1
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Pan Z, Zhao Y, Wang X, Xie X, Liu M, Zhang K, Wang L, Bai D, Foster LJ, Shu R, He G. Targeting bromodomain-containing proteins: research advances of drug discovery. MOLECULAR BIOMEDICINE 2023; 4:13. [PMID: 37142850 PMCID: PMC10159834 DOI: 10.1186/s43556-023-00127-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 04/02/2023] [Indexed: 05/06/2023] Open
Abstract
Bromodomain (BD) is an evolutionarily conserved protein module found in 46 different BD-containing proteins (BCPs). BD acts as a specific reader for acetylated lysine residues (KAc) and serves an essential role in transcriptional regulation, chromatin remodeling, DNA damage repair, and cell proliferation. On the other hand, BCPs have been shown to be involved in the pathogenesis of a variety of diseases, including cancers, inflammation, cardiovascular diseases, and viral infections. Over the past decade, researchers have brought new therapeutic strategies to relevant diseases by inhibiting the activity or downregulating the expression of BCPs to interfere with the transcription of pathogenic genes. An increasing number of potent inhibitors and degraders of BCPs have been developed, some of which are already in clinical trials. In this paper, we provide a comprehensive review of recent advances in the study of drugs that inhibit or down-regulate BCPs, focusing on the development history, molecular structure, biological activity, interaction with BCPs and therapeutic potentials of these drugs. In addition, we discuss current challenges, issues to be addressed and future research directions for the development of BCPs inhibitors. Lessons learned from the successful or unsuccessful development experiences of these inhibitors or degraders will facilitate the further development of efficient, selective and less toxic inhibitors of BCPs and eventually achieve drug application in the clinic.
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Affiliation(s)
- Zhaoping Pan
- Department of Dermatology & Venerology and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
- Laboratory of Dermatology, Clinical Institute of Inflammation and Immunology (CIII), Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Yuxi Zhao
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Disease, Department of Orthodontics and Pediatrics, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, China
| | - Xiaoyun Wang
- Department of Dermatology & Venerology and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
- Laboratory of Dermatology, Clinical Institute of Inflammation and Immunology (CIII), Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Xin Xie
- College of Medical Technology and School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Mingxia Liu
- Department of Dermatology & Venerology and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Kaiyao Zhang
- Department of Dermatology & Venerology and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Lian Wang
- Department of Dermatology & Venerology and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Ding Bai
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Disease, Department of Orthodontics and Pediatrics, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, China
| | - Leonard J Foster
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Rui Shu
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Disease, Department of Orthodontics and Pediatrics, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, China.
| | - Gu He
- Department of Dermatology & Venerology and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China.
- Laboratory of Dermatology, Clinical Institute of Inflammation and Immunology (CIII), Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610041, China.
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2
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Lu H, Zu S, Duan Z, Feng Y, Wang J, Ma J, Li Q, Chen D, Li B, Chen K, Luo C, Lin J, Lu T, Lin H. Discovery of
CECR2
Bromodomain Inhibitors with High Selectivities over
BPTF
Bromodomain. CHINESE J CHEM 2022. [DOI: 10.1002/cjoc.202200208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Haibo Lu
- School of Pharmacy, Fudan University, 826 Zhangheng Road Shanghai 201203 China
- State Key Laboratory of Drug Research, , Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road Shanghai 201203 China
| | - Shijia Zu
- State Key Laboratory of Drug Research, , Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road Shanghai 201203 China
- University of Chinese Academy of Sciences, 19 Yuquan Road Beijing 100049 China
| | - Zhe Duan
- School of Pharmacy Nanchang University Nanchang 330006 China
| | - Yueyao Feng
- Biomedical Research Center of South China, College of Life Sciences Fujian Normal University Fuzhou 350117 China
| | - Jie Wang
- Biomedical Research Center of South China, College of Life Sciences Fujian Normal University Fuzhou 350117 China
| | - Jingyi Ma
- University of Chinese Academy of Sciences, 19 Yuquan Road Beijing 100049 China
- Laboratory of Pharmaceutical Analysis, , Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Zhangjiang Hi‐Tech Park Shanghai 201203 China
| | - Qi Li
- State Key Laboratory of Drug Research, , Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road Shanghai 201203 China
| | - Dongying Chen
- University of Chinese Academy of Sciences, 19 Yuquan Road Beijing 100049 China
- Laboratory of Pharmaceutical Analysis, , Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Zhangjiang Hi‐Tech Park Shanghai 201203 China
| | - Bo Li
- State Key Laboratory of Drug Research, , Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road Shanghai 201203 China
| | - Kaixian Chen
- School of Pharmacy, Fudan University, 826 Zhangheng Road Shanghai 201203 China
- State Key Laboratory of Drug Research, , Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road Shanghai 201203 China
- University of Chinese Academy of Sciences, 19 Yuquan Road Beijing 100049 China
| | - Cheng Luo
- School of Pharmacy, Fudan University, 826 Zhangheng Road Shanghai 201203 China
- State Key Laboratory of Drug Research, , Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road Shanghai 201203 China
- University of Chinese Academy of Sciences, 19 Yuquan Road Beijing 100049 China
| | - Jin Lin
- School of Pharmacy Fujian Medical University Fuzhou 350122 China
| | - Tian Lu
- GuiZhou University of Traditional Chinese Medicine Guizhou 550025 China
| | - Hua Lin
- Biomedical Research Center of South China, College of Life Sciences Fujian Normal University Fuzhou 350117 China
- State Key Laboratory of Drug Research, , Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road Shanghai 201203 China
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3
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Lu H, Lu T, Zu S, Duan Z, Guang Y, Li Q, Ma J, Chen D, Li B, Lu W, Jiang H, Luo C, Ye D, Chen K, Lin H. Discovery of a Highly Potent CECR2 Bromodomain Inhibitor with 7H-pyrrolo[2,3-d] Pyrimidine Scaffold. Bioorg Chem 2022; 123:105768. [DOI: 10.1016/j.bioorg.2022.105768] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 03/14/2022] [Accepted: 03/24/2022] [Indexed: 12/24/2022]
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4
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Zhang M, Liu ZZ, Aoshima K, Cai WL, Sun H, Xu T, Zhang Y, An Y, Chen JF, Chan LH, Aoshima A, Lang SM, Tang Z, Che X, Li Y, Rutter SJ, Bossuyt V, Chen X, Morrow JS, Pusztai L, Rimm DL, Yin M, Yan Q. CECR2 drives breast cancer metastasis by promoting NF-κB signaling and macrophage-mediated immune suppression. Sci Transl Med 2022; 14:eabf5473. [PMID: 35108062 PMCID: PMC9003667 DOI: 10.1126/scitranslmed.abf5473] [Citation(s) in RCA: 49] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Metastasis is the major cause of cancer-related deaths due to the lack of effective therapies. Emerging evidence suggests that certain epigenetic and transcriptional regulators drive cancer metastasis and could be targeted for metastasis treatment. To identify epigenetic regulators of breast cancer metastasis, we profiled the transcriptomes of matched pairs of primary breast tumors and metastases from human patients. We found that distant metastases are more immune inert with increased M2 macrophages compared to their matched primary tumors. The acetyl-lysine reader, cat eye syndrome chromosome region candidate 2 (CECR2), was the top up-regulated epigenetic regulator in metastases associated with an increased abundance of M2 macrophages and worse metastasis-free survival. CECR2 was required for breast cancer metastasis in multiple mouse models, with more profound effect in the immunocompetent setting. Mechanistically, the nuclear factor κB (NF-κB) family member v-rel avian reticuloendotheliosis viral oncogene homolog A (RELA) recruits CECR2 to increase chromatin accessibility and activate the expression of their target genes. These target genes include multiple metastasis-promoting genes, such as TNC, MMP2, and VEGFA, and cytokine genes CSF1 and CXCL1, which are critical for immunosuppression at metastatic sites. Consistent with these results, pharmacological inhibition of CECR2 bromodomain impeded NF-κB-mediated immune suppression by macrophages and inhibited breast cancer metastasis. These results reveal that targeting CECR2 may be a strategy to treat metastatic breast cancer.
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Affiliation(s)
- Meiling Zhang
- Department of Pathology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Zongzhi Z. Liu
- Department of Pathology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Keisuke Aoshima
- Department of Pathology, Yale School of Medicine, New Haven, CT 06520, USA
- Laboratory of Comparative Pathology, Department of Veterinary Clinical Sciences, Faculty of Veterinary Medicine, Hokkaido University, Sapporo 060-0818, Japan
| | - Wesley L. Cai
- Department of Pathology, Yale School of Medicine, New Haven, CT 06520, USA
- Hillman Cancer Center, University of Pittsburgh Medical Center, Pittsburgh, PA 15232, USA
| | - Hongyin Sun
- Department of Dermatology, Hunan Engineering Research Center of Skin Health and Disease, Hunan Key Laboratory of Skin Cancer and Psoriasis, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Tianrui Xu
- Department of Dermatology, Hunan Engineering Research Center of Skin Health and Disease, Hunan Key Laboratory of Skin Cancer and Psoriasis, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Yangyi Zhang
- Department of Pathology, Yale School of Medicine, New Haven, CT 06520, USA
- Department of Dermatology, Hunan Engineering Research Center of Skin Health and Disease, Hunan Key Laboratory of Skin Cancer and Psoriasis, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Yongyan An
- Department of Pathology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Jocelyn F. Chen
- Department of Pathology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Lok Hei Chan
- Department of Pathology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Asako Aoshima
- Department of Pathology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Sabine M. Lang
- Department of Pathology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Zhenwei Tang
- Department of Dermatology, Hunan Engineering Research Center of Skin Health and Disease, Hunan Key Laboratory of Skin Cancer and Psoriasis, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Xuanlin Che
- Department of Dermatology, Hunan Engineering Research Center of Skin Health and Disease, Hunan Key Laboratory of Skin Cancer and Psoriasis, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Yao Li
- Department of Pathology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Sara J. Rutter
- Department of Pathology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Veerle Bossuyt
- Department of Pathology, Yale School of Medicine, New Haven, CT 06520, USA
| | - Xiang Chen
- Department of Dermatology, Hunan Engineering Research Center of Skin Health and Disease, Hunan Key Laboratory of Skin Cancer and Psoriasis, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Jon S. Morrow
- Department of Pathology, Yale School of Medicine, New Haven, CT 06520, USA
- Yale Cancer Center, Yale School of Medicine, New Haven, CT 06520, USA
| | - Lajos Pusztai
- Yale Cancer Center, Yale School of Medicine, New Haven, CT 06520, USA
- Breast Medical Oncology, Yale Cancer Center, Yale University, New Haven, CT 06520, USA
| | - David. L. Rimm
- Department of Pathology, Yale School of Medicine, New Haven, CT 06520, USA
- Yale Cancer Center, Yale School of Medicine, New Haven, CT 06520, USA
| | - Mingzhu Yin
- Department of Pathology, Yale School of Medicine, New Haven, CT 06520, USA
- Department of Dermatology, Hunan Engineering Research Center of Skin Health and Disease, Hunan Key Laboratory of Skin Cancer and Psoriasis, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Qin Yan
- Department of Pathology, Yale School of Medicine, New Haven, CT 06520, USA
- Yale Cancer Center, Yale School of Medicine, New Haven, CT 06520, USA
- Yale Stem Cell Center, Yale School of Medicine, New Haven, CT 06520, USA
- Yale Center for Immuno-Oncology, Yale School of Medicine, New Haven, CT 06520, USA
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5
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Warnecke A, Giesemann A. Embryology, Malformations, and Rare Diseases of the Cochlea. Laryngorhinootologie 2021; 100:S1-S43. [PMID: 34352899 PMCID: PMC8354575 DOI: 10.1055/a-1349-3824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Despite the low overall prevalence of individual rare diseases, cochlear
dysfunction leading to hearing loss represents a symptom in a large
proportion. The aim of this work was to provide a clear overview of rare
cochlear diseases, taking into account the embryonic development of the
cochlea and the systematic presentation of the different disorders. Although
rapid biotechnological and bioinformatic advances may facilitate the
diagnosis of a rare disease, an interdisciplinary exchange is often required
to raise the suspicion of a rare disease. It is important to recognize that
the phenotype of rare inner ear diseases can vary greatly not only in
non-syndromic but also in syndromic hearing disorders. Finally, it becomes
clear that the phenotype of the individual rare diseases cannot be
determined exclusively by classical genetics even in monogenetic
disorders.
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Affiliation(s)
- Athanasia Warnecke
- Klinik für Hals-, Nasen- und Ohrenheilkunde, Medizinische Hochschule Hannover, Carl-Neuberg-Straße 1, 30625 Hannover.,Deutsche Forschungsgemeinschaft Exzellenzcluster"Hearing4all" - EXC 2177/1 - Project ID 390895286
| | - Anja Giesemann
- Institut für Neuroradiologie, Medizinische Hochschule Hannover, Carl-Neuberg-Straße 1, 30625 Hannover
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6
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Clegg MA, Bamborough P, Chung CW, Craggs PD, Gordon L, Grandi P, Leveridge M, Lindon M, Liwicki GM, Michon AM, Molnar J, Rioja I, Soden PE, Theodoulou NH, Werner T, Tomkinson NCO, Prinjha RK, Humphreys PG. Application of Atypical Acetyl-lysine Methyl Mimetics in the Development of Selective Inhibitors of the Bromodomain-Containing Protein 7 (BRD7)/Bromodomain-Containing Protein 9 (BRD9) Bromodomains. J Med Chem 2020; 63:5816-5840. [PMID: 32410449 DOI: 10.1021/acs.jmedchem.0c00075] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Non-BET bromodomain-containing proteins have become attractive targets for the development of novel therapeutics targeting epigenetic pathways. To help facilitate the target validation of this class of proteins, structurally diverse small-molecule ligands and methodologies to produce selective inhibitors in a predictable fashion are in high demand. Herein, we report the development and application of atypical acetyl-lysine (KAc) methyl mimetics to take advantage of the differential stability of conserved water molecules in the bromodomain binding site. Discovery of the n-butyl group as an atypical KAc methyl mimetic allowed generation of 31 (GSK6776) as a soluble, permeable, and selective BRD7/9 inhibitor from a pyridazinone template. The n-butyl group was then used to enhance the bromodomain selectivity of an existing BRD9 inhibitor and to transform pan-bromodomain inhibitors into BRD7/9 selective compounds. Finally, a solvent-exposed vector was defined from the pyridazinone template to enable bifunctional molecule synthesis, and affinity enrichment chemoproteomic experiments were used to confirm several of the endogenous protein partners of BRD7 and BRD9, which form part of the chromatin remodeling PBAF and BAF complexes, respectively.
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Affiliation(s)
- Michael A Clegg
- GlaxoSmithKline R&D, Stevenage SG1 2NY, Hertfordshire, United Kingdom.,WestCHEM, Department of Pure and Applied Chemistry, Thomas Graham Building, University of Strathclyde, 295 Cathedral Street, Glasgow G1 1XL, United Kingdom
| | - Paul Bamborough
- GlaxoSmithKline R&D, Stevenage SG1 2NY, Hertfordshire, United Kingdom
| | - Chun-Wa Chung
- GlaxoSmithKline R&D, Stevenage SG1 2NY, Hertfordshire, United Kingdom
| | - Peter D Craggs
- GlaxoSmithKline R&D, Stevenage SG1 2NY, Hertfordshire, United Kingdom
| | - Laurie Gordon
- GlaxoSmithKline R&D, Stevenage SG1 2NY, Hertfordshire, United Kingdom
| | - Paola Grandi
- Cellzome GmbH, R&D MST GlaxoSmithKline, Meyerhofstrasse 1 69117 Heidelberg, Germany
| | - Melanie Leveridge
- GlaxoSmithKline R&D, Stevenage SG1 2NY, Hertfordshire, United Kingdom
| | - Matthew Lindon
- GlaxoSmithKline R&D, Stevenage SG1 2NY, Hertfordshire, United Kingdom
| | - Gemma M Liwicki
- GlaxoSmithKline R&D, Stevenage SG1 2NY, Hertfordshire, United Kingdom
| | - Anne-Marie Michon
- Cellzome GmbH, R&D MST GlaxoSmithKline, Meyerhofstrasse 1 69117 Heidelberg, Germany
| | - Judit Molnar
- GlaxoSmithKline R&D, Stevenage SG1 2NY, Hertfordshire, United Kingdom
| | - Inmaculada Rioja
- GlaxoSmithKline R&D, Stevenage SG1 2NY, Hertfordshire, United Kingdom
| | - Peter E Soden
- GlaxoSmithKline R&D, Stevenage SG1 2NY, Hertfordshire, United Kingdom
| | - Natalie H Theodoulou
- GlaxoSmithKline R&D, Stevenage SG1 2NY, Hertfordshire, United Kingdom.,WestCHEM, Department of Pure and Applied Chemistry, Thomas Graham Building, University of Strathclyde, 295 Cathedral Street, Glasgow G1 1XL, United Kingdom
| | - Thilo Werner
- Cellzome GmbH, R&D MST GlaxoSmithKline, Meyerhofstrasse 1 69117 Heidelberg, Germany
| | - Nicholas C O Tomkinson
- WestCHEM, Department of Pure and Applied Chemistry, Thomas Graham Building, University of Strathclyde, 295 Cathedral Street, Glasgow G1 1XL, United Kingdom
| | - Rab K Prinjha
- GlaxoSmithKline R&D, Stevenage SG1 2NY, Hertfordshire, United Kingdom
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7
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Lucas SCC, Atkinson SJ, Bamborough P, Barnett H, Chung CW, Gordon L, Mitchell DJ, Phillipou A, Prinjha RK, Sheppard RJ, Tomkinson NCO, Watson RJ, Demont EH. Optimization of Potent ATAD2 and CECR2 Bromodomain Inhibitors with an Atypical Binding Mode. J Med Chem 2020; 63:5212-5241. [DOI: 10.1021/acs.jmedchem.0c00021] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Simon C. C. Lucas
- WestCHEM, Department of Pure and Applied Chemistry, University of Strathclyde, Thomas Graham Building, 295 Cathedral Street, Glasgow G1 1XL, United Kingdom
| | | | | | | | | | | | | | | | | | | | - Nicholas C. O. Tomkinson
- WestCHEM, Department of Pure and Applied Chemistry, University of Strathclyde, Thomas Graham Building, 295 Cathedral Street, Glasgow G1 1XL, United Kingdom
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8
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Phillipou AN, Lay CS, Carver CE, Messenger C, Evans JP, Lewis AJ, Gordon LJ, Mahmood M, Greenhough LA, Sammon D, Cheng AT, Chakraborty S, Jones EJ, Lucas SCC, Gatfield KM, Brierley DJ, Craggs PD. Cellular Target Engagement Approaches to Monitor Epigenetic Reader Domain Interactions. SLAS DISCOVERY 2019; 25:163-175. [PMID: 31875412 DOI: 10.1177/2472555219896278] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Malfunctions in the basic epigenetic mechanisms such as histone modifications, DNA methylation, and chromatin remodeling are implicated in a number of cancers and immunological and neurodegenerative conditions. Within GlaxoSmithKline (GSK) we have utilized a number of variations of the NanoBRET technology for the direct measurement of compound-target engagement within native cellular environments to drive high-throughput, routine structure-activity relationship (SAR) profiling across differing epigenetic targets. NanoBRET is a variation of the bioluminescence resonance energy transfer (BRET) methodology utilizing proteins of interest fused to either NanoLuc, a small, high-emission-intensity luciferase, or HaloTag, a modified dehalogenase enzyme that can be selectively labeled with a fluorophore. The combination of these two technologies has enabled the application of NanoBRET to biological systems such as epigenetic protein-protein interactions, which have previously been challenging. By synergizing target engagement assays with more complex primary cell phenotypic assays, we have been able to demonstrate compound-target selectivity profiles to enhance cellular potency and offset potential liability risks. Additionally, we have shown that in the absence of a robust, cell phenotypic assay, it is possible to utilize NanoBRET target engagement assays to aid chemistry in progressing at a higher scale than would have otherwise been achievable. The NanoBRET target engagement assays utilized have further shown an excellent correlation with more reductionist biochemical and biophysical assay systems, clearly demonstrating the possibility of using such assay systems at scale, in tandem with, or in preference to, lower-throughput cell phenotypic approaches.
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Affiliation(s)
- Alexander N Phillipou
- Medicine Design, Medicinal Science and Technology, GlaxoSmithKline, Stevenage, Hertfordshire, UK
| | - Charles S Lay
- Medicine Design, Medicinal Science and Technology, GlaxoSmithKline, Stevenage, Hertfordshire, UK
| | - Charlotte E Carver
- Medicine Design, Medicinal Science and Technology, GlaxoSmithKline, Stevenage, Hertfordshire, UK
| | - Cassie Messenger
- Medicine Design, Medicinal Science and Technology, GlaxoSmithKline, Stevenage, Hertfordshire, UK
| | - John P Evans
- Medicine Design, Medicinal Science and Technology, GlaxoSmithKline, Stevenage, Hertfordshire, UK
| | - Antonia J Lewis
- Medicine Design, Medicinal Science and Technology, GlaxoSmithKline, Stevenage, Hertfordshire, UK
| | - Laurie J Gordon
- Medicine Design, Medicinal Science and Technology, GlaxoSmithKline, Stevenage, Hertfordshire, UK
| | - Mahnoor Mahmood
- Medicine Design, Medicinal Science and Technology, GlaxoSmithKline, Stevenage, Hertfordshire, UK
| | - Luke A Greenhough
- Medicine Design, Medicinal Science and Technology, GlaxoSmithKline, Stevenage, Hertfordshire, UK
| | - Douglas Sammon
- Medicine Design, Medicinal Science and Technology, GlaxoSmithKline, Stevenage, Hertfordshire, UK
| | - Aaron T Cheng
- Functional Genomics, Medicinal Science and Technology, GlaxoSmithKline, Collegeville, PA, USA
| | - Syandan Chakraborty
- Functional Genomics, Medicinal Science and Technology, GlaxoSmithKline, Collegeville, PA, USA
| | - Emma J Jones
- Medicine Design, Medicinal Science and Technology, GlaxoSmithKline, Stevenage, Hertfordshire, UK
| | - Simon C C Lucas
- Epigenetics Research Unit, GlaxoSmithKline, Stevenage, Hertfordshire, UK
| | - Kelly M Gatfield
- Medicine Design, Medicinal Science and Technology, GlaxoSmithKline, Stevenage, Hertfordshire, UK
| | - David J Brierley
- Medicine Design, Medicinal Science and Technology, GlaxoSmithKline, Stevenage, Hertfordshire, UK
| | - Peter D Craggs
- Medicine Design, Medicinal Science and Technology, GlaxoSmithKline, Stevenage, Hertfordshire, UK
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9
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Hilton-Proctor J, Ilyichova O, Zheng Z, Jennings I, Johnstone R, Shortt J, Mountford S, Scanlon M, Thompson P. Synthesis and elaboration of N-methylpyrrolidone as an acetamide fragment substitute in bromodomain inhibition. Bioorg Med Chem 2019; 27:115157. [DOI: 10.1016/j.bmc.2019.115157] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 10/07/2019] [Accepted: 10/08/2019] [Indexed: 01/24/2023]
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10
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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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11
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A chemical toolbox for the study of bromodomains and epigenetic signaling. Nat Commun 2019; 10:1915. [PMID: 31015424 PMCID: PMC6478789 DOI: 10.1038/s41467-019-09672-2] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 03/15/2019] [Indexed: 12/16/2022] Open
Abstract
Bromodomains (BRDs) are conserved protein interaction modules which recognize (read) acetyl-lysine modifications, however their role(s) in regulating cellular states and their potential as targets for the development of targeted treatment strategies is poorly understood. Here we present a set of 25 chemical probes, selective small molecule inhibitors, covering 29 human bromodomain targets. We comprehensively evaluate the selectivity of this probe-set using BROMOscan and demonstrate the utility of the set identifying roles of BRDs in cellular processes and potential translational applications. For instance, we discovered crosstalk between histone acetylation and the glycolytic pathway resulting in a vulnerability of breast cancer cell lines under conditions of glucose deprivation or GLUT1 inhibition to inhibition of BRPF2/3 BRDs. This chemical probe-set will serve as a resource for future applications in the discovery of new physiological roles of bromodomain proteins in normal and disease states, and as a toolset for bromodomain target validation. Bromodomains are conserved protein interaction modules that recognize acetyl-lysine modifications. Here the authors present a set of 25 selective small molecule inhibitors covering 29 human bromodomain targets and comprehensively evaluate the selectivity of this probe-set.
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Clegg MA, Tomkinson NCO, Prinjha RK, Humphreys PG. Advancements in the Development of non-BET Bromodomain Chemical Probes. ChemMedChem 2019; 14:362-385. [PMID: 30624862 DOI: 10.1002/cmdc.201800738] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Indexed: 01/07/2023]
Abstract
The bromodomain and extra terminal (BET) family of bromodomain-containing proteins (BCPs) have been the subject of extensive research over the past decade, resulting in a plethora of high-quality chemical probes for their tandem bromodomains. In turn, these chemical probes have helped reveal the profound biological role of the BET bromodomains and their role in disease, ultimately leading to a number of molecules in active clinical development. However, the BET subfamily represents just 8/61 of the known human bromodomains, and attention has now expanded to the biological role of the remaining 53 non-BET bromodomains. Rapid growth of this research area has been accompanied by a greater understanding of the requirements for an effective bromodomain chemical probe and has led to a number of new non-BET bromodomain chemical probes being developed. Advances since December 2015 are discussed, highlighting the strengths/caveats of each molecule, and the value they add toward validating the non-BET bromodomains as tractable therapeutic targets.
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Affiliation(s)
- Michael A Clegg
- Epigenetics Discovery Performance Unit, GlaxoSmithKline R&D, Stevenage, Hertfordshire, SG1 2NY, UK.,WestCHEM, Department of Pure and Applied Chemistry, University of Strathclyde, 295 Cathedral Street, Thomas Graham Building, Glasgow, G1 1XL, UK
| | - Nicholas C O Tomkinson
- WestCHEM, Department of Pure and Applied Chemistry, University of Strathclyde, 295 Cathedral Street, Thomas Graham Building, Glasgow, G1 1XL, UK
| | - Rab K Prinjha
- Epigenetics Discovery Performance Unit, GlaxoSmithKline R&D, Stevenage, Hertfordshire, SG1 2NY, UK
| | - Philip G Humphreys
- Epigenetics Discovery Performance Unit, GlaxoSmithKline R&D, Stevenage, Hertfordshire, SG1 2NY, UK
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Schiedel M, Conway SJ. Small molecules as tools to study the chemical epigenetics of lysine acetylation. Curr Opin Chem Biol 2018; 45:166-178. [DOI: 10.1016/j.cbpa.2018.06.015] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Revised: 06/08/2018] [Accepted: 06/11/2018] [Indexed: 02/06/2023]
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Aldeghi M, Ross GA, Bodkin MJ, Essex JW, Knapp S, Biggin PC. Large-scale analysis of water stability in bromodomain binding pockets with grand canonical Monte Carlo. Commun Chem 2018; 1:19. [PMID: 29863194 PMCID: PMC5978690 DOI: 10.1038/s42004-018-0019-x] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Accepted: 03/01/2018] [Indexed: 12/17/2022] Open
Abstract
Conserved water molecules are of interest in drug design, as displacement of such waters can lead to higher affinity ligands and in some cases, contribute towards selectivity. Bromodomains, small protein domains involved in the epigenetic regulation of gene transcription, display a network of four conserved water molecules in their binding pockets and have recently been the focus of intense medicinal chemistry efforts. Understanding why certain bromodomains have displaceable water molecules and others do not is extremely challenging, and it remains unclear which water molecules in a given bromodomain can be targeted for displacement. Here we estimate the stability of the conserved water molecules in 35 bromodomains via binding free energy calculations using all-atom grand canonical Monte Carlo simulations. Encouraging quantitative agreement to the available experimental evidence is found. We thus discuss the expected ease of water displacement in different bromodomains and the implications for ligand selectivity.
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Affiliation(s)
- Matteo Aldeghi
- Structural Bioinformatics and Computational Biochemistry, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, United Kingdom
| | - Gregory A. Ross
- Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York, United States
| | - Michael J. Bodkin
- Evotec (U.K.) Ltd., 114 Innovation Drive, Milton Park, Abingdon, Oxfordshire OX14 4RZ, United Kingdom
| | - Jonathan W. Essex
- School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, United Kingdom
| | - Stefan Knapp
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, United Kingdom
- Target Discovery Institute, Nuffield Department of Clinical Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, United Kingdom
| | - Philip C. Biggin
- Structural Bioinformatics and Computational Biochemistry, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, United Kingdom
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