1
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Bursch KL, Goetz CJ, Jiao G, Nuñez R, Olp MD, Dhiman A, Khurana M, Zimmermann MT, Urrutia RA, Dykhuizen EC, Smith BC. Cancer-associated polybromo-1 bromodomain 4 missense variants variably impact bromodomain ligand binding and cell growth suppression. J Biol Chem 2024; 300:107146. [PMID: 38460939 PMCID: PMC11002309 DOI: 10.1016/j.jbc.2024.107146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 02/12/2024] [Accepted: 02/29/2024] [Indexed: 03/11/2024] Open
Abstract
The polybromo, brahma-related gene 1-associated factors (PBAF) chromatin remodeling complex subunit polybromo-1 (PBRM1) contains six bromodomains that recognize and bind acetylated lysine residues on histone tails and other nuclear proteins. PBRM1 bromodomains thus provide a link between epigenetic posttranslational modifications and PBAF modulation of chromatin accessibility and transcription. As a putative tumor suppressor in several cancers, PBRM1 protein expression is often abrogated by truncations and deletions. However, ∼33% of PBRM1 mutations in cancer are missense and cluster within its bromodomains. Such mutations may generate full-length PBRM1 variant proteins with undetermined structural and functional characteristics. Here, we employed computational, biophysical, and cellular assays to interrogate the effects of PBRM1 bromodomain missense variants on bromodomain stability and function. Since mutations in the fourth bromodomain of PBRM1 (PBRM1-BD4) comprise nearly 20% of all cancer-associated PBRM1 missense mutations, we focused our analysis on PBRM1-BD4 missense protein variants. Selecting 16 potentially deleterious PBRM1-BD4 missense protein variants for further study based on high residue mutational frequency and/or conservation, we show that cancer-associated PBRM1-BD4 missense variants exhibit varied bromodomain stability and ability to bind acetylated histones. Our results demonstrate the effectiveness of identifying the unique impacts of individual PBRM1-BD4 missense variants on protein structure and function, based on affected residue location within the bromodomain. This knowledge provides a foundation for drawing correlations between specific cancer-associated PBRM1 missense variants and distinct alterations in PBRM1 function, informing future cancer personalized medicine approaches.
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Affiliation(s)
- Karina L Bursch
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin, USA; Structural Genomics Unit, Linda T. and John A. Mellowes Center for Genomic Sciences and Precision Medicine, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Christopher J Goetz
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Guanming Jiao
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana, USA
| | - Raymundo Nuñez
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Michael D Olp
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Alisha Dhiman
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana, USA
| | - Mallika Khurana
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Michael T Zimmermann
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin, USA; Structural Genomics Unit, Linda T. and John A. Mellowes Center for Genomic Sciences and Precision Medicine, Medical College of Wisconsin, Milwaukee, Wisconsin, USA; Clinical and Translational Sciences Institute, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Raul A Urrutia
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin, USA; Structural Genomics Unit, Linda T. and John A. Mellowes Center for Genomic Sciences and Precision Medicine, Medical College of Wisconsin, Milwaukee, Wisconsin, USA; Department of Surgery, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Emily C Dykhuizen
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana, USA
| | - Brian C Smith
- Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin, USA; Structural Genomics Unit, Linda T. and John A. Mellowes Center for Genomic Sciences and Precision Medicine, Medical College of Wisconsin, Milwaukee, Wisconsin, USA; Program in Chemical Biology, Medical College of Wisconsin, Milwaukee, Wisconsin, USA.
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2
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Berlin M, Cantley J, Bookbinder M, Bortolon E, Broccatelli F, Cadelina G, Chan EW, Chen H, Chen X, Cheng Y, Cheung TK, Davenport K, DiNicola D, Gordon D, Hamman BD, Harbin A, Haskell R, He M, Hole AJ, Januario T, Kerry PS, Koenig SG, Li L, Merchant M, Pérez-Dorado I, Pizzano J, Quinn C, Rose CM, Rousseau E, Soto L, Staben LR, Sun H, Tian Q, Wang J, Wang W, Ye CS, Ye X, Zhang P, Zhou Y, Yauch R, Dragovich PS. PROTACs Targeting BRM (SMARCA2) Afford Selective In Vivo Degradation over BRG1 (SMARCA4) and Are Active in BRG1 Mutant Xenograft Tumor Models. J Med Chem 2024; 67:1262-1313. [PMID: 38180485 DOI: 10.1021/acs.jmedchem.3c01781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2024]
Abstract
The identification of VHL-binding proteolysis targeting chimeras (PROTACs) that potently degrade the BRM protein (also known as SMARCA2) in SW1573 cell-based experiments is described. These molecules exhibit between 10- and 100-fold degradation selectivity for BRM over the closely related paralog protein BRG1 (SMARCA4). They also selectively impair the proliferation of the H1944 "BRG1-mutant" NSCLC cell line, which lacks functional BRG1 protein and is thus highly dependent on BRM for growth, relative to the wild-type Calu6 line. In vivo experiments performed with a subset of compounds identified PROTACs that potently and selectively degraded BRM in the Calu6 and/or the HCC2302 BRG1 mutant NSCLC xenograft models and also afforded antitumor efficacy in the latter system. Subsequent PK/PD analysis established a need to achieve strong BRM degradation (>95%) in order to trigger meaningful antitumor activity in vivo. Intratumor quantitation of mRNA associated with two genes whose transcription was controlled by BRM (PLAU and KRT80) also supported this conclusion.
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Affiliation(s)
- Michael Berlin
- Arvinas LLC, 5 Science Park, New Haven, Connecticut 06511, United States
| | - Jennifer Cantley
- Arvinas LLC, 5 Science Park, New Haven, Connecticut 06511, United States
| | - Mark Bookbinder
- Arvinas LLC, 5 Science Park, New Haven, Connecticut 06511, United States
| | - Elizabeth Bortolon
- Arvinas LLC, 5 Science Park, New Haven, Connecticut 06511, United States
| | - Fabio Broccatelli
- Genentech Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Greg Cadelina
- Arvinas LLC, 5 Science Park, New Haven, Connecticut 06511, United States
| | - Emily W Chan
- Genentech Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Huifen Chen
- Genentech Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Xin Chen
- Arvinas LLC, 5 Science Park, New Haven, Connecticut 06511, United States
| | - Yunxing Cheng
- Pharmaron Beijing, Co. Ltd., 6 Tai He Road, BDA, Beijing 100176, P. R. China
| | - Tommy K Cheung
- Genentech Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Kim Davenport
- Arvinas LLC, 5 Science Park, New Haven, Connecticut 06511, United States
| | - Dean DiNicola
- Arvinas LLC, 5 Science Park, New Haven, Connecticut 06511, United States
| | - Debbie Gordon
- Arvinas LLC, 5 Science Park, New Haven, Connecticut 06511, United States
| | - Brian D Hamman
- Arvinas LLC, 5 Science Park, New Haven, Connecticut 06511, United States
| | - Alicia Harbin
- Arvinas LLC, 5 Science Park, New Haven, Connecticut 06511, United States
| | - Roy Haskell
- Arvinas LLC, 5 Science Park, New Haven, Connecticut 06511, United States
| | - Mingtao He
- Pharmaron Beijing, Co. Ltd., 6 Tai He Road, BDA, Beijing 100176, P. R. China
| | - Alison J Hole
- Evotec (U.K.) Ltd., 95 Park Drive, Milton Park, Abingdon, Oxfordshire OX14 4RY, U.K
| | - Thomas Januario
- Genentech Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Philip S Kerry
- Evotec (U.K.) Ltd., 95 Park Drive, Milton Park, Abingdon, Oxfordshire OX14 4RY, U.K
| | - Stefan G Koenig
- Genentech Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Limei Li
- Pharmaron Beijing, Co. Ltd., 6 Tai He Road, BDA, Beijing 100176, P. R. China
| | - Mark Merchant
- Genentech Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | | | - Jennifer Pizzano
- Arvinas LLC, 5 Science Park, New Haven, Connecticut 06511, United States
| | - Connor Quinn
- Arvinas LLC, 5 Science Park, New Haven, Connecticut 06511, United States
| | - Christopher M Rose
- Genentech Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Emma Rousseau
- Arvinas LLC, 5 Science Park, New Haven, Connecticut 06511, United States
| | - Leofal Soto
- Arvinas LLC, 5 Science Park, New Haven, Connecticut 06511, United States
| | - Leanna R Staben
- Genentech Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Hongming Sun
- Pharmaron Beijing, Co. Ltd., 6 Tai He Road, BDA, Beijing 100176, P. R. China
| | - Qingping Tian
- Genentech Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Jing Wang
- Arvinas LLC, 5 Science Park, New Haven, Connecticut 06511, United States
| | - Weifeng Wang
- Pharmaron Beijing, Co. Ltd., 6 Tai He Road, BDA, Beijing 100176, P. R. China
| | - Crystal S Ye
- Genentech Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Xiaofen Ye
- Genentech Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Penghong Zhang
- Pharmaron Beijing, Co. Ltd., 6 Tai He Road, BDA, Beijing 100176, P. R. China
| | - Yuhui Zhou
- Genentech Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Robert Yauch
- Genentech Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Peter S Dragovich
- Genentech Inc., 1 DNA Way, South San Francisco, California 94080, United States
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Kaczor AA, Zięba A, Matosiuk D. The application of WaterMap-guided structure-based virtual screening in novel drug discovery. Expert Opin Drug Discov 2024; 19:73-83. [PMID: 37807912 DOI: 10.1080/17460441.2023.2267015] [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: 07/17/2023] [Accepted: 10/02/2023] [Indexed: 10/10/2023]
Abstract
INTRODUCTION Nowadays, it is widely accepted that water molecules play a key role in binding a ligand to a molecular target. Neglecting water molecules in the process of molecular recognition was the result of several failures of the structure-based drug discovery campaigns. The application of WaterMap, in particular WaterMap-guided molecular docking, enables the reasonably accurate and quick description of the location and energetics of water molecules at the ligand-protein interface. AREAS COVERED In this review, the authors shortly discuss the importance of water in drug design and discovery and provide a brief overview of the computational approaches used to predict the solvent-related effects for the purposes of presenting WaterMap in the context of other available techniques and tools. A concise description of WaterMap concept is followed by the presentation of WaterMap-assisted virtual screening literature published between 2013 and 2023. EXPERT OPINION In recent years, WaterMap software has been extensively used to support structure-based drug design, in particular structure-based virtual screening. Indeed, it is a useful tool to rescore docking results considering water molecules in the binding pocket. Although WaterMap allows for the consideration of the dynamic behavior of water molecules in the binding site, for best accuracy, its application in conjunction with other techniques such as molecular mechanics-generalized Born surface area of FEP (Free Energy Perturbation) is recommended.
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Affiliation(s)
- Agnieszka A Kaczor
- Department of Synthesis and Chemical Technology of Pharmaceutical Substances with Computer Modeling Laboratory, Faculty of Pharmacy, Lublin, Poland
- School of Pharmacy, University of Eastern Finland, Kuopio, Finland
| | - Agata Zięba
- Department of Synthesis and Chemical Technology of Pharmaceutical Substances with Computer Modeling Laboratory, Faculty of Pharmacy, Lublin, Poland
| | - Dariusz Matosiuk
- Department of Synthesis and Chemical Technology of Pharmaceutical Substances with Computer Modeling Laboratory, Faculty of Pharmacy, Lublin, Poland
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4
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Cochran AG, Flynn M. GNE-235: A Lead Compound Selective for the Second Bromodomain of PBRM1. J Med Chem 2023; 66:13116-13134. [PMID: 37702400 DOI: 10.1021/acs.jmedchem.3c01149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/14/2023]
Abstract
Bromodomains are acetyl-lysine binding modules that are found in different classes of chromatin-interacting proteins. Among these are large chromatin remodeling complexes such as BAF and PBAF (variants of human SWI/SNF). Previous work has identified chemical probes targeting a subset of the bromodomains present in the BAF and PBAF complexes. Selective inhibitors of the individual bromodomains have proven challenging to discover, as the domains are highly similar. Here, elaboration of an aminopyridazine scaffold used previously to develop probes for the bromodomains of SMARCA2, SMARCA4, and the fifth bromodomain of PBRM1 yielded compounds with both potency and unusual selectivity for the second bromodomain of PBRM1. One of these, GNE-235, and its enantiomer control GNE-234 are suggested for initial cellular investigations of the function of the second bromodomain of PBRM1.
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Affiliation(s)
- Andrea G Cochran
- Department of Biological Chemistry, Genentech, Inc., South San Francisco, California 94080, United States
| | - Megan Flynn
- Department of Biological Chemistry, Genentech, Inc., South San Francisco, California 94080, United States
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5
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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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6
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Divakaran A, Harki DA, Pomerantz WC. Recent progress and structural analyses of domain-selective BET inhibitors. Med Res Rev 2023; 43:972-1018. [PMID: 36971240 PMCID: PMC10520981 DOI: 10.1002/med.21942] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 12/21/2022] [Accepted: 02/26/2023] [Indexed: 03/29/2023]
Abstract
Epigenetic mechanisms for controlling gene expression through heritable modifications to DNA, RNA, and proteins, are essential processes in maintaining cellular homeostasis. As a result of their central role in human diseases, the proteins responsible for adding, removing, or recognizing epigenetic modifications have emerged as viable drug targets. In the case of lysine-ε-N-acetylation (Kac ), bromodomains serve as recognition modules ("readers") of this activating epigenetic mark and competition of the bromodomain-Kac interaction with small-molecule inhibitors is an attractive strategy to control aberrant bromodomain-mediated gene expression. The bromodomain and extra-terminal (BET) family proteins contain eight similar bromodomains. These BET bromodomains are among the more commonly studied bromodomain classes with numerous pan-BET inhibitors showing promising anticancer and anti-inflammatory efficacy. However, these results have yet to translate into Food and Drug Administration-approved drugs, in part due to a high degree of on-target toxicities associated with pan-BET inhibition. Improved selectivity within the BET-family has been proposed to alleviate these concerns. In this review, we analyze the reported BET-domain selective inhibitors from a structural perspective. We highlight three essential characteristics of the reported molecules in generating domain selectivity, binding affinity, and mimicking Kac molecular recognition. In several cases, we provide insight into the design of molecules with improved specificity for individual BET-bromodomains. This review provides a perspective on the current state of the field as this exciting class of inhibitors continue to be evaluated in the clinic.
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Affiliation(s)
- Anand Divakaran
- Department of Medicinal Chemistry, University of Minnesota, 2231 6th St SE, Minneapolis, MN 55455, United States
| | - Daniel A. Harki
- Department of Medicinal Chemistry, University of Minnesota, 2231 6th St SE, Minneapolis, MN 55455, United States
- Department of Chemistry, University of Minnesota, 207 Pleasant St. SE, Minneapolis, MN55455, United States
| | - William C.K. Pomerantz
- Department of Medicinal Chemistry, University of Minnesota, 2231 6th St SE, Minneapolis, MN 55455, United States
- Department of Chemistry, University of Minnesota, 207 Pleasant St. SE, Minneapolis, MN55455, United States
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7
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Shishodia S, Nuñez R, Strohmier BP, Bursch KL, Goetz CJ, Olp MD, Jensen DR, Fenske TG, Ordonez-Rubiano SC, Blau ME, Roach MK, Peterson FC, Volkman BF, Dykhuizen EC, Smith BC. Selective and Cell-Active PBRM1 Bromodomain Inhibitors Discovered through NMR Fragment Screening. J Med Chem 2022; 65:13714-13735. [PMID: 36227159 PMCID: PMC9630929 DOI: 10.1021/acs.jmedchem.2c00864] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
PBRM1 is a subunit of the PBAF chromatin remodeling complex that uniquely contains six bromodomains. PBRM1 can operate as a tumor suppressor or tumor promoter. PBRM1 is a tumor promoter in prostate cancer, contributing to migratory and immunosuppressive phenotypes. Selective chemical probes targeting PBRM1 bromodomains are desired to elucidate the association between aberrant PBRM1 chromatin binding and cancer pathogenesis and the contributions of PBRM1 to immunotherapy. Previous PBRM1 inhibitors unselectively bind SMARCA2 and SMARCA4 bromodomains with nanomolar potency. We used our protein-detected NMR screening pipeline to screen 1968 fragments against the second PBRM1 bromodomain, identifying 17 hits with Kd values from 45 μM to >2 mM. Structure-activity relationship studies on the tightest-binding hit resulted in nanomolar inhibitors with selectivity for PBRM1 over SMARCA2 and SMARCA4. These chemical probes inhibit the association of full-length PBRM1 to acetylated histone peptides and selectively inhibit growth of a PBRM1-dependent prostate cancer cell line.
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Affiliation(s)
- Shifali Shishodia
- Department of Biochemistry, Program in Chemical Biology, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, United States
| | - Raymundo Nuñez
- Department of Biochemistry, Program in Chemical Biology, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, United States
| | - Brayden P Strohmier
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana 47907, United States
| | - Karina L Bursch
- Department of Biochemistry, Program in Chemical Biology, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, United States
| | - Christopher J Goetz
- Department of Biochemistry, Program in Chemical Biology, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, United States
| | - Michael D Olp
- Department of Biochemistry, Program in Chemical Biology, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, United States
| | - Davin R Jensen
- Department of Biochemistry, Program in Chemical Biology, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, United States
| | - Tyler G Fenske
- Department of Biochemistry, Program in Chemical Biology, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, United States
| | - Sandra C Ordonez-Rubiano
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana 47907, United States
| | - Maya E Blau
- Department of Biochemistry, Program in Chemical Biology, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, United States
| | - Mallory K Roach
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana 47907, United States
| | - Francis C Peterson
- Department of Biochemistry, Program in Chemical Biology, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, United States
| | - Brian F Volkman
- 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, Purdue University, 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
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8
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Taylor AM, Bailey C, Belmont LD, Campbell R, Cantone N, Côté A, Crawford TD, Cummings R, DeMent K, Duplessis M, Flynn M, Good AC, Huang HR, Joshi S, Leblanc Y, Murray J, Nasveschuk CG, Neiss A, Poy F, Romero FA, Sandy P, Tang Y, Tsui V, Zawadzke L, Sims RJ, Audia JE, Bellon SF, Magnuson SR, Albrecht BK, Cochran AG. GNE-064: A Potent, Selective, and Orally Bioavailable Chemical Probe for the Bromodomains of SMARCA2 and SMARCA4 and the Fifth Bromodomain of PBRM1. J Med Chem 2022; 65:11177-11186. [PMID: 35930799 DOI: 10.1021/acs.jmedchem.2c00662] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Bromodomains are acetyllysine recognition domains present in a variety of human proteins. Bromodomains also bind small molecules that compete with acetyllysine, and therefore bromodomains have been targets for drug discovery efforts. Highly potent and selective ligands with good cellular permeability have been proposed as chemical probes for use in exploring the functions of many of the bromodomain proteins. We report here the discovery of a class of such inhibitors targeting the family VIII bromodomains of SMARCA2 (BRM) and SMARCA4 (BRG1), and PBRM1 (polybromo-1) bromodomain 5. We propose one example from this series, GNE-064, as a chemical probe for the bromodomains SMARCA2, SMARCA4, and PBRM1(5) with the potential for in vivo use.
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Affiliation(s)
- Alexander M Taylor
- Constellation, a Morphosys Company, 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Chris Bailey
- Constellation, a Morphosys Company, 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Lisa D Belmont
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Robert Campbell
- Constellation, a Morphosys Company, 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Nico Cantone
- Constellation, a Morphosys Company, 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Alexandre Côté
- Constellation, a Morphosys Company, 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Terry D Crawford
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Richard Cummings
- Constellation, a Morphosys Company, 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Kevin DeMent
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Martin Duplessis
- Constellation, a Morphosys Company, 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Megan Flynn
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Andrew C Good
- Constellation, a Morphosys Company, 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Hon-Ren Huang
- Constellation, a Morphosys Company, 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Shivangi Joshi
- Constellation, a Morphosys Company, 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Yves Leblanc
- Constellation, a Morphosys Company, 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, a Morphosys Company, 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Adrianne Neiss
- Constellation, a Morphosys Company, 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Florence Poy
- Constellation, a Morphosys Company, 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
| | - Peter Sandy
- Constellation, a Morphosys Company, 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Yong Tang
- Constellation, a Morphosys Company, 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Vickie Tsui
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Laura Zawadzke
- Constellation, a Morphosys Company, 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Robert J Sims
- Constellation, a Morphosys Company, 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - James E Audia
- Constellation, a Morphosys Company, 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Steven F Bellon
- Constellation, a Morphosys Company, 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
| | - Brian K Albrecht
- Constellation, a Morphosys Company, 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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9
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Yang X, Sun J, Huang X, Jin Z. Asymmetric Synthesis of Structurally Sophisticated Spirocyclic Pyrano[2,3- c]pyrazole Derivatives Bearing a Chiral Quaternary Carbon Center. Org Lett 2022; 24:5474-5479. [PMID: 35857420 DOI: 10.1021/acs.orglett.2c02211] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A carbene-catalyzed enantio- and diastereoselective [2 + 4] cycloaddition reaction is developed for quick and efficient access to structurally complex multicyclic pyrano[2,3-c]pyrazole molecules. The reaction tolerates a broad scope of substrates bearing various substitution patterns, with the multicyclic pyrano[2,3-c]pyrazole products afforded in generally good to excellent yields and optical purities. The chiral molecules obtained from this approach has found promising applications in the development of novel bacteriacides for plant protection.
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Affiliation(s)
- Xiaoqun Yang
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Huaxi District, Guiyang 550025, China
| | - Jun Sun
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Huaxi District, Guiyang 550025, China
| | - Xuan Huang
- International Joint Research Center for Molecular Science, College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen 518060, China
| | - Zhichao Jin
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Huaxi District, Guiyang 550025, China
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10
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Webb T, Craigon C, Ciulli A. Targeting epigenetic modulators using PROTAC degraders: Current status and future perspective. Bioorg Med Chem Lett 2022; 63:128653. [PMID: 35257896 DOI: 10.1016/j.bmcl.2022.128653] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 02/27/2022] [Accepted: 03/02/2022] [Indexed: 01/10/2023]
Abstract
Epigenetic modulators perform critical functions in gene expression for rapid adaption to external stimuli and are prevalent in all higher-order organisms. The establishment of a link between dysregulation of epigenetic processes and disease pathogenesis, particularly in cancer, has led to much interest in identifying drug targets. This prompted the development of small molecule inhibitors, primarily in haematological malignancies. While there have been epigenetic-targeting drugs to receive FDA approval for the treatment of cancers, many suffer from limited applicability, toxicity and the onset of drug resistance, as our understanding of the biology remains incomplete. The recent advent of genome-wide RNAi and CRISPR screens has shed new light on loss of specific proteins causing vulnerabilities of specific cancer types, highlighting the potential for exploiting synthetic lethality as a therapeutic approach. However, small molecule inhibitors have largely been unable to recapitulate phenotypic effects observed using genome-wide knockdown approaches. This mechanistic disconnect and gap are set to be addressed by targeted protein degradation. Degraders such as PROTACs targeting epigenetic proteins recapitulate CRISPR mediated genetic knockdown at the post-translational level and therefore can better exploit target druggability. Here, we review the current landscape of epigenetic drug discovery, the rationale behind and progress made in the development of PROTAC degraders, and look at future perspectives for the field.
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Affiliation(s)
- Thomas Webb
- Centre for Targeted Protein Degradation, Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH, Scotland, United Kingdom
| | - Conner Craigon
- Centre for Targeted Protein Degradation, Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH, Scotland, United Kingdom
| | - Alessio Ciulli
- Centre for Targeted Protein Degradation, Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dow Street, Dundee, DD1 5EH, Scotland, United Kingdom.
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11
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Morningstar-Kywi N, Wang K, Asbell TR, Wang Z, Giles JB, Lai J, Brill D, Sutch BT, Haworth IS. Prediction of Water Distributions and Displacement at Protein-Ligand Interfaces. J Chem Inf Model 2022; 62:1489-1497. [PMID: 35261241 DOI: 10.1021/acs.jcim.1c01266] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The retention and displacement of water molecules during formation of ligand-protein interfaces play a major role in determining ligand binding. Understanding these effects requires a method for positioning of water molecules in the bound and unbound proteins and for defining water displacement upon ligand binding. We describe an algorithm for water placement and a calculation of ligand-driven water displacement in >9000 protein-ligand complexes. The algorithm predicts approximately 38% of experimental water positions within 1.0 Å and about 83% within 1.5 Å. We further show that the predicted water molecules can complete water networks not detected in crystallographic structures of the protein-ligand complexes. The algorithm was also applied to solvation of the corresponding unbound proteins, and this allowed calculation of water displacement upon ligand binding based on differences in the water network between the bound and unbound structures. We illustrate use of this approach through comparison of water displacement by structurally related ligands at the same binding site. This method for evaluation of water displacement upon ligand binding may be of value for prediction of the effects of ligand modification in drug design.
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Affiliation(s)
- Noam Morningstar-Kywi
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, 1985 Zonal Avenue, Los Angeles, California 90089, United States
| | - Kaichen Wang
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, 1985 Zonal Avenue, Los Angeles, California 90089, United States
| | - Thomas R Asbell
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, 1985 Zonal Avenue, Los Angeles, California 90089, United States
| | - Zhaohui Wang
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, 1985 Zonal Avenue, Los Angeles, California 90089, United States
| | - Jason B Giles
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, 1985 Zonal Avenue, Los Angeles, California 90089, United States
| | - Jiawei Lai
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, 1985 Zonal Avenue, Los Angeles, California 90089, United States
| | - Dab Brill
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, 1985 Zonal Avenue, Los Angeles, California 90089, United States
| | - Brian T Sutch
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, 1985 Zonal Avenue, Los Angeles, California 90089, United States
| | - Ian S Haworth
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, 1985 Zonal Avenue, Los Angeles, California 90089, United States
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12
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Cowan AD, Ciulli A. Driving E3 Ligase Substrate Specificity for Targeted Protein Degradation: Lessons from Nature and the Laboratory. Annu Rev Biochem 2022; 91:295-319. [PMID: 35320687 DOI: 10.1146/annurev-biochem-032620-104421] [Citation(s) in RCA: 39] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Methods to direct the degradation of protein targets with proximity-inducing molecules that coopt the cellular degradation machinery are advancing in leaps and bounds, and diverse modalities are emerging. The most used and well-studied approach is to hijack E3 ligases of the ubiquitin-proteasome system. E3 ligases use specific molecular recognition to determine which proteins in the cell are ubiquitinated and degraded. This review focuses on the structural determinants of E3 ligase recruitment of natural substrates and neo-substrates obtained through monovalent molecular glues and bivalent proteolysis-targeting chimeras. We use structures to illustrate the different types of substrate recognition and assess the basis for neo-protein-protein interactions in ternary complex structures. The emerging structural and mechanistic complexity is reflective of the diverse physiological roles of protein ubiquitination. This molecular insight is also guiding the application of structure-based design approaches to the development of new and existing degraders as chemical tools and therapeutics. Expected final online publication date for the Annual Review of Biochemistry, Volume 91 is June 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Angus D Cowan
- Centre for Targeted Protein Degradation, School of Life Sciences, University of Dundee, Dundee, United Kingdom;
| | - Alessio Ciulli
- Centre for Targeted Protein Degradation, School of Life Sciences, University of Dundee, Dundee, United Kingdom;
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13
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Mélin L, Gesner E, Attwell S, Kharenko OA, van der Horst EH, Hansen HC, Gagnon A. Design and Synthesis of LM146, a Potent Inhibitor of PB1 with an Improved Selectivity Profile over SMARCA2. ACS OMEGA 2021; 6:21327-21338. [PMID: 34471737 PMCID: PMC8387997 DOI: 10.1021/acsomega.1c01555] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 07/27/2021] [Indexed: 06/01/2023]
Abstract
PB1 is a bromodomain-containing protein hypothesized to act as the nucleosome-recognition subunit of the PBAF complex. Although PB1 is a key component of the PBAF chromatin remodeling complex, its exact role has not been elucidated due to the lack of potent and selective inhibitors. Chemical probes that target specific bromodomains within the complex would constitute highly valuable tools to characterize the function and therapeutic pertinence of PB1 and of each of its bromodomains. Here, we report the design and synthesis of lead compound LM146, which displays strong stabilization of the second and fifth bromodomains of PB1 as shown by DSF. LM146 does not interact with bromodomains outside of sub-family VIII and binds to PB1(2), PB1(5), and SMARCA2B with K D values of 110, 61, and 2100 nM, respectively, providing a ∼34-fold selectivity profile for PB1(5) over SMARCA2.
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Affiliation(s)
- Léa Mélin
- Département
de Chimie, Université du Québec
à Montréal, C.P. 8888, Succ. Centre-Ville, Montréal, Québec H3C 3P8, Canada
| | - Emily Gesner
- Zenith
Epigenetics Ltd., Suite
300, 4820 Richard Road SW, Calgary, Alberta T3E 6L1, Canada
| | - Sarah Attwell
- Zenith
Epigenetics Ltd., Suite
300, 4820 Richard Road SW, Calgary, Alberta T3E 6L1, Canada
| | - Olesya A. Kharenko
- Zenith
Epigenetics Ltd., Suite
300, 4820 Richard Road SW, Calgary, Alberta T3E 6L1, Canada
| | | | - Henrik C. Hansen
- Zenith
Epigenetics Ltd., Suite
300, 4820 Richard Road SW, Calgary, Alberta T3E 6L1, Canada
| | - Alexandre Gagnon
- Département
de Chimie, Université du Québec
à Montréal, C.P. 8888, Succ. Centre-Ville, Montréal, Québec H3C 3P8, Canada
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14
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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: 58] [Impact Index Per Article: 19.3] [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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15
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Zhong YJ, Qi T, Ji YL, Huang H, Zhang X, Leng HJ, Peng C, Li JL, Han B. Highly Chemoselective [2+1] Annulation of α-Alkylidene Pyrazolones with α-Bromonitroalkenes: Synthesis of Pyrazolone-Based Vinylcyclopropanes and Computational Studies. J Org Chem 2021; 86:2582-2592. [PMID: 33423501 DOI: 10.1021/acs.joc.0c02674] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
A highly chemoselective [2+1] annulation of α-alkylidene pyrazolones with α-bromonitroalkenes has been achieved under mild conditions. α-Alkylidene pyrazolones were unprecedentedly used as a C1 synthon to participate in annulation reactions, providing access to diverse vinylcyclopropane-based pyrazolone products. In addition, a spectrum of pharmaceutically interesting pyrazole-fused pyranone oximes could be rapidly obtained through a [2+1] annulation/rearrangement sequential process. Computational studies disclosed the origin of the observed chemoselectivity of the [2+1] cycloaddition.
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Affiliation(s)
- Ya-Jun Zhong
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, People's Republic of China
| | - Ting Qi
- Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, Sichuan Industrial Institute of Antibiotics, School of Pharmacy, Chengdu University, Chengdu 610052, People's Republic of China
| | - Yan-Ling Ji
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, People's Republic of China
| | - Hua Huang
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, People's Republic of China.,Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, Sichuan Industrial Institute of Antibiotics, School of Pharmacy, Chengdu University, Chengdu 610052, People's Republic of China
| | - Xiang Zhang
- Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, Sichuan Industrial Institute of Antibiotics, School of Pharmacy, Chengdu University, Chengdu 610052, People's Republic of China
| | - Hai-Jun Leng
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, People's Republic of China.,Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, Sichuan Industrial Institute of Antibiotics, School of Pharmacy, Chengdu University, Chengdu 610052, People's Republic of China
| | - Cheng Peng
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, People's Republic of China
| | - Jun-Long Li
- Antibiotics Research and Re-evaluation Key Laboratory of Sichuan Province, Sichuan Industrial Institute of Antibiotics, School of Pharmacy, Chengdu University, Chengdu 610052, People's Republic of China
| | - Bo Han
- State Key Laboratory of Southwestern Chinese Medicine Resources, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, People's Republic of China
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16
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Yang GJ, Wang W, Lei PM, Leung CH, Ma DL. A 7-methoxybicoumarin derivative selectively inhibits BRD4 BD2 for anti-melanoma therapy. Int J Biol Macromol 2020; 164:3204-3220. [DOI: 10.1016/j.ijbiomac.2020.08.194] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 08/18/2020] [Accepted: 08/24/2020] [Indexed: 01/07/2023]
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17
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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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18
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Aksenov NA, Aksenov AV, Kirilov NK, Arutiunov NA, Aksenov DA, Maslivetc V, Zhao Z, Du L, Rubin M, Kornienko A. Nitroalkanes as electrophiles: synthesis of triazole-fused heterocycles with neuroblastoma differentiation activity. Org Biomol Chem 2020; 18:6651-6664. [PMID: 32813002 PMCID: PMC7857362 DOI: 10.1039/d0ob01007c] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
We discovered a reaction of nitroalkanes with 2-hydrazinylquinolines, 2-hydrazinylpyridines and bis-2,4-dihydrazinylpyrimidines in polyphosphoric acid (PPA) affording 1,2,4-triazolo[4,3-a]quinolines, 1,2,4-triazolo[4,3-a]pyridines and bis[1,2,4]triazolo[4,3-a:4',3'-c]pyrimidines, respectively. The reaction expands the scope of heterocyclic annulations involving phosphorylated nitronates, believed to be the electrophilic intermediates formed from nitroalkanes in PPA. Several of the synthesized triazoles showed promising anticancer activity by inducing differentiation in neuroblastoma cancer cells. Due to the urgent need for novel differentiation agents for neuroblastoma therapy, this finding warrants further evaluation of this class of compounds against neuroblastoma.
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Affiliation(s)
- Nicolai A Aksenov
- Department of Chemistry, North Caucasus Federal University, 1a Pushkin St., Stavropol 355009, Russian Federation
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19
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Nikolić AM, Živković F, Selaković Ž, Wipf P, Opsenica IM. One‐Pot Two‐Step Synthesis of Isochromene‐Fused CF
3
‐Substituted Pyrazoles. European J Org Chem 2020. [DOI: 10.1002/ejoc.202000942] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Andrea M. Nikolić
- Faculty of Chemistry University of Belgrade PO Box 51, Studentski trg 16 11158 Belgrade Serbia
| | - Filip Živković
- Faculty of Chemistry University of Belgrade PO Box 51, Studentski trg 16 11158 Belgrade Serbia
| | - Života Selaković
- Faculty of Chemistry University of Belgrade PO Box 51, Studentski trg 16 11158 Belgrade Serbia
| | - Peter Wipf
- Department of Chemistry University of Pittsburgh 219 Parkman Avenue 15260 Pittsburgh PA USA
| | - Igor M. Opsenica
- Faculty of Chemistry University of Belgrade PO Box 51, Studentski trg 16 11158 Belgrade Serbia
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20
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Liu X, Zhang X, Lv D, Yuan Y, Zheng G, Zhou D. Assays and technologies for developing proteolysis targeting chimera degraders. Future Med Chem 2020; 12:1155-1179. [PMID: 32431173 PMCID: PMC7333641 DOI: 10.4155/fmc-2020-0073] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Accepted: 03/18/2020] [Indexed: 02/06/2023] Open
Abstract
Targeted protein degradation by small-molecule degraders represents an emerging mode of action in drug discovery. Proteolysis targeting chimeras (PROTACs) are small molecules that can recruit an E3 ligase and a protein of interest (POI) into proximity, leading to induced ubiquitination and degradation of the POI by the proteasome system. To date, the design and optimization of PROTACs remain empirical due to the complicated mechanism of induced protein degradation. Nevertheless, it is increasingly appreciated that profiling step-by-step along the ubiquitin-proteasome degradation pathway using biochemical and biophysical assays are essential in understanding the structure-activity relationship and facilitating the rational design of PROTACs. This review aims to summarize these assays and to discuss the potential of expanding the toolbox with other new techniques.
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Affiliation(s)
- Xingui Liu
- Department of Pharmacodynamics, College of Pharmacy, University of Florida, 1333 Center Drive, Gainesville, FL 32610, USA
| | - Xuan Zhang
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, 1333 Center Drive, Gainesville, FL 32610, USA
| | - Dongwen Lv
- Department of Pharmacodynamics, College of Pharmacy, University of Florida, 1333 Center Drive, Gainesville, FL 32610, USA
| | - Yaxia Yuan
- Department of Pharmacodynamics, College of Pharmacy, University of Florida, 1333 Center Drive, Gainesville, FL 32610, USA
| | - Guangrong Zheng
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, 1333 Center Drive, Gainesville, FL 32610, USA
| | - Daohong Zhou
- Department of Pharmacodynamics, College of Pharmacy, University of Florida, 1333 Center Drive, Gainesville, FL 32610, USA
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21
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Pardali V, Giannakopoulou E, Balourdas DI, Myrianthopoulos V, Taylor MC, Šekutor M, Mlinarić-Majerski K, Kelly JM, Zoidis G. Lipophilic Guanylhydrazone Analogues as Promising Trypanocidal Agents: An Extended SAR Study. Curr Pharm Des 2020; 26:838-866. [DOI: 10.2174/1381612826666200210150127] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 11/19/2019] [Indexed: 12/18/2022]
Abstract
In this report, we extend the SAR analysis of a number of lipophilic guanylhydrazone analogues with
respect to in vitro growth inhibition of Trypanosoma brucei and Trypanosoma cruzi. Sleeping sickness and Chagas
disease, caused by the tropical parasites T. brucei and T. cruzi, constitute a significant socioeconomic burden
in low-income countries of sub-Saharan Africa and Latin America, respectively. Drug development is underfunded.
Moreover, current treatments are outdated and difficult to administer, while drug resistance is an emerging
concern. The synthesis of adamantane-based compounds that have potential as antitrypanosomal agents is
extensively reviewed. The critical role of the adamantane ring was further investigated by synthesizing and testing
a number of novel lipophilic guanylhydrazones. The introduction of hydrophobic bulky substituents onto the
adamantane ring generated the most active analogues, illustrating the synergistic effect of the lipophilic character
of the C1 side chain and guanylhydrazone moiety on trypanocidal activity. The n-decyl C1-substituted compound
G8 proved to be the most potent adamantane derivative against T. brucei with activity in the nanomolar range
(EC50=90 nM). Molecular simulations were also performed to better understand the structure-activity relationships
between the studied guanylhydrazone analogues and their potential enzyme target.
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Affiliation(s)
- Vasiliki Pardali
- School of Health Sciences, Department of Pharmacy, Division of Pharmaceutical Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis-Zografou, GR-15771 Athens, Greece
| | - Erofili Giannakopoulou
- School of Health Sciences, Department of Pharmacy, Division of Pharmaceutical Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis-Zografou, GR-15771 Athens, Greece
| | - Dimitrios-Ilias Balourdas
- School of Health Sciences, Department of Pharmacy, Division of Pharmaceutical Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis-Zografou, GR-15771 Athens, Greece
| | - Vassilios Myrianthopoulos
- School of Health Sciences, Department of Pharmacy, Division of Pharmaceutical Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis-Zografou, GR-15771 Athens, Greece
| | - Martin C. Taylor
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, United Kingdom
| | - Marina Šekutor
- Department of Organic Chemistry and Biochemistry, Ruder Boskovic Institute, Bijenicka cesta 54, 10 000 Zagreb, Croatia
| | - Kata Mlinarić-Majerski
- Department of Organic Chemistry and Biochemistry, Ruder Boskovic Institute, Bijenicka cesta 54, 10 000 Zagreb, Croatia
| | - John M. Kelly
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, United Kingdom
| | - Grigoris Zoidis
- School of Health Sciences, Department of Pharmacy, Division of Pharmaceutical Chemistry, National and Kapodistrian University of Athens, Panepistimiopolis-Zografou, GR-15771 Athens, Greece
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22
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Lucas SCC, Atkinson SJ, Bamborough P, Barnett H, Chung CW, Gordon L, Mitchell DJ, Phillipou A, Prinjha RK, Sheppard RJ, Tomkinson NCO, Watson RJ, Demont EH. Optimization of Potent ATAD2 and CECR2 Bromodomain Inhibitors with an Atypical Binding Mode. J Med Chem 2020; 63:5212-5241. [DOI: 10.1021/acs.jmedchem.0c00021] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Simon C. C. Lucas
- WestCHEM, Department of Pure and Applied Chemistry, University of Strathclyde, Thomas Graham Building, 295 Cathedral Street, Glasgow G1 1XL, United Kingdom
| | | | | | | | | | | | | | | | | | | | - Nicholas C. O. Tomkinson
- 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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23
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Euryops pectinatus L. Flower Extract Inhibits P-glycoprotein and Reverses Multi-Drug Resistance in Cancer Cells: A Mechanistic Study. Molecules 2020; 25:molecules25030647. [PMID: 32028621 PMCID: PMC7038149 DOI: 10.3390/molecules25030647] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2020] [Revised: 01/30/2020] [Accepted: 02/01/2020] [Indexed: 11/17/2022] Open
Abstract
Euryops pectinatus is a South African ornamental plant belonging to family Asteraceae. The present work evaluates the cytotoxic activity and phytochemical profile of the flower extract. Metabolite profiling was performed using HPLC-PDA-ESI-MS/MS. Total phenolics and flavonoids content were assessed. Cytotoxicity was evaluated against 6 different cancer cell lines using MTT assay. The possible underlying mechanism was proposed. We analyzed whether the extract could overcome the resistance of multidrug-resistant cancer cells for doxorubicin. The effect of combination of E. pectinatus with doxorubicin was also studied. Additionally, the potential inhibitory activity of the identified phytochemicals to PB1 protein was analyzed using in silico molecular docking. Twenty-five compounds were tentatively identified. Total phenolic and flavonoid contents represented 49.41 ± 0.66 and 23.37 ± 0.23 µg/mg dried flower extract, respectively. The extract showed selective cytotoxicity against Caco2 cells but its main effect goes beyond mere cytotoxicity. It showed strong inhibition of P-glycoprotein, which helps to overcome multidrug resistance to classical chemotherapeutic agents. In silico molecular docking showed that dicaffeoyl quinic acid, kaempferol-O-rutinoside, rutin, and isorhamnetin-O-rutinoside exhibited the most potent inhibitory activity to PB1 involved in tumor progression. Euryops pectinatus flower heads could have promising selective cytotoxicity alone or in combination with other chemotherapeutic agents to counteract multidrug resistance.
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24
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Schiedel M, Moroglu M, Ascough DMH, Chamberlain AER, Kamps JJAG, Sekirnik AR, Conway SJ. Chemical Epigenetics: The Impact of Chemical and Chemical Biology Techniques on Bromodomain Target Validation. Angew Chem Int Ed Engl 2019; 58:17930-17952. [DOI: 10.1002/anie.201812164] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Revised: 01/08/2019] [Indexed: 12/22/2022]
Affiliation(s)
- Matthias Schiedel
- Department of ChemistryChemistry Research LaboratoryUniversity of Oxford Mansfield Road Oxford OX1 3TA UK
| | - Mustafa Moroglu
- Department of ChemistryChemistry Research LaboratoryUniversity of Oxford Mansfield Road Oxford OX1 3TA UK
| | - David M. H. Ascough
- Department of ChemistryChemistry Research LaboratoryUniversity of Oxford Mansfield Road Oxford OX1 3TA UK
| | - Anna E. R. Chamberlain
- Department of ChemistryChemistry Research LaboratoryUniversity of Oxford Mansfield Road Oxford OX1 3TA UK
| | - Jos J. A. G. Kamps
- Department of ChemistryChemistry Research LaboratoryUniversity of Oxford Mansfield Road Oxford OX1 3TA UK
| | - Angelina R. Sekirnik
- Department of ChemistryChemistry Research LaboratoryUniversity of Oxford Mansfield Road Oxford OX1 3TA UK
| | - Stuart J. Conway
- Department of ChemistryChemistry Research LaboratoryUniversity of Oxford Mansfield Road Oxford OX1 3TA UK
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25
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Schiedel M, Moroglu M, Ascough DMH, Chamberlain AER, Kamps JJAG, Sekirnik AR, Conway SJ. Chemische Epigenetik: der Einfluss chemischer und chemo‐biologischer Techniken auf die Zielstruktur‐Validierung von Bromodomänen. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201812164] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Matthias Schiedel
- Department of ChemistryChemistry Research LaboratoryUniversity of Oxford Mansfield Road Oxford OX1 3TA Großbritannien
| | - Mustafa Moroglu
- Department of ChemistryChemistry Research LaboratoryUniversity of Oxford Mansfield Road Oxford OX1 3TA Großbritannien
| | - David M. H. Ascough
- Department of ChemistryChemistry Research LaboratoryUniversity of Oxford Mansfield Road Oxford OX1 3TA Großbritannien
| | - Anna E. R. Chamberlain
- Department of ChemistryChemistry Research LaboratoryUniversity of Oxford Mansfield Road Oxford OX1 3TA Großbritannien
| | - Jos J. A. G. Kamps
- Department of ChemistryChemistry Research LaboratoryUniversity of Oxford Mansfield Road Oxford OX1 3TA Großbritannien
| | - Angelina R. Sekirnik
- Department of ChemistryChemistry Research LaboratoryUniversity of Oxford Mansfield Road Oxford OX1 3TA Großbritannien
| | - Stuart J. Conway
- Department of ChemistryChemistry Research LaboratoryUniversity of Oxford Mansfield Road Oxford OX1 3TA Großbritannien
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26
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Farnaby W, Koegl M, Roy MJ, Whitworth C, Diers E, Trainor N, Zollman D, Steurer S, Karolyi-Oezguer J, Riedmueller C, Gmaschitz T, Wachter J, Dank C, Galant M, Sharps B, Rumpel K, Traxler E, Gerstberger T, Schnitzer R, Petermann O, Greb P, Weinstabl H, Bader G, Zoephel A, Weiss-Puxbaum A, Ehrenhöfer-Wölfer K, Wöhrle S, Boehmelt G, Rinnenthal J, Arnhof H, Wiechens N, Wu MY, Owen-Hughes T, Ettmayer P, Pearson M, McConnell DB, Ciulli A. BAF complex vulnerabilities in cancer demonstrated via structure-based PROTAC design. Nat Chem Biol 2019; 15:672-680. [PMID: 31178587 PMCID: PMC6600871 DOI: 10.1038/s41589-019-0294-6] [Citation(s) in RCA: 302] [Impact Index Per Article: 60.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 04/16/2019] [Indexed: 12/22/2022]
Abstract
Targeting subunits of BAF/PBAF chromatin remodeling complexes has been proposed as an approach to exploit cancer vulnerabilities. Here we develop PROTAC degraders of the BAF ATPase subunits SMARCA2 and SMARCA4 using a bromodomain ligand and recruitment of the E3 ubiquitin ligase VHL. High-resolution ternary complex crystal structures and biophysical investigation guided rational and efficient optimization towards ACBI1, a potent and cooperative degrader of SMARCA2, SMARCA4 and PBRM1. ACBI1 induced antiproliferative effects and cell death caused by SMARCA2 depletion in SMARCA4 mutant cancer cells, and in acute myeloid leukemia cells dependent on SMARCA4 ATPase activity. These findings exemplify a successful biophysics- and structure-based PROTAC design approach to degrade high profile drug targets and pave the way towards new therapeutics for the treatment of tumors sensitive to the loss of BAF complex ATPases.
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Affiliation(s)
- William Farnaby
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee, UK
| | - Manfred Koegl
- Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria
| | - Michael J Roy
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee, UK
| | - Claire Whitworth
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee, UK
| | - Emelyne Diers
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee, UK
| | - Nicole Trainor
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee, UK
| | - David Zollman
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee, UK
| | | | | | | | | | | | | | | | | | - Klaus Rumpel
- Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria
| | | | | | | | | | - Peter Greb
- Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria
| | | | - Gerd Bader
- Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria
| | | | | | | | - Simon Wöhrle
- Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria
| | | | | | | | - Nicola Wiechens
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, UK
| | - Meng-Ying Wu
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, UK
| | - Tom Owen-Hughes
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, UK
| | | | - Mark Pearson
- Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria
| | | | - Alessio Ciulli
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee, UK.
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27
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Yang GJ, Ko CN, Zhong HJ, Leung CH, Ma DL. Structure-Based Discovery of a Selective KDM5A Inhibitor that Exhibits Anti-Cancer Activity via Inducing Cell Cycle Arrest and Senescence in Breast Cancer Cell Lines. Cancers (Basel) 2019; 11:E92. [PMID: 30650517 PMCID: PMC6360022 DOI: 10.3390/cancers11010092] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2018] [Revised: 12/24/2018] [Accepted: 01/10/2019] [Indexed: 12/13/2022] Open
Abstract
Breast cancer is the one of the most frequent causes of female cancer mortality. KDM5A, a histone demethylase, can increase the proliferation, metastasis, and drug resistance of cancers, including breast cancer, and is thus an important therapeutic target. In the present work, we performed hierarchical virtual screening towards the KDM5A catalytic pocket from a chemical library containing 90,000 compounds. Using multiple biochemical methods, the cyclopenta[c]chromen derivative 1 was identified as the top candidate for KDM5A demethylase inhibitory activity. Compared with the well-known KDM5 inhibitor CPI-455 (18), 1 exhibited higher potency against KDM5A and much higher selectivity for KDM5A over both KDM4A and other KDM5 family members (KDM5B and KDM5C). Additionally, compound 1 repressed the proliferation of various KDM5A-overexpressing breast cancer cell lines. Mechanistically, 1 promoted accumulation of p16 and p27 by blocking KDM5A-mediated H3K4me3 demethylation, leading to cell cycle arrest and senescence. To date, compound 1 is the first cyclopenta[c]chromen-based KDM5A inhibitor reported, and may serve as a novel motif for developing more selective and efficacious pharmacological molecules targeting KDM5A. In addition, our research provides a possible anti-cancer mechanism of KDM5A inhibitors and highlights the feasibility and significance of KDM5A as a therapeutic target for KDM5A-overexpressing breast cancer.
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Affiliation(s)
- Guan-Jun Yang
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao 999078, China.
| | - Chung-Nga Ko
- Department of Chemistry, Hong Kong Baptist University, Kowloon Tong, Hong Kong 999077, China.
| | - Hai-Jing Zhong
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao 999078, China.
| | - Chung-Hang Leung
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao 999078, China.
| | - Dik-Lung Ma
- Department of Chemistry, Hong Kong Baptist University, Kowloon Tong, Hong Kong 999077, China.
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28
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Zhong H, Wang Z, Wang X, Liu H, Li D, Liu H, Yao X, Hou T. Importance of a crystalline water network in docking-based virtual screening: a case study of BRD4. Phys Chem Chem Phys 2019; 21:25276-25289. [DOI: 10.1039/c9cp04290c] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
As a member of the bromodomain and extra terminal domain (BET) protein family, bromodomain-containing protein 4 (BRD4) is an epigenetic reader and can recognize acetylated lysine residues in histones.
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Affiliation(s)
- Haiyang Zhong
- State Key Laboratory of Applied Organic Chemistry and Department of Chemistry
- Lanzhou University
- Lanzhou 730000
- China
- College of Pharmaceutical Sciences
| | - Zhe Wang
- College of Pharmaceutical Sciences
- Zhejiang University
- Hangzhou
- China
| | - Xuwen Wang
- College of Pharmaceutical Sciences
- Zhejiang University
- Hangzhou
- China
| | - Hui Liu
- College of Pharmaceutical Sciences
- Zhejiang University
- Hangzhou
- China
| | - Dan Li
- College of Pharmaceutical Sciences
- Zhejiang University
- Hangzhou
- China
| | - Huanxiang Liu
- School of Pharmacy
- Lanzhou University
- Lanzhou 730000
- China
| | - Xiaojun Yao
- State Key Laboratory of Applied Organic Chemistry and Department of Chemistry
- Lanzhou University
- Lanzhou 730000
- China
- State Key Laboratory of Quality Research in Chinese Medicine
| | - Tingjun Hou
- College of Pharmaceutical Sciences
- Zhejiang University
- Hangzhou
- China
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29
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From bench to bedside, via desktop. Recent advances in the application of cutting-edge in silico tools in the research of drugs targeting bromodomain modules. Biochem Pharmacol 2018; 159:40-51. [PMID: 30414936 DOI: 10.1016/j.bcp.2018.11.007] [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: 08/19/2018] [Accepted: 11/07/2018] [Indexed: 11/22/2022]
Abstract
The discipline of drug discovery has greatly benefited by computational tools and in silico algorithms aiming at rationalization of many related processes, from the stage of early hit identification to the preclinical phases of drug candidate validation. The various methodologies referred to as molecular modeling tools span a broad spectrum of applications, from straightforward approaches such as virtual screening of compound libraries to more advanced techniques involving the precise estimation of free energy upon binding of the candidate drug to its macromolecular target. To this end, we report an overview of specific studies where implementation of such sophisticated modeling algorithms has shown to be indispensable for addressing challenging systems and biological questions otherwise difficult to answer. We focus our attention on the emerging field of bromodomain inhibitors. Bromodomains are small modules involved in epigenetic signaling and currently comprise high-priority targets for developing both drug candidates and chemical probes for basic biomedical research. We attempt a critical presentation of selected cases utilizing cutting-edge in silico methodologies, with our main emphasis being on absolute or relative free energy simulations, on implementation of quantum-mechanics level calculations and on characterization of solvent thermodynamics. We discuss the advantages and strengths as well as the drawbacks and weaknesses of computational tools utilized in those works and we attempt to comment on specific issues related to their integration into the regular medicinal chemistry practice. Our conclusion is that while such methods indeed represent highly promising resources for further advancing the discipline, their application is not always trivial.
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30
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Mavrogeni ME, Pronios F, Zareifi D, Vasilakaki S, Lozach O, Alexopoulos L, Meijer L, Myrianthopoulos V, Mikros E. A facile consensus ranking approach enhances virtual screening robustness and identifies a cell-active DYRK1α inhibitor. Future Med Chem 2018; 10:2411-2430. [PMID: 30325204 PMCID: PMC6479281 DOI: 10.4155/fmc-2018-0198] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2018] [Accepted: 08/16/2018] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND Virtual screening is vital for contemporary drug discovery but striking performance fluctuations are commonly encountered, thus hampering error-free use. Results and Methodology: A conceptual framework is suggested for combining screening algorithms characterized by orthogonality (docking-scoring calculations, 3D shape similarity, 2D fingerprint similarity) into a simple, efficient and expansible python-based consensus ranking scheme. An original experimental dataset is created for comparing individual screening methods versus the novel approach. Its utilization leads to identification and phosphoproteomic evaluation of a cell-active DYRK1α inhibitor. CONCLUSION Consensus ranking considerably stabilizes screening performance at reasonable computational cost, whereas individual screens are heavily dependent on calculation settings. Results indicate that the novel approach, currently available as a free online tool, is highly suitable for prospective screening by nonexperts.
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Affiliation(s)
- Maria E Mavrogeni
- Department of Pharmaceutical Chemistry, School of Pharmacy, University of Athens, Panepistimiopolis Zografou, 157 71 Athens, Greece
| | - Filippos Pronios
- Department of Pharmaceutical Chemistry, School of Pharmacy, University of Athens, Panepistimiopolis Zografou, 157 71 Athens, Greece
| | - Danae Zareifi
- ProtATonce Ltd, Dimokritos Science Park, Agia Paraskevi, 153 43 Athens, Greece
| | - Sofia Vasilakaki
- Department of Pharmaceutical Chemistry, School of Pharmacy, University of Athens, Panepistimiopolis Zografou, 157 71 Athens, Greece
| | - Olivier Lozach
- Laboratoire Chimie Electrochimie Moléculaires et Chimie Analytique, University of Brest, 29238 Brest, France
| | - Leonidas Alexopoulos
- School of Mechanical Engineering, National Technical University of Athens, 157 80 Athens, Greece
| | - Laurent Meijer
- ManRos Therapeutics, Perharidy Research Center, 29680 Roscoff, Bretagne, France
| | - Vassilios Myrianthopoulos
- Department of Pharmaceutical Chemistry, School of Pharmacy, University of Athens, Panepistimiopolis Zografou, 157 71 Athens, Greece
- ‘Athena’ Research & Innovation Center, 151 25 Athens, Greece
| | - Emmanuel Mikros
- Department of Pharmaceutical Chemistry, School of Pharmacy, University of Athens, Panepistimiopolis Zografou, 157 71 Athens, Greece
- ‘Athena’ Research & Innovation Center, 151 25 Athens, Greece
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31
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Matter H, Güssregen S. Characterizing hydration sites in protein-ligand complexes towards the design of novel ligands. Bioorg Med Chem Lett 2018; 28:2343-2352. [PMID: 29880400 DOI: 10.1016/j.bmcl.2018.05.061] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Revised: 05/28/2018] [Accepted: 05/30/2018] [Indexed: 11/18/2022]
Abstract
Water is an essential part of protein binding sites and mediates interactions to ligands. Its displacement by ligand parts affects the free binding energy of resulting protein-ligand complexes. Therefore the characterization of solvation properties is important for design. Of particular interest is the propensity of localized water to be favorably displaced by a ligand. This review discusses two popular computational approaches addressing these questions, namely WaterMap based on statistical mechanics analysis of MD simulations and 3D RISM based on integral equation theory of liquids. The theoretical background and recent applications in structure-based design will be presented.
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Affiliation(s)
- Hans Matter
- Sanofi-Aventis Deutschland GmbH, Integrated Drug Discovery (IDD), Synthetic Molecular Design, Building G838, Industriepark Höchst, 65926 Frankfurt am Main, Germany.
| | - Stefan Güssregen
- Sanofi-Aventis Deutschland GmbH, Integrated Drug Discovery (IDD), Synthetic Molecular Design, Building G838, Industriepark Höchst, 65926 Frankfurt am Main, Germany
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32
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Miyao T, Bajorath J. Exploring ensembles of bioactive or virtual analogs of X-ray ligands for shape similarity searching. J Comput Aided Mol Des 2018; 32:759-767. [PMID: 29968097 DOI: 10.1007/s10822-018-0128-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2018] [Accepted: 06/30/2018] [Indexed: 12/20/2022]
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33
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Aldeghi M, Ross GA, Bodkin MJ, Essex JW, Knapp S, Biggin PC. Large-scale analysis of water stability in bromodomain binding pockets with grand canonical Monte Carlo. Commun Chem 2018; 1:19. [PMID: 29863194 PMCID: PMC5978690 DOI: 10.1038/s42004-018-0019-x] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Accepted: 03/01/2018] [Indexed: 12/17/2022] Open
Abstract
Conserved water molecules are of interest in drug design, as displacement of such waters can lead to higher affinity ligands and in some cases, contribute towards selectivity. Bromodomains, small protein domains involved in the epigenetic regulation of gene transcription, display a network of four conserved water molecules in their binding pockets and have recently been the focus of intense medicinal chemistry efforts. Understanding why certain bromodomains have displaceable water molecules and others do not is extremely challenging, and it remains unclear which water molecules in a given bromodomain can be targeted for displacement. Here we estimate the stability of the conserved water molecules in 35 bromodomains via binding free energy calculations using all-atom grand canonical Monte Carlo simulations. Encouraging quantitative agreement to the available experimental evidence is found. We thus discuss the expected ease of water displacement in different bromodomains and the implications for ligand selectivity.
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Affiliation(s)
- Matteo Aldeghi
- Structural Bioinformatics and Computational Biochemistry, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, United Kingdom
| | - Gregory A. Ross
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York, United States
| | - Michael J. Bodkin
- Evotec (U.K.) Ltd., 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire OX14 4RZ, United Kingdom
| | - Jonathan W. Essex
- School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, United Kingdom
| | - Stefan Knapp
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, United Kingdom
- Target Discovery Institute, Nuffield Department of Clinical Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, United Kingdom
| | - Philip C. Biggin
- Structural Bioinformatics and Computational Biochemistry, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, United Kingdom
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34
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Myrianthopoulos V, Lambrinidis G, Mikros E. In Silico Screening of Compound Libraries Using a Consensus of Orthogonal Methodologies. Methods Mol Biol 2018; 1824:261-277. [PMID: 30039412 DOI: 10.1007/978-1-4939-8630-9_15] [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: 12/25/2022]
Abstract
A number of diverse approaches for efficient screening of compound collections in silico are nowadays available, each with their own methodological background, successes and limitations. Implementation of such virtual screening methods has enabled an impressive acceleration in the search toward the most biologically relevant regions of chemical space and has greatly facilitated the discovery of novel biologically active molecules. It is noteworthy that the range of principles on which the available virtual screening methodologies are based is wide enough for several of these methods to be considered as orthogonal to a good extent. We hereby propose a simple and extensible protocol aiming at integrating the diverse information derived by such virtual screening methods in a consensus manner that can achieve an improvement of the hit rate obtained by individual use of those methods. The protocol can be performed in its basic version as described in this work, but it can also be extended manually by integrating a number of different screening tools and their case-specific variations to further increase the performance of virtual screening in prioritizing the most promising compounds for in vitro evaluations.
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Affiliation(s)
- Vassilios Myrianthopoulos
- Department of Pharmacy, National and Kapodistrian University of Athens, Panepistimiopolis Zografou, Athens, Greece.,"Athena" Research and Innovation Center, Athens, Greece
| | - George Lambrinidis
- Department of Pharmacy, National and Kapodistrian University of Athens, Panepistimiopolis Zografou, Athens, Greece
| | - Emmanuel Mikros
- Department of Pharmacy, National and Kapodistrian University of Athens, Panepistimiopolis Zografou, Athens, Greece. .,"Athena" Research and Innovation Center, Athens, Greece.
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35
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Myrianthopoulos V, Lozach O, Zareifi D, Alexopoulos L, Meijer L, Gorgoulis VG, Mikros E. Combined Virtual and Experimental Screening for CK1 Inhibitors Identifies a Modulator of p53 and Reveals Important Aspects of in Silico Screening Performance. Int J Mol Sci 2017; 18:ijms18102102. [PMID: 28984824 PMCID: PMC5666784 DOI: 10.3390/ijms18102102] [Citation(s) in RCA: 7] [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: 09/01/2017] [Revised: 09/25/2017] [Accepted: 10/03/2017] [Indexed: 12/02/2022] Open
Abstract
A compound collection of pronounced structural diversity was comprehensively screened for inhibitors of the DNA damage-related kinase CK1. The collection was evaluated in vitro. A potent and selective CK1 inhibitor was discovered and its capacity to modulate the endogenous levels of the CK1-regulated tumor suppressor p53 was demonstrated in cancer cell lines. Administration of 10 μM of the compound resulted in significant increase of p53 levels, reaching almost 2-fold in hepatocellular carcinoma cells. In parallel to experimental screening, two representative and orthogonal in silico screening methodologies were implemented for enabling the retrospective assessment of virtual screening performance on a case-specific basis. Results showed that both techniques performed at an acceptable and fairly comparable level, with a slight advantage of the structure-based over the ligand-based approach. However, both approaches demonstrated notable sensitivity upon parameters such as screening template choice and treatment of redundancy in the enumerated compound collection. An effort to combine insight derived by sequential implementation of the two methods afforded poor further improvement of screening performance. Overall, the presented assessment highlights the relation between improper use of enrichment metrics and misleading results, and demonstrates the inherent delicacy of in silico methods, emphasizing the challenging character of virtual screening protocol optimization.
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Affiliation(s)
| | - Olivier Lozach
- Protein Phosphorylation & Human Disease Group, Station Biologique, B. P. 74, CEDEX 29682 Roscoff, Bretagne, France.
| | | | - Leonidas Alexopoulos
- School of Mechanical Engineering, National Technical University of Athens, 15780 Athens, Greece.
| | - Laurent Meijer
- ManRos Therapeutics, Perharidy Research Center, Roscoff, 29680 Bretagne, France.
| | - Vassilis G Gorgoulis
- Department of Histology-Embryology, School of Medicine, University of Athens, Mikras Asias 75, GR-11527 Athens, Greece.
- Biomedical Research Foundation of the Academy of Athens, 11527 Athens, Greece.
- Faculty Institute of Cancer Sciences, University of Manchester, Manchester Academic Health Science Centre, M13 9NT Manchester, UK.
| | - Emmanuel Mikros
- Department of Pharmacy, University of Athens, Panepistimiopolis Zografou, GR-15771 Athens, Greece.
- "Athena" Research and Innovation Center, 15125 Athens, Greece.
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36
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Igoe N, Bayle ED, Tallant C, Fedorov O, Meier JC, Savitsky P, Rogers C, Morias Y, Scholze S, Boyd H, Cunoosamy D, Andrews DM, Cheasty A, Brennan PE, Müller S, Knapp S, Fish PV. Design of a Chemical Probe for the Bromodomain and Plant Homeodomain Finger-Containing (BRPF) Family of Proteins. J Med Chem 2017; 60:6998-7011. [PMID: 28714688 DOI: 10.1021/acs.jmedchem.7b00611] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The bromodomain and plant homeodomain finger-containing (BRPF) family are scaffolding proteins important for the recruitment of histone acetyltransferases of the MYST family to chromatin. Here, we describe NI-57 (16) as new pan-BRPF chemical probe of the bromodomain (BRD) of the BRPFs. Inhibitor 16 preferentially bound the BRD of BRPF1 and BRPF2 over BRPF3, whereas binding to BRD9 was weaker. Compound 16 has excellent selectivity over nonclass IV BRD proteins. Target engagement of BRPF1B and BRPF2 with 16 was demonstrated in nanoBRET and FRAP assays. The binding of 16 to BRPF1B was rationalized through an X-ray cocrystal structure determination, which showed a flipped binding orientation when compared to previous structures. We report studies that show 16 has functional activity in cellular assays by modulation of the phenotype at low micromolar concentrations in both cancer and inflammatory models. Pharmacokinetic data for 16 was generated in mouse with single dose administration showing favorable oral bioavailability.
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Affiliation(s)
- Niall Igoe
- UCL School of Pharmacy, University College London , 29/39 Brunswick Square, London WC1N 1AX, U.K
| | - Elliott D Bayle
- UCL School of Pharmacy, University College London , 29/39 Brunswick Square, London WC1N 1AX, U.K
| | - Cynthia Tallant
- Nuffield Department of Clinical Medicine, Structural Genomics Consortium, University of Oxford , Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, U.K
| | - Oleg Fedorov
- Nuffield Department of Clinical Medicine, Structural Genomics Consortium, University of Oxford , Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, U.K
| | - Julia C Meier
- Nuffield Department of Clinical Medicine, Structural Genomics Consortium, University of Oxford , Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, U.K
| | - Pavel Savitsky
- Nuffield Department of Clinical Medicine, Structural Genomics Consortium, University of Oxford , Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, U.K
| | - Catherine Rogers
- Nuffield Department of Clinical Medicine, Structural Genomics Consortium, University of Oxford , Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, U.K
| | - Yannick Morias
- AstraZeneca , Innovative Medicines & Early Development, Pepparedsleden 1, 431 83 Mölndal, Sweden
| | - Sarah Scholze
- AstraZeneca , Innovative Medicines & Early Development, Pepparedsleden 1, 431 83 Mölndal, Sweden
| | - Helen Boyd
- AstraZeneca , Innovative Medicines & Early Development, Pepparedsleden 1, 431 83 Mölndal, Sweden
| | - Danen Cunoosamy
- AstraZeneca , Innovative Medicines & Early Development, Pepparedsleden 1, 431 83 Mölndal, Sweden
| | - David M Andrews
- AstraZeneca Discovery Sciences , Darwin Building, Cambridge Science Park, Cambridge CB4 0FZ, U.K
| | - Anne Cheasty
- CRT Discovery Laboratories , Jonas Webb Building, Babraham Research Campus, Cambridge CB22 3AT, U.K
| | - Paul E Brennan
- Nuffield Department of Clinical Medicine, Structural Genomics Consortium, University of Oxford , Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, U.K
| | - Susanne Müller
- Nuffield Department of Clinical Medicine, Structural Genomics Consortium, University of Oxford , Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, U.K.,Buchmann Institute for Molecular Life Sciences , Max-von-Laue-Strasse 15, D-60438 Frankfurt am Main, Germany
| | - Stefan Knapp
- Nuffield Department of Clinical Medicine, Structural Genomics Consortium, University of Oxford , Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, U.K.,Buchmann Institute for Molecular Life Sciences , Max-von-Laue-Strasse 15, D-60438 Frankfurt am Main, Germany.,Institute for Pharmaceutical Chemistry, Johann Wolfgang Goethe-University , Max-von-Laue-Strasse 9, D-60438 Frankfurt am Main, Germany
| | - Paul V Fish
- UCL School of Pharmacy, University College London , 29/39 Brunswick Square, London WC1N 1AX, U.K
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37
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Bouché L, Christ CD, Siegel S, Fernández-Montalván AE, Holton SJ, Fedorov O, Ter Laak A, Sugawara T, Stöckigt D, Tallant C, Bennett J, Monteiro O, Díaz-Sáez L, Siejka P, Meier J, Pütter V, Weiske J, Müller S, Huber KVM, Hartung IV, Haendler B. Benzoisoquinolinediones as Potent and Selective Inhibitors of BRPF2 and TAF1/TAF1L Bromodomains. J Med Chem 2017; 60:4002-4022. [PMID: 28402630 PMCID: PMC5443610 DOI: 10.1021/acs.jmedchem.7b00306] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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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Affiliation(s)
- Léa Bouché
- Drug Discovery, Bayer AG , Müllerstrasse 178, 13353 Berlin, Germany
| | - Clara D Christ
- Drug Discovery, Bayer AG , Müllerstrasse 178, 13353 Berlin, Germany
| | - Stephan Siegel
- Drug Discovery, Bayer AG , Müllerstrasse 178, 13353 Berlin, Germany
| | | | - Simon J Holton
- Drug Discovery, Bayer AG , Müllerstrasse 178, 13353 Berlin, Germany
| | - Oleg Fedorov
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford , Roosevelt Drive, Oxford OX3 7DQ, U.K.,Target Discovery Institute, Nuffield Department of Clinical Medicine, University of Oxford , Roosevelt Drive, Oxford OX3 7FZ, U.K
| | | | - Tatsuo Sugawara
- Drug Discovery, Bayer AG , Müllerstrasse 178, 13353 Berlin, Germany
| | - Detlef Stöckigt
- Drug Discovery, Bayer AG , Müllerstrasse 178, 13353 Berlin, Germany
| | - Cynthia Tallant
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford , Roosevelt Drive, Oxford OX3 7DQ, U.K.,Target Discovery Institute, Nuffield Department of Clinical Medicine, University of Oxford , Roosevelt Drive, Oxford OX3 7FZ, U.K
| | - James Bennett
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford , Roosevelt Drive, Oxford OX3 7DQ, U.K.,Target Discovery Institute, Nuffield Department of Clinical Medicine, University of Oxford , Roosevelt Drive, Oxford OX3 7FZ, U.K
| | - Octovia Monteiro
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford , Roosevelt Drive, Oxford OX3 7DQ, U.K.,Target Discovery Institute, Nuffield Department of Clinical Medicine, University of Oxford , Roosevelt Drive, Oxford OX3 7FZ, U.K
| | - Laura Díaz-Sáez
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford , Roosevelt Drive, Oxford OX3 7DQ, U.K.,Target Discovery Institute, Nuffield Department of Clinical Medicine, University of Oxford , Roosevelt Drive, Oxford OX3 7FZ, U.K
| | - Paulina Siejka
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford , Roosevelt Drive, Oxford OX3 7DQ, U.K.,Target Discovery Institute, Nuffield Department of Clinical Medicine, University of Oxford , Roosevelt Drive, Oxford OX3 7FZ, U.K
| | - Julia Meier
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford , Roosevelt Drive, Oxford OX3 7DQ, U.K
| | - Vera Pütter
- Drug Discovery, Bayer AG , Müllerstrasse 178, 13353 Berlin, Germany
| | - Jörg Weiske
- Drug Discovery, Bayer AG , Müllerstrasse 178, 13353 Berlin, Germany
| | - Susanne Müller
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford , Roosevelt Drive, Oxford OX3 7DQ, U.K.,Target Discovery Institute, Nuffield Department of Clinical Medicine, University of Oxford , Roosevelt Drive, Oxford OX3 7FZ, U.K
| | - Kilian V M Huber
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford , Roosevelt Drive, Oxford OX3 7DQ, U.K.,Target Discovery Institute, Nuffield Department of Clinical Medicine, University of Oxford , Roosevelt Drive, Oxford OX3 7FZ, U.K
| | - Ingo V Hartung
- Drug Discovery, Bayer AG , Müllerstrasse 178, 13353 Berlin, Germany
| | - Bernard Haendler
- Drug Discovery, Bayer AG , Müllerstrasse 178, 13353 Berlin, Germany
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38
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Porter EG, Dykhuizen EC. Individual Bromodomains of Polybromo-1 Contribute to Chromatin Association and Tumor Suppression in Clear Cell Renal Carcinoma. J Biol Chem 2017; 292:2601-2610. [PMID: 28053089 DOI: 10.1074/jbc.m116.746875] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Revised: 12/22/2016] [Indexed: 01/09/2023] Open
Abstract
The architecture of chromatin is governed, in part, by ATP-dependent chromatin remodelers. These multiprotein complexes contain targeting domains that recognize post-translational marks on histones. One such targeting domain is the bromodomain (BD), which recognizes acetyl-lysines and recruits proteins to sites of acetylation across the genome. Polybromo1 (PBRM1), a subunit of the Polybromo-associated BRG1- or hBRM-associated factors (PBAF) chromatin remodeler, contains six tandem BDs and is frequently mutated in clear cell renal cell carcinoma (ccRCC). Mutations in the PBRM1 gene often lead to the loss of protein expression; however, missense mutations in PBRM1 have been identified and tend to cluster in the BDs, particularly BD2 and BD4, suggesting that individual BDs are critical for PBRM1 function. To study the role of these six BDs, we inactivated each of the six BDs of PBRM1 and re-expressed these mutants in Caki2 cells (ccRCC cells with the loss of function mutation in PBRM1). Four of the six BDs abrogated PBRM1 tumor suppressor function, gene regulation, and chromatin affinity with the degree of importance correlating strongly to the rate of missense mutations in patients. Furthermore, we identified BD2 as the most critical for PBRM1 and confirmed BD2-mediated association to histone H3 peptides acetylated at lysine 14 (H3K14Ac), validating the importance of this specific acetylation mark for PBRM1 binding. From these data, we conclude that four of the BDs act together to target PBRM1 to sites on chromatin; when a single BD is mutated, PBRM1 no longer controls gene expression properly, leading to increased cell proliferation.
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Affiliation(s)
- Elizabeth G Porter
- From the Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana 47907
| | - Emily C Dykhuizen
- From the Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana 47907
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