1
|
Cruz-Vicente P, Gonçalves AM, Barroca-Ferreira J, Silvestre SM, Romão MJ, Queiroz JA, Gallardo E, Passarinha LA. Unveiling the biopathway for the design of novel COMT inhibitors. Drug Discov Today 2022; 27:103328. [PMID: 35907613 DOI: 10.1016/j.drudis.2022.07.013] [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: 11/13/2021] [Revised: 06/27/2022] [Accepted: 07/25/2022] [Indexed: 12/15/2022]
Abstract
Catechol-O-methyltransferase (COMT) is an enzyme responsible for the O-methylation of biologically active catechol-based molecules. It has been associated with several neurological disorders, especially Parkinson's disease (PD), because of its involvement in catecholamine metabolism, and has been considered an important therapeutic target for central nervous system disorders. In this review, we summarize the biophysical, structural, and therapeutical relevance of COMT; the medicinal chemistry behind the development of COMT inhibitors and the application of computer-aided design to support the design of novel molecules; current methodologies for the biosynthesis, isolation, and purification of COMT; and revise existing bioanalytical approaches for the assessment of enzymatic activity in several biological matrices.
Collapse
Affiliation(s)
- Pedro Cruz-Vicente
- CICS-UBI - Health Sciences Research Centre, University of Beira Interior, 6201-506 Covilhã, Portugal; UCIBIO - Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal; Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2819-516 Caparica, Portugal
| | - Ana M Gonçalves
- CICS-UBI - Health Sciences Research Centre, University of Beira Interior, 6201-506 Covilhã, Portugal; UCIBIO - Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal; Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2819-516 Caparica, Portugal
| | - Jorge Barroca-Ferreira
- CICS-UBI - Health Sciences Research Centre, University of Beira Interior, 6201-506 Covilhã, Portugal; UCIBIO - Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal; Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2819-516 Caparica, Portugal
| | - Samuel M Silvestre
- CICS-UBI - Health Sciences Research Centre, University of Beira Interior, 6201-506 Covilhã, Portugal; CNC - Center for Neuroscience and Cell Biology, University of Coimbra, 3004-504 Coimbra, Portugal
| | - Maria J Romão
- UCIBIO - Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal; Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2819-516 Caparica, Portugal
| | - João A Queiroz
- CICS-UBI - Health Sciences Research Centre, University of Beira Interior, 6201-506 Covilhã, Portugal
| | - Eugénia Gallardo
- CICS-UBI - Health Sciences Research Centre, University of Beira Interior, 6201-506 Covilhã, Portugal; Laboratório de Fármaco-Toxicologia-UBIMedical, Universidade da Beira Interior, 6201-506 Covilhã, Portugal
| | - Luis A Passarinha
- CICS-UBI - Health Sciences Research Centre, University of Beira Interior, 6201-506 Covilhã, Portugal; UCIBIO - Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal; Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, 2819-516 Caparica, Portugal; Laboratório de Fármaco-Toxicologia-UBIMedical, Universidade da Beira Interior, 6201-506 Covilhã, Portugal.
| |
Collapse
|
2
|
Schwickert M, Fischer TR, Zimmermann RA, Hoba SN, Meidner JL, Weber M, Weber M, Stark MM, Koch J, Jung N, Kersten C, Windbergs M, Lyko F, Helm M, Schirmeister T. Discovery of Inhibitors of DNA Methyltransferase 2, an Epitranscriptomic Modulator and Potential Target for Cancer Treatment. J Med Chem 2022; 65:9750-9788. [PMID: 35849534 DOI: 10.1021/acs.jmedchem.2c00388] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Selective manipulation of the epitranscriptome could be beneficial for the treatment of cancer and also broaden the understanding of epigenetic inheritance. Inhibitors of the tRNA methyltransferase DNMT2, the enzyme catalyzing the S-adenosylmethionine-dependent methylation of cytidine 38 to 5-methylcytidine, were designed, synthesized, and analyzed for their enzyme-binding and -inhibiting properties. For rapid screening of potential DNMT2 binders, a microscale thermophoresis assay was established. Besides the natural inhibitors S-adenosyl-l-homocysteine (SAH) and sinefungin (SFG), we identified new synthetic inhibitors based on the structure of N-adenosyl-2,4-diaminobutyric acid (Dab). Structure-activity relationship studies revealed the amino acid side chain and a Y-shaped substitution pattern at the 4-position of Dab as crucial for DNMT2 inhibition. The most potent inhibitors are alkyne-substituted derivatives, exhibiting similar binding and inhibitory potencies as the natural compounds SAH and SFG. CaCo-2 assays revealed that poor membrane permeabilities of the acids and rapid hydrolysis of an ethylester prodrug might be the reasons for the insufficient activity in cellulo.
Collapse
Affiliation(s)
- Marvin Schwickert
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University Mainz, Staudinger Weg 5, D-55128 Mainz, Germany
| | - Tim R Fischer
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University Mainz, Staudinger Weg 5, D-55128 Mainz, Germany
| | - Robert A Zimmermann
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University Mainz, Staudinger Weg 5, D-55128 Mainz, Germany
| | - Sabrina N Hoba
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University Mainz, Staudinger Weg 5, D-55128 Mainz, Germany
| | - J Laurenz Meidner
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University Mainz, Staudinger Weg 5, D-55128 Mainz, Germany
| | - Marlies Weber
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University Mainz, Staudinger Weg 5, D-55128 Mainz, Germany
| | - Moritz Weber
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University Mainz, Staudinger Weg 5, D-55128 Mainz, Germany
| | - Martin M Stark
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University Mainz, Staudinger Weg 5, D-55128 Mainz, Germany
| | - Jonas Koch
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, Im Neuenheimer Feld 280, D-69120 Heidelberg, Germany
| | - Nathalie Jung
- Institute of Pharmaceutical Technology and Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany
| | - Christian Kersten
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University Mainz, Staudinger Weg 5, D-55128 Mainz, Germany
| | - Maike Windbergs
- Institute of Pharmaceutical Technology and Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Max-von-Laue-Str. 9, D-60438 Frankfurt am Main, Germany
| | - Frank Lyko
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, Im Neuenheimer Feld 280, D-69120 Heidelberg, Germany
| | - Mark Helm
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University Mainz, Staudinger Weg 5, D-55128 Mainz, Germany
| | - Tanja Schirmeister
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg University Mainz, Staudinger Weg 5, D-55128 Mainz, Germany
| |
Collapse
|
3
|
Ahmed‐Belkacem R, Debart F, Vasseur J. Bisubstrate Strategies to Target Methyltransferases. European J Org Chem 2022. [DOI: 10.1002/ejoc.202101481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
|
4
|
Discovery of Small Molecules as Membrane-Bound Catechol- O-methyltransferase Inhibitors with Interest in Parkinson's Disease: Pharmacophore Modeling, Molecular Docking and In Vitro Experimental Validation Studies. Pharmaceuticals (Basel) 2021; 15:ph15010051. [PMID: 35056108 PMCID: PMC8780549 DOI: 10.3390/ph15010051] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 12/22/2021] [Accepted: 12/28/2021] [Indexed: 12/22/2022] Open
Abstract
A pharmacophore-based virtual screening methodology was used to discover new catechol-O-methyltransferase (COMT) inhibitors with interest in Parkinson’s disease therapy. To do so, pharmacophore models were constructed using the structure of known inhibitors and then they were used in a screening in the ZINCPharmer database to discover hit molecules with the desired structural moieties and drug-likeness properties. Following this, the 50 best ranked molecules were submitted to molecular docking to better understand their atomic interactions and binding poses with the COMT (PDB#6I3C) active site. Additionally, the hits’ ADMET properties were also studied to improve the obtained results and to select the most promising compounds to advance for in-vitro studies. Then, the 10 compounds selected were purchased and studied regarding their in-vitro inhibitory potency on human recombinant membrane-bound COMT (MBCOMT), as well as their cytotoxicity in rat dopaminergic cells (N27) and human dermal fibroblasts (NHDF). Of these, the compound ZIN27985035 displayed the best results: For MBCOMT inhibition an IC50 of 17.6 nM was determined, and low cytotoxicity was observed in both cell lines (61.26 and 40.32 μM, respectively). Therefore, the promising results obtained, combined with the structure similarity with commercial COMT inhibitors, can allow for the future development of a potential new Parkinson’s disease drug candidate with improved properties.
Collapse
|
5
|
Akhtar MJ, Yar MS, Grover G, Nath R. Neurological and psychiatric management using COMT inhibitors: A review. Bioorg Chem 2020; 94:103418. [DOI: 10.1016/j.bioorg.2019.103418] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Revised: 10/27/2019] [Accepted: 10/31/2019] [Indexed: 12/18/2022]
|
6
|
Moschovou K, Melagraki G, Mavromoustakos T, Zacharia LC, Afantitis A. Cheminformatics and virtual screening studies of COMT inhibitors as potential Parkinson’s disease therapeutics. Expert Opin Drug Discov 2019; 15:53-62. [DOI: 10.1080/17460441.2020.1691165] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
| | - Georgia Melagraki
- Division of Physical Sciences & Applications, Hellenic Military Academy, Vari, Greece
| | | | | | | |
Collapse
|
7
|
Chen AY, Adamek RN, Dick BL, Credille CV, Morrison CN, Cohen SM. Targeting Metalloenzymes for Therapeutic Intervention. Chem Rev 2019; 119:1323-1455. [PMID: 30192523 PMCID: PMC6405328 DOI: 10.1021/acs.chemrev.8b00201] [Citation(s) in RCA: 161] [Impact Index Per Article: 32.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Metalloenzymes are central to a wide range of essential biological activities, including nucleic acid modification, protein degradation, and many others. The role of metalloenzymes in these processes also makes them central for the progression of many diseases and, as such, makes metalloenzymes attractive targets for therapeutic intervention. Increasing awareness of the role metalloenzymes play in disease and their importance as a class of targets has amplified interest in the development of new strategies to develop inhibitors and ultimately useful drugs. In this Review, we provide a broad overview of several drug discovery efforts focused on metalloenzymes and attempt to map out the current landscape of high-value metalloenzyme targets.
Collapse
Affiliation(s)
- Allie Y Chen
- Department of Chemistry and Biochemistry , University of California, San Diego , La Jolla , California 92093 , United States
| | - Rebecca N Adamek
- Department of Chemistry and Biochemistry , University of California, San Diego , La Jolla , California 92093 , United States
| | - Benjamin L Dick
- Department of Chemistry and Biochemistry , University of California, San Diego , La Jolla , California 92093 , United States
| | - Cy V Credille
- Department of Chemistry and Biochemistry , University of California, San Diego , La Jolla , California 92093 , United States
| | - Christine N Morrison
- Department of Chemistry and Biochemistry , University of California, San Diego , La Jolla , California 92093 , United States
| | - Seth M Cohen
- Department of Chemistry and Biochemistry , University of California, San Diego , La Jolla , California 92093 , United States
| |
Collapse
|
8
|
Lerner C, Jakob-Roetne R, Buettelmann B, Ehler A, Rudolph M, Rodríguez Sarmiento RM. Design of Potent and Druglike Nonphenolic Inhibitors for Catechol O-Methyltransferase Derived from a Fragment Screening Approach Targeting the S-Adenosyl-l-methionine Pocket. J Med Chem 2016; 59:10163-10175. [PMID: 27685665 DOI: 10.1021/acs.jmedchem.6b00927] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
A fragment screening approach designed to target specifically the S-adenosyl-l-methionine pocket of catechol O-methyl transferase allowed the identification of structurally related fragments of high ligand efficiency and with activity on the described orthogonal assays. By use of a reliable enzymatic assay together with X-ray crystallography as guidance, a series of fragment modifications revealed an SAR and, after several expansions, potent lead compounds could be obtained. For the first time nonphenolic and small low nanomolar potent, SAM competitive COMT inhibitors are reported. These compounds represent a novel series of potent COMT inhibitors that might be further optimized to new drugs useful for the treatment of Parkinson's disease, as adjuncts in levodopa based therapy, or for the treatment of schizophrenia.
Collapse
Affiliation(s)
- Christian Lerner
- Pharmaceutical Research and Early Development (pRED), Roche Innovation Center Basel, F. Hoffmann-La Roche AG, Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Roland Jakob-Roetne
- Pharmaceutical Research and Early Development (pRED), Roche Innovation Center Basel, F. Hoffmann-La Roche AG, Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Bernd Buettelmann
- Pharmaceutical Research and Early Development (pRED), Roche Innovation Center Basel, F. Hoffmann-La Roche AG, Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Andreas Ehler
- Pharmaceutical Research and Early Development (pRED), Roche Innovation Center Basel, F. Hoffmann-La Roche AG, Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Markus Rudolph
- Pharmaceutical Research and Early Development (pRED), Roche Innovation Center Basel, F. Hoffmann-La Roche AG, Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Rosa María Rodríguez Sarmiento
- Pharmaceutical Research and Early Development (pRED), Roche Innovation Center Basel, F. Hoffmann-La Roche AG, Grenzacherstrasse 124, 4070 Basel, Switzerland
| |
Collapse
|
9
|
Abstract
S-Adenosyl-L-methionine (SAM) is a sulfonium molecule with a structural hybrid of methionine and adenosine. As the second largest cofactor in the human body, its major function is to serve as methyl donor for SAM-dependent methyltransferases (MTases). The resultant transmethylation of biomolecules constitutes a significant biochemical mechanism in epigenetic regulation, cellular signaling, and metabolite degradation. Recently, numerous SAM analogs have been developed as synthetic cofactors to transfer the activated groups on MTase substrates for downstream ligation and identification. Meanwhile, new compounds built upon or derived from the SAM scaffold have been designed and tested as selective inhibitors for important MTase targets. Here, we summarized the recent development and application of SAM analogs as chemical biology tools for MTases.
Collapse
Affiliation(s)
- Jing Zhang
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, The University of Georgia, Athens, Georgia 30602, United States
| | - Yujun George Zheng
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, The University of Georgia, Athens, Georgia 30602, United States
| |
Collapse
|
10
|
Cai XC, Kapilashrami K, Luo M. Synthesis and Assays of Inhibitors of Methyltransferases. Methods Enzymol 2016; 574:245-308. [DOI: 10.1016/bs.mie.2016.01.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
|
11
|
Ehler A, Benz J, Schlatter D, Rudolph MG. Mapping the conformational space accessible to catechol-O-methyltransferase. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2014; 70:2163-74. [PMID: 25084335 PMCID: PMC4118827 DOI: 10.1107/s1399004714012917] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/28/2014] [Accepted: 06/03/2014] [Indexed: 11/10/2022]
Abstract
Methylation catalysed by catechol-O-methyltransferase (COMT) is the main pathway of catechol neurotransmitter deactivation in the prefrontal cortex. Low levels of this class of neurotransmitters are held to be causative of diseases such as schizophrenia, depression and Parkinson's disease. Inhibition of COMT may increase neurotransmitter levels, thus offering a route for treatment. Structure-based drug design hitherto seems to be based on the closed enzyme conformation. Here, a set of apo, semi-holo, holo and Michaelis form crystal structures are described that define the conformational space available to COMT and that include likely intermediates along the catalytic pathway. Domain swaps and sizeable loop movements around the active site testify to the flexibility of this enzyme, rendering COMT a difficult drug target. The low affinity of the co-substrate S-adenosylmethionine and the large conformational changes involved during catalysis highlight significant energetic investment to achieve the closed conformation. Since each conformation of COMT is a bona fide target for inhibitors, other states than the closed conformation may be promising to address. Crystallographic data for an alternative avenue of COMT inhibition, i.e. locking of the apo state by an inhibitor, are presented. The set of COMT structures may prove to be useful for the development of novel classes of inhibitors.
Collapse
Affiliation(s)
- Andreas Ehler
- Molecular Design and Chemical Biology, F. Hoffmann-La Roche, Grenzacher Strasse 124, Basel, Switzerland
| | - Jörg Benz
- Molecular Design and Chemical Biology, F. Hoffmann-La Roche, Grenzacher Strasse 124, Basel, Switzerland
| | - Daniel Schlatter
- Molecular Design and Chemical Biology, F. Hoffmann-La Roche, Grenzacher Strasse 124, Basel, Switzerland
| | - Markus G. Rudolph
- Molecular Design and Chemical Biology, F. Hoffmann-La Roche, Grenzacher Strasse 124, Basel, Switzerland
| |
Collapse
|
12
|
Ma Z, Liu H, Wu B. Structure-based drug design of catechol-O-methyltransferase inhibitors for CNS disorders. Br J Clin Pharmacol 2014; 77:410-20. [PMID: 23713800 PMCID: PMC3952716 DOI: 10.1111/bcp.12169] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2013] [Accepted: 04/25/2013] [Indexed: 12/23/2022] Open
Abstract
Catechol-O-methyltransferase (COMT) is of great importance in pharmacology because it catalyzes the metabolism (methylation) of endogenous and xenobiotic catechols. Moreover, inhibition of COMT is the drug target in the management of central nervous system (CNS) disorders such as Parkinson's disease due to its role in regulation of the dopamine level in the brain. The X-ray crystal structures for COMT have been available since 1994. The active sites for cofactor and substrate/inhibitor binding are well resolved to an atomic level, providing valuable insights into the catalytic mechanisms as well as the role of magnesium ions in catalysis. Determination of how the substrates/inhibitors bind to the protein leads to a structure-based approach that has resulted in potent and selective inhibitors. This review focuses on the design of two types of inhibitors (nitrocatechol-type and bisubstrate inhibitors) for COMT using the protein structures.
Collapse
Affiliation(s)
- Zhiguo Ma
- Division of Pharmaceutics, College of Pharmacy, Jinan UniversityGuangzhou, Guangdong, China
| | - Hongming Liu
- Division of Pharmaceutics, College of Pharmacy, Jinan UniversityGuangzhou, Guangdong, China
| | - Baojian Wu
- Division of Pharmaceutics, College of Pharmacy, Jinan UniversityGuangzhou, Guangdong, China
| |
Collapse
|
13
|
Jatana N, Sharma A, Latha N. Pharmacophore modeling and virtual screening studies to design potential COMT inhibitors as new leads. J Mol Graph Model 2012; 39:145-64. [PMID: 23280413 DOI: 10.1016/j.jmgm.2012.10.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2012] [Revised: 09/15/2012] [Accepted: 10/08/2012] [Indexed: 10/27/2022]
Abstract
Catechol-O-methyltransferase (COMT) catalyzes the methylation of catecholamines, including neurotransmitters like dopamine, epinephrine and norepinephrine, leading to their degradation. COMT has been a subject of study for its implications in numerous neurological disorders like Parkinson's disease (PD), schizophrenia, and depression. The COMT gene is associated with many allelic variants, the Val108Met polymorphism being the most clinically significant. Availability of crystal structure of both 108V and 108M forms of human soluble-COMT (S-COMT) facilitated us to use structure-based virtual screening approach to obtain new hits by screening a library of CNS permeable compounds from ZINC database. In this study, E-pharmacophore was also used to generate pharmacophore models based on a series of known COMT inhibitors. A five-point pharmacophore model consisting of one hydrogen-bond acceptor (A), two hydrogen bond donors (D), and two aromatic rings (R) was generated for both the polymorphic forms of COMT. These models were then used for filtering ZINC-CNS permeable library to obtain new hits. Physicochemical properties were also calculated for all the hits obtained from both the approaches for favorable ADME properties. These identified hits maybe of interest for further structural optimization and biological evaluation assays.
Collapse
Affiliation(s)
- Nidhi Jatana
- Bioinformatics Infrastructure Facility, Sri Venkateswara College (University of Delhi), Benito Juarez Road, Dhaula Kuan, New Delhi, India
| | | | | |
Collapse
|
14
|
Ellermann M, Lerner C, Burgy G, Ehler A, Bissantz C, Jakob-Roetne R, Paulini R, Allemann O, Tissot H, Grünstein D, Stihle M, Diederich F, Rudolph MG. Catechol-O-methyltransferase in complex with substituted 3′-deoxyribose bisubstrate inhibitors. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2012; 68:253-60. [DOI: 10.1107/s0907444912001138] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2011] [Accepted: 01/10/2012] [Indexed: 11/10/2022]
|
15
|
Ellermann M, Paulini R, Jakob‐Roetne R, Lerner C, Borroni E, Roth D, Ehler A, Schweizer WB, Schlatter D, Rudolph MG, Diederich F. Molecular Recognition at the Active Site of Catechol‐
O
‐methyltransferase (COMT): Adenine Replacements in Bisubstrate Inhibitors. Chemistry 2011; 17:6369-81. [DOI: 10.1002/chem.201003648] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2010] [Indexed: 12/29/2022]
Affiliation(s)
- Manuel Ellermann
- Laboratorium für Organische Chemie, ETH‐Zürich, Wolfgang‐Pauli‐Strasse 10, 8093 Zürich (Switzerland), Fax: (+41) 1‐632‐1109
| | - Ralph Paulini
- Laboratorium für Organische Chemie, ETH‐Zürich, Wolfgang‐Pauli‐Strasse 10, 8093 Zürich (Switzerland), Fax: (+41) 1‐632‐1109
| | - Roland Jakob‐Roetne
- Pharma Division, Präklinische Forschung, F. Hoffmann‐La Roche AG, 4070 Basel (Switzerland)
| | - Christian Lerner
- Pharma Division, Präklinische Forschung, F. Hoffmann‐La Roche AG, 4070 Basel (Switzerland)
| | - Edilio Borroni
- Pharma Division, Präklinische Forschung, F. Hoffmann‐La Roche AG, 4070 Basel (Switzerland)
| | - Doris Roth
- Pharma Division, Präklinische Forschung, F. Hoffmann‐La Roche AG, 4070 Basel (Switzerland)
| | - Andreas Ehler
- Pharma Division, Präklinische Forschung, F. Hoffmann‐La Roche AG, 4070 Basel (Switzerland)
| | - W. Bernd Schweizer
- Laboratorium für Organische Chemie, ETH‐Zürich, Wolfgang‐Pauli‐Strasse 10, 8093 Zürich (Switzerland), Fax: (+41) 1‐632‐1109
| | - Daniel Schlatter
- Pharma Division, Präklinische Forschung, F. Hoffmann‐La Roche AG, 4070 Basel (Switzerland)
| | - Markus G. Rudolph
- Pharma Division, Präklinische Forschung, F. Hoffmann‐La Roche AG, 4070 Basel (Switzerland)
| | - François Diederich
- Laboratorium für Organische Chemie, ETH‐Zürich, Wolfgang‐Pauli‐Strasse 10, 8093 Zürich (Switzerland), Fax: (+41) 1‐632‐1109
| |
Collapse
|
16
|
Le Calvez PB, Scott CJ, Migaud ME. Multisubstrate adduct inhibitors: drug design and biological tools. J Enzyme Inhib Med Chem 2010; 24:1291-318. [PMID: 19912064 DOI: 10.3109/14756360902843809] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
In drug discovery, different methods exist to create new inhibitors possessing satisfactory biological activity. The multisubstrate adduct inhibitor (MAI) approach is one of these methods, which consists of a covalent combination between analogs of the substrate and the cofactor or of the multiple substrates used by the target enzyme. Adopted as the first line of investigation for many enzymes, this method has brought insights into the enzymatic mechanism, structure, and inhibitory requirements. In this review, the MAI approach, applied to different classes of enzyme, is reported from the point of view of biological activity.
Collapse
|
17
|
Ellermann M, Jakob-Roetne R, Lerner C, Borroni E, Schlatter D, Roth D, Ehler A, Rudolph M, Diederich F. Molecular Recognition at the Active Site of Catechol-O-Methyltransferase: Energetically Favorable Replacement of a Water Molecule Imported by a Bisubstrate Inhibitor. Angew Chem Int Ed Engl 2009; 48:9092-6. [DOI: 10.1002/anie.200904410] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
|
18
|
Ellermann M, Jakob-Roetne R, Lerner C, Borroni E, Schlatter D, Roth D, Ehler A, Rudolph M, Diederich F. Molekulare Erkennung in der aktiven Tasche der Catechol-O- Methyltransferase: energetisch günstige Verdrängung eines von einem Bisubstratinhibitor importierten Wassermoleküls. Angew Chem Int Ed Engl 2009. [DOI: 10.1002/ange.200904410] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
|
19
|
Link A, Heidler P, Kaiser M, Brun R. Parallel synthesis of a series of non-functional ATP/NAD analogs with activity against trypanosomatid parasites. Mol Divers 2009; 14:215-24. [PMID: 19484371 DOI: 10.1007/s11030-009-9160-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2009] [Accepted: 05/09/2009] [Indexed: 11/29/2022]
Abstract
Non-functional analogs of the cofactors ATP and NAD are putative inhibitors of ATP- or NAD-dependant enzymes. Since pathogenic protozoa rely heavily on the salvage of purine nucleosides from the bloodstream of their host, such compounds are of interest as antiplasmodial and antitrypanosomal agents with a multitude of molecular targets. By replacing the negatively charged phosphate residues with a constrained unsaturated amide spacer and the nicotinamide moiety of NAD with various lipophilic substituents, 15 new ATP/NAD analogs were obtained in screening quantities. In these compounds, a 5'-desoxyadenosine moiety was conserved as key molecular recognition motif. The inhibition of P. falciparum and T. brucei ssp. in a whole parasite in vitro assay is reported.
Collapse
Affiliation(s)
- Andreas Link
- Institute of Pharmacy, Ernst-Moritz-Arndt-University, Friedrich-Ludwig-Jahn-Strasse 17, 17487, Greifswald, Germany.
| | | | | | | |
Collapse
|
20
|
|
21
|
Zürcher M, Diederich F. Structure-Based Drug Design: Exploring the Proper Filling of Apolar Pockets at Enzyme Active Sites. J Org Chem 2008; 73:4345-61. [DOI: 10.1021/jo800527n] [Citation(s) in RCA: 88] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Martina Zürcher
- Department of Chemistry and Applied Biosciences, Laboratorium für Organische Chemie, ETH Zürich, HCI G 313, 8093 Zürich, Switzerland
| | - François Diederich
- Department of Chemistry and Applied Biosciences, Laboratorium für Organische Chemie, ETH Zürich, HCI G 313, 8093 Zürich, Switzerland
| |
Collapse
|
22
|
Bonifácio MJ, Palma PN, Almeida L, Soares‐da‐Silva P. Catechol-O-methyltransferase and its inhibitors in Parkinson's disease. CNS DRUG REVIEWS 2008; 13:352-79. [PMID: 17894650 PMCID: PMC6494163 DOI: 10.1111/j.1527-3458.2007.00020.x] [Citation(s) in RCA: 137] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Parkinson's disease (PD) is a neurological disorder characterized by the degeneration of dopaminergic neurons, with consequent reduction in striatal dopamine levels leading to characteristic motor symptoms. The most effective treatment for this disease continues to be the dopamine replacement therapy with levodopa together with an inhibitor of aromatic amino acid decarboxylase (AADC). The efficacy of this therapy, however, decreases with time and most patients develop fluctuating responses and dyskinesias. The last decade showed that the use of catechol-O-methyltransferase inhibitors as adjuvants to the levodopa/AADC inhibitor therapy, significantly improves the clinical benefits of this therapy. The purpose of this article is to review the current knowledge on the enzyme catechol-O-methyltransferase (COMT) and the role of COMT inhibitors in PD as a new therapeutic approach to PD involving conversion of levodopa to dopamine at the target region in the brain and facilitation of the continuous action of this amine at the receptor sites. A historical overview of the discovery and development of COMT inhibitors is presented with a special emphasis on nebicapone, presently under clinical development, as well as entacapone and tolcapone, which are already approved as adjuncts in the therapy of PD. This article reviews human pharmacokinetic and pharmacodynamic properties of these drugs as well as their clinical efficacy and safety.
Collapse
Affiliation(s)
- Maria João Bonifácio
- Department of Research and Development, BIAL (Portela & Co S.A.), S Mamede do Coronado, Portugal
| | - P. Nuno Palma
- Department of Research and Development, BIAL (Portela & Co S.A.), S Mamede do Coronado, Portugal
| | - Luís Almeida
- Department of Research and Development, BIAL (Portela & Co S.A.), S Mamede do Coronado, Portugal
- Institute of Pharmacology and Therapeutics, Faculty of Medicine, Porto, Portugal
| | - Patrício Soares‐da‐Silva
- Department of Research and Development, BIAL (Portela & Co S.A.), S Mamede do Coronado, Portugal
- Institute of Pharmacology and Therapeutics, Faculty of Medicine, Porto, Portugal
| |
Collapse
|
23
|
Receptor-oriented Pharmacophore-based in silico Screening of Human Catechol O-Methyltransferase for the Design of Antiparkinsonian Drug. B KOREAN CHEM SOC 2007. [DOI: 10.5012/bkcs.2007.28.3.379] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
|
24
|
Paulini R, Trindler C, Lerner C, Brändli L, Schweizer WB, Jakob-Roetne R, Zürcher G, Borroni E, Diederich F. Bisubstrate inhibitors of catechol O-methyltransferase (COMT): the crucial role of the ribose structural unit for inhibitor binding affinity. ChemMedChem 2006; 1:340-57. [PMID: 16892369 DOI: 10.1002/cmdc.200500065] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Inhibition of the enzyme catechol O-methyltransferase offers a therapeutic handle to regulate the catabolism of catecholamine neurotransmitters, providing valuable assistance in the treatment of CNS disorders such as Parkinson's disease. A series of ribose-modified bisubstrate inhibitors of COMT featuring 2'-deoxy-, 3'-deoxy-, 2'-aminodeoxy-3'-deoxy-, and 2'-deoxy-3'-aminodeoxyribose-derived central moieties and analogues containing the carbocyclic skeleton of the natural product aristeromycin were synthesized and evaluated to investigate the molecular recognition properties of the ribose binding site in the enzyme. Key synthetic intermediates in the ribose-derived series were obtained by deoxygenative [1,2]-hydride shift rearrangement of adenosine derivatives; highlights in the synthesis of carbocyclic aristeromycin analogues include a diastereoselective cyclopropanation step and nucleobase introduction with a modified Mitsunobu protocol. In vitro biological evaluation and kinetic studies revealed dramatic effects of the ribose modification on binding affinity: 3'-deoxygenation of the ribose gave potent inhibitors (IC50 values in the nanomolar range), which stands in sharp contrast to the remarkable decrease in potency observed for 2'-deoxy derivatives (IC50 values in the micromolar range). Aminodeoxy analogues were only weakly active, whereas the change of the tetrahydrofuran skeleton to a carbocycle unexpectedly led to a complete loss of biological activity. These results confirm that the ribose structural unit of the bisubstrate inhibitors of COMT is a key element of molecular recognition and that modifications thereof are delicate and may lead to surprises.
Collapse
Affiliation(s)
- Ralph Paulini
- Laboratorium für Organische Chemie, ETH-Hönggerberg, HCI, 8093 Zürich, Switzerland
| | | | | | | | | | | | | | | | | |
Collapse
|
25
|
Paulini R, Lerner C, Diederich F, Jakob-Roetne R, Zürcher G, Borroni E. Synthesis and Biological Evaluation of Potent Bisubstrate Inhibitors of the Enzyme CatecholO-Methyltransferase (COMT) Lacking a Nitro Group. Helv Chim Acta 2006. [DOI: 10.1002/hlca.200690179] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
|
26
|
Marotti F, Bonifazi D, Gehrig R, Gallani JL, Diederich F. Fullerene- and porphyrin-appended crown ethers: Synthesis and preparation of stable langmuir and langmuir-blodgett films. Isr J Chem 2005. [DOI: 10.1560/f8ld-64mn-ravn-guav] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
|
27
|
Sahli S, Stump B, Welti T, Schweizer W, Diederich F, Blum-Kaelin D, Aebi J, Böhm HJ. A New Class of Inhibitors for the Metalloprotease Neprilysin Based on a Central Imidazole Scaffold. Helv Chim Acta 2005. [DOI: 10.1002/hlca.200590050] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
|