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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Horx P, Geyer A. High five! Methyl probes at five ring positions of phenylalanine explore the hydrophobic core dynamics of zinc finger miniproteins. Chem Sci 2021; 12:11455-11463. [PMID: 34667551 PMCID: PMC8447250 DOI: 10.1039/d1sc02346b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 07/22/2021] [Indexed: 12/02/2022] Open
Abstract
The elucidation of internal dynamics in proteins is essential for the understanding of their stability and functionality. Breaking the symmetry of the degenerate rotation of the phenyl side chain provides additional structural information and allows a detailed description of the dynamics. Based on this concept, we propose a combination of synthetic and computational methods, to study the rotational mobility of the Phe ring in a sensitive zinc finger motif. The systematic methyl hopping around the phenylalanine ring yields o-, m-, p-tolyl and xylyl side chains that provide a vast array of additional NOE contacts, allowing the precise determination of the orientation of the aromatic ring. MD simulations and metadynamics complement these findings and facilitate the generation of free energy profiles for each derivative. Previous studies used a wide temperature window in combination with NMR spectroscopy to elucidate the side chain mobility of stable proteins. The zinc finger moiety exhibits a limited thermodynamic stability in a temperature range of only 40 K, making this approach impractical for this compound class. Therefore, we have developed a method that can be applied even to thermolabile systems and facilitates the detailed investigation of protein dynamics.
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Affiliation(s)
- Philip Horx
- Philipps-University Marburg 35043 Marburg Germany
| | - Armin Geyer
- Philipps-University Marburg 35043 Marburg Germany
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3
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Rathman BM, Rowe JL, Del Valle JR. Synthesis and conformation of backbone N-aminated peptides. Methods Enzymol 2021; 656:271-294. [PMID: 34325790 DOI: 10.1016/bs.mie.2021.04.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The chemical modification of peptides is a promising approach for the design of protein-protein interaction inhibitors and peptide-based drug candidates. Among several peptidomimetic strategies, substitution of the amide backbone maintains side-chain functionality that may be important for engagement of biological targets. Backbone amide substitution has been largely limited to N-alkylation, which can promote cis amide geometry and disrupt important H-bonding interactions. In contrast, N-amination of peptides induces distinct backbone geometries and maintains H-bond donor capacity. In this chapter we discuss the conformational characteristics of designed N-amino peptides and present a detailed protocol for their synthesis on solid support. The described methods allow for backbone N-amino scanning of biologically active parent sequences.
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4
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Cao Z, Deng X, Chen C, Liu Y, Yu L, Jiang X. Synergetic catalysis of Se and Cu allowing diethoxylation of halomethylene ketones using O2 as the mild oxidant. REACT CHEM ENG 2021. [DOI: 10.1039/d0re00471e] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Catalyzed by PhSe(O)OH/Cu(OAc)2, sp3-C–H alkylation of bromomethylene ketones produced useful α-carbonyl acetals under mild conditions. Bromo-containing substrates could release HBr during the reaction, avoiding the use of acidic additives.
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Affiliation(s)
- Zhicheng Cao
- School of Chemistry and Chemical Engineering
- Yangzhou University
- Yangzhou
- China
- Shanghai Key Laboratory of Green Chemistry and Chemical Process
| | - Xin Deng
- School of Chemistry and Chemical Engineering
- Yangzhou University
- Yangzhou
- China
| | - Chao Chen
- School of Chemistry and Chemical Engineering
- Yangzhou University
- Yangzhou
- China
| | - Yonghong Liu
- School of Chemistry and Chemical Engineering
- Yangzhou University
- Yangzhou
- China
| | - Lei Yu
- School of Chemistry and Chemical Engineering
- Yangzhou University
- Yangzhou
- China
| | - Xuefeng Jiang
- Shanghai Key Laboratory of Green Chemistry and Chemical Process
- Department of Chemistry
- East China Normal University
- Shanghai 200062
- China
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5
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Ghosh U, Soni I, Kaul G, Trivedi P, Chaturvedi V, Chopra S, Kanti Chakraborty T. Synthesis and Biological Studies of Dodecameric Cationic Antimicrobial Peptides Containing Tetrahydrofuran Amino Acids. Chembiochem 2020; 21:2518-2526. [PMID: 32297461 DOI: 10.1002/cbic.202000163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 04/13/2020] [Indexed: 11/05/2022]
Abstract
We report here a concise route to synthesize various stereoisomers of tetrahydrofuran amino acids (TAAs) and the synthesis of TAA-containing linear cationic dodecapeptides. Some of these linear peptides show slightly better antimicrobial activities than their tetra- and octameric congeners, but no activity against Mycobacterium tuberculosis, for which octapeptides exhibited by far the best results; this implies that antibacterial activity is dependent on the length of these linear peptides. All the dodecapeptides described here were found to be toxic in nature against Vero cells. The study helps to delineate the optimal length of this series of linear peptides and select potential leads in the development of novel cationic peptide-based antibiotics.
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Affiliation(s)
- Uttam Ghosh
- Department of Organic Chemistry, Indian Institution of Science, Bengaluru, 560012, Karnataka, India
| | - Isha Soni
- Division of Microbiology, CSIR-Central Drug Research Institute, Lucknow, 226031, Uttar Pradesh, India
| | - Grace Kaul
- Division of Microbiology, CSIR-Central Drug Research Institute, Lucknow, 226031, Uttar Pradesh, India
| | - Priyanka Trivedi
- Division of Biochemistry, CSIR-Central Drug Research Institute, Lucknow, 226031, Uttar Pradesh, India
| | - Vinita Chaturvedi
- Division of Biochemistry, CSIR-Central Drug Research Institute, Lucknow, 226031, Uttar Pradesh, India
| | - Sidharth Chopra
- Division of Microbiology, CSIR-Central Drug Research Institute, Lucknow, 226031, Uttar Pradesh, India
| | - Tushar Kanti Chakraborty
- Department of Organic Chemistry, Indian Institution of Science, Bengaluru, 560012, Karnataka, India
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6
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Rathman BM, Allen JL, Shaw LN, Del Valle JR. Synthesis and biological evaluation of backbone-aminated analogues of gramicidin S. Bioorg Med Chem Lett 2020; 30:127283. [PMID: 32527462 DOI: 10.1016/j.bmcl.2020.127283] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 05/18/2020] [Accepted: 05/20/2020] [Indexed: 01/26/2023]
Abstract
We report the parallel synthesis of gramicidin S derivatives featuring backbone N-amino substituents. Analogues were prepared by incorporation of N-amino dipeptide subunits on solid support. Nine backbone-aminated macrocycles were evaluated for growth inhibitory activity against ESKAPE pathogens and hemolytic activity against human red blood cells. Diamination of the Orn residues in the β-strand region of gramicidin S was found to enhance broad-spectrum antimicrobial activity without a corresponding increase in hemolytic activity.
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Affiliation(s)
- Benjamin M Rathman
- Department of Chemistry & Biochemistry, University of Notre Dame, Notre Dame, IN 46556, United States
| | - Jessie L Allen
- Department of Cell Biology, Microbiology & Molecular Biology, University of South Florida, Tampa, FL 33620, United States
| | - Lindsey N Shaw
- Department of Cell Biology, Microbiology & Molecular Biology, University of South Florida, Tampa, FL 33620, United States
| | - Juan R Del Valle
- Department of Chemistry & Biochemistry, University of Notre Dame, Notre Dame, IN 46556, United States.
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7
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Chen C, Cao Z, Zhang X, Li Y, Yu L, Jiang X. Synergistic Catalysis of Se and Cu for the Activation of
α
‐H
of Methyl Ketones with Molecular Oxygen/Alcohol to Produce
α
‐Keto
Acetals
†. CHINESE J CHEM 2020. [DOI: 10.1002/cjoc.202000089] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Chao Chen
- School of Chemistry and Chemical Engineering, Yangzhou University Yangzhou Jiangsu 225002 China
| | - Zhicheng Cao
- School of Chemistry and Chemical Engineering, Yangzhou University Yangzhou Jiangsu 225002 China
- Shanghai Key Laboratory of Green Chemistry and Chemical Process, Department of Chemistry, East China Normal University Shanghai 200062 China
| | - Xu Zhang
- School of Chemistry and Chemical Engineering, Yangzhou University Yangzhou Jiangsu 225002 China
| | - Yiming Li
- Shanghai Key Laboratory of Green Chemistry and Chemical Process, Department of Chemistry, East China Normal University Shanghai 200062 China
| | - Lei Yu
- School of Chemistry and Chemical Engineering, Yangzhou University Yangzhou Jiangsu 225002 China
| | - Xuefeng Jiang
- Shanghai Key Laboratory of Green Chemistry and Chemical Process, Department of Chemistry, East China Normal University Shanghai 200062 China
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8
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Guan Q, Chen K, Chen Q, Hu J, Cheng K, Hu C, Zhu J, Jin Y, Miclet E, Alezra V, Wan Y. Development of Therapeutic Gramicidin S Analogues Bearing Plastic β,γ-Diamino Acids. ChemMedChem 2020; 15:1089-1100. [PMID: 32233075 DOI: 10.1002/cmdc.202000097] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Indexed: 12/12/2022]
Abstract
Gramicidin S (GS), one of the most widely investigated antimicrobial peptides (AMPs), is known for its robust antimicrobial activity. However, it is restricted to topical application due to undesired hemolytic activity. With the aim of obtaining nontoxic GS analogues, we describe herein a molecular approach in which the native GS β-turn region is replaced by synthetic β,γ-diamino acids (β,γ-DiAAs). Four β,γ-DiAA diastereomers were employed to mimic the β-turn structure to afford GS analogues GS3-6, which exhibit diminished hemolytic activity. A comparative structural study demonstrates that the (βR,γS)-DiAA is the most-stable β-turn mimic. To further improve the therapeutic index (e. g., high antibacterial activity and low hemolytic activity) and to extend the molecular diversity, GS5 and GS6 were used as structural scaffolds to introduce additional hydrophobic or hydrophilic groups. We show that GS6K, GS6F and GS display comparable antibacterial activity, and GS6K and GS6F have significantly decreased toxicity. Moreover, antibacterial mechanism studies suggest that GS6K kills bacteria mainly through the disruption of the membrane.
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Affiliation(s)
- Qinkun Guan
- National Pharmaceutical Engineering Center for Solid Preparation in Chinese Herbal Medicine, Jiangxi University of Traditional Chinese Medicine, 1688 Meiling Avenue, WanLi, Nanchang, 330004, P. R. China
| | - Kaisen Chen
- Department of Clinical Laboratory, The First Affiliated Hospital of Nanchang University, 17 Yongwaizheng Street, Donghu, Nanchang, 330006, P. R. China
| | - Qiang Chen
- Department of Clinical Laboratory, The First Affiliated Hospital of Nanchang University, 17 Yongwaizheng Street, Donghu, Nanchang, 330006, P. R. China
| | - Jianguo Hu
- College of Pharmacy, Jiangxi University of Traditional Chinese Medicine, 1688 Meiling Avenue, WanLi, Nanchang, 330004, P. R. China
| | - Keguang Cheng
- State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, Normal University, 15 Yuchai Road, Guilin, 541004, P. R. China
| | - Chengfei Hu
- National Pharmaceutical Engineering Center for Solid Preparation in Chinese Herbal Medicine, Jiangxi University of Traditional Chinese Medicine, 1688 Meiling Avenue, WanLi, Nanchang, 330004, P. R. China
| | - Jibao Zhu
- National Pharmaceutical Engineering Center for Solid Preparation in Chinese Herbal Medicine, Jiangxi University of Traditional Chinese Medicine, 1688 Meiling Avenue, WanLi, Nanchang, 330004, P. R. China
| | - Yi Jin
- National Pharmaceutical Engineering Center for Solid Preparation in Chinese Herbal Medicine, Jiangxi University of Traditional Chinese Medicine, 1688 Meiling Avenue, WanLi, Nanchang, 330004, P. R. China
| | - Emeric Miclet
- Laboratoire des Biomolécules, Sorbonne Université, Université PSL, CNRS, 4 Place Jussieu, Paris, 75005, France
| | - Valérie Alezra
- Laboratoire de Méthodologie, Synthèse et Molécules Thérapeutiques (ICMMO), Université Paris-Sud, UMR 8182 CNRS, Université Paris-Saclay, Bât. 410, Faculté des Sciences d'Orsay, Orsay, 91405, France
| | - Yang Wan
- National Pharmaceutical Engineering Center for Solid Preparation in Chinese Herbal Medicine, Jiangxi University of Traditional Chinese Medicine, 1688 Meiling Avenue, WanLi, Nanchang, 330004, P. R. China.,State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, Normal University, 15 Yuchai Road, Guilin, 541004, P. R. China.,Laboratoire de Méthodologie, Synthèse et Molécules Thérapeutiques (ICMMO), Université Paris-Sud, UMR 8182 CNRS, Université Paris-Saclay, Bât. 410, Faculté des Sciences d'Orsay, Orsay, 91405, France
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9
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Nicke L, Horx P, Harms K, Geyer A. Directed C(sp 3)-H arylation of tryptophan: transformation of the directing group into an activated amide. Chem Sci 2019; 10:8634-8641. [PMID: 31803437 PMCID: PMC6844298 DOI: 10.1039/c9sc03440d] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Accepted: 08/03/2019] [Indexed: 12/18/2022] Open
Abstract
The aminoquinoline-directed C–H activation was used to synthezise unnatural tryptophans for solid phase peptide synthesis for the first time.
The 8-aminoquinoline (8AQ) directed C(sp3)–H functionalization was applied in the synthesis of β-arylated tryptophan derivatives. The laborious protecting group reorganization towards α-amino acids compatible for solid phase peptide synthesis (SPPS) was cut short by the transformation of the directing group into an activated amide, which was either used directly in peptide coupling or in the gram scale synthesis of storable Fmoc-protected amino acids for SPPS. In this work, directed C–H activation and nonplanar amide chemistry complement each other for the synthesis of hybrids between phenylalanine and tryptophan with restricted side chain mobility.
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Affiliation(s)
- Lennart Nicke
- Philipps-Universität Marburg , Fachbereich Chemie , Hans Meerwein Straße , 35032 Marburg , Germany .
| | - Philip Horx
- Philipps-Universität Marburg , Fachbereich Chemie , Hans Meerwein Straße , 35032 Marburg , Germany .
| | - Klaus Harms
- Philipps-Universität Marburg , Fachbereich Chemie , Hans Meerwein Straße , 35032 Marburg , Germany .
| | - Armin Geyer
- Philipps-Universität Marburg , Fachbereich Chemie , Hans Meerwein Straße , 35032 Marburg , Germany .
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10
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Guan Q, Huang S, Jin Y, Campagne R, Alezra V, Wan Y. Recent Advances in the Exploration of Therapeutic Analogues of Gramicidin S, an Old but Still Potent Antimicrobial Peptide. J Med Chem 2019; 62:7603-7617. [DOI: 10.1021/acs.jmedchem.9b00156] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Qinkun Guan
- National Pharmaceutical Engineering Center for Solid Preparation in Chinese Herbal Medicine, Jiangxi University of Traditional Chinese Medicine, Nanchang 330006, P. R. China
| | - Shuhui Huang
- National Pharmaceutical Engineering Center for Solid Preparation in Chinese Herbal Medicine, Jiangxi University of Traditional Chinese Medicine, Nanchang 330006, P. R. China
- Jiangxi Maternal and Child Hospital, Nanchang 330006, P. R. China
| | - Yi Jin
- National Pharmaceutical Engineering Center for Solid Preparation in Chinese Herbal Medicine, Jiangxi University of Traditional Chinese Medicine, Nanchang 330006, P. R. China
| | - Rémy Campagne
- Faculté des Sciences d’Orsay, Université Paris-Sud, Laboratoire de Méthodologie, Synthèse
et Molécules Thérapeutiques, ICMMO, UMR 8182, CNRS,
Université Paris-Saclay, Bât 410, 91405 Orsay, France
| | - Valérie Alezra
- Faculté des Sciences d’Orsay, Université Paris-Sud, Laboratoire de Méthodologie, Synthèse
et Molécules Thérapeutiques, ICMMO, UMR 8182, CNRS,
Université Paris-Saclay, Bât 410, 91405 Orsay, France
| | - Yang Wan
- National Pharmaceutical Engineering Center for Solid Preparation in Chinese Herbal Medicine, Jiangxi University of Traditional Chinese Medicine, Nanchang 330006, P. R. China
- Faculté des Sciences d’Orsay, Université Paris-Sud, Laboratoire de Méthodologie, Synthèse
et Molécules Thérapeutiques, ICMMO, UMR 8182, CNRS,
Université Paris-Saclay, Bât 410, 91405 Orsay, France
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11
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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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12
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Babii O, Afonin S, Ishchenko AY, Schober T, Negelia AO, Tolstanova GM, Garmanchuk LV, Ostapchenko LI, Komarov IV, Ulrich AS. Structure–Activity Relationships of Photoswitchable Diarylethene-Based β-Hairpin Peptides as Membranolytic Antimicrobial and Anticancer Agents. J Med Chem 2018; 61:10793-10813. [DOI: 10.1021/acs.jmedchem.8b01428] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Oleg Babii
- Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology (KIT), POB 3640, 76021 Karlsruhe, Germany
| | - Sergii Afonin
- Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology (KIT), POB 3640, 76021 Karlsruhe, Germany
| | - Aleksandr Yu. Ishchenko
- Institute of High Technologies, Taras Shevchenko National University of Kyiv, Vul. Volodymyrska 60, 01601 Kyiv, Ukraine
- Enamine Ltd., Vul. Chervonotkatska 78, 02066 Kyiv, Ukraine
| | - Tim Schober
- Institute of Organic Chemistry (IOC), Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
| | - Anatoliy O. Negelia
- Institute of Biology and Medicine, Taras Shevchenko National University of Kyiv, Prosp. Hlushkova 2, 03022 Kyiv, Ukraine
| | - Ganna M. Tolstanova
- Institute of Biology and Medicine, Taras Shevchenko National University of Kyiv, Prosp. Hlushkova 2, 03022 Kyiv, Ukraine
| | - Liudmyla V. Garmanchuk
- Institute of Biology and Medicine, Taras Shevchenko National University of Kyiv, Prosp. Hlushkova 2, 03022 Kyiv, Ukraine
| | - Liudmyla I. Ostapchenko
- Institute of Biology and Medicine, Taras Shevchenko National University of Kyiv, Prosp. Hlushkova 2, 03022 Kyiv, Ukraine
| | - Igor V. Komarov
- Institute of High Technologies, Taras Shevchenko National University of Kyiv, Vul. Volodymyrska 60, 01601 Kyiv, Ukraine
- Enamine Ltd., Vul. Chervonotkatska 78, 02066 Kyiv, Ukraine
- Lumobiotics GmbH, Auerstraße 2, 76227 Karlsruhe, Germany
| | - Anne S. Ulrich
- Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology (KIT), POB 3640, 76021 Karlsruhe, Germany
- Institute of Organic Chemistry (IOC), Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
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13
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Movsisyan LD, Schäfer E, Nguyen A, Ehrmann FR, Schwab A, Rossolini T, Zimmerli D, Wagner B, Daff H, Heine A, Klebe G, Diederich F. Sugar Acetonides are a Superior Motif for Addressing the Large, Solvent-Exposed Ribose-33 Pocket of tRNA-Guanine Transglycosylase. Chemistry 2018; 24:9957-9967. [PMID: 29939431 DOI: 10.1002/chem.201801756] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Revised: 05/10/2018] [Indexed: 11/09/2022]
Abstract
The intestinal disease shigellosis caused by Shigella bacteria affects over 120 million people annually. There is an urgent demand for new drugs as resistance against common antibiotics emerges. Bacterial tRNA-guanine transglycosylase (TGT) is a druggable target and controls the pathogenicity of Shigella flexneri. We report the synthesis of sugar-functionalized lin-benzoguanines addressing the ribose-33 pocket of TGT from Zymomonas mobilis. Ligand binding was analyzed by isothermal titration calorimetry and X-ray crystallography. Pocket occupancy was optimized by variation of size and protective groups of the sugars. The participation of a polycyclic water-cluster in the recognition of the sugar moiety was revealed. Acetonide-protected ribo- and psicofuranosyl derivatives are highly potent, benefiting from structural rigidity, good solubility, and metabolic stability. We conclude that sugar acetonides have a significant but not yet broadly recognized value in drug development.
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Affiliation(s)
- Levon D Movsisyan
- Laboratorium für Organische Chemie, ETH Zurich, Vladimir-Prelog-Weg 3, HCI, 8093, Zurich, Switzerland
| | - Elisabeth Schäfer
- Laboratorium für Organische Chemie, ETH Zurich, Vladimir-Prelog-Weg 3, HCI, 8093, Zurich, Switzerland
| | - Andreas Nguyen
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35032, Marburg, Germany
| | - Frederik R Ehrmann
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35032, Marburg, Germany
| | - Anatol Schwab
- Laboratorium für Organische Chemie, ETH Zurich, Vladimir-Prelog-Weg 3, HCI, 8093, Zurich, Switzerland
| | - Thomas Rossolini
- Laboratorium für Organische Chemie, ETH Zurich, Vladimir-Prelog-Weg 3, HCI, 8093, Zurich, Switzerland
| | - Daniel Zimmerli
- F. Hoffmann-La Roche Ltd, Discovery Technologies, Bldg 92, 4070, Basel, Switzerland
| | - Björn Wagner
- F. Hoffmann-La Roche Ltd, Discovery Technologies, Bldg 92, 4070, Basel, Switzerland
| | - Hamina Daff
- F. Hoffmann-La Roche Ltd, Discovery Technologies, Bldg 92, 4070, Basel, Switzerland
| | - Andreas Heine
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35032, Marburg, Germany
| | - Gerhard Klebe
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35032, Marburg, Germany
| | - François Diederich
- Laboratorium für Organische Chemie, ETH Zurich, Vladimir-Prelog-Weg 3, HCI, 8093, Zurich, Switzerland
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14
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Hofman GJ, Ottoy E, Light ME, Kieffer B, Kuprov I, Martins JC, Sinnaeve D, Linclau B. Minimising conformational bias in fluoroprolines through vicinal difluorination. Chem Commun (Camb) 2018; 54:5118-5121. [PMID: 29717724 DOI: 10.1039/c8cc01493k] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Monofluorination at the proline 4-position results in conformational effects, which is exploited for a range of applications. However, this conformational distortion is a hindrance when the natural proline conformation is important. Here we introduce (3S,4R)-3,4-difluoroproline, in which the individual fluorine atoms instil opposite conformational effects, as a suitable probe for fluorine NMR studies.
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Affiliation(s)
- Gert-Jan Hofman
- Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, UK.
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Wan Y, Stanovych A, Gori D, Zirah S, Kouklovsky C, Alezra V. β,γ-diamino acids as building blocks for new analogues of Gramicidin S: Synthesis and biological activity. Eur J Med Chem 2018; 149:122-128. [DOI: 10.1016/j.ejmech.2018.02.053] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Revised: 02/05/2018] [Accepted: 02/16/2018] [Indexed: 01/15/2023]
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