1
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Kubyshkin V, Rubini M. Proline Analogues. Chem Rev 2024; 124:8130-8232. [PMID: 38941181 DOI: 10.1021/acs.chemrev.4c00007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/30/2024]
Abstract
Within the canonical repertoire of the amino acid involved in protein biogenesis, proline plays a unique role as an amino acid presenting a modified backbone rather than a side-chain. Chemical structures that mimic proline but introduce changes into its specific molecular features are defined as proline analogues. This review article summarizes the existing chemical, physicochemical, and biochemical knowledge about this peculiar family of structures. We group proline analogues from the following compounds: substituted prolines, unsaturated and fused structures, ring size homologues, heterocyclic, e.g., pseudoproline, and bridged proline-resembling structures. We overview (1) the occurrence of proline analogues in nature and their chemical synthesis, (2) physicochemical properties including ring conformation and cis/trans amide isomerization, (3) use in commercial drugs such as nirmatrelvir recently approved against COVID-19, (4) peptide and protein synthesis involving proline analogues, (5) specific opportunities created in peptide engineering, and (6) cases of protein engineering with the analogues. The review aims to provide a summary to anyone interested in using proline analogues in systems ranging from specific biochemical setups to complex biological systems.
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Affiliation(s)
| | - Marina Rubini
- School of Chemistry, University College Dublin, Belfield, Dublin 4, Ireland
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2
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Logvinenko IG, Sadkova IV, Tolmachova NA, Shishkina SV, Daniliuc CG, Haufe G, Kondratov IS. 4-Trifluoromethoxy proline: synthesis of stereoisomers and lipophilicity study. Org Biomol Chem 2024. [PMID: 38973538 DOI: 10.1039/d4ob00688g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/09/2024]
Abstract
All four stereoisomers of 4-CF3O-proline have been synthesized through a fluorodesulfurization approach using the corresponding 4-hydroxyprolines as starting materials. The investigation of their lipophilicity characteristics and comparison with those of other 4-substituted proline analogs demonstrated a similar impact of CF3 and CF3O groups on log D.
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Affiliation(s)
- Ivan G Logvinenko
- Enamine Ltd, Winston Churchill Str. 78, Kyiv 02094, Ukraine
- Address V.P. Kukhar Institute of Bioorganic Chemistry & Petrochemistry, National Academy of Sciences of Ukraine, Academician Kukhar Str. 1, Kyiv 02094, Ukraine
| | | | | | - Svitlana V Shishkina
- SSI "Institute for Single Crystals" of the National Academy of Sciences of Ukraine, Nauky Ave. 60, Kharkiv 61072, Ukraine
- Institute of Organic Chemistry of the National Academy of Sciences of Ukraine, Academician Kukhar Str. Str. 5, Kyiv 02660, Ukraine
| | - Constantin G Daniliuc
- Organisch-Chemisches Institut, Universität Münster, Corrensstraße 40, Münster 48149, Germany
| | - Günter Haufe
- Organisch-Chemisches Institut, Universität Münster, Corrensstraße 40, Münster 48149, Germany
- Cells-in-Motion Cluster of Excellence, Universität Münster, Waldeyerstraße 15, 48149 Münster, Germany
| | - Ivan S Kondratov
- Enamine Ltd, Winston Churchill Str. 78, Kyiv 02094, Ukraine
- Address V.P. Kukhar Institute of Bioorganic Chemistry & Petrochemistry, National Academy of Sciences of Ukraine, Academician Kukhar Str. 1, Kyiv 02094, Ukraine
- Enamine Germany GmbH, Industriepark Hoechst, G837, 65926 Frankfurt am Main, Germany.
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3
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Ganguly HK, Ludwig BA, Tressler CM, Bhatt MR, Pandey AK, Quinn CM, Bai S, Yap GPA, Zondlo NJ. 4,4-Difluoroproline as a Unique 19F NMR Probe of Proline Conformation. Biochemistry 2024; 63:1131-1146. [PMID: 38598681 DOI: 10.1021/acs.biochem.3c00697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/12/2024]
Abstract
Despite the importance of proline conformational equilibria (trans versus cis amide and exo versus endo ring pucker) on protein structure and function, there is a lack of convenient ways to probe proline conformation. 4,4-Difluoroproline (Dfp) was identified to be a sensitive 19F NMR-based probe of proline conformational biases and cis-trans isomerism. Within model compounds and disordered peptides, the diastereotopic fluorines of Dfp exhibit similar chemical shifts (ΔδFF = 0-3 ppm) when a trans X-Dfp amide bond is present. In contrast, the diastereotopic fluorines exhibit a large (ΔδFF = 5-12 ppm) difference in chemical shift in a cis X-Dfp prolyl amide bond. DFT calculations, X-ray crystallography, and solid-state NMR spectroscopy indicated that ΔδFF directly reports on the relative preference of one proline ring pucker over the other: a fluorine which is pseudo-axial (i.e., the pro-4R-F in an exo ring pucker, or the pro-4S-F in an endo ring pucker) is downfield, while a fluorine which is pseudo-equatorial (i.e., pro-4S-F when exo, or pro-4R-F when endo) is upfield. Thus, when a proline is disordered (a mixture of exo and endo ring puckers, as at trans-Pro in peptides in water), it exhibits a small Δδ. In contrast, when the Pro is ordered (i.e., when one ring pucker is strongly preferred, as in cis-Pro amide bonds, where the endo ring pucker is strongly favored), a large Δδ is observed. Dfp can be used to identify inherent induced order in peptides and to quantify proline cis-trans isomerism. Using Dfp, we discovered that the stable polyproline II helix (PPII) formed in the denatured state (8 M urea) exhibits essentially equal populations of the exo and endo proline ring puckers. In addition, the data with Dfp suggested the specific stabilization of PPII by water over other polar solvents. These data strongly support the importance of carbonyl solvation and n → π* interactions for the stabilization of PPII. Dfp was also employed to quantify proline cis-trans isomerism as a function of phosphorylation and the R406W mutation in peptides derived from the intrinsically disordered protein tau. Dfp is minimally sterically disruptive and can be incorporated in expressed proteins, suggesting its broad application in understanding proline cis-trans isomerization, protein folding, and local order in intrinsically disordered proteins.
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Affiliation(s)
- Himal K Ganguly
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Brice A Ludwig
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Caitlin M Tressler
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Megh R Bhatt
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Anil K Pandey
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Caitlin M Quinn
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Shi Bai
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Glenn P A Yap
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Neal J Zondlo
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
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4
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Patel K, Karmakar S, Tothadi S, Reddy JP, Prabhakaran P. "Fluorine Effects" in Conformational Orchestration of α/β Hybrid Peptide with a 9-membered Pseudo β-Turn Motif. Chemistry 2024; 30:e202303757. [PMID: 38165894 DOI: 10.1002/chem.202303757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Revised: 12/27/2023] [Accepted: 12/28/2023] [Indexed: 01/04/2024]
Abstract
Fluorine, the tiny robust atom, with its unique features has captured the attention of scientists in recent times, especially in drug discovery with its integration in small molecules, peptides, and proteins. However, studies to understand the 'fluorine effects' on the conformation of molecules that follow 'beyond the rule of 5' are in the infancy yet significant in molecular design and function. For the first time, using short hybrid peptide sequence as an appropriate model, we examined the substitution effect (size, stereoelectronic effect, and hydrogen bonding) using X-ray diffraction, 2D-NMR, and CD studies. The comparative study on their folding patterns with hydrogen-substituted analogs can provide valuable insights into fluorinated substrates' design.
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Affiliation(s)
- Karma Patel
- School of Chemical Sciences, Central University of Gujarat, Gandhinagar, India-, 382030
| | - Sintu Karmakar
- School of Chemical Sciences, Central University of Gujarat, Gandhinagar, India-, 382030
| | - Srinu Tothadi
- Analytical and Environmental Sciences Division and Centralized Instrument Facility (AESD&CIF), CSIR-Central Salt & Marine Chemicals Research Institute (CSMCRI), Bhavnagar, India-, 364002
| | - J Prakasha Reddy
- School of Applied Material Sciences, Central University of Gujarat, Gandhinagar, India-, 382030
| | - Panchami Prabhakaran
- School of Chemical Sciences, Central University of Gujarat, Gandhinagar, India-, 382030
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5
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Killoran PM, Capel V, D'Aloisio V, Schofield A, Aczél T, Bölcskei K, Helyes Z, von Mentzer B, Kendall DA, Coxon CR, Hutcheon GA. Novel peptide calcitonin gene-related peptide antagonists for migraine therapy. J Pharm Pharmacol 2023; 75:1581-1589. [PMID: 37742055 DOI: 10.1093/jpp/rgad081] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 08/22/2023] [Indexed: 09/25/2023]
Abstract
OBJECTIVES It has previously been shown that the peptide (34Pro,35Phe)CGRP27-37 is a potent calcitonin gene-related peptide, CGRP receptor antagonist, and in this project we aimed to improve the antagonist potency through the structural modification of truncated C-terminal CGRP peptides. METHODS Six peptide analogues were synthesized and the anti-CGRP activity confirmed using both in vitro and in vivo studies. KEY FINDINGS A 10 amino acid-containing peptide VPTDVGPFAF-NH2 (P006) was identified as a key candidate to take forward for in vivo evaluation, where it was shown to be an effective antagonist after intraperitoneal injection into mice. P006 was formulated as a preparation suitable for nasal administration by spray drying with chitosan to form mucoadhesive microcarriers (9.55 ± 0.91 mm diameter) and a loading of 0.2 mg peptide per 20 mg dose. CONCLUSIONS The project has demonstrated the potential of these novel small peptide CGRP antagonists, to undergo future preclinical evaluation as anti-migraine therapeutics.
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Affiliation(s)
- Patrick M Killoran
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Liverpool, L3 3AF, United Kingdom
| | - Vicky Capel
- NHS Health Education England, Victoria House, Fulbourn, Cambridge, CB21 5XB, United Kingdom
| | - Vera D'Aloisio
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Liverpool, L3 3AF, United Kingdom
- AmbioPharm, Inc., 1024 Dittman Court, North Augusta, SC 29842, United States
| | - Adam Schofield
- EaStCHEM School of Chemistry, The University of Edinburgh, Joseph Black Building, David, Brewster Road, Edinburgh, EH14 4AS, United Kingdom
| | - Tímea Aczél
- Department of Pharmacology and Pharmacotherapy, University of Pécs Medical School, Szigeti út 12, Pécs, Hungary
- Eötvös Lorand Research Network, Chronic Pain Research Group, University of Pécs, Szigeti út 12, Pécs, Hungary
| | - Kata Bölcskei
- Department of Pharmacology and Pharmacotherapy, University of Pécs Medical School, Szigeti út 12, Pécs, Hungary
- Eötvös Lorand Research Network, Chronic Pain Research Group, University of Pécs, Szigeti út 12, Pécs, Hungary
| | - Zsuzsanna Helyes
- Department of Pharmacology and Pharmacotherapy, University of Pécs Medical School, Szigeti út 12, Pécs, Hungary
- Eötvös Lorand Research Network, Chronic Pain Research Group, University of Pécs, Szigeti út 12, Pécs, Hungary
- PharmInVivo Ltd., Szondi Gy. u. 10. H-7629, Pécs, Hungary
- National Laboratory for Drug Research and Development, Magyar tudósok krt. 2, H-1117 Budapest, Hungary
| | - Bengt von Mentzer
- Innovipharm Limited, 2 Woodlands Lane, West Kirby, Wirral, CH48 8D, United Kingdom
| | - David A Kendall
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Liverpool, L3 3AF, United Kingdom
- Innovipharm Limited, 2 Woodlands Lane, West Kirby, Wirral, CH48 8D, United Kingdom
| | - Chris R Coxon
- EaStCHEM School of Chemistry, The University of Edinburgh, Joseph Black Building, David, Brewster Road, Edinburgh, EH14 4AS, United Kingdom
| | - Gillian A Hutcheon
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Liverpool, L3 3AF, United Kingdom
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6
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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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7
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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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8
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19F NMR Chemical Shifts Are Sensitive to Remote Functional Group Variations. J Mol Struct 2023. [DOI: 10.1016/j.molstruc.2023.135273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/09/2023]
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9
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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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10
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Diehl CJ, Ciulli A. Discovery of small molecule ligands for the von Hippel-Lindau (VHL) E3 ligase and their use as inhibitors and PROTAC degraders. Chem Soc Rev 2022; 51:8216-8257. [PMID: 35983982 PMCID: PMC9528729 DOI: 10.1039/d2cs00387b] [Citation(s) in RCA: 46] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The von Hippel-Lindau (VHL) Cullin RING E3 ligase is an essential enzyme in the ubiquitin-proteasome system that recruits substrates such as the hypoxia inducible factor for ubiquitination and subsequent proteasomal degradation. The ubiquitin-proteasome pathway can be hijacked toward non-native neo-substrate proteins using proteolysis targeting chimeras (PROTACs), bifunctional molecules designed to simultaneously bind to an E3 ligase and a target protein to induce target ubiquitination and degradation. The availability of high-quality small-molecule ligands with good binding affinity for E3 ligases is fundamental for PROTAC development. Lack of good E3 ligase ligands as starting points to develop PROTAC degraders was initially a stumbling block to the development of the field. Herein, the journey towards the design of small-molecule ligands binding to VHL is presented. We cover the structure-based design of VHL ligands, their application as inhibitors in their own right, and their implementation into rationally designed, potent PROTAC degraders of various target proteins. We highlight the key findings and learnings that have provided strong foundations for the remarkable development of targeted protein degradation, and that offer a blueprint for designing new ligands for E3 ligases beyond VHL.
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Affiliation(s)
- Claudia J Diehl
- Centre for Targeted Protein Degradation, School of Life Sciences, University of Dundee, Dundee, Scotland, UK.
| | - Alessio Ciulli
- Centre for Targeted Protein Degradation, School of Life Sciences, University of Dundee, Dundee, Scotland, UK.
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11
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Cristóbal C, Gaviña D, Alonso I, Ribagorda M, Carretero JC, Del Pozo C, Adrio J. Catalytic enantioselective intramolecular 1,3-dipolar cycloaddition of azomethine ylides with fluorinated dipolarophiles. Chem Commun (Camb) 2022; 58:7805-7808. [PMID: 35735739 DOI: 10.1039/d2cc02902b] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
An enantioselective synthesis of polycyclic fluorinated pyrrolidines has been achieved by Cu-catalyzed intramolecular 1,3-dipolar cycloaddition of azomethine ylides with fluorinated dipolarophiles. The method displays a wide scope and afforded the desired cycloadducts in high yields with up to 99% ee. These results demonstrate that fluoroalkyl substituents are excellent activating groups in this transformation.
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Affiliation(s)
- Christian Cristóbal
- Departamento de Química Orgánica, Facultad de Ciencias, C/Francisco Tomás y Valiente 7, Universidad Autónoma de Madrid, 28049 Madrid, Spain.
| | - Daniel Gaviña
- Departamento de Química Orgánica, Universidad de Valencia, E-46100 Burjassot, Spain.
| | - Inés Alonso
- Departamento de Química Orgánica, Facultad de Ciencias, C/Francisco Tomás y Valiente 7, Universidad Autónoma de Madrid, 28049 Madrid, Spain. .,Institute for Advanced Research in Chemical Sciences (IAdChem), Universidad Autónoma de Madrid, 28049 Madrid, Spain.,Centro de Innovación en Química Avanzada (ORFEO-CINQA), Spain
| | - María Ribagorda
- Departamento de Química Orgánica, Facultad de Ciencias, C/Francisco Tomás y Valiente 7, Universidad Autónoma de Madrid, 28049 Madrid, Spain. .,Institute for Advanced Research in Chemical Sciences (IAdChem), Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Juan C Carretero
- Departamento de Química Orgánica, Facultad de Ciencias, C/Francisco Tomás y Valiente 7, Universidad Autónoma de Madrid, 28049 Madrid, Spain. .,Institute for Advanced Research in Chemical Sciences (IAdChem), Universidad Autónoma de Madrid, 28049 Madrid, Spain.,Centro de Innovación en Química Avanzada (ORFEO-CINQA), Spain
| | - Carlos Del Pozo
- Departamento de Química Orgánica, Universidad de Valencia, E-46100 Burjassot, Spain.
| | - Javier Adrio
- Departamento de Química Orgánica, Facultad de Ciencias, C/Francisco Tomás y Valiente 7, Universidad Autónoma de Madrid, 28049 Madrid, Spain. .,Institute for Advanced Research in Chemical Sciences (IAdChem), Universidad Autónoma de Madrid, 28049 Madrid, Spain.,Centro de Innovación en Química Avanzada (ORFEO-CINQA), Spain
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12
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Landrieu I, Dupré E, Sinnaeve D, El Hajjar L, Smet-Nocca C. Deciphering the Structure and Formation of Amyloids in Neurodegenerative Diseases With Chemical Biology Tools. Front Chem 2022; 10:886382. [PMID: 35646824 PMCID: PMC9133342 DOI: 10.3389/fchem.2022.886382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 04/20/2022] [Indexed: 11/24/2022] Open
Abstract
Protein aggregation into highly ordered, regularly repeated cross-β sheet structures called amyloid fibrils is closely associated to human disorders such as neurodegenerative diseases including Alzheimer's and Parkinson's diseases, or systemic diseases like type II diabetes. Yet, in some cases, such as the HET-s prion, amyloids have biological functions. High-resolution structures of amyloids fibrils from cryo-electron microscopy have very recently highlighted their ultrastructural organization and polymorphisms. However, the molecular mechanisms and the role of co-factors (posttranslational modifications, non-proteinaceous components and other proteins) acting on the fibril formation are still poorly understood. Whether amyloid fibrils play a toxic or protective role in the pathogenesis of neurodegenerative diseases remains to be elucidated. Furthermore, such aberrant protein-protein interactions challenge the search of small-molecule drugs or immunotherapy approaches targeting amyloid formation. In this review, we describe how chemical biology tools contribute to new insights on the mode of action of amyloidogenic proteins and peptides, defining their structural signature and aggregation pathways by capturing their molecular details and conformational heterogeneity. Challenging the imagination of scientists, this constantly expanding field provides crucial tools to unravel mechanistic detail of amyloid formation such as semisynthetic proteins and small-molecule sensors of conformational changes and/or aggregation. Protein engineering methods and bioorthogonal chemistry for the introduction of protein chemical modifications are additional fruitful strategies to tackle the challenge of understanding amyloid formation.
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Affiliation(s)
- Isabelle Landrieu
- University Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167 - RID-AGE - Risk Factors and Molecular Determinants of Aging-Related Diseases, Lille, France
- CNRS EMR9002 Integrative Structural Biology, Lille, France
| | - Elian Dupré
- University Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167 - RID-AGE - Risk Factors and Molecular Determinants of Aging-Related Diseases, Lille, France
- CNRS EMR9002 Integrative Structural Biology, Lille, France
| | - Davy Sinnaeve
- University Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167 - RID-AGE - Risk Factors and Molecular Determinants of Aging-Related Diseases, Lille, France
- CNRS EMR9002 Integrative Structural Biology, Lille, France
| | - Léa El Hajjar
- University Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167 - RID-AGE - Risk Factors and Molecular Determinants of Aging-Related Diseases, Lille, France
- CNRS EMR9002 Integrative Structural Biology, Lille, France
| | - Caroline Smet-Nocca
- University Lille, Inserm, CHU Lille, Institut Pasteur de Lille, U1167 - RID-AGE - Risk Factors and Molecular Determinants of Aging-Related Diseases, Lille, France
- CNRS EMR9002 Integrative Structural Biology, Lille, France
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13
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Munyaradzi O, Rundell S, Bong D. Impact of bPNA Backbone Structural Constraints and Composition on Triplex Hybridization with DNA. Chembiochem 2022; 23:e202100707. [PMID: 35167719 PMCID: PMC9136932 DOI: 10.1002/cbic.202100707] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2021] [Revised: 01/18/2022] [Indexed: 11/07/2022]
Abstract
We report herein a study on the impact of bifacial peptide nucleic acid (bPNA) amino acid composition and backbone modification on DNA binding. A series of bPNA backbone variants with identical net charge were synthesized to display either 4 or 6 melamine (M) bases. These bases form thymine-melamine-thymine (TMT) base-triples, resulting in triplex hybrid stem structures with T-rich DNAs. Analyses of 6 M bPNA-DNA hybrids suggested that hybrid stability was linked to amino acid secondary structure propensities, prompting a more detailed study in shorter 4 M bPNAs. We synthesized 4 M bPNAs predisposed to adopt helical secondary structure via helix-turn nucleation in 7-residue bPNAs using double-click covalent stapling. Generally, hybrid stability improved upon stapling, but amino acid composition had a more significant effect. We also pursued an alternative strategy for bPNA structural preorganization by incorporation of residues with strong backbone amide conformational preferences such as 4R- and 4S-fluoroprolines. Notably, these derivatives exhibited an additional improvement in hybrid stability beyond both unsubstituted proline bPNA analogues and the helically patterned bPNAs. Overall, these findings demonstrate the tunability of bPNA-DNA hybrid stability through bPNA backbone structural propensities and amino acid composition.
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Affiliation(s)
- Oliver Munyaradzi
- Department of Chemistry & Biochemistry, The Ohio State University, 100 W. 18th Avenue, Columbus, Ohio, 43210, USA
| | - Sarah Rundell
- Department of Chemistry & Biochemistry, The Ohio State University, 100 W. 18th Avenue, Columbus, Ohio, 43210, USA
| | - Dennis Bong
- Department of Chemistry & Biochemistry, The Ohio State University, 100 W. 18th Avenue, Columbus, Ohio, 43210, USA
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14
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Boudreau MW, Mulligan MP, Shapiro DJ, Fan TM, Hergenrother PJ. Activators of the Anticipatory Unfolded Protein Response with Enhanced Selectivity for Estrogen Receptor Positive Breast Cancer. J Med Chem 2022; 65:3894-3912. [PMID: 35080871 PMCID: PMC9067622 DOI: 10.1021/acs.jmedchem.1c01730] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Approximately 75% of breast cancers are estrogen receptor alpha-positive (ERα+), and targeting ERα directly with ERα antagonists/degraders or indirectly with aromatase inhibitors is a successful therapeutic strategy. However, such treatments are rarely curative and development of resistance is universal. We recently reported ErSO, a compound that induces ERα-dependent cancer cell death through a mechanism distinct from clinically approved ERα drugs, via hyperactivation of the anticipatory unfolded protein response. ErSO has remarkable tumor-eradicative activity in multiple ERα+ tumor models. While ErSO has promise as a new drug, it has effects on ERα-negative (ERα-) cells in certain contexts. Herein, we construct modified versions of ErSO and identify variants with enhanced differential activity between ERα+ and ERα- cells. We report ErSO-DFP, a compound that maintains antitumor efficacy, has enhanced selectivity for ERα+ cancer cells, and is well tolerated in rodents. ErSO-DFP and related compounds represent an intriguing new class for the treatment of ERα+ cancers.
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Affiliation(s)
- Matthew W. Boudreau
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois, 61801, United States,Carl R. Woese Institute for Genomic, Biology University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Michael P. Mulligan
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States,Carl R. Woese Institute for Genomic Biology University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - David J. Shapiro
- Cancer Center at Illinois and Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Timothy M. Fan
- Carl R. Woese Institute for Genomic Biology University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States,Cancer Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States,Department of Veterinary Clinical Medicine, University of Illinois at Urbana-Champaign, Urbana, Illinois 61802, United States
| | - Paul J. Hergenrother
- Department of Chemistry and Cancer, Center at Illinois, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States,Carl R. Woese Institute for Genomic Biology University of Illinois at, Urbana-Champaign, Urbana, Illinois 61801, United States
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15
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16
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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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17
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Pons A, Decaens J, Najjar R, Otog N, Arribat M, Jolly S, Couve-Bonnaire S, Sebban M, Coadou G, Oulyadi H, Speybrouck D, Iwasa S, Charette AB, Poisson T, Jubault P. Fluorocyclopropane-Containing Proline Analogue: Synthesis and Conformation of an Item in the Peptide Chemist's Toolbox. ACS OMEGA 2022; 7:4868-4878. [PMID: 35187307 PMCID: PMC8851640 DOI: 10.1021/acsomega.1c05337] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Accepted: 12/10/2021] [Indexed: 05/27/2023]
Abstract
Over the years, numerous modifications to the structure of proline have been made in order to tune its effects on bioactive compounds. Notably, the introduction of a cyclopropane ring or a fluorine atom has produced interesting results. Herein, we describe the synthesis of a proline containing fluorocyclopropane. This modified amino acid was inserted into a tripeptide, whose conformation was studied by nuclear magnetic resonance and density functional theory calculations.
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Affiliation(s)
- Amandine Pons
- Normandie
Université, INSA Rouen, UNIROUEN, CNRS, COBRA (UMR 6014), 76000 Rouen, France
| | - Jonathan Decaens
- Normandie
Université, INSA Rouen, UNIROUEN, CNRS, COBRA (UMR 6014), 76000 Rouen, France
| | - Riham Najjar
- Normandie
Université, INSA Rouen, UNIROUEN, CNRS, COBRA (UMR 6014), 76000 Rouen, France
| | - Nansalmaa Otog
- Department
of Applied Chemistry and Life Science, Toyohashi
University of Technology, 1-1 Hibarigaoka, Tempaku, Toyohashi, Aichi 441-8580, Japan
| | - Mathieu Arribat
- Normandie
Université, INSA Rouen, UNIROUEN, CNRS, COBRA (UMR 6014), 76000 Rouen, France
| | - Sandrine Jolly
- Analytical
Sciences—Discovery Sciences, Janssen
Research & Development, a Division of Janssen-Cilag, Campus de Maigremont, CS10615, F-27106 Val de Reuil Cedex, France
| | - Samuel Couve-Bonnaire
- Normandie
Université, INSA Rouen, UNIROUEN, CNRS, COBRA (UMR 6014), 76000 Rouen, France
| | - Muriel Sebban
- Normandie
Université, INSA Rouen, UNIROUEN, CNRS, COBRA (UMR 6014), 76000 Rouen, France
| | - Gael Coadou
- Normandie
Université, INSA Rouen, UNIROUEN, CNRS, COBRA (UMR 6014), 76000 Rouen, France
| | - Hassan Oulyadi
- Normandie
Université, INSA Rouen, UNIROUEN, CNRS, COBRA (UMR 6014), 76000 Rouen, France
| | - David Speybrouck
- Analytical
Sciences—Discovery Sciences, Janssen
Research & Development, a Division of Janssen-Cilag, Campus de Maigremont, CS10615, F-27106 Val de Reuil Cedex, France
| | - Seiji Iwasa
- Department
of Applied Chemistry and Life Science, Toyohashi
University of Technology, 1-1 Hibarigaoka, Tempaku, Toyohashi, Aichi 441-8580, Japan
| | - André B. Charette
- Centre
in Green Chemistry and Catalysis, Faculty of Arts and Sciences, Department
of Chemistry, Université de Montréal, P.O. Box 6128, Station Downtown, Montréal, Québec H3C3J7, Canada
| | - Thomas Poisson
- Normandie
Université, INSA Rouen, UNIROUEN, CNRS, COBRA (UMR 6014), 76000 Rouen, France
- Institut
Universitaire de France, 1 rue Descartes, 75231 Paris, France
| | - Philippe Jubault
- Normandie
Université, INSA Rouen, UNIROUEN, CNRS, COBRA (UMR 6014), 76000 Rouen, France
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18
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Linclau B, Wang Z, Jeffries B, Graton J, Carbajo RJ, Sinnaeve D, Le Questel J, Scott JS, Chiarparin E. Relating Conformational Equilibria to Conformer‐Specific Lipophilicities: New Opportunities in Drug Discovery. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202114862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Bruno Linclau
- School of Chemistry University of Southampton Highfield, Southampton SO17 1BJ UK
- Department of Organic and Macromolecular Chemistry, Ghent University Campus Sterre, S4 Krijgslaan 281 9000 Ghent Belgium
| | - Zhong Wang
- School of Chemistry University of Southampton Highfield, Southampton SO17 1BJ UK
| | - Benjamin Jeffries
- School of Chemistry University of Southampton Highfield, Southampton SO17 1BJ UK
| | - Jérôme Graton
- CEISAM UMR CNRS 6230 Université de Nantes CNRS CEISAM UMR 6230 44000 Nantes France
| | | | - Davy Sinnaeve
- Univ. Lille Inserm Institut Pasteur de Lille CHU Lille U1167—RID-AGE—Risk Factors and Molecular Determinants of Aging-Related Diseases 59000 Lille France
- CNRS ERL9002—Integrative Structural Biology 59000 Lille France
| | - Jean‐Yves Le Questel
- CEISAM UMR CNRS 6230 Université de Nantes CNRS CEISAM UMR 6230 44000 Nantes France
| | - James S. Scott
- Medicinal Chemistry, Oncology R&D AstraZeneca Cambridge CB4 0WG UK
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19
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Linclau B, Wang Z, Jeffries B, Graton J, Carbajo RJ, Sinnaeve D, Le Questel JY, Scott JS, Chiarparin E. Relating Conformational Equilibria to Conformer-Specific Lipophilicities: New Opportunities in Drug Discovery. Angew Chem Int Ed Engl 2021; 61:e202114862. [PMID: 34913249 PMCID: PMC9304282 DOI: 10.1002/anie.202114862] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Indexed: 11/10/2022]
Abstract
Efficient drug discovery is based on a concerted effort in optimizing bioactivity and compound properties such as lipophilicity, and is guided by efficiency metrics that reflect both aspects. While conformation–activity relationships and ligand conformational control are known strategies to improve bioactivity, the use of conformer‐specific lipophilicities (logp) is much less explored. Here we show how conformer‐specific logp values can be obtained from knowledge of the macroscopic logP value, and of the equilibrium constants between the individual species in water and in octanol. This is illustrated with fluorinated amide rotamers, with integration of rotamer 19F NMR signals as a facile, direct method to obtain logp values. The difference between logp and logP optimization is highlighted, giving rise to a novel avenue for lipophilicity control in drug discovery.
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Affiliation(s)
- Bruno Linclau
- School of Chemistry, University of Southampton, Highfield, Southampton, SO17 1BJ, UK.,Department of Organic and Macromolecular Chemistry, Ghent University, Campus Sterre, S4, Krijgslaan 281, 9000, Ghent, Belgium
| | - Zhong Wang
- School of Chemistry, University of Southampton, Highfield, Southampton, SO17 1BJ, UK
| | - Benjamin Jeffries
- School of Chemistry, University of Southampton, Highfield, Southampton, SO17 1BJ, UK
| | - Jérôme Graton
- CEISAM UMR CNRS 6230, Université de Nantes, CNRS, CEISAM UMR 6230, 44000, Nantes, France
| | - Rodrigo J Carbajo
- Medicinal Chemistry, Oncology R&D, AstraZeneca, Cambridge, CB4 0WG, UK
| | - Davy Sinnaeve
- Univ. Lille, Inserm, Institut Pasteur de Lille, CHU Lille, U1167-RID-AGE-Risk Factors and Molecular, Determinants of Aging-Related Diseases, 59000, Lille, France.,CNRS, ERL9002-Integrative Structural Biology, 59000, Lille, France
| | - Jean-Yves Le Questel
- CEISAM UMR CNRS 6230, Université de Nantes, CNRS, CEISAM UMR 6230, 44000, Nantes, France
| | - James S Scott
- Medicinal Chemistry, Oncology R&D, AstraZeneca, Cambridge, CB4 0WG, UK
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20
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O' Loughlin J, Napolitano S, Rubini M. Protein Design with Fluoroprolines: 4,4-Difluoroproline Does Not Eliminate the Rate-Limiting Step of Thioredoxin Folding. Chembiochem 2021; 22:3326-3332. [PMID: 34545985 PMCID: PMC9292674 DOI: 10.1002/cbic.202100418] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Revised: 09/20/2021] [Indexed: 01/08/2023]
Abstract
C4‐substituted fluoroprolines (4R)‐fluoroproline ((4R)‐Flp) and (4S)‐fluoroproline ((4S)‐Flp) have been used in protein engineering to enhance the thermodynamic stability of peptides and proteins. The electron‐withdrawing effect of fluorine can bias the pucker of the pyrrolidine ring, influence the conformational preference of the preceding peptide bond, and can accelerate the cis/trans prolyl peptide bond isomerisation by diminishing its double bond character. The role of 4,4‐difluoroproline (Dfp) in the acceleration of the refolding rate of globular proteins bearing a proline (Pro) residue in the cis conformation in the native state remains elusive. Moreover, the impact of Dfp on the thermodynamic stability and bioactivity of globular proteins has been seldom described. In this study, we show that the incorporation of Dfp caused a redox state dependent and position dependent destabilisation of the thioredoxin (Trx) fold, while the catalytic activities of the modified proteins remained unchanged. The Pro to Dfp substitution at the conserved cisPro76 in the thioredoxin variant Trx1P did not elicited acceleration of the rate‐limiting trans‐to‐cis isomerization of the Ile75‐Pro76 peptide bond. Our results show that pucker preferences in the context of a tertiary structure could play a major role in protein folding, thus overtaking the rules determined for cis/trans isomerisation barriers determined in model peptides.
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Affiliation(s)
- Jennie O' Loughlin
- School of Chemistry, University College Dublin, Belfield, Dublin 4, Ireland
| | - Silvia Napolitano
- Department of Molecular Biology and Biophysics, ETH Zürich, Otto-Stern-Weg 5, 8093, Zürich, Switzerland
| | - Marina Rubini
- School of Chemistry, University College Dublin, Belfield, Dublin 4, Ireland
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21
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Sinnaeve D, Ben Bouzayene A, Ottoy E, Hofman GJ, Erdmann E, Linclau B, Kuprov I, Martins J, Torbeev V, Kieffer B. Fluorine NMR study of proline-rich sequences using fluoroprolines. MAGNETIC RESONANCE (GOTTINGEN, GERMANY) 2021; 2:795-813. [PMID: 37905223 PMCID: PMC10539733 DOI: 10.5194/mr-2-795-2021] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 09/28/2021] [Indexed: 11/01/2023]
Abstract
Proline homopolymer motifs are found in many proteins; their peculiar conformational and dynamic properties are often directly involved in those proteins' functions. However, the dynamics of proline homopolymers is hard to study by NMR due to a lack of amide protons and small chemical shift dispersion. Exploiting the spectroscopic properties of fluorinated prolines opens interesting perspectives to address these issues. Fluorinated prolines are already widely used in protein structure engineering - they introduce conformational and dynamical biases - but their use as 19 F NMR reporters of proline conformation has not yet been explored. In this work, we look at model peptides where Cγ -fluorinated prolines with opposite configurations of the chiral Cγ centre have been introduced at two positions in distinct polyproline segments. By looking at the effects of swapping these (4R )-fluoroproline and (4S )-fluoroproline within the polyproline segments, we were able to separate the intrinsic conformational properties of the polyproline sequence from the conformational alterations instilled by fluorination. We assess the fluoroproline 19 F relaxation properties, and we exploit the latter in elucidating binding kinetics to the SH3 (Src homology 3) domain.
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Affiliation(s)
- Davy Sinnaeve
- Univ. Lille, Inserm, Institut Pasteur de Lille, CHU Lille, U1167 – Risk Factors and Molecular Determinants of
Aging-Related Diseases (RID-AGE), 59000 Lille, France
- CNRS, ERL9002 – Integrative Structural Biology, 59000 Lille, France
| | - Abir Ben Bouzayene
- Department of Integrative Structural Biology, IGBMC, University of Strasbourg, Inserm U1258, CNRS UMR 7104, 1 rue Laurent Fries, 67404
Illkirch, France
| | - Emile Ottoy
- Department of Organic and Macromolecular Chemistry, Ghent University,
Campus Sterre, S4, Krijgslaan 281, 9000 Ghent, Belgium
| | - Gert-Jan Hofman
- Department of Organic and Macromolecular Chemistry, Ghent University,
Campus Sterre, S4, Krijgslaan 281, 9000 Ghent, Belgium
- School of Chemistry, University of Southampton, Southampton SO17 1BJ,
United Kingdom
| | - Eva Erdmann
- Department of Integrative Structural Biology, IGBMC, University of Strasbourg, Inserm U1258, CNRS UMR 7104, 1 rue Laurent Fries, 67404
Illkirch, France
| | - Bruno Linclau
- School of Chemistry, University of Southampton, Southampton SO17 1BJ,
United Kingdom
| | - Ilya Kuprov
- School of Chemistry, University of Southampton, Southampton SO17 1BJ,
United Kingdom
| | - José C. Martins
- Department of Organic and Macromolecular Chemistry, Ghent University,
Campus Sterre, S4, Krijgslaan 281, 9000 Ghent, Belgium
| | - Vladimir Torbeev
- Institut de Science et d'Ingénierie Supramoléculaires (ISIS),
International Center for Frontier Research in Chemistry (icFRC), University of Strasbourg,
CNRS UMR 7006, 67000 Strasbourg, France
| | - Bruno Kieffer
- Department of Integrative Structural Biology, IGBMC, University of Strasbourg, Inserm U1258, CNRS UMR 7104, 1 rue Laurent Fries, 67404
Illkirch, France
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22
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Jyoti Kalita S, Zhao Z, Li Z, Cheng F, Zhao Y, Huang Y. Diastereodivergent 1,3‐Dipolar Cycloaddition of α‐Fluoro‐α,β‐Unsaturated Arylketones and Azomethine Ylides: Experimental and Theoretical DFT Studies. European J Org Chem 2021. [DOI: 10.1002/ejoc.202100759] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Subarna Jyoti Kalita
- Department of Chemistry School of Chemistry Chemical Engineering and Life Science Wuhan University of Technology 122 Luoshi Road 430070 Wuhan China
| | - Zhen‐Ni Zhao
- Department of Chemistry School of Chemistry Chemical Engineering and Life Science Wuhan University of Technology 122 Luoshi Road 430070 Wuhan China
| | - Zi‐Han Li
- Department of Chemistry School of Chemistry Chemical Engineering and Life Science Wuhan University of Technology 122 Luoshi Road 430070 Wuhan China
| | - Feng Cheng
- Department of Chemistry School of Chemistry Chemical Engineering and Life Science Wuhan University of Technology 122 Luoshi Road 430070 Wuhan China
| | - Yan Zhao
- State Key Laboratory of Silicate Materials for Architectures Wuhan University of Technology 122 Luoshi Road 430070 Wuhan China
| | - Yi‐Yong Huang
- Department of Chemistry School of Chemistry Chemical Engineering and Life Science Wuhan University of Technology 122 Luoshi Road 430070 Wuhan China
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23
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Sanchez CA, Gadais C, Diarra S, Bordessa A, Lensen N, Chelain E, Brigaud T. Synthesis of enantiopure α-Tfm-proline and α-Tfm-pipecolic acid from oxazolo-pyrrolidines and -piperidines. Org Biomol Chem 2021; 19:6771-6775. [PMID: 34292288 DOI: 10.1039/d1ob01173a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Enantiopure α-Tfm-proline and α-Tfm-pipecolic acid were synthesized starting from commercially available diesters and ethyl trifluoroacetate. A Strecker type reaction on intermediate chiral Tfm-oxazolo-pyrrolidine and -piperidine provided the corresponding nitrile precursor of enantiopure (R) and (S) α-Tfm-proline and α-Tfm-pipecolic acid. The C-terminal peptide coupling reaction of α-Tfm-pipecolic acid has been successfully achieved.
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Affiliation(s)
- Clément A Sanchez
- CY Cergy Paris Université, CNRS, BioCIS, 95000, Cergy Pontoise, France.
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24
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Jana B, Barman S, Roy R, Das G, Mukherjee N, Adak A, Ghosh S. Fluorine Substituted Proline Enhances the Tubulin Binding Potential of a Tetrapeptide at the GTP Binding Pocket Causing the Inhibition of Microtubule Motility and an Antimitotic Effect. J Phys Chem B 2021; 125:8768-8780. [PMID: 34328335 DOI: 10.1021/acs.jpcb.1c04323] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The microtubule is regarded as the key target for designing anticancer and neurotherapeutic drugs due to its functional importance in eukaryotic cells including neurons. The microtubule is a dynamic hollow polymer tube consisting of α,β-tubulin heterodimer. Polymerization of α,β-tubulin heterodimer resulted in microtubule formation. GTP plays a crucial role in microtubule polymerization. It binds at the exchangeable binding site of the β-tubulin heterodimer, and it is one of the most crucial therapeutic hot spots for designing anticancer therapeutics. In this manuscript, we have shown using an in silico strategy and various in vitro and cellular experiments that the binding affinity to the tubulin and cancer therapeutic potential of an exchangeable GTP/GDP binding antimitotic tetrapeptide (SP: Ser-Leu-Arg-Pro) is increased through changing proline with the multifluorine substituted proline. This study showcases the importance of the proline amino acid and its pyrrolidine ring in the regulation of binding with tubulin at the GTP binding pocket.
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Affiliation(s)
- Batakrishna Jana
- Organic and Medicinal Chemistry and Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Jadavpur, Kolkata, West Bengal 700 032, India
| | - Surajit Barman
- Organic and Medicinal Chemistry and Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Jadavpur, Kolkata, West Bengal 700 032, India
| | - Rajsekhar Roy
- Department of Bioscience & Bioengineering, Indian Institute of Technology Jodhpur, NH 62, Surpura Bypass Road, Karwar, Rajasthan 342037, India
| | - Gaurav Das
- Organic and Medicinal Chemistry and Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Jadavpur, Kolkata, West Bengal 700 032, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India
| | - Nabanita Mukherjee
- Department of Bioscience & Bioengineering, Indian Institute of Technology Jodhpur, NH 62, Surpura Bypass Road, Karwar, Rajasthan 342037, India
| | - Anindyasundar Adak
- Organic and Medicinal Chemistry and Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Jadavpur, Kolkata, West Bengal 700 032, India
| | - Surajit Ghosh
- Organic and Medicinal Chemistry and Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Jadavpur, Kolkata, West Bengal 700 032, India.,Department of Bioscience & Bioengineering, Indian Institute of Technology Jodhpur, NH 62, Surpura Bypass Road, Karwar, Rajasthan 342037, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India
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25
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Kalita SJ, Cheng F, Fan QH, Shibata N, Huang YY. Diastereodivergent Synthesis of Chiral 4-Fluoropyrrolidines ( exo and exo') Based on the Cu(II)-Catalyzed Asymmetric 1,3-Dipolar Cycloaddition. J Org Chem 2021; 86:8695-8705. [PMID: 34124915 DOI: 10.1021/acs.joc.1c00509] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
1,3-Dipolar cycloaddition of azomethine ylides and electron deficient alkenes is widely studied for rapid installation of pyrrolidine frameworks. Despite significant advances, the major limitations of this process are creating chiral pyrrolidines bearing a quaternary stereogenic center and controlling the diastereoselectivity. Herein, we present an exo-selective asymmetric 1,3-dipolar cycloaddition to access chiral pyrrolidines with four contiguous stereogenic centers, including a fluorinated quaternary stereogenic center at C4, wherein a Cu(OAc)2/(S)-tol-BINAP catalyst and α-fluoro-α,β-unsaturated arylketone dipolarophiles are used. Epimerization promoted by 5.0 equiv of DBU at 90 °C results in the formation of chiral 4-fluoropyrrolidines (exo') while maintaining the optical purity.
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Affiliation(s)
- Subarna Jyoti Kalita
- Department of Chemistry, School of Chemistry, Chemical Engineering and Life Science, Wuhan University of Technology, 122 Luoshi Road, Wuhan 430070, China
| | - Feng Cheng
- Department of Chemistry, School of Chemistry, Chemical Engineering and Life Science, Wuhan University of Technology, 122 Luoshi Road, Wuhan 430070, China
| | - Qing-Hua Fan
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Molecular Recognition and Function, Institute of Chemistry, Chinese Academy of Sciences (CAS), Beijing 100190, China
| | - Norio Shibata
- Department of Nanopharmaceutical Sciences and Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Gokiso, Showa-ku, Nagoya 466-8555, Japan
| | - Yi-Yong Huang
- Department of Chemistry, School of Chemistry, Chemical Engineering and Life Science, Wuhan University of Technology, 122 Luoshi Road, Wuhan 430070, China
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26
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Breunig SL, Tirrell DA. Incorporation of proline analogs into recombinant proteins expressed in Escherichia coli. Methods Enzymol 2021; 656:545-571. [PMID: 34325798 DOI: 10.1016/bs.mie.2021.05.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Proline residues are unique in the extent to which they constrain the conformational space available to the protein backbone. Because the conformational preferences of proline cannot be recapitulated by any of the other proteinogenic amino acids, standard mutagenesis approaches that seek to introduce new chemical functionality at proline positions unavoidably perturb backbone flexibility. Here, we detail the incorporation of proline analogs into recombinant proteins in Escherichia coli via a residue-specific mutagenesis strategy. This approach results in global replacement of proline residues with high yields of the recombinant protein of interest, minimal genetic manipulation, and maintenance of backbone conformational constraints.
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Affiliation(s)
- Stephanie L Breunig
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, United States
| | - David A Tirrell
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, United States.
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27
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Mondal R, Agbaria M, Nairoukh Z. Fluorinated Rings: Conformation and Application. Chemistry 2021; 27:7193-7213. [PMID: 33512034 DOI: 10.1002/chem.202005425] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Indexed: 12/16/2022]
Abstract
The introduction of fluorine atoms into molecules and materials across many fields of academic and industrial research is now commonplace, owing to their unique properties. A particularly interesting feature is the impact of fluorine substitution on the relative orientation of a C-F bond when incorporated into organic molecules. In this Review, we will be discussing the conformational behavior of fluorinated aliphatic carbo- and heterocyclic systems. The conformational preference of each system is associated with various interactions introduced by fluorine substitution such as charge-dipole, dipole-dipole, and hyperconjugative interactions. The contribution of each interaction on the stabilization of the fluorinated alicyclic system, which manifests itself in low conformations, will be discussed in detail. The novelty of this feature will be demonstrated by presenting the most recent applications.
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Affiliation(s)
- Rajarshi Mondal
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Jerusalem, 9190401, Israel
| | - Mohamed Agbaria
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Jerusalem, 9190401, Israel
| | - Zackaria Nairoukh
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Jerusalem, 9190401, Israel
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28
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Motornov VA, Tabolin AA, Nelyubina YV, Nenajdenko VG, Ioffe SL. Copper-catalyzed [3 + 2]-cycloaddition of α-halonitroalkenes with azomethine ylides: facile synthesis of multisubstituted pyrrolidines and pyrroles. Org Biomol Chem 2021; 19:3413-3427. [PMID: 33899878 DOI: 10.1039/d1ob00146a] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
An efficient route for the synthesis of multifunctionalized pyrrolidines based on copper-catalyzed diastereoselective [3 + 2]-cycloaddition of nitroalkenes with azomethine ylides was developed. Novel fluorinated heterocycles - β-fluoro-β-nitropyrrolidines - were accessed via this method. The products can be prepared in good to excellent yields and with high diastereoselectivity. Subsequent transformations of pyrrolidines including oxidative aromatization into fluorinated pyrrolines and medicinally attractive β-fluoro-NH-pyrroles as well as chemoselective reduction reactions were demonstrated. Application of the developed procedures for the non-fluorinated analogues was demonstrated to lead to various β-substituted pyrrole derivatives.
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Affiliation(s)
- Vladimir A Motornov
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky prosp. 47, Moscow, 119991, Russia.
| | - Andrey A Tabolin
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky prosp. 47, Moscow, 119991, Russia.
| | - Yulia V Nelyubina
- A. N. Nesmeyanov Institute of Organoelement Compounds, Russian Academy of Sciences, Vavilov str. 28, Moscow, 119991, Russia
| | - Valentine G Nenajdenko
- Department of Chemistry, M. V. Lomonosov Moscow State University, Leninskie Gory 1, Moscow 119991, Russia
| | - Sema L Ioffe
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky prosp. 47, Moscow, 119991, Russia.
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29
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Kubyshkin V, Davis R, Budisa N. Biochemistry of fluoroprolines: the prospect of making fluorine a bioelement. Beilstein J Org Chem 2021; 17:439-460. [PMID: 33727970 PMCID: PMC7934785 DOI: 10.3762/bjoc.17.40] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 01/22/2021] [Indexed: 12/12/2022] Open
Abstract
Due to the heterocyclic structure and distinct conformational profile, proline is unique in the repertoire of the 20 amino acids coded into proteins. Here, we summarize the biochemical work on the replacement of proline with (4R)- and (4S)-fluoroproline as well as 4,4-difluoroproline in proteins done mainly in the last two decades. We first recapitulate the complex position and biochemical fate of proline in the biochemistry of a cell, discuss the physicochemical properties of fluoroprolines, and overview the attempts to use these amino acids as proline replacements in studies of protein production and folding. Fluorinated proline replacements are able to elevate the protein expression speed and yields and improve the thermodynamic and kinetic folding profiles of individual proteins. In this context, fluoroprolines can be viewed as useful tools in the biotechnological toolbox. As a prospect, we envision that proteome-wide proline-to-fluoroproline substitutions could be possible. We suggest a hypothetical scenario for the use of laboratory evolutionary methods with fluoroprolines as a suitable vehicle to introduce fluorine into living cells. This approach may enable creation of synthetic cells endowed with artificial biodiversity, containing fluorine as a bioelement.
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Affiliation(s)
- Vladimir Kubyshkin
- Department of Chemistry, University of Manitoba, 144 Dysart Rd., Winnipeg, R3T 2N2, Canada
| | - Rebecca Davis
- Department of Chemistry, University of Manitoba, 144 Dysart Rd., Winnipeg, R3T 2N2, Canada
| | - Nediljko Budisa
- Department of Chemistry, University of Manitoba, 144 Dysart Rd., Winnipeg, R3T 2N2, Canada
- Institute of Chemistry, Technical University of Berlin, Müller-Breslau-Str. 10, 10623 Berlin, Germany
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30
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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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31
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Lv J, Cheng Y. Fluoropolymers in biomedical applications: state-of-the-art and future perspectives. Chem Soc Rev 2021; 50:5435-5467. [DOI: 10.1039/d0cs00258e] [Citation(s) in RCA: 67] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Biomedical applications of fluoropolymers in gene delivery, protein delivery, drug delivery, 19F MRI, PDT, anti-fouling, anti-bacterial, cell culture, and tissue engineering.
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Affiliation(s)
- Jia Lv
- Shanghai Key Laboratory of Regulatory Biology
- School of Life Sciences
- East China Normal University
- Shanghai
- China
| | - Yiyun Cheng
- Shanghai Key Laboratory of Regulatory Biology
- School of Life Sciences
- East China Normal University
- Shanghai
- China
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32
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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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33
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Orlandi S, Cavazzini M, Capuani S, Ciardello A, Pozzi G. Synthesis and 19F NMR parameters of a perfluoro-tert-butoxy tagged L-DOPA analogue. J Fluor Chem 2020. [DOI: 10.1016/j.jfluchem.2020.109596] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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34
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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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35
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Muralidharan A, Schmidt JR, Yethiraj A. Solvation Induced Ring Puckering Effect in Fluorinated Prolines and Its Inclusion in Classical Force Fields. J Phys Chem B 2020; 124:5899-5906. [PMID: 32551633 DOI: 10.1021/acs.jpcb.0c04312] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Strategic incorporation of fluorinated prolines can accelerate folding and increase thermal stability of proteins. It has been suggested that this behavior emerges from puckering effects induced by fluorination of the proline ring. We use electronic structure calculations to characterize the potential energy surface (PES) along puckering coordinates for a simple dipeptide model of proline and its fluorinated derivatives. Significant shifts in puckering trends between gas phase and implicit solvent calculations shed light on the effect of solvation on electronic structure and conformational preferences of the ring. This solvation induced puckering effect is previously unknown in the context of prolines. The PES based on implicit solvent is then utilized to construct a correction for a classical force field. The corrected force field accurately captures the experimental conformational equilibrium including the coupling between ring puckering and cis-trans isomerism in fluorinated prolines. This method can be extended to other rings and substituents besides fluorine.
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Affiliation(s)
- Ajay Muralidharan
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconson 53706, United States
| | - J R Schmidt
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconson 53706, United States
| | - Arun Yethiraj
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconson 53706, United States
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36
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Benhamou RI, Abe M, Choudhary S, Meyer SM, Angelbello AJ, Disney MD. Optimization of the Linker Domain in a Dimeric Compound that Degrades an r(CUG) Repeat Expansion in Cells. J Med Chem 2020; 63:7827-7839. [PMID: 32657583 DOI: 10.1021/acs.jmedchem.0c00558] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
RNA repeat expansions are responsible for more than 30 incurable diseases. Among them is myotonic dystrophy type 1 (DM1), the most common form of adult on-set muscular dystrophy. DM1 is caused by an r(CUG) repeat expansion [r(CUG)exp] located in the 3' untranslated region (UTR) of the dystrophia myotonica protein kinase gene. This repeat expansion is highly structured, forming a periodic array of 5'CUG/3'GUC internal loop motifs. We therefore designed dimeric compounds that simultaneously bind two of these motifs by connecting two RNA-binding modules with peptoid linkers of different geometries and lengths. The optimal linker contains two proline residues and enhances compound affinity. Equipping this molecule with a bleomycin A5 cleaving module converts the simple binding compound into a potent allele-selective cleaver of r(CUG)exp. This study shows that the linker in modularly assembled ligands targeting RNA can be optimized to afford potent biological activity.
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Affiliation(s)
- Raphael I Benhamou
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Masahito Abe
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Shruti Choudhary
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Samantha M Meyer
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Alicia J Angelbello
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Matthew D Disney
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, Florida 33458, United States
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37
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Tressler CM, Zondlo NJ. Perfluoro- tert-Butyl Hydroxyprolines as Sensitive, Conformationally Responsive Molecular Probes: Detection of Protein Kinase Activity by 19F NMR. ACS Chem Biol 2020; 15:1096-1103. [PMID: 32125821 DOI: 10.1021/acschembio.0c00131] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
19F NMR spectroscopy provides the ability to quantitatively analyze single species in complex solutions but is often limited by the modest sensitivity inherent to NMR. 4R- and 4S-Perfluoro-tert-buyl hydroxyproline contain 9 equivalent fluorines, in amino acids with strong conformational preferences. In order to test the ability to use these amino acids as sensitive probes of protein modifications, the perfluoro-tert-buyl hydroxyprolines were incorporated into substrate peptides of the protein kinases PKA and Akt. Peptides containing each diastereomeric proline were rapidly phosphorylated by each protein kinase and exhibited 19F chemical shift changes as a result of phosphorylation. The sensitivity of the perfluoro-tert-butyl group allowed quantitative analysis of the kinetics of phosphorylation over three half-lives at single-digit micromolar concentrations of each species. The distinct conformational preferences of these amino acids allowed the optimization of the substrate with a conformationally matched amino acid, in order to maximize the rate of phosphorylation. PKA preferred the 4R-amino acid at the -1 position, whereas the closely related AGC kinase Akt preferred the 4S-amino acid. These data, combined with analysis of structures of the Michaelis complexes of these kinases in the PDB, suggest that PKA recognizes the PPII conformation at the P-1 position relative to the phosphorylation site, while Akt/PKB recognizes an extended conformation at this position. These results suggest that conformational targeting may be employed to increase specificity in recognition by protein kinases. Perfluoro-tert-butyl hydroxyprolines were applied to the real-time detection and quantification of PKA activity and inhibition of PKA activity in HeLa cell extracts via 19F NMR spectroscopy. The coupling of proline ring pucker with main chain conformation suggests broad application of perfluoro-tert-butyl hydroxyprolines in molecular sensing and imaging.
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Affiliation(s)
- Caitlin M. Tressler
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Neal J. Zondlo
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
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38
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Ganguly HK, Basu G. Conformational landscape of substituted prolines. Biophys Rev 2020; 12:25-39. [PMID: 31953795 PMCID: PMC7040156 DOI: 10.1007/s12551-020-00621-8] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 01/09/2020] [Indexed: 12/16/2022] Open
Abstract
The cyclic side chain of the amino acid proline confers unique conformational restraints on its backbone and side chain dihedral angles. This affects two equilibria-one at the backbone (cis/trans) and the other at the side chain (endo/exo). Substitutions on the proline ring impose additional steric and stereoelectronic effects that can further modulate both these equilibria, which in turn can also affect the backbone dihedral angle (ϕ, ψ) preferences. In this review, we have explored the conformational landscape of several termini capped mono-(2-, 3-, 4-, and 5-) substituted proline derivatives in the Cambridge Structural Database, correlating observed conformations with the nature of substituents and deciphering the underlying interactions for the observed structural biases. The impact of incorporating these derivatives within model peptides and proteins are also discussed for selected cases. Several of these substituents have been used to introduce bioorthogonal functionality and modulate structure-specific ligand recognition or used as spectroscopic probes. The incorporation of these diversely applicable functional groups, coupled with their ability to define an amino acid conformation via stereoelectronic effects, have a broad appeal among chemical biologists, molecular biophysicists, and medicinal chemists.
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Affiliation(s)
- Himal Kanti Ganguly
- Department of Biophysics, Bose Institute, P-1/12 CIT scheme VII M, Kolkata, 700054, India.
| | - Gautam Basu
- Department of Biophysics, Bose Institute, P-1/12 CIT scheme VII M, Kolkata, 700054, India.
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39
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Maguire OR, Taylor B, Higgins EM, Rees M, Cobb SL, Simpkins NS, Hayes CJ, O'Donoghue AC. Unusually high α-proton acidity of prolyl residues in cyclic peptides. Chem Sci 2020; 11:7722-7729. [PMID: 34094148 PMCID: PMC8159430 DOI: 10.1039/d0sc02508a] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The acidity of the α-proton in peptides has an essential role in numerous biochemical reactions and underpins their stereochemical integrity, which is critical to their biological function. We report a detailed kinetic and computational study of the acidity of the α-proton in two cyclic peptide systems: diketopiperazine (DKP) and triketopiperazine (TKP). The kinetic acidity (protofugality) of the α-protons were determined though hydrogen deuterium exchange studies in aqueous solutions. The acidities of the α-proton in prolyl residues were increased by 3–89 fold relative to other amino acid residues (prolyl > glycyl ≫ alanyl > tyrosyl). Experimental and computational evidence for the stereoelectronic origins of this enhanced prolyl reactivity is presented. TKPs were 106-fold more reactive than their DKP analogues towards deprotonation, which we attribute to the advanced development of aromaticity in the earlier transition state for proton transfer in these cases. A Brønsted linear free energy analysis of the reaction data was conducted to provide estimates of α-proton pKas. Kinetic and computational studies reveal that prolyl residues in cyclic peptides are substantially more acidic than other residues due to a stereoelectronic effect.![]()
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Affiliation(s)
| | - Bethany Taylor
- Department of Chemistry
- Durham University
- Durham DH1 3LE
- UK
| | | | - Matthew Rees
- School of Chemistry
- University of Birmingham
- Birmingham
- UK
| | - Steven L. Cobb
- Department of Chemistry
- Durham University
- Durham DH1 3LE
- UK
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40
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Capaccio V, Sicignano M, Rodríguez RI, Della Sala G, Alemán J. Asymmetric Synthesis of α-Trifluoromethylthio-β-Amino Acids under Phase Transfer Catalysis. Org Lett 2019; 22:219-223. [DOI: 10.1021/acs.orglett.9b04195] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Vito Capaccio
- Organic Chemistry Department, Módulo 1, Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Marina Sicignano
- Dipartimento di Chimica e Biologia “A. Zambelli”, Università degli Studi di Salerno, Via Giovanni Paolo II 132, 84084 Fisciano, SA, Italy
| | - Ricardo I. Rodríguez
- Organic Chemistry Department, Módulo 1, Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Giorgio Della Sala
- Dipartimento di Chimica e Biologia “A. Zambelli”, Università degli Studi di Salerno, Via Giovanni Paolo II 132, 84084 Fisciano, SA, Italy
| | - José Alemán
- Organic Chemistry Department, Módulo 1, Universidad Autónoma de Madrid, 28049 Madrid, Spain
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41
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Mei H, Han J, Klika KD, Izawa K, Sato T, Meanwell NA, Soloshonok VA. Applications of fluorine-containing amino acids for drug design. Eur J Med Chem 2019; 186:111826. [PMID: 31740056 DOI: 10.1016/j.ejmech.2019.111826] [Citation(s) in RCA: 124] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 10/21/2019] [Accepted: 10/26/2019] [Indexed: 01/26/2023]
Abstract
Fluorine-containing amino acids are becoming increasingly prominent in new drugs due to two general trends in the modern pharmaceutical industry. Firstly, the growing acceptance of peptides and modified peptides as drugs; and secondly, fluorine editing has become a prevalent protocol in drug-candidate optimization. Accordingly, fluorine-containing amino acids represent one of the more promising and rapidly developing areas of research in organic, bio-organic and medicinal chemistry. The goal of this Review article is to highlight the current state-of-the-art in this area by profiling 42 selected compounds that combine fluorine and amino acid structural elements. The compounds under discussion represent pharmaceutical drugs currently on the market, or in clinical trials as well as examples of drug-candidates that although withdrawn from development had a significant impact on the progress of medicinal chemistry and/or provided a deeper understanding of the nature and mechanism of biological action. For each compound, we present features of biological activity, a brief history of the design principles and the development of the synthetic approach, focusing on the source of tailor-made amino acid structures and fluorination methods. General aspects of the medicinal chemistry of fluorine-containing amino acids and synthetic methodology are briefly discussed.
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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
| | - Karel D Klika
- Molecular Structure Analysis, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, D-69120 Heidelberg, Germany
| | - Kunisuke Izawa
- Hamari Chemicals Ltd., 1-4-29 Kunijima, Higashi-Yodogawa-ku, Osaka, 533-0024, Japan.
| | - Tatsunori Sato
- Hamari Chemicals Ltd., 1-4-29 Kunijima, Higashi-Yodogawa-ku, Osaka, 533-0024, Japan
| | - Nicholas A Meanwell
- Department of Discovery Chemistry, Bristol-Myers Squibb Research and Development, PO Box 4000, Princeton, NJ, 08543-4000, United States.
| | - Vadim A Soloshonok
- Department of Organic Chemistry I, University of the Basque Country UPV/EHU, Paseo Manuel Lardizábal 3, 20018, San Sebastián, Spain; IKERBASQUE, Basque Foundation for Science, María Díaz de Haro 3, Plaza Bizkaia, 48013, Bilbao, Spain.
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42
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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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43
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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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44
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Barrett SD, Holt MC, Kramer JB, Germain B, Ho CS, Ciske FL, Kornilov A, Colombo JM, Uzieblo A, O’Malley JP, Owen TA, Stein AJ, Morano MI. Difluoromethylene at the γ-Lactam α-Position Improves 11-Deoxy-8-aza-PGE1 Series EP4 Receptor Binding and Activity: 11-Deoxy-10,10-difluoro-8-aza-PGE1 Analog (KMN-159) as a Potent EP4 Agonist. J Med Chem 2019; 62:4731-4741. [PMID: 30964292 DOI: 10.1021/acs.jmedchem.9b00336] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
A series of small-molecule full agonists of the prostaglandin E2 type 4 (EP4) receptor have been generated and evaluated for binding affinity and cellular potency. KMN-80 and its gem-difluoro analog KMN-159 possess high selectivity relative to other prostanoid receptors. Difluoro substitution is positioned alpha to the lactam ring carbonyl and results in KMN-159's fivefold increase in potency versus KMN-80. The two analogs exhibit electronic and conformational variations, including altered nitrogen hybridization and lactam ring puckering, that may drive the observed difluoro-associated increased potency within this four-compound series.
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Affiliation(s)
- Stephen D. Barrett
- Cayman Chemical Company, Inc., 1180 East Ellsworth Road, Ann Arbor, Michigan 48108, United States
| | - Melissa C. Holt
- Cayman Chemical Company, Inc., 1180 East Ellsworth Road, Ann Arbor, Michigan 48108, United States
| | - James B. Kramer
- Cayman Chemical Company, Inc., 1180 East Ellsworth Road, Ann Arbor, Michigan 48108, United States
| | - Bradlee Germain
- Cayman Chemical Company, Inc., 1180 East Ellsworth Road, Ann Arbor, Michigan 48108, United States
| | - Chi S. Ho
- Cayman Chemical Company, Inc., 1180 East Ellsworth Road, Ann Arbor, Michigan 48108, United States
| | - Fred L. Ciske
- Cayman Chemical Company, Inc., 1180 East Ellsworth Road, Ann Arbor, Michigan 48108, United States
| | - Andrei Kornilov
- Cayman Chemical Company, Inc., 1180 East Ellsworth Road, Ann Arbor, Michigan 48108, United States
| | - Joseph M. Colombo
- Cayman Chemical Company, Inc., 1180 East Ellsworth Road, Ann Arbor, Michigan 48108, United States
| | - Adam Uzieblo
- Cayman Chemical Company, Inc., 1180 East Ellsworth Road, Ann Arbor, Michigan 48108, United States
| | - James P. O’Malley
- Myometrics, LLC, 216 Howard Street, New London, Connecticut 06320, United States
| | - Thomas A. Owen
- Myometrics, LLC, 216 Howard Street, New London, Connecticut 06320, United States
- Ramapo College of New Jersey, 505 Ramapo Valley Road, Mahwah, New Jersey 07430, United States
| | - Adam J. Stein
- Cayman Chemical Company, Inc., 1180 East Ellsworth Road, Ann Arbor, Michigan 48108, United States
| | - Maria I. Morano
- Cayman Chemical Company, Inc., 1180 East Ellsworth Road, Ann Arbor, Michigan 48108, United States
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45
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Hofman GJ, Ottoy E, Light ME, Kieffer B, Martins JC, Kuprov I, Sinnaeve D, Linclau B. Synthesis and Conformational Properties of 3,4-Difluoro-l-prolines. J Org Chem 2019; 84:3100-3120. [PMID: 30777755 DOI: 10.1021/acs.joc.8b02920] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Fluorinated proline derivatives have found diverse applications in areas ranging from medicinal chemistry over structural biochemistry to organocatalysis. Depending on the stereochemistry of monofluorination at the proline 3- or 4-position, different effects on the conformational properties of proline (ring pucker, cis/ trans isomerization) are introduced. With fluorination at both 3- and 4-positions, matching or mismatching effects can occur depending on the relative stereochemistry. Here we report, in full, the syntheses and conformational properties of three out of the four possible 3,4-difluoro-l-proline diastereoisomers. The yet unreported conformational properties are described for (3 S,4 S)- and (3 R,4 R)-difluoro-l-proline, which are shown to bias ring pucker and cis/ trans ratios on the same order of magnitude as their respective monofluorinated progenitors, although with significantly faster amide cis/ trans isomerization rates. The reported analogues thus expand the scope of available fluorinated proline analogues as tools to tailor proline's distinct conformational and dynamical properties, allowing for the interrogation of its role in, for instance, protein stability or folding.
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Affiliation(s)
- Gert-Jan Hofman
- School of Chemistry , University of Southampton , Highfield, Southampton SO17 1BJ , United Kingdom.,Department of Organic and Macromolecular Chemistry , Ghent University , Campus Sterre, S4, Krijgslaan 281 , Ghent B-9000 , Belgium
| | - Emile Ottoy
- Department of Organic and Macromolecular Chemistry , Ghent University , Campus Sterre, S4, Krijgslaan 281 , Ghent B-9000 , Belgium
| | - Mark E Light
- School of Chemistry , University of Southampton , Highfield, Southampton SO17 1BJ , United Kingdom
| | - Bruno Kieffer
- Biomolecular NMR , University of Strasbourg , IGBMC, CNRS UMR 7104, INSERM U1258, 1 rue Laurent Fries/BP 10142 , Illkirch Cedex 67404 , France
| | - Jose C Martins
- Department of Organic and Macromolecular Chemistry , Ghent University , Campus Sterre, S4, Krijgslaan 281 , Ghent B-9000 , Belgium
| | - Ilya Kuprov
- School of Chemistry , University of Southampton , Highfield, Southampton SO17 1BJ , United Kingdom
| | - Davy Sinnaeve
- Department of Organic and Macromolecular Chemistry , Ghent University , Campus Sterre, S4, Krijgslaan 281 , Ghent B-9000 , Belgium
| | - Bruno Linclau
- School of Chemistry , University of Southampton , Highfield, Southampton SO17 1BJ , United Kingdom
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46
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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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