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Martiren NL, Bajicoff S, Bellizzi Y, Blank VC, Roguin LP, Cornier PG, Mata EG, Delpiccolo CML. Synthetic Strategies Towards the Generation of Penicillin-Containing Hybrids in the Search for Anticancer Activity. Chem Biodivers 2025; 22:e202402198. [PMID: 39264823 DOI: 10.1002/cbdv.202402198] [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: 09/07/2024] [Accepted: 09/12/2024] [Indexed: 09/14/2024]
Abstract
An extended library of hybrids that combined a penicillin derivative with a peptoid moiety was designed and synthetized using either a solid-phase or a mixed solid-phase/solution-phase strategy. The library was further evaluated for antiproliferative activity. While none of the different synthesized compounds showed significant cytotoxicity against a normal cell line, tumor cell results drew several conclusions, when comparing with our reference, the highly active triazolylpeptidyl penicillin derivative, TAF7f. Thus, when the 1,2,3-triazole group was exchanged by its "retro-inverse" analogue, no change was noted in the activity of the hybrids; however, better performance was generally obtained if the triazole is replaced by a glycine moiety. Additionally, the absence of hydrogen bond donor groups decreased the compounds activity, which could explain that, in general, this set of derivatives were less active than their peptide-containing analogues. From this study, is indisputable that, regardless of the type of chain (peptide, peptoid or mixture) attached to penicillin, an isobutyl side chain placed in the position closest to penicillin and a benzyl in the next position are determinant for the activity.
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Affiliation(s)
- Nadia L Martiren
- Instituto de Química Rosario (CONICET-UNR), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, S2002LRK, Rosario, Argentina
| | - Sofia Bajicoff
- Instituto de Química y Fisicoquímica Biológicas (IQUIFIB), Departamento de Química Biológica, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Junín 956, C1113AA, Buenos Aires, Argentina
| | - Yanina Bellizzi
- Instituto de Química y Fisicoquímica Biológicas (IQUIFIB), Departamento de Química Biológica, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Junín 956, C1113AA, Buenos Aires, Argentina
| | - Viviana C Blank
- Instituto de Química y Fisicoquímica Biológicas (IQUIFIB), Departamento de Química Biológica, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Junín 956, C1113AA, Buenos Aires, Argentina
| | - Leonor P Roguin
- Instituto de Química y Fisicoquímica Biológicas (IQUIFIB), Departamento de Química Biológica, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Junín 956, C1113AA, Buenos Aires, Argentina
| | - Patricia G Cornier
- Instituto de Química Rosario (CONICET-UNR), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, S2002LRK, Rosario, Argentina
| | - Ernesto G Mata
- Instituto de Química Rosario (CONICET-UNR), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, S2002LRK, Rosario, Argentina
| | - Carina M L Delpiccolo
- Instituto de Química Rosario (CONICET-UNR), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, S2002LRK, Rosario, Argentina
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2
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Hintzen JCJ, Mecinović J. Peptide-based inhibitors of epigenetic proteins. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2024; 212:25-65. [PMID: 40122647 DOI: 10.1016/bs.pmbts.2024.04.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/25/2025]
Abstract
Epigenetic drug discovery has become an integral part of medicinal chemistry in the past two decades. Targeting epigenetic proteins-enzymes that modify histone proteins and DNA (writers and erasers) and proteins that recognize such modifications (readers)-has been firmly established as a medicinal strategy for treatment of many human diseases, including cancer and neurological disorders. In this chapter, we systematically describe peptide-based inhibitors of structurally and functionally diverse classes of epigenetic proteins. We show that epigenetic writers, such as DNA methyltransferases, histone methyltransferases and histone acetyltransferases, can be efficiently inhibited by peptides possessing nonproteinogenic amino acids. Moreover, the activity of epigenetic erasers, including TET enzymes, histone demethylases, and histone deacetylases, can be selectively modulated by diverse linear and cyclic peptides. Furthermore, we discuss chromatin-binding epigenetic reader proteins that can be inhibited by histone-mimicking peptides. Overall, this chapter highlights that peptides provide an important molecular platform for epigenetic drug discovery programmes in academia and industry.
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Affiliation(s)
- Jordi C J Hintzen
- Department of Chemistry and Molecular Biology, Wallenberg Center for Molecular and Translational Medicine, University of Gothenburg, Göteborg, Sweden.
| | - Jasmin Mecinović
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense, Denmark.
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3
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Feng Y, Qirjollari A, Fawaz MV, Cancilla MT, Gonzalez RJ, Pearson K. Rapid and Definitive Identification of Cyclic Peptide Soft Spots by Isotope-Labeled Reductive Dimethylation and Mass Spectrometry Fragmentation. Anal Chem 2024; 96:7756-7762. [PMID: 38690743 DOI: 10.1021/acs.analchem.4c01372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2024]
Abstract
Cyclic peptides are an emerging therapeutic modality over the past few decades. To identify drug candidates with sufficient proteolytic stability for oral administration, it is critical to pinpoint the amide bond hydrolysis sites, or soft spots, to better understand their metabolism and provide guidance on further structure optimization. However, the unambiguous characterization of cyclic peptide soft spots remains a significant challenge during early stage discovery studies, as amide bond hydrolysis forms a linearized isobaric sequence with the addition of a water molecule, regardless of the amide hydrolysis location. In this study, an innovative strategy was developed to enable the rapid and definitive identification of cyclic peptide soft spots by isotope-labeled reductive dimethylation and mass spectrometry fragmentation. The dimethylated immonium ion with enhanced MS signal at a distinctive m/z in MS/MS fragmentation spectra reveals the N-terminal amino acid on a linearized peptide sequence definitively and, thus, significantly simplifies the soft spot identification workflow. This approach has been evaluated to demonstrate the potential of isotope-labeled dimethylation to be a powerful analytical tool in cyclic peptide drug discovery and development.
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Affiliation(s)
- Yu Feng
- Nonclinical Drug Safety, MRL, Merck & Co., Inc., 770 Sumneytown Pike, West Point, Pennsylvania 19486, United States
| | - Athanasia Qirjollari
- Nonclinical Drug Safety, MRL, Merck & Co., Inc., 770 Sumneytown Pike, West Point, Pennsylvania 19486, United States
| | - Maria V Fawaz
- Pharmacokinetics, Dynamics, Metabolism, and Bioanalytics, MRL, Merck & Co., Inc., 770 Sumneytown Pike, West Point, Pennsylvania 19486, United States
| | - Mark T Cancilla
- Pharmacokinetics, Dynamics, Metabolism, and Bioanalytics, MRL, Merck & Co., Inc., 770 Sumneytown Pike, West Point, Pennsylvania 19486, United States
| | - Raymond J Gonzalez
- Nonclinical Drug Safety, MRL, Merck & Co., Inc., 770 Sumneytown Pike, West Point, Pennsylvania 19486, United States
| | - Kara Pearson
- Nonclinical Drug Safety, MRL, Merck & Co., Inc., 770 Sumneytown Pike, West Point, Pennsylvania 19486, United States
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4
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Zhang C, Liu F, Zhang Y, Song C. Macrocycles and macrocyclization in anticancer drug discovery: Important pieces of the puzzle. Eur J Med Chem 2024; 268:116234. [PMID: 38401189 DOI: 10.1016/j.ejmech.2024.116234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 02/10/2024] [Accepted: 02/11/2024] [Indexed: 02/26/2024]
Abstract
Increasing disease-related proteins have been identified as novel therapeutic targets. Macrocycles are emerging as potential solutions, bridging the gap between conventional small molecules and biomacromolecules in drug discovery. Inspired by successful macrocyclic drugs of natural origins, macrocycles are attracting more attention for enhanced binding affinity and target selectivity. Due to the conformation constraint and structure preorganization, macrocycles can reach bioactive conformations more easily than parent acyclic compounds. Also, rational macrocyclization combined with sequent structural modification will help improve oral bioavailability and combat drug resistance. This review introduces various strategies to enhance membrane permeability in macrocyclization and subsequent modification, such as N-methylation, intramolecular hydrogen bonding modulation, isomerization, and reversible bicyclization. Several case studies highlight macrocyclic inhibitors targeting kinases, HDAC, and protein-protein interactions. Finally, some macrocyclic agents targeting tumor microenvironments are illustrated.
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Affiliation(s)
- Chao Zhang
- Laboratory for Food and Medicine Homologous Natural Resources Development and Utilization, Belgorod College of Food Sciences, Dezhou University, Dezhou, 253023, China
| | - Fenfen Liu
- Laboratory for Food and Medicine Homologous Natural Resources Development and Utilization, Belgorod College of Food Sciences, Dezhou University, Dezhou, 253023, China
| | - Youming Zhang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China.
| | - Chun Song
- Laboratory for Food and Medicine Homologous Natural Resources Development and Utilization, Belgorod College of Food Sciences, Dezhou University, Dezhou, 253023, China; State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China.
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5
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Wang HM, Seo CD, Lee KJ, Park JH, Lim HS. Evaluation of the cell permeability of bicyclic peptoids and bicyclic peptide-peptoid hybrids. Bioorg Chem 2022; 127:105976. [DOI: 10.1016/j.bioorg.2022.105976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 06/14/2022] [Accepted: 06/16/2022] [Indexed: 11/02/2022]
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6
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Affiliation(s)
- Assunta D'Amato
- University of Salerno: Universita degli Studi di Salerno Chemistry and Biology "A. Zambelli" Via Giovanni Paolo II, 132 84084 Fisciano ITALY
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7
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Therapeutic peptides: current applications and future directions. Signal Transduct Target Ther 2022; 7:48. [PMID: 35165272 PMCID: PMC8844085 DOI: 10.1038/s41392-022-00904-4] [Citation(s) in RCA: 751] [Impact Index Per Article: 250.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 01/13/2022] [Accepted: 01/17/2022] [Indexed: 02/08/2023] Open
Abstract
Peptide drug development has made great progress in the last decade thanks to new production, modification, and analytic technologies. Peptides have been produced and modified using both chemical and biological methods, together with novel design and delivery strategies, which have helped to overcome the inherent drawbacks of peptides and have allowed the continued advancement of this field. A wide variety of natural and modified peptides have been obtained and studied, covering multiple therapeutic areas. This review summarizes the efforts and achievements in peptide drug discovery, production, and modification, and their current applications. We also discuss the value and challenges associated with future developments in therapeutic peptides.
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8
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Warnock TMC, Rajkumar S, Fitzpatrick MP, Serpell CJ, Dingwall P, Knipe PC. Chiral, sequence-definable foldamer-derived macrocycles. Chem Sci 2021; 12:15632-15636. [PMID: 35003593 PMCID: PMC8654020 DOI: 10.1039/d1sc05021d] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 11/03/2021] [Indexed: 12/22/2022] Open
Abstract
Nature's oligomeric macromolecules have been a long-standing source of inspiration for chemists producing foldamers. Natural systems are frequently conformationally stabilised by macrocyclisation, yet this approach has been rarely adopted in the field of foldamer chemistry. Here we present a new class of chiral cyclic trimers and tetramers formed by macrocyclisation of open-chain foldamer precursors. Symmetrical products are obtained via a [2 + 2] self-assembly approach, while full sequence control is demonstrated through linear synthesis and cyclisation of an unsymmetrical trimer. Structural characterisation is achieved through a combined X-ray and DFT approach, which indicates the tetramers adopt a near-planar conformation, while the trimers adopt a shallow bowl-like shape. Finally, a proof-of-concept experiment is conducted to demonstrate the macrocycles' capacity for cation binding. Dipole-controlled pre-organization enables the cyclization of sequence-defined foldamers into macrocycles. The structure and properties of trimeric and tetrameric macrocycles are explored, and their ability to bind cationic guests is demonstrated.![]()
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Affiliation(s)
- Toyah M C Warnock
- School of Chemistry and Chemical Engineering, Queen's University Belfast David Keir Building Belfast BT9 5AG UK
| | | | - Matthew P Fitzpatrick
- School of Chemistry and Chemical Engineering, Queen's University Belfast David Keir Building Belfast BT9 5AG UK
| | - Christopher J Serpell
- School of Physical Sciences, University of Kent Ingram Building Canterbury Kent CT2 7NH UK
| | - Paul Dingwall
- School of Chemistry and Chemical Engineering, Queen's University Belfast David Keir Building Belfast BT9 5AG UK
| | - Peter C Knipe
- School of Chemistry and Chemical Engineering, Queen's University Belfast David Keir Building Belfast BT9 5AG UK
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9
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Herlan CN, Sonnefeld A, Gloge T, Brückel J, Schlee LC, Muhle-Goll C, Nieger M, Bräse S. Macrocyclic Tetramers-Structural Investigation of Peptide-Peptoid Hybrids. Molecules 2021; 26:molecules26154548. [PMID: 34361700 PMCID: PMC8348019 DOI: 10.3390/molecules26154548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 07/23/2021] [Accepted: 07/24/2021] [Indexed: 11/16/2022] Open
Abstract
Outstanding affinity and specificity are the main characteristics of peptides, rendering them interesting compounds for basic and medicinal research. However, their biological applicability is limited due to fast proteolytic degradation. The use of mimetic peptoids overcomes this disadvantage, though they lack stereochemical information at the α-carbon. Hybrids composed of amino acids and peptoid monomers combine the unique properties of both parent classes. Rigidification of the backbone increases the affinity towards various targets. However, only little is known about the spatial structure of such constrained hybrids. The determination of the three-dimensional structure is a key step for the identification of new targets as well as the rational design of bioactive compounds. Herein, we report the synthesis and the structural elucidation of novel tetrameric macrocycles. Measurements were taken in solid and solution states with the help of X-ray scattering and NMR spectroscopy. The investigations made will help to find diverse applications for this new, promising compound class.
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Affiliation(s)
- Claudine Nicole Herlan
- Institute of Organic Chemistry, Karlsruhe Institute of Technology, Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany; (C.N.H.); (J.B.); (L.C.S.)
| | - Anna Sonnefeld
- Institute for Biological Interfaces 4, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany; (A.S.); (T.G.); (C.M.-G.)
| | - Thomas Gloge
- Institute for Biological Interfaces 4, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany; (A.S.); (T.G.); (C.M.-G.)
| | - Julian Brückel
- Institute of Organic Chemistry, Karlsruhe Institute of Technology, Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany; (C.N.H.); (J.B.); (L.C.S.)
| | - Luisa Chiara Schlee
- Institute of Organic Chemistry, Karlsruhe Institute of Technology, Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany; (C.N.H.); (J.B.); (L.C.S.)
| | - Claudia Muhle-Goll
- Institute for Biological Interfaces 4, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany; (A.S.); (T.G.); (C.M.-G.)
| | - Martin Nieger
- Department of Chemistry, University of Helsinki, P.O. Box 55 (A.I. Virtasen aukio 1), FIN-00014 Helsinki, Finland;
| | - Stefan Bräse
- Institute of Organic Chemistry, Karlsruhe Institute of Technology, Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany; (C.N.H.); (J.B.); (L.C.S.)
- Institute of Biological and Chemical Systems—Functional Molecular Systems, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
- Correspondence:
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10
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Melesina J, Simoben CV, Praetorius L, Bülbül EF, Robaa D, Sippl W. Strategies To Design Selective Histone Deacetylase Inhibitors. ChemMedChem 2021; 16:1336-1359. [PMID: 33428327 DOI: 10.1002/cmdc.202000934] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Indexed: 12/15/2022]
Abstract
This review classifies drug-design strategies successfully implemented in the development of histone deacetylase (HDAC) inhibitors, which have many applications including cancer treatment. Our focus is on especially demanded selective HDAC inhibitors and their structure-activity relationships in relation to corresponding protein structures. The main part of the paper is divided into six subsections each narrating how optimization of one of six structural features can influence inhibitor selectivity. It starts with the impact of the zinc binding group on selectivity, continues with the optimization of the linker placed in the substrate binding tunnel as well as the adjustment of the cap group interacting with the surface of the protein, and ends with the addition of groups targeting class-specific sub-pockets: the side-pocket-, lower-pocket- and foot-pocket-targeting groups. The review is rounded off with a conclusion and an outlook on the future of HDAC inhibitor design.
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Affiliation(s)
- Jelena Melesina
- Institute of Pharmacy, Martin Luther University of Halle - Wittenberg, Kurt Mothes Straße 3, 06120, Halle (Saale), Germany
| | - Conrad V Simoben
- Institute of Pharmacy, Martin Luther University of Halle - Wittenberg, Kurt Mothes Straße 3, 06120, Halle (Saale), Germany
| | - Lucas Praetorius
- Institute of Pharmacy, Martin Luther University of Halle - Wittenberg, Kurt Mothes Straße 3, 06120, Halle (Saale), Germany
| | - Emre F Bülbül
- Institute of Pharmacy, Martin Luther University of Halle - Wittenberg, Kurt Mothes Straße 3, 06120, Halle (Saale), Germany
| | - Dina Robaa
- Institute of Pharmacy, Martin Luther University of Halle - Wittenberg, Kurt Mothes Straße 3, 06120, Halle (Saale), Germany
| | - Wolfgang Sippl
- Institute of Pharmacy, Martin Luther University of Halle - Wittenberg, Kurt Mothes Straße 3, 06120, Halle (Saale), Germany
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11
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Affiliation(s)
- Francesco De Riccardis
- Department of Chemistry and Biology “A. Zambelli”; University of Salerno; Via Giovani Paolo II, 132 84084 Fisciano SA Italy
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12
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Solid-Phase Insertion of N-mercaptoalkylglycine Residues into Peptides. Molecules 2019; 24:molecules24234261. [PMID: 31766740 PMCID: PMC6930625 DOI: 10.3390/molecules24234261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 11/18/2019] [Accepted: 11/20/2019] [Indexed: 11/18/2022] Open
Abstract
N-mercaptoalkylglycine residues were inserted into peptides by reacting N-free amino groups of peptides, which were initially synthesized on 2-chlorotrityl resin (Cltr) using the Fmoc/tBu method, with bromoacetic acid and subsequent nucleophilic replacement of the bromide by reacting with S-4-methoxytrityl- (Mmt)/S-trityl- (Trt) protected aminothiols. The synthesized thiols containing peptide–peptoid hybrids were cleaved from the resin, either protected by treatment with dichloromethane (DCM)/trifluoroethanol (TFE)/acetic acid (AcOH) (7:2:1), or deprotected (fully or partially) by treatment with trifluoroacetic acid (TFA) solution using triethylsilane (TES) as a scavenger.
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13
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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: 1.8] [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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14
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Abstract
Over the past two decades, developing medical applications for peptides has, and continues to be a highly active area of research. At present there are over 60 peptide-based drugs on the market and more than 140 in various stages of clinical trials. The interest in peptide-based therapeutics arises from their biocompatibility and their ability to form defined secondary and tertiary structures, resulting in a high selectivity for complex targets. However, there are significant challenges associated with the development of peptide-based therapeutics, namely peptides are readily metabolised in vivo. Peptoids are an emerging class of peptidomimetic and they offer an alternative to peptides. Peptoids are comprised of N-substituted glycines where side-chains are located on the nitrogen atom of the amide backbone rather than the α-carbon as is the case in peptides. This change in structure confers a high degree of resistance to proteolytic degradation but the absence of any backbone hydrogen bonding means that peptoids exhibit a high degree of conformational flexibility. Cyclisation has been explored as one possible route to rigidify peptoid structures, making them more selective, and, therefore more desirable as potential therapeutics. This review outlines the various strategies that have been developed over the last decade to access new types of macrocyclic peptoids.
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Affiliation(s)
| | - Steven L. Cobb
- Department of ChemistryDurham UniversitySouth RoadDurhamDH1 3LEUK
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15
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Boehm M, Beaumont K, Jones R, Kalgutkar AS, Zhang L, Atkinson K, Bai G, Brown JA, Eng H, Goetz GH, Holder BR, Khunte B, Lazzaro S, Limberakis C, Ryu S, Shapiro MJ, Tylaska L, Yan J, Turner R, Leung SSF, Ramaseshan M, Price DA, Liras S, Jacobson MP, Earp DJ, Lokey RS, Mathiowetz AM, Menhaji-Klotz E. Discovery of Potent and Orally Bioavailable Macrocyclic Peptide-Peptoid Hybrid CXCR7 Modulators. J Med Chem 2017; 60:9653-9663. [PMID: 29045152 DOI: 10.1021/acs.jmedchem.7b01028] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The chemokine receptor CXCR7 is an attractive target for a variety of diseases. While several small-molecule modulators of CXCR7 have been reported, peptidic macrocycles may provide advantages in terms of potency, selectivity, and reduced off-target activity. We produced a series of peptidic macrocycles that incorporate an N-linked peptoid functionality where the peptoid group enabled us to explore side-chain diversity well beyond that of natural amino acids. At the same time, theoretical calculations and experimental assays were used to track and reduce the polarity while closely monitoring the physicochemical properties. This strategy led to the discovery of macrocyclic peptide-peptoid hybrids with high CXCR7 binding affinities (Ki < 100 nM) and measurable passive permeability (Papp > 5 × 10-6 cm/s). Moreover, bioactive peptide 25 (Ki = 9 nM) achieved oral bioavailability of 18% in rats, which was commensurate with the observed plasma clearance values upon intravenous administration.
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Affiliation(s)
- Markus Boehm
- Pfizer Worldwide Research & Development , Cambridge, Massachusetts 02139, United States
| | - Kevin Beaumont
- Pfizer Worldwide Research & Development , Cambridge, Massachusetts 02139, United States
| | - Rhys Jones
- Pfizer Worldwide Research & Development , Cambridge, Massachusetts 02139, United States
| | - Amit S Kalgutkar
- Pfizer Worldwide Research & Development , Cambridge, Massachusetts 02139, United States
| | - Liying Zhang
- Pfizer Worldwide Research & Development , Cambridge, Massachusetts 02139, United States
| | - Karen Atkinson
- Pfizer Worldwide Research & Development , Groton, Connecticut 06340, United States
| | - Guoyun Bai
- Pfizer Worldwide Research & Development , Groton, Connecticut 06340, United States
| | - Janice A Brown
- Pfizer Worldwide Research & Development , Groton, Connecticut 06340, United States
| | - Heather Eng
- Pfizer Worldwide Research & Development , Groton, Connecticut 06340, United States
| | - Gilles H Goetz
- Pfizer Worldwide Research & Development , Groton, Connecticut 06340, United States
| | - Brian R Holder
- Pfizer Worldwide Research & Development , Groton, Connecticut 06340, United States
| | - Bhagyashree Khunte
- Pfizer Worldwide Research & Development , Groton, Connecticut 06340, United States
| | - Sarah Lazzaro
- Pfizer Worldwide Research & Development , Groton, Connecticut 06340, United States
| | - Chris Limberakis
- Pfizer Worldwide Research & Development , Groton, Connecticut 06340, United States
| | - Sangwoo Ryu
- Pfizer Worldwide Research & Development , Groton, Connecticut 06340, United States
| | - Michael J Shapiro
- Pfizer Worldwide Research & Development , Groton, Connecticut 06340, United States
| | - Laurie Tylaska
- Pfizer Worldwide Research & Development , Groton, Connecticut 06340, United States
| | - Jiangli Yan
- Pfizer Worldwide Research & Development , Groton, Connecticut 06340, United States
| | - Rushia Turner
- Chemistry and Biochemistry, University of California , Santa Cruz, California 95064, United States
| | - Siegfried S F Leung
- Department of Pharmaceutical Chemistry, University of California , San Francisco, California 94158, United States.,Circle Pharma , South San Francisco, California 94080, United States
| | - Mahesh Ramaseshan
- Circle Pharma , South San Francisco, California 94080, United States
| | - David A Price
- Pfizer Worldwide Research & Development , Cambridge, Massachusetts 02139, United States
| | - Spiros Liras
- Pfizer Worldwide Research & Development , Cambridge, Massachusetts 02139, United States
| | - Matthew P Jacobson
- Department of Pharmaceutical Chemistry, University of California , San Francisco, California 94158, United States
| | - David J Earp
- Circle Pharma , South San Francisco, California 94080, United States
| | - R Scott Lokey
- Chemistry and Biochemistry, University of California , Santa Cruz, California 95064, United States
| | - Alan M Mathiowetz
- Pfizer Worldwide Research & Development , Cambridge, Massachusetts 02139, United States
| | - Elnaz Menhaji-Klotz
- Pfizer Worldwide Research & Development , Cambridge, Massachusetts 02139, United States
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16
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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: 3.4] [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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17
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Furukawa A, Townsend CE, Schwochert J, Pye CR, Bednarek MA, Lokey RS. Passive Membrane Permeability in Cyclic Peptomer Scaffolds Is Robust to Extensive Variation in Side Chain Functionality and Backbone Geometry. J Med Chem 2016; 59:9503-9512. [PMID: 27690434 DOI: 10.1021/acs.jmedchem.6b01246] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Synthetic and natural cyclic peptides provide a testing ground for studying membrane permeability in nontraditional drug scaffolds. Cyclic peptomers, which incorporate peptide and N-alkylglycine (peptoid) residues, combine the stereochemical and geometric complexity of peptides with the functional group diversity accessible to peptoids. We synthesized cyclic peptomer libraries by split-pool techniques, separately permuting side chain and backbone geometry, and analyzed their membrane permeabilities using the parallel artificial membrane permeability assay. Nearly half of the side chain permutations had permeability coefficients (Papp) > 1 × 10-6 cm/s. Some backbone geometries enhanced permeability due to their ability to form more stable intramolecular hydrogen bond networks compared with other scaffolds. These observations suggest that hexameric cyclic peptomers can have good passive permeability even in the context of extensive side chain and backbone variation, and that high permeability can generally be achieved within a relatively wide lipophilicity range.
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Affiliation(s)
- Akihiro Furukawa
- Department of Chemistry and Biochemistry, University of California, Santa Cruz , 1156 High Street, Santa Cruz, California 95064, United States.,Modality Research Laboratories, Daiichi Sankyo Co., Ltd. , 1-2-58 Hiromachi, Shinagawa-ku, Tokyo 140-8710, Japan
| | - Chad E Townsend
- Department of Chemistry and Biochemistry, University of California, Santa Cruz , 1156 High Street, Santa Cruz, California 95064, United States
| | - Joshua Schwochert
- Department of Chemistry and Biochemistry, University of California, Santa Cruz , 1156 High Street, Santa Cruz, California 95064, United States
| | - Cameron R Pye
- Department of Chemistry and Biochemistry, University of California, Santa Cruz , 1156 High Street, Santa Cruz, California 95064, United States
| | - Maria A Bednarek
- Department of Antibody Discovery & Protein Engineering, Medimmune Ltd. , Cambridge CB21 6GH, United Kingdom
| | - R Scott Lokey
- Department of Chemistry and Biochemistry, University of California, Santa Cruz , 1156 High Street, Santa Cruz, California 95064, United States
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18
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Li Y, Seto E. HDACs and HDAC Inhibitors in Cancer Development and Therapy. Cold Spring Harb Perspect Med 2016; 6:cshperspect.a026831. [PMID: 27599530 DOI: 10.1101/cshperspect.a026831] [Citation(s) in RCA: 845] [Impact Index Per Article: 93.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Over the last several decades, it has become clear that epigenetic abnormalities may be one of the hallmarks of cancer. Posttranslational modifications of histones, for example, may play a crucial role in cancer development and progression by modulating gene transcription, chromatin remodeling, and nuclear architecture. Histone acetylation, a well-studied posttranslational histone modification, is controlled by the opposing activities of histone acetyltransferases (HATs) and histone deacetylases (HDACs). By removing acetyl groups, HDACs reverse chromatin acetylation and alter transcription of oncogenes and tumor suppressor genes. In addition, HDACs deacetylate numerous nonhistone cellular substrates that govern a wide array of biological processes including cancer initiation and progression. This review will discuss the role of HDACs in cancer and the therapeutic potential of HDAC inhibitors (HDACi) as emerging drugs in cancer treatment.
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Affiliation(s)
- Yixuan Li
- George Washington University Cancer Center, Department of Biochemistry and Molecular Medicine, George Washington University, Washington, DC 20037
| | - Edward Seto
- George Washington University Cancer Center, Department of Biochemistry and Molecular Medicine, George Washington University, Washington, DC 20037
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19
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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: 1.4] [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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20
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Mukherjee S, Zhou G, Michel C, Voelz VA. Insights into Peptoid Helix Folding Cooperativity from an Improved Backbone Potential. J Phys Chem B 2015; 119:15407-17. [PMID: 26584227 DOI: 10.1021/acs.jpcb.5b09625] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Peptoids (N-substituted oligoglycines) are biomimetic polymers that can fold into a variety of unique structural scaffolds. Peptoid helices, which result from the incorporation of bulky chiral side chains, are a key peptoid structural motif whose formation has not yet been accurately modeled in molecular simulations. Here, we report that a simple modification of the backbone φ-angle potential in GAFF is able to produce well-folded cis-amide helices of (S)-N-(1-phenylethyl)glycine (Nspe), consistent with experiment. We validate our results against both QM calculations and NMR experiments. For this latter task, we make quantitative comparisons to sparse NOE data using the Bayesian Inference of Conformational Populations (BICePs) algorithm, a method we have recently developed for this purpose. We then performed extensive REMD simulations of Nspe oligomers as a function of chain length and temperature to probe the molecular forces driving cooperative helix formation. Analysis of simulation data by Lifson-Roig helix-coil theory show that the modified potential predicts much more cooperative folding for Nspe helices. Unlike peptides, per-residue entropy changes for helix nucleation and extension are mostly positive, suggesting that steric bulk provides the main driving force for folding. We expect these results to inform future work aimed at predicting and designing peptoid peptidomimetics and tertiary assemblies of peptoid helices.
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Affiliation(s)
- Sudipto Mukherjee
- Department of Chemistry, Temple University , Philadelphia, Pennsylvania 19122, United States
| | - Guangfeng Zhou
- Department of Chemistry, Temple University , Philadelphia, Pennsylvania 19122, United States
| | - Chris Michel
- Department of Chemistry, Temple University , Philadelphia, Pennsylvania 19122, United States
| | - Vincent A Voelz
- Department of Chemistry, Temple University , Philadelphia, Pennsylvania 19122, United States
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21
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Abstract
For a long time, peptides were considered unsuitable for drug development due to their inherently poor pharmacokinetic properties and proteolytic susceptibility. However, this paradigm has changed significantly in the past decade with the approval of numerous antibodies and proteins as drugs. In parallel, research in the field of synthetic molecules that are able to mimic or complement folding patterns exhibited by biopolymers, but are not recognized by proteases, have received considerable attention as well. Such entities were coined "foldamers" by Professor Gellman in an Account published in this journal in the late 1990s. Oligomers of N-alkylated 3-aminopropionic acid residues have been called β-peptoids due to their structural similarity to β-peptides and peptoids (N-alkylglycines), respectively. Because bona fide foldamer behavior has been demonstrated for both parent architectures, we wondered if the β-peptoids could serve as a successful addition to the known ensemble of peptidomimetic foldamers. When we entered this field, only the seminal description of libraries of β-peptoid dimers and trimers by Hamper et al. had been published a number of years earlier [ J. Org. Chem. 1998 , 63 , 708 ]. Perhaps somewhat naïvely in retrospect, we envisioned that elongation of chain length combined with introduction of bulky α-chiral side chains would deliver folded structures as reported for the α-peptoid counterparts. Initially, we, and others, were unsucessful in obtaining stable secondary structures of β-peptoid oligomers, and instead, these residues were either incorporated in cyclic structures or in combination with other types of residues to give peptidomimetic constructs with heterogeneous backbones. Amphiphilic architectures with various membrane-targeting activities, such as mimics of antimicrobial peptides or cell-penetrating peptides, have thus been particularly successful. Introduction of β-peptoid residues in histone deacetylase inhibitors mimicking nonribosomal cyclotetrapeptides have also been reported. In the present Account, we will sketch the scientific journey that ultimately delivered robustly folded β-peptoid oligomers. Contributions involving biological evaluation of peptidomimetic constructs containing β-peptoid residues, as mentioned above, which were investigated leading up to these recently reported high-resolution helical structures, will thus be discussed. On the basis of the work described in this Account, we envision that β-peptoids will find future utility as peptidomimetics for biomedical investigation containing both heterogeneous and homogeneous backbones. The recent demonstration of control over the secondary structure of a homogeneous β-peptoid backbone now enables structure-based design of scaffolds with predictable display of desired functionalities in three dimensions.
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Affiliation(s)
- Jonas S. Laursen
- Center for Biopharmaceuticals & Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, DK-2100, Copenhagen, Denmark
| | - Jens Engel-Andreasen
- Center for Biopharmaceuticals & Department of Drug Design and Pharmacology, University of Copenhagen, Universitetsparken 2, DK-2100, Copenhagen, Denmark
| | - 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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22
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Schwochert J, Turner R, Thang M, Berkeley RF, Ponkey AR, Rodriguez KM, Leung SSF, Khunte B, Goetz G, Limberakis C, Kalgutkar AS, Eng H, Shapiro MJ, Mathiowetz AM, Price DA, Liras S, Jacobson MP, Lokey RS. Peptide to Peptoid Substitutions Increase Cell Permeability in Cyclic Hexapeptides. Org Lett 2015; 17:2928-31. [PMID: 26046483 DOI: 10.1021/acs.orglett.5b01162] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The effect of peptide-to-peptoid substitutions on the passive membrane permeability of an N-methylated cyclic hexapeptide is examined. In general, substitutions maintained permeability but increased conformational heterogeneity. Diversification with nonproteinogenic side chains increased permeability up to 3-fold. Additionally, the conformational impact of peptoid substitutions within a β-turn are explored. Based on these results, the strategic incorporation of peptoid residues into cyclic peptides can maintain or improve cell permeability, while increasing access to diverse side-chain functionality.
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Affiliation(s)
- Joshua Schwochert
- †Chemistry and Biochemistry University of California, Santa Cruz, California 95064, United States
| | - Rushia Turner
- †Chemistry and Biochemistry University of California, Santa Cruz, California 95064, United States
| | - Melissa Thang
- †Chemistry and Biochemistry University of California, Santa Cruz, California 95064, United States
| | - Ray F Berkeley
- †Chemistry and Biochemistry University of California, Santa Cruz, California 95064, United States
| | - Alexandra R Ponkey
- †Chemistry and Biochemistry University of California, Santa Cruz, California 95064, United States
| | - Kelsie M Rodriguez
- †Chemistry and Biochemistry University of California, Santa Cruz, California 95064, United States
| | - Siegfried S F Leung
- ‡Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158, United States
| | - Bhagyashree Khunte
- ∥World Wide Medicinal Chemistry, Groton Laboratories, Pfizer Inc. Groton, Connecticut 06340, United States
| | - Gilles Goetz
- ∥World Wide Medicinal Chemistry, Groton Laboratories, Pfizer Inc. Groton, Connecticut 06340, United States
| | - Chris Limberakis
- ∥World Wide Medicinal Chemistry, Groton Laboratories, Pfizer Inc. Groton, Connecticut 06340, United States
| | - Amit S Kalgutkar
- §Pharmacokinetics and Drug Metabolism, Cambridge Laboratories, Pfizer Inc. Cambridge, Massachusetts 02139, United States
| | - Heather Eng
- ⊥Pharmacokinetics and Drug Metabolism, Groton Laboratories, Pfizer Inc. Groton, Connecticut 06340, United States
| | - Michael J Shapiro
- ∥World Wide Medicinal Chemistry, Groton Laboratories, Pfizer Inc. Groton, Connecticut 06340, United States
| | - Alan M Mathiowetz
- ○World Wide Medicinal Chemistry, Cambridge Laboratories, Pfizer Inc. Cambridge, Massachusetts 02139, United States
| | - David A Price
- ○World Wide Medicinal Chemistry, Cambridge Laboratories, Pfizer Inc. Cambridge, Massachusetts 02139, United States
| | - Spiros Liras
- ○World Wide Medicinal Chemistry, Cambridge Laboratories, Pfizer Inc. Cambridge, Massachusetts 02139, United States
| | - Matthew P Jacobson
- ‡Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94158, United States
| | - R Scott Lokey
- †Chemistry and Biochemistry University of California, Santa Cruz, California 95064, United States
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23
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Lee KJ, Lim HS. Facile Method To Sequence Cyclic Peptides/Peptoids via One-Pot Ring-Opening/Cleavage Reaction. Org Lett 2014; 16:5710-3. [DOI: 10.1021/ol502788e] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Kang Ju Lee
- Department of Chemistry, Pohang University of Science and Technology (POSTECH), Pohang 790-784, South Korea
| | - Hyun-Suk Lim
- Department of Chemistry, Pohang University of Science and Technology (POSTECH), Pohang 790-784, South Korea
- Department of Biochemistry and Molecular
Biology, Indiana University School of Medicine, Indianapolis, Indiana 46202, United States
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24
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25
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Structure-Activity Relationship Study of Spider Polyamine Toxins as Inhibitors of Ionotropic Glutamate Receptors. ChemMedChem 2014; 9:2661-70. [DOI: 10.1002/cmdc.201402278] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2014] [Indexed: 12/14/2022]
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26
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Culf AS, Čuperlović-Culf M, Léger DA, Decken A. Small head-to-tail macrocyclic α-peptoids. Org Lett 2014; 16:2780-3. [PMID: 24797336 DOI: 10.1021/ol501102b] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
A convenient and efficient methodology for the head-to-tail macrocyclization of small 3-mer, 4-mer, and 5-mer α-peptoid acids (9-, 12-, and 15-atom N-substituted glycine oligomers) is described. The cyclic trimer has a ccc amide sequence in the crystal structure, whereas the tetramer has ctct and the pentamer has ttccc stereochemistry. NMR analysis reveals rigid structures in solution. These synthetic macrocycles may prove useful in medicinal and materials applications.
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Affiliation(s)
- Adrian S Culf
- Atlantic Cancer Research Institute , 35 Providence Street, Moncton, NB E1C 8X3, Canada
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27
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Wałęsa R, Broda MA. Solvent effects on the conformational preferences of model peptoids. MP2 study. J Pept Sci 2014; 20:203-11. [PMID: 24520015 DOI: 10.1002/psc.2601] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2013] [Revised: 11/12/2013] [Accepted: 11/22/2013] [Indexed: 01/04/2023]
Abstract
The influence of aqueous environment on the main-chain conformation (ω0 , ϕ, and ψ dihedral angles) of two model peptoids: N-acetyl-N-methylglycine N'-methylamide (Ac-N(Me)-Gly-NHMe) (1) and N-acetyl-N-methylglycine N',N'-dimethylamide (Ac-N(Me)-Gly-NMe₂) (2) was investigated by MP2/6-311++G(d,p) method. The Ramachandran maps of both studied molecules with cis and trans configuration of the N-terminal amide bond in the gas phase and in water environment were obtained and all energy minima localized. The polarizable continuum model was applied to estimate the solvation effect on conformation. Energy minima of the Ac-N(Me)-Gly-NHMe and Ac-N(Me)-Gly-NMe₂ have been analyzed in terms of the possible hydrogen bonds and C = O dipole attraction. To validate the theoretical results obtained, conformations of the similar structures gathered in the Cambridge Crystallographic Data Centre were analyzed. Obtained results indicate that aqueous environment in model peptoids 1 and 2 favors the conformation F (ϕ and ψ = -70º, 180º), and additionally significantly increases the percentage of structures with cis configuration of N-terminal amide bond in studied compounds.
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28
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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: 1.4] [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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29
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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: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2013] [Indexed: 12/21/2022]
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30
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Lawson KV, Rose TE, Harran PG. Template-induced macrocycle diversity through large ring-forming alkylations of tryptophan. Tetrahedron 2013; 69:7683-7691. [PMID: 23976797 DOI: 10.1016/j.tet.2013.05.060] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Macrocyclic peptidomimetics are valuable in research and serve as lead compounds in drug discovery efforts. New methods to prepare such structures are of considerable interest. In this pilot study, we show that an organic template harboring a latent cinnamyl cation participates in novel Friedel-Crafts macrocyclization reactions with tryptophan. Upon joining the template to Trp-Trp-Tyr, a single operation efficiently generates eight unique macrocycles. Each has been isolated and thoroughly characterized. Product distribution as a function of Brønsted and/or Lewis acidic conditions was explored, and outcomes were compared to rearrangements induced within a corresponding tyrosine-linked cyclic ether. The solution structure of a new macrocyclic pyrroloindoline was solved using a combination of two-dimensional NMR methods and molecular mechanics simulations. Template-induced structural diversification of peptide sequences harboring aromatic residues has potential to create myriad macrocycles that target surfaces involved in protein-protein interactions.
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Affiliation(s)
- Kenneth V Lawson
- Department of Chemistry and Biochemistry, University of California Los Angeles, 607 Charles E. Young Drive East, Los Angeles, CA 90095-1569 (USA)
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31
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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: 2.3] [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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32
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Zhang Y, Yang P, Chou CJ, Liu C, Wang X, Xu W. Development of N-Hydroxycinnamamide-Based Histone Deacetylase Inhibitors with Indole-Containing Cap Group. ACS Med Chem Lett 2013; 4:235-238. [PMID: 23493449 DOI: 10.1021/ml300366t] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
A novel series of histone deacetylase inhibitors combining N-hydroxycinnamamide bioactive fragment and indole bioactive fragment was designed and synthesized. Several compounds (17c, 17g, 17h, 17j and 17k) exhibited comparable even superior total HDACs inhibitory activity and in vitro antiproliferative activities relative to the approved drug SAHA. A representative compound 17a with moderate HDACs inhibition was progressed to isoform selectivity profile, western blot analysis and in vivo antitumor assay. Although HDACs isoform selectivity of 17a was similar to that of SAHA, our western blot results indicated that intracellular effects of 17a at 1 μM were class I selective. It was noteworthy that the effect on histone H4 acetylation of SAHA decreased with time while the effect on histone H4 acetylation of 17a maintained even increased. Most importantly, compound 17a exhibited promising in vivo antitumor activity in a U937 xenograft model.
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Affiliation(s)
- Yingjie Zhang
- Department of Medicinal Chemistry,
School of Pharmacy, Shandong University, Ji’nan, Shandong, 250012, People’s Republic of China
| | - Penghui Yang
- Department of Medicinal Chemistry,
School of Pharmacy, Shandong University, Ji’nan, Shandong, 250012, People’s Republic of China
| | - C. James Chou
- Department of Drug Discovery
and Biomedical Sciences, South Carolina College of Pharmacy, Medical University of South Carolina, Charleston, South
Carolina, 29425, United States United States
| | - Chunxi Liu
- Department of Pharmaceutics, School
of Pharmacy, Shandong University, Ji’nan,
Shandong, 250012, People’s Republic of China
| | - Xuejian Wang
- Postdoctoral Workstation, Biomedical Industry Park Management Office, Weifang,
Shandong, 261205, People’s Republic of China
| | - Wenfang Xu
- Department of Medicinal Chemistry,
School of Pharmacy, Shandong University, Ji’nan, Shandong, 250012, People’s Republic of China
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33
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Laursen JS, Engel-Andreasen J, Fristrup P, Harris P, Olsen CA. Cis-trans amide bond rotamers in β-peptoids and peptoids: evaluation of stereoelectronic effects in backbone and side chains. J Am Chem Soc 2013; 135:2835-44. [PMID: 23343406 DOI: 10.1021/ja312532x] [Citation(s) in RCA: 116] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Non-natural peptide analogs have significant potential for the development of new materials and pharmacologically active ligands. One such architecture, the β-peptoids (N-alkyl-β-alanines), has found use in a variety of biologically active compounds but has been sparsely studied with respect to folding propensity. Thus, we here report an investigation of the effect of structural variations on the cis-trans amide bond rotamer equilibria in a selection of monomer model systems. In addition to various side chain effects, which correlated well with previous studies of α-peptoids, we present the synthesis and investigation of cis-trans isomerism in the first examples of peptoids and β-peptoids containing thioamide bonds as well as trifluoroacetylated peptoids and β-peptoids. These systems revealed an increase in the preference for cis-amides as compared to their parent compounds and thus provide novel strategies for affecting the folding of peptoid constructs. By using NMR spectroscopy, X-ray crystallographic analysis, and density functional theory calculations, we present evidence for the presence of thioamide-aromatic interactions through C(sp(2))-H···S(amide) hydrogen bonding, which stabilize certain peptoid conformations.
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Affiliation(s)
- Jonas S Laursen
- Department of Chemistry, Technical University of Denmark, Kemitorvet 207, DK-2800, Kongens Lyngby, Denmark
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Caumes C, Hjelmgaard T, Roy O, Reynaud M, Servent D, Taillefumier C, Faure S. Synthesis and binding affinities for sst receptors of cyclic peptoid SRIF-mimetics. MEDCHEMCOMM 2012. [DOI: 10.1039/c2md20265d] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Synthesis of the first all-peptoid SRIF (Somatotropin Release-Inhibiting Factor) analogues and evaluation of their binding affinities for the five human somatostatin receptors (hsst1–5).
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Affiliation(s)
- Cécile Caumes
- Clermont Universités
- Université Blaise Pascal
- Institut de Chimie de Clermont-Ferrand (ICCF)
- 63000 Clermont-Ferrand
- France
| | - Thomas Hjelmgaard
- Clermont Universités
- Université Blaise Pascal
- Institut de Chimie de Clermont-Ferrand (ICCF)
- 63000 Clermont-Ferrand
- France
| | - Olivier Roy
- Clermont Universités
- Université Blaise Pascal
- Institut de Chimie de Clermont-Ferrand (ICCF)
- 63000 Clermont-Ferrand
- France
| | - Morgane Reynaud
- CEA
- iBiTecS
- Service d'Ingénierie Moléculaire des Protéines (SIMOPRO)
- 91191 Gif sur Yvette
- France
| | - Denis Servent
- CEA
- iBiTecS
- Service d'Ingénierie Moléculaire des Protéines (SIMOPRO)
- 91191 Gif sur Yvette
- France
| | - Claude Taillefumier
- Clermont Universités
- Université Blaise Pascal
- Institut de Chimie de Clermont-Ferrand (ICCF)
- 63000 Clermont-Ferrand
- France
| | - Sophie Faure
- Clermont Universités
- Université Blaise Pascal
- Institut de Chimie de Clermont-Ferrand (ICCF)
- 63000 Clermont-Ferrand
- France
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