1
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Just D, Palivec V, Bártová K, Bednárová L, Pazderková M, Císařová I, Martinez-Seara H, Jahn U. Foldamers controlled by functional triamino acids: structural investigation of α/γ-hybrid oligopeptides. Commun Chem 2024; 7:114. [PMID: 38796536 PMCID: PMC11128005 DOI: 10.1038/s42004-024-01201-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 05/14/2024] [Indexed: 05/28/2024] Open
Abstract
Peptide-like foldamers controlled by normal amide backbone hydrogen bonding have been extensively studied, and their folding patterns largely rely on configurational and conformational constraints induced by the steric properties of backbone substituents at appropriate positions. In contrast, opportunities to influence peptide secondary structure by functional groups forming individual hydrogen bond networks have not received much attention. Here, peptide-like foldamers consisting of alternating α,β,γ-triamino acids 3-amino-4-(aminomethyl)-2-methylpyrrolidine-3-carboxylate (AAMP) and natural amino acids glycine and alanine are reported, which were obtained by solution phase peptide synthesis. They form ordered secondary structures, which are dominated by a three-dimensional bridged triazaspiranoid-like hydrogen bond network involving the non-backbone amino groups, the backbone amide hydrogen bonds, and the relative configuration of the α,β,γ-triamino and α-amino acid building blocks. This additional stabilization leads to folding in both nonpolar organic as well as in aqueous environments. The three-dimensional arrangement of the individual foldamers is supported by X-ray crystallography, NMR spectroscopy, chiroptical methods, and molecular dynamics simulations.
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Affiliation(s)
- David Just
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo náměstí 2, 16610, Prague 6, Czech Republic
| | - Vladimír Palivec
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo náměstí 2, 16610, Prague 6, Czech Republic
| | - Kateřina Bártová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo náměstí 2, 16610, Prague 6, Czech Republic
| | - Lucie Bednárová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo náměstí 2, 16610, Prague 6, Czech Republic
| | - Markéta Pazderková
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo náměstí 2, 16610, Prague 6, Czech Republic
| | - Ivana Císařová
- Department of Inorganic Chemistry, Faculty of Science, Charles University in Prague, Hlavova 2030/8, 12843, Prague 2, Czech Republic
| | - Hector Martinez-Seara
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo náměstí 2, 16610, Prague 6, Czech Republic.
| | - Ullrich Jahn
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo náměstí 2, 16610, Prague 6, Czech Republic.
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2
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Ma X, Beard AM, Burgess SA, Darlak M, Newman JA, Nogle LM, Pietrafitta MJ, Smith DA, Wang X, Yue L. General Synthesis of Conformationally Constrained Noncanonical Amino Acids with C( sp3)-Rich Benzene Bioisosteres. J Org Chem 2024; 89:5010-5018. [PMID: 38532573 DOI: 10.1021/acs.joc.4c00225] [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: 03/28/2024]
Abstract
Recent years have seen novel modalities emerge for the treatment of human diseases resulting in an increase in beyond rule of 5 (bRo5) chemical matter. As a result, synthetic innovations aiming to enable rapid access to complex bRo5 molecular entities have become increasingly valuable for medicinal chemists' toolkits. Herein, we report the general synthesis of a new class of noncanonical amino acids (ncAA) with a cyclopropyl backbone to achieve conformational constraint and bearing C(sp3)-rich benzene bioisosteres. We also demonstrate preliminary studies toward utilities of these ncAA as building blocks for medicinal chemistry research.
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Affiliation(s)
- Xiaoshen Ma
- Department of Discovery Chemistry, Merck & Co., Inc., 33 Ave. Louis Pasteur, Boston, Massachusetts 02215, United States
| | - Adam M Beard
- Department of Discovery Chemistry, Merck & Co., Inc., 33 Ave. Louis Pasteur, Boston, Massachusetts 02215, United States
| | - Samantha A Burgess
- Analytical Research & Development, Merck & Co., Inc., 33 Ave. Louis Pasteur, Boston, Massachusetts 02215, United States
| | - Miroslawa Darlak
- Department of Discovery Chemistry, Merck & Co., Inc., 33 Ave. Louis Pasteur, Boston, Massachusetts 02215, United States
| | - Justin A Newman
- Analytical Research and Development, Merck & Co., Inc., 126 E. Lincoln Ave., Rahway, New Jersey 07065, United States
| | - Lisa M Nogle
- Department of Discovery Chemistry, Merck & Co., Inc., 33 Ave. Louis Pasteur, Boston, Massachusetts 02215, United States
| | - Mark J Pietrafitta
- Department of Discovery Chemistry, Merck & Co., Inc., 33 Ave. Louis Pasteur, Boston, Massachusetts 02215, United States
| | - David A Smith
- Department of Discovery Chemistry, Merck & Co., Inc., 33 Ave. Louis Pasteur, Boston, Massachusetts 02215, United States
| | - Xiao Wang
- Analytical Research and Development, Merck & Co., Inc., 126 E. Lincoln Ave., Rahway, New Jersey 07065, United States
| | - Lei Yue
- Department of Discovery Chemistry, Merck & Co., Inc., 33 Ave. Louis Pasteur, Boston, Massachusetts 02215, United States
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3
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Bolzonello A, Morbiato L, Tundo S, Sella L, Baccelli I, Echeverrigaray S, Musetti R, De Zotti M, Favaron F. Peptide Analogs of a Trichoderma Peptaibol Effectively Control Downy Mildew in the Vineyard. PLANT DISEASE 2023; 107:2643-2652. [PMID: 36724095 DOI: 10.1094/pdis-09-22-2064-re] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Plasmopara viticola, the agent of grapevine downy mildew, causes enormous economic damage, and its control is primarily based on the use of synthetic fungicides. The European Union policies promote reducing reliance on synthetic plant protection products. Biocontrol agents such as Trichoderma spp. constitute a resource for the development of biopesticides. Trichoderma spp. produce secondary metabolites such as peptaibols, but the poor water solubility of peptaibols limits their practical use as agrochemicals. To identify new potential bio-inspired molecules effective against P. viticola, various water-soluble peptide analogs of the peptaibol trichogin were synthesized. In grapevine leaf disk assays, the peptides analogs at a concentration of 50 μM completely prevented P. viticola infection after zoosporangia inoculation. Microscopic observations of one of the most effective peptides showed that it causes membrane lysis and cytoplasmic granulation in both zoosporangia and zoospores. Among the effective peptides, 4r was selected for a 2-year field trial experiment. In the vineyard, the peptide administered at 100 μM (equivalent to 129.3 g/ha) significantly reduced the disease incidence and severity on both leaves and bunches, with protection levels similar to those obtained using a cupric fungicide. In the second-year field trial, reduced dosages of the peptide were also tested, and even at the peptide concentration reduced by 50 or 75%, a significant decrease in the disease incidence and severity was obtained at the end of the trial. The peptide did not show any phytotoxic effect. Previously, peptide 4r had been demonstrated to be active against other fungal pathogens, including the grapevine fungus Botrytis cinerea. Thus, this peptide may be a candidate for a broad-spectrum fungicide whose biological properties deserve further investigation.
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Affiliation(s)
- Angela Bolzonello
- Department of Land, Environment, Agriculture, and Forestry (TESAF), University of Padova, Legnaro I-35020, Italy
| | - Laura Morbiato
- Department of Chemistry, University of Padova, Padova I-35131, Italy
| | - Silvio Tundo
- Department of Land, Environment, Agriculture, and Forestry (TESAF), University of Padova, Legnaro I-35020, Italy
| | - Luca Sella
- Department of Land, Environment, Agriculture, and Forestry (TESAF), University of Padova, Legnaro I-35020, Italy
| | - Ivan Baccelli
- Institute for Sustainable Plant Protection, National Research Council of Italy, Sesto Fiorentino I-50019, Italy
| | - Sergio Echeverrigaray
- Institute of Biotechnology, University of Caxias do Sul, Caxias do Sul, RS 95070-560, Brazil
| | - Rita Musetti
- Department of Land, Environment, Agriculture, and Forestry (TESAF), University of Padova, Legnaro I-35020, Italy
| | - Marta De Zotti
- Department of Chemistry, University of Padova, Padova I-35131, Italy
| | - Francesco Favaron
- Department of Land, Environment, Agriculture, and Forestry (TESAF), University of Padova, Legnaro I-35020, Italy
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4
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Morbiato L, Quaggia C, Menilli L, Dalla Torre C, Barbon A, De Zotti M. Synthesis, Conformational Analysis and Antitumor Activity of the Naturally Occurring Antimicrobial Medium-Length Peptaibol Pentadecaibin and Spin-Labeled Analogs Thereof. Int J Mol Sci 2023; 24:13396. [PMID: 37686199 PMCID: PMC10487733 DOI: 10.3390/ijms241713396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 08/04/2023] [Accepted: 08/11/2023] [Indexed: 09/10/2023] Open
Abstract
Peptaibols are proteolysis-resistant, membrane-active peptides. Their remarkably stable helical 3D-structures are key for their bioactivity. They can insert themselves into the lipid bilayer as barrel staves, or lay on its surface like carpets, depending on both their length and the thickness of the lipid bilayer. Medium-length peptaibols are of particular interest for studying the peptide-membrane interaction because their length allows them to adopt either orientation as a function of the membrane thickness, which, in turn, might even result in an enhanced selectivity. Electron paramagnetic resonance (EPR) is the election technique used to this aim, but it requires the synthesis of spin-labeled medium-length peptaibols, which, in turn, is hampered by the poor reactivity of the Cα-tetrasubstituted residues featured in their sequences. After several years of trial and error, we are now able to give state-of-the-art advice for a successful synthesis of nitroxide-containing peptaibols, avoiding deleted sequences, side reactions and difficult purification steps. Herein, we describe our strategy and itsapplication to the synthesis of spin-labeled analogs of the recently discovered, natural, medium-length peptaibol pentadecaibin. We studied the antitumor activity of pentadecaibin and its analogs, finding potent cytotoxicity against human triple-negative breast cancer and ovarian cancer. Finally, our analysis of the peptide conformational preferences and membrane interaction proved that pentadecaibinspin-labeling does not alter the biological features of the native sequence and is suitable for further EPR studies. The nitroxide-containing pentadecaibins, and their synthetic strategy described herein, will help to shed light on the mechanism of the peptide-membrane interaction of medium-length peptaibols.
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Affiliation(s)
- Laura Morbiato
- Department of Chemical Sciences, University of Padova, 35131 Padova, Italy; (L.M.); (C.Q.); (C.D.T.); (A.B.)
| | - Celeste Quaggia
- Department of Chemical Sciences, University of Padova, 35131 Padova, Italy; (L.M.); (C.Q.); (C.D.T.); (A.B.)
| | - Luca Menilli
- Department of Biology, University of Padova, 35131 Padova, Italy;
| | - Chiara Dalla Torre
- Department of Chemical Sciences, University of Padova, 35131 Padova, Italy; (L.M.); (C.Q.); (C.D.T.); (A.B.)
| | - Antonio Barbon
- Department of Chemical Sciences, University of Padova, 35131 Padova, Italy; (L.M.); (C.Q.); (C.D.T.); (A.B.)
| | - Marta De Zotti
- Department of Chemical Sciences, University of Padova, 35131 Padova, Italy; (L.M.); (C.Q.); (C.D.T.); (A.B.)
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5
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Oba M, Nakajima S, Misao K, Yokoo H, Tanaka M. Effect of helicity and hydrophobicity on cell-penetrating ability of arginine-rich peptides. Bioorg Med Chem 2023; 91:117409. [PMID: 37441862 DOI: 10.1016/j.bmc.2023.117409] [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: 05/11/2023] [Revised: 07/03/2023] [Accepted: 07/04/2023] [Indexed: 07/15/2023]
Abstract
Arginine (Arg)-rich peptides are one of the typical cell-penetrating peptides (CPPs), which can deliver membrane-impermeable compounds into intracellular compartments. Guanidino groups in Arg-rich peptides are critical for their high cell-penetrating ability, although it remains unclear whether peptide secondary structures contribute to this ability. In the current study, we designed four Arg-rich peptides containing α,α-disubstituted α-amino acids (dAAs), which prefer to adopt a helical structure. The four dAA-containing peptides adopted slightly different peptide secondary structures, from a random structure to a helical structure, with different hydrophobicities. In these peptides, dipropylglycine-containing peptide exhibited the highest helicity and hydrophobicity, and showed the best cell-penetrating ability. These findings suggested that the helicity and hydrophobicity of Arg-rich peptides contributes to their high cell-penetrating ability.
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Affiliation(s)
- Makoto Oba
- Medical Chemistry, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 1-5 Shimogamohangi-cho, Sakyo-ku, Kyoto 606-0823, Japan.
| | - Shun Nakajima
- Graduate School of Biomedical Sciences, Nagasaki University, 1-14 Bunkyo-machi, Nagasaki 852-8521, Japan
| | - Kurumi Misao
- Graduate School of Biomedical Sciences, Nagasaki University, 1-14 Bunkyo-machi, Nagasaki 852-8521, Japan
| | - Hidetomo Yokoo
- Medical Chemistry, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 1-5 Shimogamohangi-cho, Sakyo-ku, 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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6
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Hickey J, Sindhikara D, Zultanski SL, Schultz DM. Beyond 20 in the 21st Century: Prospects and Challenges of Non-canonical Amino Acids in Peptide Drug Discovery. ACS Med Chem Lett 2023; 14:557-565. [PMID: 37197469 PMCID: PMC10184154 DOI: 10.1021/acsmedchemlett.3c00037] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 03/29/2023] [Indexed: 05/19/2023] Open
Abstract
Life is constructed primarily using a toolbox of 20 canonical amino acids-relying upon these building blocks for the assembly of proteins and peptides that regulate nearly every cellular task, including cell structure, function, and maintenance. While Nature continues to be a source of inspiration for drug discovery, medicinal chemists are not beholden to only 20 canonical amino acids and have begun to explore non-canonical amino acids (ncAAs) for the construction of designer peptides with improved drug-like properties. However, as our toolbox of ncAAs expands, drug hunters are encountering new challenges in approaching the iterative peptide design-make-test-analyze cycle with a seemingly boundless set of building blocks. This Microperspective focuses on new technologies that are accelerating ncAA interrogation in peptide drug discovery (including HELM notation, late-stage functionalization, and biocatalysis) while shedding light on areas where further investment could not only accelerate the discovery of new medicines but also improve downstream development.
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Affiliation(s)
- Jennifer
L. Hickey
- Department
of Medicinal Chemistry, Merck & Co.,
Inc., Kenilworth, New Jersey 07033, United States
| | - Dan Sindhikara
- Department
of Modeling and Informatics, Merck &
Co., Inc., Kenilworth, New Jersey 07033, United States
| | - Susan L. Zultanski
- Department
of Process Research & Development, Merck
& Co., Inc., Rahway, New Jersey 07065, United States
| | - Danielle M. Schultz
- Department
of Process Research & Development, Merck
& Co., Inc., Rahway, New Jersey 07065, United States
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7
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Tapia SM, Macías LG, Pérez-Torrado R, Daroqui N, Manzanares P, Querol A, Barrio E. A novel aminotransferase gene and its regulator acquired in Saccharomyces by a horizontal gene transfer event. BMC Biol 2023; 21:102. [PMID: 37158891 PMCID: PMC10169451 DOI: 10.1186/s12915-023-01566-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 03/16/2023] [Indexed: 05/10/2023] Open
Abstract
BACKGROUND Horizontal gene transfer (HGT) is an evolutionary mechanism of adaptive importance, which has been deeply studied in wine S. cerevisiae strains, where those acquired genes conferred improved traits related to both transport and metabolism of the nutrients present in the grape must. However, little is known about HGT events that occurred in wild Saccharomyces yeasts and how they determine their phenotypes. RESULTS Through a comparative genomic approach among Saccharomyces species, we detected a subtelomeric segment present in the S. uvarum, S. kudriavzevii, and S. eubayanus species, belonging to the first species to diverge in the Saccharomyces genus, but absent in the other Saccharomyces species. The segment contains three genes, two of which were characterized, named DGD1 and DGD2. DGD1 encodes dialkylglicine decarboxylase, whose specific substrate is the non-proteinogenic amino acid 2-aminoisobutyric acid (AIB), a rare amino acid present in some antimicrobial peptides of fungal origin. DGD2 encodes putative zinc finger transcription factor, which is essential to induce the AIB-dependent expression of DGD1. Phylogenetic analysis showed that DGD1 and DGD2 are closely related to two adjacent genes present in Zygosaccharomyces. CONCLUSIONS The presented results show evidence of an early HGT event conferring new traits to the ancestor of the Saccharomyces genus that could be lost in the evolutionary more recent Saccharomyces species, perhaps due to loss of function during the colonization of new habitats.
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Affiliation(s)
- Sebastián M Tapia
- Instituto de Agroquímica y Tecnología de los Alimentos, IATA-CSIC, Paterna, Spain
| | - Laura G Macías
- Instituto de Agroquímica y Tecnología de los Alimentos, IATA-CSIC, Paterna, Spain
| | | | - Noemi Daroqui
- Instituto de Agroquímica y Tecnología de los Alimentos, IATA-CSIC, Paterna, Spain
| | - Paloma Manzanares
- Instituto de Agroquímica y Tecnología de los Alimentos, IATA-CSIC, Paterna, Spain
| | - Amparo Querol
- Instituto de Agroquímica y Tecnología de los Alimentos, IATA-CSIC, Paterna, Spain
| | - Eladio Barrio
- Instituto de Agroquímica y Tecnología de los Alimentos, IATA-CSIC, Paterna, Spain.
- Departament de Genètica, Universitat de València, Valencia, Spain.
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8
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Anticancer and Targeting Activity of Phytopharmaceutical Structural Analogs of a Natural Peptide from Trichoderma longibrachiatum and Related Peptide-Decorated Gold Nanoparticles. Int J Mol Sci 2023; 24:ijms24065537. [PMID: 36982610 PMCID: PMC10057332 DOI: 10.3390/ijms24065537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 03/08/2023] [Accepted: 03/13/2023] [Indexed: 03/18/2023] Open
Abstract
In the large field of bioactive peptides, peptaibols represent a unique class of compounds. They are membrane-active peptides, produced by fungi of the genus Trichoderma and known to elicit plant defenses. Among the short-length peptaibols, trichogin GA IV is nonhemolytic, proteolysis-resistant, antibacterial, and cytotoxic. Several trichogin analogs are endowed with potent activity against phytopathogens, thus representing a sustainable alternative to copper for plant protection. In this work, we tested the activity of trichogin analogs against a breast cancer cell line and a normal cell line of the same derivation. Lys-containing trichogins showed an IC50 below 12 µM, a peptide concentration not significantly affecting the viability of normal cells. Two analogs were found to be membrane-active but noncytotoxic. They were anchored to gold nanoparticles (GNPs) and further investigated for their ability to act as targeting agents. GNP uptake by cancer cells increased with peptide decoration, while it decreased in the corresponding normal epithelial cells. This work highlights the promising biological properties of peptaibol analogs in the field of cancer therapy either as cytotoxic molecules or as active targeting agents in drug delivery.
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9
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Balázs D, Marik T, Szekeres A, Vágvölgyi C, Kredics L, Tyagi C. Structure-activity correlations for peptaibols obtained from clade Longibrachiatum of Trichoderma: A combined experimental and computational approach. Comput Struct Biotechnol J 2023; 21:1860-1873. [PMID: 36915379 PMCID: PMC10006723 DOI: 10.1016/j.csbj.2023.02.046] [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: 07/26/2022] [Revised: 02/23/2023] [Accepted: 02/23/2023] [Indexed: 03/06/2023] Open
Abstract
Integrated disease management and plant protection have been discussed with much fervor in the past decade due to the rising environmental concerns of using industrially produced pesticides. Members of the genus Trichoderma are a subject of considerable research today due to their several properties as biocontrol agents. In our study, the peptaibol production of Trichoderma longibrachiatum SZMC 1775, T. longibrachiatum f. bissettii SZMC 12546, T. reesei SZMC 22616, T. reesei SZMC 22614, T. saturnisporum SZMC 22606 and T. effusum SZMC 22611 were investigated to elucidate structure-activity relationships (SARs) between the properties of peptaibols and their 3D structures. The effects of peptaibol mixtures obtained from every Trichoderma strain were examined against nine commonly known bacteria. The lowest minimum inhibitory concentrations (MIC, mg ml-1) were exerted by T. longibrachiatum f. bissettii SZMC 12546 against Gram-positive bacteria, which was also able to inhibit the plant pathogenic Gram-negative Rhizobium radiobacter. Accelerated molecular dynamics (aMD) simulations were performed in aqueous solvent to explore the folding dynamics of 12 selected peptaibol sequences. The most characteristic difference between the peptaibols from group A and B relies in the 'Gly-Leu-Aib-Pro' and 'Gly-Aib-Aib-Pro' motifs ('Aib' stands for α-aminoisobutyric acid), which imparted a significant effect on the folding dynamics in water and might be correlated with their expressed bioactivity. In our aMD simulation experiments, Group A peptaibols showed more restricted folding dynamics with well-folded helical conformations as the most stable representative structures. This structural stability and dynamics may contribute to their bioactivity against the selected bacterial species.
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Affiliation(s)
- Dóra Balázs
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Közép fasor 52, H-6726 Szeged, Hungary
- Doctoral School of Biology, Faculty of Science and Informatics, University of Szeged, Közép fasor 52, H-6726 Szeged, Hungary
| | - Tamás Marik
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Közép fasor 52, H-6726 Szeged, Hungary
| | - András Szekeres
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Közép fasor 52, H-6726 Szeged, Hungary
| | - Csaba Vágvölgyi
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Közép fasor 52, H-6726 Szeged, Hungary
| | - László Kredics
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Közép fasor 52, H-6726 Szeged, Hungary
| | - Chetna Tyagi
- Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Közép fasor 52, H-6726 Szeged, Hungary
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10
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Bellavita R, Maione A, Braccia S, Sinoca M, Galdiero S, Galdiero E, Falanga A. Myxinidin-Derived Peptide against Biofilms Caused by Cystic Fibrosis Emerging Pathogens. Int J Mol Sci 2023; 24:ijms24043092. [PMID: 36834512 PMCID: PMC9964602 DOI: 10.3390/ijms24043092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 01/30/2023] [Accepted: 02/02/2023] [Indexed: 02/09/2023] Open
Abstract
Chronic lung infections in cystic fibrosis (CF) patients are triggered by multidrug-resistant bacteria such as Pseudomonas aeruginosa, Achromobacter xylosoxidans, and Stenotrophomonas maltophilia. The CF airways are considered ideal sites for the colonization and growth of bacteria and fungi that favor the formation of mixed biofilms that are difficult to treat. The inefficacy of traditional antibiotics reinforces the need to find novel molecules able to fight these chronic infections. Antimicrobial peptides (AMPs) represent a promising alternative for their antimicrobial, anti-inflammatory, and immunomodulatory activities. We developed a more serum-stable version of the peptide WMR (WMR-4) and investigated its ability to inhibit and eradicate C. albicans, S. maltophilia, and A. xylosoxidans biofilms in both in vitro and in vivo studies. Our results suggest that the peptide is able better to inhibit than to eradicate both mono and dual-species biofilms, which is further confirmed by the downregulation of some genes involved in biofilm formation or in quorum-sensing signaling. Biophysical data help to elucidate its mode of action, showing a strong interaction of WMR-4 with lipopolysaccharide (LPS) and its insertion in liposomes mimicking Gram-negative and Candida membranes. Our results support the promising therapeutic application of AMPs in the treatment of mono- and dual-species biofilms during chronic infections in CF patients.
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Affiliation(s)
- Rosa Bellavita
- Department of Pharmacy, School of Medicine, University of Naples ‘Federico II’, Via Domenico Montesano 49, 80131 Naples, Italy
| | - Angela Maione
- Department of Biology, University of Naples ‘Federico II’, Via Cinthia, 80126 Naples, Italy
| | - Simone Braccia
- Department of Pharmacy, School of Medicine, University of Naples ‘Federico II’, Via Domenico Montesano 49, 80131 Naples, Italy
| | - Marica Sinoca
- Department of Biology, University of Naples ‘Federico II’, Via Cinthia, 80126 Naples, Italy
| | - Stefania Galdiero
- Department of Pharmacy, School of Medicine, University of Naples ‘Federico II’, Via Domenico Montesano 49, 80131 Naples, Italy
| | - Emilia Galdiero
- Department of Biology, University of Naples ‘Federico II’, Via Cinthia, 80126 Naples, Italy
| | - Annarita Falanga
- Department of Agricultural Sciences, University of Naples ‘Federico II’, Via dell’ Università 100, 80055 Portici, Italy
- Correspondence: ; Tel.: +39-081-253-4525
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11
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Joaquin D, Mansfield SA, Chanthakhoun JC, LeSueur AK, Blackburn TA, Castle SL. Synthesis and Studies of Bulky Cycloalkyl α,β-Dehydroamino Acids that Enhance Proteolytic Stability. Org Lett 2022; 24:5329-5333. [PMID: 35839437 PMCID: PMC10243721 DOI: 10.1021/acs.orglett.2c01962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Three new bulky cycloalkyl α,β-dehydroamino acids (ΔAAs) have been designed and synthesized. Each residue enhances the rigidity of model peptides and their stability to proteolysis, with larger ring sizes exhibiting greater effects. Peptides containing bulky cycloalkyl ΔAAs are inert to conjugate addition by a nucleophilic thiol. The results suggest that these residues will be effective tools for improving the proteolytic stability of bioactive peptides.
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Affiliation(s)
- Daniel Joaquin
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States
| | - Samuel A Mansfield
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States
| | - Joseph C Chanthakhoun
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States
| | - Austin K LeSueur
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States
| | - Tiffani A Blackburn
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States
| | - Steven L Castle
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States
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12
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Passivating the Omicron SARS-CoV-2 variant with self-assembled nano peptides: Specificity, stability, and no cytotoxicity. OPENNANO 2022. [PMCID: PMC9245369 DOI: 10.1016/j.onano.2022.100054] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The SARS-CoV-2 Omicron variant is called a “variant of concern” (VOC) which has spread all over the world at a faster rate than even the first SARS-CoV-2 outbreak despite travel restrictions. In order to combat the health consequences from a SARS-CoV-2 Omicron variant infection, the objective of the present in vitro study was to develop self-assembled nano peptides to attach to the virus and inhibit its attachment and entry into mammalian cells for replication. For this purpose, two amphipathic peptides containing hydrophobic and hydrophilic peptides and an unnatural amino acid (such as 2-aminoisobutyric acid (U)) were designed to attach to the less mutated virus envelope rather than more frequently mutated S-protein region: NapFFTLUFLTUTEKKKK and NapFFMLUFLMUMEKKKK. These peptides were synthesized using the solid phase peptide synthesis method and were characterized for mammalian cell infection using well-established pseudo virus assays. In vitro results showed that the two self-assembled nano peptides significantly inhibited the ability of the SARS-CoV-2 Omicron variant virus to infect mammalian cells and replicate with IC50 values of 0.5 and 360 mg/ml for NapFFTLUFLTUTEKKKK and NapFFMLUFLMUMEKKKK, respectively. Most impressively, 1 mg/ml of NapFFTLUFLTUTEKKKK resulted in a 2 log reduction in pseudovirus replication after just 15 min at a viral load of 106 copies/ml. Results further confirmed that the peptides continued to passivate the SARS-CoV-2 Omicron variant for up to one week and were stable in cell culture media before being added to the virus. Mechanistically, in vitro results showed selective binding of the peptides to the SARS-CoV-2 Omicron variant envelop protein over the more frequently mutated spike protein up to one week demonstrating the stability of the peptides. Cytotoxicity studies with fibroblasts also showed no toxicity when exposed to the peptides for 72 h. In summary, the present results strongly suggest that the two peptides developed in this study should be further researched for a wide range of anti-SARS-CoV-2 virus applications, including the present Omicron and future mutations.
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13
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Wang X, Li J, Hayashi Y. Highly Sterically Hindered Peptide Bond Formation between α,α-Disubstituted α-Amino Acids and N-Alkyl Cysteines Using α,α-Disubstituted α-Amidonitrile. J Am Chem Soc 2022; 144:10145-10150. [PMID: 35658430 DOI: 10.1021/jacs.2c02993] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Peptides and proteins attract enormous attention in many fields of academia and industry. The introduction of unusual amino acids such as α,α-disubstituted α-amino acids or N-alkyl α-amino acids into normal peptide backbones is a well-utilized and useful tool for the modification of properties such as conformation, biological activity, and pharmacological profile. Despite the significant interest in sterically hindered peptides, research on peptides bearing an amide bond between an α,α-disubstituted α-amino acid and an N-alkyl α-amino acid remains underexplored because of the lack of an efficient synthetic approach. Herein, we describe a high-yielding synthetic method to access such extremely sterically hindered peptide bonds between amino acids. The reaction takes place between a peptide with an α,α-disubstituted α-amidonitrile and a second peptide bearing an N-alkyl cysteine, without a coupling reagent.
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Affiliation(s)
- Xiaoling Wang
- Department of Chemistry, Graduate School of Science, Tohoku University, 6-3 Aramaki Aza-Aoba, Aoba-ku, Sendai, Miyagi 980-8578, Japan
| | - Jing Li
- Department of Chemistry, Graduate School of Science, Tohoku University, 6-3 Aramaki Aza-Aoba, Aoba-ku, Sendai, Miyagi 980-8578, Japan
| | - Yujiro Hayashi
- Department of Chemistry, Graduate School of Science, Tohoku University, 6-3 Aramaki Aza-Aoba, Aoba-ku, Sendai, Miyagi 980-8578, Japan
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14
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Wada SI, Shibaike A, Hayashi J, Urata H. Influence of Aib-Containing Amphipathic Helical Chain Length in MAP(Aib)-cRGD as Carrier for siRNA Delivery. Chem Biodivers 2021; 19:e202100728. [PMID: 34842340 DOI: 10.1002/cbdv.202100728] [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: 09/06/2021] [Accepted: 11/29/2021] [Indexed: 11/09/2022]
Abstract
MAP(Aib)-cRGD, which is a conjugate of an α-aminoisobutyric acid (Aib)-containing amphipathic helical peptide [MAP(Aib)] with a αv β3 integrin binding ligand, cRGD, at the C-terminus of the helical peptide, has been developed for siRNA delivery into cells. In this work, we synthesized three peptides containing 19 (PI), 18 (PII), and 17 (PIII) amino acid residues in the helical peptide, which lack Aib, Leu-Aib, and Lys-Leu-Aib residues present in the C-terminus of the helical peptide of the parent MAP(Aib)-cRGD, respectively. MAP(Aib)-cRGD showed the siRNA delivery into cells and the RNAi effect both in the presence and in the absence of serum in reaction media. In contrast, PI delivered siRNA into cells, and this was followed by the RNAi effect in only serum-free reaction media. On the other hand, siRNA delivery was abolished by the further reduction of the number of residues (PII and PIII) in the C-terminus. Our data indicate that the Aib-containing helical part requires 20 residues in the conjugation of the helical peptide with cRGD for the construction of carrier for siRNA delivery into cells.
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Affiliation(s)
- Shun-Ichi Wada
- Department of Bioorganic Chemistry, Faculty of Pharmacy, Osaka Medical and Pharmaceutical University, 4-20-1 Nasahara, Takatsuki, Osaka, 569-1094, Japan
| | - Akira Shibaike
- Department of Bioorganic Chemistry, Faculty of Pharmacy, Osaka Medical and Pharmaceutical University, 4-20-1 Nasahara, Takatsuki, Osaka, 569-1094, Japan
| | - Junsuke Hayashi
- Department of Bioorganic Chemistry, Faculty of Pharmacy, Osaka Medical and Pharmaceutical University, 4-20-1 Nasahara, Takatsuki, Osaka, 569-1094, Japan
| | - Hidehito Urata
- Department of Bioorganic Chemistry, Faculty of Pharmacy, Osaka Medical and Pharmaceutical University, 4-20-1 Nasahara, Takatsuki, Osaka, 569-1094, Japan
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15
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Pane AJ, Yu W, Aytenfisu A, Tunyi J, Venable RM, MacKerell AD, Pastor RW. Development of CHARMM Additive Potential Energy Parameters for α-Methyl Amino Acids. J Phys Chem B 2021; 125:11687-11696. [PMID: 34652160 PMCID: PMC8627904 DOI: 10.1021/acs.jpcb.1c07202] [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: 11/28/2022]
Abstract
Potential energy parameters for α-methyl amino acids were generated with ab initio calculations on α-methyl-N-acetylalanyl-N'-methylamide (the α-methyl "alanine dipeptide") which served as an input to a grid-based correction to the backbone torsional potential (known as CMAP) consistent with the CHARMM36m additive protein force field. The new parameters were validated by comparison with experimentally determined helicities of the 22 residue C-terminal peptide (H10) from apolipoprotein A1 and five α-methylated variants in water and 0.3:0.7 trifluoroethanol (TFE)/water. Conventional molecular dynamics simulation totaling 30 μs for each peptide is in overall good agreement with the experiment, including the increased helicity in 30% TFE. An additional 500 ns of simulation using two-dimensional dihedral biasing (bpCMAP) replica exchange reduced left-handed conformations, increased right-handed helices, and thereby mostly decreased agreement with the experiment. Analysis of side chain-side chain salt bridges suggests that the overestimation of the helical content may be, in part, due to such interactions. The increased helicity of the peptides in 30% TFE arises from decreased hydrogen bonding of the backbone atoms to water and a concomitant increase in intramolecular backbone hydrogen bonds.
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Affiliation(s)
- Anthony J Pane
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Rockville, Maryland 20892, United States
| | - Wenbo Yu
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, 20 Penn Street, Baltimore, Maryland 21201, United States
| | - Asaminew Aytenfisu
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, 20 Penn Street, Baltimore, Maryland 21201, United States
| | - Jude Tunyi
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Rockville, Maryland 20892, United States
| | - Richard M Venable
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Rockville, Maryland 20892, United States
| | - Alexander D MacKerell
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, 20 Penn Street, Baltimore, Maryland 21201, United States
| | - Richard W Pastor
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Rockville, Maryland 20892, United States
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16
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Kodama Y, Imai S, Fujimoto J, Sato K, Mase N, Narumi T. Stereoselective synthesis of highly functionalized ( Z)-chloroalkene dipeptide isosteres containing an α,α-disubstituted amino acid. Chem Commun (Camb) 2021; 57:6915-6918. [PMID: 34152343 DOI: 10.1039/d1cc02952e] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Described here is the first stereoselective synthesis of highly functionalized chloroalkene dipeptide isosteres containing an α,α-disubstituted amino acid (ααAA). This synthesis requires the construction of a quaternary carbon center, and this challenge was overcome by the Aza-Darzens condensation of ketimine with α,α-dichloroenolate, producing 2-chloroaziridines with quaternary carbon centers including spirocyclic motifs, which are valuable for the previously elusive synthesis of various ααAA-containing chloroalkene isosteres.
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Affiliation(s)
- Yuki Kodama
- Graduate School of Science and Technology, Shizuoka University, 3-5-1 Johoku, Hamamatsu, Shizuoka, 432-8561, Japan.
| | - Saki Imai
- Course of Applied Chemistry and Biochemical Engineering, Department of Engineering, Graduate School of Integrated Science and Technology, Shizuoka University, 3-5-1 Johoku, Hamamatsu, Shizuoka, 432-8561, Japan
| | - Junko Fujimoto
- Department of Applied Chemistry and Biochemical Engineering, Faculty of Engineering, Shizuoka University, Shizuoka, 432-8561, Japan
| | - Kohei Sato
- Graduate School of Science and Technology, Shizuoka University, 3-5-1 Johoku, Hamamatsu, Shizuoka, 432-8561, Japan. and Course of Applied Chemistry and Biochemical Engineering, Department of Engineering, Graduate School of Integrated Science and Technology, Shizuoka University, 3-5-1 Johoku, Hamamatsu, Shizuoka, 432-8561, Japan and Department of Applied Chemistry and Biochemical Engineering, Faculty of Engineering, Shizuoka University, Shizuoka, 432-8561, Japan
| | - Nobuyuki Mase
- Graduate School of Science and Technology, Shizuoka University, 3-5-1 Johoku, Hamamatsu, Shizuoka, 432-8561, Japan. and Course of Applied Chemistry and Biochemical Engineering, Department of Engineering, Graduate School of Integrated Science and Technology, Shizuoka University, 3-5-1 Johoku, Hamamatsu, Shizuoka, 432-8561, Japan and Department of Applied Chemistry and Biochemical Engineering, Faculty of Engineering, Shizuoka University, Shizuoka, 432-8561, Japan and Green Energy Research Division, Research Institute of Green Science and Technology, Shizuoka University, 3-5-1 Johoku, Hamamatsu, Shizuoka, 432-8561, Japan
| | - Tetsuo Narumi
- Graduate School of Science and Technology, Shizuoka University, 3-5-1 Johoku, Hamamatsu, Shizuoka, 432-8561, Japan. and Course of Applied Chemistry and Biochemical Engineering, Department of Engineering, Graduate School of Integrated Science and Technology, Shizuoka University, 3-5-1 Johoku, Hamamatsu, Shizuoka, 432-8561, Japan and Department of Applied Chemistry and Biochemical Engineering, Faculty of Engineering, Shizuoka University, Shizuoka, 432-8561, Japan and Green Chemistry Research Division, Research Institute of Green Science and Technology, Shizuoka University, 3-5-1 Johoku, Hamamatsu, Shizuoka, 432-8561, Japan
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17
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Kato T, Kita Y, Iwanari K, Asano A, Oba M, Tanaka M, Doi M. Synthesis of six-membered carbocyclic ring α,α-disubstituted amino acids and arginine-rich peptides to investigate the effect of ring size on the properties of the peptide. Bioorg Med Chem 2021; 38:116111. [PMID: 33838611 DOI: 10.1016/j.bmc.2021.116111] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 03/04/2021] [Accepted: 03/05/2021] [Indexed: 01/08/2023]
Abstract
Cell-penetrating peptides (CPPs) have been attracting attention as tools for intracellular delivery of membrane-impermeant functional molecules. Among the variety of CPPs that have been developed, many are composed of both natural and unnatural amino acids. We previously synthesized α,α-disubstituted α-amino acids (dAAs) containing a five-membered carbocyclic ring in its side chain and revealed the utility of dAAs for the development of novel CPPs. In the present study, we designed a six-membered carbocyclic ring dAA with an amino group on the ring and introduced it into arginine (Arg)-rich peptides to further investigate the value of dAAs for developing CPPs. We also assessed the effects of the size of the dAA carbocyclic ring on cellular uptake of dAA-containing peptides. The stability of the peptide's secondary structure and its membrane permeability were both greater in dAA-containing peptides than in an Arg nonapeptide. However, the number of carbon atoms in the dAA side chain ring had little effect. Nevertheless, these results show the utility of cyclic dAAs in the design of novel CPPs containing unnatural amino acids.
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Affiliation(s)
- Takuma Kato
- Osaka University of Pharmaceutical Sciences, 4-20-1 Nasahara, Takatsuki, Osaka 569-1094, Japan.
| | - Yuki Kita
- Osaka University of Pharmaceutical Sciences, 4-20-1 Nasahara, Takatsuki, Osaka 569-1094, Japan
| | - Kazuki Iwanari
- Osaka University of Pharmaceutical Sciences, 4-20-1 Nasahara, Takatsuki, Osaka 569-1094, Japan
| | - Akiko Asano
- Osaka University of Pharmaceutical Sciences, 4-20-1 Nasahara, Takatsuki, Osaka 569-1094, Japan
| | - Makoto Oba
- Graduate School of Medicine, Kyoto Prefectural University of Medicine, 1-5 Shimogamohangi-Cho, Sakyo-Ku, Kyoto 606-0823, Japan
| | - Masakazu Tanaka
- Graduate School of Biomedical Sciences, Nagasaki University, 1-14 Bunkyo-machi, Nagasaki 852-8521, Japan
| | - Mitsunobu Doi
- Osaka University of Pharmaceutical Sciences, 4-20-1 Nasahara, Takatsuki, Osaka 569-1094, Japan
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18
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Lu J, Xu H, Xia J, Ma J, Xu J, Li Y, Feng J. D- and Unnatural Amino Acid Substituted Antimicrobial Peptides With Improved Proteolytic Resistance and Their Proteolytic Degradation Characteristics. Front Microbiol 2020; 11:563030. [PMID: 33281761 PMCID: PMC7688903 DOI: 10.3389/fmicb.2020.563030] [Citation(s) in RCA: 99] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Accepted: 10/22/2020] [Indexed: 01/10/2023] Open
Abstract
The transition of antimicrobial peptides (AMPs) from the laboratory to market has been severely hindered by their instability toward proteases in biological systems. In the present study, we synthesized derivatives of the cationic AMP Pep05 (KRLFKKLLKYLRKF) by substituting L-amino acid residues with D- and unnatural amino acids, such as D-lysine, D-arginine, L-2,4-diaminobutanoic acid (Dab), L-2,3-diaminopropionic acid (Dap), L-homoarginine, 4-aminobutanoic acid (Aib), and L-thienylalanine, and evaluated their antimicrobial activities, toxicities, and stabilities toward trypsin, plasma proteases, and secreted bacterial proteases. In addition to measuring changes in the concentration of the intact peptides, LC-MS was used to identify the degradation products of the modified AMPs in the presence of trypsin and plasma proteases to determine degradation pathways and examine whether the amino acid substitutions afforded improved proteolytic resistance. The results revealed that both D- and unnatural amino acids enhanced the stabilities of the peptides toward proteases. The derivative DP06, in which all of the L-lysine and L-arginine residues were replaced by D-amino acids, displayed remarkable stability and mild toxicity in vitro but only slight activity and severe toxicity in vivo, indicating a significant difference between the in vivo and in vitro results. Unexpectedly, we found that the incorporation of a single Aib residue at the N-terminus of compound UP09 afforded remarkably enhanced plasma stability and improved activity in vivo. Hence, this derivative may represent a candidate AMP for further optimization, providing a new strategy for the design of novel AMPs with improved bioavailability.
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Affiliation(s)
- Jianguang Lu
- Key State Laboratory of Drug Innovation and Pharmaceutical Technology, China State Institute of Pharmaceutical Industry, Shanghai, China.,Department of Peptide Drugs R&D, Shanghai Duomirui Biotechnology Co., Ltd., Shanghai, China
| | - Hongjiang Xu
- Key State Laboratory of Drug Innovation and Pharmaceutical Technology, China State Institute of Pharmaceutical Industry, Shanghai, China.,Department of Drug Evaluation and Research, Chia Tai Tianqing Pharmaceutical Group Co., Ltd., Nanjing, China
| | - Jianghua Xia
- Key State Laboratory of Drug Innovation and Pharmaceutical Technology, China State Institute of Pharmaceutical Industry, Shanghai, China
| | - Jie Ma
- Department of Peptide Drugs R&D, Shanghai Duomirui Biotechnology Co., Ltd., Shanghai, China
| | - Jun Xu
- Department of Peptide Drugs R&D, Shanghai Duomirui Biotechnology Co., Ltd., Shanghai, China
| | - Yanan Li
- Key State Laboratory of Drug Innovation and Pharmaceutical Technology, China State Institute of Pharmaceutical Industry, Shanghai, China.,School of Pharmacy, Fudan University, Shanghai, China
| | - Jun Feng
- Key State Laboratory of Drug Innovation and Pharmaceutical Technology, China State Institute of Pharmaceutical Industry, Shanghai, China.,Department of Peptide Drugs R&D, Shanghai Duomirui Biotechnology Co., Ltd., Shanghai, China
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19
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De Zotti M, Sella L, Bolzonello A, Gabbatore L, Peggion C, Bortolotto A, Elmaghraby I, Tundo S, Favaron F. Targeted Amino Acid Substitutions in a Trichoderma Peptaibol Confer Activity against Fungal Plant Pathogens and Protect Host Tissues from Botrytis cinerea Infection. Int J Mol Sci 2020; 21:E7521. [PMID: 33053906 PMCID: PMC7589190 DOI: 10.3390/ijms21207521] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 09/28/2020] [Accepted: 10/09/2020] [Indexed: 02/07/2023] Open
Abstract
Fungal species belonging to the Trichoderma genus are commonly used as biocontrol agents against several crop pathogens. Among their secondary metabolites, peptaibols are helical, antimicrobial peptides, which are structurally stable even under extreme pH and temperature conditions. The promise of peptaibols as agrochemicals is, however, hampered by poor water solubility, which inhibits efficient delivery for practical use in crop protection. Using a versatile synthetic strategy, based on green chemistry procedures, we produced water-soluble analogs of the short-length peptaibol trichogin. Although natural trichogin was inactive against the tested fungal plant pathogens (Botrytis cinerea, Bipolaris sorokiniana, Fusarium graminearum, and Penicillium expansum), three analogs completely inhibited fungal growth at low micromolar concentrations. The most effective peptides significantly reduced disease symptoms by B. cinerea on common bean and grapevine leaves and ripe grape berries without visible phytotoxic effects. An in-depth conformational analysis featuring a 3D-structure-activity relationship study indicated that the relative spatial position of cationic residues is crucial for increasing peptide fungicidal activity.
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Affiliation(s)
- Marta De Zotti
- Department of Chemistry, University of Padova, Via Marzolo 1, 35131 Padova, Italy; (L.G.); (C.P.); (A.B.)
| | - Luca Sella
- Department of Land, Environment, Agriculture and Forestry, University of Padova, Viale dell’Università 16, 35020 Legnaro (Padova), Italy; (L.S.); (A.B.); (I.E.); (S.T.); (F.F.)
| | - Angela Bolzonello
- Department of Land, Environment, Agriculture and Forestry, University of Padova, Viale dell’Università 16, 35020 Legnaro (Padova), Italy; (L.S.); (A.B.); (I.E.); (S.T.); (F.F.)
| | - Laura Gabbatore
- Department of Chemistry, University of Padova, Via Marzolo 1, 35131 Padova, Italy; (L.G.); (C.P.); (A.B.)
| | - Cristina Peggion
- Department of Chemistry, University of Padova, Via Marzolo 1, 35131 Padova, Italy; (L.G.); (C.P.); (A.B.)
| | - Alessandro Bortolotto
- Department of Chemistry, University of Padova, Via Marzolo 1, 35131 Padova, Italy; (L.G.); (C.P.); (A.B.)
- Department of Land, Environment, Agriculture and Forestry, University of Padova, Viale dell’Università 16, 35020 Legnaro (Padova), Italy; (L.S.); (A.B.); (I.E.); (S.T.); (F.F.)
| | - Ibrahim Elmaghraby
- Department of Land, Environment, Agriculture and Forestry, University of Padova, Viale dell’Università 16, 35020 Legnaro (Padova), Italy; (L.S.); (A.B.); (I.E.); (S.T.); (F.F.)
- Agricultural Research Center, Central Laboratory of Organic Agriculture 9, Cairo Univ. St., Giza 12619, Egypt
| | - Silvio Tundo
- Department of Land, Environment, Agriculture and Forestry, University of Padova, Viale dell’Università 16, 35020 Legnaro (Padova), Italy; (L.S.); (A.B.); (I.E.); (S.T.); (F.F.)
| | - Francesco Favaron
- Department of Land, Environment, Agriculture and Forestry, University of Padova, Viale dell’Università 16, 35020 Legnaro (Padova), Italy; (L.S.); (A.B.); (I.E.); (S.T.); (F.F.)
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20
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Terada K, Gimenez-Dejoz J, Miyagi Y, Oikawa K, Tsuchiya K, Numata K. Artificial Cell-Penetrating Peptide Containing Periodic α-Aminoisobutyric Acid with Long-Term Internalization Efficiency in Human and Plant Cells. ACS Biomater Sci Eng 2020; 6:3287-3298. [DOI: 10.1021/acsbiomaterials.0c00182] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Kayo Terada
- Biomacromolecules Research Team, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Joan Gimenez-Dejoz
- Biomacromolecules Research Team, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Yu Miyagi
- Biomacromolecules Research Team, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Kazusato Oikawa
- Biomacromolecules Research Team, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Kousuke Tsuchiya
- Biomacromolecules Research Team, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Keiji Numata
- Biomacromolecules Research Team, RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
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21
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Patel K, Kushwaha P, Kumar S, Kumar R. Lysine and α-Aminoisobutyric Acid Conjugated Bioinspired Polydopamine Surfaces for the Enhanced Antibacterial Performance of the Foley Catheter. ACS APPLIED BIO MATERIALS 2019; 2:5799-5809. [PMID: 35021573 DOI: 10.1021/acsabm.9b00794] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Khushbu Patel
- Department of Applied Chemistry, S.V. National Institute of Technology, Surat-395007, Gujarat, India
| | - Prem Kushwaha
- Centre for Biochemistry and Microbial Science, School of Basic and Applied Sciences, Central University of Punjab, Bathinda-151001, Punjab, India
| | - Shashank Kumar
- Centre for Biochemistry and Microbial Science, School of Basic and Applied Sciences, Central University of Punjab, Bathinda-151001, Punjab, India
| | - Rajender Kumar
- Department of Applied Chemistry, S.V. National Institute of Technology, Surat-395007, Gujarat, India
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22
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Taniguchi K, Wada SI, Ito Y, Hayashi J, Inomata Y, Lee SW, Tanaka T, Komura K, Akao Y, Urata H, Uchiyama K. α-Aminoisobutyric Acid-Containing Amphipathic Helical Peptide-Cyclic RGD Conjugation as a Potential Drug Delivery System for MicroRNA Replacement Therapy in Vitro. Mol Pharm 2019; 16:4542-4550. [PMID: 31596588 DOI: 10.1021/acs.molpharmaceut.9b00680] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Replacement therapy with tumor suppressive microRNA (TS-miRNA) might be the next-generation oligonucleotide therapy; however, a novel drug delivery system (DDS) is required. Recently, we developed the cell-penetrating peptide, model amphipathic peptide with α-aminoisobutyric acid (MAP(Aib)), as a carrier for oligonucleotide delivery to cells. In this study, we examined whether a modified MAP(Aib) analogue, MAP(Aib)-cRGD, could be a DDS for TS-miRNA replacement therapy. MIR145-5p, a representative TS-miRNA especially in colorectal cancer, was selected. The MAP(Aib)-cRGD dose was adjusted for MIR145-5p delivery to cells using peripheral blood mononuclear cells and degradation analysis. AlexaFluor488-labeled MIR145-5p incorporation into cells and negative regulation of MIR145-5p-targeting genes demonstrated MAP(Aib)-cRGD's functionality as a miRNA DDS. Treating MIR145-5p with MAP(Aib)-cRGD also revealed various anticancer effects, such as cell viability, invasion inhibition, and apoptosis induction in WiDr cells. Altogether, these findings suggest that MAP(Aib)-cRGD could be a DDS for TS-miRNA replacement therapy, but in vivo investigations are required.
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Affiliation(s)
| | - Shun-Ichi Wada
- Department of Bioorganic Chemistry , Osaka University of Pharmaceutical Sciences , 4-20-1 Nasahara , Takatsuki , Osaka 569-1094 , Japan
| | | | - Junsuke Hayashi
- Department of Bioorganic Chemistry , Osaka University of Pharmaceutical Sciences , 4-20-1 Nasahara , Takatsuki , Osaka 569-1094 , Japan
| | | | | | | | | | - Yukihiro Akao
- United Graduate School of Drug Discovery and Medical Information Sciences , Gifu University , 1-1 Yanagido , Gifu 501-1193 , Japan
| | - Hidehito Urata
- Department of Bioorganic Chemistry , Osaka University of Pharmaceutical Sciences , 4-20-1 Nasahara , Takatsuki , Osaka 569-1094 , Japan
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23
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Oba M, Nagano Y, Kato T, Tanaka M. Secondary structures and cell-penetrating abilities of arginine-rich peptide foldamers. Sci Rep 2019; 9:1349. [PMID: 30718681 PMCID: PMC6362038 DOI: 10.1038/s41598-018-38063-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Accepted: 12/19/2018] [Indexed: 11/09/2022] Open
Abstract
Foldamers, which are folded oligomers with well-defined conformations, have been recently reported to have a good cell-penetrating ability. α,α-Disubstituted α-amino acids are one such promising tool for the design of peptide foldamers. Here, we prepared four types of L-arginine-rich nonapeptides containing L-leucine or α,α-disubstituted α-amino acids, and evaluated their secondary structures and cell-penetrating abilities in order to elucidate a correlation between them. Peptides containing α,α-disubstituted α-amino acids had similar resistance to protease digestion but showed different secondary structures. Intracellular uptake assays revealed that the helicity of peptides was important for their cell-penetrating abilities. These findings suggested that a peptide foldamer with a stable helical structure could be promising for the design of cell-penetrating peptides.
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Affiliation(s)
- Makoto Oba
- Graduate School Biomedical Sciences, Nagasaki University, 1-14 Bunkyo-machi, Nagasaki, 852-8521, Japan.
| | - Yu Nagano
- Graduate School Biomedical Sciences, Nagasaki University, 1-14 Bunkyo-machi, Nagasaki, 852-8521, Japan
| | - Takuma Kato
- Graduate School Biomedical Sciences, Nagasaki University, 1-14 Bunkyo-machi, Nagasaki, 852-8521, Japan
- Osaka University of Pharmaceutical Sciences, 40-20-1 Nasahara, Takatsuki, Osaka, 569-1094, Japan
| | - Masakazu Tanaka
- Graduate School Biomedical Sciences, Nagasaki University, 1-14 Bunkyo-machi, Nagasaki, 852-8521, Japan
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Just D, Hernandez-Guerra D, Kritsch S, Pohl R, Císařová I, Jones PG, Mackman R, Bahador G, Jahn U. Lithium Chloride Catalyzed Asymmetric Domino Aza-Michael Addition/[3 + 2] Cycloaddition Reactions for the Synthesis of Spiro- and Bicyclic α,β,γ-Triamino Acid Derivatives. European J Org Chem 2018. [DOI: 10.1002/ejoc.201800585] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- David Just
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences; Flemingovo nám. 2 166 10 Prague 6 Czech Republic
| | - Daniel Hernandez-Guerra
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences; Flemingovo nám. 2 166 10 Prague 6 Czech Republic
| | - Susanne Kritsch
- Fachbereich Chemie; Technische Universität Braunschweig; Hagenring 30 38106 Braunschweig Germany
| | - Radek Pohl
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences; Flemingovo nám. 2 166 10 Prague 6 Czech Republic
| | - Ivana Císařová
- Department of Inorganic Chemistry; Faculty of Science; Charles University; Hlavova 2030/8 128 43 Prague 2 Czech Republic
| | - Peter G. Jones
- Fachbereich Chemie; Technische Universität Braunschweig; Hagenring 30 38106 Braunschweig Germany
| | - Richard Mackman
- Gilead Sciences, Inc.; 333 Lakeside Drive 94404 Foster City CA USA
| | - Gina Bahador
- Gilead Sciences, Inc.; 333 Lakeside Drive 94404 Foster City CA USA
| | - Ullrich Jahn
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences; Flemingovo nám. 2 166 10 Prague 6 Czech Republic
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25
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Kato T, Oba M, Nishida K, Tanaka M. Cell-Penetrating Peptides Using Cyclic α,α-Disubstituted α-Amino Acids with Basic Functional Groups. ACS Biomater Sci Eng 2018; 4:1368-1376. [PMID: 33418667 DOI: 10.1021/acsbiomaterials.8b00180] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In the delivery of cell-impermeable molecules, cell-penetrating peptides (CPPs) have been attracting increasing attention as intracellular delivery tools. In the present study, we designed four types of cyclic α,α-disubstituted α-amino acids (dAAs) with basic functional groups on their five-membered rings and different chiralities at the α-position and introduced them into arginine (Arg)-rich peptides. The evaluation of cell-penetrating abilities indicated that these peptides exhibited better cell permeabilities than an Arg nonapeptide. Furthermore, peptides containing dAAs delivered plasmid DNA (pDNA) better than a commercially available transfection reagent with a longer incubation time. These results demonstrate that the introduction of cyclic dAAs with basic functional groups into Arg-rich peptides is an effective strategy for the design of CPPs as a pDNA delivery tool.
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Affiliation(s)
- Takuma Kato
- Graduate School of Biomedical Sciences, Nagasaki University, 1-14 Bunkyo-machi, Nagasaki 852-8521, Japan.,Osaka University of Pharmaceutical Sciences, 40-20-1 Nasahara, Takatsuki, Osaka 569-1094, Japan
| | - Makoto Oba
- Graduate School of Biomedical Sciences, Nagasaki University, 1-14 Bunkyo-machi, Nagasaki 852-8521, Japan
| | - Koyo Nishida
- Graduate School of Biomedical Sciences, Nagasaki University, 1-14 Bunkyo-machi, Nagasaki 852-8521, Japan
| | - Masakazu Tanaka
- Graduate School of Biomedical Sciences, Nagasaki University, 1-14 Bunkyo-machi, Nagasaki 852-8521, Japan
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26
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Jo M, Won SW, Lee DG, Jung JK, Kim S, Kwak YS. An efficient synthetic protocol for amide derivatives of Boc-2-aminoisobutyrate. Arch Pharm Res 2018; 41:259-264. [DOI: 10.1007/s12272-018-1009-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Accepted: 02/11/2018] [Indexed: 11/30/2022]
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27
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Das S, Ben Haj Salah K, Wenger E, Martinez J, Kotarba J, Andreu V, Ruiz N, Savini F, Stella L, Didierjean C, Legrand B, Inguimbert N. Enhancing the Antimicrobial Activity of Alamethicin F50/5 by Incorporating N-terminal Hydrophobic Triazole Substituents. Chemistry 2017; 23:17964-17972. [DOI: 10.1002/chem.201703569] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Indexed: 01/20/2023]
Affiliation(s)
- Sanjit Das
- USR 3278 CRIOBE, PSL Research University, EPHE-UPVD-CNRS; Université de Perpignan Via Domitia, Laboratoire d'Excellence « CORAIL » Bâtiment T; 58 avenue P. Alduy 66860 Perpignan France)
| | - Khoubaib Ben Haj Salah
- USR 3278 CRIOBE, PSL Research University, EPHE-UPVD-CNRS; Université de Perpignan Via Domitia, Laboratoire d'Excellence « CORAIL » Bâtiment T; 58 avenue P. Alduy 66860 Perpignan France)
| | - Emmanuel Wenger
- CRM2 (UMR UL-CNRS 7036) Faculté des Sciences et Technologies; Université de Lorraine; 70239 Boulevard des Aiguillettes 54506 Vandoeuvre-lès-Nancy France)
| | - Jean Martinez
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247 CNRS; Université de Montpellier; 15 avenue Charles Flahault, BP 14491 34093 Montpellier Cedex 5 France
| | | | | | - Nicolas Ruiz
- Laboratoire Mer Molécules Santé.; Université de Nantes, UFR de Sciences pharmaceutiques et biologiques; 9 rue Bias-BP 61112 44035 Nantes France
| | - Filippo Savini
- Dipartimento di Scienze e Tecnologie Chimiche; Università di Roma, Tor Vergata; Via della Ricerca Scientifica 00133 Roma Italy)
| | - Lorenzo Stella
- Dipartimento di Scienze e Tecnologie Chimiche; Università di Roma, Tor Vergata; Via della Ricerca Scientifica 00133 Roma Italy)
| | - Claude Didierjean
- CRM2 (UMR UL-CNRS 7036) Faculté des Sciences et Technologies; Université de Lorraine; 70239 Boulevard des Aiguillettes 54506 Vandoeuvre-lès-Nancy France)
| | - Baptiste Legrand
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247 CNRS; Université de Montpellier; 15 avenue Charles Flahault, BP 14491 34093 Montpellier Cedex 5 France
| | - Nicolas Inguimbert
- USR 3278 CRIOBE, PSL Research University, EPHE-UPVD-CNRS; Université de Perpignan Via Domitia, Laboratoire d'Excellence « CORAIL » Bâtiment T; 58 avenue P. Alduy 66860 Perpignan France)
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28
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Wada SI, Takesada A, Nagamura Y, Sogabe E, Ohki R, Hayashi J, Urata H. Structure-activity relationship study of Aib-containing amphipathic helical peptide-cyclic RGD conjugates as carriers for siRNA delivery. Bioorg Med Chem Lett 2017; 27:5378-5381. [PMID: 29157863 DOI: 10.1016/j.bmcl.2017.11.018] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Accepted: 11/08/2017] [Indexed: 12/22/2022]
Abstract
The conjugation of Aib-containing amphipathic helical peptide with cyclo(-Arg-Gly-Asp-d-Phe-Cys-) (cRGDfC) at the C-terminus of the helix peptide (PI) has been reported to be useful for constructing a carrier for targeted siRNA delivery into cells. In order to explore structure-activity relationships for the development of potential carriers for siRNA delivery, we synthesized conjugates of Aib-containing amphipathic helical peptide with cRGDfC at the N-terminus (PII) and both the N- and C-termini (PIII) of the helical peptide. Furthermore, to examine the influence of PI helical chain length on siRNA delivery, truncated peptides containing 16 (PIV), 12 (PV), and 8 (PVI) amino acid residues at the N-terminus of the helical chain were synthesized. PII and PIII, as well as PI, could deliver anti-luciferase siRNA into cells to induce the knockdown of luciferase stably expressed in cells. In contrast, all of the truncated peptides were unlikely to transport siRNA into cells.
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Affiliation(s)
- Shun-Ichi Wada
- Laboratory of Bioorganic Chemistry, Osaka University of Pharmaceutical Sciences, 4-20-1 Nasahara, Takatsuki, Osaka 569-1094, Japan.
| | - Anna Takesada
- Laboratory of Bioorganic Chemistry, Osaka University of Pharmaceutical Sciences, 4-20-1 Nasahara, Takatsuki, Osaka 569-1094, Japan
| | - Yurie Nagamura
- Laboratory of Bioorganic Chemistry, Osaka University of Pharmaceutical Sciences, 4-20-1 Nasahara, Takatsuki, Osaka 569-1094, Japan
| | - Eri Sogabe
- Laboratory of Bioorganic Chemistry, Osaka University of Pharmaceutical Sciences, 4-20-1 Nasahara, Takatsuki, Osaka 569-1094, Japan
| | - Rieko Ohki
- Laboratory of Bioorganic Chemistry, Osaka University of Pharmaceutical Sciences, 4-20-1 Nasahara, Takatsuki, Osaka 569-1094, Japan
| | - Junsuke Hayashi
- Laboratory of Bioorganic Chemistry, Osaka University of Pharmaceutical Sciences, 4-20-1 Nasahara, Takatsuki, Osaka 569-1094, Japan
| | - Hidehito Urata
- Laboratory of Bioorganic Chemistry, Osaka University of Pharmaceutical Sciences, 4-20-1 Nasahara, Takatsuki, Osaka 569-1094, Japan
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29
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Henninot A, Collins JC, Nuss JM. The Current State of Peptide Drug Discovery: Back to the Future? J Med Chem 2017; 61:1382-1414. [PMID: 28737935 DOI: 10.1021/acs.jmedchem.7b00318] [Citation(s) in RCA: 648] [Impact Index Per Article: 92.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Over the past decade, peptide drug discovery has experienced a revival of interest and scientific momentum, as the pharmaceutical industry has come to appreciate the role that peptide therapeutics can play in addressing unmet medical needs and how this class of compounds can be an excellent complement or even preferable alternative to small molecule and biological therapeutics. In this Perspective, we give a concise description of the recent progress in peptide drug discovery in a holistic manner, highlighting enabling technological advances affecting nearly every aspect of this field: from lead discovery, to synthesis and optimization, to peptide drug delivery. An emphasis is placed on describing research efforts to overcome the inherent weaknesses of peptide drugs, in particular their poor pharmacokinetic properties, and how these efforts have been critical to the discovery, design, and subsequent development of novel therapeutics.
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Affiliation(s)
- Antoine Henninot
- Ferring Research Institute , 4245 Sorrento Valley Boulevard, San Diego, California 92121, United States
| | - James C Collins
- Ferring Research Institute , 4245 Sorrento Valley Boulevard, San Diego, California 92121, United States
| | - John M Nuss
- Ferring Research Institute , 4245 Sorrento Valley Boulevard, San Diego, California 92121, United States
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30
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Oba M, Kunitake M, Kato T, Ueda A, Tanaka M. Enhanced and Prolonged Cell-Penetrating Abilities of Arginine-Rich Peptides by Introducing Cyclic α,α-Disubstituted α-Amino Acids with Stapling. Bioconjug Chem 2017; 28:1801-1806. [PMID: 28603971 DOI: 10.1021/acs.bioconjchem.7b00190] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Cell-penetrating peptides are receiving increasing attention as drug delivery tools, and the search for peptides with high cell-penetrating ability and negligible cytotoxicity has become a critical research topic. Herein, cyclic α,α-disubstituted α-amino acids were introduced into arginine-rich peptides and an additional staple was provided in the side chain. The peptides designed in the present study showed more enhanced and prolonged cell-penetrating abilities than an arginine nonapeptide due to high resistance to protease and conformationally stable helical structures.
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Affiliation(s)
- Makoto Oba
- Graduate School of Biomedical Sciences, Nagasaki University , 1-14 Bunkyo-machi, Nagasaki 852-8521, Japan
| | - Masayuki Kunitake
- Graduate School of Biomedical Sciences, Nagasaki University , 1-14 Bunkyo-machi, Nagasaki 852-8521, Japan
| | - Takuma Kato
- Graduate School of Biomedical Sciences, Nagasaki University , 1-14 Bunkyo-machi, Nagasaki 852-8521, Japan
| | - Atsushi Ueda
- Graduate School of Biomedical Sciences, Nagasaki University , 1-14 Bunkyo-machi, Nagasaki 852-8521, Japan
| | - Masakazu Tanaka
- Graduate School of Biomedical Sciences, Nagasaki University , 1-14 Bunkyo-machi, Nagasaki 852-8521, Japan
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31
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Checco JW, Gellman SH. Iterative Nonproteinogenic Residue Incorporation Yields α/β-Peptides with a Helix-Loop-Helix Tertiary Structure and High Affinity for VEGF. Chembiochem 2017; 18:291-299. [PMID: 27897370 DOI: 10.1002/cbic.201600545] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Indexed: 12/12/2022]
Abstract
Inhibition of specific protein-protein interactions is attractive for a range of therapeutic applications, but the large and irregularly shaped contact surfaces involved in many such interactions make it challenging to design synthetic antagonists. Here, we describe the development of backbone-modified peptides containing both α- and β-amino acid residues (α/β-peptides) that target the receptor-binding surface of vascular endothelial growth factor (VEGF). Our approach is based on the Z-domain, which adopts a three-helix bundle tertiary structure. We show how a two-helix "mini-Z-domain" can be modified to contain β and other nonproteinogenic residues while retaining the target-binding epitope by using iterative unnatural residue incorporation. The resulting α/β-peptides are less susceptible to proteolysis than is their parent α-peptide, and some of these α/β-peptides match the full-length Z-domain in terms of affinity for receptor-recognition surfaces on the VEGF homodimer.
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Affiliation(s)
- James W Checco
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin, 53706, USA
| | - Samuel H Gellman
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin, 53706, USA
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32
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Effects of Aib residues insertion on the structural–functional properties of the frog skin-derived peptide esculentin-1a(1–21)NH2. Amino Acids 2016; 49:139-150. [DOI: 10.1007/s00726-016-2341-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Accepted: 09/28/2016] [Indexed: 10/20/2022]
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33
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Cromm PM, Spiegel J, Küchler P, Dietrich L, Kriegesmann J, Wendt M, Goody RS, Waldmann H, Grossmann TN. Protease-Resistant and Cell-Permeable Double-Stapled Peptides Targeting the Rab8a GTPase. ACS Chem Biol 2016; 11:2375-82. [PMID: 27336832 DOI: 10.1021/acschembio.6b00386] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Small GTPases comprise a family of highly relevant targets in chemical biology and medicinal chemistry research and have been considered "undruggable" due to the persisting lack of effective synthetic modulators and suitable binding pockets. As molecular switches, small GTPases control a multitude of pivotal cellular functions, and their dysregulation is associated with many human diseases such as various forms of cancer. Rab-GTPases represent the largest subfamily of small GTPases and are master regulators of vesicular transport interacting with various proteins via flat and extensive protein-protein interactions (PPIs). The only reported synthetic inhibitor of a PPI involving an activated Rab GTPase is the hydrocarbon stapled peptide StRIP3. However, this macrocyclic peptide shows low proteolytic stability and cell permeability. Here, we report the design of a bioavailable StRIP3 analogue that harbors two hydrophobic cross-links and exhibits increased binding affinity, combined with robust cellular uptake and extremely high proteolytic stability. Localization experiments reveal that this double-stapled peptide and its target protein Rab8a accumulate in the same cellular compartments. The reported approach offers a strategy for the implementation of biostability into conformationally constrained peptides while supporting cellular uptake and target affinity, thereby conveying drug-like properties.
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Affiliation(s)
- Philipp M. Cromm
- Department
of Chemical Biology, Max-Planck-Institute of Molecular Physiology, Otto-Hahn-Strasse 11, D-44227 Dortmund, Germany
- Technische Universität Dortmund, Fakultät
für Chemie und Chemische Biologie, Otto-Hahn-Strasse 6, D-44227 Dortmund, Germany
- Chemical Genomics Centre of the Max Planck Society, Otto-Hahn-Strasse 15, D-44227 Dortmund, Germany
| | - Jochen Spiegel
- Department
of Chemical Biology, Max-Planck-Institute of Molecular Physiology, Otto-Hahn-Strasse 11, D-44227 Dortmund, Germany
- Technische Universität Dortmund, Fakultät
für Chemie und Chemische Biologie, Otto-Hahn-Strasse 6, D-44227 Dortmund, Germany
- Chemical Genomics Centre of the Max Planck Society, Otto-Hahn-Strasse 15, D-44227 Dortmund, Germany
| | - Philipp Küchler
- Department
of Chemical Biology, Max-Planck-Institute of Molecular Physiology, Otto-Hahn-Strasse 11, D-44227 Dortmund, Germany
- Technische Universität Dortmund, Fakultät
für Chemie und Chemische Biologie, Otto-Hahn-Strasse 6, D-44227 Dortmund, Germany
| | - Laura Dietrich
- Technische Universität Dortmund, Fakultät
für Chemie und Chemische Biologie, Otto-Hahn-Strasse 6, D-44227 Dortmund, Germany
- Chemical Genomics Centre of the Max Planck Society, Otto-Hahn-Strasse 15, D-44227 Dortmund, Germany
| | - Julia Kriegesmann
- Technische Universität Dortmund, Fakultät
für Chemie und Chemische Biologie, Otto-Hahn-Strasse 6, D-44227 Dortmund, Germany
- Chemical Genomics Centre of the Max Planck Society, Otto-Hahn-Strasse 15, D-44227 Dortmund, Germany
- VU University Amsterdam, Department of Chemistry & Pharmaceutical Sciences, De Boelelaan 1083, 1081 HV, Amsterdam, The Netherlands
| | - Mathias Wendt
- Technische Universität Dortmund, Fakultät
für Chemie und Chemische Biologie, Otto-Hahn-Strasse 6, D-44227 Dortmund, Germany
- Chemical Genomics Centre of the Max Planck Society, Otto-Hahn-Strasse 15, D-44227 Dortmund, Germany
- VU University Amsterdam, Department of Chemistry & Pharmaceutical Sciences, De Boelelaan 1083, 1081 HV, Amsterdam, The Netherlands
| | - Roger S. Goody
- Structural
Biochemistry, Max-Planck-Institute of Molecular Physiology, Otto-Hahn-Strasse
11, D-44227 Dortmund, Germany
| | - Herbert Waldmann
- Department
of Chemical Biology, Max-Planck-Institute of Molecular Physiology, Otto-Hahn-Strasse 11, D-44227 Dortmund, Germany
- Technische Universität Dortmund, Fakultät
für Chemie und Chemische Biologie, Otto-Hahn-Strasse 6, D-44227 Dortmund, Germany
| | - Tom N. Grossmann
- Technische Universität Dortmund, Fakultät
für Chemie und Chemische Biologie, Otto-Hahn-Strasse 6, D-44227 Dortmund, Germany
- Chemical Genomics Centre of the Max Planck Society, Otto-Hahn-Strasse 15, D-44227 Dortmund, Germany
- VU University Amsterdam, Department of Chemistry & Pharmaceutical Sciences, De Boelelaan 1083, 1081 HV, Amsterdam, The Netherlands
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Palomo V, Díaz SA, Stewart MH, Susumu K, Medintz IL, Dawson PE. 3,4-Dihydroxyphenylalanine Peptides as Nonperturbative Quantum Dot Sensors of Aminopeptidase. ACS NANO 2016; 10:6090-9. [PMID: 27206058 PMCID: PMC4968404 DOI: 10.1021/acsnano.6b01682] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Fluorescence-based assays for hydrolases that cleave within the substrate (endopeptidases) are common, while developing substrates for proteases that selectively cleave from peptide termini (exopeptidases) is more challenging, since the termini are specifically recognized by the enzyme and cannot be modified to facilitate a Förster resonance energy transfer (FRET)-based approach. The development of a robust system that enables the quenching of fluorescent particles by simple amino acid side chains would find broad utility for peptide sensors and would be advantageous for exopeptidases. Here we describe a quantum dot (QD)-based electron transfer (ET) sensor that is able to allow direct, quantitative monitoring of both exopeptidase and endopeptidase activity. The incorporation of 3,4-dihydroxyphenylalanine (DOPA) into the sequence of a peptide allows for the quenching of QD photoluminescence through an ET mechanism. DOPA is a nonproteinogenic amino acid that can replace a phenylalanine or tyrosine residue in a peptide sequence without severely altering structural properties, allowing for its introduction at multiple positions within a biologically active peptide substrate. Consequently, the quenching system presented here is ideally suited for incorporation into diverse peptide substrates for enzyme recognition, digestion, and activity sensing. Our findings suggest a broad utility of a small ET-capable amino acid side chain in detecting enzyme activity through ET-mediated QD luminescence quenching.
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Affiliation(s)
- Valle Palomo
- Department of Chemistry, The Scripps Research Institute, La Jolla, California, 92037 (USA)
| | - Sebastián A. Díaz
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C., 20375 (USA)
| | - Michael H. Stewart
- Optical Sciences Division, Code 5611, U.S. Naval Research Laboratory, Washington, D.C., 20375 (USA)
| | - Kimihiro Susumu
- Optical Sciences Division, Code 5611, U.S. Naval Research Laboratory, Washington, D.C., 20375 (USA)
| | - Igor L. Medintz
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C., 20375 (USA)
| | - Philip E. Dawson
- Department of Chemistry, The Scripps Research Institute, La Jolla, California, 92037 (USA)
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35
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Kato T, Yamashita H, Misawa T, Nishida K, Kurihara M, Tanaka M, Demizu Y, Oba M. Plasmid DNA delivery by arginine-rich cell-penetrating peptides containing unnatural amino acids. Bioorg Med Chem 2016; 24:2681-7. [PMID: 27132868 DOI: 10.1016/j.bmc.2016.04.031] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Revised: 04/13/2016] [Accepted: 04/16/2016] [Indexed: 10/21/2022]
Abstract
Cell-penetrating peptides (CPPs) have been developed as drug, protein, and gene delivery tools. In the present study, arginine (Arg)-rich CPPs containing unnatural amino acids were designed to deliver plasmid DNA (pDNA). The transfection ability of one of the Arg-rich CPPs examined here was more effective than that of the Arg nonapeptide, which is the most frequently used CPP. The transfection efficiencies of Arg-rich CPPs increased with longer post-incubation times and were significantly higher at 48-h and 72-h post-incubation than that of the commercially available transfection reagent TurboFect. These Arg-rich CPPs were complexed with pDNA for a long time in cells and effectively escaped from the late endosomes/lysosomes into the cytoplasm. These results will be helpful for designing novel CPPs for pDNA delivery.
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Affiliation(s)
- Takuma Kato
- Graduate School of Biomedical Sciences, Nagasaki University, 1-14 Bunkyo-machi, Nagasaki 852-8521, Japan
| | - Hiroko Yamashita
- Division of Organic Chemistry, National Institute of Health Sciences, Setagaya, Tokyo 158-8501, Japan; Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama 226-8501, Japan
| | - Takashi Misawa
- Division of Organic Chemistry, National Institute of Health Sciences, Setagaya, Tokyo 158-8501, Japan
| | - Koyo Nishida
- Graduate School of Biomedical Sciences, Nagasaki University, 1-14 Bunkyo-machi, Nagasaki 852-8521, Japan
| | - Masaaki Kurihara
- Division of Organic Chemistry, National Institute of Health Sciences, Setagaya, Tokyo 158-8501, Japan; Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama 226-8501, Japan
| | - Masakazu Tanaka
- Graduate School of Biomedical Sciences, Nagasaki University, 1-14 Bunkyo-machi, Nagasaki 852-8521, Japan
| | - Yosuke Demizu
- Division of Organic Chemistry, National Institute of Health Sciences, Setagaya, Tokyo 158-8501, Japan.
| | - Makoto Oba
- Graduate School of Biomedical Sciences, Nagasaki University, 1-14 Bunkyo-machi, Nagasaki 852-8521, Japan.
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36
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Mainz ER, Dobes NC, Allbritton NL. Pronase E-Based Generation of Fluorescent Peptide Fragments: Tracking Intracellular Peptide Fate in Single Cells. Anal Chem 2015; 87:7987-95. [PMID: 26171808 PMCID: PMC6026012 DOI: 10.1021/acs.analchem.5b01929] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The ability to track intracellular peptide proteolysis at the single cell level is of growing interest, particularly as short peptide sequences continue to play important roles as biosensors, therapeutics, and endogenous participants in antigen processing and intracellular signaling. We describe a rapid and inexpensive methodology to generate fluorescent peptide fragments from a parent sequence with diverse chemical properties, including aliphatic, nonpolar, basic, acidic, and non-native amino acids. Four peptide sequences with existing biochemical applications were fragmented using incubation with Pronase E and/or formic acid, and in each case a complete set of fluorescent fragments was generated for use as proteolysis standards in chemical cytometry. Fragment formation and identity was monitored with capillary electrophoresis with laser-induced fluorescence detection (CE-LIF) and matrix assisted laser desorption ionization-time-of-flight mass spectrometry (MALDI-MS) to confirm the presence of all sequences and yield fragmentation profiles across Pronase E concentrations which can readily be used by others. As a pilot study, Pronase E-generated standards from an Abl kinase sensor and an ovalbumin antigenic peptide were then employed to identify proteolysis products arising from the metabolism of these sequences in single cells. The Abl kinase sensor fragmented at 4.2 ± 4.8 zmol μM(-1) s(-1) and the majority of cells possessed similar fragment identities. In contrast, an ovalbumin epitope peptide was degraded at 8.9 ± 0.1 zmol μM(-1) s(-1), but with differential fragment formation between individual cells. Overall, Pronase E-generated peptide standards were a rapid and efficient method to identify proteolysis products from cells.
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Affiliation(s)
- Emilie R. Mainz
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | - Nicholas C. Dobes
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | - Nancy L. Allbritton
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599, USA
- Department of Biomedical Engineering, University of North Carolina, Chapel Hill, North Carolina 27599, USA and North Carolina State University, Raleigh, North Carolina 27695, US
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37
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Abstract
A small library of truncated/lipid-conjugated neuromedin U (NmU) analogs was synthesized and tested in vitro using an intracellular calcium signaling assay. The selected, most active analogs were then tested in vivo, and showed potent anorexigenic effects in a diet-induced obese (DIO) mouse model. The most promising compound, NM4-C16 was effective in a once-weekly-dose regimen. Collectively, our findings suggest that short, lipidated analogs of NmU are suitable leads for the development of novel anti-obesity therapeutics.
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38
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Yamashita H, Demizu Y, Misawa T, Shoda T, Kurihara M. Synthesis of a bis-cationic α,α-disubstituted amino acid (9-amino-bispidine-9-carboxylic acid) and its effects on the conformational properties of peptides. Tetrahedron 2015. [DOI: 10.1016/j.tet.2015.02.076] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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39
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Targeting diverse protein-protein interaction interfaces with α/β-peptides derived from the Z-domain scaffold. Proc Natl Acad Sci U S A 2015; 112:4552-7. [PMID: 25825775 DOI: 10.1073/pnas.1420380112] [Citation(s) in RCA: 86] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Peptide-based agents derived from well-defined scaffolds offer an alternative to antibodies for selective and high-affinity recognition of large and topologically complex protein surfaces. Here, we describe a strategy for designing oligomers containing both α- and β-amino acid residues ("α/β-peptides") that mimic several peptides derived from the three-helix bundle "Z-domain" scaffold. We show that α/β-peptides derived from a Z-domain peptide targeting vascular endothelial growth factor (VEGF) can structurally and functionally mimic the binding surface of the parent peptide while exhibiting significantly decreased susceptibility to proteolysis. The tightest VEGF-binding α/β-peptide inhibits the VEGF165-induced proliferation of human umbilical vein endothelial cells. We demonstrate the versatility of this strategy by showing how principles underlying VEGF signaling inhibitors can be rapidly extended to produce Z-domain-mimetic α/β-peptides that bind to two other protein partners, IgG and tumor necrosis factor-α. Because well-established selection techniques can identify high-affinity Z-domain derivatives from large DNA-encoded libraries, our findings should enable the design of biostable α/β-peptides that bind tightly and specifically to diverse targets of biomedical interest. Such reagents would be useful for diagnostic and therapeutic applications.
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40
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Blum AP, Kammeyer JK, Yin J, Crystal DT, Rush AM, Gilson MK, Gianneschi NC. Peptides displayed as high density brush polymers resist proteolysis and retain bioactivity. J Am Chem Soc 2014; 136:15422-37. [PMID: 25314576 PMCID: PMC4227725 DOI: 10.1021/ja5088216] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
We describe a strategy for rendering peptides resistant to proteolysis by formulating them as high-density brush polymers. The utility of this approach is demonstrated by polymerizing well-established cell-penetrating peptides (CPPs) and showing that the resulting polymers are not only resistant to proteolysis but also maintain their ability to enter cells. The scope of this design concept is explored by studying the proteolytic resistance of brush polymers composed of peptides that are substrates for either thrombin or a metalloprotease. Finally, we demonstrate that the proteolytic susceptibility of peptide brush polymers can be tuned by adjusting the density of the polymer brush and offer in silico models to rationalize this finding. We contend that this strategy offers a plausible method of preparing peptides for in vivo use, where rapid digestion by proteases has traditionally restricted their utility.
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Affiliation(s)
- Angela P Blum
- Department of Chemistry & Biochemistry, ‡Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego , La Jolla, California 92093, United States
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41
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Kato T, Oba M, Nishida K, Tanaka M. Cell-Penetrating Helical Peptides Having l-Arginines and Five-Membered Ring α,α-Disubstituted α-Amino Acids. Bioconjug Chem 2014; 25:1761-8. [DOI: 10.1021/bc5003949] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Takuma Kato
- Graduate School of Biomedical
Sciences, Nagasaki University, 1-14 Bunkyo-machi, Nagasaki 852-8521, Japan
| | - Makoto Oba
- Graduate School of Biomedical
Sciences, Nagasaki University, 1-14 Bunkyo-machi, Nagasaki 852-8521, Japan
| | - Koyo Nishida
- Graduate School of Biomedical
Sciences, Nagasaki University, 1-14 Bunkyo-machi, Nagasaki 852-8521, Japan
| | - Masakazu Tanaka
- Graduate School of Biomedical
Sciences, Nagasaki University, 1-14 Bunkyo-machi, Nagasaki 852-8521, Japan
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42
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Yamashita H, Demizu Y, Shoda T, Sato Y, Oba M, Tanaka M, Kurihara M. Amphipathic short helix-stabilized peptides with cell-membrane penetrating ability. Bioorg Med Chem 2014; 22:2403-8. [DOI: 10.1016/j.bmc.2014.03.005] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2014] [Revised: 02/28/2014] [Accepted: 03/04/2014] [Indexed: 10/25/2022]
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43
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Žukauskaitė A, Moretto A, Peggion C, De Zotti M, Šačkus A, Formaggio F, De Kimpe N, Mangelinckx S. Synthesis and Conformational Study of Model Peptides ContainingN-Substituted 3-Aminoazetidine-3-carboxylic Acids. European J Org Chem 2014. [DOI: 10.1002/ejoc.201301741] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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44
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Milov AD, Tsvetkov YD, Bortolus M, Maniero AL, Gobbo M, Toniolo C, Formaggio F. Synthesis and conformational properties of a TOAC doubly spin-labeled analog of the medium-length, membrane active peptaibiotic ampullosporin a as revealed by cd, fluorescence, and EPR spectroscopies. Biopolymers 2014; 102:40-8. [DOI: 10.1002/bip.22362] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2013] [Revised: 07/10/2013] [Accepted: 07/12/2013] [Indexed: 11/10/2022]
Affiliation(s)
- Alexander D. Milov
- Institute of Chemical Kinetics and Combustion; Novosibirsk 630090 Russian Federation
| | - Yuri D. Tsvetkov
- Institute of Chemical Kinetics and Combustion; Novosibirsk 630090 Russian Federation
| | - Marco Bortolus
- Department of Chemical Sciences; University of Padova; 35131 Padova Italy
| | - Anna Lisa Maniero
- Department of Chemical Sciences; University of Padova; 35131 Padova Italy
| | - Marina Gobbo
- Department of Chemical Sciences; University of Padova; 35131 Padova Italy
- Institute of Biomolecular Chemistry; Padova Unit, CNR 35131 Padova Italy
| | - Claudio Toniolo
- Department of Chemical Sciences; University of Padova; 35131 Padova Italy
- Institute of Biomolecular Chemistry; Padova Unit, CNR 35131 Padova Italy
| | - Fernando Formaggio
- Department of Chemical Sciences; University of Padova; 35131 Padova Italy
- Institute of Biomolecular Chemistry; Padova Unit, CNR 35131 Padova Italy
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45
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Wada SI, Hashimoto Y, Kawai Y, Miyata K, Tsuda H, Nakagawa O, Urata H. Effect of Ala replacement with Aib in amphipathic cell-penetrating peptide on oligonucleotide delivery into cells. Bioorg Med Chem 2013; 21:7669-73. [PMID: 24216093 DOI: 10.1016/j.bmc.2013.10.029] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2013] [Revised: 10/18/2013] [Accepted: 10/19/2013] [Indexed: 11/28/2022]
Abstract
A number of cell-penetrating peptides (CPPs) have been characterized and their usefulness as delivery tools has been clarified. As one of the CPPs, model amphipathic peptide (MAP) was developed by integrating both hydrophobic and hydrophilic amino acids in its sequence. In our previous work, we designed MAP(Aib) by replacing five alanine (Ala) residues on the hydrophobic face of the helix in the MAP sequence with α-aminoisobutyric acid (Aib) residues, and the replacement resulted in higher helix propensity, stronger resistance to protease, and higher cell membrane permeability than MAP. As a next step, we examined the efficiency of oligonucleotide (ODN) delivery into cells by MAP(Aib) in comparison with that by MAP. The electrostatically formed MAP(Aib)/ODN complex was more easily taken up by cells than the MAP/ODN complex, and the ODN delivery by MAP(Aib) was via an endocytic pathway. We demonstrated that the incorporation of Aib residues into CPPs enhances the delivery of hydrophilic molecules, such as ODN, into cells.
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Affiliation(s)
- Shun-Ichi Wada
- Laboratory of Bioorganic Chemistry, Osaka University of Pharmaceutical Sciences, 4-20-1 Nasahara, Takatsuki, Osaka 569-1094, Japan.
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46
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Antimicrobial lipopeptaibol trichogin GA IV: role of the three Aib residues on conformation and bioactivity. Amino Acids 2012; 43:1761-77. [DOI: 10.1007/s00726-012-1261-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2012] [Accepted: 02/28/2012] [Indexed: 11/26/2022]
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47
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De Zotti M, Biondi B, Peggion C, Formaggio F, Park Y, Hahm KS, Toniolo C. Trichogin GA IV: a versatile template for the synthesis of novel peptaibiotics. Org Biomol Chem 2011; 10:1285-99. [PMID: 22179201 DOI: 10.1039/c1ob06178j] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Trichogin GA IV, isolated from the fungus Trichoderma longibrachiatum, is the prototype of lipopeptaibols, the sub-class of short-length peptaibiotics exhibiting membrane-modifying properties. This peptaibol is predominantly folded in a mixed 3(10)-/α- helical conformation with a clear, albeit modest, amphiphilic character, which is likely to be responsible for its capability to perturb bacterial membranes and to induce cell death. In previous papers, we reported on the interesting biological properties of trichogin GA IV, namely its good activity against Gram positive bacteria, in particular methicillin-resistant S. aureus strains, its stability towards proteolytic degradation, and its low hemolytic activity. Aiming at broadening the antimicrobial activity spectrum by increasing the peptide helical amphiphilicity, in this work we synthesized, by solution and solid-phase methodologies, purified and fully characterized a set of trichogin GA IV analogs in which the four Gly residues at positions 2, 5, 6, 9, lying in the poorly hydrophilic face of the helical structure, are substituted by one (position 2, 5, 6 or 9), two (positions 5 and 6), three (positions 2, 5, and 9), and four (positions 2, 5, 6, and 9) Lys residues. The conformational preferences of the Lys-containing analogs were assessed by FT-IR absorption, CD and 2D-NMR techniques in aqueous, organic, and membrane-mimetic environments. Interestingly, it turns out that the presence of charged residues induces a transition of the helical conformation adopted by the peptaibols (from 3(10)- to α-helix) as a function of pH in a reversible process. The role played in the analogs by the markedly increased amphiphilicity was further tested by fluorescence leakage experiments in model membranes, protease resistance, antibacterial and antifungal activities, cytotoxicity, and hemolysis. Taken together, our biological results provide evidence that some of the least substituted among these analogs are good candidates for the development of new membrane-active antimicrobial agents.
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Affiliation(s)
- Marta De Zotti
- ICB, Padova Unit, CNR, Department of Chemistry, University of Padova, 35131, Padova, Italy
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48
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Frydman-Marom A, Convertino M, Pellarin R, Lampel A, Shaltiel-Karyo R, Segal D, Caflisch A, Shalev DE, Gazit E. Structural basis for inhibiting β-amyloid oligomerization by a non-coded β-breaker-substituted endomorphin analogue. ACS Chem Biol 2011; 6:1265-76. [PMID: 21892833 DOI: 10.1021/cb200103h] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The distribution of endomorphins (EM) 1 and 2 in the human brain inversely correlates with cerebral neurodegeneration in Alzheimer's disease (AD), implying a protective role. These endogenous opioid peptides incorporate aromatic residues and a β-breaker motif, as seen in several optimized inhibitors of Aβ aggregation. The activity of native endomorphins was studied, as well as the rationally designed analogue Aib-1, which includes a remarkably efficient β-breaker, α-aminoisobutyric acid (Aib). In vitro and GFP fusion protein assays showed that Aib-1 interacted with Aβ and markedly inhibited the formation of toxic oligomer and fibril growth. Moreover, Aib-1 prevented the toxicity of Aβ toward neuronal PC12 cells and markedly rectified reduced longevity of an AD fly model. Atomistic simulations and NMR-derived solution structures revealed that Aib-1 significantly reduced the propensity of Aβ to aggregate due to multimode interactions including aromatic, hydrophobic, and polar contacts. We suggest that hindering the self-assembly process by interfering with the aromatic core of amyloidogenic peptides may pave the way toward developing therapeutic agents to treat amyloid-associated diseases.
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Affiliation(s)
- Anat Frydman-Marom
- Department of Molecular Microbiology & Biotechnology, Tel-Aviv University, Tel-Aviv 69978, Israel
| | - Marino Convertino
- Department of Biochemistry, University of Zurich, CH-8057 Zurich, Switzerland
| | - Riccardo Pellarin
- Department of Biochemistry, University of Zurich, CH-8057 Zurich, Switzerland
| | - Ayala Lampel
- Department of Molecular Microbiology & Biotechnology, Tel-Aviv University, Tel-Aviv 69978, Israel
| | - Ronit Shaltiel-Karyo
- Department of Molecular Microbiology & Biotechnology, Tel-Aviv University, Tel-Aviv 69978, Israel
| | - Daniel Segal
- Department of Molecular Microbiology & Biotechnology, Tel-Aviv University, Tel-Aviv 69978, Israel
| | - Amedeo Caflisch
- Department of Biochemistry, University of Zurich, CH-8057 Zurich, Switzerland
| | - Deborah E. Shalev
- Wolfson Centre for Applied Structural Biology, Hebrew University of Jerusalem, Safra Campus, Givat Ram, Jerusalem 91904, Israel
| | - Ehud Gazit
- Department of Molecular Microbiology & Biotechnology, Tel-Aviv University, Tel-Aviv 69978, Israel
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49
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Wada SI, Tsuda H, Okada T, Urata H. Cellular uptake of Aib-containing amphipathic helix peptide. Bioorg Med Chem Lett 2011; 21:5688-91. [DOI: 10.1016/j.bmcl.2011.08.030] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2011] [Revised: 08/02/2011] [Accepted: 08/05/2011] [Indexed: 11/27/2022]
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50
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De Zotti M, Biondi B, Peggion C, Park Y, Hahm KS, Formaggio F, Toniolo C. Synthesis, preferred conformation, protease stability, and membrane activity of heptaibin, a medium-length peptaibiotic. J Pept Sci 2011; 17:585-94. [PMID: 21495119 DOI: 10.1002/psc.1364] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2011] [Accepted: 01/18/2011] [Indexed: 11/11/2022]
Abstract
The medium-length peptaibiotics are characterized by a primary structure of 14-16 amino acid residues. Despite the interesting antibiotic and antifungal properties exhibited by these membrane-active peptides, their exact mechanism of action is still unknown. Here, we present our results on heptaibin, a 14-amino acid peptaibiotic found to exhibit antimicrobial activity against Staphylococcus aureus. We carried out the very challenging synthesis of heptaibin on solid phase and a detailed conformational analysis in solution. The peptaibiotic is folded in a mixed 3₁₀-/α-helix conformation which exhibits a remarkable amphiphilic character. We also find that it is highly stable toward degradation by proteolytic enzymes and nonhemolytic. Finally, fluorescence leakage experiments using small unilamellar vesicles of three different compositions revealed that heptaibin, although uncharged, is a selective compound for permeabilization of model membranes mimicking the overall negatively charged surface of Gram-positive bacteria. This latter finding is in agreement with the originally published antimicrobial activity data.
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Affiliation(s)
- Marta De Zotti
- ICB, Padova Unit, CNR, Department of Chemistry, University of Padova, via Marzolo 1, 35131 Padova, Italy.
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