1
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Repositioning of Quinazolinedione-Based Compounds on Soluble Epoxide Hydrolase (sEH) through 3D Structure-Based Pharmacophore Model-Driven Investigation. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27123866. [PMID: 35744994 PMCID: PMC9228872 DOI: 10.3390/molecules27123866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 06/08/2022] [Accepted: 06/14/2022] [Indexed: 12/01/2022]
Abstract
The development of new bioactive compounds represents one of the main purposes of the drug discovery process. Various tools can be employed to identify new drug candidates against pharmacologically relevant biological targets, and the search for new approaches and methodologies often represents a critical issue. In this context, in silico drug repositioning procedures are required even more in order to re-evaluate compounds that already showed poor biological results against a specific biological target. 3D structure-based pharmacophoric models, usually built for specific targets to accelerate the identification of new promising compounds, can be employed for drug repositioning campaigns as well. In this work, an in-house library of 190 synthesized compounds was re-evaluated using a 3D structure-based pharmacophoric model developed on soluble epoxide hydrolase (sEH). Among the analyzed compounds, a small set of quinazolinedione-based molecules, originally selected from a virtual combinatorial library and showing poor results when preliminarily investigated against heat shock protein 90 (Hsp90), was successfully repositioned against sEH, accounting the related built 3D structure-based pharmacophoric model. The promising results here obtained highlight the reliability of this computational workflow for accelerating the drug discovery/repositioning processes.
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2
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Chang CC, Pan SF, Wu MH, Cheng CT, Su YR, Jiang SJ, Hsu HJ. Combinatorial Virtual Screening Revealed a Novel Scaffold for TNKS Inhibition to Combat Colorectal Cancer. Biomedicines 2022; 10:143. [PMID: 35052822 PMCID: PMC8773749 DOI: 10.3390/biomedicines10010143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 12/30/2021] [Accepted: 01/06/2022] [Indexed: 02/04/2023] Open
Abstract
The abnormal Wnt signaling pathway leads to a high expression of β-catenin, which causes several types of cancer, particularly colorectal cancer (CRC). The inhibition of tankyrase (TNKS) activity can reduce cancer cell growth, invasion, and resistance to treatment by blocking the Wnt signaling pathway. A pharmacophore search and pharmacophore docking were performed to identify potential TNKS inhibitors in the training databases. The weighted MM/PBSA binding free energy of the docking model was calculated to rank the databases. The reranked results indicated that 26.98% of TNKS inhibitors that were present in the top 5% of compounds in the database and near an ideal value ranked 28.57%. The National Cancer Institute database was selected for formal virtual screening, and 11 potential TNKS inhibitors were identified. An enzyme-based experiment was performed to demonstrate that of the 11 potential TNKS inhibitors, NSC295092 and NSC319963 had the most potential. Finally, Wnt pathway analysis was performed through a cell-based assay, which indicated that NSC319963 is the most likely TNKS inhibitor (pIC50 = 5.59). The antiproliferation assay demonstrated that NSC319963 can decrease colorectal cancer cell growth; therefore, the proposed method successfully identified a novel TNKS inhibitor that can alleviate CRC.
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Affiliation(s)
- Chun-Chun Chang
- Department of Laboratory Medicine, Hualien Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, Hualien 97004, Taiwan;
- Department of Laboratory Medicine and Biotechnology, College of Medicine, Tzu Chi University, Hualien 97004, Taiwan; (M.-H.W.); (Y.-R.S.)
| | - Sheng-Feng Pan
- Department of Biochemistry, School of Medicine, Tzu Chi University, Hualien 97004, Taiwan;
| | - Min-Huang Wu
- Department of Laboratory Medicine and Biotechnology, College of Medicine, Tzu Chi University, Hualien 97004, Taiwan; (M.-H.W.); (Y.-R.S.)
| | - Chun-Tse Cheng
- Department of Life Sciences, College of Medicine, Tzu Chi University, Hualien 97004, Taiwan;
| | - Yan-Rui Su
- Department of Laboratory Medicine and Biotechnology, College of Medicine, Tzu Chi University, Hualien 97004, Taiwan; (M.-H.W.); (Y.-R.S.)
| | - Shinn-Jong Jiang
- Department of Biochemistry, School of Medicine, Tzu Chi University, Hualien 97004, Taiwan;
| | - Hao-Jen Hsu
- Department of Biochemistry, School of Medicine, Tzu Chi University, Hualien 97004, Taiwan;
- Department of Life Sciences, College of Medicine, Tzu Chi University, Hualien 97004, Taiwan;
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3
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Bzówka M, Mitusińska K, Hopko K, Góra A. Computational insights into the known inhibitors of human soluble epoxide hydrolase. Drug Discov Today 2021; 26:1914-1921. [PMID: 34082135 DOI: 10.1016/j.drudis.2021.05.017] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Revised: 04/20/2021] [Accepted: 05/25/2021] [Indexed: 01/22/2023]
Abstract
Human soluble epoxide hydrolase (hsEH) is involved in the hydrolysis of epoxyeicosatrienoic acids (EETs), which have potent anti-inflammatory properties. Given that EET conversion generates nonbioactive molecules, inhibition of this enzyme would be beneficial. Past decades of work on hsEH inhibitors resulted in numerous potential compounds, of which a hundred hsEH-ligand complexes were crystallized and deposited in the Protein Data Bank (PDB). We analyzed all deposited hsEH-ligand complexes to gain insight into the binding of inhibitors and to provide feedback on the future drug design processes. We also reviewed computationally driven strategies that were used to propose novel hsEH inhibitors.
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Affiliation(s)
- Maria Bzówka
- Tunneling Group, Biotechnology Centre, ul. Krzywoustego 8, Silesian University of Technology, Gliwice 44-100, Poland; Department of Organic Chemistry, Bioorganic Chemistry and Biotechnology, ul. Krzywoustego 4, Faculty of Chemistry, Silesian University of Technology, Gliwice 44-100, Poland
| | - Karolina Mitusińska
- Tunneling Group, Biotechnology Centre, ul. Krzywoustego 8, Silesian University of Technology, Gliwice 44-100, Poland
| | - Katarzyna Hopko
- Biotechnology Centre, ul. Krzywoustego 8, Silesian University of Technology, Gliwice 44-100, Poland
| | - Artur Góra
- Tunneling Group, Biotechnology Centre, ul. Krzywoustego 8, Silesian University of Technology, Gliwice 44-100, Poland.
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4
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Sirish P, Thai PN, Lee JH, Yang J, Zhang X, Ren L, Li N, Timofeyev V, Lee KSS, Nader CE, Rowland DJ, Yechikov S, Ganaga S, Young N, Lieu DK, Yamoah EN, Hammock BD, Chiamvimonvat N. Suppression of inflammation and fibrosis using soluble epoxide hydrolase inhibitors enhances cardiac stem cell-based therapy. Stem Cells Transl Med 2020; 9:1570-1584. [PMID: 32790136 PMCID: PMC7695637 DOI: 10.1002/sctm.20-0143] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2020] [Revised: 05/03/2020] [Accepted: 05/30/2020] [Indexed: 01/29/2023] Open
Abstract
Stem cell replacement offers a great potential for cardiac regenerative therapy. However, one of the critical barriers to stem cell therapy is a significant loss of transplanted stem cells from ischemia and inflammation in the host environment. Here, we tested the hypothesis that inhibition of the soluble epoxide hydrolase (sEH) enzyme using sEH inhibitors (sEHIs) to decrease inflammation and fibrosis in the host myocardium may increase the survival of the transplanted human induced pluripotent stem cell derived-cardiomyocytes (hiPSC-CMs) in a murine postmyocardial infarction model. A specific sEHI (1-trifluoromethoxyphenyl-3-(1-propionylpiperidine-4-yl)urea [TPPU]) and CRISPR/Cas9 gene editing were used to test the hypothesis. TPPU results in a significant increase in the retention of transplanted cells compared with cell treatment alone. The increase in the retention of hiPSC-CMs translates into an improvement in the fractional shortening and a decrease in adverse remodeling. Mechanistically, we demonstrate a significant decrease in oxidative stress and apoptosis not only in transplanted hiPSC-CMs but also in the host environment. CRISPR/Cas9-mediated gene silencing of the sEH enzyme reduces cleaved caspase-3 in hiPSC-CMs challenged with angiotensin II, suggesting that knockdown of the sEH enzyme protects the hiPSC-CMs from undergoing apoptosis. Our findings demonstrate that suppression of inflammation and fibrosis using an sEHI represents a promising adjuvant to cardiac stem cell-based therapy. Very little is known regarding the role of this class of compounds in stem cell-based therapy. There is consequently an enormous opportunity to uncover a potentially powerful class of compounds, which may be used effectively in the clinical setting.
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Affiliation(s)
- Padmini Sirish
- Division of Cardiovascular MedicineUniversity of CaliforniaDavisCaliforniaUSA,Department of Veterans AffairsNorthern California Health Care SystemMatherCaliforniaUSA
| | - Phung N. Thai
- Division of Cardiovascular MedicineUniversity of CaliforniaDavisCaliforniaUSA
| | - Jeong Han Lee
- Department of Physiology and Cell BiologyUniversity of Nevada, RenoRenoNevadaUSA
| | - Jun Yang
- Department of Entomology and Nematology and Comprehensive Cancer CenterUniversity of CaliforniaDavisCaliforniaUSA
| | - Xiao‐Dong Zhang
- Division of Cardiovascular MedicineUniversity of CaliforniaDavisCaliforniaUSA,Department of Veterans AffairsNorthern California Health Care SystemMatherCaliforniaUSA
| | - Lu Ren
- Division of Cardiovascular MedicineUniversity of CaliforniaDavisCaliforniaUSA
| | - Ning Li
- Division of Cardiovascular MedicineUniversity of CaliforniaDavisCaliforniaUSA
| | - Valeriy Timofeyev
- Division of Cardiovascular MedicineUniversity of CaliforniaDavisCaliforniaUSA
| | - Kin Sing Stephen Lee
- Department of Entomology and Nematology and Comprehensive Cancer CenterUniversity of CaliforniaDavisCaliforniaUSA
| | - Carol E. Nader
- Division of Cardiovascular MedicineUniversity of CaliforniaDavisCaliforniaUSA
| | - Douglas J. Rowland
- Center for Molecular and Genomic ImagingUniversity of CaliforniaDavisCaliforniaUSA
| | - Sergey Yechikov
- Division of Cardiovascular MedicineUniversity of CaliforniaDavisCaliforniaUSA
| | - Svetlana Ganaga
- Department of SurgeryUniversity of CaliforniaDavisCaliforniaUSA
| | - Nilas Young
- Department of SurgeryUniversity of CaliforniaDavisCaliforniaUSA
| | - Deborah K. Lieu
- Division of Cardiovascular MedicineUniversity of CaliforniaDavisCaliforniaUSA
| | - Ebenezer N. Yamoah
- Department of Physiology and Cell BiologyUniversity of Nevada, RenoRenoNevadaUSA
| | - Bruce D. Hammock
- Department of Entomology and Nematology and Comprehensive Cancer CenterUniversity of CaliforniaDavisCaliforniaUSA
| | - Nipavan Chiamvimonvat
- Division of Cardiovascular MedicineUniversity of CaliforniaDavisCaliforniaUSA,Department of Veterans AffairsNorthern California Health Care SystemMatherCaliforniaUSA,Department of PharmacologyUniversity of CaliforniaDavisCaliforniaUSA
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5
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Hiesinger K, Schott A, Kramer JS, Blöcher R, Witt F, Wittmann SK, Steinhilber D, Pogoryelov D, Gerstmeier J, Werz O, Proschak E. Design of Dual Inhibitors of Soluble Epoxide Hydrolase and LTA 4 Hydrolase. ACS Med Chem Lett 2020; 11:298-302. [PMID: 32184960 DOI: 10.1021/acsmedchemlett.9b00330] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Accepted: 10/30/2019] [Indexed: 11/30/2022] Open
Abstract
Multitarget anti-inflammatory drugs interfering with the arachidonic acid cascade exhibit superior efficacy. In this study, a prototype dual inhibitor of soluble epoxide hydrolase (sEH) and LTA4 hydrolase (LTA4H) with submicromolar activity toward both targets has been designed and synthesized. Preliminary structure-activity relationship studies were performed to identify optimal substitution patterns. X-ray structure analysis of a promising dual inhibitor in complex with sEH, as well as molecular docking with LTA4H provided a rationale for further optimization. Hereby, scaffold extension was successfully applied to yield potent dual sEH/LTA4H inhibitors. The spectrum of pro- and anti-inflammatory lipid mediators was evaluated in M1 and M2 macrophages, stimulated with LPS, and incubated with the most promising compound 14. The effect of 14 on the inflammatory lipid mediator profile characterizes dual sEH/LTA4H inhibitors as an interesting option for future anti-inflammatory agent investigations.
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Affiliation(s)
- Kerstin Hiesinger
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Strasse 9, 60438 Frankfurt, Germany
| | - Annika Schott
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Strasse 9, 60438 Frankfurt, Germany
| | - Jan S. Kramer
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Strasse 9, 60438 Frankfurt, Germany
| | - René Blöcher
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Strasse 9, 60438 Frankfurt, Germany
| | - Finja Witt
- Department of Pharmaceutical/Medicinal Chemistry, Institute of Pharmacy, Friedrich-Schiller-University Jena, Philosophenweg 14, 07743 Jena, Germany
| | - Sandra K. Wittmann
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Strasse 9, 60438 Frankfurt, Germany
| | - Dieter Steinhilber
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Strasse 9, 60438 Frankfurt, Germany
| | - Denys Pogoryelov
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Strasse 9, 60438 Frankfurt, Germany
| | - Jana Gerstmeier
- Department of Pharmaceutical/Medicinal Chemistry, Institute of Pharmacy, Friedrich-Schiller-University Jena, Philosophenweg 14, 07743 Jena, Germany
| | - Oliver Werz
- Department of Pharmaceutical/Medicinal Chemistry, Institute of Pharmacy, Friedrich-Schiller-University Jena, Philosophenweg 14, 07743 Jena, Germany
| | - Ewgenij Proschak
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Strasse 9, 60438 Frankfurt, Germany
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6
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Bhagwati S, Siddiqi MI. Identification of potential soluble epoxide hydrolase (sEH) inhibitors by ligand-based pharmacophore model and biological evaluation. J Biomol Struct Dyn 2019; 38:4956-4966. [DOI: 10.1080/07391102.2019.1691659] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- Sudha Bhagwati
- Molecular and Structural Biology Division, CSIR-Central Drug Research Institute (CSIR-CDRI), Lucknow, India
| | - Mohammad Imran Siddiqi
- Molecular and Structural Biology Division, CSIR-Central Drug Research Institute (CSIR-CDRI), Lucknow, India
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7
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da Silva Rocha SF, Olanda CG, Fokoue HH, Sant'Anna CM. Virtual Screening Techniques in Drug Discovery: Review and Recent Applications. Curr Top Med Chem 2019; 19:1751-1767. [DOI: 10.2174/1568026619666190816101948] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 06/21/2019] [Accepted: 07/29/2019] [Indexed: 11/22/2022]
Abstract
The discovery of bioactive molecules is an expensive and time-consuming process and new
strategies are continuously searched for in order to optimize this process. Virtual Screening (VS) is one
of the recent strategies that has been explored for the identification of candidate bioactive molecules.
The number of new techniques and software that can be applied in this strategy has grown considerably
in recent years, so, before their use, it is necessary to understand the basics an also the limitations behind
each one to get the most out of them. It is also necessary to assess the real contributions of this strategy
so that more significant progress can be made in the future. In this context, this review aims to discuss
some important points related to VS, including the use of virtual ligand and biotarget libraries, structurebased
and ligand-based VS techniques, as well as to present recent cases where this strategy was successfully
applied.
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Affiliation(s)
- Sheisi F.L. da Silva Rocha
- Programa de Pos-Graduacao em Quimica, Instituto de Quimica, Universidade Federal Rural do Rio de Janeiro, Seropedica, Brazil
| | - Carolina G. Olanda
- Programa de Pos-Graduacao em Quimica, Instituto de Quimica, Universidade Federal Rural do Rio de Janeiro, Seropedica, Brazil
| | - Harold H. Fokoue
- Laboratorio de Avaliacao e Síntese de Substancias Bioativas (LASSBio), Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Carlos M.R. Sant'Anna
- Programa de Pos-Graduacao em Quimica, Instituto de Quimica, Universidade Federal Rural do Rio de Janeiro, Seropedica, Brazil
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8
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Schierle S, Flauaus C, Heitel P, Willems S, Schmidt J, Kaiser A, Weizel L, Goebel T, Kahnt AS, Geisslinger G, Steinhilber D, Wurglics M, Rovati GE, Schmidtko A, Proschak E, Merk D. Boosting Anti-Inflammatory Potency of Zafirlukast by Designed Polypharmacology. J Med Chem 2018; 61:5758-5764. [DOI: 10.1021/acs.jmedchem.8b00458] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Simone Schierle
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Straße 9, D-60438 Frankfurt, Germany
| | - Cathrin Flauaus
- Institute of Pharmacology, College of Pharmacy, Goethe University Frankfurt, Max-von-Laue-Straße 9, D-60438 Frankfurt, Germany
| | - Pascal Heitel
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Straße 9, D-60438 Frankfurt, Germany
| | - Sabine Willems
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Straße 9, D-60438 Frankfurt, Germany
| | - Jurema Schmidt
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Straße 9, D-60438 Frankfurt, Germany
| | - Astrid Kaiser
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Straße 9, D-60438 Frankfurt, Germany
| | - Lilia Weizel
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Straße 9, D-60438 Frankfurt, Germany
| | - Tamara Goebel
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Straße 9, D-60438 Frankfurt, Germany
| | - Astrid S. Kahnt
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Straße 9, D-60438 Frankfurt, Germany
| | - Gerd Geisslinger
- Institute of Clinical Pharmacology, Goethe University Frankfurt, Theodor-Stern-Kai 7, D-60590 Frankfurt, Germany
| | - Dieter Steinhilber
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Straße 9, D-60438 Frankfurt, Germany
| | - Mario Wurglics
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Straße 9, D-60438 Frankfurt, Germany
| | - G. Enrico Rovati
- Institute of Pharmacological Sciences, University of Milan, Via Balzaretti 9, I-20133 Milan, Italy
| | - Achim Schmidtko
- Institute of Pharmacology, College of Pharmacy, Goethe University Frankfurt, Max-von-Laue-Straße 9, D-60438 Frankfurt, Germany
| | - Ewgenij Proschak
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Straße 9, D-60438 Frankfurt, Germany
| | - Daniel Merk
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Straße 9, D-60438 Frankfurt, Germany
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9
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Lee KSS, Henriksen NM, Ng CJ, Yang J, Jia W, Morisseau C, Andaya A, Gilson MK, Hammock BD. Probing the orientation of inhibitor and epoxy-eicosatrienoic acid binding in the active site of soluble epoxide hydrolase. Arch Biochem Biophys 2016; 613:1-11. [PMID: 27983948 DOI: 10.1016/j.abb.2016.10.017] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2016] [Revised: 10/26/2016] [Accepted: 10/27/2016] [Indexed: 11/30/2022]
Abstract
Soluble epoxide hydrolase (sEH) is an important therapeutic target of many diseases, such as chronic obstructive pulmonary disease (COPD) and diabetic neuropathic pain. It acts by hydrolyzing and thus regulating specific bioactive long chain polyunsaturated fatty acid epoxides (lcPUFA), like epoxyeicosatrienoic acids (EETs). To better predict which epoxides could be hydrolyzed by sEH, one needs to dissect the important factors and structural requirements that govern the binding of the substrates to sEH. This knowledge allows further exploration of the physiological role played by sEH. Unfortunately, a crystal structure of sEH with a substrate bound has not yet been reported. In this report, new photoaffinity mimics of a sEH inhibitor and EET regioisomers were prepared and used in combination with peptide sequencing and computational modeling, to identify the binding orientation of different regioisomers and enantiomers of EETs into the catalytic cavity of sEH. Results indicate that the stereochemistry of the epoxide plays a crucial role in dictating the binding orientation of the substrate.
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Affiliation(s)
- Kin Sing Stephen Lee
- Department of Entomology and Nematology, UCD Comprehensive Cancer Center, University of California at Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Niel M Henriksen
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego, 9500 Gilman Drive, MC 0736, La Jolla, CA 92093, USA
| | - Connie J Ng
- Department of Entomology and Nematology, UCD Comprehensive Cancer Center, University of California at Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Jun Yang
- Department of Entomology and Nematology, UCD Comprehensive Cancer Center, University of California at Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Weitao Jia
- Campus Mass Spectrometry Facilities, University of California at Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Christophe Morisseau
- Department of Entomology and Nematology, UCD Comprehensive Cancer Center, University of California at Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Armann Andaya
- Campus Mass Spectrometry Facilities, University of California at Davis, One Shields Avenue, Davis, CA 95616, USA
| | - Michael K Gilson
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California at San Diego, 9500 Gilman Drive, MC 0736, La Jolla, CA 92093, USA
| | - Bruce D Hammock
- Department of Entomology and Nematology, UCD Comprehensive Cancer Center, University of California at Davis, One Shields Avenue, Davis, CA 95616, USA.
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10
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Thao NP, Luyen BTT, Kim JH, Jo AR, Dat NT, Kiem PV, Minh CV, Kim YH. Identification, characterization, kinetics, and molecular docking of flavonoid constituents from Archidendron clypearia (Jack.) Nielsen leaves and twigs. Bioorg Med Chem 2016; 24:3125-32. [PMID: 27246857 DOI: 10.1016/j.bmc.2016.05.034] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2016] [Revised: 05/10/2016] [Accepted: 05/19/2016] [Indexed: 01/29/2023]
Abstract
In our search for natural soluble epoxide hydrolase (sEH) inhibitors from plants, we found that the methanolic extract of the leaves and twigs of Archidendron clypearia (Jack.) Nielsen (Fabaceae) significantly inhibits sEH in vitro. In a phytochemical investigation of the water layer of A. clypearia, we isolated two new chalcones, clypesides A-B (1-2), 13 flavonoid derivatives (3-15) and established their structures based on an extensive 1D and 2D NMR, CD data, and MS analysis. All of the flavonoid derivatives inhibited sEH enzymatic activity in a dose-dependent manner, with IC50 values ranging from 10.0±0.4 to 30.1±2.1μM. A kinetic analysis of compounds 4, 8-10, 12, 13, and 15 revealed that the compounds 8-10 were non-competitive, 4, 13, and 15 were mixed-type, and 12 was competitive inhibitors. Additionally, molecular docking increased our understanding of their receptor-ligand binding. These results demonstrated that flavonoid derivatives from A. clypearia are potential sEH inhibitors.
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Affiliation(s)
- Nguyen Phuong Thao
- College of Pharmacy, Chungnam National University, Daejeon 305-764, Republic of Korea; Institute of Marine Biochemistry (IMBC), Vietnam Academy of Science and Technology (VAST), 18 Hoang Quoc Viet, Caugiay, Hanoi, Viet Nam
| | - Bui Thi Thuy Luyen
- College of Pharmacy, Chungnam National University, Daejeon 305-764, Republic of Korea
| | - Jang Hoon Kim
- Department of Horticultural Environment, National Institute of Horticultural and Herbal Science, RDA, Wanju-gun 440-310, Republic of Korea
| | - Ah Reum Jo
- College of Pharmacy, Chungnam National University, Daejeon 305-764, Republic of Korea
| | - Nguyen Tien Dat
- Institute of Marine Biochemistry (IMBC), Vietnam Academy of Science and Technology (VAST), 18 Hoang Quoc Viet, Caugiay, Hanoi, Viet Nam
| | - Phan Van Kiem
- Institute of Marine Biochemistry (IMBC), Vietnam Academy of Science and Technology (VAST), 18 Hoang Quoc Viet, Caugiay, Hanoi, Viet Nam
| | - Chau Van Minh
- Institute of Marine Biochemistry (IMBC), Vietnam Academy of Science and Technology (VAST), 18 Hoang Quoc Viet, Caugiay, Hanoi, Viet Nam
| | - Young Ho Kim
- College of Pharmacy, Chungnam National University, Daejeon 305-764, Republic of Korea.
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11
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Waltenberger B, Garscha U, Temml V, Liers J, Werz O, Schuster D, Stuppner H. Discovery of Potent Soluble Epoxide Hydrolase (sEH) Inhibitors by Pharmacophore-Based Virtual Screening. J Chem Inf Model 2016; 56:747-62. [DOI: 10.1021/acs.jcim.5b00592] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Birgit Waltenberger
- Institute
of Pharmacy/Pharmacognosy and Center for
Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80-82, A-6020 Innsbruck, Austria
| | - Ulrike Garscha
- Chair
of Pharmaceutical/Medicinal Chemistry, Institute of Pharmacy, University of Jena, Philosophenweg 14, D-07743 Jena, Germany
| | - Veronika Temml
- Institute
of Pharmacy/Pharmacognosy and Center for
Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80-82, A-6020 Innsbruck, Austria
| | - Josephine Liers
- Chair
of Pharmaceutical/Medicinal Chemistry, Institute of Pharmacy, University of Jena, Philosophenweg 14, D-07743 Jena, Germany
| | - Oliver Werz
- Chair
of Pharmaceutical/Medicinal Chemistry, Institute of Pharmacy, University of Jena, Philosophenweg 14, D-07743 Jena, Germany
| | | | - Hermann Stuppner
- Institute
of Pharmacy/Pharmacognosy and Center for
Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80-82, A-6020 Innsbruck, Austria
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12
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Thao NP, Luyen BTT, Kim JH, Jo AR, Yang SY, Dat NT, Van Minh C, Kim YH. Soluble epoxide hydrolase inhibitory activity by rhizomes of Kaempferia parviflora Wall. ex Baker. Med Chem Res 2016. [DOI: 10.1007/s00044-016-1525-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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13
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Xue Y, Olsson T, Johansson CA, Öster L, Beisel HG, Rohman M, Karis D, Bäckström S. Fragment Screening of Soluble Epoxide Hydrolase for Lead Generation-Structure-Based Hit Evaluation and Chemistry Exploration. ChemMedChem 2016; 11:497-508. [PMID: 26845235 DOI: 10.1002/cmdc.201500575] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Indexed: 12/20/2022]
Abstract
Soluble epoxide hydrolase (sEH) is involved in the regulation of many biological processes by metabolizing the key bioactive lipid mediator, epoxyeicosatrienoic acids. For the development of sEH inhibitors with improved physicochemical properties, we performed both a fragment screening and a high-throughput screening aiming at an integrated hit evaluation and lead generation. Followed by a joint dose-response analysis to confirm the hits, the identified actives were then effectively triaged by a structure-based hit-classification approach to three prioritized series. Two distinct scaffolds were identified as tractable starting points for potential lead chemistry work. The oxoindoline series bind at the right-hand side of the active-site pocket with hydrogen bonds to the protein. The 2-phenylbenzimidazole-4-sulfonamide series bind at the central channel with significant induced fit, which has not been previously reported. On the basis of the encouraging initial results, we envision that a new lead series with improved properties could be generated if a vector is found that could merge the cyclohexyl functionality of the oxoindoline series with the trifluoromethyl moiety of the 2-phenylbenzimidazole-4-sulfonamide series.
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Affiliation(s)
- Yafeng Xue
- Department Discovery Sciences, AstraZeneca R&D Gothenburg, Pepparedsleden 1, 431 83, Mölndal, Sweden
| | - Thomas Olsson
- Department Medicinal Chemistry, CVMD iMED, AstraZeneca R&D Gothenburg, Pepparedsleden 1, 431 83, Mölndal, Sweden
| | - Carina A Johansson
- Department Discovery Sciences, AstraZeneca R&D Gothenburg, Pepparedsleden 1, 431 83, Mölndal, Sweden
| | - Linda Öster
- Department Discovery Sciences, AstraZeneca R&D Gothenburg, Pepparedsleden 1, 431 83, Mölndal, Sweden
| | - Hans-Georg Beisel
- Department Medicinal Chemistry, CVMD iMED, AstraZeneca R&D Gothenburg, Pepparedsleden 1, 431 83, Mölndal, Sweden
| | - Mattias Rohman
- Department Discovery Sciences, AstraZeneca R&D Gothenburg, Pepparedsleden 1, 431 83, Mölndal, Sweden
| | - David Karis
- Department Medicinal Chemistry, CVMD iMED, AstraZeneca R&D Gothenburg, Pepparedsleden 1, 431 83, Mölndal, Sweden
| | - Stefan Bäckström
- Department Discovery Sciences, AstraZeneca R&D Gothenburg, Pepparedsleden 1, 431 83, Mölndal, Sweden.
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Sun YN, Li W, Song SB, Yan XT, Zhao Y, Jo AR, Kang JS, Young Ho K. A new phenolic derivative with soluble epoxide hydrolase and nuclear factor-kappaB inhibitory activity from the aqueous extract of Acacia catechu. Nat Prod Res 2015; 30:2085-92. [DOI: 10.1080/14786419.2015.1114937] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Ya Nan Sun
- College of Pharmacy, Chungnam National University, Daejeon, Korea
| | - Wei Li
- School of Biotechnology, Yeungnam University, Gyeongsan, Korea
| | - Seok Bean Song
- Gyeongbuk Institute for Bio-industry (GIB), Andong City, Korea
| | - Xi Tao Yan
- Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Science, Northwest A & F University, Yangling, China
| | - Yan Zhao
- College of Pharmacy, Chungnam National University, Daejeon, Korea
| | - A. Reum Jo
- College of Pharmacy, Chungnam National University, Daejeon, Korea
| | - Jong Seong Kang
- College of Pharmacy, Chungnam National University, Daejeon, Korea
| | - Kim Young Ho
- College of Pharmacy, Chungnam National University, Daejeon, Korea
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15
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Amano Y, Tanabe E, Yamaguchi T. Identification of N-ethylmethylamine as a novel scaffold for inhibitors of soluble epoxide hydrolase by crystallographic fragment screening. Bioorg Med Chem 2015; 23:2310-7. [DOI: 10.1016/j.bmc.2015.03.083] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Revised: 03/30/2015] [Accepted: 03/31/2015] [Indexed: 11/30/2022]
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16
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Li W, Kim JH, Zhou W, Shim SH, Ma JY, Kim YH. Soluble epoxide hydrolase inhibitory activity of phenolic components from the rhizomes and roots of Gentiana scabra. Biosci Biotechnol Biochem 2015; 79:907-11. [PMID: 25588498 DOI: 10.1080/09168451.2014.1002451] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Two new (1 and 2) and seven known phenolic compounds were isolated from a methanol extract of the rhizomes and roots of Gentiana scabra. Their structures were identified by spectroscopic analysis and comparing with reported values. The inhibitory effects of each compound on soluble epoxide hydrolase (sEH) were evaluated. Among them, compounds 2, 6, and 9 potently inhibited sEH activity.
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Affiliation(s)
- Wei Li
- a School of Biotechnology , Yeungnam University , Gyeongsan , Korea
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17
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Sun YN, Li W, Kim JH, Yan XT, Kim JE, Yang SY, Kim YH. Chemical constituents from the root of Polygonum multiflorum and their soluble epoxide hydrolase inhibitory activity. Arch Pharm Res 2014; 38:998-1004. [DOI: 10.1007/s12272-014-0520-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2014] [Accepted: 11/16/2014] [Indexed: 12/19/2022]
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18
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Amano Y, Yamaguchi T, Tanabe E. Structural insights into binding of inhibitors to soluble epoxide hydrolase gained by fragment screening and X-ray crystallography. Bioorg Med Chem 2014; 22:2427-34. [DOI: 10.1016/j.bmc.2014.03.001] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2013] [Revised: 02/27/2014] [Accepted: 03/01/2014] [Indexed: 12/22/2022]
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19
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Morisseau C, Pakhomova S, Hwang SH, Newcomer ME, Hammock BD. Inhibition of soluble epoxide hydrolase by fulvestrant and sulfoxides. Bioorg Med Chem Lett 2013; 23:3818-21. [PMID: 23684894 DOI: 10.1016/j.bmcl.2013.04.083] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2013] [Accepted: 04/29/2013] [Indexed: 11/17/2022]
Abstract
The soluble epoxide hydrolase (sEH) is a key enzyme in the metabolism of epoxy-fatty acids, signaling molecules involved in numerous biologies. Toward finding novel inhibitors of sEH, a library of known drugs was tested for inhibition of sEH. We found that fulvestrant, an anticancer agent, is a potent (KI=26 nM) competitive inhibitor of sEH. From this observation, we found that alkyl-sulfoxides represent a new kind of pharmacophore for the inhibition of sEH.
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Affiliation(s)
- Christophe Morisseau
- Department of Entomology and UCD Comprehensive Cancer Center, University of California, One Shields Avenue, Davis, CA 95616, USA.
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