1
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Thomas AM, Serafini M, Grant EK, Coombs EAJ, Bluck JP, Schiedel M, McDonough MA, Reynolds JK, Lee B, Platt M, Sharlandjieva V, Biggin PC, Duarte F, Milne TA, Bush JT, Conway SJ. Mutate and Conjugate: A Method to Enable Rapid In-Cell Target Validation. ACS Chem Biol 2023; 18:2405-2417. [PMID: 37874862 PMCID: PMC10660337 DOI: 10.1021/acschembio.3c00437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 09/22/2023] [Accepted: 10/05/2023] [Indexed: 10/26/2023]
Abstract
Target validation remains a challenge in drug discovery, which leads to a high attrition rate in the drug discovery process, particularly in Phase II clinical trials. Consequently, new approaches to enhance target validation are valuable tools to improve the drug discovery process. Here, we report the combination of site-directed mutagenesis and electrophilic fragments to enable the rapid identification of small molecules that selectively inhibit the mutant protein. Using the bromodomain-containing protein BRD4 as an example, we employed a structure-based approach to identify the L94C mutation in the first bromodomain of BRD4 [BRD4(1)] as having a minimal effect on BRD4(1) function. We then screened a focused, KAc mimic-containing fragment set and a diverse fragment library against the mutant and wild-type proteins and identified a series of fragments that showed high selectivity for the mutant protein. These compounds were elaborated to include an alkyne click tag to enable the attachment of a fluorescent dye. These clickable compounds were then assessed in HEK293T cells, transiently expressing BRD4(1)WT or BRD4(1)L94C, to determine their selectivity for BRD4(1)L94C over other possible cellular targets. One compound was identified that shows very high selectivity for BRD4(1)L94C over all other proteins. This work provides a proof-of-concept that the combination of site-directed mutagenesis and electrophilic fragments, in a mutate and conjugate approach, can enable rapid identification of small molecule inhibitors for an appropriately mutated protein of interest. This technology can be used to assess the cellular phenotype of inhibiting the protein of interest, and the electrophilic ligand provides a starting point for noncovalent ligand development.
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Affiliation(s)
- Adam M. Thomas
- Department
of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Marta Serafini
- Department
of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Emma K. Grant
- Department
of Chemical Biology, GSK, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, United Kingdom
| | - Edward A. J. Coombs
- Department
of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Joseph P. Bluck
- Department
of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, United Kingdom
- Department
of Biochemistry, South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Matthias Schiedel
- Department
of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Michael A. McDonough
- Department
of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Jessica K. Reynolds
- Department
of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Bernadette Lee
- Department
of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Michael Platt
- Department
of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Vassilena Sharlandjieva
- MRC
Molecular Haematology Unit, MRC Weatherall Institute of Molecular
Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DS, United
Kingdom
| | - Philip C. Biggin
- Department
of Biochemistry, South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Fernanda Duarte
- Department
of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Thomas A. Milne
- MRC
Molecular Haematology Unit, MRC Weatherall Institute of Molecular
Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DS, United
Kingdom
| | - Jacob T. Bush
- Department
of Chemical Biology, GSK, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, United Kingdom
| | - Stuart J. Conway
- Department
of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, United Kingdom
- Department
of Chemistry & Biochemistry, University
of California Los Angeles, 607 Charles E. Young Drive East, P.O. Box 951569, Los Angeles, California 90095-1569, United States
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2
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Guo J, Zheng Q, Peng Y. BET proteins: Biological functions and therapeutic interventions. Pharmacol Ther 2023; 243:108354. [PMID: 36739915 DOI: 10.1016/j.pharmthera.2023.108354] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Revised: 01/29/2023] [Accepted: 01/31/2023] [Indexed: 02/05/2023]
Abstract
Bromodomain and extra-terminal (BET) family member proteins (BRD2, BRD3, BRD4 and BRDT) play a pivotal role in interpreting the epigenetic information of histone Kac modification, thus controlling gene expression, remodeling chromatin structures and avoid replicative stress-induced DNA damages. Abnormal activation of BET proteins is tightly correlated to various human diseases, including cancer. Therefore, BET bromodomain inhibitors (BBIs) were considered as promising therapeutics to treat BET-related diseases, raising >70 clinical trials in the past decades. Despite preliminary effects achieved, drug resistance and adverse events represent two major challenges for current BBIs development. In this review, we will introduce the biological functions of BET proteins in both physiological and pathological conditions; and summarize the progress in current BBI drug development. Moreover, we will also discuss the major challenges in the front of BET inhibitor development and provide rational strategies to overcome these obstacles.
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Affiliation(s)
- Jiawei Guo
- Laboratory of Molecular Oncology, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Qingquan Zheng
- Laboratory of Molecular Oncology, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Yong Peng
- Laboratory of Molecular Oncology, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China; Frontier Medical Center, Tianfu Jincheng Laboratory, Chengdu, 610212, China.
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3
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Troelsen KS, Calder EDD, Skwarska A, Sneddon D, Hammond EM, Conway SJ. Zap-Pano: a Photocaged Prodrug of the KDAC Inhibitor Panobinostat. ChemMedChem 2021; 16:3691-3700. [PMID: 34259396 PMCID: PMC9291796 DOI: 10.1002/cmdc.202100403] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 07/02/2021] [Indexed: 01/04/2023]
Abstract
We report the synthesis and biological evaluation of a light‐activated (caged) prodrug of the KDAC inhibitor panobinostat (Zap‐Pano). We demonstrate that addition of the 4,5‐dimethoxy‐2‐nitrobenzyl group to the hydroxamic acid oxygen results in an inactive prodrug. In two cancer cell lines we show that photolysis of this compound releases panobinostat and an unexpected carboxamide analogue of panobinostat. Photolysis of Zap‐Pano causes an increase in H3K9Ac and H3K18Ac, consistent with KDAC inhibition, in an oesophageal cancer cell line (OE21). Irradiation of OE21 cells in the presence of Zap‐Pano results in apoptotic cell death. This compound is a useful research tool, allowing spatial and temporal control over release of panobinostat.
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Affiliation(s)
- Kathrin S Troelsen
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK.,Department of Oncology, Oxford Institute for Radiation Oncology, University of Oxford, Oxford, OX3 7DQ, UK.,Department of Drug Design and Pharmacology, University of Copenhagen, Jagtvej 162, 2100, Copenhagen, Denmark
| | - Ewen D D Calder
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK
| | - Anna Skwarska
- Department of Oncology, Oxford Institute for Radiation Oncology, University of Oxford, Oxford, OX3 7DQ, UK
| | - Deborah Sneddon
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK
| | - Ester M Hammond
- Department of Oncology, Oxford Institute for Radiation Oncology, University of Oxford, Oxford, OX3 7DQ, UK
| | - Stuart J Conway
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK
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4
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Brand M, Clayton J, Moroglu M, Schiedel M, Picaud S, Bluck JP, Skwarska A, Bolland H, Chan AKN, Laurin CMC, Scorah AR, See L, Rooney TPC, Andrews KH, Fedorov O, Perell G, Kalra P, Vinh KB, Cortopassi WA, Heitel P, Christensen KE, Cooper RI, Paton RS, Pomerantz WCK, Biggin PC, Hammond EM, Filippakopoulos P, Conway SJ. Controlling Intramolecular Interactions in the Design of Selective, High-Affinity Ligands for the CREBBP Bromodomain. J Med Chem 2021; 64:10102-10123. [PMID: 34255515 PMCID: PMC8311651 DOI: 10.1021/acs.jmedchem.1c00348] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
![]()
CREBBP (CBP/KAT3A)
and its paralogue EP300 (KAT3B) are lysine acetyltransferases
(KATs) that are essential for human development. They each comprise
10 domains through which they interact with >400 proteins, making
them important transcriptional co-activators and key nodes in the
human protein–protein interactome. The bromodomains of CREBBP
and EP300 enable the binding of acetylated lysine residues from histones
and a number of other important proteins, including p53, p73, E2F,
and GATA1. Here, we report a work to develop a high-affinity, small-molecule
ligand for the CREBBP and EP300 bromodomains [(−)-OXFBD05]
that shows >100-fold selectivity over a representative member of
the
BET bromodomains, BRD4(1). Cellular studies using this ligand demonstrate
that the inhibition of the CREBBP/EP300 bromodomain in HCT116 colon
cancer cells results in lowered levels of c-Myc and a reduction in
H3K18 and H3K27 acetylation. In hypoxia (<0.1% O2),
the inhibition of the CREBBP/EP300 bromodomain results in the enhanced
stabilization of HIF-1α.
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Affiliation(s)
- Michael Brand
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K
| | - James Clayton
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K
| | - Mustafa Moroglu
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K
| | - Matthias Schiedel
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K
| | - Sarah Picaud
- Nuffield Department of Clinical Medicine, Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 3TA, U.K
| | - Joseph P Bluck
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K.,Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, U.K
| | - Anna Skwarska
- Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford OX3 7DQ, U.K
| | - Hannah Bolland
- Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford OX3 7DQ, U.K
| | - Anthony K N Chan
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K
| | - Corentine M C Laurin
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K
| | - Amy R Scorah
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K
| | - Larissa See
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K
| | - Timothy P C Rooney
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K
| | - Katrina H Andrews
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K
| | - Oleg Fedorov
- Nuffield Department of Clinical Medicine, Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 3TA, U.K
| | - Gabriella Perell
- Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455, United States
| | - Prakriti Kalra
- Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455, United States
| | - Kayla B Vinh
- Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455, United States
| | - Wilian A Cortopassi
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K
| | - Pascal Heitel
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K
| | - Kirsten E Christensen
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K
| | - Richard I Cooper
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K
| | - Robert S Paton
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K.,Department of Chemistry, Colorado State University, 1301 Center Ave, Ft. Collins, Colorado 80523-1872, United States
| | - William C K Pomerantz
- Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455, United States
| | - Philip C Biggin
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, U.K
| | - Ester M Hammond
- Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford OX3 7DQ, U.K
| | - Panagis Filippakopoulos
- Nuffield Department of Clinical Medicine, Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 3TA, U.K
| | - Stuart J Conway
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K
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5
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Nguyen HHT, Yeoh LM, Chisholm SA, Duffy MF. Developments in drug design strategies for bromodomain protein inhibitors to target Plasmodium falciparum parasites. Expert Opin Drug Discov 2019; 15:415-425. [PMID: 31870185 DOI: 10.1080/17460441.2020.1704251] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Introduction: Bromodomains (BRDs) bind to acetylated lysine residues, often on histones. The BRD proteins can contribute to gene regulation either directly through enzymatic activity or indirectly through recruitment of chromatin-modifying complexes or transcription factors. There is no evidence of direct orthologues of the Plasmodium falciparum BRD proteins (PfBDPs) outside the apicomplexans. PfBDPs are expressed during the parasite's life cycle in both the human host's blood and in the mosquito. PfBDPs could also prove to be promising targets for novel antimalarials, which are urgently required to address increasing drug resistance.Areas covered: This review discusses recent studies of the biology of PfBDPs, current target-based strategies for PfBDP inhibitor discovery, and different approaches to the important step of validating the specificity of hit compounds for PfBDPs.Expert opinion: The novelty of Plasmodium BRDs suggests that they could be targeted by selective compounds. Chemical series that showed promise in screens against human BRDs could be leveraged to create targeted compound libraries, as could hits from P. falciparum phenotypic screens. These targeted libraries and hits could be screened in target-based strategies aimed at discovery and optimization of novel inhibitors of PfBDPs. A key task for the field is to generate parasite assays to validate the hit compounds' specificity for PfBDPs.
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Affiliation(s)
- Hanh H T Nguyen
- The School of BioSciences, Bio21 Institute, The University of Melbourne, Melbourne, Australia.,The Dept of Medicine and Radiology, Royal Melbourne Hospital, University of Melbourne, Melbourne, Australia
| | - Lee M Yeoh
- The School of BioSciences, Bio21 Institute, The University of Melbourne, Melbourne, Australia
| | - Scott A Chisholm
- The School of BioSciences, Bio21 Institute, The University of Melbourne, Melbourne, Australia
| | - Michael F Duffy
- The School of BioSciences, Bio21 Institute, The University of Melbourne, Melbourne, Australia.,The Dept of Medicine and Radiology, Royal Melbourne Hospital, University of Melbourne, Melbourne, Australia
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6
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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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7
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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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8
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Abstract
Less than a decade ago, it was shown that bromodomains, acetyl lysine 'reader' modules found in proteins with varied functions, were highly tractable small-molecule targets. This is an unusual property for protein-protein or protein-peptide interaction domains, and it prompted a wave of chemical probe discovery to understand the biological potential of new agents that targeted bromodomains. The original examples, inhibitors of the bromodomain and extra-terminal (BET) class of bromodomains, showed enticing anti-inflammatory and anticancer activities, and several compounds have since advanced to human clinical trials. Here, we review the current state of BET inhibitor biology in relation to clinical development, and we discuss the next wave of bromodomain inhibitors with clinical potential in oncology and non-oncology indications. The lessons learned from BET inhibitor programmes should affect efforts to develop drugs that target non-BET bromodomains and other epigenetic readers.
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9
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Yang SM, Yoshioka M, Strovel JW, Urban DJ, Hu X, Hall MD, Jadhav A, Maloney DJ. Lead optimization and efficacy evaluation of quinazoline-based BET family inhibitors for potential treatment of cancer and inflammatory diseases. Bioorg Med Chem Lett 2019; 29:1220-1226. [PMID: 30905542 DOI: 10.1016/j.bmcl.2019.03.014] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Revised: 03/06/2019] [Accepted: 03/10/2019] [Indexed: 12/25/2022]
Abstract
Extensive optimization of quinazoline-based lead 8 is described. The structure-activity relationship studies indicate the S-configuration is preferred for the phenylmorpholine substitution. Together with incorporation of a (2-hydroxyl-2-methylpropyl)pyrazole moiety at the 2-position leads to analogs with comparable potency and marked improvement in the pharmacokinetic profile over our previously reported lead compounds. Further in vivo efficacy studies in Kasumi-1 xenograft mouse model demonstrates that the selected inhibitors are well tolerated and highly efficacious in the inhibition of tumor growth. Additionally, the representative analog 19 also demonstrated significant improvement of arthritis severity in a collagen-induced arthritis (CIA) mouse model. These results indicate potential use of these quinazoline-based BET inhibitors for treatment of cancer and inflammatory diseases. A brief discussion of the co-crystallized structure of 19 with BRD4 (BD1) is also highlighted.
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Affiliation(s)
- Shyh-Ming Yang
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD 20850, United States.
| | - Makoto Yoshioka
- ConverGene LLC., 3093 Beverly Lane, Unit C, Cambridge, MD 21613, United States
| | - Jeffrey W Strovel
- ConverGene LLC., 3093 Beverly Lane, Unit C, Cambridge, MD 21613, United States
| | - Daniel J Urban
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD 20850, United States
| | - Xin Hu
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD 20850, United States
| | - Matthew D Hall
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD 20850, United States
| | - Ajit Jadhav
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD 20850, United States
| | - David J Maloney
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD 20850, United States.
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10
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Yang SM, Urban DJ, Yoshioka M, Strovel JW, Fletcher S, Wang AQ, Xu X, Shah P, Hu X, Hall MD, Jadhav A, Maloney DJ. Discovery and lead identification of quinazoline-based BRD4 inhibitors. Bioorg Med Chem Lett 2018; 28:3483-3488. [PMID: 30268702 DOI: 10.1016/j.bmcl.2018.08.039] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2018] [Revised: 08/28/2018] [Accepted: 08/29/2018] [Indexed: 01/09/2023]
Abstract
A new series of quinazoline-based analogs as potent bromodomain-containing protein 4 (BRD4) inhibitors is described. The structure-activity relationships on 2- and 4-position of quinazoline ring, and the substitution at 6-position that mimic the acetylated lysine are discussed. A co-crystallized structure of 48 (CN750) with BRD4 (BD1) including key inhibitor-protein interactions is also highlighted. Together with preliminary rodent pharmacokinetic results, a new lead (65, CN427) is identified which is suitable for further lead optimization.
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Affiliation(s)
- Shyh-Ming Yang
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD 20850, United States.
| | - Daniel J Urban
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD 20850, United States
| | - Makoto Yoshioka
- ConverGene LLC., 3093 Beverly Lane, Unit C, Cambridge, MD 21613, United States
| | - Jeffrey W Strovel
- ConverGene LLC., 3093 Beverly Lane, Unit C, Cambridge, MD 21613, United States
| | - Steven Fletcher
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, 20 North Pine Street, Baltimore, MD 21201, United States
| | - Amy Q Wang
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD 20850, United States
| | - Xin Xu
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD 20850, United States
| | - Pranav Shah
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD 20850, United States
| | - Xin Hu
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD 20850, United States
| | - Matthew D Hall
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD 20850, United States
| | - Ajit Jadhav
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD 20850, United States
| | - David J Maloney
- National Center for Advancing Translational Sciences, National Institutes of Health, 9800 Medical Center Drive, Rockville, MD 20850, United States.
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11
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Schiedel M, Conway SJ. Small molecules as tools to study the chemical epigenetics of lysine acetylation. Curr Opin Chem Biol 2018; 45:166-178. [DOI: 10.1016/j.cbpa.2018.06.015] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Revised: 06/08/2018] [Accepted: 06/11/2018] [Indexed: 02/06/2023]
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12
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Jennings LE, Schiedel M, Hewings DS, Picaud S, Laurin CMC, Bruno PA, Bluck JP, Scorah AR, See L, Reynolds JK, Moroglu M, Mistry IN, Hicks A, Guzanov P, Clayton J, Evans CNG, Stazi G, Biggin PC, Mapp AK, Hammond EM, Humphreys PG, Filippakopoulos P, Conway SJ. BET bromodomain ligands: Probing the WPF shelf to improve BRD4 bromodomain affinity and metabolic stability. Bioorg Med Chem 2018; 26:2937-2957. [PMID: 29776834 DOI: 10.1016/j.bmc.2018.05.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 04/30/2018] [Accepted: 05/02/2018] [Indexed: 12/20/2022]
Abstract
Ligands for the bromodomain and extra-terminal domain (BET) family of bromodomains have shown promise as useful therapeutic agents for treating a range of cancers and inflammation. Here we report that our previously developed 3,5-dimethylisoxazole-based BET bromodomain ligand (OXFBD02) inhibits interactions of BRD4(1) with the RelA subunit of NF-κB, in addition to histone H4. This ligand shows a promising profile in a screen of the NCI-60 panel but was rapidly metabolised (t½ = 39.8 min). Structure-guided optimisation of compound properties led to the development of the 3-pyridyl-derived OXFBD04. Molecular dynamics simulations assisted our understanding of the role played by an internal hydrogen bond in altering the affinity of this series of molecules for BRD4(1). OXFBD04 shows improved BRD4(1) affinity (IC50 = 166 nM), optimised physicochemical properties (LE = 0.43; LLE = 5.74; SFI = 5.96), and greater metabolic stability (t½ = 388 min).
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Affiliation(s)
- Laura E Jennings
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Matthias Schiedel
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - David S Hewings
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Sarah Picaud
- Nuffield Department of Clinical Medicine, Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 3TA, United Kingdom
| | - Corentine M C Laurin
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Paul A Bruno
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, United States; Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109-2216, United States; Program in Chemical Biology, University of Michigan, Ann Arbor, MI 48109-2216, United States
| | - Joseph P Bluck
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, United Kingdom; Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Amy R Scorah
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Larissa See
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Jessica K Reynolds
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Mustafa Moroglu
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Ishna N Mistry
- CRUK/MRC Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Old Road Campus Research Building, Oxford OX3 7DQ, United Kingdom
| | - Amy Hicks
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Pavel Guzanov
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - James Clayton
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Charles N G Evans
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Giulia Stazi
- Department of Chemistry and Technologies of Drugs, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Philip C Biggin
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Anna K Mapp
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, United States; Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109-2216, United States; Program in Chemical Biology, University of Michigan, Ann Arbor, MI 48109-2216, United States
| | - Ester M Hammond
- CRUK/MRC Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Old Road Campus Research Building, Oxford OX3 7DQ, United Kingdom
| | - Philip G Humphreys
- Epigenetics Discovery Performance Unit, GlaxoSmithKline R&D, Stevenage Hertfordshire SG1 2NY, United Kingdom
| | - Panagis Filippakopoulos
- Nuffield Department of Clinical Medicine, Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 3TA, United Kingdom
| | - Stuart J Conway
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, United Kingdom.
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13
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Leveridge M, Chung CW, Gross JW, Phelps CB, Green D. Integration of Lead Discovery Tactics and the Evolution of the Lead Discovery Toolbox. SLAS DISCOVERY 2018; 23:881-897. [PMID: 29874524 DOI: 10.1177/2472555218778503] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
There has been much debate around the success rates of various screening strategies to identify starting points for drug discovery. Although high-throughput target-based and phenotypic screening has been the focus of this debate, techniques such as fragment screening, virtual screening, and DNA-encoded library screening are also increasingly reported as a source of new chemical equity. Here, we provide examples in which integration of more than one screening approach has improved the campaign outcome and discuss how strengths and weaknesses of various methods can be used to build a complementary toolbox of approaches, giving researchers the greatest probability of successfully identifying leads. Among others, we highlight case studies for receptor-interacting serine/threonine-protein kinase 1 and the bromo- and extra-terminal domain family of bromodomains. In each example, the unique insight or chemistries individual approaches provided are described, emphasizing the synergy of information obtained from the various tactics employed and the particular question each tactic was employed to answer. We conclude with a short prospective discussing how screening strategies are evolving, what this screening toolbox might look like in the future, how to maximize success through integration of multiple tactics, and scenarios that drive selection of one combination of tactics over another.
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Affiliation(s)
- Melanie Leveridge
- 1 GlaxoSmithKline Drug Design and Selection, Platform Technology and Science, Stevenage, Hertfordshire, UK
| | - Chun-Wa Chung
- 1 GlaxoSmithKline Drug Design and Selection, Platform Technology and Science, Stevenage, Hertfordshire, UK
| | - Jeffrey W Gross
- 2 GlaxoSmithKline Drug Design and Selection, Platform Technology and Science, Collegeville, PA, USA
| | - Christopher B Phelps
- 3 GlaxoSmithKline Drug Design and Selection, Platform Technology and Science, Cambridge, MA, USA
| | - Darren Green
- 1 GlaxoSmithKline Drug Design and Selection, Platform Technology and Science, Stevenage, Hertfordshire, UK
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14
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Zhou Y, Hussain M, Kuang G, Zhang J, Tu Y. Mechanistic insights into peptide and ligand binding of the ATAD2-bromodomain via atomistic simulations disclosing a role of induced fit and conformational selection. Phys Chem Chem Phys 2018; 20:23222-23232. [DOI: 10.1039/c8cp03860k] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Atomistic simulations of the ATAD2-bromodomain disclose a role of induced fit and conformational selection upon ligand and peptide binding.
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Affiliation(s)
- Yang Zhou
- Department of Theoretical Chemistry and Biology
- KTH Royal Institute of Technology
- AlbaNova University Center
- Stockholm
- Sweden
| | - Muzammal Hussain
- Guangdong Provincial Key Laboratory of Biocomputing
- Institute of Chemical Biology
- Guangzhou Institutes of Biomedicine and Health
- Chinese Academy of Sciences
- Guangzhou 510530
| | - Guanglin Kuang
- Department of Theoretical Chemistry and Biology
- KTH Royal Institute of Technology
- AlbaNova University Center
- Stockholm
- Sweden
| | - Jiancun Zhang
- Guangdong Provincial Key Laboratory of Biocomputing
- Institute of Chemical Biology
- Guangzhou Institutes of Biomedicine and Health
- Chinese Academy of Sciences
- Guangzhou 510530
| | - Yaoquan Tu
- Department of Theoretical Chemistry and Biology
- KTH Royal Institute of Technology
- AlbaNova University Center
- Stockholm
- Sweden
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15
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W Young D. Using Fragment Based Drug Discovery to Target Epigenetic Regulators in Cancer. ACTA ACUST UNITED AC 2017. [DOI: 10.15406/mojbb.2017.04.00062] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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16
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Carlino L, Rastelli G. Dual Kinase-Bromodomain Inhibitors in Anticancer Drug Discovery: A Structural and Pharmacological Perspective. J Med Chem 2016; 59:9305-9320. [DOI: 10.1021/acs.jmedchem.6b00438] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Luca Carlino
- Department
of Life Sciences, University of Modena and Reggio Emilia, Modena 41125, Italy
| | - Giulio Rastelli
- Department
of Life Sciences, University of Modena and Reggio Emilia, Modena 41125, Italy
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17
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Galdeano C, Ciulli A. Selectivity on-target of bromodomain chemical probes by structure-guided medicinal chemistry and chemical biology. Future Med Chem 2016; 8:1655-80. [PMID: 27193077 PMCID: PMC5321501 DOI: 10.4155/fmc-2016-0059] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Accepted: 04/22/2016] [Indexed: 12/18/2022] Open
Abstract
Targeting epigenetic proteins is a rapidly growing area for medicinal chemistry and drug discovery. Recent years have seen an explosion of interest in developing small molecules binding to bromodomains, the readers of acetyl-lysine modifications. A plethora of co-crystal structures has motivated focused fragment-based design and optimization programs within both industry and academia. These efforts have yielded several compounds entering the clinic, and many more are increasingly being used as chemical probes to interrogate bromodomain biology. High selectivity of chemical probes is necessary to ensure biological activity is due to an on-target effect. Here, we review the state-of-the-art of bromodomain-targeting compounds, focusing on the structural basis for their on-target selectivity or lack thereof. We also highlight chemical biology approaches to enhance on-target selectivity.
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Affiliation(s)
- Carles Galdeano
- Division of Biological Chemistry & Drug Discovery, School of Life Sciences, University of Dundee, James Black Centre, Dow Street, Dundee, DD1 5EH, UK
- Institut de Biomedicina de la Universitat de Barcelona (IBUB) & Departament de Fisicoquímica, Facultat de Farmàcia, Universitat de Barcelona, Av. Joan XXIII s/n, 08028 Barcelona, Spain
| | - Alessio Ciulli
- Division of Biological Chemistry & Drug Discovery, School of Life Sciences, University of Dundee, James Black Centre, Dow Street, Dundee, DD1 5EH, UK
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18
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Theodoulou NH, Tomkinson NCO, Prinjha RK, Humphreys PG. Clinical progress and pharmacology of small molecule bromodomain inhibitors. Curr Opin Chem Biol 2016; 33:58-66. [DOI: 10.1016/j.cbpa.2016.05.028] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Revised: 05/25/2016] [Accepted: 05/30/2016] [Indexed: 11/26/2022]
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19
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Abstract
Histone posttranslational modifications represent a versatile set of epigenetic marks involved not only in dynamic cellular processes, such as transcription and DNA repair, but also in the stable maintenance of repressive chromatin. In this article, we review many of the key and newly identified histone modifications known to be deregulated in cancer and how this impacts function. The latter part of the article addresses the challenges and current status of the epigenetic drug development process as it applies to cancer therapeutics.
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Affiliation(s)
- James E Audia
- Constellation Pharmaceuticals, Cambridge, Massachusetts 02142
| | - Robert M Campbell
- Eli Lilly and Company, Lilly Corporate Center, Indianapolis, Indiana 46285
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20
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Unzue A, Zhao H, Lolli G, Dong J, Zhu J, Zechner M, Dolbois A, Caflisch A, Nevado C. The “Gatekeeper” Residue Influences the Mode of Binding of Acetyl Indoles to Bromodomains. J Med Chem 2016; 59:3087-97. [DOI: 10.1021/acs.jmedchem.5b01757] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Andrea Unzue
- Department of Chemistry and ‡Department of
Biochemistry, University of Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Hongtao Zhao
- Department of Chemistry and ‡Department of
Biochemistry, University of Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Graziano Lolli
- Department of Chemistry and ‡Department of
Biochemistry, University of Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Jing Dong
- Department of Chemistry and ‡Department of
Biochemistry, University of Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Jian Zhu
- Department of Chemistry and ‡Department of
Biochemistry, University of Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Melanie Zechner
- Department of Chemistry and ‡Department of
Biochemistry, University of Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Aymeric Dolbois
- Department of Chemistry and ‡Department of
Biochemistry, University of Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Amedeo Caflisch
- Department of Chemistry and ‡Department of
Biochemistry, University of Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Cristina Nevado
- Department of Chemistry and ‡Department of
Biochemistry, University of Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
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21
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Theodoulou NH, Tomkinson NCO, Prinjha RK, Humphreys PG. Progress in the Development of non-BET Bromodomain Chemical Probes. ChemMedChem 2016; 11:477-87. [PMID: 26749027 DOI: 10.1002/cmdc.201500540] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Revised: 12/09/2015] [Indexed: 12/19/2022]
Abstract
The bromodomain and extra terminal (BET) family of bromodomains have been the focus of extensive research, leading to the development of many potent, selective chemical probes and recent clinical assets. The profound biology associated with BET bromodomain inhibition has provided a convincing rationale for targeting bromodomains for the treatment of disease. However, the BET family represents just eight of the at least 56 human bromodomains identified to date. Until recently, there has been significantly less interest in non-BET bromodomains, leaving a vast area of research and the majority of this new target class yet to be thoroughly investigated. It has been widely reported that several non-BET bromodomain containing proteins are associated with various diseases including cancer and HIV. Therefore, the development of chemical probes for non-BET bromodomains will facilitate elucidation of their precise biological roles and potentially lead to the development of new medicines. This review summarises the progress made towards the development of non-BET bromodomain chemical probes to date. In addition, we highlight the potential for future work in this new and exciting area.
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Affiliation(s)
- Natalie H Theodoulou
- Epinova Epigenetics Discovery Performance Unit, GlaxoSmithKline R&D, Stevenage, Hertfordshire, SG1 2NY, UK.,WestCHEM, Department of Pure and Applied Chemistry, Thomas Graham Building, University of Strathclyde, 295 Cathedral Street, Glasgow, G1 1XL, UK
| | - Nicholas C O Tomkinson
- WestCHEM, Department of Pure and Applied Chemistry, Thomas Graham Building, University of Strathclyde, 295 Cathedral Street, Glasgow, G1 1XL, UK
| | - Rab K Prinjha
- Epinova Epigenetics Discovery Performance Unit, GlaxoSmithKline R&D, Stevenage, Hertfordshire, SG1 2NY, UK
| | - Philip G Humphreys
- Epinova Epigenetics Discovery Performance Unit, GlaxoSmithKline R&D, Stevenage, Hertfordshire, SG1 2NY, UK.
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22
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Bamborough P, Chung CW, Furze RC, Grandi P, Michon AM, Sheppard RJ, Barnett H, Diallo H, Dixon DP, Douault C, Jones EJ, Karamshi B, Mitchell DJ, Prinjha RK, Rau C, Watson RJ, Werner T, Demont EH. Structure-Based Optimization of Naphthyridones into Potent ATAD2 Bromodomain Inhibitors. J Med Chem 2015; 58:6151-78. [PMID: 26230603 DOI: 10.1021/acs.jmedchem.5b00773] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
ATAD2 is a bromodomain-containing protein whose overexpression is linked to poor outcomes in a number of different cancer types. To date, no potent and selective inhibitors of the bromodomain have been reported. This article describes the structure-based optimization of a series of naphthyridones from micromolar leads with no selectivity over the BET bromodomains to inhibitors with sub-100 nM ATAD2 potency and 100-fold BET selectivity.
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Affiliation(s)
| | | | | | - Paola Grandi
- ∥Cellzome GmbH, Molecular Discovery Research, GlaxoSmithKline, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Anne-Marie Michon
- ∥Cellzome GmbH, Molecular Discovery Research, GlaxoSmithKline, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | | | | | | | | | | | | | | | | | | | - Christina Rau
- ∥Cellzome GmbH, Molecular Discovery Research, GlaxoSmithKline, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | | | - Thilo Werner
- ∥Cellzome GmbH, Molecular Discovery Research, GlaxoSmithKline, Meyerhofstrasse 1, 69117 Heidelberg, Germany
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23
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Clark AM, Ekins S. Open Source Bayesian Models. 2. Mining a "Big Dataset" To Create and Validate Models with ChEMBL. J Chem Inf Model 2015; 55:1246-60. [PMID: 25995041 DOI: 10.1021/acs.jcim.5b00144] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
In an associated paper, we have described a reference implementation of Laplacian-corrected naïve Bayesian model building using extended connectivity (ECFP)- and molecular function class fingerprints of maximum diameter 6 (FCFP)-type fingerprints. As a follow-up, we have now undertaken a large-scale validation study in order to ensure that the technique generalizes to a broad variety of drug discovery datasets. To achieve this, we have used the ChEMBL (version 20) database and split it into more than 2000 separate datasets, each of which consists of compounds and measurements with the same target and activity measurement. In order to test these datasets with the two-state Bayesian classification, we developed an automated algorithm for detecting a suitable threshold for active/inactive designation, which we applied to all collections. With these datasets, we were able to establish that our Bayesian model implementation is effective for the large majority of cases, and we were able to quantify the impact of fingerprint folding on the receiver operator curve cross-validation metrics. We were also able to study the impact that the choice of training/testing set partitioning has on the resulting recall rates. The datasets have been made publicly available to be downloaded, along with the corresponding model data files, which can be used in conjunction with the CDK and several mobile apps. We have also explored some novel visualization methods which leverage the structural origins of the ECFP/FCFP fingerprints to attribute regions of a molecule responsible for positive and negative contributions to activity. The ability to score molecules across thousands of relevant datasets across organisms also may help to access desirable and undesirable off-target effects as well as suggest potential targets for compounds derived from phenotypic screens.
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Affiliation(s)
- Alex M Clark
- †Molecular Materials Informatics, Inc., 1900 St. Jacques No. 302, Montreal H3J 2S1, Quebec, Canada
| | - Sean Ekins
- ‡Collaborations Pharmaceuticals, Inc., 5616 Hilltop Needmore Road, Fuquay-Varina, North Carolina 27526, United States.,§Collaborations in Chemistry, 5616 Hilltop Needmore Road, Fuquay-Varina, North Carolina 27526, United States.,∥Collaborative Drug Discovery, 1633 Bayshore Highway, Suite 342, Burlingame, California 94010, United States
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24
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Magee TV. Progress in discovery of small-molecule modulators of protein-protein interactions via fragment screening. Bioorg Med Chem Lett 2015; 25:2461-8. [PMID: 25971770 DOI: 10.1016/j.bmcl.2015.04.089] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Revised: 04/21/2015] [Accepted: 04/27/2015] [Indexed: 11/16/2022]
Abstract
Protein-protein interactions (PPIs) present a formidable challenge to medicinal chemistry. The extended and open nature of many binding sites at protein interfaces has made it difficult to find useful chemical matter by traditional screening methods using standard screening libraries. This Digest focuses on the progress that has been made in discovering small-molecule modulators for a diverse selection of PPI targets using fragment screening and highlights the utility of this strategy in this context.
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Affiliation(s)
- Thomas V Magee
- Worldwide Medicinal Chemistry, Pfizer Inc, 610 Main Street, Cambridge, MA 02139, USA.
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25
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Theodoulou NH, Bamborough P, Bannister AJ, Becher I, Bit RA, Che KH, Chung CW, Dittmann A, Drewes G, Drewry DH, Gordon L, Grandi P, Leveridge M, Lindon M, Michon AM, Molnar J, Robson SC, Tomkinson NCO, Kouzarides T, Prinjha RK, Humphreys PG. Discovery of I-BRD9, a Selective Cell Active Chemical Probe for Bromodomain Containing Protein 9 Inhibition. J Med Chem 2015; 59:1425-39. [PMID: 25856009 DOI: 10.1021/acs.jmedchem.5b00256] [Citation(s) in RCA: 162] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Acetylation of histone lysine residues is one of the most well-studied post-translational modifications of chromatin, selectively recognized by bromodomain "reader" modules. Inhibitors of the bromodomain and extra terminal domain (BET) family of bromodomains have shown profound anticancer and anti-inflammatory properties, generating much interest in targeting other bromodomain-containing proteins for disease treatment. Herein, we report the discovery of I-BRD9, the first selective cellular chemical probe for bromodomain-containing protein 9 (BRD9). I-BRD9 was identified through structure-based design, leading to greater than 700-fold selectivity over the BET family and 200-fold over the highly homologous bromodomain-containing protein 7 (BRD7). I-BRD9 was used to identify genes regulated by BRD9 in Kasumi-1 cells involved in oncology and immune response pathways and to the best of our knowledge, represents the first selective tool compound available to elucidate the cellular phenotype of BRD9 bromodomain inhibition.
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Affiliation(s)
- Natalie H Theodoulou
- Epinova Discovery Performance Unit, GlaxoSmithKline R&D , Stevenage, Hertfordshire SG1 2NY, U.K.,WestCHEM, Department of Pure and Applied Chemistry, Thomas Graham Building, University of Strathclyde , 295 Cathedral Street, Glasgow G1 1XL, U.K
| | - Paul Bamborough
- Computational & Structural Chemistry, Molecular Discovery Research, GlaxoSmithKline R&D , Stevenage, Hertfordshire SG1 2NY, U.K
| | - Andrew J Bannister
- Department of Pathology, Gurdon Institute , Tennis Court Road, Cambridge CB2 1QN, U.K
| | - Isabelle Becher
- Cellzome GmbH, Molecular Discovery Research, GlaxoSmithKline R&D , Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Rino A Bit
- Epinova Discovery Performance Unit, GlaxoSmithKline R&D , Stevenage, Hertfordshire SG1 2NY, U.K
| | - Ka Hing Che
- Department of Pathology, Gurdon Institute , Tennis Court Road, Cambridge CB2 1QN, U.K
| | - Chun-wa Chung
- Computational & Structural Chemistry, Molecular Discovery Research, GlaxoSmithKline R&D , Stevenage, Hertfordshire SG1 2NY, U.K
| | - Antje Dittmann
- Cellzome GmbH, Molecular Discovery Research, GlaxoSmithKline R&D , Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Gerard Drewes
- Cellzome GmbH, Molecular Discovery Research, GlaxoSmithKline R&D , Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - David H Drewry
- Department of Chemical Biology, GlaxoSmithKline , Research Triangle Park, North Carolina 27709, United States
| | - Laurie Gordon
- Biological Sciences, Molecular Discovery Research, GlaxoSmithKline R&D , Stevenage, Hertfordshire SG1 2NY, U.K
| | - Paola Grandi
- Cellzome GmbH, Molecular Discovery Research, GlaxoSmithKline R&D , Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Melanie Leveridge
- Biological Sciences, Molecular Discovery Research, GlaxoSmithKline R&D , Stevenage, Hertfordshire SG1 2NY, U.K
| | - Matthew Lindon
- Epinova Discovery Performance Unit, GlaxoSmithKline R&D , Stevenage, Hertfordshire SG1 2NY, U.K
| | - Anne-Marie Michon
- Cellzome GmbH, Molecular Discovery Research, GlaxoSmithKline R&D , Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Judit Molnar
- Epinova Discovery Performance Unit, GlaxoSmithKline R&D , Stevenage, Hertfordshire SG1 2NY, U.K
| | - Samuel C Robson
- Department of Pathology, Gurdon Institute , Tennis Court Road, Cambridge CB2 1QN, U.K
| | - Nicholas C O Tomkinson
- WestCHEM, Department of Pure and Applied Chemistry, Thomas Graham Building, University of Strathclyde , 295 Cathedral Street, Glasgow G1 1XL, U.K
| | - Tony Kouzarides
- Department of Pathology, Gurdon Institute , Tennis Court Road, Cambridge CB2 1QN, U.K
| | - Rab K Prinjha
- Epinova Discovery Performance Unit, GlaxoSmithKline R&D , Stevenage, Hertfordshire SG1 2NY, U.K
| | - Philip G Humphreys
- Epinova Discovery Performance Unit, GlaxoSmithKline R&D , Stevenage, Hertfordshire SG1 2NY, U.K
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26
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Brand M, Measures AM, Wilson BG, Cortopassi WA, Alexander R, Höss M, Hewings DS, Rooney TPC, Paton RS, Conway SJ. Small molecule inhibitors of bromodomain-acetyl-lysine interactions. ACS Chem Biol 2015; 10:22-39. [PMID: 25549280 DOI: 10.1021/cb500996u] [Citation(s) in RCA: 137] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Bromodomains are protein modules that bind to acetylated lysine residues. Their interaction with histone proteins suggests that they function as "readers" of histone lysine acetylation, a component of the proposed "histone code". Bromodomain-containing proteins are often found as components of larger protein complexes with roles in fundamental cellular process including transcription. The publication of two potent ligands for the BET bromodomains in 2010 demonstrated that small molecules can inhibit the bromodomain-acetyl-lysine protein-protein interaction. These molecules display strong phenotypic effects in a number of cell lines and affect a range of cancers in vivo. This work stimulated intense interest in developing further ligands for the BET bromodomains and the design of ligands for non-BET bromodomains. Here we review the recent progress in the field with particular attention paid to ligand design, the assays employed in early ligand discovery, and the use of computational approaches to inform ligand design.
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Affiliation(s)
- Michael Brand
- Department
of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K
| | - Angelina M. Measures
- Department
of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K
| | - Brian G. Wilson
- Department
of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K
| | - Wilian A. Cortopassi
- Department
of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K
- Department
of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QZ, U.K
| | | | | | - David S. Hewings
- Department
of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K
| | - Timothy P. C. Rooney
- Department
of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K
| | - Robert S. Paton
- Department
of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K
- Department
of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QZ, U.K
| | - Stuart J. Conway
- Department
of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K
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