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Li J, Moumbock AFA, Qaseem A, Xu Q, Feng Y, Wang D, Günther S. AroCageDB: A Web-Based Resource for Aromatic Cage Binding Sites and Their Intrinsic Ligands. J Chem Inf Model 2021; 61:5327-5330. [PMID: 34738791 DOI: 10.1021/acs.jcim.1c00927] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
While aromatic cages have extensively been investigated in the context of structural biology, molecular recognition, and drug discovery, there exist to date no comprehensive resource for proteins sharing this conserved structural motif. To this end, we parsed the Protein Data Bank and thus constructed the Aromatic Cage Database (AroCageDB), a database for investigating the binding pocket descriptors and ligand binding space of aromatic-cage-containing proteins (ACCPs). AroCageDB contains 487 unique ACCPs bound to 890 unique ligands, for a total of 1636 complexes. This web-accessible database provides a user-friendly interface for the interactive visualization of ligand-bound ACCP structures, with a variety of search options that will open up opportunities for structural analyses and drug discovery campaigns. AroCageDB is freely available at http://www.pharmbioinf.uni-freiburg.de/arocagedb/.
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Affiliation(s)
- Jianyu Li
- Institute of Pharmaceutical Sciences, Faculty of Chemistry and Pharmacy, Albert-Ludwigs-Universität Freiburg, Hermann-Herder-Straße 9, D-79104 Freiburg, Germany
| | - Aurélien F A Moumbock
- Institute of Pharmaceutical Sciences, Faculty of Chemistry and Pharmacy, Albert-Ludwigs-Universität Freiburg, Hermann-Herder-Straße 9, D-79104 Freiburg, Germany
| | - Ammar Qaseem
- Institute of Pharmaceutical Sciences, Faculty of Chemistry and Pharmacy, Albert-Ludwigs-Universität Freiburg, Hermann-Herder-Straße 9, D-79104 Freiburg, Germany
| | - Qianqing Xu
- Institute of Pharmaceutical Sciences, Faculty of Chemistry and Pharmacy, Albert-Ludwigs-Universität Freiburg, Hermann-Herder-Straße 9, D-79104 Freiburg, Germany
| | - Yue Feng
- Institute of Pharmaceutical Sciences, Faculty of Chemistry and Pharmacy, Albert-Ludwigs-Universität Freiburg, Hermann-Herder-Straße 9, D-79104 Freiburg, Germany
| | - Dan Wang
- Institute of Pharmaceutical Sciences, Faculty of Chemistry and Pharmacy, Albert-Ludwigs-Universität Freiburg, Hermann-Herder-Straße 9, D-79104 Freiburg, Germany
| | - Stefan Günther
- Institute of Pharmaceutical Sciences, Faculty of Chemistry and Pharmacy, Albert-Ludwigs-Universität Freiburg, Hermann-Herder-Straße 9, D-79104 Freiburg, Germany
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2
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Horenstein NA, Stokes C, Papke RL. Sulfonium Ligands of the α7 nAChR. Molecules 2021; 26:5643. [PMID: 34577114 PMCID: PMC8464850 DOI: 10.3390/molecules26185643] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 09/13/2021] [Accepted: 09/13/2021] [Indexed: 11/16/2022] Open
Abstract
The α7 nicotinic acetylcholine receptor (nAChR) is an important target given its role in cognitive function as well as in the cholinergic anti-inflammatory pathway, where ligands that are effective at stabilizing desensitized states of the receptor are of particular interest. The typical structural element associated with a good desensitizer is the ammonium pharmacophore, but recent work has identified that a trivalent sulfur, in the positively charged sulfonium form, can substitute for the nitrogen in the ammonium pharmacophore. However, the breadth and scope of employing the sulfonium group is largely unexplored. In this work, we have surveyed a disparate group of sulfonium compounds for their functional activity with α7 as well as other nAChR subtypes. Amongst them, we found that there is a wide range of ability to induce α7 desensitization, with 4-hydroxyphenyldimethylsulfonium and suplatast sulfonium salts being the most desensitizing. The smallest sulfonium compound, trimethylsulfonium, was a partial agonist for α7 and other neuronal nAChR. Molecular docking into the α7 receptor extracellular domain revealed preferred poses in the orthosteric binding site for all but one compound, with typical cation-pi interactions as seen with traditional ammonium compounds. A number of the compounds tested may serve as useful platforms for further development of α7 desensitizing ability and for receptor subtype selectivity.
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Affiliation(s)
| | - Clare Stokes
- Department of Pharmacology and Therapeutics, University of Florida, Gainesville, FL 32610-0267, USA; (C.S.); (R.L.P.)
| | - Roger L. Papke
- Department of Pharmacology and Therapeutics, University of Florida, Gainesville, FL 32610-0267, USA; (C.S.); (R.L.P.)
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Debyser Z, Bruggemans A, Van Belle S, Janssens J, Christ F. LEDGINs, Inhibitors of the Interaction Between HIV-1 Integrase and LEDGF/p75, Are Potent Antivirals with a Potential to Cure HIV Infection. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1322:97-114. [PMID: 34258738 DOI: 10.1007/978-981-16-0267-2_4] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
Abstract
A permanent cure remains the greatest challenge in the field of HIV research. In order to reach this goal, a profound understanding of the molecular mechanisms controlling HIV integration and transcription is needed. Here we provide an overview of recent advances in the field. Lens epithelium-derived growth factor p75 (LEDGF/p75), a transcriptional coactivator, tethers and targets the HIV integrase into transcriptionally active regions of the chromatin through an interaction with the epigenetic mark H3K36me2/3. This finding prompted us to propose a "block-and-lock" strategy to retarget HIV integration into deep latency. A decade ago, we pioneered protein-protein interaction inhibitors for HIV and discovered LEDGINs. LEDGINs are small molecule inhibitors of the interaction between the integrase binding domain (IBD) of LEDGF/p75 and HIV integrase. They modify integration site selection and therefore might be molecules with a "block-and-lock" mechanism of action. Here we will describe how LEDGINs may become part in the future functional cure strategies.
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Affiliation(s)
- Zeger Debyser
- Molecular Virology and Gene Therapy, Department of Pharmacological and Pharmaceutical Sciences, KU Leuven, Leuven, Belgium.
| | - Anne Bruggemans
- Molecular Virology and Gene Therapy, Department of Pharmacological and Pharmaceutical Sciences, KU Leuven, Leuven, Belgium
| | - Siska Van Belle
- Molecular Virology and Gene Therapy, Department of Pharmacological and Pharmaceutical Sciences, KU Leuven, Leuven, Belgium
| | - Julie Janssens
- Molecular Virology and Gene Therapy, Department of Pharmacological and Pharmaceutical Sciences, KU Leuven, Leuven, Belgium
| | - Frauke Christ
- Molecular Virology and Gene Therapy, Department of Pharmacological and Pharmaceutical Sciences, KU Leuven, Leuven, Belgium
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Li J, Moumbock AFA, Günther S. Exploring Cocrystallized Aromatic Cage Binders to Target Histone Methylation Reader Proteins. J Chem Inf Model 2020; 60:5225-5233. [DOI: 10.1021/acs.jcim.0c00765] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Jianyu Li
- Institute of Pharmaceutical Sciences, Albert-Ludwigs-Universität Freiburg, Hermann-Herder-Straße 9, D-79104 Freiburg, Germany
| | - Aurélien F. A. Moumbock
- Institute of Pharmaceutical Sciences, Albert-Ludwigs-Universität Freiburg, Hermann-Herder-Straße 9, D-79104 Freiburg, Germany
| | - Stefan Günther
- Institute of Pharmaceutical Sciences, Albert-Ludwigs-Universität Freiburg, Hermann-Herder-Straße 9, D-79104 Freiburg, Germany
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5
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Protein-protein and protein-chromatin interactions of LEDGF/p75 as novel drug targets. DRUG DISCOVERY TODAY. TECHNOLOGIES 2017; 24:25-31. [PMID: 29233296 DOI: 10.1016/j.ddtec.2017.11.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Revised: 11/02/2017] [Accepted: 11/09/2017] [Indexed: 11/21/2022]
Abstract
Lens epithelium-derived growth factor p75 (LEDGF/p75), a transcriptional co-activator, plays an important role in tethering protein complexes to the chromatin. Through this tethering function LEDGF/p75 is implicated in a diverse set of human diseases including HIV infection and mixed lineage leukemia, an aggressive form of cancer with poor prognosis. Here we provide an overview of recent progress in resolving protein-protein and protein-chromatin interaction mechanisms of LEDGF/p75. This review will focus on two well-characterized domains, the PWWP domain and the integrase binding domain (IBD). The PWWP domain interacts with methylated lysine 36 in histone H3, a marker of actively transcribed genes. The IBD interacts with the IBD binding motif, available in cellular binding partners of LEDGF/p75. Each domain forms an interesting new target for drug discovery.
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Abstract
A network of reader proteins and enzymes precisely controls gene transcription through the dynamic addition, removal, and recognition of post-translational modifications (PTMs) of histone tails. Histone PTMs work in concert with this network to regulate gene transcription through the histone code, and the dysregulation of PTM maintenance is linked to a large number of diseases, including many types of cancer. A wealth of research aims to elucidate the functions of this code, but our understanding of the effects of PTMs, specifically the methylation of lysine (Lys) and arginine (Arg), is lacking. The development of new tools to study PTMs relies on a sophisticated understanding of the mechanisms that drive protein and small molecule recognition in water. In this review, we outline the physical organic concepts that drive the molecular recognition of Lys and Arg methylation by reader proteins and draw comparisons to the binding mechanisms of small molecule receptors for methylated Lys and Arg that have been developed recently.
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Affiliation(s)
- Joshua E. Beaver
- Department of Chemistry, University of North Carolina, CB 3290, Chapel Hill, North Carolina 27599, United States
| | - Marcey L. Waters
- Department of Chemistry, University of North Carolina, CB 3290, Chapel Hill, North Carolina 27599, United States
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Wagner T, Robaa D, Sippl W, Jung M. Mind the Methyl: Methyllysine Binding Proteins in Epigenetic Regulation. ChemMedChem 2014; 9:466-83. [DOI: 10.1002/cmdc.201300422] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2013] [Indexed: 11/07/2022]
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Blancafort P, Jin J, Frye S. Writing and rewriting the epigenetic code of cancer cells: from engineered proteins to small molecules. Mol Pharmacol 2012; 83:563-76. [PMID: 23150486 DOI: 10.1124/mol.112.080697] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
The epigenomic era has revealed a well-connected network of molecular processes that shape the chromatin landscape. These processes comprise abnormal methylomes, transcriptosomes, genome-wide histone post-transcriptional modifications patterns, histone variants, and noncoding RNAs. The mapping of these processes in large scale by chromatin immunoprecipitation sequencing and other methodologies in both cancer and normal cells reveals novel therapeutic opportunities for anticancer intervention. The goal of this minireview is to summarize pharmacological strategies to modify the epigenetic landscape of cancer cells. These approaches include the use of novel small molecule inhibitors of epigenetic processes specifically deregulated in cancer cells and the design of engineered proteins able to stably reprogram the epigenetic code in cancer cells in a way that is similar to normal cells.
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Affiliation(s)
- Pilar Blancafort
- School of Anatomy, Physiology, and Human Biology, M309, the University of Western Australia, 35 Stirling Highway, Crawley, 6009, WA, Australia.
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Lu Q, Quinn AM, Patel MP, Semus SF, Graves AP, Bandyopadhyay D, Pope AJ, Thrall SH. Perspectives on the discovery of small-molecule modulators for epigenetic processes. ACTA ACUST UNITED AC 2012; 17:555-71. [PMID: 22392809 DOI: 10.1177/1087057112437763] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Epigenetic gene regulation is a critical process controlling differentiation and development, the malfunction of which may underpin a variety of diseases. In this article, we review the current landscape of small-molecule epigenetic modulators including drugs on the market, key compounds in clinical trials, and chemical probes being used in epigenetic mechanistic studies. Hit identification strategies for the discovery of small-molecule epigenetic modulators are summarized with respect to writers, erasers, and readers of histone marks. Perspectives are provided on opportunities for new hit discovery approaches, some of which may define the next generation of therapeutic intervention strategies for epigenetic processes.
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Affiliation(s)
- Quinn Lu
- GlaxoSmithKline, Collegeville, Pennsylvania, USA.
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Daze KD, Pinter T, Beshara CS, Ibraheem A, Minaker SA, Ma MCF, Courtemanche RJM, Campbell RE, Hof F. Supramolecular hosts that recognize methyllysines and disrupt the interaction between a modified histone tail and its epigenetic reader protein. Chem Sci 2012. [DOI: 10.1039/c2sc20583a] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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12
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Orabi EA, Lamoureux G. Cation−π and π–π Interactions in Aqueous Solution Studied Using Polarizable Potential Models. J Chem Theory Comput 2011; 8:182-93. [DOI: 10.1021/ct200569x] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Esam A. Orabi
- Department of Chemistry and Biochemistry and Centre for Research in Molecular Modeling, Concordia University, Montréal, Québec H4B 1R6, Canada
| | - Guillaume Lamoureux
- Department of Chemistry and Biochemistry and Centre for Research in Molecular Modeling, Concordia University, Montréal, Québec H4B 1R6, Canada
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Eisert RJ, Waters ML. Tuning HP1α Chromodomain Selectivity for Di- and Trimethyllysine. Chembiochem 2011; 12:2786-90. [DOI: 10.1002/cbic.201100555] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2011] [Indexed: 01/16/2023]
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Herold JM, Ingerman LA, Gao C, Frye SV. Drug discovery toward antagonists of methyl-lysine binding proteins. CURRENT CHEMICAL GENOMICS 2011; 5:51-61. [PMID: 22145013 PMCID: PMC3229088 DOI: 10.2174/1875397301005010051] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/26/2011] [Revised: 02/22/2011] [Accepted: 04/25/2011] [Indexed: 12/04/2022]
Abstract
The recognition of methyl-lysine and -arginine residues on both histone and other proteins by specific "reader" elements is important for chromatin regulation, gene expression, and control of cell-cycle progression. Recently the crucial role of these reader proteins in cancer development and dedifferentiation has emerged, owing to the increased interest among the scientific community. The methyl-lysine and -arginine readers are a large and very diverse set of effector proteins and targeting them with small molecule probes in drug discovery will inevitably require a detailed understanding of their structural biology and mechanism of binding. In the following review, the critical elements of methyl-lysine and -arginine recognition will be summarized with respect to each protein family and initial results in assay development, probe design, and drug discovery will be highlighted.
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Affiliation(s)
| | | | | | - Stephen V Frye
- Center for Integrated Chemical Biology and Drug Discovery, UNC Eshelman School of Pharmacy, Division of Medicinal Chemistry and Natural Products, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
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15
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Herold JM, Wigle TJ, Norris JL, Lam R, Korboukh VK, Gao C, Ingerman LA, Kireev DB, Senisterra G, Vedadi M, Tripathy A, Brown PJ, Arrowsmith CH, Jin J, Janzen WP, Frye SV. Small-molecule ligands of methyl-lysine binding proteins. J Med Chem 2011; 54:2504-11. [PMID: 21417280 PMCID: PMC3109722 DOI: 10.1021/jm200045v] [Citation(s) in RCA: 99] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Proteins which bind methylated lysines ("readers" of the histone code) are important components in the epigenetic regulation of gene expression and can also modulate other proteins that contain methyl-lysine such as p53 and Rb. Recognition of methyl-lysine marks by MBT domains leads to compaction of chromatin and a repressed transcriptional state. Antagonists of MBT domains would serve as probes to interrogate the functional role of these proteins and initiate the chemical biology of methyl-lysine readers as a target class. Small-molecule MBT antagonists were designed based on the structure of histone peptide-MBT complexes and their interaction with MBT domains determined using a chemiluminescent assay and ITC. The ligands discovered antagonize native histone peptide binding, exhibiting 5-fold stronger binding affinity to L3MBTL1 than its preferred histone peptide. The first cocrystal structure of a small molecule bound to L3MBTL1 was determined and provides new insights into binding requirements for further ligand design.
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Affiliation(s)
- J. Martin Herold
- Center for Integrated Chemical Biology and Drug Discovery, UNC Eshelman School of Pharmacy, Division of Medicinal Chemistry and Natural Products, University of North Carolina at Chapel Hill Chapel Hill, North Carolina 27599, USA
| | - Tim J. Wigle
- Center for Integrated Chemical Biology and Drug Discovery, UNC Eshelman School of Pharmacy, Division of Medicinal Chemistry and Natural Products, University of North Carolina at Chapel Hill Chapel Hill, North Carolina 27599, USA
| | - Jacqueline L. Norris
- Center for Integrated Chemical Biology and Drug Discovery, UNC Eshelman School of Pharmacy, Division of Medicinal Chemistry and Natural Products, University of North Carolina at Chapel Hill Chapel Hill, North Carolina 27599, USA
| | - Robert Lam
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, M5G 1L7, Ontario, Canada
| | - Victoria K. Korboukh
- Center for Integrated Chemical Biology and Drug Discovery, UNC Eshelman School of Pharmacy, Division of Medicinal Chemistry and Natural Products, University of North Carolina at Chapel Hill Chapel Hill, North Carolina 27599, USA
| | - Cen Gao
- Center for Integrated Chemical Biology and Drug Discovery, UNC Eshelman School of Pharmacy, Division of Medicinal Chemistry and Natural Products, University of North Carolina at Chapel Hill Chapel Hill, North Carolina 27599, USA
| | - Lindsey A. Ingerman
- Center for Integrated Chemical Biology and Drug Discovery, UNC Eshelman School of Pharmacy, Division of Medicinal Chemistry and Natural Products, University of North Carolina at Chapel Hill Chapel Hill, North Carolina 27599, USA
| | - Dmitri B. Kireev
- Center for Integrated Chemical Biology and Drug Discovery, UNC Eshelman School of Pharmacy, Division of Medicinal Chemistry and Natural Products, University of North Carolina at Chapel Hill Chapel Hill, North Carolina 27599, USA
| | - Guillermo Senisterra
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, M5G 1L7, Ontario, Canada
| | - Masoud Vedadi
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, M5G 1L7, Ontario, Canada
| | - Ashutosh Tripathy
- Department of Biochemistry and Biophysics, UNC Macromolecular Interactions Facility, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Peter J. Brown
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, M5G 1L7, Ontario, Canada
| | - Cheryl H. Arrowsmith
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, M5G 1L7, Ontario, Canada
| | - Jian Jin
- Center for Integrated Chemical Biology and Drug Discovery, UNC Eshelman School of Pharmacy, Division of Medicinal Chemistry and Natural Products, University of North Carolina at Chapel Hill Chapel Hill, North Carolina 27599, USA
| | - William P. Janzen
- Center for Integrated Chemical Biology and Drug Discovery, UNC Eshelman School of Pharmacy, Division of Medicinal Chemistry and Natural Products, University of North Carolina at Chapel Hill Chapel Hill, North Carolina 27599, USA
| | - Stephen V. Frye
- Center for Integrated Chemical Biology and Drug Discovery, UNC Eshelman School of Pharmacy, Division of Medicinal Chemistry and Natural Products, University of North Carolina at Chapel Hill Chapel Hill, North Carolina 27599, USA
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Targeting Methyl Lysine. ANNUAL REPORTS IN MEDICINAL CHEMISTRY 2010. [DOI: 10.1016/s0065-7743(10)45020-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/08/2023]
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