1
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Miles SA, Nillama JA, Hunter L. Tinker, Tailor, Soldier, Spy: The Diverse Roles That Fluorine Can Play within Amino Acid Side Chains. Molecules 2023; 28:6192. [PMID: 37687021 PMCID: PMC10489206 DOI: 10.3390/molecules28176192] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 08/17/2023] [Accepted: 08/17/2023] [Indexed: 09/10/2023] Open
Abstract
Side chain-fluorinated amino acids are useful tools in medicinal chemistry and protein science. In this review, we outline some general strategies for incorporating fluorine atom(s) into amino acid side chains and for elaborating such building blocks into more complex fluorinated peptides and proteins. We then describe the diverse benefits that fluorine can offer when located within amino acid side chains, including enabling 19F NMR and 18F PET imaging applications, enhancing pharmacokinetic properties, controlling molecular conformation, and optimizing target-binding.
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Affiliation(s)
| | | | - Luke Hunter
- School of Chemistry, The University of New South Wales (UNSW), Sydney 2052, Australia
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2
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Killoran PM, Hanson GSM, Verhoork SJM, Smith M, Del Gobbo D, Lian L, Coxon CR. Probing Peptidylprolyl Bond cis/trans Status Using Distal 19 F NMR Reporters. Chemistry 2023; 29:e202203017. [PMID: 36550088 PMCID: PMC10946801 DOI: 10.1002/chem.202203017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 12/21/2022] [Accepted: 12/22/2022] [Indexed: 12/24/2022]
Abstract
A method for measuring peptidylprolyl bond cis-trans conformational status in peptide models is described, using 4-fluorophenylalanine (4FPhe) as a distal reporter for 19 F NMR. The %cis-Pro population was measured for peptides of the general structure Ac-X-Pro-Z-Ala-Ala-4FPhe (X and Z are proteinogenic amino acids) at pH 7.4, and provided conformational populations consistent with literature values obtained by more complex methods. This approach was applied to probe the prolyl bond status in pentapeptide models of the intrinsically disordered C-terminal region of α-synuclein, which mirrored the preferences in the Ac-X-Pro-Z-Ala-4FPhe models. Advantageously, the 19 F reporter group does not need to be adjacent to or attached to proline to provide quantifiable signals and distal 4-fluorophenylalanines can be placed so as not to influence prolyl bond conformation. Finally, we demonstrated that the prolyl bond status is not significantly affected by pH when there are ionisable amino acid residues at the carboxyl side of proline, which makes 19 F NMR an invaluable tool with which to study proline isomerism at a range of pHs and in different solvents and buffers.
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Affiliation(s)
- Patrick M. Killoran
- School of Pharmacy and Biomolecular SciencesLiverpool John Moores UniversityLiverpoolMerseysideL3 3AFUK
| | - George S. M. Hanson
- EaStChem School of ChemistryThe University of Edinburgh Joseph Black BuildingDavid Brewster RoadEdinburghEH14 4ASUK
| | - Sanne J. M. Verhoork
- School of Pharmacy and Biomolecular SciencesLiverpool John Moores UniversityLiverpoolMerseysideL3 3AFUK
| | - Madeleine Smith
- School of Pharmacy and Biomolecular SciencesLiverpool John Moores UniversityLiverpoolMerseysideL3 3AFUK
| | - Davide Del Gobbo
- School of Pharmacy and Biomolecular SciencesLiverpool John Moores UniversityLiverpoolMerseysideL3 3AFUK
| | - Lu‐Yun Lian
- Institute of SystemsMolecular and Integrative BiologyThe University of LiverpoolCrown StreetLiverpoolL69 7ZBUK
| | - Christopher R. Coxon
- EaStChem School of ChemistryThe University of Edinburgh Joseph Black BuildingDavid Brewster RoadEdinburghEH14 4ASUK
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3
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Daniecki NJ, Bhatt MR, Yap GPA, Zondlo NJ. Proline C-H Bonds as Loci for Proline Assembly via C-H/O Interactions. Chembiochem 2022; 23:e202200409. [PMID: 36129371 DOI: 10.1002/cbic.202200409] [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: 07/20/2022] [Revised: 09/20/2022] [Indexed: 01/25/2023]
Abstract
Proline residues within proteins lack a traditional hydrogen bond donor. However, the hydrogens of the proline ring are all sterically accessible, with polarized C-H bonds at Hα and Hδ that exhibit greater partial positive character and can be utilized as alternative sites for molecular recognition. C-H/O interactions, between proline C-H bonds and oxygen lone pairs, have been previously identified as modes of recognition within protein structures and for higher-order assembly of protein structures. In order to better understand intermolecular recognition of proline residues, a series of proline derivatives was synthesized, including 4R-hydroxyproline nitrobenzoate methyl ester, acylated on the proline nitrogen with bromoacetyl and glycolyl groups, and Boc-4S-(4-iodophenyl)hydroxyproline methyl amide. All three derivatives exhibited multiple close intermolecular C-H/O interactions in the crystallographic state, with H⋅⋅⋅O distances as close as 2.3 Å. These observed distances are well below the 2.72 Å sum of the van der Waals radii of H and O, and suggest that these interactions are particularly favorable. In order to generalize these results, we further analyzed the role of C-H/O interactions in all previously crystallized derivatives of these amino acids, and found that all 26 structures exhibited close intermolecular C-H/O interactions. Finally, we analyzed all proline residues in the Cambridge Structural Database of small-molecule crystal structures. We found that the majority of these structures exhibited intermolecular C-H/O interactions at proline C-H bonds, suggesting that C-H/O interactions are an inherent and important mode for recognition of and higher-order assembly at proline residues. Due to steric accessibility and multiple polarized C-H bonds, proline residues are uniquely positioned as sites for binding and recognition via C-H/O interactions.
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Affiliation(s)
- Noah J Daniecki
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, USA
| | - Megh R Bhatt
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, USA
| | - Glenn P A Yap
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, USA
| | - Neal J Zondlo
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, USA
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4
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Chernykh AV, Aloshyn D, Kuchkovska YO, Daniliuc CG, Tolmachova NA, Kondratov IS, Zozulya S, Grygorenko OO, Haufe G. Impact of β-perfluoroalkyl substitution of proline on the proteolytic stability of its peptide derivatives. Org Biomol Chem 2022; 20:9337-9350. [PMID: 36107003 DOI: 10.1039/d2ob01430k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
A series of all stereoisomers of β-CF3 or β-C2F5 substituted prolines and their dipeptide derivatives were synthesized. Mouse plasma stability assay was carried out to study the impact of fluoroalkyl substituents on the proteolytic stability of proline-derived peptides. The effect of the (R)-/(S)-configuration at the C-2 atom in combination with electronic and steric effects imposed by fluoroalkyl groups was addressed to rationalize the difference in the half-life stability of diastereomeric β-CF3-Pro-Gly and β-C2F5-Pro-Gly derivatives and compared to those of parent (S)-Pro-Gly and (R)-Pro-Gly dipeptides. The steric effect was predominant when the β-CF3 or β-C2F5 group was placed properly to create a spatial interference within the pockets of proteases, thereby protecting the substances from degradation (e.g., for cis-isomeric derivatives). Otherwise, a smaller electronic effect accelerating proteolysis was in charge (i.e., for the (2S,3S) isomers).
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Affiliation(s)
- Anton V Chernykh
- Enamine Ltd., Chervonotkatska Street 78, Kyïv 02094, Ukraine. .,Taras Shevchenko National University of Kyïv, Volodymyrska Street 60, Kyïv 01601, Ukraine.
| | - Danylo Aloshyn
- Bienta/Enamine Ltd., Chervonotkatska Street 78, Kyïv 02094, Ukraine
| | | | - Constantin G Daniliuc
- Organisch-Chemisches Institut, Westfälische Wilhelms-Universität Münster, Corrensstrasse 40, 48149 Münster, Germany
| | | | - Ivan S Kondratov
- Enamine Ltd., Chervonotkatska Street 78, Kyïv 02094, Ukraine. .,V.P. Kukhar Institute of Bioorganic Chemistry & Petrochemistry, National Academy of Sciences of, Ukraine, Murmanska Street 1, Kyïv 02660, Ukraine
| | - Sergey Zozulya
- Bienta/Enamine Ltd., Chervonotkatska Street 78, Kyïv 02094, Ukraine
| | - Oleksandr O Grygorenko
- Enamine Ltd., Chervonotkatska Street 78, Kyïv 02094, Ukraine. .,Taras Shevchenko National University of Kyïv, Volodymyrska Street 60, Kyïv 01601, Ukraine.
| | - Günter Haufe
- Organisch-Chemisches Institut, Westfälische Wilhelms-Universität Münster, Corrensstrasse 40, 48149 Münster, Germany.,Cells-in-Motion Cluster of Excellence, Universität Münster, Waldeyerstraße 15, 48149 Münster, Germany
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5
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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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6
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Natural and Synthetic Halogenated Amino Acids-Structural and Bioactive Features in Antimicrobial Peptides and Peptidomimetics. Molecules 2021; 26:molecules26237401. [PMID: 34885985 PMCID: PMC8659048 DOI: 10.3390/molecules26237401] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [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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7
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Sloand JN, Miller MA, Medina SH. Fluorinated peptide biomaterials. Pept Sci (Hoboken) 2021; 113:e24184. [PMID: 34541446 PMCID: PMC8448251 DOI: 10.1002/pep2.24184] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 06/30/2020] [Indexed: 12/20/2022]
Abstract
Fluorinated compounds, while rarely used by nature, are emerging as fundamental ingredients in biomedical research, with applications in drug discovery, metabolomics, biospectroscopy, and, as the focus of this review, peptide/protein engineering. Leveraging the fluorous effect to direct peptide assembly has evolved an entirely new class of organofluorine building blocks from which unique and bioactive materials can be constructed. Here, we discuss three distinct peptide fluorination strategies used to design and induce peptide assembly into nano-, micro-, and macrosupramolecular states that potentiate high-ordered organization into material scaffolds. These fluorine-tailored peptide assemblies employ the unique fluorous environment to boost biofunctionality for a broad range of applications, from drug delivery to antibacterial coatings. This review provides foundational tactics for peptide fluorination and discusses the utility of these fluorous-directed hierarchical structures as material platforms in diverse biomedical applications.
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Affiliation(s)
- Janna N Sloand
- Department of Biomedical Engineering, Penn State University, University Park, Pennsylvania, USA
| | - Michael A Miller
- Department of Biomedical Engineering, Penn State University, University Park, Pennsylvania, USA
| | - Scott H Medina
- Department of Biomedical Engineering, Penn State University, University Park, Pennsylvania, USA
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8
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Sanchez CA, Gadais C, Chaume G, Girard S, Chelain E, Brigaud T. Enantiopure 5-CF 3-Proline: Synthesis, Incorporation in Peptides, and Tuning of the Peptide Bond Geometry. Org Lett 2021; 23:382-387. [PMID: 33369434 DOI: 10.1021/acs.orglett.0c03880] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The straightforward synthesis of enantiopure 5-(R)-and 5-(S)-trifluoromethylproline is reported. The key steps are a Ruppert-Prakash reagent addition on l-pyroglutamic esters followed by an elimination reaction and a selective reduction. The solution-phase and solid-phase incorporation of this unprotected enantiopure fluorinated amino acid in a short peptide chain was demonstrated. Compared to proline, the CF3 group provides a decrease of the trans to cis amide bond isomerization energy and an increase of the cis conformer population.
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Affiliation(s)
- Clément A Sanchez
- CNRS, BioCIS, CY Cergy Paris Université, 95000 Cergy Pontoise, France.,CNRS, BioCIS, Université Paris-Saclay, 92290 Châtenay-Malabry, France
| | - Charlène Gadais
- CNRS, BioCIS, CY Cergy Paris Université, 95000 Cergy Pontoise, France.,CNRS, BioCIS, Université Paris-Saclay, 92290 Châtenay-Malabry, France
| | - Grégory Chaume
- CNRS, BioCIS, CY Cergy Paris Université, 95000 Cergy Pontoise, France.,CNRS, BioCIS, Université Paris-Saclay, 92290 Châtenay-Malabry, France
| | - Sylvaine Girard
- CNRS, BioCIS, CY Cergy Paris Université, 95000 Cergy Pontoise, France.,CNRS, BioCIS, Université Paris-Saclay, 92290 Châtenay-Malabry, France
| | - Evelyne Chelain
- CNRS, BioCIS, CY Cergy Paris Université, 95000 Cergy Pontoise, France.,CNRS, BioCIS, Université Paris-Saclay, 92290 Châtenay-Malabry, France
| | - Thierry Brigaud
- CNRS, BioCIS, CY Cergy Paris Université, 95000 Cergy Pontoise, France.,CNRS, BioCIS, Université Paris-Saclay, 92290 Châtenay-Malabry, France
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9
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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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10
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Brittain WDG, Lloyd CM, Cobb SL. Synthesis of complex unnatural fluorine-containing amino acids. J Fluor Chem 2020; 239:109630. [PMID: 33144742 PMCID: PMC7583769 DOI: 10.1016/j.jfluchem.2020.109630] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 08/12/2020] [Accepted: 08/12/2020] [Indexed: 01/01/2023]
Abstract
The area of fluorinated amino acid synthesis has seen rapid growth over the past decade. As reports of singly fluorinated natural amino acid derivatives have grown, researchers have turned their attention to develop methodology to access complex proteinogenic examples. A variety of reaction conditions have been employed in this area, exploiting new advances in the wider synthetic community such as photocatalysis and palladium cross-coupling. In addition, novel fluorinated functional groups have also been incorporated into amino acids, with SFX and perfluoro moieties now appearing with more frequency in the literature. This review focuses on synthetic methodology for accessing complex non-proteinogenic amino acids, along with amino acids containing multiple fluorine atoms such as CF3, SF5 and perfluoroaromatic groups.
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Affiliation(s)
| | - Carissa M Lloyd
- Department of Chemistry, Durham University, Durham DH1 3LE, United Kingdom
| | - Steven L Cobb
- Department of Chemistry, Durham University, Durham DH1 3LE, United Kingdom
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11
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Kubyshkin V. Polarity effects in 4-fluoro- and 4-(trifluoromethyl)prolines. Beilstein J Org Chem 2020; 16:1837-1852. [PMID: 32765799 PMCID: PMC7385359 DOI: 10.3762/bjoc.16.151] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 07/06/2020] [Indexed: 12/14/2022] Open
Abstract
Fluorine-containing analogues of proline are valuable tools in engineering and NMR spectroscopic studies of peptides and proteins. Their use relies on the fundamental understanding of the interplay between the substituents and the main chain groups of the amino acid residue. This study aims to showcase the polarity-related effects that arise from the interaction between the functional groups in molecular models. Properties such as conformation, acid-base transition, and amide-bond isomerism were examined for diastereomeric 4-fluoroprolines, 4-(trifluoromethyl)prolines, and 1,1-difluoro-5-azaspiro[2.4]heptane-6-carboxylates. The preferred conformation on the proline ring originated from a preferential axial positioning for a single fluorine atom, and an equatorial positioning for a trifluoromethyl- or a difluoromethylene group. This orientation of the substituents explains the observed trends in the pK a values, lipophilicity, and the kinetics of the amide bond rotation. The study also provides a set of evidences that the transition state of the amide-bond rotation in peptidyl-prolyl favors C4-exo conformation of the pyrrolidine ring.
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12
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Kitamura Electrophilic Fluorination Using HF as a Source of Fluorine. MOLECULES (BASEL, SWITZERLAND) 2020; 25:molecules25092116. [PMID: 32366048 PMCID: PMC7248860 DOI: 10.3390/molecules25092116] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/04/2020] [Revised: 04/22/2020] [Accepted: 04/27/2020] [Indexed: 12/30/2022]
Abstract
This review article focused on the innovative procedure for electrophilic fluorination using HF and in situ generation of the required electrophilic species derived from hypervalent iodine compounds. The areas of synthetic application of this approach include fluorination of 1,3-dicarbonyl compounds, aryl-alkyl ketones, styrene derivatives, α,β-unsaturated ketones and alcohols, homoallyl amine and homoallyl alcohol derivatives, 3-butenoic acids and alkynes.
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13
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Trofymchuk S, Bugera MY, Klipkov AA, Razhyk B, Semenov S, Tarasenko K, Starova VS, Zaporozhets OA, Tananaiko OY, Alekseenko AN, Pustovit Y, Kiriakov O, Gerus II, Tolmachev AA, Mykhailiuk PK. Deoxofluorination of (Hetero)aromatic Acids. J Org Chem 2020; 85:3110-3124. [PMID: 31928000 DOI: 10.1021/acs.joc.9b03011] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Diverse trifluoromethyl-substituted compounds were synthesized by deoxofluorination of cinnamic and (hetero)aromatic carboxylic acids with sulfur tetrafluoride. The obtained products were used as starting materials in the preparation of novel fluorinated amino acids, anilines, and aliphatic amines - valuable building blocks for medicinal chemistry and agrochemistry.
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Affiliation(s)
| | - Maksym Ya Bugera
- Enamine Ltd., Chervonotkatska 78, Kyiv 02094, Ukraine.,V.P. Kukhar Institute of Bioorganic Chemistry and Petrochemistry NAS of Ukraine, Murmanskaya 1, Kyiv 02094, Ukraine
| | - Anton A Klipkov
- Enamine Ltd., Chervonotkatska 78, Kyiv 02094, Ukraine.,V.P. Kukhar Institute of Bioorganic Chemistry and Petrochemistry NAS of Ukraine, Murmanskaya 1, Kyiv 02094, Ukraine
| | - Bohdan Razhyk
- Enamine Ltd., Chervonotkatska 78, Kyiv 02094, Ukraine
| | | | - Karen Tarasenko
- V.P. Kukhar Institute of Bioorganic Chemistry and Petrochemistry NAS of Ukraine, Murmanskaya 1, Kyiv 02094, Ukraine.,UkrOrgSyntez Ltd. (UORSY), 29 Schorsa Street, Kyiv 01133, Ukraine
| | - Viktoriia S Starova
- Chemistry Department, Taras Shevchenko National University of Kyiv, Volodymyrska 64, Kyiv 01601, Ukraine
| | - Olga A Zaporozhets
- Chemistry Department, Taras Shevchenko National University of Kyiv, Volodymyrska 64, Kyiv 01601, Ukraine
| | - Oksana Yu Tananaiko
- Chemistry Department, Taras Shevchenko National University of Kyiv, Volodymyrska 64, Kyiv 01601, Ukraine
| | | | - Yurii Pustovit
- Institute of Organic Chemistry NAS of Ukraine, Murmanskaya 5, Kyiv 02094, Ukraine
| | | | - Igor I Gerus
- V.P. Kukhar Institute of Bioorganic Chemistry and Petrochemistry NAS of Ukraine, Murmanskaya 1, Kyiv 02094, Ukraine
| | - Andrei A Tolmachev
- Enamine Ltd., Chervonotkatska 78, Kyiv 02094, Ukraine.,Chemistry Department, Taras Shevchenko National University of Kyiv, Volodymyrska 64, Kyiv 01601, Ukraine
| | - Pavel K Mykhailiuk
- Enamine Ltd., Chervonotkatska 78, Kyiv 02094, Ukraine.,Chemistry Department, Taras Shevchenko National University of Kyiv, Volodymyrska 64, Kyiv 01601, Ukraine
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14
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Mei H, Han J, White S, Butler G, Soloshonok VA. Perfluoro-3-ethyl-2,4-dimethyl-3-pentyl persistent radical: A new reagent for direct, metal-free radical trifluoromethylation and polymer initiation. J Fluor Chem 2019. [DOI: 10.1016/j.jfluchem.2019.109370] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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15
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Kubyshkin V, Grage SL, Ulrich AS, Budisa N. Bilayer thickness determines the alignment of model polyproline helices in lipid membranes. Phys Chem Chem Phys 2019; 21:22396-22408. [PMID: 31577299 DOI: 10.1039/c9cp02996f] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Our understanding of protein folds relies fundamentally on the set of secondary structures found in the proteomes. Yet, there also exist intriguing structures and motifs that are underrepresented in natural biopolymeric systems. One example is the polyproline II helix, which is usually considered to have a polar character and therefore does not form membrane spanning sections of membrane proteins. In our work, we have introduced specially designed polyproline II helices into the hydrophobic membrane milieu and used 19F NMR to monitor the helix alignment in oriented lipid bilayers. Our results show that these artificial hydrophobic peptides can adopt several different alignment states. If the helix is shorter than the thickness of the hydrophobic core of the membrane, it is submerged into the bilayer with its long axis parallel to the membrane plane. The polyproline helix adopts a transmembrane alignment when its length exceeds the bilayer thickness. If the peptide length roughly matches the lipid thickness, a coexistence of both states is observed. We thus show that the lipid thickness plays a determining role in the occurrence of a transmembrane polyproline II helix. We also found that the adaptation of polyproline II helices to hydrophobic mismatch is in some notable aspects different from α-helices. Finally, our results prove that the polyproline II helix is a competent structure for the construction of transmembrane peptide segments, despite the fact that no such motif has ever been reported in natural systems.
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Affiliation(s)
- Vladimir Kubyshkin
- Institute of Chemistry, Technical University of Berlin, Müller-Breslau-Str. 10, Berlin 10623, Germany and Department of Chemistry, University of Manitoba, Dysart Rd. 144, Winnipeg MB R3T 2N2, Canada.
| | - Stephan L Grage
- Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology (KIT), P.O.B. 3640, Karlsruhe 76021, Germany
| | - Anne S Ulrich
- Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology (KIT), P.O.B. 3640, Karlsruhe 76021, Germany and Institute of Organic Chemistry, KIT, Fritz-Haber-Weg 6, Karlsruhe 76131, Germany
| | - Nediljko Budisa
- Institute of Chemistry, Technical University of Berlin, Müller-Breslau-Str. 10, Berlin 10623, Germany and Department of Chemistry, University of Manitoba, Dysart Rd. 144, Winnipeg MB R3T 2N2, Canada.
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16
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Gadais C, Van Holsbeeck K, Moors SLC, Buyst D, Fehér K, Van Hecke K, Tourwé D, Brigaud T, Martin C, De Proft F, Pytkowicz J, Martins JC, Chaume G, Ballet S. Trifluoromethylated Proline Surrogates as Part of "Pro-Pro" Turn-Inducing Templates. Chembiochem 2019; 20:2513-2518. [PMID: 31062451 DOI: 10.1002/cbic.201900294] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Indexed: 12/27/2022]
Abstract
Proline is often found as a turn inducer in peptide or protein domains. Exploitation of its restricted conformational freedom led to the development of the d-Pro-l-Pro (corresponding to (R)-Pro-(S)-Pro) segment as a "templating" unit, frequently used in the design of β-hairpin peptidomimetics, in which conformational stability is, however, inherently linked to the cis-trans isomerization of the prolyl amide bonds. In this context, the stereoelectronic properties of the CF3 group can aid in conformational control. Herein, the impact of α-trifluoromethylated proline analogues is examined for the design of enhanced β-turn inducers. A theoretical conformational study permitted the dipeptide (R)-Pro-(R)-TfmOxa (TfmOxa: 2-trifluoromethyloxazolidine-2-carboxylic acid) to be selected as a template with an increased trans-cis rotational energy barrier. NMR spectroscopic analysis of the Ac-(R)-Pro-(R)-TfmOxa-(S)-Val-OtBu β-turn model, obtained through an original synthetic pathway, validated the prevalence of a major trans-trans conformer and indicated the presence of an internal hydrogen bond. Altogether, it was shown that the (R)-Pro-(R)-TfmOxa template fulfilled all crucial β-turn-inducer criteria.
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Affiliation(s)
- Charlène Gadais
- Research Group of Organic Chemistry, Departments of Bioengineering Sciences and Chemistry, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium
| | - Kevin Van Holsbeeck
- Research Group of Organic Chemistry, Departments of Bioengineering Sciences and Chemistry, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium.,NMR and Structure Analysis Unit, Department of Organic and Macromolecular Chemistry, Ghent University, Krijgslaan 281, 9000, Gent, Belgium
| | - Samuel L C Moors
- Eenheid Algemene Chemie (ALGC), Department of Chemistry, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium
| | - Dieter Buyst
- NMR and Structure Analysis Unit, Department of Organic and Macromolecular Chemistry, Ghent University, Krijgslaan 281, 9000, Gent, Belgium
| | - Krisztina Fehér
- NMR and Structure Analysis Unit, Department of Organic and Macromolecular Chemistry, Ghent University, Krijgslaan 281, 9000, Gent, Belgium
| | - Kristof Van Hecke
- XStruct Bio-Inorganic Group, Department of Chemistry, Ghent University, Krijgslaan 281, 9000, Gent, Belgium
| | - Dirk Tourwé
- Research Group of Organic Chemistry, Departments of Bioengineering Sciences and Chemistry, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium
| | - Thierry Brigaud
- Laboratoire de Chimie Biologique, Université de Cergy-Pontoise, 5 Mail Gay-Lussac, 95031, Cergy-Pontoise cedex, France
| | - Charlotte Martin
- Research Group of Organic Chemistry, Departments of Bioengineering Sciences and Chemistry, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium
| | - Frank De Proft
- Eenheid Algemene Chemie (ALGC), Department of Chemistry, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium
| | - Julien Pytkowicz
- Laboratoire de Chimie Biologique, Université de Cergy-Pontoise, 5 Mail Gay-Lussac, 95031, Cergy-Pontoise cedex, France
| | - José C Martins
- NMR and Structure Analysis Unit, Department of Organic and Macromolecular Chemistry, Ghent University, Krijgslaan 281, 9000, Gent, Belgium
| | - Grégory Chaume
- Laboratoire de Chimie Biologique, Université de Cergy-Pontoise, 5 Mail Gay-Lussac, 95031, Cergy-Pontoise cedex, France
| | - Steven Ballet
- Research Group of Organic Chemistry, Departments of Bioengineering Sciences and Chemistry, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium
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17
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Malquin N, Rahgoshay K, Lensen N, Chaume G, Miclet E, Brigaud T. CF 2H as a hydrogen bond donor group for the fine tuning of peptide bond geometry with difluoromethylated pseudoprolines. Chem Commun (Camb) 2019; 55:12487-12490. [PMID: 31566647 DOI: 10.1039/c9cc05771d] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
CF2H-Pseudoprolines obtained from difluoroacetaldehyde hemiacetal and serine are stable proline surrogates. The consequence of the incorporation of the CF2H group is an important decrease of the trans to cis amide bond isomerization energy and a remarkable stabilisation of the cis conformer by an hydrogen bond.
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Affiliation(s)
- N Malquin
- Laboratory of Chemical Biology (LCB, EA 4505), Université de Cergy-Pontoise, 5 Mail Gay-Lussac, 95000 Cergy-Pontoise, France.
| | - K Rahgoshay
- Laboratory of Chemical Biology (LCB, EA 4505), Université de Cergy-Pontoise, 5 Mail Gay-Lussac, 95000 Cergy-Pontoise, France.
| | - N Lensen
- Laboratory of Chemical Biology (LCB, EA 4505), Université de Cergy-Pontoise, 5 Mail Gay-Lussac, 95000 Cergy-Pontoise, France.
| | - G Chaume
- Laboratory of Chemical Biology (LCB, EA 4505), Université de Cergy-Pontoise, 5 Mail Gay-Lussac, 95000 Cergy-Pontoise, France.
| | - E Miclet
- Sorbonne Université, École Normale Supérieure, PSL University, CNRS, Laboratoire des Biomolécules, 75005 Paris, France
| | - T Brigaud
- Laboratory of Chemical Biology (LCB, EA 4505), Université de Cergy-Pontoise, 5 Mail Gay-Lussac, 95000 Cergy-Pontoise, France.
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18
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Kubyshkin V. Stabilization of the triple helix in collagen mimicking peptides. Org Biomol Chem 2019; 17:8031-8047. [PMID: 31464337 DOI: 10.1039/c9ob01646e] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Collagen mimics are peptides designed to reproduce structural features of natural collagen. A triple helix is the first element in the hierarchy of collagen folding. It is an assembly of three parallel peptide chains stabilized by packing and interchain hydrogen bonds. In this review we summarize the existing chemical approaches towards stabilization of this structure including the most recent developments. Currently proposed methods include manipulation of the amino acid composition, application of unnatural amino acid analogues, stimuli-responsive modifications, chain tethering approaches, peptide amphiphiles, modifications that target interchain interactions and more. This ability to manipulate the triple helix as a supramolecular self-assembly contributes to our understanding of the collagen folding. It also provides essential information needed to design collagen-based biomaterials of the future.
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Affiliation(s)
- Vladimir Kubyshkin
- Institute of Chemistry, University of Manitoba, Dysart Rd. 144, R3T 2N2, Winnipeg, Manitoba, Canada.
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19
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Mei H, Han J, Takeda R, Sakamoto T, Miwa T, Minamitsuji Y, Moriwaki H, Abe H, Soloshonok VA. Practical Method for Preparation of ( S)-2-Amino-5,5,5-trifluoropentanoic Acid via Dynamic Kinetic Resolution. ACS OMEGA 2019; 4:11844-11851. [PMID: 31460294 PMCID: PMC6682081 DOI: 10.1021/acsomega.9b01537] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2019] [Accepted: 06/25/2019] [Indexed: 05/08/2023]
Abstract
This work reports an operationally convenient ∼20 g scale synthesis of (S)-2-amino-5,5,5-trifluoropentanoic acid and its Fmoc-derivative via dynamic kinetic resolution of the corresponding racemate.
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Affiliation(s)
- Haibo Mei
- College
of Chemical Engineering Nanjing Forestry University, Nanjing 210037, China
| | - Jianlin Han
- College
of Chemical Engineering Nanjing Forestry University, Nanjing 210037, China
| | - Ryosuke Takeda
- Hamari
Chemicals Ltd., 1-4-29 Kunijima, Higashi-Yodogawa-ku, Osaka 533-0024, Japan
- Department
of Organic Chemistry I, Faculty of Chemistry, University of the Basque Country UPV/EHU, Paseo Manuel Lardizábal 3, San Sebastián 20018, Spain
| | - Tsubasa Sakamoto
- Hamari
Chemicals Ltd., 1-4-29 Kunijima, Higashi-Yodogawa-ku, Osaka 533-0024, Japan
| | - Toshio Miwa
- Hamari
Chemicals Ltd., 1-4-29 Kunijima, Higashi-Yodogawa-ku, Osaka 533-0024, Japan
| | - Yutaka Minamitsuji
- Hamari
Chemicals Ltd., 1-4-29 Kunijima, Higashi-Yodogawa-ku, Osaka 533-0024, Japan
| | - Hiroki Moriwaki
- Hamari
Chemicals Ltd., 1-4-29 Kunijima, Higashi-Yodogawa-ku, Osaka 533-0024, Japan
| | - Hidenori Abe
- Hamari
Chemicals Ltd., 1-4-29 Kunijima, Higashi-Yodogawa-ku, Osaka 533-0024, Japan
| | - Vadim A. Soloshonok
- Department
of Organic Chemistry I, Faculty of Chemistry, University of the Basque Country UPV/EHU, Paseo Manuel Lardizábal 3, San Sebastián 20018, Spain
- IKERBASQUE—Basque
Foundation for Science, María
Díaz de Haro 3, Plaza Bizkaia, Bilbao 48013, Spain
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20
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Rabasa-Alcañiz F, Hammerl D, Sánchez-Merino A, Tejero T, Merino P, Fustero S, del Pozo C. Asymmetric synthesis of polycyclic 3-fluoroalkylproline derivatives by intramolecular azomethine ylide cycloaddition. Org Chem Front 2019. [DOI: 10.1039/c9qo00525k] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The asymmetric intramolecular dipolar cycloaddition of azomethine ylides was developed for fluorinated dipolarophiles, being the RF group crucial for selectivity.
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Affiliation(s)
| | - Daniel Hammerl
- Departamento de Química Orgánica
- Universidad de Valencia
- E-46100 Burjassot
- Spain
| | | | - Tomás Tejero
- Instituto de Síntesis Química y Catálisis Homogénea (ISQCH)
- Universidad de Zaragoza
- 50009 Zaragoza
- Spain
| | - Pedro Merino
- Instituto de Biocomputación y Fisica de Sistemas Complejos (BIFI)
- Universidad de Zaragoza
- 50009 Zaragoza
- Spain
| | - Santos Fustero
- Departamento de Química Orgánica
- Universidad de Valencia
- E-46100 Burjassot
- Spain
- Laboratorio de Moléculas Orgánicas
| | - Carlos del Pozo
- Departamento de Química Orgánica
- Universidad de Valencia
- E-46100 Burjassot
- Spain
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21
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Hutskalova V, Mykhailiuk PK. Pd-Catalyzed directedCH-(hetero)arylation of cyclic α-amino acids: effects of substituents and the ring size. Org Biomol Chem 2019; 17:4342-4349. [DOI: 10.1039/c9ob00393b] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
A systematic study on the directed Pd-catalyzed (hetero)arylation of 26 substituted cyclic α-amino acids at the C(3)-atom was performed. For the first time, the 7- and 8-membered cyclic amino acids were introduced to C–H activation. 8–Aminoquinoline was used as a directing group.
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Affiliation(s)
- Valeriia Hutskalova
- Enamine Ltd
- Kyiv 02094
- Ukraine
- Department of Chemistry
- National Taras Shevchenko University of Kyiv
| | - Pavel K. Mykhailiuk
- Enamine Ltd
- Kyiv 02094
- Ukraine
- Department of Chemistry
- National Taras Shevchenko University of Kyiv
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22
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Levterov VV, Michurin O, Borysko PO, Zozulya S, Sadkova IV, Tolmachev AA, Mykhailiuk PK. Photochemical In-Flow Synthesis of 2,4-Methanopyrrolidines: Pyrrolidine Analogues with Improved Water Solubility and Reduced Lipophilicity. J Org Chem 2018; 83:14350-14361. [PMID: 30358395 DOI: 10.1021/acs.joc.8b02071] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
A practical synthesis of 2,4-methanopyrrolidines was elaborated. The key synthetic step was an intramolecular photochemical [2 + 2]-cycloaddition of an acrylic acid derivative in flow. In spite of a higher molecular weight, 2,4-methanopyrrolidines were shown to have higher solubility in water and lower lipophilicity than pyrrolidines, important characteristics of bioactive molecules in drug design.
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Affiliation(s)
- Vadym V Levterov
- Enamine, Ltd. , Chervonotkatska 78 , Kyiv 02094 , Ukraine (www.enamine.net)
| | - Oleg Michurin
- Enamine, Ltd. , Chervonotkatska 78 , Kyiv 02094 , Ukraine (www.enamine.net)
| | - Petro O Borysko
- Bienta, Chervonotkatska 78 , Kyiv 02094 , Ukraine (www.bienta.net)
| | - Sergey Zozulya
- Bienta, Chervonotkatska 78 , Kyiv 02094 , Ukraine (www.bienta.net)
| | - Iryna V Sadkova
- Enamine, Ltd. , Chervonotkatska 78 , Kyiv 02094 , Ukraine (www.enamine.net)
| | - Andrey A Tolmachev
- Enamine, Ltd. , Chervonotkatska 78 , Kyiv 02094 , Ukraine (www.enamine.net).,Department of Chemistry , Taras Shevchenko National University of Kyiv , Volodymyrska 64 , Kyiv 01601 , Ukraine (www.mykhailiukchem.org)
| | - Pavel K Mykhailiuk
- Enamine, Ltd. , Chervonotkatska 78 , Kyiv 02094 , Ukraine (www.enamine.net).,Department of Chemistry , Taras Shevchenko National University of Kyiv , Volodymyrska 64 , Kyiv 01601 , Ukraine (www.mykhailiukchem.org)
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23
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Verhoork SJM, Killoran PM, Coxon CR. Fluorinated Prolines as Conformational Tools and Reporters for Peptide and Protein Chemistry. Biochemistry 2018; 57:6132-6143. [DOI: 10.1021/acs.biochem.8b00787] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Sanne J. M. Verhoork
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Byrom Street Campus, Liverpool L3 3AF, U.K
| | - Patrick M. Killoran
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Byrom Street Campus, Liverpool L3 3AF, U.K
| | - Christopher R. Coxon
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Byrom Street Campus, Liverpool L3 3AF, U.K
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24
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Testa A, Lucas X, Castro GV, Chan KH, Wright JE, Runcie AC, Gadd MS, Harrison WTA, Ko EJ, Fletcher D, Ciulli A. 3-Fluoro-4-hydroxyprolines: Synthesis, Conformational Analysis, and Stereoselective Recognition by the VHL E3 Ubiquitin Ligase for Targeted Protein Degradation. J Am Chem Soc 2018; 140:9299-9313. [PMID: 29949369 PMCID: PMC6430500 DOI: 10.1021/jacs.8b05807] [Citation(s) in RCA: 87] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
![]()
Hydroxylation and
fluorination of proline alters the pyrrolidine
ring pucker and the trans:cis amide bond ratio in a stereochemistry-dependent
fashion, affecting molecular recognition of proline-containing molecules
by biological systems. While hydroxyprolines and fluoroprolines are
common motifs in medicinal and biological chemistry, the synthesis
and molecular properties of prolines containing both modifications,
i.e., fluoro-hydroxyprolines, have not been described. Here we present
a practical and facile synthesis of all four diastereoisomers of 3-fluoro-4-hydroxyprolines
(F-Hyps), starting from readily available 4-oxo-l-proline
derivatives. Small-molecule X-ray crystallography, NMR spectroscopy,
and quantum mechanical calculations are consistent with fluorination
at C3 having negligible effects on the hydrogen bond donor
capacity of the C4 hydroxyl, but inverting the natural
preference of Hyp from C4-exo to C4-endo pucker.
In spite of this, F-Hyps still bind to the von Hippel–Lindau
(VHL) E3 ligase, which naturally recognizes C4-exo Hyp
in a stereoselective fashion. Co-crystal structures and electrostatic
potential calculations support and rationalize the observed preferential
recognition for (3R,4S)-F-Hyp over
the corresponding (3S,4S) epimer
by VHL. We show that (3R,4S)-F-Hyp
provides bioisosteric Hyp substitution in both hypoxia-inducible factor
1 alpha (HIF-1α) substrate peptides and peptidomimetic ligands
that form part of PROTAC (proteolysis targeting chimera) conjugates
for targeted protein degradation. Despite a weakened affinity, Hyp
substitution with (3S,4S)-F-Hyp
within the PROTAC MZ1 led to Brd4-selective cellular degradation at
concentrations >100-fold lower than the binary Kd for VHL. We anticipate that the disclosed chemistry
of 3-fluoro-4-hydroxyprolines
and their application as VHL ligands for targeted protein degradation
will be of wide interest to medicinal organic chemists, chemical biologists,
and drug discoverers alike.
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Affiliation(s)
- Andrea Testa
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences , University of Dundee , James Black Centre, Dow Street , Dundee DD1 5EH , Scotland, U.K
| | - Xavier Lucas
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences , University of Dundee , James Black Centre, Dow Street , Dundee DD1 5EH , Scotland, U.K
| | - Guilherme V Castro
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences , University of Dundee , James Black Centre, Dow Street , Dundee DD1 5EH , Scotland, U.K
| | - Kwok-Ho Chan
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences , University of Dundee , James Black Centre, Dow Street , Dundee DD1 5EH , Scotland, U.K
| | - Jane E Wright
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences , University of Dundee , James Black Centre, Dow Street , Dundee DD1 5EH , Scotland, U.K
| | - Andrew C Runcie
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences , University of Dundee , James Black Centre, Dow Street , Dundee DD1 5EH , Scotland, U.K
| | - Morgan S Gadd
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences , University of Dundee , James Black Centre, Dow Street , Dundee DD1 5EH , Scotland, U.K
| | - William T A Harrison
- Department of Chemistry , University of Aberdeen , Meston Walk , Aberdeen AB24 3UE , Scotland, U.K
| | - Eun-Jung Ko
- Drug Discovery Unit, Division of Biological Chemistry and Drug Discovery, School of Life Sciences , University of Dundee , James Black Centre, Dow Street , Dundee DD1 5EH , Scotland, U.K
| | - Daniel Fletcher
- Drug Discovery Unit, Division of Biological Chemistry and Drug Discovery, School of Life Sciences , University of Dundee , James Black Centre, Dow Street , Dundee DD1 5EH , Scotland, U.K
| | - Alessio Ciulli
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences , University of Dundee , James Black Centre, Dow Street , Dundee DD1 5EH , Scotland, U.K
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25
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Michurin OM, Tolmachova K, Afonin S, Babii O, Grage SL, Ulrich AS, Komarov IV, Radchenko DS. Conformationally Constrained Mono-Fluorinated Arginine as a Cationic Label for Solid-State 19
F NMR Analysis of Membrane-Bound Peptides. European J Org Chem 2018. [DOI: 10.1002/ejoc.201800473] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
| | - Kateryna Tolmachova
- Enamine Ltd.; vul. Chervonotkatska 78 02094 Kyiv Ukraine
- Institute of Bioorganic Chemistry and Petrochemistry; National Academy of Sciences of Ukraine; vul. Murmanska 1 02660 Kyiv Ukraine
| | - Sergii Afonin
- Institute of Biological Interfaces (IBG-2); Karlsruhe Institute of Technology (KIT); POB 3640 76021 Karlsruhe Germany
| | - Oleg Babii
- Institute of Organic Chemistry (IOC); KIT; Fritz-Haber-Weg 6 76131 Karlsruhe Germany
| | - Stephan L. Grage
- Institute of Biological Interfaces (IBG-2); Karlsruhe Institute of Technology (KIT); POB 3640 76021 Karlsruhe Germany
| | - Anne S. Ulrich
- Institute of Biological Interfaces (IBG-2); Karlsruhe Institute of Technology (KIT); POB 3640 76021 Karlsruhe Germany
- Institute of Organic Chemistry (IOC); KIT; Fritz-Haber-Weg 6 76131 Karlsruhe Germany
| | - Igor V. Komarov
- Taras Shevchenko National University of Kyiv; Taras Shevchenko National University of Kyiv; vul. Volodymyrska 60 01601 Kyiv Ukraine
| | - Dmytro S. Radchenko
- Enamine Ltd.; vul. Chervonotkatska 78 02094 Kyiv Ukraine
- Taras Shevchenko National University of Kyiv; Taras Shevchenko National University of Kyiv; vul. Volodymyrska 60 01601 Kyiv Ukraine
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26
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Hao J, Milcent T, Retailleau P, Soloshonok VA, Ongeri S, Crousse B. Asymmetric Synthesis of Cyclic Fluorinated Amino Acids. European J Org Chem 2018. [DOI: 10.1002/ejoc.201800255] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Jing Hao
- BioCIS, Univ. Paris-Sud, CNRS; Université Paris-Saclay; 92290 Châtenay-Malabry France
| | - Thierry Milcent
- BioCIS, Univ. Paris-Sud, CNRS; Université Paris-Saclay; 92290 Châtenay-Malabry France
| | - Pascal Retailleau
- Institut de Chimie des Substances Naturelles; CNRS UPR 2301; Université Paris-Saclay; 1, avenue de la Terrasse 91198 Gif-sur-Yvette France
| | - Vadim A. Soloshonok
- Department of Organic Chemistry I; Faculty of Chemistry; University of the Basque Country, UPV/EHU; 20018 San Sebastian Spain
| | - Sandrine Ongeri
- BioCIS, Univ. Paris-Sud, CNRS; Université Paris-Saclay; 92290 Châtenay-Malabry France
| | - Benoit Crousse
- BioCIS, Univ. Paris-Sud, CNRS; Université Paris-Saclay; 92290 Châtenay-Malabry France
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27
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Abstract
The third most abundant polypeptide conformation in nature, the polyproline-II helix, is a polar, extended secondary structure with a local organization stabilized by intercarbonyl interactions within the peptide chain. Here we design a hydrophobic polyproline-II helical peptide based on an oligomeric octahydroindole-2-carboxylic acid scaffold and demonstrate its transmembrane alignment in model lipid bilayers by means of solid-state 19F NMR. As result, we provide a first example of a purely artificial transmembrane peptide with a structural organization that is not based on hydrogen-bonding.
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Affiliation(s)
- Vladimir Kubyshkin
- Institute of Chemistry , Technical University of Berlin , Müller-Breslau-Strasse 10 , Berlin 10623 , Germany
| | - Stephan L Grage
- Institute of Biological Interfaces (IBG-2) , Karlsruhe Institute of Technology (KIT) , P.O.B. 3640, Karlsruhe 76021 , Germany
| | - Jochen Bürck
- Institute of Biological Interfaces (IBG-2) , Karlsruhe Institute of Technology (KIT) , P.O.B. 3640, Karlsruhe 76021 , Germany
| | - Anne S Ulrich
- Institute of Biological Interfaces (IBG-2) , Karlsruhe Institute of Technology (KIT) , P.O.B. 3640, Karlsruhe 76021 , Germany
- Institute of Organic Chemistry , KIT , Fritz-Haber-Weg 6 , Karlsruhe 76131 , Germany
| | - Nediljko Budisa
- Institute of Chemistry , Technical University of Berlin , Müller-Breslau-Strasse 10 , Berlin 10623 , Germany
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28
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Bychek RM, Levterov VV, Sadkova IV, Tolmachev AA, Mykhailiuk PK. Synthesis of Functionalized Difluorocyclopropanes: Unique Building Blocks for Drug Discovery. Chemistry 2018; 24:12291-12297. [DOI: 10.1002/chem.201705708] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Indexed: 01/16/2023]
Affiliation(s)
| | | | | | - Andrey A. Tolmachev
- Enamine Ltd.; Chervonotkatska 78 Kyiv 02094 Ukraine
- Department of Chemistry; Taras Shevchenko National University of Kyiv; Volodymyrska 64 Kyiv 01601 Ukraine
| | - Pavel K. Mykhailiuk
- Enamine Ltd.; Chervonotkatska 78 Kyiv 02094 Ukraine
- Department of Chemistry; Taras Shevchenko National University of Kyiv; Volodymyrska 64 Kyiv 01601 Ukraine
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29
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New insights into the influence of monofluorination on dimyristoylphosphatidylcholine membrane properties: A solid-state NMR study. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2018; 1860:654-663. [DOI: 10.1016/j.bbamem.2017.12.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Revised: 11/29/2017] [Accepted: 12/04/2017] [Indexed: 10/18/2022]
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30
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Abstract
Amide rotation of peptidyl-prolyl fragments is an important factor in backbone structure organization of proteins. Computational studies have indicated that this rotation preferentially proceeds through a defined transition-state structure (syn/exo). Here, we complement the computational findings by determining the amide bond rotation barriers for derivatives of the two symmetric proline analogues, meso and racemic pyrrolidine-2,5-dicarboxylic acids. The rotations around these residues represent syn/exo-syn/exo and anti/endo-syn/exo hybrid transition states for the meso and racemic diastereomer, respectively. The rotation barriers are lower for the former rotation by about 9 kJ mol-1 (aqueous medium), suggesting a strong preference for the syn/exo (clockwise) rotation over the anti/endo (anticlockwise) rotation. The results show that both hybrid rotation processes are enthalpically driven but respond differently to solvent polarity changes due to the different transition state dipole-dipole interactions.
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Affiliation(s)
- Vladimir Kubyshkin
- Biocatalysis Group, Institute of Chemistry, Technical University of Berlin, Müller-Breslau-Str. 10, Berlin 10623, Germany.
| | - Nediljko Budisa
- Biocatalysis Group, Institute of Chemistry, Technical University of Berlin, Müller-Breslau-Str. 10, Berlin 10623, Germany.
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31
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Tolmachova NA, Kondratov IS, Dolovanyuk VG, Pridma SO, Chernykh AV, Daniliuc CG, Haufe G. Synthesis of new fluorinated proline analogues from polyfluoroalkyl β-ketoacetals and ethyl isocyanoacetate. Chem Commun (Camb) 2018; 54:9683-9686. [DOI: 10.1039/c8cc05912h] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
New straightforward synthetic approach to hitherto unknown cis-/trans-CF3-prolines and other 3-polyfluoroalkyl proline analogues.
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Affiliation(s)
| | - Ivan S. Kondratov
- Enamine Ltd
- Kyiv
- Ukraine
- Institute of Bioorganic Chemistry and Petrochemistry
- National Academy of Sciences of Ukraine
| | - Violetta G. Dolovanyuk
- Institute of Bioorganic Chemistry and Petrochemistry
- National Academy of Sciences of Ukraine
- Kyiv
- Ukraine
| | | | | | | | - Günter Haufe
- Organisch-Chemisches Institut
- Universität Münster
- Münster 48149
- Germany
- Cells-in-Motion Cluster of Excellence
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32
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Kubyshkin V, Pridma S, Budisa N. Comparative effects of trifluoromethyl- and methyl-group substitutions in proline. NEW J CHEM 2018. [DOI: 10.1039/c8nj02631a] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
What is the outcome of trifluoromethyl-/methyl-substitution in each position of the proline ring? Look inside to find out.
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Affiliation(s)
- Vladimir Kubyshkin
- Biocatalysis Group
- Institute of Chemistry
- Technical University of Berlin
- Berlin 10623
- Germany
| | | | - Nediljko Budisa
- Biocatalysis Group
- Institute of Chemistry
- Technical University of Berlin
- Berlin 10623
- Germany
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33
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Kubyshkin V, Budisa N. Hydrolysis, polarity, and conformational impact of C-terminal partially fluorinated ethyl esters in peptide models. Beilstein J Org Chem 2017; 13:2442-2457. [PMID: 29234471 PMCID: PMC5704756 DOI: 10.3762/bjoc.13.241] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Accepted: 10/19/2017] [Indexed: 12/17/2022] Open
Abstract
Fluorinated moieties are highly valuable to chemists due to the sensitive NMR detectability of the 19F nucleus. Fluorination of molecular scaffolds can also selectively influence a molecule's polarity, conformational preferences and chemical reactivity, properties that can be exploited for various chemical applications. A powerful route for incorporating fluorine atoms in biomolecules is last-stage fluorination of peptide scaffolds. One of these methods involves esterification of the C-terminus of peptides using a diazomethane species. Here, we provide an investigation of the physicochemical consequences of peptide esterification with partially fluorinated ethyl groups. Derivatives of N-acetylproline are used to model the effects of fluorination on the lipophilicity, hydrolytic stability and on conformational properties. The conformational impact of the 2,2-difluoromethyl ester on several neutral and charged oligopeptides was also investigated. Our results demonstrate that partially fluorinated esters undergo variable hydrolysis in biologically relevant buffers. The hydrolytic stability can be tailored over a broad pH range by varying the number of fluorine atoms in the ester moiety or by introducing adjacent charges in the peptide sequence.
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Affiliation(s)
- Vladimir Kubyshkin
- Biocatalysis group, Institute of Chemistry, Technical University of Berlin, Müller-Breslau-Strasse 10, Berlin 10623, Germany
| | - Nediljko Budisa
- Biocatalysis group, Institute of Chemistry, Technical University of Berlin, Müller-Breslau-Strasse 10, Berlin 10623, Germany
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34
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Chalyk BA, Butko MV, Yanshyna OO, Gavrilenko KS, Druzhenko TV, Mykhailiuk PK. Synthesis of Spirocyclic Pyrrolidines: Advanced Building Blocks for Drug Discovery. Chemistry 2017; 23:16782-16786. [PMID: 28800185 DOI: 10.1002/chem.201702362] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Indexed: 01/24/2023]
Abstract
In the context of drug discovery, novel spirocyclic pyrrolidines have been synthesized in two steps from common three- to seven-membered-ring (hetero)alicyclic ketones. The key transformation is a reaction between an electron-deficient exocyclic alkene and an in situ generated N-benzyl azomethine ylide. The developed method has been used to synthesize the central diamine core of the known antibacterial agents Sitafloxacin and Olamufloxacin.
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Affiliation(s)
| | - Maryna V Butko
- Enamine Ltd., Chervonotkatska 78, Kyiv, 02094, Ukraine.,Department of Chemical Technology, National Technical University of Ukraine, "Igor Sikorsky Kyiv Polytechnic Institute", Prosp. Peremohy 37, Kyiv, 03056, Ukraine
| | - Oksana O Yanshyna
- Enamine Ltd., Chervonotkatska 78, Kyiv, 02094, Ukraine.,Institute of High Technologies, Taras Shevchenko National University of Kyiv, Volodymyrska 60, Kyiv, 01601, Ukraine
| | - Konstantin S Gavrilenko
- Enamine Ltd., Chervonotkatska 78, Kyiv, 02094, Ukraine.,ChemBioCenter, Taras Shevchenko National University of Kyiv, Volodymyrska 64, Kyiv, 01601, Ukraine
| | - Tetiana V Druzhenko
- Enamine Ltd., Chervonotkatska 78, Kyiv, 02094, Ukraine.,Institute of High Technologies, Taras Shevchenko National University of Kyiv, Volodymyrska 60, Kyiv, 01601, Ukraine
| | - Pavel K Mykhailiuk
- Enamine Ltd., Chervonotkatska 78, Kyiv, 02094, Ukraine.,Department of Chemistry, Taras Shevchenko National University of Kyiv, Volodymyrska 64, Kyiv, 01601, Ukraine
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35
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Chalyk BA, Isakov AA, Butko MV, Hrebeniuk KV, Savych OV, Kucher OV, Gavrilenko KS, Druzhenko TV, Yarmolchuk VS, Zozulya S, Mykhailiuk PK. Synthesis of 6-Azaspiro[4.3]alkanes: Innovative Scaffolds for Drug Discovery. European J Org Chem 2017. [DOI: 10.1002/ejoc.201700536] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
| | - Andrei A. Isakov
- Enamine Ltd.; Chervonotkatska 78 02094 Kyiv Ukraine
- Department of Chemistry; Taras Shevchenko National University of Kyiv; Volodymyrska 64 01601 Kyiv Ukraine
| | - Maryna V. Butko
- Enamine Ltd.; Chervonotkatska 78 02094 Kyiv Ukraine
- Department of Chemical Technology; National Technical University of Ukraine “Igor Sikorsky Kyiv Polytechnic Institute”; Prosp. Peremohy 37 03056 Kyiv Ukraine
| | | | - Olena V. Savych
- Enamine Ltd.; Chervonotkatska 78 02094 Kyiv Ukraine
- Department of Chemistry; Taras Shevchenko National University of Kyiv; Volodymyrska 64 01601 Kyiv Ukraine
| | - Olexandr V. Kucher
- Enamine Ltd.; Chervonotkatska 78 02094 Kyiv Ukraine
- Institute of Bioorganic Chemistry and Petrochemistry; National Academy of Sciences of Ukraine; Murmanska Street 1 02094 Kyiv Ukraine
| | - Konstantin S. Gavrilenko
- Enamine Ltd.; Chervonotkatska 78 02094 Kyiv Ukraine
- ChemBioCenter; Taras Shevchenko National University of Kyiv; Volodymyrska 64 01601 Kyiv Ukraine
| | - Tetiana V. Druzhenko
- Enamine Ltd.; Chervonotkatska 78 02094 Kyiv Ukraine
- Institute of High Technologies; Taras Shevchenko National University of Kyiv; Hlushkova Avenue, 4G 03022 Kyiv Ukraine
| | - Vladimir S. Yarmolchuk
- Enamine Ltd.; Chervonotkatska 78 02094 Kyiv Ukraine
- Institute of High Technologies; Taras Shevchenko National University of Kyiv; Hlushkova Avenue, 4G 03022 Kyiv Ukraine
| | - Sergey Zozulya
- Enamine Ltd.; Chervonotkatska 78 02094 Kyiv Ukraine
- ChemBioCenter; Taras Shevchenko National University of Kyiv; Volodymyrska 64 01601 Kyiv Ukraine
| | - Pavel K. Mykhailiuk
- Department of Chemistry; Taras Shevchenko National University of Kyiv; Volodymyrska 64 01601 Kyiv Ukraine
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36
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Mykhailiuk PK, Kubyshkin V, Bach T, Budisa N. Peptidyl-Prolyl Model Study: How Does the Electronic Effect Influence the Amide Bond Conformation? J Org Chem 2017; 82:8831-8841. [DOI: 10.1021/acs.joc.7b00803] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Pavel K. Mykhailiuk
- Taras Shevchenko National University of Kyiv, Chemistry Department, Volodymyrska 64, 01601 Kyiv, Ukraine
- Enamine Limited, Chervonotkatska 78, 01103 Kyiv, Ukraine
| | - Vladimir Kubyshkin
- Institute
of Chemistry, Technical University of Berlin, Müller-Breslau-Strasse 10, 10623 Berlin, Germany
| | - Thorsten Bach
- Lehrstuhl
für Organische Chemie I, Technische Universität München, Lichtenbergstrasse 4, 85747 Garching, Germany
| | - Nediljko Budisa
- Institute
of Chemistry, Technical University of Berlin, Müller-Breslau-Strasse 10, 10623 Berlin, Germany
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37
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Kirichok AA, Shton I, Kliachyna M, Pishel I, Mykhailiuk PK. 1-Substituted 2-Azaspiro[3.3]heptanes: Overlooked Motifs for Drug Discovery. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201703801] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
| | - Iryna Shton
- Enamine Ltd./Bienta; Chervonotkatska 78 02094 Kyiv Ukraine
| | | | - Iryna Pishel
- Enamine Ltd./Bienta; Chervonotkatska 78 02094 Kyiv Ukraine
| | - Pavel K. Mykhailiuk
- Taras Shevchenko National University of Kyiv; Chemistry Department; Volodymyrska 64 01601 Kyiv Ukraine
- Enamine Ltd./Bienta; Chervonotkatska 78 02094 Kyiv Ukraine
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38
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Kirichok AA, Shton I, Kliachyna M, Pishel I, Mykhailiuk PK. 1-Substituted 2-Azaspiro[3.3]heptanes: Overlooked Motifs for Drug Discovery. Angew Chem Int Ed Engl 2017; 56:8865-8869. [PMID: 28510279 DOI: 10.1002/anie.201703801] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Revised: 05/15/2017] [Indexed: 01/28/2023]
Abstract
The 2-substituted piperidine core is found in drugs (18 FDA-approved drugs), however, their spirocyclic analogues remain unknown. Described here is the synthesis of spirocyclic analogues for 2-substituted piperidines and a demonstration of their validation in drug discovery.
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Affiliation(s)
| | - Iryna Shton
- Enamine Ltd./Bienta, Chervonotkatska 78, 02094, Kyiv, Ukraine
| | - Maria Kliachyna
- Enamine Ltd./Bienta, Chervonotkatska 78, 02094, Kyiv, Ukraine
| | - Iryna Pishel
- Enamine Ltd./Bienta, Chervonotkatska 78, 02094, Kyiv, Ukraine
| | - Pavel K Mykhailiuk
- Taras Shevchenko National University of Kyiv, Chemistry Department, Volodymyrska 64, 01601, Kyiv, Ukraine.,Enamine Ltd./Bienta, Chervonotkatska 78, 02094, Kyiv, Ukraine
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39
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Michurin OM, Afonin S, Berditsch M, Daniliuc CG, Ulrich AS, Komarov IV, Radchenko DS. Delivering Structural Information on the Polar Face of Membrane‐Active Peptides:
19
F‐NMR Labels with a Cationic Side Chain. Angew Chem Int Ed Engl 2016; 55:14595-14599. [DOI: 10.1002/anie.201607161] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2016] [Revised: 09/14/2016] [Indexed: 12/16/2022]
Affiliation(s)
| | - Sergii Afonin
- Institute of Biological Interfaces (IBG-2) Karlsruhe Institute of Technology (KIT) POB 3640 76021 Karlsruhe Germany
| | - Marina Berditsch
- Institute of Organic Chemistry (IOC) KIT Fritz-Haber-Weg 6 76131 Karlsruhe Germany
| | - Constantin G. Daniliuc
- Institute of Organic Chemistry Westfalische Wilhelms-Universität Münster Corrensstrasse 40 48149 Münster Germany
| | - Anne S. Ulrich
- Institute of Biological Interfaces (IBG-2) Karlsruhe Institute of Technology (KIT) POB 3640 76021 Karlsruhe Germany
- Institute of Organic Chemistry (IOC) KIT Fritz-Haber-Weg 6 76131 Karlsruhe Germany
| | - Igor V. Komarov
- Institute of High Technologies Taras Shevchenko National University of Kyiv vul. Volodymyrska 60 01601 Kyiv Ukraine
| | - Dmytro S. Radchenko
- Enamine Ltd. vul. Chervonotkatska 78 02094 Kyiv Ukraine
- Institute of Organic Chemistry (IOC) KIT Fritz-Haber-Weg 6 76131 Karlsruhe Germany
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40
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Michurin OM, Afonin S, Berditsch M, Daniliuc CG, Ulrich AS, Komarov IV, Radchenko DS. Delivering Structural Information on the Polar Face of Membrane-Active Peptides: 19
F-NMR Labels with a Cationic Side Chain. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201607161] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
| | - Sergii Afonin
- Institute of Biological Interfaces (IBG-2); Karlsruhe Institute of Technology (KIT); POB 3640 76021 Karlsruhe Germany
| | - Marina Berditsch
- Institute of Organic Chemistry (IOC); KIT; Fritz-Haber-Weg 6 76131 Karlsruhe Germany
| | - Constantin G. Daniliuc
- Institute of Organic Chemistry; Westfalische Wilhelms-Universität Münster; Corrensstrasse 40 48149 Münster Germany
| | - Anne S. Ulrich
- Institute of Biological Interfaces (IBG-2); Karlsruhe Institute of Technology (KIT); POB 3640 76021 Karlsruhe Germany
- Institute of Organic Chemistry (IOC); KIT; Fritz-Haber-Weg 6 76131 Karlsruhe Germany
| | - Igor V. Komarov
- Institute of High Technologies; Taras Shevchenko National University of Kyiv; vul. Volodymyrska 60 01601 Kyiv Ukraine
| | - Dmytro S. Radchenko
- Enamine Ltd.; vul. Chervonotkatska 78 02094 Kyiv Ukraine
- Institute of Organic Chemistry (IOC); KIT; Fritz-Haber-Weg 6 76131 Karlsruhe Germany
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41
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Kokhan SO, Tymtsunik AV, Grage SL, Afonin S, Babii O, Berditsch M, Strizhak AV, Bandak D, Platonov MO, Komarov IV, Ulrich AS, Mykhailiuk PK. Design, Synthesis, and Application of an Optimized Monofluorinated Aliphatic Label for Peptide Studies by Solid-State 19
F NMR Spectroscopy. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201608116] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Serhii O. Kokhan
- Enamine Ltd; Chervonotkatska 78 02094 Kyiv Ukraine
- Institute of High Technologies; Taras Shevchenko National University of Kyiv; Volodymyrska 60 01601 Kyiv Ukraine
| | - Andriy V. Tymtsunik
- Enamine Ltd; Chervonotkatska 78 02094 Kyiv Ukraine
- Institute of High Technologies; Taras Shevchenko National University of Kyiv; Volodymyrska 60 01601 Kyiv Ukraine
| | - Stephan L. Grage
- Institute of Biological Interfaces (IBG-2); Karlsruhe Institute of Technology (KIT); POB 3640 76021 Karlsruhe Germany
| | - Sergii Afonin
- Institute of Biological Interfaces (IBG-2); Karlsruhe Institute of Technology (KIT); POB 3640 76021 Karlsruhe Germany
| | - Oleg Babii
- Institute of Organic Chemistry (IOC); KIT; Fritz-Haber-Weg 6 76131 Karlsruhe Germany
| | - Marina Berditsch
- Institute of Organic Chemistry (IOC); KIT; Fritz-Haber-Weg 6 76131 Karlsruhe Germany
| | | | | | | | - Igor V. Komarov
- Institute of High Technologies; Taras Shevchenko National University of Kyiv; Volodymyrska 60 01601 Kyiv Ukraine
| | - Anne S. Ulrich
- Institute of Biological Interfaces (IBG-2); Karlsruhe Institute of Technology (KIT); POB 3640 76021 Karlsruhe Germany
- Institute of Organic Chemistry (IOC); KIT; Fritz-Haber-Weg 6 76131 Karlsruhe Germany
| | - Pavel K. Mykhailiuk
- Enamine Ltd; Chervonotkatska 78 02094 Kyiv Ukraine
- Chemistry Department; Taras Shevchenko National University of Kyiv; Volodymyrska 64 01601 Kyiv Ukraine
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42
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Kokhan SO, Tymtsunik AV, Grage SL, Afonin S, Babii O, Berditsch M, Strizhak AV, Bandak D, Platonov MO, Komarov IV, Ulrich AS, Mykhailiuk PK. Design, Synthesis, and Application of an Optimized Monofluorinated Aliphatic Label for Peptide Studies by Solid‐State
19
F NMR Spectroscopy. Angew Chem Int Ed Engl 2016; 55:14788-14792. [DOI: 10.1002/anie.201608116] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Indexed: 02/06/2023]
Affiliation(s)
- Serhii O. Kokhan
- Enamine Ltd Chervonotkatska 78 02094 Kyiv Ukraine
- Institute of High Technologies Taras Shevchenko National University of Kyiv Volodymyrska 60 01601 Kyiv Ukraine
| | - Andriy V. Tymtsunik
- Enamine Ltd Chervonotkatska 78 02094 Kyiv Ukraine
- Institute of High Technologies Taras Shevchenko National University of Kyiv Volodymyrska 60 01601 Kyiv Ukraine
| | - Stephan L. Grage
- Institute of Biological Interfaces (IBG-2) Karlsruhe Institute of Technology (KIT) POB 3640 76021 Karlsruhe Germany
| | - Sergii Afonin
- Institute of Biological Interfaces (IBG-2) Karlsruhe Institute of Technology (KIT) POB 3640 76021 Karlsruhe Germany
| | - Oleg Babii
- Institute of Organic Chemistry (IOC) KIT Fritz-Haber-Weg 6 76131 Karlsruhe Germany
| | - Marina Berditsch
- Institute of Organic Chemistry (IOC) KIT Fritz-Haber-Weg 6 76131 Karlsruhe Germany
| | | | | | | | - Igor V. Komarov
- Institute of High Technologies Taras Shevchenko National University of Kyiv Volodymyrska 60 01601 Kyiv Ukraine
| | - Anne S. Ulrich
- Institute of Biological Interfaces (IBG-2) Karlsruhe Institute of Technology (KIT) POB 3640 76021 Karlsruhe Germany
- Institute of Organic Chemistry (IOC) KIT Fritz-Haber-Weg 6 76131 Karlsruhe Germany
| | - Pavel K. Mykhailiuk
- Enamine Ltd Chervonotkatska 78 02094 Kyiv Ukraine
- Chemistry Department Taras Shevchenko National University of Kyiv Volodymyrska 64 01601 Kyiv Ukraine
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43
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Simon J, Pytkowicz J, Lensen N, Chaume G, Brigaud T. Incorporation of Trifluoromethylated Proline and Surrogates into Peptides: Application to the Synthesis of Fluorinated Analogues of the Neuroprotective Glycine-Proline-Glutamate (GPE) Tripeptide. J Org Chem 2016; 81:5381-92. [DOI: 10.1021/acs.joc.6b00704] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Julien Simon
- Laboratoire de Chimie Biologique (LCB), Université de Cergy-Pontoise, EA 4505, 5 Mail Gay-Lussac, 95000 Cergy-Pontoise, France
| | - Julien Pytkowicz
- Laboratoire de Chimie Biologique (LCB), Université de Cergy-Pontoise, EA 4505, 5 Mail Gay-Lussac, 95000 Cergy-Pontoise, France
| | - Nathalie Lensen
- Laboratoire de Chimie Biologique (LCB), Université de Cergy-Pontoise, EA 4505, 5 Mail Gay-Lussac, 95000 Cergy-Pontoise, France
| | - Grégory Chaume
- Laboratoire de Chimie Biologique (LCB), Université de Cergy-Pontoise, EA 4505, 5 Mail Gay-Lussac, 95000 Cergy-Pontoise, France
| | - Thierry Brigaud
- Laboratoire de Chimie Biologique (LCB), Université de Cergy-Pontoise, EA 4505, 5 Mail Gay-Lussac, 95000 Cergy-Pontoise, France
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44
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Levchenko K, Datsenko OP, Serhiichuk O, Tolmachev A, Iaroshenko VO, Mykhailiuk PK. Copper-Catalyzed O-Difluoromethylation of Functionalized Aliphatic Alcohols: Access to Complex Organic Molecules with an OCF2H Group. J Org Chem 2016; 81:5803-13. [DOI: 10.1021/acs.joc.6b00628] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
| | | | - Oleh Serhiichuk
- Department
of Organic Chemistry, Kiev Polytechnic Institute, Pr. Pobedy 37, 03056 Kiev, Ukraine
| | | | - Viktor O. Iaroshenko
- Homogeneous
Catalysis and Molecular Design Research Group at Center of Molecular
and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza
112, PL-90-363 Łódź, Poland
| | - Pavel K. Mykhailiuk
- Enamine,
Ltd., 78 Chervonotkatska str., 02094 Kyiv, Ukraine
- Department
of Chemistry, Taras Shevchenko National University of Kyiv, Volodymyrska
Street, 64, Kyiv 01601, Ukraine
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45
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Kubyshkin V, Budisa N. cis-trans-Amide isomerism of the 3,4-dehydroproline residue, the 'unpuckered' proline. Beilstein J Org Chem 2016; 12:589-93. [PMID: 27340450 PMCID: PMC4901939 DOI: 10.3762/bjoc.12.57] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Accepted: 03/08/2016] [Indexed: 11/23/2022] Open
Abstract
Proline (Pro) is an outstanding amino acid in various biochemical and physicochemical perspectives, especially when considering the cis–trans isomerism of the peptidyl-Pro amide bond. Elucidation of the roles of Pro in chemical or biological systems and engineering of its features can be addressed with various Pro analogues. Here we report an experimental work investigating the basic physicochemical properties of two Pro analogues which possess a 3,4-double bond: 3,4-dehydroproline and 4-trifluoromethyl-3,4-dehydroproline. Both indicate a flat pyrroline ring in their crystal structures, in agreement with previous theoretical calculations. In solution, the peptide mimics exhibit an almost unchanged equilibrium of the trans/cis ratios compared to that of Pro and 4-trifluoromethylproline derivatives. Finally we demonstrate that the 3,4-double bond in the investigated structures leads to an increase of the amide rotational barriers, presumably due to an interplay with the transition state.
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Affiliation(s)
- Vladimir Kubyshkin
- Institute of Chemistry, Technical University of Berlin, Müller-Breslau-Str., 10, 10623, Berlin, Germany
| | - Nediljko Budisa
- Institute of Chemistry, Technical University of Berlin, Müller-Breslau-Str., 10, 10623, Berlin, Germany
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46
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Kubyshkin V, Durkin P, Budisa N. Energetic contribution to both acidity and conformational stability in peptide models. NEW J CHEM 2016. [DOI: 10.1039/c5nj03611a] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The acidity difference of the amide rotamers has been revised for a large set ofN-acetyl amino acids.
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Affiliation(s)
- Vladimir Kubyshkin
- Biocatalysis Group
- Institute of Chemistry
- Technical University of Berlin
- Berlin
- Germany
| | - Patrick Durkin
- Biocatalysis Group
- Institute of Chemistry
- Technical University of Berlin
- Berlin
- Germany
| | - Nediljko Budisa
- Biocatalysis Group
- Institute of Chemistry
- Technical University of Berlin
- Berlin
- Germany
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