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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Pfukwa NBC, Rautenbach M, Hunt NT, Olaoye OO, Kumar V, Parker AW, Minnes L, Neethling PH. Temperature-Induced Effects on the Structure of Gramicidin S. J Phys Chem B 2023; 127:3774-3786. [PMID: 37125750 DOI: 10.1021/acs.jpcb.2c06115] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
We report on the structure of Gramicidin S (GS) in a model membrane mimetic environment represented by the amphipathic solvent 1-octanol using one-dimensional (1D) and two-dimensional (2D) IR spectroscopy. To explore potential structural changes of GS, we also performed a series of spectroscopic measurements at differing temperatures. By analyzing the amide I band and using 2D-IR spectral changes, results could be associated to the disruption of aggregates/oligomers, as well as structural and conformational changes happening in the concentrated solution of GS. The ability of 2D-IR to enable differentiation in melting transitions of oligomerized GS structures is attributed to the sensitivity of the technique to vibrational coupling. Two melting transition temperatures were identified; at Tm1 in the range 41-47 °C where the GS aggregates/oligomers disassemble and at Tm2 = 57 ± 2 °C where there is significant change involving GS β-sheet-type hydrogen bonds, whereby it is proposed that there is loss of interpeptide hydrogen bonds and we are left with mainly intrapeptide β-sheet and β-turn hydrogen bonds of the smaller oligomers. Further analysis with quantum mechanical/molecular mechanics (QM/MM) simulations and second derivative results highlighted the participation of active GS side chains. Ultimately, this work contributes toward understanding the GS structure and the formulation of GS analogues with improved bioactivity.
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Affiliation(s)
- Ngaatendwe B C Pfukwa
- Department of Physics, Laser Research Institute, Stellenbosch University, Private Bag X1, Matieland 7602, South Africa
| | - Marina Rautenbach
- BIOPEP Peptide Group, Department of Biochemistry, Stellenbosch University, Private Bag X1, Matieland 7602, South Africa
| | - Neil T Hunt
- Department of Chemistry and York Biomedical Research Institute, University of York, Heslington, York YO10 5DD, U.K
| | - Olufemi O Olaoye
- Department of Physics, Laser Research Institute, Stellenbosch University, Private Bag X1, Matieland 7602, South Africa
| | - Vikas Kumar
- BIOPEP Peptide Group, Department of Biochemistry, Stellenbosch University, Private Bag X1, Matieland 7602, South Africa
| | - Anthony W Parker
- Department of Physics, Laser Research Institute, Stellenbosch University, Private Bag X1, Matieland 7602, South Africa
- Research Complex at Harwell, Rutherford Appleton Laboratory, STFC Central Laser Facility, Harwell Science and Innovation Campus, Didcot, Oxon OX11 0QX, U.K
| | - Lucy Minnes
- Department of Physics, University of Strathclyde, SUPA, 107 Rottenrow East, Glasgow G4 0NG, U.K
| | - Pieter H Neethling
- Department of Physics, Laser Research Institute, Stellenbosch University, Private Bag X1, Matieland 7602, South Africa
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3
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Asano A, Minami C, Matsuoka S, Kato T, Doi M. An Ornithine-Free Gramicidin S Analogue Using Norleucine, Cyclo(Val-Nle-Leu-D-Phe-Pro) 2, Forms Helically Aligned β-Sheets. Chem Pharm Bull (Tokyo) 2021; 69:1097-1103. [PMID: 34719592 DOI: 10.1248/cpb.c21-00548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The structure of an ornithine (Orn)-free Gramicidin S (GS) analogue, cyclo(Val-Nle-Leu-D-Phe-Pro)2 (NGS), was studied. Its circular dichroism (CD) spectrum showed that NGS has a structure similar to GS, though the value of [θ] indicated smaller β-turn and sheet populations. This is probably because the Nle side chain could not form intramolecular hydrogen bonds stabilizing the sheet structure. The chemical shift perturbation of αH and JNH-αH were similar in GS and NGS. Three independent NGS molecules formed intramolecular β-sheet structures in crystal. The turn structures of D-Phe-Pro moieties were classed as type II' β-turns, but one part was unclassed. The molecules were arranged in a twisting manner, which resulted in the formation of a helical sheet. Similar structural characteristics were observed previously in a Leu-type, Orn-free GS analogue and in GS trifluoroacetic acid salt.
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Affiliation(s)
- Akiko Asano
- Faculty of Pharmacy, Osaka Medical and Pharmaceutical University
| | - Chisato Minami
- Faculty of Pharmacy, Osaka Medical and Pharmaceutical University
| | - Shiori Matsuoka
- Faculty of Pharmacy, Osaka Medical and Pharmaceutical University
| | - Takuma Kato
- Faculty of Pharmacy, Osaka Medical and Pharmaceutical University
| | - Mitsunobu Doi
- Faculty of Pharmacy, Osaka Medical and Pharmaceutical University
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4
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Zhu J, Hu C, Zeng Z, Deng X, Zeng L, Xie S, Fang Y, Jin Y, Alezra V, Wan Y. Polymyxin B-inspired non-hemolytic tyrocidine A analogues with significantly enhanced activity against gram-negative bacteria: How cationicity impacts cell specificity and antibacterial mechanism. Eur J Med Chem 2021; 221:113488. [PMID: 33991963 DOI: 10.1016/j.ejmech.2021.113488] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 03/31/2021] [Accepted: 04/18/2021] [Indexed: 11/25/2022]
Abstract
Naturally occurring cyclic antimicrobial peptides (AMPs) such as tyrocidine A (Tyrc A) and gramicidin S (GS) are appealing targets for the development of novel antibiotics. However, their therapeutic potentials are limited by undesired hemolytic activity and relatively poor activity against Gram-negative bacteria. Inspired by polycationic lipopeptide polymyxin B (PMB), the so called 'last-resort' antibiotic for the treatment of infections caused by multidrug-resistant Gram-negative bacteria, we synthesized and biologically evaluated a series of polycationic analogues derived from Tyrc A. We were able to obtain peptide 8 that possesses 5 positive charges exhibiting potent activities against both Gram-negative and Gram-positive bacteria along with totally diminished hemolytic activity. Intriguingly, antibacterial mechanism studies revealed that, rather than the 'pore forming' model that possessed by Tyrc A, peptide 8 likely diffuses membrane in a 'detergent-like' manner. Furthermore, when treating mice with peritonitis-sepsis, peptide 8 showed excellent antibacterial and anti-inflammatory activities in vivo.
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Affiliation(s)
- Jibao Zhu
- National Pharmaceutical Engineering Center for Solid Preparation in Chinese Herbal Medicine, Jiangxi University of Traditional Chinese Medicine, Nanchang, 330004, PR China
| | - Chengfei Hu
- National Pharmaceutical Engineering Center for Solid Preparation in Chinese Herbal Medicine, Jiangxi University of Traditional Chinese Medicine, Nanchang, 330004, PR China
| | - Zizhen Zeng
- National Pharmaceutical Engineering Center for Solid Preparation in Chinese Herbal Medicine, Jiangxi University of Traditional Chinese Medicine, Nanchang, 330004, PR China
| | - Xiaoyu Deng
- Minist Educ, Key Lab Modern Preparat TCM, Jiangxi University of Traditional Chinese Medicine, Nanchang, 330004, PR China
| | - Lingbing Zeng
- Department of Clinical Laboratory, The First Affiliated Hospital of Nanchang University, 17 Yongwaizheng Street, Donghu, Nanchang, 330006, PR China
| | - Saisai Xie
- National Pharmaceutical Engineering Center for Solid Preparation in Chinese Herbal Medicine, Jiangxi University of Traditional Chinese Medicine, Nanchang, 330004, PR China
| | - Yuanying Fang
- National Pharmaceutical Engineering Center for Solid Preparation in Chinese Herbal Medicine, Jiangxi University of Traditional Chinese Medicine, Nanchang, 330004, PR China
| | - Yi Jin
- National Pharmaceutical Engineering Center for Solid Preparation in Chinese Herbal Medicine, Jiangxi University of Traditional Chinese Medicine, Nanchang, 330004, PR China
| | - Valérie Alezra
- Laboratoire de Méthodologie, Synthèse et Molécules Thérapeutiques (ICMMO), UMR 8182, CNRS, Université Paris-Saclay, Bât 410, Facultédes Sciences D'Orsay, Orsay, 291405, France
| | - Yang Wan
- National Pharmaceutical Engineering Center for Solid Preparation in Chinese Herbal Medicine, Jiangxi University of Traditional Chinese Medicine, Nanchang, 330004, PR China; Laboratoire de Méthodologie, Synthèse et Molécules Thérapeutiques (ICMMO), UMR 8182, CNRS, Université Paris-Saclay, Bât 410, Facultédes Sciences D'Orsay, Orsay, 291405, France; State Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources, Guangxi Normal University, 15 Yuchai Road, Guilin, 541004, PR China.
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5
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Legrand B, Maillard LT. α,β-Unsaturated γ-Peptide Foldamers. Chempluschem 2021; 86:629-645. [PMID: 33856125 DOI: 10.1002/cplu.202100045] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 03/31/2021] [Indexed: 01/01/2023]
Abstract
Despite their concomitant emergence in the 1990s, γ-peptide foldamers have not developed as fast as β-peptide foldamers and to date, only a few γ-oligomer structures have been reported, and with sparse applications. Among these examples, sequences containing α,β-unsaturated γ-amino acids have recently drawn attention since the Z/E configurations of the double bond provide opposite planar restrictions leading to divergent conformational behaviors, from helix to extended structures. In this Review, we give a comprehensive overview of the developments of γ-peptide foldamers containing α,β-unsaturated γ-amino acids with examples of applications for health and catalysis, as well as materials science.
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Affiliation(s)
- Baptiste Legrand
- Institut des Biomolécules Max Mousseron, IBMM, University of Montpellier, ENSCM, CNRS, Montpellier, France., 15 Av. Charles Flahault BP 14 491, 34093, Montpellier Cedex 5, France
| | - Ludovic T Maillard
- Institut des Biomolécules Max Mousseron, IBMM, University of Montpellier, ENSCM, CNRS, Montpellier, France., 15 Av. Charles Flahault BP 14 491, 34093, Montpellier Cedex 5, France
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6
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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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7
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Bonnel C, Legrand B, Simon M, Clavié M, Masnou A, Jumas-Bilak E, Kang YK, Licznar-Fajardo P, Maillard LT, Masurier N. Tailoring the Physicochemical Properties of Antimicrobial Peptides onto a Thiazole-Based γ-Peptide Foldamer. J Med Chem 2020; 63:9168-9180. [DOI: 10.1021/acs.jmedchem.0c00077] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Clément Bonnel
- Institut des Biomolécules Max Mousseron, UMR 5247, CNRS, UM, ENSCM, UFR des Sciences Pharmaceutiques et Biologiques, 15 Avenue Charles Flahault, 34093 Montpellier Cedex 5, France
| | - Baptiste Legrand
- Institut des Biomolécules Max Mousseron, UMR 5247, CNRS, UM, ENSCM, UFR des Sciences Pharmaceutiques et Biologiques, 15 Avenue Charles Flahault, 34093 Montpellier Cedex 5, France
| | - Matthieu Simon
- Institut des Biomolécules Max Mousseron, UMR 5247, CNRS, UM, ENSCM, UFR des Sciences Pharmaceutiques et Biologiques, 15 Avenue Charles Flahault, 34093 Montpellier Cedex 5, France
| | - Margaux Clavié
- Institut des Biomolécules Max Mousseron, UMR 5247, CNRS, UM, ENSCM, UFR des Sciences Pharmaceutiques et Biologiques, 15 Avenue Charles Flahault, 34093 Montpellier Cedex 5, France
| | - Agnès Masnou
- Laboratoire HydroSciences Montpellier, UMR 5569, CNRS, UM, IRD, Département d’Hygiène Hospitalière−CHU Montpellier, 34095 Montpellier, France
| | - Estelle Jumas-Bilak
- Laboratoire HydroSciences Montpellier, UMR 5569, CNRS, UM, IRD, Département d’Hygiène Hospitalière−CHU Montpellier, 34095 Montpellier, France
| | - Young Kee Kang
- Department of Chemistry, Chungbuk National University, Cheongju, Chungbuk 28644, Republic of Korea
| | - Patricia Licznar-Fajardo
- Laboratoire HydroSciences Montpellier, UMR 5569, CNRS, UM, IRD, Département d’Hygiène Hospitalière−CHU Montpellier, 34095 Montpellier, France
| | - Ludovic T. Maillard
- Institut des Biomolécules Max Mousseron, UMR 5247, CNRS, UM, ENSCM, UFR des Sciences Pharmaceutiques et Biologiques, 15 Avenue Charles Flahault, 34093 Montpellier Cedex 5, France
| | - Nicolas Masurier
- Institut des Biomolécules Max Mousseron, UMR 5247, CNRS, UM, ENSCM, UFR des Sciences Pharmaceutiques et Biologiques, 15 Avenue Charles Flahault, 34093 Montpellier Cedex 5, France
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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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Asano A, Matsuoka S, Minami C, Kato T, Doi M. [Leu 2]Gramicidin S preserves the structural properties of its parent peptide and forms helically aligned β-sheets. ACTA CRYSTALLOGRAPHICA SECTION C-STRUCTURAL CHEMISTRY 2019; 75:1336-1343. [PMID: 31589149 DOI: 10.1107/s2053229619011872] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 08/28/2019] [Indexed: 11/11/2022]
Abstract
For crystallographic analysis, Leu was substituted for Orn in Gramicidin S (LGS) to suppress interactions with hydrophilic solvent molecules, which increased the flexibility of the Orn side chains, leading to disorder within the crystals. The asymmetric unit (C62H94N10O10·1.296C3H8O·1.403H2O) contains three LGS molecules (A, B and C) forming β-turn and intramolecular β-sheet structures. With the exception of one motif in molecule C, D-Phe-Pro turn motifs (Phe is phenylalanine and Pro is proline) were classed as type II' β-turns. The peptide backbones twist slightly to the right along the long axis of the molecule. The puckering of Pro is in a Cγ-endo or twisted Cγ-endo-Cβ-exo form. Flanking molecules are arranged such that the angles (A...B = 104°, B...C = 139° and C...A = 117°) form helical β-sheets. Solvent molecules interact with the peptide backbones supporting the β-sheets. The forms of the replacement Leu side chains are consistent with the e-form of the Orn side chain in GS analogues. No hydrophilic region composed of solvent molecules, such as that observed in Gramicidin S hydrochloride (GS·HCl) crystals, was found. The perturbation of αH chemical shifts and coupling constants of CONH showed that the structural properties of GS·HCl and LGS are similar to each other in solution. CD spectra also supported the structural similarity. With the sequence cyclo(-Val-Leu-Leu-D-Phe-Pro-)2 (Val is valine and Leu is leucine), LGS lacks the amphiphilicity and antimicrobial activity of parental Gramicidin S (GS). However, the structure of LGS reflects the structural characteristics of GS and no disordering inconvenient for structural analysis was found. Thus, LGS could be a novel scaffold useful for studying β-turn and sheet structures.
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Affiliation(s)
- Akiko Asano
- Osaka University of Pharmaceutical Sciences, 4-20-1 Nasahara, Takatsuki, Osaka 569-1094, Japan
| | - Shiori Matsuoka
- Osaka University of Pharmaceutical Sciences, 4-20-1 Nasahara, Takatsuki, Osaka 569-1094, Japan
| | - Chisato Minami
- Osaka University of Pharmaceutical Sciences, 4-20-1 Nasahara, Takatsuki, Osaka 569-1094, Japan
| | - Takuma Kato
- Osaka University of Pharmaceutical Sciences, 4-20-1 Nasahara, Takatsuki, Osaka 569-1094, Japan
| | - Mitsinobu Doi
- Osaka University of Pharmaceutical Sciences, 4-20-1 Nasahara, Takatsuki, Osaka 569-1094, Japan
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10
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Ali LMA, Simon M, El Cheikh K, Aguesseau-Kondrotas J, Godefroy A, Nguyen C, Garcia M, Morère A, Gary-Bobo M, Maillard L. Topological Requirements for CI-M6PR-Mediated Cell Uptake. Bioconjug Chem 2019; 30:2533-2538. [DOI: 10.1021/acs.bioconjchem.9b00590] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Lamiaa M. A. Ali
- Institut des Biomolécules Max Mousseron, UMR CNRS-UM-ENSCM
5247, UFR des Sciences Pharmaceutiques et Biologiques, 15 Avenue Charles Flahault, 34093 Montpellier Cedex 5, France
- Biochemistry Department, Medical Research Institute, Alexandria University, 21561 Alexandria, Egypt
| | - Matthieu Simon
- Institut des Biomolécules Max Mousseron, UMR CNRS-UM-ENSCM
5247, UFR des Sciences Pharmaceutiques et Biologiques, 15 Avenue Charles Flahault, 34093 Montpellier Cedex 5, France
| | - Khaled El Cheikh
- NanoMedSyn, Avenue Charles Flahault, 34093 Montpellier Cedex
05, France
| | - Julie Aguesseau-Kondrotas
- Institut des Biomolécules Max Mousseron, UMR CNRS-UM-ENSCM
5247, UFR des Sciences Pharmaceutiques et Biologiques, 15 Avenue Charles Flahault, 34093 Montpellier Cedex 5, France
| | - Anastasia Godefroy
- Institut des Biomolécules Max Mousseron, UMR CNRS-UM-ENSCM
5247, UFR des Sciences Pharmaceutiques et Biologiques, 15 Avenue Charles Flahault, 34093 Montpellier Cedex 5, France
- NanoMedSyn, Avenue Charles Flahault, 34093 Montpellier Cedex
05, France
| | - Christophe Nguyen
- Institut des Biomolécules Max Mousseron, UMR CNRS-UM-ENSCM
5247, UFR des Sciences Pharmaceutiques et Biologiques, 15 Avenue Charles Flahault, 34093 Montpellier Cedex 5, France
| | - Marcel Garcia
- NanoMedSyn, Avenue Charles Flahault, 34093 Montpellier Cedex
05, France
| | - Alain Morère
- Institut des Biomolécules Max Mousseron, UMR CNRS-UM-ENSCM
5247, UFR des Sciences Pharmaceutiques et Biologiques, 15 Avenue Charles Flahault, 34093 Montpellier Cedex 5, France
| | - Magali Gary-Bobo
- Institut des Biomolécules Max Mousseron, UMR CNRS-UM-ENSCM
5247, UFR des Sciences Pharmaceutiques et Biologiques, 15 Avenue Charles Flahault, 34093 Montpellier Cedex 5, France
| | - Ludovic Maillard
- Institut des Biomolécules Max Mousseron, UMR CNRS-UM-ENSCM
5247, UFR des Sciences Pharmaceutiques et Biologiques, 15 Avenue Charles Flahault, 34093 Montpellier Cedex 5, France
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11
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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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12
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Abstract
The rise of antibiotic resistant bacteria requires unconventional strategies toward efficient chemotherapeutic agents, preferably with alternative mechanisms of action. The bacterial cell membrane has become an appealing target since its essential and highly conservative structure are key challenges to resistance mechanisms. Inspired by natural antimicrobial peptides, research on membrane-targeting antimicrobials has been growing out of the peptide space. The pursuit of more druggable molecules led to the discovery that the pharmacophore of antimicrobial peptides is smaller than anticipated. Several promising classes of membrane-targeting antimicrobials have been discovered, such as ceragenins, reutericyclines, carbohydrate amphiphiles - among others. This review will discuss the most recent findings on membrane-targeting antibiotics, focusing on small molecules outside the antimicrobial peptide molecular space.
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13
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Konda M, Ghosh T, Mobin SM, Das AK. Intertwined gababutin-based supramolecular double helix. NEW J CHEM 2019. [DOI: 10.1039/c8nj05009k] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
A dimer-assembly driven supramolecular double helix is observed for the gababutin-based short peptide sequence and this architecture exhibits electrochemical features.
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Affiliation(s)
- Maruthi Konda
- Department of Chemistry
- Indian Institute of Technology Indore
- Indore 453552
- India
| | - Tapas Ghosh
- Department of Chemistry
- Indian Institute of Technology Indore
- Indore 453552
- India
| | - Shaikh M. Mobin
- Department of Chemistry
- Indian Institute of Technology Indore
- Indore 453552
- India
| | - Apurba K. Das
- Department of Chemistry
- Indian Institute of Technology Indore
- Indore 453552
- India
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14
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Yeoh YQ, Yu J, Polyak SW, Horsley JR, Abell AD. Photopharmacological Control of Cyclic Antimicrobial Peptides. Chembiochem 2018; 19:2591-2597. [DOI: 10.1002/cbic.201800618] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2018] [Indexed: 12/20/2022]
Affiliation(s)
- Yuan Qi Yeoh
- ARC Centre of Excellence for Nanoscale BioPhotonics (CNBP)Department of ChemistryThe University of Adelaide, North Terrace Adelaide SA 5005 Australia
| | - Jingxian Yu
- ARC Centre of Excellence for Nanoscale BioPhotonics (CNBP)Department of ChemistryThe University of Adelaide, North Terrace Adelaide SA 5005 Australia
| | - Steven W. Polyak
- School of Biological SciencesDepartment of Molecular and Cellular BiologyThe University of Adelaide, North Terrace Adelaide SA 5005 Australia
| | - John R. Horsley
- ARC Centre of Excellence for Nanoscale BioPhotonics (CNBP)Department of ChemistryThe University of Adelaide, North Terrace Adelaide SA 5005 Australia
| | - Andrew D. Abell
- ARC Centre of Excellence for Nanoscale BioPhotonics (CNBP)Department of ChemistryThe University of Adelaide, North Terrace Adelaide SA 5005 Australia
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15
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Simon M, Ali LMA, El Cheikh K, Aguesseau J, Gary-Bobo M, Garcia M, Morère A, Maillard LT. Can Heterocyclic γ-Peptides Provide Polyfunctional Platforms for Synthetic Glycocluster Construction? Chemistry 2018; 24:11426-11432. [PMID: 29846978 DOI: 10.1002/chem.201802032] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Indexed: 01/03/2023]
Abstract
Sugars play key roles in many molecular and cellular communication processes involving a family of proteins named lectins. The low affinity associated with sugar recognition is generally counterbalanced by the multivalent nature of the interaction. While many polyglycosylated architectures have been described, only a few studies focused on the impact of topology variations of the multivalent structures on the interaction with lectin proteins. One major interest of our group concerns the design of new highly predictable and stable molecular pseudo-peptide architectures for therapeutic applications. In such a context, we described a class of constrained heterocyclic γ-amino acids built around a thiazole ring, named ATCs. ATC oligomers are helical molecules resulting from the formation of a highly stable C9 hydrogen-bonding pattern. Following our program, we herein address the potential of ATC oligomers as tunable scaffolds for the development of original multivalent glycoclusters.
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Affiliation(s)
- Matthieu Simon
- Institut des Biomolécules Max Mousseron, UMR CNRS-UM-ENSCM 5247, UFR des Sciences Pharmaceutiques et Biologiques, 15 Avenue Charles Flahault, 34093, Montpellier Cedex 5, France
| | - Lamiaa M A Ali
- Institut des Biomolécules Max Mousseron, UMR CNRS-UM-ENSCM 5247, UFR des Sciences Pharmaceutiques et Biologiques, 15 Avenue Charles Flahault, 34093, Montpellier Cedex 5, France.,On sabbatical leave from: Medical Research Institute, Alexandria University, Egypt
| | - Khaled El Cheikh
- Institut des Biomolécules Max Mousseron, UMR CNRS-UM-ENSCM 5247, UFR des Sciences Pharmaceutiques et Biologiques, 15 Avenue Charles Flahault, 34093, Montpellier Cedex 5, France
| | - Julie Aguesseau
- Institut des Biomolécules Max Mousseron, UMR CNRS-UM-ENSCM 5247, UFR des Sciences Pharmaceutiques et Biologiques, 15 Avenue Charles Flahault, 34093, Montpellier Cedex 5, France
| | - Magali Gary-Bobo
- Institut des Biomolécules Max Mousseron, UMR CNRS-UM-ENSCM 5247, UFR des Sciences Pharmaceutiques et Biologiques, 15 Avenue Charles Flahault, 34093, Montpellier Cedex 5, France
| | - Marcel Garcia
- Institut des Biomolécules Max Mousseron, UMR CNRS-UM-ENSCM 5247, UFR des Sciences Pharmaceutiques et Biologiques, 15 Avenue Charles Flahault, 34093, Montpellier Cedex 5, France
| | - Alain Morère
- Institut des Biomolécules Max Mousseron, UMR CNRS-UM-ENSCM 5247, UFR des Sciences Pharmaceutiques et Biologiques, 15 Avenue Charles Flahault, 34093, Montpellier Cedex 5, France
| | - Ludovic T Maillard
- Institut des Biomolécules Max Mousseron, UMR CNRS-UM-ENSCM 5247, UFR des Sciences Pharmaceutiques et Biologiques, 15 Avenue Charles Flahault, 34093, Montpellier Cedex 5, France
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16
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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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17
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Laurencin M, Simon M, Fleury Y, Baudy-Floc'h M, Bondon A, Legrand B. Selectivity Modulation and Structure of α/aza-β3
Cyclic Antimicrobial Peptides. Chemistry 2018; 24:6191-6201. [DOI: 10.1002/chem.201800152] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Indexed: 12/26/2022]
Affiliation(s)
| | - Matthieu Simon
- Institut des Biomolécules Max Mousseron (IBMM); Univ Montpellier, CNRS, UM, ENSCM; 15 Avenue Charles Flahault 34093 Montpellier Cedex 5 France
- Université de Rennes, CNRS; ISCR-UMR 6226; 35000 Rennes France
| | - Yannick Fleury
- Chimie Marines, IUEM; Université de Brest, EA 3884; 6 rue de l'Université 29000 Quimper France
| | | | - Arnaud Bondon
- Université de Rennes, CNRS; ISCR-UMR 6226; 35000 Rennes France
| | - Baptiste Legrand
- Institut des Biomolécules Max Mousseron (IBMM); Univ Montpellier, CNRS, UM, ENSCM; 15 Avenue Charles Flahault 34093 Montpellier Cedex 5 France
- Université de Rennes, CNRS; ISCR-UMR 6226; 35000 Rennes France
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18
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Singh G, Azmi S, Ghosh JK, Ampapathi RS, Pal S. Synthesis and Conformational Studies of Taa-Containingo-Nitrobenzenesulfonamide- (o-Nosyl-) Protected GS Analogs to Prove the Importance of 6RStereochemistry of Taa over 6S. ChemistrySelect 2018. [DOI: 10.1002/slct.201800003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Gajendra Singh
- NMR Research Centre; Division of SAIF; CSIR-Central Drug Research Institute; Lucknow 226031 India
- Academy of Scientific and Innovative Research; New Delhi 110001 India
| | - Sarfuddin Azmi
- Molecular and Structural Biology Division; CSIR-Central Drug Research Institute; Lucknow 226031 India
- Present Address: Research Centre; Prince Sultan Military Medical City, Riyadh, Kingdom of; Saudi Arabia
| | - Jimut Kanti Ghosh
- Molecular and Structural Biology Division; CSIR-Central Drug Research Institute; Lucknow 226031 India
| | - Ravi Sankar Ampapathi
- NMR Research Centre; Division of SAIF; CSIR-Central Drug Research Institute; Lucknow 226031 India
- Academy of Scientific and Innovative Research; New Delhi 110001 India
| | - Sudip Pal
- Medicinal & Process Chemistry Division; CSIR-Central Drug Research Institute; Lucknow 226031 India
- Department of Chemistry, School of Physical Sciences; Sikkim University (A Central University); Gangtok 737102 India
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19
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Bonnel C, Legrand B, Bantignies JL, Petitjean H, Martinez J, Masurier N, Maillard LT. FT-IR and NMR structural markers for thiazole-based γ-peptide foldamers. Org Biomol Chem 2018; 14:8664-8669. [PMID: 27714174 DOI: 10.1039/c6ob01594h] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Nuclear magnetic resonance (NMR) spectroscopy has been established as a potent method for the determination of foldamer structures in solution. However, the NMR techniques could be limited by averaging, so additional experimental techniques are often needed to fully endorse the folding properties of a sequence. We have recently demonstrated that oligo-γ-peptides composed of 4-amino(methyl)-1,3-thiazole-5-carboxylic acids (ATCs) adopt an original helical fold stabilized by hydrogen bonds forming C9 pseudocycles. The main objective of the present work is to reinvestigate the folding of ATC oligomer 1 in order to identify reliable FT-IR and NMR structural markers that are of value for tracking the degree of organization of ATC-based peptides.
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Affiliation(s)
- C Bonnel
- Institut des Biomolécules Max Mousseron, UMR 5247, Université de Montpellier, CNRS, ENSCM, UFR des Sciences Pharmaceutiques et Biologiques, 15 Avenue Charles Flahault, 34093 Montpellier Cedex 5, France.
| | - B Legrand
- Institut des Biomolécules Max Mousseron, UMR 5247, Université de Montpellier, CNRS, ENSCM, UFR des Sciences Pharmaceutiques et Biologiques, 15 Avenue Charles Flahault, 34093 Montpellier Cedex 5, France.
| | - J-L Bantignies
- LC2 - UMR 5221 Université de Montpellier, CNRS, Place Eugène Bataillon, 34095 Montpellier, France
| | - H Petitjean
- Institut Charles Gerhardt, UMR 5253 CNRS/ENSCM/UM, Matériaux Avancés pour la Catalyse et la Santé, Ecole Nationale Supérieure de Chimie, 8 rue de l'Ecole Normale, 34296 Montpellier Cedex 5, France
| | - J Martinez
- Institut des Biomolécules Max Mousseron, UMR 5247, Université de Montpellier, CNRS, ENSCM, UFR des Sciences Pharmaceutiques et Biologiques, 15 Avenue Charles Flahault, 34093 Montpellier Cedex 5, France.
| | - N Masurier
- Institut des Biomolécules Max Mousseron, UMR 5247, Université de Montpellier, CNRS, ENSCM, UFR des Sciences Pharmaceutiques et Biologiques, 15 Avenue Charles Flahault, 34093 Montpellier Cedex 5, France.
| | - L T Maillard
- Institut des Biomolécules Max Mousseron, UMR 5247, Université de Montpellier, CNRS, ENSCM, UFR des Sciences Pharmaceutiques et Biologiques, 15 Avenue Charles Flahault, 34093 Montpellier Cedex 5, France.
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20
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Wan Y, Auberger N, Thétiot-Laurent S, Bouillère F, Zulauf A, He J, Courtiol-Legourd S, Guillot R, Kouklovsky C, Cote des Combes S, Pacaud C, Devillers I, Alezra V. Constrained Cyclic β,γ-Diamino Acids from Glutamic Acid: Synthesis of Both Diastereomers and Unexpected Kinetic Resolution. European J Org Chem 2018. [DOI: 10.1002/ejoc.201701477] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Yang Wan
- Laboratoire de Méthodologie, Synthèse et Molécules Thérapeutiques; ICMMO; UMR 8182, CNRS, Univ. Paris-Sud; Université Paris-Saclay; Faculté des Sciences d'Orsay; Bât 410 91405 Orsay France
| | - Nicolas Auberger
- Laboratoire de Méthodologie, Synthèse et Molécules Thérapeutiques; ICMMO; UMR 8182, CNRS, Univ. Paris-Sud; Université Paris-Saclay; Faculté des Sciences d'Orsay; Bât 410 91405 Orsay France
| | - Sophie Thétiot-Laurent
- Laboratoire de Méthodologie, Synthèse et Molécules Thérapeutiques; ICMMO; UMR 8182, CNRS, Univ. Paris-Sud; Université Paris-Saclay; Faculté des Sciences d'Orsay; Bât 410 91405 Orsay France
| | - Francelin Bouillère
- Laboratoire de Méthodologie, Synthèse et Molécules Thérapeutiques; ICMMO; UMR 8182, CNRS, Univ. Paris-Sud; Université Paris-Saclay; Faculté des Sciences d'Orsay; Bât 410 91405 Orsay France
| | - Anaïs Zulauf
- Laboratoire de Méthodologie, Synthèse et Molécules Thérapeutiques; ICMMO; UMR 8182, CNRS, Univ. Paris-Sud; Université Paris-Saclay; Faculté des Sciences d'Orsay; Bât 410 91405 Orsay France
| | - Jiefang He
- Laboratoire de Méthodologie, Synthèse et Molécules Thérapeutiques; ICMMO; UMR 8182, CNRS, Univ. Paris-Sud; Université Paris-Saclay; Faculté des Sciences d'Orsay; Bât 410 91405 Orsay France
| | - Stéphanie Courtiol-Legourd
- Laboratoire de Méthodologie, Synthèse et Molécules Thérapeutiques; ICMMO; UMR 8182, CNRS, Univ. Paris-Sud; Université Paris-Saclay; Faculté des Sciences d'Orsay; Bât 410 91405 Orsay France
| | - Régis Guillot
- Laboratoire de Méthodologie, Synthèse et Molécules Thérapeutiques; ICMMO; UMR 8182, CNRS, Univ. Paris-Sud; Université Paris-Saclay; Faculté des Sciences d'Orsay; Bât 410 91405 Orsay France
| | - Cyrille Kouklovsky
- Laboratoire de Méthodologie, Synthèse et Molécules Thérapeutiques; ICMMO; UMR 8182, CNRS, Univ. Paris-Sud; Université Paris-Saclay; Faculté des Sciences d'Orsay; Bât 410 91405 Orsay France
| | - Sylvain Cote des Combes
- Sanofi Recherche et Développement; 1 avenue Pierre Brossolette 91385 Chilly Mazarin CEDEX France
| | - Christophe Pacaud
- Sanofi Recherche et Développement; 1 avenue Pierre Brossolette 91385 Chilly Mazarin CEDEX France
| | - Ingrid Devillers
- Sanofi Recherche et Développement; 1 avenue Pierre Brossolette 91385 Chilly Mazarin CEDEX France
| | - Valérie Alezra
- Laboratoire de Méthodologie, Synthèse et Molécules Thérapeutiques; ICMMO; UMR 8182, CNRS, Univ. Paris-Sud; Université Paris-Saclay; Faculté des Sciences d'Orsay; Bât 410 91405 Orsay France
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21
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Kotmale AS, Sangtani E, Gonnade RG, Sarkar D, Burade S, Rajamohanan PR, Sanjayan GJ. Conformational studies of Ant–Pro motif-incorporated cyclic peptides: gramicidin S and avellanin. NEW J CHEM 2018. [DOI: 10.1039/c7nj03701e] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Conformational studies suggest that an AntDPro motif-incorporated synthetic gramicidin S analog retains β-sheet conformation, while its truncated analog avellanin disturbs the β-sheet conformation.
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Affiliation(s)
- Amol S. Kotmale
- Division of Organic Chemistry
- CSIR-National Chemical Laboratory (CSIR-NCL)
- Pune 411 008
- India
- Central NMR Facility
| | - Ekta Sangtani
- Center for Materials Characterization
- CSIR-National Chemical Laboratory (CSIR-NCL)
- Pune 411 008
- India
| | - Rajesh G. Gonnade
- Center for Materials Characterization
- CSIR-National Chemical Laboratory (CSIR-NCL)
- Pune 411 008
- India
| | - Dhiman Sarkar
- Combichem-Bioresource Center
- Organic Chemistry Division
- CSIR-National Chemical Laboratory
- Pune 411008
- India
| | - Sachin Burade
- Department of Chemistry
- Savitribai Phule Pune University
- Pune
- India
| | | | - Gangadhar J. Sanjayan
- Division of Organic Chemistry
- CSIR-National Chemical Laboratory (CSIR-NCL)
- Pune 411 008
- India
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22
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Bonnel C, Legrand B, Simon M, Martinez J, Bantignies JL, Kang YK, Wenger E, Hoh F, Masurier N, Maillard LT. C9/12
Ribbon-Like Structures in Hybrid Peptides Alternating α- and Thiazole-Based γ-Amino Acids. Chemistry 2017; 23:17584-17591. [DOI: 10.1002/chem.201704001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Indexed: 11/08/2022]
Affiliation(s)
- Clément Bonnel
- Institut des Biomolécules Max Mousseron; UMR CNRS-UM-ENSCM 5247, UFR des Sciences Pharmaceutiques et Biologiques; 15 Avenue Charles Flahault 34093 Montpellier Cedex 5 France
| | - Baptiste Legrand
- Institut des Biomolécules Max Mousseron; UMR CNRS-UM-ENSCM 5247, UFR des Sciences Pharmaceutiques et Biologiques; 15 Avenue Charles Flahault 34093 Montpellier Cedex 5 France
| | - Matthieu Simon
- Institut des Biomolécules Max Mousseron; UMR CNRS-UM-ENSCM 5247, UFR des Sciences Pharmaceutiques et Biologiques; 15 Avenue Charles Flahault 34093 Montpellier Cedex 5 France
| | - Jean Martinez
- Institut des Biomolécules Max Mousseron; UMR CNRS-UM-ENSCM 5247, UFR des Sciences Pharmaceutiques et Biologiques; 15 Avenue Charles Flahault 34093 Montpellier Cedex 5 France
| | | | - Young Kee Kang
- Department of Chemistry; Chungbuk National University, Cheongju; Chungbuk 28644 Republic of Korea
| | - Emmanuel Wenger
- Laboratoire de Cristallographie, Résonance Magnétique et Modélisation; Université de Lorraine, CNRS, UMR 7036; Nancy France
| | - Francois Hoh
- Centre de Biochimie Structurale, CNRS UMR 5048-INSERM 1054; University of Montpellier; Montpellier France
| | - Nicolas Masurier
- Institut des Biomolécules Max Mousseron; UMR CNRS-UM-ENSCM 5247, UFR des Sciences Pharmaceutiques et Biologiques; 15 Avenue Charles Flahault 34093 Montpellier Cedex 5 France
| | - Ludovic T. Maillard
- Institut des Biomolécules Max Mousseron; UMR CNRS-UM-ENSCM 5247, UFR des Sciences Pharmaceutiques et Biologiques; 15 Avenue Charles Flahault 34093 Montpellier Cedex 5 France
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23
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Teo CY, Tejo BA, Leow ATC, Salleh AB, Abdul Rahman MB. Novel furan-containing peptide-based inhibitors of protein arginine deiminase type IV (PAD4). Chem Biol Drug Des 2017; 90:1134-1146. [PMID: 28581157 DOI: 10.1111/cbdd.13033] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Revised: 03/13/2017] [Accepted: 05/15/2017] [Indexed: 01/12/2023]
Abstract
Protein arginine deiminase type IV (PAD4) is responsible for the posttranslational conversion of peptidylarginine to peptidylcitrulline. Citrullinated protein is the autoantigen in rheumatoid arthritis, and therefore, PAD4 is currently a promising therapeutic target for the disease. Recently, we reported the importance of the furan ring in the structure of PAD4 inhibitors. In this study, the furan ring was incorporated into peptides to act as the "warhead" of the inhibitors for PAD4. IC50 studies showed that the furan-containing peptide-based inhibitors were able to inhibit PAD4 to a better extent than the furan-containing small molecules that were previously reported. The best peptide-based inhibitor inhibited PAD4 reversibly and competitively with an IC50 value of 243.2 ± 2.4 μm. NMR spectroscopy and NMR-restrained molecular dynamic simulations revealed that the peptide-based inhibitor had a random structure. Molecular docking studies showed that the peptide-based inhibitor entered the binding site and interacted with the essential amino acids involved in the catalytic activity. The peptide-based inhibitor could be further developed into a therapeutic drug for rheumatoid arthritis.
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Affiliation(s)
- Chian Ying Teo
- Department of Pharmaceutical Chemistry, School of Pharmacy, International Medical University, Kuala Lumpur, Malaysia
| | - Bimo A Tejo
- Faculty of Applied Sciences, UCSI University, Kuala Lumpur, Malaysia
| | - Adam Thean Chor Leow
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Malaysia
| | - Abu Bakar Salleh
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Malaysia
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24
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Pal S, Ghosh U, Singh G, Alam F, Singh S, Chopra S, Sinha S, Ampapathi RS, Chakraborty TK. Synthesis, Conformational Studies and Biological Profiles of Tetrahydrofuran Amino-Acid-Containing Cationic Antitubercular Peptides. ASIAN J ORG CHEM 2017. [DOI: 10.1002/ajoc.201700183] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Sudip Pal
- Medicinal & Process Chemistry Division; CSIR-Central Drug Research Institute; Lucknow 226031 India
| | - Uttam Ghosh
- Department of Organic Chemistry; Indian Institute of Science; Bangalore 560012 India
| | - Gajendra Singh
- NMR Research Centre, Division of SAIF; CSIR-Central Drug Research Institute; Lucknow 226031 India
- Academy of Scientific and Innovative Research; New Delhi 110001 India
| | - Faiyaz Alam
- NMR Research Centre, Division of SAIF; CSIR-Central Drug Research Institute; Lucknow 226031 India
- Academy of Scientific and Innovative Research; New Delhi 110001 India
| | - Shyam Singh
- Biochemistry Division; CSIR-Central Drug Research Institute; Lucknow 226031 India
| | - Sidharth Chopra
- Microbiology Division; CSIR-Central Drug Research Institute; Lucknow 226031 India
| | - Sudhir Sinha
- Biochemistry Division; CSIR-Central Drug Research Institute; Lucknow 226031 India
| | - Ravi Sankar Ampapathi
- NMR Research Centre, Division of SAIF; CSIR-Central Drug Research Institute; Lucknow 226031 India
- Academy of Scientific and Innovative Research; New Delhi 110001 India
| | - Tushar Kanti Chakraborty
- Medicinal & Process Chemistry Division; CSIR-Central Drug Research Institute; Lucknow 226031 India
- Department of Organic Chemistry; Indian Institute of Science; Bangalore 560012 India
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25
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Interaction of aurein 1.2 and its analogue with DPPC lipid bilayer. J Biol Phys 2017; 43:127-137. [PMID: 28130642 DOI: 10.1007/s10867-016-9438-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Accepted: 12/14/2016] [Indexed: 01/17/2023] Open
Abstract
Antibacterial peptides have potential as novel therapeutic agents for bacterial infections. Aurein 1.2 is one of the smallest antibacterial peptides extracted from an anuran. LLAA is a more active analogue of aurein 1.2. Antibacterial peptides usually accomplish their function by interacting with bacterial membrane selectively. In this study, we tried to find the reasons for the stronger antibacterial activity of LLAA compared with aurein 1.2. For this purpose, the interaction of aurein 1.2 and LLAA with dipalmitoylphosphatidylcholine (DPPC) was investigated by molecular dynamics (MD) simulation. In addition, the structure of peptides and their antibacterial activity were investigated by circular dichroism (CD) and dilution test method, respectively. MD results showed that LLAA is more flexible compared with aurein 1.2. Furthermore, LLAA loses its structure more than aurein 1.2 in the DPPC bilayer. A higher amount of water molecules penetrate into bilayer in the presence of LLAA relative to aurein 1.2. According to the antibacterial result that indicated LLAA is remarkably more active than aurein 1.2, it can be concluded that flexibility of the peptide is a determining factor in antibacterial activity. Probably, flexibility of the peptides facilitates formation of effective pores in the lipid bilayer.
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26
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Kang YK, Yoo IK. Propensities of peptides containing the Asn-Gly segment to form β-turn and β-hairpin structures. Biopolymers 2016; 105:653-64. [DOI: 10.1002/bip.22863] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Revised: 04/21/2016] [Accepted: 04/25/2016] [Indexed: 12/28/2022]
Affiliation(s)
- Young Kee Kang
- Department of Chemistry and BK21 PLUS Research Team; Chungbuk National University; Cheongju Chungbuk 28644 Republic of Korea
| | - In Kee Yoo
- Department of Chemistry and BK21 PLUS Research Team; Chungbuk National University; Cheongju Chungbuk 28644 Republic of Korea
- LG Research Park, LG Household & Health Care; Daejeon 34114 Republic of Korea
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27
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Chalyk BA, Kandaurova IY, Hrebeniuk KV, Manoilenko OV, Kulik IB, Iminov RT, Kubyshkin V, Tverdokhlebov AV, Ablialimov OK, Mykhailiuk PK. A base promoted multigram synthesis of aminoisoxazoles: valuable building blocks for drug discovery and peptidomimetics. RSC Adv 2016. [DOI: 10.1039/c6ra02365g] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
An easy access to a large panel of aminoisoxazoles starting from commonly available amino acids.
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Affiliation(s)
| | | | | | | | - Irene B. Kulik
- Institute of Bioorganic Chemistry & Petrochemistry
- NAS of Ukraine
- Kyiv 02660
- Ukraine
| | | | | | | | | | - Pavel K. Mykhailiuk
- Enamine Ltd
- 01103 Kyiv
- Ukraine
- Department of Chemistry
- Taras Shevchenko National University of Kyiv
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28
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Kang YK, Park HS. Propensities to form the β-turn and β-hairpin structures of d-Pro-Gly and Aib- d-Ala containing peptides: a computational study. NEW J CHEM 2016. [DOI: 10.1039/c6nj00614k] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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29
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Pal S, Ghosh U, Ampapathi RS, Chakraborty TK. Recent Studies on Gramicidin S Analog Structure and Antimicrobial Activity. ACTA ACUST UNITED AC 2015. [DOI: 10.1007/7081_2015_188] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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30
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Kang YK, Park HS. Hairpin formation promoted by the heterochiral dinipecotic acid segment: A DFT study. Biopolymers 2015; 103:609-17. [PMID: 26015319 DOI: 10.1002/bip.22687] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2015] [Revised: 05/22/2015] [Accepted: 05/22/2015] [Indexed: 01/16/2023]
Abstract
Conformational preferences for the turn and β-hairpin structures of Ala-based peptides [Ac-Ala(n)-(R)-Nip-(S)-Nip-Ala(n)-X (n = 0-2; X = NHMe or NMe2)] containing nipecotic acid (Nip) residues were carried out using the density functional M06-2X and the implicit solvation model SMD in CH2Cl2 and/or water. The turn structure of the (R)-Nip-(S)-Nip segment with a C10 H-bond between two terminal groups was found to be most preferred (populated at 98.9%) in CH2Cl2; this structure is consistent with IR and (1)H NMR results. The stabilities of the β-hairpins containing the (R)-Nip-(S)-Nip segment as a turn motif relative to the extended structures increased with peptide sequence length. The relative strengths of the H-bonds between the carbonyl oxygen and the amide hydrogen appeared to be responsible for stabilizing the turn and β-hairpin structures in CH2Cl2. In addition, the (R)-Nip-(S)-Nip segment exhibited the capability to be incorporated into one of the two β-turn motifs of gramicidin S (GS). The structure of this GS derivative (GS-Nip2 ) was generally similar to the native peptide but was less hydrophobic and it is therefore expected to exhibit lower hemolytic activity; however, further experiments are needed to evaluate its antimicrobial activity. The structure of GS-Nip2 was somewhat more flexible than GS in solvents of higher polarity. Thus, our calculated results regarding the turn and β-hairpin motifs of the (R)-Nip-(S)-Nip segment indicate that this structure might be useful for the design of bioactive macrocyclic peptides containing β-hairpin mimics as well as binding epitopes in protein-protein and protein-nucleic acid recognitions.
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Affiliation(s)
- Young Kee Kang
- Department of Chemistry and BK21 PLUS Research Team, Chungbuk National University, Cheongju, Chungbuk, 362-763, Republic of Korea
| | - Hae Sook Park
- Department of Nursing, Cheju Halla University, Cheju, 690-708, Republic of Korea
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31
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Beno BR, Yeung KS, Bartberger MD, Pennington LD, Meanwell NA. A Survey of the Role of Noncovalent Sulfur Interactions in Drug Design. J Med Chem 2015; 58:4383-438. [DOI: 10.1021/jm501853m] [Citation(s) in RCA: 468] [Impact Index Per Article: 52.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Brett R. Beno
- Department of Computer-Assisted Drug Design, Bristol-Myers Squibb Research and Development, 5 Research Parkway Wallingford Connecticut 06492, United States
| | - Kap-Sun Yeung
- Department of Discovery Chemistry, Bristol-Myers Squibb Research and Development, 5 Research Parkway Wallingford Connecticut 06492, United States
| | - Michael D. Bartberger
- Department of Therapeutic Discovery, Amgen Inc., One Amgen Center Drive Thousand Oaks California 91320, United States
| | - Lewis D. Pennington
- Department of Therapeutic Discovery, Amgen Inc., One Amgen Center Drive Thousand Oaks California 91320, United States
| | - Nicholas A. Meanwell
- Department of Discovery Chemistry, Bristol-Myers Squibb Research and Development, 5 Research Parkway Wallingford Connecticut 06492, United States
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32
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Mathieu L, Bonnel C, Masurier N, Maillard LT, Martinez J, Lisowski V. Cross-Claisen Condensation ofN-Fmoc-Amino Acids - A Short Route to Heterocyclic γ-Amino Acids. European J Org Chem 2015. [DOI: 10.1002/ejoc.201500012] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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33
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34
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Abstract
Oligo-γ-peptides based on 2-aminocyclopentylacetic acid (γAc5a) with a cyclopentyl constraint on the Cβ–Cγ bond and homochiral (1S,2S) configurations preferentially adopt the right-handed 14-helix foldamers in the gas phase and in solution.
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Affiliation(s)
- Young Kee Kang
- Department of Chemistry and BK21 PLUS Research Team
- Chungbuk National University
- Cheongju
- Republic of Korea
| | - Joo Yun Lee
- Department of Chemistry and BK21 PLUS Research Team
- Chungbuk National University
- Cheongju
- Republic of Korea
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35
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Lee JH, Park HS, Kang YK. Conformational preferences of β-sheet structures in cyclopropane-containing γ-peptides. NEW J CHEM 2015. [DOI: 10.1039/c5nj00545k] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Oligo-γ-peptides based on 2-(aminomethyl)cyclopropanecarboxylic acid (γAmc3) with a cyclopropane constraint on the Cα–Cβ bond preferentially formed parallel β-sheets rather than antiparallel β-sheets due to the stronger N–H⋯O H-bonds in the parallel conformation.
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Affiliation(s)
- Ji Hyang Lee
- Department of Chemistry and BK21 PLUS Research Team
- Chungbuk National University
- Cheongju
- Republic of Korea
| | - Hae Sook Park
- Department of Nursing
- Cheju Halla University
- Cheju 690-708
- Republic of Korea
| | - Young Kee Kang
- Department of Chemistry and BK21 PLUS Research Team
- Chungbuk National University
- Cheongju
- Republic of Korea
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36
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Pal S, Singh G, Singh S, Tripathi JK, Ghosh JK, Sinha S, Ampapathi RS, Chakraborty TK. Tetrahydrofuran amino acid-containing gramicidin S analogues with improved biological profiles. Org Biomol Chem 2015; 13:6789-802. [DOI: 10.1039/c5ob00622h] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Replacement of thed-Phe-Pro units of GS with novel C6-Bn-substituted tetrahydrofuran amino acid minimized its cytotoxicity while preserving its antimicrobial activity, with a few analogs showing selective anti-TB activity as well.
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Affiliation(s)
- Sudip Pal
- Medicinal and Process Chemistry Division
- CSIR-Central Drug Research Institute
- Lucknow-226031
- India
| | - Gajendra Singh
- Centre for Nuclear Magnetic Resonance
- SAIF
- CSIR-Central Drug Research Institute
- Lucknow-226031
- India
| | - Shyam Singh
- Biochemistry Division
- CSIR-Central Drug Research Institute
- Lucknow-226031
- India
| | - Jitendra Kumar Tripathi
- Molecular and Structural Biology Division
- CSIR-Central Drug Research Institute
- Lucknow-226031
- India
| | - Jimut Kanti Ghosh
- Molecular and Structural Biology Division
- CSIR-Central Drug Research Institute
- Lucknow-226031
- India
| | - Sudhir Sinha
- Biochemistry Division
- CSIR-Central Drug Research Institute
- Lucknow-226031
- India
| | - Ravi Sankar Ampapathi
- Centre for Nuclear Magnetic Resonance
- SAIF
- CSIR-Central Drug Research Institute
- Lucknow-226031
- India
| | - Tushar Kanti Chakraborty
- Medicinal and Process Chemistry Division
- CSIR-Central Drug Research Institute
- Lucknow-226031
- India
- Department of Organic Chemistry
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37
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Nair RV, Baravkar SB, Ingole TS, Sanjayan GJ. Synthetic turn mimetics and hairpin nucleators: Quo Vadimus? Chem Commun (Camb) 2014; 50:13874-84. [PMID: 25051222 DOI: 10.1039/c4cc03114h] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Structural mimicry of peptides has witnessed perceptible progress in the last three decades. Reverse turn and β-hairpin units are the smallest secondary structural motifs that are some of the most scrutinized functional cores of peptides and proteins. The practice of mimicking, without altering the function of the bioactive core, ranges from conformational locking of the basic skeleton to total replacement of structural architecture using synthetic analogues. Development of heterogeneous backbones--using unnatural residues in place of natural ones--has broadened further opportunities for efficient structural rigidification. This feature article endeavours to trail the path of progress achieved hitherto and envisage the possibilities that lie ahead in the development of synthetic turn mimetics and hairpin nucleators.
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Affiliation(s)
- Roshna V Nair
- Division of Organic Chemistry, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411 008, India.
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