1
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Pan D, Huang Y, Jiang D, Zhang Y, Wu M, Han M, Jin X. Discovery of an EP300 Inhibitor using Structure-based Virtual Screening and Bioactivity Evaluation. Curr Pharm Des 2024; 30:CPD-EPUB-140778. [PMID: 38835125 PMCID: PMC11348464 DOI: 10.2174/0113816128298051240529113313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Revised: 05/01/2024] [Accepted: 05/08/2024] [Indexed: 06/06/2024]
Abstract
BACKGROUND EP300 (E1A binding protein p300) played a significant role in serial diseases such as cancer, neurodegenerative disease. Therefore, it became a significant target. METHODS Targeting EP300 discovery of a novel drug to alleviate these diseases. In this paper, 17 candidate compounds were obtained using a structure-based virtual screening approach, 4449-0460, with an IC50 of 5.89 ± 2.08 uM, which was identified by the EP300 bioactivity test. 4449-0460 consisted of three rings. The middle benzene ring connected the 5-ethylideneimidazolidine-2,4-dione group and the 3-F-Phenylmethoxy group. RESULTS Furthermore, the interaction mechanism between 4449-0460 and EP300 was explored by combining molecular dynamics (MD) simulations and binding free energy calculation methods. CONCLUSION The binding free energy of EP300 with 4449-0460 was -10.93 kcal/mol, and mainly came from the nonpolar energy term (ΔGnonpolar). Pro1074, Phe1075, Val1079, Leu1084, and Val1138 were the key residues in EP300/4449-0460 binding with more -1 kcal/mol energy contribution. 4449-0460 was a promising inhibitor targeting EP300, which had implications for the development of drugs for EP300-related diseases.
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Affiliation(s)
- Dabo Pan
- Department of Medical Technology, Qiandongnan Vocational and Technical College for Nationalities, Kaili 556000, China
- Department of Pharmacy, The Second Affiliated Hospital of Guizhou Medical University, Guizhou Medical University, Kaili 556000, China
| | - Yaxuan Huang
- Department of Medical Technology, Qiandongnan Vocational and Technical College for Nationalities, Kaili 556000, China
| | - Dewen Jiang
- Department of Medical Technology, Qiandongnan Vocational and Technical College for Nationalities, Kaili 556000, China
| | - Yonghao Zhang
- Department of Medical Technology, Qiandongnan Vocational and Technical College for Nationalities, Kaili 556000, China
| | - Mingkai Wu
- Department of Medical Technology, Qiandongnan Vocational and Technical College for Nationalities, Kaili 556000, China
| | - Minzhen Han
- Department of Pharmacy, The Second Affiliated Hospital of Guizhou Medical University, Guizhou Medical University, Kaili 556000, China
| | - Xiaojie Jin
- College of Pharmacy, Gansu University of Chinese Medicine, Lanzhou 730000, China
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2
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Hall A, Chatzopoulou M, Frost J. Bioisoteres for carboxylic acids: From ionized isosteres to novel unionized replacements. Bioorg Med Chem 2024; 104:117653. [PMID: 38579492 DOI: 10.1016/j.bmc.2024.117653] [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: 11/08/2023] [Revised: 02/05/2024] [Accepted: 02/19/2024] [Indexed: 04/07/2024]
Abstract
Carboxylic acids are key pharmacophoric elements in many molecules. They can be seen as a problem by some, due to perceived permeability challenges, potential for high plasma protein binding and the risk of forming reactive metabolites due to acyl-glucuronidation. By others they are viewed more favorably as they can decrease lipophilicity by adding an ionizable center which can be beneficial for solubility, and can add enthalpic interactions with the target protein. However, there are many instances where the replacement of a carboxylic acid with a bioisosteric group is required. This has led to the development of a number of ionizable groups which sufficiently mimic the carboxylic acid functionality whilst improving, for example, the metabolic profile of the molecule in question. An alternative strategy involves replacement of the carboxylate by neutral functional groups. This review initially details carefully selected examples whereby tetrazoles, acyl sulfonamides or isoxazolols have been beneficially utilized as carboxylic acid bioisosteres altering physicohemical properties, interactions with the target and metabolism and/or pharmacokinetics, before delving further into the binding mode of carboxylic acid derivatives with their target proteins. This analysis highlights new ways to consider the replacement of carboxylic acids by neutral bioisosteric groups which either rely on hydrogen bonds or cation-π interactions. It should serve as a useful guide for scientists working in drug discovery.
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Affiliation(s)
- Adrian Hall
- UCB, Chemin du Foriest, Braine l'Alleud, Belgium, 1420 UCB, 216 Bath Road, Slough SL1 3WE, UK.
| | - Maria Chatzopoulou
- UCB, Chemin du Foriest, Braine l'Alleud, Belgium, 1420 UCB, 216 Bath Road, Slough SL1 3WE, UK
| | - James Frost
- UCB, Chemin du Foriest, Braine l'Alleud, Belgium, 1420 UCB, 216 Bath Road, Slough SL1 3WE, UK
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3
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Zhao W, Li H, Ge Q, Cong H, Yang S. Synthesis of Dihydroquinoxalinones from Biomass-Derived Keto Acids and o-Phenylenediamines. J Org Chem 2024; 89:3987-3994. [PMID: 38437716 DOI: 10.1021/acs.joc.3c02821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2024]
Abstract
A novel catalyst-free cascade amination/cyclization/reduction reaction was developed for the synthesis of various Dihydroquinoxalinones under mild conditions from accessible biomass-derived keto acids and 1,2-phenylenediamines with ammonia borane as a hydrogen donor. This single-step approach enables a simple and eco-friendly route toward the direct synthesis of 12 kinds of Dihydroquinoxalinones in moderate to excellent yields in the green solvent dimethyl carbonate. The results of deuterium-labeling experiments and density function calculations demonstrate that the reductive process proceeds along a double hydrogen transfer pathway. An acceptable yield of Dihydroquinoxalinone can be afforded in a gram-scale experiment, illustrating the practicality of the as-reported reaction system.
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Affiliation(s)
- Wenfeng Zhao
- Key Laboratory of Macrocyclic and Supramolecular Chemistry of Guizhou Province, School of Chemistry and Chemical Engineering, Guizhou University, Guiyang 550025, China
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering (Ministry of Education), State-Local Joint Engineering Lab for Comprehensive Utilization of Biomass, Center for R&D of Fine Chemicals, Guizhou University, Guiyang 550025, China
| | - Hu Li
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering (Ministry of Education), State-Local Joint Engineering Lab for Comprehensive Utilization of Biomass, Center for R&D of Fine Chemicals, Guizhou University, Guiyang 550025, China
| | - Qingmei Ge
- Key Laboratory of Macrocyclic and Supramolecular Chemistry of Guizhou Province, School of Chemistry and Chemical Engineering, Guizhou University, Guiyang 550025, China
| | - Hang Cong
- Key Laboratory of Macrocyclic and Supramolecular Chemistry of Guizhou Province, School of Chemistry and Chemical Engineering, Guizhou University, Guiyang 550025, China
| | - Song Yang
- State Key Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering (Ministry of Education), State-Local Joint Engineering Lab for Comprehensive Utilization of Biomass, Center for R&D of Fine Chemicals, Guizhou University, Guiyang 550025, China
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4
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Xiang Q, Wu T, Zhang C, Wang C, Xu H, Hu Q, Hu J, Luo G, Zhuang X, Wu X, Zhang Y, Xu Y. Discovery of a potent and selective CBP bromodomain inhibitor (Y08262) for treating acute myeloid leukemia. Bioorg Chem 2024; 142:106950. [PMID: 37924753 DOI: 10.1016/j.bioorg.2023.106950] [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: 09/24/2023] [Revised: 10/22/2023] [Accepted: 10/27/2023] [Indexed: 11/06/2023]
Abstract
The bromodomain of CREB (cyclic-AMP response element binding protein) binding protein (CBP) is an epigenetic "reader" and plays a key role in transcriptional regulation. CBP bromodomain is considered to be a promising therapeutic target for acute myeloid leukemia (AML). Herein, we report the discovery of a series of 1-(indolizin-3-yl)ethan-1-one derivatives as potent, and selective CBP bromodomain inhibitors focused on improving cellular potency. One of the most promising compounds, 7e (Y08262), inhibits the CBP bromodomain at the nanomolar level (IC50 = 73.1 nM) with remarkable selectivity. In addition, the new inhibitor also displays potent inhibitory activities in AML cell lines. Collectively, this study provides a new lead compound for further validation of CBP bromodomain as a molecular target for AML drug development.
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Affiliation(s)
- Qiuping Xiang
- Ningbo No. 2 Hospital, Ningbo, Zhejiang 315010, China; Guoke Ningbo Life Science and Health Industry Research Institute, Ningbo, Zhejiang 315010, China.
| | - Tianbang Wu
- Key Laboratory of Structure-Based Drugs Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, China; Center for Chemical Biology and Drug Discovery, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, No. 190 Kaiyuan Avenue, Guangzhou 510530, China
| | - Cheng Zhang
- Center for Chemical Biology and Drug Discovery, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, No. 190 Kaiyuan Avenue, Guangzhou 510530, China
| | - Chao Wang
- Center for Chemical Biology and Drug Discovery, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, No. 190 Kaiyuan Avenue, Guangzhou 510530, China
| | - Hongrui Xu
- Center for Chemical Biology and Drug Discovery, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, No. 190 Kaiyuan Avenue, Guangzhou 510530, China; GMU-GIBH Joint School of Life Sciences, Guangzhou Medical University, Guangzhou 511436, China
| | - Qingqing Hu
- Center for Chemical Biology and Drug Discovery, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, No. 190 Kaiyuan Avenue, Guangzhou 510530, China
| | - Jiankang Hu
- Center for Chemical Biology and Drug Discovery, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, No. 190 Kaiyuan Avenue, Guangzhou 510530, China; University of Chinese Academy of Sciences, No. 19 Yuquan Road, Beijing 100049, China
| | - Guolong Luo
- Center for Chemical Biology and Drug Discovery, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, No. 190 Kaiyuan Avenue, Guangzhou 510530, China
| | - Xiaoxi Zhuang
- Center for Chemical Biology and Drug Discovery, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, No. 190 Kaiyuan Avenue, Guangzhou 510530, China
| | - Xishan Wu
- Center for Chemical Biology and Drug Discovery, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, No. 190 Kaiyuan Avenue, Guangzhou 510530, China
| | - Yan Zhang
- Center for Chemical Biology and Drug Discovery, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, No. 190 Kaiyuan Avenue, Guangzhou 510530, China.
| | - Yong Xu
- Key Laboratory of Structure-Based Drugs Design & Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, China; Center for Chemical Biology and Drug Discovery, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, No. 190 Kaiyuan Avenue, Guangzhou 510530, China; China-New Zealand Joint Laboratory on Biomedicine and Health, Guangzhou 510530, China; State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China.
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5
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Schiedel M, McArdle DJB, Padalino G, Chan AKN, Forde-Thomas J, McDonough M, Whiteland H, Beckmann M, Cookson R, Hoffmann KF, Conway SJ. Small Molecule Ligands of the BET-like Bromodomain, SmBRD3, Affect Schistosoma mansoni Survival, Oviposition, and Development. J Med Chem 2023; 66:15801-15822. [PMID: 38048437 PMCID: PMC10726355 DOI: 10.1021/acs.jmedchem.3c01321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 10/15/2023] [Accepted: 11/01/2023] [Indexed: 12/06/2023]
Abstract
Schistosomiasis is a disease affecting >200 million people worldwide, but its treatment relies on a single agent, praziquantel. To investigate new avenues for schistosomiasis control, we have conducted the first systematic analysis of bromodomain-containing proteins (BCPs) in a causative species, Schistosoma mansoni. Having identified 29 putative bromodomains (BRDs) in 22 S. mansoni proteins, we selected SmBRD3, a tandem BRD-containing BCP that shows high similarity to the human bromodomain and extra terminal domain (BET) family, for further studies. Screening 697 small molecules identified the human BET BRD inhibitor I-BET726 as a ligand for SmBRD3. An X-ray crystal structure of I-BET726 bound to the second BRD of SmBRD3 [SmBRD3(2)] enabled rational design of a quinoline-based ligand (15) with an ITC Kd = 364 ± 26.3 nM for SmBRD3(2). The ethyl ester pro-drug of compound 15 (compound 22) shows substantial effects on sexually immature larval schistosomula, sexually mature adult worms, and snail-infective miracidia in ex vivo assays.
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Affiliation(s)
- Matthias Schiedel
- Department
of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K.
| | - Darius J. B. McArdle
- Department
of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K.
| | - Gilda Padalino
- The
Department of Life Sciences (DLS), Aberystwyth
University, Wales SY23 3DA, U.K.
| | - Anthony K. N. Chan
- Department
of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K.
| | | | - Michael McDonough
- Department
of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K.
| | - Helen Whiteland
- The
Department of Life Sciences (DLS), Aberystwyth
University, Wales SY23 3DA, U.K.
| | - Manfred Beckmann
- The
Department of Life Sciences (DLS), Aberystwyth
University, Wales SY23 3DA, U.K.
| | - Rosa Cookson
- GlaxoSmithKline
R&D, Stevenage, Hertfordshire SG1 2NY, U.K.
| | - Karl F. Hoffmann
- The
Department of Life Sciences (DLS), Aberystwyth
University, Wales SY23 3DA, U.K.
| | - Stuart J. Conway
- Department
of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K.
- Department
of Chemistry & Biochemistry, University
of California Los Angeles, 607 Charles E. Young Drive East, P.O. Box 951569, Los Angeles, California 90095-1569, United States
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6
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Wei G, Zheng D, Li C, Chen Z, Wu XF. Divergent Synthesis of Trifluoromethyl-Substituted 1,2-Dihydroquinoxalines and Diimines by Cascade Reactions of CF 3-Imidoyl Sulfoxonium Ylides with Azo Compounds. Org Lett 2023; 25:7046-7050. [PMID: 37721372 DOI: 10.1021/acs.orglett.3c02718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/19/2023]
Abstract
A base-mediated cascade reaction of CF3-imidoyl sulfoxonium ylides and azo compounds has been achieved, allowing for facile access to trifluoromethyl-substituted 1,2-dihydroquinoxalines and diimines in moderate to excellent yields. Noteworthy is that the unusual N-N bond cleavage and rearrangement of azo compounds are involved in the transformations.
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Affiliation(s)
- Guangming Wei
- Department of Chemistry, Key Laboratory of Surface & Interface Science of Polymer Materials of Zhejiang Province, Zhejiang Sci-Tech University, Hangzhou 310018, China
| | - Dongling Zheng
- Department of Chemistry, Key Laboratory of Surface & Interface Science of Polymer Materials of Zhejiang Province, Zhejiang Sci-Tech University, Hangzhou 310018, China
| | - Chen Li
- Department of Chemistry, Key Laboratory of Surface & Interface Science of Polymer Materials of Zhejiang Province, Zhejiang Sci-Tech University, Hangzhou 310018, China
| | - Zhengkai Chen
- Department of Chemistry, Key Laboratory of Surface & Interface Science of Polymer Materials of Zhejiang Province, Zhejiang Sci-Tech University, Hangzhou 310018, China
| | - Xiao-Feng Wu
- Dalian National Laboratory for Clean Energy, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, Liaoning China
- Leibniz-Institut für Katalyse e. V., Albert-Einstein-Straβe 29a, 18059 Rostock, Germany
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7
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Liu M, Zhang K, Li Q, Pang H, Pan Z, Huang X, Wang L, Wu F, He G. Recent Advances on Small-Molecule Bromodomain-Containing Histone Acetyltransferase Inhibitors. J Med Chem 2023; 66:1678-1699. [PMID: 36695774 DOI: 10.1021/acs.jmedchem.2c01638] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
In recent years, substantial research has been conducted on molecular mechanisms and inhibitors targeting bromodomains (BRDs) and extra-terminal (BET) family proteins. On this basis, non-BET BRD is gradually becoming a research hot spot. BRDs are abundant in histone acetyltransferase (HAT)-associated activating transcription factors, and BRD-containing HATs have been linked to cancer, inflammation, and viral replication. Therefore, the development of BRD-containing HATs as chemical probes is useful for understanding the specific biological roles of BRDs in diseases and drug discovery. Several types of BRD-containing HATs, including CBP/P300, PCAF/GCN5, and TAF1, are discussed in this context in terms of their structures, functions, and small-molecule inhibitors. Additionally, progress in BRD inhibitors/chemical probes and proteolysis targeting chimeras in terms of drug design, biological activity, and disease application are summarized. These findings provide insights into the development of BRD inhibitors as potential drug candidates for various diseases.
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Affiliation(s)
- Mingxia Liu
- Department of Dermatology and Department of Pharmacy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, P. R. China.,Laboratory of Dermatology, Clinical Institute of Inflammation and Immunology (CIII), Frontiers Science Center for Disease-related Molecular Network and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu 610041, China
| | - Kaiyao Zhang
- Department of Dermatology and Department of Pharmacy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, P. R. China.,Laboratory of Dermatology, Clinical Institute of Inflammation and Immunology (CIII), Frontiers Science Center for Disease-related Molecular Network and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu 610041, China
| | - Qinjue Li
- West China School of Public Health, Sichuan University, Chengdu, Sichuan 610041, P. R. China
| | - Haiying Pang
- Laboratory of Dermatology, Clinical Institute of Inflammation and Immunology (CIII), Frontiers Science Center for Disease-related Molecular Network and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu 610041, China
| | - Zhaoping Pan
- Department of Dermatology and Department of Pharmacy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, P. R. China
| | - Xiaowei Huang
- Department of Dermatology and Department of Pharmacy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, P. R. China
| | - Lian Wang
- Department of Dermatology and Department of Pharmacy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, P. R. China
| | - Fengbo Wu
- Department of Dermatology and Department of Pharmacy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, P. R. China
| | - Gu He
- Department of Dermatology and Department of Pharmacy, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, P. R. China.,Laboratory of Dermatology, Clinical Institute of Inflammation and Immunology (CIII), Frontiers Science Center for Disease-related Molecular Network and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center of Biotherapy, Chengdu 610041, China
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8
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Bhat MF, Luján AP, Saifuddin M, Poelarends GJ. Chemoenzymatic Asymmetric Synthesis of Complex Heterocycles: Dihydrobenzoxazinones and Dihydroquinoxalinones. ACS Catal 2022; 12:11421-11427. [PMID: 36158903 PMCID: PMC9486952 DOI: 10.1021/acscatal.2c03008] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 08/25/2022] [Indexed: 01/08/2023]
Affiliation(s)
- Mohammad Faizan Bhat
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Alejandro Prats Luján
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Mohammad Saifuddin
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Gerrit J. Poelarends
- Department of Chemical and Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
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9
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Xu H, Luo G, Wu T, Hu J, Wang C, Wu X, Zhang Y, Xu Y, Xiang Q. Structural insights revealed by the cocrystal structure of CCS1477 in complex with CBP bromodomain. Biochem Biophys Res Commun 2022; 623:17-22. [PMID: 35868068 DOI: 10.1016/j.bbrc.2022.07.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 07/05/2022] [Accepted: 07/06/2022] [Indexed: 11/30/2022]
Abstract
Inhibition of the bromodomain of the CREB (cyclic-AMP response element-binding protein) binding protein (CBP) is a particularly promising new therapeutic approach for cancer. Benzimidazole derivatives CCS1477 and its analogues (8 and 9) are highly potent and selective CBP bromodomain inhibitors, with Kd values of 26.4, 37.0, and 34.3 nM in ITC assay, respectively. Among these compounds, CCS1477 is undergoing phase Ib/IIa clinical trials for the treatment of various cancers. Thus, we determined the co-crystal structures of CCS1477 and its analogues in complex with CBP bromodomain and revealed the detailed binding modes. Furthermore, overlapping with other reported co-crystal structures allowed us to identify that interaction with Arg1173, LPF shelf, and ZA channel was critical for keeping strong biological activity and selectivity. Collectively, this study provided a structural basis for CBP bromodomain inhibitors design.
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Affiliation(s)
- Hongrui Xu
- GMU-GIBH Joint School of Life Sciences, Guangzhou Medical University, Guangzhou, 511436, China
| | - Guolong Luo
- Center for Chemical Biology and Drug Discovery, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China; University of Chinese Academy of Sciences, No.19 Yuquan Road, Beijing, 100049, China
| | - Tianbang Wu
- Center for Chemical Biology and Drug Discovery, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China; Key Laboratory of Structure-Based Drug Design and Discovery of Ministry of Education, Shenyang Pharmaceutical University, Shenyang, 110016, China
| | - Jiankang Hu
- Center for Chemical Biology and Drug Discovery, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China; University of Chinese Academy of Sciences, No.19 Yuquan Road, Beijing, 100049, China
| | - Chao Wang
- Center for Chemical Biology and Drug Discovery, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China; University of Chinese Academy of Sciences, No.19 Yuquan Road, Beijing, 100049, China
| | - Xishan Wu
- Center for Chemical Biology and Drug Discovery, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China
| | - Yan Zhang
- Center for Chemical Biology and Drug Discovery, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.
| | - Yong Xu
- Guangdong Provincial Key Laboratory of Biocomputing, Joint School of Life Sciences, Guangzhou Medical University, Guangzhou, 510530, China; China-New Zealand Joint Laboratory on Biomedicine and Health, Guangzhou, 510530, China; State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, 510530, China.
| | - Qiuping Xiang
- Hwa Mei Hospital, University of Chinese Academy of Sciences, Ningbo, 315000, China; Ningbo Institute of Life and Health Industry, University of Chinese Academy of Sciences, Ningbo, 315000, China.
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10
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Design, synthesis and biological evaluation of (R)-5-methylpyrrolidin-2-ones as p300 bromodomain inhibitors with Anti-Tumor activities in multiple tumor lines. Bioorg Chem 2022; 124:105803. [DOI: 10.1016/j.bioorg.2022.105803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 04/05/2022] [Accepted: 04/08/2022] [Indexed: 11/21/2022]
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11
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Xia F, Lu YQ, Sun P, Guo QY, Shi QL, Zhang JZ, Qiu C. A formal [4 + 2] annulation of diamines and prop-2-ynyl sulfonium salts for the synthesis of tetrahydroquinoxalines. Org Biomol Chem 2022; 20:8415-8419. [DOI: 10.1039/d2ob01590k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
A formal [4 + 2] annulation of diamines and prop-2-ynyl sulfonium salts was developed.
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Affiliation(s)
- Fei Xia
- Artemisinin Research Center, and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Yu-Qian Lu
- Artemisinin Research Center, and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Peng Sun
- Artemisinin Research Center, and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Qiu-Yan Guo
- Artemisinin Research Center, and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Qiao-Li Shi
- Artemisinin Research Center, and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Jun-Zhe Zhang
- Artemisinin Research Center, and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
| | - Chong Qiu
- Artemisinin Research Center, and Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China
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12
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Yao Z, Zhang X, Luo Z, Pan Y, Zhao H, Li B, Xu L, Shi Q, Fan Q. Na
2
S
2
O
8
‐Mediated Tandem One‐Pot Construction of 3,3‐Disubsituted 3,4‐Dihydroquinoxalin‐2(1
H
)‐ones with 4‐Alkyl‐1,4‐dihydropyridines as Alkyl Radical Sources. ASIAN J ORG CHEM 2022. [DOI: 10.1002/ajoc.202100609] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Zhen Yao
- Department of Chemistry Renmin University of China Beijing 100872 P. R. China
| | - Xin Zhang
- Department of Chemistry Renmin University of China Beijing 100872 P. R. China
| | - Zhenli Luo
- Department of Chemistry Renmin University of China Beijing 100872 P. R. China
| | - Yixiao Pan
- Department of Chemistry Renmin University of China Beijing 100872 P. R. China
| | - Haoqiang Zhao
- Department of Chemistry Renmin University of China Beijing 100872 P. R. China
| | - Bohan Li
- Department of Chemistry Renmin University of China Beijing 100872 P. R. China
| | - Lijin Xu
- Department of Chemistry Renmin University of China Beijing 100872 P. R. China
| | - Qian Shi
- College of Chemistry & Materials Engineering Wenzhou University Wenzhou 325035 P. R. China
| | - Qing‐Hua Fan
- Institute of Chemistry Chinese Academy of Sciences
- University of Chinese Academy of Sciences Beijing 100190 P. R. China
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13
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Xiang Q, Wang C, Wu T, Zhang C, Hu Q, Luo G, Hu J, Zhuang X, Zou L, Shen H, Wu X, Zhang Y, Kong X, Liu J, Xu Y. Design, Synthesis, and Biological Evaluation of 1-(Indolizin-3-yl)ethan-1-ones as CBP Bromodomain Inhibitors for the Treatment of Prostate Cancer. J Med Chem 2021; 65:785-810. [PMID: 34962793 DOI: 10.1021/acs.jmedchem.1c01864] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
CREB (cyclic-AMP responsive element binding protein) binding protein (CBP) is a potential target for prostate cancer treatment. Herein, we report the structural optimization of a series of 1-(indolizin-3-yl)ethan-1-one compounds as new selective CBP bromodomain inhibitors, aiming to improve cellular potency and metabolic stability. This process led to compound 9g (Y08284), which possesses good liver microsomal stability and pharmacokinetic properties (F = 25.9%). Furthermore, the compound is able to inhibit CBP bromodomain as well as the proliferation, colony formation, and migration of prostate cancer cells. Additionally, the new inhibitor shows promising antitumor efficacy in a 22Rv1 xenograft model (TGI = 88%). This study provides new lead compounds for further development of drugs for the treatment of 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, Guangzhou Medical University, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Chao Wang
- Guangdong Provincial Key Laboratory of Biocomputing, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Guangzhou Medical University, Chinese Academy of Sciences, Guangzhou 510530, China.,University of Chinese Academy of Sciences, No. 19 Yuquan Road, Beijing 100049, China
| | - Tianbang Wu
- Guangdong Provincial Key Laboratory of Biocomputing, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Guangzhou Medical University, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Cheng Zhang
- Guangdong Provincial Key Laboratory of Biocomputing, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Guangzhou Medical University, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Qingqing Hu
- Guangdong Provincial Key Laboratory of Biocomputing, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Guangzhou Medical University, Chinese Academy of Sciences, Guangzhou 510530, China.,University of Chinese Academy of Sciences, No. 19 Yuquan Road, Beijing 100049, China
| | - Guolong Luo
- Guangdong Provincial Key Laboratory of Biocomputing, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Guangzhou Medical University, Chinese Academy of Sciences, Guangzhou 510530, China.,University of Chinese Academy of Sciences, No. 19 Yuquan Road, Beijing 100049, China
| | - Jiankang Hu
- Guangdong Provincial Key Laboratory of Biocomputing, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Guangzhou Medical University, Chinese Academy of Sciences, Guangzhou 510530, China.,University of Chinese Academy of Sciences, No. 19 Yuquan Road, Beijing 100049, China
| | - Xiaoxi Zhuang
- Guangdong Provincial Key Laboratory of Biocomputing, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Guangzhou Medical University, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Lingjiao Zou
- Guangdong Provincial Key Laboratory of Biocomputing, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Guangzhou Medical University, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Hui Shen
- Guangdong Provincial Key Laboratory of Biocomputing, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Guangzhou Medical University, Chinese Academy of Sciences, Guangzhou 510530, China.,University of Chinese Academy of Sciences, No. 19 Yuquan Road, Beijing 100049, China
| | - Xishan Wu
- Guangdong Provincial Key Laboratory of Biocomputing, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Guangzhou Medical University, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Yan Zhang
- Guangdong Provincial Key Laboratory of Biocomputing, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Guangzhou Medical University, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Xiangqian Kong
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Jinsong Liu
- State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
| | - Yong Xu
- Guangdong Provincial Key Laboratory of Biocomputing, Joint School of Life Sciences, Guangzhou Institutes of Biomedicine and Health, Guangzhou Medical University, Chinese Academy of Sciences, Guangzhou 510530, China.,China-New Zealand Joint Laboratory on Biomedicine and Health, Guangzhou 510530, China.,State Key Laboratory of Respiratory Disease, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China
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14
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Huang J, Chen W, Liang J, Yang Q, Fan Y, Chen MW, Peng Y. α-Keto Acids as Triggers and Partners for the Synthesis of Quinazolinones, Quinoxalinones, Benzooxazinones, and Benzothiazoles in Water. J Org Chem 2021; 86:14866-14882. [PMID: 34624963 DOI: 10.1021/acs.joc.1c01497] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A general and efficient method for the synthesis of quinazolinones, quinoxalinones, benzooxazinones, and benzothiazoles from the reactions of α-keto acids with 2-aminobenzamides, benzene-1,2-diamines, 2-aminophenols, and 2-aminobenzenethiols, respectively, is described. The reactions were conducted under catalyst-free conditions, using water as the sole solvent with no additive required, and successfully applied to the synthesis of sildenafil. More importantly, these reactions can be conducted on a mass scale, and the products can be easily purified through filtration and washing with ethanol (or crystallized).
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Affiliation(s)
- Jian Huang
- Key Laboratory for Green Chemistry of Jiangxi Province, Key Laboratory of Functional Small Molecules for Ministry of Education, Jiangxi Normal University, 99 Ziyang Avenue, Nanchang 330022, China
| | - Wei Chen
- Key Laboratory for Green Chemistry of Jiangxi Province, Key Laboratory of Functional Small Molecules for Ministry of Education, Jiangxi Normal University, 99 Ziyang Avenue, Nanchang 330022, China
| | - Jiazhi Liang
- Key Laboratory for Green Chemistry of Jiangxi Province, Key Laboratory of Functional Small Molecules for Ministry of Education, Jiangxi Normal University, 99 Ziyang Avenue, Nanchang 330022, China
| | - Qin Yang
- Key Laboratory for Green Chemistry of Jiangxi Province, Key Laboratory of Functional Small Molecules for Ministry of Education, Jiangxi Normal University, 99 Ziyang Avenue, Nanchang 330022, China
| | - Yan Fan
- Key Laboratory for Green Chemistry of Jiangxi Province, Key Laboratory of Functional Small Molecules for Ministry of Education, Jiangxi Normal University, 99 Ziyang Avenue, Nanchang 330022, China
| | - Mu-Wang Chen
- Key Laboratory for Green Chemistry of Jiangxi Province, Key Laboratory of Functional Small Molecules for Ministry of Education, Jiangxi Normal University, 99 Ziyang Avenue, Nanchang 330022, China
| | - Yiyuan Peng
- Key Laboratory for Green Chemistry of Jiangxi Province, Key Laboratory of Functional Small Molecules for Ministry of Education, Jiangxi Normal University, 99 Ziyang Avenue, Nanchang 330022, China
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15
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Volpe C, Meninno S, Crescenzi C, Mancinelli M, Mazzanti A, Lattanzi A. Catalytic Enantioselective Access to Dihydroquinoxalinones via Formal α‐Halo Acyl Halide Synthon in One Pot. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202110173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Chiara Volpe
- Dipartimento di Chimica e Biologia “A. Zambelli” Università di Salerno Via Giovanni Paolo II 132-84084 Fisciano Italy
| | - Sara Meninno
- Dipartimento di Chimica e Biologia “A. Zambelli” Università di Salerno Via Giovanni Paolo II 132-84084 Fisciano Italy
| | - Carlo Crescenzi
- Dipartimento di Farmacia Università di Salerno Via Giovanni Paolo II 132-84084 Fisciano Italy
| | - Michele Mancinelli
- Dipartimento di Chimica Industriale Università di Bologna Viale Risorgimento 4-40136 Bologna Italy
| | - Andrea Mazzanti
- Dipartimento di Chimica Industriale Università di Bologna Viale Risorgimento 4-40136 Bologna Italy
| | - Alessandra Lattanzi
- Dipartimento di Chimica e Biologia “A. Zambelli” Università di Salerno Via Giovanni Paolo II 132-84084 Fisciano Italy
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16
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Volpe C, Meninno S, Crescenzi C, Mancinelli M, Mazzanti A, Lattanzi A. Catalytic Enantioselective Access to Dihydroquinoxalinones via Formal α-Halo Acyl Halide Synthon in One Pot. Angew Chem Int Ed Engl 2021; 60:23819-23826. [PMID: 34437760 PMCID: PMC8596509 DOI: 10.1002/anie.202110173] [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: 07/29/2021] [Indexed: 11/25/2022]
Abstract
An enantioselective one-pot catalytic strategy to dihydroquinoxalinones, featuring novel 1-phenylsulfonyl-1-cyano enantioenriched epoxides as masked α-halo acyl halide synthons, followed by a domino ring-opening cyclization (DROC), is documented. A popular quinine-derived urea served as the catalyst in two out of the three steps performed in the same solvent using commercially available aldehydes, (phenylsulfonyl)acetonitrile, cumyl hydroperoxide and 1,2-phenylendiamines. Medicinally relevant 3-aryl/alkyl-substituted heterocycles are isolated in generally good to high overall yield and high enantioselectivity (up to 99 % ee). A rare example of excellent reusability of an organocatalyst at higher scale, subjected to oxidative conditions, is demonstrated. Mechanistically, labile α-ketosulfone has been detected as the intermediate involved in the DROC process. Theoretical calculations on the key epoxidation step rationalize the observed stereocontrol, highlighting the important role played by the sulfone group.
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Affiliation(s)
- Chiara Volpe
- Dipartimento di Chimica e Biologia “A. Zambelli”Università di SalernoVia Giovanni Paolo II132-84084FiscianoItaly
| | - Sara Meninno
- Dipartimento di Chimica e Biologia “A. Zambelli”Università di SalernoVia Giovanni Paolo II132-84084FiscianoItaly
| | - Carlo Crescenzi
- Dipartimento di FarmaciaUniversità di SalernoVia Giovanni Paolo II132-84084FiscianoItaly
| | - Michele Mancinelli
- Dipartimento di Chimica IndustrialeUniversità di BolognaViale Risorgimento4-40136BolognaItaly
| | - Andrea Mazzanti
- Dipartimento di Chimica IndustrialeUniversità di BolognaViale Risorgimento4-40136BolognaItaly
| | - Alessandra Lattanzi
- Dipartimento di Chimica e Biologia “A. Zambelli”Università di SalernoVia Giovanni Paolo II132-84084FiscianoItaly
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17
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Brand M, Clayton J, Moroglu M, Schiedel M, Picaud S, Bluck JP, Skwarska A, Bolland H, Chan AKN, Laurin CMC, Scorah AR, See L, Rooney TPC, Andrews KH, Fedorov O, Perell G, Kalra P, Vinh KB, Cortopassi WA, Heitel P, Christensen KE, Cooper RI, Paton RS, Pomerantz WCK, Biggin PC, Hammond EM, Filippakopoulos P, Conway SJ. Controlling Intramolecular Interactions in the Design of Selective, High-Affinity Ligands for the CREBBP Bromodomain. J Med Chem 2021; 64:10102-10123. [PMID: 34255515 PMCID: PMC8311651 DOI: 10.1021/acs.jmedchem.1c00348] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
![]()
CREBBP (CBP/KAT3A)
and its paralogue EP300 (KAT3B) are lysine acetyltransferases
(KATs) that are essential for human development. They each comprise
10 domains through which they interact with >400 proteins, making
them important transcriptional co-activators and key nodes in the
human protein–protein interactome. The bromodomains of CREBBP
and EP300 enable the binding of acetylated lysine residues from histones
and a number of other important proteins, including p53, p73, E2F,
and GATA1. Here, we report a work to develop a high-affinity, small-molecule
ligand for the CREBBP and EP300 bromodomains [(−)-OXFBD05]
that shows >100-fold selectivity over a representative member of
the
BET bromodomains, BRD4(1). Cellular studies using this ligand demonstrate
that the inhibition of the CREBBP/EP300 bromodomain in HCT116 colon
cancer cells results in lowered levels of c-Myc and a reduction in
H3K18 and H3K27 acetylation. In hypoxia (<0.1% O2),
the inhibition of the CREBBP/EP300 bromodomain results in the enhanced
stabilization of HIF-1α.
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Affiliation(s)
- Michael Brand
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K
| | - James Clayton
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K
| | - Mustafa Moroglu
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K
| | - Matthias Schiedel
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K
| | - Sarah Picaud
- Nuffield Department of Clinical Medicine, Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 3TA, U.K
| | - Joseph P Bluck
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K.,Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, U.K
| | - Anna Skwarska
- Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford OX3 7DQ, U.K
| | - Hannah Bolland
- Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford OX3 7DQ, U.K
| | - Anthony K N Chan
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K
| | - Corentine M C Laurin
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K
| | - Amy R Scorah
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K
| | - Larissa See
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K
| | - Timothy P C Rooney
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K
| | - Katrina H Andrews
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K
| | - Oleg Fedorov
- Nuffield Department of Clinical Medicine, Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 3TA, U.K
| | - Gabriella Perell
- Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455, United States
| | - Prakriti Kalra
- Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455, United States
| | - Kayla B Vinh
- Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455, United States
| | - Wilian A Cortopassi
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K
| | - Pascal Heitel
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K
| | - Kirsten E Christensen
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K
| | - Richard I Cooper
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K
| | - Robert S Paton
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K.,Department of Chemistry, Colorado State University, 1301 Center Ave, Ft. Collins, Colorado 80523-1872, United States
| | - William C K Pomerantz
- Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455, United States
| | - Philip C Biggin
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, U.K
| | - Ester M Hammond
- Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford OX3 7DQ, U.K
| | - Panagis Filippakopoulos
- Nuffield Department of Clinical Medicine, Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 3TA, U.K
| | - Stuart J Conway
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, U.K
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18
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Flynn NR, Ward MD, Schleiff MA, Laurin CMC, Farmer R, Conway SJ, Boysen G, Swamidass SJ, Miller GP. Bioactivation of Isoxazole-Containing Bromodomain and Extra-Terminal Domain (BET) Inhibitors. Metabolites 2021; 11:metabo11060390. [PMID: 34203690 PMCID: PMC8232216 DOI: 10.3390/metabo11060390] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 06/04/2021] [Accepted: 06/08/2021] [Indexed: 12/15/2022] Open
Abstract
The 3,5-dimethylisoxazole motif has become a useful and popular acetyl-lysine mimic employed in isoxazole-containing bromodomain and extra-terminal (BET) inhibitors but may introduce the potential for bioactivations into toxic reactive metabolites. As a test, we coupled deep neural models for quinone formation, metabolite structures, and biomolecule reactivity to predict bioactivation pathways for 32 BET inhibitors and validate the bioactivation of select inhibitors experimentally. Based on model predictions, inhibitors were more likely to undergo bioactivation than reported non-bioactivated molecules containing isoxazoles. The model outputs varied with substituents indicating the ability to scale their impact on bioactivation. We selected OXFBD02, OXFBD04, and I-BET151 for more in-depth analysis. OXFBD’s bioactivations were evenly split between traditional quinones and novel extended quinone-methides involving the isoxazole yet strongly favored the latter quinones. Subsequent experimental studies confirmed the formation of both types of quinones for OXFBD molecules, yet traditional quinones were the dominant reactive metabolites. Modeled I-BET151 bioactivations led to extended quinone-methides, which were not verified experimentally. The differences in observed and predicted bioactivations reflected the need to improve overall bioactivation scaling. Nevertheless, our coupled modeling approach predicted BET inhibitor bioactivations including novel extended quinone methides, and we experimentally verified those pathways highlighting potential concerns for toxicity in the development of these new drug leads.
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Affiliation(s)
- Noah R. Flynn
- Department of Pathology and Immunology, Washington University-St. Louis, St. Louis, MO 63130, USA; (N.R.F.); (M.D.W.); (R.F.)
| | - Michael D. Ward
- Department of Pathology and Immunology, Washington University-St. Louis, St. Louis, MO 63130, USA; (N.R.F.); (M.D.W.); (R.F.)
| | - Mary A. Schleiff
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA;
| | | | - Rohit Farmer
- Department of Pathology and Immunology, Washington University-St. Louis, St. Louis, MO 63130, USA; (N.R.F.); (M.D.W.); (R.F.)
| | - Stuart J. Conway
- Department of Chemistry, University of Oxford, Oxford OX1 3TA, UK; (C.M.C.L.); (S.J.C.)
| | - Gunnar Boysen
- Department of Environmental and Occupational Health, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA;
| | - S. Joshua Swamidass
- Department of Pathology and Immunology, Washington University-St. Louis, St. Louis, MO 63130, USA; (N.R.F.); (M.D.W.); (R.F.)
- Correspondence: (S.J.S.); (G.P.M.)
| | - Grover P. Miller
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA;
- Correspondence: (S.J.S.); (G.P.M.)
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19
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Waddell AR, Huang H, Liao D. CBP/p300: Critical Co-Activators for Nuclear Steroid Hormone Receptors and Emerging Therapeutic Targets in Prostate and Breast Cancers. Cancers (Basel) 2021; 13:2872. [PMID: 34201346 PMCID: PMC8229436 DOI: 10.3390/cancers13122872] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 05/29/2021] [Accepted: 05/31/2021] [Indexed: 01/10/2023] Open
Abstract
The CREB-binding protein (CBP) and p300 are two paralogous lysine acetyltransferases (KATs) that were discovered in the 1980s-1990s. Since their discovery, CBP/p300 have emerged as important regulatory proteins due to their ability to acetylate histone and non-histone proteins to modulate transcription. Work in the last 20 years has firmly established CBP/p300 as critical regulators for nuclear hormone signaling pathways, which drive tumor growth in several cancer types. Indeed, CBP/p300 are critical co-activators for the androgen receptor (AR) and estrogen receptor (ER) signaling in prostate and breast cancer, respectively. The AR and ER are stimulated by sex hormones and function as transcription factors to regulate genes involved in cell cycle progression, metabolism, and other cellular functions that contribute to oncogenesis. Recent structural studies of the AR/p300 and ER/p300 complexes have provided critical insights into the mechanism by which p300 interacts with and activates AR- and ER-mediated transcription. Breast and prostate cancer rank the first and forth respectively in cancer diagnoses worldwide and effective treatments are urgently needed. Recent efforts have identified specific and potent CBP/p300 inhibitors that target the acetyltransferase activity and the acetytllysine-binding bromodomain (BD) of CBP/p300. These compounds inhibit AR signaling and tumor growth in prostate cancer. CBP/p300 inhibitors may also be applicable for treating breast and other hormone-dependent cancers. Here we provide an in-depth account of the critical roles of CBP/p300 in regulating the AR and ER signaling pathways and discuss the potential of CBP/p300 inhibitors for treating prostate and breast cancer.
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Affiliation(s)
- Aaron R. Waddell
- UF Health Cancer Center, Department of Anatomy and Cell Biology, University Florida College of Medicine, 2033 Mowry Road, Gainesville, FL 32610, USA;
| | - Haojie Huang
- Departments of Biochemistry and Molecular Biology and Urology, Mayo Clinic College of Medicine and Science, 200 First St. SW, Rochester, MN 55905, USA;
| | - Daiqing Liao
- UF Health Cancer Center, Department of Anatomy and Cell Biology, University Florida College of Medicine, 2033 Mowry Road, Gainesville, FL 32610, USA;
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20
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Favalli N, Bassi G, Pellegrino C, Millul J, De Luca R, Cazzamalli S, Yang S, Trenner A, Mozaffari NL, Myburgh R, Moroglu M, Conway SJ, Sartori AA, Manz MG, Lerner RA, Vogt PK, Scheuermann J, Neri D. Stereo- and regiodefined DNA-encoded chemical libraries enable efficient tumour-targeting applications. Nat Chem 2021; 13:540-548. [PMID: 33833446 PMCID: PMC8405038 DOI: 10.1038/s41557-021-00660-y] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 02/10/2021] [Indexed: 02/01/2023]
Abstract
The encoding of chemical compounds with amplifiable DNA tags facilitates the discovery of small-molecule ligands for proteins. To investigate the impact of stereo- and regiochemistry on ligand discovery, we synthesized a DNA-encoded library of 670,752 derivatives based on 2-azido-3-iodophenylpropionic acids. The library was selected against multiple proteins and yielded specific ligands. The selection fingerprints obtained for a set of protein targets of pharmaceutical relevance clearly showed the preferential enrichment of ortho-, meta- or para-regioisomers, which was experimentally verified by affinity measurements in the absence of DNA. The discovered ligands included novel selective enzyme inhibitors and binders to tumour-associated antigens, which enabled conditional chimeric antigen receptor T-cell activation and tumour targeting.
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Affiliation(s)
- Nicholas Favalli
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH Zurich), Zurich, Switzerland
| | - Gabriele Bassi
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH Zurich), Zurich, Switzerland
| | - Christian Pellegrino
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH Zurich), Zurich, Switzerland
| | | | | | | | - Su Yang
- Department of Molecular Medicine, Scripps Research Institute, La Jolla, CA, USA
| | - Anika Trenner
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Nour L Mozaffari
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Renier Myburgh
- Department of Medical Oncology and Hematology, University Hospital Zurich and University of Zurich, Comprehensive Cancer Center Zurich (CCCZ), Zurich, Switzerland
| | - Mustafa Moroglu
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Oxford, UK
| | - Stuart J Conway
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Oxford, UK
| | - Alessandro A Sartori
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Markus G Manz
- Department of Medical Oncology and Hematology, University Hospital Zurich and University of Zurich, Comprehensive Cancer Center Zurich (CCCZ), Zurich, Switzerland
| | - Richard A Lerner
- Department of Chemistry, Scripps Research Institute, La Jolla, CA, USA
| | - Peter K Vogt
- Department of Molecular Medicine, Scripps Research Institute, La Jolla, CA, USA
| | - Jörg Scheuermann
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH Zurich), Zurich, Switzerland.
| | - Dario Neri
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH Zurich), Zurich, Switzerland.
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21
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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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22
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Bassi G, Favalli N, Vuk M, Catalano M, Martinelli A, Trenner A, Porro A, Yang S, Tham CL, Moroglu M, Yue WW, Conway SJ, Vogt PK, Sartori AA, Scheuermann J, Neri D. A Single-Stranded DNA-Encoded Chemical Library Based on a Stereoisomeric Scaffold Enables Ligand Discovery by Modular Assembly of Building Blocks. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2020; 7:2001970. [PMID: 33240760 PMCID: PMC7675038 DOI: 10.1002/advs.202001970] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 08/17/2020] [Indexed: 06/11/2023]
Abstract
A versatile and Lipinski-compliant DNA-encoded library (DEL), comprising 366 600 glutamic acid derivatives coupled to oligonucleotides serving as amplifiable identification barcodes is designed, constructed, and characterized. The GB-DEL library, constructed in single-stranded DNA format, allows de novo identification of specific binders against several pharmaceutically relevant proteins. Moreover, hybridization of the single-stranded DEL with a set of known protein ligands of low to medium affinity coupled to a complementary DNA strand results in self-assembled selectable chemical structures, leading to the identification of affinity-matured compounds.
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Affiliation(s)
- Gabriele Bassi
- Department of Chemistry and Applied BiosciencesETH ZürichZürich8092Switzerland
| | - Nicholas Favalli
- Department of Chemistry and Applied BiosciencesETH ZürichZürich8092Switzerland
| | - Miriam Vuk
- Department of Chemistry and Applied BiosciencesETH ZürichZürich8092Switzerland
| | - Marco Catalano
- Department of Chemistry and Applied BiosciencesETH ZürichZürich8092Switzerland
| | - Adriano Martinelli
- Department of Chemistry and Applied BiosciencesETH ZürichZürich8092Switzerland
| | - Anika Trenner
- Institute of Molecular Cancer ResearchUniversity of ZürichZürich8006Switzerland
| | - Antonio Porro
- Institute of Molecular Cancer ResearchUniversity of ZürichZürich8006Switzerland
| | - Su Yang
- Scripps Research InstituteDepartment of Molecular MedicineLa JollaCA92037USA
| | - Chuin Lean Tham
- Structural Genomic Consortium (SGC)Nuffield Department of MedicineUniversity of OxfordOxfordOX1 2JDUK
| | - Mustafa Moroglu
- Department of ChemistryChemistry Research LaboratoryUniversity of OxfordMansfield RoadOxfordOX1 3TAUK
| | - Wyatt W. Yue
- Structural Genomic Consortium (SGC)Nuffield Department of MedicineUniversity of OxfordOxfordOX1 2JDUK
| | - Stuart J. Conway
- Department of ChemistryChemistry Research LaboratoryUniversity of OxfordMansfield RoadOxfordOX1 3TAUK
| | - Peter K. Vogt
- Scripps Research InstituteDepartment of Molecular MedicineLa JollaCA92037USA
| | | | - Jörg Scheuermann
- Department of Chemistry and Applied BiosciencesETH ZürichZürich8092Switzerland
| | - Dario Neri
- Department of Chemistry and Applied BiosciencesETH ZürichZürich8092Switzerland
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23
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Xiong Y, Zhang M, Li Y. Recent Advances in the Development of CBP/p300 Bromodomain Inhibitors. Curr Med Chem 2020; 27:5583-5598. [DOI: 10.2174/0929867326666190731141055] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2019] [Revised: 07/01/2019] [Accepted: 07/02/2019] [Indexed: 12/22/2022]
Abstract
CBP and p300 are two closely related Histone Acetyltransferases (HATs) that interact
with numerous transcription factors and act to increase the expression of their target genes. Both
proteins contain a bromodomain flanking the HAT catalytic domain that is important in binding of
CBP/p300 to chromatin, which offers an opportunity to develop protein-protein interaction inhibitors.
Since their discovery in 2006, CBP/p300 bromodomains have attracted much interest as promising
new epigenetic targets for diverse human diseases, including inflammation, cancer, autoimmune
disorders, and cardiovascular disease. Herein, we present a comprehensive review of the
structure, function, and inhibitors of CBP/p300 bromodomains developed in the last several years,
which is expected to be beneficial to relevant studies.
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Affiliation(s)
- Ying Xiong
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China
| | - Mingming Zhang
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, Shanghai 201203, China
| | - Yingxia Li
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, Shanghai 201203, China
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24
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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: 77] [Impact Index Per Article: 19.3] [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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25
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Discovery of selective inhibitors for cyclic AMP response element-binding protein: a combined ligand and structure-based resources pipeline. Anticancer Drugs 2020; 30:363-373. [PMID: 30499778 DOI: 10.1097/cad.0000000000000727] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Bromodomains are epigenetic readers of acetyl-lysine involved in chromatin remodeling and transcriptional regulations. Over the past few years, extensive research has been carried out to discover small-molecule inhibitors against bromodomains to treat various diseases. Cyclic AMP response element-binding protein (CREBBP) bromodomain has emerged as a hot target for cancer therapy. This study aims at discovering new inhibitors against CREBBP bromodomain using ligand-based molecular docking. A library of 2168 lead-like compounds were docked into the Kac binding site of CREBBP bromodomain. On the basis of the energy score and interaction analysis, six compounds were selected. In order to validate the stability of these six protein-ligand complexes 20 ns molecular dynamics simulations and principal component analyses were carried out. Based on the different analyses these six compounds may provide valuable information for developing CREBBP selective inhibitors.
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26
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Catalano M, Moroglu M, Balbi P, Mazzieri F, Clayton J, Andrews KH, Bigatti M, Scheuermann J, Conway SJ, Neri D. Selective Fragments for the CREBBP Bromodomain Identified from an Encoded Self-assembly Chemical Library. ChemMedChem 2020; 15:1752-1756. [PMID: 32686307 DOI: 10.1002/cmdc.202000528] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Indexed: 12/21/2022]
Abstract
DNA-encoded chemical libraries (DECLs) are collections of chemical moieties individually coupled to distinctive DNA barcodes. Compounds can be displayed either at the end of a single DNA strand (i. e., single-pharmacophore libraries) or at the extremities of two complementary DNA strands (i. e., dual-pharmacophore libraries). In this work, we describe the use of a dual-pharmacophore encoded self-assembly chemical (ESAC) library for the affinity maturation of a known 4,5-dihydrobenzodiazepinone ring (THBD) acetyl-lysine (KAc) mimic for the cyclic-AMP response element binding protein (CREB) binding protein (CREBBP or CBP) bromodomain. The new pair of fragments discovered from library selection showed a sub-micromolar affinity for the CREBBP bromodomain in fluorescence polarization and ELISA assays, and selectivity against BRD4(1).
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Affiliation(s)
- Marco Catalano
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH Zürich), Vladimir-Prelog-Weg 4, 8093, Zürich, Switzerland
| | - Mustafa Moroglu
- Department of Chemistry, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK
| | - Petra Balbi
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH Zürich), Vladimir-Prelog-Weg 4, 8093, Zürich, Switzerland
| | - Federica Mazzieri
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH Zürich), Vladimir-Prelog-Weg 4, 8093, Zürich, Switzerland
| | - James Clayton
- Department of Chemistry, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK
| | - Katrina H Andrews
- Department of Chemistry, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK
| | | | - Jörg Scheuermann
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH Zürich), Vladimir-Prelog-Weg 4, 8093, Zürich, Switzerland
| | - Stuart J Conway
- Department of Chemistry, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK
| | - Dario Neri
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH Zürich), Vladimir-Prelog-Weg 4, 8093, Zürich, Switzerland
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27
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Hassanzadeh P. Towards the quantum-enabled technologies for development of drugs or delivery systems. J Control Release 2020; 324:260-279. [DOI: 10.1016/j.jconrel.2020.04.050] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2019] [Revised: 04/28/2020] [Accepted: 04/29/2020] [Indexed: 12/20/2022]
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28
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Substituted 1-methyl-4-phenylpyrrolidin-2-ones – Fragment-based design of N-methylpyrrolidone-derived bromodomain inhibitors. Eur J Med Chem 2020; 191:112120. [DOI: 10.1016/j.ejmech.2020.112120] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 01/16/2020] [Accepted: 02/03/2020] [Indexed: 01/12/2023]
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29
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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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30
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Hu J, Tian CQ, Damaneh MS, Li Y, Cao D, Lv K, Yu T, Meng T, Chen D, Wang X, Chen L, Li J, Song SS, Huan XJ, Qin L, Shen J, Wang YQ, Miao ZH, Xiong B. Structure-Based Discovery and Development of a Series of Potent and Selective Bromodomain and Extra-Terminal Protein Inhibitors. J Med Chem 2019; 62:8642-8663. [PMID: 31490070 DOI: 10.1021/acs.jmedchem.9b01094] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
BRD4 has recently emerged as a promising drug target. Therefore, identifying novel inhibitors with distinct properties could enrich their use in anticancer treatment. Guided by the cocrystal structure of hit compound 4 harboring a five-membered-ring linker motif, we quickly identified lead compound 7, which exhibited good antitumor effects in an MM.1S xenograft model by oral administration. Encouraged by its high potency and interesting scaffold, we performed further lead optimization to generate a novel potent series of bromodomain and extra-terminal (BET) inhibitors with a (1,2,4-triazol-5-yl)-3,4-dihydroquinoxalin-2(1H)-one structure. Among them, compound 19 was found to have the best balance of activity, stability, and antitumor efficacy. After confirming its low brain penetration, we conducted comprehensive preclinical studies, including a multiple-species pharmacokinetics profile, extensive cellular mechanism studies, hERG assay, and in vivo antitumor growth effect testing, and we found that compound 19 is a potential BET protein drug candidate for the treatment of cancer.
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Affiliation(s)
- Jianping Hu
- University of Chinese Academy of Sciences , NO.19A Yuquan Road , Beijing 100049 , China
| | - Chang-Qing Tian
- University of Chinese Academy of Sciences , NO.19A Yuquan Road , Beijing 100049 , China
| | | | | | | | - Kaikai Lv
- University of Chinese Academy of Sciences , NO.19A Yuquan Road , Beijing 100049 , China
| | | | | | | | | | | | | | | | | | - Lihuai Qin
- Center for Chemical Biology and Drug Discovery, Department of Pharmacological Sciences, Tisch Cancer Institute , Icahn School of Medicine at Mount Sinai , New York , New York 10029 , United States
| | | | - Ying-Qing Wang
- University of Chinese Academy of Sciences , NO.19A Yuquan Road , Beijing 100049 , China
| | - Ze-Hong Miao
- University of Chinese Academy of Sciences , NO.19A Yuquan Road , Beijing 100049 , China
| | - Bing Xiong
- University of Chinese Academy of Sciences , NO.19A Yuquan Road , Beijing 100049 , China
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31
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Xu Z, Zhang Q, Shi J, Zhu W. Underestimated Noncovalent Interactions in Protein Data Bank. J Chem Inf Model 2019; 59:3389-3399. [PMID: 31294978 DOI: 10.1021/acs.jcim.9b00258] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Noncovalent interactions (NCIs) play essential roles in the structure and function of biomacromolecules. There are various NCIs, e.g., hydrogen bonds (HBs), cation-π and π-π interactions, and ionic bonds, among which HBs are the most widespread and well-studied. By utilizing the ratio of the observed HBs over pseudo HBs (1.0 Å longer than the HB distance criteria without angle constraints), we demonstrated that HBs in both protein-ligand and protein-protein interfaces are overlooked in structures deposited in PDB. After the QM/MM optimization of 12 protein-ligand complexes, we showed that the overlooked HBs could be recovered. With a systematic search in the PDB, we found that the HB number per residue (NHB/R) in proteins decreases as structural resolution becomes lower, implying that HBs are overlooked even today, regardless of the type of refinement approach used. Similarly, cation-π, π-π, and ionic interactions were found to be significantly lost, manifesting the universal underestimation of various NCIs. Considering the vital role of NCIs, it is important to recover the NCIs to facilitate drug design, to explore protein-protein interaction, and to study protein structure and function.
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Affiliation(s)
- Zhijian Xu
- CAS Key Laboratory of Receptor Research, Drug Discovery and Design Center , Shanghai Institute of Materia Medica, Chinese Academy of Sciences , Shanghai 201203 , China
| | - Qian Zhang
- Department of Computer Science and Technology , East China Normal University , Shanghai 200241 , China
| | - Jiye Shi
- CAS Key Laboratory of Receptor Research, Drug Discovery and Design Center , Shanghai Institute of Materia Medica, Chinese Academy of Sciences , Shanghai 201203 , China
| | - Weiliang Zhu
- CAS Key Laboratory of Receptor Research, Drug Discovery and Design Center , Shanghai Institute of Materia Medica, Chinese Academy of Sciences , Shanghai 201203 , China.,Open Studio for Druggability Research of Marine Natural Products , Pilot National Laboratory for Marine Science and Technology (Qingdao) , Qingdao 266237 , China
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32
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Huang R, Chen X, Mou C, Luo G, Li Y, Li X, Xue W, Jin Z, Chi YR. Carbene-Catalyzed α-Carbon Amination of Chloroaldehydes for Enantioselective Access to Dihydroquinoxaline Derivatives. Org Lett 2019; 21:4340-4344. [PMID: 31117715 DOI: 10.1021/acs.orglett.9b01520] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
An NHC-catalyzed α-carbon amination of chloroaldehydes was developed. Cyclohexadiene-1,2-diimines are used as amination reagents and four-atom synthons. Our reaction affords optically enriched dihydroquinoxalines that are core structures in natural products and synthetic bioactive molecules.
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Affiliation(s)
- Ruoyan Huang
- Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education , Guizhou University , Huaxi District , Guiyang 550025 , China
| | - Xingkuan Chen
- Division of Chemistry & Biological Chemistry, School of Physical & Mathematical Sciences , Nanyang Technological University , Singapore 637371 , Singapore
| | - Chengli Mou
- Guizhou University of Traditional Chinese Medicine , Huaxi District , Guiyang 550025 , China
| | - Guoyong Luo
- Guizhou University of Traditional Chinese Medicine , Huaxi District , Guiyang 550025 , China
| | - Yongjia Li
- Division of Chemistry & Biological Chemistry, School of Physical & Mathematical Sciences , Nanyang Technological University , Singapore 637371 , Singapore
| | - Xiangyang Li
- Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education , Guizhou University , Huaxi District , Guiyang 550025 , China
| | - Wei Xue
- Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education , Guizhou University , Huaxi District , Guiyang 550025 , China
| | - Zhichao Jin
- Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education , Guizhou University , Huaxi District , Guiyang 550025 , China
| | - Yonggui Robin Chi
- Laboratory Breeding Base of Green Pesticide and Agricultural Bioengineering, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education , Guizhou University , Huaxi District , Guiyang 550025 , China.,Division of Chemistry & Biological Chemistry, School of Physical & Mathematical Sciences , Nanyang Technological University , Singapore 637371 , Singapore
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33
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Chan AKN, Chen CW. Rewiring the Epigenetic Networks in MLL-Rearranged Leukemias: Epigenetic Dysregulation and Pharmacological Interventions. Front Cell Dev Biol 2019; 7:81. [PMID: 31157223 PMCID: PMC6529847 DOI: 10.3389/fcell.2019.00081] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2019] [Accepted: 04/30/2019] [Indexed: 12/26/2022] Open
Abstract
Leukemias driven by chromosomal translocation of the mixed-lineage leukemia gene (MLL or KMT2A) are highly prevalent in pediatric oncology. The poor survival rate and lack of an effective targeted therapy for patients with MLL-rearranged (MLL-r) leukemias emphasize an urgent need for improved knowledge and novel therapeutic approaches for these malignancies. The resulting chimeric products of MLL gene rearrangements, i.e., MLL-fusion proteins (MLL-FPs), are capable of transforming hematopoietic stem/progenitor cells (HSPCs) into leukemic blasts. The ability of MLL-FPs to reprogram HSPCs toward leukemia requires the involvement of multiple chromatin effectors, including the histone 3 lysine 79 methyltransferase DOT1L, the chromatin epigenetic reader BRD4, and the super elongation complex. These epigenetic regulators constitute a complicated network that dictates maintenance of the leukemia program, and therefore represent an important cluster of therapeutic opportunities. In this review, we will discuss the role of MLL and its fusion partners in normal HSPCs and hematopoiesis, including the links between chromatin effectors, epigenetic landscapes, and leukemia development, and summarize current approaches to therapeutic targeting of MLL-r leukemias.
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Affiliation(s)
| | - Chun-Wei Chen
- Department of Systems Biology, Beckman Research Institute of City of Hope, Duarte, CA, United States
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34
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Li D, Ollevier T. Iron- or Zinc-Mediated Synthetic Approach to Enantiopure Dihydroquinoxalinones. European J Org Chem 2018. [DOI: 10.1002/ejoc.201801639] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Dazhi Li
- Département de chimie; Université Laval; 1045 avenue de la Médecine Québec, QC, G1V 0A6 Canada
| | - Thierry Ollevier
- Département de chimie; Université Laval; 1045 avenue de la Médecine Québec, QC, G1V 0A6 Canada
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35
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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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36
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From bench to bedside, via desktop. Recent advances in the application of cutting-edge in silico tools in the research of drugs targeting bromodomain modules. Biochem Pharmacol 2018; 159:40-51. [PMID: 30414936 DOI: 10.1016/j.bcp.2018.11.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2018] [Accepted: 11/07/2018] [Indexed: 11/22/2022]
Abstract
The discipline of drug discovery has greatly benefited by computational tools and in silico algorithms aiming at rationalization of many related processes, from the stage of early hit identification to the preclinical phases of drug candidate validation. The various methodologies referred to as molecular modeling tools span a broad spectrum of applications, from straightforward approaches such as virtual screening of compound libraries to more advanced techniques involving the precise estimation of free energy upon binding of the candidate drug to its macromolecular target. To this end, we report an overview of specific studies where implementation of such sophisticated modeling algorithms has shown to be indispensable for addressing challenging systems and biological questions otherwise difficult to answer. We focus our attention on the emerging field of bromodomain inhibitors. Bromodomains are small modules involved in epigenetic signaling and currently comprise high-priority targets for developing both drug candidates and chemical probes for basic biomedical research. We attempt a critical presentation of selected cases utilizing cutting-edge in silico methodologies, with our main emphasis being on absolute or relative free energy simulations, on implementation of quantum-mechanics level calculations and on characterization of solvent thermodynamics. We discuss the advantages and strengths as well as the drawbacks and weaknesses of computational tools utilized in those works and we attempt to comment on specific issues related to their integration into the regular medicinal chemistry practice. Our conclusion is that while such methods indeed represent highly promising resources for further advancing the discipline, their application is not always trivial.
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Zhu J, Dong J, Batiste L, Unzue A, Dolbois A, Pascanu V, Śledź P, Nevado C, Caflisch A. Binding Motifs in the CBP Bromodomain: An Analysis of 20 Crystal Structures of Complexes with Small Molecules. ACS Med Chem Lett 2018; 9:929-934. [PMID: 30258543 DOI: 10.1021/acsmedchemlett.8b00286] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Accepted: 08/08/2018] [Indexed: 01/01/2023] Open
Abstract
We analyze 20 crystal structures of complexes between the CBP bromodomain and small-molecule ligands that belong to eight different chemotypes identified by docking. The binding motif of the moiety that mimics the natural ligand (acetylated side chain of lysine) at the bottom of the binding pocket is conserved. In stark contrast, the rest of the ligands form different interactions with different side chains and backbone polar groups on the outer rim of the binding pocket. Hydrogen bonds are direct or water-bridged. van der Waals contacts are optimized by rotations of hydrophobic side chains and a slight inward displacement of the ZA loop. Rare types of interactions are observed for some of the ligands.
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38
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Jennings LE, Schiedel M, Hewings DS, Picaud S, Laurin CMC, Bruno PA, Bluck JP, Scorah AR, See L, Reynolds JK, Moroglu M, Mistry IN, Hicks A, Guzanov P, Clayton J, Evans CNG, Stazi G, Biggin PC, Mapp AK, Hammond EM, Humphreys PG, Filippakopoulos P, Conway SJ. BET bromodomain ligands: Probing the WPF shelf to improve BRD4 bromodomain affinity and metabolic stability. Bioorg Med Chem 2018; 26:2937-2957. [PMID: 29776834 DOI: 10.1016/j.bmc.2018.05.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 04/30/2018] [Accepted: 05/02/2018] [Indexed: 12/20/2022]
Abstract
Ligands for the bromodomain and extra-terminal domain (BET) family of bromodomains have shown promise as useful therapeutic agents for treating a range of cancers and inflammation. Here we report that our previously developed 3,5-dimethylisoxazole-based BET bromodomain ligand (OXFBD02) inhibits interactions of BRD4(1) with the RelA subunit of NF-κB, in addition to histone H4. This ligand shows a promising profile in a screen of the NCI-60 panel but was rapidly metabolised (t½ = 39.8 min). Structure-guided optimisation of compound properties led to the development of the 3-pyridyl-derived OXFBD04. Molecular dynamics simulations assisted our understanding of the role played by an internal hydrogen bond in altering the affinity of this series of molecules for BRD4(1). OXFBD04 shows improved BRD4(1) affinity (IC50 = 166 nM), optimised physicochemical properties (LE = 0.43; LLE = 5.74; SFI = 5.96), and greater metabolic stability (t½ = 388 min).
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Affiliation(s)
- Laura E Jennings
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Matthias Schiedel
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - David S Hewings
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Sarah Picaud
- Nuffield Department of Clinical Medicine, Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 3TA, United Kingdom
| | - Corentine M C Laurin
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Paul A Bruno
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, United States; Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109-2216, United States; Program in Chemical Biology, University of Michigan, Ann Arbor, MI 48109-2216, United States
| | - Joseph P Bluck
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, United Kingdom; Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Amy R Scorah
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Larissa See
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Jessica K Reynolds
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Mustafa Moroglu
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Ishna N Mistry
- CRUK/MRC Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Old Road Campus Research Building, Oxford OX3 7DQ, United Kingdom
| | - Amy Hicks
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Pavel Guzanov
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - James Clayton
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Charles N G Evans
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, United Kingdom
| | - Giulia Stazi
- Department of Chemistry and Technologies of Drugs, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Philip C Biggin
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
| | - Anna K Mapp
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, United States; Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109-2216, United States; Program in Chemical Biology, University of Michigan, Ann Arbor, MI 48109-2216, United States
| | - Ester M Hammond
- CRUK/MRC Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Old Road Campus Research Building, Oxford OX3 7DQ, United Kingdom
| | - Philip G Humphreys
- Epigenetics Discovery Performance Unit, GlaxoSmithKline R&D, Stevenage Hertfordshire SG1 2NY, United Kingdom
| | - Panagis Filippakopoulos
- Nuffield Department of Clinical Medicine, Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 3TA, United Kingdom
| | - Stuart J Conway
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, United Kingdom.
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Lu W, Zhang R, Jiang H, Zhang H, Luo C. Computer-Aided Drug Design in Epigenetics. Front Chem 2018; 6:57. [PMID: 29594101 PMCID: PMC5857607 DOI: 10.3389/fchem.2018.00057] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2018] [Accepted: 02/23/2018] [Indexed: 12/31/2022] Open
Abstract
Epigenetic dysfunction has been widely implicated in several diseases especially cancers thus highlights the therapeutic potential for chemical interventions in this field. With rapid development of computational methodologies and high-performance computational resources, computer-aided drug design has emerged as a promising strategy to speed up epigenetic drug discovery. Herein, we make a brief overview of major computational methods reported in the literature including druggability prediction, virtual screening, homology modeling, scaffold hopping, pharmacophore modeling, molecular dynamics simulations, quantum chemistry calculation, and 3D quantitative structure activity relationship that have been successfully applied in the design and discovery of epi-drugs and epi-probes. Finally, we discuss about major limitations of current virtual drug design strategies in epigenetics drug discovery and future directions in this field.
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Affiliation(s)
- Wenchao 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, China
- Department of Pharmacy, University of Chinese Academy of Sciences, Beijing, China
| | - Rukang 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, China
- Department of Pharmacy, University of Chinese Academy of Sciences, Beijing, 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, China
- Department of Pharmacy, University of Chinese Academy of Sciences, Beijing, China
| | - Huimin 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, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 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, China
- Department of Pharmacy, University of Chinese Academy of Sciences, Beijing, China
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40
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In silico quest of selective naphthyl-based CREBBP bromodomain inhibitor. In Silico Pharmacol 2018; 6:1. [PMID: 30607314 DOI: 10.1007/s40203-018-0038-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Accepted: 03/02/2018] [Indexed: 10/17/2022] Open
Abstract
The reader proteins like bromodomains have recently gained increased attentions in the area of epigenetic drug discovery, as they are the potent regulators in gene transcription process. Among the other bromodomains, cAMP response element-binding protein (CREB) binding protein or CREBBP bomodomain involved in various cancer progressions and therefore, efforts to develop specific inhibitors of CREBBP bomodomain are of clinical value. In this study, we tried to identify selective CREBBP bromodomain inhibitor, which was accomplished by using molecular docking, free energy calculation and molecular dynamics (MD) simulation studies, considering a series of naphthyl based compounds. The docking procedure was validated by comparing root mean square deviations (RMSDs) of crystallographic complex to docked complex. Favorable electrostatic interactions with the Arg1173 side chain were considered to attain selectivity for CREBBP bromodomain over other human bromodomain subfamilies. We found that naphthyl-based compounds have greater binding affinities towards the CREBBP bromodomain, and formed non-bonded interactions with various side chain residues that are important for bromodomain inhibition. From detailed investigation by induced fit docking, compound 31 was found to have favorable electrostatic interactions with the Arg1173 side chain by forming conventional hydrogen bonds. This result was further confirmed by analyzing hydrogen bond occupancy and bonding distance during the molecular dynamics simulation. We believe that these findings offer useful insight for the designing of target specific new bromodomain inhibitor and also promote further structure guided synthesis of analogues for identification of potent CREBBP bromodomain inhibitors as well as detailed in vitro and in vivo analyses.
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Batiste L, Unzue A, Dolbois A, Hassler F, Wang X, Deerain N, Zhu J, Spiliotopoulos D, Nevado C, Caflisch A. Chemical Space Expansion of Bromodomain Ligands Guided by in Silico Virtual Couplings (AutoCouple). ACS CENTRAL SCIENCE 2018; 4:180-188. [PMID: 29532017 PMCID: PMC5833004 DOI: 10.1021/acscentsci.7b00401] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Indexed: 10/24/2023]
Abstract
Expanding the chemical space and simultaneously ensuring synthetic accessibility is of upmost importance, not only for the discovery of effective binders for novel protein classes but, more importantly, for the development of compounds against hard-to-drug proteins. Here, we present AutoCouple, a de novo approach to computational ligand design focused on the diversity-oriented generation of chemical entities via virtual couplings. In a benchmark application, chemically diverse compounds with low-nanomolar potency for the CBP bromodomain and high selectivity against the BRD4(1) bromodomain were achieved by the synthesis of about 50 derivatives of the original fragment. The binding mode was confirmed by X-ray crystallography, target engagement in cells was demonstrated, and antiproliferative activity was showcased in three cancer cell lines. These results reveal AutoCouple as a useful in silico coupling method to expand the chemical space in hit optimization campaigns resulting in potent, selective, and cell permeable bromodomain ligands.
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Affiliation(s)
- Laurent Batiste
- Department
of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057, Zürich, Switzerland
| | - Andrea Unzue
- Department
of Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057, Zürich, Switzerland
| | - Aymeric Dolbois
- Department
of Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057, Zürich, Switzerland
| | - Fabrice Hassler
- Department
of Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057, Zürich, Switzerland
| | - Xuan Wang
- Department
of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057, Zürich, Switzerland
- Department
of Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057, Zürich, Switzerland
| | - Nicholas Deerain
- Department
of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057, Zürich, Switzerland
| | - Jian Zhu
- Department
of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057, Zürich, Switzerland
| | - Dimitrios Spiliotopoulos
- Department
of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057, Zürich, Switzerland
| | - Cristina Nevado
- Department
of Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057, Zürich, Switzerland
| | - Amedeo Caflisch
- Department
of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057, Zürich, Switzerland
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42
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Kanyiva KS, Horiuchi M, Shibata T. Metal-Free N-H/C-H Coupling for Efficient Asymmetric Synthesis of Chiral Dihydroquinoxalinones from Readily Available α-Amino Acids. European J Org Chem 2018. [DOI: 10.1002/ejoc.201800012] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Kyalo Stephen Kanyiva
- Global Center for Science and Engineering; School of Advanced Science and Engineering; Waseda University; Shinjuku 8555 Tokyo 169- Japan
| | - Masashi Horiuchi
- Department of Chemistry and Biochemistry; School of Advanced Science and Engineering; Waseda University; Shinjuku 8555 Tokyo 169- Japan
| | - Takanori Shibata
- Department of Chemistry and Biochemistry; School of Advanced Science and Engineering; Waseda University; Shinjuku 8555 Tokyo 169- Japan
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43
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Hu J, Wang Y, Li Y, Cao D, Xu L, Song S, Damaneh MS, Li J, Chen Y, Wang X, Chen L, Shen J, Miao Z, Xiong B. Structure-based optimization of a series of selective BET inhibitors containing aniline or indoline groups. Eur J Med Chem 2018. [PMID: 29525435 DOI: 10.1016/j.ejmech.2018.02.070] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Recently, several kinase inhibitors were found to also inhibit bromodomains, providing a new strategy for the discovery of bromodomain inhibitors. Along this line, starting from PLK1-BRD4 dual inhibitor BI-2536, we discovered a new series of dihydroquinoxalin-2(1H)-one with aniline and indoline WPF binders as selective BRD4 inhibitors. They showed better BRD4-BD1 potency and negligible PLK1 kinase activity comparing with BI-2536. Additionally, dihydroquinoxalin-2(1H)-ones containing indoline group showed profound activities in molecular and cellular based assays. Throughout the study, compounds 9, 28 and 37 showed significant inhibitory activity for c-Myc or PD-L1 protein expression and mRNA transcription both at concentration of 0.2 and 1 μM. Compound 9 was found possessing the best balance of binding affinity, in vitro metabolic stability and in vivo pharmacokinetic properties. Therefore, it was selected for in vivo pharmacological study. By using MM.1S cell derived xenograft model, we confirmed compound 9 showed comparable in vivo tumor inhibition to phase II investigation drug I-BET762, which, together with the novel WPF binder, further indicated the utility of this series of BRD4 inhibitors.
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Affiliation(s)
- Jianping Hu
- Department of Medicinal Chemistry, 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, NO.19A Yuquan Road, Beijing 100049, China
| | - Yingqing Wang
- Division of Anti-tumor Pharmacology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Yanlian Li
- Department of Medicinal Chemistry, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Danyan Cao
- Department of Medicinal Chemistry, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Lin Xu
- Division of Anti-tumor Pharmacology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - ShanShan Song
- Division of Anti-tumor Pharmacology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Mohammadali Soleimani Damaneh
- Division of Anti-tumor Pharmacology, 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, NO.19A Yuquan Road, Beijing 100049, China
| | - Jian Li
- Department of Medicinal Chemistry, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Yuelei Chen
- Department of Medicinal Chemistry, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Xin Wang
- Department of Medicinal Chemistry, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Lin Chen
- Department of Medicinal Chemistry, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Jingkang Shen
- Department of Medicinal Chemistry, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Zehong Miao
- Division of Anti-tumor Pharmacology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China.
| | - Bing Xiong
- Department of Medicinal Chemistry, 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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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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45
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Theoretical research in structure characteristics of different inhibitors and differences of binding modes with CBP bromodomain. Bioorg Med Chem 2018; 26:712-720. [DOI: 10.1016/j.bmc.2017.12.040] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Revised: 12/18/2017] [Accepted: 12/24/2017] [Indexed: 12/12/2022]
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46
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Kumar K, Woo SM, Siu T, Cortopassi WA, Duarte F, Paton RS. Cation-π interactions in protein-ligand binding: theory and data-mining reveal different roles for lysine and arginine. Chem Sci 2018; 9:2655-2665. [PMID: 29719674 PMCID: PMC5903419 DOI: 10.1039/c7sc04905f] [Citation(s) in RCA: 152] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Accepted: 01/20/2018] [Indexed: 12/22/2022] Open
Abstract
The interactions of neutral aromatic ligands with cationic arginine, histidine and lysine amino acid residues have been studied with ab initio calculations, symmetry adapted perturbation theory (SAPT), and a systematic meta-analysis of X-ray structures.
We have studied the cation–π interactions of neutral aromatic ligands with the cationic amino acid residues arginine, histidine and lysine using ab initio calculations, symmetry adapted perturbation theory (SAPT), and a systematic meta-analysis of all available Protein Data Bank (PDB) X-ray structures. Quantum chemical potential energy surfaces (PES) for these interactions were obtained at the DLPNO-CCSD(T) level of theory and compared against the empirical distribution of 2012 unique protein–ligand cation–π interactions found in X-ray crystal structures. We created a workflow to extract these structures from the PDB, filtering by interaction type and residue pKa. The gas phase cation–π interaction of lysine is the strongest by more than 10 kcal mol–1, but the empirical distribution of 582 X-ray structures lies away from the minimum on the interaction PES. In contrast, 1381 structures involving arginine match the underlying calculated PES with good agreement. SAPT analysis revealed that underlying differences in the balance of electrostatic and dispersion contributions are responsible for this behavior in the context of the protein environment. The lysine–arene interaction, dominated by electrostatics, is greatly weakened by a surrounding dielectric medium and causes it to become essentially negligible in strength and without a well-defined equilibrium separation. The arginine–arene interaction involves a near equal mix of dispersion and electrostatic attraction, which is weakened to a much smaller degree by the surrounding medium. Our results account for the paucity of cation–π interactions involving lysine, even though this is a more common residue than arginine. Aromatic ligands are most likely to interact with cationic arginine residues as this interaction is stronger than for lysine in higher polarity surroundings.
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Affiliation(s)
- Kiran Kumar
- Chemistry Research Laboratory , University of Oxford , 12 Mansfield Road , Oxford OX1 3TA , UK .
| | - Shin M Woo
- Chemistry Research Laboratory , University of Oxford , 12 Mansfield Road , Oxford OX1 3TA , UK .
| | - Thomas Siu
- Chemistry Research Laboratory , University of Oxford , 12 Mansfield Road , Oxford OX1 3TA , UK .
| | - Wilian A Cortopassi
- Chemistry Research Laboratory , University of Oxford , 12 Mansfield Road , Oxford OX1 3TA , UK .
| | - Fernanda Duarte
- EaStCHEM School of Chemistry , University of Edinburgh , Joseph Black Building, David Brewster Road , Edinburgh EH9 3FJ , UK .
| | - Robert S Paton
- Chemistry Research Laboratory , University of Oxford , 12 Mansfield Road , Oxford OX1 3TA , UK .
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47
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Wang Q, An X, Xu J, Wang Y, Liu L, Leung ELH, Yao X. Classical molecular dynamics and metadynamics simulations decipher the mechanism of CBP30 selectively inhibiting CBP/p300 bromodomains. Org Biomol Chem 2018; 16:6521-6530. [DOI: 10.1039/c8ob01526k] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The selective inhibition mechanism of CBP30 towards CBP/p300 over BRD4-BD1/BD2 bromodomains was revealed by conventional molecular dynamics and metadynamics simulations.
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Affiliation(s)
- Qianqian Wang
- State Key Laboratory of Quality Research in Chinese Medicine/Macau Institute for Applied Research in Medicine and Health
- Macau University of Science and Technology
- Macau
- China
| | - Xiaoli An
- State Key Laboratory of Applied Organic Chemistry and Department of Chemistry
- Lanzhou University
- Lanzhou
- China
| | - Jiahui Xu
- State Key Laboratory of Quality Research in Chinese Medicine/Macau Institute for Applied Research in Medicine and Health
- Macau University of Science and Technology
- Macau
- China
| | - Yuwei Wang
- State Key Laboratory of Quality Research in Chinese Medicine/Macau Institute for Applied Research in Medicine and Health
- Macau University of Science and Technology
- Macau
- China
| | - Liang Liu
- State Key Laboratory of Quality Research in Chinese Medicine/Macau Institute for Applied Research in Medicine and Health
- Macau University of Science and Technology
- Macau
- China
| | - Elaine Lai-Han Leung
- State Key Laboratory of Quality Research in Chinese Medicine/Macau Institute for Applied Research in Medicine and Health
- Macau University of Science and Technology
- Macau
- China
| | - Xiaojun Yao
- State Key Laboratory of Quality Research in Chinese Medicine/Macau Institute for Applied Research in Medicine and Health
- Macau University of Science and Technology
- Macau
- China
- State Key Laboratory of Applied Organic Chemistry and Department of Chemistry
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48
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Lai KW, Romero FA, Tsui V, Beresini MH, de Leon Boenig G, Bronner SM, Chen K, Chen Z, Choo EF, Crawford TD, Cyr P, Kaufman S, Li Y, Liao J, Liu W, Ly J, Murray J, Shen W, Wai J, Wang F, Zhu C, Zhu X, Magnuson S. Design and synthesis of a biaryl series as inhibitors for the bromodomains of CBP/P300. Bioorg Med Chem Lett 2018; 28:15-23. [DOI: 10.1016/j.bmcl.2017.11.025] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Revised: 11/07/2017] [Accepted: 11/13/2017] [Indexed: 11/26/2022]
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49
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Bronner SM, Murray J, Romero FA, Lai KW, Tsui V, Cyr P, Beresini MH, de Leon Boenig G, Chen Z, Choo EF, Clark KR, Crawford TD, Jayaram H, Kaufman S, Li R, Li Y, Liao J, Liang X, Liu W, Ly J, Maher J, Wai J, Wang F, Zheng A, Zhu X, Magnuson S. A Unique Approach to Design Potent and Selective Cyclic Adenosine Monophosphate Response Element Binding Protein, Binding Protein (CBP) Inhibitors. J Med Chem 2017; 60:10151-10171. [PMID: 29155580 DOI: 10.1021/acs.jmedchem.7b01372] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The epigenetic regulator CBP/P300 presents a novel therapeutic target for oncology. Previously, we disclosed the development of potent and selective CBP bromodomain inhibitors by first identifying pharmacophores that bind the KAc region and then building into the LPF shelf. Herein, we report the "hybridization" of a variety of KAc-binding fragments with a tetrahydroquinoline scaffold that makes optimal interactions with the LPF shelf, imparting enhanced potency and selectivity to the hybridized ligand. To demonstrate the utility of our hybridization approach, two analogues containing unique Asn binders and the optimized tetrahydroquinoline moiety were rapidly optimized to yield single-digit nanomolar inhibitors of CBP with exquisite selectivity over BRD4(1) and the broader bromodomain family.
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Affiliation(s)
- Sarah M Bronner
- Genentech, Inc. , 1 DNA Way, South San Francisco, California 94080, United States
| | - Jeremy Murray
- Genentech, Inc. , 1 DNA Way, South San Francisco, California 94080, United States
| | - F Anthony Romero
- Genentech, Inc. , 1 DNA Way, South San Francisco, California 94080, United States
| | - Kwong Wah Lai
- Wuxi Apptec Co., Ltd. , 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, People's Republic of China
| | - Vickie Tsui
- Genentech, Inc. , 1 DNA Way, South San Francisco, California 94080, United States
| | - Patrick Cyr
- Genentech, Inc. , 1 DNA Way, South San Francisco, California 94080, United States
| | - Maureen H Beresini
- Genentech, Inc. , 1 DNA Way, South San Francisco, California 94080, United States
| | | | - Zhongguo Chen
- Wuxi Apptec Co., Ltd. , 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, People's Republic of China
| | - Edna F Choo
- Genentech, Inc. , 1 DNA Way, South San Francisco, California 94080, United States
| | - Kevin R Clark
- Genentech, Inc. , 1 DNA Way, South San Francisco, California 94080, United States
| | - Terry D Crawford
- Genentech, Inc. , 1 DNA Way, South San Francisco, California 94080, United States
| | - Hariharan Jayaram
- Editas Medicine, Inc. , 11 Hurley Street, Cambridge, Massachusetts 02141, United States
| | - Susan Kaufman
- Genentech, Inc. , 1 DNA Way, South San Francisco, California 94080, United States
| | - Ruina Li
- Genentech, Inc. , 1 DNA Way, South San Francisco, California 94080, United States
| | - Yingjie Li
- Wuxi Apptec Co., Ltd. , 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, People's Republic of China
| | - Jiangpeng Liao
- Wuxi Apptec Co., Ltd. , 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, People's Republic of China
| | - Xiaorong Liang
- Genentech, Inc. , 1 DNA Way, South San Francisco, California 94080, United States
| | - Wenfeng Liu
- Wuxi Apptec Co., Ltd. , 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, People's Republic of China
| | - Justin Ly
- Genentech, Inc. , 1 DNA Way, South San Francisco, California 94080, United States
| | - Jonathan Maher
- Genentech, Inc. , 1 DNA Way, South San Francisco, California 94080, United States
| | - John Wai
- Wuxi Apptec Co., Ltd. , 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, People's Republic of China
| | - Fei Wang
- Wuxi Apptec Co., Ltd. , 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, People's Republic of China
| | - Aijun Zheng
- Wuxi Apptec Co., Ltd. , 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, People's Republic of China
| | - Xiaoyu Zhu
- Wuxi Apptec Co., Ltd. , 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, People's Republic of China
| | - Steven Magnuson
- Genentech, Inc. , 1 DNA Way, South San Francisco, California 94080, United States
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50
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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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