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Nieto-Domínguez M, Sako A, Enemark-Rasmussen K, Gotfredsen CH, Rago D, Nikel PI. Enzymatic synthesis of mono- and trifluorinated alanine enantiomers expands the scope of fluorine biocatalysis. Commun Chem 2024; 7:104. [PMID: 38724655 PMCID: PMC11082193 DOI: 10.1038/s42004-024-01188-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 04/24/2024] [Indexed: 05/12/2024] Open
Abstract
Fluorinated amino acids serve as an entry point for establishing new-to-Nature chemistries in biological systems, and novel methods are needed for the selective synthesis of these building blocks. In this study, we focused on the enzymatic synthesis of fluorinated alanine enantiomers to expand fluorine biocatalysis. The alanine dehydrogenase from Vibrio proteolyticus and the diaminopimelate dehydrogenase from Symbiobacterium thermophilum were selected for in vitro production of (R)-3-fluoroalanine and (S)-3-fluoroalanine, respectively, using 3-fluoropyruvate as the substrate. Additionally, we discovered that an alanine racemase from Streptomyces lavendulae, originally selected for setting an alternative enzymatic cascade leading to the production of these non-canonical amino acids, had an unprecedented catalytic efficiency in β-elimination of fluorine from the monosubstituted fluoroalanine. The in vitro enzymatic cascade based on the dehydrogenases of V. proteolyticus and S. thermophilum included a cofactor recycling system, whereby a formate dehydrogenase from Pseudomonas sp. 101 (either native or engineered) coupled formate oxidation to NAD(P)H formation. Under these conditions, the reaction yields for (R)-3-fluoroalanine and (S)-3-fluoroalanine reached >85% on the fluorinated substrate and proceeded with complete enantiomeric excess. The selected dehydrogenases also catalyzed the conversion of trifluoropyruvate into trifluorinated alanine as a first-case example of fluorine biocatalysis with amino acids carrying a trifluoromethyl group.
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Affiliation(s)
- Manuel Nieto-Domínguez
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Aboubakar Sako
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | | | | | - Daniela Rago
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Pablo I Nikel
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark.
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2
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Tanács D, Berkecz R, Bozsó Z, Tóth GK, Armstrong DW, Péter A, Ilisz I. Liquid Chromatographic Enantioseparation of Newly Synthesized Fluorinated Tryptophan Analogs Applying Macrocyclic Glycopeptides-Based Chiral Stationary Phases Utilizing Core-Shell Particles. Int J Mol Sci 2024; 25:4719. [PMID: 38731937 PMCID: PMC11083430 DOI: 10.3390/ijms25094719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 04/16/2024] [Accepted: 04/24/2024] [Indexed: 05/13/2024] Open
Abstract
Due to the favorable features obtained through the incorporation of fluorine atom(s), fluorinated drugs are a group with emerging pharmaceutical importance. As their commercial availability is still very limited, to expand the range of possible candidates, new fluorinated tryptophan analogs were synthesized. Control of enantiopurity during the synthesis procedure requires that highly efficient enantioseparation methods be available. In this work, the enantioseparation of seven fluorinated tryptophans and tryptophan was studied and compared systematically to (i) develop analytical methods for enantioselective separations and (ii) explore the chromatographic features of the fluorotrytophans. For enantioresolution, macrocyclic glycopeptide-based selectors linked to core-shell particles were utilized, applying liquid chromatography-based methods. Application of the polar-ionic mode resulted in asymmetric and broadened peaks, while reversed-phase conditions, together with mobile-phase additives, resulted in baseline separation for all studied fluorinated tryptophans. The marked differences observed between the methanol and acetonitrile-containing eluent systems can be explained by the different solvation abilities of the bulk solvents of the applied mobile phases. Among the studied chiral selectors, teicoplanin and teicoplanin aglycone were found to work effectively. Under optimized conditions, baseline separations were achieved within 6 min. Ionic interactions were semi-quantitatively characterized and found to not influence enantiorecognition. Interestingly, fluorination of the analytes does not lead to marked changes in the chromatographic characteristics of the methanol-containing eluents, while larger differences were noticed when the polar but aprotic acetonitrile was applied. Experiments conducted on the influence of the separation temperature indicated that the separations are enthalpically driven, with only one exception. Enantiomeric elution order was found to be constant on both teicoplanin and teicoplanin aglycone-based chiral stationary phases (L < D) under all applied chromatographic conditions.
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Affiliation(s)
- Dániel Tanács
- Institute of Pharmaceutical Analysis, University of Szeged, H-6720 Szeged, Hungary; (D.T.); (R.B.); (A.P.)
| | - Róbert Berkecz
- Institute of Pharmaceutical Analysis, University of Szeged, H-6720 Szeged, Hungary; (D.T.); (R.B.); (A.P.)
| | - Zsolt Bozsó
- Department of Medical Chemistry, University of Szeged, H-6720 Szeged, Hungary; (Z.B.); (G.K.T.)
| | - Gábor K. Tóth
- Department of Medical Chemistry, University of Szeged, H-6720 Szeged, Hungary; (Z.B.); (G.K.T.)
| | - Daniel W. Armstrong
- Department of Chemistry and Biochemistry, University of Texas at Arlington, Arlington, TX 76019-0065, USA;
| | - Antal Péter
- Institute of Pharmaceutical Analysis, University of Szeged, H-6720 Szeged, Hungary; (D.T.); (R.B.); (A.P.)
| | - István Ilisz
- Institute of Pharmaceutical Analysis, University of Szeged, H-6720 Szeged, Hungary; (D.T.); (R.B.); (A.P.)
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3
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Demir Ğ, Valjakka J, Turunen O, Aktaş F, Binay B. Cloning and expression heterologous alanine dehydrogenase genes: Investigation of reductive amination potential of L-alanine dehydrogenases for green synthesis of alanine derivatives. Heliyon 2024; 10:e26899. [PMID: 38463761 PMCID: PMC10923667 DOI: 10.1016/j.heliyon.2024.e26899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 02/09/2024] [Accepted: 02/21/2024] [Indexed: 03/12/2024] Open
Abstract
Unnatural amino acids (UAAs) offer significant promise in a wide range of applications, including drug discovery, the custom design of peptides and proteins, and their utility and use as markers for monitoring molecular interactions in biological research. The synthesis of UAAs presents a formidable challenge and can be classified into two primary categories: enzymatic and chemical synthesis. Notably, the enzymatic route, specifically asymmetric synthesis, emerges as a an attractive method for procuring enantiopure UAAs with high efficiency, owing to its streamlined and concise reaction mechanism. The current study investigated the reductive amination activity mechanisms of alanine dehydrogenase (L-AlaDH), sourced from a combination of newly and previously characterized microorganisms. Our principal aim was to evaluate the catalytic efficiency of these L-AlaDH enzymes concerning a range of specific ketoacids and pyruvate to ascertain their capability for facilitating the production of both natural and unnatural amino acids. After the characterization processes, mutation points for TtAlaDH were determined and as a result of the mutations, mutants that could use ketocaproate and ketovalerate more effectively than the wild type were obtained. Among the enzymes studied, MetAlaDH exhibited the highest specific activity against pyruvate, 173 U/mg, and a KM value of 1.3 mM. VlAlaDH displayed the most favourable catalytic efficiency with a rate constant of 170 s-1mM-1. On the other hand, AfAlaDH demonstrated the highest catalytic efficiency against α-ketobutyrate (34.0 s-1mM-1) and α-ketovalerate (2.7 s-1mM-1). Of the enzymes investigated in the study, TtAlaDH exhibited the highest effectiveness among bacterial enzymes in catalyzing ketocaproate with a measured catalytic efficiency of about 0.6 s-1mM-1 and a KM value of approximately 0.3 mM. These findings provide valuable insights into the substrate specificity and catalytic performance of L-AlaDHs, enhancing our understanding of their potential applications in various biocatalytic processes.
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Affiliation(s)
- Ğarip Demir
- Department of Molecular Biology and Genetics, Gebze Technical University, 41400, Gebze, Kocaeli, Turkey
| | - Jarkko Valjakka
- Faculty of Medicine and Health Technology, Tampere University, FI-33100, Tampere, Finland
| | - Ossi Turunen
- School of Forest Sciences, University of Eastern Finland, FI-80101, Joensuu, Finland
| | - Fatih Aktaş
- Faculty of Engineering, Düzce University, 81600, Düzce, Turkey
| | - Barış Binay
- Department of Bioengineering, Gebze Technical University, 41400, Gebze, Kocaeli, Turkey
- BAUZYME Biotechnology Co., Gebze Technical University Technopark, 41400, Gebze, Kocaeli, Turkey
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4
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Liu K, Jiang L, Ma S, Song Z, Wang L, Zhang Q, Xu R, Yang L, Wu J, Yu H. An evolved pyrrolysyl-tRNA synthetase with polysubstrate specificity expands the toolbox for engineering enzymes with incorporation of noncanonical amino acids. BIORESOUR BIOPROCESS 2023; 10:92. [PMID: 38647798 PMCID: PMC10991234 DOI: 10.1186/s40643-023-00712-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 12/03/2023] [Indexed: 04/25/2024] Open
Abstract
Aminoacyl-tRNA synthetase (aaRS) is a core component for genetic code expansion (GCE), a powerful technique that enables the incorporation of noncanonical amino acids (ncAAs) into a protein. The aaRS with polyspecificity can be exploited in incorporating additional ncAAs into a protein without the evolution of new, orthogonal aaRS/tRNA pair, which hence provides a useful tool for probing the enzyme mechanism or expanding protein function. A variant (N346A/C348A) of pyrrolysyl-tRNA synthetase from Methanosarcina mazei (MmPylRS) exhibited a wide substrate scope of accepting over 40 phenylalanine derivatives. However, for most of the substrates, the incorporation efficiency was low. Here, a MbPylRS (N311A/C313A) variant was constructed that showed higher ncAA incorporation efficiency than its homologous MmPylRS (N346A/C348A). Next, N-terminal of MbPylRS (N311A/C313A) was engineered by a greedy combination of single variants identified previously, resulting in an IPE (N311A/C313A/V31I/T56P/A100E) variant with significantly improved activity against various ncAAs. Activity of IPE was then tested toward 43 novel ncAAs, and 16 of them were identified to be accepted by the variant. The variant hence could incorporate nearly 60 ncAAs in total into proteins. With the utility of this variant, eight various ncAAs were then incorporated into a lanthanide-dependent alcohol dehydrogenase PedH. Incorporation of phenyllactic acid improved the catalytic efficiency of PedH toward methanol by 1.8-fold, indicating the role of modifying protein main chain in enzyme engineering. Incorporation of O-tert-Butyl-L-tyrosine modified the enantioselectivity of PedH by influencing the interactions between substrate and protein. Enzymatic characterization and molecular dynamics simulations revealed the mechanism of ncAAs affecting PedH catalysis. This study provides a PylRS variant with high activity and substrate promiscuity, which increases the utility of GCE in enzyme mechanism illustration and engineering.
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Affiliation(s)
- Ke Liu
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, Zhejiang, China
| | - Ling Jiang
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, Zhejiang, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Centre, Hangzhou, 311200, Zhejiang, China
| | - Shuang Ma
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, Zhejiang, China
| | - Zhongdi Song
- Key Laboratory of Pollution Exposure and Health Intervention of Zhejiang Province, Interdisciplinary Research Academy, Zhejiang Shuren University, Hangzhou, 310015, Zhejiang, China.
| | - Lun Wang
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, Zhejiang, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Centre, Hangzhou, 311200, Zhejiang, China
| | - Qunfeng Zhang
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, Zhejiang, China
| | - Renhao Xu
- Hangzhou 14th Middle School, Hangzhou, 310006, Zhejiang, China
| | - Lirong Yang
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, Zhejiang, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Centre, Hangzhou, 311200, Zhejiang, China
| | - Jianping Wu
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, Zhejiang, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Centre, Hangzhou, 311200, Zhejiang, China
| | - Haoran Yu
- Institute of Bioengineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou, 310027, Zhejiang, China.
- ZJU-Hangzhou Global Scientific and Technological Innovation Centre, Hangzhou, 311200, Zhejiang, China.
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5
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Gregorc J, Lensen N, Chaume G, Iskra J, Brigaud T. Trifluoromethylthiolation of Tryptophan and Tyrosine Derivatives: A Tool for Enhancing the Local Hydrophobicity of Peptides. J Org Chem 2023; 88:13169-13177. [PMID: 37672679 PMCID: PMC10507666 DOI: 10.1021/acs.joc.3c01373] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Indexed: 09/08/2023]
Abstract
The incorporation of fluorinated groups into peptides significantly affects their biophysical properties. We report herein the synthesis of Fmoc-protected trifluoromethylthiolated tyrosine (CF3S-Tyr) and tryptophan (CF3S-Trp) analogues on a gram scale (77-93% yield) and demonstrate their use as highly hydrophobic fluorinated building blocks for peptide chemistry. The developed methodology was successfully applied to the late-stage regioselective trifluoromethylthiolation of Trp residues in short peptides (66-80% yield) and the synthesis of various CF3S-analogues of biologically active monoamines. To prove the concept, Fmoc-(CF3S)Tyr and -Trp were incorporated into the endomorphin-1 chain (EM-1) and into model tripeptides by solid-phase peptide synthesis. A remarkable enhancement of the local hydrophobicity of the trifluoromethylthiolated peptides was quantified by the chromatographic hydrophobicity index determination method, demonstrating the high potential of CF3S-containing amino acids for the rational design of bioactive peptides.
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Affiliation(s)
- Jure Gregorc
- Chair
of Organic Chemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, Večna pot 113, Ljubljana 1000, Slovenia
- CY
Cergy Paris Université, CNRS, BioCIS, Cergy Pontoise 95000, France
- Université
Paris-Saclay, CNRS, BioCIS, Orsay 91400, France
| | - Nathalie Lensen
- CY
Cergy Paris Université, CNRS, BioCIS, Cergy Pontoise 95000, France
- Université
Paris-Saclay, CNRS, BioCIS, Orsay 91400, France
| | - Grégory Chaume
- CY
Cergy Paris Université, CNRS, BioCIS, Cergy Pontoise 95000, France
- Université
Paris-Saclay, CNRS, BioCIS, Orsay 91400, France
| | - Jernej Iskra
- Chair
of Organic Chemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, Večna pot 113, Ljubljana 1000, Slovenia
| | - Thierry Brigaud
- CY
Cergy Paris Université, CNRS, BioCIS, Cergy Pontoise 95000, France
- Université
Paris-Saclay, CNRS, BioCIS, Orsay 91400, France
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6
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Isenegger PG, Josephson B, Gaunt B, Davy MJ, Gouverneur V, Baldwin AJ, Davis BG. Posttranslational, site-directed photochemical fluorine editing of protein sidechains to probe residue oxidation state via 19F-nuclear magnetic resonance. Nat Protoc 2023; 18:1543-1562. [PMID: 36806799 DOI: 10.1038/s41596-022-00800-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 11/23/2022] [Indexed: 02/22/2023]
Abstract
The fluorination of amino acid residues represents a near-isosteric alteration with the potential to report on biological pathways, yet the site-directed editing of carbon-hydrogen (C-H) bonds in complex biomolecules to carbon-fluorine (C-F) bonds is challenging, resulting in its limited exploitation. Here, we describe a protocol for the posttranslational and site-directed alteration of native γCH2 to γCF2 in protein sidechains. This alteration allows the installation of difluorinated sidechain analogs of proteinogenic amino acids, in both native and modified states. This chemical editing is robust, mild, fast and highly efficient, exploiting photochemical- and radical-mediated C-C bonds grafted onto easy-to-access cysteine-derived dehydroalanine-containing proteins as starting materials. The heteroaryl-sulfonyl reagent required for generating the key carbon-centered C• radicals that install the sidechain can be synthesized in two to six steps from commercially available precursors. This workflow allows the nonexpert to create fluorinated proteins within 24 h, starting from a corresponding purified cysteine-containing protein precursor, without the need for bespoke biological systems. As an example, we readily introduce three γCF2-containing methionines in all three progressive oxidation states (sulfide, sulfoxide and sulfone) as D-/L- forms into histone eH3.1 at site 4 (a relevant lysine to methionine oncomutation site), and each can be detected by 19F-nuclear magnetic resonance of the γCF2 group, as well as the two diastereomers of the sulfoxide, even when found in a complex protein mixture of all three. The site-directed editing of C-H→C-F enables the use of γCF2 as a highly sensitive, 'zero-size-zero-background' label in protein sidechains, which may be used to probe biological phenomena, protein structures and/or protein-ligand interactions by 19F-based detection methods.
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Affiliation(s)
| | | | - Ben Gaunt
- The Rosalind Franklin Institute, Oxfordshire, UK
| | - Matthew J Davy
- The Rosalind Franklin Institute, Oxfordshire, UK.,Department of Pharmacology, University of Oxford, Oxford, UK
| | | | - Andrew J Baldwin
- Department of Chemistry, University of Oxford, Oxford, UK. .,The Rosalind Franklin Institute, Oxfordshire, UK. .,Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford, UK.
| | - Benjamin G Davis
- Department of Chemistry, University of Oxford, Oxford, UK. .,The Rosalind Franklin Institute, Oxfordshire, UK. .,Department of Pharmacology, University of Oxford, Oxford, UK.
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7
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El-Bestawy EM, Tolba AM, Rashad WA. Morphological, ultrastructural, and biochemical changes induced by sodium fluoride in the tongue of adult male albino rat and the ameliorative effect of resveratrol. Anat Cell Biol 2022; 55:483-496. [PMID: 36168808 PMCID: PMC9747341 DOI: 10.5115/acb.22.088] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2022] [Revised: 06/05/2022] [Accepted: 06/21/2022] [Indexed: 01/02/2023] Open
Abstract
Little knowledge is available about the effects of fluoride exposure on the tongue. This study evaluated the effects of sodium fluoride (NaF) on the tongue ultrastructure and detected the ameliorative effects of resveratrol. Forty adult albino rats were separated into 4 groups: the control group was given a balanced diet and purified water. The NaF treated group: received 10 mg/kg/d dissolved in 2.5 ml distilled water once daily for 30 days orally. The NaF+resveratrol group: received NaF 10 mg/kg/d orally together with resveratrol in a dose of 30 mg/kg daily for 30 days. The resveratrol group was subjected to resveratrol in a dose of 30 mg/kg/d by oral gavage for 30 days. Sections were stained with hematoxylin & eosin, and Masson's trichrome. Tumor necrosis factor α immunohistochemical study and electron microscopic examinations were done. The oxidative stress markers malondialdehyde, antioxidant reduced glutathione, and the total antioxidant capacity were measured. The NaF group revealed ulceration, necrotic muscle fibers, distorted papillae and a significant increase in malondialdehyde level, and a significant decrease in glutathione and the total antioxidant levels. In the NaF+resveratrol group, pathological changes were less, and the oxidant levels were decreased by the administration of resveratrol with NaF. In conclusion, NaF adversely affects the ultrastructure of the adult rat tongue and resveratrol can ameliorate this effect.
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Affiliation(s)
- Emtethal M. El-Bestawy
- Department of Human Anatomy and Embryology, Faculty of Medicine, Zagazig University, Sharqia Governorate, Egypt
| | - Asmaa M. Tolba
- Department of Human Anatomy and Embryology, Faculty of Medicine, Zagazig University, Sharqia Governorate, Egypt,Corresponding author: Asmaa M. Tolba, Department of Human Anatomy and Embryology, Faculty of Medicine, Zagazig University, Sharqia Governorate 44519, Egypt, E-mail:
| | - Walaa A. Rashad
- Department of Human Anatomy and Embryology, Faculty of Medicine, Zagazig University, Sharqia Governorate, Egypt
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8
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Tao XW, Yi LN, Huang MY, Fu Y, Yang Q. Direct C(sp 3)-H Polyfluoroarylation: Access to Polyfluoroaryl Amino Acids via Rh-Catalyzed Selective C-F Bond Cleavage. J Org Chem 2022; 87:14476-14486. [PMID: 36226632 DOI: 10.1021/acs.joc.2c01906] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
A catalytic selective C-F bond alkylation method for polyfluoroarene with glycinates and derivatives in the presence of a DavePhos-ligated Rh catalyst was developed. This method avoids the preactivation of alkylating reagents and provides an efficient and straightforward route to synthesize a series of polyfluoroaryl amino acids via C(sp3)-H functionalization. This reaction proceeds under mild conditions and exhibits high reactivity and excellent chemoselectivities. Meanwhile, the synthetic potential of this method was demonstrated by gram-scale synthesis, and further transformations proved the application value of the products as well.
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Affiliation(s)
- Xuan-Wen Tao
- Key Laboratory of General Chemistry of the National Ethnic Affairs Commission, College of Chemistry and Environment, Southwest Minzu University, Chengdu 610041, China
| | - Li-Na Yi
- Key Laboratory of General Chemistry of the National Ethnic Affairs Commission, College of Chemistry and Environment, Southwest Minzu University, Chengdu 610041, China
| | - Meng-Yi Huang
- Key Laboratory of General Chemistry of the National Ethnic Affairs Commission, College of Chemistry and Environment, Southwest Minzu University, Chengdu 610041, China
| | - Yun Fu
- Key Laboratory of General Chemistry of the National Ethnic Affairs Commission, College of Chemistry and Environment, Southwest Minzu University, Chengdu 610041, China
| | - Qiang Yang
- Key Laboratory of General Chemistry of the National Ethnic Affairs Commission, College of Chemistry and Environment, Southwest Minzu University, Chengdu 610041, China
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9
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Maleckis A, Abdelkader EH, Herath ID, Otting G. Synthesis of fluorinated leucines, valines and alanines for use in protein NMR. Org Biomol Chem 2022; 20:2424-2432. [PMID: 35262139 DOI: 10.1039/d2ob00145d] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Efficient syntheses of fluorinated leucines, valines and alanines are described. The synthetic routes provide expedient access to various 13C/15N/D isotopologues requiring solely readily available and inexpensive isotope containing reagents such as NaBD4, carbon-13C dioxide and sodium azide-1-15N. The lightly fluorinated leucines and valines were found to be good substrates for cell-free protein expression and even 3-fluoroalanine, which is highly toxic to bacteria in vivo, could be incorporated into proteins this way. 19F-NMR spectra of the protein GB1 produced with these amino acids showed large chemical shift dispersions. Particularly high incorporation yields and clean 19F-NMR spectra were obtained for GB1 produced with valine residues, which had been synthesized with a single fluorine substituting a hydrogen stereospecifically in one of the methyl groups.
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Affiliation(s)
- Ansis Maleckis
- Latvian Institute of Organic Synthesis, Aizkraukles 21, LV-1006, Riga, Latvia.
| | - Elwy H Abdelkader
- ARC Centre of Excellence for Innovations in Peptide & Protein Science, Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia.
| | - Iresha D Herath
- ARC Centre of Excellence for Innovations in Peptide & Protein Science, Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia.
| | - Gottfried Otting
- ARC Centre of Excellence for Innovations in Peptide & Protein Science, Research School of Chemistry, Australian National University, Canberra, ACT 2601, Australia.
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10
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Mykhailiuk PK. Fluorine-Containing Prolines: Synthetic Strategies, Applications, and Opportunities. J Org Chem 2022; 87:6961-7005. [PMID: 35175772 DOI: 10.1021/acs.joc.1c02956] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Fluorinated prolines play an important role in peptide studies, protein engineering, medicinal chemistry, drug discovery, and agrochemistry. Since the first synthesis of 4-fluoroprolines by Gottlieb and Witkop in 1965, their popularity started to grow exponentially. For example, during the past two decades, all isomeric trifluoromethyl-substituted prolines have been synthesized. In this Perspective, chemical properties and applications of fluorinated prolines are discussed. Synthetic approaches to all known fluorine-containing prolines are also discussed and analyzed. This analysis unexpectedly revealed an unsolved problem: in strict contrast to fluoro- and trifluoromethyl-substituted prolines, the corresponding analogues with fluoromethyl and difluoromethyl groups are mostly unknown. At the end of the paper, structures of several interesting, yet unknown, fluorinated prolines are disclosed─a good opportunity for chemists to make them.
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11
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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] [MESH Headings] [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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12
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Mardirossian M, Rubini M, Adamo MFA, Scocchi M, Saviano M, Tossi A, Gennaro R, Caporale A. Natural and Synthetic Halogenated Amino Acids-Structural and Bioactive Features in Antimicrobial Peptides and Peptidomimetics. Molecules 2021; 26:7401. [PMID: 34885985 PMCID: PMC8659048 DOI: 10.3390/molecules26237401] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 11/16/2021] [Accepted: 11/26/2021] [Indexed: 11/17/2022] Open
Abstract
The 3D structure and surface characteristics of proteins and peptides are crucial for interactions with receptors or ligands and can be modified to some extent to modulate their biological roles and pharmacological activities. The introduction of halogen atoms on the side-chains of amino acids is a powerful tool for effecting this type of tuning, influencing both the physico-chemical and structural properties of the modified polypeptides, helping to first dissect and then rationally modify features that affect their mode of action. This review provides examples of the influence of different types of halogenation in amino acids that replace native residues in proteins and peptides. Examples of synthetic strategies for obtaining halogenated amino acids are also provided, focusing on some representative compounds and their biological effects. The role of halogenation in native and designed antimicrobial peptides (AMPs) and their mimetics is then discussed. These are in the spotlight for the development of new antimicrobial drugs to counter the rise of antibiotic-resistant pathogens. AMPs represent an interesting model to study the role that natural halogenation has on their mode of action and also to understand how artificially halogenated residues can be used to rationally modify and optimize AMPs for pharmaceutical purposes.
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Affiliation(s)
- Mario Mardirossian
- Department of Medicine, Surgery and Health Sciences, University of Trieste, Piazza dell’Ospitale, 1, 34125 Trieste, Italy
| | - Marina Rubini
- School of Chemistry, University College Dublin, Belfield, Dublin 4, Ireland;
| | - Mauro F. A. Adamo
- Department of Chemistry, Centre for Synthesis and Chemical Biology (CSCB), RCSI, 123 St. Stephens Green, Dublin 2, Ireland;
| | - Marco Scocchi
- Department of Life Sciences, University of Trieste, Via L. Giorgieri, 5, Q Building, 34127 Trieste, Italy; (M.S.); (A.T.); (R.G.)
| | - Michele Saviano
- Institute of Crystallography (IC), National Research Council (CNR), Via Amendola, 122, 70126 Bari, Italy;
| | - Alessandro Tossi
- Department of Life Sciences, University of Trieste, Via L. Giorgieri, 5, Q Building, 34127 Trieste, Italy; (M.S.); (A.T.); (R.G.)
| | - Renato Gennaro
- Department of Life Sciences, University of Trieste, Via L. Giorgieri, 5, Q Building, 34127 Trieste, Italy; (M.S.); (A.T.); (R.G.)
| | - Andrea Caporale
- Institute of Crystallography (IC), National Research Council (CNR), c/o Area Science Park, S.S. 14 Km 163.5, Basovizza, 34149 Trieste, Italy
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13
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Base-Mediated Claisen Rearrangement of CF 3-Containing Bisallyl Ethers. Molecules 2021; 26:molecules26144365. [PMID: 34299639 PMCID: PMC8304132 DOI: 10.3390/molecules26144365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 07/05/2021] [Accepted: 07/14/2021] [Indexed: 11/27/2022] Open
Abstract
We have previously clarified that the strongly electron-withdrawing CF3 group nicely affected the base-mediated proton shift of CF3-containing propargylic or allylic alcohols to afford the corresponding α,β-unsaturated or saturated ketones, respectively, which was applied this time to the Claisen rearrangement after O-allylation of the allylic alcohols with a CF3 group, followed by isomerization to the corresponding allyl vinyl ethers via the proton shift, enabling the desired rearrangement in a tandem fashion, or in a stepwise manner, the latter of which was proved to have attained an excellent diastereoselectivity with the aid of a palladium catalyst.
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14
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Han ZZ, Dong T, Ming XX, Kuang F, Zhang CP. Synthesis and Biological Evaluation of CF 3 Se-Substituted α-Amino Acid Derivatives. ChemMedChem 2021; 16:3177-3180. [PMID: 34268896 DOI: 10.1002/cmdc.202100451] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 07/14/2021] [Indexed: 11/07/2022]
Abstract
Several CF3 Se-substituted α-amino acid derivatives, such as (R)-2-amino-3-((trifluoromethyl)selanyl)propanoates (5 a/6 a), (S)-2-amino-4-((trifluoromethyl)selanyl)butanoates (5 b/6 b), (2R,3R)-2-amino-3-((trifluoromethyl)selanyl)butanoates (5 c/6 c), (R)-2-((S)-2-amino-3-phenylpropanamido)-3-((trifluoromethyl)selanyl)propanoates (11 a/12 a), and (R)-2-(2-aminoacetamido)-3-((trifluoromethyl)selanyl)propanoates (11 b/12 b), were readily synthesized from natural amino acids and [Me4 N][SeCF3 ]. The primary in vitro cytotoxicity assays revealed that compounds 6 a, 11 a and 12 a were more effective cell growth inhibitors than the other tested CF3 Se-substituted derivatives towards MCF-7, HCT116, and SK-OV-3 cells, with their IC50 values being less than 10 μM for MCF-7 and HCT116 cells. This study indicated the potentials of CF3 Se moiety as a pharmaceutically relevant group in the design and synthesis of novel biologically active molecules.
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Affiliation(s)
- Zhou-Zhou Han
- School of Chemistry, Chemical Engineering and Life Science, Wuhan University of Technology, 205 Luoshi Road, Wuhan, 430070, China
| | - Tao Dong
- School of Chemistry, Chemical Engineering and Life Science, Wuhan University of Technology, 205 Luoshi Road, Wuhan, 430070, China
| | - Xiao-Xia Ming
- School of Chemistry, Chemical Engineering and Life Science, Wuhan University of Technology, 205 Luoshi Road, Wuhan, 430070, China
| | - Fu Kuang
- Department of phase I clinical trial center, the Second Affiliated Hospital of Chongqing Medical University, Chongqing, 40010, China
| | - Cheng-Pan Zhang
- School of Chemistry, Chemical Engineering and Life Science, Wuhan University of Technology, 205 Luoshi Road, Wuhan, 430070, China
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15
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Rozhin P, Charitidis C, Marchesan S. Self-Assembling Peptides and Carbon Nanomaterials Join Forces for Innovative Biomedical Applications. Molecules 2021; 26:4084. [PMID: 34279424 PMCID: PMC8271590 DOI: 10.3390/molecules26134084] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 06/30/2021] [Accepted: 07/02/2021] [Indexed: 02/07/2023] Open
Abstract
Self-assembling peptides and carbon nanomaterials have attracted great interest for their respective potential to bring innovation in the biomedical field. Combination of these two types of building blocks is not trivial in light of their very different physico-chemical properties, yet great progress has been made over the years at the interface between these two research areas. This concise review will analyze the latest developments at the forefront of research that combines self-assembling peptides with carbon nanostructures for biological use. Applications span from tissue regeneration, to biosensing and imaging, and bioelectronics.
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Affiliation(s)
- Petr Rozhin
- Chemical and Pharmaceutical Sciences Department, University of Trieste, 34127 Trieste, Italy;
| | - Costas Charitidis
- School of Chemical Engineering, National Technical University of Athens, Iroon Polytechneiou 9, Zografou, 157 80 Athens, Greece;
| | - Silvia Marchesan
- Chemical and Pharmaceutical Sciences Department, University of Trieste, 34127 Trieste, Italy;
- INSTM, Unit of Trieste, 34127 Trieste, Italy
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16
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Bellotto O, Cringoli MC, Perathoner S, Fornasiero P, Marchesan S. Peptide Gelators to Template Inorganic Nanoparticle Formation. Gels 2021; 7:14. [PMID: 33540722 PMCID: PMC7930985 DOI: 10.3390/gels7010014] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2021] [Revised: 01/27/2021] [Accepted: 01/30/2021] [Indexed: 12/28/2022] Open
Abstract
The use of peptides to template inorganic nanoparticle formation has attracted great interest as a green route to advance structures with innovative physicochemical properties for a variety of applications that range from biomedicine and sensing, to catalysis. In particular, short-peptide gelators offer the advantage of providing dynamic supramolecular environments for the templating effect on the formation of inorganic nanoparticles directly in the resulting gels, and ideally without using further reductants or chemical reagents. This mini-review describes the recent progress in the field to outline future research directions towards dynamic functional materials that exploit the synergy between supramolecular chemistry, nanoscience, and the interface between organic and inorganic components for advanced performance.
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Affiliation(s)
- Ottavia Bellotto
- Chemical and Pharmaceutical Sciences Department, University of Trieste, 34127 Trieste, Italy; (O.B.); (M.C.C.); (P.F.)
| | - Maria C. Cringoli
- Chemical and Pharmaceutical Sciences Department, University of Trieste, 34127 Trieste, Italy; (O.B.); (M.C.C.); (P.F.)
- INSTM, Unit of Trieste, 34127 Trieste, Italy
| | - Siglinda Perathoner
- Dipartimento di Scienze Chimiche, Biologiche, Farmaceutiche e Ambientali, University of Messina, 98168 Messina, Italy;
- INSTM, Unit of Messina, 98168 Messina, Italy
| | - Paolo Fornasiero
- Chemical and Pharmaceutical Sciences Department, University of Trieste, 34127 Trieste, Italy; (O.B.); (M.C.C.); (P.F.)
- INSTM, Unit of Trieste, 34127 Trieste, Italy
- Istituto di Chimica dei Composti Organometallici, Consiglio Nazionale delle Ricerche (ICCOM-CNR), 34127 Trieste, Italy
| | - Silvia Marchesan
- Chemical and Pharmaceutical Sciences Department, University of Trieste, 34127 Trieste, Italy; (O.B.); (M.C.C.); (P.F.)
- INSTM, Unit of Trieste, 34127 Trieste, Italy
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17
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Stoletova NV, Moshchenkov AD, Smol'yakov AF, Gugkaeva ZT, Maleev VI, Katayev D, Larionov VA. Asymmetric Synthesis of Perfluoroalkylated α‐Amino Acids through Generated Radicals Using a Chiral Ni(II) Complex. Helv Chim Acta 2020. [DOI: 10.1002/hlca.202000193] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Nadezhda V. Stoletova
- A.N. Nesmeyanov Institute of Organoelement Compounds of Russian Academy of Sciences (INEOS RAS) Vavilov Str. 28 RU-119991 Moscow Russian Federation
| | - Andrey D. Moshchenkov
- A.N. Nesmeyanov Institute of Organoelement Compounds of Russian Academy of Sciences (INEOS RAS) Vavilov Str. 28 RU-119991 Moscow Russian Federation
- Higher Chemical College of the Russian Academy of Sciences Dmitry Mendeleev University of Chemical Technology of Russia Miusskaya sq. 9 RU-125047 Moscow Russian Federation
| | - Alexander F. Smol'yakov
- A.N. Nesmeyanov Institute of Organoelement Compounds of Russian Academy of Sciences (INEOS RAS) Vavilov Str. 28 RU-119991 Moscow Russian Federation
| | - Zalina T. Gugkaeva
- A.N. Nesmeyanov Institute of Organoelement Compounds of Russian Academy of Sciences (INEOS RAS) Vavilov Str. 28 RU-119991 Moscow Russian Federation
| | - Victor I. Maleev
- A.N. Nesmeyanov Institute of Organoelement Compounds of Russian Academy of Sciences (INEOS RAS) Vavilov Str. 28 RU-119991 Moscow Russian Federation
| | - Dmitry Katayev
- Department of Chemistry and Applied Biosciences Swiss Federal Institute of Technology ETH Zürich Vladimir-Prelog-Weg 2 CH-8093 Zürich Switzerland
| | - Vladimir A. Larionov
- A.N. Nesmeyanov Institute of Organoelement Compounds of Russian Academy of Sciences (INEOS RAS) Vavilov Str. 28 RU-119991 Moscow Russian Federation
- Peoples' Friendship University of Russia (RUDN University) Miklukho-Maklaya Str. 6 RU-117198 Moscow Russian Federation
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