1
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Majekodunmi T, Britton D, Montclare JK. Engineered Proteins and Materials Utilizing Residue-Specific Noncanonical Amino Acid Incorporation. Chem Rev 2024. [PMID: 39008623 DOI: 10.1021/acs.chemrev.3c00855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/17/2024]
Abstract
The incorporation of noncanonical amino acids into proteins and protein-based materials has significantly expanded the repertoire of available protein structures and chemistries. Through residue-specific incorporation, protein properties can be globally modified, resulting in the creation of novel proteins and materials with diverse and tailored characteristics. In this review, we highlight recent advancements in residue-specific incorporation techniques as well as the applications of the engineered proteins and materials. Specifically, we discuss their utility in bio-orthogonal noncanonical amino acid tagging (BONCAT), fluorescent noncanonical amino acid tagging (FUNCAT), threonine-derived noncanonical amino acid tagging (THRONCAT), cross-linking, fluorination, and enzyme engineering. This review underscores the importance of noncanonical amino acid incorporation as a tool for the development of tailored protein properties to meet diverse research and industrial needs.
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Affiliation(s)
- Temiloluwa Majekodunmi
- Department of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York 11201, United States
| | - Dustin Britton
- Department of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York 11201, United States
| | - Jin Kim Montclare
- Department of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York 11201, United States
- Department of Biomedical Engineering, New York University Tandon School of Engineering, Brooklyn, New York 11201, United States
- Bernard and Irene Schwartz Center for Biomedical Imaging, Department of Radiology, New York University School of Medicine, New York, New York 10016, United States
- Department of Chemistry, New York University, New York, New York 10012, United States
- Department of Biomaterials, New York University College of Dentistry, New York, New York 10010, United States
- Department of Radiology, New York University Langone Health, New York, New York 10016, United States
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2
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Kothapalli Y, Jones RA, Chu CK, Singh US. Synthesis of Fluorinated Nucleosides/Nucleotides and Their Antiviral Properties. Molecules 2024; 29:2390. [PMID: 38792251 PMCID: PMC11124531 DOI: 10.3390/molecules29102390] [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: 04/02/2024] [Revised: 05/10/2024] [Accepted: 05/13/2024] [Indexed: 05/26/2024] Open
Abstract
The FDA has approved several drugs based on the fluorinated nucleoside pharmacophore, and numerous drugs are currently in clinical trials. Fluorine-containing nucleos(t)ides offer significant antiviral and anticancer activity. The insertion of a fluorine atom, either in the base or sugar of nucleos(t)ides, alters its electronic and steric parameters and transforms the lipophilicity, pharmacodynamic, and pharmacokinetic properties of these moieties. The fluorine atom restricts the oxidative metabolism of drugs and provides enzymatic metabolic stability towards the glycosidic bond of the nucleos(t)ide. The incorporation of fluorine also demonstrates additional hydrogen bonding interactions in receptors with enhanced biological profiles. The present article discusses the synthetic methodology and antiviral activities of FDA-approved drugs and ongoing fluoro-containing nucleos(t)ide drug candidates in clinical trials.
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Affiliation(s)
| | | | - Chung K. Chu
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, GA 30602, USA; (Y.K.); (R.A.J.)
| | - Uma S. Singh
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, GA 30602, USA; (Y.K.); (R.A.J.)
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3
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Chowdhary S, Pelzer T, Saathoff M, Quaas E, Pendl J, Fulde M, Koksch B. Fine‐tuning the antimicrobial activity of β‐hairpin peptides with fluorinated amino acids. Pept Sci (Hoboken) 2023. [DOI: 10.1002/pep2.24306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/11/2023]
Affiliation(s)
- Suvrat Chowdhary
- Institute of Chemistry and Biochemistry Freie Universität Berlin Berlin Germany
| | - Tim Pelzer
- Institute of Chemistry and Biochemistry Freie Universität Berlin Berlin Germany
| | - Mareike Saathoff
- Institute of Microbiology and Epizootics, Centre of Infection Medicine Freie Universität Berlin Berlin Germany
| | - Elisa Quaas
- Institute of Chemistry and Biochemistry, Core Facility SupraFAB Freie Universität Berlin Berlin Germany
| | - Johanna Pendl
- Institute of Veterinary Anatomy Freie Universität Berlin Berlin Germany
| | - Marcus Fulde
- Institute of Microbiology and Epizootics, Centre of Infection Medicine Freie Universität Berlin Berlin Germany
- Veterinary Centre for Resistance Research (TZR) Freie Universität Berlin Berlin Germany
| | - Beate Koksch
- Institute of Chemistry and Biochemistry Freie Universität Berlin Berlin Germany
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4
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Fluorinated Protein and Peptide Materials for Biomedical Applications. Pharmaceuticals (Basel) 2022; 15:ph15101201. [PMID: 36297312 PMCID: PMC9609677 DOI: 10.3390/ph15101201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 09/22/2022] [Accepted: 09/26/2022] [Indexed: 11/17/2022] Open
Abstract
Fluorination represents one of the most powerful modern design strategies to impart biomacromolecules with unique functionality, empowering them for widespread application in the biomedical realm. However, the properties of fluorinated protein materials remain unpredictable due to the heavy context-dependency of the surrounding atoms influenced by fluorine’s strong electron-withdrawing tendencies. This review aims to discern patterns and elucidate design principles governing the biochemical synthesis and rational installation of fluorine into protein and peptide sequences for diverse biomedical applications. Several case studies are presented to deconvolute the overgeneralized fluorous stabilization effect and critically examine the duplicitous nature of the resultant enhanced chemical and thermostability as it applies to use as biomimetic therapeutics, drug delivery vehicles, and bioimaging modalities.
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5
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Bilska-Markowska M, Jankowski W, Hoffmann M, Kaźmierczak M. Design and Synthesis of New α-hydroxy β-fluoro/β-trifluoromethyl and Unsaturated Phosphonates from Carbohydrate-Derived Building Blocks via Pudovik and Horner–Wadsworth–Emmons Reactions. Molecules 2022; 27:molecules27175404. [PMID: 36080169 PMCID: PMC9457578 DOI: 10.3390/molecules27175404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 08/21/2022] [Accepted: 08/22/2022] [Indexed: 11/16/2022] Open
Abstract
Herein, we present the application of fluorinated carbohydrate-derived building blocks for α-hydroxy β-fluoro/β-trifluoromethyl and unsaturated phosphonates synthesis. Pudovik and Horner–Wadsworth–Emmons reactions were applied to achieve this goal. The proposed pathway of the key reactions is supported by the experimental results, as well as quantum chemical calculations. The structure of the products was established by spectroscopic (1D, 2D NMR) and spectrometric (MS) techniques. Based on our data received, we claim that the progress of the Pudovik and HWE reactions is significantly influenced by the acidic protons present in the molecules as assessed by pKa values of the reagent.
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Affiliation(s)
- Monika Bilska-Markowska
- Faculty of Chemistry, Adam Mickiewicz University, Uniwersytetu Poznańskiego 8, 61-614 Poznań, Poland
| | - Wojciech Jankowski
- Faculty of Chemistry, Adam Mickiewicz University, Uniwersytetu Poznańskiego 8, 61-614 Poznań, Poland
| | - Marcin Hoffmann
- Faculty of Chemistry, Adam Mickiewicz University, Uniwersytetu Poznańskiego 8, 61-614 Poznań, Poland
| | - Marcin Kaźmierczak
- Faculty of Chemistry, Adam Mickiewicz University, Uniwersytetu Poznańskiego 8, 61-614 Poznań, Poland
- Centre for Advanced Technologies, Adam Mickiewicz University, Uniwersytetu Poznańskiego 10, 61-614 Poznań, Poland
- Correspondence:
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6
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Hohmann T, Dyrks M, Chowdhary S, Weber M, Nguyen D, Moschner J, Koksch B. Gram-Scale Asymmetric Synthesis of Fluorinated Amino Acids Using a Chiral Nickel(II) Complex. J Org Chem 2022; 87:10592-10604. [PMID: 35926217 DOI: 10.1021/acs.joc.2c00522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Fluorinated amino acids play an important role in the field of peptide and protein engineering. Although numerous syntheses have been published in recent decades, strategies that allow routine access to fluorinated amino acids on a gram-scale have been poorly described. Furthermore, the described pathways that gain fluorinated amino acids are based on different synthetic strategies, making a uniform approach that uses similar starting materials highly beneficial. Chiral Ni(II) complexes were introduced as powerful tools in the synthesis of noncanonical amino acids. In this work, we present a strategy for the synthesis of a diverse range of fluorinated amino acids based on the corresponding Ni(II) complex from which the products can be obtained in enantiopure form (99% ee) on a gram-scale. In addition, we describe an optimized procedure for the synthesis of alkyl iodide building blocks that are required for the alkylation reactions with the corresponding Ni(II) complex. Finally, we characterized the synthesized fluorinated amino acids with regard to their hydrophobicity and α-helix propensity.
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Affiliation(s)
- Thomas Hohmann
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Arnimallee 20, Berlin, 14195Berlin, Germany
| | - Michael Dyrks
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Arnimallee 20, Berlin, 14195Berlin, Germany
| | - Suvrat Chowdhary
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Arnimallee 20, Berlin, 14195Berlin, Germany
| | - Manuela Weber
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Fabeckstraße 34/36, Berlin, 14195Berlin, Germany
| | - Duy Nguyen
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Arnimallee 20, Berlin, 14195Berlin, Germany
| | - Johann Moschner
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Arnimallee 20, Berlin, 14195Berlin, Germany
| | - Beate Koksch
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Arnimallee 20, Berlin, 14195Berlin, Germany
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7
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Ghosh P, Nandy T, Singh PC, Ghosh D. Substitution enables significant new decay channels for a non-canonical amino acid. Phys Chem Chem Phys 2022; 24:17695-17702. [PMID: 35838114 DOI: 10.1039/d2cp00465h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
UV-Vis absorption spectra and emission peaks of indole and 7-fluoroindole are measured and it is observed that 7-fluoroindole quenches the fluorescence signals significantly compared to indole. This observation is elucidated via reconstruction of the potential energy surfaces, determination of the conical intersections, and dynamical studies. It is observed that a single fluorine substitution on indole leads to the appearance of several accessible low-energy conical intersections that cause fast nonradiative decay. In this paper, we have investigated the nonradiative processes of Ind and 7F-Ind theoretically using high-level methods, such as EOM-EE-CCSD, SA-CASSCF, MS-CASPT2/6-311++G(d,p) levels of theory, to study these pathways and their feasibility.
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Affiliation(s)
- Paulami Ghosh
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Kolkata 700032, India.
| | - Tonima Nandy
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Kolkata 700032, India.
| | - Prashant C Singh
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Kolkata 700032, India.
| | - Debashree Ghosh
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Kolkata 700032, India.
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8
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Engineering of enzymes using non-natural amino acids. Biosci Rep 2022; 42:231590. [PMID: 35856922 PMCID: PMC9366748 DOI: 10.1042/bsr20220168] [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: 05/16/2022] [Revised: 07/05/2022] [Accepted: 07/20/2022] [Indexed: 11/17/2022] Open
Abstract
In enzyme engineering, the main targets for enhancing properties are enzyme activity, stereoselective specificity, stability, substrate range, and the development of unique functions. With the advent of genetic code extension technology, non-natural amino acids (nnAAs) are able to be incorporated into proteins in a site-specific or residue-specific manner, which breaks the limit of 20 natural amino acids for protein engineering. Benefitting from this approach, numerous enzymes have been engineered with nnAAs for improved properties or extended functionality. In this review, we focus on applications and strategies for using nnAAs in enzyme engineering. Notably, approaches to computational modelling of enzymes with nnAAs are also addressed. Finally, we discuss the bottlenecks that currently need to be addressed in order to realise the broader prospects of this genetic code extension technique.
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9
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Gawor A, Gajewski Z, Paczek L, Czarkowska-Paczek B, Konopka A, Wryk G, Bulska E. Fluorine-Containing Drug Administration in Rats Results in Fluorination of Selected Proteins in Liver and Brain Tissue. Int J Mol Sci 2022; 23:ijms23084202. [PMID: 35457021 PMCID: PMC9028303 DOI: 10.3390/ijms23084202] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Revised: 03/31/2022] [Accepted: 04/09/2022] [Indexed: 12/26/2022] Open
Abstract
In many pharmaceuticals, a hydrogen atom or hydroxyl group is replaced by a fluorine to increase bioavailability and biostability. The fate of fluorine released from fluorine-containing drugs is not well investigated. The aim of this study was to examine possible fluorination of proteins in rat liver and brain after administration of the fluorinated drug cinacalcet. We assigned 18 Wistar rats to a control group (n = 6) and a group treated with cinacalcet (2 mg kg−1/body weight, 5 days/week), divided into 7 day (n = 6) and 21 day (n = 6) treatment subgroups. Fluorinated proteins were identified using a free proteomics approach; chromatographic separation and analysis by high-resolution mass spectrometry; peptide/protein identification using the Mascot search algorithm; manual verification of an experimentally generated MS/MS spectrum with the theoretical MS/MS spectrum of identified fluorinated peptides. Three fluorinated proteins (spectrin beta chain; carbamoyl-phosphate synthase [ammonia], mitochondrial; 6-phosphofructo-2-kinase/fructose-2, 6-bisphosphatase 1) were identified in the liver and four (spectrin beta chain, dihydropyrimidinase-related protein 4, prominin-2, dihydropyrimidinase-related protein 4) in the brain tissue after 21 days of cinacalcet treatment, but not in the control group. Introduction of fluorine into an organism by administration of fluorinated drugs results in tissue-specific fluorination of proteins.
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Affiliation(s)
- Andrzej Gawor
- Biological and Chemical Research Centre, Faculty of Chemistry, University of Warsaw, Zwirki i Wigury 101, 02-089 Warsaw, Poland; (A.G.); (A.K.); (G.W.); (E.B.)
| | - Zdzislaw Gajewski
- Center for Translational Medicine, Warsaw University of Life Science, Nowoursynowska 100, 02-797 Warsaw, Poland;
| | - Leszek Paczek
- Department of Immunology, Transplantology and Internal Diseases, Medical University of Warsaw, Nowogrodzka 59, 02-006 Warsaw, Poland;
- Department of Bioinformatics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Bozena Czarkowska-Paczek
- Department of Clinical Nursing, Medical University of Warsaw, Ciolka Street 27, 01-445 Warsaw, Poland
- Correspondence: ; Tel./Fax: +48-22-836-0972
| | - Anna Konopka
- Biological and Chemical Research Centre, Faculty of Chemistry, University of Warsaw, Zwirki i Wigury 101, 02-089 Warsaw, Poland; (A.G.); (A.K.); (G.W.); (E.B.)
| | - Grzegorz Wryk
- Biological and Chemical Research Centre, Faculty of Chemistry, University of Warsaw, Zwirki i Wigury 101, 02-089 Warsaw, Poland; (A.G.); (A.K.); (G.W.); (E.B.)
| | - Ewa Bulska
- Biological and Chemical Research Centre, Faculty of Chemistry, University of Warsaw, Zwirki i Wigury 101, 02-089 Warsaw, Poland; (A.G.); (A.K.); (G.W.); (E.B.)
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10
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Gou FH, Ma MJ, Wang AJ, Zhao L, Wang H, Tong J, Wang Z, Wang Z, He CY. Nickel-Catalyzed Cross-Coupling of Amino-Acid-Derived Alkylzinc Reagents with Alkyl Bromides/Chlorides: Access to Diverse Unnatural Amino Acids. Org Lett 2022; 24:240-244. [PMID: 34958223 DOI: 10.1021/acs.orglett.1c03884] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Unnatural α-amino acids are important synthetic targets in the field of peptide science. Herein we report an efficient, versatile, and straightforward strategy for the synthesis of homophenylalanine derivatives via the nickel-catalyzed Csp3-Csp3 cross-coupling of (fluoro)benzyl bromides/chlorides with natural α-amino-acid-derived alkylzinc reagents. The current protocol features the advantages of a low-cost nickel catalyst system, synthetic convenience, and the tolerance of rich functionality and stereochemistry.
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Affiliation(s)
- Fei-Hu Gou
- Key Laboratory of Biocatalysis & Chiral Drug Synthesis of Guizhou Province, Generic Drug Research Center of Guizhou Province, Zunyi Medical University, Zunyi, Guizhou 563000, China
| | - Ming-Jian Ma
- Key Laboratory of Biocatalysis & Chiral Drug Synthesis of Guizhou Province, Generic Drug Research Center of Guizhou Province, Zunyi Medical University, Zunyi, Guizhou 563000, China
| | - An-Jun Wang
- Key Laboratory of Biocatalysis & Chiral Drug Synthesis of Guizhou Province, Generic Drug Research Center of Guizhou Province, Zunyi Medical University, Zunyi, Guizhou 563000, China
| | - Liang Zhao
- Key Laboratory of Biocatalysis & Chiral Drug Synthesis of Guizhou Province, Generic Drug Research Center of Guizhou Province, Zunyi Medical University, Zunyi, Guizhou 563000, China
| | - Haoyang Wang
- Laboratory of Mass Spectrometry Analysis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, China
| | - Jie Tong
- School of Medicine, Yale University, New Haven, Connecticut 06510, United States
| | - Ze Wang
- Key Laboratory of Biocatalysis & Chiral Drug Synthesis of Guizhou Province, Generic Drug Research Center of Guizhou Province, Zunyi Medical University, Zunyi, Guizhou 563000, China
| | - Zhen Wang
- School of Pharmaceutical Science, University of South China, Hengyang 421001, China
| | - Chun-Yang He
- Key Laboratory of Biocatalysis & Chiral Drug Synthesis of Guizhou Province, Generic Drug Research Center of Guizhou Province, Zunyi Medical University, Zunyi, Guizhou 563000, China
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11
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Mondal R, Agbaria M, Nairoukh Z. Fluorinated Rings: Conformation and Application. Chemistry 2021; 27:7193-7213. [PMID: 33512034 DOI: 10.1002/chem.202005425] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Indexed: 12/16/2022]
Abstract
The introduction of fluorine atoms into molecules and materials across many fields of academic and industrial research is now commonplace, owing to their unique properties. A particularly interesting feature is the impact of fluorine substitution on the relative orientation of a C-F bond when incorporated into organic molecules. In this Review, we will be discussing the conformational behavior of fluorinated aliphatic carbo- and heterocyclic systems. The conformational preference of each system is associated with various interactions introduced by fluorine substitution such as charge-dipole, dipole-dipole, and hyperconjugative interactions. The contribution of each interaction on the stabilization of the fluorinated alicyclic system, which manifests itself in low conformations, will be discussed in detail. The novelty of this feature will be demonstrated by presenting the most recent applications.
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Affiliation(s)
- Rajarshi Mondal
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Jerusalem, 9190401, Israel
| | - Mohamed Agbaria
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Jerusalem, 9190401, Israel
| | - Zackaria Nairoukh
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Jerusalem, 9190401, Israel
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12
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Glossop HD, De Zoysa GH, Pilkington LI, Barker D, Sarojini V. Fluorinated O-phenylserine residues enhance the broad-spectrum antimicrobial activity of ultrashort cationic lipopeptides. J Fluor Chem 2021. [DOI: 10.1016/j.jfluchem.2020.109685] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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13
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Jia H, Qiao B, Jiang Z. Photoredox Catalytic Radical Coupling to Access β-Fluoro α-Amino Acid Derivatives. ACTA CHIMICA SINICA 2021. [DOI: 10.6023/a21090432] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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14
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Montalbán-López M, Scott TA, Ramesh S, Rahman IR, van Heel AJ, Viel JH, Bandarian V, Dittmann E, Genilloud O, Goto Y, Grande Burgos MJ, Hill C, Kim S, Koehnke J, Latham JA, Link AJ, Martínez B, Nair SK, Nicolet Y, Rebuffat S, Sahl HG, Sareen D, Schmidt EW, Schmitt L, Severinov K, Süssmuth RD, Truman AW, Wang H, Weng JK, van Wezel GP, Zhang Q, Zhong J, Piel J, Mitchell DA, Kuipers OP, van der Donk WA. New developments in RiPP discovery, enzymology and engineering. Nat Prod Rep 2021; 38:130-239. [PMID: 32935693 PMCID: PMC7864896 DOI: 10.1039/d0np00027b] [Citation(s) in RCA: 389] [Impact Index Per Article: 129.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Covering: up to June 2020Ribosomally-synthesized and post-translationally modified peptides (RiPPs) are a large group of natural products. A community-driven review in 2013 described the emerging commonalities in the biosynthesis of RiPPs and the opportunities they offered for bioengineering and genome mining. Since then, the field has seen tremendous advances in understanding of the mechanisms by which nature assembles these compounds, in engineering their biosynthetic machinery for a wide range of applications, and in the discovery of entirely new RiPP families using bioinformatic tools developed specifically for this compound class. The First International Conference on RiPPs was held in 2019, and the meeting participants assembled the current review describing new developments since 2013. The review discusses the new classes of RiPPs that have been discovered, the advances in our understanding of the installation of both primary and secondary post-translational modifications, and the mechanisms by which the enzymes recognize the leader peptides in their substrates. In addition, genome mining tools used for RiPP discovery are discussed as well as various strategies for RiPP engineering. An outlook section presents directions for future research.
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15
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Miller MA, Sletten EM. Perfluorocarbons in Chemical Biology. Chembiochem 2020; 21:3451-3462. [PMID: 32628804 PMCID: PMC7736518 DOI: 10.1002/cbic.202000297] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 07/03/2020] [Indexed: 01/10/2023]
Abstract
Perfluorocarbons, saturated carbon chains in which all the hydrogen atoms are replaced with fluorine, form a separate phase from both organic and aqueous solutions. Though perfluorinated compounds are not found in living systems, they can be used to modify biomolecules to confer orthogonal behavior within natural systems, such as improved stability, engineered assembly, and cell-permeability. Perfluorinated groups also provide handles for purification, mass spectrometry, and 19 F NMR studies in complex environments. Herein, we describe how the unique properties of perfluorocarbons have been employed to understand and manipulate biological systems.
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Affiliation(s)
- Margeaux A Miller
- Department of Chemistry and Biochemistry, University of California, Los Angeles, 607 Charles E Young Dr E, Los Angeles, CA, 90095, USA
| | - Ellen M Sletten
- Department of Chemistry and Biochemistry, University of California, Los Angeles, 607 Charles E Young Dr E, Los Angeles, CA, 90095, USA
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16
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Yang B, Liu H, Liu Z, Doenen R, Nash MA. Influence of Fluorination on Single-Molecule Unfolding and Rupture Pathways of a Mechanostable Protein Adhesion Complex. NANO LETTERS 2020; 20:8940-8950. [PMID: 33191756 PMCID: PMC7729889 DOI: 10.1021/acs.nanolett.0c04178] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 11/08/2020] [Indexed: 05/25/2023]
Abstract
We investigated the influence of fluorination on unfolding and unbinding reaction pathways of a mechanostable protein complex comprising the tandem dyad XModule-Dockerin bound to Cohesin. Using single-molecule atomic force spectroscopy, we mapped the energy landscapes governing the unfolding and unbinding reactions. We then used sense codon suppression to substitute trifluoroleucine in place of canonical leucine globally in XMod-Doc. Although TFL substitution thermally destabilized XMod-Doc, it had little effect on XMod-Doc:Coh binding affinity at equilibrium. When we mechanically dissociated global TFL-substituted XMod-Doc from Coh, we observed the emergence of a new unbinding pathway with a lower energy barrier. Counterintuitively, when fluorination was restricted to Doc, we observed mechano-stabilization of the non-fluorinated neighboring XMod domain. This suggests that intramolecular deformation is modulated by fluorination and highlights the differences between equilibrium thermostability and non-equilibrium mechanostability. Future work is poised to investigate fluorination as a means to modulate mechanical properties of synthetic proteins and hydrogels.
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Affiliation(s)
- Byeongseon Yang
- Department
of Chemistry, University of Basel, 4058 Basel, Switzerland
- Department
of Biosystems Science and Engineering, ETH
Zurich, 4058 Basel, Switzerland
| | - Haipei Liu
- Department
of Chemistry, University of Basel, 4058 Basel, Switzerland
- Department
of Biosystems Science and Engineering, ETH
Zurich, 4058 Basel, Switzerland
| | - Zhaowei Liu
- Department
of Chemistry, University of Basel, 4058 Basel, Switzerland
- Department
of Biosystems Science and Engineering, ETH
Zurich, 4058 Basel, Switzerland
| | - Regina Doenen
- Department
of Chemistry, University of Basel, 4058 Basel, Switzerland
- Department
of Biosystems Science and Engineering, ETH
Zurich, 4058 Basel, Switzerland
| | - Michael A. Nash
- Department
of Chemistry, University of Basel, 4058 Basel, Switzerland
- Department
of Biosystems Science and Engineering, ETH
Zurich, 4058 Basel, Switzerland
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17
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Muralidharan A, Schmidt JR, Yethiraj A. Solvation Induced Ring Puckering Effect in Fluorinated Prolines and Its Inclusion in Classical Force Fields. J Phys Chem B 2020; 124:5899-5906. [PMID: 32551633 DOI: 10.1021/acs.jpcb.0c04312] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Strategic incorporation of fluorinated prolines can accelerate folding and increase thermal stability of proteins. It has been suggested that this behavior emerges from puckering effects induced by fluorination of the proline ring. We use electronic structure calculations to characterize the potential energy surface (PES) along puckering coordinates for a simple dipeptide model of proline and its fluorinated derivatives. Significant shifts in puckering trends between gas phase and implicit solvent calculations shed light on the effect of solvation on electronic structure and conformational preferences of the ring. This solvation induced puckering effect is previously unknown in the context of prolines. The PES based on implicit solvent is then utilized to construct a correction for a classical force field. The corrected force field accurately captures the experimental conformational equilibrium including the coupling between ring puckering and cis-trans isomerism in fluorinated prolines. This method can be extended to other rings and substituents besides fluorine.
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Affiliation(s)
- Ajay Muralidharan
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconson 53706, United States
| | - J R Schmidt
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconson 53706, United States
| | - Arun Yethiraj
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconson 53706, United States
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18
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Biswas B, Singh PC. The role of fluorocarbon group in the hydrogen bond network, photophysical and solvation dynamics of fluorinated molecules. J Fluor Chem 2020. [DOI: 10.1016/j.jfluchem.2019.109414] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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19
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Fluorine-19 NMR spectroscopy of fluorinated analogs of tritrpticin highlights a distinct role for Tyr residues in antimicrobial peptides. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1862:183260. [DOI: 10.1016/j.bbamem.2020.183260] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 02/17/2020] [Accepted: 02/19/2020] [Indexed: 02/08/2023]
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20
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Schätti J, Köhler V, Mayor M, Fein YY, Geyer P, Mairhofer L, Gerlich S, Arndt M. Matter-wave interference and deflection of tripeptides decorated with fluorinated alkyl chains. JOURNAL OF MASS SPECTROMETRY : JMS 2020; 55:e4514. [PMID: 32363659 PMCID: PMC7317408 DOI: 10.1002/jms.4514] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/29/2019] [Revised: 03/11/2020] [Accepted: 03/13/2020] [Indexed: 06/11/2023]
Abstract
Studies of neutral biomolecules in the gas phase allow for the study of molecular properties in the absence of solvent and charge effects, thus complementing spectroscopic and analytical methods in solution or in ion traps. Some properties, such as the static electronic susceptibility, are best accessed in experiments that act on the motion of the neutral molecules in an electric field. Here, we screen seven peptides for their thermal stability and electron impact ionizability. We identify two tripeptides as sufficiently volatile and thermostable to be evaporated and interfered in the long-baseline universal matter-wave interferometer. Monitoring the deflection of the interferometric molecular nanopattern in a tailored external electric field allows us to measure the static molecular susceptibility of Ala-Trp-Ala and Ala-Ala-Trp bearing fluorinated alkyl chains at C- and N-termini. The respective values are 4 π ε 0 × 330 ± 150 Å 3 and 4 π ε 0 × 270 ± 80 Å 3 .
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Affiliation(s)
- Jonas Schätti
- Department of ChemistryUniversity of BaselCH‐St. Johannsring 1Basel4056Switzerland
| | - Valentin Köhler
- Department of ChemistryUniversity of BaselCH‐St. Johannsring 1Basel4056Switzerland
| | - Marcel Mayor
- Department of ChemistryUniversity of BaselCH‐St. Johannsring 1Basel4056Switzerland
- Institute of NanotechnologyKarlsruhe Institute of TechnologyHermann‐von‐Helmholtz‐Platz 1, 76344Eggenstein‐LeopoldshafenGermany
- Lehn Institute of Functional Materials (LIFM)Sun Yat‐Sen University (SYSU)XinGangXi Rd. 135, 510275GuangzhouChina
| | - Yaakov Y. Fein
- Faculty of PhysicsUniversity of ViennaBoltzmanngasse 5, 1090ViennaAustria
| | - Philipp Geyer
- Faculty of PhysicsUniversity of ViennaBoltzmanngasse 5, 1090ViennaAustria
| | - Lukas Mairhofer
- Faculty of PhysicsUniversity of ViennaBoltzmanngasse 5, 1090ViennaAustria
| | - Stefan Gerlich
- Faculty of PhysicsUniversity of ViennaBoltzmanngasse 5, 1090ViennaAustria
| | - Markus Arndt
- Faculty of PhysicsUniversity of ViennaBoltzmanngasse 5, 1090ViennaAustria
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21
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Abularrage NS, Levandowski BJ, Raines RT. Synthesis and Diels-Alder Reactivity of 4-Fluoro-4-Methyl-4 H-Pyrazoles. Int J Mol Sci 2020; 21:ijms21113964. [PMID: 32486503 PMCID: PMC7312747 DOI: 10.3390/ijms21113964] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 05/22/2020] [Accepted: 05/24/2020] [Indexed: 02/01/2023] Open
Abstract
4H-Pyrazoles are emerging scaffolds for “click” chemistry. Late-stage fluorination with Selectfluor® is found to provide a reliable route to 4-fluoro-4-methyl-4H-pyrazoles. 4-Fluoro-4-methyl-3,5-diphenyl-4H-pyrazole (MFP) manifested 7-fold lower Diels–Alder reactivity than did 4,4-difluoro-3,5-diphenyl-4H-pyrazole (DFP), but higher stability in the presence of biological nucleophiles. Calculations indicate that a large decrease in the hyperconjugative antiaromaticity in MFP relative to DFP does not lead to a large loss in Diels–Alder reactivity because the ground-state structure of MFP avoids hyperconjugative antiaromaticity by distorting into an envelope-like conformation like that in the Diels–Alder transition state. This predistortion enhances the reactivity of MFP and offsets the decrease in reactivity from the diminished hyperconjugative antiaromaticity.
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22
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Brewitz L, Noda H, Kumagai N, Shibasaki M. (
2R
,
3S
)‐3,4,4,4‐Tetrafluorovaline: A Fluorinated Bioisostere of Isoleucine. European J Org Chem 2020. [DOI: 10.1002/ejoc.202000109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Lennart Brewitz
- Institute of Microbial Chemistry (BIKAKEN) Tokyo Kamiosaki 3‐14‐23, Shinagawa‐ku 141‐0021 Tokyo Japan
| | - Hidetoshi Noda
- Institute of Microbial Chemistry (BIKAKEN) Tokyo Kamiosaki 3‐14‐23, Shinagawa‐ku 141‐0021 Tokyo Japan
| | - Naoya Kumagai
- Institute of Microbial Chemistry (BIKAKEN) Tokyo Kamiosaki 3‐14‐23, Shinagawa‐ku 141‐0021 Tokyo Japan
| | - Masakatsu Shibasaki
- Institute of Microbial Chemistry (BIKAKEN) Tokyo Kamiosaki 3‐14‐23, Shinagawa‐ku 141‐0021 Tokyo Japan
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23
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Li M, Wang S, Xu J, Xu S, Liu H. pH/Redox-Controlled Interaction between Lipid Membranes and Peptide Derivatives with a "Helmet". J Phys Chem B 2019; 123:6784-6791. [PMID: 31306021 DOI: 10.1021/acs.jpcb.9b05367] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
How to reduce the cytotoxicity of antitumor peptides to normal cells remains an ongoing challenge. Here, we designed a pH/redox-responsive supramolecular structure (Pep-V⊂P-PEG) composed of a peptide modified with viologen (Pep-V) and polyethylene glycol bearing pillar[5]arene (P-PEG) as a "helmet". By shielding the hydrophobic moiety of the peptide derivative with pillar[5]arene via host-guest interactions, its disruption on normal cells can be effectively reduced. At acidic pH, the supramolecular structure can selectively adsorb onto negatively charged lipid membranes because of electrostatic interactions. Owing to redox responsiveness of the viologen group, Pep-V could be separated from P-PEG after the addition of reductants and inserted into lipid bilayers, which leads to membrane disruption. Cargo leakage of liposome models was investigated to understand Pep-V⊂P-PEG-induced liposomal membrane disruption under different pH values and redox conditions. Results showed that Pep-V⊂P-PEG caused almost no cargo leakage from (1,2-dipalmitoyl-sn-glycerol-3-phosphocholine) liposomes at pH 7.4 but significant leakage from negatively charged (1,2-dipalmitoyl-sn-glycerol-3-phospho-(1-rac-glyerol)) liposomes at pH 5.0 under a reducing environment. Pep-V⊂P-PEG displayed low destructive effects on mimic normal cells and significant disruption to mimic tumor cells when exposed to a reducing environment that is expected to be a potential antitumor agent.
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Affiliation(s)
- Mengya Li
- Key Laboratory for Advanced Materials, School of Chemistry and Molecular Engineering , East China University of Science and Technology , Shanghai 200237 , PR China
| | - Sijia Wang
- College of Pharmacy , Henan University of Chinese Medicine , Zhengzhou 450046 , PR China
| | - Jun Xu
- Key Laboratory for Advanced Materials, School of Chemistry and Molecular Engineering , East China University of Science and Technology , Shanghai 200237 , PR China
| | - Shouhong Xu
- Key Laboratory for Advanced Materials, School of Chemistry and Molecular Engineering , East China University of Science and Technology , Shanghai 200237 , PR China
| | - Honglai Liu
- Key Laboratory for Advanced Materials, School of Chemistry and Molecular Engineering , East China University of Science and Technology , Shanghai 200237 , PR China
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24
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Tungstosulfonic acid-catalyzed green synthesis and bioassay of α-aminophosphonates. MONATSHEFTE FUR CHEMIE 2019. [DOI: 10.1007/s00706-019-2385-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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25
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Sukach V, Melnykov S, Bertho S, Diachenko I, Retailleau P, Vovk M, Gillaizeau I. Access to Unprotected β-Fluoroalkyl β-Amino Acids and Their α-Hydroxy Derivatives. Org Lett 2019; 21:2340-2345. [PMID: 30873840 DOI: 10.1021/acs.orglett.9b00622] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Unprotected β-(het)aryl-β-fluoroalkyl β-amino acids and their α-hydroxy derivatives can be readily obtained using a decarboxylative Mannich-type reaction without protection/deprotection steps. This protocol utilizes lithium hexamethyldisilazide and (het)arylfluoroalkyl ketones to generate NH-ketimine intermediates. The mild reaction conditions allow the preparation of original fluorinated β-amino acids as useful building blocks in a practical and scalable manner.
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Affiliation(s)
- Volodymyr Sukach
- Le Studium Loire Valley Institute for Advanced Studies , 1, rue Dupanloup , Orléans 45000 , France.,Institute of Organic and Analytical Chemistry, ICOA UMR 7311 CNRS , Université d'Orléans , rue de Chartres , Orléans 45100 , France
| | - Serhii Melnykov
- Institute of Organic Chemistry of NAS of Ukraine , 5, Murmanska Str ., Kyiv 02660 , Ukraine.,Enamine LTD , 78 Chervonotkats'ka Str. , Kyiv 02094 , Ukraine
| | - Sylvain Bertho
- Institute of Organic and Analytical Chemistry, ICOA UMR 7311 CNRS , Université d'Orléans , rue de Chartres , Orléans 45100 , France
| | - Iryna Diachenko
- Institute of Organic and Analytical Chemistry, ICOA UMR 7311 CNRS , Université d'Orléans , rue de Chartres , Orléans 45100 , France
| | - Pascal Retailleau
- Institut de Chimie des Substances Naturelles, CNRS UPR 2301, Université Paris-Sud, Université Paris-Saclay, Avenue de la Terrasse , Gif-sur-Yvette 91198 , France
| | - Mykhailo Vovk
- Institute of Organic Chemistry of NAS of Ukraine , 5, Murmanska Str ., Kyiv 02660 , Ukraine
| | - Isabelle Gillaizeau
- Institute of Organic and Analytical Chemistry, ICOA UMR 7311 CNRS , Université d'Orléans , rue de Chartres , Orléans 45100 , France
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26
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Xing H, Lu M, Yang T, Liu H, Sun Y, Zhao X, Xu H, Yang L, Ding P. Structure-function relationships of nonviral gene vectors: Lessons from antimicrobial polymers. Acta Biomater 2019; 86:15-40. [PMID: 30590184 DOI: 10.1016/j.actbio.2018.12.041] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2018] [Revised: 11/22/2018] [Accepted: 12/21/2018] [Indexed: 01/13/2023]
Abstract
In recent years, substantial advances have been achieved in the design and synthesis of nonviral gene vectors. However, lack of effective and biocompatible vectors still remains a major challenge that hinders their application in clinical settings. In the past decade, there has been a rapid expansion of cationic antimicrobial polymers, due to their potent, rapid, and broad-spectrum biocidal activity against resistant microbes, and biocompatible features. Given that antimicrobial polymers share common features with nonviral gene vectors in various aspects, such as membrane affinity, functional groups, physicochemical characteristics, and unique macromolecular architectures, these polymers may provide us with inspirations to overcome challenges in the design of novel vectors toward more safe and efficient gene delivery in clinic. Building off these observations, we provide here an overview of the structure-function relationships of polymers for both antimicrobial applications and gene delivery by elaborating some key structural parameters, including functional groups, charge density, hydrophobic/hydrophilic balance, MW, and macromolecular architectures. By borrowing a leaf from antimicrobial agents, great advancement in the development of newer nonviral gene vectors with high transfection efficiency and biocompatibility will be more promising. STATEMENT OF SIGNIFICANCE: The development of gene delivery is still in the preclinical stage for the lack of effective and biocompatible vectors. Given that antimicrobial polymers share common features with gene vectors in various aspects, such as membrane affinity, functional groups, physicochemical characteristics, and unique macromolecular architectures, these polymers may provide us with inspirations to overcome challenges in the design of novel vectors toward more safe and efficient gene delivery in clinic. In this review, we systematically summarized the structure-function relationships of antimicrobial polymers and gene vectors, with which the design of more advanced nonviral gene vectors is anticipated to be further boosted in the future.
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Affiliation(s)
- Haonan Xing
- School of Pharmacy, Shenyang Pharmaceutical University, Shenyang, China
| | - Mei Lu
- School of Pharmacy, Shenyang Pharmaceutical University, Shenyang, China
| | - Tianzhi Yang
- Department of Basic Pharmaceutical Sciences, School of Pharmacy, Husson University, Bangor, ME, USA
| | - Hui Liu
- School of Pharmacy, Shenyang Pharmaceutical University, Shenyang, China
| | - Yanping Sun
- School of Pharmacy, Shenyang Pharmaceutical University, Shenyang, China
| | - Xiaoyun Zhao
- School of Life Science and Biopharmaceutics, Shenyang Pharmaceutical University, Shenyang, China
| | - Hui Xu
- School of Pharmacy, Shenyang Pharmaceutical University, Shenyang, China
| | - Li Yang
- School of Pharmacy, Shenyang Pharmaceutical University, Shenyang, China.
| | - Pingtian Ding
- School of Pharmacy, Shenyang Pharmaceutical University, Shenyang, China.
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27
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Sim J, Campbell MW, Molander GA. Synthesis of α-Fluoro-α-Amino Acid Derivatives via Photoredox-Catalyzed Carbofluorination. ACS Catal 2019; 9:1558-1563. [PMID: 31588366 DOI: 10.1021/acscatal.8b04284] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
A mild, metal-free, regioselective carbofluorination of dehydroalanine derivatives has been developed. Alkyl radicals resulting from visible-light photoredox catalysis engage in a radical conjugate addition to dehydroalanine, with subsequent fluorination of the newly generated radical to afford an α-fluoro-α-amino acid. By using a highly oxidizing organic photocatalyst, this process incorporates non-stabilized primary, secondary, and tertiary alkyl radicals derived from commercially available alkyltrifluoroborates to furnish a wide range of fluorinated unnatural amino acids.
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Affiliation(s)
- Jaehoon Sim
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, Pennsylvania 19104-6323, United States
| | - Mark W. Campbell
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, Pennsylvania 19104-6323, United States
| | - Gary A. Molander
- Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, Pennsylvania 19104-6323, United States
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28
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Nandy T, Mondal S, Singh PC. Solvent organization around the noncanonical part of tyrosine modulates its fluorescence properties. Phys Chem Chem Phys 2019; 21:6042-6050. [DOI: 10.1039/c8cp06410e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Solvent interactions with the fluorocarbon group of noncanonical amino acids are the cause of their diverse fluorescence behaviors, which implies their usefulness as solvent-sensitive environmental sensors in many biological processes.
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Affiliation(s)
- Tonima Nandy
- Department of Spectroscopy
- Indian Association for the Cultivation of Science
- Kolkata
- India
| | - Saptarsi Mondal
- Department of Spectroscopy
- Indian Association for the Cultivation of Science
- Kolkata
- India
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29
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Auger M, Lefèvre T, Otis F, Voyer N, Auger M. Lipid membrane interactions of a fluorinated peptide with potential ion channel-forming ability. Pept Sci (Hoboken) 2019. [DOI: 10.1002/pep2.24051] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Maud Auger
- Regroupement québécois de Recherche sur la Fonction, l'Ingénierie et les Applications des Protéines (PROTEO), Centre de Recherche sur les Matériaux Avancés (CERMA), Centre Québécois sur les Matériaux Fonctionnels (CQMF), Département de Chimie, Université Laval, 1045 avenue de la Médecine; Québec QC Canada G1V 0A6
| | - Thierry Lefèvre
- Regroupement québécois de Recherche sur la Fonction, l'Ingénierie et les Applications des Protéines (PROTEO), Centre de Recherche sur les Matériaux Avancés (CERMA), Centre Québécois sur les Matériaux Fonctionnels (CQMF), Département de Chimie, Université Laval, 1045 avenue de la Médecine; Québec QC Canada G1V 0A6
| | - François Otis
- PROTEO, Département de chimie; Université Laval, 1045 avenue de la Médecine; Québec QC Canada G1V 0A6
| | - Normand Voyer
- PROTEO, Département de chimie; Université Laval, 1045 avenue de la Médecine; Québec QC Canada G1V 0A6
| | - Michèle Auger
- Regroupement québécois de Recherche sur la Fonction, l'Ingénierie et les Applications des Protéines (PROTEO), Centre de Recherche sur les Matériaux Avancés (CERMA), Centre Québécois sur les Matériaux Fonctionnels (CQMF), Département de Chimie, Université Laval, 1045 avenue de la Médecine; Québec QC Canada G1V 0A6
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30
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Wei Q, Ma Y, Li L, Liu Q, Liu Z, Liu G. Synthesis of Quaternary α-Fluorinated α-Amino Acid Derivatives via Coordinating Cu(II) Catalytic α-C(sp 3)-H Direct Fluorination. Org Lett 2018; 20:7100-7103. [PMID: 30362773 DOI: 10.1021/acs.orglett.8b03044] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A coordinating, copper-catalyzed direct α-C(sp3)-H fluorination method has been developed to prepare vital quaternary α-fluorinated α-amino acid derivatives. A Cu(II) catalytic SET oxidative addition mechanism is proposed, involving a key fluoride-coupled Cu(II) charge transfer complex. The protocol can tolerate a rich variety of α-amino acids, for which the auxiliary group is removed in high yield and substituted for the direct preparation of dipeptide derivatives with detachable, single absolute configurations of the target compounds.
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Affiliation(s)
- Qiang Wei
- Tsinghua-Peking Center for Life Sciences, School of Life Sciences , Tsinghua University , Beijing 100084 , China
| | - Yao Ma
- Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College , Beijing 100050 , China
| | - Li Li
- Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College , Beijing 100050 , China
| | - Qingfei Liu
- School of Pharmaceutical Sciences , Tsinghua University , Beijing 100084 , China
| | - Zijie Liu
- Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College , Beijing 100050 , China
| | - Gang Liu
- Tsinghua-Peking Center for Life Sciences, School of Life Sciences , Tsinghua University , Beijing 100084 , China.,School of Pharmaceutical Sciences , Tsinghua University , Beijing 100084 , China
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31
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Xu Y, Correia I, Ha-Duong T, Kihal N, Soulier JL, Kaffy J, Crousse B, Lequin O, Ongeri S. The use of 4,4,4-trifluorothreonine to stabilize extended peptide structures and mimic β-strands. Beilstein J Org Chem 2018; 13:2842-2853. [PMID: 29564012 PMCID: PMC5753055 DOI: 10.3762/bjoc.13.276] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Accepted: 12/13/2017] [Indexed: 01/06/2023] Open
Abstract
Pentapeptides having the sequence R-HN-Ala-Val-X-Val-Leu-OMe, where the central residue X is L-serine, L-threonine, (2S,3R)-L-CF3-threonine and (2S,3S)-L-CF3-threonine were prepared. The capacity of (2S,3S)- and (2S,3R)-CF3-threonine analogues to stabilize an extended structure when introduced in the central position of pentapeptides is demonstrated by NMR conformational studies and molecular dynamics simulations. CF3-threonine containing pentapeptides are more prone to mimic β-strands than their natural Ser and Thr pentapeptide analogues. The proof of concept that these fluorinated β-strand mimics are able to disrupt protein–protein interactions involving β-sheet structures is provided. The CF3-threonine containing pentapeptides interact with the amyloid peptide Aβ1-42 in order to reduce the protein–protein interactions mediating its aggregation process.
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Affiliation(s)
- Yaochun Xu
- Molécules Fluorées et Chimie Médicinale, BioCIS, Univ. Paris-Sud, CNRS, Université Paris Saclay, 5 rue Jean-Baptiste Clément, 92296 Châtenay-Malabry Cedex, France
| | - Isabelle Correia
- Sorbonne Universités, UPMC Univ Paris 06, Ecole Normale Supérieure, PSL Research University, CNRS, Laboratoire des Biomolécules, 4 place Jussieu, 75252 Paris Cedex 05, France
| | - Tap Ha-Duong
- Molécules Fluorées et Chimie Médicinale, BioCIS, Univ. Paris-Sud, CNRS, Université Paris Saclay, 5 rue Jean-Baptiste Clément, 92296 Châtenay-Malabry Cedex, France
| | - Nadjib Kihal
- Molécules Fluorées et Chimie Médicinale, BioCIS, Univ. Paris-Sud, CNRS, Université Paris Saclay, 5 rue Jean-Baptiste Clément, 92296 Châtenay-Malabry Cedex, France
| | - Jean-Louis Soulier
- Molécules Fluorées et Chimie Médicinale, BioCIS, Univ. Paris-Sud, CNRS, Université Paris Saclay, 5 rue Jean-Baptiste Clément, 92296 Châtenay-Malabry Cedex, France
| | - Julia Kaffy
- Molécules Fluorées et Chimie Médicinale, BioCIS, Univ. Paris-Sud, CNRS, Université Paris Saclay, 5 rue Jean-Baptiste Clément, 92296 Châtenay-Malabry Cedex, France
| | - Benoît Crousse
- Molécules Fluorées et Chimie Médicinale, BioCIS, Univ. Paris-Sud, CNRS, Université Paris Saclay, 5 rue Jean-Baptiste Clément, 92296 Châtenay-Malabry Cedex, France
| | - Olivier Lequin
- Sorbonne Universités, UPMC Univ Paris 06, Ecole Normale Supérieure, PSL Research University, CNRS, Laboratoire des Biomolécules, 4 place Jussieu, 75252 Paris Cedex 05, France
| | - Sandrine Ongeri
- Molécules Fluorées et Chimie Médicinale, BioCIS, Univ. Paris-Sud, CNRS, Université Paris Saclay, 5 rue Jean-Baptiste Clément, 92296 Châtenay-Malabry Cedex, France
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32
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Perfluorophenyl phosphonate analogues of aromatic amino acids: Synthesis, X-ray and DFT studies. Tetrahedron 2018. [DOI: 10.1016/j.tet.2018.01.019] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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33
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Das S, Ben Haj Salah K, Wenger E, Martinez J, Kotarba J, Andreu V, Ruiz N, Savini F, Stella L, Didierjean C, Legrand B, Inguimbert N. Enhancing the Antimicrobial Activity of Alamethicin F50/5 by Incorporating N-terminal Hydrophobic Triazole Substituents. Chemistry 2017; 23:17964-17972. [DOI: 10.1002/chem.201703569] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Indexed: 01/20/2023]
Affiliation(s)
- Sanjit Das
- USR 3278 CRIOBE, PSL Research University, EPHE-UPVD-CNRS; Université de Perpignan Via Domitia, Laboratoire d'Excellence « CORAIL » Bâtiment T; 58 avenue P. Alduy 66860 Perpignan France)
| | - Khoubaib Ben Haj Salah
- USR 3278 CRIOBE, PSL Research University, EPHE-UPVD-CNRS; Université de Perpignan Via Domitia, Laboratoire d'Excellence « CORAIL » Bâtiment T; 58 avenue P. Alduy 66860 Perpignan France)
| | - Emmanuel Wenger
- CRM2 (UMR UL-CNRS 7036) Faculté des Sciences et Technologies; Université de Lorraine; 70239 Boulevard des Aiguillettes 54506 Vandoeuvre-lès-Nancy France)
| | - Jean Martinez
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247 CNRS; Université de Montpellier; 15 avenue Charles Flahault, BP 14491 34093 Montpellier Cedex 5 France
| | | | | | - Nicolas Ruiz
- Laboratoire Mer Molécules Santé.; Université de Nantes, UFR de Sciences pharmaceutiques et biologiques; 9 rue Bias-BP 61112 44035 Nantes France
| | - Filippo Savini
- Dipartimento di Scienze e Tecnologie Chimiche; Università di Roma, Tor Vergata; Via della Ricerca Scientifica 00133 Roma Italy)
| | - Lorenzo Stella
- Dipartimento di Scienze e Tecnologie Chimiche; Università di Roma, Tor Vergata; Via della Ricerca Scientifica 00133 Roma Italy)
| | - Claude Didierjean
- CRM2 (UMR UL-CNRS 7036) Faculté des Sciences et Technologies; Université de Lorraine; 70239 Boulevard des Aiguillettes 54506 Vandoeuvre-lès-Nancy France)
| | - Baptiste Legrand
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247 CNRS; Université de Montpellier; 15 avenue Charles Flahault, BP 14491 34093 Montpellier Cedex 5 France
| | - Nicolas Inguimbert
- USR 3278 CRIOBE, PSL Research University, EPHE-UPVD-CNRS; Université de Perpignan Via Domitia, Laboratoire d'Excellence « CORAIL » Bâtiment T; 58 avenue P. Alduy 66860 Perpignan France)
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Şologan M, Boccalon M, Bidoggia S, Gentilini C, Pasquato L, Pengo P. Self-sorting in mixed fluorinated/hydrogenated assemblies. Supramol Chem 2017. [DOI: 10.1080/10610278.2017.1386307] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Maria Şologan
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Trieste, Italy
| | - Mariangela Boccalon
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Trieste, Italy
| | - Silvia Bidoggia
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Trieste, Italy
| | - Cristina Gentilini
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Trieste, Italy
| | - Lucia Pasquato
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Trieste, Italy
| | - Paolo Pengo
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Trieste, Italy
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35
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Kasten K, Slawin AMZ, Smith AD. Enantioselective Synthesis of β-Fluoro-β-aryl-α-aminopentenamides by Organocatalytic [2,3]-Sigmatropic Rearrangement. Org Lett 2017; 19:5182-5185. [PMID: 28885031 DOI: 10.1021/acs.orglett.7b02452] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The tetramisole-promoted catalytic enantioselective [2,3]-sigmatropic rearrangement of quaternary ammonium salts bearing a (Z)-3-fluoro-3-arylprop-2-ene group generates, after addition of benzylamine, a range of β-fluoro-β-aryl-α-aminopentenamides containing a stereogenic tertiary fluorine substituent. Cyclic and acyclic nitrogen substituents as well as various aromatic substituents are tolerated, giving the β-fluoro-β-aryl-α-aminopentenamide products in up to 76% yield, 96:4 dr, and 98:2 er.
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Affiliation(s)
- Kevin Kasten
- EaStCHEM, School of Chemistry, University of St Andrews , North Haugh, St Andrews, Fife, KY16 9ST, U.K
| | - Alexandra M Z Slawin
- EaStCHEM, School of Chemistry, University of St Andrews , North Haugh, St Andrews, Fife, KY16 9ST, U.K
| | - Andrew D Smith
- EaStCHEM, School of Chemistry, University of St Andrews , North Haugh, St Andrews, Fife, KY16 9ST, U.K
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Mondal S, Chaterjee S, Halder R, Jana B, Singh PC. Role of Dispersive Fluorous Interaction in the Solvation Dynamics of the Perfluoro Group Containing Molecules. J Phys Chem B 2017; 121:7681-7688. [PMID: 28737391 DOI: 10.1021/acs.jpcb.7b03420] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Perfluoro group containing molecules possess an important self-aggregation property through the fluorous (F···F) interaction which makes them useful for diverse applications such as medicinal chemistry, separation techniques, polymer technology, and biology. In this article, we have investigated the solvation dynamics of coumarin-153 (C153) and coumarin-6H (C6H) in ethanol (ETH), 2-fluoroethanol (MFE), and 2,2,2-trifluoroethanol (TFE) using the femtosecond upconversion technique and molecular dynamics (MD) simulation to understand the role of fluorous interaction between the solute and solvent molecules in the solvation dynamics of perfluoro group containing molecules. The femtosecond upconversion data show that the time scales of solvation dynamics of C6H in ETH, MFE, and TFE are approximately the same whereas the solvation dynamics of C153 in TFE is slow as compared to that of ETH and MFE. It has also been observed that the time scale of solvation dynamics of C6H in ETH and MFE is higher than that of C153 in the same solvents. MD simulation results show a qualitative agreement with the experimental data in terms of the time scale of the slow components of the solvation for all the systems. The experimental and simulation studies combined lead to the conclusion that the solvation dynamics of C6H in all solvents as well as C153 in ETH and MFE is mostly governed by the charge distribution of ester moieties (C═O and O) of dye molecules whereas the solvation of C153 in TFE is predominantly due to the dispersive fluorous interaction (F···F) between the perfluoro groups of the C153 and solvent molecules.
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Affiliation(s)
- Saptarsi Mondal
- Department of Spectroscopy, and ‡Department of Physical Chemistry, Indian Association for the Cultivation of Science , Kolkata, India
| | - Soumit Chaterjee
- Department of Spectroscopy, and ‡Department of Physical Chemistry, Indian Association for the Cultivation of Science , Kolkata, India
| | - Ritaban Halder
- Department of Spectroscopy, and ‡Department of Physical Chemistry, Indian Association for the Cultivation of Science , Kolkata, India
| | - Biman Jana
- Department of Spectroscopy, and ‡Department of Physical Chemistry, Indian Association for the Cultivation of Science , Kolkata, India
| | - Prashant Chandra Singh
- Department of Spectroscopy, and ‡Department of Physical Chemistry, Indian Association for the Cultivation of Science , Kolkata, India
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A combined molecular dynamics simulation, atoms in molecule analysis and IR study on the biologically important bulk fluorinated ethanols to understand the role of weak interactions in their cluster formation and hydrogen bond network. J Mol Liq 2017. [DOI: 10.1016/j.molliq.2017.05.098] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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38
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Mondal S, Halder R, Biswas B, Jana B, Singh PC. Solvent organization around the perfluoro group of coumarin 153 governs its photophysical properties: An experimental and simulation study of coumarin dyes in ethanol as well as fluorinated ethanol solvents. J Chem Phys 2017; 144:184504. [PMID: 27179492 DOI: 10.1063/1.4948704] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The self-aggregation property of the perfluoro group containing molecules makes it important in the research fields of biology and polymer and organic synthesis. In the quest of understanding the role of the perfluoro group on the photophysical properties of perfluoro-containing molecules in biologically important fluoroethanol solvents, we have applied photophysical as well as molecular dynamics simulation techniques to explore the properties of perfluoro groups containing molecule coumarin-153 (C153) in ethanol (ETH), monofluoroethanol (MFE), difluoroethanol (DFE), and trifluoroethanol (TFE) and compared them with the molecules without perfluoro moiety, namely coumarin-6H (C6H) and coumarin-480 (C480). In contrast to C6H and C480, the excited state lifetime of C153 in fluorinated ETHs is not monotonic. The excited state lifetime of C153 decreases in MFE and DFE as compared to ETH, whereas in TFE, it increases as compared to MFE and DFE. Molecular dynamics simulation reveals that the carbon terminal away from the OH group of fluorinated ETHs has a preferential orientation near the perfluoro (CF3) group of C153. In MFE and DFE, the CF3 group of C153 prefers to have a CF2-F⋯H -(CHF) type of electrostatic interaction over CF2-F⋯F -(CH2) kind of dispersion interaction which increases the rate of nonradiative decay, probably due to the electrostatic nature of the CF2-F⋯H -(CHF) hydrogen bond. On the other hand, in TFE, C-F⋯ F-C type of dispersion interaction, also known as fluorous interaction, takes place between the CF3 groups of C153 and TFE which decreases the rate of nonradiative rate as compared to MFE and DFE, leading to the increased lifetime of C153 in TFE. Photophysical and MD simulation studies clearly depict that the structural organization of solvents and their interaction with the fluorocarbon group are crucial factors for the photophysical behavior of the fluorocarbon containing molecules.
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Affiliation(s)
- Saptarsi Mondal
- Department of Spectroscopy, Indian Association for the Cultivation of Science, Kolkata 700032, India
| | - Ritaban Halder
- Department of Physical Chemistry, Indian Association for the Cultivation of Science, Kolkata 700032, India
| | - Biswajit Biswas
- Department of Spectroscopy, Indian Association for the Cultivation of Science, Kolkata 700032, India
| | - Biman Jana
- Department of Physical Chemistry, Indian Association for the Cultivation of Science, Kolkata 700032, India
| | - Prashant Chandra Singh
- Department of Spectroscopy, Indian Association for the Cultivation of Science, Kolkata 700032, India
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Zarandi M, Cai R, Kovacs M, Popovics P, Szalontay L, Cui T, Sha W, Jaszberenyi M, Varga J, Zhang X, Block NL, Rick FG, Halmos G, Schally AV. Synthesis and structure-activity studies on novel analogs of human growth hormone releasing hormone (GHRH) with enhanced inhibitory activities on tumor growth. Peptides 2017; 89:60-70. [PMID: 28130121 DOI: 10.1016/j.peptides.2017.01.009] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Revised: 01/10/2017] [Accepted: 01/23/2017] [Indexed: 12/21/2022]
Abstract
The syntheses and biological evaluations of new GHRH analogs of Miami (MIA) series with greatly increased anticancer activity are described. In the design and synthesis of these analogs, the following previous substitutions were conserved: D-Arg2, Har9, Abu15, and Nle27. Most new analogs had Ala at position 8. Since replacements of both Lys12 and Lys21 with Orn increased resistance against enzymatic degradation, these modifications were kept. The substitutions of Arg at both positions 11 and 20 by His were also conserved. We kept D-Arg28, Har29 -NH2 at the C-terminus or inserted Agm or 12-amino dodecanoic acid amide at position 30. We incorporated pentafluoro-Phe (Fpa5), instead of Cpa, at position 6 and Tyr(Me) at position 10 and ω-amino acids at N-terminus of some analogs. These GHRH analogs were prepared by solid-phase methodology and purified by HPLC. The evaluation of the activity of the analogs on GH release was carried out in vitro on rat pituitaries and in vivo in male rats. Receptor binding affinities were measured in vitro by the competitive binding analysis. The inhibitory activity of the analogs on tumor proliferation in vitro was tested in several human cancer cell lines such as HEC-1A endometrial adenocarcinoma, HCT-15 colorectal adenocarcinoma, and LNCaP prostatic carcinoma. For in vivo tests, various cell lines including PC-3 prostate cancer, HEC-1A endometrial adenocarcinoma, HT diffuse mixed β cell lymphoma, and ACHN renal cell carcinoma cell lines were xenografted into nude mice and treated subcutaneously with GHRH antagonists at doses of 1-5μg/day. Analogs MIA-602, MIA-604, MIA-610, and MIA-640 showed the highest binding affinities, 30, 58, 48, and 73 times higher respectively, than GHRH (1-29) NH2. Treatment of LNCaP and HCT-15 cells with 5μM MIA-602 or MIA-690 decreased proliferation by 40%-80%. In accord with previous tests in various human cancer lines, analog MIA-602 showed high inhibitory activity in vivo on growth of PC-3 prostate cancer, HT-mixed β cell lymphoma, HEC-1A endometrial adenocarcinoma and ACHN renal cell carcinoma. Thus, GHRH analogs of the Miami series powerfully suppress tumor growth, but have only a weak endocrine GH inhibitory activity. The suppression of tumor growth could be induced in part by the downregulation of GHRH receptors levels.
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Affiliation(s)
- Marta Zarandi
- Endocrine, Polypeptide, and Cancer Institute, Veterans Affairs Medical Center, Miami, FL, United States; South Florida VA Foundation for Research and Education, Miami, FL, United States; Department of Pathology, Department of Medicine, University of Miami Miller School of Medicine, Miami, FL, United States
| | - Renzhi Cai
- Endocrine, Polypeptide, and Cancer Institute, Veterans Affairs Medical Center, Miami, FL, United States; South Florida VA Foundation for Research and Education, Miami, FL, United States; Department of Pathology, Department of Medicine, University of Miami Miller School of Medicine, Miami, FL, United States; Division of Endocrinology, Department of Medicine, University of Miami Miller School of Medicine, Miami, FL, United States
| | - Magdolna Kovacs
- Endocrine, Polypeptide, and Cancer Institute, Veterans Affairs Medical Center, Miami, FL, United States; South Florida VA Foundation for Research and Education, Miami, FL, United States; Department of Pathology, Department of Medicine, University of Miami Miller School of Medicine, Miami, FL, United States
| | - Petra Popovics
- Endocrine, Polypeptide, and Cancer Institute, Veterans Affairs Medical Center, Miami, FL, United States; South Florida VA Foundation for Research and Education, Miami, FL, United States; Division of Endocrinology, Department of Medicine, University of Miami Miller School of Medicine, Miami, FL, United States
| | - Luca Szalontay
- Endocrine, Polypeptide, and Cancer Institute, Veterans Affairs Medical Center, Miami, FL, United States; South Florida VA Foundation for Research and Education, Miami, FL, United States; Department of Pathology, Department of Medicine, University of Miami Miller School of Medicine, Miami, FL, United States
| | - Tengjiao Cui
- Endocrine, Polypeptide, and Cancer Institute, Veterans Affairs Medical Center, Miami, FL, United States; South Florida VA Foundation for Research and Education, Miami, FL, United States; Department of Pathology, Department of Medicine, University of Miami Miller School of Medicine, Miami, FL, United States; Division of Endocrinology, Department of Medicine, University of Miami Miller School of Medicine, Miami, FL, United States
| | - Wei Sha
- Endocrine, Polypeptide, and Cancer Institute, Veterans Affairs Medical Center, Miami, FL, United States; Division of Endocrinology, Department of Medicine, University of Miami Miller School of Medicine, Miami, FL, United States; Division of Hematology/Oncology, Department of Medicine, University of Miami Miller School of Medicine, Miami, FL, United States; Sylvester Comprehensive Cancer Center, Miami, FL, United States
| | - Miklos Jaszberenyi
- Endocrine, Polypeptide, and Cancer Institute, Veterans Affairs Medical Center, Miami, FL, United States; South Florida VA Foundation for Research and Education, Miami, FL, United States; Department of Pathology, Department of Medicine, University of Miami Miller School of Medicine, Miami, FL, United States
| | - Jozsef Varga
- Endocrine, Polypeptide, and Cancer Institute, Veterans Affairs Medical Center, Miami, FL, United States
| | - XianYang Zhang
- Endocrine, Polypeptide, and Cancer Institute, Veterans Affairs Medical Center, Miami, FL, United States; South Florida VA Foundation for Research and Education, Miami, FL, United States; Interdisciplinary Stem Cell Institute, University of Miami Miller School of Medicine, Miami, FL, United States
| | - Norman L Block
- South Florida VA Foundation for Research and Education, Miami, FL, United States; Department of Pathology, Department of Medicine, University of Miami Miller School of Medicine, Miami, FL, United States; Sylvester Comprehensive Cancer Center, Miami, FL, United States; Interdisciplinary Stem Cell Institute, University of Miami Miller School of Medicine, Miami, FL, United States
| | - Ferenc G Rick
- Endocrine, Polypeptide, and Cancer Institute, Veterans Affairs Medical Center, Miami, FL, United States; South Florida VA Foundation for Research and Education, Miami, FL, United States; Department of Urology, Florida International University, Herbert Wertheim College of Medicine, Miami, FL, United States
| | - Gabor Halmos
- Endocrine, Polypeptide, and Cancer Institute, Veterans Affairs Medical Center, Miami, FL, United States; South Florida VA Foundation for Research and Education, Miami, FL, United States
| | - Andrew V Schally
- Endocrine, Polypeptide, and Cancer Institute, Veterans Affairs Medical Center, Miami, FL, United States; South Florida VA Foundation for Research and Education, Miami, FL, United States; Department of Pathology, Department of Medicine, University of Miami Miller School of Medicine, Miami, FL, United States; Division of Endocrinology, Department of Medicine, University of Miami Miller School of Medicine, Miami, FL, United States; Division of Hematology/Oncology, Department of Medicine, University of Miami Miller School of Medicine, Miami, FL, United States; Sylvester Comprehensive Cancer Center, Miami, FL, United States.
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40
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Völler JS, Dulic M, Gerling-Driessen UIM, Biava H, Baumann T, Budisa N, Gruic-Sovulj I, Koksch B. Discovery and Investigation of Natural Editing Function against Artificial Amino Acids in Protein Translation. ACS CENTRAL SCIENCE 2017; 3:73-80. [PMID: 28149956 PMCID: PMC5269655 DOI: 10.1021/acscentsci.6b00339] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Indexed: 05/24/2023]
Abstract
Fluorine being not substantially present in the chemistry of living beings is an attractive element in tailoring novel chemical, biophysical, and pharmacokinetic properties of peptides and proteins. The hallmark of ribosome-mediated artificial amino acid incorporation into peptides and proteins is a broad substrate tolerance, which is assumed to rely on the absence of evolutionary pressure for efficient editing of artificial amino acids. We used the well-characterized editing proficient isoleucyl-tRNA synthetase (IleRS) from Escherichia coli to investigate the crosstalk of aminoacylation and editing activities against fluorinated amino acids. We show that translation of trifluoroethylglycine (TfeGly) into proteins is prevented by hydrolysis of TfeGly-tRNAIle in the IleRS post-transfer editing domain. The remarkable observation is that dissociation of TfeGly-tRNAIle from IleRS is significantly slowed down. This finding is in sharp contrast to natural editing reactions by tRNA synthetases wherein fast editing rates for the noncognate substrates are essential to outcompete fast aa-tRNA dissociation rates. Using a post-transfer editing deficient mutant of IleRS (IleRSAla10), we were able to achieve ribosomal incorporation of TfeGly in vivo. Our work expands the knowledge of ribosome-mediated artificial amino acid translation with detailed analysis of natural editing function against an artificial amino acid providing an impulse for further systematic investigations and engineering of the translation and editing of unusual amino acids.
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Affiliation(s)
- Jan-Stefan Völler
- Institute
of Chemistry and Biochemistry − Organic Chemistry, Freie Universität Berlin, Takustrasse 3, 14195 Berlin, Germany
- Department
of Chemistry, Technische Universität
Berlin, Müller-Breslau-Strasse 10, 10623 Berlin, Germany
| | - Morana Dulic
- Department
of Chemistry, Faculty of Science, University
of Zagreb, Horvatovac
102a, 10000 Zagreb, Croatia
| | - Ulla I. M. Gerling-Driessen
- Institute
of Chemistry and Biochemistry − Organic Chemistry, Freie Universität Berlin, Takustrasse 3, 14195 Berlin, Germany
| | - Hernan Biava
- Department
of Chemistry, Technische Universität
Berlin, Müller-Breslau-Strasse 10, 10623 Berlin, Germany
| | - Tobias Baumann
- Department
of Chemistry, Technische Universität
Berlin, Müller-Breslau-Strasse 10, 10623 Berlin, Germany
| | - Nediljko Budisa
- Department
of Chemistry, Technische Universität
Berlin, Müller-Breslau-Strasse 10, 10623 Berlin, Germany
| | - Ita Gruic-Sovulj
- Department
of Chemistry, Faculty of Science, University
of Zagreb, Horvatovac
102a, 10000 Zagreb, Croatia
| | - Beate Koksch
- Institute
of Chemistry and Biochemistry − Organic Chemistry, Freie Universität Berlin, Takustrasse 3, 14195 Berlin, Germany
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41
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Chernykh AV, Feskov IO, Chernykh AV, Kondratov IS, Tolmachova N, Radchenko DS, Daniliuc CG, Haufe G. Synthesis and Physical-Chemical Properties ofcis- andtrans-1-Amino-3-fluoro-3-methylcyclobutanecarboxylic Acids. European J Org Chem 2016. [DOI: 10.1002/ejoc.201600953] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Anton V. Chernykh
- Enamine Ltd; Chervonotkatska St 78 02094 Kyiv Ukraine
- Institute of Organic Chemistry; National Academy of Sciences of Ukraine; Murmanska Str. 5 02660 Kyiv Ukraine
| | - Illia O. Feskov
- Enamine Ltd; Chervonotkatska St 78 02094 Kyiv Ukraine
- Institute of Bioorganic Chemistry and Petrochemistry; National Academy of Sciences of Ukraine; Murmanska Str. 1 02660 Kyiv Ukraine
| | | | - Ivan S. Kondratov
- Enamine Ltd; Chervonotkatska St 78 02094 Kyiv Ukraine
- Institute of Bioorganic Chemistry and Petrochemistry; National Academy of Sciences of Ukraine; Murmanska Str. 1 02660 Kyiv Ukraine
| | - Nataliya Tolmachova
- Enamine Ltd; Chervonotkatska St 78 02094 Kyiv Ukraine
- Institute of Bioorganic Chemistry and Petrochemistry; National Academy of Sciences of Ukraine; Murmanska Str. 1 02660 Kyiv Ukraine
| | - Dmytro S. Radchenko
- Enamine Ltd; Chervonotkatska St 78 02094 Kyiv Ukraine
- Institute of High Technologies; Taras Shevchenko National University of Kyiv; Volodymyrska 60 01601 Kyiv Ukraine
| | - Constantin G. Daniliuc
- Organisch-Chemisches Institut; Universität Münster; Corrensstraße 40 48149 Münster Germany
| | - Günter Haufe
- Organisch-Chemisches Institut; Universität Münster; Corrensstraße 40 48149 Münster Germany
- Cells-in-Motion Cluster of Excellence; Universität Münster; Waldeyerstraße 15 48149 Münster Germany
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Şologan M, Cantarutti C, Bidoggia S, Polizzi S, Pengo P, Pasquato L. Routes to the preparation of mixed monolayers of fluorinated and hydrogenated alkanethiolates grafted on the surface of gold nanoparticles. Faraday Discuss 2016; 191:527-543. [PMID: 27459891 DOI: 10.1039/c6fd00016a] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
The use of binary blends of hydrogenated and fluorinated alkanethiolates represents an interesting approach to the construction of anisotropic hybrid organic-inorganic nanoparticles since the fluorinated and hydrogenated components are expected to self-sort on the nanoparticle surface because of their reciprocal phobicity. These mixed monolayers are therefore strongly non-ideal binary systems. The synthetic routes we explored to achieve mixed monolayer gold nanoparticles displaying hydrogenated and fluorinated ligands clearly show that the final monolayer composition is a non-linear function of the initial reaction mixture. Our data suggest that, under certain geometrical constraints, nucleation and growth of fluorinated domains could be the initial event in the formation of these mixed monolayers. The onset of domain formation depends on the structure of the fluorinated and hydrogenated species. The solubility of the mixed monolayer nanoparticles displayed a marked discontinuity as a function of the monolayer composition. When the fluorinated component content is small, the nanoparticle systems are fully soluble in chloroform, at intermediate content the nanoparticles become soluble in hexane and eventually they become soluble in fluorinated solvents only. The ranges of monolayer compositions in which the solubility transitions are observed depend on the nature of the thiols composing the monolayer.
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Affiliation(s)
- Maria Şologan
- Department of Chemical and Pharmaceutical Sciences and INSTM Trieste Unit, University of Trieste, via L. Giorgieri 1, 34127 Trieste, Italy.
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Abstract
As methods to incorporate noncanonical amino acid residues into proteins have become more powerful, interest in their use to modify the physical and biological properties of proteins and enzymes has increased. This chapter discusses the use of highly fluorinated analogs of hydrophobic amino acids, for example, hexafluoroleucine, in protein design. In particular, fluorinated residues have proven to be generally effective in increasing the thermodynamic stability of proteins. The chapter provides an overview of the different fluorinated amino acids that have been used in protein design and the various methods available for producing fluorinated proteins. It discusses model proteins systems into which highly fluorinated amino acids have been introduced and the reasons why fluorinated residues are generally stabilizing, with particular reference to thermodynamic and structural studies from our laboratory. Lastly, details of the methodology we have developed to measure the thermodynamic stability of oligomeric fluorinated proteins are presented, as this may be generally applicable to many proteins.
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Affiliation(s)
- E N G Marsh
- University of Michigan, Ann Arbor, MI, United States.
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45
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Zheng C, Qiu Q, Hao L, Li H. Studies on the halogen substituted β-amino acids and their Cu(II) coordination complexes in crystallography. Chem Res Chin Univ 2016. [DOI: 10.1007/s40242-016-5333-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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46
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Kasireddy C, Bann JG, Mitchell-Koch KR. Demystifying fluorine chemical shifts: electronic structure calculations address origins of seemingly anomalous (19)F-NMR spectra of fluorohistidine isomers and analogues. Phys Chem Chem Phys 2015; 17:30606-12. [PMID: 26524669 PMCID: PMC4643390 DOI: 10.1039/c5cp05502d] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Fluorine NMR spectroscopy is a powerful tool for studying biomolecular structure, dynamics, and ligand binding, yet the origins of (19)F chemical shifts are not well understood. Herein, we use electronic structure calculations to describe the changes in (19)F chemical shifts of 2F- and 4F-histidine/(5-methyl)-imidazole upon acid titration. While the protonation of the 2F species results in a deshielded chemical shift, protonation of the 4F isomer results in an opposite, shielded chemical shift. The deshielding of 2F-histidine/(5-methyl)-imidazole upon protonation can be rationalized by concomitant decreases in charge density on fluorine and a reduced dipole moment. These correlations do not hold for 4F-histidine/(5-methyl)-imidazole, however. Molecular orbital calculations reveal that for the 4F species, there are no lone pair electrons on the fluorine until protonation. Analysis of a series of 4F-imidazole analogues, all with delocalized fluorine electron density, indicates that the deshielding of (19)F chemical shifts through substituent effects correlates with increased C-F bond polarity. In summary, the delocalization of fluorine electrons in the neutral 4F species, with gain of a lone pair upon protonation may help explain the difficulty in developing a predictive framework for fluorine chemical shifts. Ideas debated by chemists over 40 years ago, regarding fluorine's complex electronic effects, are shown to have relevance for understanding and predicting fluorine NMR spectra.
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Affiliation(s)
- Chandana Kasireddy
- Department of Chemistry, Wichita State University, 1845 Fairmount, Wichita, Kansas 67260-0051, USA.
| | - James G Bann
- Department of Chemistry, Wichita State University, 1845 Fairmount, Wichita, Kansas 67260-0051, USA.
| | - Katie R Mitchell-Koch
- Department of Chemistry, Wichita State University, 1845 Fairmount, Wichita, Kansas 67260-0051, USA.
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Liu Z, Jenkinson SF, Vermaas T, Adachi I, Wormald MR, Hata Y, Kurashima Y, Kaji A, Yu CY, Kato A, Fleet GWJ. 3-Fluoroazetidinecarboxylic Acids and trans,trans-3,4-Difluoroproline as Peptide Scaffolds: Inhibition of Pancreatic Cancer Cell Growth by a Fluoroazetidine Iminosugar. J Org Chem 2015; 80:4244-58. [DOI: 10.1021/acs.joc.5b00463] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Zilei Liu
- Chemistry
Research Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3TA, U.K
| | - Sarah F. Jenkinson
- Chemistry
Research Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3TA, U.K
| | - Tom Vermaas
- Chemistry
Research Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3TA, U.K
| | - Isao Adachi
- Department
of Hospital Pharmacy, University of Toyama, Toyama 930-0194, Japan
| | - Mark R. Wormald
- Glycobiology
Institute, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, U.K
| | - Yukako Hata
- Faculty
of Pharmaceutical Sciences, Hokuriku University, Kanazawa 920-1181, Japan
| | - Yukiko Kurashima
- Faculty
of Pharmaceutical Sciences, Hokuriku University, Kanazawa 920-1181, Japan
| | - Akira Kaji
- Faculty
of Pharmaceutical Sciences, Hokuriku University, Kanazawa 920-1181, Japan
| | - Chu-Yi Yu
- CAS
Key Laboratory of Molecular Recognition and Function, Institute of
Chemistry, Chinese Academy of Sciences, Beijing 100190, P.R. China
- National
Engineering Research Center for Carbohydrate Synthesis, Jiangxi Normal University, Nanchang 330022, P.R. China
| | - Atsushi Kato
- Department
of Hospital Pharmacy, University of Toyama, Toyama 930-0194, Japan
| | - George W. J. Fleet
- Chemistry
Research Laboratory, Department of Chemistry, University of Oxford, Oxford OX1 3TA, U.K
- National
Engineering Research Center for Carbohydrate Synthesis, Jiangxi Normal University, Nanchang 330022, P.R. China
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48
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Davies SG, Fletcher AM, Frost AB, Roberts PM, Thomson JE. Asymmetric Synthesis of Substituted anti-β-Fluorophenylalanines. Org Lett 2015; 17:2254-7. [DOI: 10.1021/acs.orglett.5b00880] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Stephen G. Davies
- Department of Chemistry,
Chemistry Research Laboratory, University of Oxford, Mansfield
Road, Oxford OX1 3TA, U.K
| | - Ai M. Fletcher
- Department of Chemistry,
Chemistry Research Laboratory, University of Oxford, Mansfield
Road, Oxford OX1 3TA, U.K
| | - Aileen B. Frost
- Department of Chemistry,
Chemistry Research Laboratory, University of Oxford, Mansfield
Road, Oxford OX1 3TA, U.K
| | - Paul M. Roberts
- Department of Chemistry,
Chemistry Research Laboratory, University of Oxford, Mansfield
Road, Oxford OX1 3TA, U.K
| | - James E. Thomson
- Department of Chemistry,
Chemistry Research Laboratory, University of Oxford, Mansfield
Road, Oxford OX1 3TA, U.K
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49
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Currin A, Swainston N, Day PJ, Kell DB. Synthetic biology for the directed evolution of protein biocatalysts: navigating sequence space intelligently. Chem Soc Rev 2015; 44:1172-239. [PMID: 25503938 PMCID: PMC4349129 DOI: 10.1039/c4cs00351a] [Citation(s) in RCA: 251] [Impact Index Per Article: 27.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Indexed: 12/21/2022]
Abstract
The amino acid sequence of a protein affects both its structure and its function. Thus, the ability to modify the sequence, and hence the structure and activity, of individual proteins in a systematic way, opens up many opportunities, both scientifically and (as we focus on here) for exploitation in biocatalysis. Modern methods of synthetic biology, whereby increasingly large sequences of DNA can be synthesised de novo, allow an unprecedented ability to engineer proteins with novel functions. However, the number of possible proteins is far too large to test individually, so we need means for navigating the 'search space' of possible protein sequences efficiently and reliably in order to find desirable activities and other properties. Enzymologists distinguish binding (Kd) and catalytic (kcat) steps. In a similar way, judicious strategies have blended design (for binding, specificity and active site modelling) with the more empirical methods of classical directed evolution (DE) for improving kcat (where natural evolution rarely seeks the highest values), especially with regard to residues distant from the active site and where the functional linkages underpinning enzyme dynamics are both unknown and hard to predict. Epistasis (where the 'best' amino acid at one site depends on that or those at others) is a notable feature of directed evolution. The aim of this review is to highlight some of the approaches that are being developed to allow us to use directed evolution to improve enzyme properties, often dramatically. We note that directed evolution differs in a number of ways from natural evolution, including in particular the available mechanisms and the likely selection pressures. Thus, we stress the opportunities afforded by techniques that enable one to map sequence to (structure and) activity in silico, as an effective means of modelling and exploring protein landscapes. Because known landscapes may be assessed and reasoned about as a whole, simultaneously, this offers opportunities for protein improvement not readily available to natural evolution on rapid timescales. Intelligent landscape navigation, informed by sequence-activity relationships and coupled to the emerging methods of synthetic biology, offers scope for the development of novel biocatalysts that are both highly active and robust.
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Affiliation(s)
- Andrew Currin
- Manchester Institute of Biotechnology , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK . ; http://dbkgroup.org/; @dbkell ; Tel: +44 (0)161 306 4492
- School of Chemistry , The University of Manchester , Manchester M13 9PL , UK
- Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM) , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK
| | - Neil Swainston
- Manchester Institute of Biotechnology , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK . ; http://dbkgroup.org/; @dbkell ; Tel: +44 (0)161 306 4492
- Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM) , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK
- School of Computer Science , The University of Manchester , Manchester M13 9PL , UK
| | - Philip J. Day
- Manchester Institute of Biotechnology , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK . ; http://dbkgroup.org/; @dbkell ; Tel: +44 (0)161 306 4492
- Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM) , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK
- Faculty of Medical and Human Sciences , The University of Manchester , Manchester M13 9PT , UK
| | - Douglas B. Kell
- Manchester Institute of Biotechnology , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK . ; http://dbkgroup.org/; @dbkell ; Tel: +44 (0)161 306 4492
- School of Chemistry , The University of Manchester , Manchester M13 9PL , UK
- Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM) , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK
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50
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Odar C, Winkler M, Wiltschi B. Fluoro amino acids: A rarity in nature, yet a prospect for protein engineering. Biotechnol J 2015; 10:427-46. [DOI: 10.1002/biot.201400587] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Revised: 12/08/2014] [Accepted: 01/09/2015] [Indexed: 01/01/2023]
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