1
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Li P, Shi M, Yang K, Jing T, Kang Z, Hu W, Qian Y. Diastereoselective Synthesis of 4-Hydroxy-2-quinolinones via Formal [2 + 4] Cycloaddition Reactions Using α-Diazo Pyrazoleamides as C2 Synthons. Org Lett 2024; 26:5554-5559. [PMID: 38912750 DOI: 10.1021/acs.orglett.4c01956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/25/2024]
Abstract
A rhodium-catalyzed highly stereoselective formal [2 + 4]-cycloaddition reaction of α-diazo pyrazoleamides and 2-aminophenyl ketones that produces 4-hydroxy-2-quinolinones in good yields with excellent diastereoselectivities has been developed. A pyrazolium ylide species that is generated from α-diazo pyrazoleamides is used as a C2 synthon for this cycloaddition. This protocol offers an efficient approach to a variety of 4-hydroxy-2-quinolinones featuring sequential quaternary centers.
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Affiliation(s)
- Pei Li
- State Key Laboratory of Anti-Infective Drug Discovery and Development, Guangdong Provincial Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Maoqing Shi
- State Key Laboratory of Anti-Infective Drug Discovery and Development, Guangdong Provincial Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Kaixin Yang
- State Key Laboratory of Anti-Infective Drug Discovery and Development, Guangdong Provincial Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Tongfei Jing
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan 528400, China
| | - Zhenghui Kang
- Zhongshan Institute for Drug Discovery, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Zhongshan 528400, China
| | - Wenhao Hu
- State Key Laboratory of Anti-Infective Drug Discovery and Development, Guangdong Provincial Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Yu Qian
- State Key Laboratory of Anti-Infective Drug Discovery and Development, Guangdong Provincial Key Laboratory of Chiral Molecule and Drug Discovery, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
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2
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Hai H, Qin S, Zhang Y, Liu W, Feng J, Guo H, Kühn FE, Liu Y. Visible Light-Induced Regioselective Intermolecular [2 + 2]-Cycloaddition of Alkyne and 2(1 H)-Quinolone Derivatives. J Org Chem 2024. [PMID: 38190649 DOI: 10.1021/acs.joc.3c02685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2024]
Abstract
We have developed a visible light-induced intermolecular [2 + 2]-cycloaddition reaction between alkenes and alkynes using thioxanthone and Cu(OTf)2 as cocatalysts. Various quinolin-2(1H)-ones, featuring diverse substituted groups, were successfully employed in this reaction, resulting in the synthesis of a series of 4,8b-dihydrocyclobuta[c]quinolin-3(2aH)-ones. Our methodology presents a novel synthetic approach for alkene-alkyne [2 + 2]-cycloaddition, delivering cyclobutene derivatives with exceptional regioselectivity.
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Affiliation(s)
- Hao Hai
- Academy for Engineering and Technology, Fudan University, 220 Handan Road, Shanghai 200433, P. R. China
| | - Shaoheng Qin
- Molecular Catalysis, Department of Chemistry and Catalysis Research Center, School of Natural Sciences, Technical University Munich, Lichtenbergstr. 4, 85747 Garching bei München, Germany
| | - Yanzhi Zhang
- Department of Breast Surgery, Fudan University Shanghai Cancer Center/Cancer Institute, Shanghai 200032, P. R. China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, P. R. China
| | - Wangsheng Liu
- Department of Chemistry, Fudan University, 2005 Songhu Road, Shanghai 200438, P. R. China
| | - Jin Feng
- Department of Chemistry, Fudan University, 2005 Songhu Road, Shanghai 200438, P. R. China
| | - Hao Guo
- Academy for Engineering and Technology, Fudan University, 220 Handan Road, Shanghai 200433, P. R. China
- Department of Chemistry, Fudan University, 2005 Songhu Road, Shanghai 200438, P. R. China
| | - Fritz E Kühn
- Molecular Catalysis, Department of Chemistry and Catalysis Research Center, School of Natural Sciences, Technical University Munich, Lichtenbergstr. 4, 85747 Garching bei München, Germany
| | - Yin Liu
- Department of Breast Surgery, Fudan University Shanghai Cancer Center/Cancer Institute, Shanghai 200032, P. R. China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, P. R. China
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3
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Zhang W, Ning R, Ran T, Peng Q, Liu Y, Lu T, Chen Y, Jiang M, Jiao Y. Development of 3-acetylindole derivatives that selectively target BRPF1 as new inhibitors of receptor activator of NF-κB ligand (RANKL)-Induced osteoclastogenesis. Bioorg Med Chem 2023; 96:117440. [PMID: 37951134 DOI: 10.1016/j.bmc.2023.117440] [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: 07/06/2023] [Revised: 08/03/2023] [Accepted: 08/07/2023] [Indexed: 11/13/2023]
Abstract
Bromodomain and PHD finger-containing (BRPF) proteins function as epigenetic readers that specifically recognize acetylated lysine residues on histone tails. The acetyl-lysine binding pocket of BRPF has emerged as an attractive target for the development of protein interaction inhibitors owing to its potential druggability. In this study, we identified 3-acetylindoles as bone antiresorptive agents with a novel scaffold by performing structure-based virtual screening and hit optimization. Among those derivatives, compound 18 exhibited potent and selective inhibitory activities against BRPF1B (IC50 = 102 nM) as well as outstanding inhibitory activity against osteoclastogenesis (73.8% @ 1 μM) and differentiation (IC50 = 0.19 μM) without cytotoxicity. Besides, cellular mechanism assays demonstrated that compound 18 exhibited a strong bone antiresorptive effect by modulating the RANKL/RANK/NFATc1 pathway. Structural and functional studies on BRPF1 inhibitors aid in making advances to understand the epigenetic mechanisms of bone cell development and create innovative therapeutics for treating bone metastases from solid tumors and other bone erosive diseases.
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Affiliation(s)
- Wenqiang Zhang
- School of Sciences, China Pharmaceutical University, 639 Longmian Avenue, Nanjing 211198, PR China
| | - Ruonan Ning
- Department of Orthopaedics, Shanghai Key Laboratory for Prevention and Treatment of Bone and Joint Diseases, Shanghai Institute of Traumatology and Orthopaedics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, 197 Ruijin 2nd Road, Shanghai 200025, PR China
| | - Ting Ran
- Drug and Vaccine Research Center, Guangzhou Laboratory, Guangzhou 510005, PR China
| | - Qi Peng
- School of Sciences, China Pharmaceutical University, 639 Longmian Avenue, Nanjing 211198, PR China
| | - Yong Liu
- School of Sciences, China Pharmaceutical University, 639 Longmian Avenue, Nanjing 211198, PR China
| | - Tao Lu
- School of Sciences, China Pharmaceutical University, 639 Longmian Avenue, Nanjing 211198, PR China; State Key Laboratory of Natural Medicines, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing 210009, PR China.
| | - Yadong Chen
- School of Sciences, China Pharmaceutical University, 639 Longmian Avenue, Nanjing 211198, PR China.
| | - Min Jiang
- Department of Orthopaedics, Shanghai Key Laboratory for Prevention and Treatment of Bone and Joint Diseases, Shanghai Institute of Traumatology and Orthopaedics, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, 197 Ruijin 2nd Road, Shanghai 200025, PR China.
| | - Yu Jiao
- School of Sciences, China Pharmaceutical University, 639 Longmian Avenue, Nanjing 211198, PR China.
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4
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Ordonez-Rubiano SC, Maschinot CA, Wang S, Sood S, Baracaldo-Lancheros LF, Strohmier BP, McQuade AJ, Smith BC, Dykhuizen EC. Rational Design and Development of Selective BRD7 Bromodomain Inhibitors and Their Activity in Prostate Cancer. J Med Chem 2023; 66:11250-11270. [PMID: 37552884 PMCID: PMC10641717 DOI: 10.1021/acs.jmedchem.3c00671] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/10/2023]
Abstract
Bromodomain-containing proteins are readers of acetylated lysine and play important roles in cancer. Bromodomain-containing protein 7 (BRD7) is implicated in multiple malignancies; however, there are no selective chemical probes to study its function in disease. Using crystal structures of BRD7 and BRD9 bromodomains (BDs) bound to BRD9-selective ligands, we identified a binding pocket exclusive to BRD7. We synthesized a series of ligands designed to occupy this binding region and identified two inhibitors with increased selectivity toward BRD7, 1-78 and 2-77, which bind with submicromolar affinity to the BRD7 BD. Our binding mode analyses indicate that these ligands occupy a uniquely accessible binding cleft in BRD7 and maintain key interactions with the asparagine and tyrosine residues critical for acetylated lysine binding. Finally, we validated the utility and selectivity of the compounds in cell-based models of prostate cancer.
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Affiliation(s)
- Sandra C Ordonez-Rubiano
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University. Robert Heine Pharmacy Building 575 Stadium Mall Drive, West Lafayette, Indiana 47907, United States
| | - Chad A Maschinot
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University. Robert Heine Pharmacy Building 575 Stadium Mall Drive, West Lafayette, Indiana 47907, United States
| | - Sijie Wang
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University. Robert Heine Pharmacy Building 575 Stadium Mall Drive, West Lafayette, Indiana 47907, United States
| | - Surbhi Sood
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University. Robert Heine Pharmacy Building 575 Stadium Mall Drive, West Lafayette, Indiana 47907, United States
| | - Luisa F Baracaldo-Lancheros
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University. Robert Heine Pharmacy Building 575 Stadium Mall Drive, West Lafayette, Indiana 47907, United States
| | - Brayden P Strohmier
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University. Robert Heine Pharmacy Building 575 Stadium Mall Drive, West Lafayette, Indiana 47907, United States
| | - Alexander J McQuade
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University. Robert Heine Pharmacy Building 575 Stadium Mall Drive, West Lafayette, Indiana 47907, United States
| | - Brian C Smith
- Department of Biochemistry, Program in Chemical Biology, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, United States
| | - Emily C Dykhuizen
- Department of Medicinal Chemistry and Molecular Pharmacology, College of Pharmacy, Purdue University. Robert Heine Pharmacy Building 575 Stadium Mall Drive, West Lafayette, Indiana 47907, United States
- Purdue Center for Cancer Research, College of Pharmacy, Purdue University, 201 S University St., West Lafayette, Indiana 47907, United States
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5
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Gajjela BK, Zhou MM. Bromodomain inhibitors and therapeutic applications. Curr Opin Chem Biol 2023; 75:102323. [PMID: 37207401 PMCID: PMC10524616 DOI: 10.1016/j.cbpa.2023.102323] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 04/14/2023] [Accepted: 04/18/2023] [Indexed: 05/21/2023]
Abstract
The bromodomain acts to recognize acetylated lysine in histones and transcription proteins and plays a fundamental role in chromatin-based cellular processes including gene transcription and chromatin remodeling. Many bromodomain proteins, particularly the bromodomain and extra terminal domain (BET) protein BRD4 have been implicated in cancers and inflammatory disorders and recognized as attractive drug targets. Although clinical studies of many BET bromodomain inhibitors have made substantial progress toward harnessing the therapeutic potential of targeting the bromodomain proteins, the development of this new class of epigenetic drugs is met with challenges, especially on-target dose-limiting toxicity. In this review, we highlight the current development of new-generation small molecule inhibitors for the BET and non-BET bromodomain proteins and discuss the research strategies used to target different bromodomain proteins for a wide array of human diseases including cancers and inflammatory disorders.
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Affiliation(s)
- Bharath Kumar Gajjela
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY, 10029, United States
| | - Ming-Ming Zhou
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY, 10029, United States.
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6
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Pan Z, Zhao Y, Wang X, Xie X, Liu M, Zhang K, Wang L, Bai D, Foster LJ, Shu R, He G. Targeting bromodomain-containing proteins: research advances of drug discovery. MOLECULAR BIOMEDICINE 2023; 4:13. [PMID: 37142850 PMCID: PMC10159834 DOI: 10.1186/s43556-023-00127-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 04/02/2023] [Indexed: 05/06/2023] Open
Abstract
Bromodomain (BD) is an evolutionarily conserved protein module found in 46 different BD-containing proteins (BCPs). BD acts as a specific reader for acetylated lysine residues (KAc) and serves an essential role in transcriptional regulation, chromatin remodeling, DNA damage repair, and cell proliferation. On the other hand, BCPs have been shown to be involved in the pathogenesis of a variety of diseases, including cancers, inflammation, cardiovascular diseases, and viral infections. Over the past decade, researchers have brought new therapeutic strategies to relevant diseases by inhibiting the activity or downregulating the expression of BCPs to interfere with the transcription of pathogenic genes. An increasing number of potent inhibitors and degraders of BCPs have been developed, some of which are already in clinical trials. In this paper, we provide a comprehensive review of recent advances in the study of drugs that inhibit or down-regulate BCPs, focusing on the development history, molecular structure, biological activity, interaction with BCPs and therapeutic potentials of these drugs. In addition, we discuss current challenges, issues to be addressed and future research directions for the development of BCPs inhibitors. Lessons learned from the successful or unsuccessful development experiences of these inhibitors or degraders will facilitate the further development of efficient, selective and less toxic inhibitors of BCPs and eventually achieve drug application in the clinic.
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Affiliation(s)
- Zhaoping Pan
- Department of Dermatology & Venerology and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
- Laboratory of Dermatology, Clinical Institute of Inflammation and Immunology (CIII), Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Yuxi Zhao
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Disease, Department of Orthodontics and Pediatrics, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, China
| | - Xiaoyun Wang
- Department of Dermatology & Venerology and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
- Laboratory of Dermatology, Clinical Institute of Inflammation and Immunology (CIII), Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Xin Xie
- College of Medical Technology and School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Mingxia Liu
- Department of Dermatology & Venerology and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Kaiyao Zhang
- Department of Dermatology & Venerology and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Lian Wang
- Department of Dermatology & Venerology and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Ding Bai
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Disease, Department of Orthodontics and Pediatrics, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, China
| | - Leonard J Foster
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Rui Shu
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Disease, Department of Orthodontics and Pediatrics, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, China.
| | - Gu He
- Department of Dermatology & Venerology and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China.
- Laboratory of Dermatology, Clinical Institute of Inflammation and Immunology (CIII), Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610041, China.
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7
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Ghelli Luserna di Rorà A, Jandoubi M, Martinelli G, Simonetti G. Targeting Proliferation Signals and the Cell Cycle Machinery in Acute Leukemias: Novel Molecules on the Horizon. Molecules 2023; 28:molecules28031224. [PMID: 36770891 PMCID: PMC9920029 DOI: 10.3390/molecules28031224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 01/04/2023] [Accepted: 01/24/2023] [Indexed: 01/28/2023] Open
Abstract
Uncontrolled proliferative signals and cell cycle dysregulation due to genomic or functional alterations are important drivers of the expansion of undifferentiated blast cells in acute myeloid leukemia (AML) and acute lymphoblastic leukemia (ALL) cells. Therefore, they are largely studied as potential therapeutic targets in the field. We here present the most recent advancements in the evaluation of novel compounds targeting cell cycle proteins or oncogenic mechanisms, including those showing an antiproliferative effect in acute leukemia, independently of the identification of a specific target. Several new kinase inhibitors have been synthesized that showed effectiveness in a nanomolar to micromolar concentration range as inhibitors of FLT3 and its mutant forms, a highly attractive therapeutic target due to its driver role in a significant fraction of AML cases. Moreover, we introduce novel molecules functioning as microtubule-depolymerizing or P53-restoring agents, G-quadruplex-stabilizing molecules and CDK2, CHK1, PI3Kδ, STAT5, BRD4 and BRPF1 inhibitors. We here discuss their mechanisms of action, including the downstream intracellular changes induced by in vitro treatment, hematopoietic toxicity, in vivo bio-availability and efficacy in murine xenograft models. The promising activity profile demonstrated by some of these candidates deserves further development towards clinical investigation.
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Affiliation(s)
- Andrea Ghelli Luserna di Rorà
- Biosciences Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, Via Piero Maroncelli 40, 47014 Meldola, Italy
- Fondazione Pisana per Scienza ONLUS, 56017 San Giuliano Terme, Italy
| | - Mouna Jandoubi
- Biosciences Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, Via Piero Maroncelli 40, 47014 Meldola, Italy
| | - Giovanni Martinelli
- Scientific Directorate, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, Via Piero Maroncelli 40, 47014 Meldola, Italy
- Correspondence:
| | - Giorgia Simonetti
- Biosciences Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, Via Piero Maroncelli 40, 47014 Meldola, Italy
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Kumar A, Emdad L, Fisher PB, Das SK. Targeting epigenetic regulation for cancer therapy using small molecule inhibitors. Adv Cancer Res 2023; 158:73-161. [PMID: 36990539 DOI: 10.1016/bs.acr.2023.01.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
Abstract
Cancer cells display pervasive changes in DNA methylation, disrupted patterns of histone posttranslational modification, chromatin composition or organization and regulatory element activities that alter normal programs of gene expression. It is becoming increasingly clear that disturbances in the epigenome are hallmarks of cancer, which are targetable and represent attractive starting points for drug creation. Remarkable progress has been made in the past decades in discovering and developing epigenetic-based small molecule inhibitors. Recently, epigenetic-targeted agents in hematologic malignancies and solid tumors have been identified and these agents are either in current clinical trials or approved for treatment. However, epigenetic drug applications face many challenges, including low selectivity, poor bioavailability, instability and acquired drug resistance. New multidisciplinary approaches are being designed to overcome these limitations, e.g., applications of machine learning, drug repurposing, high throughput virtual screening technologies, to identify selective compounds with improved stability and better bioavailability. We provide an overview of the key proteins that mediate epigenetic regulation that encompass histone and DNA modifications and discuss effector proteins that affect the organization of chromatin structure and function as well as presently available inhibitors as potential drugs. Current anticancer small-molecule inhibitors targeting epigenetic modified enzymes that have been approved by therapeutic regulatory authorities across the world are highlighted. Many of these are in different stages of clinical evaluation. We also assess emerging strategies for combinatorial approaches of epigenetic drugs with immunotherapy, standard chemotherapy or other classes of agents and advances in the design of novel epigenetic therapies.
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9
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Lal Gupta P, Carlson HA. Cosolvent Simulations with Fragment-Bound Proteins Identify Hot Spots to Direct Lead Growth. J Chem Theory Comput 2022; 18:3829-3844. [PMID: 35533286 DOI: 10.1021/acs.jctc.1c01054] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
In drug design, chemical groups are sequentially added to improve a weak-binding fragment into a tight-binding lead molecule. Often, the direction to make these additions is unclear, and there are numerous chemical modifications to choose. Lead development can be guided by crystal structures of the fragment-bound protein, but this alone is unable to capture structural changes like closing or opening of the binding site and any side-chain movements. Accounting for adaptation of the site requires a dynamic approach. Here, we use molecular dynamics calculations of small organic solvents with protein-fragment pairs to reveal the nearest "hot spots". These close hot spots show the direction to make appropriate additions and suggest types of chemical modifications that could improve binding affinity. Mixed-solvent molecular dynamics (MixMD) is a cosolvent simulation technique that is well established for finding binding "hot spots" in active sites and allosteric sites of proteins. We simulated 20 fragment-bound and apo forms of key pharmaceutical targets to map out hot spots for potential lead space. Furthermore, we analyzed whether the presence of a fragment facilitates the probes' binding in the lead space, a type of binding cooperativity. To the best of our knowledge, this is the first use of cosolvent MD conducted with bound inhibitors in the simulation. Our work provides a general framework to extract molecular features of binding sites to choose chemical groups for growing lead molecules. Of the 20 systems, 17 systems were well mapped by MixMD. For the three not-mapped systems, two had lead growth out into solution away from the protein, and the third had very small modifications which indicated no nearby hot spots. Therefore, our lack of mapping in three systems was appropriate given the experimental data (true-negative cases). The simulations are run for very short time scales, making this method tractable for use in the pharmaceutical industry.
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Affiliation(s)
- Pancham Lal Gupta
- Department of Medicinal Chemistry, College of Pharmacy, 428 Church Street, Ann Arbor, Michigan 48109-1065, United States
| | - Heather A Carlson
- Department of Medicinal Chemistry, College of Pharmacy, 428 Church Street, Ann Arbor, Michigan 48109-1065, United States
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10
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Mazodze CM, Petersen WF. Silver-catalysed double decarboxylative addition-cyclisation-elimination cascade sequence for the synthesis of quinolin-2-ones. Org Biomol Chem 2022; 20:3469-3474. [PMID: 35420621 DOI: 10.1039/d2ob00521b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
An atom-efficient silver-catalysed double carboxylative strategy for the one-step synthesis of quinolin-2-ones via an addition-cyclisation-elimination cascade sequence of oxamic acids to acrylic acids, mediated either thermally or photochemically, is reported. The reaction was applicable to the synthesis of a broad range of quinolin-2-ones and featured a double-disconnection approach that constructed the quinolin-2-one core via the formal and direct addition of a C(sp2)-H/C(sp2)-H olefin moiety to a phenylformamide precursor.
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Affiliation(s)
- C Munashe Mazodze
- Department of Chemistry, University of Cape Town, Rondebosch, Cape Town, 7700, South Africa.
| | - Wade F Petersen
- Department of Chemistry, University of Cape Town, Rondebosch, Cape Town, 7700, South Africa.
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11
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Duan YC, Zhang SJ, Shi XJ, Jin LF, Yu T, Song Y, Guan YY. Research progress of dual inhibitors targeting crosstalk between histone epigenetic modulators for cancer therapy. Eur J Med Chem 2021; 222:113588. [PMID: 34107385 DOI: 10.1016/j.ejmech.2021.113588] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Revised: 05/09/2021] [Accepted: 05/25/2021] [Indexed: 12/13/2022]
Abstract
Abnormal epigenetics is a critical hallmark of human cancers. Anticancer drug discovery directed at histone epigenetic modulators has gained impressive advances with six drugs available for cancer therapy and numerous other candidates undergoing clinical trials. However, limited therapeutic profile, drug resistance, narrow safety margin, and dose-limiting toxicities pose intractable challenges for their clinical utility. Because histone epigenetic modulators undergo intricate crosstalk and act cooperatively to shape an aberrant epigenetic profile, co-targeting histone epigenetic modulators with a different mechanism of action has rapidly emerged as an attractive strategy to overcome the limitations faced by the single-target epigenetic inhibitors. In this review, we summarize in detail the crosstalk of histone epigenetic modulators in regulating gene transcription and the progress of dual epigenetic inhibitors targeting this crosstalk.
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Affiliation(s)
- Ying-Chao Duan
- School of Pharmacy, Xinxiang Medical University, 453003, Xinxiang, Henan Province, PR China.
| | - Shao-Jie Zhang
- School of Pharmacy, Xinxiang Medical University, 453003, Xinxiang, Henan Province, PR China
| | - Xiao-Jing Shi
- Laboratory Animal Center, Academy of Medical Science, Zhengzhou University, 450052, Zhengzhou, Henan Province, PR China
| | - Lin-Feng Jin
- School of Pharmacy, Xinxiang Medical University, 453003, Xinxiang, Henan Province, PR China
| | - Tong Yu
- School of Pharmacy, Xinxiang Medical University, 453003, Xinxiang, Henan Province, PR China
| | - Yu Song
- School of Pharmacy, Xinxiang Medical University, 453003, Xinxiang, Henan Province, PR China
| | - Yuan-Yuan Guan
- School of Pharmacy, Xinxiang Medical University, 453003, Xinxiang, Henan Province, PR China.
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12
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Abstract
It is well established that medicinal chemists should depart from the flat, sp2-dominated nature of traditional drugs and incorporate complexities of bioactive natural products, such as sp3-richness, 3D topology and chirality. There is a gray area, however, in the relevance of newly developed chemical scaffolds that exhibit these complexities but do not correlate to anything observed in nature. This can leave synthetic methodologists searching for structural similarities between their newly developed products and known natural products in search of justification. This article offers a perspective on how these types of complex 'abiotic' scaffolds can be appreciated purely on the basis of their structural novelty, and identifies the unique advantages arising when a complex chemical entity unrecognized by nature is introduced to biological systems.
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13
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Design, synthesis, and biological evaluation of dual targeting inhibitors of histone deacetylase 6/8 and bromodomain BRPF1. Eur J Med Chem 2020; 200:112338. [PMID: 32497960 DOI: 10.1016/j.ejmech.2020.112338] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 04/09/2020] [Accepted: 04/13/2020] [Indexed: 01/19/2023]
Abstract
Histone modifying proteins, specifically histone deacetylases (HDACs) and bromodomains, have emerged as novel promising targets for anticancer therapy. In the current work, based on available crystal structures and docking studies, we designed dual inhibitors of both HDAC6/8 and the bromodomain and PHD finger containing protein 1 (BRPF1). Biochemical and biophysical tests showed that compounds 23a,b and 37 are nanomolar inhibitors of both target proteins. Detailed structure-activity relationships were deduced for the synthesized inhibitors which were supported by extensive docking and molecular dynamics studies. Cellular testing in acute myeloid leukemia (AML) cells showed only a weak effect, most probably because of the poor permeability of the inhibitors. We also aimed to analyse the target engagement and the cellular activity of the novel inhibitors by determining the protein acetylation levels in cells by western blotting (tubulin vs histone acetylation), and by assessing their effects on various cancer cell lines.
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14
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Bhattacharya D, Tomar R, Babu SA. Conversion of 2,3‐Dihydrobenzo[
b
][1,4]dioxine‐2‐carboxamides to 3‐Oxoquinolin‐2(1
H
)‐ones via Ring‐Opening and Formal 6‐
endo
‐trig Cyclization‐Involved Heck Reactions. ASIAN J ORG CHEM 2020. [DOI: 10.1002/ajoc.202000096] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Debabrata Bhattacharya
- Department of Chemical SciencesIndian Institute of Science Education and Research (IISER) Mohali Knowledge City, Sector 81, SAS Nagar, Mohali, Manauli P.O., Punjab, 140306 (India)
| | - Radha Tomar
- Department of Chemical SciencesIndian Institute of Science Education and Research (IISER) Mohali Knowledge City, Sector 81, SAS Nagar, Mohali, Manauli P.O., Punjab, 140306 (India)
| | - Srinivasarao Arulananda Babu
- Department of Chemical SciencesIndian Institute of Science Education and Research (IISER) Mohali Knowledge City, Sector 81, SAS Nagar, Mohali, Manauli P.O., Punjab, 140306 (India)
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15
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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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16
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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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17
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Klein BJ, Cox KL, Jang SM, Côté J, Poirier MG, Kutateladze TG. Molecular Basis for the PZP Domain of BRPF1 Association with Chromatin. Structure 2019; 28:105-110.e3. [PMID: 31711755 DOI: 10.1016/j.str.2019.10.014] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 09/27/2019] [Accepted: 10/22/2019] [Indexed: 11/25/2022]
Abstract
The assembly of human histone acetyltransferase MOZ/MORF complexes relies on the scaffolding bromodomain plant homeodomain (PHD) finger 1 (BRPF1) subunit. The PHD-zinc-knuckle-PHD module of BRPF1 (BRPF1PZP) has been shown to associate with the histone H3 tail and DNA; however, the molecular mechanism underlying recognition of H3 and the relationship between the histone and DNA-binding activities remain unclear. In this study, we report the crystal structure of BRPF1PZP bound to the H3 tail and characterize the role of the bipartite interaction in the engagement of BRPF1PZP with the nucleosome core particle (NCP). We find that although both interactions of BRPF1PZP with the H3 tail and DNA are required for tight binding to NCP and for acetyltransferase function of the BRPF1-MORF-ING5-MEAF6 complex, binding to extranucleosomal DNA dominates. Our findings suggest that functionally active BRPF1PZP might be important in stabilization of the MOZ/MORF complexes at chromatin with accessible DNA.
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Affiliation(s)
- Brianna J Klein
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Khan L Cox
- Department of Physics, Ohio State University, Columbus, OH 43210, USA
| | - Suk Min Jang
- Laval University Cancer Research Center, CHU de Québec-UL Research Center-Oncology Division, Quebec City, QC G1R 3S3, Canada
| | - Jacques Côté
- Laval University Cancer Research Center, CHU de Québec-UL Research Center-Oncology Division, Quebec City, QC G1R 3S3, Canada
| | - Michael G Poirier
- Department of Physics, Ohio State University, Columbus, OH 43210, USA.
| | - Tatiana G Kutateladze
- Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA.
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18
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Abstract
Less than a decade ago, it was shown that bromodomains, acetyl lysine 'reader' modules found in proteins with varied functions, were highly tractable small-molecule targets. This is an unusual property for protein-protein or protein-peptide interaction domains, and it prompted a wave of chemical probe discovery to understand the biological potential of new agents that targeted bromodomains. The original examples, inhibitors of the bromodomain and extra-terminal (BET) class of bromodomains, showed enticing anti-inflammatory and anticancer activities, and several compounds have since advanced to human clinical trials. Here, we review the current state of BET inhibitor biology in relation to clinical development, and we discuss the next wave of bromodomain inhibitors with clinical potential in oncology and non-oncology indications. The lessons learned from BET inhibitor programmes should affect efforts to develop drugs that target non-BET bromodomains and other epigenetic readers.
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19
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Lenci E, Trabocchi A. Smart Design of Small‐Molecule Libraries: When Organic Synthesis Meets Cheminformatics. Chembiochem 2019; 20:1115-1123. [DOI: 10.1002/cbic.201800751] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Indexed: 12/25/2022]
Affiliation(s)
- Elena Lenci
- Department of Chemistry “Ugo Schiff”University of Florence Via della Lastruccia 13 50019 Sesto Fiorentino Florence Italy
| | - Andrea Trabocchi
- Department of Chemistry “Ugo Schiff”University of Florence Via della Lastruccia 13 50019 Sesto Fiorentino Florence Italy
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20
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Clegg MA, Tomkinson NCO, Prinjha RK, Humphreys PG. Advancements in the Development of non-BET Bromodomain Chemical Probes. ChemMedChem 2019; 14:362-385. [PMID: 30624862 DOI: 10.1002/cmdc.201800738] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Indexed: 01/07/2023]
Abstract
The bromodomain and extra terminal (BET) family of bromodomain-containing proteins (BCPs) have been the subject of extensive research over the past decade, resulting in a plethora of high-quality chemical probes for their tandem bromodomains. In turn, these chemical probes have helped reveal the profound biological role of the BET bromodomains and their role in disease, ultimately leading to a number of molecules in active clinical development. However, the BET subfamily represents just 8/61 of the known human bromodomains, and attention has now expanded to the biological role of the remaining 53 non-BET bromodomains. Rapid growth of this research area has been accompanied by a greater understanding of the requirements for an effective bromodomain chemical probe and has led to a number of new non-BET bromodomain chemical probes being developed. Advances since December 2015 are discussed, highlighting the strengths/caveats of each molecule, and the value they add toward validating the non-BET bromodomains as tractable therapeutic targets.
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Affiliation(s)
- Michael A Clegg
- Epigenetics Discovery Performance Unit, GlaxoSmithKline R&D, Stevenage, Hertfordshire, SG1 2NY, UK.,WestCHEM, Department of Pure and Applied Chemistry, University of Strathclyde, 295 Cathedral Street, Thomas Graham Building, Glasgow, G1 1XL, UK
| | - Nicholas C O Tomkinson
- WestCHEM, Department of Pure and Applied Chemistry, University of Strathclyde, 295 Cathedral Street, Thomas Graham Building, Glasgow, G1 1XL, UK
| | - Rab K Prinjha
- Epigenetics Discovery Performance Unit, GlaxoSmithKline R&D, Stevenage, Hertfordshire, SG1 2NY, UK
| | - Philip G Humphreys
- Epigenetics Discovery Performance Unit, GlaxoSmithKline R&D, Stevenage, Hertfordshire, SG1 2NY, UK
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21
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Mio C, Bulotta S, Russo D, Damante G. Reading Cancer: Chromatin Readers as Druggable Targets for Cancer Treatment. Cancers (Basel) 2019; 11:cancers11010061. [PMID: 30634442 PMCID: PMC6356452 DOI: 10.3390/cancers11010061] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 12/30/2018] [Accepted: 01/03/2019] [Indexed: 02/07/2023] Open
Abstract
The epigenetic machinery deputed to control histone post-translational modifications is frequently dysregulated in cancer cells. With epigenetics being naturally reversible, it represents a good target for therapies directed to restore normal gene expression. Since the discovery of Bromodomain and Extra Terminal (BET) inhibitors, a great effort has been spent investigating the effects of chromatin readers’ inhibition, specifically the class of proteins assigned to bind acetylated and methylated residues. So far, focused studies have been produced on epigenetic regulation, dissecting a specific class of epigenetic-related proteins or investigating epigenetic therapy in a specific tumor type. In this review, recent steps toward drug discovery on the different classes of chromatin readers have been outlined, highlighting the pros and cons of current therapeutic approaches.
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Affiliation(s)
- Catia Mio
- Department of Medical Area, University of Udine, 33100 Udine, Italy.
| | - Stefania Bulotta
- Department of Health Sciences, "Magna Graecia" University of Catanzaro, 88100 Catanzaro, Italy.
| | - Diego Russo
- Department of Health Sciences, "Magna Graecia" University of Catanzaro, 88100 Catanzaro, Italy.
| | - Giuseppe Damante
- Department of Medical Area, University of Udine, 33100 Udine, Italy.
- Medical Genetics Institute, University Hospital of Udine, 33100 Udine, Italy.
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22
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Mortenson PN, Erlanson DA, de Esch IJP, Jahnke W, Johnson CN. Fragment-to-Lead Medicinal Chemistry Publications in 2017. J Med Chem 2018; 62:3857-3872. [PMID: 30462504 DOI: 10.1021/acs.jmedchem.8b01472] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
This Miniperspective is the third in a series reviewing fragment-to-lead publications from a given year. Following our reviews for 2015 and 2016, this Miniperspective provides tabulated summaries of relevant articles published in 2017 along with some general observations. In addition, we discuss insights obtained from analysis of the combined data set of 85 examples from all three years of publications.
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Affiliation(s)
- Paul N Mortenson
- Astex Pharmaceuticals , 436 Cambridge Science Park, Milton Road , Cambridge CB4 0QA , United Kingdom
| | - Daniel A Erlanson
- Carmot Therapeutics Inc. , 740 Heinz Avenue , Berkeley , California 94710 , United States
| | - Iwan J P de Esch
- Division of Medicinal Chemistry, Amsterdam Institute for Molecules, Medicines and Systems (AIMMS) , Vrije Universiteit Amsterdam , De Boelelaan 1108 , 1081 HZ , Amsterdam , The Netherlands
| | - Wolfgang Jahnke
- Chemical Biology and Therapeutics , Novartis Institutes for Biomedical Research , 4002 Basel , Switzerland
| | - Christopher N Johnson
- Astex Pharmaceuticals , 436 Cambridge Science Park, Milton Road , Cambridge CB4 0QA , United Kingdom
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23
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Vaijayanthi T, Pandian GN, Sugiyama H. Chemical Control System of Epigenetics. CHEM REC 2018; 18:1833-1853. [DOI: 10.1002/tcr.201800067] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Accepted: 10/07/2018] [Indexed: 12/28/2022]
Affiliation(s)
- Thangavel Vaijayanthi
- Department of ChemistryGraduate School of ScienceKyoto University Kitashirakawa-Oiwakecho, Sakyo-ku Kyoto 606-8502, Japan
| | - Ganesh N. Pandian
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS)Kyoto University Yoshida-Ushinomaecho, Sakyo-ku Kyoto 606-8501 Japan
| | - Hiroshi Sugiyama
- Department of ChemistryGraduate School of ScienceKyoto University Kitashirakawa-Oiwakecho, Sakyo-ku Kyoto 606-8502, Japan
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS)Kyoto University Yoshida-Ushinomaecho, Sakyo-ku Kyoto 606-8501 Japan
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24
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Charoenpol A, Meesin J, Khaikate O, Reutrakul V, Pohmakotr M, Leowanawat P, Soorukram D, Kuhakarn C. Synthesis of 3-substituted quinolin-2(1H)-ones via the cyclization of o-alkynylisocyanobenzenes. Org Biomol Chem 2018; 16:7050-7054. [PMID: 30239546 DOI: 10.1039/c8ob01882k] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
A facile synthesis of various functionalized 3-substituted quinolin-2(1H)-ones through Ag(i) nitrate-catalyzed cyclization of o-alkynylisocyanobenzenes is described. The reaction allows rapid and convenient access to 3-substituted quinolin-2(1H)-one scaffolds in moderate to good yields.
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Affiliation(s)
- Ailada Charoenpol
- Department of Chemistry and Center of Excellence for Innovation in Chemistry (PERCH-CIC), Faculty of Science, Mahidol University, Rama 6 Road, Bangkok 10400, Thailand.
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25
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Schiedel M, Conway SJ. Small molecules as tools to study the chemical epigenetics of lysine acetylation. Curr Opin Chem Biol 2018; 45:166-178. [DOI: 10.1016/j.cbpa.2018.06.015] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Revised: 06/08/2018] [Accepted: 06/11/2018] [Indexed: 02/06/2023]
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26
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Zhu J, Zhou C, Caflisch A. Structure-based discovery of selective BRPF1 bromodomain inhibitors. Eur J Med Chem 2018; 155:337-352. [PMID: 29902720 DOI: 10.1016/j.ejmech.2018.05.037] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Revised: 04/05/2018] [Accepted: 05/23/2018] [Indexed: 11/19/2022]
Abstract
Bromodomain and plant homeodomain (PHD) finger containing protein 1 (BRPF1) is a member of subfamily IV of the human bromodomains. Experimental evidence suggests that BRPF1 is involved in leukemia. In a previous high-throughput docking campaign we identified several chemotypes targeting the BRPF1 bromodomain. Here, pharmacophore searches using the binding modes of two of these chemotypes resulted in two new series of ligands of the BRPF1 bromodomain. The 2,3-dioxo-quinoxaline 21 exhibits a 2-μM affinity for the BRPF1 bromodomain in two different competition binding assays, and more than 100-fold selectivity for BRPF1 against other members of subfamily IV and representatives of other subfamilies. Cellular activity is confirmed by a viability assay in a leukemia cell line. Isothermal titration calorimetry measurements reveal enthalpy-driven binding for compounds 21, 26 (KD = 3 μM), and the 2,4-dimethyl-oxazole derivative 42 (KD = 10 μM). Multiple molecular dynamics simulations and a dozen co-crystal structures at high resolution provide useful information for further optimization of affinity for the BRPF1 bromodomain.
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Affiliation(s)
- Jian Zhu
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland
| | - Chunxian Zhou
- Department of Pathology, Shanghai University of Traditional Chinese Medicine, Cailun Road 1200, Pudong District, Shanghai, China
| | - Amedeo Caflisch
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland.
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27
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Research progress of selective small molecule bromodomain-containing protein 9 inhibitors. Future Med Chem 2018; 10:895-906. [PMID: 29620420 DOI: 10.4155/fmc-2017-0243] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The bromodomain proteins, known as the key targets in epigenetics, are 'readers' of acetylated lysine of histones. As a member of bromodomain proteins, bromodomain-containing protein 9 (BRD9) is a subunit of mammalian SWI/SNF chromatin remodeling complexes. However, the biological functions and the potential application in therapeutics of BRD9 remain ambiguous due to a lack of selective small molecule inhibitors of BRD9. Recently, series of chemical ligands against BRD9 were developed by different research institutes. Here, we reviewed the development and characterization of reported BRD9 inhibitors, which will be the foundation of further chemical design and biological evaluation.
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28
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Foley DJ, Craven PGE, Collins PM, Doveston RG, Aimon A, Talon R, Churcher I, von Delft F, Marsden SP, Nelson A. Synthesis and Demonstration of the Biological Relevance of sp 3 -rich Scaffolds Distantly Related to Natural Product Frameworks. Chemistry 2017; 23:15227-15232. [PMID: 28983993 PMCID: PMC5703167 DOI: 10.1002/chem.201704169] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Indexed: 12/18/2022]
Abstract
The productive exploration of chemical space is an enduring challenge in chemical biology and medicinal chemistry. Natural products are biologically relevant, and their frameworks have facilitated chemical tool and drug discovery. A "top-down" synthetic approach is described that enabled a range of complex bridged intermediates to be converted with high step efficiency into 26 diverse sp3 -rich scaffolds. The scaffolds have local natural product-like features, but are only distantly related to specific natural product frameworks. To assess biological relevance, a set of 52 fragments was prepared, and screened by high-throughput crystallography against three targets from two protein families (ATAD2, BRD1 and JMJD2D). In each case, 3D fragment hits were identified that would serve as distinctive starting points for ligand discovery. This demonstrates that frameworks that are distantly related to natural products can facilitate discovery of new biologically relevant regions within chemical space.
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Affiliation(s)
- Daniel J. Foley
- Astbury Centre for Structural Molecular BiologyUniversity of LeedsLeedsLS2 9JTUK
- School of ChemistryUniversity of LeedsLeedsLS2 9JTUK
| | - Philip G. E. Craven
- Astbury Centre for Structural Molecular BiologyUniversity of LeedsLeedsLS2 9JTUK
- School of ChemistryUniversity of LeedsLeedsLS2 9JTUK
| | - Patrick M. Collins
- Diamond Light Source LtdHarwell Science and Innovation CampusDidcotOX11 0QXUK
| | - Richard G. Doveston
- Astbury Centre for Structural Molecular BiologyUniversity of LeedsLeedsLS2 9JTUK
- School of ChemistryUniversity of LeedsLeedsLS2 9JTUK
| | - Anthony Aimon
- Astbury Centre for Structural Molecular BiologyUniversity of LeedsLeedsLS2 9JTUK
- School of ChemistryUniversity of LeedsLeedsLS2 9JTUK
| | - Romain Talon
- Structural Genomics Consortium, Nuffield Department of MedicineUniversity of Oxford, Roosevelt DriveOxfordOX3 7DQUK
| | - Ian Churcher
- GlaxoSmithKline Medicines Research CentreStevenageSG1 2NYUK,BenevolentBio, ChurchwayLondonNW1 1LWUK
| | - Frank von Delft
- Diamond Light Source LtdHarwell Science and Innovation CampusDidcotOX11 0QXUK
- Structural Genomics Consortium, Nuffield Department of MedicineUniversity of Oxford, Roosevelt DriveOxfordOX3 7DQUK
| | | | - Adam Nelson
- Astbury Centre for Structural Molecular BiologyUniversity of LeedsLeedsLS2 9JTUK
- School of ChemistryUniversity of LeedsLeedsLS2 9JTUK
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29
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Meier JC, Tallant C, Fedorov O, Witwicka H, Hwang SY, van Stiphout RG, Lambert JP, Rogers C, Yapp C, Gerstenberger BS, Fedele V, Savitsky P, Heidenreich D, Daniels DL, Owen DR, Fish PV, Igoe NM, Bayle ED, Haendler B, Oppermann UC, Buffa F, Brennan PE, Müller S, Gingras AC, Odgren PR, Birnbaum MJ, Knapp S. Selective Targeting of Bromodomains of the Bromodomain-PHD Fingers Family Impairs Osteoclast Differentiation. ACS Chem Biol 2017; 12:2619-2630. [PMID: 28849908 PMCID: PMC5662925 DOI: 10.1021/acschembio.7b00481] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2017] [Accepted: 08/29/2017] [Indexed: 01/16/2023]
Abstract
Histone acetyltransferases of the MYST family are recruited to chromatin by BRPF scaffolding proteins. We explored functional consequences and the therapeutic potential of inhibitors targeting acetyl-lysine dependent protein interaction domains (bromodomains) present in BRPF1-3 in bone maintenance. We report three potent and selective inhibitors: one (PFI-4) with high selectivity for the BRPF1B isoform and two pan-BRPF bromodomain inhibitors (OF-1, NI-57). The developed inhibitors displaced BRPF bromodomains from chromatin and did not inhibit cell growth and proliferation. Intriguingly, the inhibitors impaired RANKL-induced differentiation of primary murine bone marrow cells and human primary monocytes into bone resorbing osteoclasts by specifically repressing transcriptional programs required for osteoclastogenesis. The data suggest a key role of BRPF in regulating gene expression during osteoclastogenesis, and the excellent druggability of these bromodomains may lead to new treatment strategies for patients suffering from bone loss or osteolytic malignant bone lesions.
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Affiliation(s)
- Julia C. Meier
- Target Discovery
Institute and Structural Genomics Consortium, Oxford University, Oxford, United Kingom
| | - Cynthia Tallant
- Target Discovery
Institute and Structural Genomics Consortium, Oxford University, Oxford, United Kingom
| | - Oleg Fedorov
- Target Discovery
Institute and Structural Genomics Consortium, Oxford University, Oxford, United Kingom
| | - Hanna Witwicka
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, Worcester, Massachusetts, United States
| | - Sung-Yong Hwang
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, Worcester, Massachusetts, United States
| | - Ruud G. van Stiphout
- Department of Oncology, Oxford University, Old Road Campus Research Building, Oxford OX3 7DQ, United Kingdom
| | - Jean-Philippe Lambert
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, Ontario M5G 1X5, Canada
| | - Catherine Rogers
- Target Discovery
Institute and Structural Genomics Consortium, Oxford University, Oxford, United Kingom
| | - Clarence Yapp
- Target Discovery
Institute and Structural Genomics Consortium, Oxford University, Oxford, United Kingom
| | - Brian S. Gerstenberger
- Pfizer Worldwide Medicinal
Chemistry, 610 Main Street, Cambridge, Massachusetts 02139, United States
| | - Vita Fedele
- Target Discovery
Institute and Structural Genomics Consortium, Oxford University, Oxford, United Kingom
| | - Pavel Savitsky
- Target Discovery
Institute and Structural Genomics Consortium, Oxford University, Oxford, United Kingom
| | - David Heidenreich
- Goethe-University Frankfurt, Institute of Pharmaceutical Chemistry, Riedberg Campus, 60438 Frankfurt am Main, Germany
| | | | - Dafydd R. Owen
- Pfizer Worldwide Medicinal
Chemistry, 610 Main Street, Cambridge, Massachusetts 02139, United States
| | - Paul V. Fish
- Department
of Pharmaceutical & Biological Chemistry, UCL School of Pharmacy, University College London, 29-39 Brunswick Square, London, WC1N 1AX, United
Kingdom
| | - Niall M. Igoe
- Department
of Pharmaceutical & Biological Chemistry, UCL School of Pharmacy, University College London, 29-39 Brunswick Square, London, WC1N 1AX, United
Kingdom
| | - Elliott D. Bayle
- Department
of Pharmaceutical & Biological Chemistry, UCL School of Pharmacy, University College London, 29-39 Brunswick Square, London, WC1N 1AX, United
Kingdom
| | - Bernard Haendler
- Drug Discovery, Bayer Pharma
AG, Müllerstrasse
178, D-13353 Berlin, Germany
| | | | - Francesca Buffa
- Department of Oncology, Oxford University, Old Road Campus Research Building, Oxford OX3 7DQ, United Kingdom
| | - Paul E. Brennan
- Target Discovery
Institute and Structural Genomics Consortium, Oxford University, Oxford, United Kingom
| | - Susanne Müller
- Target Discovery
Institute and Structural Genomics Consortium, Oxford University, Oxford, United Kingom
- Buchmann Institute for Life Sciences (BMLS), Riedberg Campus, 60438 Frankfurt am Main, Germany
| | - Anne Claude Gingras
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, Ontario M5G 1X5, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Paul R. Odgren
- Department of Cell and Developmental Biology, University of Massachusetts Medical School, Worcester, Massachusetts, United States
| | - Mark J. Birnbaum
- Department of Biology, Merrimack College, North Andover, Massachusetts, United States
| | - Stefan Knapp
- Target Discovery
Institute and Structural Genomics Consortium, Oxford University, Oxford, United Kingom
- Buchmann Institute for Life Sciences (BMLS), Riedberg Campus, 60438 Frankfurt am Main, Germany
- Goethe-University Frankfurt, Institute of Pharmaceutical Chemistry, Riedberg Campus, 60438 Frankfurt am Main, Germany
- German Cancer Network (DKTK), Frankfurt site, 60438 Frankfurt am Main, Germany
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30
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Igoe N, Bayle ED, Tallant C, Fedorov O, Meier JC, Savitsky P, Rogers C, Morias Y, Scholze S, Boyd H, Cunoosamy D, Andrews DM, Cheasty A, Brennan PE, Müller S, Knapp S, Fish PV. Design of a Chemical Probe for the Bromodomain and Plant Homeodomain Finger-Containing (BRPF) Family of Proteins. J Med Chem 2017; 60:6998-7011. [PMID: 28714688 DOI: 10.1021/acs.jmedchem.7b00611] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The bromodomain and plant homeodomain finger-containing (BRPF) family are scaffolding proteins important for the recruitment of histone acetyltransferases of the MYST family to chromatin. Here, we describe NI-57 (16) as new pan-BRPF chemical probe of the bromodomain (BRD) of the BRPFs. Inhibitor 16 preferentially bound the BRD of BRPF1 and BRPF2 over BRPF3, whereas binding to BRD9 was weaker. Compound 16 has excellent selectivity over nonclass IV BRD proteins. Target engagement of BRPF1B and BRPF2 with 16 was demonstrated in nanoBRET and FRAP assays. The binding of 16 to BRPF1B was rationalized through an X-ray cocrystal structure determination, which showed a flipped binding orientation when compared to previous structures. We report studies that show 16 has functional activity in cellular assays by modulation of the phenotype at low micromolar concentrations in both cancer and inflammatory models. Pharmacokinetic data for 16 was generated in mouse with single dose administration showing favorable oral bioavailability.
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Affiliation(s)
- Niall Igoe
- UCL School of Pharmacy, University College London , 29/39 Brunswick Square, London WC1N 1AX, U.K
| | - Elliott D Bayle
- UCL School of Pharmacy, University College London , 29/39 Brunswick Square, London WC1N 1AX, U.K
| | - Cynthia Tallant
- Nuffield Department of Clinical Medicine, Structural Genomics Consortium, University of Oxford , Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, U.K
| | - Oleg Fedorov
- Nuffield Department of Clinical Medicine, Structural Genomics Consortium, University of Oxford , Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, U.K
| | - Julia C Meier
- Nuffield Department of Clinical Medicine, Structural Genomics Consortium, University of Oxford , Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, U.K
| | - Pavel Savitsky
- Nuffield Department of Clinical Medicine, Structural Genomics Consortium, University of Oxford , Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, U.K
| | - Catherine Rogers
- Nuffield Department of Clinical Medicine, Structural Genomics Consortium, University of Oxford , Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, U.K
| | - Yannick Morias
- AstraZeneca , Innovative Medicines & Early Development, Pepparedsleden 1, 431 83 Mölndal, Sweden
| | - Sarah Scholze
- AstraZeneca , Innovative Medicines & Early Development, Pepparedsleden 1, 431 83 Mölndal, Sweden
| | - Helen Boyd
- AstraZeneca , Innovative Medicines & Early Development, Pepparedsleden 1, 431 83 Mölndal, Sweden
| | - Danen Cunoosamy
- AstraZeneca , Innovative Medicines & Early Development, Pepparedsleden 1, 431 83 Mölndal, Sweden
| | - David M Andrews
- AstraZeneca Discovery Sciences , Darwin Building, Cambridge Science Park, Cambridge CB4 0FZ, U.K
| | - Anne Cheasty
- CRT Discovery Laboratories , Jonas Webb Building, Babraham Research Campus, Cambridge CB22 3AT, U.K
| | - Paul E Brennan
- Nuffield Department of Clinical Medicine, Structural Genomics Consortium, University of Oxford , Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, U.K
| | - Susanne Müller
- Nuffield Department of Clinical Medicine, Structural Genomics Consortium, University of Oxford , Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, U.K.,Buchmann Institute for Molecular Life Sciences , Max-von-Laue-Strasse 15, D-60438 Frankfurt am Main, Germany
| | - Stefan Knapp
- Nuffield Department of Clinical Medicine, Structural Genomics Consortium, University of Oxford , Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, U.K.,Buchmann Institute for Molecular Life Sciences , Max-von-Laue-Strasse 15, D-60438 Frankfurt am Main, Germany.,Institute for Pharmaceutical Chemistry, Johann Wolfgang Goethe-University , Max-von-Laue-Strasse 9, D-60438 Frankfurt am Main, Germany
| | - Paul V Fish
- UCL School of Pharmacy, University College London , 29/39 Brunswick Square, London WC1N 1AX, U.K
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Petersen WF, Taylor RJK, Donald JR. Photoredox-catalyzed procedure for carbamoyl radical generation: 3,4-dihydroquinolin-2-one and quinolin-2-one synthesis. Org Biomol Chem 2017; 15:5831-5845. [PMID: 28664204 DOI: 10.1039/c7ob01274h] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
A reductive approach for carbamoyl radical generation from N-hydroxyphthalimido oxamides under photoredox catalysis is outlined. This strategy was applied to the synthesis of 3,4-dihydroquinolin-2-ones via the intermolecular addition/cyclization of carbamoyl radicals with electron deficient olefins in a mild, redox-neutral manner. Under a general set of reaction conditions, diversely substituted 3,4-dihydroquinolin-2-ones, including spirocyclic systems can be prepared. By using chlorine-substituted olefins, aromatic quinolin-2-ones can also be accessed.
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Affiliation(s)
- Wade F Petersen
- Department of Chemistry, University of York, Heslington, York, YO10 5DD, UK.
| | - Richard J K Taylor
- Department of Chemistry, University of York, Heslington, York, YO10 5DD, UK.
| | - James R Donald
- Department of Chemistry, University of York, Heslington, York, YO10 5DD, UK.
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32
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Bouché L, Christ CD, Siegel S, Fernández-Montalván AE, Holton SJ, Fedorov O, Ter Laak A, Sugawara T, Stöckigt D, Tallant C, Bennett J, Monteiro O, Díaz-Sáez L, Siejka P, Meier J, Pütter V, Weiske J, Müller S, Huber KVM, Hartung IV, Haendler B. Benzoisoquinolinediones as Potent and Selective Inhibitors of BRPF2 and TAF1/TAF1L Bromodomains. J Med Chem 2017; 60:4002-4022. [PMID: 28402630 PMCID: PMC5443610 DOI: 10.1021/acs.jmedchem.7b00306] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
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Bromodomains
(BD) are readers of lysine acetylation marks present
in numerous proteins associated with chromatin. Here we describe a
dual inhibitor of the bromodomain and PHD finger (BRPF) family member
BRPF2 and the TATA box binding protein-associated factors TAF1 and
TAF1L. These proteins are found in large chromatin complexes and play
important roles in transcription regulation. The substituted benzoisoquinolinedione
series was identified by high-throughput screening, and subsequent
structure–activity relationship optimization allowed generation
of low nanomolar BRPF2 BD inhibitors with strong selectivity against
BRPF1 and BRPF3 BDs. In addition, a strong inhibition of TAF1/TAF1L
BD2 was measured for most derivatives. The best compound of the series
was BAY-299, which is a very potent, dual inhibitor with an IC50 of 67 nM for BRPF2 BD, 8 nM for TAF1 BD2, and 106 nM for
TAF1L BD2. Importantly, no activity was measured for BRD4 BDs. Furthermore,
cellular activity was evidenced using a BRPF2– or TAF1–histone
H3.3 or H4 interaction assay.
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Affiliation(s)
- Léa Bouché
- Drug Discovery, Bayer AG , Müllerstrasse 178, 13353 Berlin, Germany
| | - Clara D Christ
- Drug Discovery, Bayer AG , Müllerstrasse 178, 13353 Berlin, Germany
| | - Stephan Siegel
- Drug Discovery, Bayer AG , Müllerstrasse 178, 13353 Berlin, Germany
| | | | - Simon J Holton
- Drug Discovery, Bayer AG , Müllerstrasse 178, 13353 Berlin, Germany
| | - Oleg Fedorov
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford , Roosevelt Drive, Oxford OX3 7DQ, U.K.,Target Discovery Institute, Nuffield Department of Clinical Medicine, University of Oxford , Roosevelt Drive, Oxford OX3 7FZ, U.K
| | | | - Tatsuo Sugawara
- Drug Discovery, Bayer AG , Müllerstrasse 178, 13353 Berlin, Germany
| | - Detlef Stöckigt
- Drug Discovery, Bayer AG , Müllerstrasse 178, 13353 Berlin, Germany
| | - Cynthia Tallant
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford , Roosevelt Drive, Oxford OX3 7DQ, U.K.,Target Discovery Institute, Nuffield Department of Clinical Medicine, University of Oxford , Roosevelt Drive, Oxford OX3 7FZ, U.K
| | - James Bennett
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford , Roosevelt Drive, Oxford OX3 7DQ, U.K.,Target Discovery Institute, Nuffield Department of Clinical Medicine, University of Oxford , Roosevelt Drive, Oxford OX3 7FZ, U.K
| | - Octovia Monteiro
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford , Roosevelt Drive, Oxford OX3 7DQ, U.K.,Target Discovery Institute, Nuffield Department of Clinical Medicine, University of Oxford , Roosevelt Drive, Oxford OX3 7FZ, U.K
| | - Laura Díaz-Sáez
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford , Roosevelt Drive, Oxford OX3 7DQ, U.K.,Target Discovery Institute, Nuffield Department of Clinical Medicine, University of Oxford , Roosevelt Drive, Oxford OX3 7FZ, U.K
| | - Paulina Siejka
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford , Roosevelt Drive, Oxford OX3 7DQ, U.K.,Target Discovery Institute, Nuffield Department of Clinical Medicine, University of Oxford , Roosevelt Drive, Oxford OX3 7FZ, U.K
| | - Julia Meier
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford , Roosevelt Drive, Oxford OX3 7DQ, U.K
| | - Vera Pütter
- Drug Discovery, Bayer AG , Müllerstrasse 178, 13353 Berlin, Germany
| | - Jörg Weiske
- Drug Discovery, Bayer AG , Müllerstrasse 178, 13353 Berlin, Germany
| | - Susanne Müller
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford , Roosevelt Drive, Oxford OX3 7DQ, U.K.,Target Discovery Institute, Nuffield Department of Clinical Medicine, University of Oxford , Roosevelt Drive, Oxford OX3 7FZ, U.K
| | - Kilian V M Huber
- Structural Genomics Consortium, Nuffield Department of Clinical Medicine, University of Oxford , Roosevelt Drive, Oxford OX3 7DQ, U.K.,Target Discovery Institute, Nuffield Department of Clinical Medicine, University of Oxford , Roosevelt Drive, Oxford OX3 7FZ, U.K
| | - Ingo V Hartung
- Drug Discovery, Bayer AG , Müllerstrasse 178, 13353 Berlin, Germany
| | - Bernard Haendler
- Drug Discovery, Bayer AG , Müllerstrasse 178, 13353 Berlin, Germany
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33
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