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Grimm LM, Setiadi J, Tkachenko B, Schreiner PR, Gilson MK, Biedermann F. The temperature-dependence of host-guest binding thermodynamics: experimental and simulation studies. Chem Sci 2023; 14:11818-11829. [PMID: 37920355 PMCID: PMC10619620 DOI: 10.1039/d3sc01975f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Accepted: 09/24/2023] [Indexed: 11/04/2023] Open
Abstract
The thermodynamic parameters of host-guest binding can be used to describe, understand, and predict molecular recognition events in aqueous systems. However, interpreting binding thermodynamics remains challenging, even for these relatively simple molecules, as they are determined by both direct and solvent-mediated host-guest interactions. In this contribution, we focus on the contributions of water to binding by studying binding thermodynamics, both experimentally and computationally, for a series of nearly rigid, electrically neutral host-guest systems and report the temperature-dependent thermodynamic binding contributions ΔGb(T), ΔHb(T), ΔSb(T), and ΔCp,b. Combining isothermal titration calorimetry (ITC) measurements with molecular dynamics (MD) simulations, we provide insight into the binding forces at play for the macrocyclic hosts cucurbit[n]uril (CBn, n = 7-8) and β-cyclodextrin (β-CD) with a range of guest molecules. We find consistently negative changes in heat capacity on binding (ΔCp,b) for all systems studied herein - as well as for literature host-guest systems - indicating increased enthalpic driving forces for binding at higher temperatures. We ascribe these trends to solvation effects, as the solvent properties of water deteriorate as temperature rises. Unlike the entropic and enthalpic contributions to binding, with their differing signs and magnitudes for the classical and non-classical hydrophobic effect, heat capacity changes appear to be a unifying and more general feature of host-guest complex formation in water. This work has implications for understanding protein-ligand interactions and other complex systems in aqueous environments.
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Affiliation(s)
- Laura M Grimm
- Institute of Nanotechnology (INT), Karlsruhe Institute of Technology (KIT) Hermann-von-Helmholtz Platz 1 76344 Eggenstein-Leopoldshafen Germany
| | - Jeffry Setiadi
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego 9255 Pharmacy Lane La Jolla CA 92093 USA
| | - Boryslav Tkachenko
- Institute of Organic Chemistry, Justus Liebig University Giessen Heinrich-Buff-Ring 17 35392 Giessen Germany
| | - Peter R Schreiner
- Institute of Organic Chemistry, Justus Liebig University Giessen Heinrich-Buff-Ring 17 35392 Giessen Germany
| | - Michael K Gilson
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego 9255 Pharmacy Lane La Jolla CA 92093 USA
| | - Frank Biedermann
- Institute of Nanotechnology (INT), Karlsruhe Institute of Technology (KIT) Hermann-von-Helmholtz Platz 1 76344 Eggenstein-Leopoldshafen Germany
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2
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Meanwell NA. The pyridazine heterocycle in molecular recognition and drug discovery. Med Chem Res 2023; 32:1-69. [PMID: 37362319 PMCID: PMC10015555 DOI: 10.1007/s00044-023-03035-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Accepted: 02/06/2023] [Indexed: 03/17/2023]
Abstract
The pyridazine ring is endowed with unique physicochemical properties, characterized by weak basicity, a high dipole moment that subtends π-π stacking interactions and robust, dual hydrogen-bonding capacity that can be of importance in drug-target interactions. These properties contribute to unique applications in molecular recognition while the inherent polarity, low cytochrome P450 inhibitory effects and potential to reduce interaction of a molecule with the cardiac hERG potassium channel add additional value in drug discovery and development. The recent approvals of the gonadotropin-releasing hormone receptor antagonist relugolix (24) and the allosteric tyrosine kinase 2 inhibitor deucravacitinib (25) represent the first examples of FDA-approved drugs that incorporate a pyridazine ring. In this review, the properties of the pyridazine ring are summarized in comparison to the other azines and its potential in drug discovery is illustrated through vignettes that explore applications that take advantage of the inherent physicochemical properties as an approach to solving challenges associated with candidate optimization. Graphical Abstract
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3
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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.
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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.
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4
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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.
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5
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Zhou S, Huang G. Some important inhibitors and mechanisms of rheumatoid arthritis. Chem Biol Drug Des 2021; 99:930-943. [PMID: 34942050 DOI: 10.1111/cbdd.14015] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 12/17/2021] [Accepted: 12/21/2021] [Indexed: 11/29/2022]
Abstract
Rheumatoid arthritis is a chronic disease that seriously affects human health and quality of life, and it is one of the main causes of labor loss and disability. Many countries have listed rheumatoid arthritis as one of the national a key diseases to tackle. The pathogenesis of RA in humans is still unknown, and medical researchers believe that the pathogenesis of RA may be the result of a combination of genetic and environmental factors. RA is an incurable condition that can only be controlled and treated with conventional drugs. In this paper, the pathologic features and pathogenesis of RA were introduced, and the research progress of new anti-rheumatoid arthritis chemical drugs in recent years was reviewed.
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Affiliation(s)
- Shiyang Zhou
- Chongqing Chemical Industry Vocational College, Chongqing, 401228, China.,College of Chemistry, Chongqing Normal University, Chongqing, 401331, China
| | - Gangliang Huang
- College of Chemistry, Chongqing Normal University, Chongqing, 401331, China
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6
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Tykwinski RR, Nierengarten JF. François Diederich’s legacy. Chem 2021. [DOI: 10.1016/j.chempr.2021.04.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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7
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Iijima H, Takebe K, Suzuki M, Kobayashi H, Takamiya T, Saito H, Niwa N, Kuwada-Kusunose T. Crystal Structure of Catechol O-Methyltransferase Complexed with Nitecapone. Chem Pharm Bull (Tokyo) 2020; 68:447-451. [DOI: 10.1248/cpb.c20-00011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
| | - Katsuki Takebe
- Oral and Maxillofacial Surgery II, Osaka University Graduate School of Dentistry
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8
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Cornelissen NV, Michailidou F, Muttach F, Rau K, Rentmeister A. Nucleoside-modified AdoMet analogues for differential methyltransferase targeting. Chem Commun (Camb) 2020; 56:2115-2118. [PMID: 31970375 PMCID: PMC7030947 DOI: 10.1039/c9cc07807j] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Methyltransferases (MTases) modify a wide range of biomolecules using S-adenosyl-l-methionine (AdoMet) as the cosubstrate. Synthetic AdoMet analogues are powerful tools to site-specifically introduce a variety of functional groups and exhibit potential to be converted only by distinct MTases. Extending the size of the substituent at the sulfur/selenium atom provides selectivity among MTases but is insufficient to discriminate between promiscuous MTases. We present a panel of AdoMet analogues differing in the nucleoside moiety (NM-AdoMets). These NM-AdoMets were efficiently produced by a previously uncharacterized methionine adenosyltransferase (MAT) from methionine and ATP analogues, such as ITP and N6-propargyl-ATP. The N6-modification changed the relative activity of three representative MTases up to 13-fold resulting in discrimination of substrates for the methyl transfer and could also be combined with transfer of allyl and propargyl groups.
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Affiliation(s)
- Nicolas V Cornelissen
- Department of Chemistry, Institute of Biochemistry, University of Muenster, Wilhelm-Klemm-Straße 2, D-48149 Muenster, Germany.
| | - Freideriki Michailidou
- Department of Chemistry, Institute of Biochemistry, University of Muenster, Wilhelm-Klemm-Straße 2, D-48149 Muenster, Germany.
| | - Fabian Muttach
- Department of Chemistry, Institute of Biochemistry, University of Muenster, Wilhelm-Klemm-Straße 2, D-48149 Muenster, Germany.
| | - Kristina Rau
- Department of Chemistry, Institute of Biochemistry, University of Muenster, Wilhelm-Klemm-Straße 2, D-48149 Muenster, Germany.
| | - Andrea Rentmeister
- Department of Chemistry, Institute of Biochemistry, University of Muenster, Wilhelm-Klemm-Straße 2, D-48149 Muenster, Germany.
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9
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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]
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10
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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
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11
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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.
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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
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12
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Atdjian C, Iannazzo L, Braud E, Ethève-Quelquejeu M. Synthesis of SAM-Adenosine Conjugates for the Study of m 6
A-RNA Methyltransferases. European J Org Chem 2018. [DOI: 10.1002/ejoc.201800798] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Colette Atdjian
- Laboratoire de Chimie et de Biochimie Pharmacologiques et Toxicologiques; Team “Chemistry of RNAs, nucleosides, peptides and heterocycles”; Université Paris Descartes; UMR 8601; 75005 Paris France
| | - Laura Iannazzo
- Laboratoire de Chimie et de Biochimie Pharmacologiques et Toxicologiques; Team “Chemistry of RNAs, nucleosides, peptides and heterocycles”; Université Paris Descartes; UMR 8601; 75005 Paris France
| | - Emmanuelle Braud
- Laboratoire de Chimie et de Biochimie Pharmacologiques et Toxicologiques; Team “Chemistry of RNAs, nucleosides, peptides and heterocycles”; Université Paris Descartes; UMR 8601; 75005 Paris France
| | - Mélanie Ethève-Quelquejeu
- Laboratoire de Chimie et de Biochimie Pharmacologiques et Toxicologiques; Team “Chemistry of RNAs, nucleosides, peptides and heterocycles”; Université Paris Descartes; UMR 8601; 75005 Paris France
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13
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Oxindole-based SYK and JAK3 dual inhibitors for rheumatoid arthritis: designing, synthesis and biological evaluation. Future Med Chem 2017; 9:1193-1211. [DOI: 10.4155/fmc-2017-0037] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Aim: Autoimmune disorders have complex pathophysiology and focus is laid on the development of multitargeted agents. Two well-established kinases: SYK and JAK3, were considered to design dual inhibitors as potential therapeutics using various molecular-modeling approaches. Mehodology: Pharmacophore models for SYK and JAK3 were generated using oxindole-based inhibitors. Furthermore, an in-house database was designed that was screened against the best selected models. The obtained hits were employed for docking analysis and subjected to MM-GBSA analysis and molecular dynamic simulation. Results: Top five oxindole derivatives were synthesized and evaluated for in vitro SYK and JAK3 activity. The most active compound 4a was evaluated for in vivo antiarthritic activity. It showed significant anti-arthritic activity. Conclusion: Thus, the designed inhibitors resulted in potential therapeutic agents for rheumatoid arthritis.
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14
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Diederich F, Trapp N, Wörle M. Small Molecule Crystallography in the Laboratory of Organic Chemistry at ETH Zürich. Isr J Chem 2016. [DOI: 10.1002/ijch.201600030] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- François Diederich
- Laboratory of Organic Chemistry; Department of Chemistry and Applied Biosciences; ETH Zurich; Vladimir-Prelog-Weg 3 8093 Zurich Switzerland
| | - Nils Trapp
- Laboratory of Organic Chemistry; Department of Chemistry and Applied Biosciences; ETH Zurich; Vladimir-Prelog-Weg 3 8093 Zurich Switzerland
| | - Michael Wörle
- Laboratory of Inorganic Chemistry; Department of Chemistry and Applied Biosciences; ETH Zurich; Vladimir-Prelog-Weg 1 8093 Zurich Switzerland
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15
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Abstract
On the basis of many literature measurements, a critical overview is given on essential noncovalent interactions in synthetic supramolecular complexes, accompanied by analyses with selected proteins. The methods, which can be applied to derive binding increments for single noncovalent interactions, start with the evaluation of consistency and additivity with a sufficiently large number of different host-guest complexes by applying linear free energy relations. Other strategies involve the use of double mutant cycles, of molecular balances, of dynamic combinatorial libraries, and of crystal structures. Promises and limitations of these strategies are discussed. Most of the analyses stem from solution studies, but a few also from gas phase. The empirically derived interactions are then presented on the basis of selected complexes with respect to ion pairing, hydrogen bonding, electrostatic contributions, halogen bonding, π-π-stacking, dispersive forces, cation-π and anion-π interactions, and contributions from the hydrophobic effect. Cooperativity in host-guest complexes as well as in self-assembly, and entropy factors are briefly highlighted. Tables with typical values for single noncovalent free energies and polarity parameters are in the Supporting Information.
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Affiliation(s)
- Frank Biedermann
- Institute of Nanotechnology, Karlsruhe Institute of Technology (KIT) , Hermann-von-Helmholtz Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Hans-Jörg Schneider
- FR Organische Chemie der Universität des Saarlandes , D-66041 Saarbrücken, Germany
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16
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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.
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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
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17
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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]
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18
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Persch E, Dumele O, Diederich F. Molekulare Erkennung in chemischen und biologischen Systemen. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201408487] [Citation(s) in RCA: 102] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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19
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Persch E, Dumele O, Diederich F. Molecular recognition in chemical and biological systems. Angew Chem Int Ed Engl 2015; 54:3290-327. [PMID: 25630692 DOI: 10.1002/anie.201408487] [Citation(s) in RCA: 419] [Impact Index Per Article: 46.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2014] [Indexed: 12/13/2022]
Abstract
Structure-based ligand design in medicinal chemistry and crop protection relies on the identification and quantification of weak noncovalent interactions and understanding the role of water. Small-molecule and protein structural database searches are important tools to retrieve existing knowledge. Thermodynamic profiling, combined with X-ray structural and computational studies, is the key to elucidate the energetics of the replacement of water by ligands. Biological receptor sites vary greatly in shape, conformational dynamics, and polarity, and require different ligand-design strategies, as shown for various case studies. Interactions between dipoles have become a central theme of molecular recognition. Orthogonal interactions, halogen bonding, and amide⋅⋅⋅π stacking provide new tools for innovative lead optimization. The combination of synthetic models and biological complexation studies is required to gather reliable information on weak noncovalent interactions and the role of water.
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Affiliation(s)
- Elke Persch
- Laboratorium für Organische Chemie, Departement Chemie und Angewandte Biowissenschaften, ETH Zürich, Vladimir-Prelog-Weg 3, 8093 Zürich (Switzerland)
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20
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Barandun LJ, Ehrmann FR, Zimmerli D, Immekus F, Giroud M, Grünenfelder C, Schweizer WB, Bernet B, Betz M, Heine A, Klebe G, Diederich F. Replacement of Water Molecules in a Phosphate Binding Site by Furanoside-Appendedlin-Benzoguanine Ligands of tRNA-Guanine Transglycosylase (TGT). Chemistry 2014; 21:126-35. [DOI: 10.1002/chem.201405764] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Indexed: 11/09/2022]
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21
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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.
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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
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22
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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.
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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
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23
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Whalen KL, Spies MA. Flooding enzymes: quantifying the contributions of interstitial water and cavity shape to ligand binding using extended linear response free energy calculations. J Chem Inf Model 2013; 53:2349-59. [PMID: 24111836 PMCID: PMC3782002 DOI: 10.1021/ci400244x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
Glutamate
racemase (GR) is a cofactor independent amino acid racemase that has
recently garnered increasing attention as an antimicrobial drug target.
There are numerous high resolution crystal structures of GR, yet these
are invariably bound to either d-glutamate or very weakly
bound oxygen-based salts. Recent in silico screens have identified
a number of new competitive inhibitor scaffolds, which are not based
on d-Glu, but exploit many of the same hydrogen bond donor
positions. In silico studies on 1-H-benzimidazole-2-sulfonic
acid (BISA) show that the sulfonic acid points to the back of the
GR active site, in the most buried region, analogous to the C2-carboxylate
binding position in the GR-d-glutamate complex. Furthermore,
BISA has been shown to be the strongest nonamino acid competitive
inhibitor. Previously published computational studies have suggested
that a portion of this binding strength is derived from complexation
with a more closed active site, relative to weaker ligands, and in
which the internal water network is more isolated from the bulk solvent.
In order to validate key contacts between the buried sulfonate moiety
of BISA and moieties in the back of the enzyme active site, as well
as to probe the energetic importance of the potentially large number
of interstitial waters contacted by the BISA scaffold, we have designed
several mutants of Asn75. GR-N75A removes a key hydrogen bond donor
to the sulfonate of BISA, but also serves to introduce an additional
interstitial water, due to the newly created space of the mutation.
GR- N75L should also show the loss of a hydrogen bond donor to the
sulfonate of BISA, but does not (a priori) seem to permit an additional
interstitial water contact. In order to investigate the dynamics,
structure, and energies of this water-mediated complexation, we have
employed the extended linear response (ELR) approach for the calculation
of binding free energies to GR, using the YASARA2 knowledge based
force field on a set of ten GR complexes, and yielding an R-squared
value of 0.85 and a RMSE of 2.0 kJ/mol. Surprisingly, the inhibitor
set produces a uniformly large interstitial water contribution to
the electrostatic interaction energy (⟨Vel⟩), ranging from 30 to >50%, except for the natural
substrate (d-glutamate), which has only a 7% contribution
of ⟨Vel⟩ from water. The
broader implications for predicting and exploiting significant interstitial
water contacts in ligand–enzyme complexation are discussed.
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Affiliation(s)
- Katie L Whalen
- College of Pharmacy, Division of Medicinal and Natural Products Chemistry, and ‡Carver College of Medicine, Department of Biochemistry, The University of Iowa , Iowa City, Iowa 52242, United States
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24
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Grego A, Müller A, Weinstock IA. Stepwise-Resolved Thermodynamics of Hydrophobic Self-Assembly. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201303083] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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25
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Grego A, Müller A, Weinstock IA. Stepwise-Resolved Thermodynamics of Hydrophobic Self-Assembly. Angew Chem Int Ed Engl 2013; 52:8358-62. [DOI: 10.1002/anie.201303083] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2013] [Indexed: 11/11/2022]
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26
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García-Sosa AT. Hydration Properties of Ligands and Drugs in Protein Binding Sites: Tightly-Bound, Bridging Water Molecules and Their Effects and Consequences on Molecular Design Strategies. J Chem Inf Model 2013; 53:1388-405. [DOI: 10.1021/ci3005786] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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27
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Hewings D, Fedorov O, Filippakopoulos P, Martin S, Picaud S, Tumber A, Wells C, Olcina MM, Freeman K, Gill A, Ritchie AJ, Sheppard DW, Russell AJ, Hammond EM, Knapp S, Brennan PE, Conway SJ. Optimization of 3,5-dimethylisoxazole derivatives as potent bromodomain ligands. J Med Chem 2013; 56:3217-27. [PMID: 23517011 PMCID: PMC3640414 DOI: 10.1021/jm301588r] [Citation(s) in RCA: 110] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2012] [Indexed: 12/14/2022]
Abstract
The bromodomain protein module, which binds to acetylated lysine, is emerging as an important epigenetic therapeutic target. We report the structure-guided optimization of 3,5-dimethylisoxazole derivatives to develop potent inhibitors of the BET (bromodomain and extra terminal domain) bromodomain family with good ligand efficiency. X-ray crystal structures of the most potent compounds reveal key interactions required for high affinity at BRD4(1). Cellular studies demonstrate that the phenol and acetate derivatives of the lead compounds showed strong antiproliferative effects on MV4;11 acute myeloid leukemia cells, as shown for other BET bromodomain inhibitors and genetic BRD4 knockdown, whereas the reported compounds showed no general cytotoxicity in other cancer cell lines tested.
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Affiliation(s)
- David
S. Hewings
- Department of Chemistry, Chemistry
Research Laboratory, University of Oxford, Mansfield Road, Oxford, OX1 3TA, U.K
- Nuffield Department of Clinical
Medicine, Structural Genomics Consortium, University
of Oxford, Old Road Campus Research Building, Roosevelt
Drive, Oxford, OX3 3TA, U.K
| | - Oleg Fedorov
- Nuffield Department of Clinical
Medicine, Structural Genomics Consortium, University
of Oxford, Old Road Campus Research Building, Roosevelt
Drive, Oxford, OX3 3TA, U.K
| | - Panagis Filippakopoulos
- Nuffield Department of Clinical
Medicine, Structural Genomics Consortium, University
of Oxford, Old Road Campus Research Building, Roosevelt
Drive, Oxford, OX3 3TA, U.K
| | - Sarah Martin
- Nuffield Department of Clinical
Medicine, Structural Genomics Consortium, University
of Oxford, Old Road Campus Research Building, Roosevelt
Drive, Oxford, OX3 3TA, U.K
| | - Sarah Picaud
- Nuffield Department of Clinical
Medicine, Structural Genomics Consortium, University
of Oxford, Old Road Campus Research Building, Roosevelt
Drive, Oxford, OX3 3TA, U.K
| | - Anthony Tumber
- Nuffield Department of Clinical
Medicine, Structural Genomics Consortium, University
of Oxford, Old Road Campus Research Building, Roosevelt
Drive, Oxford, OX3 3TA, U.K
| | - Christopher Wells
- Nuffield Department of Clinical
Medicine, Structural Genomics Consortium, University
of Oxford, Old Road Campus Research Building, Roosevelt
Drive, Oxford, OX3 3TA, U.K
| | - Monica M. Olcina
- Department of Oncology, Cancer
Research UK/MRC Gray Institute for Radiation Oncology and Biology, University of Oxford, Old Road Campus Research Building,
Oxford, OX3 7DQ, U.K
| | - Katherine Freeman
- Department of Chemistry, Chemistry
Research Laboratory, University of Oxford, Mansfield Road, Oxford, OX1 3TA, U.K
| | - Andrew Gill
- BioFocus, Chesterford Research Park, Saffron Walden,
Essex, CB10 1XL, U.K
| | - Alison J. Ritchie
- BioFocus, Chesterford Research Park, Saffron Walden,
Essex, CB10 1XL, U.K
| | - David W. Sheppard
- BioFocus, Chesterford Research Park, Saffron Walden,
Essex, CB10 1XL, U.K
| | - Angela J. Russell
- Department of Chemistry, Chemistry
Research Laboratory, University of Oxford, Mansfield Road, Oxford, OX1 3TA, U.K
| | - Ester M. Hammond
- Department of Oncology, Cancer
Research UK/MRC Gray Institute for Radiation Oncology and Biology, University of Oxford, Old Road Campus Research Building,
Oxford, OX3 7DQ, U.K
| | - Stefan Knapp
- Nuffield Department of Clinical
Medicine, Structural Genomics Consortium, University
of Oxford, Old Road Campus Research Building, Roosevelt
Drive, Oxford, OX3 3TA, U.K
| | - Paul E. Brennan
- Nuffield Department of Clinical
Medicine, Structural Genomics Consortium, University
of Oxford, Old Road Campus Research Building, Roosevelt
Drive, Oxford, OX3 3TA, U.K
| | - Stuart J. Conway
- Department of Chemistry, Chemistry
Research Laboratory, University of Oxford, Mansfield Road, Oxford, OX1 3TA, U.K
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28
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Zhu Z, Fahrenbach AC, Li H, Barnes JC, Liu Z, Dyar SM, Zhang H, Lei J, Carmieli R, Sarjeant AA, Stern CL, Wasielewski MR, Stoddart JF. Controlling Switching in Bistable [2]Catenanes by Combining Donor–Acceptor and Radical–Radical Interactions. J Am Chem Soc 2012; 134:11709-20. [DOI: 10.1021/ja3037355] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Zhixue Zhu
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston,
Illinois 60208, United States
| | - Albert C. Fahrenbach
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston,
Illinois 60208, United States
- NanoCentury KAIST Institute
and Graduate School of EEWS (WCU), Korea Advanced Institute of Science and Technology, 373-1 Guseong Dong, Yuseong
Gu, Daejeon 305-701, Republic of Korea
| | - Hao Li
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston,
Illinois 60208, United States
| | - Jonathan C. Barnes
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston,
Illinois 60208, United States
- NanoCentury KAIST Institute
and Graduate School of EEWS (WCU), Korea Advanced Institute of Science and Technology, 373-1 Guseong Dong, Yuseong
Gu, Daejeon 305-701, Republic of Korea
| | - Zhichang Liu
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston,
Illinois 60208, United States
| | - Scott M. Dyar
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston,
Illinois 60208, United States
- Argonne-Northwestern Solar Energy
Research (ANSER) Center, Northwestern University, Evanston, Illinois 60208, United States
| | - Huacheng Zhang
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston,
Illinois 60208, United States
| | - Juying Lei
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston,
Illinois 60208, United States
| | - Raanan Carmieli
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston,
Illinois 60208, United States
- Argonne-Northwestern Solar Energy
Research (ANSER) Center, Northwestern University, Evanston, Illinois 60208, United States
| | - Amy A. Sarjeant
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston,
Illinois 60208, United States
| | - Charlotte L. Stern
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston,
Illinois 60208, United States
| | - Michael R. Wasielewski
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston,
Illinois 60208, United States
- Argonne-Northwestern Solar Energy
Research (ANSER) Center, Northwestern University, Evanston, Illinois 60208, United States
| | - J. Fraser Stoddart
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston,
Illinois 60208, United States
- NanoCentury KAIST Institute
and Graduate School of EEWS (WCU), Korea Advanced Institute of Science and Technology, 373-1 Guseong Dong, Yuseong
Gu, Daejeon 305-701, Republic of Korea
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29
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Barandun LJ, Immekus F, Kohler PC, Tonazzi S, Wagner B, Wendelspiess S, Ritschel T, Heine A, Kansy M, Klebe G, Diederich F. From lin-benzoguanines to lin-benzohypoxanthines as ligands for Zymomonas mobilis tRNA-guanine transglycosylase: replacement of protein-ligand hydrogen bonding by importing water clusters. Chemistry 2012; 18:9246-57. [PMID: 22736391 DOI: 10.1002/chem.201200809] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2012] [Indexed: 11/12/2022]
Abstract
The foodborne illness shigellosis is caused by Shigella bacteria that secrete the highly cytotoxic Shiga toxin, which is also formed by the closely related enterohemorrhagic Escherichia coli (EHEC). It has been shown that tRNA-guanine transglycosylase (TGT) is essential for the pathogenicity of Shigella flexneri. Herein, the molecular recognition properties of a guanine binding pocket in Zymomonas mobilis TGT are investigated with a series of lin-benzohypoxanthine- and lin-benzoguanine-based inhibitors that bear substituents to occupy either the ribose-33 or the ribose-34 pocket. The three inhibitor scaffolds differ by the substituent at C(6) being H, NH(2), or NH-alkyl. These differences lead to major changes in the inhibition constants, pK(a) values, and binding modes. Compared to the lin-benzoguanines, with an exocyclic NH(2) at C(6), the lin-benzohypoxanthines without an exocyclic NH(2) group have a weaker affinity as several ionic protein-ligand hydrogen bonds are lost. X-ray cocrystal structure analysis reveals that a new water cluster is imported into the space vacated by the lacking NH(2) group and by a conformational shift of the side chain of catalytic Asp102. In the presence of an N-alkyl group at C(6) in lin-benzoguanine ligands, this water cluster is largely maintained but replacement of one of the water molecules in the cluster leads to a substantial loss in binding affinity. This study provides new insight into the role of water clusters at enzyme active sites and their challenging substitution by ligand parts, a topic of general interest in contemporary structure-based drug design.
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Affiliation(s)
- Luzi Jakob Barandun
- Laboratorium für Organische Chemie, ETH Zürich, Hönggerberg, HCI, 8093 Zurich, Switzerland
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30
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Fabris F, De Lucchi O, Nardini I, Crisma M, Mazzanti A, Mason SA, Lemée-Cailleau MH, Scaramuzzo FA, Zonta C. (+)-syn-Benzotriborneol an enantiopure C3-symmetric receptor for water. Org Biomol Chem 2012; 10:2464-9. [PMID: 22349254 DOI: 10.1039/c2ob06774a] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
(+)-syn-Benzotriborneol forms stable complexes with one molecule of water. This is due to the ability of the host to form three hydrogen bonds with water, to act simultaneously as a hydrogen-bond acceptor and donor, and to a perfect geometrical match between the pair. We report experimental (X-ray and neutron diffraction, VT NMR, DSC, TGA) and stereochemical studies carried out to elucidate and quantify the molecular and thermodynamic aspects of this supramolecular complex.
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Affiliation(s)
- Fabrizio Fabris
- Dipartimento di Scienze Molecolari e Nanosistemi, Università Ca' Foscari di Venezia Dorsoduro 2137, I-30123, Venezia, Italy.
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31
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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]
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32
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Salonen LM, Holland MC, Kaib PSJ, Haap W, Benz J, Mary JL, Kuster O, Schweizer WB, Banner DW, Diederich F. Molecular recognition at the active site of factor Xa: cation-π interactions, stacking on planar peptide surfaces, and replacement of structural water. Chemistry 2011; 18:213-22. [PMID: 22162109 DOI: 10.1002/chem.201102571] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2011] [Indexed: 11/10/2022]
Abstract
Factor Xa, a serine protease from the blood coagulation cascade, is an ideal enzyme for molecular recognition studies, as its active site is highly shape-persistent and features distinct, concave sub-pockets. We developed a family of non-peptidic, small-molecule inhibitors with a central tricyclic core orienting a neutral heterocyclic substituent into the S1 pocket and a quaternary ammonium ion into the aromatic box in the S4 pocket. The substituents were systematically varied to investigate cation-π interactions in the S4 pocket, optimal heterocyclic stacking on the flat peptide walls lining the S1 pocket, and potential water replacements in both the S1 and the S4 pockets. Structure-activity relationships were established to reveal and quantify contributions to the binding free enthalpy, resulting from single-atom replacements or positional changes in the ligands. A series of high-affinity ligands with inhibitory constants down to K(i)=2 nM were obtained and their proposed binding geometries confirmed by X-ray co-crystal structures of protein-ligand complexes.
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Affiliation(s)
- Laura M Salonen
- Laboratorium für Organische Chemie, ETH Zürich, Wolfgang-Pauli-Strasse 10, HCI, 8093 Zürich, Switzerland
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33
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Hardegger LA, Kuhn B, Spinnler B, Anselm L, Ecabert R, Stihle M, Gsell B, Thoma R, Diez J, Benz J, Plancher JM, Hartmann G, Isshiki Y, Morikami K, Shimma N, Haap W, Banner DW, Diederich F. Halogen bonding at the active sites of human cathepsin L and MEK1 kinase: efficient interactions in different environments. ChemMedChem 2011; 6:2048-54. [PMID: 21898833 DOI: 10.1002/cmdc.201100353] [Citation(s) in RCA: 104] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2011] [Indexed: 01/25/2023]
Abstract
In two series of small-molecule ligands, one inhibiting human cathepsin L (hcatL) and the other MEK1 kinase, biological affinities were found to strongly increase when an aryl ring of the inhibitors is substituted with the larger halogens Cl, Br, and I, but to decrease upon F substitution. X-ray co-crystal structure analyses revealed that the higher halides engage in halogen bonding (XB) with a backbone C=O in the S3 pocket of hcatL and in a back pocket of MEK1. While the S3 pocket is located at the surface of the enzyme, which provides a polar environment, the back pocket in MEK1 is deeply buried in the protein and is of pronounced apolar character. This study analyzes environmental effects on XB in protein-ligand complexes. It is hypothesized that energetic gains by XB are predominantly not due to water replacements but originate from direct interactions between the XB donor (Caryl-X) and the XB acceptor (C=O) in the correct geometry. New X-ray co-crystal structures in the same crystal form (space group P2(1)2(1)2(1)) were obtained for aryl chloride, bromide, and iodide ligands bound to hcatL. These high-resolution structures reveal that the backbone C=O group of Gly61 in most hcatL co-crystal structures maintains water solvation while engaging in XB. An aryl-CF3-substituted ligand of hcatL with an unexpectedly high affinity was found to adopt the same binding geometry as the aryl halides, with the CF3 group pointing to the C=O group of Gly61 in the S3 pocket. In this case, a repulsive F2C-F⋅⋅⋅O=C contact apparently is energetically overcompensated by other favorable protein-ligand contacts established by the CF3 group.
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Affiliation(s)
- Leo A Hardegger
- Laboratorium für Organische Chemie, ETH Zürich, Wolfgang-Pauli-Strasse 10, HCI, 8093 Zürich, Switzerland
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34
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Witschel MC, Höffken HW, Seet M, Parra L, Mietzner T, Thater F, Niggeweg R, Röhl F, Illarionov B, Rohdich F, Kaiser J, Fischer M, Bacher A, Diederich F. Inhibitoren des Herbizid-Targets IspD: Bindung in einer allosterischen Tasche. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201102281] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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35
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Witschel MC, Höffken HW, Seet M, Parra L, Mietzner T, Thater F, Niggeweg R, Röhl F, Illarionov B, Rohdich F, Kaiser J, Fischer M, Bacher A, Diederich F. Inhibitors of the Herbicidal Target IspD: Allosteric Site Binding. Angew Chem Int Ed Engl 2011; 50:7931-5. [DOI: 10.1002/anie.201102281] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2011] [Indexed: 11/07/2022]
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36
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Salonen LM, Ellermann M, Diederich F. Aromatische Ringe in chemischer und biologischer Erkennung: Energien und Strukturen. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201007560] [Citation(s) in RCA: 245] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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37
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Salonen LM, Ellermann M, Diederich F. Aromatic rings in chemical and biological recognition: energetics and structures. Angew Chem Int Ed Engl 2011; 50:4808-42. [PMID: 21538733 DOI: 10.1002/anie.201007560] [Citation(s) in RCA: 1165] [Impact Index Per Article: 89.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2010] [Indexed: 12/12/2022]
Abstract
This review describes a multidimensional treatment of molecular recognition phenomena involving aromatic rings in chemical and biological systems. It summarizes new results reported since the appearance of an earlier review in 2003 in host-guest chemistry, biological affinity assays and biostructural analysis, data base mining in the Cambridge Structural Database (CSD) and the Protein Data Bank (PDB), and advanced computational studies. Topics addressed are arene-arene, perfluoroarene-arene, S⋅⋅⋅aromatic, cation-π, and anion-π interactions, as well as hydrogen bonding to π systems. The generated knowledge benefits, in particular, structure-based hit-to-lead development and lead optimization both in the pharmaceutical and in the crop protection industry. It equally facilitates the development of new advanced materials and supramolecular systems, and should inspire further utilization of interactions with aromatic rings to control the stereochemical outcome of synthetic transformations.
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Affiliation(s)
- Laura M Salonen
- Laboratory of Organic Chemistry, Department of Chemistry and Applied Biosciences, ETH Zurich, Hönggerberg, HCI, 8093 Zurich, Switzerland
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38
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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
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