1
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Strachowska M, Robaszkiewicz A. Characteristics of anticancer activity of CBP/p300 inhibitors - Features of their classes, intracellular targets and future perspectives of their application in cancer treatment. Pharmacol Ther 2024; 257:108636. [PMID: 38521246 DOI: 10.1016/j.pharmthera.2024.108636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 03/11/2024] [Accepted: 03/14/2024] [Indexed: 03/25/2024]
Abstract
Due to the contribution of highly homologous acetyltransferases CBP and p300 to transcription elevation of oncogenes and other cancer promoting factors, these enzymes emerge as possible epigenetic targets of anticancer therapy. Extensive efforts in search for small molecule inhibitors led to development of compounds targeting histone acetyltransferase catalytic domain or chromatin-interacting bromodomain of CBP/p300, as well as dual BET and CBP/p300 inhibitors. The promising anticancer efficacy in in vitro and mice models led CCS1477 and NEO2734 to clinical trials. However, none of the described inhibitors is perfectly specific to CBP/p300 since they share similarity of a key functional domains with other enzymes, which are critically associated with cancer progression and their antagonists demonstrate remarkable clinical efficacy in cancer therapy. Therefore, we revise the possible and clinically relevant off-targets of CBP/p300 inhibitors that can be blocked simultaneously with CBP/p300 thereby improving the anticancer potential of CBP/p300 inhibitors and pharmacokinetic predicting data such as absorption, distribution, metabolism, excretion (ADME) and toxicity.
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Affiliation(s)
- Magdalena Strachowska
- University of Lodz, Faculty of Biology and Environmental Protection, Department of General Biophysics, Pomorska 141/143, 90-236 Lodz, Poland; University of Lodz, Bio-Med-Chem Doctoral School of the University of Lodz and Lodz Institutes of the Polish Academy of Sciences, Banacha 12 /16, 90-237 Lodz, Poland.
| | - Agnieszka Robaszkiewicz
- University of Lodz, Faculty of Biology and Environmental Protection, Department of General Biophysics, Pomorska 141/143, 90-236 Lodz, Poland; Johns Hopkins University School of Medicine, Institute of Fundamental and Basic Research, 600 5(th) Street South, Saint Petersburg FL33701, United States of America.
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2
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Shi M, Zheng X, Zhou Y, Yin Y, Lu Z, Zou Z, Hu Y, Liang Y, Chen T, Yang Y, Jing M, Lei D, Yang P, Li X. Selectivity Mechanism of Pyrrolopyridone Analogues Targeting Bromodomain 2 of Bromodomain-Containing Protein 4 from Molecular Dynamics Simulations. ACS OMEGA 2023; 8:33658-33674. [PMID: 37744850 PMCID: PMC10515184 DOI: 10.1021/acsomega.3c03935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/04/2023] [Accepted: 08/25/2023] [Indexed: 09/26/2023]
Abstract
Bromodomain and extra-terminal domain (BET) proteins play an important role in epigenetic regulation and are linked to several diseases; therefore, they are interesting targets. BET has two bromodomains: bromodomain 1 (BD1) and BD2. Selective targeting of BD1 or BD2 may produce different activities and greater effects than pan-BD inhibitors. However, the selective mechanism of the specific core must be studied at the atomic level. This study determined the effectiveness of pyrrolopyridone analogues to selectively inhibit BD2 using a pan-BD inhibitor (ABBV-075) and a selective-BD2 inhibitor (ABBV-744). Molecular dynamics simulations and calculations of binding free energies were used to systematically study the selectivity of BD2 inhibition by the pyrrolopyridone analogues. Overall, the pyrrolopyridone analogue inhibitors targeting BD2 interacted mainly with the following amino acid pairs between bromodomain-containing protein 4 (BRD4)-BD1 and BRD4-BD2 complexes: I146/V439, N140/N433, D144/H437, P82/P375, V87/V380, D88/D381, and Y139/Y432. The pyrrolopyridone analogues targeting BRD4-BD2 were divided into five regions based on selectivity mechanism. These results suggest that the R3 and R5 regions of pyrrolopyridone analogues can be modified to improve the selectivity between BRD4-BD1 and BRD4-BD2. The selectivity of BD2 inhibition by pyrrolopyridone analogues can be used to design novel BD2 inhibitors based on a pyrrolopyridone core.
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Affiliation(s)
- Mingsong Shi
- NHC
Key Laboratory of Nuclear Technology Medical Transformation, Mianyang
Central Hospital, School of Medicine, University
of Electronic Science and Technology of China, Mianyang 621099, Sichuan, China
- Innovation
Center of Nursing Research, Nursing Key Laboratory of Sichuan Province,
West China Hospital, Sichuan University, Chengdu 610041, Sichuan, China
| | - Xueting Zheng
- NHC
Key Laboratory of Nuclear Technology Medical Transformation, Mianyang
Central Hospital, School of Medicine, University
of Electronic Science and Technology of China, Mianyang 621099, Sichuan, China
| | - Yan Zhou
- NHC
Key Laboratory of Nuclear Technology Medical Transformation, Mianyang
Central Hospital, School of Medicine, University
of Electronic Science and Technology of China, Mianyang 621099, Sichuan, China
| | - Yuan Yin
- NHC
Key Laboratory of Nuclear Technology Medical Transformation, Mianyang
Central Hospital, School of Medicine, University
of Electronic Science and Technology of China, Mianyang 621099, Sichuan, China
| | - Zhou Lu
- NHC
Key Laboratory of Nuclear Technology Medical Transformation, Mianyang
Central Hospital, School of Medicine, University
of Electronic Science and Technology of China, Mianyang 621099, Sichuan, China
| | - Zhiyan Zou
- NHC
Key Laboratory of Nuclear Technology Medical Transformation, Mianyang
Central Hospital, School of Medicine, University
of Electronic Science and Technology of China, Mianyang 621099, Sichuan, China
| | - Yan Hu
- NHC
Key Laboratory of Nuclear Technology Medical Transformation, Mianyang
Central Hospital, School of Medicine, University
of Electronic Science and Technology of China, Mianyang 621099, Sichuan, China
| | - Yuanyuan Liang
- NHC
Key Laboratory of Nuclear Technology Medical Transformation, Mianyang
Central Hospital, School of Medicine, University
of Electronic Science and Technology of China, Mianyang 621099, Sichuan, China
| | - Tingting Chen
- NHC
Key Laboratory of Nuclear Technology Medical Transformation, Mianyang
Central Hospital, School of Medicine, University
of Electronic Science and Technology of China, Mianyang 621099, Sichuan, China
| | - Yuhan Yang
- NHC
Key Laboratory of Nuclear Technology Medical Transformation, Mianyang
Central Hospital, School of Medicine, University
of Electronic Science and Technology of China, Mianyang 621099, Sichuan, China
| | - Meng Jing
- Department
of Pathology, Mianyang Central Hospital, School of Medicine, University of Electronic Science and Technology of
China, Mianyang 621099, Sichuan, China
| | - Dan Lei
- School
of Life Science and Engineering, Southwest
University of Science and Technology, Mianyang 621010, Sichuan, China
| | - Pei Yang
- Department
of Hepatobiliary Surgery, Mianyang Central Hospital, School of Medicine, University of Electronic Science and Technology of
China, Mianyang 621099, Sichuan, China
| | - Xiaoan Li
- NHC
Key Laboratory of Nuclear Technology Medical Transformation, Mianyang
Central Hospital, School of Medicine, University
of Electronic Science and Technology of China, Mianyang 621099, Sichuan, China
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3
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Sterling J, Baker JR, McCluskey A, Munoz L. Systematic literature review reveals suboptimal use of chemical probes in cell-based biomedical research. Nat Commun 2023; 14:3228. [PMID: 37270653 PMCID: PMC10239480 DOI: 10.1038/s41467-023-38952-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2022] [Accepted: 05/23/2023] [Indexed: 06/05/2023] Open
Abstract
Chemical probes have reached a prominent role in biomedical research, but their impact is governed by experimental design. To gain insight into the use of chemical probes, we conducted a systematic review of 662 publications, understood here as primary research articles, employing eight different chemical probes in cell-based research. We summarised (i) concentration(s) at which chemical probes were used in cell-based assays, (ii) inclusion of structurally matched target-inactive control compounds and (iii) orthogonal chemical probes. Here, we show that only 4% of analysed eligible publications used chemical probes within the recommended concentration range and included inactive compounds as well as orthogonal chemical probes. These findings indicate that the best practice with chemical probes is yet to be implemented in biomedical research. To achieve this, we propose 'the rule of two': At least two chemical probes (either orthogonal target-engaging probes, and/or a pair of a chemical probe and matched target-inactive compound) to be employed at recommended concentrations in every study.
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Affiliation(s)
- Jayden Sterling
- Faculty of Medicine and Health, Charles Perkins Centre, The University of Sydney, Camperdown, NSW, 2006, Australia
| | - Jennifer R Baker
- Discipline of Chemistry, School of Environmental and Life Sciences, The University of Newcastle, Callaghan, NSW, 2308, Australia
| | - Adam McCluskey
- Discipline of Chemistry, School of Environmental and Life Sciences, The University of Newcastle, Callaghan, NSW, 2308, Australia
| | - Lenka Munoz
- Faculty of Medicine and Health, Charles Perkins Centre, The University of Sydney, Camperdown, NSW, 2006, Australia.
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4
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Agnarelli A, Mitchell S, Caalim G, Wood CD, Milton‐Harris L, Chevassut T, West MJ, Mancini EJ. Dissecting the impact of bromodomain inhibitors on the Interferon Regulatory Factor 4-MYC oncogenic axis in multiple myeloma. Hematol Oncol 2022; 40:417-429. [PMID: 35544413 PMCID: PMC9543246 DOI: 10.1002/hon.3016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 04/19/2022] [Accepted: 05/06/2022] [Indexed: 11/21/2022]
Abstract
B-cell progenitor fate determinant interferon regulatory factor 4 (IRF4) exerts key roles in the pathogenesis and progression of multiple myeloma (MM), a currently incurable plasma cell malignancy. Aberrant expression of IRF4 and the establishment of a positive auto-regulatory loop with oncogene MYC, drives a MM specific gene-expression program leading to the abnormal expansion of malignant immature plasma cells. Targeting the IRF4-MYC oncogenic loop has the potential to provide a selective and effective therapy for MM. Here we evaluate the use of bromodomain inhibitors to target the IRF4-MYC axis through combined inhibition of their known epigenetic regulators, BRD4 and CBP/EP300. Although all inhibitors induced cell death, we found no synergistic effect of targeting both of these regulators on the viability of MM cell-lines. Importantly, for all inhibitors over a time period up to 72 h, we detected reduced IRF4 mRNA, but a limited decrease in IRF4 protein expression or mRNA levels of downstream target genes. This indicates that inhibitor-induced loss of cell viability is not mediated through reduced IRF4 protein expression, as previously proposed. Further analysis revealed a long half-life of IRF4 protein in MM cells. In support of our experimental observations, gene network modeling of MM suggests that bromodomain inhibition is exerted primarily through MYC and not IRF4. These findings suggest that despite the autofeedback positive regulatory loop between IRF4 and MYC, bromodomain inhibitors are not effective at targeting IRF4 in MM and that novel therapeutic strategies should focus on the direct inhibition or degradation of IRF4.
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Affiliation(s)
- Alessandro Agnarelli
- Biochemistry and BiomedicineSchool of Life SciencesUniversity of SussexBrightonUK
| | - Simon Mitchell
- Brighton and Sussex Medical SchoolUniversity of SussexBrightonUK
| | - Gillian Caalim
- Biochemistry and BiomedicineSchool of Life SciencesUniversity of SussexBrightonUK
| | - C. David Wood
- Biochemistry and BiomedicineSchool of Life SciencesUniversity of SussexBrightonUK
| | - Leanne Milton‐Harris
- Biochemistry and BiomedicineSchool of Life SciencesUniversity of SussexBrightonUK
| | | | - Michelle J. West
- Biochemistry and BiomedicineSchool of Life SciencesUniversity of SussexBrightonUK
| | - Erika J. Mancini
- Biochemistry and BiomedicineSchool of Life SciencesUniversity of SussexBrightonUK
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5
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Edmonds AK, Oakes CS, Hassell-Hart S, Bruyère D, Tizzard GJ, Coles SJ, Felix R, Maple HJ, Marsh GP, Spencer J. Scale-up and optimization of the synthesis of dual CBP/BRD4 inhibitor ISOX-DUAL. Org Biomol Chem 2022; 20:4021-4029. [PMID: 35506991 DOI: 10.1039/d2ob00609j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
ISOX-DUAL is a dual inhibitor of CBP/p300 (IC50 = 0.65 μM) and BRD4 (IC50 = 1.5 μM) bromodomains, and a useful chemical probe for epigenetic research. Aspects of the published synthetic route to this compound and its analogues are small-scale, poor-yielding or simply unamenable to scale-up without optimization. Herein we describe the development of a refined synthesis that circumvents the challenges of the original report, with notable improvements to several of the key synthetic transformations. Moreover, a general Suzuki Miyaura protocol for the late stage installation of alternative dimethyl-isoxazole acetyl-lysine (KAc) binding motifs is presented.
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Affiliation(s)
- Anthony K Edmonds
- Chemistry Department, School of Life Sciences, University of Sussex, Falmer, Brighton, BN1 9QJ, UK.
| | - Catherine S Oakes
- Bio-Techne (Tocris), The Watkins Building, Atlantic Road, Bristol, BS11 9QD, UK
| | - Storm Hassell-Hart
- Chemistry Department, School of Life Sciences, University of Sussex, Falmer, Brighton, BN1 9QJ, UK.
| | - Didier Bruyère
- Bio-Techne (Tocris), The Watkins Building, Atlantic Road, Bristol, BS11 9QD, UK
| | - Graham J Tizzard
- National Crystallography Service, School of Chemistry, University of Southampton, Southampton, SO17 1BJ, UK
| | - Simon J Coles
- National Crystallography Service, School of Chemistry, University of Southampton, Southampton, SO17 1BJ, UK
| | - Robert Felix
- Bio-Techne (Tocris), The Watkins Building, Atlantic Road, Bristol, BS11 9QD, UK
| | - Hannah J Maple
- Bio-Techne (Tocris), The Watkins Building, Atlantic Road, Bristol, BS11 9QD, UK
| | - Graham P Marsh
- Bio-Techne (Tocris), The Watkins Building, Atlantic Road, Bristol, BS11 9QD, UK
| | - John Spencer
- Chemistry Department, School of Life Sciences, University of Sussex, Falmer, Brighton, BN1 9QJ, UK. .,Sussex Drug Discovery Centre, School of Life Sciences, University of Sussex, Falmer, Brighton, BN1 9QJ, UK
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6
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Ghiboub M, Elfiky AMI, de Winther MPJ, Harker NR, Tough DF, de Jonge WJ. Selective Targeting of Epigenetic Readers and Histone Deacetylases in Autoimmune and Inflammatory Diseases: Recent Advances and Future Perspectives. J Pers Med 2021; 11:336. [PMID: 33922725 PMCID: PMC8145108 DOI: 10.3390/jpm11050336] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 04/16/2021] [Accepted: 04/19/2021] [Indexed: 02/07/2023] Open
Abstract
Histone deacetylases (HDACs) and bromodomain-containing proteins (BCPs) play a key role in chromatin remodeling. Based on their ability to regulate inducible gene expression in the context of inflammation and cancer, HDACs and BCPs have been the focus of drug discovery efforts, and numerous small-molecule inhibitors have been developed. However, dose-limiting toxicities of the first generation of inhibitors, which typically target multiple HDACs or BCPs, have limited translation to the clinic. Over the last decade, an increasing effort has been dedicated to designing class-, isoform-, or domain-specific HDAC or BCP inhibitors, as well as developing strategies for cell-specific targeted drug delivery. Selective inhibition of the epigenetic modulators is helping to elucidate the functions of individual epigenetic proteins and has the potential to yield better and safer therapeutic strategies. In accordance with this idea, several in vitro and in vivo studies have reported the ability of more selective HDAC/BCP inhibitors to recapitulate the beneficial effects of pan-inhibitors with less unwanted adverse events. In this review, we summarize the most recent advances with these strategies, discussing advantages and limitations of these approaches as well as some therapeutic perspectives, focusing on autoimmune and inflammatory diseases.
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Affiliation(s)
- Mohammed Ghiboub
- Tytgat Institute for Liver and Intestinal Research, Amsterdam Gastroenterology Endocrinology Metabolism Research Institute, Amsterdam University Medical Centers, University of Amsterdam, 1105 BK Amsterdam, The Netherlands; (M.G.); (A.M.I.E.)
- Adaptive Immunity Research Unit, Medicines Research Centre, GlaxoSmithKline, Stevenage SG1 2NY, UK; (N.R.H.); (D.F.T.)
| | - Ahmed M. I. Elfiky
- Tytgat Institute for Liver and Intestinal Research, Amsterdam Gastroenterology Endocrinology Metabolism Research Institute, Amsterdam University Medical Centers, University of Amsterdam, 1105 BK Amsterdam, The Netherlands; (M.G.); (A.M.I.E.)
- Adaptive Immunity Research Unit, Medicines Research Centre, GlaxoSmithKline, Stevenage SG1 2NY, UK; (N.R.H.); (D.F.T.)
| | - Menno P. J. de Winther
- Department of Medical Biochemistry, Amsterdam University Medical Centers, University of Amsterdam, 1105 AZ Amsterdam, The Netherlands;
- Department of Medicine, Institute for Cardiovascular Prevention (IPEK), 80336 Munich, Germany
| | - Nicola R. Harker
- Adaptive Immunity Research Unit, Medicines Research Centre, GlaxoSmithKline, Stevenage SG1 2NY, UK; (N.R.H.); (D.F.T.)
| | - David F. Tough
- Adaptive Immunity Research Unit, Medicines Research Centre, GlaxoSmithKline, Stevenage SG1 2NY, UK; (N.R.H.); (D.F.T.)
| | - Wouter J. de Jonge
- Tytgat Institute for Liver and Intestinal Research, Amsterdam Gastroenterology Endocrinology Metabolism Research Institute, Amsterdam University Medical Centers, University of Amsterdam, 1105 BK Amsterdam, The Netherlands; (M.G.); (A.M.I.E.)
- Department of Surgery, University of Bonn, 53127 Bonn, Germany
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7
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Muthengi A, Wimalasena VK, Yosief HO, Bikowitz MJ, Sigua LH, Wang T, Li D, Gaieb Z, Dhawan G, Liu S, Erickson J, Amaro RE, Schönbrunn E, Qi J, Zhang W. Development of Dimethylisoxazole-Attached Imidazo[1,2- a]pyridines as Potent and Selective CBP/P300 Inhibitors. J Med Chem 2021; 64:5787-5801. [PMID: 33872011 DOI: 10.1021/acs.jmedchem.0c02232] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The use of epigenetic bromodomain inhibitors as anticancer therapeutics has transitioned from targeting bromodomain extraterminal domain (BET) proteins into targeting non-BET bromodomains. The two most relevant non-BET bromodomain oncology targets are cyclic AMP response element-binding protein (CBP) and E1A binding protein P300 (EP300). To explore the growing CBP/EP300 interest, we developed a highly efficient two-step synthetic route for dimethylisoxazole-attached imidazo[1,2-a]pyridine scaffold-containing inhibitors. Our efficient two-step reactions enabled high-throughput synthesis of compounds designed by molecular modeling, which together with structure-activity relationship (SAR) studies facilitated an overarching understanding of selective targeting of CBP/EP300 over non-BET bromodomains. This led to the identification of a new potent and selective CBP/EP300 bromodomain inhibitor, UMB298 (compound 23, CBP IC50 72 nM and bromodomain 4, BRD4 IC50 5193 nM). The SAR we established is in good agreement with literature-reported CBP inhibitors, such as CBP30, and demonstrates the advantage of utilizing our two-step approach for inhibitor development of other bromodomains.
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Affiliation(s)
- Alex Muthengi
- Center for Green Chemistry and Department of Chemistry, University of Massachusetts Boston, 100 Morrissey Boulevard, Boston, Massachusetts 02125, United States
| | - Virangika K Wimalasena
- Department of Cancer Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, Massachusetts 02215, United States
| | - Hailemichael O Yosief
- Center for Green Chemistry and Department of Chemistry, University of Massachusetts Boston, 100 Morrissey Boulevard, Boston, Massachusetts 02125, United States
| | - Melissa J Bikowitz
- Drug Discovery Department, Moffit Cancer Center, Tampa, Florida 33612, United States.,Department of Molecular Medicine, USF Morsani College of Medicine, University of South Florida, Tampa, Florida 33612, United States
| | - Logan H Sigua
- Department of Cancer Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, Massachusetts 02215, United States
| | - Tingjian Wang
- Department of Cancer Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, Massachusetts 02215, United States
| | - Deyao Li
- Department of Cancer Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, Massachusetts 02215, United States
| | - Zied Gaieb
- Department of Chemistry & Biochemistry, University of California, San Diego, 9500 Gilman Dr, LA Jolla, California 92093, United States
| | - Gagan Dhawan
- Department of Biomedical Science, Acharya Narendra Dev College, University of Delhi, Delhi, New Delhi 110019, India
| | - Shuai Liu
- Center for Green Chemistry and Department of Chemistry, University of Massachusetts Boston, 100 Morrissey Boulevard, Boston, Massachusetts 02125, United States
| | - Jon Erickson
- Center for Green Chemistry and Department of Chemistry, University of Massachusetts Boston, 100 Morrissey Boulevard, Boston, Massachusetts 02125, United States
| | - Rommie E Amaro
- Department of Chemistry & Biochemistry, University of California, San Diego, 9500 Gilman Dr, LA Jolla, California 92093, United States
| | - Ernst Schönbrunn
- Drug Discovery Department, Moffit Cancer Center, Tampa, Florida 33612, United States.,Department of Molecular Medicine, USF Morsani College of Medicine, University of South Florida, Tampa, Florida 33612, United States
| | - Jun Qi
- Department of Cancer Biology, Dana-Farber Cancer Institute, 450 Brookline Avenue, Boston, Massachusetts 02215, United States.,Department of Medicine, Harvard Medical School, 220 Longwood Avenue, Boston, Massachusetts 02115, United States
| | - Wei Zhang
- Center for Green Chemistry and Department of Chemistry, University of Massachusetts Boston, 100 Morrissey Boulevard, Boston, Massachusetts 02125, United States
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8
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Wu S, Wang L, Zhang L, Xu X, Zhao J. Molecular dynamics insights into binding selectivity of inhibitors toward BRD4 and CBP. Chem Phys Lett 2021. [DOI: 10.1016/j.cplett.2021.138435] [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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9
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Wu SL, Zhao J, Sun HB, Li HY, Yin YY, Zhang LL. Insights into interaction mechanism of inhibitors E3T, E3H and E3B with CREB binding protein by using molecular dynamics simulations and MM-GBSA calculations. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2021; 32:221-246. [PMID: 33661069 DOI: 10.1080/1062936x.2021.1887351] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 02/04/2021] [Indexed: 06/12/2023]
Abstract
CREB binding protein (CBP) and its paralog E1A binding protein (p300) are related to the development of inflammatory diseases, cancers and other diseases, and have been potential targets for the treatment of human diseases. In this work, interaction mechanism of three small molecules E3T, E3H, and E3B with CBP was investigated by employing molecular dynamics (MD) simulations, principal component analysis (PCA), and molecular mechanics/generalized born surface area (MM-GBSA) method. The results indicate that inhibitor bindings cause the changes of movement modes and structural flexibility of CBP, and van der Waals interactions mostly drive associations of inhibitors with CBP. In the meantime, the results based on inhibitor-residue interactions not only show that eight residues of CBP can strongly interact with E3T, E3H and E3B but also verify that the CH-CH, CH-π, and π-π interactions are responsible for vital contributions in associations of E3T, E3H and E3B with CBP. In addition, the H-O radial distribution functions (RDFs) were computed to assess the stability of hydrogen bonding interactions between inhibitors and CBP, and the obtained information identifies several key hydrogen bonds playing key roles in bindings of E3T, E3H and E3B to CBP. Potential new inhibitors have been proposed.
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Affiliation(s)
- S L Wu
- School of Science, Shandong Jiaotong University, Jinan, China
| | - J Zhao
- School of Science, Shandong Jiaotong University, Jinan, China
| | - H B Sun
- School of Science, Shandong Jiaotong University, Jinan, China
| | - H Y Li
- School of Science, Shandong Jiaotong University, Jinan, China
| | - Y Y Yin
- School of Science, Shandong Jiaotong University, Jinan, China
| | - L L Zhang
- School of Science, Shandong Jiaotong University, Jinan, China
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10
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Li TY, Sleiman MB, Li H, Gao AW, Mottis A, Bachmann AM, El Alam G, Li X, Goeminne LJE, Schoonjans K, Auwerx J. The transcriptional coactivator CBP/p300 is an evolutionarily conserved node that promotes longevity in response to mitochondrial stress. ACTA ACUST UNITED AC 2021; 1:165-178. [PMID: 33718883 PMCID: PMC7116894 DOI: 10.1038/s43587-020-00025-z] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Organisms respond to mitochondrial stress by activating multiple defense pathways including the mitochondrial unfolded protein response (UPRmt). However, how UPRmt regulators are orchestrated to transcriptionally activate stress responses remains largely unknown. Here we identified CBP-1, the worm ortholog of the mammalian acetyltransferases CBP/p300, as an essential regulator of the UPRmt, as well as mitochondrial stress-induced immune response, reduction of amyloid-β aggregation and lifespan extension in Caenorhabditis elegans. Mechanistically, CBP-1 acts downstream of histone demethylases, JMJD-1.2/JMJD-3.1, and upstream of UPRmt transcription factors including ATFS-1, to systematically induce a broad spectrum of UPRmt genes and execute multiple beneficial functions. In mouse and human populations, transcript levels of CBP/p300 positively correlate with UPRmt transcripts and longevity. Furthermore, CBP/p300 inhibition disrupts, while forced expression of p300 is sufficient to activate, the UPRmt in mammalian cells. These results highlight an evolutionarily conserved mechanism that determines mitochondrial stress response, and promotes health and longevity through CBP/p300.
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Affiliation(s)
- Terytty Yang Li
- Laboratory of Integrative Systems Physiology, Interfaculty Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Maroun Bou Sleiman
- Laboratory of Integrative Systems Physiology, Interfaculty Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.,Laboratory of Metabolic Signaling, Interfaculty Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Hao Li
- Laboratory of Integrative Systems Physiology, Interfaculty Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Arwen W Gao
- Laboratory of Integrative Systems Physiology, Interfaculty Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Adrienne Mottis
- Laboratory of Integrative Systems Physiology, Interfaculty Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Alexis Maximilien Bachmann
- Laboratory of Integrative Systems Physiology, Interfaculty Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Gaby El Alam
- Laboratory of Integrative Systems Physiology, Interfaculty Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Xiaoxu Li
- Laboratory of Integrative Systems Physiology, Interfaculty Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Ludger J E Goeminne
- Laboratory of Integrative Systems Physiology, Interfaculty Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Kristina Schoonjans
- Laboratory of Metabolic Signaling, Interfaculty Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Johan Auwerx
- Laboratory of Integrative Systems Physiology, Interfaculty Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
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11
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Current development of CBP/p300 inhibitors in the last decade. Eur J Med Chem 2020; 209:112861. [PMID: 33045661 DOI: 10.1016/j.ejmech.2020.112861] [Citation(s) in RCA: 75] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 09/16/2020] [Accepted: 09/17/2020] [Indexed: 01/10/2023]
Abstract
CBP/p300, functioning as histone acetyltransferases and transcriptional co-factors, represents an attractive target for various diseases, including malignant tumor. The development of small-molecule inhibitors targeting the bromodomain and HAT domains of CBP/p300 has aroused broad interests of medicinal chemist in expectation of providing new hope for anti-cancer treatment. In particular, the CBP/p300 bromodomain inhibitor CCS1477, identified by CellCentric, is currently undergone clinical evaluation for the treatment of haematological malignancies and prostate cancer. In this review, we depict the development of CBP/p300 inhibitors reported from 2010 to 2020 and particularly highlight their structure-activity relationships (SARs), binding modes, selectivity and pharmacological functions with the aim to facilitate rational design and development of CBP/p300 inhibitors.
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12
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Zhang FC, Sun ZY, Liao LP, Zuo Y, Zhang D, Wang J, Chen YT, Xiao SH, Jiang H, Lu T, Xu P, Yue LY, Du DH, Zhang H, Liu CP, Luo C. Discovery of novel CBP bromodomain inhibitors through TR-FRET-based high-throughput screening. Acta Pharmacol Sin 2020; 41:286-292. [PMID: 31253937 PMCID: PMC7468272 DOI: 10.1038/s41401-019-0256-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Revised: 05/16/2019] [Accepted: 05/21/2019] [Indexed: 12/12/2022] Open
Abstract
The cAMP-responsive element binding protein (CREB) binding protein (CBP) and adenoviral E1A-binding protein (P300) are two closely related multifunctional transcriptional coactivators. Both proteins contain a bromodomain (BrD) adjacent to the histone acetyl transferase (HAT) catalytic domain, which serves as a promising drug target for cancers and immune system disorders. Several potent and selective small-molecule inhibitors targeting CBP BrD have been reported, but thus far small-molecule inhibitors targeting BrD outside of the BrD and extraterminal domain (BET) family are especially lacking. Here, we established and optimized a TR-FRET-based high-throughput screening platform for the CBP BrD and acetylated H4 peptide. Through an HTS assay against an in-house chemical library containing 20 000 compounds, compound DC_CP20 was discovered as a novel CBP BrD inhibitor with an IC50 value of 744.3 nM. This compound bound to CBP BrD with a KD value of 4.01 μM in the surface plasmon resonance assay. Molecular modeling revealed that DC_CP20 occupied the Kac-binding region firmly through hydrogen bonding with the conserved residue N1168. At the celluslar level, DC_CP20 dose-dependently inhibited the proliferation of human leukemia MV4-11 cells with an IC50 value of 19.2 μM and markedly downregulated the expression of the c-Myc in the cells. Taken together, the discovery of CBP BrD inhibitor DC_CP20 provides a novel chemical scaffold for further medicinal chemistry optimization and a potential chemical probe for CBP-related biological function research. In addition, this inhibitor may serve as a promising therapeutic strategy for MLL leukemia by targeting CBP BrD protein.
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Affiliation(s)
- Feng-Cai Zhang
- School of Pharmacy, Nanchang University, Nanchang, 330006, China
| | - Zhong-Ya Sun
- School of Life and Technology, Harbin Institute of Technology, Harbin, 150001, China
- Drug Discovery and Design Center, CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Li-Ping Liao
- Drug Discovery and Design Center, CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yu Zuo
- School of Pharmacy, Nanchang University, Nanchang, 330006, China
- Drug Discovery and Design Center, CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Dan Zhang
- Drug Discovery and Design Center, CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- Department of Pharmacy, Guizhou University of Traditional Chinese Medicine, Guiyang, 550025, China
| | - Jun Wang
- Drug Discovery and Design Center, CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- Jiangsu Key Laboratory for High Technology Research of TCM Formulae, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Yan-Tao Chen
- Drug Discovery and Design Center, CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Sen-Hao Xiao
- Drug Discovery and Design Center, CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hao Jiang
- Drug Discovery and Design Center, CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Tian Lu
- Drug Discovery and Design Center, CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- Jiangsu Key Laboratory for High Technology Research of TCM Formulae, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Pan Xu
- Drug Discovery and Design Center, CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Li-Yan Yue
- Drug Discovery and Design Center, CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Dao-Hai Du
- Drug Discovery and Design Center, CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- Jiangsu Key Laboratory for High Technology Research of TCM Formulae, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Hao Zhang
- Drug Discovery and Design Center, CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Chuan-Peng Liu
- School of Life and Technology, Harbin Institute of Technology, Harbin, 150001, China.
| | - Cheng Luo
- Drug Discovery and Design Center, CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China.
- Department of Pharmacy, Guizhou University of Traditional Chinese Medicine, Guiyang, 550025, China.
- Jiangsu Key Laboratory for High Technology Research of TCM Formulae, Nanjing University of Chinese Medicine, Nanjing, 210023, China.
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13
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Small Molecules Targeting the Specific Domains of Histone-Mark Readers in Cancer Therapy. Molecules 2020; 25:molecules25030578. [PMID: 32013155 PMCID: PMC7037402 DOI: 10.3390/molecules25030578] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 01/20/2020] [Accepted: 01/22/2020] [Indexed: 12/11/2022] Open
Abstract
Epigenetic modifications (or epigenetic tags) on DNA and histones not only alter the chromatin structure, but also provide a recognition platform for subsequent protein recruitment and enable them to acquire executive instructions to carry out specific intracellular biological processes. In cells, different epigenetic-tags on DNA and histones are often recognized by the specific domains in proteins (readers), such as bromodomain (BRD), chromodomain (CHD), plant homeodomain (PHD), Tudor domain, Pro-Trp-Trp-Pro (PWWP) domain and malignant brain tumor (MBT) domain. Recent accumulating data reveal that abnormal intracellular histone modifications (histone marks) caused by tumors can be modulated by small molecule-mediated changes in the activity of the above domains, suggesting that small molecules targeting histone-mark reader domains may be the trend of new anticancer drug development. Here, we summarize the protein domains involved in histone-mark recognition, and introduce recent research findings about small molecules targeting histone-mark readers in cancer therapy.
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14
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Histone acetyltransferase and Polo-like kinase 3 inhibitors prevent rat galactose-induced cataract. Sci Rep 2019; 9:20085. [PMID: 31882756 PMCID: PMC6934598 DOI: 10.1038/s41598-019-56414-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 12/06/2019] [Indexed: 01/01/2023] Open
Abstract
Diabetic cataracts can occur at an early age, causing visual impairment or blindness. The detailed molecular mechanisms of diabetic cataract formation remain incompletely understood, and there is no well-documented prophylactic agent. Galactose-fed rats and ex vivo treatment of lenses with galactose are used as models of diabetic cataract. To assess the role of histone acetyltransferases, we conducted cataract prevention screening with known histone acetyltransferase (HAT) inhibitors. Ex vivo treatment with a HAT inhibitor strongly inhibited the formation of lens turbidity in high-galactose conditions, while addition of a histone deacetylase (HDAC) inhibitor aggravated turbidity. We conducted a microarray to identify genes differentially regulated by HATs and HDACs, leading to discovery of a novel cataract causative factor, Plk3. Plk3 mRNA levels correlated with the degree of turbidity, and Plk3 inhibition alleviated galactose-induced cataract formation. These findings indicate that epigenetically controlled Plk3 influences cataract formation. Our results demonstrate a novel approach for prevention of diabetic cataract using HAT and Plk3 inhibitors.
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15
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Y08197 is a novel and selective CBP/EP300 bromodomain inhibitor for the treatment of prostate cancer. Acta Pharmacol Sin 2019; 40:1436-1447. [PMID: 31097763 DOI: 10.1038/s41401-019-0237-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Accepted: 04/11/2019] [Indexed: 12/21/2022] Open
Abstract
In advanced prostate cancer, CREB (cAMP-responsive element-binding protein) binding protein (CBP) and its homolog EP300 are highly expressed; targeting the bromodomain of CBP is a new strategy for the treatment of prostate cancer. In the current study we identified Y08197, a novel 1-(indolizin-3-yl) ethanone derivative, as a selective inhibitor of CBP/EP300 bromodomain and explored its antitumor activity against prostate cancer cell lines in vitro. In the AlphaScreen assay, we demonstrated that Y08197 dose-dependently inhibited the CBP bromodomain with an IC50 value at 100.67 ± 3.30 nM. Y08197 also exhibited high selectivity for CBP/EP300 over other bromodomain-containing proteins. In LNCaP, 22Rv1 and VCaP prostate cancer cells, treatment with Y08197 (1, 5 μM) strongly affected downstream signaling transduction, thus markedly inhibiting the expression of androgen receptor (AR)-regulated genes PSA, KLK2, TMPRSS2, and oncogenes C-MYC and ERG. Notably, Y08197 potently inhibited cell growth in several AR-positive prostate cancer cell lines including LNCaP, 22Rv1, VCaP, and C4-2B. In 22Rv1 prostate cancer cells, treatment with Y08197 (1, 4, 16 μM) dose-dependently induced G0/G1 phase arrest and apoptosis. Furthermore, treatment with Y08197 (5 μM) significantly decreased ERG-induced invasive capacity of 22Rv1 prostate cancer cells detected in wound-healing assay and cell migration assay. Taken together, CBP/EP300 inhibitor Y08197 represents a promising lead compound for development as new therapeutics for the treatment of castration-resistant prostate cancer.
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16
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Abstract
Less than a decade ago, it was shown that bromodomains, acetyl lysine 'reader' modules found in proteins with varied functions, were highly tractable small-molecule targets. This is an unusual property for protein-protein or protein-peptide interaction domains, and it prompted a wave of chemical probe discovery to understand the biological potential of new agents that targeted bromodomains. The original examples, inhibitors of the bromodomain and extra-terminal (BET) class of bromodomains, showed enticing anti-inflammatory and anticancer activities, and several compounds have since advanced to human clinical trials. Here, we review the current state of BET inhibitor biology in relation to clinical development, and we discuss the next wave of bromodomain inhibitors with clinical potential in oncology and non-oncology indications. The lessons learned from BET inhibitor programmes should affect efforts to develop drugs that target non-BET bromodomains and other epigenetic readers.
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17
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Wang XS, Guan SY, Liu A, Yue J, Hu LN, Zhang K, Yang LK, Lu L, Tian Z, Zhao MG, Liu SB. Anxiolytic effects of Formononetin in an inflammatory pain mouse model. Mol Brain 2019; 12:36. [PMID: 30961625 PMCID: PMC6454770 DOI: 10.1186/s13041-019-0453-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2019] [Accepted: 03/25/2019] [Indexed: 12/24/2022] Open
Abstract
Chronic pain is commonly accompanied with anxiety disorder, which complicates treatment. In this study, we investigated the analgesic and anxiolytic effects of Formononetin (FMNT), an active component of traditional Chinese medicine red clover (Trifolium pratense L.) that is capable of protecting neurons from N-methyl-D-aspartate (NMDA)-evoked excitotoxic injury, on mice suffering from complete Freund’s adjuvant (CFA)-induced chronic inflammatory pain. The results show that FMNT administration significantly reduces anxiety-like behavior but does not affect the nociceptive threshold in CFA-injected mice. The treatment reverses the upregulation of NMDA, GluA1, and GABAA receptors, as well as PSD95 and CREB in the basolateral amygdala (BLA). The effects of FMNT on NMDA receptors and CREB binding protein (CBP) were further confirmed by the potential structure combination between these compounds, which was analyzed by in silico docking technology. FMNT also inhibits the activation of the NF-κB signaling pathway and microglia in the BLA of mice suffering from chronic inflammatory pain. Therefore, the anxiolytic effects of FMNT are partially due to the attenuation of inflammation and neuronal hyperexcitability through the inhibition of NMDA receptor and CBP in the BLA.
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Affiliation(s)
- Xin-Shang Wang
- Department of Pharmacology, School of Pharmacy, and Precision Pharmacy & Drug Development Center, Department of Pharmacy, Tangdu Hospital, Fourth Military Medical University, Xi'an, 710032, China
| | - Shao-Yu Guan
- Department of Pharmacology, School of Pharmacy, and Precision Pharmacy & Drug Development Center, Department of Pharmacy, Tangdu Hospital, Fourth Military Medical University, Xi'an, 710032, China
| | - An Liu
- Department of Pharmacology, School of Pharmacy, and Precision Pharmacy & Drug Development Center, Department of Pharmacy, Tangdu Hospital, Fourth Military Medical University, Xi'an, 710032, China
| | - Jiao Yue
- Department of Pharmacology, School of Pharmacy, and Precision Pharmacy & Drug Development Center, Department of Pharmacy, Tangdu Hospital, Fourth Military Medical University, Xi'an, 710032, China
| | - Li-Ning Hu
- Department of Pharmacology, School of Pharmacy, and Precision Pharmacy & Drug Development Center, Department of Pharmacy, Tangdu Hospital, Fourth Military Medical University, Xi'an, 710032, China
| | - Kun Zhang
- Department of Pharmacology, School of Pharmacy, and Precision Pharmacy & Drug Development Center, Department of Pharmacy, Tangdu Hospital, Fourth Military Medical University, Xi'an, 710032, China
| | - Liu-Kun Yang
- Department of Pharmacology, School of Pharmacy, and Precision Pharmacy & Drug Development Center, Department of Pharmacy, Tangdu Hospital, Fourth Military Medical University, Xi'an, 710032, China
| | - Liang Lu
- Department of Pharmacology, School of Pharmacy, and Precision Pharmacy & Drug Development Center, Department of Pharmacy, Tangdu Hospital, Fourth Military Medical University, Xi'an, 710032, China
| | - Zhen Tian
- Department of Pharmacology, School of Pharmacy, and Precision Pharmacy & Drug Development Center, Department of Pharmacy, Tangdu Hospital, Fourth Military Medical University, Xi'an, 710032, China.,The 154th Central Hospital of PLA, Xinyang, 464000, China
| | - Ming-Gao Zhao
- Department of Pharmacology, School of Pharmacy, and Precision Pharmacy & Drug Development Center, Department of Pharmacy, Tangdu Hospital, Fourth Military Medical University, Xi'an, 710032, China
| | - Shui-Bing Liu
- Department of Pharmacology, School of Pharmacy, and Precision Pharmacy & Drug Development Center, Department of Pharmacy, Tangdu Hospital, Fourth Military Medical University, Xi'an, 710032, China.
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18
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Garcia-Carpizo V, Ruiz-Llorente S, Sarmentero J, González-Corpas A, Barrero MJ. CREBBP/EP300 Bromodomain Inhibition Affects the Proliferation of AR-Positive Breast Cancer Cell Lines. Mol Cancer Res 2019; 17:720-730. [DOI: 10.1158/1541-7786.mcr-18-0719] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Revised: 10/10/2018] [Accepted: 12/14/2018] [Indexed: 11/16/2022]
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19
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van Zundert GCP, Hudson BM, de Oliveira SHP, Keedy DA, Fonseca R, Heliou A, Suresh P, Borrelli K, Day T, Fraser JS, van den Bedem H. qFit-ligand Reveals Widespread Conformational Heterogeneity of Drug-Like Molecules in X-Ray Electron Density Maps. J Med Chem 2018; 61:11183-11198. [PMID: 30457858 DOI: 10.1021/acs.jmedchem.8b01292] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Proteins and ligands sample a conformational ensemble that governs molecular recognition, activity, and dissociation. In structure-based drug design, access to this conformational ensemble is critical to understand the balance between entropy and enthalpy in lead optimization. However, ligand conformational heterogeneity is currently severely underreported in crystal structures in the Protein Data Bank, owing in part to a lack of automated and unbiased procedures to model an ensemble of protein-ligand states into X-ray data. Here, we designed a computational method, qFit-ligand, to automatically resolve conformationally averaged ligand heterogeneity in crystal structures, and applied it to a large set of protein receptor-ligand complexes. In an analysis of the cancer related BRD4 domain, we found that up to 29% of protein crystal structures bound with drug-like molecules present evidence of unmodeled, averaged, relatively isoenergetic conformations in ligand-receptor interactions. In many retrospective cases, these alternate conformations were adventitiously exploited to guide compound design, resulting in improved potency or selectivity. Combining qFit-ligand with high-throughput screening or multitemperature crystallography could therefore augment the structure-based drug design toolbox.
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Affiliation(s)
| | - Brandi M Hudson
- Department of Bioengineering and Therapeutic Sciences , UCSF , San Francisco , California 94158 , United States
| | - Saulo H P de Oliveira
- SLAC National Accelerator Laboratory , Stanford University , Menlo Park , California 94025 United States
| | - Daniel A Keedy
- Department of Bioengineering and Therapeutic Sciences , UCSF , San Francisco , California 94158 , United States
| | - Rasmus Fonseca
- Department of Molecular and Cellular Physiology , Stanford University , Stanford , California 94305 , United States
| | - Amelie Heliou
- LIX, Ecole Polytechnique, CNRS, Inria , Université Paris-Saclay , 91128 Palaiseau , France
| | - Pooja Suresh
- Department of Bioengineering and Therapeutic Sciences , UCSF , San Francisco , California 94158 , United States
| | | | - Tyler Day
- Schrödinger , New York , New York 10036 , United States
| | - James S Fraser
- Department of Bioengineering and Therapeutic Sciences , UCSF , San Francisco , California 94158 , United States
| | - Henry van den Bedem
- Department of Bioengineering and Therapeutic Sciences , UCSF , San Francisco , California 94158 , United States.,SLAC National Accelerator Laboratory , Stanford University , Menlo Park , California 94025 United States
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20
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Wang S, Tsui V, Crawford TD, Audia JE, Burdick DJ, Beresini MH, Côté A, Cummings R, Duplessis M, Flynn EM, Hewitt MC, Huang HR, Jayaram H, Jiang Y, Joshi S, Murray J, Nasveschuk CG, Pardo E, Poy F, Romero FA, Tang Y, Taylor AM, Wang J, Xu Z, Zawadzke LE, Zhu X, Albrecht BK, Magnuson SR, Bellon S, Cochran AG. GNE-371, a Potent and Selective Chemical Probe for the Second Bromodomains of Human Transcription-Initiation-Factor TFIID Subunit 1 and Transcription-Initiation-Factor TFIID Subunit 1-like. J Med Chem 2018; 61:9301-9315. [DOI: 10.1021/acs.jmedchem.8b01225] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Shumei Wang
- Genentech Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Vickie Tsui
- Genentech Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Terry D. Crawford
- Genentech Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - James E. Audia
- Constellation Pharmaceuticals, 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Daniel J. Burdick
- Genentech Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Maureen H. Beresini
- Genentech Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | | | - Richard Cummings
- Constellation Pharmaceuticals, 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Martin Duplessis
- Constellation Pharmaceuticals, 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - E. Megan Flynn
- Genentech Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Michael C. Hewitt
- Constellation Pharmaceuticals, 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Hon-Ren Huang
- Constellation Pharmaceuticals, 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Hariharan Jayaram
- Constellation Pharmaceuticals, 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Ying Jiang
- Wuxi Apptec Company, Ltd., 288 Fute Zhong Road, Waigaoqiao
Free Trade Zone, Shanghai 200131, People’s Republic of China
| | - Shivangi Joshi
- Constellation Pharmaceuticals, 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Jeremy Murray
- Genentech Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Christopher G. Nasveschuk
- Constellation Pharmaceuticals, 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Eneida Pardo
- Constellation Pharmaceuticals, 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Florence Poy
- Constellation Pharmaceuticals, 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - F. Anthony Romero
- Genentech Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Yong Tang
- Constellation Pharmaceuticals, 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Alexander M. Taylor
- Constellation Pharmaceuticals, 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Jian Wang
- Wuxi Apptec Company, Ltd., 288 Fute Zhong Road, Waigaoqiao
Free Trade Zone, Shanghai 200131, People’s Republic of China
| | - Zhaowu Xu
- Wuxi Apptec Company, Ltd., 288 Fute Zhong Road, Waigaoqiao
Free Trade Zone, Shanghai 200131, People’s Republic of China
| | - Laura E. Zawadzke
- Constellation Pharmaceuticals, 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Xiaoyu Zhu
- Wuxi Apptec Company, Ltd., 288 Fute Zhong Road, Waigaoqiao
Free Trade Zone, Shanghai 200131, People’s Republic of China
| | - Brian K. Albrecht
- Constellation Pharmaceuticals, 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Steven R. Magnuson
- Genentech Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Steve Bellon
- Constellation Pharmaceuticals, 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Andrea G. Cochran
- Genentech Inc., 1 DNA Way, South San Francisco, California 94080, United States
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21
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Garcia-Carpizo V, Ruiz-Llorente S, Sarmentero J, Graña-Castro O, Pisano DG, Barrero MJ. CREBBP/EP300 bromodomains are critical to sustain the GATA1/MYC regulatory axis in proliferation. Epigenetics Chromatin 2018; 11:30. [PMID: 29884215 PMCID: PMC5992658 DOI: 10.1186/s13072-018-0197-x] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2018] [Accepted: 05/27/2018] [Indexed: 02/06/2023] Open
Abstract
Background The reported antitumor activity of the BET family bromodomain inhibitors has prompted the development of inhibitors against other bromodomains. However, the human genome encodes more than 60 different bromodomains and most of them remain unexplored. Results We report that the bromodomains of the histone acetyltransferases CREBBP/EP300 are critical to sustain the proliferation of human leukemia and lymphoma cell lines. EP300 is very abundant at super-enhancers in K562 and is coincident with sites of GATA1 and MYC occupancy. In accordance, CREBBP/EP300 bromodomain inhibitors interfere with GATA1- and MYC-driven transcription, causing the accumulation of cells in the G0/G1 phase of the cell cycle. The CREBBP/CBP30 bromodomain inhibitor CBP30 displaces CREBBP and EP300 from GATA1 and MYC binding sites at enhancers, resulting in a decrease in the levels of histone acetylation at these regulatory regions and consequently reduced gene expression of critical genes controlled by these transcription factors. Conclusions Our data shows that inhibition of CREBBP/EP300 bromodomains can interfere with oncogene-driven transcriptional programs in cancer cells and consequently hold therapeutic potential. Electronic supplementary material The online version of this article (10.1186/s13072-018-0197-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Veronica Garcia-Carpizo
- CNIO-Lilly Epigenetics Laboratory, Spanish National Cancer Research Center (CNIO), Melchor Fernandez Almagro 3, 28029, Madrid, Spain
| | - Sergio Ruiz-Llorente
- CNIO-Lilly Epigenetics Laboratory, Spanish National Cancer Research Center (CNIO), Melchor Fernandez Almagro 3, 28029, Madrid, Spain
| | - Jacinto Sarmentero
- CNIO-Lilly Epigenetics Laboratory, Spanish National Cancer Research Center (CNIO), Melchor Fernandez Almagro 3, 28029, Madrid, Spain
| | - Osvaldo Graña-Castro
- Bioinformatics Unit, Spanish National Cancer Research Center (CNIO), Melchor Fernandez Almagro 3, 28029, Madrid, Spain
| | - David G Pisano
- Bioinformatics Unit, Spanish National Cancer Research Center (CNIO), Melchor Fernandez Almagro 3, 28029, Madrid, Spain
| | - Maria J Barrero
- CNIO-Lilly Epigenetics Laboratory, Spanish National Cancer Research Center (CNIO), Melchor Fernandez Almagro 3, 28029, Madrid, Spain.
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22
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Abstract
Chromatin packaging of DNA provides a framework for transcriptional regulation. Modifications to DNA and histone proteins in nucleosomes lead to conformational changes, alterations in the recruitment of transcriptional complexes, and ultimately modulation of gene expression. We provide a focused review of control mechanisms that help modulate the activation and deactivation of gene transcription specifically through histone acetylation writers and readers in cancer. The chemistry of these modifications is subject to clinically actionable targeting, including state-of-the-art strategies to inhibit basic oncogenic mechanisms related to histone acetylation. Although discussed in the context of acute leukemia, the concepts of acetylation writers and readers are not cell-type-specific and are generalizable to other cancers. We review the challenges and resistance mechanisms encountered to date in the development of such therapeutics and postulate how such challenges may be overcome. Because these fundamental cellular mechanisms are dysregulated in cancer biology, continued research and in-depth understanding of histone acetylation reading and writing are desired to further define optimal therapeutic strategies to affect gene activity to target cancer effectively.
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23
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Xiang Q, Wang C, Zhang Y, Xue X, Song M, Zhang C, Li C, Wu C, Li K, Hui X, Zhou Y, Smaill JB, Patterson AV, Wu D, Ding K, Xu Y. Discovery and optimization of 1-(1H-indol-1-yl)ethanone derivatives as CBP/EP300 bromodomain inhibitors for the treatment of castration-resistant prostate cancer. Eur J Med Chem 2018; 147:238-252. [PMID: 29448139 DOI: 10.1016/j.ejmech.2018.01.087] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Revised: 01/11/2018] [Accepted: 01/26/2018] [Indexed: 01/08/2023]
Abstract
The CREB (cAMP responsive element binding protein) binding protein (CBP) and its homolog EP300 have emerged as new therapeutic targets for the treatment of cancer and inflammatory diseases. Here we report the identification, optimization and evaluation of 1-(1H-indol-1-yl)ethanone derivatives as CBP/EP300 inhibitors starting from fragment-based virtual screening (FBVS). A cocrystal structure of the inhibitor (22e) in complex with CBP provides a solid structural basis for further optimization. The most potent compound 32h binds to the CBP bromodomain and has an IC50 value of 0.037 μM in the AlphaScreen assay which was 2 times more potent than the reported CBP bromodomain inhibitor SGC-CBP30 in our hands. 32h also exhibit high selectivity for CBP/EP300 over other bromodomain-containing proteins. Notably, the ester derivative (29h) of compound 32h markedly inhibits cell growth in several prostate cancer cell lines including LNCaP, 22Rv1 and LNCaP derived C4-2B. Compound 29h suppresses the mRNA expression of full length AR (AR-FL), AR target genes and other oncogene in LNCaP cells. 29h also reduces the expression of PSA, the biomarker of prostate cancer. CBP/EP300 inhibitor 29h represents a promising lead compound for the development of new therapeutics for the treatment of castration-resistant prostate cancer.
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Affiliation(s)
- Qiuping Xiang
- Guangdong Provincial Key Laboratory of Biocomputing, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, China; University of Chinese Academy of Sciences, No. 19 Yuquan Road, Beijing 100049, China
| | - Chao Wang
- Guangdong Provincial Key Laboratory of Biocomputing, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, China; School of Pharmaceutical Sciences, Jilin University, Changchun, China, No. 1266 Fujin Road, Chaoyang District, Changchun, Jilin 130021, China
| | - Yan Zhang
- Guangdong Provincial Key Laboratory of Biocomputing, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, China; University of Chinese Academy of Sciences, No. 19 Yuquan Road, Beijing 100049, China
| | - Xiaoqian Xue
- Guangdong Provincial Key Laboratory of Biocomputing, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, China; University of Chinese Academy of Sciences, No. 19 Yuquan Road, Beijing 100049, China
| | - Ming Song
- Guangdong Provincial Key Laboratory of Biocomputing, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, China
| | - Cheng Zhang
- Guangdong Provincial Key Laboratory of Biocomputing, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, China; School of Pharmaceutical Sciences, Jilin University, Changchun, China, No. 1266 Fujin Road, Chaoyang District, Changchun, Jilin 130021, 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 Medical University, Guangzhou, China; School of Pharmaceutical Sciences, Jilin University, Changchun, China, No. 1266 Fujin Road, Chaoyang District, Changchun, Jilin 130021, China
| | - Chun Wu
- Guangdong Provincial Key Laboratory of Biocomputing, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, China
| | - Kuai Li
- Guangdong Provincial Key Laboratory of Biocomputing, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, China
| | - Xiaoyan Hui
- State Key Laboratory of Pharmaceutical Biotechnology, Department of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region
| | - Yulai Zhou
- School of Pharmaceutical Sciences, Jilin University, Changchun, China, No. 1266 Fujin Road, Chaoyang District, Changchun, Jilin 130021, China
| | - Jeff B Smaill
- University of Auckland, Auckland Cancer Society Research Centre, School of Medical Sciences, Private Bag 92019, Auckland, New Zealand
| | - Adam V Patterson
- University of Auckland, Auckland Cancer Society Research Centre, School of Medical Sciences, Private Bag 92019, Auckland, New Zealand
| | - Donghai Wu
- Guangdong Provincial Key Laboratory of Biocomputing, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, China
| | - Ke Ding
- School of Pharmacy, Jinan University, 601 Huangpu Avenue West, Guangzhou 510632, China
| | - Yong Xu
- Guangdong Provincial Key Laboratory of Biocomputing, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou Medical University, Guangzhou, China.
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24
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Alqinyah M, Hooks SB. Regulating the regulators: Epigenetic, transcriptional, and post-translational regulation of RGS proteins. Cell Signal 2017; 42:77-87. [PMID: 29042285 DOI: 10.1016/j.cellsig.2017.10.007] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Revised: 10/06/2017] [Accepted: 10/13/2017] [Indexed: 12/11/2022]
Abstract
Regulators of G protein signaling (RGS) are a family of proteins classically known to accelerate the intrinsic GTPase activity of G proteins, which results in accelerated inactivation of heterotrimeric G proteins and inhibition of G protein coupled receptor signaling. RGS proteins play major roles in essential cellular processes, and dysregulation of RGS protein expression is implicated in multiple diseases, including cancer, cardiovascular and neurodegenerative diseases. The expression of RGS proteins is highly dynamic and is regulated by epigenetic, transcriptional and post-translational mechanisms. This review summarizes studies that report dysregulation of RGS protein expression in disease states, and presents examples of drugs that regulate RGS protein expression. Additionally, this review discusses, in detail, the transcriptional and post-transcriptional mechanisms regulating RGS protein expression, and further assesses the therapeutic potential of targeting these mechanisms. Understanding the molecular mechanisms controlling the expression of RGS proteins is essential for the development of therapeutics that indirectly modulate G protein signaling by regulating expression of RGS proteins.
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Affiliation(s)
- Mohammed Alqinyah
- Department of Pharmaceutical and Biomedical Sciences, University of Georgia, Athens, GA, USA
| | - Shelley B Hooks
- Department of Pharmaceutical and Biomedical Sciences, University of Georgia, Athens, GA, USA.
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25
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Hügle M, Lucas X, Ostrovskyi D, Regenass P, Gerhardt S, Einsle O, Hau M, Jung M, Breit B, Günther S, Wohlwend D. Beyond the BET Family: Targeting CBP/p300 with 4‐Acyl Pyrroles. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201705516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Martin Hügle
- Institut für Biochemie Albert-Ludwigs-Universität Freiburg Albertstrasse 21 79104 Freiburg Germany
| | - Xavier Lucas
- School of Life Sciences Division of Biological Chemistry and Drug Discovery University of Dundee, James Black Centre Dow Street Dundee DD1 5EH UK
| | - Dmytro Ostrovskyi
- Institut für Organische Chemie Albert-Ludwigs-Universität Freiburg Albertstrasse 21 79104 Freiburg Germany
| | - Pierre Regenass
- Institut für Organische Chemie Albert-Ludwigs-Universität Freiburg Albertstrasse 21 79104 Freiburg Germany
| | - Stefan Gerhardt
- Institut für Biochemie Albert-Ludwigs-Universität Freiburg Albertstrasse 21 79104 Freiburg Germany
| | - Oliver Einsle
- Institut für Biochemie Albert-Ludwigs-Universität Freiburg Albertstrasse 21 79104 Freiburg Germany
- Freiburg Institute for Advanced Studies (FRIAS) Albert-Ludwigs-Universität Freiburg Albertstrasse 21 79104 Freiburg Germany
- BIOSS Centre for Biological Signalling Studies Albert-Ludwigs-Universität Freiburg Albertstr. 21 79104 Freiburg Germany
| | - Mirjam Hau
- Institut für Pharmazeutische Wissenschaften Albert-Ludwigs-Universität Freiburg Hermann-Herder-Strasse 9 79104 Freiburg Germany
| | - Manfred Jung
- Institut für Pharmazeutische Wissenschaften Albert-Ludwigs-Universität Freiburg Hermann-Herder-Strasse 9 79104 Freiburg Germany
| | - Bernhard Breit
- Freiburg Institute for Advanced Studies (FRIAS) Albert-Ludwigs-Universität Freiburg Albertstrasse 21 79104 Freiburg Germany
- Institut für Organische Chemie Albert-Ludwigs-Universität Freiburg Albertstrasse 21 79104 Freiburg Germany
| | - Stefan Günther
- Institut für Pharmazeutische Wissenschaften Albert-Ludwigs-Universität Freiburg Hermann-Herder-Strasse 9 79104 Freiburg Germany
- Freiburg Institute for Advanced Studies (FRIAS) Albert-Ludwigs-Universität Freiburg Albertstrasse 21 79104 Freiburg Germany
| | - Daniel Wohlwend
- Institut für Biochemie Albert-Ludwigs-Universität Freiburg Albertstrasse 21 79104 Freiburg Germany
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26
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Yan G, Hou M, Luo J, Pu C, Hou X, Lan S, Li R. Pharmacophore-based virtual screening, molecular docking, molecular dynamics simulation, and biological evaluation for the discovery of novel BRD4 inhibitors. Chem Biol Drug Des 2017; 91:478-490. [PMID: 28901664 DOI: 10.1111/cbdd.13109] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Revised: 08/21/2017] [Accepted: 08/22/2017] [Indexed: 02/05/2023]
Abstract
Bromodomain is a recognition module in the signal transduction of acetylated histone. BRD4, one of the bromodomain members, is emerging as an attractive therapeutic target for several types of cancer. Therefore, in this study, an attempt has been made to screen compounds from an integrated database containing 5.5 million compounds for BRD4 inhibitors using pharmacophore-based virtual screening, molecular docking, and molecular dynamics simulations. As a result, two molecules of twelve hits were found to be active in bioactivity tests. Among the molecules, compound 5 exhibited potent anticancer activity, and the IC50 values against human cancer cell lines MV4-11, A375, and HeLa were 4.2, 7.1, and 11.6 μm, respectively. After that, colony formation assay, cell cycle, apoptosis analysis, wound-healing migration assay, and Western blotting were carried out to learn the bioactivity of compound 5.
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Affiliation(s)
- Guoyi Yan
- Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Sichuan, China
| | - Manzhou Hou
- Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Sichuan, China
| | - Jiang Luo
- Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Sichuan, China
| | - Chunlan Pu
- Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Sichuan, China
| | - Xueyan Hou
- Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Sichuan, China
| | - Suke Lan
- Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Sichuan, China
| | - Rui Li
- Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Sichuan, China
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27
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Hügle M, Lucas X, Ostrovskyi D, Regenass P, Gerhardt S, Einsle O, Hau M, Jung M, Breit B, Günther S, Wohlwend D. Beyond the BET Family: Targeting CBP/p300 with 4-Acyl Pyrroles. Angew Chem Int Ed Engl 2017; 56:12476-12480. [PMID: 28766825 DOI: 10.1002/anie.201705516] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Revised: 07/21/2017] [Indexed: 11/07/2022]
Abstract
Bromodomain and extra-terminal domain (BET) inhibitors are widely used both as chemical tools to study the biological role of their targets in living organisms and as candidates for drug development against several cancer variants and human disorders. However, non-BET bromodomains such as those in p300 and CBP are less studied. XDM-CBP is a highly potent and selective inhibitor for the bromodomains of CBP and p300 derived from a pan-selective BET BRD-binding fragment. Along with X-ray crystal-structure analysis and thermodynamic profiling, XDM-CBP was used in screenings of several cancer cell lines in vitro to study its inhibitory potential on cancer cell proliferation. XDM-CBP is demonstrated to be a potent and selective CBP/p300 inhibitor that acts on specific cancer cell lines, in particular malignant melanoma, breast cancer, and leukemia.
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Affiliation(s)
- Martin Hügle
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Albertstrasse 21, 79104, Freiburg, Germany
| | - Xavier Lucas
- School of Life Sciences, Division of Biological Chemistry and Drug Discovery, University of Dundee, James Black Centre, Dow Street, Dundee, DD1 5EH, UK
| | - Dmytro Ostrovskyi
- Institut für Organische Chemie, Albert-Ludwigs-Universität Freiburg, Albertstrasse 21, 79104, Freiburg, Germany
| | - Pierre Regenass
- Institut für Organische Chemie, Albert-Ludwigs-Universität Freiburg, Albertstrasse 21, 79104, Freiburg, Germany
| | - Stefan Gerhardt
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Albertstrasse 21, 79104, Freiburg, Germany
| | - Oliver Einsle
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Albertstrasse 21, 79104, Freiburg, Germany
- Freiburg Institute for Advanced Studies (FRIAS), Albert-Ludwigs-Universität Freiburg, Albertstrasse 21, 79104, Freiburg, Germany
- BIOSS Centre for Biological Signalling Studies, Albert-Ludwigs-Universität Freiburg, Albertstr. 21, 79104, Freiburg, Germany
| | - Mirjam Hau
- Institut für Pharmazeutische Wissenschaften, Albert-Ludwigs-Universität Freiburg, Hermann-Herder-Strasse 9, 79104, Freiburg, Germany
| | - Manfred Jung
- Institut für Pharmazeutische Wissenschaften, Albert-Ludwigs-Universität Freiburg, Hermann-Herder-Strasse 9, 79104, Freiburg, Germany
| | - Bernhard Breit
- Freiburg Institute for Advanced Studies (FRIAS), Albert-Ludwigs-Universität Freiburg, Albertstrasse 21, 79104, Freiburg, Germany
- Institut für Organische Chemie, Albert-Ludwigs-Universität Freiburg, Albertstrasse 21, 79104, Freiburg, Germany
| | - Stefan Günther
- Institut für Pharmazeutische Wissenschaften, Albert-Ludwigs-Universität Freiburg, Hermann-Herder-Strasse 9, 79104, Freiburg, Germany
- Freiburg Institute for Advanced Studies (FRIAS), Albert-Ludwigs-Universität Freiburg, Albertstrasse 21, 79104, Freiburg, Germany
| | - Daniel Wohlwend
- Institut für Biochemie, Albert-Ludwigs-Universität Freiburg, Albertstrasse 21, 79104, Freiburg, Germany
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28
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Zucconi BE, Cole PA. Allosteric regulation of epigenetic modifying enzymes. Curr Opin Chem Biol 2017; 39:109-115. [PMID: 28689145 DOI: 10.1016/j.cbpa.2017.05.015] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Accepted: 05/29/2017] [Indexed: 12/14/2022]
Abstract
Epigenetic enzymes including histone modifying enzymes are key regulators of gene expression in normal and disease processes. Many drug development strategies to target histone modifying enzymes have focused on ligands that bind to enzyme active sites, but allosteric pockets offer potentially attractive opportunities for therapeutic development. Recent biochemical studies have revealed roles for small molecule and peptide ligands binding outside of the active sites in modulating the catalytic activities of histone modifying enzymes. Here we highlight several examples of allosteric regulation of epigenetic enzymes and discuss the biological significance of these findings.
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Affiliation(s)
- Beth E Zucconi
- Department of Pharmacology and Molecular Sciences, Johns Hopkins School of Medicine, 725 N. Wolfe St., Baltimore, MD 21205, USA.
| | - Philip A Cole
- Department of Pharmacology and Molecular Sciences, Johns Hopkins School of Medicine, 725 N. Wolfe St., Baltimore, MD 21205, USA.
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29
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Field SD, Arkin J, Li J, Jones LH. Selective Downregulation of JAK2 and JAK3 by an ATP-Competitive pan-JAK Inhibitor. ACS Chem Biol 2017; 12:1183-1187. [PMID: 28318222 DOI: 10.1021/acschembio.7b00116] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
PF-956980 has been used previously as a JAK3-selective chemical probe in numerous cell-based experiments. Here, we report that not only is PF-956980 a pan-JAK ATP-competitive inhibitor but it also causes selective reduction of endogenous JAK2 and JAK3 protein levels in human primary immune cells (in a time-dependent manner), leaving the other JAK family members (JAK1 and TYK2) unchanged. We found that PF-956980 selectively downregulated JAK2 and JAK3 mRNA, corresponding to changes observed at the protein level. This work highlights therapeutic opportunities for the development of pharmacological inhibitors that also modulate the expression of their cognate binding proteins.
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Affiliation(s)
- S. Denise Field
- Medicine
Design, Pfizer, 610 Main Street, Cambridge, Massachusetts 02139, United States
| | - Jacob Arkin
- Medicine
Design, Pfizer, 610 Main Street, Cambridge, Massachusetts 02139, United States
| | - Jing Li
- Medicine
Design, 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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30
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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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31
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Tetsu O, McCormick F. ETS-targeted therapy: can it substitute for MEK inhibitors? Clin Transl Med 2017; 6:16. [PMID: 28474232 PMCID: PMC5418169 DOI: 10.1186/s40169-017-0147-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Accepted: 04/11/2017] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND The RAS/MAPK pathway has been intensively studied in cancer. Constitutive activation of ERK1 and ERK2 is frequently found in cancer cells from a variety of tissues. In clinical practice and clinical trials, small molecules targeting receptor tyrosine kinases or components in the MAPK cascade are used for treatment. MEK1 and MEK2 are ideal targets because these enzymes are physiologically important and have narrow substrate specificities and distinctive structural characteristics. Despite success in pre-clinical testing, only two MEK inhibitors, trametinib and cobimetinib, have been approved, both for treatment of BRAF-mutant melanoma. Surprisingly, the efficacy of MEK inhibitors in other tumors has been disappointing. These facts suggest the need for a different approach. We here consider transcription factor ETS1 and ETS2 as alternate therapeutic targets because they are major MAPK downstream effectors. MAIN TEXT The lack of clinical efficacy of MEK inhibitors is attributed mostly to a subsequent loss of negative feedback regulation in the MAPK pathway. To overcome this obstacle, second-generation MEK inhibitors, so-called "feedback busters," have been developed. However, their efficacy is still unsatisfactory in the majority of cancers. To substitute ETS-targeted therapy, therapeutic strategies to modulate the transcription factor in cancer must be considered. Chemical targeting of ETS1 for proteolysis is a promising strategy; Src and USP9X inhibitors might achieve this by accelerating ETS1 protein turnover. Targeting the ETS1 interface might have great therapeutic value because ETS1 dimerizes itself or with other transcription factors to regulate target genes. In addition, transcriptional cofactors, including CBP/p300 and BRD4, represent intriguing targets for both ETS1 and ETS2. CONCLUSIONS ETS-targeted therapy appears to be promising. However, it may have a potential problem. It might inhibit autoregulatory negative feedback loops in the MAPK pathway, with consequent resistance to cell death by ERK1 and ERK2 activation. Further research is warranted to explore clinically applicable ways to inhibit ETS1 and ETS2.
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Affiliation(s)
- Osamu Tetsu
- Department of Otolaryngology-Head and Neck Surgery, School of Medicine, University of California, San Francisco, San Francisco, CA, 94143, USA. .,UCSF Helen Diller Family Comprehensive Cancer Center, School of Medicine, University of California, San Francisco, San Francisco, CA, 94143, USA.
| | - Frank McCormick
- UCSF Helen Diller Family Comprehensive Cancer Center, School of Medicine, University of California, San Francisco, San Francisco, CA, 94143, USA
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32
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Bromodomains in Protozoan Parasites: Evolution, Function, and Opportunities for Drug Development. Microbiol Mol Biol Rev 2017; 81:81/1/e00047-16. [PMID: 28077462 DOI: 10.1128/mmbr.00047-16] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Parasitic infections remain one of the most pressing global health concerns of our day, affecting billions of people and producing unsustainable economic burdens. The rise of drug-resistant parasites has created an urgent need to study their biology in hopes of uncovering new potential drug targets. It has been established that disrupting gene expression by interfering with lysine acetylation is detrimental to survival of apicomplexan (Toxoplasma gondii and Plasmodium spp.) and kinetoplastid (Leishmania spp. and Trypanosoma spp.) parasites. As "readers" of lysine acetylation, bromodomain proteins have emerged as key gene expression regulators and a promising new class of drug target. Here we review recent studies that demonstrate the essential roles played by bromodomain-containing proteins in parasite viability, invasion, and stage switching and present work showing the efficacy of bromodomain inhibitors as novel antiparasitic agents. In addition, we performed a phylogenetic analysis of bromodomain proteins in representative pathogens, some of which possess unique features that may be specific to parasite processes and useful in future drug development.
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33
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Humphreys PG, Bamborough P, Chung CW, Craggs PD, Gordon L, Grandi P, Hayhow TG, Hussain J, Jones KL, Lindon M, Michon AM, Renaux JF, Suckling CJ, Tough DF, Prinjha RK. Discovery of a Potent, Cell Penetrant, and Selective p300/CBP-Associated Factor (PCAF)/General Control Nonderepressible 5 (GCN5) Bromodomain Chemical Probe. J Med Chem 2017; 60:695-709. [DOI: 10.1021/acs.jmedchem.6b01566] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
| | | | | | | | | | - Paola Grandi
- Cellzome
GmbH, Molecular Discovery Research, GlaxoSmithKline, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | | | | | | | | | - Anne-Marie Michon
- Cellzome
GmbH, Molecular Discovery Research, GlaxoSmithKline, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | | | - Colin J. Suckling
- WestCHEM,
Department of Pure and Applied Chemistry, University of Strathclyde, Thomas Graham Building, 295 Cathedral Street, Glasgow, G1 1XL, United Kingdom
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34
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Abstract
Aberrations in the epigenetic landscape are a hallmark of cancer. Alterations in enzymes that are “writers,” “erasers,” or “readers” of histone modification marks are common. Bromodomains are “readers” that bind acetylated lysines in histone tails. Their most important function is the regulation of gene transcription by the recruitment of different molecular partners. Moreover, proteins containing bromodomains are also epigenetic regulators, although little is known about the specific function of these domains. In recent years, there has been increasing interest in developing small molecules that can target specific bromodomains. First, this has helped clarify biological functions of bromodomain-containing proteins. Secondly, it opens a new front for combatting cancer. In this review we will describe the structures and mechanisms associated with Bromodomain and Extra-Terminal motif (BET) inhibitors and non-BET inhibitors, their current status of development, and their promising role as anti-cancer agents.
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Affiliation(s)
- Montserrat Pérez-Salvia
- a Cancer Epigenetics and Biology Program (PEBC) , Bellvitge Biomedical Research Institute (IDIBELL) , Barcelona , Catalonia , Spain
| | - Manel Esteller
- a Cancer Epigenetics and Biology Program (PEBC) , Bellvitge Biomedical Research Institute (IDIBELL) , Barcelona , Catalonia , Spain.,b Department of Physiological Sciences II, School of Medicine , University of Barcelona , Barcelona , Catalonia , Spain.,c Institució Catalana de Recerca i Estudis Avançats (ICREA) , Barcelona , Catalonia , Spain
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35
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Crawford TD, Romero FA, Lai KW, Tsui V, Taylor AM, de Leon Boenig G, Noland CL, Murray J, Ly J, Choo EF, Hunsaker TL, Chan EW, Merchant M, Kharbanda S, Gascoigne KE, Kaufman S, Beresini MH, Liao J, Liu W, Chen KX, Chen Z, Conery AR, Côté A, Jayaram H, Jiang Y, Kiefer JR, Kleinheinz T, Li Y, Maher J, Pardo E, Poy F, Spillane KL, Wang F, Wang J, Wei X, Xu Z, Xu Z, Yen I, Zawadzke L, Zhu X, Bellon S, Cummings R, Cochran AG, Albrecht BK, Magnuson S. Discovery of a Potent and Selective in Vivo Probe (GNE-272) for the Bromodomains of CBP/EP300. J Med Chem 2016; 59:10549-10563. [PMID: 27682507 DOI: 10.1021/acs.jmedchem.6b01022] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The single bromodomain of the closely related transcriptional regulators CBP/EP300 is a target of much recent interest in cancer and immune system regulation. A co-crystal structure of a ligand-efficient screening hit and the CBP bromodomain guided initial design targeting the LPF shelf, ZA loop, and acetylated lysine binding regions. Structure-activity relationship studies allowed us to identify a more potent analogue. Optimization of permeability and microsomal stability and subsequent improvement of mouse hepatocyte stability afforded 59 (GNE-272, TR-FRET IC50 = 0.02 μM, BRET IC50 = 0.41 μM, BRD4(1) IC50 = 13 μM) that retained the best balance of cell potency, selectivity, and in vivo PK. Compound 59 showed a marked antiproliferative effect in hematologic cancer cell lines and modulates MYC expression in vivo that corresponds with antitumor activity in an AML tumor model.
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Affiliation(s)
- Terry D Crawford
- Genentech, Inc. 1 DNA Way, South San Francisco, California 94080, United States
| | - F Anthony Romero
- Genentech, Inc. 1 DNA Way, South San Francisco, California 94080, United States
| | - Kwong Wah Lai
- Wuxi Apptec Co., Ltd. , 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, People's Republic of China
| | - Vickie Tsui
- Genentech, Inc. 1 DNA Way, South San Francisco, California 94080, United States
| | - Alexander M Taylor
- Constellation Pharmaceuticals, Inc. 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | | | - Cameron L Noland
- Genentech, Inc. 1 DNA Way, South San Francisco, California 94080, United States
| | - Jeremy Murray
- Genentech, Inc. 1 DNA Way, South San Francisco, California 94080, United States
| | - Justin Ly
- Genentech, Inc. 1 DNA Way, South San Francisco, California 94080, United States
| | - Edna F Choo
- Genentech, Inc. 1 DNA Way, South San Francisco, California 94080, United States
| | - Thomas L Hunsaker
- Genentech, Inc. 1 DNA Way, South San Francisco, California 94080, United States
| | - Emily W Chan
- Genentech, Inc. 1 DNA Way, South San Francisco, California 94080, United States
| | - Mark Merchant
- Genentech, Inc. 1 DNA Way, South San Francisco, California 94080, United States
| | - Samir Kharbanda
- Genentech, Inc. 1 DNA Way, South San Francisco, California 94080, United States
| | - Karen E Gascoigne
- Genentech, Inc. 1 DNA Way, South San Francisco, California 94080, United States
| | - Susan Kaufman
- Genentech, Inc. 1 DNA Way, South San Francisco, California 94080, United States
| | - Maureen H Beresini
- Genentech, Inc. 1 DNA Way, South San Francisco, California 94080, United States
| | - Jiangpeng Liao
- Wuxi Apptec Co., Ltd. , 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, People's Republic of China
| | - Wenfeng Liu
- Wuxi Apptec Co., Ltd. , 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, People's Republic of China
| | - Kevin X Chen
- Wuxi Apptec Co., Ltd. , 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, People's Republic of China
| | - Zhongguo Chen
- Wuxi Apptec Co., Ltd. , 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, People's Republic of China
| | - Andrew R Conery
- Constellation Pharmaceuticals, Inc. 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Alexandre Côté
- Constellation Pharmaceuticals, Inc. 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Hariharan Jayaram
- Constellation Pharmaceuticals, Inc. 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Ying Jiang
- Wuxi Apptec Co., Ltd. , 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, People's Republic of China
| | - James R Kiefer
- Genentech, Inc. 1 DNA Way, South San Francisco, California 94080, United States
| | - Tracy Kleinheinz
- Genentech, Inc. 1 DNA Way, South San Francisco, California 94080, United States
| | - Yingjie Li
- Wuxi Apptec Co., Ltd. , 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, People's Republic of China
| | - Jonathan Maher
- Genentech, Inc. 1 DNA Way, South San Francisco, California 94080, United States
| | - Eneida Pardo
- Constellation Pharmaceuticals, Inc. 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Florence Poy
- Constellation Pharmaceuticals, Inc. 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Kerry L Spillane
- Constellation Pharmaceuticals, Inc. 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Fei Wang
- Wuxi Apptec Co., Ltd. , 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, People's Republic of China
| | - Jian Wang
- Wuxi Apptec Co., Ltd. , 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, People's Republic of China
| | - Xiaocang Wei
- Wuxi Apptec Co., Ltd. , 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, People's Republic of China
| | - Zhaowu Xu
- Wuxi Apptec Co., Ltd. , 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, People's Republic of China
| | - Zhongya Xu
- Wuxi Apptec Co., Ltd. , 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, People's Republic of China
| | - Ivana Yen
- Genentech, Inc. 1 DNA Way, South San Francisco, California 94080, United States
| | - Laura Zawadzke
- Constellation Pharmaceuticals, Inc. 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Xiaoyu Zhu
- Wuxi Apptec Co., Ltd. , 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, People's Republic of China
| | - Steven Bellon
- Constellation Pharmaceuticals, Inc. 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Richard Cummings
- Constellation Pharmaceuticals, Inc. 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Andrea G Cochran
- Genentech, Inc. 1 DNA Way, South San Francisco, California 94080, United States
| | - Brian K Albrecht
- Constellation Pharmaceuticals, Inc. 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Steven Magnuson
- Genentech, Inc. 1 DNA Way, South San Francisco, California 94080, United States
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36
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Moustakim M, Clark PGK, Hay DA, Dixon DJ, Brennan PE. Chemical probes and inhibitors of bromodomains outside the BET family. MEDCHEMCOMM 2016; 7:2246-2264. [PMID: 29170712 PMCID: PMC5644722 DOI: 10.1039/c6md00373g] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Accepted: 09/06/2016] [Indexed: 01/03/2023]
Abstract
Significant progress has been made in discovering inhibitors and chemical probes of bromodomains, epigenetic readers of lysine acetylation.
In the last five years, the development of inhibitors of bromodomains has emerged as an area of intensive worldwide research. Emerging evidence has implicated a number of non-BET bromodomains in the onset and progression of diseases such as cancer, HIV infection and inflammation. The development and use of small molecule chemical probes has been fundamental to pre-clinical evaluation of bromodomains as targets. Recent efforts are described highlighting the development of potent, selective and cell active non-BET bromodomain inhibitors and their therapeutic potential. Over half of typical bromodomains now have reported ligands, but those with atypical binding site residues remain resistant to chemical probe discovery efforts.
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Affiliation(s)
- Moses Moustakim
- Department of Chemistry, University of Oxford, Oxford OX1 3TA, UK.,Structural Genomics Consortium, University of Oxford, OX3 7DQ, UK. .,Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, OX3 7FZ, UK
| | - Peter G K Clark
- Department of Chemistry, Simon Fraser University, Burnaby V5A 1S6, Canada
| | - Duncan A Hay
- Evotec (UK) Ltd, 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire OX14 4RZ, UK
| | - Darren J Dixon
- Department of Chemistry, University of Oxford, Oxford OX1 3TA, UK
| | - Paul E Brennan
- Structural Genomics Consortium, University of Oxford, OX3 7DQ, UK. .,Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, OX3 7FZ, UK
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37
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Theodoulou NH, Tomkinson NCO, Prinjha RK, Humphreys PG. Clinical progress and pharmacology of small molecule bromodomain inhibitors. Curr Opin Chem Biol 2016; 33:58-66. [DOI: 10.1016/j.cbpa.2016.05.028] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Revised: 05/25/2016] [Accepted: 05/30/2016] [Indexed: 11/26/2022]
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38
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Crawford TD, Tsui V, Flynn EM, Wang S, Taylor AM, Côté A, Audia JE, Beresini MH, Burdick DJ, Cummings R, Dakin LA, Duplessis M, Good AC, Hewitt MC, Huang HR, Jayaram H, Kiefer JR, Jiang Y, Murray J, Nasveschuk CG, Pardo E, Poy F, Romero FA, Tang Y, Wang J, Xu Z, Zawadzke LE, Zhu X, Albrecht BK, Magnuson SR, Bellon S, Cochran AG. Diving into the Water: Inducible Binding Conformations for BRD4, TAF1(2), BRD9, and CECR2 Bromodomains. J Med Chem 2016; 59:5391-402. [PMID: 27219867 DOI: 10.1021/acs.jmedchem.6b00264] [Citation(s) in RCA: 84] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The biological role played by non-BET bromodomains remains poorly understood, and it is therefore imperative to identify potent and highly selective inhibitors to effectively explore the biology of individual bromodomain proteins. A ligand-efficient nonselective bromodomain inhibitor was identified from a 6-methyl pyrrolopyridone fragment. Small hydrophobic substituents replacing the N-methyl group were designed directing toward the conserved bromodomain water pocket, and two distinct binding conformations were then observed. The substituents either directly displaced and rearranged the conserved solvent network, as in BRD4(1) and TAF1(2), or induced a narrow hydrophobic channel adjacent to the lipophilic shelf, as in BRD9 and CECR2. The preference of distinct substituents for individual bromodomains provided selectivity handles useful for future lead optimization efforts for selective BRD9, CECR2, and TAF1(2) inhibitors.
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Affiliation(s)
- Terry D Crawford
- Genentech, Inc. 1 DNA Way, South San Francisco, California 94080, United States
| | - Vickie Tsui
- Genentech, Inc. 1 DNA Way, South San Francisco, California 94080, United States
| | - E Megan Flynn
- Genentech, Inc. 1 DNA Way, South San Francisco, California 94080, United States
| | - Shumei Wang
- Genentech, Inc. 1 DNA Way, South San Francisco, California 94080, United States
| | - Alexander M Taylor
- Constellation Pharmaceuticals, Inc. 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Alexandre Côté
- Constellation Pharmaceuticals, Inc. 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - James E Audia
- Constellation Pharmaceuticals, Inc. 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Maureen H Beresini
- Genentech, Inc. 1 DNA Way, South San Francisco, California 94080, United States
| | - Daniel J Burdick
- Genentech, Inc. 1 DNA Way, South San Francisco, California 94080, United States
| | - Richard Cummings
- Constellation Pharmaceuticals, Inc. 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Les A Dakin
- Constellation Pharmaceuticals, Inc. 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Martin Duplessis
- Constellation Pharmaceuticals, Inc. 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Andrew C Good
- Constellation Pharmaceuticals, Inc. 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Michael C Hewitt
- Constellation Pharmaceuticals, Inc. 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Hon-Ren Huang
- Constellation Pharmaceuticals, Inc. 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Hariharan Jayaram
- Constellation Pharmaceuticals, Inc. 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - James R Kiefer
- Genentech, Inc. 1 DNA Way, South San Francisco, California 94080, United States
| | - Ying Jiang
- Wuxi AppTec Co., Ltd. , 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, People's Republic of China
| | - Jeremy Murray
- Genentech, Inc. 1 DNA Way, South San Francisco, California 94080, United States
| | - Christopher G Nasveschuk
- Constellation Pharmaceuticals, Inc. 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Eneida Pardo
- Constellation Pharmaceuticals, Inc. 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Florence Poy
- Constellation Pharmaceuticals, Inc. 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - F Anthony Romero
- Genentech, Inc. 1 DNA Way, South San Francisco, California 94080, United States
| | - Yong Tang
- Constellation Pharmaceuticals, Inc. 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Jian Wang
- Wuxi AppTec Co., Ltd. , 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, People's Republic of China
| | - Zhaowu Xu
- Wuxi AppTec Co., Ltd. , 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, People's Republic of China
| | - Laura E Zawadzke
- Constellation Pharmaceuticals, Inc. 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Xiaoyu Zhu
- Wuxi AppTec Co., Ltd. , 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, People's Republic of China
| | - Brian K Albrecht
- Constellation Pharmaceuticals, Inc. 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Steven R Magnuson
- Genentech, Inc. 1 DNA Way, South San Francisco, California 94080, United States
| | - Steve Bellon
- Constellation Pharmaceuticals, Inc. 215 First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Andrea G Cochran
- Genentech, Inc. 1 DNA Way, South San Francisco, California 94080, United States
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39
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Taylor AM, Côté A, Hewitt MC, Pastor R, Leblanc Y, Nasveschuk CG, Romero FA, Crawford T, Cantone N, Jayaram H, Setser J, Murray J, Beresini MH, de Leon
Boenig G, Chen Z, Conery A, Cummings RT, Dakin LA, Flynn EM, Huang OW, Kaufman S, Keller PJ, Kiefer JR, Lai T, Li Y, Liao J, Liu W, Lu H, Pardo E, Tsui V, Wang J, Wang Y, Xu Z, Yan F, Yu D, Zawadzke L, Zhu X, Zhu X, Sims RJ, Cochran AG, Bellon S, Audia J, Magnuson S, Albrecht BK. Fragment-Based Discovery of a Selective and Cell-Active Benzodiazepinone CBP/EP300 Bromodomain Inhibitor (CPI-637). ACS Med Chem Lett 2016; 7:531-6. [PMID: 27190605 PMCID: PMC4867486 DOI: 10.1021/acsmedchemlett.6b00075] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Accepted: 03/15/2016] [Indexed: 12/11/2022] Open
Abstract
CBP and EP300 are highly homologous, bromodomain-containing transcription coactivators involved in numerous cellular pathways relevant to oncology. As part of our effort to explore the potential therapeutic implications of selectively targeting bromodomains, we set out to identify a CBP/EP300 bromodomain inhibitor that was potent both in vitro and in cellular target engagement assays and was selective over the other members of the bromodomain family. Reported here is a series of cell-potent and selective probes of the CBP/EP300 bromodomains, derived from the fragment screening hit 4-methyl-1,3,4,5-tetrahydro-2H-benzo[b][1,4]diazepin-2-one.
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Affiliation(s)
- Alexander M. Taylor
- Constellation
Pharmaceuticals, 215
First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Alexandre Côté
- Constellation
Pharmaceuticals, 215
First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Michael C. Hewitt
- Constellation
Pharmaceuticals, 215
First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Richard Pastor
- Genentech,
Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Yves Leblanc
- Constellation
Pharmaceuticals, 215
First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Christopher G. Nasveschuk
- Constellation
Pharmaceuticals, 215
First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - F. Anthony Romero
- Genentech,
Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Terry
D. Crawford
- Genentech,
Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Nico Cantone
- Constellation
Pharmaceuticals, 215
First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Hariharan Jayaram
- Constellation
Pharmaceuticals, 215
First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Jeremy Setser
- Constellation
Pharmaceuticals, 215
First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Jeremy Murray
- Genentech,
Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Maureen H. Beresini
- Genentech,
Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | | | - Zhongguo Chen
- Wuxi
AppTec Co., Ltd., 288
Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, People’s
Republic of China
| | - Andrew
R. Conery
- Constellation
Pharmaceuticals, 215
First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Richard T. Cummings
- Constellation
Pharmaceuticals, 215
First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Leslie A. Dakin
- Constellation
Pharmaceuticals, 215
First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - E. Megan Flynn
- Genentech,
Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Oscar W. Huang
- Genentech,
Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Susan Kaufman
- Genentech,
Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Patricia J. Keller
- Constellation
Pharmaceuticals, 215
First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - James R. Kiefer
- Genentech,
Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Tommy Lai
- Wuxi
AppTec Co., Ltd., 288
Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, People’s
Republic of China
| | - Yingjie Li
- Wuxi
AppTec Co., Ltd., 288
Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, People’s
Republic of China
| | - Jiangpeng Liao
- Wuxi
AppTec Co., Ltd., 288
Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, People’s
Republic of China
| | - Wenfeng Liu
- Wuxi
AppTec Co., Ltd., 288
Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, People’s
Republic of China
| | - Henry Lu
- Wuxi
AppTec Co., Ltd., 288
Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, People’s
Republic of China
| | - Eneida Pardo
- Constellation
Pharmaceuticals, 215
First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Vickie Tsui
- Genentech,
Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Jian Wang
- Wuxi
AppTec Co., Ltd., 288
Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, People’s
Republic of China
| | - Yongyun Wang
- Wuxi
AppTec Co., Ltd., 288
Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, People’s
Republic of China
| | - Zhaowu Xu
- Wuxi
AppTec Co., Ltd., 288
Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, People’s
Republic of China
| | - Fen Yan
- Wuxi
AppTec Co., Ltd., 288
Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, People’s
Republic of China
| | - Dong Yu
- Wuxi
AppTec Co., Ltd., 288
Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, People’s
Republic of China
| | - Laura Zawadzke
- Constellation
Pharmaceuticals, 215
First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Xiaoqin Zhu
- Wuxi
AppTec Co., Ltd., 288
Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, People’s
Republic of China
| | - Xiaoyu Zhu
- Wuxi
AppTec Co., Ltd., 288
Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, People’s
Republic of China
| | - Robert J. Sims
- Constellation
Pharmaceuticals, 215
First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Andrea G. Cochran
- Genentech,
Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Steve Bellon
- Constellation
Pharmaceuticals, 215
First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - James
E. Audia
- Constellation
Pharmaceuticals, 215
First Street, Suite 200, Cambridge, Massachusetts 02142, United States
| | - Steven Magnuson
- Genentech,
Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Brian K. Albrecht
- Constellation
Pharmaceuticals, 215
First Street, Suite 200, Cambridge, Massachusetts 02142, United States
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40
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Affiliation(s)
- Lyn H Jones
- a Worldwide Medicinal Chemistry, Pfizer , Cambridge , MA , USA
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41
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Theodoulou NH, Tomkinson NCO, Prinjha RK, Humphreys PG. Progress in the Development of non-BET Bromodomain Chemical Probes. ChemMedChem 2016; 11:477-87. [PMID: 26749027 DOI: 10.1002/cmdc.201500540] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Revised: 12/09/2015] [Indexed: 12/19/2022]
Abstract
The bromodomain and extra terminal (BET) family of bromodomains have been the focus of extensive research, leading to the development of many potent, selective chemical probes and recent clinical assets. The profound biology associated with BET bromodomain inhibition has provided a convincing rationale for targeting bromodomains for the treatment of disease. However, the BET family represents just eight of the at least 56 human bromodomains identified to date. Until recently, there has been significantly less interest in non-BET bromodomains, leaving a vast area of research and the majority of this new target class yet to be thoroughly investigated. It has been widely reported that several non-BET bromodomain containing proteins are associated with various diseases including cancer and HIV. Therefore, the development of chemical probes for non-BET bromodomains will facilitate elucidation of their precise biological roles and potentially lead to the development of new medicines. This review summarises the progress made towards the development of non-BET bromodomain chemical probes to date. In addition, we highlight the potential for future work in this new and exciting area.
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Affiliation(s)
- Natalie H Theodoulou
- Epinova Epigenetics Discovery Performance Unit, GlaxoSmithKline R&D, Stevenage, Hertfordshire, SG1 2NY, UK.,WestCHEM, Department of Pure and Applied Chemistry, Thomas Graham Building, University of Strathclyde, 295 Cathedral Street, Glasgow, G1 1XL, UK
| | - Nicholas C O Tomkinson
- WestCHEM, Department of Pure and Applied Chemistry, Thomas Graham Building, University of Strathclyde, 295 Cathedral Street, Glasgow, G1 1XL, UK
| | - Rab K Prinjha
- Epinova Epigenetics Discovery Performance Unit, GlaxoSmithKline R&D, Stevenage, Hertfordshire, SG1 2NY, UK
| | - Philip G Humphreys
- Epinova Epigenetics Discovery Performance Unit, GlaxoSmithKline R&D, Stevenage, Hertfordshire, SG1 2NY, UK.
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