1
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Bernauer T, Nitsche V, Kaiser J, Gertzen CGW, Höfner G, Niessen KV, Seeger T, Steinritz D, Worek F, Gohlke H, Wanner KT, Paintner FF. Synthesis and biological evaluation of novel MB327 analogs as resensitizers for desensitized nicotinic acetylcholine receptors after intoxication with nerve agents. Toxicol Lett 2024; 397:151-162. [PMID: 38759939 DOI: 10.1016/j.toxlet.2024.05.011] [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: 02/12/2024] [Revised: 05/06/2024] [Accepted: 05/14/2024] [Indexed: 05/19/2024]
Abstract
Poisoning with organophosphorus compounds, which can lead to a cholinergic crisis due to the inhibition of acetylcholinesterase and the subsequent accumulation of acetylcholine (ACh) in the synaptic cleft, is a serious problem for which treatment options are currently insufficient. Our approach to broadening the therapeutic spectrum is to use agents that interact directly with desensitized nicotinic acetylcholine receptors (nAChRs) in order to induce functional recovery after ACh overstimulation. Although MB327, one of the most prominent compounds investigated in this context, has already shown positive properties in terms of muscle force recovery, this compound is not suitable for use as a therapeutic agent due to its insufficient potency. By means of in silico studies based on our recently presented allosteric binding pocket at the nAChR, i.e. the MB327-PAM-1 binding site, three promising MB327 analogs with a 4-aminopyridinium ion partial structure (PTM0056, PTM0062, and PTM0063) were identified. In this study, we present the synthesis and biological evaluation of a series of new analogs of the aforementioned compounds with a 4-aminopyridinium ion partial structure (PTM0064-PTM0072), as well as hydroxy-substituted analogs of MB327 (PTMD90-0012 and PTMD90-0015) designed to substitute entropically unfavorable water clusters identified during molecular dynamics simulations. The compounds were characterized in terms of their binding affinity towards the aforementioned binding site by applying the UNC0642 MS Binding Assays and in terms of their muscle force reactivation in rat diaphragm myography. More potent compounds were identified compared to MB327, as some of them showed a higher affinity towards MB327-PAM-1 and also a higher recovery of neuromuscular transmission at lower compound concentrations. To improve the treatment of organophosphate poisoning, direct targeting of nAChRs with appropriate compounds is a key step, and this study is an important contribution to this research.
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Affiliation(s)
- Tamara Bernauer
- Department of Pharmacy - Center for Drug Research, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Valentin Nitsche
- Department of Pharmacy - Center for Drug Research, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Jesko Kaiser
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Christoph G W Gertzen
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Georg Höfner
- Department of Pharmacy - Center for Drug Research, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Karin V Niessen
- Bundeswehr Institute of Pharmacology and Toxicology, Munich, Germany
| | - Thomas Seeger
- Bundeswehr Institute of Pharmacology and Toxicology, Munich, Germany
| | - Dirk Steinritz
- Bundeswehr Institute of Pharmacology and Toxicology, Munich, Germany
| | - Franz Worek
- Bundeswehr Institute of Pharmacology and Toxicology, Munich, Germany
| | - Holger Gohlke
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany; John von Neumann Institute for Computing (NIC), Jülich Supercomputing Centre (JSC), Institute of Biological Information Processing (IBI-7: Structural Biochemistry) & Institute of Bio- and Geosciences (IBG-4: Bioinformatics), Forschungszentrum Jülich, Jülich, Germany
| | - Klaus T Wanner
- Department of Pharmacy - Center for Drug Research, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Franz F Paintner
- Department of Pharmacy - Center for Drug Research, Ludwig-Maximilians-Universität München, Munich, Germany.
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2
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Ordonez-Rubiano SC, Maschinot CA, Wang S, Sood S, Baracaldo-Lancheros LF, Strohmier BP, McQuade AJ, Smith BC, Dykhuizen EC. Rational Design and Development of Selective BRD7 Bromodomain Inhibitors and Their Activity in Prostate Cancer. J Med Chem 2023; 66:11250-11270. [PMID: 37552884 PMCID: PMC10641717 DOI: 10.1021/acs.jmedchem.3c00671] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/10/2023]
Abstract
Bromodomain-containing proteins are readers of acetylated lysine and play important roles in cancer. Bromodomain-containing protein 7 (BRD7) is implicated in multiple malignancies; however, there are no selective chemical probes to study its function in disease. Using crystal structures of BRD7 and BRD9 bromodomains (BDs) bound to BRD9-selective ligands, we identified a binding pocket exclusive to BRD7. We synthesized a series of ligands designed to occupy this binding region and identified two inhibitors with increased selectivity toward BRD7, 1-78 and 2-77, which bind with submicromolar affinity to the BRD7 BD. Our binding mode analyses indicate that these ligands occupy a uniquely accessible binding cleft in BRD7 and maintain key interactions with the asparagine and tyrosine residues critical for acetylated lysine binding. Finally, we validated the utility and selectivity of the compounds in cell-based models of prostate cancer.
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Affiliation(s)
- Sandra C Ordonez-Rubiano
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University. Robert Heine Pharmacy Building 575 Stadium Mall Drive, West Lafayette, Indiana 47907, United States
| | - Chad A Maschinot
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University. Robert Heine Pharmacy Building 575 Stadium Mall Drive, West Lafayette, Indiana 47907, United States
| | - Sijie Wang
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University. Robert Heine Pharmacy Building 575 Stadium Mall Drive, West Lafayette, Indiana 47907, United States
| | - Surbhi Sood
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University. Robert Heine Pharmacy Building 575 Stadium Mall Drive, West Lafayette, Indiana 47907, United States
| | - Luisa F Baracaldo-Lancheros
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University. Robert Heine Pharmacy Building 575 Stadium Mall Drive, West Lafayette, Indiana 47907, United States
| | - Brayden P Strohmier
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University. Robert Heine Pharmacy Building 575 Stadium Mall Drive, West Lafayette, Indiana 47907, United States
| | - Alexander J McQuade
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University. Robert Heine Pharmacy Building 575 Stadium Mall Drive, West Lafayette, Indiana 47907, United States
| | - Brian C Smith
- Department of Biochemistry, Program in Chemical Biology, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, United States
| | - Emily C Dykhuizen
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University. Robert Heine Pharmacy Building 575 Stadium Mall Drive, West Lafayette, Indiana 47907, United States
- Purdue Center for Cancer Research, College of Pharmacy, Purdue University, 201 S University St., West Lafayette, Indiana 47907, United States
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Ravindra MP, Lee M, Dimova S, Steven CF, Bluntzer MTJ, Brunton VG, Hulme AN. Stretching the Bisalkyne Raman Spectral Palette Reveals a New Electrophilic Covalent Motif. Chemistry 2023; 29:e202300953. [PMID: 37014262 PMCID: PMC10946950 DOI: 10.1002/chem.202300953] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Revised: 04/03/2023] [Accepted: 04/04/2023] [Indexed: 04/05/2023]
Abstract
Small heteroaryl-diyne (Het-DY) tags with distinct vibrational frequencies, and physiologically relevant cLog P were designed for multiplexed bioorthogonal Raman imaging. Pd-Cu catalyzed coupling, combined with the use of Lei ligand, was shown to improve overall yields of the desired heterocoupled Het-DY tags, minimizing the production of homocoupled side-products. Spectral data were in agreement with the trends predicted by DFT calculations and systematic introduction of electron- rich/poor rings stretched the frequency limit of aryl-capped diynes (2209-2243 cm-1 ). The improved Log P of these Het-DY tags was evident from their diffuse distribution in cellular uptake studies and functionalizing tags with organelle markers allowed the acquisition of location-specific biological images. LC-MS- and NMR-based assays showed that some heteroaryl-capped internal alkynes are potential nucleophile traps with structure-dependent reactivity. These biocompatible Het-DY tags, equipped with covalent reactivity, open up new avenues for Raman bioorthogonal imaging.
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Affiliation(s)
- Manasa Punaha Ravindra
- School of ChemistryUniversity of EdinburghJoseph Black Building, David Brewster RoadEdinburghEH9 3FJUK
| | - Martin Lee
- Edinburgh Cancer ResearchInstitute of Genetics & CancerUniversity of EdinburghCrewe Road SouthEdinburghEH4 2XRUK
| | - Silviya Dimova
- Edinburgh Cancer ResearchInstitute of Genetics & CancerUniversity of EdinburghCrewe Road SouthEdinburghEH4 2XRUK
| | - Craig F. Steven
- School of ChemistryUniversity of EdinburghJoseph Black Building, David Brewster RoadEdinburghEH9 3FJUK
- Edinburgh Cancer ResearchInstitute of Genetics & CancerUniversity of EdinburghCrewe Road SouthEdinburghEH4 2XRUK
| | - Marie T. J. Bluntzer
- School of ChemistryUniversity of EdinburghJoseph Black Building, David Brewster RoadEdinburghEH9 3FJUK
| | - Valerie G. Brunton
- Edinburgh Cancer ResearchInstitute of Genetics & CancerUniversity of EdinburghCrewe Road SouthEdinburghEH4 2XRUK
| | - Alison N. Hulme
- School of ChemistryUniversity of EdinburghJoseph Black Building, David Brewster RoadEdinburghEH9 3FJUK
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4
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Ali MM, Naz S, Ashraf S, Knapp S, Ul-Haq Z. Epigenetic modulation by targeting bromodomain containing protein 9 (BRD9): Its therapeutic potential and selective inhibition. Int J Biol Macromol 2023; 230:123428. [PMID: 36709803 DOI: 10.1016/j.ijbiomac.2023.123428] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Revised: 01/20/2023] [Accepted: 01/21/2023] [Indexed: 01/27/2023]
Abstract
The bromodomain-containing protein 9, a component of the SWI/SNF chromatin remodeling complex, functions as an 'epigenetic reader' selectively recognizing acetyl-lysine marks. It regulates chromatin structure and gene expression by recruitment of acetylated transcriptional regulators and by modulating the function of remodeling complexes. Recent data suggests that BRD9 plays an important role in regulating cellular growth and it has been suggested to drive progression of several malignant diseases such as cervical cancer, and acute myeloid leukemia. Its role in tumorigenesis suggests that selective BRD9 inhibitors may have therapeutic value in cancer therapy. Currently, there has been increasing interest in developing small molecules that can specifically target BRD9 or the closely related bromodomain protein BRD7. Available chemical probes will help to clarify biological functions of BRD9 and its potential for cancer therapy. Since the report of the first BRD9 inhibitor LP99 in 2015, numerous inhibitors have been developed. In this review, we summarized the biological roles of BRD9, structural details and the progress made in the development of BRD9 inhibitors.
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Affiliation(s)
- Maria Mushtaq Ali
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi-75270, Pakistan
| | - Sehrish Naz
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi-75270, Pakistan
| | - Sajda Ashraf
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi-75270, Pakistan
| | - Stefan Knapp
- Institute for Pharmaceutical Chemistry, Goethe University Frankfurt, Max von Lauestrasse 9, 60438 Frankfurt, Germany; Structural Genomics Consortium, Buchmann Institute for Life Sciences, Goethe University Frankfurt, Max von Lauestrasse 15, 60438 Frankfurt, Germany
| | - Zaheer Ul-Haq
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi-75270, Pakistan.
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5
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Fuchs JR, Schulte BC, Fuchs JW, Agulnik M. Emerging targeted and cellular therapies in the treatment of advanced and metastatic synovial sarcoma. Front Oncol 2023; 13:1123464. [PMID: 36761952 PMCID: PMC9905840 DOI: 10.3389/fonc.2023.1123464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 01/09/2023] [Indexed: 01/26/2023] Open
Abstract
Synovial sarcoma is a soft tissue sarcoma accounting for approximately 1,000 cases per year in the United States. Currently, standard treatment of advanced and metastatic synovial sarcoma is anthracycline-based chemotherapy. While advanced synovial sarcoma is more responsive to chemotherapy compared to other soft tissue sarcomas, survival rates are poor, with a median survival time of less than 18 months. Enhanced understanding of tumor antigen expression and molecular mechanisms behind synovial sarcoma provide potential targets for treatment. Adoptive Cell Transfer using engineered T-cell receptors is in clinical trials for treatment of synovial sarcoma, specifically targeting New York esophageal squamous cell carcinoma-1 (NY-ESO-1), preferentially expressed antigen in melanoma (PRAME), and melanoma antigen-A4 (MAGE-A4). In this review, we explore the opportunities and challenges of these treatments. We also describe artificial adjuvant vector cells (aAVCs) and BRD9 inhibitors, two additional potential targets for treatment of advanced synovial sarcoma. This review demonstrates the progress that has been made in treatment of synovial sarcoma and highlights the future study and qualification needed to implement these technologies as standard of care.
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Affiliation(s)
- Joseph R. Fuchs
- Department of Medicine, McGaw Medical Center of Northwestern University, Chicago, IL, United States
| | - Brian C. Schulte
- Department of Medicine, University of California, San Francisco, San Francisco, CA, United States
| | - Jeffrey W. Fuchs
- Department of Medicine, McGaw Medical Center of Northwestern University, Chicago, IL, United States
| | - Mark Agulnik
- Medical Oncology and Therapeutics Research, City of Hope Comprehensive Cancer Center, Duarte, CA, United States,*Correspondence: Mark Agulnik,
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6
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Ali MM, Ashraf S, Nure-e-Alam M, Qureshi U, Khan KM, Ul-Haq Z. Identification of Selective BRD9 Inhibitor via Integrated Computational Approach. Int J Mol Sci 2022; 23:13513. [PMID: 36362300 PMCID: PMC9655433 DOI: 10.3390/ijms232113513] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 10/25/2022] [Accepted: 10/28/2022] [Indexed: 04/12/2024] Open
Abstract
Bromodomain-containing protein 9 (BRD9), a member of the bromodomain and extra terminal domain (BET) protein family, works as an epigenetic reader. BRD9 has been considered an essential drug target for cancer, inflammatory diseases, and metabolic disorders. Due to its high similarity among other isoforms, no effective treatment of BRD9-associated disorders is available. For the first time, we performed a detailed comparative analysis among BRD9, BRD7, and BRD4. The results indicate that residues His42, Gly43, Ala46, Ala54, Val105, and Leu109 can confer the BRD9 isoform selectivity. The predicted crucial residues were further studied. The pharmacophore model's features were precisely mapped with some key residues including, Gly43, Phe44, Phe45, Asn100, and Tyr106, all of which play a crucial role in BRD9 inhibition. Docking-based virtual screening was utilized with the consideration of the conserved water network in the binding cavity to identify the potential inhibitors of BRD9. In this workflow, 714 compounds were shortlisted. To attain selectivity, 109 compounds were re-docked to BRD7 for negative selection. Finally, four compounds were selected for molecular dynamics studies. Our studies pave the way for the identification of new compounds and their role in causing noticeable, functional differences in isoforms and between orthologues.
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Affiliation(s)
- Maria Mushtaq Ali
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan
| | - Sajda Ashraf
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan
| | - Mohammad Nure-e-Alam
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
| | - Urooj Qureshi
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan
| | - Khalid Mohammed Khan
- H.E.J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan
- Department of Clinical Pharmacy, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam 31441, Saudi Arabia
| | - Zaheer Ul-Haq
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan
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7
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De Vita S, Chini MG, Bifulco G, Lauro G. Insights into the Ligand Binding to Bromodomain-Containing Protein 9 (BRD9): A Guide to the Selection of Potential Binders by Computational Methods. Molecules 2021; 26:molecules26237192. [PMID: 34885774 PMCID: PMC8659208 DOI: 10.3390/molecules26237192] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 11/24/2021] [Accepted: 11/25/2021] [Indexed: 11/16/2022] Open
Abstract
The estimation of the binding of a set of molecules against BRD9 protein was carried out through an in silico molecular dynamics-driven exhaustive analysis to guide the identification of potential novel ligands. Starting from eight crystal structures of this protein co-complexed with known binders and one apo form, we conducted an exhaustive molecular docking/molecular dynamics (MD) investigation. To balance accuracy and an affordable calculation time, the systems were simulated for 100 ns in explicit solvent. Moreover, one complex was simulated for 1 µs to assess the influence of simulation time on the results. A set of MD-derived parameters was computed and compared with molecular docking-derived and experimental data. MM-GBSA and the per-residue interaction energy emerged as the main indicators for the good interaction between the specific binder and the protein counterpart. To assess the performance of the proposed analysis workflow, we tested six molecules featuring different binding affinities for BRD9, obtaining promising outcomes. Further insights were reported to highlight the influence of the starting structure on the molecular dynamics simulations evolution. The data confirmed that a ranking of BRD9 binders using key parameters arising from molecular dynamics is advisable to discard poor ligands before moving on with the synthesis and the biological tests.
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Affiliation(s)
- Simona De Vita
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II 132, 84084 Fisciano, Italy; (S.D.V.); (G.B.)
| | - Maria Giovanna Chini
- Department of Biosciences and Territory, University of Molise, Contrada Fonte Lappone, Pesche, 86090 Isernia, Italy;
| | - Giuseppe Bifulco
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II 132, 84084 Fisciano, Italy; (S.D.V.); (G.B.)
| | - Gianluigi Lauro
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II 132, 84084 Fisciano, Italy; (S.D.V.); (G.B.)
- Correspondence: ; Tel.: +39-(0)89-969176; Fax: +39-(0)89-969602
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8
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Pierri M, Gazzillo E, Chini MG, Ferraro MG, Piccolo M, Maione F, Irace C, Bifulco G, Bruno I, Terracciano S, Lauro G. Introducing structure-based three-dimensional pharmacophore models for accelerating the discovery of selective BRD9 binders. Bioorg Chem 2021; 118:105480. [PMID: 34823196 DOI: 10.1016/j.bioorg.2021.105480] [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: 08/08/2021] [Revised: 11/03/2021] [Accepted: 11/07/2021] [Indexed: 01/18/2023]
Abstract
A well-structured in silico workflow is here reported for disclosing structure-based pharmacophore models against bromodomain-containing protein 9 (BRD9), accelerating virtual screening campaigns and facilitating the identification of novel binders. Specifically, starting from 23 known ligands co-crystallized with BRD9, three-dimensional pharmacophore models, namely placed in a reference protein structure, were developed. Specifically, we here introduce a fragment-related pharmacophore model, useful for the identification of new promising small chemical probes targeting the protein region responsible of the acetyllysine recognition, and two further pharmacophore models useful for the selection of compounds featuring drug-like properties. A pharmacophore-driven virtual screening campaign was then performed to facilitate the selection of new selective BRD9 ligands, starting from a large library of commercially available molecules. The identification of a promising BRD9 binder (7) prompted us to re-iterate this computational workflow on a second focused in-house built library of synthesizable compounds and, eventually, three further novel BRD9 binders were disclosed (8-10). Moreover, all these compounds were tested among a panel comprising other nine bromodomains, showing a high selectivity for BRD9. Preclinical bioscreens for potential anticancer activity highlighted compound 7 as that showing the most promising biological effects, proving the reliability of this in silico pipeline and confirming the applicability of the here introduced structure-based three-dimensional (3D) pharmacophore models as straightforward tools for the selection of new BRD9 ligands.
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Affiliation(s)
- Martina Pierri
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II 132, Fisciano 84084, Italy; PhD Program in Drug Discovery and Development, University of Salerno, Via Giovanni Paolo II 132, Fisciano 84084, Italy
| | - Erica Gazzillo
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II 132, Fisciano 84084, Italy; PhD Program in Drug Discovery and Development, University of Salerno, Via Giovanni Paolo II 132, Fisciano 84084, Italy
| | - Maria Giovanna Chini
- Department of Biosciences and Territory, University of Molise, C.da Fonte Lappone, Pesche 86090, Italy
| | - Maria Grazia Ferraro
- Department of Pharmacy, School of Medicine and Surgery, University of Naples, Via Domenico Montesano 49, Naples 80131, Italy
| | - Marialuisa Piccolo
- Department of Pharmacy, School of Medicine and Surgery, University of Naples, Via Domenico Montesano 49, Naples 80131, Italy
| | - Francesco Maione
- Department of Pharmacy, School of Medicine and Surgery, University of Naples, Via Domenico Montesano 49, Naples 80131, Italy
| | - Carlo Irace
- Department of Pharmacy, School of Medicine and Surgery, University of Naples, Via Domenico Montesano 49, Naples 80131, Italy
| | - Giuseppe Bifulco
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II 132, Fisciano 84084, Italy
| | - Ines Bruno
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II 132, Fisciano 84084, Italy
| | - Stefania Terracciano
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II 132, Fisciano 84084, Italy.
| | - Gianluigi Lauro
- Department of Pharmacy, University of Salerno, Via Giovanni Paolo II 132, Fisciano 84084, Italy.
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9
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Sar S, Guha S, Prabakar T, Maiti D, Sen S. Blue Light-Emitting Diode-Mediated In Situ Generation of Pyridinium and Isoquinolinium Ylides from Aryl Diazoesters: Their Application in the Synthesis of Diverse Dihydroindolizine. J Org Chem 2021; 86:11736-11747. [PMID: 34369766 DOI: 10.1021/acs.joc.1c01209] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Blue light-emitting diode-mediated environmentally sustainable three component reactions among pyridine/isoquinoline 1/2, aryl diazoesters 3, and acrylic ester/3-alkenyl oxindoles 5/6 provide various dihydroindolizines 7 to 9 in excellent yield. The principle of the strategy is photolytic generation of nitrogen ylides from N-heteroarenes and aryl diazoesters and their subsequent [3 + 2] cycloaddition reaction with dipolarophiles. Detailed mechanistic analysis of the transformation through control experiments establishes this strategy as the foundation for the photolytic multicomponent reaction.
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Affiliation(s)
- Saibal Sar
- Department of Chemistry, School of Natural Sciences, Shiv Nadar University Dadri, Chithera, Gautam Buddha Nagar, Uttar Pradesh 201314, India
| | - Souvik Guha
- Department of Chemistry, School of Natural Sciences, Shiv Nadar University Dadri, Chithera, Gautam Buddha Nagar, Uttar Pradesh 201314, India
| | - Tejas Prabakar
- Department of Chemistry, School of Natural Sciences, Shiv Nadar University Dadri, Chithera, Gautam Buddha Nagar, Uttar Pradesh 201314, India
| | - Debajit Maiti
- Department of Chemistry, School of Natural Sciences, Shiv Nadar University Dadri, Chithera, Gautam Buddha Nagar, Uttar Pradesh 201314, India
| | - Subhabrata Sen
- Department of Chemistry, School of Natural Sciences, Shiv Nadar University Dadri, Chithera, Gautam Buddha Nagar, Uttar Pradesh 201314, India
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10
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Wang Q, Shao X, Leung ELH, Chen Y, Yao X. Selectively targeting individual bromodomain: Drug discovery and molecular mechanisms. Pharmacol Res 2021; 172:105804. [PMID: 34450309 DOI: 10.1016/j.phrs.2021.105804] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 08/03/2021] [Accepted: 08/04/2021] [Indexed: 12/21/2022]
Abstract
Bromodomain-containing proteins include bromodomain and extra-terminal (BET) and non-BET families. Due to the conserved bromodomain (BD) module between BD-containing proteins, and especially BETs with each member having two BDs (BD1 and BD2), the high degree of structural similarity makes BD-selective inhibitors much difficult to be designed. However, increasing evidences emphasized that individual BDs had distinct functions and different cellular phenotypes after pharmacological inhibition, and selectively targeting one of the BDs could result in a different efficacy and tolerability profile. This review is to summarize the pioneering progress of BD-selective inhibitors targeting BET and non-BET proteins, focusing on their structural features, biological activity, therapeutic application and experimental/theoretical mechanisms. The present proteolysis targeting chimeras (PROTAC) degraders targeting BDs, and clinical status of BD-selective inhibitors were also analyzed, providing a new insight into future direction of bromodomain-selective drug discovery.
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Affiliation(s)
- Qianqian Wang
- Chronic Disease Research Center, Medical College, Dalian University, Dalian 116622, China
| | - Xiaomin Shao
- Chronic Disease Research Center, Medical College, Dalian University, Dalian 116622, China
| | - Elaine Lai Han Leung
- Dr. Neher's Biophysics Laboratory for Innovative Drug Discovery, State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Taipa, Macau(SAR) 999078, China
| | - Yingqing Chen
- Chronic Disease Research Center, Medical College, Dalian University, Dalian 116622, China.
| | - Xiaojun Yao
- Dr. Neher's Biophysics Laboratory for Innovative Drug Discovery, State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Taipa, Macau(SAR) 999078, China.
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11
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Wanior M, Krämer A, Knapp S, Joerger AC. Exploiting vulnerabilities of SWI/SNF chromatin remodelling complexes for cancer therapy. Oncogene 2021; 40:3637-3654. [PMID: 33941852 PMCID: PMC8154588 DOI: 10.1038/s41388-021-01781-x] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 03/15/2021] [Accepted: 04/06/2021] [Indexed: 02/08/2023]
Abstract
Multi-subunit ATPase-dependent chromatin remodelling complexes SWI/SNF (switch/sucrose non-fermentable) are fundamental epigenetic regulators of gene transcription. Functional genomic studies revealed a remarkable mutation prevalence of SWI/SNF-encoding genes in 20-25% of all human cancers, frequently driving oncogenic programmes. Some SWI/SNF-mutant cancers are hypersensitive to perturbations in other SWI/SNF subunits, regulatory proteins and distinct biological pathways, often resulting in sustained anticancer effects and synthetic lethal interactions. Exploiting these vulnerabilities is a promising therapeutic strategy. Here, we review the importance of SWI/SNF chromatin remodellers in gene regulation as well as mechanisms leading to assembly defects and their role in cancer development. We will focus in particular on emerging strategies for the targeted therapy of SWI/SNF-deficient cancers using chemical probes, including proteolysis targeting chimeras, to induce synthetic lethality.
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Affiliation(s)
- Marek Wanior
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Frankfurt am Main, Germany
- Structural Genomics Consortium (SGC), Buchmann Institute for Molecular Life Sciences (BMLS), Frankfurt am Main, Germany
| | - Andreas Krämer
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Frankfurt am Main, Germany
- Structural Genomics Consortium (SGC), Buchmann Institute for Molecular Life Sciences (BMLS), Frankfurt am Main, Germany
- Frankfurt Cancer Institute (FCI), Frankfurt am Main, Germany
| | - Stefan Knapp
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Frankfurt am Main, Germany.
- Structural Genomics Consortium (SGC), Buchmann Institute for Molecular Life Sciences (BMLS), Frankfurt am Main, Germany.
- Frankfurt Cancer Institute (FCI), Frankfurt am Main, Germany.
- German Translational Cancer Network (DKTK) site Frankfurt/Mainz, Frankfurt am Main, Germany.
| | - Andreas C Joerger
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Frankfurt am Main, Germany.
- Structural Genomics Consortium (SGC), Buchmann Institute for Molecular Life Sciences (BMLS), Frankfurt am Main, Germany.
- German Translational Cancer Network (DKTK) site Frankfurt/Mainz, Frankfurt am Main, Germany.
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12
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Su K, Guo X, Zhu L, Liu Y, Lu Y, Chen B. Indolizine synthesis via radical cyclization and demethylation of sulfoxonium ylides and 2-(pyridin-2-yl)acetate derivatives. Org Chem Front 2021. [DOI: 10.1039/d1qo00550b] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
A novel radical cross-coupling/cyclization of 2-(pyridin-2-yl)acetate derivatives and sulfoxonium ylides is developed, which provides a straightforward access to structurally diverse methylthio-substituted indolizine.
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Affiliation(s)
- Kexin Su
- State Key Laboratory of Applied Organic Chemistry
- Department of Chemistry
- Lanzhou University
- Lanzhou
- China
| | - Xin Guo
- School of Chemistry and Chemical Engineering
- North Minzu University
- Yinchuan
- China
| | - Liangwei Zhu
- State Key Laboratory of Applied Organic Chemistry
- Department of Chemistry
- Lanzhou University
- Lanzhou
- China
| | - Yafeng Liu
- School of Chemistry and Chemical Engineering
- North Minzu University
- Yinchuan
- China
| | - Yixuan Lu
- State Key Laboratory of Applied Organic Chemistry
- Department of Chemistry
- Lanzhou University
- Lanzhou
- China
| | - Baohua Chen
- State Key Laboratory of Applied Organic Chemistry
- Department of Chemistry
- Lanzhou University
- Lanzhou
- China
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13
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Schifferer L, García Mancheño O. Metal‐ and Solvent‐Free, One‐Pot Synthesis of 3‐Unsubstituted Benzoindolizines. European J Org Chem 2020. [DOI: 10.1002/ejoc.202001245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Lukas Schifferer
- Organic Chemistry Institute Münster University Corrensstraße 36 48149 Münster Germany
| | - Olga García Mancheño
- Organic Chemistry Institute Münster University Corrensstraße 36 48149 Münster Germany
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14
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Wanior M, Preuss F, Ni X, Krämer A, Mathea S, Göbel T, Heidenreich D, Simonyi S, Kahnt AS, Joerger AC, Knapp S. Pan-SMARCA/PB1 Bromodomain Inhibitors and Their Role in Regulating Adipogenesis. J Med Chem 2020; 63:14680-14699. [PMID: 33216538 DOI: 10.1021/acs.jmedchem.0c01242] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Accessibility of the human genome is modulated by the ATP-driven SWI/SNF chromatin remodeling multiprotein complexes BAF (BRG1/BRM-associated factor) and PBAF (polybromo-associated BAF factor), which involves reading of acetylated histone tails by the bromodomain-containing proteins SMARCA2 (BRM), SMARCA4 (BRG1), and polybromo-1. Dysregulation of chromatin remodeling leads to aberrant cell proliferation and differentiation. Here, we have characterized a set of potent and cell-active bromodomain inhibitors with pan-selectivity for canonical family VIII bromodomains. Targeted SWI/SNF bromodomain inhibition blocked the expression of key genes during adipogenesis, including the transcription factors PPARγ and C/EBPα, and impaired the differentiation of 3T3-L1 murine fibroblasts into adipocytes. Our data highlight the role of SWI/SNF bromodomains in adipogenesis and provide a framework for the development of SWI/SNF bromodomain inhibitors for indirect targeting of key transcription factors regulating cell differentiation.
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Affiliation(s)
- Marek Wanior
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany.,Structural Genomics Consortium (SGC), Buchmann Institute for Molecular Life Sciences (BMLS), Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | - Franziska Preuss
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany.,Structural Genomics Consortium (SGC), Buchmann Institute for Molecular Life Sciences (BMLS), Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | - Xiaomin Ni
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany.,Structural Genomics Consortium (SGC), Buchmann Institute for Molecular Life Sciences (BMLS), Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | - Andreas Krämer
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany.,Structural Genomics Consortium (SGC), Buchmann Institute for Molecular Life Sciences (BMLS), Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany.,Frankfurt Cancer Institute (FCI), Paul-Ehrlich-Str. 42-44, 60596 Frankfurt am Main, Germany
| | - Sebastian Mathea
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany.,Structural Genomics Consortium (SGC), Buchmann Institute for Molecular Life Sciences (BMLS), Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | - Tamara Göbel
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
| | - David Heidenreich
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany.,Structural Genomics Consortium (SGC), Buchmann Institute for Molecular Life Sciences (BMLS), Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | - Svenja Simonyi
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
| | - Astrid S Kahnt
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
| | - Andreas C Joerger
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany.,Structural Genomics Consortium (SGC), Buchmann Institute for Molecular Life Sciences (BMLS), Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany.,German Translational Cancer Network (DKTK), Frankfurt/Mainz Site, 60438 Frankfurt am Main, Germany
| | - Stefan Knapp
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany.,Structural Genomics Consortium (SGC), Buchmann Institute for Molecular Life Sciences (BMLS), Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany.,German Translational Cancer Network (DKTK), Frankfurt/Mainz Site, 60438 Frankfurt am Main, Germany.,Frankfurt Cancer Institute (FCI), Paul-Ehrlich-Str. 42-44, 60596 Frankfurt am Main, Germany
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15
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Innis SM, Cabot B. GBAF, a small BAF sub-complex with big implications: a systematic review. Epigenetics Chromatin 2020; 13:48. [PMID: 33143733 PMCID: PMC7607862 DOI: 10.1186/s13072-020-00370-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 10/23/2020] [Indexed: 12/01/2022] Open
Abstract
ATP-dependent chromatin remodeling by histone-modifying enzymes and chromatin remodeling complexes is crucial for maintaining chromatin organization and facilitating gene transcription. In the SWI/SNF family of ATP-dependent chromatin remodelers, distinct complexes such as BAF, PBAF, GBAF, esBAF and npBAF/nBAF are of particular interest regarding their implications in cellular differentiation and development, as well as in various diseases. The recently identified BAF subcomplex GBAF is no exception to this, and information is emerging linking this complex and its components to crucial events in mammalian development. Furthermore, given the essential nature of many of its subunits in maintaining effective chromatin remodeling function, it comes as no surprise that aberrant expression of GBAF complex components is associated with disease development, including neurodevelopmental disorders and numerous malignancies. It becomes clear that building upon our knowledge of GBAF and BAF complex function will be essential for advancements in both mammalian reproductive applications and the development of more effective therapeutic interventions and strategies. Here, we review the roles of the SWI/SNF chromatin remodeling subcomplex GBAF and its subunits in mammalian development and disease.
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Affiliation(s)
- Sarah M Innis
- Department of Animal Sciences, Purdue University, West Lafayette, IN, USA
| | - Birgit Cabot
- Department of Animal Sciences, Purdue University, West Lafayette, IN, USA.
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16
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Abstract
INTRODUCTION Indolizines are structural isomers with indoles. Although several indole-based commercial drugs are available in the market, none of the indolizine-based drugs are available up-to-date. Natural and synthetic indolizines have a wide-range of pharmaceutical importance such as antitumor, antimycobacterial, antagonist, and antiproliferative activities. This prompted us to search and collect all possible data about the pharmacological importance of indolizine to open an avenue to the researchers in exploring more medicinal applications of such biologically important compounds. AREAS COVERED The current review article covers the advancements in the biological and pharmacological activities of indolizine-based compounds during the last decade. The covered areas of this work involved anticancer, anti-HIV-1, anti-inflammatory, antimicrobial, anti-tubercular, larvicidal, anti-schizophrenia, CRTh2 antagonist's activities in addition to enzymatic inhibitory activity. EXPERT OPINION The discovery of indolizine drugs will be a major breakthrough as compared with their widely available drug-containing indole isosteres. Major work collected here was focused on anticancer, anti-tubercular, anti-inflammatory, and enzymatic inhibitory activities. The SAR study of the reported biologically active indolizines is summarized throughout the review whenever highlighted to the rationale the behavior of inhibitory action. Several indolizines with certain functions provided great enhancement in the therapeutic activities comparing with reference drugs.
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Affiliation(s)
- Kamal M Dawood
- Department of Chemistry, Faculty of Science, Cairo University , Giza, Egypt
| | - Ashraf A Abbas
- Department of Chemistry, Faculty of Science, Cairo University , Giza, Egypt
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17
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Clegg MA, Bamborough P, Chung CW, Craggs PD, Gordon L, Grandi P, Leveridge M, Lindon M, Liwicki GM, Michon AM, Molnar J, Rioja I, Soden PE, Theodoulou NH, Werner T, Tomkinson NCO, Prinjha RK, Humphreys PG. Application of Atypical Acetyl-lysine Methyl Mimetics in the Development of Selective Inhibitors of the Bromodomain-Containing Protein 7 (BRD7)/Bromodomain-Containing Protein 9 (BRD9) Bromodomains. J Med Chem 2020; 63:5816-5840. [PMID: 32410449 DOI: 10.1021/acs.jmedchem.0c00075] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Non-BET bromodomain-containing proteins have become attractive targets for the development of novel therapeutics targeting epigenetic pathways. To help facilitate the target validation of this class of proteins, structurally diverse small-molecule ligands and methodologies to produce selective inhibitors in a predictable fashion are in high demand. Herein, we report the development and application of atypical acetyl-lysine (KAc) methyl mimetics to take advantage of the differential stability of conserved water molecules in the bromodomain binding site. Discovery of the n-butyl group as an atypical KAc methyl mimetic allowed generation of 31 (GSK6776) as a soluble, permeable, and selective BRD7/9 inhibitor from a pyridazinone template. The n-butyl group was then used to enhance the bromodomain selectivity of an existing BRD9 inhibitor and to transform pan-bromodomain inhibitors into BRD7/9 selective compounds. Finally, a solvent-exposed vector was defined from the pyridazinone template to enable bifunctional molecule synthesis, and affinity enrichment chemoproteomic experiments were used to confirm several of the endogenous protein partners of BRD7 and BRD9, which form part of the chromatin remodeling PBAF and BAF complexes, respectively.
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Affiliation(s)
- Michael A Clegg
- GlaxoSmithKline R&D, Stevenage SG1 2NY, Hertfordshire, United Kingdom.,WestCHEM, Department of Pure and Applied Chemistry, Thomas Graham Building, University of Strathclyde, 295 Cathedral Street, Glasgow G1 1XL, United Kingdom
| | - Paul Bamborough
- GlaxoSmithKline R&D, Stevenage SG1 2NY, Hertfordshire, United Kingdom
| | - Chun-Wa Chung
- GlaxoSmithKline R&D, Stevenage SG1 2NY, Hertfordshire, United Kingdom
| | - Peter D Craggs
- GlaxoSmithKline R&D, Stevenage SG1 2NY, Hertfordshire, United Kingdom
| | - Laurie Gordon
- GlaxoSmithKline R&D, Stevenage SG1 2NY, Hertfordshire, United Kingdom
| | - Paola Grandi
- Cellzome GmbH, R&D MST GlaxoSmithKline, Meyerhofstrasse 1 69117 Heidelberg, Germany
| | - Melanie Leveridge
- GlaxoSmithKline R&D, Stevenage SG1 2NY, Hertfordshire, United Kingdom
| | - Matthew Lindon
- GlaxoSmithKline R&D, Stevenage SG1 2NY, Hertfordshire, United Kingdom
| | - Gemma M Liwicki
- GlaxoSmithKline R&D, Stevenage SG1 2NY, Hertfordshire, United Kingdom
| | - Anne-Marie Michon
- Cellzome GmbH, R&D MST GlaxoSmithKline, Meyerhofstrasse 1 69117 Heidelberg, Germany
| | - Judit Molnar
- GlaxoSmithKline R&D, Stevenage SG1 2NY, Hertfordshire, United Kingdom
| | - Inmaculada Rioja
- GlaxoSmithKline R&D, Stevenage SG1 2NY, Hertfordshire, United Kingdom
| | - Peter E Soden
- GlaxoSmithKline R&D, Stevenage SG1 2NY, Hertfordshire, United Kingdom
| | - Natalie H Theodoulou
- GlaxoSmithKline R&D, Stevenage SG1 2NY, Hertfordshire, United Kingdom.,WestCHEM, Department of Pure and Applied Chemistry, Thomas Graham Building, University of Strathclyde, 295 Cathedral Street, Glasgow G1 1XL, United Kingdom
| | - Thilo Werner
- Cellzome GmbH, R&D MST GlaxoSmithKline, Meyerhofstrasse 1 69117 Heidelberg, Germany
| | - Nicholas C O Tomkinson
- WestCHEM, Department of Pure and Applied Chemistry, Thomas Graham Building, University of Strathclyde, 295 Cathedral Street, Glasgow G1 1XL, United Kingdom
| | - Rab K Prinjha
- GlaxoSmithKline R&D, Stevenage SG1 2NY, Hertfordshire, United Kingdom
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18
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Wang LF, Wang Y, Yang ZY, Zhao J, Sun HB, Wu SL. Revealing binding selectivity of inhibitors toward bromodomain-containing proteins 2 and 4 using multiple short molecular dynamics simulations and free energy analyses. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2020; 31:373-398. [PMID: 32496901 DOI: 10.1080/1062936x.2020.1748107] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 03/24/2020] [Indexed: 06/11/2023]
Abstract
Emerging evidences indicate bromodomain-containing proteins 2 and 4 (BRD2 and BRD4) play critical roles in cancers, inflammations, cardiovascular diseases and other pathologies. Multiple short molecular dynamics (MSMD) simulations combined with molecular mechanics generalized Born surface area (MM-GBSA) method were applied to investigate the binding selectivity of three inhibitors 87D, 88M and 89G towards BRD2 over BRD4. The root-mean-square fluctuation (RMSF) analysis indicates that the structural flexibility of BRD4 is stronger than that of BRD2. Moreover the calculated distances between the Cα atoms in the centres of the ZA_loop and BC_loop of BRD4 are also bigger than that of BRD2. The rank of binding free energies calculated using MM-GBSA method agrees well with that determined by experimental data. The results show that 87D can bind more favourably to BRD2 than BRD4, while 88M has better selectivity on BRD4 over BRD2. Residue-based free-energy decomposition method was utilized to estimate the inhibitor-residue interaction spectrum and the results not only identify the hot interaction spots of inhibitors with BRD2 and BRD4, but also demonstrate that several common residues, including (W370, W374), (P371, P375), (V376, V380) and (L381, L385) belonging to (BRD2, BRD4), generate significant binding difference of inhibitors to BRD2 and BRD4.
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Affiliation(s)
- L F Wang
- School of Science, Shandong Jiaotong University , Jinan, China
| | - Y Wang
- School of Science, Shandong Jiaotong University , Jinan, China
| | - Z Y Yang
- Department of Physics, Jiangxi Agricultural University , Nanchang, China
| | - J Zhao
- School of Science, Shandong Jiaotong University , Jinan, China
| | - H B Sun
- School of Science, Shandong Jiaotong University , Jinan, China
| | - S L Wu
- School of Science, Shandong Jiaotong University , Jinan, China
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19
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Wang Y, Wang LF, Zhang LL, Sun HB, Zhao J. Molecular mechanism of inhibitor bindings to bromodomain-containing protein 9 explored based on molecular dynamics simulations and calculations of binding free energies. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2020; 31:149-170. [PMID: 31851834 DOI: 10.1080/1062936x.2019.1701075] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 12/02/2019] [Indexed: 06/10/2023]
Abstract
Recently, bromodomain-containing protein 9 (BRD9) has been a prospective therapeutic target for anticancer drug design. Molecular dynamics (MD) simulations combined with molecular mechanics generalized Born surface area (MM-GBSA) method were adopted to explore binding modes of three inhibitors (5SW, 5U2, and 5U6) to BRD9 and identify the hot spot of the inhibitor-BRD9 binding. The results indicate that the inhibitor 5SW has the strongest binding ability to BRD9 among the current three inhibitors. Furthermore, the rank of the binding free energies predicted by MM-GBSA approach agrees with that determined by the experimental values. In addition, inhibitor-residue interactions were computed by using residue-based free-energy decomposition method and the results suggest that residue His42 produces the CH-H interactions, residues Asn100, Ile53 and Val49 produce the CH-[Formula: see text] interactions with three inhibitors and Tyr106, Phe45 and Phe44 generate the π-π interactions with inhibitors. Notably, the residue Asn140 forms hydrogen bonding interactions with three inhibitors. This research is expected to provide useful molecular basis and dynamics information at atomic levels for the design of potent inhibitors inhibiting the activity of BRD9.
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Affiliation(s)
- Y Wang
- School of Science, Shandong Jiaotong University, Jinan, China
| | - L F Wang
- School of Science, Shandong Jiaotong University, Jinan, China
| | - L L Zhang
- School of Science, Shandong Jiaotong University, Jinan, China
| | - H B Sun
- School of Science, Shandong Jiaotong University, Jinan, China
| | - J Zhao
- School of Science, Shandong Jiaotong University, Jinan, China
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20
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Lu CJ, Yu X, Chen YT, Song QB, Wang H. Indolizine synthesis via copper-catalyzed cyclization of gem-difluoroalkenes and 2-(pyridin-2-yl)acetate derivatives. Org Chem Front 2020. [DOI: 10.1039/d0qo00553c] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
A novel and versatile approach to construct substituted indolizines through copper-catalyzed coupling cyclization of 2-(pyridin-2-yl)acetate with gem-difluoroalkenes has been developed.
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Affiliation(s)
- Chuan-Jun Lu
- College of Chemistry and Chemical Engineering
- Qingdao University
- China
- College of Chemical Engineering
- Zhejiang University of Technology
| | - Xin Yu
- College of Chemical Engineering
- Zhejiang University of Technology
- Hangzhou 310014
- China
| | - Yu-Ting Chen
- College of Chemical Engineering
- Zhejiang University of Technology
- Hangzhou 310014
- China
| | - Qing-Bao Song
- College of Chemical Engineering
- Zhejiang University of Technology
- Hangzhou 310014
- China
| | - Hong Wang
- College of Chemical Engineering
- Zhejiang University of Technology
- Hangzhou 310014
- China
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21
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Dong S, Huang J, Sha H, Qiu L, Hu W, Xu X. Copper-catalyzed formal [1 + 2 + 2]-annulation of alkyne-tethered diazoacetates and pyridines: access to polycyclic indolizines. Org Biomol Chem 2020; 18:1926-1932. [DOI: 10.1039/d0ob00222d] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
A copper-catalyzed formal [1 + 2 + 2]-annulation of alkyne-tethered diazo compounds with pyridines, which affords polycyclic fused indolizine derivatives with broad substrate generality, has been reported.
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Affiliation(s)
- Shanliang Dong
- College of Chemistry
- Chemical Engineering and Materials Science
- Soochow University
- Suzhou 215123
- China
| | - Jingjing Huang
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery
- School of Pharmaceutical Sciences
- Sun Yat-sen University
- Guangzhou 510006
- China
| | - Hongkai Sha
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery
- School of Pharmaceutical Sciences
- Sun Yat-sen University
- Guangzhou 510006
- China
| | - Lihua Qiu
- College of Chemistry
- Chemical Engineering and Materials Science
- Soochow University
- Suzhou 215123
- China
| | - Wenhao Hu
- Guangdong Key Laboratory of Chiral Molecule and Drug Discovery
- School of Pharmaceutical Sciences
- Sun Yat-sen University
- Guangzhou 510006
- China
| | - Xinfang Xu
- College of Chemistry
- Chemical Engineering and Materials Science
- Soochow University
- Suzhou 215123
- China
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22
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Li F, Tang X, Xu Y, Wang C, Zhang L, Zhang J, Liu J, Li Z, Wang L. Hemoglobin-Catalyzed Synthesis of Indolizines Under Mild Conditions. European J Org Chem 2019. [DOI: 10.1002/ejoc.201901591] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Fengxi Li
- Key Laboratory of Molecular Enzymology and Engineering of Ministry of Education School of Life Sciences; Jilin University; 130023 Changchun P. R. China
| | - Xuyong Tang
- Key Laboratory of Molecular Enzymology and Engineering of Ministry of Education School of Life Sciences; Jilin University; 130023 Changchun P. R. China
| | - Yaning Xu
- Key Laboratory of Molecular Enzymology and Engineering of Ministry of Education School of Life Sciences; Jilin University; 130023 Changchun P. R. China
| | - Chunyu Wang
- State Key Laboratory of Supramolecular Structure and Materials; Jilin University; 130023 Changchun P. R. China
| | - Liu Zhang
- Key Laboratory of Molecular Enzymology and Engineering of Ministry of Education School of Life Sciences; Jilin University; 130023 Changchun P. R. China
| | - Jiaxin Zhang
- Key Laboratory of Molecular Enzymology and Engineering of Ministry of Education School of Life Sciences; Jilin University; 130023 Changchun P. R. China
| | - Jiaxu Liu
- Key Laboratory of Molecular Enzymology and Engineering of Ministry of Education School of Life Sciences; Jilin University; 130023 Changchun P. R. China
| | - Zhengqiang Li
- Key Laboratory of Molecular Enzymology and Engineering of Ministry of Education School of Life Sciences; Jilin University; 130023 Changchun P. R. China
| | - Lei Wang
- Key Laboratory of Molecular Enzymology and Engineering of Ministry of Education School of Life Sciences; Jilin University; 130023 Changchun P. R. China
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23
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Zaware N, Zhou MM. Bromodomain biology and drug discovery. Nat Struct Mol Biol 2019; 26:870-879. [PMID: 31582847 DOI: 10.1038/s41594-019-0309-8] [Citation(s) in RCA: 141] [Impact Index Per Article: 28.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Accepted: 08/21/2019] [Indexed: 12/20/2022]
Abstract
The bromodomain (BrD) is a conserved structural module found in chromatin- and transcription-associated proteins that acts as the primary reader for acetylated lysine residues. This basic activity endows BrD proteins with versatile functions in the regulation of protein-protein interactions mediating chromatin-templated gene transcription, DNA recombination, replication and repair. Consequently, BrD proteins are involved in the pathogenesis of numerous human diseases. In this Review, we highlight our current understanding of BrD biology, and discuss the latest development of small-molecule inhibitors targeting BrDs as emerging epigenetic therapies for cancer and inflammatory disorders.
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Affiliation(s)
- Nilesh Zaware
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Ming-Ming Zhou
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
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24
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Abstract
Less than a decade ago, it was shown that bromodomains, acetyl lysine 'reader' modules found in proteins with varied functions, were highly tractable small-molecule targets. This is an unusual property for protein-protein or protein-peptide interaction domains, and it prompted a wave of chemical probe discovery to understand the biological potential of new agents that targeted bromodomains. The original examples, inhibitors of the bromodomain and extra-terminal (BET) class of bromodomains, showed enticing anti-inflammatory and anticancer activities, and several compounds have since advanced to human clinical trials. Here, we review the current state of BET inhibitor biology in relation to clinical development, and we discuss the next wave of bromodomain inhibitors with clinical potential in oncology and non-oncology indications. The lessons learned from BET inhibitor programmes should affect efforts to develop drugs that target non-BET bromodomains and other epigenetic readers.
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25
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Huang L, Li H, Li L, Niu L, Seupel R, Wu C, Cheng W, Chen C, Ding B, Brennan PE, Yang S. Discovery of Pyrrolo[3,2-d]pyrimidin-4-one Derivatives as a New Class of Potent and Cell-Active Inhibitors of P300/CBP-Associated Factor Bromodomain. J Med Chem 2019; 62:4526-4542. [PMID: 30998845 DOI: 10.1021/acs.jmedchem.9b00096] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Luyi Huang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu 610041, P. R. China
| | - Hui Li
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu 610041, P. R. China
| | - Linli Li
- Key Laboratory of Drug Targeting and Drug Delivery System of Ministry of Education, West China School of Pharmacy, Sichuan University, Sichuan 610041, P. R. China
| | - Lu Niu
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu 610041, P. R. China
| | - Raina Seupel
- Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, U.K
- Target Discovery Institute, University of Oxford, NDM Research Building, Roosevelt Drive, Oxford OX3 7FZ, U.K
| | - Chengyong Wu
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu 610041, P. R. China
| | - Wei Cheng
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu 610041, P. R. China
| | - Chong Chen
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu 610041, P. R. China
| | - Bisen Ding
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu 610041, P. R. China
| | - Paul E. Brennan
- Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, U.K
- Target Discovery Institute, University of Oxford, NDM Research Building, Roosevelt Drive, Oxford OX3 7FZ, U.K
| | - Shengyong Yang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu 610041, P. R. China
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26
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Genomic characterization of genes encoding histone acetylation modulator proteins identifies therapeutic targets for cancer treatment. Nat Commun 2019; 10:733. [PMID: 30760718 PMCID: PMC6374416 DOI: 10.1038/s41467-019-08554-x] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 01/18/2019] [Indexed: 02/07/2023] Open
Abstract
A growing emphasis in anticancer drug discovery efforts has been on targeting histone acetylation modulators. Here we comprehensively analyze the genomic alterations of the genes encoding histone acetylation modulator proteins (HAMPs) in the Cancer Genome Atlas cohort and observe that HAMPs have a high frequency of focal copy number alterations and recurrent mutations, whereas transcript fusions of HAMPs are relatively rare genomic events in common adult cancers. Collectively, 86.3% (63/73) of HAMPs have recurrent alterations in at least 1 cancer type and 16 HAMPs, including 9 understudied HAMPs, are identified as putative therapeutic targets across multiple cancer types. For example, the recurrent focal amplification of BRD9 is observed in 9 cancer types and genetic depletion of BRD9 inhibits tumor growth. Our systematic genomic analysis of HAMPs across a large-scale cancer specimen cohort may facilitate the identification and prioritization of potential drug targets and selection of suitable patients for precision treatment. Targeting histone acetylation modulators (HAMPs) is a promising avenue of drug discovery in cancer research. Here, the authors integrate multi-dimensional genomic profiles to systematically investigate recurrent genomic alterations in HAMPs, identifying potential therapeutic targets for precision epigenetic treatment.
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27
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Zoppi V, Hughes SJ, Maniaci C, Testa A, Gmaschitz T, Wieshofer C, Koegl M, Riching KM, Daniels DL, Spallarossa A, Ciulli A. Iterative Design and Optimization of Initially Inactive Proteolysis Targeting Chimeras (PROTACs) Identify VZ185 as a Potent, Fast, and Selective von Hippel-Lindau (VHL) Based Dual Degrader Probe of BRD9 and BRD7. J Med Chem 2018; 62:699-726. [PMID: 30540463 PMCID: PMC6348446 DOI: 10.1021/acs.jmedchem.8b01413] [Citation(s) in RCA: 190] [Impact Index Per Article: 31.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
![]()
Developing
PROTACs to redirect the ubiquitination activity of E3
ligases and potently degrade a target protein within cells can be
a lengthy and unpredictable process, and it remains unclear whether
any combination of E3 and target might be productive for degradation.
We describe a probe-quality degrader for a ligase–target pair
deemed unsuitable: the von Hippel–Lindau (VHL) and BRD9, a
bromodomain-containing subunit of the SWI/SNF chromatin remodeling
complex BAF. VHL-based degraders could be optimized from suboptimal
compounds in two rounds by systematically varying conjugation patterns
and linkers and monitoring cellular degradation activities, kinetic
profiles, and ubiquitination, as well as ternary complex formation
thermodynamics. The emerged structure–activity relationships
guided the discovery of VZ185, a potent, fast, and selective degrader
of BRD9 and of its close homolog BRD7. Our findings qualify a new
chemical tool for BRD7/9 knockdown and provide a roadmap for PROTAC
development against seemingly incompatible target–ligase combinations.
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Affiliation(s)
- Vittoria Zoppi
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, James Black Centre , University of Dundee , Dow Street , DD1 5EH , Dundee , Scotland , United Kingdom.,Dipartimento di Farmacia, Sezione di Chimica del Farmaco e del Prodotto Cosmetico , Università degli Studi di Genova , Viale Benedetto XV 3 , 16132 Genova , Italy
| | - Scott J Hughes
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, James Black Centre , University of Dundee , Dow Street , DD1 5EH , Dundee , Scotland , United Kingdom
| | - Chiara Maniaci
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, James Black Centre , University of Dundee , Dow Street , DD1 5EH , Dundee , Scotland , United Kingdom.,Medical Research Council Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, James Black Centre , University of Dundee , Dow Street , DD1 5EH , Dundee , Scotland , United Kingdom
| | - Andrea Testa
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, James Black Centre , University of Dundee , Dow Street , DD1 5EH , Dundee , Scotland , United Kingdom
| | | | | | - Manfred Koegl
- Boehringer Ingelheim RCV GmbH & Co. KG , 1221 Vienna , Austria
| | - Kristin M Riching
- Promega Corporation , 2800 Woods Hollow Road , Madison , Wisconsin 53711 , United States
| | - Danette L Daniels
- Promega Corporation , 2800 Woods Hollow Road , Madison , Wisconsin 53711 , United States
| | - Andrea Spallarossa
- Dipartimento di Farmacia, Sezione di Chimica del Farmaco e del Prodotto Cosmetico , Università degli Studi di Genova , Viale Benedetto XV 3 , 16132 Genova , Italy
| | - Alessio Ciulli
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, James Black Centre , University of Dundee , Dow Street , DD1 5EH , Dundee , Scotland , United Kingdom
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28
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Moustakim M, Christott T, Monteiro OP, Bennett J, Giroud C, Ward J, Rogers CM, Smith P, Panagakou I, Díaz‐Sáez L, Felce SL, Gamble V, Gileadi C, Halidi N, Heidenreich D, Chaikuad A, Knapp S, Huber KVM, Farnie G, Heer J, Manevski N, Poda G, Al‐awar R, Dixon DJ, Brennan PE, Fedorov O. Discovery of an MLLT1/3 YEATS Domain Chemical Probe. Angew Chem Int Ed Engl 2018; 57:16302-16307. [PMID: 30288907 PMCID: PMC6348381 DOI: 10.1002/anie.201810617] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Indexed: 11/10/2022]
Abstract
YEATS domain (YD) containing proteins are an emerging class of epigenetic targets in drug discovery. Dysregulation of these modified lysine-binding proteins has been linked to the onset and progression of cancers. We herein report the discovery and characterisation of the first small-molecule chemical probe, SGC-iMLLT, for the YD of MLLT1 (ENL/YEATS1) and MLLT3 (AF9/YEATS3). SGC-iMLLT is a potent and selective inhibitor of MLLT1/3-histone interactions. Excellent selectivity over other human YD proteins (YEATS2/4) and bromodomains was observed. Furthermore, our probe displays cellular target engagement of MLLT1 and MLLT3. The first small-molecule X-ray co-crystal structures with the MLLT1 YD are also reported. This first-in-class probe molecule can be used to understand MLLT1/3-associated biology and the therapeutic potential of small-molecule YD inhibitors.
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Affiliation(s)
- Moses Moustakim
- Structural Genomics Consortium & Target Discovery InstituteUniversity of Oxford, NDMRBOld Road CampusOxford, OX3 7DQ &OX3 7FZUK
- Department of ChemistryUniversity of OxfordChemistry Research LaboratoryMansfield RoadOxfordOX1 3TAUK
| | - Thomas Christott
- Structural Genomics Consortium & Target Discovery InstituteUniversity of Oxford, NDMRBOld Road CampusOxford, OX3 7DQ &OX3 7FZUK
| | - Octovia P. Monteiro
- Structural Genomics Consortium & Target Discovery InstituteUniversity of Oxford, NDMRBOld Road CampusOxford, OX3 7DQ &OX3 7FZUK
| | - James Bennett
- Structural Genomics Consortium & Target Discovery InstituteUniversity of Oxford, NDMRBOld Road CampusOxford, OX3 7DQ &OX3 7FZUK
| | - Charline Giroud
- Structural Genomics Consortium & Target Discovery InstituteUniversity of Oxford, NDMRBOld Road CampusOxford, OX3 7DQ &OX3 7FZUK
| | - Jennifer Ward
- Structural Genomics Consortium & Target Discovery InstituteUniversity of Oxford, NDMRBOld Road CampusOxford, OX3 7DQ &OX3 7FZUK
| | - Catherine M. Rogers
- Structural Genomics Consortium & Target Discovery InstituteUniversity of Oxford, NDMRBOld Road CampusOxford, OX3 7DQ &OX3 7FZUK
| | - Paul Smith
- Structural Genomics Consortium & Target Discovery InstituteUniversity of Oxford, NDMRBOld Road CampusOxford, OX3 7DQ &OX3 7FZUK
| | - Ioanna Panagakou
- Structural Genomics Consortium & Target Discovery InstituteUniversity of Oxford, NDMRBOld Road CampusOxford, OX3 7DQ &OX3 7FZUK
| | - Laura Díaz‐Sáez
- Structural Genomics Consortium & Target Discovery InstituteUniversity of Oxford, NDMRBOld Road CampusOxford, OX3 7DQ &OX3 7FZUK
| | - Suet Ling Felce
- Structural Genomics Consortium & Botnar Research CentreUniversity of OxfordWindmill RoadOxfordOX3 7LDUK
| | - Vicki Gamble
- Structural Genomics Consortium & Botnar Research CentreUniversity of OxfordWindmill RoadOxfordOX3 7LDUK
| | - Carina Gileadi
- Structural Genomics Consortium & Botnar Research CentreUniversity of OxfordWindmill RoadOxfordOX3 7LDUK
| | - Nadia Halidi
- Structural Genomics Consortium & Botnar Research CentreUniversity of OxfordWindmill RoadOxfordOX3 7LDUK
| | - David Heidenreich
- Institute for Pharmaceutical Chemistry and Buchmann Institute for Life SciencesJohann Wolfgang Goethe-University60438Frankfurt am MainGermany
| | - Apirat Chaikuad
- Structural Genomics Consortium & Target Discovery InstituteUniversity of Oxford, NDMRBOld Road CampusOxford, OX3 7DQ &OX3 7FZUK
- Institute for Pharmaceutical Chemistry and Buchmann Institute for Life SciencesJohann Wolfgang Goethe-University60438Frankfurt am MainGermany
| | - Stefan Knapp
- Structural Genomics Consortium & Target Discovery InstituteUniversity of Oxford, NDMRBOld Road CampusOxford, OX3 7DQ &OX3 7FZUK
- Institute for Pharmaceutical Chemistry and Buchmann Institute for Life SciencesJohann Wolfgang Goethe-University60438Frankfurt am MainGermany
| | - Kilian V. M. Huber
- Structural Genomics Consortium & Target Discovery InstituteUniversity of Oxford, NDMRBOld Road CampusOxford, OX3 7DQ &OX3 7FZUK
| | - Gillian Farnie
- Structural Genomics Consortium & Botnar Research CentreUniversity of OxfordWindmill RoadOxfordOX3 7LDUK
| | | | | | - Gennady Poda
- Drug Discovery ProgramOntario Institute for Cancer ResearchTorontoONCanada
- Leslie Dan Faculty of PharmacyUniversity of TorontoTorontoONCanada
| | - Rima Al‐awar
- Drug Discovery ProgramOntario Institute for Cancer ResearchTorontoONCanada
- Department of Pharmacology and ToxicologyUniversity of TorontoTorontoONCanada
| | - Darren J. Dixon
- Department of ChemistryUniversity of OxfordChemistry Research LaboratoryMansfield RoadOxfordOX1 3TAUK
| | - Paul E. Brennan
- Structural Genomics Consortium & Target Discovery InstituteUniversity of Oxford, NDMRBOld Road CampusOxford, OX3 7DQ &OX3 7FZUK
- Alzheimer's Research (UK) Oxford Drug Discovery InstituteNuffield Department of MedicineUniversity of OxfordNDM Research BuildingRoosevelt DriveOxfordOX3 7FZUK
| | - Oleg Fedorov
- Structural Genomics Consortium & Target Discovery InstituteUniversity of Oxford, NDMRBOld Road CampusOxford, OX3 7DQ &OX3 7FZUK
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29
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Moustakim M, Christott T, Monteiro OP, Bennett J, Giroud C, Ward J, Rogers CM, Smith P, Panagakou I, Díaz-Sáez L, Felce SL, Gamble V, Gileadi C, Halidi N, Heidenreich D, Chaikuad A, Knapp S, Huber KVM, Farnie G, Heer J, Manevski N, Poda G, Al-awar R, Dixon DJ, Brennan PE, Fedorov O. Entdeckung einer chemischen Sonde für MLLT1/3-YEATS-Domänen. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201810617] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Moses Moustakim
- Structural Genomics Consortium & Target Discovery Institute; University of Oxford, NDMRB; Old Road Campus Oxford OX3 7DQ & OX3 7FZ Großbritannien
- Department of Chemistry; University of Oxford; Chemistry Research Laboratory; Mansfield Road Oxford OX1 3TA Großbritannien
| | - Thomas Christott
- Structural Genomics Consortium & Target Discovery Institute; University of Oxford, NDMRB; Old Road Campus Oxford OX3 7DQ & OX3 7FZ Großbritannien
| | - Octovia P. Monteiro
- Structural Genomics Consortium & Target Discovery Institute; University of Oxford, NDMRB; Old Road Campus Oxford OX3 7DQ & OX3 7FZ Großbritannien
| | - James Bennett
- Structural Genomics Consortium & Target Discovery Institute; University of Oxford, NDMRB; Old Road Campus Oxford OX3 7DQ & OX3 7FZ Großbritannien
| | - Charline Giroud
- Structural Genomics Consortium & Target Discovery Institute; University of Oxford, NDMRB; Old Road Campus Oxford OX3 7DQ & OX3 7FZ Großbritannien
| | - Jennifer Ward
- Structural Genomics Consortium & Target Discovery Institute; University of Oxford, NDMRB; Old Road Campus Oxford OX3 7DQ & OX3 7FZ Großbritannien
| | - Catherine M. Rogers
- Structural Genomics Consortium & Target Discovery Institute; University of Oxford, NDMRB; Old Road Campus Oxford OX3 7DQ & OX3 7FZ Großbritannien
| | - Paul Smith
- Structural Genomics Consortium & Target Discovery Institute; University of Oxford, NDMRB; Old Road Campus Oxford OX3 7DQ & OX3 7FZ Großbritannien
| | - Ioanna Panagakou
- Structural Genomics Consortium & Target Discovery Institute; University of Oxford, NDMRB; Old Road Campus Oxford OX3 7DQ & OX3 7FZ Großbritannien
| | - Laura Díaz-Sáez
- Structural Genomics Consortium & Target Discovery Institute; University of Oxford, NDMRB; Old Road Campus Oxford OX3 7DQ & OX3 7FZ Großbritannien
| | - Suet Ling Felce
- Structural Genomics Consortium & Botnar Research Centre; University of Oxford; Windmill Road Oxford OX3 7LD Großbritannien
| | - Vicki Gamble
- Structural Genomics Consortium & Botnar Research Centre; University of Oxford; Windmill Road Oxford OX3 7LD Großbritannien
| | - Carina Gileadi
- Structural Genomics Consortium & Botnar Research Centre; University of Oxford; Windmill Road Oxford OX3 7LD Großbritannien
| | - Nadia Halidi
- Structural Genomics Consortium & Botnar Research Centre; University of Oxford; Windmill Road Oxford OX3 7LD Großbritannien
| | - David Heidenreich
- Institute for Pharmaceutical Chemistry and Buchmann Institute for Life Sciences; Johann Wolfgang Goethe-University; 60438 Frankfurt am Main Deutschland
| | - Apirat Chaikuad
- Structural Genomics Consortium & Target Discovery Institute; University of Oxford, NDMRB; Old Road Campus Oxford OX3 7DQ & OX3 7FZ Großbritannien
- Institute for Pharmaceutical Chemistry and Buchmann Institute for Life Sciences; Johann Wolfgang Goethe-University; 60438 Frankfurt am Main Deutschland
| | - Stefan Knapp
- Structural Genomics Consortium & Target Discovery Institute; University of Oxford, NDMRB; Old Road Campus Oxford OX3 7DQ & OX3 7FZ Großbritannien
- Institute for Pharmaceutical Chemistry and Buchmann Institute for Life Sciences; Johann Wolfgang Goethe-University; 60438 Frankfurt am Main Deutschland
| | - Kilian V. M. Huber
- Structural Genomics Consortium & Target Discovery Institute; University of Oxford, NDMRB; Old Road Campus Oxford OX3 7DQ & OX3 7FZ Großbritannien
| | - Gillian Farnie
- Structural Genomics Consortium & Botnar Research Centre; University of Oxford; Windmill Road Oxford OX3 7LD Großbritannien
| | - Jag Heer
- UCB Pharma Ltd; Slough SL1 3WE UK
| | | | - Gennady Poda
- Drug Discovery Program; Ontario Institute for Cancer Research; Toronto ON Kanada
- Leslie Dan Faculty of Pharmacy; University of Toronto; Toronto ON Kanada
| | - Rima Al-awar
- Drug Discovery Program; Ontario Institute for Cancer Research; Toronto ON Kanada
- Department of Pharmacology and Toxicology; University of Toronto; Toronto ON Kanada
| | - Darren J. Dixon
- Department of Chemistry; University of Oxford; Chemistry Research Laboratory; Mansfield Road Oxford OX1 3TA Großbritannien
| | - Paul E. Brennan
- Structural Genomics Consortium & Target Discovery Institute; University of Oxford, NDMRB; Old Road Campus Oxford OX3 7DQ & OX3 7FZ Großbritannien
- Alzheimer's Research (UK) Oxford Drug Discovery Institute; Nuffield Department of Medicine; University of Oxford; NDM Research Building; Roosevelt Drive Oxford OX3 7FZ Großbritannien
| | - Oleg Fedorov
- Structural Genomics Consortium & Target Discovery Institute; University of Oxford, NDMRB; Old Road Campus Oxford OX3 7DQ & OX3 7FZ Großbritannien
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30
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Abstract
Amongst nitrogen heterocycles of different ring sizes and oxidation statuses, dihydropyridines (DHP) occupy a prominent role due to their synthetic versatility and occurrence in medicinally relevant compounds. One of the most straightforward synthetic approaches to polysubstituted DHP derivatives is provided by nucleophilic dearomatization of readily assembled pyridines. In this article, we collect and summarize nucleophilic dearomatization reactions of - pyridines reported in the literature between 2010 and mid-2018, complementing and updating previous reviews published in the early 2010s dedicated to various aspects of pyridine chemistry. Since functionalization of the pyridine nitrogen, rendering a (transient) pyridinium ion, is usually required to render the pyridine nucleus sufficiently electrophilic to suffer the attack of a nucleophile, the material is organized according to the type of N-functionalization. A variety of nucleophilic species (organometallic reagents, enolates, heteroaromatics, umpoled aldehydes) can be productively engaged in pyridine dearomatization reactions, including catalytic asymmetric implementations, providing useful and efficient synthetic platforms to (enantioenriched) DHPs. Conversely, pyridine nitrogen functionalization can also lead to pyridinium ylides. These dipolar species can undergo a variety of dipolar cycloaddition reactions with electron-poor dipolarophiles, affording polycyclic frameworks and embedding a DHP moiety in their structures.
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31
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Song LT, Tu J, Liu RR, Zhu M, Meng YJ, Zhai HL. Molecular mechanism study of several inhibitors binding to BRD9 bromodomain based on molecular simulations. J Biomol Struct Dyn 2018; 37:2970-2979. [DOI: 10.1080/07391102.2018.1502097] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Li Ting Song
- College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou, P. R. China
| | - Jing Tu
- College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou, P. R. China
| | - Rui Rui Liu
- College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou, P. R. China
| | - Min Zhu
- College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou, P. R. China
| | - Ya Jie Meng
- College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou, P. R. China
| | - Hong Lin Zhai
- College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou, P. R. China
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32
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Moustakim M, Felce SL, Zaarour N, Farnie G, McCann FE, Brennan PE. Target Identification Using Chemical Probes. Methods Enzymol 2018; 610:27-58. [PMID: 30390803 DOI: 10.1016/bs.mie.2018.09.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Chemical probes are small molecules with potency and selectivity for a single or small number of protein targets. A good chemical probe engages its target intracellularly and is accompanied by a chemically similar, but inactive molecule to be used as a negative control in cellular phenotypic screening. The utility of these chemical probes is ultimately governed by how well they are developed and characterized. Chemical probes either as single entities, or in chemical probes sets are being increasingly used to interrogate the biological relevance of a target in a disease model. This chapter lays out the core properties of chemical probes, summarizes the seminal and emerging techniques used to demonstrate robust intracellular target engagement. Translation of target engagement assays to disease-relevant phenotypic assays using primary patient-derived cells and tissues is also reviewed. Two examples of epigenetic chemical probe discovery and utility are presented whereby target engagement pointed to novel disease associations elucidated from poorly understood protein targets. Finally, a number of examples are discussed whereby chemical probe sets, or "chemogenomic libraries" are used to illuminate new target-disease links which may represent future directions for chemical probe utility.
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Affiliation(s)
- Moses Moustakim
- Nuffield Department of Medicine, Structural Genomics Consortium, University of Oxford, Oxford, United Kingdom; Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Oxford, United Kingdom; Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Oxford, United Kingdom
| | - Suet Ling Felce
- Nuffield Department of Orthopedics, Rheumatology and Musculoskeletal Sciences, Botnar Research Centre, University of Oxford, Oxford, United Kingdom
| | - Nancy Zaarour
- Nuffield Department of Orthopedics, Rheumatology and Musculoskeletal Sciences, Botnar Research Centre, University of Oxford, Oxford, United Kingdom; Kennedy Institute of Rheumatology, University of Oxford, Oxford, United Kingdom
| | - Gillian Farnie
- Nuffield Department of Medicine, Structural Genomics Consortium, University of Oxford, Oxford, United Kingdom; Nuffield Department of Orthopedics, Rheumatology and Musculoskeletal Sciences, Botnar Research Centre, University of Oxford, Oxford, United Kingdom.
| | - Fiona E McCann
- Nuffield Department of Orthopedics, Rheumatology and Musculoskeletal Sciences, Botnar Research Centre, University of Oxford, Oxford, United Kingdom; Kennedy Institute of Rheumatology, University of Oxford, Oxford, United Kingdom.
| | - Paul E Brennan
- Nuffield Department of Medicine, Structural Genomics Consortium, University of Oxford, Oxford, United Kingdom; Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Oxford, United Kingdom; Nuffield Department of Medicine, Alzheimer's Research UK Oxford Drug Discovery Institute, University of Oxford, Oxford, United Kingdom.
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33
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Su J, Liu X, Zhang S, Yan F, Zhang Q, Chen J. Insight into selective mechanism of class of I-BRD9 inhibitors toward BRD9 based on molecular dynamics simulations. Chem Biol Drug Des 2018; 93:163-176. [PMID: 30225973 DOI: 10.1111/cbdd.13398] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Revised: 08/10/2018] [Accepted: 09/02/2018] [Indexed: 02/06/2023]
Abstract
Recently, bromodomain-containing protein 9 (BRD9), 7 (BRD7), and 4 (BRD4) have been potential targets of anticancer drug design. Molecular dynamic simulations followed by molecular mechanics Poisson-Boltzmann surface area calculation were performed to study the selective mechanism of I-BRD9 inhibitor H1B and its derivatives N1D, TVU, and 5V2 toward BRD9 and BRD4. The rank of our calculated binding free energies agrees with that of the experimental data. The results show that binding free energy of H1B to BRD7 is slightly lower than that of H1B to BRD9, and all four inhibitors bind more tightly to BRD9 than to BRD4. Decomposition of binding free energies into individual residues implies that Ile164 and Asn211 in BRD7 and Ile53 and Asn100 in BRD9 play a significant role in the selectivity of H1B toward BRD7 and BRD9. Besides, several key residues Phe44, Ile53, Asn100, Thr104 in BRD9 and Pro82, Lys91, Asn140, Asp144 in BRD4 that are located in the ZA-loop and BC-loop provide significant contributions to binding selectivity of inhibitors to BRD9 and BRD4. This study is expected to provide important theoretical guidance for rational designs of highly selective inhibitors targeting BRD9 and BRD4.
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Affiliation(s)
- Jing Su
- School of Physics and Electronics, Shandong Normal University, Jinan, China
| | - Xinguo Liu
- School of Physics and Electronics, Shandong Normal University, Jinan, China
| | - Shaolong Zhang
- School of Physics and Electronics, Shandong Normal University, Jinan, China
| | - Fangfang Yan
- School of Physics and Electronics, Shandong Normal University, Jinan, China
| | - Qinggang Zhang
- School of Physics and Electronics, Shandong Normal University, Jinan, China
| | - Jianzhong Chen
- School of Science, Shandong Jiaotong University, Jinan, China
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34
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Wang S, Tsui V, Crawford TD, Audia JE, Burdick DJ, Beresini MH, Côté A, Cummings R, Duplessis M, Flynn EM, Hewitt MC, Huang HR, Jayaram H, Jiang Y, Joshi S, Murray J, Nasveschuk CG, Pardo E, Poy F, Romero FA, Tang Y, Taylor AM, Wang J, Xu Z, Zawadzke LE, Zhu X, Albrecht BK, Magnuson SR, Bellon S, Cochran AG. GNE-371, a Potent and Selective Chemical Probe for the Second Bromodomains of Human Transcription-Initiation-Factor TFIID Subunit 1 and Transcription-Initiation-Factor TFIID Subunit 1-like. J Med Chem 2018; 61:9301-9315. [DOI: 10.1021/acs.jmedchem.8b01225] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Shumei Wang
- Genentech Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Vickie Tsui
- Genentech Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Terry D. Crawford
- Genentech Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - James E. Audia
- Constellation Pharmaceuticals, 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Daniel J. Burdick
- Genentech Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Maureen H. Beresini
- Genentech Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | | | - Richard Cummings
- Constellation Pharmaceuticals, 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Martin Duplessis
- Constellation Pharmaceuticals, 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - E. Megan Flynn
- Genentech Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Michael C. Hewitt
- Constellation Pharmaceuticals, 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Hon-Ren Huang
- Constellation Pharmaceuticals, 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Hariharan Jayaram
- Constellation Pharmaceuticals, 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Ying Jiang
- Wuxi Apptec Company, Ltd., 288 Fute Zhong Road, Waigaoqiao
Free Trade Zone, Shanghai 200131, People’s Republic of China
| | - Shivangi Joshi
- Constellation Pharmaceuticals, 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Jeremy Murray
- Genentech Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Christopher G. Nasveschuk
- Constellation Pharmaceuticals, 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Eneida Pardo
- Constellation Pharmaceuticals, 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Florence Poy
- Constellation Pharmaceuticals, 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - F. Anthony Romero
- Genentech Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Yong Tang
- Constellation Pharmaceuticals, 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Alexander M. Taylor
- Constellation Pharmaceuticals, 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Jian Wang
- Wuxi Apptec Company, Ltd., 288 Fute Zhong Road, Waigaoqiao
Free Trade Zone, Shanghai 200131, People’s Republic of China
| | - Zhaowu Xu
- Wuxi Apptec Company, Ltd., 288 Fute Zhong Road, Waigaoqiao
Free Trade Zone, Shanghai 200131, People’s Republic of China
| | - Laura E. Zawadzke
- Constellation Pharmaceuticals, 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Xiaoyu Zhu
- Wuxi Apptec Company, Ltd., 288 Fute Zhong Road, Waigaoqiao
Free Trade Zone, Shanghai 200131, People’s Republic of China
| | - Brian K. Albrecht
- Constellation Pharmaceuticals, 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Steven R. Magnuson
- Genentech Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Steve Bellon
- Constellation Pharmaceuticals, 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Andrea G. Cochran
- Genentech Inc., 1 DNA Way, South San Francisco, California 94080, United States
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35
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Research progress of selective small molecule bromodomain-containing protein 9 inhibitors. Future Med Chem 2018; 10:895-906. [PMID: 29620420 DOI: 10.4155/fmc-2017-0243] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The bromodomain proteins, known as the key targets in epigenetics, are 'readers' of acetylated lysine of histones. As a member of bromodomain proteins, bromodomain-containing protein 9 (BRD9) is a subunit of mammalian SWI/SNF chromatin remodeling complexes. However, the biological functions and the potential application in therapeutics of BRD9 remain ambiguous due to a lack of selective small molecule inhibitors of BRD9. Recently, series of chemical ligands against BRD9 were developed by different research institutes. Here, we reviewed the development and characterization of reported BRD9 inhibitors, which will be the foundation of further chemical design and biological evaluation.
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36
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Batiste L, Unzue A, Dolbois A, Hassler F, Wang X, Deerain N, Zhu J, Spiliotopoulos D, Nevado C, Caflisch A. Chemical Space Expansion of Bromodomain Ligands Guided by in Silico Virtual Couplings (AutoCouple). ACS CENTRAL SCIENCE 2018; 4:180-188. [PMID: 29532017 PMCID: PMC5833004 DOI: 10.1021/acscentsci.7b00401] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Indexed: 10/24/2023]
Abstract
Expanding the chemical space and simultaneously ensuring synthetic accessibility is of upmost importance, not only for the discovery of effective binders for novel protein classes but, more importantly, for the development of compounds against hard-to-drug proteins. Here, we present AutoCouple, a de novo approach to computational ligand design focused on the diversity-oriented generation of chemical entities via virtual couplings. In a benchmark application, chemically diverse compounds with low-nanomolar potency for the CBP bromodomain and high selectivity against the BRD4(1) bromodomain were achieved by the synthesis of about 50 derivatives of the original fragment. The binding mode was confirmed by X-ray crystallography, target engagement in cells was demonstrated, and antiproliferative activity was showcased in three cancer cell lines. These results reveal AutoCouple as a useful in silico coupling method to expand the chemical space in hit optimization campaigns resulting in potent, selective, and cell permeable bromodomain ligands.
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Affiliation(s)
- Laurent Batiste
- Department
of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057, Zürich, Switzerland
| | - Andrea Unzue
- Department
of Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057, Zürich, Switzerland
| | - Aymeric Dolbois
- Department
of Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057, Zürich, Switzerland
| | - Fabrice Hassler
- Department
of Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057, Zürich, Switzerland
| | - Xuan Wang
- Department
of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057, Zürich, Switzerland
- Department
of Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057, Zürich, Switzerland
| | - Nicholas Deerain
- Department
of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057, Zürich, Switzerland
| | - Jian Zhu
- Department
of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057, Zürich, Switzerland
| | - Dimitrios Spiliotopoulos
- Department
of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057, Zürich, Switzerland
| | - Cristina Nevado
- Department
of Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057, Zürich, Switzerland
| | - Amedeo Caflisch
- Department
of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057, Zürich, Switzerland
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37
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Douglas T, Pordea A, Dowden J. Iron-Catalyzed Indolizine Synthesis from Pyridines, Diazo Compounds, and Alkynes. Org Lett 2017; 19:6396-6399. [DOI: 10.1021/acs.orglett.7b03252] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Tim Douglas
- School
of Chemistry and ‡Department of Chemical and Environmental Engineering, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom
| | - Anca Pordea
- School
of Chemistry and ‡Department of Chemical and Environmental Engineering, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom
| | - James Dowden
- School
of Chemistry and ‡Department of Chemical and Environmental Engineering, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom
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38
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Differential gene expression profiles according to the Association for the Study of Lung Cancer/American Thoracic Society/European Respiratory Society histopathological classification in lung adenocarcinoma subtypes. Hum Pathol 2017; 66:188-199. [DOI: 10.1016/j.humpath.2017.06.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Revised: 05/26/2017] [Accepted: 06/01/2017] [Indexed: 12/29/2022]
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39
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Chemical modulators for epigenome reader domains as emerging epigenetic therapies for cancer and inflammation. Curr Opin Chem Biol 2017; 39:116-125. [PMID: 28689146 DOI: 10.1016/j.cbpa.2017.06.012] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Revised: 05/30/2017] [Accepted: 06/03/2017] [Indexed: 12/12/2022]
Abstract
Site-specific lysine acetylation and methylation on histones are critical post-translational modifications (PTMs) that govern ordered gene transcription in chromatin. Mis-regulation of these histone PTM-mediated processes has been shown to be associated with human diseases. Since the 2010 landmark reports of small molecules (+)-JQ1 and I-BET762 that target the acetyl-lysine 'reader' Bromodomain and Extra Terminal domain (BET) proteins, there have been relentless efforts to develop epigenetic therapy with small molecules to modulate molecular interactions of epigenome reader domain proteins with PTMs. In addition to BET, the other emerging targets include non-BET acetyl-lysine and methyl-lysine reader domains. This review covers the key chemical modulators of the aforementioned epigenome reader proteins.
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40
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Crawford TD, Vartanian S, Côté A, Bellon S, Duplessis M, Flynn EM, Hewitt M, Huang HR, Kiefer JR, Murray J, Nasveschuk CG, Pardo E, Romero FA, Sandy P, Tang Y, Taylor AM, Tsui V, Wang J, Wang S, Zawadzke L, Albrecht BK, Magnuson SR, Cochran AG, Stokoe D. Inhibition of bromodomain-containing protein 9 for the prevention of epigenetically-defined drug resistance. Bioorg Med Chem Lett 2017; 27:3534-3541. [PMID: 28606761 DOI: 10.1016/j.bmcl.2017.05.063] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Revised: 05/19/2017] [Accepted: 05/20/2017] [Indexed: 01/29/2023]
Abstract
Bromodomain-containing protein 9 (BRD9), an epigenetic "reader" of acetylated lysines on post-translationally modified histone proteins, is upregulated in multiple cancer cell lines. To assess the functional role of BRD9 in cancer cell lines, we identified a small-molecule inhibitor of the BRD9 bromodomain. Starting from a pyrrolopyridone lead, we used structure-based drug design to identify a potent and highly selective in vitro tool compound 11, (GNE-375). While this compound showed minimal effects in cell viability or gene expression assays, it showed remarkable potency in preventing the emergence of a drug tolerant population in EGFR mutant PC9 cells treated with EGFR inhibitors. Such tolerance has been linked to an altered epigenetic state, and 11 decreased BRD9 binding to chromatin, and this was associated with decreased expression of ALDH1A1, a gene previously shown to be important in drug tolerance. BRD9 inhibitors may therefore show utility in preventing epigenetically-defined drug resistance.
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Affiliation(s)
- Terry D Crawford
- Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, United States.
| | - Steffan Vartanian
- Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, United States
| | - Alexandre Côté
- Constellation Pharmaceuticals, 215 First Street, Suite 200, Cambridge, MA 02142, United States
| | - Steve Bellon
- Constellation Pharmaceuticals, 215 First Street, Suite 200, Cambridge, MA 02142, United States
| | - Martin Duplessis
- Constellation Pharmaceuticals, 215 First Street, Suite 200, Cambridge, MA 02142, United States
| | - E Megan Flynn
- Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, United States
| | - Michael Hewitt
- Constellation Pharmaceuticals, 215 First Street, Suite 200, Cambridge, MA 02142, United States
| | - Hon-Ren Huang
- Constellation Pharmaceuticals, 215 First Street, Suite 200, Cambridge, MA 02142, United States
| | - James R Kiefer
- Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, United States
| | - Jeremy Murray
- Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, United States
| | | | - Eneida Pardo
- Constellation Pharmaceuticals, 215 First Street, Suite 200, Cambridge, MA 02142, United States
| | - F Anthony Romero
- Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, United States
| | - Peter Sandy
- Constellation Pharmaceuticals, 215 First Street, Suite 200, Cambridge, MA 02142, United States
| | - Yong Tang
- Constellation Pharmaceuticals, 215 First Street, Suite 200, Cambridge, MA 02142, United States
| | - Alexander M Taylor
- Constellation Pharmaceuticals, 215 First Street, Suite 200, Cambridge, MA 02142, United States
| | - Vickie Tsui
- Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, United States
| | - Jian Wang
- Wuxi Apptec Co., Ltd., 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, PR China
| | - Shumei Wang
- Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, United States
| | - Laura Zawadzke
- Constellation Pharmaceuticals, 215 First Street, Suite 200, Cambridge, MA 02142, United States
| | - Brian K Albrecht
- Constellation Pharmaceuticals, 215 First Street, Suite 200, Cambridge, MA 02142, United States
| | - Steven R Magnuson
- Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, United States
| | - Andrea G Cochran
- Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, United States
| | - David Stokoe
- Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, United States.
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41
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Mammalian SWI/SNF complexes in cancer: emerging therapeutic opportunities. Curr Opin Genet Dev 2017; 42:56-67. [PMID: 28391084 DOI: 10.1016/j.gde.2017.02.004] [Citation(s) in RCA: 115] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Revised: 01/23/2017] [Accepted: 02/07/2017] [Indexed: 02/08/2023]
Abstract
Mammalian SWI/SNF (BAF) chromatin remodeling complexes orchestrate a diverse set of chromatin alterations which impact transcriptional output. Recent whole-exome sequencing efforts have revealed that the genes encoding subunits of mSWI/SNF complexes are mutated in over 20% of cancers, spanning a wide range of tissue types. The majority of mutations result in loss of subunit protein expression, implicating mSWI/SNF subunits as tumor suppressors. mSWI/SNF-deficient cancers remain a therapeutic challenge, owing to a lack of potent and selective agents which target complexes or unique pathway dependencies generated by mSWI/SNF subunit perturbations. Here, we review the current landscape of mechanistic insights and emerging therapeutic opportunities for human malignancies driven by mSWI/SNF complex perturbation.
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42
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Humphreys PG, Bamborough P, Chung CW, Craggs PD, Gordon L, Grandi P, Hayhow TG, Hussain J, Jones KL, Lindon M, Michon AM, Renaux JF, Suckling CJ, Tough DF, Prinjha RK. Discovery of a Potent, Cell Penetrant, and Selective p300/CBP-Associated Factor (PCAF)/General Control Nonderepressible 5 (GCN5) Bromodomain Chemical Probe. J Med Chem 2017; 60:695-709. [DOI: 10.1021/acs.jmedchem.6b01566] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
| | | | | | | | | | - Paola Grandi
- Cellzome
GmbH, Molecular Discovery Research, GlaxoSmithKline, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | | | | | | | | | - Anne-Marie Michon
- Cellzome
GmbH, Molecular Discovery Research, GlaxoSmithKline, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | | | - Colin J. Suckling
- WestCHEM,
Department of Pure and Applied Chemistry, University of Strathclyde, Thomas Graham Building, 295 Cathedral Street, Glasgow, G1 1XL, United Kingdom
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43
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Moustakim M, Clark PGK, Hay DA, Dixon DJ, Brennan PE. Chemical probes and inhibitors of bromodomains outside the BET family. MEDCHEMCOMM 2016; 7:2246-2264. [PMID: 29170712 PMCID: PMC5644722 DOI: 10.1039/c6md00373g] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Accepted: 09/06/2016] [Indexed: 01/03/2023]
Abstract
Significant progress has been made in discovering inhibitors and chemical probes of bromodomains, epigenetic readers of lysine acetylation.
In the last five years, the development of inhibitors of bromodomains has emerged as an area of intensive worldwide research. Emerging evidence has implicated a number of non-BET bromodomains in the onset and progression of diseases such as cancer, HIV infection and inflammation. The development and use of small molecule chemical probes has been fundamental to pre-clinical evaluation of bromodomains as targets. Recent efforts are described highlighting the development of potent, selective and cell active non-BET bromodomain inhibitors and their therapeutic potential. Over half of typical bromodomains now have reported ligands, but those with atypical binding site residues remain resistant to chemical probe discovery efforts.
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Affiliation(s)
- Moses Moustakim
- Department of Chemistry, University of Oxford, Oxford OX1 3TA, UK.,Structural Genomics Consortium, University of Oxford, OX3 7DQ, UK. .,Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, OX3 7FZ, UK
| | - Peter G K Clark
- Department of Chemistry, Simon Fraser University, Burnaby V5A 1S6, Canada
| | - Duncan A Hay
- Evotec (UK) Ltd, 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire OX14 4RZ, UK
| | - Darren J Dixon
- Department of Chemistry, University of Oxford, Oxford OX1 3TA, UK
| | - Paul E Brennan
- Structural Genomics Consortium, University of Oxford, OX3 7DQ, UK. .,Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, OX3 7FZ, UK
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44
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Galdeano C, Ciulli A. Selectivity on-target of bromodomain chemical probes by structure-guided medicinal chemistry and chemical biology. Future Med Chem 2016; 8:1655-80. [PMID: 27193077 PMCID: PMC5321501 DOI: 10.4155/fmc-2016-0059] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Accepted: 04/22/2016] [Indexed: 12/18/2022] Open
Abstract
Targeting epigenetic proteins is a rapidly growing area for medicinal chemistry and drug discovery. Recent years have seen an explosion of interest in developing small molecules binding to bromodomains, the readers of acetyl-lysine modifications. A plethora of co-crystal structures has motivated focused fragment-based design and optimization programs within both industry and academia. These efforts have yielded several compounds entering the clinic, and many more are increasingly being used as chemical probes to interrogate bromodomain biology. High selectivity of chemical probes is necessary to ensure biological activity is due to an on-target effect. Here, we review the state-of-the-art of bromodomain-targeting compounds, focusing on the structural basis for their on-target selectivity or lack thereof. We also highlight chemical biology approaches to enhance on-target selectivity.
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Affiliation(s)
- Carles Galdeano
- Division of Biological Chemistry & Drug Discovery, School of Life Sciences, University of Dundee, James Black Centre, Dow Street, Dundee, DD1 5EH, UK
- Institut de Biomedicina de la Universitat de Barcelona (IBUB) & Departament de Fisicoquímica, Facultat de Farmàcia, Universitat de Barcelona, Av. Joan XXIII s/n, 08028 Barcelona, Spain
| | - Alessio Ciulli
- Division of Biological Chemistry & Drug Discovery, School of Life Sciences, University of Dundee, James Black Centre, Dow Street, Dundee, DD1 5EH, UK
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45
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Clark PGK, Dixon DJ, Brennan PE. Development of chemical probes for the bromodomains of BRD7 and BRD9. DRUG DISCOVERY TODAY. TECHNOLOGIES 2016; 19:73-80. [PMID: 27769361 DOI: 10.1016/j.ddtec.2016.05.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Revised: 05/09/2016] [Accepted: 05/17/2016] [Indexed: 12/15/2022]
Abstract
The bromodomain family of proteins are 'readers' of acetylated lysines of histones, a key mark in the epigenetic code of gene regulation. Without high quality chemical probes with which to study these proteins, their biological function, and potential use in therapeutics, remains unknown. Recently, a number of chemical ligands were reported for the previously unprobed bromodomain proteins BRD7 and BRD9. Herein the development and characterisation of probes against these proteins is detailed, including the preliminary biological activity of BRD7 and BRD9 assessed using these probes. Future studies utilising these chemically-diverse compounds in parallel will allow for a confident assessment of the role of BRD7/9, and give multiple entry points into any subsequent pharmaceutical programs.
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Affiliation(s)
- Peter G K Clark
- Department of Chemistry, University of Oxford, Oxford OX1 3TA, UK
| | - Darren J Dixon
- Department of Chemistry, University of Oxford, Oxford OX1 3TA, UK
| | - Paul E Brennan
- Structural Genomics Consortium, Target Discovery Institute, and Alzheimer's Research UK Oxford Drug Discovery Institute, Nuffield Dept of Medicine, Oxford OX3 7FZ, UK.
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46
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Theodoulou NH, Tomkinson NCO, Prinjha RK, Humphreys PG. Clinical progress and pharmacology of small molecule bromodomain inhibitors. Curr Opin Chem Biol 2016; 33:58-66. [DOI: 10.1016/j.cbpa.2016.05.028] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Revised: 05/25/2016] [Accepted: 05/30/2016] [Indexed: 11/26/2022]
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47
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Spiliotopoulos D, Caflisch A. Fragment-based in silico screening of bromodomain ligands. DRUG DISCOVERY TODAY. TECHNOLOGIES 2016; 19:81-90. [PMID: 27769362 DOI: 10.1016/j.ddtec.2016.06.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Revised: 06/09/2016] [Accepted: 06/15/2016] [Indexed: 01/31/2023]
Abstract
We review the results of fragment-based high-throughput docking to the N-terminal bromodomain of BRD4 and the CREBBP bromodomain. In both docking campaigns the ALTA (anchor-based library tailoring) procedure was used to reduce the size of the initial library by selecting for flexible docking only the molecules that contain a fragment with favorable predicted binding energy. Ranking by a force field-based energy with solvation has resulted in small-molecule hits with low-micromolar affinity and favorable ligand efficiency. Importantly, the binding modes predicted by docking have been validated by X-ray crystallography. One of the hits for the CREBBP bromodomain has been optimized by medicinal chemistry into a series of potent and selective ligands.
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Affiliation(s)
| | - Amedeo Caflisch
- Department of Biochemistry, University of Zurich, CH-8057 Zurich, Switzerland.
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48
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Crawford TD, Tsui V, Flynn EM, Wang S, Taylor AM, Côté A, Audia JE, Beresini MH, Burdick DJ, Cummings R, Dakin LA, Duplessis M, Good AC, Hewitt MC, Huang HR, Jayaram H, Kiefer JR, Jiang Y, Murray J, Nasveschuk CG, Pardo E, Poy F, Romero FA, Tang Y, Wang J, Xu Z, Zawadzke LE, Zhu X, Albrecht BK, Magnuson SR, Bellon S, Cochran AG. Diving into the Water: Inducible Binding Conformations for BRD4, TAF1(2), BRD9, and CECR2 Bromodomains. J Med Chem 2016; 59:5391-402. [PMID: 27219867 DOI: 10.1021/acs.jmedchem.6b00264] [Citation(s) in RCA: 81] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The biological role played by non-BET bromodomains remains poorly understood, and it is therefore imperative to identify potent and highly selective inhibitors to effectively explore the biology of individual bromodomain proteins. A ligand-efficient nonselective bromodomain inhibitor was identified from a 6-methyl pyrrolopyridone fragment. Small hydrophobic substituents replacing the N-methyl group were designed directing toward the conserved bromodomain water pocket, and two distinct binding conformations were then observed. The substituents either directly displaced and rearranged the conserved solvent network, as in BRD4(1) and TAF1(2), or induced a narrow hydrophobic channel adjacent to the lipophilic shelf, as in BRD9 and CECR2. The preference of distinct substituents for individual bromodomains provided selectivity handles useful for future lead optimization efforts for selective BRD9, CECR2, and TAF1(2) inhibitors.
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Affiliation(s)
- Terry D Crawford
- Genentech, Inc. 1 DNA Way, South San Francisco, California 94080, United States
| | - Vickie Tsui
- Genentech, Inc. 1 DNA Way, South San Francisco, California 94080, United States
| | - E Megan Flynn
- Genentech, Inc. 1 DNA Way, South San Francisco, California 94080, United States
| | - Shumei Wang
- Genentech, Inc. 1 DNA Way, South San Francisco, California 94080, United States
| | - Alexander M Taylor
- Constellation Pharmaceuticals, Inc. 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Alexandre Côté
- Constellation Pharmaceuticals, Inc. 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - James E Audia
- Constellation Pharmaceuticals, Inc. 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Maureen H Beresini
- Genentech, Inc. 1 DNA Way, South San Francisco, California 94080, United States
| | - Daniel J Burdick
- Genentech, Inc. 1 DNA Way, South San Francisco, California 94080, United States
| | - Richard Cummings
- Constellation Pharmaceuticals, Inc. 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Les A Dakin
- Constellation Pharmaceuticals, Inc. 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Martin Duplessis
- Constellation Pharmaceuticals, Inc. 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Andrew C Good
- Constellation Pharmaceuticals, Inc. 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Michael C Hewitt
- Constellation Pharmaceuticals, Inc. 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Hon-Ren Huang
- Constellation Pharmaceuticals, Inc. 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Hariharan Jayaram
- Constellation Pharmaceuticals, Inc. 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - James R Kiefer
- Genentech, Inc. 1 DNA Way, South San Francisco, California 94080, United States
| | - Ying Jiang
- Wuxi AppTec Co., Ltd. , 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, People's Republic of China
| | - Jeremy Murray
- Genentech, Inc. 1 DNA Way, South San Francisco, California 94080, United States
| | - Christopher G Nasveschuk
- Constellation Pharmaceuticals, Inc. 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Eneida Pardo
- Constellation Pharmaceuticals, Inc. 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Florence Poy
- Constellation Pharmaceuticals, Inc. 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - F Anthony Romero
- Genentech, Inc. 1 DNA Way, South San Francisco, California 94080, United States
| | - Yong Tang
- Constellation Pharmaceuticals, Inc. 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Jian Wang
- Wuxi AppTec Co., Ltd. , 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, People's Republic of China
| | - Zhaowu Xu
- Wuxi AppTec Co., Ltd. , 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, People's Republic of China
| | - Laura E Zawadzke
- Constellation Pharmaceuticals, Inc. 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Xiaoyu Zhu
- Wuxi AppTec Co., Ltd. , 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, People's Republic of China
| | - Brian K Albrecht
- Constellation Pharmaceuticals, Inc. 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Steven R Magnuson
- Genentech, Inc. 1 DNA Way, South San Francisco, California 94080, United States
| | - Steve Bellon
- Constellation Pharmaceuticals, Inc. 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Andrea G Cochran
- Genentech, Inc. 1 DNA Way, South San Francisco, California 94080, United States
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49
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Affiliation(s)
- Rezaul M. Karim
- Drug Discovery Department, Moffitt Cancer Center, Tampa, Florida 33612, United States
- Department of Molecular Medicine, University of South Florida, Tampa, Florida 33612, United States
| | - Ernst Schönbrunn
- Drug Discovery Department, Moffitt Cancer Center, Tampa, Florida 33612, United States
- Department of Molecular Medicine, University of South Florida, Tampa, Florida 33612, United States
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Unzue A, Zhao H, Lolli G, Dong J, Zhu J, Zechner M, Dolbois A, Caflisch A, Nevado C. The “Gatekeeper” Residue Influences the Mode of Binding of Acetyl Indoles to Bromodomains. J Med Chem 2016; 59:3087-97. [DOI: 10.1021/acs.jmedchem.5b01757] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Andrea Unzue
- Department of Chemistry and ‡Department of
Biochemistry, University of Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Hongtao Zhao
- Department of Chemistry and ‡Department of
Biochemistry, University of Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Graziano Lolli
- Department of Chemistry and ‡Department of
Biochemistry, University of Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Jing Dong
- Department of Chemistry and ‡Department of
Biochemistry, University of Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Jian Zhu
- Department of Chemistry and ‡Department of
Biochemistry, University of Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Melanie Zechner
- Department of Chemistry and ‡Department of
Biochemistry, University of Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Aymeric Dolbois
- Department of Chemistry and ‡Department of
Biochemistry, University of Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Amedeo Caflisch
- Department of Chemistry and ‡Department of
Biochemistry, University of Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Cristina Nevado
- Department of Chemistry and ‡Department of
Biochemistry, University of Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
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