1
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Wasko J, Wolszczak M, Zajaczkowska Z, Dudek M, Kolesinska B. Human serum albumin as a potential drug delivery system for N-methylated hot spot insulin analogs inhibiting hormone aggregation. Bioorg Chem 2024; 143:107104. [PMID: 38194903 DOI: 10.1016/j.bioorg.2024.107104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 12/20/2023] [Accepted: 01/03/2024] [Indexed: 01/11/2024]
Abstract
The purpose of this study was to investigate whether Human Serum Albumin (HSA) can bind N-methylated analogs of hot spots of native insulin. Three N-methylated derivatives of the A13-A19 fragment of native insulin were used: L(N-Me)YQLENY (1), LYQ(N-Me)LENY (2), and L(N-Me)YQ(N-Me)LENY (3). The studied N-methylated insulin fragments possess inhibiting potential against hormone aggregation. A variety of research techniques, including spectroscopic methods and microscopy assays, were used to study the interaction of HSA with the N-methylated insulin fragments. Based on spectroscopic measurements with Congo Red and Thioflavin T, all the analyzed N-methylated peptides were able to interact with the HSA surface. The CD spectrum registered for HSA in the presence of L(N-Me)YQLENY showed the smallest content of α-helix conformation, indicating the most compact HSA structure. Based on the results of MST, the dissociation constants (Kd) for complexes of HSA and peptides 1-3 were 19.2 nM (complex 1), 15.6 nM (complex 2), and 8.07 nM (complex 3). Microscopy assays, dynamic light scattering measurements as well as computer simulation of protein-ligand interaction also confirmed the possibility of docking the N-methylated inhibitors within HSA.
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Affiliation(s)
- Joanna Wasko
- Institute of Organic Chemistry, Faculty of Chemistry, Lodz University of Technology, Zeromskiego 116, Poland.
| | - Marian Wolszczak
- Institute of Applied Radiation Chemistry, Faculty of Chemistry, Lodz University of Technology, Wroblewskiego 15, Poland.
| | - Zuzanna Zajaczkowska
- Institute of Organic Chemistry, Faculty of Chemistry, Lodz University of Technology, Zeromskiego 116, Poland.
| | - Mariusz Dudek
- Institute of Materials Science and Engineering, The Faculty of Mechanical Engineering, Lodz University of Technology, Stefanowskiego 1/15, Poland.
| | - Beata Kolesinska
- Institute of Organic Chemistry, Faculty of Chemistry, Lodz University of Technology, Zeromskiego 116, Poland.
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2
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Crone KK, Jomori T, Miller FS, Gralnick JA, Elias MH, Freeman MF. RiPP enzyme heterocomplex structure-guided discovery of a bacterial borosin α- N-methylated peptide natural product. RSC Chem Biol 2023; 4:804-816. [PMID: 37799586 PMCID: PMC10549244 DOI: 10.1039/d3cb00093a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 08/18/2023] [Indexed: 10/07/2023] Open
Abstract
Amide peptide backbone methylation is a characteristic post-translational modification found in a family of ribosomally synthesized and post-translationally modified peptide natural products (RiPPs) called borosins. Previously, we bioinformatically identified >1500 putative borosin pathways in bacteria; however, none of the pathways were associated with a known secondary metabolite. Through in-depth characterization of a borosin pathway in Shewanella oneidensis MR-1, we have now identified a bacterially derived borosin natural product named Shewanellamide A. Borosin identification was facilitated by the creation and analysis of a series of precursor variants and crystallographic interrogation of variant precursor and methyltransferase complexes. Along with assaying two proteases from S. oneidensis, probable boundaries for proteolytic maturation of the metabolite were projected and confirmed via comparison of S. oneidensis knockout and overexpression strains. All in all, the S. oneidensis natural product was found to be a 16-mer linear peptide featuring two backbone methylations, establishing Shewanellamide A as one of the few borosin metabolites yet identified, and the first from bacteria.
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Affiliation(s)
- K K Crone
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota - Twin Cities St. Paul 55108 USA
| | - T Jomori
- The BioTechnology Institute, University of Minnesota - Twin Cities St. Paul 55108 USA
| | - F S Miller
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota - Twin Cities St. Paul 55108 USA
| | - J A Gralnick
- The BioTechnology Institute, University of Minnesota - Twin Cities St. Paul 55108 USA
- Department of Plant and Microbial Biology, University of Minnesota - Twin Cities St. Paul 55108 USA
| | - M H Elias
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota - Twin Cities St. Paul 55108 USA
- The BioTechnology Institute, University of Minnesota - Twin Cities St. Paul 55108 USA
| | - M F Freeman
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota - Twin Cities St. Paul 55108 USA
- The BioTechnology Institute, University of Minnesota - Twin Cities St. Paul 55108 USA
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3
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Rajewski BH, Wright MM, Gerrein TA, Del Valle JR. N-Aminoglycine and Its Derivatives Stabilize PPII Secondary Structure. Org Lett 2023; 25:4366-4370. [PMID: 37276840 DOI: 10.1021/acs.orglett.3c01502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The identification of unnatural residues that stabilize polyproline type 2 (PPII) folds can aid in the design of peptidomimetics targeting PPII-binding domains. Here, we examine the impact of peptide backbone N-amination on PPII helix stability and find N-aminoglycine (aGly) to be an effective PPII promoter. Further derivatization of an aGly-containing peptide affords N'-alkylated analogues with increased helical propensity. Backbone N-amination of glycine represents a convenient approach to stabilize PPII conformation and allows for the diversity-oriented synthesis of optimally constrained folds.
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Affiliation(s)
- Benjamin H Rajewski
- Department of Chemistry & Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Madison M Wright
- Department of Chemistry & Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Taylor A Gerrein
- Department of Chemistry & Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Juan R Del Valle
- Department of Chemistry & Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, United States
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4
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Calabretta LO, Yang J, Raines RT. N α -Methylation of arginine: Implications for cell-penetrating peptides. J Pept Sci 2022; 29:e3468. [PMID: 36494904 PMCID: PMC10073267 DOI: 10.1002/psc.3468] [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: 09/29/2022] [Revised: 12/05/2022] [Accepted: 12/06/2022] [Indexed: 12/14/2022]
Abstract
The field of cell-penetrating peptides is dominated by the use of oligomers of arginine residues. Octanol-water partitioning in the presence of an anionic lipid is a validated proxy for cell-penetrative efficacy. Here, we add one, two, or three N-methyl groups to Ac-Arg-NH2 and examine the effects on octanol-water partitioning. In the absence of an anionic lipid, none of these arginine derivatives can be detected in the octanol layer. In the presence of sodium dodecanoate, however, increasing N-methylation correlates with increasing partitioning into octanol, which is predictive of higher cell-penetrative ability. We then evaluated fully Nα -methylated oligoarginine peptides and observed an increase in their cellular penetration compared with canonical oligoarginine peptides in some contexts. These findings indicate that a simple modification, Nα -methylation, can enhance the performance of cell-penetrating peptides.
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Affiliation(s)
- Lindsey O Calabretta
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Jinyi Yang
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Ronald T Raines
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
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5
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Gupta N, Wilczek M, Dobrzycki L, Pulka-Ziach K. Structural Consequences of N‐methylation of N‐terminus in Oligourea Foldamers. Chempluschem 2022; 87:e202200199. [DOI: 10.1002/cplu.202200199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 07/22/2022] [Indexed: 11/11/2022]
Affiliation(s)
- Naveen Gupta
- University of Warsaw: Uniwersytet Warszawski Faculty of Chemistry Pastuera 1 02-093 Warsaw POLAND
| | - Marcin Wilczek
- University of Warsaw: Uniwersytet Warszawski Faculty of Chemistry Pasteura 1 02-093 Warsaw POLAND
| | - Lukasz Dobrzycki
- University of Warsaw: Uniwersytet Warszawski Faculty of Chemistry Zwirki i Wigury 101 02-089 Warsaw POLAND
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6
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Yokomine M, Morimoto J, Fukuda Y, Shiratori Y, Kuroda D, Ueda T, Takeuchi K, Tsumoto K, Sando S. Oligo(N-methylalanine) as a Peptide-Based Molecular Scaffold with a Minimal Structure and High Density of Functionalizable Sites. Angew Chem Int Ed Engl 2022; 61:e202200119. [PMID: 35088931 DOI: 10.1002/anie.202200119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Indexed: 12/26/2022]
Abstract
Functionalizable synthetic molecules with nanometer sizes and defined shapes in water are useful as molecular scaffolds to mimic the functions of biomacromolecules and develop chemical tools for manipulating biomacromolecules. Herein, we propose oligo(N-methylalanine) (oligo-NMA) as a peptide-based molecular scaffold with a minimal structure and a high density of functionalizable sites. Oligo-NMA forms a defined shape in water without hydrogen-bonding networks or ring constraints, which enables the molecule to act as a scaffold with minimal atomic composition. Furthermore, functional groups can be readily introduced on the nitrogens and α-carbons of oligo-NMA. Computational and NMR spectroscopic analysis suggested that the backbone structure of oligo-NMA is not largely affected by functionalization. Moreover, the usefulness of oligo-NMA was demonstrated by the design of protein ligands. The ease of synthesis, minimal structure, and high functionalization flexibility makes oligo-NMA a useful scaffold for chemical and biological applications.
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Affiliation(s)
- Marin Yokomine
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Jumpei Morimoto
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan.,Precursory Research for Embryonic Science and Technology (PRESTO), Japan Science and Technology Agency (JST), 4-1-8 Honcho, Kawaguchi, Saitama, 332-0012, Japan
| | - Yasuhiro Fukuda
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Yota Shiratori
- Department of Bioengineering, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Daisuke Kuroda
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan.,Department of Bioengineering, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Takumi Ueda
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Koh Takeuchi
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Kouhei Tsumoto
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan.,Department of Bioengineering, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan.,Institute of Medical Science, The University of Tokyo, 4-6-1, Shirokanedai, Minato-ku, Tokyo, 108-8639, Japan
| | - Shinsuke Sando
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan.,Department of Bioengineering, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
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7
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Yokomine M, Morimoto J, Fukuda Y, Shiratori Y, Kuroda D, Ueda T, Takeuchi K, Tsumoto K, Sando S. Oligo(N‐methylalanine) as a Peptide‐Based Molecular Scaffold with a Minimal Structure and High Density of Functionalizable Sites. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202200119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Marin Yokomine
- The University of Tokyo: Tokyo Daigaku Department of Chemistry and Biotechnology 7-3-1 Hongo, Bunkyo-ku 113-8656 Tokyo JAPAN
| | - Jumpei Morimoto
- The University of Tokyo: Tokyo Daigaku Chemistry and Biotechnology 7-3-1 Hongo, Bunkyo-ku 113-8656 Tokyo JAPAN
| | - Yasuhiro Fukuda
- The University of Tokyo: Tokyo Daigaku Chemistry and Biotechnolgy 7-3-1 Hongo, Bunkyo-ku 113-8656 Tokyo JAPAN
| | - Yota Shiratori
- The University of Tokyo: Tokyo Daigaku Chemistry and Biotechnology 7-3-1 Hongo, Bunkyo-ku 113-8656 Tokyo JAPAN
| | - Daisuke Kuroda
- The University of Tokyo: Tokyo Daigaku Bioengineering 7-3-1 Hongo, Bunkyo-ku 113-8656 Tokyo JAPAN
| | - Takumi Ueda
- The University of Tokyo: Tokyo Daigaku Graduate school of pharmaceutical sciences 7-3-1 Hongo, Bunkyo-ku 113-0033 Tokyo JAPAN
| | - Koh Takeuchi
- The University of Tokyo: Tokyo Daigaku Graduate school of pharmaceutical sciences 7-3-1 Hongo, Bunkyo-ku 113-0033 Tokyo JAPAN
| | - Kouhei Tsumoto
- The University of Tokyo: Tokyo Daigaku Institute of medical science 4-6-1, Shirokanedai, Minato-ku 108-8639 Tokyo JAPAN
| | - Shinsuke Sando
- The University of Tokyo Department of Chemistry and Biotechnology, Graduate School of Engineering Hongo 7-3-1, Bunkyo-ku 113-8656 Tokyo JAPAN
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8
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Morimoto J, Sando S. Peptoids with Substituents on the Backbone Carbons as Conformationally Constrained Synthetic Oligoamides. J SYN ORG CHEM JPN 2020. [DOI: 10.5059/yukigoseikyokaishi.78.1076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
| | - Shinsuke Sando
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo
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9
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Suo R, Watanabe R, Takada K, Suzuki T, Oikawa H, Itoi S, Sugita H, Matsunaga S. Heptavalinamide A, an Extensively N-Methylated Linear Nonapeptide from a Cyanobacterium Symploca sp. and Development of a Highly Sensitive Analysis of N,N-Dimethylvaline by LCMS. Org Lett 2020; 22:1254-1258. [DOI: 10.1021/acs.orglett.9b04420] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Rei Suo
- Laboratory of Aquatic Natural Products Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Bunkyo-ku, Tokyo 113-8657, Japan
- College of Bioresource Sciences, Nihon University, 1866 Kameino, Fujisawa, Kanagawa 252-0880, Japan
| | - Ryuichi Watanabe
- National Research Institute of Fisheries Science, 2-12-4 Fukuura,
Kanazawa-ku, Yokohama, Kanagawa 236-8648, Japan
| | - Kentaro Takada
- School of Marine Biosciences, Kitasato University, 1-15-1 Kitasato, Minami-ku, Sagamihara, Kanagawa 252-0373, Japan
| | - Toshiyuki Suzuki
- National Research Institute of Fisheries Science, 2-12-4 Fukuura,
Kanazawa-ku, Yokohama, Kanagawa 236-8648, Japan
| | - Hiroshi Oikawa
- National Research Institute of Fisheries Science, 2-12-4 Fukuura,
Kanazawa-ku, Yokohama, Kanagawa 236-8648, Japan
| | - Shiro Itoi
- College of Bioresource Sciences, Nihon University, 1866 Kameino, Fujisawa, Kanagawa 252-0880, Japan
| | - Haruo Sugita
- College of Bioresource Sciences, Nihon University, 1866 Kameino, Fujisawa, Kanagawa 252-0880, Japan
| | - Shigeki Matsunaga
- Laboratory of Aquatic Natural Products Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Bunkyo-ku, Tokyo 113-8657, Japan
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10
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Morimoto J, Fukuda Y, Kuroda D, Watanabe T, Yoshida F, Asada M, Nakamura T, Senoo A, Nagatoishi S, Tsumoto K, Sando S. A Peptoid with Extended Shape in Water. J Am Chem Soc 2019; 141:14612-14623. [DOI: 10.1021/jacs.9b04371] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Jumpei Morimoto
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Yasuhiro Fukuda
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Daisuke Kuroda
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
- Department of Bioengineering, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Takumu Watanabe
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Fumihiko Yoshida
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Mizue Asada
- Department of Materials Molecular Science, Institute for Molecular Science, 38 Nishigo-naka, Myodaiji, Okazaki 444-8585, Japan
| | - Toshikazu Nakamura
- Department of Materials Molecular Science, Institute for Molecular Science, 38 Nishigo-naka, Myodaiji, Okazaki 444-8585, Japan
| | - Akinobu Senoo
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Satoru Nagatoishi
- Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
| | - Kouhei Tsumoto
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
- Department of Bioengineering, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
- Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
| | - Shinsuke Sando
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
- Department of Bioengineering, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
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11
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Lee KJ, Sable GA, Shin MK, Lim HS. Oligomers of α-ABpeptoid/β 3 -peptide hybrid. Biopolymers 2019; 110:e23289. [PMID: 31150108 DOI: 10.1002/bip.23289] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 05/08/2019] [Accepted: 05/14/2019] [Indexed: 12/20/2022]
Abstract
Peptoids, oligomers of N-substituted glycines, have been attracting increasing interest due to their advantageous properties as peptidomimetics. However, due to the lack of chiral centers and amide hydrogen atoms, peptoids, in general, do not form folding structures except that they have α-chiral side chains. We have recently developed "peptoids with backbone chirality" as a new class of peptoid foldamers called α-ABpeptoids and demonstrated that they could have folding conformations owing to the methyl groups on chiral α-carbons in the backbone structure. Here we report α-ABpeptoid/β3 -peptide oligomers as a unique peptidomimetic structure with a heterogeneous backbone. This hybrid structure contains a mixed α-ABpeptoid and β3 -peptide residues arranged in an alternate manner. These α-ABpeptoid/β3 -peptide oligomers could form intramolecular hydrogen bonding and have better cell permeability relative to pure peptide sequences. These oligomers were shown to adopt ordered folding structures based on circular dichroism studies. Overall, α-ABpeptoid/β3 -peptide oligomers may represent a novel class of peptidomimetic foldamers and will find a wide range of applications in biomedical and material sciences.
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Affiliation(s)
- Kang Ju Lee
- Department of Chemistry and Division of Advanced Material Science, Pohang University of Science and Technology (POSTECH), Pohang, South Korea
| | - Ganesh A Sable
- Department of Chemistry and Division of Advanced Material Science, Pohang University of Science and Technology (POSTECH), Pohang, South Korea
| | - Min-Kyung Shin
- Department of Chemistry and Division of Advanced Material Science, Pohang University of Science and Technology (POSTECH), Pohang, South Korea
| | - Hyun-Suk Lim
- Department of Chemistry and Division of Advanced Material Science, Pohang University of Science and Technology (POSTECH), Pohang, South Korea
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12
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He Y, Hoi H, Abraham S, Montemagno CD. Highly permeable biomimetic reverse osmosis membrane with amphiphilic peptide stabilized aquaporin as water filtering agent. J Appl Polym Sci 2017. [DOI: 10.1002/app.46169] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Yuan He
- Ingenuity Lab; 11421 Saskatchewan Drive NW, Edmonton Alberta T6G 2M9 Canada
- Department of Chemical Materials Engineering; University of Alberta; Edmonton Alberta T6G 2V4 Canada
| | - Hiofan Hoi
- Ingenuity Lab; 11421 Saskatchewan Drive NW, Edmonton Alberta T6G 2M9 Canada
- Department of Chemical Materials Engineering; University of Alberta; Edmonton Alberta T6G 2V4 Canada
| | - Sinoj Abraham
- Ingenuity Lab; 11421 Saskatchewan Drive NW, Edmonton Alberta T6G 2M9 Canada
- Department of Chemical Materials Engineering; University of Alberta; Edmonton Alberta T6G 2V4 Canada
| | - Carlo D. Montemagno
- Ingenuity Lab; 11421 Saskatchewan Drive NW, Edmonton Alberta T6G 2M9 Canada
- Department of Chemical Materials Engineering; University of Alberta; Edmonton Alberta T6G 2V4 Canada
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13
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Sarnowski MP, Kang CW, Elbatrawi YM, Wojtas L, Del Valle JR. Peptide N-Amination Supports β-Sheet Conformations. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201609395] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Matthew P. Sarnowski
- Department of Chemistry; University of South Florida; 4202 E. Fowler Avenue Tampa FL 33620 USA
| | - Chang Won Kang
- Department of Chemistry; University of South Florida; 4202 E. Fowler Avenue Tampa FL 33620 USA
| | - Yassin M. Elbatrawi
- Department of Chemistry; University of South Florida; 4202 E. Fowler Avenue Tampa FL 33620 USA
| | - Lukasz Wojtas
- Department of Chemistry; University of South Florida; 4202 E. Fowler Avenue Tampa FL 33620 USA
| | - Juan R. Del Valle
- Department of Chemistry; University of South Florida; 4202 E. Fowler Avenue Tampa FL 33620 USA
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14
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Sarnowski MP, Kang CW, Elbatrawi YM, Wojtas L, Del Valle JR. Peptide N-Amination Supports β-Sheet Conformations. Angew Chem Int Ed Engl 2017; 56:2083-2086. [DOI: 10.1002/anie.201609395] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2016] [Revised: 12/12/2016] [Indexed: 12/12/2022]
Affiliation(s)
- Matthew P. Sarnowski
- Department of Chemistry; University of South Florida; 4202 E. Fowler Avenue Tampa FL 33620 USA
| | - Chang Won Kang
- Department of Chemistry; University of South Florida; 4202 E. Fowler Avenue Tampa FL 33620 USA
| | - Yassin M. Elbatrawi
- Department of Chemistry; University of South Florida; 4202 E. Fowler Avenue Tampa FL 33620 USA
| | - Lukasz Wojtas
- Department of Chemistry; University of South Florida; 4202 E. Fowler Avenue Tampa FL 33620 USA
| | - Juan R. Del Valle
- Department of Chemistry; University of South Florida; 4202 E. Fowler Avenue Tampa FL 33620 USA
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15
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Selective homocoupling of phenylboronic acid over supported Pd nanoparticle in biphase solvent. CATAL COMMUN 2017. [DOI: 10.1016/j.catcom.2016.11.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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16
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Lee KJ, Lee WS, Yun H, Hyun YJ, Seo CD, Lee CW, Lim HS. Oligomers of N-Substituted β(2)-Homoalanines: Peptoids with Backbone Chirality. Org Lett 2016; 18:3678-81. [PMID: 27404658 DOI: 10.1021/acs.orglett.6b01726] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
A new class of peptoid-based peptidomimetics composed of oligomers of N-substituted β(2)-homoalanines is reported. Design, solid-phase synthesis, and preliminary circular dichroism studies of oligomers of N-alkylated β(2)-homoalanines consisting of up to 8-mers are described.
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Affiliation(s)
- Kang Ju Lee
- Departments of Chemistry and Advanced Material Science, Pohang University of Science and Technology (POSTECH) , Pohang 37673, South Korea
| | - Woo Sirl Lee
- Departments of Chemistry and Advanced Material Science, Pohang University of Science and Technology (POSTECH) , Pohang 37673, South Korea
| | - Hyosuk Yun
- Department of Chemistry, Chonnam National University , Gwangju 61186, South Korea
| | - Yu-Jung Hyun
- Departments of Chemistry and Advanced Material Science, Pohang University of Science and Technology (POSTECH) , Pohang 37673, South Korea
| | - Chang Deok Seo
- Departments of Chemistry and Advanced Material Science, Pohang University of Science and Technology (POSTECH) , Pohang 37673, South Korea
| | - Chul Won Lee
- Department of Chemistry, Chonnam National University , Gwangju 61186, South Korea
| | - Hyun-Suk Lim
- Departments of Chemistry and Advanced Material Science, Pohang University of Science and Technology (POSTECH) , Pohang 37673, South Korea.,Department of Biochemistry and Molecular Biology, Indiana University School of Medicine , Indianapolis, Indiana 46202, United States
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17
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Doran TM, Sarkar M, Kodadek T. Chemical Tools To Monitor and Manipulate Adaptive Immune Responses. J Am Chem Soc 2016; 138:6076-94. [PMID: 27115249 PMCID: PMC5332222 DOI: 10.1021/jacs.6b02954] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Methods to monitor and manipulate the immune system are of enormous clinical interest. For example, the development of vaccines represents one of the earliest and greatest accomplishments of the biomedical research enterprise. More recently, drugs capable of "reawakening" the immune system to cancer have generated enormous excitement. But, much remains to be done. All drugs available today that manipulate the immune system cannot distinguish between "good" and "bad" immune responses and thus drive general and systemic immune suppression or activation. Indeed, with the notable exception of vaccines, our ability to monitor and manipulate antigen-specific immune responses is in its infancy. Achieving this finer level of control would be highly desirable. For example, it might allow the pharmacological editing of pathogenic immune responses without restricting the ability of the immune system to defend against infection. On the diagnostic side, a method to comprehensively monitor the circulating, antigen-specific antibody population could provide a treasure trove of clinically useful biomarkers, since many diseases expose the immune system to characteristic molecules that are deemed foreign and elicit the production of antibodies against them. This Perspective will discuss the state-of-the-art of this area with a focus on what we consider seminal opportunities for the chemistry community to contribute to this important field.
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Affiliation(s)
- Todd M. Doran
- Departments of Chemistry & Cancer Biology, The Scripps Research
Institute, 130 Scripps Way, Jupiter, FL 33458
| | - Mohosin Sarkar
- Departments of Chemistry & Cancer Biology, The Scripps Research
Institute, 130 Scripps Way, Jupiter, FL 33458
| | - Thomas Kodadek
- Departments of Chemistry & Cancer Biology, The Scripps Research
Institute, 130 Scripps Way, Jupiter, FL 33458
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18
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Pels K, Kodadek T. Solid-phase synthesis of diverse peptide tertiary amides by reductive amination. ACS COMBINATORIAL SCIENCE 2015; 17:152-5. [PMID: 25695359 DOI: 10.1021/acscombsci.5b00007] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The synthesis of libraries of conformationally constrained peptide-like oligomers is an important goal in combinatorial chemistry. In this regard an attractive building block is the N-alkylated peptide, also known as a peptide tertiary amide (PTA). PTAs are conformationally constrained because of allylic 1,3 strain interactions. We report here an improved synthesis of these species on solid supports through the use of reductive amination chemistry using amino acid-terminated, bead-displayed oligomers and diverse aldehydes. The utility of this chemistry is demonstrated by the synthesis of a library of 10,000 mixed peptoid-PTA oligomers.
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Affiliation(s)
- Kevin Pels
- Departments of Chemistry
and Cancer Biology, The Scripps Research Institute, 130 Scripps
Way, Jupiter, Florida 33458, United States
| | - Thomas Kodadek
- Departments of Chemistry
and Cancer Biology, The Scripps Research Institute, 130 Scripps
Way, Jupiter, Florida 33458, United States
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19
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Gao Y, Amar S, Pahwa S, Fields G, Kodadek T. Rapid lead discovery through iterative screening of one bead one compound libraries. ACS COMBINATORIAL SCIENCE 2015; 17:49-59. [PMID: 25434974 PMCID: PMC4294594 DOI: 10.1021/co500154e] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Primary hits that arise from screening one bead one compound (OBOC) libraries against a target of interest rarely have high potency. However, there has been little work focused on the development of an efficient workflow for primary hit improvement. In this study, we show that by characterizing the binding constants for all of the hits that arise from a screen, structure-activity relationship (SAR) data can be obtained to inform the design of "derivative libraries" of a primary hit that can then be screened under more demanding conditions to obtain improved compounds. Here, we demonstrate the rapid improvement of a primary hit against matrix metalloproteinase-14 using this approach.
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Affiliation(s)
- Yu Gao
- Departments
of Chemistry and Cancer Biology The Scripps Research Institutem 130
Scripps Way, Jupiter, Florida 33458, United States
| | - Sabrina Amar
- Torrey Pines Institute for Molecular Studies 11350 SW Village Parkway, Port St. Lucie, Florida 34987, United States
| | - Sonia Pahwa
- Torrey Pines Institute for Molecular Studies 11350 SW Village Parkway, Port St. Lucie, Florida 34987, United States
| | - Gregg Fields
- Torrey Pines Institute for Molecular Studies 11350 SW Village Parkway, Port St. Lucie, Florida 34987, United States
| | - Thomas Kodadek
- Departments
of Chemistry and Cancer Biology The Scripps Research Institutem 130
Scripps Way, Jupiter, Florida 33458, United States
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20
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Ochiai H, Komuro T, Hiramatsu H. The Extinction Coefficient of N-Methylated Aβ30–40 Depends on the Position of N-Methylation. CHEM LETT 2015. [DOI: 10.1246/cl.140851] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Hironori Ochiai
- Graduate School of Pharmaceutical Sciences, Tohoku University
| | - Tomoyuki Komuro
- Graduate School of Pharmaceutical Sciences, Tohoku University
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21
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Unudurthi SD, Hotta K, Kim CY. Engineering the polyproline II propensity of a class II major histocompatibility complex ligand peptide. ACS Chem Biol 2013; 8:2383-7. [PMID: 24001370 DOI: 10.1021/cb400594q] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Our immune system constantly samples peptides found inside the body as a means to detect foreign pathogens, infected cells, and tumorous cells. T cells, which carry out the critical task of distinguishing self from nonself peptides, can only survey peptides that are presented by the major histocompatibility complex protein. We investigated how the secondary structure of a peptide, namely, the polyproline II helix content, influences major histocompatibility complex binding. We synthesized 12 analogues of the wheat gluten derived α-I-gliadin peptide and tested their binding to the celiac disease associated HLA-DQ2 protein. Our analogue library represents a broad spectrum of polyproline II propensities, ranging from random coil structure to high polyproline II helix content. Overall, there was no noticeable correlation between the peptide polyproline II helix content and HLA-DQ2 binding. One analogue peptide, which has low polyproline II helix content, showed a 4.5-fold superior binding compared to native α-I-gliadin.
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Affiliation(s)
- Sathya Dev Unudurthi
- Department of Biological
Sciences, National University of Singapore, 14 Science Drive 4, 117543 Singapore
| | - Kinya Hotta
- Department of Biological
Sciences, National University of Singapore, 14 Science Drive 4, 117543 Singapore
| | - Chu-Young Kim
- Department of Biological
Sciences, National University of Singapore, 14 Science Drive 4, 117543 Singapore
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22
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Engineered nanostructured β-sheet peptides protect membrane proteins. Nat Methods 2013; 10:759-61. [PMID: 23817067 PMCID: PMC3753066 DOI: 10.1038/nmeth.2533] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2012] [Accepted: 05/06/2013] [Indexed: 12/12/2022]
Abstract
We have designed β-strand peptides (BP) that stabilize integral membrane proteins (IMP). BPs self-assemble in solution as filaments and become restructured upon association with IMPs; the resulting IMP/BP complexes resist aggregation when diluted in detergent-free buffer and are examined as stable, single particles with low detergent background by electron microscopy. This enables clear visualization of a spectrum of flexible conformations in the highly dynamic ATP-binding cassette (ABC) transporter MsbA.
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23
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Gao Y, Kodadek T. Synthesis and screening of stereochemically diverse combinatorial libraries of peptide tertiary amides. CHEMISTRY & BIOLOGY 2013; 20:360-9. [PMID: 23521794 PMCID: PMC3885906 DOI: 10.1016/j.chembiol.2013.01.013] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2012] [Revised: 12/16/2012] [Accepted: 01/04/2013] [Indexed: 02/03/2023]
Abstract
Large combinatorial libraries of N-substituted peptides would be an attractive source of protein ligands, because these compounds are known to be conformationally constrained, whereas standard peptides or peptoids are conformationally mobile. Here, we report an efficient submonomer solid-phase synthetic route to these compounds and demonstrate that it can be used to create high quality libraries. A model screening experiment and analysis of the hits indicates that the rigidity afforded by the stereocenters is critical for high affinity binding.
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Affiliation(s)
- Yu Gao
- Scripps Florida (130 Scripps way, Jupiter, FL, 33458)
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24
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Pratim Bose P, Chatterjee U, Nerelius C, Govender T, Norström T, Gogoll A, Sandegren A, Göthelid E, Johansson J, Arvidsson PI. Poly-N-methylated amyloid beta-peptide (Abeta) C-terminal fragments reduce Abeta toxicity in vitro and in Drosophila melanogaster. J Med Chem 2010; 52:8002-9. [PMID: 19908889 DOI: 10.1021/jm901092h] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Alzheimer's disease (AD), an age related neurodegenerative disorder, threatens to become a major health-economic problem. Assembly of 40- or 42-residue amyloid beta-peptides (Abeta) into neurotoxic oligo-/polymeric beta-sheet structures is an important pathogenic feature in AD, thus, inhibition of this process has been explored to prevent or treat AD. The C-terminal part plays an important role in Abeta aggregation, but most Abeta aggregation inhibitors have targeted the central region around residues 16-23. Herein, we synthesized hexapeptides with varying extents of N-methylation based on residues 32-37 of Abeta, to target its C-terminal region. We measured the peptides' abilities to retard beta-sheet and fibril formation of Abeta and to reduce Abeta neurotoxicity. A penta-N-methylated peptide was more efficient than peptides with 0, 2, or 3 N-methyl groups. This penta-N-methylated peptide moreover increased life span and locomotor activity in Drosophila melanogaster flies overexpressing human Abeta(1-42).
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Affiliation(s)
- Partha Pratim Bose
- Department of Biochemistry and Organic Chemistry, Uppsala University, Uppsala, Sweden
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25
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Sharif S, Singh M, Kim SJ, Schaefer J. Staphylococcus aureus peptidoglycan tertiary structure from carbon-13 spin diffusion. J Am Chem Soc 2009; 131:7023-30. [PMID: 19419167 DOI: 10.1021/ja808971c] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The cell-wall peptidoglycan of Staphylococcus aureus is a heterogeneous, highly cross-linked polymer of unknown tertiary structure. We have partially characterized this structure by measuring spin diffusion from (13)C labels in pentaglycyl cross-linking segments to natural-abundance (13)C in the surrounding intact cell walls. The measurements were performed using a version of centerband-only detection of exchange (CODEX). The cell walls were isolated from S. aureus grown in media containing [1-(13)C]glycine. The CODEX spin diffusion rates established that the pentaglycyl bridge of one peptidoglycan repeat unit of S. aureus is within 5 A of the glycan chain of another repeat unit. This surprising proximity is interpreted in terms of a model for the peptidoglycan lattice in which all peptide stems in a plane perpendicular to the glycan mainchain are parallel to one another.
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Affiliation(s)
- Shasad Sharif
- Department of Chemistry, Washington University, St. Louis, Missouri 63130, USA
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26
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Lu C, DesMarteau DD. Construction of N-1H,1H-perfluoroalkylated peptide bonds. Chem Commun (Camb) 2008:208-10. [DOI: 10.1039/b712617d] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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27
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Moretto A, Crisma M, Kaptein B, Broxterman QB, Toniolo C. N-methylation of N(alpha)-acylated, fully C(alpha)-methylated, linear, folded peptides: synthetic and conformational aspects. Biopolymers 2007; 84:553-65. [PMID: 16802303 DOI: 10.1002/bip.20560] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Peptides characterized by single or multiple N-methylated, C(alpha)-trisubstituted (e.g., protein) amino acids are of great interest in medicinal chemistry. Several naturally occurring peptides, remarkably stable to enzymatic attacks, are based on N-methylated residues. The classical conditions (CH(3)I/Ag(2)O in DMF, 24 h, room temperature) for N-methylation of the peptide function are useful tools for distinguishing solvent exposed from intramolecularly H-bonded -CO-NH- groups in peptides. In this work we have extended this reaction to N(alpha)-acylated, linear peptides based exclusively on helicogenic C(alpha)-tetrasubstituted alpha-amino acids, e.g., Aib (alpha-aminoisobutyric acid) or (alphaMe)Nva (C(alpha)-methyl norvaline) residues. Under the experimental conditions used, only amide monomethylation (on the N-terminal, acylated, residue) takes place. Methylation of internal peptide groups linking two C(alpha)-tetrasubstituted residues was not observed. Our FT-IR absorption, NMR, and X-ray diffraction investigations support the view that the beta-turn and 3(10)-helical conformations preferred by the original peptides are not dramatically perturbed in the derivatives monomethylated at position 1. In particular, the tertiary amide bonds are trans. Conversely, the packing modes in the crystals are strongly influenced by the reduction of the number of H-bonding donors. The MeXxx-Xxx peptide bond is readily disrupted under mild acidic conditions.
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Affiliation(s)
- Alessandro Moretto
- Institute of Biomolecular Chemistry, CNR, Department of Chemistry, University of Padova, 35131 Padova, Italy
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