danahay H, Harris JL. Discovery of inhibitors of the channel-activating protease prostasin (CAP1/PRSS8) utilizing structure-based design. Bioorg Med Chem Lett 2008; 18:5895-9. [DOI: 10.1016/j.bmcl.2008.08.029] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2008] [Revised: 08/08/2008] [Accepted: 08/11/2008] [Indexed: 11/15/2022]
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41
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Li H, Yang H, Liebeskind LS. Synthesis of high enantiopurity N-protected alpha-amino ketones by thiol ester-organostannane cross-coupling using pH-neutral conditions. Org Lett 2008; 10:4375-8. [PMID: 18759432 DOI: 10.1021/ol8018456] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
An efficient synthesis of high enantiopurity N-protected alpha-amino ketones is described. Complementing other studies using boronic acids and thiol esters, this Cu(I) diphenylphosphinate (CuDPP)-mediated, palladium-catalyzed coupling of alpha-amino thiol esters with aryl, heteroaryl, allyl, and alkenyl organostannanes gives N-protected alpha-amino ketones in high yields with high enantiopurity (in almost all cases) under mild and pH-neutral reaction conditions. The viability of pi-deficient heteroarylstannanes is an advantage of this reaction compared to the related boronic acid system.
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Affiliation(s)
- Hao Li
- Department of Chemistry, Emory University, 1515 Dickey Drive, Atlanta, Georgia 30322, USA.
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42
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Debaene F, Da Silva JA, Pianowski Z, Duran FJ, Winssinger N. Expanding the scope of PNA-encoded libraries: divergent synthesis of libraries targeting cysteine, serine and metallo-proteases as well as tyrosine phosphatases. Tetrahedron 2007. [DOI: 10.1016/j.tet.2007.03.033] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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43
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Gavrilyuk JI, Evindar G, Chen JY, Batey RA. Peptide-Heterocycle Hybrid Molecules: Solid-Phase-Supported Synthesis of Substituted N-Terminal 5-Aminotetrazole Peptides via Electrocyclization of Peptidic Imidoylazides. ACTA ACUST UNITED AC 2007; 9:644-51. [PMID: 17580974 DOI: 10.1021/cc060119p] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A method for the synthesis of polypeptides modified with a tetrazole ring at the N-terminus is described. Reaction of the N-terminal amino group of solid-supported peptides with arylisothiocyanates generates thiourea intermediates, which upon treatment with Mukaiyama's reagent (2-chloro-1-methylpyridinium iodide) generate electrophilic carbodiimide functionality. Trapping by the azide anion and electrocyclization of the intermediate imidoylazide generates an aryl-substituted 5-aminotetrazole at the N-terminus of the peptide. To prevent competitive cyclization of a neighboring amide N-H into the carbodiimide, there should not be a free N-H at the [X-1] position relative to the activated carbodiimide. Protection of the N-H group at this position or incorporation of a secondary amino acid is thus required for optimal tetrazole formation. Cleavage from the resin releases the hybrid molecules incorporating a 5-aminotetrazole ring conjugated onto a peptidic fragment.
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Affiliation(s)
- Julia I Gavrilyuk
- Davenport Chemical Laboratories, Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, ON, Canada M5S 3H6
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44
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Wu EL, Mei Y, Han K, Zhang JZH. Quantum and molecular dynamics study for binding of macrocyclic inhibitors to human alpha-thrombin. Biophys J 2007; 92:4244-53. [PMID: 17384076 PMCID: PMC1877793 DOI: 10.1529/biophysj.106.099150] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2006] [Accepted: 02/12/2007] [Indexed: 11/18/2022] Open
Abstract
Molecular dynamics simulations followed by quantum mechanical calculation and Molecular Mechanics Poisson-Boltzmann Surface Area (MM-PBSA) analysis have been carried out to study binding of proline- and pyrazinone-based macrocyclic inhibitors (L86 and T76) to human alpha-thrombin. Detailed binding interaction energies between these inhibitors and individual protein fragments are calculated using DFT method based on a new quantum mechanical approach for computing protein-ligand interaction energy. The analysis of detailed interaction energies provides insight on the protein-ligand binding mechanism. Study shows that T76 and L86 bind to thrombin in a very similar "inhibition mode" except that T76 has relatively weaker binding interaction with Glu(217). The analysis from quantum calculation of binding interaction is consistent with the MM-PBSA calculation of binding free energy, and the calculated free energies for L86/T76-thrombin binding agree well with the experimental data.
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Affiliation(s)
- Emilia L Wu
- Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
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45
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Romero FA, Du W, Hwang I, Rayl TJ, Kimball FS, Leung D, Hoover HS, Apodaca RL, Breitenbucher JG, Cravatt BF, Boger DL. Potent and selective alpha-ketoheterocycle-based inhibitors of the anandamide and oleamide catabolizing enzyme, fatty acid amide hydrolase. J Med Chem 2007; 50:1058-68. [PMID: 17279740 PMCID: PMC2531193 DOI: 10.1021/jm0611509] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A study of the structure-activity relationships (SAR) of 2f (OL-135), a potent inhibitor of fatty acid amide hydrolase (FAAH), is detailed, targeting the 5-position of the oxazole. Examination of a series of substituted benzene derivatives (12-14) revealed that the optimal position for substitution was the meta-position with selected members approaching or exceeding the potency of 2f. Concurrent with these studies, the effect of substitution on the pyridine ring of 2f was also examined. A series of small, nonaromatic C5-substituents was also explored and revealed that the K(i) follows a well-defined correlation with the Hammett sigma(p) constant (rho = 3.01, R2 = 0.91) in which electron-withdrawing substituents enhance potency, leading to inhibitors with K(i)s as low as 400 pM (20n). Proteomic-wide screening of the inhibitors revealed that most are exquisitely selective for FAAH over all other mammalian proteases, reversing the 100-fold preference of 20a (C5 substituent = H) for the enzyme TGH.
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Affiliation(s)
- F. Anthony Romero
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037
| | - Wu Du
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037
| | - Inkyu Hwang
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037
| | - Thomas J. Rayl
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037
| | - F. Scott Kimball
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037
| | - Donmienne Leung
- Department of Cell Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037
| | - Heather S. Hoover
- Department of Cell Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037
| | - Richard L. Apodaca
- Johnson & Johnson Pharmaceutical Research and Development, L.L.C., 3210 Merryfield Row, San Diego, CA 92121
| | - J. Guy Breitenbucher
- Johnson & Johnson Pharmaceutical Research and Development, L.L.C., 3210 Merryfield Row, San Diego, CA 92121
| | - Benjamin F. Cravatt
- Department of Cell Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037
| | - Dale L. Boger
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037
- The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037
- *CORRESPONDING AUTHOR: Dale L. Boger, Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Rd., La Jolla, CA 92037. Phone: 858-784-7522. Fax: 858-784-7550. E-mail:
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46
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Ator MA, Mallamo JP, Williams M. Overview of Drug Discovery and Development. ACTA ACUST UNITED AC 2006; Chapter 9:Unit9.9. [PMID: 22294181 DOI: 10.1002/0471141755.ph0909s35] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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47
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Maryanoff BE, McComsey DF, Costanzo MJ, Yabut SC, Lu T, Player MR, Giardino EC, Damiano BP. Exploration of potential prodrugs of RWJ-445167, an oxyguanidine-based dual inhibitor of thrombin and factor Xa. Chem Biol Drug Des 2006; 68:29-36. [PMID: 16923023 DOI: 10.1111/j.1747-0285.2006.00408.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Compound 2 (RWJ-445167; 3DP-10017), a dual inhibitor of thrombin and factor Xa, was advanced into human clinical studies. However, its oral bioavailability in humans proved to be below acceptable limits. To address this issue, we explored a prodrug approach involving numerous guanidine derivatives. Prodrug candidates of classes A (carbamate derivatives), B (imidate derivatives), and C (alkyl and acyl derivatives), compounds 3-6, were synthesized and evaluated for anticoagulant activity at 2 h after oral administration to rats. In comparison to the parent drug (2), little worthwhile improvement was observed for the prodrug candidates.
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Affiliation(s)
- Bruce E Maryanoff
- Vascular Research Team, Johnson & Johnson Pharmaceutical Research & Development, Spring House, PA 19477-0776, USA.
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48
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Romero FA, Hwang I, Boger DL. Delineation of a fundamental alpha-ketoheterocycle substituent effect for use in the design of enzyme inhibitors. J Am Chem Soc 2006; 128:14004-5. [PMID: 17061864 PMCID: PMC2501112 DOI: 10.1021/ja064522b] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The synthesis and examination of a systematic series of 5-substituted 2-keto oxazoles as inhibitors of fatty acid amide hydrolase (FAAH) defined a fundamental substituent effect that led to the discovery of inhibitors with Ki's as low as 400 pM. The intrinsic basis of the relationship (-log Ki vs sigmap), which relates Ki with the Hammett sigmap constant of the substituent, the magnitude of the effect (rho = 3.01), and its predictive value (R2 = 0.91) suggest a widespread applicability in studies beyond FAAH.
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Affiliation(s)
- F. Anthony Romero
- Department of Chemistry and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037
| | - Inkyu Hwang
- Department of Chemistry and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037
| | - Dale L. Boger
- Department of Chemistry and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037
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49
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Abstract
Common methodologies of computer-assisted drug design focus on noncovalent enzyme-ligand interactions. We introduced enzyme isoselective inhibition trend analysis as a tool for the expert analysis of covalent reversible inhibitors. The methodology is applied to predict the binding affinities of a series of transition-state analogue inhibitors of medicinally important serine and cysteine hydrolases. These inhibitors are isoselective: they have identical noncovalent recognition fragments (RS) and different reactive chemical fragments (CS). Furthermore, it is possible to predict the binding affinities of a series of isoselective inhibitors toward a prototype enzyme and to extrapolate the data to a target medicinally important enzyme of the same family. Rational design of CS fragments followed by conventional RS optimization could be used as a novel approach to drug design.
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Affiliation(s)
- Michael Shokhen
- The Julius Spokojny Bioorganic Chemistry Laboratory, Department of Chemistry, Bar Ilan University, Ramat Gan 52900, Israel.
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Gavrilyuk JI, Evindar G, Batey RA. Peptide−Heterocycle Hybrid Molecules: Solid-Phase Synthesis of a 400-Member Library of N-Terminal 2-Iminohydantoin Peptides. ACTA ACUST UNITED AC 2006; 8:237-46. [PMID: 16529519 DOI: 10.1021/cc050090+] [Citation(s) in RCA: 14] [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
A method for the heterocyclic modification of the N-terminus of a peptide is described. Reaction of the N-terminal amino group of solid-supported peptides with arylisothiocyanates generates a thiourea intermediate, as in the first step of Edman degradation. Treatment of the resin-supported peptide-thioureas with Mukaiyama's reagent (2-chloro-1-methylpyridinium iodide) generates an electrophilic carbodiimide functionality, which undergoes rapid intramolecular trapping by the adjacent amide group to give a 2-iminohydantoin ring at the N-terminus of the peptide. The dehydrothiolation step in the presence of Mukaiyama's reagent prevents Edman degradation from occurring, in essence leading to a "diversion" of the Edman degradation. Cleavage from the resin then releases the hybrid molecules incorporating a 2-iminohydantoin ring conjugated onto a peptidic fragment. A 400-member library of the iminohydantoin-peptide hybrids was synthesized using this approach, starting from a chlorotrityl resin-supported tripeptides.
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Affiliation(s)
- Julia I Gavrilyuk
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario, Canada M5S 3H6
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