1
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Hansen T, Danková D, Bæk M, Grlaš L, Olsen CA. Sulfur(VI) Fluoride Exchange Chemistry in Solid-Phase Synthesis of Compound Arrays: Discovery of Histone Deacetylase Inhibitors. JACS AU 2024; 4:1854-1862. [PMID: 38818074 PMCID: PMC11134391 DOI: 10.1021/jacsau.4c00042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 03/18/2024] [Accepted: 03/19/2024] [Indexed: 06/01/2024]
Abstract
Multistep synthesis performed on solid support is a powerful means to generate small-molecule libraries for the discovery of chemical probes to dissect biological mechanisms as well as for drug discovery. Therefore, expansion of the collection of robust chemical transformations amenable to solid-phase synthesis is desirable for achieving chemically diverse libraries for biological testing. Here, we show that sulfur(VI) fluoride exchange (SuFEx) chemistry, exemplified by pairing phenols with aryl fluorosulfates, can be used for the solid-phase synthesis of biologically active compounds. As a case study, we designed and synthesized a library of 84 hydroxamic acid-containing small molecules, providing a rich source of inhibitors with diverse selectivity profiles across the human histone deacetylase enzyme family. Among other discoveries, we identified a scaffold that furnished inhibitors of HDAC11 with exquisite selectivity in vitro and a selective inhibitor of HDAC6 that was shown to affect the acetylation of α-tubulin over histone sites H3K18, H3K27, as well as SMC3 in cultured cells. Our results encourage the further use of SuFEx chemistry for the synthesis of diverse small-molecule libraries and provide insight for future design of selective HDAC inhibitors.
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Affiliation(s)
| | | | | | - Linda Grlaš
- Center for Biopharmaceuticals
and Department of Drug Design and Pharmacology, Faculty of Health
and Medical Sciences, University of Copenhagen, Jagtvej 160, DK-2100 Copenhagen, Denmark
| | - Christian A. Olsen
- Center for Biopharmaceuticals
and Department of Drug Design and Pharmacology, Faculty of Health
and Medical Sciences, University of Copenhagen, Jagtvej 160, DK-2100 Copenhagen, Denmark
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2
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Li C, Jin K. Chemical Strategies towards the Development of Effective Anticancer Peptides. Curr Med Chem 2024; 31:1839-1873. [PMID: 37170992 DOI: 10.2174/0929867330666230426111157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 01/28/2023] [Accepted: 02/24/2023] [Indexed: 05/13/2023]
Abstract
Cancer is increasingly recognized as one of the primary causes of death and has become a multifaceted global health issue. Modern medical science has made significant advancements in the diagnosis and therapy of cancer over the past decade. The detrimental side effects, lack of efficacy, and multidrug resistance of conventional cancer therapies have created an urgent need for novel anticancer therapeutics or treatments with low cytotoxicity and drug resistance. The pharmaceutical groups have recognized the crucial role that peptide therapeutic agents can play in addressing unsatisfied healthcare demands and how these become great supplements or even preferable alternatives to biological therapies and small molecules. Anticancer peptides, as a vibrant therapeutic strategy against various cancer cells, have demonstrated incredible anticancer potential due to high specificity and selectivity, low toxicity, and the ability to target the surface of traditional "undruggable" proteins. This review will provide the research progression of anticancer peptides, mainly focusing on the discovery and modifications along with the optimization and application of these peptides in clinical practice.
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Affiliation(s)
- Cuicui Li
- Key Laboratory of Chemical Biology (Ministry of Education), Department of Medicinal Chemistry, School of Pharmacy, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, China
| | - Kang Jin
- Key Laboratory of Chemical Biology (Ministry of Education), Department of Medicinal Chemistry, School of Pharmacy, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, China
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3
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Mukherjee A, Zamani F, Suzuki T. Evolution of Slow-Binding Inhibitors Targeting Histone Deacetylase Isoforms. J Med Chem 2023; 66:11672-11700. [PMID: 37651268 DOI: 10.1021/acs.jmedchem.3c01160] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
Abstract
Because the overexpression of histone deacetylase enzymes (HDACs) has been linked to numerous diseases, including various cancers and neurodegenerative disorders, HDAC inhibitors have emerged as promising therapeutic agents. However, most HDAC inhibitors lack both subclass and isoform selectivity, which leads to potential toxicity. Unlike classical hydroxamate HDAC inhibitors, slow-binding HDAC inhibitors form tight and prolonged bonds with HDAC enzymes. This distinct mechanism of action improves both selectivity and toxicity profiles, which makes slow-binding HDAC inhibitors a promising class of therapeutic agents for various diseases. Therefore, the development of slow-binding HDAC inhibitors that can effectively target a wide range of HDAC isoforms is crucial. This Perspective provides valuable insights into the potential and progress of slow-binding HDAC inhibitors as promising drug candidates for the treatment of various diseases.
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Affiliation(s)
| | - Farzad Zamani
- SANKEN, Osaka University, Mihogaoka, Ibaraki, Osaka 567-0047, Japan
| | - Takayoshi Suzuki
- SANKEN, Osaka University, Mihogaoka, Ibaraki, Osaka 567-0047, Japan
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4
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Amin SA, Khatun S, Gayen S, Das S, Jha T. Are inhibitors of histone deacetylase 8 (HDAC8) effective in hematological cancers especially acute myeloid leukemia (AML) and acute lymphoblastic leukemia (ALL)? Eur J Med Chem 2023; 258:115594. [PMID: 37429084 DOI: 10.1016/j.ejmech.2023.115594] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 06/17/2023] [Accepted: 06/23/2023] [Indexed: 07/12/2023]
Abstract
Histone deacetylase 8 (HDAC8) aberrantly deacetylates histone and non-histone proteins. These include structural maintenance of chromosome 3 (SMC3) cohesin protein, retinoic acid induced 1 (RAI1), p53, etc and thus, regulating diverse processes such as leukemic stem cell (LSC) transformation and maintenance. HDAC8, one of the crucial HDACs, affects the gene silencing process in solid and hematological cancer progressions especially on acute myeloid leukemia (AML) and acute lymphoblastic leukemia (ALL). A specific HDAC8 inhibitor PCI-34051 showed promising results against both T-cell lymphoma and AML. Here, we summarize the role of HDAC8 in hematological malignancies, especially in AML and ALL. This article also introduces the structure/function of HDAC8 and a special attention has been paid to address the HDAC8 enzyme selectivity issue in hematological cancer especially against AML and ALL.
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Affiliation(s)
- Sk Abdul Amin
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, 700032, India; Department of Pharmaceutical Technology, JIS University, 81, Nilgunj Road, Agarpara, Kolkata, West Bengal, India.
| | - Samima Khatun
- Laboratory of Drug Design and Discovery, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, 700032, India
| | - Shovanlal Gayen
- Laboratory of Drug Design and Discovery, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, 700032, India.
| | - Sanjib Das
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, 700032, India
| | - Tarun Jha
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata, 700032, India.
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5
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Fumo VM, Roberts RC, Zhang J, O'Reilly MC. Diastereoselective synthesis of cyclic tetrapeptide pseudoxylallemycin A illuminates the impact of base during macrolactamization. Org Biomol Chem 2023; 21:1056-1069. [PMID: 36628602 PMCID: PMC11311250 DOI: 10.1039/d2ob02126a] [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] [Indexed: 01/07/2023]
Abstract
Therapeutic agents with unique molecular structures and new mechanisms of action are needed to confront the phenomenon of multidrug resistance among bacteria. Pseudoxylallemycins, cyclic tetrapeptide (CTP) natural products, have exhibited modest antibiotic activity, but their synthesis has proven challenging. Inherent ring strain in CTPs decreases the rate of cyclization in lieu of polymerization and racemization pathways, which has resulted in previous syntheses describing mixtures of diastereomers containing predominantly an undesired epimer. We have optimized the cyclization step of pseudoxylallemycin A to favor production of the natural diastereomer; notably, variation of the base, temperature, and solvent with peptide coupling reagent propylphosphonic anhydride (T3P) afforded exquisite selectivity for the natural product in as high as 97 : 3 DR, and our conditions can provide the natural product in up to 32% overall yield through 8 steps. Employing weaker bases than those typically used in peptide coupling reactions led to the greatest improvement in diastereoselectivity, and these studies demonstrated that the identity of the amine base has enormous impact on the rate of C-terminal epimerization when T3P is used, a variable usually considered of lesser consequence when combined with typical amide coupling reagents. Toward fully characterizing pseudoxylallemycin stereoisomers, variable temperature NMR was described as a tool to more clearly analyze CTPs that exhibit multiple conformational states. These synthetic and spectroscopic insights were applied toward synthesizing several natural product analogues, and their antibacterial activity was examined using microdilution assays.
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Affiliation(s)
- Vincent M Fumo
- Department of Chemistry, Villanova University, 800 E Lancaster Ave, Villanova, Pennsylvania 19085, USA.
| | - R Charlie Roberts
- Department of Chemistry, Villanova University, 800 E Lancaster Ave, Villanova, Pennsylvania 19085, USA.
| | - Jieyu Zhang
- Department of Chemistry, Villanova University, 800 E Lancaster Ave, Villanova, Pennsylvania 19085, USA.
| | - Matthew C O'Reilly
- Department of Chemistry, Villanova University, 800 E Lancaster Ave, Villanova, Pennsylvania 19085, USA.
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6
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Brusa I, Sondo E, Falchi F, Pedemonte N, Roberti M, Cavalli A. Proteostasis Regulators in Cystic Fibrosis: Current Development and Future Perspectives. J Med Chem 2022; 65:5212-5243. [PMID: 35377645 PMCID: PMC9014417 DOI: 10.1021/acs.jmedchem.1c01897] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
In cystic fibrosis (CF), the deletion of phenylalanine 508 (F508del) in the CF transmembrane conductance regulator (CFTR) leads to misfolding and premature degradation of the mutant protein. These defects can be targeted with pharmacological agents named potentiators and correctors. During the past years, several efforts have been devoted to develop and approve new effective molecules. However, their clinical use remains limited, as they fail to fully restore F508del-CFTR biological function. Indeed, the search for CFTR correctors with different and additive mechanisms has recently increased. Among them, drugs that modulate the CFTR proteostasis environment are particularly attractive to enhance therapy effectiveness further. This Perspective focuses on reviewing the recent progress in discovering CFTR proteostasis regulators, mainly describing the design, chemical structure, and structure-activity relationships. The opportunities, challenges, and future directions in this emerging and promising field of research are discussed, as well.
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Affiliation(s)
- Irene Brusa
- Department of Pharmacy and Biotechnology, University of Bologna, 40126 Bologna, Italy.,Computational & Chemical Biology, Istituto Italiano di Tecnologia, 16163 Genova, Italy
| | - Elvira Sondo
- UOC Genetica Medica, IRCCS Istituto Giannina Gaslini, 16147 Genova, Italy
| | | | | | - Marinella Roberti
- Department of Pharmacy and Biotechnology, University of Bologna, 40126 Bologna, Italy
| | - Andrea Cavalli
- Department of Pharmacy and Biotechnology, University of Bologna, 40126 Bologna, Italy.,Computational & Chemical Biology, Istituto Italiano di Tecnologia, 16163 Genova, Italy
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7
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Moreno-Yruela C, Bæk M, Vrsanova AE, Schulte C, Maric HM, Olsen CA. Hydroxamic acid-modified peptide microarrays for profiling isozyme-selective interactions and inhibition of histone deacetylases. Nat Commun 2021; 12:62. [PMID: 33397936 PMCID: PMC7782793 DOI: 10.1038/s41467-020-20250-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 11/19/2020] [Indexed: 02/07/2023] Open
Abstract
Histones control gene expression by regulating chromatin structure and function. The posttranslational modifications (PTMs) on the side chains of histones form the epigenetic landscape, which is tightly controlled by epigenetic modulator enzymes and further recognized by so-called reader domains. Histone microarrays have been widely applied to investigate histone-reader interactions, but not the transient interactions of Zn2+-dependent histone deacetylase (HDAC) eraser enzymes. Here, we synthesize hydroxamic acid-modified histone peptides and use them in femtomolar microarrays for the direct capture and detection of the four class I HDAC isozymes. Follow-up functional assays in solution provide insights into their suitability to discover HDAC substrates and inhibitors with nanomolar potency and activity in cellular assays. We conclude that similar hydroxamic acid-modified histone peptide microarrays and libraries could find broad application to identify class I HDAC isozyme-specific substrates and facilitate the development of isozyme-selective HDAC inhibitors and probes.
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Affiliation(s)
- Carlos Moreno-Yruela
- Center for Biopharmaceuticals & Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, DK-2100, Copenhagen, Denmark
| | - Michael Bæk
- Center for Biopharmaceuticals & Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, DK-2100, Copenhagen, Denmark
| | - Adela-Eugenie Vrsanova
- Center for Biopharmaceuticals & Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, DK-2100, Copenhagen, Denmark.,Institute of Applied Biosciences & Department of Food Chemistry and Toxicology, Karlsruhe Institute of Technology, Adenauerring 20a, D-76131, Karlsruhe, Germany.,Division of Proteomics of Stem Cells and Cancer, DKFZ German Cancer Research Center, Im Neuenhemier Feld 581, D-69120, Heidelberg, Germany
| | - Clemens Schulte
- Rudolf Virchow Center, Center for Integrative and Translational Bioimaging, University of Würzburg, Josef-Schneider-Str. 2, D-97080, Würzburg, Germany
| | - Hans M Maric
- Rudolf Virchow Center, Center for Integrative and Translational Bioimaging, University of Würzburg, Josef-Schneider-Str. 2, D-97080, Würzburg, Germany.
| | - Christian A Olsen
- Center for Biopharmaceuticals & Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, DK-2100, Copenhagen, Denmark.
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8
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Brosowsky J, Lutterbeck M, Liebich A, Keller M, Herp D, Vogelmann A, Jung M, Breit B. Syntheses of Thailandepsin B Pseudo-Natural Products: Access to New Highly Potent HDAC Inhibitors via Late-Stage Modification. Chemistry 2020; 26:16241-16245. [PMID: 32725698 PMCID: PMC7756392 DOI: 10.1002/chem.202002449] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2020] [Indexed: 01/08/2023]
Abstract
New Thailandepsin B pseudo‐natural products have been prepared. Our synthetic strategy offers the possibility to introduce varying warheads via late stage modification. Additionally, it gives access to the asymmetric branched allylic ester moiety of the natural product in a highly diastereoselective manner applying rhodium‐catalyzed hydrooxycarbonylation. The newly developed pseudo‐natural products are extremely potent and selective HDAC inhibitors. The non‐proteinogenic amino acid d‐norleucine was obtained enantioselectively by a recently developed method of rhodium‐catalyzed hydroamination.
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Affiliation(s)
- Jana Brosowsky
- Institut für Organische ChemieAlbert-Ludwigs-Universität FreiburgAlbertstr. 2179104FreiburgGermany
| | - Monika Lutterbeck
- Institut für Organische ChemieAlbert-Ludwigs-Universität FreiburgAlbertstr. 2179104FreiburgGermany
| | - Amelie Liebich
- Institut für Organische ChemieAlbert-Ludwigs-Universität FreiburgAlbertstr. 2179104FreiburgGermany
| | - Manfred Keller
- Institut für Organische ChemieAlbert-Ludwigs-Universität FreiburgAlbertstr. 2179104FreiburgGermany
| | - Daniel Herp
- Institut für Pharmazeutische WissenschaftenAlbert-Ludwigs-Universität FreiburgAlbertstr. 2579104FreiburgGermany
| | - Anja Vogelmann
- Institut für Pharmazeutische WissenschaftenAlbert-Ludwigs-Universität FreiburgAlbertstr. 2579104FreiburgGermany
| | - Manfred Jung
- Institut für Pharmazeutische WissenschaftenAlbert-Ludwigs-Universität FreiburgAlbertstr. 2579104FreiburgGermany
| | - Bernhard Breit
- Institut für Organische ChemieAlbert-Ludwigs-Universität FreiburgAlbertstr. 2179104FreiburgGermany
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9
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Jwad R, Weissberger D, Hunter L. Strategies for Fine-Tuning the Conformations of Cyclic Peptides. Chem Rev 2020; 120:9743-9789. [PMID: 32786420 DOI: 10.1021/acs.chemrev.0c00013] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Cyclic peptides are promising scaffolds for drug development, attributable in part to their increased conformational order compared to linear peptides. However, when optimizing the target-binding or pharmacokinetic properties of cyclic peptides, it is frequently necessary to "fine-tune" their conformations, e.g., by imposing greater rigidity, by subtly altering certain side chain vectors, or by adjusting the global shape of the macrocycle. This review systematically examines the various types of structural modifications that can be made to cyclic peptides in order to achieve such conformational control.
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Affiliation(s)
- Rasha Jwad
- Department of Chemistry, College of Science, Al-Nahrain University, Baghdad, Iraq
| | - Daniel Weissberger
- School of Chemistry, University of New South Wales (UNSW) Sydney, New South Wales 2052, Australia
| | - Luke Hunter
- School of Chemistry, University of New South Wales (UNSW) Sydney, New South Wales 2052, Australia
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10
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Jing X, Jin K. A gold mine for drug discovery: Strategies to develop cyclic peptides into therapies. Med Res Rev 2019; 40:753-810. [PMID: 31599007 DOI: 10.1002/med.21639] [Citation(s) in RCA: 96] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 09/05/2019] [Accepted: 09/26/2019] [Indexed: 12/19/2022]
Abstract
As a versatile therapeutic modality, peptides attract much attention because of their great binding affinity, low toxicity, and the capability of targeting traditionally "undruggable" protein surfaces. However, the deficiency of cell permeability and metabolic stability always limits the success of in vitro bioactive peptides as drug candidates. Peptide macrocyclization is one of the most established strategies to overcome these limitations. Over the past decades, more than 40 cyclic peptide drugs have been clinically approved, the vast majority of which are derived from natural products. The de novo discovered cyclic peptides on the basis of rational design and in vitro evolution, have also enabled the binding with targets for which nature provides no solutions. The current review summarizes different classes of cyclic peptides with diverse biological activities, and presents an overview of various approaches to develop cyclic peptide-based drug candidates, drawing upon series of examples to illustrate each strategy.
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Affiliation(s)
- Xiaoshu Jing
- Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Kang Jin
- Department of Medicinal Chemistry, School of Pharmacy, Shandong University, Jinan, Shandong, China
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11
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Elek GZ, Koppel K, Zubrytski DM, Konrad N, Järving I, Lopp M, Kananovich DG. Divergent Access to Histone Deacetylase Inhibitory Cyclopeptides via a Late-Stage Cyclopropane Ring Cleavage Strategy. Short Synthesis of Chlamydocin. Org Lett 2019; 21:8473-8478. [PMID: 31596600 DOI: 10.1021/acs.orglett.9b03305] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A unified step-economical strategy for accessing histone deacetylase inhibitory peptides is proposed, based on the late-stage installation of multiple zinc-binding functionalities via the cleavage of the strained cyclopropane ring in the common pluripotent cyclopropanol precursor. The efficacy of the proposed diversity-oriented approach has been validated by short stereoselective synthesis of natural product chlamydocin, containing a challenging-to-install fragment of (2S,9S)-2-amino-8-oxo-9,10-epoxydecanoic acid (Aoe) and a range of its analogues, derivatives of 2-amino-8-oxodecanoic and 2-aminosuberic acids.
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Affiliation(s)
- Gábor Zoltán Elek
- Tallinn University of Technology , School of Science, Department of Chemistry and Biotechnology , Akadeemia tee 15 , 12618 Tallinn , Estonia
| | - Kaur Koppel
- Tallinn University of Technology , School of Science, Department of Chemistry and Biotechnology , Akadeemia tee 15 , 12618 Tallinn , Estonia
| | - Dzmitry M Zubrytski
- Belarusian State University , Department of Organic Chemistry , Leningradskaya 14 , 220050 Minsk , Belarus
| | - Nele Konrad
- Tallinn University of Technology , School of Science, Department of Chemistry and Biotechnology , Akadeemia tee 15 , 12618 Tallinn , Estonia
| | - Ivar Järving
- Tallinn University of Technology , School of Science, Department of Chemistry and Biotechnology , Akadeemia tee 15 , 12618 Tallinn , Estonia
| | - Margus Lopp
- Tallinn University of Technology , School of Science, Department of Chemistry and Biotechnology , Akadeemia tee 15 , 12618 Tallinn , Estonia
| | - Dzmitry G Kananovich
- Tallinn University of Technology , School of Science, Department of Chemistry and Biotechnology , Akadeemia tee 15 , 12618 Tallinn , Estonia
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12
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Janssens Y, Wynendaele E, Vanden Berghe W, De Spiegeleer B. Peptides as epigenetic modulators: therapeutic implications. Clin Epigenetics 2019; 11:101. [PMID: 31300053 PMCID: PMC6624906 DOI: 10.1186/s13148-019-0700-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 07/03/2019] [Indexed: 12/13/2022] Open
Abstract
Peptides originating from different sources (endogenous, food derived, environmental, and synthetic) are able to influence different aspects of epigenetic regulation. Endogenous short peptides, resulting from proteolytic cleavage of proteins or upon translation of non-annotated out of frame transcripts, can block DNA methylation and hereby regulate gene expression. Peptides entering the body by digestion of food-related proteins can modulate DNA methylation and/or histone acetylation while environmental peptides, synthesized by bacteria, fungi, and marine sponges, mainly inhibit histone deacetylation. In addition, synthetic peptides that reverse or inhibit different epigenetic modifications of both histones and the DNA can be developed as well. Next to these DNA and histone modifications, peptides can also influence the expression of non-coding RNAs such as lncRNAs and the maturation of miRNAs. Seen the advantages over small molecules, the development of peptide therapeutics is an interesting approach to treat diseases with a strong epigenetic basis like cancer and Alzheimer’s disease. To date, only a limited number of drugs with a proven epigenetic mechanism of action have been approved by the FDA of which two (romidepsin and nesiritide) are peptides. A large knowledge gap concerning epigenetic effects of peptides is present, and this class of molecules deserves more attention in the development as epigenetic modulators. In addition, none of the currently approved peptide drugs are under investigation for their potential effects on epigenetics, hampering drug repositioning of these peptides to other indications with an epigenetic etiology.
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Affiliation(s)
- Yorick Janssens
- Drug Quality and Registration (DruQuaR) group, Faculty of Pharmaceutical Sciences, Ghent University, Ottergemsesteenweg 460, 9000, Ghent, Belgium
| | - Evelien Wynendaele
- Drug Quality and Registration (DruQuaR) group, Faculty of Pharmaceutical Sciences, Ghent University, Ottergemsesteenweg 460, 9000, Ghent, Belgium
| | - Wim Vanden Berghe
- Protein Science, Proteomics and Epigenetic Signaling (PPES), Department Biomedical Sciences, University of Antwerp, Universiteitsplein 1, 2610, Wilrijk, Belgium
| | - Bart De Spiegeleer
- Drug Quality and Registration (DruQuaR) group, Faculty of Pharmaceutical Sciences, Ghent University, Ottergemsesteenweg 460, 9000, Ghent, Belgium.
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13
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Almaliti J, Miller B, Pietraszkiewicz H, Glukhov E, Naman CB, Kline T, Hanson J, Li X, Zhou S, Valeriote FA, Gerwick WH. Exploration of the carmaphycins as payloads in antibody drug conjugate anticancer agents. Eur J Med Chem 2019; 161:416-432. [PMID: 30384045 PMCID: PMC6248884 DOI: 10.1016/j.ejmech.2018.10.024] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Revised: 09/25/2018] [Accepted: 10/09/2018] [Indexed: 02/06/2023]
Abstract
Antibody-drug conjugates (ADCs) represent a new dimension of anticancer chemotherapeutics, with warheads to date generally involving either antitubulin or DNA-directed agents to achieve low-to sub-nanomolar potency. However, other potent cytotoxins working by different pharmacological mechanisms are under investigation, such as α,β-epoxyketone based proteasome inhibitors. These proteasome active agents are an emerging class of anticancer drug that possesses ultra-potent cytotoxicity to some cancer cell lines. The carmaphycins are representatives of this latter class that we isolated and characterized from a marine cyanobacterium, and these as well as several synthetic analogues exhibit this level of potency. In the current work, we investigated the use of these highly potent cytotoxic compounds as warheads in the design of novel ADCs. We designed and synthesized a library of carmaphycin B analogues that contain amine handles, enabling their attachment to an antibody linker. The basicity of these incorporated amine handles was shown to strongly affect their cytotoxic properties. Linear amines resulted in the greatest reduction in cytotoxicity whereas less basic aromatic amines retained potent activity as demonstrated by a 4-sulfonylaniline derivative. These investigations resulted in identifying the P2 residue in the carmaphycins as the most suitable site for linker attachment point, and hence, we synthesized a highly potent analogue of carmaphycin B that contained a 4-sulfonylaniline handle as an attachment point for the linker antibody.
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Affiliation(s)
- Jehad Almaliti
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, 92093, United States; Department Pharmaceutical Sciences, College of Pharmacy, The University of Jordan, Amman, 11942, Jordan
| | - Bailey Miller
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, 92093, United States
| | - Halina Pietraszkiewicz
- Department of Internal Medicine, Division of Hematology and Oncology, Henry Ford Hospital, Detroit, MI, 48202, USA
| | - Evgenia Glukhov
- Department Pharmaceutical Sciences, College of Pharmacy, The University of Jordan, Amman, 11942, Jordan
| | - C Benjamin Naman
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, 92093, United States; College of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, Zhejiang, 315211, China
| | - Toni Kline
- Sutro Biopharma, South San Francisco, CA, 94080, United States
| | - Jeffrey Hanson
- Sutro Biopharma, South San Francisco, CA, 94080, United States
| | - Xiaofan Li
- Sutro Biopharma, South San Francisco, CA, 94080, United States
| | - Sihong Zhou
- Sutro Biopharma, South San Francisco, CA, 94080, United States
| | - Frederick A Valeriote
- Department of Internal Medicine, Division of Hematology and Oncology, Henry Ford Hospital, Detroit, MI, 48202, USA
| | - William H Gerwick
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, 92093, United States; Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, 92093, United States.
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14
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Histone deacetylase 8 (HDAC8) and its inhibitors with selectivity to other isoforms: An overview. Eur J Med Chem 2018; 164:214-240. [PMID: 30594678 DOI: 10.1016/j.ejmech.2018.12.039] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2018] [Revised: 12/04/2018] [Accepted: 12/16/2018] [Indexed: 01/08/2023]
Abstract
The histone deacetylases (HDACs) enzymes provided crucial role in transcriptional regulation of cells through deacetylation of nuclear histone proteins. Discoveries related to the HDAC8 enzyme activity signified the importance of HDAC8 isoform in cell proliferation, tumorigenesis, cancer, neuronal disorders, parasitic/viral infections and other epigenetic regulations. The pan-HDAC inhibitors can confront these conditions but have chances to affect epigenetic functions of other HDAC isoforms. Designing of selective HDAC8 inhibitors is a key feature to combat the pathophysiological and diseased conditions involving the HDAC8 activity. This review is concerned about the structural and positional aspects of HDAC8 in the HDAC family. It also covers the contributions of HDAC8 in the pathophysiological conditions, a preliminary discussion about the recent scenario of HDAC8 inhibitors. This review might help to deliver the structural, functional and computational information in order to identify and design potent and selective HDAC8 inhibitors for target specific treatment of diseases involving HDAC8 enzymatic activity.
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15
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Structure–activity relationships of hydroxamate-based histone deacetylase-8 inhibitors: reality behind anticancer drug discovery. Future Med Chem 2017; 9:2211-2237. [PMID: 29182018 DOI: 10.4155/fmc-2017-0130] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The pan-histone deacetylase (HDAC) inhibitors comprise a fish-like structural orientation where hydrophobic aryl- and zinc-binding groups act as head and tail, respectively of a fish. The linker moiety correlates the body of the fish linking head and tail groups. Despite these pan-HDAC inhibitors, selective HDAC-8 inhibitors are still in demand as a safe remedy. HDAC-8 is involved in invasion and metastasis in cancer. This review deals with the rationale behind HDAC-8 inhibitory activity and selectivity along with detailed structure–activity relationships of diverse hydroxamate-based HDAC-8 inhibitors. HDAC-8 inhibitory potency may be increased by modifying the fish-like pharmacophoric features of such type of pan-HDAC inhibitors. This review may provide a preliminary basis to design and optimize new lead molecules with higher HDAC-8 inhibitory activity. This work may surely enlighten in providing useful information in the field of target-specific anticancer therapy.
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16
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Recent advances in the discovery of potent and selective HDAC6 inhibitors. Eur J Med Chem 2017; 143:1406-1418. [PMID: 29133060 DOI: 10.1016/j.ejmech.2017.10.040] [Citation(s) in RCA: 99] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Revised: 10/14/2017] [Accepted: 10/14/2017] [Indexed: 01/07/2023]
Abstract
Histone deacetylase HDAC6, a member of the class IIb HDAC family, is unique among HDAC enzymes in having two active catalytic domains, and has unique physiological function. In addition to the modification of histone, HDAC6 targets specific substrates including α-tubulin and HSP90, and are involved in protein trafficking and degradation, cell shape and migration. Selective HDAC6 inhibitors are an emerging class of pharmaceuticals due to the involvement of HDAC6 in different pathways related to neurodegenerative diseases, cancer, and immunology. Therefore, extensive investigations have been made in the discovery of selective HDAC6 inhibitors. Based on their different zinc binding groups (ZBGs), in this review, HDAC6 inhibitors are grouped as hydroxamic acids, a sulfur containing ZBG based derivatives and other ZBG-derived compounds, and their enzymatic inhibitory activity, selectivity and other biological activities are introduced and summarized.
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17
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Kitir B, Maolanon AR, Ohm RG, Colaço AR, Fristrup P, Madsen AS, Olsen CA. Chemical Editing of Macrocyclic Natural Products and Kinetic Profiling Reveal Slow, Tight-Binding Histone Deacetylase Inhibitors with Picomolar Affinities. Biochemistry 2017; 56:5134-5146. [DOI: 10.1021/acs.biochem.7b00725] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Betül Kitir
- Center
for Biopharmaceuticals and Department for Drug Design and Pharmacology,
Faculty of Health and Medical Sciences, University of Copenhagen, DK-2100 Copenhagen, Denmark
| | - Alex R. Maolanon
- Center
for Biopharmaceuticals and Department for Drug Design and Pharmacology,
Faculty of Health and Medical Sciences, University of Copenhagen, DK-2100 Copenhagen, Denmark
| | - Ragnhild G. Ohm
- Center
for Biopharmaceuticals and Department for Drug Design and Pharmacology,
Faculty of Health and Medical Sciences, University of Copenhagen, DK-2100 Copenhagen, Denmark
| | - Ana R. Colaço
- Department
of Chemistry, Technical University of Denmark, DK-2800 Kongens
Lyngby, Denmark
| | - Peter Fristrup
- Department
of Chemistry, Technical University of Denmark, DK-2800 Kongens
Lyngby, Denmark
| | - Andreas S. Madsen
- Center
for Biopharmaceuticals and Department for Drug Design and Pharmacology,
Faculty of Health and Medical Sciences, University of Copenhagen, DK-2100 Copenhagen, Denmark
| | - Christian A. Olsen
- Center
for Biopharmaceuticals and Department for Drug Design and Pharmacology,
Faculty of Health and Medical Sciences, University of Copenhagen, DK-2100 Copenhagen, Denmark
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18
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Marshall GR, Ballante F. Limiting Assumptions in the Design of Peptidomimetics. Drug Dev Res 2017; 78:245-267. [DOI: 10.1002/ddr.21406] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Garland R. Marshall
- Department of Biochemistry and Molecular Biophysics; Washington University School of Medicine; St. Louis Missouri 63110
| | - Flavio Ballante
- Department of Biochemistry and Molecular Biophysics; Washington University School of Medicine; St. Louis Missouri 63110
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19
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Mendoza-Sanchez R, Corless VB, Nguyen QNN, Bergeron-Brlek M, Frost J, Adachi S, Tantillo DJ, Yudin AK. Cyclols Revisited: Facile Synthesis of Medium-Sized Cyclic Peptides. Chemistry 2017; 23:13319-13322. [PMID: 28771904 DOI: 10.1002/chem.201703616] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Indexed: 12/21/2022]
Abstract
Medium-sized rings, particularly the corresponding cyclic peptides, are challenging synthetic targets. In the present study, we report an approach to medium-sized cyclic peptides through targeted formation and collapse of cyclol intermediates. This methodology operates on β-amino imides derived from 2,5-diketopiperazines and offers a straightforward transition from frequently examined scaffolds in drug discovery to a rarely visited class of medium-sized rings.
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Affiliation(s)
- Rodrigo Mendoza-Sanchez
- Davenport Research Laboratories, Department of Chemistry, University of Toronto, 80 St. George St., Toronto, ON, M5S 3H6, Canada
| | - Victoria B Corless
- Davenport Research Laboratories, Department of Chemistry, University of Toronto, 80 St. George St., Toronto, ON, M5S 3H6, Canada
| | - Q Nhu N Nguyen
- Department of Chemistry, University of California Davis, 1 Shields Avenue, Davis, CA, USA
| | - Milan Bergeron-Brlek
- Davenport Research Laboratories, Department of Chemistry, University of Toronto, 80 St. George St., Toronto, ON, M5S 3H6, Canada
| | - John Frost
- Davenport Research Laboratories, Department of Chemistry, University of Toronto, 80 St. George St., Toronto, ON, M5S 3H6, Canada
| | - Shinya Adachi
- Davenport Research Laboratories, Department of Chemistry, University of Toronto, 80 St. George St., Toronto, ON, M5S 3H6, Canada
| | - Dean J Tantillo
- Department of Chemistry, University of California Davis, 1 Shields Avenue, Davis, CA, USA
| | - Andrei K Yudin
- Davenport Research Laboratories, Department of Chemistry, University of Toronto, 80 St. George St., Toronto, ON, M5S 3H6, Canada
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20
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Barnash KD, Lamb KN, James LI, Frye SV. Peptide Technologies in the Development of Chemical Tools for Chromatin-Associated Machinery. Drug Dev Res 2017. [DOI: 10.1002/ddr.21398] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Kimberly D. Barnash
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy; University of North Carolina at Chapel Hill; Chapel Hill North Carolina 27599
| | - Kelsey N. Lamb
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy; University of North Carolina at Chapel Hill; Chapel Hill North Carolina 27599
| | - Lindsey I. James
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy; University of North Carolina at Chapel Hill; Chapel Hill North Carolina 27599
| | - Stephen V. Frye
- Center for Integrative Chemical Biology and Drug Discovery, Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy; University of North Carolina at Chapel Hill; Chapel Hill North Carolina 27599
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21
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Lai JI, Leman LJ, Ku S, Vickers CJ, Olsen CA, Montero A, Ghadiri MR, Gottesfeld JM. Cyclic tetrapeptide HDAC inhibitors as potential therapeutics for spinal muscular atrophy: Screening with iPSC-derived neuronal cells. Bioorg Med Chem Lett 2017. [PMID: 28648462 DOI: 10.1016/j.bmcl.2017.06.027] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Spinal muscular atrophy (SMA) is an autosomal recessive neuromuscular disorder that is caused by inactivating mutations in the Survival of motor neuron 1 (SMN1) gene, resulting in decreased SMN protein expression. Humans possess a paralog gene, SMN2, which contains a splicing defect in exon 7 leading to diminished expression of full-length, fully functional SMN protein. Increasing SMN2 expression has been a focus of therapeutic development for SMA. Multiple studies have reported the efficacy of histone deacetylase inhibitors (HDACi) in this regard. However, clinical trials involving HDACi have been unsatisfactory, possibly because previous efforts to identify HDACi to treat SMA have employed non-neuronal cells as the screening platform. To address this issue, we generated an SMA-patient specific, induced pluripotent stem cell (iPSC) derived neuronal cell line that contains homogenous Tuj1+neurons. We screened a small library of cyclic tetrapeptide HDACi using this SMA neuronal platform and discovered compounds that elevate SMN2 expression by an impressive twofold or higher. These candidates are also capable of forming gems intranuclearly in SMA neurons, demonstrating biological activity. Our study identifies new potential HDACi therapeutics for SMA screened using a disease-relevant SMA neuronal cellular model.
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Affiliation(s)
- Jiun-I Lai
- Department of Cell and Molecular Biology, The Scripps Research Institute, La Jolla, CA, USA; National Yang-Ming University, Taipei, Taiwan; National Yang-Ming University Hospital, Ilan, Taiwan
| | - Luke J Leman
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
| | - Sherman Ku
- Department of Cell and Molecular Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Chris J Vickers
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
| | - Christian A Olsen
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA; Center for Biopharmaceuticals and Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark
| | - Ana Montero
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
| | - M Reza Ghadiri
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
| | - Joel M Gottesfeld
- Department of Cell and Molecular Biology, The Scripps Research Institute, La Jolla, CA, USA.
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22
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Chen CC, Wang SF, Su YY, Lin YA, Lin PC. Copper(I)-Mediated Denitrogenative Macrocyclization for the Synthesis of Cyclic α3
β-Tetrapeptide Analogues. Chem Asian J 2017; 12:1326-1337. [DOI: 10.1002/asia.201700339] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Revised: 03/23/2017] [Indexed: 12/23/2022]
Affiliation(s)
- Chun-Chi Chen
- Department of Chemistry; Nation Sun Yat-sen University; 70 Lienhai Rd. Kaohsiung 80424 Taiwan
| | - Sheng-Fu Wang
- Department of Chemistry; Nation Sun Yat-sen University; 70 Lienhai Rd. Kaohsiung 80424 Taiwan
| | - Yung-Yu Su
- Department of Chemistry; Nation Sun Yat-sen University; 70 Lienhai Rd. Kaohsiung 80424 Taiwan
| | - Yuya A. Lin
- Department of Chemistry; Nation Sun Yat-sen University; 70 Lienhai Rd. Kaohsiung 80424 Taiwan
| | - Po-Chiao Lin
- Department of Chemistry; Nation Sun Yat-sen University; 70 Lienhai Rd. Kaohsiung 80424 Taiwan
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23
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Maolanon AR, Kristensen HME, Leman LJ, Ghadiri MR, Olsen CA. Natural and Synthetic Macrocyclic Inhibitors of the Histone Deacetylase Enzymes. Chembiochem 2016; 18:5-49. [DOI: 10.1002/cbic.201600519] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Indexed: 12/18/2022]
Affiliation(s)
- Alex R. Maolanon
- Center for Biopharmaceuticals and; Department of Drug Design and Pharmacology; University of Copenhagen; Universitetsparken 2 2100 Copenhagen Denmark
| | - Helle M. E. Kristensen
- Center for Biopharmaceuticals and; Department of Drug Design and Pharmacology; University of Copenhagen; Universitetsparken 2 2100 Copenhagen Denmark
| | - Luke J. Leman
- Department of Chemistry; The Skaggs Institute for Chemical Biology; The Scripps Research Institute; 10550 North Torrey Pines Road La Jolla CA 92037 USA
| | - M. Reza Ghadiri
- Department of Chemistry; The Skaggs Institute for Chemical Biology; The Scripps Research Institute; 10550 North Torrey Pines Road La Jolla CA 92037 USA
| | - Christian A. Olsen
- Center for Biopharmaceuticals and; Department of Drug Design and Pharmacology; University of Copenhagen; Universitetsparken 2 2100 Copenhagen Denmark
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24
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Wilbs J, Middendorp SJ, Heinis C. Improving the Binding Affinity of in-Vitro-Evolved Cyclic Peptides by Inserting Atoms into the Macrocycle Backbone. Chembiochem 2016; 17:2299-2303. [DOI: 10.1002/cbic.201600336] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Indexed: 12/20/2022]
Affiliation(s)
- Jonas Wilbs
- Institute of Chemical Sciences and Engineering; Ecole Polytechnique Fédérale de Lausanne; EPFL); 1015 Lausanne Switzerland
| | - Simon J. Middendorp
- Institute of Chemical Sciences and Engineering; Ecole Polytechnique Fédérale de Lausanne; EPFL); 1015 Lausanne Switzerland
| | - Christian Heinis
- Institute of Chemical Sciences and Engineering; Ecole Polytechnique Fédérale de Lausanne; EPFL); 1015 Lausanne Switzerland
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25
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Salih N, Adams H, Jackson RFW. Synthesis of ω-Oxo Amino Acids and trans-5-Substituted Proline Derivatives Using Cross-Metathesis of Unsaturated Amino Acids. J Org Chem 2016; 81:8386-93. [DOI: 10.1021/acs.joc.6b01571] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Nabaz Salih
- Department of Chemistry, The University of Sheffield, Dainton Building, Sheffield S3 7HF, U.K
| | - Harry Adams
- Department of Chemistry, The University of Sheffield, Dainton Building, Sheffield S3 7HF, U.K
| | - Richard F. W. Jackson
- Department of Chemistry, The University of Sheffield, Dainton Building, Sheffield S3 7HF, U.K
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26
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Xin D, Burgess K. Anthranilic acid-containing cyclic tetrapeptides: at the crossroads of conformational rigidity and synthetic accessibility. Org Biomol Chem 2016; 14:5049-58. [PMID: 27173439 PMCID: PMC4916954 DOI: 10.1039/c6ob00693k] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Each amino acid in a peptide contributes three atom units to main-chains, hence natural cyclic peptides can be 9, 12, 15, …. i.e. 3n membered-rings, where n is the number of amino acids. Cyclic peptides that are 9 or 12-membered ring compounds tend to be hard to prepare because of strain, while their one amino acid homologs (15-membered cyclic pentapeptides) are not conformationally homogeneous unless constrained by strategically placed proline or d-amino acid residues. We hypothesized that replacing one genetically encoded amino acid in a cyclic tetrapeptide with a rigid β-amino acid would render peptidomimetic designs that rest at a useful crossroads between synthetic accessibility and conformational rigidity. Thus this research explored non-proline containing 13-membered ring peptides 1 featuring one anthranilic acid (Anth) residue. Twelve cyclic peptides of this type were prepared, and in doing so the viability of both solution- and solid-phase methods was demonstrated. The library produced contained a complete set of four diastereoisomers of the sequence 1aaf (i.e. cyclo-AlaAlaPheAnth). Without exception, these four diastereoisomers each adopted one predominant conformation in solution; basically these conformations feature amide N-H vectors puckering above and below the equatorial plane, and approximately oriented their N-H[combining low line] atoms towards the polar axis. Moreover, the shapes of these conformers varied in a logical and predictable way (NOE, temperature coefficient, D/H exchange, circular dichroism). Comparisons were made of the side-chain orientations presented by compounds 1aaa in solution with ideal secondary structures and protein-protein interaction interfaces. Various 1aaa stereoisomers in solution present side-chains in similar orientations to regular and inverse γ-turns, and to the most common β-turns (types I and II). Consistent with this, compounds 1aaa have a tendency to mimic various turns and bends at protein-protein interfaces. Finally, proteolytic- and hydrolytic stabilities of the compounds at different pHs indicate they are robust relative to related linear peptides, and rates of permeability through an artificial membrane indicate their structures are conducive to cell permeability.
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Affiliation(s)
- Dongyue Xin
- Department of Chemistry, Texas A & M University, Box 30012, College Station, TX 77842, USA.
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27
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Magpusao AN, Rutledge K, Hamlin TA, Lawrence J, Mercado BQ, Leadbeater NE, Peczuh MW. Rules of Macrocycle Topology: A [13]‐Macrodilactone Case Study. Chemistry 2016; 22:6001-11. [DOI: 10.1002/chem.201504684] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Revised: 02/23/2016] [Indexed: 12/29/2022]
Affiliation(s)
- Anniefer N. Magpusao
- Department of Chemistry University of Connecticut 55 N. Eagleville Road, U3060 Storrs CT 06269-3060 USA
| | - Kelli Rutledge
- Department of Chemistry University of Connecticut 55 N. Eagleville Road, U3060 Storrs CT 06269-3060 USA
| | - Trevor A. Hamlin
- Department of Chemistry University of Connecticut 55 N. Eagleville Road, U3060 Storrs CT 06269-3060 USA
- Department of Theoretical Chemistry VU University Amsterdam De Boelelaan 1083 1081 HV Amsterdam The Netherlands
| | - Jean‐Marc Lawrence
- Department of Chemistry University of Connecticut 55 N. Eagleville Road, U3060 Storrs CT 06269-3060 USA
| | - Brandon Q. Mercado
- Department of Chemistry Yale University 225 Prospect Street New Haven CT 06520 USA
| | - Nicholas E. Leadbeater
- Department of Chemistry University of Connecticut 55 N. Eagleville Road, U3060 Storrs CT 06269-3060 USA
| | - Mark W. Peczuh
- Department of Chemistry University of Connecticut 55 N. Eagleville Road, U3060 Storrs CT 06269-3060 USA
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28
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Mukherjee JP, Sil S, Chattopadhyay SK. A modular approach to cyclic tetrapeptides related to histone deacetylase inhibition: synthesis of epi-microsporin A. Tetrahedron Lett 2016. [DOI: 10.1016/j.tetlet.2016.01.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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29
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Kim B, Hong J. An overview of naturally occurring histone deacetylase inhibitors. Curr Top Med Chem 2015; 14:2759-82. [PMID: 25487010 DOI: 10.2174/1568026615666141208105614] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Revised: 11/26/2014] [Accepted: 11/29/2014] [Indexed: 12/13/2022]
Abstract
Histone deacetylases (HDACs) have recently emerged as key elements in epigenetic control of gene expression. Due to the implication of HDACs in a variety of diseases ranging from cancer to neurodegenerative disorder, HDAC inhibitors have received increased attention in recent years. Over the last few decades, a myriad of HDAC inhibitors containing a wide variety of structural features have been identified from natural sources. Here, we review the discovery, synthesis, biological properties, and modes of action of these naturally occurring HDAC inhibitors and consider their implications for future research.
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Affiliation(s)
| | - Jiyong Hong
- Duke University, Department of Chemistry, 124 Science Drive, Box 90346, Durham, NC 27708, USA.
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30
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Yudin AK. Macrocycles: lessons from the distant past, recent developments, and future directions. Chem Sci 2015; 6:30-49. [PMID: 28553456 PMCID: PMC5424464 DOI: 10.1039/c4sc03089c] [Citation(s) in RCA: 337] [Impact Index Per Article: 37.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Accepted: 11/01/2014] [Indexed: 12/20/2022] Open
Abstract
A noticeable increase in molecular complexity of drug targets has created an unmet need in the therapeutic agents that are larger than traditional small molecules. Macrocycles, which are cyclic compounds comprising 12 atoms or more, are now recognized as molecules that "are up to the task" to interrogate extended protein interfaces. However, because macrocycles (particularly the ones based on peptides) are equipped with large polar surface areas, achieving cellular permeability and bioavailability is anything but straightforward. While one might consider this to be the Achilles' heel of this class of compounds, the synthetic community continues to develop creative approaches toward the synthesis of macrocycles and their site-selective modification. This perspective provides an overview of both mechanistic and structural issues that bear on macrocycles as a unique class of molecules. The reader is offered a historical foray into some of the classic studies that have resulted in the current renaissance of macrocycles. In addition, an attempt is made to overview the more recent developments that give hope that macrocycles might indeed turn into a useful therapeutic modality.
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Affiliation(s)
- Andrei K Yudin
- Department of Chemistry , University of Toronto , 80 St. George Street , Toronto , Ontario M5S 3H6 , Canada . ; Blog: http://www.amphoteros.com
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31
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Maolanon AR, Villadsen JS, Christensen NJ, Hoeck C, Friis T, Harris P, Gotfredsen CH, Fristrup P, Olsen CA. Methyl Effect in Azumamides Provides Insight Into Histone Deacetylase Inhibition by Macrocycles. J Med Chem 2014; 57:9644-57. [DOI: 10.1021/jm501399d] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Alex R. Maolanon
- Department
of Chemistry, Technical University of Denmark, Kemitorvet 207, DK-2800 Kongens Lyngby, Denmark
| | - Jesper S. Villadsen
- Department
of Chemistry, Technical University of Denmark, Kemitorvet 207, DK-2800 Kongens Lyngby, Denmark
| | - Niels J. Christensen
- Department
of Chemistry, Technical University of Denmark, Kemitorvet 207, DK-2800 Kongens Lyngby, Denmark
| | - Casper Hoeck
- Department
of Chemistry, Technical University of Denmark, Kemitorvet 207, DK-2800 Kongens Lyngby, Denmark
| | - Tina Friis
- Department
of Clinical Biochemistry, Immunology and Genetics, Statens Serum Institut, Artillerivej 5, DK-2300 Copenhagen, Denmark
| | - Pernille Harris
- Department
of Chemistry, Technical University of Denmark, Kemitorvet 207, DK-2800 Kongens Lyngby, Denmark
| | - Charlotte H. Gotfredsen
- Department
of Chemistry, Technical University of Denmark, Kemitorvet 207, DK-2800 Kongens Lyngby, Denmark
| | - Peter Fristrup
- Department
of Chemistry, Technical University of Denmark, Kemitorvet 207, DK-2800 Kongens Lyngby, Denmark
| | - Christian A. Olsen
- Department
of Chemistry, Technical University of Denmark, Kemitorvet 207, DK-2800 Kongens Lyngby, Denmark
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33
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Jiang J, Chen X, Feng J, Wu Q, Zhu D. Substrate profile of an ω-transaminase from Burkholderia vietnamiensis and its potential for the production of optically pure amines and unnatural amino acids. ACTA ACUST UNITED AC 2014. [DOI: 10.1016/j.molcatb.2013.11.013] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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34
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35
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Maity I, Parmar HS, Rasale DB, Das AK. Self-programmed nanovesicle to nanofiber transformation of a dipeptide appended bolaamphiphile and its dose dependent cytotoxic behaviour. J Mater Chem B 2014; 2:5272-5279. [DOI: 10.1039/c4tb00365a] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
A fluorescent nanostructured peptide bolaamphiphile hydrogel shows dose-dependent behaviour towards cytotoxicity and cell-proliferation.
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Affiliation(s)
- Indrajit Maity
- Department of Chemistry
- Indian Institute of Technology Indore
- Indore, India
| | | | | | - Apurba K. Das
- Department of Chemistry
- Indian Institute of Technology Indore
- Indore, India
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36
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Villadsen JS, Kitir B, Wich K, Friis T, Madsen AS, Olsen CA. An azumamide C analogue without the zinc-binding functionality. MEDCHEMCOMM 2014. [DOI: 10.1039/c4md00252k] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Histone deacetylase (HDAC) inhibitors have attracted considerable attention due to their promise as therapeutic agents.
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Affiliation(s)
| | - Betül Kitir
- Department of Chemistry
- Technical University of Denmark
- Kongens Lyngby
- Denmark
| | | | - Tina Friis
- Department of Clinical Biochemistry
- Immunology and Genetics (KBIG)
- Statens Serum Institut
- Copenhagen
- Denmark
| | - Andreas S. Madsen
- Department of Chemistry
- Technical University of Denmark
- Kongens Lyngby
- Denmark
| | - Christian A. Olsen
- Department of Chemistry
- Technical University of Denmark
- Kongens Lyngby
- Denmark
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37
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Madsen AS, Kristensen HME, Lanz G, Olsen CA. The Effect of Various Zinc Binding Groups on Inhibition of Histone Deacetylases 1-11. ChemMedChem 2013; 9:614-26. [DOI: 10.1002/cmdc.201300433] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2013] [Indexed: 12/21/2022]
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38
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Villadsen JS, Stephansen HM, Maolanon AR, Harris P, Olsen CA. Total synthesis and full histone deacetylase inhibitory profiling of Azumamides A-E as well as β²- epi-Azumamide E and β³-epi-Azumamide E. J Med Chem 2013; 56:6512-20. [PMID: 23865683 DOI: 10.1021/jm4008449] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Cyclic tetrapeptide and depsipeptide natural products have proven useful as biological probes and drug candidates due to their potent activities as histone deacetylase (HDAC) inhibitors. Here, we present the syntheses of a class of cyclic tetrapeptide HDAC inhibitors, the azumamides, by a concise route in which the key step in preparation of the noncanonical disubstituted β-amino acid building block was an Ellman-type Mannich reaction. By tweaking the reaction conditions during this transformation, we gained access to the natural products as well as two epimeric homologues. Thus, the first total syntheses of azumamides B-D corroborated the originally assigned structures, and the synthetic efforts enabled the first full profiling of HDAC inhibitory properties of the entire selection of azumamides A-E. This revealed unexpected differences in the relative potencies within the class and showed that azumamides C and E are both potent inhibitors of HDAC10 and HDAC11.
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Affiliation(s)
- Jesper S Villadsen
- Department of Chemistry, Technical University of Denmark, Kemitorvet 207, Kongens Lyngby DK-2800, Denmark
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39
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Caumes C, Fernandes C, Roy O, Hjelmgaard T, Wenger E, Didierjean C, Taillefumier C, Faure S. Cyclic α,β-tetrapeptoids: sequence-dependent cyclization and conformational preference. Org Lett 2013; 15:3626-9. [PMID: 23806006 DOI: 10.1021/ol401478j] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The presence of at least one N-Cα branched side chain is crucial for successful cyclization of α,β-tetrapeptoids. The ctct amide sequence revealed in the crystal structure of the 14-membered cyclotetrapeptoid 8 is also the most populated conformation in solution and is reminiscent of the predominant amide arrangement of the 12-membered cyclic tetrapeptides (CTPs).
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Affiliation(s)
- Cécile Caumes
- Clermont Université, Université Blaise Pascal, Institut de Chimie de Clermont-Ferrand, BP10448, F-63000 Clermont-Ferrand, France
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40
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Chakraborty S, Tyagi P, Tai DF, Lee GH, Peng SM. A lead (II) 3D coordination polymer based on a marine cyclic peptide motif. Molecules 2013; 18:4972-85. [PMID: 23624650 PMCID: PMC6270303 DOI: 10.3390/molecules18054972] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2013] [Revised: 04/16/2013] [Accepted: 04/24/2013] [Indexed: 11/23/2022] Open
Abstract
The crystal structure of a naturally occurring cyclic tetrapeptide cyclo(Gly-L-Ser-L-Pro-L-Glu) [cyclo(GSPE)] was obtained. The conformation of synthesized cyclo(GSPE) fixes the coordination to lead ion in a 1:1 ratio. This cyclo(GSPE)-Pb complex was constructed as an asymmetric 3D network in the crystalline state. The polymerization of a heavy metal ion with a rigid asymmetric cyclic tetrapeptide represents the first example of a new class of macrocyclic complexes.
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Affiliation(s)
| | - Pooja Tyagi
- Department of Chemistry, National Dong-Hwa University, Hualien 974, Taiwan
| | - Dar-Fu Tai
- Department of Chemistry, National Dong-Hwa University, Hualien 974, Taiwan
| | - Gene-Hsiang Lee
- Department of Chemistry, National Taiwan University, Taipei 106, Taiwan
| | - Shie-Ming Peng
- Department of Chemistry, National Taiwan University, Taipei 106, Taiwan
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41
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Traoré M, Mietton F, Maubon D, Peuchmaur M, Francisco Hilário F, Pereira de Freitas R, Bougdour A, Curt A, Maynadier M, Vial H, Pelloux H, Hakimi MA, Wong YS. Flexible Synthesis and Evaluation of Diverse Anti-Apicomplexa Cyclic Peptides. J Org Chem 2013; 78:3655-75. [DOI: 10.1021/jo4001492] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Mariam Traoré
- Département de Pharmacochimie Moléculaire, Université Joseph Fourier-Grenoble 1, CNRS UMR 5063, CNRS ICMG FR 2607, bâtiment André
Rassat, 470 rue de la Chimie, F-38041 Grenoble Cedex 9, France
| | - Flore Mietton
- Laboratoire Adaptation et Pathogénie des Micro-organismes, Université Joseph Fourier-Grenoble 1, CNRS UMR 5163, BP 170, F-38042 Grenoble Cedex 9, France
| | - Danièle Maubon
- Laboratoire Adaptation et Pathogénie des Micro-organismes, Université Joseph Fourier-Grenoble 1, CNRS UMR 5163, BP 170, F-38042 Grenoble Cedex 9, France
- Laboratoire de Parasitologie-Mycologie, Département des Agents Infectieux, Centre Hospitalier Universitaire, BP
217, 38043 Grenoble cedex 9, France
| | - Marine Peuchmaur
- Département de Pharmacochimie Moléculaire, Université Joseph Fourier-Grenoble 1, CNRS UMR 5063, CNRS ICMG FR 2607, bâtiment André
Rassat, 470 rue de la Chimie, F-38041 Grenoble Cedex 9, France
| | - Flaviane Francisco Hilário
- Département de Pharmacochimie Moléculaire, Université Joseph Fourier-Grenoble 1, CNRS UMR 5063, CNRS ICMG FR 2607, bâtiment André
Rassat, 470 rue de la Chimie, F-38041 Grenoble Cedex 9, France
- Departamento de Quı́mica, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais,
Brasil
- CAPES Foundation, Ministry of Education of Brazil, Brasilia DF 70040-020, Brazil
| | | | - Alexandre Bougdour
- Laboratoire Adaptation et Pathogénie des Micro-organismes, Université Joseph Fourier-Grenoble 1, CNRS UMR 5163, BP 170, F-38042 Grenoble Cedex 9, France
| | - Aurélie Curt
- Laboratoire Adaptation et Pathogénie des Micro-organismes, Université Joseph Fourier-Grenoble 1, CNRS UMR 5163, BP 170, F-38042 Grenoble Cedex 9, France
- Laboratoire de Parasitologie-Mycologie, Département des Agents Infectieux, Centre Hospitalier Universitaire, BP
217, 38043 Grenoble cedex 9, France
| | - Marjorie Maynadier
- Dynamique
des Interactions Membranaires Normales et Pathologiques, Université de Montpellier 2,
CNRS UMR 5235, CP 107, Place E. Bataillon, F-34095 Montpellier Cedex
5, France
| | - Henri Vial
- Dynamique
des Interactions Membranaires Normales et Pathologiques, Université de Montpellier 2,
CNRS UMR 5235, CP 107, Place E. Bataillon, F-34095 Montpellier Cedex
5, France
| | - Hervé Pelloux
- Laboratoire Adaptation et Pathogénie des Micro-organismes, Université Joseph Fourier-Grenoble 1, CNRS UMR 5163, BP 170, F-38042 Grenoble Cedex 9, France
- Laboratoire de Parasitologie-Mycologie, Département des Agents Infectieux, Centre Hospitalier Universitaire, BP
217, 38043 Grenoble cedex 9, France
| | - Mohamed-Ali Hakimi
- Laboratoire Adaptation et Pathogénie des Micro-organismes, Université Joseph Fourier-Grenoble 1, CNRS UMR 5163, BP 170, F-38042 Grenoble Cedex 9, France
| | - Yung-Sing Wong
- Département de Pharmacochimie Moléculaire, Université Joseph Fourier-Grenoble 1, CNRS UMR 5063, CNRS ICMG FR 2607, bâtiment André
Rassat, 470 rue de la Chimie, F-38041 Grenoble Cedex 9, France
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42
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Olsen CA, Montero A, Leman LJ, Ghadiri MR. Macrocyclic peptoid-Peptide hybrids as inhibitors of class I histone deacetylases. ACS Med Chem Lett 2012; 3:749-53. [PMID: 24900543 DOI: 10.1021/ml300162r] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2012] [Accepted: 08/07/2012] [Indexed: 01/04/2023] Open
Abstract
We report the design, synthesis, and biological evaluation of the first macrocyclic peptoid-containing histone deacetylase (HDAC) inhibitors. The compounds selectively inhibit human class I HDAC isoforms in vitro, with no inhibition of the tubulin deacetylase activity associated with class IIb HDAC6 in cultured Jurkat cells. Compared to the natural product apicidin (1), one inhibitor (compound 10) showed equivalent potency against K-562 cells, but was more cytoselective across a panel of cancer cell lines.
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Affiliation(s)
- Christian A. Olsen
- Department of Chemistry and The Skaggs Institute for
Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United
States
| | - Ana Montero
- Department of Chemistry and The Skaggs Institute for
Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United
States
| | - Luke J. Leman
- Department of Chemistry and The Skaggs Institute for
Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United
States
| | - M. Reza Ghadiri
- Department of Chemistry and The Skaggs Institute for
Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United
States
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43
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Madsen AS, Olsen CA. Profiling of Substrates for Zinc-dependent Lysine Deacylase Enzymes: HDAC3 Exhibits Decrotonylase Activity In Vitro. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201203754] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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44
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Madsen AS, Olsen CA. Profiling of substrates for zinc-dependent lysine deacylase enzymes: HDAC3 exhibits decrotonylase activity in vitro. Angew Chem Int Ed Engl 2012; 51:9083-7. [PMID: 22890609 DOI: 10.1002/anie.201203754] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2012] [Revised: 07/19/2012] [Indexed: 12/27/2022]
Abstract
Systematic screening of the activities of the eleven human zinc-dependent lysine deacylases against a series of fluorogenic substrates as well as kinetic evaluation revealed substrates for screenings of histone deacetylases HDAC10 and HDAC11 at reasonably low enzyme concentrations. Furthermore, HDAC3 in complex with nuclear receptor corepressor 1 (HDAC3-NCoR1) was shown to harbor decrotonylase activity in vitro.
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Affiliation(s)
- Andreas S Madsen
- Department of Chemistry, Technical University of Denmark, Kgs. Lyngby, 2800 Denmark
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45
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Vickers CJ, Olsen CA, Leman LJ, Ghadiri MR. Discovery of HDAC Inhibitors That Lack an Active Site Zn(2+)-Binding Functional Group. ACS Med Chem Lett 2012; 3:505-8. [PMID: 24900500 DOI: 10.1021/ml300081u] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2012] [Accepted: 04/26/2012] [Indexed: 01/06/2023] Open
Abstract
Natural and synthetic histone deacetylase (HDAC) inhibitors generally derive their strong binding affinity and high potency from a key functional group that binds to the Zn(2+) ion within the enzyme active site. However, this feature is also thought to carry the potential liability of undesirable off-target interactions with other metalloenzymes. As a step toward mitigating this issue, here, we describe the design, synthesis, and structure-activity characterizations of cyclic α3β-tetrapeptide HDAC inhibitors that lack the presumed indispensable Zn(2+)-binding group. The lead compounds (e.g., 15 and 26) display good potency against class 1 HDACs and are active in tissue culture against various human cancer cell lines. Importantly, enzymological analysis of 26 indicates that the cyclic α3β-tetrapeptide is a fast-on/off competitive inhibitor of HDACs 1-3 with K i values of 49, 33, and 37 nM, respectively. Our proof of principle study supports the idea that novel classes of HDAC inhibitors, which interact at the active-site opening, but not with the active site Zn(2+), can have potential in drug design.
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Affiliation(s)
- Chris J. Vickers
- Department of Chemistry and The Skaggs Institute for
Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United
States
| | - Christian A. Olsen
- Department of Chemistry and The Skaggs Institute for
Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United
States
| | - Luke J. Leman
- Department of Chemistry and The Skaggs Institute for
Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United
States
| | - M. Reza Ghadiri
- Department of Chemistry and The Skaggs Institute for
Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United
States
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46
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White CJ, Yudin AK. A versatile scaffold for site-specific modification of cyclic tetrapeptides. Org Lett 2012; 14:2898-901. [PMID: 22612626 DOI: 10.1021/ol301178r] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
A novel scaffold that can be used to prepare conformationally homogeneous cyclic tetrapeptides equipped with a β-amino acid residue is disclosed. It is shown that regioselective structural modification can be accomplished using thiols and azide nucleophiles, commonly associated with rich downstream chemistry. The method should find application in efforts to constrain privileged tripeptide sequences in rigid molecular scaffolds.
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Affiliation(s)
- Christopher J White
- Davenport Research Laboratories, Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario, M5S 3H6, Canada
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47
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Rudat J, Brucher BR, Syldatk C. Transaminases for the synthesis of enantiopure beta-amino acids. AMB Express 2012; 2:11. [PMID: 22293122 PMCID: PMC3281772 DOI: 10.1186/2191-0855-2-11] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2012] [Accepted: 01/31/2012] [Indexed: 11/29/2022] Open
Abstract
Optically pure β-amino acids constitute interesting building blocks for peptidomimetics and a great variety of pharmaceutically important compounds. Their efficient synthesis still poses a major challenge. Transaminases (also known as aminotransferases) possess a great potential for the synthesis of optically pure β-amino acids. These pyridoxal 5'-dependent enzymes catalyze the transfer of an amino group from a donor substrate to an acceptor, thus enabling the synthesis of a wide variety of chiral amines and amino acids. Transaminases can be applied either for the kinetic resolution of racemic compounds or the asymmetric synthesis starting from a prochiral substrate. This review gives an overview over microbial transaminases with activity towards β-amino acids and their substrate spectra. It also outlines current strategies for the screening of new biocatalysts. Particular emphasis is placed on activity assays which are applicable to high-throughput screening.
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48
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Sharma A, Sharma S, Tripathi RP, Ampapathi RS. Robust Turn Structures in α3β Cyclic Tetrapeptides Induced and Controlled by Carbo-β3 Amino Acid. J Org Chem 2012; 77:2001-7. [DOI: 10.1021/jo2019834] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Anindra Sharma
- Divisions
of Medicinal and Process Chemistry and ‡NMR Centre, SAIF, Central Drug Research Institute (CSIR), Lucknow-226001,
India
| | - Shrikant Sharma
- Divisions
of Medicinal and Process Chemistry and ‡NMR Centre, SAIF, Central Drug Research Institute (CSIR), Lucknow-226001,
India
| | - Rama P. Tripathi
- Divisions
of Medicinal and Process Chemistry and ‡NMR Centre, SAIF, Central Drug Research Institute (CSIR), Lucknow-226001,
India
| | - Ravi Sankar Ampapathi
- Divisions
of Medicinal and Process Chemistry and ‡NMR Centre, SAIF, Central Drug Research Institute (CSIR), Lucknow-226001,
India
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49
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Ha K, Monbaliu JCM, Williams BC, Pillai GG, Ocampo CE, Zeller M, Stevens CV, Katritzky AR. A convenient synthesis of difficult medium-sized cyclic peptides by Staudinger mediated ring-closure. Org Biomol Chem 2012; 10:8055-8. [DOI: 10.1039/c2ob25996f] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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50
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Hutt DM, Olsen CA, Vickers CJ, Herman D, Chalfant MA, Montero A, Leman LJ, Burkle R, Maryanoff BE, Balch WE, Ghadiri MR. Potential Agents for Treating Cystic Fibrosis: Cyclic Tetrapeptides that Restore Trafficking and Activity of ΔF508-CFTR. ACS Med Chem Lett 2011; 2:703-707. [PMID: 21984958 DOI: 10.1021/ml200136e] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Cystic fibrosis (CF) is a loss-of-function disease caused by mutations in the CF transmembrane conductance regulator (CFTR) protein, a chloride ion channel that localizes to the apical plasma membrane of epithelial cells. The most common form of the disease results from the deletion of phenylalanine-508 (ΔF508), leading to the accumulation of CFTR in the endoplasmic reticulum with a concomitant loss of chloride flux. We discovered that cyclic tetrapeptides, such as 11, 14, and 15, are able to correct the trafficking defect and restore cell surface activity of ΔF508-CFTR. Although this class of cyclic tetrapeptides is known to contain inhibitors of certain histone deacetylase (HDAC) isoforms, their HDAC inhibitory potencies did not directly correlate with their ability to rescue ΔF508-CFTR. In full HDAC profiling, 15 strongly inhibited HDACs 1, 2, 3, 10 and 11, but not HDACs 4-9. Although 15 had less potent IC(50) values than reference agent vorinostat (2) in HDAC profiling, it was markedly more potent than 2 in rescuing ΔF508-CFTR. We suggest that specific HDACs can have a differential influence on correcting ΔF508-CFTR, which may reflect both deacetylase and protein scaffolding actions.
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Affiliation(s)
- Darren M. Hutt
- Departments of †Cell Biology, ‡Chemical Physiology, and §Chemistry, and ∥The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Christian A. Olsen
- Departments of †Cell Biology, ‡Chemical Physiology, and §Chemistry, and ∥The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Chris J. Vickers
- Departments of †Cell Biology, ‡Chemical Physiology, and §Chemistry, and ∥The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - David Herman
- Departments of †Cell Biology, ‡Chemical Physiology, and §Chemistry, and ∥The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Monica A. Chalfant
- Departments of †Cell Biology, ‡Chemical Physiology, and §Chemistry, and ∥The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Ana Montero
- Departments of †Cell Biology, ‡Chemical Physiology, and §Chemistry, and ∥The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Luke J. Leman
- Departments of †Cell Biology, ‡Chemical Physiology, and §Chemistry, and ∥The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Renner Burkle
- Departments of †Cell Biology, ‡Chemical Physiology, and §Chemistry, and ∥The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Bruce E. Maryanoff
- Departments of †Cell Biology, ‡Chemical Physiology, and §Chemistry, and ∥The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - William E. Balch
- Departments of †Cell Biology, ‡Chemical Physiology, and §Chemistry, and ∥The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - M. Reza Ghadiri
- Departments of †Cell Biology, ‡Chemical Physiology, and §Chemistry, and ∥The Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
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