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Wang Z, Lu J, Hao A, Xing P. Odd-Even Law Mediated Supramolecular Chirality of Luminescent Dipeptides for Chiroptical Energy Transfer. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024:e2405698. [PMID: 39263767 DOI: 10.1002/smll.202405698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2024] [Revised: 08/27/2024] [Indexed: 09/13/2024]
Abstract
Inherent luminescent short peptides essentially provide opportunities to rationally manipulate supramolecular chirality and chiral luminescence. Herein, a facile protocol to construct a series of naphthalimide-appended dipeptides is reported that show ultrasound wave-activated supramolecular chirality regulated by odd-even law. Naphthalimide luminophores are conjugated to the dipeptide skeleton with variable alkyl spacers. The presence of tyrosine interferes the kinetic aggregation into achiral nanoparticles without chirality transfer to supramolecular scale. However, ultrasound treatment initiates the nanoparticle-to-helix transition accompanied with the appeared chiral optics, including Cotton effect and circularly polarized luminescence (CPL). The supramolecular chiral parameters, including handedness of helices and chiroptical behaviors, follow the odd-even law of alkyl spacers in dipeptides bearing non-substituted naphthalimides. The amine-substitution boosted the quantum yields of dipeptide whereas no odd-even effect. The two types of dipeptides constituted ideal energy transfer pairs that enable the efficient energy transfer as well as the transportation of odd-even law to dipeptides containing substituted naphthalimides. This work sheds light on the construction of luminescent dipeptides with applications in precise control over chirality transportation and chiral luminescence.
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Affiliation(s)
- Zhuoer Wang
- Key Laboratory of Colloid and Interface Chemistry of Ministry of Education, School of Chemistry and Chemical Engineering, Shandong University, Jinan, 250100, P. R. China
| | - Jiahui Lu
- Key Laboratory of Colloid and Interface Chemistry of Ministry of Education, School of Chemistry and Chemical Engineering, Shandong University, Jinan, 250100, P. R. China
| | - Aiyou Hao
- Key Laboratory of Colloid and Interface Chemistry of Ministry of Education, School of Chemistry and Chemical Engineering, Shandong University, Jinan, 250100, P. R. China
| | - Pengyao Xing
- Key Laboratory of Colloid and Interface Chemistry of Ministry of Education, School of Chemistry and Chemical Engineering, Shandong University, Jinan, 250100, P. R. China
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2
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Tomohara K, Kusaba S, Masui M, Uchida T, Nambu H, Nose T. Ammonium carboxylates in the ammonia-Ugi reaction: one-pot synthesis of α,α-disubstituted amino acid derivatives including unnatural dipeptides. Org Biomol Chem 2024; 22:6999-7005. [PMID: 39118586 DOI: 10.1039/d4ob00924j] [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: 08/10/2024]
Abstract
Despite the remarkable developments of the Ugi reaction and its variants, the use of ammonia in the Ugi reaction has long been recognized as impractical and unsuccessful. Indeed, the ammonia-Ugi reaction often requires harsh reaction conditions, such as heating and microwave irradiation, and competes with the Passerini reaction, thereby resulting in low yields. This study describes a robust and practical ammonia-Ugi reaction protocol. Using originally prepared ammonium carboxylates in trifluoroethanol, the ammonia-Ugi reaction proceeded at room temperature in high yields and showed a broad substrate scope, thus synthesizing a variety of α,α-disubstituted amino acid derivatives, including unnatural dipeptides. The reaction required no condensing agents and proceeded without racemization of the chiral stereocenter of α-amino acids. Furthermore, using this protocol, we quickly synthesized a novel dipeptide, D-Leu-Aic-NH-CH2Ph(p-F), which exhibited a potent inhibitory activity against α-chymotrypsin with a Ki value of 0.091 μM.
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Affiliation(s)
- Keisuke Tomohara
- Faculty of Arts and Science, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, 819-0395, Japan
- Faculty and Graduate School of Pharmaceutical Science, Kyoto Pharmaceutical University, 1 Misasagishichono-cho, Yamashina-ku, Kyoto 607-8412, Japan.
| | - Satoru Kusaba
- Graduate School of Science, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, 819-0395, Japan.
| | - Mana Masui
- Faculty and Graduate School of Pharmaceutical Science, Kyoto Pharmaceutical University, 1 Misasagishichono-cho, Yamashina-ku, Kyoto 607-8412, Japan.
| | - Tatsuya Uchida
- Faculty of Arts and Science, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, 819-0395, Japan
- Graduate School of Science, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, 819-0395, Japan.
- International Institute for Carbon-Neutral Energy Research, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, 819-0395, Japan
| | - Hisanori Nambu
- Faculty and Graduate School of Pharmaceutical Science, Kyoto Pharmaceutical University, 1 Misasagishichono-cho, Yamashina-ku, Kyoto 607-8412, Japan.
| | - Takeru Nose
- Faculty of Arts and Science, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, 819-0395, Japan
- Graduate School of Science, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, 819-0395, Japan.
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3
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Biondi B, Formaggio F, Toniolo C, Peggion C, Crisma M. Isolated α-turns in peptides: a selected literature survey. J Pept Sci 2023:e3476. [PMID: 36603599 DOI: 10.1002/psc.3476] [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: 10/28/2022] [Revised: 12/21/2022] [Accepted: 12/26/2022] [Indexed: 01/07/2023]
Abstract
The results of classifying into various types the 68 examples of isolated α-turns in the X-ray diffraction crystal structures of peptides documented in the literature are presented and discussed in this review article. α-Turns characterized by the trans disposition of all ω torsion angles are common for the backbone linear peptides investigated. In contrast, the cis arrangement of the N-terminal (ωi + 1 ) torsion angle, among those generated by the three residues internal to the α-turn, is a peculiar feature of 65% of the cyclic peptides. Among linear and cyclic peptides featuring the all-trans disposition of the ω torsion angles, only one third of the α-turns display φ,ψ values not too far from those characterizing regular α-helices. In general, our findings, taken together, suggest that a significant conformational diversity is compatible with the formation of an intramolecularly H-bonded C13 -member pseudocycle (α-turn) in linear and cyclic peptides.
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Affiliation(s)
- Barbara Biondi
- CNR-Institute of Biomolecular Chemistry, Padova Unit, Padua, Italy
| | - Fernando Formaggio
- CNR-Institute of Biomolecular Chemistry, Padova Unit, Padua, Italy.,Department of Chemical Sciences, University of Padova, Padua, Italy
| | - Claudio Toniolo
- CNR-Institute of Biomolecular Chemistry, Padova Unit, Padua, Italy.,Department of Chemical Sciences, University of Padova, Padua, Italy
| | - Cristina Peggion
- CNR-Institute of Biomolecular Chemistry, Padova Unit, Padua, Italy.,Department of Chemical Sciences, University of Padova, Padua, Italy
| | - Marco Crisma
- CNR-Institute of Biomolecular Chemistry, Padova Unit, Padua, Italy
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4
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Ueda A, Makura Y, Kakazu S, Kato T, Umeno T, Hirayama K, Doi M, Oba M, Tanaka M. E-Selective Ring-Closing Metathesis in α-Helical Stapled Peptides Using Carbocyclic α,α-Disubstituted α-Amino Acids. Org Lett 2022; 24:1049-1054. [PMID: 35073100 DOI: 10.1021/acs.orglett.1c04256] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We present an E-selective ring-closing metathesis reaction in α-helical stapled peptides at positions i and i + 4. The use of two chiral carbocyclic α,α-disubstituted α-amino acids, (1S,3S)-Ac5c3OAll and (1R,3S)-Ac5c3OAll, provides a high E-selectivity of a ≤59:1 E:Z ratio, while mixtures with E:Z ratios of 2.1-0.5:1 were produced with standard acyclic (S)-(4-pentenyl)alanine amino acids. A stapled octapeptide composed of (1S,3S)- and (1R,3S)-Ac5c3OAll amino acids showed a right-handed α-helical crystal structure.
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Affiliation(s)
- Atsushi Ueda
- Graduate School of Biomedical Sciences, Nagasaki University, 1-14 Bunkyo-machi, Nagasaki 852-8521, Japan
| | - Yui Makura
- Graduate School of Biomedical Sciences, Nagasaki University, 1-14 Bunkyo-machi, Nagasaki 852-8521, Japan
| | - Sana Kakazu
- Graduate School of Biomedical Sciences, Nagasaki University, 1-14 Bunkyo-machi, Nagasaki 852-8521, Japan
| | - Takuma Kato
- Faculty of Pharmacy, Osaka Medical and Pharmaceutical University, Osaka 569-1094, Japan
| | - Tomohiro Umeno
- Graduate School of Biomedical Sciences, Nagasaki University, 1-14 Bunkyo-machi, Nagasaki 852-8521, Japan
| | - Kazuhiro Hirayama
- Graduate School of Biomedical Sciences, Nagasaki University, 1-14 Bunkyo-machi, Nagasaki 852-8521, Japan
| | - Mitsunobu Doi
- Faculty of Pharmacy, Osaka Medical and Pharmaceutical University, Osaka 569-1094, Japan
| | - Makoto Oba
- Graduate School of Biomedical Sciences, Nagasaki University, 1-14 Bunkyo-machi, Nagasaki 852-8521, Japan
- Graduate School of Medicine, Kyoto Prefectural University of Medicine, Kyoto 606-0823, Japan
| | - Masakazu Tanaka
- Graduate School of Biomedical Sciences, Nagasaki University, 1-14 Bunkyo-machi, Nagasaki 852-8521, Japan
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5
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Gupta MK, Jena CK, Balachandra C, Sharma NK. Unusual Pseudopeptides: Syntheses and Structural Analyses of Ethylenediprolyl Peptides and Their Metal Complexes with Cu(II) Ion. J Org Chem 2021; 86:16327-16336. [PMID: 34783560 DOI: 10.1021/acs.joc.1c01676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The synthetic unnatural amino acids and their peptides as peptidomimetics have shown remarkable structural and functional properties. In the repertoire of synthetic peptides, pseudopeptides have emerged as attractive small peptidomimetics that are capable of forming the characteristic secondary structures in the solid/solution phase, as in natural peptides. This report describes the synthesis and structural analyses of novel pseudopeptides as ethylenediprolyl (etpro) tetra/hexapeptides, comprising a chiral diaminedicarboxylate scaffold. Their NMR and CD spectral analyses strongly support the formation of the β-turn-type structures in organic solvents (ACN/MeOH). Further, the single-crystal X-ray studies of tetrapseudopeptide confirm the formation of a unique self-assembly structure as β-strand type in the solid state through hydrogen bonding. Importantly, their diamine moiety influences the formation of Cu-complexes with Cu(II) ions. A tetrapseudopeptide monocarboxylate-Cu(II) complex forms the single crystal that is studied by the single-crystal X-ray diffractometer. The crystal structure of the tetrapseudopeptide-Cu(II) complex confirms the formation of the distorted square planar geometry structure, almost like the amyloid β(Aβ)-peptide-Cu(II) complex structural geometry. Hence, these etpro-pseudopeptides are emerging peptidomimatics that form β-turn types of structures and metal complexes mainly with Cu(II) ions. These molecules could be considered for the development of peptide-based catalysts and peptide-based therapeutic drug candidates.
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Affiliation(s)
- Manish K Gupta
- National Institute of Science Education and Research (NISER)-Bhubaneswar, Jatni Campus, Bhubaneswar 752050, India.,Homi Bhabha National Institute (HBNI), Mumbai 400094, India
| | - Chinmay K Jena
- National Institute of Science Education and Research (NISER)-Bhubaneswar, Jatni Campus, Bhubaneswar 752050, India.,Homi Bhabha National Institute (HBNI), Mumbai 400094, India
| | - Chenikkayala Balachandra
- National Institute of Science Education and Research (NISER)-Bhubaneswar, Jatni Campus, Bhubaneswar 752050, India.,Homi Bhabha National Institute (HBNI), Mumbai 400094, India
| | - Nagendra K Sharma
- National Institute of Science Education and Research (NISER)-Bhubaneswar, Jatni Campus, Bhubaneswar 752050, India.,Homi Bhabha National Institute (HBNI), Mumbai 400094, India
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6
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Adasme-Carreño F, Caballero J, Ireta J. PSIQUE: Protein Secondary Structure Identification on the Basis of Quaternions and Electronic Structure Calculations. J Chem Inf Model 2021; 61:1789-1800. [PMID: 33769809 DOI: 10.1021/acs.jcim.0c01343] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The secondary structure is important in protein structure analysis, classification, and modeling. We have developed a novel method for secondary structure assignment, termed PSIQUE, based on the potential energy surface (PES) of polyalanine obtained using an infinitely long chain model and density functional theory calculations. First, uniform protein segments are determined in terms of a difference of quaternions between neighboring amino acids along the protein backbone. Then, the identification of the secondary structure motifs is carried out based on the minima found in the PES. PSIQUE shows good agreement with other secondary structure assignment methods. However, it provides better discrimination of subtle secondary structures (e.g., helix types) and termini and produces more uniform segments while also accounting for local distortions. Overall, PSIQUE provides a precise and reliable assignment of secondary structures, so it should be helpful for the detailed characterization of the protein structure.
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Affiliation(s)
- Francisco Adasme-Carreño
- Departamento de Bioinformática, Centro de Bioinformática, Simulación y Modelado (CBSM), Facultad de Ingeniería, Universidad de Talca, Campus Talca, 1 Poniente No. 1141, Casilla 721, Talca 3460000, Chile
| | - Julio Caballero
- Departamento de Bioinformática, Centro de Bioinformática, Simulación y Modelado (CBSM), Facultad de Ingeniería, Universidad de Talca, Campus Talca, 1 Poniente No. 1141, Casilla 721, Talca 3460000, Chile
| | - Joel Ireta
- Departamento de Química, División de Ciencias Básicas e Ingeniería, Universidad Autónoma Metropolitana-Iztapalapa, A.P. 55-534, Ciudad de Mexico 09340, Mexico
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7
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Di Silvio S, Bologna F, Milli L, Giuri D, Zanna N, Castellucci N, Monari M, Calvaresi M, Górecki M, Angelici G, Tomasini C, Pescitelli G. Elusive π-helical peptide foldamers spotted by chiroptical studies. Org Biomol Chem 2020; 18:865-877. [PMID: 31845697 DOI: 10.1039/c9ob02313e] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
A series of oligomers containing alternate l-Ala and pGlu (pyroglutamic acid) both in the L and D form have been prepared and conformationally investigated by X-ray, NMR, UV/ECD, IR/VCD and molecular modelling. X-ray diffraction analysis was possible for the shortest oligomers LL-1 and LD-1. Molecular dynamics simulations of the oligomers demonstrated that the energy landscapes of the LL-series are broad. In contrast, the energy landscapes of the LD-series are characterized by well-defined minima corresponding to specific conformational structures. A single well-defined minimum exists in the energy landscape of the largest oligomer LD-8, corresponding to a precise conformation, characterized by i + 5 →i N-HO[double bond, length as m-dash]C hydrogen bonds, typical of a π-helix. ECD and VCD spectra were measured to identify the chiroptical profiles of the oligomers. The most striking element in the ECD spectra of the LD-series is their exceptionally strong intensity, which confirms that these polypeptides attain a high degree of helical order. VCD spectra for the LD-series are well reproduced by frequency calculations when π-helix folds are employed as input structures, suggesting that a symmetrical VCD couplet around 1720 cm-1 can be taken as the VCD signature of π-helices.
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Affiliation(s)
- Sergio Di Silvio
- Dipartimento di Chimica "Giacomo Ciamician", Alma Mater Studiorum Università di Bologna, Via F. Selmi 2, 40126 Bologna, Italy.
| | - Fabio Bologna
- Dipartimento di Chimica "Giacomo Ciamician", Alma Mater Studiorum Università di Bologna, Via F. Selmi 2, 40126 Bologna, Italy.
| | - Lorenzo Milli
- Dipartimento di Chimica "Giacomo Ciamician", Alma Mater Studiorum Università di Bologna, Via F. Selmi 2, 40126 Bologna, Italy.
| | - Demetra Giuri
- Dipartimento di Chimica "Giacomo Ciamician", Alma Mater Studiorum Università di Bologna, Via F. Selmi 2, 40126 Bologna, Italy.
| | - Nicola Zanna
- Dipartimento di Chimica "Giacomo Ciamician", Alma Mater Studiorum Università di Bologna, Via F. Selmi 2, 40126 Bologna, Italy.
| | - Nicola Castellucci
- Dipartimento di Chimica "Giacomo Ciamician", Alma Mater Studiorum Università di Bologna, Via F. Selmi 2, 40126 Bologna, Italy.
| | - Magda Monari
- Dipartimento di Chimica "Giacomo Ciamician", Alma Mater Studiorum Università di Bologna, Via F. Selmi 2, 40126 Bologna, Italy.
| | - Matteo Calvaresi
- Dipartimento di Chimica "Giacomo Ciamician", Alma Mater Studiorum Università di Bologna, Via F. Selmi 2, 40126 Bologna, Italy.
| | - Marcin Górecki
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via Moruzzi 13, 56124 Pisa, Italy. and Institute of Organic Chemistry, Polish Academy of Sciences, Warsaw 01-224, Poland
| | - Gaetano Angelici
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via Moruzzi 13, 56124 Pisa, Italy.
| | - Claudia Tomasini
- Dipartimento di Chimica "Giacomo Ciamician", Alma Mater Studiorum Università di Bologna, Via F. Selmi 2, 40126 Bologna, Italy.
| | - Gennaro Pescitelli
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via Moruzzi 13, 56124 Pisa, Italy.
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