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Kumar V, Chunchagatta Lakshman PK, Prasad TK, Manjunath K, Bairy S, Vasu AS, Ganavi B, Jasti S, Kamariah N. Target-based drug discovery: Applications of fluorescence techniques in high throughput and fragment-based screening. Heliyon 2024; 10:e23864. [PMID: 38226204 PMCID: PMC10788520 DOI: 10.1016/j.heliyon.2023.e23864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 12/14/2023] [Accepted: 12/14/2023] [Indexed: 01/17/2024] Open
Abstract
Target-based discovery of first-in-class therapeutics demands an in-depth understanding of the molecular mechanisms underlying human diseases. Precise measurements of cellular and biochemical activities are critical to gain mechanistic knowledge of biomolecules and their altered function in disease conditions. Such measurements enable the development of intervention strategies for preventing or treating diseases by modulation of desired molecular processes. Fluorescence-based techniques are routinely employed for accurate and robust measurements of in-vitro activity of molecular targets and for discovering novel chemical molecules that modulate the activity of molecular targets. In the current review, the authors focus on the applications of fluorescence-based high throughput screening (HTS) and fragment-based ligand discovery (FBLD) techniques such as fluorescence polarization (FP), Förster resonance energy transfer (FRET), fluorescence thermal shift assay (FTSA) and microscale thermophoresis (MST) for the discovery of chemical probe to exploring target's role in disease biology and ultimately, serve as a foundation for drug discovery. Some recent advancements in these techniques for compound library screening against important classes of drug targets, such as G-protein-coupled receptors (GPCRs) and GTPases, as well as phosphorylation- and acetylation-mediated protein-protein interactions, are discussed. Overall, this review presents a landscape of how these techniques paved the way for the discovery of small-molecule modulators and biologics against these targets for therapeutic benefits.
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Affiliation(s)
| | | | - Thazhe Kootteri Prasad
- Centre for Chemical Biology & Therapeutics, inStem & NCBS, Bellary Road, Bangalore, 560065, India
| | - Kavyashree Manjunath
- Centre for Chemical Biology & Therapeutics, inStem & NCBS, Bellary Road, Bangalore, 560065, India
| | - Sneha Bairy
- Centre for Chemical Biology & Therapeutics, inStem & NCBS, Bellary Road, Bangalore, 560065, India
| | - Akshaya S. Vasu
- Centre for Chemical Biology & Therapeutics, inStem & NCBS, Bellary Road, Bangalore, 560065, India
| | - B. Ganavi
- Centre for Chemical Biology & Therapeutics, inStem & NCBS, Bellary Road, Bangalore, 560065, India
| | - Subbarao Jasti
- Centre for Chemical Biology & Therapeutics, inStem & NCBS, Bellary Road, Bangalore, 560065, India
| | - Neelagandan Kamariah
- Centre for Chemical Biology & Therapeutics, inStem & NCBS, Bellary Road, Bangalore, 560065, India
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2
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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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3
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Gupta S, Park SE, Mozaffari S, El-Aarag B, Parang K, Tiwari RK. Design, Synthesis, and Antiproliferative Activity of Benzopyran-4-One-Isoxazole Hybrid Compounds. Molecules 2023; 28:molecules28104220. [PMID: 37241960 DOI: 10.3390/molecules28104220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 05/12/2023] [Accepted: 05/16/2023] [Indexed: 05/28/2023] Open
Abstract
The biological significance of benzopyran-4-ones as cytotoxic agents against multi-drug resistant cancer cell lines and isoxazoles as anti-inflammatory agents in cellular assays prompted us to design and synthesize their hybrid compounds and explore their antiproliferative activity against a panel of six cancer cell lines and two normal cell lines. Compounds 5a-d displayed significant antiproliferative activities against all the cancer cell lines tested, and IC50 values were in the range of 5.2-22.2 μM against MDA-MB-231 cancer cells, while they were minimally cytotoxic to the HEK-293 and LLC-PK1 normal cell lines. The IC50 values of 5a-d against normal HEK-293 cells were in the range of 102.4-293.2 μM. Compound 5a was screened for kinase inhibitory activity, proteolytic human serum stability, and apoptotic activity. The compound was found inactive towards different kinases, while it completely degraded after 2 h of incubation with human serum. At 5 μM concentration, it induced apoptosis in MDA-MB-231 by 50.8%. Overall, these findings suggest that new benzopyran-4-one-isoxazole hybrid compounds, particularly 5a-d, are selective anticancer agents, potentially safe for human cells, and could be synthesized at low cost. Additionally, Compound 5a exhibits potential anticancer activity mediated via inhibition of cancer cell proliferation and induction of apoptosis.
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Affiliation(s)
- Shilpi Gupta
- Center for Targeted Drug Delivery, Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Harry and Diane Rinker Health Science Campus, Irvine, CA 92618-1908, USA
- Department of Chemistry, Hindu College, Sonipat 131001, India
| | - Shang Eun Park
- Center for Targeted Drug Delivery, Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Harry and Diane Rinker Health Science Campus, Irvine, CA 92618-1908, USA
| | - Saghar Mozaffari
- Center for Targeted Drug Delivery, Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Harry and Diane Rinker Health Science Campus, Irvine, CA 92618-1908, USA
| | - Bishoy El-Aarag
- Center for Targeted Drug Delivery, Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Harry and Diane Rinker Health Science Campus, Irvine, CA 92618-1908, USA
- Biochemistry Division, Chemistry Department, Faculty of Science, Menoufia University, Shebin El-Koom 32512, Egypt
| | - Keykavous Parang
- Center for Targeted Drug Delivery, Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Harry and Diane Rinker Health Science Campus, Irvine, CA 92618-1908, USA
| | - Rakesh Kumar Tiwari
- Center for Targeted Drug Delivery, Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Harry and Diane Rinker Health Science Campus, Irvine, CA 92618-1908, USA
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Pan Z, Zhao Y, Wang X, Xie X, Liu M, Zhang K, Wang L, Bai D, Foster LJ, Shu R, He G. Targeting bromodomain-containing proteins: research advances of drug discovery. MOLECULAR BIOMEDICINE 2023; 4:13. [PMID: 37142850 PMCID: PMC10159834 DOI: 10.1186/s43556-023-00127-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 04/02/2023] [Indexed: 05/06/2023] Open
Abstract
Bromodomain (BD) is an evolutionarily conserved protein module found in 46 different BD-containing proteins (BCPs). BD acts as a specific reader for acetylated lysine residues (KAc) and serves an essential role in transcriptional regulation, chromatin remodeling, DNA damage repair, and cell proliferation. On the other hand, BCPs have been shown to be involved in the pathogenesis of a variety of diseases, including cancers, inflammation, cardiovascular diseases, and viral infections. Over the past decade, researchers have brought new therapeutic strategies to relevant diseases by inhibiting the activity or downregulating the expression of BCPs to interfere with the transcription of pathogenic genes. An increasing number of potent inhibitors and degraders of BCPs have been developed, some of which are already in clinical trials. In this paper, we provide a comprehensive review of recent advances in the study of drugs that inhibit or down-regulate BCPs, focusing on the development history, molecular structure, biological activity, interaction with BCPs and therapeutic potentials of these drugs. In addition, we discuss current challenges, issues to be addressed and future research directions for the development of BCPs inhibitors. Lessons learned from the successful or unsuccessful development experiences of these inhibitors or degraders will facilitate the further development of efficient, selective and less toxic inhibitors of BCPs and eventually achieve drug application in the clinic.
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Affiliation(s)
- Zhaoping Pan
- Department of Dermatology & Venerology and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
- Laboratory of Dermatology, Clinical Institute of Inflammation and Immunology (CIII), Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Yuxi Zhao
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Disease, Department of Orthodontics and Pediatrics, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, China
| | - Xiaoyun Wang
- Department of Dermatology & Venerology and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
- Laboratory of Dermatology, Clinical Institute of Inflammation and Immunology (CIII), Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Xin Xie
- College of Medical Technology and School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Mingxia Liu
- Department of Dermatology & Venerology and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Kaiyao Zhang
- Department of Dermatology & Venerology and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Lian Wang
- Department of Dermatology & Venerology and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Ding Bai
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Disease, Department of Orthodontics and Pediatrics, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, China
| | - Leonard J Foster
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Rui Shu
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Disease, Department of Orthodontics and Pediatrics, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, China.
| | - Gu He
- Department of Dermatology & Venerology and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China.
- Laboratory of Dermatology, Clinical Institute of Inflammation and Immunology (CIII), Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610041, China.
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FT-6876, a Potent and Selective Inhibitor of CBP/p300, is Active in Preclinical Models of Androgen Receptor-Positive Breast Cancer. Target Oncol 2023; 18:269-285. [PMID: 36826464 PMCID: PMC10042772 DOI: 10.1007/s11523-023-00949-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/30/2023] [Indexed: 02/25/2023]
Abstract
BACKGROUND Patients with triple-negative breast cancer (TNBC) expressing the androgen receptor (AR) respond poorly to neoadjuvant chemotherapy, although AR antagonists have shown promising clinical activity, suggesting these tumors are AR-dependent. cAMP responsive element binding protein (CREB)-binding protein (CBP) and p300 are transcriptional co-activators for the AR, a key driver of AR+ breast and prostate cancer, and may provide a novel therapeutic target in AR+ TNBC. OBJECTIVES The aim of this study was to determine the therapeutic potential of FT-6876, a new CBP/p300 bromodomain inhibitor, in breast cancer models with a range of AR levels in vitro and in vivo. METHODS Effects of FT-6876 on the CBP/p300 pathway were determined by combining chromatin immunoprecipitation (ChIP) with precision run-on sequencing (PRO-seq) complemented with H3K27 acetylation (Ac) and transcriptional profiling. The antiproliferative effect of FT-6876 was also measured in vitro and in vivo. RESULTS We describe the discovery of FT-6876, a potent and selective CBP/p300 bromodomain inhibitor. The combination of ChIP and PRO-seq confirmed the reduction in H3K27Ac at specific promoter sites concurrent with a decrease in CBP/p300 on the chromatin and a reduction in nascent RNA and enhancer RNA. This was associated with a time- and concentration-dependent reduction in H3K37Ac associated with a decrease in AR and estrogen receptor (ER) target gene expression. This led to a time-dependent growth inhibition in AR+ models, correlated with AR expression. Tumor growth inhibition was also observed in AR+ tumor models of TNBC and ER+ breast cancer subtypes with consistent pharmacokinetics and pharmacodynamics. CONCLUSION Our findings demonstrate FT-6876 as a promising new CBP/p300 bromodomain inhibitor, with efficacy in preclinical models of AR+ breast cancer.
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6
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Mahmoudi AE, Tachallait H, Moutaoukil Z, Arshad S, Karrouchi K, Benhida R, Bougrin K. Ultrasound‐Assisted Green Synthesis of 3,5‐Disubstituted Isoxazole Secondary Sulfonamides via One‐Pot Five‐Component Reaction using CaCl
2
/K
2
CO
3
as Pre‐Catalyst in Water. ChemistrySelect 2022. [DOI: 10.1002/slct.202203072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Ayoub El Mahmoudi
- Equipe de Chimie des Plantes et de Synthèse Organique et Bioorganique URAC23 Faculty of Science B.P. 1014 Geophysics Natural Patrimony and Green Chemistry (GEOPAC) Research Center Mohammed V University in Rabat Morocco
| | - Hamza Tachallait
- Equipe de Chimie des Plantes et de Synthèse Organique et Bioorganique URAC23 Faculty of Science B.P. 1014 Geophysics Natural Patrimony and Green Chemistry (GEOPAC) Research Center Mohammed V University in Rabat Morocco
- Chemical & Biochemical Sciences Green-Process Engineering (CBS) Mohammed VI Polytechnic University Lot 660, Hay Moulay Rachid Benguerir Morocco
| | - Zakaria Moutaoukil
- Chemical & Biochemical Sciences Green-Process Engineering (CBS) Mohammed VI Polytechnic University Lot 660, Hay Moulay Rachid Benguerir Morocco
- Université Côte d'Azur CNRS Institut de Chimie de Nice UMR CNRS 7272 - 06108 Nice France
| | - Suhana Arshad
- X-ray Crystallography Unit School of Physics Universiti Sains Malaysia 11800 USM Penang Malaysia
| | - Khalid Karrouchi
- Laboratory of Analytical Chemistry and Bromatology Faculty of Medicine and Pharmacy Mohammed V University in Rabat Morocco
| | - Rachid Benhida
- Chemical & Biochemical Sciences Green-Process Engineering (CBS) Mohammed VI Polytechnic University Lot 660, Hay Moulay Rachid Benguerir Morocco
- Université Côte d'Azur CNRS Institut de Chimie de Nice UMR CNRS 7272 - 06108 Nice France
| | - Khalid Bougrin
- Equipe de Chimie des Plantes et de Synthèse Organique et Bioorganique URAC23 Faculty of Science B.P. 1014 Geophysics Natural Patrimony and Green Chemistry (GEOPAC) Research Center Mohammed V University in Rabat Morocco
- Chemical & Biochemical Sciences Green-Process Engineering (CBS) Mohammed VI Polytechnic University Lot 660, Hay Moulay Rachid Benguerir Morocco
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7
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Mattei A, Hong RS, Dietrich H, Firaha D, Helfferich J, Liu YM, Sasikumar K, Abraham NS, Miglani Bhardwaj R, Neumann MA, Sheikh AY. Efficient Crystal Structure Prediction for Structurally Related Molecules with Accurate and Transferable Tailor-Made Force Fields. J Chem Theory Comput 2022; 18:5725-5738. [PMID: 35930763 PMCID: PMC9476662 DOI: 10.1021/acs.jctc.2c00451] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Crystal structure prediction (CSP) his generally used to complement experimental solid form screening and applied to individual molecules in drug development. The fast development of algorithms and computing resources offers the opportunity to use CSP earlier and for a broader range of applications in the drug design cycle. This study presents a novel paradigm of CSP specifically designed for structurally related molecules, referred to as Quick-CSP. The approach prioritizes more accurate physics through robust and transferable tailor-made force fields (TMFFs), such that significant efficiency gains are achieved through the reduction of expensive ab initio calculations. The accuracy of the TMFF is increased by the introduction of electrostatic multipoles, and the fragment-based force field parameterization scheme is demonstrated to be transferable for a family of chemically related molecules. The protocol is benchmarked with structurally related compounds from the Bromodomain and Extraterminal (BET) domain inhibitors series. A new convergence criterion is introduced that aims at performing only as many ab initio optimizations of crystal structures as required to locate the bottom of the crystal energy landscape within a user-defined accuracy. The overall approach provides significant cost savings ranging from three- to eight-fold less than the full-CSP workflow. The reported advancements expand the scope and utility of the underlying CSP building blocks as well as their novel reassembly to other applications earlier in the drug design cycle to guide molecule design and selection.
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Affiliation(s)
- Alessandra Mattei
- Solid State Chemistry, Research & Development, AbbVie Inc., 1 N Waukegan Road, North Chicago, Illinois 60064, United States
| | - Richard S Hong
- Solid State Chemistry, Research & Development, AbbVie Inc., 1 N Waukegan Road, North Chicago, Illinois 60064, United States
| | - Hanno Dietrich
- Avant-garde Materials Simulation, GmbH, Alte Str. 2, 79249 Merzhausen, Germany
| | - Dzmitry Firaha
- Avant-garde Materials Simulation, GmbH, Alte Str. 2, 79249 Merzhausen, Germany
| | - Julian Helfferich
- Avant-garde Materials Simulation, GmbH, Alte Str. 2, 79249 Merzhausen, Germany
| | - Yifei Michelle Liu
- Avant-garde Materials Simulation, GmbH, Alte Str. 2, 79249 Merzhausen, Germany
| | - Kiran Sasikumar
- Avant-garde Materials Simulation, GmbH, Alte Str. 2, 79249 Merzhausen, Germany
| | - Nathan S Abraham
- Solid State Chemistry, Research & Development, AbbVie Inc., 1 N Waukegan Road, North Chicago, Illinois 60064, United States
| | - Rajni Miglani Bhardwaj
- Solid State Chemistry, Research & Development, AbbVie Inc., 1 N Waukegan Road, North Chicago, Illinois 60064, United States
| | - Marcus A Neumann
- Avant-garde Materials Simulation, GmbH, Alte Str. 2, 79249 Merzhausen, Germany
| | - Ahmad Y Sheikh
- Solid State Chemistry, Research & Development, AbbVie Inc., 1 N Waukegan Road, North Chicago, Illinois 60064, United States
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8
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Holdgate GA, Bardelle C, Lanne A, Read J, O'Donovan DH, Smith JM, Selmi N, Sheppard R. Drug discovery for epigenetics targets. Drug Discov Today 2021; 27:1088-1098. [PMID: 34728375 DOI: 10.1016/j.drudis.2021.10.020] [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: 06/20/2021] [Revised: 09/19/2021] [Accepted: 10/27/2021] [Indexed: 12/28/2022]
Abstract
Dysregulation of the epigenome is associated with the onset and progression of several diseases, including cancer, autoimmune, cardiovascular, and neurological disorders. Members from the three families of epigenetic proteins (readers, writers, and erasers) have been shown to be druggable using small-molecule inhibitors. Increasing knowledge of the role of epigenetics in disease and the reversibility of these modifications explain why pharmacological intervention is an attractive strategy for tackling epigenetic-based disease. In this review, we provide an overview of epigenetics drug targets, focus on approaches used for initial hit identification, and describe the subsequent role of structure-guided chemistry optimisation of initial hits to clinical candidates. We also highlight current challenges and future potential for epigenetics-based therapies.
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Affiliation(s)
- Geoffrey A Holdgate
- High-throughput Screening, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Alderley Park, UK.
| | - Catherine Bardelle
- High-throughput Screening, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Alderley Park, UK
| | - Alice Lanne
- High-throughput Screening, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Alderley Park, UK
| | - Jon Read
- Structure and Biophysics, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | | | | | - Nidhal Selmi
- iLAB, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Robert Sheppard
- Medicinal Chemistry, Cardiovascular, Renal, Metabolism R&D, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
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9
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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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10
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Jones KL, Beaumont DM, Bernard SG, Bit RA, Campbell SP, Chung CW, Cutler L, Demont EH, Dennis K, Gordon L, Gray JR, Haase MV, Lewis AJ, McCleary S, Mitchell DJ, Moore SM, Parr N, Robb OJ, Smithers N, Soden PE, Suckling CJ, Taylor S, Walker AL, Watson RJ, Prinjha RK. Discovery of a Novel Bromodomain and Extra Terminal Domain (BET) Protein Inhibitor, I-BET282E, Suitable for Clinical Progression. J Med Chem 2021; 64:12200-12227. [PMID: 34387088 DOI: 10.1021/acs.jmedchem.1c00855] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The functions of the bromodomain and extra terminal (BET) family of proteins have been implicated in a wide range of diseases, particularly in the oncology and immuno-inflammatory areas, and several inhibitors are under investigation in the clinic. To mitigate the risk of attrition of these compounds due to structurally related toxicity findings, additional molecules from distinct chemical series were required. Here we describe the structure- and property-based optimization of the in vivo tool molecule I-BET151 toward I-BET282E, a molecule with properties suitable for progression into clinical studies.
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Affiliation(s)
- Katherine L Jones
- GlaxoSmithKline, Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire, SG1 2NY, U.K
| | - Dominic M Beaumont
- GlaxoSmithKline, Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire, SG1 2NY, U.K
| | - Sharon G Bernard
- GlaxoSmithKline, Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire, SG1 2NY, U.K
| | - Rino A Bit
- GlaxoSmithKline, Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire, SG1 2NY, U.K
| | - Simon P Campbell
- GlaxoSmithKline, Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire, SG1 2NY, U.K
| | - Chun-Wa Chung
- GlaxoSmithKline, Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire, SG1 2NY, U.K
| | - Leanne Cutler
- GlaxoSmithKline, Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire, SG1 2NY, U.K
| | - Emmanuel H Demont
- GlaxoSmithKline, Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire, SG1 2NY, U.K
| | - Kate Dennis
- GlaxoSmithKline, Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire, SG1 2NY, U.K
| | - Laurie Gordon
- GlaxoSmithKline, Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire, SG1 2NY, U.K
| | - James R Gray
- GlaxoSmithKline, Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire, SG1 2NY, U.K
| | - Michael V Haase
- GlaxoSmithKline, Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire, SG1 2NY, U.K
| | - Antonia J Lewis
- GlaxoSmithKline, Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire, SG1 2NY, U.K
| | - Scott McCleary
- GlaxoSmithKline, Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire, SG1 2NY, U.K
| | - Darren J Mitchell
- GlaxoSmithKline, Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire, SG1 2NY, U.K
| | - Susanne M Moore
- GlaxoSmithKline, Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire, SG1 2NY, U.K
| | - Nigel Parr
- GlaxoSmithKline, Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire, SG1 2NY, U.K
| | - Olivia J Robb
- GlaxoSmithKline, Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire, SG1 2NY, U.K
| | - Nicholas Smithers
- GlaxoSmithKline, Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire, SG1 2NY, U.K
| | - Peter E Soden
- GlaxoSmithKline, Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire, SG1 2NY, U.K
| | - Colin J Suckling
- Department of Pure & Applied Chemistry, University of Strathclyde, Glasgow, G1 1XL, U.K
| | - Simon Taylor
- GlaxoSmithKline, Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire, SG1 2NY, U.K
| | - Ann L Walker
- GlaxoSmithKline, Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire, SG1 2NY, U.K
| | - Robert J Watson
- GlaxoSmithKline, Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire, SG1 2NY, U.K
| | - Rab K Prinjha
- GlaxoSmithKline, Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire, SG1 2NY, U.K
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11
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Gaikwad NB, Bansod S, Mara A, Garise R, Srinivas N, Godugu C, Yaddanapudi VM. Design, synthesis, and biological evaluation of N-(4-substituted)-3-phenylisoxazolo[5,4-d]pyrimidin-4-amine derivatives as apoptosis-inducing cytotoxic agents. Bioorg Med Chem Lett 2021; 49:128294. [PMID: 34333139 DOI: 10.1016/j.bmcl.2021.128294] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 07/22/2021] [Accepted: 07/24/2021] [Indexed: 11/25/2022]
Abstract
A library of new 3-phenylisoxazolo[5,4-d]pyrimidines (8-10) was designed based on a scaffold hybridization technique incorporating the important pharmacophoric features of 4-aminopyrimidine and phenyl isoxazole scaffold which is renowned for its BET inhibition activity. The designed molecules were synthesized and evaluated with the NCI-60 cell line panel. Examination by NCI-60 cell lines at single-dose and the five-dose study showed that compound 10h exhibited promising growth inhibitory effects with GI50 values on various cancer cell lines such as HCT-15 (Colon Cancer)-0.0221 μM, MDA-MB-435 (Melanoma) - 0.0318 μM, SNB-75(CNS Cancer)-0.0263 μM, and MCF7 (Breast Cancer)-0.0372 μM. Further studies to know the mechanism of action of 10h based on the phase-contrast microscopic evaluation, DAPI, acridine orange/ethidium bromide (AO/EB) staining, and annexin V-FITC assays revealed that elevation in the intracellular ROS leads to alteration in mitochondrial membrane potential which in turn induced the apoptosis in BT-474 cancer cells, which could be the plausible mechanism of action for compound 10h.
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Affiliation(s)
- Nikhil Baliram Gaikwad
- Department of Chemical Sciences, National Institute of Pharmaceutical Education and Research (NIPER), Balanagar, Hyderabad, Telangana 500037, India
| | - Sapana Bansod
- Department of Biological Sciences, National Institute of Pharmaceutical Education and Research (NIPER), Balanagar, Hyderabad, Telangana 500037, India
| | - Alekhya Mara
- Department of Chemical Sciences, National Institute of Pharmaceutical Education and Research (NIPER), Balanagar, Hyderabad, Telangana 500037, India
| | - Ramana Garise
- Department of Chemical Sciences, National Institute of Pharmaceutical Education and Research (NIPER), Balanagar, Hyderabad, Telangana 500037, India
| | - Nanduri Srinivas
- Department of Chemical Sciences, National Institute of Pharmaceutical Education and Research (NIPER), Balanagar, Hyderabad, Telangana 500037, India
| | - Chandraiah Godugu
- Department of Biological Sciences, National Institute of Pharmaceutical Education and Research (NIPER), Balanagar, Hyderabad, Telangana 500037, India
| | - Venkata Madhavi Yaddanapudi
- Department of Chemical Sciences, National Institute of Pharmaceutical Education and Research (NIPER), Balanagar, Hyderabad, Telangana 500037, India.
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12
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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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13
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Quinlan RBA, Brennan PE. Chemogenomics for drug discovery: clinical molecules from open access chemical probes. RSC Chem Biol 2021; 2:759-795. [PMID: 34458810 PMCID: PMC8341094 DOI: 10.1039/d1cb00016k] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 03/25/2021] [Indexed: 12/12/2022] Open
Abstract
In recent years chemical probes have proved valuable tools for the validation of disease-modifying targets, facilitating investigation of target function, safety, and translation. Whilst probes and drugs often differ in their properties, there is a belief that chemical probes are useful for translational studies and can accelerate the drug discovery process by providing a starting point for small molecule drugs. This review seeks to describe clinical candidates that have been inspired by, or derived from, chemical probes, and the process behind their development. By focusing primarily on examples of probes developed by the Structural Genomics Consortium, we examine a variety of epigenetic modulators along with other classes of probe.
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Affiliation(s)
- Robert B A Quinlan
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford Old Road Campus Oxford OX3 7FZ UK
| | - Paul E Brennan
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford Old Road Campus Oxford OX3 7FZ UK
- Alzheimer's Research (UK) Oxford Drug Discovery Institute, Nuffield Department of Medicine, University of Oxford Oxford OX3 7FZ UK
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14
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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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15
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Neha K, Wakode S. Contemporary advances of cyclic molecules proposed for inflammation. Eur J Med Chem 2021; 221:113493. [PMID: 34029774 DOI: 10.1016/j.ejmech.2021.113493] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 04/18/2021] [Accepted: 04/19/2021] [Indexed: 12/15/2022]
Abstract
This review stretches insight about the advancement (2011-2021) of synthesized non-heterocyclic, heterocyclic and natural occurring cyclic molecules for inflammation. While inflammation is very significant in the abolition of pathogens and other causes of soreness, a protracted inflammatory procedure takes to outcomes in chronic disease that might finally affect in organ failure or damage. Thus, restraining the provocative process by the use of anti-inflammatory agents is chief in controlling this damage. It also reveals other pursuit along with their anti-inflammatory activity. Molecular docking studies represent most suitable PDB (Protein Data Bank) ID for the synthesized heterocyclic molecules with their selective inhibitor. It discusses the findings presented in recent research papers and provides understanding to researchers intended for the growth of newer combinations/molecules having littler side things.
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Affiliation(s)
- Kumari Neha
- Department of Pharmaceutical Chemistry, Delhi Institute of Pharmaceutical Sciences and Research (DIPSAR), DPSR University, New Delhi, India
| | - Sharad Wakode
- Department of Pharmaceutical Chemistry, Delhi Institute of Pharmaceutical Sciences and Research (DIPSAR), DPSR University, New Delhi, India.
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16
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Feng Z, Chen A, Shi J, Zhou D, Shi W, Qiu Q, Liu X, Huang W, Li J, Qian H, Zhang W. Design, synthesis, and biological activity evaluation of a series of novel sulfonamide derivatives as BRD4 inhibitors against acute myeloid leukemia. Bioorg Chem 2021; 111:104849. [PMID: 33798846 DOI: 10.1016/j.bioorg.2021.104849] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2020] [Revised: 03/18/2021] [Accepted: 03/19/2021] [Indexed: 12/12/2022]
Abstract
Accumulating researches have contributed much effect to discover novel chemotherapeutic drug for leukemia with expeditious curative effect, of which bromodomain-containing protein 4 (BRD4) inhibitor is considered as a eutherapeutic drug which has presented efficient cell proliferation suppression effect. In this study, we disclosed a series of phenylisoxazole sulfonamide derivatives as potent BRD4 inhibitors. Especially, compound 58 exhibited robust inhibitory potency toward BRD4-BD1 and BRD4-BD2 with IC50 values of 70 and 140 nM, respectively. In addition, compound 58 significantly suppressed cell proliferation of leukemia cell lines HL-60 and MV4-11 with IC50 values of 1.21 and 0.15 μM. In-depth study of the biological mechanism of compound 58 exerted its tumor suppression effect via down-regulating the level of oncogene c-myc. Moreover, in vivo pharmacokinetics (PK) study was conducted and the results demonstrated better pharmacokinetics features versus (+)-JQ1. In summary, our study discovers that compound 58 represents as a novel BRD4 inhibitor for further investigation in development of leukemia inhibitor with potentiality.
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Affiliation(s)
- Ziying Feng
- Center of Drug Discovery, State Key Laboratory of Natural Medicines, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing 210009, PR China
| | - Aiping Chen
- College of Pharmacy, Nanjing University of Chinese Medicine, 138 Xianlin Avenue, Nanjing 210023, PR China; Center for Drug Evaluation, NMPA, 128 Jianguo Road, Beijing 100022, PR China
| | - Jing Shi
- Center for Drug Evaluation, NMPA, 128 Jianguo Road, Beijing 100022, PR China
| | - Daoguang Zhou
- Center of Drug Discovery, State Key Laboratory of Natural Medicines, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing 210009, PR China
| | - Wei Shi
- Center of Drug Discovery, State Key Laboratory of Natural Medicines, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing 210009, PR China
| | - Qianqian Qiu
- Center of Drug Discovery, State Key Laboratory of Natural Medicines, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing 210009, PR China
| | - Xinhong Liu
- Center of Drug Discovery, State Key Laboratory of Natural Medicines, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing 210009, PR China
| | - Wenlong Huang
- Center of Drug Discovery, State Key Laboratory of Natural Medicines, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing 210009, PR China
| | - Jieming Li
- Henan University of Traditional Chinese Medicine, Zhengzhou, 450046, Henan, PR China.
| | - Hai Qian
- Center of Drug Discovery, State Key Laboratory of Natural Medicines, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing 210009, PR China; Jiangsu Key Laboratory of Drug Discovery for Metabolic Disease, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing 210009, PR China.
| | - Wenjie Zhang
- Center of Drug Discovery, State Key Laboratory of Natural Medicines, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing 210009, PR China; Jiangsu Key Laboratory of Drug Discovery for Metabolic Disease, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing 210009, PR China.
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17
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Hong RS, Mattei A, Sheikh AY, Bhardwaj RM, Bellucci MA, McDaniel KF, Pierce MO, Sun G, Li S, Wang L, Mondal S, Ji J, Borchardt TB. Novel Physics-Based Ensemble Modeling Approach That Utilizes 3D Molecular Conformation and Packing to Access Aqueous Thermodynamic Solubility: A Case Study of Orally Available Bromodomain and Extraterminal Domain Inhibitor Lead Optimization Series. J Chem Inf Model 2021; 61:1412-1426. [PMID: 33661005 DOI: 10.1021/acs.jcim.0c01410] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Drug design with patient centricity for ease of administration and pill burden requires robust understanding of the impact of chemical modifications on relevant physicochemical properties early in lead optimization. To this end, we have developed a physics-based ensemble approach to predict aqueous thermodynamic crystalline solubility, with a 2D chemical structure as the input. Predictions for the bromodomain and extraterminal domain (BET) inhibitor series show very close match (0.5 log unit) with measured thermodynamic solubility for cases with low crystal anisotropy and good match (1 log unit) for high anisotropy structures. The importance of thermodynamic solubility is clearly demonstrated by up to a 4 log unit drop in solubility compared to kinetic (amorphous) solubility in some cases and implications thereof, for instance on human dose. We have also demonstrated that incorporating predicted crystal structures in thermodynamic solubility prediction is necessary to differentiate (up to 4 log unit) between solubility of molecules within the series. Finally, our physics-based ensemble approach provides valuable structural insights into the origins of 3-D conformational landscapes, crystal polymorphism, and anisotropy that can be leveraged for both drug design and development.
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Affiliation(s)
- Richard S Hong
- Research & Development, AbbVie Inc., 1 N Waukegan Road, North Chicago, Illinois 60064, United States
| | - Alessandra Mattei
- Research & Development, AbbVie Inc., 1 N Waukegan Road, North Chicago, Illinois 60064, United States
| | - Ahmad Y Sheikh
- Research & Development, AbbVie Inc., 1 N Waukegan Road, North Chicago, Illinois 60064, United States
| | - Rajni Miglani Bhardwaj
- Research & Development, AbbVie Inc., 1 N Waukegan Road, North Chicago, Illinois 60064, United States
| | - Michael A Bellucci
- XtalPi, Inc., 245 Main Street, Cambridge, Massachusetts 02142, United States
| | - Keith F McDaniel
- Research & Development, AbbVie Inc., 1 N Waukegan Road, North Chicago, Illinois 60064, United States
| | - M Olivia Pierce
- Schrödinger Inc., 120 W 45th Street, New York, New York 10036, United States
| | - Guangxu Sun
- XtalPi, Inc., 245 Main Street, Cambridge, Massachusetts 02142, United States
| | - Sizhu Li
- XtalPi, Inc., 245 Main Street, Cambridge, Massachusetts 02142, United States
| | - Lingle Wang
- Schrödinger Inc., 120 W 45th Street, New York, New York 10036, United States
| | - Sayan Mondal
- Schrödinger Inc., 120 W 45th Street, New York, New York 10036, United States
| | - Jianguo Ji
- Research & Development, AbbVie Inc., 1 N Waukegan Road, North Chicago, Illinois 60064, United States
| | - Thomas B Borchardt
- Research & Development, AbbVie Inc., 1 N Waukegan Road, North Chicago, Illinois 60064, United States
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18
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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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19
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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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20
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Prieto-Martínez FD, Medina-Franco JL. Current advances on the development of BET inhibitors: insights from computational methods. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2020; 122:127-180. [PMID: 32951810 DOI: 10.1016/bs.apcsb.2020.06.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Epigenetics was coined almost 70 years ago for the description of heritable phenotype without altering DNA sequences. Research on the field has uncovered significant roles of such mechanisms, that account for the biogenesis of several diseases. Further studies have led the way for drug development which targets epi-enzymes, mainly for cancer treatment. Of the numerous epi-targets involved with histone acetylation, bromodomains have captured the spotlight of drug discovery focused on novel therapies. However, due to high sequence identity, the development of potent and selective inhibitors poses a significant challenge. Herein, we discuss recent computational developments on BET inhibitors and other methods that may be applied for drug discovery in general. As a proof-of-concept, we discuss a virtual screening to identify novel BET inhibitors based on coumarin derivatives. From public data, we identified putative structure-activity relationships of coumarin scaffold and propose R-group modifications for BET selectivity. Results showed that the optimization and design of novel coumarins could be further explored.
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Affiliation(s)
- Fernando D Prieto-Martínez
- Department of Pharmacy, School of Chemistry, National Autonomous University of Mexico, Mexico City, Mexico
| | - José L Medina-Franco
- Department of Pharmacy, School of Chemistry, National Autonomous University of Mexico, Mexico City, Mexico
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21
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The main directions and recent trends in the synthesis and use of isoxazoles. Chem Heterocycl Compd (N Y) 2020. [DOI: 10.1007/s10593-020-02718-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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22
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Dorababu A. Pharmacology Profile of Recently Developed Multi‐Functional Azoles; SAR‐Based Predictive Structural Modification. ChemistrySelect 2020. [DOI: 10.1002/slct.202000294] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Atukuri Dorababu
- Department of Studies in ChemistrySRMPP Govt. First Grade College Huvinahadagali 583219, Karnataka India
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23
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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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24
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Wellaway CR, Amans D, Bamborough P, Barnett H, Bit RA, Brown JA, Carlson NR, Chung CW, Cooper AWJ, Craggs PD, Davis RP, Dean TW, Evans JP, Gordon L, Harada IL, Hirst DJ, Humphreys PG, Jones KL, Lewis AJ, Lindon MJ, Lugo D, Mahmood M, McCleary S, Medeiros P, Mitchell DJ, O’Sullivan M, Le Gall A, Patel VK, Patten C, Poole DL, Shah RR, Smith JE, Stafford KAJ, Thomas PJ, Vimal M, Wall ID, Watson RJ, Wellaway N, Yao G, Prinjha RK. Discovery of a Bromodomain and Extraterminal Inhibitor with a Low Predicted Human Dose through Synergistic Use of Encoded Library Technology and Fragment Screening. J Med Chem 2020; 63:714-746. [DOI: 10.1021/acs.jmedchem.9b01670] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
| | - Dominique Amans
- GSK, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Paul Bamborough
- GSK, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Heather Barnett
- GSK, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Rino A. Bit
- GSK, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Jack A. Brown
- GSK, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Neil R. Carlson
- GSK, 200 Cambridge Park Drive, Cambridge, Massachusetts 02140, United States
| | - Chun-wa Chung
- GSK, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, U.K
| | | | - Peter D. Craggs
- GSK, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Robert P. Davis
- GSK, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Tony W. Dean
- GSK, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, U.K
| | - John P. Evans
- GSK, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Laurie Gordon
- GSK, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, U.K
| | | | - David J. Hirst
- GSK, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, U.K
| | | | | | | | | | - Dave Lugo
- GSK, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Mahnoor Mahmood
- GSK, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Scott McCleary
- GSK, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Patricia Medeiros
- GSK, 200 Cambridge Park Drive, Cambridge, Massachusetts 02140, United States
| | | | | | - Armelle Le Gall
- GSK, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, U.K
| | | | - Chris Patten
- GSK, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Darren L. Poole
- GSK, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Rishi R. Shah
- GSK, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Jane E. Smith
- GSK, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, U.K
| | | | | | - Mythily Vimal
- GSK, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, U.K
| | - Ian D. Wall
- GSK, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, U.K
| | | | | | - Gang Yao
- GSK, 200 Cambridge Park Drive, Cambridge, Massachusetts 02140, United States
| | - Rab K. Prinjha
- GSK, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, U.K
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25
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Alonso VL, Tavernelli LE, Pezza A, Cribb P, Ritagliati C, Serra E. Aim for the Readers! Bromodomains As New Targets Against Chagas’ Disease. Curr Med Chem 2019; 26:6544-6563. [DOI: 10.2174/0929867325666181031132007] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Revised: 10/04/2018] [Accepted: 10/08/2018] [Indexed: 12/11/2022]
Abstract
Bromodomains recognize and bind acetyl-lysine residues present in histone and non-histone
proteins in a specific manner. In the last decade they have raised as attractive targets for drug discovery
because the miss-regulation of human bromodomains was discovered to be involved in the development
of a large spectrum of diseases. However, targeting eukaryotic pathogens bromodomains
continues to be almost unexplored. We and others have reported the essentiality of diverse bromodomain-
containing proteins in protozoa, offering a new opportunity for the development of antiparasitic
drugs, especially for Trypansoma cruzi, the causative agent of Chagas’ disease. Mammalian bromodomains
were classified in eight groups based on sequence similarity but parasitic bromodomains are very
divergent proteins and are hard to assign them to any of these groups, suggesting that selective inhibitors
can be obtained. In this review, we describe the importance of lysine acetylation and bromodomains
in T. cruzi as well as the current knowledge on mammalian bromodomains. Also, we summarize
the myriad of small-molecules under study to treat different pathologies and which of them have been
tested in trypanosomatids and other protozoa. All the information available led us to propose that
T. cruzi bromodomains should be considered as important potential targets and the search for smallmolecules
to inhibit them should be empowered.
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Affiliation(s)
- Victoria Lucia Alonso
- Facultad de Ciencias Bioquimicas y Farmaceuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | | | - Alejandro Pezza
- Instituto de Biologia Molecular y Celular de Rosario (IBR-CONICET), Rosario, Argentina
| | - Pamela Cribb
- Instituto de Biologia Molecular y Celular de Rosario (IBR-CONICET), Rosario, Argentina
| | - Carla Ritagliati
- Instituto de Biologia Molecular y Celular de Rosario (IBR-CONICET), Rosario, Argentina
| | - Esteban Serra
- Instituto de Biologia Molecular y Celular de Rosario (IBR-CONICET), Rosario, Argentina
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26
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Schiedel M, Moroglu M, Ascough DMH, Chamberlain AER, Kamps JJAG, Sekirnik AR, Conway SJ. Chemical Epigenetics: The Impact of Chemical and Chemical Biology Techniques on Bromodomain Target Validation. Angew Chem Int Ed Engl 2019; 58:17930-17952. [DOI: 10.1002/anie.201812164] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Revised: 01/08/2019] [Indexed: 12/22/2022]
Affiliation(s)
- Matthias Schiedel
- Department of ChemistryChemistry Research LaboratoryUniversity of Oxford Mansfield Road Oxford OX1 3TA UK
| | - Mustafa Moroglu
- Department of ChemistryChemistry Research LaboratoryUniversity of Oxford Mansfield Road Oxford OX1 3TA UK
| | - David M. H. Ascough
- Department of ChemistryChemistry Research LaboratoryUniversity of Oxford Mansfield Road Oxford OX1 3TA UK
| | - Anna E. R. Chamberlain
- Department of ChemistryChemistry Research LaboratoryUniversity of Oxford Mansfield Road Oxford OX1 3TA UK
| | - Jos J. A. G. Kamps
- Department of ChemistryChemistry Research LaboratoryUniversity of Oxford Mansfield Road Oxford OX1 3TA UK
| | - Angelina R. Sekirnik
- Department of ChemistryChemistry Research LaboratoryUniversity of Oxford Mansfield Road Oxford OX1 3TA UK
| | - Stuart J. Conway
- Department of ChemistryChemistry Research LaboratoryUniversity of Oxford Mansfield Road Oxford OX1 3TA UK
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27
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Hilton-Proctor J, Ilyichova O, Zheng Z, Jennings I, Johnstone R, Shortt J, Mountford S, Scanlon M, Thompson P. Synthesis and elaboration of N-methylpyrrolidone as an acetamide fragment substitute in bromodomain inhibition. Bioorg Med Chem 2019; 27:115157. [DOI: 10.1016/j.bmc.2019.115157] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 10/07/2019] [Accepted: 10/08/2019] [Indexed: 01/24/2023]
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28
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Schiedel M, Moroglu M, Ascough DMH, Chamberlain AER, Kamps JJAG, Sekirnik AR, Conway SJ. Chemische Epigenetik: der Einfluss chemischer und chemo‐biologischer Techniken auf die Zielstruktur‐Validierung von Bromodomänen. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201812164] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Matthias Schiedel
- Department of ChemistryChemistry Research LaboratoryUniversity of Oxford Mansfield Road Oxford OX1 3TA Großbritannien
| | - Mustafa Moroglu
- Department of ChemistryChemistry Research LaboratoryUniversity of Oxford Mansfield Road Oxford OX1 3TA Großbritannien
| | - David M. H. Ascough
- Department of ChemistryChemistry Research LaboratoryUniversity of Oxford Mansfield Road Oxford OX1 3TA Großbritannien
| | - Anna E. R. Chamberlain
- Department of ChemistryChemistry Research LaboratoryUniversity of Oxford Mansfield Road Oxford OX1 3TA Großbritannien
| | - Jos J. A. G. Kamps
- Department of ChemistryChemistry Research LaboratoryUniversity of Oxford Mansfield Road Oxford OX1 3TA Großbritannien
| | - Angelina R. Sekirnik
- Department of ChemistryChemistry Research LaboratoryUniversity of Oxford Mansfield Road Oxford OX1 3TA Großbritannien
| | - Stuart J. Conway
- Department of ChemistryChemistry Research LaboratoryUniversity of Oxford Mansfield Road Oxford OX1 3TA Großbritannien
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29
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Barak DS, Dahatonde DJ, Batra S. Microwave‐Assisted Metal‐Free Decarboxylative Iodination/Bromination of Isoxazole‐4‐carboxylic Acids. ASIAN J ORG CHEM 2019. [DOI: 10.1002/ajoc.201900572] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Dinesh S. Barak
- Medicinal and Process Chemistry DivisionCSIR-Central Drug Research Institute, Sector 10, Jankipuram Extension Sitapur Road Lucknow 226031, Uttar Pradesh India
| | - Dipak J. Dahatonde
- Medicinal and Process Chemistry DivisionCSIR-Central Drug Research Institute, Sector 10, Jankipuram Extension Sitapur Road Lucknow 226031, Uttar Pradesh India
| | - Sanjay Batra
- Medicinal and Process Chemistry DivisionCSIR-Central Drug Research Institute, Sector 10, Jankipuram Extension Sitapur Road Lucknow 226031, Uttar Pradesh India
- Academy of Scientific and Innovative ResearchCSIR- Human Resource Development Centre (CSIR-HRDC) Campus, Sector 19, Kamla Nehru Nagar Ghaziabad- 201002, Uttar Pradesh India
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30
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Jiang X, Yu J, Zhou Z, Kongsted J, Song Y, Pannecouque C, De Clercq E, Kang D, Poongavanam V, Liu X, Zhan P. Molecular design opportunities presented by solvent‐exposed regions of target proteins. Med Res Rev 2019; 39:2194-2238. [DOI: 10.1002/med.21581] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2018] [Revised: 03/09/2019] [Accepted: 03/16/2019] [Indexed: 12/24/2022]
Affiliation(s)
- Xiangyi Jiang
- Department of Medicinal ChemistryKey Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University Jinan Shandong People's Republic of China
| | - Ji Yu
- Department of Medicinal ChemistryKey Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University Jinan Shandong People's Republic of China
| | - Zhongxia Zhou
- Department of Medicinal ChemistryKey Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University Jinan Shandong People's Republic of China
| | - Jacob Kongsted
- Department of Physics, Chemistry and PharmacyUniversity of Southern Denmark Odense Denmark
| | - Yuning Song
- Department of Clinical PharmacyQilu Hospital of Shandong University Jinan China
| | - Christophe Pannecouque
- Rega Institute for Medical ResearchLaboratory of Virology and Chemotherapy Leuven Belgium
| | - Erik De Clercq
- Rega Institute for Medical ResearchLaboratory of Virology and Chemotherapy Leuven Belgium
| | - Dongwei Kang
- Department of Medicinal ChemistryKey Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University Jinan Shandong People's Republic of China
| | | | - Xinyong Liu
- Department of Medicinal ChemistryKey Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University Jinan Shandong People's Republic of China
| | - Peng Zhan
- Department of Medicinal ChemistryKey Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University Jinan Shandong People's Republic of China
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31
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Huang B, Chen W, Zhao T, Li Z, Jiang X, Ginex T, Vílchez D, Luque FJ, Kang D, Gao P, Zhang J, Tian Y, Daelemans D, De Clercq E, Pannecouque C, Zhan P, Liu X. Exploiting the Tolerant Region I of the Non-Nucleoside Reverse Transcriptase Inhibitor (NNRTI) Binding Pocket: Discovery of Potent Diarylpyrimidine-Typed HIV-1 NNRTIs against Wild-Type and E138K Mutant Virus with Significantly Improved Water Solubility and Favorable Safety Profiles. J Med Chem 2019; 62:2083-2098. [PMID: 30721060 DOI: 10.1021/acs.jmedchem.8b01729] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Boshi Huang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, PR China
| | - Wenmin Chen
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, PR China
| | - Tong Zhao
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, PR China
| | - Zhenyu Li
- Department of Pharmacy, Shandong Provincial Hospital Affiliated to Shandong University, Jinan 250021 Shandong, China
| | - Xiangyi Jiang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, PR China
| | - Tiziana Ginex
- Department of Nutrition, Food Science and Gastronomy, Faculty of Pharmacy, Campus Torribera, Institute of Biomedicine (IBUB) and Institute of Theoretical and Computational Chemistry (IQTCUB), University of Barcelona, 08921 Santa Coloma de Gramenet, Spain
| | - David Vílchez
- Department of Nutrition, Food Science and Gastronomy, Faculty of Pharmacy, Campus Torribera, Institute of Biomedicine (IBUB) and Institute of Theoretical and Computational Chemistry (IQTCUB), University of Barcelona, 08921 Santa Coloma de Gramenet, Spain
| | - Francisco Javier Luque
- Department of Nutrition, Food Science and Gastronomy, Faculty of Pharmacy, Campus Torribera, Institute of Biomedicine (IBUB) and Institute of Theoretical and Computational Chemistry (IQTCUB), University of Barcelona, 08921 Santa Coloma de Gramenet, Spain
| | - Dongwei Kang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, PR China
| | - Ping Gao
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, PR China
| | - Jian Zhang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, PR China
| | - Ye Tian
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, PR China
| | - Dirk Daelemans
- Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, K.U. Leuven, Herestraat 49 Postbus 1043 (09.A097), B-3000 Leuven, Belgium
| | - Erik De Clercq
- Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, K.U. Leuven, Herestraat 49 Postbus 1043 (09.A097), B-3000 Leuven, Belgium
| | - Christophe Pannecouque
- Rega Institute for Medical Research, Laboratory of Virology and Chemotherapy, K.U. Leuven, Herestraat 49 Postbus 1043 (09.A097), B-3000 Leuven, Belgium
| | - Peng Zhan
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, PR China
| | - Xinyong Liu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, 44 West Culture Road, 250012 Jinan, Shandong, PR China
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32
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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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33
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Song LT, Tu J, Liu RR, Zhu M, Meng YJ, Zhai HL. Molecular mechanism study of several inhibitors binding to BRD9 bromodomain based on molecular simulations. J Biomol Struct Dyn 2018; 37:2970-2979. [DOI: 10.1080/07391102.2018.1502097] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Li Ting Song
- College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou, P. R. China
| | - Jing Tu
- College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou, P. R. China
| | - Rui Rui Liu
- College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou, P. R. China
| | - Min Zhu
- College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou, P. R. China
| | - Ya Jie Meng
- College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou, P. R. China
| | - Hong Lin Zhai
- College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou, P. R. China
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34
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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: 104] [Impact Index Per Article: 17.3] [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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35
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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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36
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Zhu B, Li F, Lu B, Chang J, Jiang Z. Organocatalytic Enantioselective Vinylogous Aldol Reaction of 5-Alkyl-4-Nitroisoxazoles to Paraformaldehyde. J Org Chem 2018; 83:11350-11358. [DOI: 10.1021/acs.joc.8b01573] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- Bo Zhu
- Henan Key Laboratory of Organic Functional Molecule and Drug Innovation, School of Chemistry and Chemical Engineering, Henan Normal University, Xinxiang, Henan 453007, P. R. China
| | - Fuyuan Li
- Key Laboratory of Natural Medicine and Immuno-Engineering of Henan Province, Henan University, Kaifeng, Henan 475004, P. R. China
| | - Bohua Lu
- Henan Key Laboratory of Organic Functional Molecule and Drug Innovation, School of Chemistry and Chemical Engineering, Henan Normal University, Xinxiang, Henan 453007, P. R. China
| | - Junbiao Chang
- Henan Key Laboratory of Organic Functional Molecule and Drug Innovation, School of Chemistry and Chemical Engineering, Henan Normal University, Xinxiang, Henan 453007, P. R. China
| | - Zhiyong Jiang
- Henan Key Laboratory of Organic Functional Molecule and Drug Innovation, School of Chemistry and Chemical Engineering, Henan Normal University, Xinxiang, Henan 453007, P. R. China
- Key Laboratory of Natural Medicine and Immuno-Engineering of Henan Province, Henan University, Kaifeng, Henan 475004, P. R. China
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37
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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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38
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Xue X, Zhang Y, Wang C, Zhang M, Xiang Q, Wang J, Wang A, Li C, Zhang C, Zou L, Wang R, Wu S, Lu Y, Chen H, Ding K, Li G, Xu Y. Benzoxazinone-containing 3,5-dimethylisoxazole derivatives as BET bromodomain inhibitors for treatment of castration-resistant prostate cancer. Eur J Med Chem 2018; 152:542-559. [PMID: 29758518 DOI: 10.1016/j.ejmech.2018.04.034] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 04/04/2018] [Accepted: 04/16/2018] [Indexed: 12/18/2022]
Abstract
The bromodomain and extra-terminal proteins (BET) have emerged as promising therapeutic targets for the treatment of castration-resistant prostate cancer (CRPC). We report the design, synthesis and evaluation of a new series of benzoxazinone-containing 3,5-dimethylisoxazole derivatives as selective BET inhibitors. One of the new compounds, (R)-12 (Y02234), binds to BRD4(1) with a Kd value of 110 nM and blocks bromodomain and acetyl lysine interactions with an IC50 value of 100 nM. It also exhibits selectivity for BET over non-BET bromodomain proteins and demonstrates reasonable anti-proliferation and colony formation inhibition effect in prostate cancer cell lines such as 22Rv1 and C4-2B. The BRD4 inhibitor (R)-12 also significantly suppresses the expression of ERG, Myc and AR target gene PSA at the mRNA level in prostate cancer cells. Treatment with (R)-12 significantly suppresses the tumor growth of prostate cancer (TGI = 70%) in a 22Rv1-derived xenograft model. These data suggest that compound (R)-12 is a promising lead compound for the development of a new class of therapeutics for the treatment of CRPC.
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Affiliation(s)
- Xiaoqian Xue
- Guangdong Provincial Key Laboratory of Biocomputing, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, Guangzhou Medical University, Guangzhou 511436 China; University of Chinese Academy of Sciences, No. 19 Yuquan Road, Beijing 100049, 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 510530, Guangzhou Medical University, Guangzhou 511436 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 510530, Guangzhou Medical University, Guangzhou 511436 China
| | - Maofeng Zhang
- Guangdong Provincial Key Laboratory of Biocomputing, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, Guangzhou Medical University, Guangzhou 511436 China; University of Chinese Academy of Sciences, No. 19 Yuquan Road, Beijing 100049, China
| | - Qiuping Xiang
- Guangdong Provincial Key Laboratory of Biocomputing, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, Guangzhou Medical University, Guangzhou 511436 China; University of Chinese Academy of Sciences, No. 19 Yuquan Road, Beijing 100049, China
| | - Junjian Wang
- Department of Biochemistry and Molecular Medicine, School of Medicine, University of California, Davis, Sacramento, CA, USA
| | - Anhui Wang
- State Key Laboratory of Fine Chemicals, School of Chemistry, Dalian University of Technology, Dalian 116023, China; Laboratory of Molecular Modeling and Design, State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Chenchang Li
- Guangdong Provincial Key Laboratory of Biocomputing, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, Guangzhou Medical University, Guangzhou 511436 China; School of Pharmaceutical Sciences, Jilin University, No. 1266 Fujin Road, Chaoyang District, Changchun, Jilin 130021, 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 510530, Guangzhou Medical University, Guangzhou 511436 China; School of Pharmaceutical Sciences, Jilin University, No. 1266 Fujin Road, Chaoyang District, Changchun, Jilin 130021, China
| | - Lingjiao Zou
- Guangdong Provincial Key Laboratory of Biocomputing, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, Guangzhou Medical University, Guangzhou 511436 China; University of Chinese Academy of Sciences, No. 19 Yuquan Road, Beijing 100049, China
| | - Rui Wang
- Guangdong Provincial Key Laboratory of Biocomputing, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, Guangzhou Medical University, Guangzhou 511436 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 510530, Guangzhou Medical University, Guangzhou 511436 China; School of Pharmaceutical Sciences, Jilin University, No. 1266 Fujin Road, Chaoyang District, Changchun, Jilin 130021, China
| | - Yongzhi Lu
- Guangdong Provincial Key Laboratory of Biocomputing, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, Guangzhou Medical University, Guangzhou 511436 China
| | - Hongwu Chen
- Department of Biochemistry and Molecular Medicine, School of Medicine, University of California, Davis, Sacramento, CA, USA
| | - Ke Ding
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Guohui Li
- Laboratory of Molecular Modeling and Design, State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, 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 510530, Guangzhou Medical University, Guangzhou 511436 China.
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39
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Research progress of selective small molecule bromodomain-containing protein 9 inhibitors. Future Med Chem 2018; 10:895-906. [PMID: 29620420 DOI: 10.4155/fmc-2017-0243] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The bromodomain proteins, known as the key targets in epigenetics, are 'readers' of acetylated lysine of histones. As a member of bromodomain proteins, bromodomain-containing protein 9 (BRD9) is a subunit of mammalian SWI/SNF chromatin remodeling complexes. However, the biological functions and the potential application in therapeutics of BRD9 remain ambiguous due to a lack of selective small molecule inhibitors of BRD9. Recently, series of chemical ligands against BRD9 were developed by different research institutes. Here, we reviewed the development and characterization of reported BRD9 inhibitors, which will be the foundation of further chemical design and biological evaluation.
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40
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Ali I, Conrad RJ, Verdin E, Ott M. Lysine Acetylation Goes Global: From Epigenetics to Metabolism and Therapeutics. Chem Rev 2018; 118:1216-1252. [PMID: 29405707 PMCID: PMC6609103 DOI: 10.1021/acs.chemrev.7b00181] [Citation(s) in RCA: 232] [Impact Index Per Article: 38.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Post-translational acetylation of lysine residues has emerged as a key regulatory mechanism in all eukaryotic organisms. Originally discovered in 1963 as a unique modification of histones, acetylation marks are now found on thousands of nonhistone proteins located in virtually every cellular compartment. Here we summarize key findings in the field of protein acetylation over the past 20 years with a focus on recent discoveries in nuclear, cytoplasmic, and mitochondrial compartments. Collectively, these findings have elevated protein acetylation as a major post-translational modification, underscoring its physiological relevance in gene regulation, cell signaling, metabolism, and disease.
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Affiliation(s)
- Ibraheem Ali
- Gladstone Institute of Virology and Immunology, San Francisco, California 94158, United States
- University of California, San Francisco, Department of Medicine, San Francisco, California 94158, United States
| | - Ryan J. Conrad
- Gladstone Institute of Virology and Immunology, San Francisco, California 94158, United States
- University of California, San Francisco, Department of Medicine, San Francisco, California 94158, United States
| | - Eric Verdin
- Buck Institute for Research on Aging, Novato, California 94945, United States
| | - Melanie Ott
- Gladstone Institute of Virology and Immunology, San Francisco, California 94158, United States
- University of California, San Francisco, Department of Medicine, San Francisco, California 94158, United States
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41
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Affiliation(s)
- Yanli Yin
- College of Bioengineering; Henan University of Technology; Zhengzhou Henan 450001 P.R. China
- Key Laboratory of Natural Medicine and Immuno-Engineering of Henan Province; Henan University; Kaifeng Henan 475004 P.R. China
| | - Zhiyong Jiang
- College of Bioengineering; Henan University of Technology; Zhengzhou Henan 450001 P.R. China
- Key Laboratory of Natural Medicine and Immuno-Engineering of Henan Province; Henan University; Kaifeng Henan 475004 P.R. China
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42
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Recognition of hyperacetylated N-terminus of H2AZ by TbBDF2 from Trypanosoma brucei. Biochem J 2017; 474:3817-3830. [DOI: 10.1042/bcj20170619] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Revised: 10/05/2017] [Accepted: 10/09/2017] [Indexed: 12/17/2022]
Abstract
Histone modification plays an important role in various biological processes, including gene expression regulation. Bromodomain, as one of histone readers, recognizes specifically the ε-N-lysine acetylation (KAc) of histone. Although the bromodomains and histone acetylation sites of Trypanosoma brucei (T. brucei), a lethal parasite responsible for sleeping sickness in human and nagana in cattle, have been identified, how acetylated histones are recognized by bromodomains is still unknown. Here, the bromodomain factor 2 (TbBDF2) from T. brucei was identified to be located in the nucleolus and bind to the hyperacetylated N-terminus of H2AZ which dimerizes with H2BV. The bromodomain of TbBDF2 (TbBDF2-BD) displays a conserved fold that comprises a left-handed bundle of four α-helices (αZ, αA, αB, αC), linked by loop regions of variable length (ZA and BC loops), which form the KAc-binding pocket. NMR chemical shift perturbation further revealed that TbBDF2-BD binds to the hyperacetylated N-terminus of H2AZ through its KAc-binding pocket. By structure-based virtual screening combining with the ITC experiment, a small molecule compound, GSK2801, was shown to have high affinity to TbBDF2-BD. GSK2801 and the hyperacetylated N-terminus of H2AZ have similar binding sites on TbBDF2-BD. In addition, GSK2801 competitively inhibits the hyperacetylated N-terminus of H2AZ binding to TbBDF2-BD. After treatment of GSK2801, cell growth was inhibited and localization of TbBDF2 was disrupted. Our results report a novel bromodomain-histone recognition by TbBDF2-BD and imply that TbBDF2 may serve as a potential chemotherapeutic target for the treatment of trypanosomiasis.
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43
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W Young D. Using Fragment Based Drug Discovery to Target Epigenetic Regulators in Cancer. ACTA ACUST UNITED AC 2017. [DOI: 10.15406/mojbb.2017.04.00062] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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44
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Allen B, Mehta S, Ember SWJ, Zhu JY, Schönbrunn E, Ayad NG, Schürer SC. Identification of a Novel Class of BRD4 Inhibitors by Computational Screening and Binding Simulations. ACS OMEGA 2017; 2:4760-4771. [PMID: 28884163 PMCID: PMC5579542 DOI: 10.1021/acsomega.7b00553] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Accepted: 07/27/2017] [Indexed: 06/07/2023]
Abstract
Computational screening is a method to prioritize small-molecule compounds based on the structural and biochemical attributes built from ligand and target information. Previously, we have developed a scalable virtual screening workflow to identify novel multitarget kinase/bromodomain inhibitors. In the current study, we identified several novel N-[3-(2-oxo-pyrrolidinyl)phenyl]-benzenesulfonamide derivatives that scored highly in our ensemble docking protocol. We quantified the binding affinity of these compounds for BRD4(BD1) biochemically and generated cocrystal structures, which were deposited in the Protein Data Bank. As the docking poses obtained in the virtual screening pipeline did not align with the experimental cocrystal structures, we evaluated the predictions of their precise binding modes by performing molecular dynamics (MD) simulations. The MD simulations closely reproduced the experimentally observed protein-ligand cocrystal binding conformations and interactions for all compounds. These results suggest a computational workflow to generate experimental-quality protein-ligand binding models, overcoming limitations of docking results due to receptor flexibility and incomplete sampling, as a useful starting point for the structure-based lead optimization of novel BRD4(BD1) inhibitors.
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Affiliation(s)
- Bryce
K. Allen
- Department
of Molecular and Cellular Pharmacology, Miller School
of Medicine, Center for Computational Science, Center for Therapeutic Innovation Miller School
of Medicine, Miami Project to Cure Paralysis, Department of Psychiatry and Behavioral
Sciences, Miller School of Medicine, and Sylvester Comprehensive Cancer Center,
Miller School of Medicine, University of
Miami, Miami, Florida 33136, United States
| | - Saurabh Mehta
- Department
of Molecular and Cellular Pharmacology, Miller School
of Medicine, Center for Computational Science, Center for Therapeutic Innovation Miller School
of Medicine, Miami Project to Cure Paralysis, Department of Psychiatry and Behavioral
Sciences, Miller School of Medicine, and Sylvester Comprehensive Cancer Center,
Miller School of Medicine, University of
Miami, Miami, Florida 33136, United States
- Department
of Applied Chemistry, Delhi
Technological University, Delhi 110042, India
| | - Stuart W. J. Ember
- Drug
Discovery Department, H. Lee Moffitt Cancer
Center and Research Institute, Tampa, Florida 33612-9416, United States
| | - Jin-Yi Zhu
- Drug
Discovery Department, H. Lee Moffitt Cancer
Center and Research Institute, Tampa, Florida 33612-9416, United States
| | - Ernst Schönbrunn
- Drug
Discovery Department, H. Lee Moffitt Cancer
Center and Research Institute, Tampa, Florida 33612-9416, United States
| | - Nagi G. Ayad
- Department
of Molecular and Cellular Pharmacology, Miller School
of Medicine, Center for Computational Science, Center for Therapeutic Innovation Miller School
of Medicine, Miami Project to Cure Paralysis, Department of Psychiatry and Behavioral
Sciences, Miller School of Medicine, and Sylvester Comprehensive Cancer Center,
Miller School of Medicine, University of
Miami, Miami, Florida 33136, United States
| | - Stephan C. Schürer
- Department
of Molecular and Cellular Pharmacology, Miller School
of Medicine, Center for Computational Science, Center for Therapeutic Innovation Miller School
of Medicine, Miami Project to Cure Paralysis, Department of Psychiatry and Behavioral
Sciences, Miller School of Medicine, and Sylvester Comprehensive Cancer Center,
Miller School of Medicine, University of
Miami, Miami, Florida 33136, United States
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45
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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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46
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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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47
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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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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: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
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Bromodomains
(BD) are readers of lysine acetylation marks present
in numerous proteins associated with chromatin. Here we describe a
dual inhibitor of the bromodomain and PHD finger (BRPF) family member
BRPF2 and the TATA box binding protein-associated factors TAF1 and
TAF1L. These proteins are found in large chromatin complexes and play
important roles in transcription regulation. The substituted benzoisoquinolinedione
series was identified by high-throughput screening, and subsequent
structure–activity relationship optimization allowed generation
of low nanomolar BRPF2 BD inhibitors with strong selectivity against
BRPF1 and BRPF3 BDs. In addition, a strong inhibition of TAF1/TAF1L
BD2 was measured for most derivatives. The best compound of the series
was BAY-299, which is a very potent, dual inhibitor with an IC50 of 67 nM for BRPF2 BD, 8 nM for TAF1 BD2, and 106 nM for
TAF1L BD2. Importantly, no activity was measured for BRD4 BDs. Furthermore,
cellular activity was evidenced using a BRPF2– or TAF1–histone
H3.3 or H4 interaction assay.
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Affiliation(s)
- Léa Bouché
- Drug Discovery, Bayer AG , Müllerstrasse 178, 13353 Berlin, Germany
| | - Clara D Christ
- Drug Discovery, Bayer AG , Müllerstrasse 178, 13353 Berlin, Germany
| | - Stephan Siegel
- Drug Discovery, Bayer AG , Müllerstrasse 178, 13353 Berlin, Germany
| | | | - Simon J Holton
- Drug Discovery, Bayer AG , Müllerstrasse 178, 13353 Berlin, Germany
| | - Oleg Fedorov
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford , Roosevelt Drive, Oxford OX3 7DQ, U.K.,Target Discovery Institute, Nuffield Department of Clinical Medicine, University of Oxford , Roosevelt Drive, Oxford OX3 7FZ, U.K
| | | | - Tatsuo Sugawara
- Drug Discovery, Bayer AG , Müllerstrasse 178, 13353 Berlin, Germany
| | - Detlef Stöckigt
- Drug Discovery, Bayer AG , Müllerstrasse 178, 13353 Berlin, Germany
| | - Cynthia Tallant
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford , Roosevelt Drive, Oxford OX3 7DQ, U.K.,Target Discovery Institute, Nuffield Department of Clinical Medicine, University of Oxford , Roosevelt Drive, Oxford OX3 7FZ, U.K
| | - James Bennett
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford , Roosevelt Drive, Oxford OX3 7DQ, U.K.,Target Discovery Institute, Nuffield Department of Clinical Medicine, University of Oxford , Roosevelt Drive, Oxford OX3 7FZ, U.K
| | - Octovia Monteiro
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford , Roosevelt Drive, Oxford OX3 7DQ, U.K.,Target Discovery Institute, Nuffield Department of Clinical Medicine, University of Oxford , Roosevelt Drive, Oxford OX3 7FZ, U.K
| | - Laura Díaz-Sáez
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford , Roosevelt Drive, Oxford OX3 7DQ, U.K.,Target Discovery Institute, Nuffield Department of Clinical Medicine, University of Oxford , Roosevelt Drive, Oxford OX3 7FZ, U.K
| | - Paulina Siejka
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford , Roosevelt Drive, Oxford OX3 7DQ, U.K.,Target Discovery Institute, Nuffield Department of Clinical Medicine, University of Oxford , Roosevelt Drive, Oxford OX3 7FZ, U.K
| | - Julia Meier
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford , Roosevelt Drive, Oxford OX3 7DQ, U.K
| | - Vera Pütter
- Drug Discovery, Bayer AG , Müllerstrasse 178, 13353 Berlin, Germany
| | - Jörg Weiske
- Drug Discovery, Bayer AG , Müllerstrasse 178, 13353 Berlin, Germany
| | - Susanne Müller
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford , Roosevelt Drive, Oxford OX3 7DQ, U.K.,Target Discovery Institute, Nuffield Department of Clinical Medicine, University of Oxford , Roosevelt Drive, Oxford OX3 7FZ, U.K
| | - Kilian V M Huber
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford , Roosevelt Drive, Oxford OX3 7DQ, U.K.,Target Discovery Institute, Nuffield Department of Clinical Medicine, University of Oxford , Roosevelt Drive, Oxford OX3 7FZ, U.K
| | - Ingo V Hartung
- Drug Discovery, Bayer AG , Müllerstrasse 178, 13353 Berlin, Germany
| | - Bernard Haendler
- Drug Discovery, Bayer AG , Müllerstrasse 178, 13353 Berlin, Germany
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49
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Padmanabhan B, Mathur S, Manjula R, Tripathi S. Bromodomain and extra-terminal (BET) family proteins: New therapeutic targets in major diseases. J Biosci 2017; 41:295-311. [PMID: 27240990 DOI: 10.1007/s12038-016-9600-6] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The bromodomains and extra-terminal domain (BET) family proteins recognize acetylated chromatin through their bromodomains (BDs) and help in regulating gene expression. BDs are chromatin 'readers': by interacting with acetylated lysines on the histone tails, they recruit chromatin-regulating proteins on the promoter region to regulate gene expression and repression. Extensive efforts have been employed by scientific communities worldwide to identify and develop potential inhibitors of BET family BDs to regulate protein expression by inhibiting acetylated histone (H3/H4) interactions. Several small molecule inhibitors have been reported, which not only have high affinity but also have high specificity to BET BDs. These developments make BET family proteins an important therapeutic targets for major diseases such as cancer, neurological disorders, obesity and inflammation. Here, we review and discuss the structural biology of BET family BDs and their applications in major diseases.
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Affiliation(s)
- Balasundaram Padmanabhan
- Department of Biophysics, National Institute of Mental Health and Neurosciences (NIMHANS), Bangalore 560 029, India
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50
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