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A miniaturized mode-of-action profiling platform enables high throughput characterization of the molecular and cellular dynamics of EZH2 inhibition. Sci Rep 2024; 14:1739. [PMID: 38242973 PMCID: PMC10799085 DOI: 10.1038/s41598-023-50964-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Accepted: 12/28/2023] [Indexed: 01/21/2024] Open
Abstract
The market approval of Tazemetostat (TAZVERIK) for the treatment of follicular lymphoma and epithelioid sarcoma has established "enhancer of zeste homolog 2" (EZH2) as therapeutic target in oncology. Despite their structural similarities and common mode of inhibition, Tazemetostat and other EZH2 inhibitors display differentiated pharmacological profiles based on their target residence time. Here we established high throughput screening methods based on time-resolved fluorescence energy transfer, scintillation proximity and high content analysis microscopy to quantify the biochemical and cellular binding of a chemically diverse collection of EZH2 inhibitors. These assays allowed to further characterize the interplay between EZH2 allosteric modulation by methylated histone tails (H3K27me3) and inhibitor binding, and to evaluate the impact of EZH2's clinically relevant mutant Y641N on drug target residence times. While all compounds in this study exhibited slower off-rates, those with clinical candidate status display significantly slower target residence times in wild type EZH2 and disease-related mutants. These inhibitors interact in a more entropy-driven fashion and show the most persistent effects in cellular washout and antiproliferative efficacy experiments. Our work provides mechanistic insights for the largest cohort of EZH2 inhibitors reported to date, demonstrating that-among several other binding parameters-target residence time is the best predictor of cellular efficacy.
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Treating Cancer by Spindle Assembly Checkpoint Abrogation: Discovery of Two Clinical Candidates, BAY 1161909 and BAY 1217389, Targeting MPS1 Kinase. J Med Chem 2020; 63:8025-8042. [PMID: 32338514 DOI: 10.1021/acs.jmedchem.9b02035] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Inhibition of monopolar spindle 1 (MPS1) kinase represents a novel approach to cancer treatment: instead of arresting the cell cycle in tumor cells, cells are driven into mitosis irrespective of DNA damage and unattached/misattached chromosomes, resulting in aneuploidy and cell death. Starting points for our optimization efforts with the goal to identify MPS1 inhibitors were two HTS hits from the distinct chemical series "triazolopyridines" and "imidazopyrazines". The major initial issue of the triazolopyridine series was the moderate potency of the HTS hits. The imidazopyrazine series displayed more than 10-fold higher potencies; however, in the early project phase, this series suffered from poor metabolic stability. Here, we outline the evolution of the two hit series to clinical candidates BAY 1161909 and BAY 1217389 and reveal how both clinical candidates bind to the ATP site of MPS1 kinase, while addressing different pockets utilizing different binding interactions, along with their synthesis and preclinical characterization in selected in vivo efficacy models.
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Abstract
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ATAD2
(ANCCA) is an epigenetic regulator and transcriptional cofactor,
whose overexpression has been linked to the progress of various cancer
types. Here, we report a DNA-encoded library screen leading to the
discovery of BAY-850, a potent and isoform selective inhibitor that
specifically induces ATAD2 bromodomain dimerization and prevents interactions
with acetylated histones in vitro, as well as with
chromatin in cells. These features qualify BAY-850 as a chemical probe
to explore ATAD2 biology.
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Abstract 980: BAY-299, a novel chemical probe for in-depth analysis of the function of the bromodomain proteins BRPF2 and TAF1. Cancer Res 2017. [DOI: 10.1158/1538-7445.am2017-980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
With the exception of the bromodomain and extra-terminal domain BET subgroup, little is known about the role of bromodomain (BD) containing proteins in cancer so that there is a dire need for chemical probes addressing other family members. The bromodomain and PHD-finger (BRPF) family encompasses three paralogs, BRPF1, BRPF2 and BRPF3, which are all found in histone acetyltransferase (HAT) complexes. BRPF2 is a scaffold protein and its knock-out leads to embryonic lethality at E15.5, potentially due to its role in embryonic stem cell differentiation. Here we present the structure-activity relationship (SAR) and characterization of the first selective BRPF2 chemical probe BAY-299, with additionnal strong activity at TAF1, a major component of the basal transcription initiation complex TFIID. BAY-299 shows in vitro activity for BRPF2 (IC50 = 67 nM) and TAF1 second bromodomain (BD2; IC50 = 8 nM) in the TR-FRET assay, as well as in the cellular NanoBRET assay [IC50 (BRPF2) = 575 nM; IC50 (TAF1 BD2) = 825 nM]. To the best of our knowledge BAY-299 is the only disclosed inhibitor showing BRPF2 selectivity over its two paralogues BRPF1 and BRPF3. It belongs to the 1,3-benzimidazolone scaffold and bears a novel substitution which is responsible for its high BRPF2 selectivity and also for its inactivity on BET BDs. The dual inhibitory properties of BAY-299 against BRPF2 and TAF1 make it an ideal research tool for further investigation of these two proteins in physiological and pathological processes.
Citation Format: Lea Bouche, Clara D. Christ, Stephan Siegel, Cynthia Tallant, Amaury E. Fernández-Montalván, Kilian V. Huber, Verra Pütter, Susanne Müller, Oleg Fedorov, Antonius ter Laak, Tatsuo Sugawara, Detlef Stöckigt, Julia Meier, Simon J. Holton, Ingo V. Hartung, Bernard Haendler. BAY-299, a novel chemical probe for in-depth analysis of the function of the bromodomain proteins BRPF2 and TAF1 [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 980. doi:10.1158/1538-7445.AM2017-980
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Abstract
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Bromodomains
(BD) are readers of lysine acetylation marks present
in numerous proteins associated with chromatin. Here we describe a
dual inhibitor of the bromodomain and PHD finger (BRPF) family member
BRPF2 and the TATA box binding protein-associated factors TAF1 and
TAF1L. These proteins are found in large chromatin complexes and play
important roles in transcription regulation. The substituted benzoisoquinolinedione
series was identified by high-throughput screening, and subsequent
structure–activity relationship optimization allowed generation
of low nanomolar BRPF2 BD inhibitors with strong selectivity against
BRPF1 and BRPF3 BDs. In addition, a strong inhibition of TAF1/TAF1L
BD2 was measured for most derivatives. The best compound of the series
was BAY-299, which is a very potent, dual inhibitor with an IC50 of 67 nM for BRPF2 BD, 8 nM for TAF1 BD2, and 106 nM for
TAF1L BD2. Importantly, no activity was measured for BRD4 BDs. Furthermore,
cellular activity was evidenced using a BRPF2– or TAF1–histone
H3.3 or H4 interaction assay.
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Discovery and Characterization of a Highly Potent and Selective Aminopyrazoline-Based in Vivo Probe (BAY-598) for the Protein Lysine Methyltransferase SMYD2. J Med Chem 2016; 59:4578-600. [PMID: 27075367 PMCID: PMC4917279 DOI: 10.1021/acs.jmedchem.5b01890] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
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Protein
lysine methyltransferases have recently emerged as a new target class
for the development of inhibitors that modulate gene transcription
or signaling pathways. SET and MYND domain containing protein 2 (SMYD2)
is a catalytic SET domain containing methyltransferase reported to
monomethylate lysine residues on histone and nonhistone proteins.
Although several studies have uncovered an important role of SMYD2
in promoting cancer by protein methylation, the biology of SMYD2 is
far from being fully understood. Utilization of highly potent and
selective chemical probes for target validation has emerged as a concept
which circumvents possible limitations of knockdown experiments and,
in particular, could result in an improved exploration of drug targets
with a complex underlying biology. Here, we report the development
of a potent, selective, and cell-active, substrate-competitive inhibitor
of SMYD2, which is the first reported inhibitor suitable for in vivo
target validation studies in rodents.
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Extensive Study on the Minor Constituents of the Essential Oil ofEucalyptus divesSchau. Type. JOURNAL OF ESSENTIAL OIL RESEARCH 2006. [DOI: 10.1080/10412905.2006.9699180] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Abstract
In the past flavor research and the development of new flavorings were constantly driven by the interaction of flavor analysis, structure elucidation, and chemical synthesis accompanied by sensory. Highly potent flavor compounds were identified in numerous food products and helped to establish a powerful toolbox for flavorists. Nowadays we experience the merging of various scientific disciplines, for example medicine, biology, chemistry, and various technologies in the field of flavor research, which shows direct impact on our understanding of flavors. At the same time modern life has profoundly changed our eating habits. This situation generates new challenges for product development teams, which represent all facets of technologies. This paper will illustrate different examples for the evolution of product-oriented flavor research and future trends.
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Liquid chromatography/mass spectrometry and liquid chromatography/nuclear magnetic resonance as complementary analytical techniques for unambiguous identification of polymethoxylated flavones in residues from molecular distillation of orange peel oils (Citrus sinensis). JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2006; 54:274-8. [PMID: 16417279 DOI: 10.1021/jf051606f] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Liquid chromatography/mass spectrometry and liquid chromatography/nuclear magnetic resonance techniques with ultraviolet/diode array detection were used as complementary analytical tools for the reliable identification of polymethoxylated flavones in residues from molecular distillation of cold-pressed peel oils of Citrus sinensis. After development of a liquid chromatographic separation procedure, the presence of several polymethoxy flavones such as sinensetin, nobiletin, tangeretin, quercetogetin, heptamethoxyflavone, and other derivatives was unambiguously confirmed. In addition, proceranone, an acetylated tetranortriterpenoid with limonoid structure, was identified for the first time in citrus.
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High-performance liquid chromatographic, capillary electrophoretic and capillary electrophoretic-electrospray ionisation mass spectrometric analysis of selected alkaloid groups. J Chromatogr A 2002; 967:85-113. [PMID: 12219932 DOI: 10.1016/s0021-9673(02)00037-7] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Systems for efficient separation of selected alkaloid groups by high performance liquid chromatography (HPLC), capillary electrophoresis (CE) and capillary electrophoresis coupled with electrospray ionisation mass spectrometry (CE-ESI-MS) are described. The optimized HPLC system was applied for the separation of 23 standard indole alkaloids as well as for qualitative and quantitative analyses of crude alkaloid extracts of Rauvolfia serpentina X Rhazya stricta hybrid cell cultures. The developed conditions for CE analysis proved to be efficient for separation of mixtures of standard indole and beta-carboline alkaloids. The described buffer system is also applicable in the combination of CE with electrospray ionisation mass spectrometry. This analytical technique allowed the separation and identification of components of standard indole alkaloid mixture as well as crude extracts of R. serpentina roots, R. serpentina cell suspension cultures and cortex of Aspidosperma quebracho-blanco. The influence of buffer composition and analyte structures on separation is discussed.
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Abstract
About 1000 catalytic or stoichiometric asymmetric reactions of racemic compounds or prochiral substrates bearing enantiotopic groups can be analyzed per day. In this highly efficient method the enantioselectivity is determined by electrospray ionization mass spectrometry using isotopically labeled substrates. The picture shows the mass spectrum of the mixture obtained upon hydrolysis of 1 to afford the pseudo-enantiomeric products 2 and 3.
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Contra-Binding Rotation in Al+−L Complexes (L = C6H6, C4H4O, C5H6, C4H4NH): A New Degenerate Rearrangement. Organometallics 1999. [DOI: 10.1021/om9809015] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Synthesis, structure and characterization of zinc(II), copper(II), zinc(II) barium(II) and copper(II) barium(II) complexes of macrocyclic heteronucleating ligands based on isothiosemicarbazide. Inorganica Chim Acta 1998. [DOI: 10.1016/s0020-1693(98)00198-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Theoretical and Experimental Study on the Bond Dissociation Energies of Al(Methane) +, Al(Acetylene) +, Al(Ethene) +, and Al(Ethane) +. J Phys Chem A 1998. [DOI: 10.1021/jp9818986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Analysis of Rauwolfia Alkaloids Employing Capillary Electrophoresis-Mass Spectrometry. ACTA ACUST UNITED AC 1997. [DOI: 10.1080/10575639708043638] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Analysis of basic pharmaceuticals by capillary electrophoresis in coated capillaries and on-line mass spectrometric detection. J Chromatogr A 1996. [DOI: 10.1016/s0021-9673(96)00511-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Theoretical and Experimental Studies on the Bond Dissociation Energies of Al(methane)+, Al(acetylene)+, Al(ethene)+, and Al(ethane)+. ACTA ACUST UNITED AC 1996. [DOI: 10.1021/jp960060k] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Application of density functional theory /Hartree-Fock hybrid methods. Geometries and bond dissociation energies of Al+ complexes. Chem Phys Lett 1996. [DOI: 10.1016/0009-2614(96)00024-3] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Catalytic gas-phase oxidation of olefins mediated by Fe(C6H6)+ and a comparison of Fe(L)+ complexes (L = benzene, pyridine, naphthalene). ACTA ACUST UNITED AC 1995. [DOI: 10.1002/jlac.199519950253] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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24
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Reactivity Tuning by Ligand Effects: Gas-Phase Reactions of Fe(C6H6)O+ versus “Bare” FeO+. ACTA ACUST UNITED AC 1994. [DOI: 10.1002/cber.19941271222] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Ligand Effects on the Gas-Phase Reactions of (π-L)FeI Complexes withn-Pentanenitrile. ACTA ACUST UNITED AC 1993. [DOI: 10.1002/cber.19931261134] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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OH Bond Activation in the Gas Phase: The Reactions of Water and Methanol with[FeCH3]+. ACTA ACUST UNITED AC 1992. [DOI: 10.1002/anie.199206031] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Transition-Metal-Induced Generation of C2H4 from 1,7-Octadiene: Regiospecific Activation of Internal CC Bonds instead of Metathesis-like Coupling of Terminal CH2 Groups. Angew Chem Int Ed Engl 1990. [DOI: 10.1002/anie.199004021] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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