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Yin J, Birman VB. Phenazine-Based Oligomers as Redox-Responsive Molecular Actuators. J Org Chem 2022; 87:15744-15753. [PMID: 36354745 DOI: 10.1021/acs.joc.2c01445] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Nanosized butterfly-coil foldamers containing alternating phenazine-1,6-dicarboxamide and 2,5-dialkoxyterephthalamide moieties have been demonstrated to undergo extension-contraction in response to changing their oxidation state. Both the chemical (catalytic hydrogenation/aerial oxidation) and electrochemical versions of this process have been shown to be clean and fully reversible.
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Affiliation(s)
- Jingwei Yin
- Washington University Department of Chemistry, Campus Box 1134, One Brookings Drive, Saint Louis, Missouri 63130, United States
| | - Vladimir B Birman
- Washington University Department of Chemistry, Campus Box 1134, One Brookings Drive, Saint Louis, Missouri 63130, United States
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2
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Cardoso MH, Chan LY, Cândido ES, Buccini DF, Rezende SB, Torres MDT, Oshiro KGN, Silva ÍC, Gonçalves S, Lu TK, Santos NC, de la Fuente-Nunez C, Craik DJ, Franco OL. An N-capping asparagine-lysine-proline (NKP) motif contributes to a hybrid flexible/stable multifunctional peptide scaffold. Chem Sci 2022; 13:9410-9424. [PMID: 36093022 PMCID: PMC9383710 DOI: 10.1039/d1sc06998e] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 07/10/2022] [Indexed: 11/21/2022] Open
Abstract
Structural diversity drives multiple biological activities and mechanisms of action in linear peptides. Here we describe an unusual N-capping asparagine-lysine-proline (NKP) motif that confers a hybrid multifunctional scaffold to a computationally designed peptide (PaDBS1R7). PaDBS1R7 has a shorter α-helix segment than other computationally designed peptides of similar sequence but with key residue substitutions. Although this motif acts as an α-helix breaker in PaDBS1R7, the Asn5 presents exclusive N-capping effects, forming a belt to establish hydrogen bonds for an amphipathic α-helix stabilization. The combination of these different structural profiles was described as a coil/N-cap/α-helix scaffold, which was also observed in diverse computational peptide mutants. Biological studies revealed that all peptides displayed antibacterial activities. However, only PaDBS1R7 displayed anticancer properties, eradicated Pseudomonas aeruginosa biofilms, decreased bacterial counts by 100-1000-fold in vivo, reduced lipopolysaccharide-induced macrophages stress, and stimulated fibroblast migration for wound healing. This study extends our understanding of an N-capping NKP motif to engineering hybrid multifunctional peptide drug candidates with potent anti-infective and immunomodulatory properties.
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Affiliation(s)
- Marlon H Cardoso
- S-Inova Biotech, Programa de Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco Avenida Tamandaré 6000 Campo Grande - MS 79117900 Brazil
- Centro de Análises Proteômicas e Bioquímicas, Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília SGAN 916 Módulo B, Asa Norte, Brasília - DF 70790160 Brazil
- Programa de Pós-Graduação em Patologia Molecular, Faculdade de Medicina, Universidade de Brasília, Campus Darcy Ribeiro Asa Norte Brasília - DF 70910900 Brazil
- Instituto de Biociências (INBIO), Universidade Federal de Mato Grosso do Sul, Cidade Universitária 79070900 Campo Grande Mato Grosso do Sul Brazil
| | - Lai Y Chan
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland Brisbane QLD, 4072 Australia
| | - Elizabete S Cândido
- S-Inova Biotech, Programa de Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco Avenida Tamandaré 6000 Campo Grande - MS 79117900 Brazil
- Centro de Análises Proteômicas e Bioquímicas, Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília SGAN 916 Módulo B, Asa Norte, Brasília - DF 70790160 Brazil
| | - Danieli F Buccini
- S-Inova Biotech, Programa de Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco Avenida Tamandaré 6000 Campo Grande - MS 79117900 Brazil
| | - Samilla B Rezende
- S-Inova Biotech, Programa de Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco Avenida Tamandaré 6000 Campo Grande - MS 79117900 Brazil
| | - Marcelo D T Torres
- Machine Biology Group, Departments of Psychiatry and Microbiology, Institute for Biomedical Informatics, Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, Departments of Bioengineering and Chemical and Biomolecular Engineering, School of Engineering and Applied Science, Penn Institute for Computational Science, University of Pennsylvania Philadelphia Pennsylvania USA
| | - Karen G N Oshiro
- S-Inova Biotech, Programa de Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco Avenida Tamandaré 6000 Campo Grande - MS 79117900 Brazil
- Programa de Pós-Graduação em Patologia Molecular, Faculdade de Medicina, Universidade de Brasília, Campus Darcy Ribeiro Asa Norte Brasília - DF 70910900 Brazil
| | - Ítala C Silva
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa Lisbon Portugal
| | - Sónia Gonçalves
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa Lisbon Portugal
| | - Timothy K Lu
- Synthetic Biology Group, MIT Synthetic Biology Center, The Center for Microbiome Informatics and Therapeutics, Research Laboratory of Electronics, Department of Biological Engineering, Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology Cambridge - MA 02139 USA
| | - Nuno C Santos
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa Lisbon Portugal
| | - Cesar de la Fuente-Nunez
- Machine Biology Group, Departments of Psychiatry and Microbiology, Institute for Biomedical Informatics, Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, Departments of Bioengineering and Chemical and Biomolecular Engineering, School of Engineering and Applied Science, Penn Institute for Computational Science, University of Pennsylvania Philadelphia Pennsylvania USA
| | - David J Craik
- Institute for Molecular Bioscience, Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland Brisbane QLD, 4072 Australia
| | - Octávio L Franco
- S-Inova Biotech, Programa de Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco Avenida Tamandaré 6000 Campo Grande - MS 79117900 Brazil
- Centro de Análises Proteômicas e Bioquímicas, Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília SGAN 916 Módulo B, Asa Norte, Brasília - DF 70790160 Brazil
- Programa de Pós-Graduação em Patologia Molecular, Faculdade de Medicina, Universidade de Brasília, Campus Darcy Ribeiro Asa Norte Brasília - DF 70910900 Brazil
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3
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Nandi S, Sarkar R, Jaiswar A, Roy S, Haldar D. Miniature β-Hairpin Mimetic by Intramolecular Hydrogen Bond and C-H···π Interactions. ACS OMEGA 2022; 7:17245-17252. [PMID: 35647431 PMCID: PMC9134230 DOI: 10.1021/acsomega.2c01168] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Accepted: 04/28/2022] [Indexed: 06/15/2023]
Abstract
Canonically, protein β-hairpin motifs are stabilized by intramolecular hydrogen bonds. Here, we attempt to develop a rational design recipe for a miniature hairpin structure stabilized by hydrogen bonding as well as C-H···π interaction and try to understand how such a stabilization effect varies with different functional groups at each terminus. Database analysis shows that the α-amino acids with an aromatic side chain will not favor that kind of C-H···π stabilized hairpin structure. However, hybrid tripeptides with an N-terminal Boc-Trp-Aib corner residue and C-terminal aromatic ω-amino acids fold into the hairpin conformation with a central β-turn/open-turn that is reinforced by a C-H···π interaction. The CCDC database analysis further confirms that this C-H···π stabilized hairpin motif is general for Boc-protected tripeptides containing Aib in the middle and aromatic functionality at the C-terminus. The different α-amino acids like Leu/Ala/Phe/Pro/Ser at the N-terminus have a minor influence on the C-H···π interaction and stabilities of the folded structures in solid-state. However, the hybrid peptides exhibit different degrees of conformational heterogeneity both in the solid and solution phase, which is common for this kind of flexible small molecule. Conformational heterogeneity in the solution phase including the C-H···π stabilized β-hairpin structures are characterized by the molecular dynamics (MD) simulations explaining their plausible origin at an atomistic level.
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Affiliation(s)
- Sujay
Kumar Nandi
- Department
of Chemical Sciences, Indian Institute of
Science Education and Research Kolkata, Mohanpur , Nadia, West Bengal 741246, India
| | - Raju Sarkar
- Department
of Chemical Sciences, Indian Institute of
Science Education and Research Kolkata, Mohanpur , Nadia, West Bengal 741246, India
| | - Akhilesh Jaiswar
- Department
of Chemical Sciences, Indian Institute of
Science Education and Research Kolkata, Mohanpur , Nadia, West Bengal 741246, India
| | - Susmita Roy
- Department
of Chemical Sciences, Indian Institute of
Science Education and Research Kolkata, Mohanpur , Nadia, West Bengal 741246, India
| | - Debasish Haldar
- Department
of Chemical Sciences, Indian Institute of
Science Education and Research Kolkata, Mohanpur , Nadia, West Bengal 741246, India
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Sun XY, Zhong Y, Li YH, Miller DP, Buttan S, Wu XX, Zhang Y, Tang Q, Tan HW, Zhu J, Liu R, Zurek E, Lu ZL, Gong B. Reliable folding of hybrid tetrapeptides into short β-hairpins. CHINESE CHEM LETT 2022. [DOI: 10.1016/j.cclet.2021.06.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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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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Integration of [12]aneN3 and Acenaphtho[1,2-b]quinoxaline as non-viral gene vectors with two-photon property for enhanced DNA/siRNA delivery and bioimaging. Bioorg Chem 2021; 113:104983. [PMID: 34029935 DOI: 10.1016/j.bioorg.2021.104983] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 05/01/2021] [Accepted: 05/07/2021] [Indexed: 12/20/2022]
Abstract
Two-photon fluorescent Acenaphtho[1,2-b]quinoxaline (ANQ) and the hydrophilic di-(triazole-[12]aneN3) moieties were combined through an alkyl chain (ANQ-A-M) or a β-hairpin motif with two aromatic γ-amino acid residues (ANQ-H-M) to explore their capabilities for in vitro and in vivo gene delivery and tracing. ANQ-A-M and ANQ-H-M showed the same maximum absorption at 420 nm, and their fluorescent intensities around 650 nm were varied in different solvents and became poor in the protic solvents. Gel electrophoresis assays indicated that both compounds completely retarded the migration of pDNA at 20 μM in the presence of DOPE. However, the DNA condensation with ANQ-H-M was not reversible, and the particle size of the corresponding complexes were larger indicated from the SEM and DLS measurements. In vitro transfections indicated ANQ-A-M/DOPE achieved Luciferase and GFP expressions were to be 7.9- and 5.7-fold of those by Lipo2000 in A549 cells respectively. However, ANQ-H-M showed very poor transfection efficiency in Luciferase expression. With the help of single/two-photon fluorescence imaging it clearly demonstrated that the successful transfection of ANQ-A-M was attributed to its cellular uptake, apparent lysosomal escape, and reversible release of DNA; and the poor transfection of ANQ-H-M was resulted from the aggregation of the DNA complexes which prevented them from the cellular uptake, and also the strong binding ability which is not easy to release DNA. ANQ-A-M/DOPE also exhibited robust gene silencing (83% knockdown of Luciferase) and GFP expression (2.47-fold higher) efficiency compared with Lipo2000 in A549 and zebrafish, respectively. The work demonstrated that the linkage structure between fluorescent and di(triazole-[12]aneN3) played the important role for their gene delivery performance, and that ANQ-A-M represents a vector with the strong transfection efficiency in vitro and in vivo as well as the efficient real time bioimaging properties, which is potential for the development in biomedical research.
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Liu JY, Sun XY, Tang Q, Song JJ, Li XQ, Gong B, Liu R, Lu ZL. An unnatural tripeptide structure containing intramolecular double H-bonds mimics a turn hairpin conformation. Org Biomol Chem 2021; 19:4359-4363. [PMID: 33908557 DOI: 10.1039/d1ob00526j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
A series of unnatural tripeptides, each consisting of two aromatic γ-amino acid residues and an ϖ-amino acid residue, are designed to probe their folding into hairpin conformations. The ϖ-amino acid residues, with aliphatic or aromatic spacers of different sizes, serve as the loop of the hairpins. Studies based on one-dimensional (1D) 1H NMR performed at different concentrations, solvent polarity, and temperature, along with 2D-NMR studies, demonstrated that the doubly H-bonded aromatic γ-amino acid residues play important roles in driving these tripeptides into the hairpin conformation. The loop based on 5-aminovaleric acid, which offers a four-carbon (CH2)4 spacer, enhanced the stability of the corresponding hairpin, while loops having a shorter, a longer and a more rigid spacer disfavored the formation of the hairpins. Results from computational studies are in good agreement with the experimental observations. Furthermore, the crystal structure of peptide 1b revealed the expected hairpin conformation in the solid state. This turn motif, which contains H-bonded aromatic γ-amino acid residues as the core unit and an ϖ-amino acid residue serving as the loop, provides a new platform that can be used to obtain a variety of turn conformations by incorporating diverse amino acids into the loops.
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Affiliation(s)
- Jin-Yu Liu
- Key Laboratory of Radiopharmaceuticals, MOE; College of Chemistry, Beijing Normal University, Xinjiekouwai Street 19, Beijing 100875, China.
| | - Xue-Yi Sun
- Key Laboratory of Radiopharmaceuticals, MOE; College of Chemistry, Beijing Normal University, Xinjiekouwai Street 19, Beijing 100875, China.
| | - Quan Tang
- Key Laboratory of Radiopharmaceuticals, MOE; College of Chemistry, Beijing Normal University, Xinjiekouwai Street 19, Beijing 100875, China.
| | - Jun-Jie Song
- Key Laboratory of Radiopharmaceuticals, MOE; College of Chemistry, Beijing Normal University, Xinjiekouwai Street 19, Beijing 100875, China.
| | - Xiao-Qi Li
- Key Laboratory of Radiopharmaceuticals, MOE; College of Chemistry, Beijing Normal University, Xinjiekouwai Street 19, Beijing 100875, China.
| | - Bing Gong
- Department of Chemistry, The State University of New York at Buffalo, Buffalo, New York 14260, USA
| | - Rui Liu
- Key Laboratory of Radiopharmaceuticals, MOE; College of Chemistry, Beijing Normal University, Xinjiekouwai Street 19, Beijing 100875, China.
| | - Zhong-Lin Lu
- Key Laboratory of Radiopharmaceuticals, MOE; College of Chemistry, Beijing Normal University, Xinjiekouwai Street 19, Beijing 100875, China.
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Zhong Y, Tang Q, Miller DP, Zurek E, Liu R, Lu ZL, Gong B. Major Factors for the Persistent Folding of Hybrid α, β, γ-Hybrid Peptides Into Hairpins. Front Chem 2020; 8:530083. [PMID: 33134269 PMCID: PMC7550740 DOI: 10.3389/fchem.2020.530083] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 08/31/2020] [Indexed: 11/13/2022] Open
Abstract
Factors responsible for the persistent adoption of hairpin conformations by hybrid oligopeptides, each having a central β/α dipeptide segment flanked by aromatic γ-amino acid (γAr) residues, are probed. Our recent studies revealed that tetrapeptide 1 and 2, having central dipeptide segments consisting of β-alanine (β-Ala) and glycine (Gly), and L-β-homophenylalanine (L-β-homoPhe) and Gly residues, respectively, that are flanked by γAr residues, fold into well-defined, expanded β-turns with doubly H-bonded γAr residues. Replacing the γAr residues of 1 and 2 with L-Val and L-Leu residues results in tetrapetides 1 ' and 2 ' that fail to fold into defined conformations, which confirms the decisive role played by the H-bonded γAr residues in the promoting folding of 1 and 2. Attaching L-Val and L-Leu residues to the termini of 1 affords hexapeptide 1a. With an additional H-bond between its L-Val and L-Leu residues, peptide 1a folds into a hairpin with higher stability than that of 1, indicating that the expanded β-turn can nucleate and stabilize β-hairpin with longer β-strands. Attaching L-Val and L-Leu residues to the termini of 2 affords hexapeptide 2a. Substituting the L-β-homoPhe residue of 2a with a D-β-homoPhe residue gives hexapeptide 2b. Surprisingly, hexapeptide 2a fold into a hairpin showing the similar stability as those of tetrapeptides 1 and 2. Hexapeptide 2b, with its combination of a D-β-homoPhe residue and the L-Val/L-Leu pair, fold into a hairpin that is significantly more stable than the other hybrid peptides, demonstrating that a combination of hetero-chirality between the β-amino acid residue of the dipeptide loop and the α-amino acid residues of the β-strands enhances the stability of the resultant β-hairpin.
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Affiliation(s)
- Yulong Zhong
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, NY, United States
| | - Quan Tang
- College of Chemistry, Beijing Normal University, Beijing, China
| | - Daniel P. Miller
- Department of Chemistry, Hofstra University, Hempstead, NY, United States
| | - Eva Zurek
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, NY, United States
| | - Rui Liu
- College of Chemistry, Beijing Normal University, Beijing, China
| | - Zhong-Lin Lu
- College of Chemistry, Beijing Normal University, Beijing, China
| | - Bing Gong
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, NY, United States
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