1
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Karrenbrock M, Rizzi V, Procacci P, Gervasio FL. Addressing Suboptimal Poses in Nonequilibrium Alchemical Calculations. J Phys Chem B 2024; 128:1595-1605. [PMID: 38323915 DOI: 10.1021/acs.jpcb.3c06516] [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: 02/08/2024]
Abstract
Alchemical transformations can be used to quantitatively estimate absolute binding free energies at a reasonable computational cost. However, most of the approaches currently in use require knowledge of the correct (crystallographic) pose. In this paper, we present a combined Hamiltonian replica exchange nonequilibrium alchemical method that allows us to reliably calculate absolute binding free energies, even when starting from suboptimal initial binding poses. Performing a preliminary Hamiltonian replica exchange enhances the sampling of slow degrees of freedom of the ligand and the target, allowing the system to populate the correct binding pose when starting from an approximate docking pose. We apply the method on 6 ligands of the first bromodomain of the BRD4 bromodomain-containing protein. For each ligand, we start nonequilibrium alchemical transformations from both the crystallographic pose and the top-scoring docked pose that are often significantly different. We show that the method produces statistically equivalent binding free energies, making it a useful tool for computational drug discovery pipelines.
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Affiliation(s)
- Maurice Karrenbrock
- School of Pharmaceutical Sciences, University of Geneva, Rue Michel-Servet 1, CH-1206 Geneva, Switzerland
| | - Valerio Rizzi
- School of Pharmaceutical Sciences, University of Geneva, Rue Michel-Servet 1, CH-1206 Geneva, Switzerland
| | - Piero Procacci
- Chemistry Department, University of Florence, Via della Lastruccia 3-13, 50019 Sesto Fiorentino, Italy
| | - Francesco Luigi Gervasio
- School of Pharmaceutical Sciences, University of Geneva, Rue Michel-Servet 1, CH-1206 Geneva, Switzerland
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, CH-1206 Geneva, Switzerland
- Chemistry Department, University College London (UCL), WC1E 6BT London, U.K
- Swiss Bioinformatics Institute, University of Geneva, CH-1206 Geneva, Switzerland
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2
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Li Y, Shen Z, Ratia K, Zhao J, Huang F, Dubrovyskyii O, Indukuri D, Fu J, Lozano Ramos O, Thatcher GRJ, Xiong R. Structure-Guided Design and Synthesis of Pyridinone-Based Selective Bromodomain and Extra-Terminal Domain (BET)-First Bromodomain (BD1) Inhibitors. J Med Chem 2024; 67:2712-2731. [PMID: 38295759 DOI: 10.1021/acs.jmedchem.3c01837] [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: 02/02/2024]
Abstract
The bromodomain and extra-terminal domain (BET) proteins are epigenetic readers, regulating transcription via two highly homologous tandem bromodomains, BD1 and BD2. Clinical development of nonselective pan-BD BET inhibitors has been challenging, partly due to dose-limiting side effects such as thrombocytopenia. This has prompted the push for domain-selective BET inhibitors to achieve a more favorable therapeutic window. We report a structure-guided drug design campaign that led to the development of a potent BD1-selective BET inhibitor, 33 (XL-126), with a Kd of 8.9 nM and 185-fold BD1/BD2 selectivity. The high selectivity was first assayed by SPR, validated by a secondary time-resolved fluorescence energy transfer assay, and further corroborated by BROMOscan (∼57-373 fold selectivity). The cocrystal of 33 with BRD4 BD1 and BD2 demonstrates the source of selectivity: repulsion with His437 and lost binding with the leucine clamp. Notably, the BD1 selectivity of BET inhibitor 33 leads to both the preservation of platelets and potent anti-inflammatory efficacy.
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Affiliation(s)
- Yangfeng Li
- UICentre (Drug Discovery@UIC), University of Illinois at Chicago, 833 S Wood Street, Chicago, Illinois 60612, United States
| | - Zhengnan Shen
- UICentre (Drug Discovery@UIC), University of Illinois at Chicago, 833 S Wood Street, Chicago, Illinois 60612, United States
| | - Kiira Ratia
- UICentre (Drug Discovery@UIC), University of Illinois at Chicago, 833 S Wood Street, Chicago, Illinois 60612, United States
- Department of Pharmaceutical Sciences, University of Illinois College of Pharmacy, University of Illinois at Chicago, 833 S Wood Street, Chicago, Illinois 60612, United States
- Research Resources Center, University of Illinois at Chicago, Chicago, Illinois 60612, United States
| | - Jiong Zhao
- Department of Pharmaceutical Sciences, University of Illinois College of Pharmacy, University of Illinois at Chicago, 833 S Wood Street, Chicago, Illinois 60612, United States
| | - Fei Huang
- UICentre (Drug Discovery@UIC), University of Illinois at Chicago, 833 S Wood Street, Chicago, Illinois 60612, United States
| | - Oleksii Dubrovyskyii
- UICentre (Drug Discovery@UIC), University of Illinois at Chicago, 833 S Wood Street, Chicago, Illinois 60612, United States
| | - Divakar Indukuri
- Department of Pharmacology & Toxicology, University of Arizona, Tucson, Arizona 85721, United States
| | - Jiqiang Fu
- Department of Pharmacology & Toxicology, University of Arizona, Tucson, Arizona 85721, United States
| | - Omar Lozano Ramos
- Department of Pharmacology & Toxicology, University of Arizona, Tucson, Arizona 85721, United States
| | - Gregory R J Thatcher
- UICentre (Drug Discovery@UIC), University of Illinois at Chicago, 833 S Wood Street, Chicago, Illinois 60612, United States
- Department of Pharmaceutical Sciences, University of Illinois College of Pharmacy, University of Illinois at Chicago, 833 S Wood Street, Chicago, Illinois 60612, United States
| | - Rui Xiong
- UICentre (Drug Discovery@UIC), University of Illinois at Chicago, 833 S Wood Street, Chicago, Illinois 60612, United States
- Department of Pharmaceutical Sciences, University of Illinois College of Pharmacy, University of Illinois at Chicago, 833 S Wood Street, Chicago, Illinois 60612, United States
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3
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Schiedel M, McArdle DJB, Padalino G, Chan AKN, Forde-Thomas J, McDonough M, Whiteland H, Beckmann M, Cookson R, Hoffmann KF, Conway SJ. Small Molecule Ligands of the BET-like Bromodomain, SmBRD3, Affect Schistosoma mansoni Survival, Oviposition, and Development. J Med Chem 2023; 66:15801-15822. [PMID: 38048437 PMCID: PMC10726355 DOI: 10.1021/acs.jmedchem.3c01321] [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: 07/21/2023] [Revised: 10/15/2023] [Accepted: 11/01/2023] [Indexed: 12/06/2023]
Abstract
Schistosomiasis is a disease affecting >200 million people worldwide, but its treatment relies on a single agent, praziquantel. To investigate new avenues for schistosomiasis control, we have conducted the first systematic analysis of bromodomain-containing proteins (BCPs) in a causative species, Schistosoma mansoni. Having identified 29 putative bromodomains (BRDs) in 22 S. mansoni proteins, we selected SmBRD3, a tandem BRD-containing BCP that shows high similarity to the human bromodomain and extra terminal domain (BET) family, for further studies. Screening 697 small molecules identified the human BET BRD inhibitor I-BET726 as a ligand for SmBRD3. An X-ray crystal structure of I-BET726 bound to the second BRD of SmBRD3 [SmBRD3(2)] enabled rational design of a quinoline-based ligand (15) with an ITC Kd = 364 ± 26.3 nM for SmBRD3(2). The ethyl ester pro-drug of compound 15 (compound 22) shows substantial effects on sexually immature larval schistosomula, sexually mature adult worms, and snail-infective miracidia in ex vivo assays.
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Affiliation(s)
- Matthias Schiedel
- Department
of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K.
| | - Darius J. B. McArdle
- Department
of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K.
| | - Gilda Padalino
- The
Department of Life Sciences (DLS), Aberystwyth
University, Wales SY23 3DA, U.K.
| | - Anthony K. N. Chan
- Department
of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K.
| | | | - Michael McDonough
- Department
of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K.
| | - Helen Whiteland
- The
Department of Life Sciences (DLS), Aberystwyth
University, Wales SY23 3DA, U.K.
| | - Manfred Beckmann
- The
Department of Life Sciences (DLS), Aberystwyth
University, Wales SY23 3DA, U.K.
| | - Rosa Cookson
- GlaxoSmithKline
R&D, Stevenage, Hertfordshire SG1 2NY, U.K.
| | - Karl F. Hoffmann
- The
Department of Life Sciences (DLS), Aberystwyth
University, Wales SY23 3DA, U.K.
| | - Stuart J. Conway
- Department
of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K.
- 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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4
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Li Y, Chu X, Yin Y, Li H, Fu H, Feng X, Deng Y, Ge J. Design, synthesis, and evaluation of 4-(3-(3,5-dimethylisoxazol-4-yl)benzyl)phthalazin-1(2H)-one derivatives: potent BRD4 inhibitors with anti-breast cancer activity. Front Pharmacol 2023; 14:1289003. [PMID: 38099141 PMCID: PMC10720709 DOI: 10.3389/fphar.2023.1289003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 11/13/2023] [Indexed: 12/17/2023] Open
Abstract
BRD4 inhibitors have demonstrated promising potential in cancer therapy. However, their therapeutic efficacy in breast cancer varies depending on the breast cancer subtype, particularly in the treatment of TNBC. In this study, we designed and synthesized 94 derivatives of 4-(3-(3,5-dimethylisoxazol-4-yl)benzyl)phthalazin-1(2H)-one to evaluate their inhibitory activities against BRD4. Notably, compound DDT26 exhibited the most potent inhibitory effect on BRD4, with an IC50 value of 0.237 ± 0.093 μM. DDT26 demonstrated significant anti-proliferative activity against both TNBC cell lines and MCF-7 cells. Intriguingly, the phthalazinone moiety of DDT26 mimicked the PAPR1 substrate, resulting in DDT26 displaying a moderate inhibitory effect on PARP1 with an IC50 value of 4.289 ± 1.807 μM. Further, DDT26 was shown to modulate the expression of c-MYC and γ-H2AX, induce DNA damage, inhibit cell migration and colony formation, and arrest the cell cycle at the G1 phase in MCF-7 cells. Our findings present potential lead compounds for the development of potent anti-breast cancer agents targeting BRD4.
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Affiliation(s)
- Yingpeng Li
- College of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Xinhong Chu
- College of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Yu Yin
- College of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Hongkun Li
- College of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Hui Fu
- College of Integrative Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Xinchi Feng
- College of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Yanru Deng
- College of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin, China
| | - Jun Ge
- College of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin, China
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5
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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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6
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Russell C, Carter JL, Borgia JM, Bush J, Calderón F, Gabarró R, Conway SJ, Mottram JC, Wilkinson AJ, Jones NG. Bromodomain Factor 5 as a Target for Antileishmanial Drug Discovery. ACS Infect Dis 2023; 9:2340-2357. [PMID: 37906637 PMCID: PMC10644352 DOI: 10.1021/acsinfecdis.3c00431] [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: 08/22/2023] [Revised: 10/16/2023] [Accepted: 10/16/2023] [Indexed: 11/02/2023]
Abstract
Leishmaniases are a collection of neglected tropical diseases caused by kinetoplastid parasites in the genus Leishmania. Current chemotherapies are severely limited, and the need for new antileishmanials is of pressing international importance. Bromodomains are epigenetic reader domains that have shown promising therapeutic potential for cancer therapy and may also present an attractive target to treat parasitic diseases. Here, we investigate Leishmania donovani bromodomain factor 5 (LdBDF5) as a target for antileishmanial drug discovery. LdBDF5 contains a pair of bromodomains (BD5.1 and BD5.2) in an N-terminal tandem repeat. We purified recombinant bromodomains of L. donovani BDF5 and determined the structure of BD5.2 by X-ray crystallography. Using a histone peptide microarray and fluorescence polarization assay, we identified binding interactions of LdBDF5 bromodomains with acetylated peptides derived from histones H2B and H4. In orthogonal biophysical assays including thermal shift assays, fluorescence polarization, and NMR, we showed that BDF5 bromodomains bind to human bromodomain inhibitors SGC-CBP30, bromosporine, and I-BRD9; moreover, SGC-CBP30 exhibited activity against Leishmania promastigotes in cell viability assays. These findings exemplify the potential BDF5 holds as a possible drug target in Leishmania and provide a foundation for the future development of optimized antileishmanial compounds targeting this epigenetic reader protein.
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Affiliation(s)
- Catherine
N. Russell
- York
Structural Biology Laboratory and York Biomedical Research Institute,
Department of Chemistry, University of York, York YO10 5DD, U.K.
| | - Jennifer L. Carter
- Department
of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K.
| | - Juliet M. Borgia
- York
Structural Biology Laboratory and York Biomedical Research Institute,
Department of Chemistry, University of York, York YO10 5DD, U.K.
| | - Jacob Bush
- GSK, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, U.K.
| | | | | | - Stuart J. Conway
- Department
of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K.
| | - Jeremy C. Mottram
- York
Biomedical Research Institute, Department of Biology, University of York, York YO10 5NG, U.K.
| | - Anthony J. Wilkinson
- York
Structural Biology Laboratory and York Biomedical Research Institute,
Department of Chemistry, University of York, York YO10 5DD, U.K.
| | - Nathaniel G. Jones
- York
Biomedical Research Institute, Department of Biology, University of York, York YO10 5NG, U.K.
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7
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Wang S, Argikar UA, Cheruzel L, Cho S, Crouch RD, Dhaware D, Heck CJS, Johnson KM, Kalgutkar AS, King L, Liu J, Ma B, Maw H, Miller GP, Seneviratne HK, Takahashi RH, Wei C, Khojasteh SC. Bioactivation and reactivity research advances - 2022 year in review‡. Drug Metab Rev 2023; 55:267-300. [PMID: 37608698 DOI: 10.1080/03602532.2023.2244193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 06/05/2023] [Indexed: 08/24/2023]
Abstract
With the 50th year mark since the launch of Drug Metabolism and Disposition journal, the field of drug metabolism and bioactivation has advanced exponentially in the past decades (Guengerich 2023).This has, in a major part, been due to the continued advances across the whole spectrum of applied technologies in hardware, software, machine learning (ML), and artificial intelligence (AI). LC-MS platforms continue to evolve to support key applications in the field, and automation is also improving the accuracy, precision, and throughput of these supporting assays. In addition, sample generation and processing is being aided by increased diversity and quality of reagents and bio-matrices so that what is being analyzed is more relevant and translatable. The application of in silico platforms (applied software, ML, and AI) is also making great strides, and in tandem with the more traditional approaches mentioned previously, is significantly advancing our understanding of bioactivation pathways and how these play a role in toxicity. All of this continues to allow the area of bioactivation to evolve in parallel with associated fields to help bring novel or improved medicines to patients with urgent or unmet needs.Shuai Wang and Cyrus Khojasteh, on behalf of the authors.
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Affiliation(s)
- Shuai Wang
- Department of Drug Metabolism and Pharmacokinetics, Genentech, Inc., South San Francisco, CA, USA
| | - Upendra A Argikar
- Non-clinical Development, Bill and Melinda Gates Medical Research Institute, Cambridge, MA, USA
| | - Lionel Cheruzel
- Department of Drug Metabolism and Pharmacokinetics, Genentech, Inc., South San Francisco, CA, USA
| | - Sungjoon Cho
- Department of Drug Metabolism and Pharmacokinetics, Genentech, Inc., South San Francisco, CA, USA
| | - Rachel D Crouch
- Department of Pharmacy and Pharmaceutical Sciences, Lipscomb University College of Pharmacy, Nashville, TN, USA
| | | | - Carley J S Heck
- Medicine Design, Pfizer Worldwide Research, Development and Medical, Groton, CT, USA
| | - Kevin M Johnson
- Drug Metabolism and Pharmacokinetics, Inotiv, Maryland Heights, MO, USA
| | - Amit S Kalgutkar
- Medicine Design, Pfizer Worldwide Research, Development and Medical, Cambridge, MA, USA
| | - Lloyd King
- Quantitative Drug Discovery, UCB Biopharma UK, Slough, UK
| | - Joyce Liu
- Department of Drug Metabolism and Pharmacokinetics, Genentech, Inc., South San Francisco, CA, USA
| | - Bin Ma
- Department of Drug Metabolism and Pharmacokinetics, Genentech, Inc., South San Francisco, CA, USA
| | - Hlaing Maw
- Drug Metabolism and Pharmacokinetics, Boehringer Ingelheim Pharmaceuticals, Inc., Ridgefield, CT, USA
| | - Grover P Miller
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Herana Kamal Seneviratne
- Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, Baltimore, MD, USA
| | | | - Cong Wei
- Drug Metabolism and Pharmacokinetics, Biogen Inc., Cambridge, MA, USA
| | - S Cyrus Khojasteh
- Department of Drug Metabolism and Pharmacokinetics, Genentech, Inc., South San Francisco, CA, USA
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8
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Ghous F, Shukla S, Singh R, Parveen S, Banerjee M, Bishnoi A. Synthesis, Crystal Structure, Computational Investigation, Molecular Docking Analysis and Anti-lung Cancer Activity of Novel (Z)-3-amino-2-(cyclohexylidenehydrazono)thiazolidin-4-one. J Mol Struct 2023. [DOI: 10.1016/j.molstruc.2023.135462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
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9
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Edmonds AK, Oakes CS, Hassell-Hart S, Bruyère D, Tizzard GJ, Coles SJ, Felix R, Maple HJ, Marsh GP, Spencer J. Scale-up and optimization of the synthesis of dual CBP/BRD4 inhibitor ISOX-DUAL. Org Biomol Chem 2022; 20:4021-4029. [PMID: 35506991 DOI: 10.1039/d2ob00609j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
ISOX-DUAL is a dual inhibitor of CBP/p300 (IC50 = 0.65 μM) and BRD4 (IC50 = 1.5 μM) bromodomains, and a useful chemical probe for epigenetic research. Aspects of the published synthetic route to this compound and its analogues are small-scale, poor-yielding or simply unamenable to scale-up without optimization. Herein we describe the development of a refined synthesis that circumvents the challenges of the original report, with notable improvements to several of the key synthetic transformations. Moreover, a general Suzuki Miyaura protocol for the late stage installation of alternative dimethyl-isoxazole acetyl-lysine (KAc) binding motifs is presented.
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Affiliation(s)
- Anthony K Edmonds
- Chemistry Department, School of Life Sciences, University of Sussex, Falmer, Brighton, BN1 9QJ, UK.
| | - Catherine S Oakes
- Bio-Techne (Tocris), The Watkins Building, Atlantic Road, Bristol, BS11 9QD, UK
| | - Storm Hassell-Hart
- Chemistry Department, School of Life Sciences, University of Sussex, Falmer, Brighton, BN1 9QJ, UK.
| | - Didier Bruyère
- Bio-Techne (Tocris), The Watkins Building, Atlantic Road, Bristol, BS11 9QD, UK
| | - Graham J Tizzard
- National Crystallography Service, School of Chemistry, University of Southampton, Southampton, SO17 1BJ, UK
| | - Simon J Coles
- National Crystallography Service, School of Chemistry, University of Southampton, Southampton, SO17 1BJ, UK
| | - Robert Felix
- Bio-Techne (Tocris), The Watkins Building, Atlantic Road, Bristol, BS11 9QD, UK
| | - Hannah J Maple
- Bio-Techne (Tocris), The Watkins Building, Atlantic Road, Bristol, BS11 9QD, UK
| | - Graham P Marsh
- Bio-Techne (Tocris), The Watkins Building, Atlantic Road, Bristol, BS11 9QD, UK
| | - John Spencer
- Chemistry Department, School of Life Sciences, University of Sussex, Falmer, Brighton, BN1 9QJ, UK. .,Sussex Drug Discovery Centre, School of Life Sciences, University of Sussex, Falmer, Brighton, BN1 9QJ, UK
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10
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Xiang Q, Luo G, Zhang C, Hu Q, Wang C, Wu T, Xu H, Hu J, Zhuang X, Zhang M, Wu S, Xu J, Zhang Y, Liu J, Xu Y. Discovery, optimization and evaluation of 1-(indolin-1-yl)ethan-1-ones as novel selective TRIM24/BRPF1 bromodomain inhibitors. Eur J Med Chem 2022; 236:114311. [PMID: 35385803 DOI: 10.1016/j.ejmech.2022.114311] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 03/15/2022] [Accepted: 03/19/2022] [Indexed: 12/12/2022]
Abstract
TRIM24 (tripartite motif-containing protein 24) and BRPF1 (bromodomain and PHD finger containing protein 1) are epigenetics "readers" and potential therapeutic targets for cancer and other diseases. Here we describe the structure-guided design of 1-(indolin-1-yl)ethan-1-ones as novel TRIM24/BRPF1 bromodomain inhibitors. The representative compound 20l (Y08624) is a new TRIM24/BRPF1 dual inhibitor, with IC50 values of 0.98 and 1.16 μM, respectively. Cellular activity of 20l was validated by viability assay in prostate cancer (PC) cell lines. In PC xenograft models, 20l suppressed tumor growth (50 mg/kg/day, TGI = 53%) without exhibiting noticeable toxicity. Compound 20l represents a versatile starting point for the development of more potent TRIM24/BRPF1 inhibitors.
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Affiliation(s)
- Qiuping Xiang
- Guangdong Provincial Key Laboratory of Biocomputing, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 510530, China.
| | - Guolong Luo
- Guangdong Provincial Key Laboratory of Biocomputing, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 510530, China; University of Chinese Academy of Sciences, No. 19 Yuquan Road, Beijing, 100049, China
| | - Cheng Zhang
- Guangdong Provincial Key Laboratory of Biocomputing, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 510530, China
| | - Qingqing Hu
- Guangdong Provincial Key Laboratory of Biocomputing, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 510530, China; University of Chinese Academy of Sciences, No. 19 Yuquan Road, Beijing, 100049, China
| | - Chao Wang
- Guangdong Provincial Key Laboratory of Biocomputing, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 510530, China; University of Chinese Academy of Sciences, No. 19 Yuquan Road, Beijing, 100049, China
| | - Tianbang Wu
- Guangdong Provincial Key Laboratory of Biocomputing, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 510530, China; Key Laboratory of Structure-Based Drug Design and Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang, 110016, China
| | - Hongrui Xu
- GMU-GIBH Joint School of Life Sciences, Guangzhou Medical University, Guangzhou, 511436, China
| | - Jiankang Hu
- Guangdong Provincial Key Laboratory of Biocomputing, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 510530, China; University of Chinese Academy of Sciences, No. 19 Yuquan Road, Beijing, 100049, China
| | - Xiaoxi Zhuang
- Guangdong Provincial Key Laboratory of Biocomputing, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 510530, China
| | - Maofeng Zhang
- College of Pharmacy, Taizhou Polytechnic College, Taizhou, 225300, China
| | - Shuang Wu
- Guangdong Provincial Key Laboratory of Biocomputing, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 510530, China
| | - Jinxin Xu
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Yan Zhang
- Guangdong Provincial Key Laboratory of Biocomputing, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 510530, China
| | - Jinsong Liu
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Yong Xu
- Guangdong Provincial Key Laboratory of Biocomputing, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, 510530, China; State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China; China-New Zealand Joint Laboratory on Biomedicine and Health, Guangzhou, 510530, China.
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11
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Humphreys PG, Atkinson SJ, Bamborough P, Bit RA, Chung CW, Craggs PD, Cutler L, Davis R, Ferrie A, Gong G, Gordon LJ, Gray M, Harrison LA, Hayhow TG, Haynes A, Henley N, Hirst DJ, Holyer ID, Lindon MJ, Lovatt C, Lugo D, McCleary S, Molnar J, Osmani Q, Patten C, Preston A, Rioja I, Seal JT, Smithers N, Sun F, Tang D, Taylor S, Theodoulou NH, Thomas C, Watson RJ, Wellaway CR, Zhu L, Tomkinson NCO, Prinjha RK. Design, Synthesis, and Characterization of I-BET567, a Pan-Bromodomain and Extra Terminal (BET) Bromodomain Oral Candidate. J Med Chem 2022; 65:2262-2287. [PMID: 34995458 DOI: 10.1021/acs.jmedchem.1c01747] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Through regulation of the epigenome, the bromodomain and extra terminal (BET) family of proteins represent important therapeutic targets for the treatment of human disease. Through mimicking the endogenous N-acetyl-lysine group and disrupting the protein-protein interaction between histone tails and the bromodomain, several small molecule pan-BET inhibitors have progressed to oncology clinical trials. This work describes the medicinal chemistry strategy and execution to deliver an orally bioavailable tetrahydroquinoline (THQ) pan-BET candidate. Critical to the success of this endeavor was a potency agnostic analysis of a data set of 1999 THQ BET inhibitors within the GSK collection which enabled identification of appropriate lipophilicity space to deliver compounds with a higher probability of desired oral candidate quality properties. SAR knowledge was leveraged via Free-Wilson analysis within this design space to identify a small group of targets which ultimately delivered I-BET567 (27), a pan-BET candidate inhibitor that demonstrated efficacy in mouse models of oncology and inflammation.
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Affiliation(s)
| | | | - Paul Bamborough
- GlaxoSmithKline R&D, Stevenage, Hertfordshire SG1 2NY, United Kingdom
| | - Rino A Bit
- GlaxoSmithKline R&D, Stevenage, Hertfordshire SG1 2NY, United Kingdom
| | - Chun-Wa Chung
- GlaxoSmithKline R&D, Stevenage, Hertfordshire SG1 2NY, United Kingdom
| | - Peter D Craggs
- GlaxoSmithKline R&D, Stevenage, Hertfordshire SG1 2NY, United Kingdom
| | - Leanne Cutler
- GlaxoSmithKline R&D, Stevenage, Hertfordshire SG1 2NY, United Kingdom
| | - Rob Davis
- GlaxoSmithKline R&D, Stevenage, Hertfordshire SG1 2NY, United Kingdom
| | - Alan Ferrie
- GlaxoSmithKline R&D, Stevenage, Hertfordshire SG1 2NY, United Kingdom
| | - GangLi Gong
- WuXi Shanghai STA Pharmaceutical R&D Co., Ltd., No. 90 Delin Road, WaiGaoQiao Free Trade Zone, Shanghai 200131, China
| | - Laurie J Gordon
- GlaxoSmithKline R&D, Stevenage, Hertfordshire SG1 2NY, United Kingdom
| | - Matthew Gray
- GlaxoSmithKline R&D, Stevenage, Hertfordshire SG1 2NY, United Kingdom
| | - Lee A Harrison
- GlaxoSmithKline R&D, Stevenage, Hertfordshire SG1 2NY, United Kingdom
| | - Thomas G Hayhow
- GlaxoSmithKline R&D, Stevenage, Hertfordshire SG1 2NY, United Kingdom
| | - Andrea Haynes
- GlaxoSmithKline R&D, Stevenage, Hertfordshire SG1 2NY, United Kingdom
| | - Nick Henley
- GlaxoSmithKline R&D, Stevenage, Hertfordshire SG1 2NY, United Kingdom
| | - David J Hirst
- GlaxoSmithKline R&D, Stevenage, Hertfordshire SG1 2NY, United Kingdom
| | - Ian D Holyer
- GlaxoSmithKline R&D, Stevenage, Hertfordshire SG1 2NY, United Kingdom
| | - Matthew J Lindon
- GlaxoSmithKline R&D, Stevenage, Hertfordshire SG1 2NY, United Kingdom
| | - Cerys Lovatt
- GlaxoSmithKline R&D, Stevenage, Hertfordshire SG1 2NY, United Kingdom
| | - David Lugo
- GlaxoSmithKline R&D, Stevenage, Hertfordshire SG1 2NY, United Kingdom
| | - Scott McCleary
- GlaxoSmithKline R&D, Stevenage, Hertfordshire SG1 2NY, United Kingdom
| | - Judit Molnar
- GlaxoSmithKline R&D, Stevenage, Hertfordshire SG1 2NY, United Kingdom
| | - Qendresa Osmani
- GlaxoSmithKline R&D, Stevenage, Hertfordshire SG1 2NY, United Kingdom
| | - Chris Patten
- GlaxoSmithKline R&D, Stevenage, Hertfordshire SG1 2NY, United Kingdom
| | - Alex Preston
- GlaxoSmithKline R&D, Stevenage, Hertfordshire SG1 2NY, United Kingdom
| | - Inmaculada Rioja
- GlaxoSmithKline R&D, Stevenage, Hertfordshire SG1 2NY, United Kingdom
| | - Jonathan T Seal
- GlaxoSmithKline R&D, Stevenage, Hertfordshire SG1 2NY, United Kingdom
| | - Nicholas Smithers
- GlaxoSmithKline R&D, Stevenage, Hertfordshire SG1 2NY, United Kingdom
| | - Fenglai Sun
- WuXi Shanghai STA Pharmaceutical R&D Co., Ltd., No. 90 Delin Road, WaiGaoQiao Free Trade Zone, Shanghai 200131, China
| | - Dalin Tang
- WuXi Shanghai STA Pharmaceutical R&D Co., Ltd., No. 90 Delin Road, WaiGaoQiao Free Trade Zone, Shanghai 200131, China
| | - Simon Taylor
- GlaxoSmithKline R&D, Stevenage, Hertfordshire SG1 2NY, United Kingdom
| | - Natalie H Theodoulou
- GlaxoSmithKline R&D, Stevenage, Hertfordshire SG1 2NY, United Kingdom.,WestCHEM, Department of Pure and Applied Chemistry, University of Strathclyde, Thomas Graham Building, 295 Cathedral Street, Glasgow G1 1XL, United Kingdom
| | - Clare Thomas
- GlaxoSmithKline R&D, Stevenage, Hertfordshire SG1 2NY, United Kingdom
| | - Robert J Watson
- GlaxoSmithKline R&D, Stevenage, Hertfordshire SG1 2NY, United Kingdom
| | | | - Linrong Zhu
- WuXi Shanghai STA Pharmaceutical R&D Co., Ltd., No. 90 Delin Road, WaiGaoQiao Free Trade Zone, Shanghai 200131, China
| | - 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
| | - Rab K Prinjha
- GlaxoSmithKline R&D, Stevenage, Hertfordshire SG1 2NY, United Kingdom
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12
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Wu TB, Xiang QP, Wang C, Wu C, Zhang C, Zhang MF, Liu ZX, Zhang Y, Xiao LJ, Xu Y. Y06014 is a selective BET inhibitor for the treatment of prostate cancer. Acta Pharmacol Sin 2021; 42:2120-2131. [PMID: 33654218 DOI: 10.1038/s41401-021-00614-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 01/13/2021] [Indexed: 12/14/2022] Open
Abstract
Bromodomain and extra-terminal proteins (BETs) are potential targets for the therapeutic treatment of prostate cancer (PC). Herein, we report the design, the synthesis, and a structure-activity relationship study of 6-(3,5-dimethylisoxazol-4-yl)benzo[cd]indol-2(1H)-one derivative as novel selective BET inhibitors. One representative compound, 19 (Y06014), bound to BRD4(1) in the low micromolar range and demonstrated high selectivity for BRD4(1) over other non-BET bromodomain-containing proteins. This molecule also potently inhibited cell growth, colony formation, and mRNA expression of AR-regulated genes in PC cell lines. Y06014 also shows stronger activity than the second-generation antiandrogen enzalutamide. Y06014 may serve as a new small molecule probe for further validation of BET as a molecular target for PC drug development.
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13
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Vaidergorn MM, da Silva Emery F, Ganesan A. From Hit Seeking to Magic Bullets: The Successful Union of Epigenetic and Fragment Based Drug Discovery (EPIDD + FBDD). J Med Chem 2021; 64:13980-14010. [PMID: 34591474 DOI: 10.1021/acs.jmedchem.1c00787] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
We review progress in the application of fragment-based drug discovery (FBDD) to epigenetic drug discovery (EPIDD) targeted at epigenetic writer and eraser enzymes as well as reader domains over the last 15 years. The greatest successes to date are in prospecting for bromodomain binding ligands. From a diverse array of fragment hits, multiple potent and selective compounds ensued, including the oncology clinical candidates mivebresib, ABBV-744, pelabresib, and PLX51107.
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Affiliation(s)
- Miguel M Vaidergorn
- School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, São Paulo 14040-903, Brazil
| | - Flavio da Silva Emery
- School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, São Paulo 14040-903, Brazil
| | - A Ganesan
- School of Pharmacy, University of East Anglia, Norwich NR4 7TJ, United Kingdom
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14
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Laurin CMC, Bluck JP, Chan AKN, Keller M, Boczek A, Scorah AR, See KFL, Jennings LE, Hewings DS, Woodhouse F, Reynolds JK, Schiedel M, Humphreys PG, Biggin PC, Conway SJ. Fragment-Based Identification of Ligands for Bromodomain-Containing Factor 3 of Trypanosoma cruzi. ACS Infect Dis 2021; 7:2238-2249. [PMID: 33203208 DOI: 10.1021/acsinfecdis.0c00618] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The Trypanosoma cruzi (T. cruzi) parasite is the cause of Chagas disease, a neglected disease endemic in South America. The life cycle of the T. cruzi parasite is complex and includes transitions between distinct life stages. This change in phenotype (without a change in genotype) could be controlled by epigenetic regulation, and might involve the bromodomain-containing factors 1-5 (TcBDF1-5). However, little is known about the function of the TcBDF1-5. Here we describe a fragment-based approach to identify ligands for T. cruzi bromodomain-containing factor 3 (TcBDF3). We expressed a soluble construct of TcBDF3 in E. coli, and used this to develop a range of biophysical assays for this protein. Fragment screening identified 12 compounds that bind to the TcBDF3 bromodomain. On the basis of this screen, we developed functional ligands containing a fluorescence or 19F reporter group, and a photo-crosslinking probe for TcBDF3. These tool compounds will be invaluable in future studies on the function of TcBDF3 and will provide insight into the biology of T. cruzi.
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Affiliation(s)
- Corentine M. C. Laurin
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK
| | - Joseph P. Bluck
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK
- Department of Biochemistry, University of Oxford, 3 Parks Road, Oxford OX1 3QU, UK
| | - Anthony K. N. Chan
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK
| | - Michelle Keller
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK
| | - Andrew Boczek
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK
| | - Amy R. Scorah
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK
| | - K. F. Larissa See
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK
| | - Laura E. Jennings
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK
| | - David S. Hewings
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK
| | - Fern Woodhouse
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK
| | - Jessica K. Reynolds
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK
| | - Matthias Schiedel
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK
| | | | - Philip C. Biggin
- Department of Biochemistry, University of Oxford, 3 Parks Road, Oxford OX1 3QU, UK
| | - Stuart J. Conway
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, UK
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15
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Saito H, Shimokawa J, Yorimitsu H. The dioxasilepanyl group as a versatile organometallic unit: studies on stability, reactivity, and utility. Chem Sci 2021; 12:9546-9555. [PMID: 34349929 PMCID: PMC8278973 DOI: 10.1039/d1sc02083h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 06/05/2021] [Indexed: 12/15/2022] Open
Abstract
Organic synthesis is performed based on precise choices of functional groups and reactions employed. In a multistep synthesis, an ideal functional group should be compatible with various reaction conditions and unaltered until it is subjected to a selective conversion. The current study was set out to search for a silicon functionality that meets these criteria. Here we have established a new silicon-based synthetic methodology centred on a bulky 7-membered dialkoxysilyl group (2,4,4,7,7-pentamethyl-1,3,2-dioxasilepan-2-yl) that uniquely has both stability and on-demand reactivity. The exceptional stability of this functional group was corroborated by both experimental and computational studies which demonstrated that key factors for its stability were a 7-membered structure and steric hindrance. In turn, the dioxasilepanyl group was found to become reactive and to be easily transformed in the presence of appropriate activators. Combined with the development of easy and robust methods to introduce the dioxasilepanyl group onto aryl rings, these findings have allowed a shorter and more efficient synthesis of a bioactive molecule, thus demonstrating the potential utility of the easily accessible dioxasilepanyl group in organic synthesis.
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Affiliation(s)
- Hayate Saito
- Department of Chemistry, Graduate School of Science, Kyoto University Sakyo-ku Kyoto 606-8502 Japan
| | - Jun Shimokawa
- Department of Chemistry, Graduate School of Science, Kyoto University Sakyo-ku Kyoto 606-8502 Japan
| | - Hideki Yorimitsu
- Department of Chemistry, Graduate School of Science, Kyoto University Sakyo-ku Kyoto 606-8502 Japan
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16
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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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17
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Flynn NR, Ward MD, Schleiff MA, Laurin CMC, Farmer R, Conway SJ, Boysen G, Swamidass SJ, Miller GP. Bioactivation of Isoxazole-Containing Bromodomain and Extra-Terminal Domain (BET) Inhibitors. Metabolites 2021; 11:metabo11060390. [PMID: 34203690 PMCID: PMC8232216 DOI: 10.3390/metabo11060390] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 06/04/2021] [Accepted: 06/08/2021] [Indexed: 12/15/2022] Open
Abstract
The 3,5-dimethylisoxazole motif has become a useful and popular acetyl-lysine mimic employed in isoxazole-containing bromodomain and extra-terminal (BET) inhibitors but may introduce the potential for bioactivations into toxic reactive metabolites. As a test, we coupled deep neural models for quinone formation, metabolite structures, and biomolecule reactivity to predict bioactivation pathways for 32 BET inhibitors and validate the bioactivation of select inhibitors experimentally. Based on model predictions, inhibitors were more likely to undergo bioactivation than reported non-bioactivated molecules containing isoxazoles. The model outputs varied with substituents indicating the ability to scale their impact on bioactivation. We selected OXFBD02, OXFBD04, and I-BET151 for more in-depth analysis. OXFBD’s bioactivations were evenly split between traditional quinones and novel extended quinone-methides involving the isoxazole yet strongly favored the latter quinones. Subsequent experimental studies confirmed the formation of both types of quinones for OXFBD molecules, yet traditional quinones were the dominant reactive metabolites. Modeled I-BET151 bioactivations led to extended quinone-methides, which were not verified experimentally. The differences in observed and predicted bioactivations reflected the need to improve overall bioactivation scaling. Nevertheless, our coupled modeling approach predicted BET inhibitor bioactivations including novel extended quinone methides, and we experimentally verified those pathways highlighting potential concerns for toxicity in the development of these new drug leads.
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Affiliation(s)
- Noah R. Flynn
- Department of Pathology and Immunology, Washington University-St. Louis, St. Louis, MO 63130, USA; (N.R.F.); (M.D.W.); (R.F.)
| | - Michael D. Ward
- Department of Pathology and Immunology, Washington University-St. Louis, St. Louis, MO 63130, USA; (N.R.F.); (M.D.W.); (R.F.)
| | - Mary A. Schleiff
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA;
| | | | - Rohit Farmer
- Department of Pathology and Immunology, Washington University-St. Louis, St. Louis, MO 63130, USA; (N.R.F.); (M.D.W.); (R.F.)
| | - Stuart J. Conway
- Department of Chemistry, University of Oxford, Oxford OX1 3TA, UK; (C.M.C.L.); (S.J.C.)
| | - Gunnar Boysen
- Department of Environmental and Occupational Health, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA;
| | - S. Joshua Swamidass
- Department of Pathology and Immunology, Washington University-St. Louis, St. Louis, MO 63130, USA; (N.R.F.); (M.D.W.); (R.F.)
- Correspondence: (S.J.S.); (G.P.M.)
| | - Grover P. Miller
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA;
- Correspondence: (S.J.S.); (G.P.M.)
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18
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Duan YC, Zhang SJ, Shi XJ, Jin LF, Yu T, Song Y, Guan YY. Research progress of dual inhibitors targeting crosstalk between histone epigenetic modulators for cancer therapy. Eur J Med Chem 2021; 222:113588. [PMID: 34107385 DOI: 10.1016/j.ejmech.2021.113588] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Revised: 05/09/2021] [Accepted: 05/25/2021] [Indexed: 12/13/2022]
Abstract
Abnormal epigenetics is a critical hallmark of human cancers. Anticancer drug discovery directed at histone epigenetic modulators has gained impressive advances with six drugs available for cancer therapy and numerous other candidates undergoing clinical trials. However, limited therapeutic profile, drug resistance, narrow safety margin, and dose-limiting toxicities pose intractable challenges for their clinical utility. Because histone epigenetic modulators undergo intricate crosstalk and act cooperatively to shape an aberrant epigenetic profile, co-targeting histone epigenetic modulators with a different mechanism of action has rapidly emerged as an attractive strategy to overcome the limitations faced by the single-target epigenetic inhibitors. In this review, we summarize in detail the crosstalk of histone epigenetic modulators in regulating gene transcription and the progress of dual epigenetic inhibitors targeting this crosstalk.
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Affiliation(s)
- Ying-Chao Duan
- School of Pharmacy, Xinxiang Medical University, 453003, Xinxiang, Henan Province, PR China.
| | - Shao-Jie Zhang
- School of Pharmacy, Xinxiang Medical University, 453003, Xinxiang, Henan Province, PR China
| | - Xiao-Jing Shi
- Laboratory Animal Center, Academy of Medical Science, Zhengzhou University, 450052, Zhengzhou, Henan Province, PR China
| | - Lin-Feng Jin
- School of Pharmacy, Xinxiang Medical University, 453003, Xinxiang, Henan Province, PR China
| | - Tong Yu
- School of Pharmacy, Xinxiang Medical University, 453003, Xinxiang, Henan Province, PR China
| | - Yu Song
- School of Pharmacy, Xinxiang Medical University, 453003, Xinxiang, Henan Province, PR China
| | - Yuan-Yuan Guan
- School of Pharmacy, Xinxiang Medical University, 453003, Xinxiang, Henan Province, PR China.
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19
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Epigenetic Effects of Benzene in Hematologic Neoplasms: The Altered Gene Expression. Cancers (Basel) 2021; 13:cancers13102392. [PMID: 34069279 PMCID: PMC8156840 DOI: 10.3390/cancers13102392] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 05/06/2021] [Accepted: 05/11/2021] [Indexed: 12/12/2022] Open
Abstract
Simple Summary Benzene is produced by diverse petroleum transformation processes and it is widely employed in industry despite its oncogenic effects. In fact, occupational exposure to benzene may cause hematopoietic malignancy. The leukemogenic action of benzene is particularly complex. Possible processes of onset of hematological malignancies have been recognized as a genotoxic action and the provocation of immunosuppression. However, benzene can induce modifications that do not involve alterations in the DNA sequence, the so-called epigenetics changes. Acquired epigenetic modification may also induce leukemogenesis, as benzene may alter nuclear receptors, and cause changes at the protein level, thereby modifying the function of regulatory proteins, including oncoproteins and tumor suppressor proteins. Abstract Benzene carcinogenic ability has been reported, and chronic exposure to benzene can be one of the risk elements for solid cancers and hematological neoplasms. Benzene is acknowledged as a myelotoxin, and it is able to augment the risk for the onset of acute myeloid leukemia, myelodysplastic syndromes, aplastic anemia, and lymphomas. Possible mechanisms of benzene initiation of hematological tumors have been identified, as a genotoxic effect, an action on oxidative stress and inflammation and the provocation of immunosuppression. However, it is becoming evident that genetic alterations and the other causes are insufficient to fully justify several phenomena that influence the onset of hematologic malignancies. Acquired epigenetic alterations may participate with benzene leukemogenesis, as benzene may affect nuclear receptors, and provoke post-translational alterations at the protein level, thereby touching the function of regulatory proteins, comprising oncoproteins and tumor suppressor proteins. DNA hypomethylation correlates with stimulation of oncogenes, while the hypermethylation of CpG islands in promoter regions of specific tumor suppressor genes inhibits their transcription and stimulates the onset of tumors. The discovery of the systems of epigenetic induction of benzene-caused hematological tumors has allowed the possibility to operate with pharmacological interventions able of stopping or overturning the negative effects of benzene.
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20
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Synthesis and biological evaluation of novel isoxazole-piperazine hybrids as potential anti-cancer agents with inhibitory effect on liver cancer stem cells. Eur J Med Chem 2021; 221:113489. [PMID: 33951549 DOI: 10.1016/j.ejmech.2021.113489] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 04/15/2021] [Accepted: 04/16/2021] [Indexed: 02/07/2023]
Abstract
In our effort for the development of novel anticancer therapeutics, a series of isoxazole-piperazine analogues were prepared, and primarily screened for their antiproliferative potential against hepatocellular carcinoma (HCC; Huh7/Mahlavu) and breast (MCF-7) cancer cells. All compounds demonstrated potent to moderate cytotoxicity on all cell lines with IC50 values in the range of 0.09-11.7 μM. Further biological studies with 6a and 13d in HCC cells have shown that both compounds induced G1 or G2/M arrests resulting in apoptotic cell death. Subsequent analysis of proteins involved in cell cycle progression as well as proliferation of HCC cells revealed that 6a and 13d may affect cellular survival pathways differently depending on the mutation profiles of cells (p53 and PTEN), epidermal/mesenchymal characteristics, and activation of cell mechanisms through p53 dependent/independent pathways. Lastly, we have demonstrated the potential anti-stemness properties of these compounds in which the proportion of liver CSCs in Huh7 cells (CD133+/EpCAM+) were significantly reduced by 6a and 13d. Furthermore, both compounds caused a significant reduction in expression of stemness markers, NANOG or OCT4 proteins, in Mahlavu and Huh7 cells, as well as resulted in a decreased sphere formation capacity in Huh7 cells. Together, these novel isoxazole-piperazine derivatives may possess potential as leads for development of effective anti-cancer drugs against HCC cells with stem cell-like properties.
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21
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Current status in the discovery of dual BET/HDAC inhibitors. Bioorg Med Chem Lett 2021; 38:127829. [PMID: 33685790 DOI: 10.1016/j.bmcl.2021.127829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The development of desired multitarget agents may provide an attractive and cost-effective complement or alternative to drug combinations. Bromodomain and extraterminal domain (BET) and histone deacetylase (HDAC), as important epigenetic modulators, are attractive targets in drug discovery and development. Considering the fact that BET and HDAC inhibitors exert a synergistic effect on cellular processes in cancer cells, the design of dual BET/HDAC inhibitors may be a rational strategy to improve the efficacy of their single-target drugs for tumor treatment. In the current review, we depict the development of dual BET/HDAC inhibitors and particularly highlight their structure-activity relationships (SARs), binding modes, and biological functions with the aim to facilitate rational drug design and develop more dual BET/HDAC inhibitors.
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22
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Synthesis, evaluation and in silico studies of novel BRD4 bromodomain inhibitors bearing a benzo[d]isoxazol scaffold. J CHEM SCI 2021. [DOI: 10.1007/s12039-020-01874-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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23
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Muddassir M, Soni K, Sangani CB, Alarifi A, Afzal M, Abduh NAY, Duan Y, Bhadja P. Bromodomain and BET family proteins as epigenetic targets in cancer therapy: their degradation, present drugs, and possible PROTACs. RSC Adv 2021; 11:612-636. [PMID: 35746919 PMCID: PMC9133982 DOI: 10.1039/d0ra07971e] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 11/28/2020] [Indexed: 12/27/2022] Open
Abstract
Alteration in the pattern of epigenetic marking leads to cancer, neurological disorders, inflammatory problems etc. These changes are due to aberration in histone modification enzymes that function as readers, writers and erasers. Bromodomains (BDs) and BET proteins that recognize acetylation of chromatin regulate gene expression. To block the function of any of these BrDs and/or BET protein can be a controlling agent in disorders such as cancer. BrDs and BET proteins are now emerging as targets for new therapeutic development. Traditional drugs like enzyme inhibitors and protein–protein inhibitors have many limitations. Recently Proteolysis-Targeting Chimeras (PROTACs) have become an advanced tool in therapeutic intervention as they remove disease causing proteins. This review provides an overview of the development and mechanisms of PROTACs for BRD and BET protein regulation in cancer and advanced possibilities of genetic technologies in therapeutics. Alteration in the pattern of epigenetic marking leads to cancer, neurological disorders, inflammatory problems etc.![]()
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Affiliation(s)
- Mohd. Muddassir
- Department of Chemistry
- College of Science
- King Saud University
- Riyadh 11451
- KSA
| | - Kunjal Soni
- Shri Maneklal M. Patel Institute of Sciences and Research
- Kadi Sarva Vishwavidyalaya University
- Gandhinagar
- India
| | - Chetan B. Sangani
- Shri Maneklal M. Patel Institute of Sciences and Research
- Kadi Sarva Vishwavidyalaya University
- Gandhinagar
- India
| | - Abdullah Alarifi
- Department of Chemistry
- College of Science
- King Saud University
- Riyadh 11451
- KSA
| | - Mohd. Afzal
- Department of Chemistry
- College of Science
- King Saud University
- Riyadh 11451
- KSA
| | - Naaser A. Y. Abduh
- Department of Chemistry
- College of Science
- King Saud University
- Riyadh 11451
- KSA
| | - Yongtao Duan
- Henan Provincial Key Laboratory of Children's Genetics and Metabolic Diseases
- Zhengzhou Children's Hospital
- Zhengzhou University
- Zhengzhou 450018
- China
| | - Poonam Bhadja
- Arthropod Ecology and Biological Control Research Group
- Ton Duc Thang University
- Ho Chi Minh City
- Vietnam
- Faculty of Environment and Labour Safety
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24
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Current status in the discovery of dual BET/HDAC inhibitors. Bioorg Med Chem Lett 2021; 31:127671. [PMID: 33229136 DOI: 10.1016/j.bmcl.2020.127671] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Revised: 10/22/2020] [Accepted: 11/01/2020] [Indexed: 12/13/2022]
Abstract
The development of desired multitarget agents may provide an attractive and cost-effective complement or alternative to drug combinations. BET and HDAC, as important epigenetic modulators, are both attractive targets in drug discovery and development. Considering the fact that BET and HDAC inhibitors exert a synergistic effect on cellular processes in cancer cells, the design of dual BET/HDAC inhibitors may be a rational strategy to improve the efficacy of their single-target drugs for tumor treatment. In current review, we depict the development of dual BET/HDAC inhibitors and particularly highlight their SARs, binding modes and biological functions with the aim to facilitate rational design and develop more dual BET/HDAC inhibitors.
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25
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Zaib S, Khan I. Synthetic and medicinal chemistry of phthalazines: Recent developments, opportunities and challenges. Bioorg Chem 2020; 105:104425. [PMID: 33157344 DOI: 10.1016/j.bioorg.2020.104425] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 09/22/2020] [Accepted: 10/20/2020] [Indexed: 12/14/2022]
Abstract
Fused diaza-heterocycles constitute the core structure of numerous bioactive natural products and effective therapeutic drugs. Among them, phthalazines have been recognized as remarkable structural leads in medicinal chemistry due to their wide application in pharmaceutical and agrochemical industries. Accessing such challenging pharmaceutical agents/drug candidates with high chemical complexity through synthetically efficient approaches remains an attractive goal in the contemporary medicinal chemistry and drug discovery arena. In this review, we focus on the recent developments in the synthetic routes towards the generation of phthalazine-based active pharmaceutical ingredients and their biological potential against various targets. The general reaction scope of these innovative and easily accessible strategies was emphasized focusing on the functional group tolerance, substrate and coupling partner compatibility/limitation, the choice of catalyst, and product diversification. These processes were also accompanied by the mechanistic insights where deemed appropriate to demonstrate meaningful information. Moreover, the rapid examination of the structure-activity relationship analyses around the phthalazine core enabled by the pharmacophore replacement/integration revealed the generation of robust, efficient, and more selective compounds with pronounced biological effects. A large variety of in silico methods and ADME profiling tools were also employed to provide a global appraisal of the pharmacokinetics profile of diaza-heterocycles. Thus, the discovery of new structural leads offers the promise of improving treatments for various tropical diseases such as tuberculosis, leishmaniasis, malaria, Chagas disease, among many others including various cancers, atherosclerosis, HIV, inflammatory, and cardiovascular diseases. We hope this review would serve as an informative collection of structurally diverse molecules enabling the generation of mature, high-quality, and innovative routes to support the drug discovery endeavors.
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Affiliation(s)
- Sumera Zaib
- Department of Biochemistry, Faculty of Life Sciences, University of Central Punjab, Lahore 54590, Pakistan
| | - Imtiaz Khan
- Department of Chemistry and Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, United Kingdom.
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26
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Discovery of selective inhibitors for cyclic AMP response element-binding protein: a combined ligand and structure-based resources pipeline. Anticancer Drugs 2020; 30:363-373. [PMID: 30499778 DOI: 10.1097/cad.0000000000000727] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Bromodomains are epigenetic readers of acetyl-lysine involved in chromatin remodeling and transcriptional regulations. Over the past few years, extensive research has been carried out to discover small-molecule inhibitors against bromodomains to treat various diseases. Cyclic AMP response element-binding protein (CREBBP) bromodomain has emerged as a hot target for cancer therapy. This study aims at discovering new inhibitors against CREBBP bromodomain using ligand-based molecular docking. A library of 2168 lead-like compounds were docked into the Kac binding site of CREBBP bromodomain. On the basis of the energy score and interaction analysis, six compounds were selected. In order to validate the stability of these six protein-ligand complexes 20 ns molecular dynamics simulations and principal component analyses were carried out. Based on the different analyses these six compounds may provide valuable information for developing CREBBP selective inhibitors.
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27
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Lv K, Chen W, Chen D, Mou J, Zhang H, Fan T, Li Y, Cao D, Wang X, Chen L, Shen J, Pei D, Xiong B. Rational Design and Evaluation of 6-(Pyrimidin-2-ylamino)-3,4-dihydroquinoxalin-2(1 H)-ones as Polypharmacological Inhibitors of BET and Kinases. J Med Chem 2020; 63:9787-9802. [PMID: 32787081 DOI: 10.1021/acs.jmedchem.0c00962] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Cancer exhibits diverse heterogeneity with a complicated molecular basis that usually harbors genetic and epigenetic abnormality, which poses a big challenge for single-target agents. In the current work, we proposed a hybrid strategy by incorporating pharmacophores that bind to the acetylated lysine binding pocket of BET proteins with a typical kinase hinge binder to generate novel polypharmacological inhibitors of BET and kinases. Through elaborating the core structure of 6-(pyrimidin-2-ylamino)-3,4-dihydroquinoxalin-2(1H)-one, we demonstrated that this rational design can produce high potent inhibitors of CDK9 and BET proteins. In this series, compound 40 was identified as the potential lead compound with balanced activities of BRD4 (IC50 = 12.7 nM) and CDK9 (IC50 = 22.4 nM), as well as good antiproliferative activities on a small cancer cell panel. Together, the current study provided a new method for the discovery of bromodomain and kinase dual inhibitors rather than only being discovered by serendipity.
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Affiliation(s)
- Kaikai Lv
- Department of Medicinal Chemistry, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China.,University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - Weicong Chen
- Department of Pathology, Xuzhou Medical University, 209 Tongshan Road, Xuzhou 221006, China
| | - Danqi Chen
- Department of Medicinal Chemistry, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Jie Mou
- Jiangsu Key Laboratory of New Drug and Clinical Pharmacy, School of Pharmacy, Xuzhou Medical University, 209 Tongshan Road, Xuzhou 221006, China
| | - Huijie Zhang
- Department of Medicinal Chemistry, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China.,University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - Tiantian Fan
- Department of Medicinal Chemistry, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China.,University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing 100049, China
| | - Yanlian Li
- Department of Medicinal Chemistry, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Danyan Cao
- Department of Medicinal Chemistry, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Xin Wang
- Department of Medicinal Chemistry, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Lin Chen
- Department of Medicinal Chemistry, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Jingkang Shen
- Department of Medicinal Chemistry, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Dongsheng Pei
- Department of Pathology, Xuzhou Medical University, 209 Tongshan Road, Xuzhou 221006, China
| | - Bing Xiong
- Department of Medicinal Chemistry, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
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28
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Wellaway CR, Bamborough P, Bernard SG, Chung CW, Craggs PD, Cutler L, Demont EH, Evans JP, Gordon L, Karamshi B, Lewis AJ, Lindon MJ, Mitchell DJ, Rioja I, Soden PE, Taylor S, Watson RJ, Willis R, Woolven JM, Wyspiańska BS, Kerr WJ, Prinjha RK. Structure-Based Design of a Bromodomain and Extraterminal Domain (BET) Inhibitor Selective for the N-Terminal Bromodomains That Retains an Anti-inflammatory and Antiproliferative Phenotype. J Med Chem 2020; 63:9020-9044. [DOI: 10.1021/acs.jmedchem.0c00566] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Christopher R. Wellaway
- GSK, Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, United Kingdom
| | - Paul Bamborough
- GSK, Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, United Kingdom
| | - Sharon G. Bernard
- GSK, Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, United Kingdom
| | - Chun-wa Chung
- GSK, Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, United Kingdom
| | - Peter D. Craggs
- GSK, Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, United Kingdom
| | - Leanne Cutler
- GSK, Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, United Kingdom
| | - Emmanuel H. Demont
- GSK, Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, United Kingdom
| | - John P. Evans
- GSK, Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, United Kingdom
| | - Laurie Gordon
- GSK, Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, United Kingdom
| | - Bhumika Karamshi
- GSK, Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, United Kingdom
| | - Antonia J. Lewis
- GSK, Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, United Kingdom
| | - Matthew J. Lindon
- GSK, Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, United Kingdom
| | - Darren J. Mitchell
- GSK, Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, United Kingdom
| | - Inmaculada Rioja
- GSK, Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, United Kingdom
| | - Peter E. Soden
- GSK, Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, United Kingdom
| | - Simon Taylor
- GSK, Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, United Kingdom
| | - Robert J. Watson
- GSK, Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, United Kingdom
| | - Rob Willis
- GSK, Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, United Kingdom
| | - James M. Woolven
- GSK, Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, United Kingdom
| | - Beata S. Wyspiańska
- GSK, Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, United Kingdom
| | - William J. Kerr
- Department of Pure and Applied Chemistry, WestCHEM, University of Strathclyde, 295 Cathedral Street, Glasgow G1 1XL, United Kingdom
| | - Rab K. Prinjha
- GSK, Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, United Kingdom
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29
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Zhao YL, Ma LL, Liu XD, Sui Y, Chai HF. The crystal structure of 2- p-fluorophenyl-5-dihydroxymethyl-1,3,4-oxadiazole, C 9H 7FN 2O 3. Z KRIST-NEW CRYST ST 2020. [DOI: 10.1515/ncrs-2019-0901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
C9H7FN2O3, triclinic, P1̅ (no. 2), a = 14.467(3) Å, b = 7.4629(14) Å, c = 8.9512(18) Å, α = 90°, β = 104.759(4)°, γ = 90°, V = 934.5(3) Å3, Z = 4, R
gt(F) = 0.0421, wR
ref(F
2) = 0.1173, T = 273 K.
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Affiliation(s)
- Yong-Li Zhao
- School of Pharmaceutical Sciences, Guizhou University of Traditional Chinese Medicine , Guiyang 550025 , P.R. China
| | - Lan-Lan Ma
- School of Pharmaceutical Sciences, Guizhou University , Guiyang 550025 , P.R. China
| | - Xue-Di Liu
- School of Pharmaceutical Sciences, Guizhou University of Traditional Chinese Medicine , Guiyang 550025 , P.R. China
| | - Yi Sui
- School of Pharmaceutical Sciences, Guizhou University of Traditional Chinese Medicine , Guiyang 550025 , P.R. China
| | - Hui-Fang Chai
- School of Pharmaceutical Sciences, Guizhou University of Traditional Chinese Medicine , Guiyang 550025 , P.R. China
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30
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Zia M, Hameed S, Ahmad I, Tabassum N, Yousaf S. Synthesis, characterization, electrochemical and DNA binding studies of regio-isomeric sulfonyl esters of substituted isoxazoles. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2019.127230] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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31
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Design, synthesis and biological evaluation of 3,5-dimethylisoxazole and pyridone derivatives as BRD4 inhibitors. Bioorg Med Chem Lett 2019; 29:126577. [DOI: 10.1016/j.bmcl.2019.07.036] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2019] [Revised: 07/05/2019] [Accepted: 07/22/2019] [Indexed: 11/22/2022]
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32
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Long D, Qin Y, Wu Q, Zou X, Zhou Z. Synthesis, Crystal Structure, and DFT Study of 4-(3,5-Dimethylisoxazol-4-yl)Benzene-1,2-Diol. J STRUCT CHEM+ 2019. [DOI: 10.1134/s0022476619080146] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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33
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Malyshev MD, Baburkin PO, Adamyan AN, Khizhnyak SD, Pakhomov PM, Komarov PV. Molecular Dynamics Simulation of the Aging Process of the Cysteine-Silver Solution. J STRUCT CHEM+ 2019. [DOI: 10.1134/s0022476619080158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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34
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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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35
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Design, synthesis and biological evaluation of novel indole derivatives as potential HDAC/BRD4 dual inhibitors and anti-leukemia agents. Bioorg Chem 2019; 84:410-417. [DOI: 10.1016/j.bioorg.2018.12.011] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Revised: 12/03/2018] [Accepted: 12/10/2018] [Indexed: 12/12/2022]
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36
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Bai P, Wey HY, Patnaik D, Lu X, Lan Y, Rokka J, Stephanie F, Haggarty SJ, Wang C. Positron emission tomography probes targeting bromodomain and extra-terminal (BET) domains to enable in vivo neuroepigenetic imaging. Chem Commun (Camb) 2019; 55:12932-12935. [DOI: 10.1039/c9cc06734e] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Novel PET radiotracer of BET proteins enable in vivo neuroepigenetic imaging.
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Affiliation(s)
- Ping Bai
- Chengdu Institute of Biology
- Chinese Academy of Sciences
- Chengdu 610041
- P. R. China
- Athinoula A. Martinos Center for Biomedical Imaging
| | - Hsiao-Ying Wey
- Athinoula A. Martinos Center for Biomedical Imaging
- Department of Radiology
- Massachusetts General Hospital, Harvard Medical School
- Charlestown
- USA
| | - Debasis Patnaik
- Chemical Neurobiology Laboratory
- Center for Genomic Medicine
- Department of Neurology
- Massachusetts General Hospital
- Harvard Medical School
| | - Xiaoxia Lu
- Chengdu Institute of Biology
- Chinese Academy of Sciences
- Chengdu 610041
- P. R. China
| | - Yu Lan
- Athinoula A. Martinos Center for Biomedical Imaging
- Department of Radiology
- Massachusetts General Hospital, Harvard Medical School
- Charlestown
- USA
| | - Johanna Rokka
- Athinoula A. Martinos Center for Biomedical Imaging
- Department of Radiology
- Massachusetts General Hospital, Harvard Medical School
- Charlestown
- USA
| | - Fiedler Stephanie
- Athinoula A. Martinos Center for Biomedical Imaging
- Department of Radiology
- Massachusetts General Hospital, Harvard Medical School
- Charlestown
- USA
| | - Stephen J. Haggarty
- Chemical Neurobiology Laboratory
- Center for Genomic Medicine
- Department of Neurology
- Massachusetts General Hospital
- Harvard Medical School
| | - Changning Wang
- Athinoula A. Martinos Center for Biomedical Imaging
- Department of Radiology
- Massachusetts General Hospital, Harvard Medical School
- Charlestown
- USA
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37
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Sperandio D, Aktoudianakis V, Babaoglu K, Chen X, Elbel K, Chin G, Corkey B, Du J, Jiang B, Kobayashi T, Mackman R, Martinez R, Yang H, Zablocki J, Kusam S, Jordan K, Webb H, Bates JG, Lad L, Mish M, Niedziela-Majka A, Metobo S, Sapre A, Hung M, Jin D, Fung W, Kan E, Eisenberg G, Larson N, Newby ZER, Lansdon E, Tay C, Neve RM, Shevick SL, Breckenridge DG. Structure-guided discovery of a novel, potent, and orally bioavailable 3,5-dimethylisoxazole aryl-benzimidazole BET bromodomain inhibitor. Bioorg Med Chem 2018; 27:457-469. [PMID: 30606676 DOI: 10.1016/j.bmc.2018.11.020] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Revised: 11/05/2018] [Accepted: 11/13/2018] [Indexed: 12/12/2022]
Abstract
The bromodomain and extra-terminal (BET) family of proteins, consisting of the bromodomains containing protein 2 (BRD2), BRD3, BRD4, and the testis-specific BRDT, are key epigenetic regulators of gene transcription and has emerged as an attractive target for anticancer therapy. Herein, we describe the discovery of a novel potent BET bromodomain inhibitor, using a systematic structure-based approach focused on improving potency, metabolic stability, and permeability. The optimized dimethylisoxazole aryl-benzimidazole inhibitor exhibited high potency towards BRD4 and related BET proteins in biochemical and cell-based assays and inhibited tumor growth in two proof-of-concept preclinical animal models.
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Affiliation(s)
- David Sperandio
- Department of Medicinal Chemistry, Gilead Sciences, Inc., 333 Lakeside Drive, Foster City, CA 94404, USA.
| | - Vangelis Aktoudianakis
- Department of Medicinal Chemistry, Gilead Sciences, Inc., 333 Lakeside Drive, Foster City, CA 94404, USA
| | - Kerim Babaoglu
- Department of Structural Chemistry, Gilead Sciences, Inc., 333 Lakeside Drive, Foster City, CA 94404, USA
| | - Xiaowu Chen
- Department of Structural Chemistry, Gilead Sciences, Inc., 333 Lakeside Drive, Foster City, CA 94404, USA
| | - Kristyna Elbel
- Department of Medicinal Chemistry, Gilead Sciences, Inc., 333 Lakeside Drive, Foster City, CA 94404, USA
| | - Gregory Chin
- Department of Medicinal Chemistry, Gilead Sciences, Inc., 333 Lakeside Drive, Foster City, CA 94404, USA
| | - Britton Corkey
- Department of Medicinal Chemistry, Gilead Sciences, Inc., 333 Lakeside Drive, Foster City, CA 94404, USA
| | - Jinfa Du
- Department of Medicinal Chemistry, Gilead Sciences, Inc., 333 Lakeside Drive, Foster City, CA 94404, USA
| | - Bob Jiang
- Department of Medicinal Chemistry, Gilead Sciences, Inc., 333 Lakeside Drive, Foster City, CA 94404, USA
| | - Tetsuya Kobayashi
- Department of Medicinal Chemistry, Gilead Sciences, Inc., 333 Lakeside Drive, Foster City, CA 94404, USA
| | - Richard Mackman
- Department of Medicinal Chemistry, Gilead Sciences, Inc., 333 Lakeside Drive, Foster City, CA 94404, USA
| | - Ruben Martinez
- Department of Medicinal Chemistry, Gilead Sciences, Inc., 333 Lakeside Drive, Foster City, CA 94404, USA
| | - Hai Yang
- Department of Medicinal Chemistry, Gilead Sciences, Inc., 333 Lakeside Drive, Foster City, CA 94404, USA
| | - Jeff Zablocki
- Department of Medicinal Chemistry, Gilead Sciences, Inc., 333 Lakeside Drive, Foster City, CA 94404, USA
| | - Saritha Kusam
- Department of Biology, Gilead Sciences, Inc., 333 Lakeside Drive, Foster City, CA 94404, USA
| | - Kim Jordan
- Department of Biology, Gilead Sciences, Inc., 333 Lakeside Drive, Foster City, CA 94404, USA
| | - Heather Webb
- Department of Biology, Gilead Sciences, Inc., 333 Lakeside Drive, Foster City, CA 94404, USA
| | - Jamie G Bates
- Department of Biology, Gilead Sciences, Inc., 333 Lakeside Drive, Foster City, CA 94404, USA
| | - Latesh Lad
- Department of Biology, Gilead Sciences, Inc., 333 Lakeside Drive, Foster City, CA 94404, USA
| | - Michael Mish
- Department of Medicinal Chemistry, Gilead Sciences, Inc., 333 Lakeside Drive, Foster City, CA 94404, USA
| | - Anita Niedziela-Majka
- Department of Biology, Gilead Sciences, Inc., 333 Lakeside Drive, Foster City, CA 94404, USA
| | - Sammy Metobo
- Department of Medicinal Chemistry, Gilead Sciences, Inc., 333 Lakeside Drive, Foster City, CA 94404, USA
| | - Annapurna Sapre
- Department of Biology, Gilead Sciences, Inc., 333 Lakeside Drive, Foster City, CA 94404, USA
| | - Magdeleine Hung
- Department of Biology, Gilead Sciences, Inc., 333 Lakeside Drive, Foster City, CA 94404, USA
| | - Debi Jin
- Department of Biology, Gilead Sciences, Inc., 333 Lakeside Drive, Foster City, CA 94404, USA
| | - Wanchi Fung
- Department of Biology, Gilead Sciences, Inc., 333 Lakeside Drive, Foster City, CA 94404, USA
| | - Elaine Kan
- Department of Biology, Gilead Sciences, Inc., 333 Lakeside Drive, Foster City, CA 94404, USA
| | - Gene Eisenberg
- Department of Drug Metabolism, Gilead Sciences, Inc., 333 Lakeside Drive, Foster City, CA 94404, USA
| | - Nate Larson
- Department of Biology, Gilead Sciences, Inc., 333 Lakeside Drive, Foster City, CA 94404, USA
| | - Zachary E R Newby
- Department of Structural Chemistry, Gilead Sciences, Inc., 333 Lakeside Drive, Foster City, CA 94404, USA
| | - Eric Lansdon
- Department of Structural Chemistry, Gilead Sciences, Inc., 333 Lakeside Drive, Foster City, CA 94404, USA
| | - Chin Tay
- Department of Biology, Gilead Sciences, Inc., 333 Lakeside Drive, Foster City, CA 94404, USA
| | - Richard M Neve
- Department of Biology, Gilead Sciences, Inc., 333 Lakeside Drive, Foster City, CA 94404, USA
| | - Sophia L Shevick
- Department of Medicinal Chemistry, Gilead Sciences, Inc., 333 Lakeside Drive, Foster City, CA 94404, USA
| | - David G Breckenridge
- Department of Biology, Gilead Sciences, Inc., 333 Lakeside Drive, Foster City, CA 94404, USA
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38
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Duan Y, Guan Y, Qin W, Zhai X, Yu B, Liu H. Targeting Brd4 for cancer therapy: inhibitors and degraders. MEDCHEMCOMM 2018; 9:1779-1802. [PMID: 30542529 PMCID: PMC6238758 DOI: 10.1039/c8md00198g] [Citation(s) in RCA: 103] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Accepted: 08/03/2018] [Indexed: 12/24/2022]
Abstract
Bromodomain-containing protein 4 (Brd4) plays an important role in mediating the expression of genes involved in cancers and non-cancer diseases such as inflammatory diseases and acute heart failure. Inactivating Brd4 or downregulating its expression inhibits cancer development, leading to the current interest in Brd4 as a promising anticancer drug target. Numerous Brd4 inhibitors have been studied in recent years and some of them are currently in various phases of clinical trials. Recently, selective degradation of target proteins by small bifunctional molecules (PROTACs) has emerged as an attractive drug discovery approach owing to the advantages it could offer over traditional small-molecule inhibitors. A number of Brd4 degraders have been reported and showed more efficient anticancer activities than just protein inhibition. In this review, we will discuss recent findings in the discovery and development of small-molecule inhibitors and degraders that target Brd4 as a potential anticancer agent.
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Affiliation(s)
- Yingchao Duan
- School of Pharmacy , Xinxiang Medical University , Xinxiang , Henan 453003 , China
| | - Yuanyuan Guan
- School of Pharmacy , Xinxiang Medical University , Xinxiang , Henan 453003 , China
| | - Wenping Qin
- School of Pharmacy , Xinxiang Medical University , Xinxiang , Henan 453003 , China
| | - Xiaoyu Zhai
- School of Pharmacy , Xinxiang Medical University , Xinxiang , Henan 453003 , China
| | - Bin Yu
- Key Laboratory of Advanced Pharmaceutical Technology , Ministry of Education of China , Co-innovation Center of Henan Province for New Drug R & D and Preclinical Safety , Institute of Drug Discovery and Development , School of Pharmaceutical Sciences , Zhengzhou University , 100 Kexue Avenue , Zhengzhou , Henan 450001 , China . ;
| | - Hongmin Liu
- Key Laboratory of Advanced Pharmaceutical Technology , Ministry of Education of China , Co-innovation Center of Henan Province for New Drug R & D and Preclinical Safety , Institute of Drug Discovery and Development , School of Pharmaceutical Sciences , Zhengzhou University , 100 Kexue Avenue , Zhengzhou , Henan 450001 , China . ;
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39
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Çalışkan B, Sinoplu E, İbiş K, Akhan Güzelcan E, Çetin Atalay R, Banoglu E. Synthesis and cellular bioactivities of novel isoxazole derivatives incorporating an arylpiperazine moiety as anticancer agents. J Enzyme Inhib Med Chem 2018; 33:1352-1361. [PMID: 30251900 PMCID: PMC6161610 DOI: 10.1080/14756366.2018.1504041] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
In our endeavour towards the development of effective anticancer therapeutics, a novel series of isoxazole-piperazine hybrids were synthesized and evaluated for their cytotoxic activities against human liver (Huh7 and Mahlavu) and breast (MCF-7) cancer cell lines. Within series, compounds 5l-o showed the most potent cytotoxicity on all cell lines with IC50 values in the range of 0.3–3.7 μM. To explore the mechanistic aspects fundamental to the observed activity, further biological studies with 5m and 5o in liver cancer cells were carried out. We have demonstrated that 5m and 5o induce oxidative stress in PTEN adequate Huh7 and PTEN deficient Mahlavu human liver cancer cells leading to apoptosis and cell cycle arrest at different phases. Further analysis of the proteins involved in apoptosis and cell cycle revealed that 5m and 5o caused an inhibition of cell survival pathway through Akt hyperphosphorylation and apoptosis and cell cycle arrest through p53 protein activation.
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Affiliation(s)
- Burcu Çalışkan
- a Department of Pharmaceutical Chemistry, Faculty of Pharmacy , Gazi University , Ankara , Turkey
| | - Esra Sinoplu
- b Department of Bioinformatics , Middle East Technical University , Ankara , Turkey
| | - Kübra İbiş
- a Department of Pharmaceutical Chemistry, Faculty of Pharmacy , Gazi University , Ankara , Turkey
| | - Ece Akhan Güzelcan
- b Department of Bioinformatics , Middle East Technical University , Ankara , Turkey
| | - Rengül Çetin Atalay
- b Department of Bioinformatics , Middle East Technical University , Ankara , Turkey
| | - Erden Banoglu
- a Department of Pharmaceutical Chemistry, Faculty of Pharmacy , Gazi University , Ankara , Turkey
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40
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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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41
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Zhu J, Zhou C, Caflisch A. Structure-based discovery of selective BRPF1 bromodomain inhibitors. Eur J Med Chem 2018; 155:337-352. [PMID: 29902720 DOI: 10.1016/j.ejmech.2018.05.037] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Revised: 04/05/2018] [Accepted: 05/23/2018] [Indexed: 11/19/2022]
Abstract
Bromodomain and plant homeodomain (PHD) finger containing protein 1 (BRPF1) is a member of subfamily IV of the human bromodomains. Experimental evidence suggests that BRPF1 is involved in leukemia. In a previous high-throughput docking campaign we identified several chemotypes targeting the BRPF1 bromodomain. Here, pharmacophore searches using the binding modes of two of these chemotypes resulted in two new series of ligands of the BRPF1 bromodomain. The 2,3-dioxo-quinoxaline 21 exhibits a 2-μM affinity for the BRPF1 bromodomain in two different competition binding assays, and more than 100-fold selectivity for BRPF1 against other members of subfamily IV and representatives of other subfamilies. Cellular activity is confirmed by a viability assay in a leukemia cell line. Isothermal titration calorimetry measurements reveal enthalpy-driven binding for compounds 21, 26 (KD = 3 μM), and the 2,4-dimethyl-oxazole derivative 42 (KD = 10 μM). Multiple molecular dynamics simulations and a dozen co-crystal structures at high resolution provide useful information for further optimization of affinity for the BRPF1 bromodomain.
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Affiliation(s)
- Jian Zhu
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland
| | - Chunxian Zhou
- Department of Pathology, Shanghai University of Traditional Chinese Medicine, Cailun Road 1200, Pudong District, Shanghai, China
| | - Amedeo Caflisch
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland.
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42
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Li X, Zhang J, Zhao L, Yang Y, Zhang H, Zhou J. Design, Synthesis, and in vitro Biological Evaluation of 3,5-Dimethylisoxazole Derivatives as BRD4 Inhibitors. ChemMedChem 2018; 13:1363-1368. [DOI: 10.1002/cmdc.201800074] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2018] [Revised: 04/23/2018] [Indexed: 11/10/2022]
Affiliation(s)
- Xiangyang Li
- Department of Medicinal Chemistry; China Pharmaceutical University; Nanjing 210009 P.R. China
| | - Jian Zhang
- Center of Drug Discovery; Jiangsu Key Laboratory of Drug Discovery for Metabolic Disease; China Pharmaceutical University; Nanjing 210009 P.R. China
| | - Leilei Zhao
- Center of Drug Discovery; Jiangsu Key Laboratory of Drug Discovery for Metabolic Disease; China Pharmaceutical University; Nanjing 210009 P.R. China
| | - Yifei Yang
- Department of Medicinal Chemistry; China Pharmaceutical University; Nanjing 210009 P.R. China
| | - Huibin Zhang
- Center of Drug Discovery; Jiangsu Key Laboratory of Drug Discovery for Metabolic Disease; China Pharmaceutical University; Nanjing 210009 P.R. China
| | - Jinpei Zhou
- Department of Medicinal Chemistry; China Pharmaceutical University; Nanjing 210009 P.R. China
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43
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Taneja N, Peddinti RK. Metal-free direct C-arylation of 1,3-dicarbonyl compounds and ethyl cyanoacetate: a platform to access diverse arrays of meta-functionalized phenols. Chem Commun (Camb) 2018; 54:11423-11426. [DOI: 10.1039/c8cc06235h] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
A base mediated, highly convenient strategy for the direct C-arylation of 1,3-dicarbonyls and cyanoacetate with various phenol derivatives as aryl partners is presented.
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Affiliation(s)
- Neha Taneja
- Department of Chemistry Indian Institute of Technology
- India
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44
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Bronner SM, Murray J, Romero FA, Lai KW, Tsui V, Cyr P, Beresini MH, de Leon Boenig G, Chen Z, Choo EF, Clark KR, Crawford TD, Jayaram H, Kaufman S, Li R, Li Y, Liao J, Liang X, Liu W, Ly J, Maher J, Wai J, Wang F, Zheng A, Zhu X, Magnuson S. A Unique Approach to Design Potent and Selective Cyclic Adenosine Monophosphate Response Element Binding Protein, Binding Protein (CBP) Inhibitors. J Med Chem 2017; 60:10151-10171. [PMID: 29155580 DOI: 10.1021/acs.jmedchem.7b01372] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The epigenetic regulator CBP/P300 presents a novel therapeutic target for oncology. Previously, we disclosed the development of potent and selective CBP bromodomain inhibitors by first identifying pharmacophores that bind the KAc region and then building into the LPF shelf. Herein, we report the "hybridization" of a variety of KAc-binding fragments with a tetrahydroquinoline scaffold that makes optimal interactions with the LPF shelf, imparting enhanced potency and selectivity to the hybridized ligand. To demonstrate the utility of our hybridization approach, two analogues containing unique Asn binders and the optimized tetrahydroquinoline moiety were rapidly optimized to yield single-digit nanomolar inhibitors of CBP with exquisite selectivity over BRD4(1) and the broader bromodomain family.
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Affiliation(s)
- Sarah M Bronner
- Genentech, Inc. , 1 DNA Way, South San Francisco, California 94080, United States
| | - Jeremy Murray
- Genentech, Inc. , 1 DNA Way, South San Francisco, California 94080, United States
| | - F Anthony Romero
- Genentech, Inc. , 1 DNA Way, South San Francisco, California 94080, United States
| | - Kwong Wah Lai
- Wuxi Apptec Co., Ltd. , 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, People's Republic of China
| | - Vickie Tsui
- Genentech, Inc. , 1 DNA Way, South San Francisco, California 94080, United States
| | - Patrick Cyr
- Genentech, Inc. , 1 DNA Way, South San Francisco, California 94080, United States
| | - Maureen H Beresini
- Genentech, Inc. , 1 DNA Way, South San Francisco, California 94080, United States
| | | | - Zhongguo Chen
- Wuxi Apptec Co., Ltd. , 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, People's Republic of China
| | - Edna F Choo
- Genentech, Inc. , 1 DNA Way, South San Francisco, California 94080, United States
| | - Kevin R Clark
- Genentech, Inc. , 1 DNA Way, South San Francisco, California 94080, United States
| | - Terry D Crawford
- Genentech, Inc. , 1 DNA Way, South San Francisco, California 94080, United States
| | - Hariharan Jayaram
- Editas Medicine, Inc. , 11 Hurley Street, Cambridge, Massachusetts 02141, United States
| | - Susan Kaufman
- Genentech, Inc. , 1 DNA Way, South San Francisco, California 94080, United States
| | - Ruina Li
- Genentech, Inc. , 1 DNA Way, South San Francisco, California 94080, United States
| | - Yingjie Li
- Wuxi Apptec Co., Ltd. , 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, People's Republic of China
| | - Jiangpeng Liao
- Wuxi Apptec Co., Ltd. , 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, People's Republic of China
| | - Xiaorong Liang
- Genentech, Inc. , 1 DNA Way, South San Francisco, California 94080, United States
| | - Wenfeng Liu
- Wuxi Apptec Co., Ltd. , 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, People's Republic of China
| | - Justin Ly
- Genentech, Inc. , 1 DNA Way, South San Francisco, California 94080, United States
| | - Jonathan Maher
- Genentech, Inc. , 1 DNA Way, South San Francisco, California 94080, United States
| | - John Wai
- Wuxi Apptec Co., Ltd. , 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, People's Republic of China
| | - Fei Wang
- Wuxi Apptec Co., Ltd. , 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, People's Republic of China
| | - Aijun Zheng
- Wuxi Apptec Co., Ltd. , 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, People's Republic of China
| | - Xiaoyu Zhu
- Wuxi Apptec Co., Ltd. , 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, People's Republic of China
| | - Steven Magnuson
- Genentech, Inc. , 1 DNA Way, South San Francisco, California 94080, United States
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45
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Yan G, Hou M, Luo J, Pu C, Hou X, Lan S, Li R. Pharmacophore-based virtual screening, molecular docking, molecular dynamics simulation, and biological evaluation for the discovery of novel BRD4 inhibitors. Chem Biol Drug Des 2017; 91:478-490. [PMID: 28901664 DOI: 10.1111/cbdd.13109] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Revised: 08/21/2017] [Accepted: 08/22/2017] [Indexed: 02/05/2023]
Abstract
Bromodomain is a recognition module in the signal transduction of acetylated histone. BRD4, one of the bromodomain members, is emerging as an attractive therapeutic target for several types of cancer. Therefore, in this study, an attempt has been made to screen compounds from an integrated database containing 5.5 million compounds for BRD4 inhibitors using pharmacophore-based virtual screening, molecular docking, and molecular dynamics simulations. As a result, two molecules of twelve hits were found to be active in bioactivity tests. Among the molecules, compound 5 exhibited potent anticancer activity, and the IC50 values against human cancer cell lines MV4-11, A375, and HeLa were 4.2, 7.1, and 11.6 μm, respectively. After that, colony formation assay, cell cycle, apoptosis analysis, wound-healing migration assay, and Western blotting were carried out to learn the bioactivity of compound 5.
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Affiliation(s)
- Guoyi Yan
- Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Sichuan, China
| | - Manzhou Hou
- Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Sichuan, China
| | - Jiang Luo
- Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Sichuan, China
| | - Chunlan Pu
- Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Sichuan, China
| | - Xueyan Hou
- Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Sichuan, China
| | - Suke Lan
- Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Sichuan, China
| | - Rui Li
- Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Sichuan, China
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46
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Radwan M, Serya R. Fragment-Based Drug Discovery in the Bromodomain and Extra-Terminal Domain Family. Arch Pharm (Weinheim) 2017; 350. [PMID: 28714212 DOI: 10.1002/ardp.201700147] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Revised: 06/27/2017] [Accepted: 06/28/2017] [Indexed: 12/21/2022]
Abstract
Bromodomain and extra-terminal domain (BET) inhibition has emerged recently as a potential therapeutic target for the treatment of many human disorders such as atherosclerosis, inflammatory disorders, chronic obstructive pulmonary disease (COPD), some viral infections, and cancer. Since the discovery of the two potent inhibitors, I-BET762 and JQ1, different research groups have used different techniques to develop novel potent and selective inhibitors. In this review, we will be concerned with the trials that used fragment-based drug discovery (FBDD) approaches to discover or optimize BET inhibitors, also showing fragments that can be further optimized in future projects to reach novel potent BET inhibitors.
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Affiliation(s)
| | - Rabah Serya
- Faculty of Pharmacy, Ain Shams University, Cairo, Egypt
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47
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Denny RA, Flick AC, Coe J, Langille J, Basak A, Liu S, Stock I, Sahasrabudhe P, Bonin P, Hay DA, Brennan PE, Pletcher M, Jones LH, Chekler ELP. Structure-Based Design of Highly Selective Inhibitors of the CREB Binding Protein Bromodomain. J Med Chem 2017; 60:5349-5363. [DOI: 10.1021/acs.jmedchem.6b01839] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- R. Aldrin Denny
- Medicine
Design, Pfizer, 610 Main Street, Cambridge Massachusetts 02139, United States
| | - Andrew C. Flick
- Medicine
Design, Pfizer, Eastern Point Road, Groton Connecticut 06340, United States
| | - Jotham Coe
- Medicine
Design, Pfizer, Eastern Point Road, Groton Connecticut 06340, United States
| | | | - Arindrajit Basak
- Medicine
Design, Pfizer, Eastern Point Road, Groton Connecticut 06340, United States
| | - Shenping Liu
- Structural
Biology and Biophysics, Medicine Design, Pfizer, Eastern Point
Road, Groton Connecticut 06340, United States
| | - Ingrid Stock
- Primary
Pharmacology Group, Pfizer, Eastern Point Road, Groton Connecticut 06340, United States
| | - Parag Sahasrabudhe
- Structural
Biology and Biophysics, Medicine Design, Pfizer, Eastern Point
Road, Groton Connecticut 06340, United States
| | - Paul Bonin
- Primary
Pharmacology Group, Pfizer, Eastern Point Road, Groton Connecticut 06340, United States
| | - Duncan A. Hay
- Evotec (UK) Ltd., 114 Innovation
Drive, Milton Park, Abingdon, Oxfordshire OX14 4RZ, UK
- Structural
Genomics Consortium, Target Discovery Institute, ARUK Oxford Drug
Discovery Institute, University of Oxford, NDM Research Building, Roosevelt
Drive, Oxford OX3 7FZ, U.K
| | - Paul E. Brennan
- Structural
Genomics Consortium, Target Discovery Institute, ARUK Oxford Drug
Discovery Institute, University of Oxford, NDM Research Building, Roosevelt
Drive, Oxford OX3 7FZ, U.K
| | - Mathew Pletcher
- Rare
Disease Research Unit, Pfizer, 610 Main Street, Cambridge Massachusetts 02139, United States
| | - Lyn H. Jones
- Medicine
Design, Pfizer, 610 Main Street, Cambridge Massachusetts 02139, United States
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48
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Zhao Y, Bai L, Liu L, McEachern D, Stuckey JA, Meagher JL, Yang CY, Ran X, Zhou B, Hu Y, Li X, Wen B, Zhao T, Li S, Sun D, Wang S. Structure-Based Discovery of 4-(6-Methoxy-2-methyl-4-(quinolin-4-yl)-9H-pyrimido[4,5-b]indol-7-yl)-3,5-dimethylisoxazole (CD161) as a Potent and Orally Bioavailable BET Bromodomain Inhibitor. J Med Chem 2017; 60:3887-3901. [PMID: 28463487 DOI: 10.1021/acs.jmedchem.7b00193] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
We have designed and synthesized 9H-pyrimido[4,5-b]indole-containing compounds to obtain potent and orally bioavailable BET inhibitors. By incorporation of an indole or a quinoline moiety to the 9H-pyrimido[4,5-b]indole core, we identified a series of small molecules showing high binding affinities to BET proteins and low nanomolar potencies in inhibition of cell growth in acute leukemia cell lines. One such compound, 4-(6-methoxy-2-methyl-4-(quinolin-4-yl)-9H-pyrimido[4,5-b]indol-7-yl)-3,5-dimethylisoxazole (31) has excellent microsomal stability and good oral pharmacokinetics in rats and mice. Orally administered, 31 achieves significant antitumor activity in the MV4;11 leukemia and MDA-MB-231 triple-negative breast cancer xenograft models in mice. Determination of the cocrystal structure of 31 with BRD4 BD2 provides a structural basis for its high binding affinity to BET proteins. Testing its binding affinities against other bromodomain-containing proteins shows that 31 is a highly selective inhibitor of BET proteins. Our data show that 31 is a potent, selective, and orally active BET inhibitor.
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Affiliation(s)
- Yujun Zhao
- Comprehensive Cancer Center and Departments of Internal Medicine, Pharmacology, and Medicinal Chemistry, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Longchuan Bai
- Comprehensive Cancer Center and Departments of Internal Medicine, Pharmacology, and Medicinal Chemistry, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Liu Liu
- Comprehensive Cancer Center and Departments of Internal Medicine, Pharmacology, and Medicinal Chemistry, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Donna McEachern
- Comprehensive Cancer Center and Departments of Internal Medicine, Pharmacology, and Medicinal Chemistry, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Jeanne A Stuckey
- Life Sciences Institute and Department of Biological Chemistry, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Jennifer L Meagher
- Life Sciences Institute and Department of Biological Chemistry, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Chao-Yie Yang
- Comprehensive Cancer Center and Departments of Internal Medicine, Pharmacology, and Medicinal Chemistry, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Xu Ran
- Comprehensive Cancer Center and Departments of Internal Medicine, Pharmacology, and Medicinal Chemistry, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Bing Zhou
- Comprehensive Cancer Center and Departments of Internal Medicine, Pharmacology, and Medicinal Chemistry, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Yang Hu
- Comprehensive Cancer Center and Departments of Internal Medicine, Pharmacology, and Medicinal Chemistry, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Xiaoqin Li
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Bo Wen
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Ting Zhao
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Siwei Li
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Duxin Sun
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Michigan , Ann Arbor, Michigan 48109, United States
| | - Shaomeng Wang
- Comprehensive Cancer Center and Departments of Internal Medicine, Pharmacology, and Medicinal Chemistry, University of Michigan , Ann Arbor, Michigan 48109, United States
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49
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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
![]()
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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50
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Chen Z, Zhang H, Liu S, Xie Y, Jiang H, Lu W, Xu H, Yue L, Zhang Y, Ding H, Zheng M, Yu K, Chen K, Jiang H, Luo C. Discovery of novel trimethoxy-ring BRD4 bromodomain inhibitors: AlphaScreen assay, crystallography and cell-based assay. MEDCHEMCOMM 2017; 8:1322-1331. [PMID: 30108844 DOI: 10.1039/c7md00083a] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Accepted: 03/16/2017] [Indexed: 12/19/2022]
Abstract
As a member of the bromodomain and extra terminal domain (BET) protein family, BRD4 is closely related to cancers and other diseases. Small-molecule BRD4 inhibitors have already demonstrated promising potential for the therapy of BRD4-related cancers. In this study, we report the discovery and evaluation of a novel category of BRD4 inhibitors, which share a trimethoxy ring and target the first bromodomain of the human BRD4 protein. The IC50 value of the most potent compound, DC-BD-03, is 2.01 μM. In addition, a high-resolution crystal structure of the compound DC-BD-29 with the first bromodomain of BRD4 was determined, which revealed the binding mode and facilitated further structure-based optimization. These compounds exhibited anti-proliferation activity, caused cell cycle arrest, and induced apoptosis in human leukemia MV4-11 cells. Thus, the results presented in this study indicated the potential of this series of compounds as drug candidates for the therapy of BRD4-related cancers.
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Affiliation(s)
- Zhifeng Chen
- Drug Discovery and Design Center , State Key Laboratory of Drug Research , Shanghai Institute of Materia Medica , Chinese Academy of Sciences , 555 Zuchongzhi Road , Shanghai 201203 , China . ; ; ; Tel: +86 21 50806600.,School of Life Science and Technology , ShanghaiTech University , 100 Haike Road , Shanghai 201210 , China.,University of Chinese Academy of Sciences , 19 Yuquan Road , Beijing 100049 , China
| | - Hao Zhang
- Drug Discovery and Design Center , State Key Laboratory of Drug Research , Shanghai Institute of Materia Medica , Chinese Academy of Sciences , 555 Zuchongzhi Road , Shanghai 201203 , China . ; ; ; Tel: +86 21 50806600.,University of Chinese Academy of Sciences , 19 Yuquan Road , Beijing 100049 , China
| | - Shien Liu
- Drug Discovery and Design Center , State Key Laboratory of Drug Research , Shanghai Institute of Materia Medica , Chinese Academy of Sciences , 555 Zuchongzhi Road , Shanghai 201203 , China . ; ; ; Tel: +86 21 50806600.,University of Chinese Academy of Sciences , 19 Yuquan Road , Beijing 100049 , China
| | - Yiqian Xie
- School of Pharmacy , Shanghai University of Traditional Chinese Medicine , China
| | - Hao Jiang
- Drug Discovery and Design Center , State Key Laboratory of Drug Research , Shanghai Institute of Materia Medica , Chinese Academy of Sciences , 555 Zuchongzhi Road , Shanghai 201203 , China . ; ; ; Tel: +86 21 50806600.,University of Chinese Academy of Sciences , 19 Yuquan Road , Beijing 100049 , China
| | - Wenchao Lu
- Drug Discovery and Design Center , State Key Laboratory of Drug Research , Shanghai Institute of Materia Medica , Chinese Academy of Sciences , 555 Zuchongzhi Road , Shanghai 201203 , China . ; ; ; Tel: +86 21 50806600.,University of Chinese Academy of Sciences , 19 Yuquan Road , Beijing 100049 , China
| | - Heng Xu
- Drug Discovery and Design Center , State Key Laboratory of Drug Research , Shanghai Institute of Materia Medica , Chinese Academy of Sciences , 555 Zuchongzhi Road , Shanghai 201203 , China . ; ; ; Tel: +86 21 50806600.,University of Chinese Academy of Sciences , 19 Yuquan Road , Beijing 100049 , China
| | - Liyan Yue
- Drug Discovery and Design Center , State Key Laboratory of Drug Research , Shanghai Institute of Materia Medica , Chinese Academy of Sciences , 555 Zuchongzhi Road , Shanghai 201203 , China . ; ; ; Tel: +86 21 50806600.,University of Chinese Academy of Sciences , 19 Yuquan Road , Beijing 100049 , China
| | - Yuanyuan Zhang
- Drug Discovery and Design Center , State Key Laboratory of Drug Research , Shanghai Institute of Materia Medica , Chinese Academy of Sciences , 555 Zuchongzhi Road , Shanghai 201203 , China . ; ; ; Tel: +86 21 50806600
| | - Hong Ding
- Drug Discovery and Design Center , State Key Laboratory of Drug Research , Shanghai Institute of Materia Medica , Chinese Academy of Sciences , 555 Zuchongzhi Road , Shanghai 201203 , China . ; ; ; Tel: +86 21 50806600.,School of Pharmacy , Shanghai University of Traditional Chinese Medicine , China
| | - Mingyue Zheng
- Drug Discovery and Design Center , State Key Laboratory of Drug Research , Shanghai Institute of Materia Medica , Chinese Academy of Sciences , 555 Zuchongzhi Road , Shanghai 201203 , China . ; ; ; Tel: +86 21 50806600
| | - Kunqian Yu
- Drug Discovery and Design Center , State Key Laboratory of Drug Research , Shanghai Institute of Materia Medica , Chinese Academy of Sciences , 555 Zuchongzhi Road , Shanghai 201203 , China . ; ; ; Tel: +86 21 50806600
| | - Kaixian Chen
- Drug Discovery and Design Center , State Key Laboratory of Drug Research , Shanghai Institute of Materia Medica , Chinese Academy of Sciences , 555 Zuchongzhi Road , Shanghai 201203 , China . ; ; ; Tel: +86 21 50806600
| | - Hualiang Jiang
- Drug Discovery and Design Center , State Key Laboratory of Drug Research , Shanghai Institute of Materia Medica , Chinese Academy of Sciences , 555 Zuchongzhi Road , Shanghai 201203 , China . ; ; ; Tel: +86 21 50806600.,School of Life Science and Technology , ShanghaiTech University , 100 Haike Road , Shanghai 201210 , China.,University of Chinese Academy of Sciences , 19 Yuquan Road , Beijing 100049 , China
| | - Cheng Luo
- Drug Discovery and Design Center , State Key Laboratory of Drug Research , Shanghai Institute of Materia Medica , Chinese Academy of Sciences , 555 Zuchongzhi Road , Shanghai 201203 , China . ; ; ; Tel: +86 21 50806600.,University of Chinese Academy of Sciences , 19 Yuquan Road , Beijing 100049 , China
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