@article{MTMT:34294004, title = {Non-Covalent Interactions Enforce Conformation in Switchable and Water-Soluble Diketopiperazine-Pyridine Foldamers}, url = {https://m2.mtmt.hu/api/publication/34294004}, author = {McCann, Sinead and Roe, William E. and Agnew, Hannah E. and Knipe, Peter C.}, doi = {10.1002/anie.202307180}, journal-iso = {ANGEW CHEM INT EDIT}, journal = {ANGEWANDTE CHEMIE-INTERNATIONAL EDITION}, volume = {62}, unique-id = {34294004}, issn = {1433-7851}, abstract = {To reach their potential as mimics of the dynamic molecules present in biological systems, foldamers must be designed to display stimulus-responsive behavior. Here we report such a foldamer architecture based on alternating pyridine-diketopiperazine linkers. Epimerization is conveniently prevented through a copper-catalyzed coupling protocol. The compounds' native unswitched conformation is first discovered in the solid and solution state. The foldamers can be solubilized in DMSO and pH 9.5 buffer, retaining conformational control to a large degree. Lastly, dynamic switching is demonstrated through treatment with acid, leading to behaviour we describe as stimulus-responsive sidechain reconfiguration.}, keywords = {CONFORMATION; FOLDAMERS; Crystallography; NMR spectroscopy; MOLECULAR SWITCHES}, year = {2023}, eissn = {1521-3773} } @article{MTMT:34616533, title = {Antimicrobial and Adjuvant Potencies of Di-n-alkyl Substituted Diazalariat Ethers}, url = {https://m2.mtmt.hu/api/publication/34616533}, author = {Patel, Mohit B. and Spikes, Helena and Bailey, Robert S. and Connell, Thomas and Gill, Hannah and Gokel, Michael R. and Harris, Rebecca and Meisel, Joseph W. and Negin, Saeedeh and Yin, Shanheng Andrew and Gokel, George W.}, doi = {10.3390/antibiotics12101513}, journal-iso = {ANTIBIOTICS-BASEL}, journal = {ANTIBIOTICS}, volume = {12}, unique-id = {34616533}, abstract = {Lariat ethers are macrocyclic polyethers-crown ethers-to which sidearms are appended. 4,13-Diaza-18-crown-6 having twin alkyl chains at the nitrogens show biological activity. They exhibit antibiotic activity, but when co-administered at with an FDA-approved antibiotic, the latter's potency is often strongly enhanced. Potency enhancements and resistance reversals have been documented in vitro for a range of Gram-negative and Gram-positive bacteria with a variety of antimicrobials. Strains of E. coli and Staphylococcus aureus having resistance to a range of drugs have been studied and the potency enhancements (checkerboards) are reported here. Drugs included in the present study are ampicillin, cefepime, chlortetracycline, ciprofloxacin, doxycycline, kanamycin, minocycline, norfloxacin, oxycycline, penicillin G, and tetracycline. Enhancements of norfloxacin potency against S. aureus 1199B of up to 128-fold were observed. The properties of these lariat ethers have been studied to determine solubility, their membrane penetration, cytotoxicity and mammalian cell survival, and their effect on bacterial efflux pumps. It is shown that in some cases, the lariat ethers have complex antimicrobials with considerable selectivity. Based on these observations, including 1:1 complexation between lariat ethers and antimicrobials and the cytotoxicity of the MeI salts showing a separation index of 32-fold, they hold significant potential for further development.}, keywords = {BACTERIA; CYTOTOXICITY; Antibiotic resistance; membrane permeability; adjuvant; Antibiotic; crown ether; EFFLUX PUMPS; Resistance reversal; lariat ether}, year = {2023}, eissn = {2079-6382} } @article{MTMT:33903404, title = {Engineering discrete synthetic macromolecules for biomedical applications}, url = {https://m2.mtmt.hu/api/publication/33903404}, author = {Shen, Aizong and Zhang, Lei and Xie, Yanbo and Zhu, Xueyu and Hu, Jinming and Liu, Shiyong}, doi = {10.1016/j.nantod.2022.101728}, journal-iso = {NANO TODAY}, journal = {NANO TODAY}, volume = {48}, unique-id = {33903404}, issn = {1748-0132}, abstract = {Synthetic polymers have been extensively used in biomedical fields for imaging and therapeutic purposes. These macromolecular nanomedicines have shown unique advantages, such as increased blood circulation time, decreased systemic toxicity, and improved therapeutic outcomes. However, the polydisperse mole-cular weight of conventional polymers greatly hampers the reproducibility and clinical translations of macromolecular nanomedicines. Unlike conventional polymers with molecular weight distributions, dis-crete polymers are characterized by precise molecular weight and no molecular weight distribution (D = 1.0). Although discrete polymers have similar chemical structures and compositions to those of their dis-perse counterparts, they can show drastically distinct physiochemical properties and thus different bio-medical performance. In this review, we summarize the recent achievements of discrete polymers in optical imaging, magnetic resonance (MR) imaging, and therapeutic applications. In addition, the representative methods used to synthesize discrete polymers are briefly discussed. Although this field represents an emerging research direction, preliminary results are encouraging and promising in many aspects. Due to the structural similarity of discrete and disperse polymers, their precise structures and improved performance may greatly facilitate their clinical translation into precision nanomedicines. We hope that more effort will be devoted to the development of highly efficient synthetic strategies and the conduction of (pre)clinical studies of discrete polymers. An in-depth understanding of the structure-property relationships of discrete polymers can be advantageous to boost their practical applications. (c) 2022 Elsevier Ltd. All rights reserved.}, keywords = {Magnetic Resonance Imaging; Optical imaging; Precision nanomedicine; Discrete polymer}, year = {2023}, eissn = {1878-044X}, orcid-numbers = {Hu, Jinming/0000-0002-6969-1343; Liu, Shiyong/0000-0002-9789-6282} } @article{MTMT:34294003, title = {Proteolytically Stable Diaza-Peptide Foldamers Mimic Helical Hot Spots of Protein-Protein Interactions and Act as Natural Chaperones}, url = {https://m2.mtmt.hu/api/publication/34294003}, author = {Shi, Chenghui and Kaffy, Julia and Ha-Duong, Tap and Gallard, Jean-Francois and Pruvost, Alain and Mabondzo, Aloise and Ciccone, Lidia and Ongeri, Sandrine and Tonali, Nicolo}, doi = {10.1021/acs.jmedchem.3c00611}, journal-iso = {J MED CHEM}, journal = {JOURNAL OF MEDICINAL CHEMISTRY}, volume = {66}, unique-id = {34294003}, issn = {0022-2623}, abstract = {A novel class of peptidomimetic foldamers based on diaza-peptide units are reported. Circular dichroism, attenuated total reflection -Fourier transform infrared, NMR, and molecular dynamics studies demonstrate that unlike the natural parent nonapeptide, the specific incorporation of one diaza-peptide unit at the N-terminus allows helical folding in water, which is further reinforced by the introduction of a second unit at the C-terminus. The ability of these foldamers to resist proteolysis, to mimic the small helical hot spot of transthyretin-amyloid ss (A ss) cross-interaction, and to decrease pathological A ss aggregation demonstrates that the introduction of diaza-peptide units is a valid approach for designing mimics or inhibitors of protein-protein interaction and other therapeutic peptidomimetics. This study also reveals that small peptide foldamers can play the same role as physiological chaperone proteins and opens a new way to design inhibitors of amyloid protein aggregation, a hallmark of more than 20 serious human diseases such as Alzheimer's disease.}, year = {2023}, eissn = {1520-4804}, pages = {12005-12017}, orcid-numbers = {Ha-Duong, Tap/0000-0002-0847-2948; Ongeri, Sandrine/0000-0002-2118-7324} } @article{MTMT:34044318, title = {Comparative Study of Molecular Mechanics Force Fields for β-Peptidic Foldamers: Folding and Self-Association}, url = {https://m2.mtmt.hu/api/publication/34044318}, author = {Wacha, András Ferenc and Varga, Zoltán and Beke-Somfai, Tamás}, doi = {10.1021/acs.jcim.3c00175}, journal-iso = {J CHEM INF MODEL}, journal = {JOURNAL OF CHEMICAL INFORMATION AND MODELING}, volume = {63}, unique-id = {34044318}, issn = {1549-9596}, year = {2023}, eissn = {1549-960X}, pages = {3799-3813}, orcid-numbers = {Wacha, András Ferenc/0000-0002-9609-0893; Varga, Zoltán/0000-0002-5741-2669} } @article{MTMT:32695477, title = {Introducing the Chiral Constrained α-Trifluoromethylalanine in Aib Foldamers to Control, Quantify and Assign the Helical Screw-Sense**}, url = {https://m2.mtmt.hu/api/publication/32695477}, author = {Bodero, L. and Guitot, K. and Lensen, N. and Lequin, O. and Brigaud, T. and Ongeri, S. and Chaume, G.}, doi = {10.1002/chem.202103887}, journal-iso = {CHEM-EUR J}, journal = {CHEMISTRY-A EUROPEAN JOURNAL}, volume = {28}, unique-id = {32695477}, issn = {0947-6539}, abstract = {Oligomers of α-aminoisobutyric acid (Aib) are achiral peptides that adopt 310 helical structures with equal population of left- and right-handed conformers. The screw-sense preference of the helical chain may be controlled by a single chiral residue located at one terminus. 1H and 19F NMR, X-ray crystallography and circular dichroism studies on new Aib oligomers show that the incorporation of a chiral quaternary α-trifluoromethylalanine at their N-terminus induces a reversal of the screw-sense preference of the 310-helix compared to that of a non-fluorinated analogue having an l-α-methyl valine residue. This work demonstrates that, among the many particular properties of introducing a trifluoromethyl group into foldamers, its stereo-electronic properties are of major interest to control the helical screw sense. Its use as an easy-to-handle 19F NMR probe to reliably determine both the magnitude of the screw-sense preference and its sign assignment is also of remarkable interest. © 2021 Wiley-VCH GmbH.}, keywords = {PROTEIN SECONDARY STRUCTURE; FOLDAMERS; FOLDAMERS; OLIGOMERS; Models, Molecular; molecular model; Circular Dichroism; Circular Dichroism; Circular Dichroism; Bone Screws; amino acids; conformational analysis; helical structures; helical structures; DICHROISM; Protein Structure, Secondary; ALANINE; ALANINE; X ray crystallography; PROPERTY; Electronic properties; bone screw; Screws; fluorinated peptides; N terminus; Helical chains; 3 10 helix; Aminoisobutyric acid; Helical screws; Lefthanded; Right handed; alpha-trifluoromethylalanine}, year = {2022}, eissn = {1521-3765} } @article{MTMT:32695478, title = {Shaping Macromolecules for Sensing Applications—From Polymer Hydrogels to Foldamers}, url = {https://m2.mtmt.hu/api/publication/32695478}, author = {Giuffrida, S.G. and Forysiak, W. and Cwynar, P. and Szweda, R.}, doi = {10.3390/polym14030580}, journal-iso = {POLYMERS-BASEL}, journal = {POLYMERS}, volume = {14}, unique-id = {32695478}, abstract = {Sensors are tools for detecting, recognizing, and recording signals from the surrounding environment. They provide measurable information on chemical or physical changes, and thus are widely used in diagnosis, environment monitoring, food quality checks, or process control. Polymers are versatile materials that find a broad range of applications in sensory devices for the bio-medical sector and beyond. Sensory materials are expected to exhibit a measurable change of properties in the presence of an analyte or a stimulus, characterized by high sensitivity and selectivity of the signal. Signal parameters can be tuned by material features connected with the restriction of macromolecule shape by crosslinking or folding. Gels are crosslinked, three-dimensional networks that can form cavities of different sizes and forms, which can be adapted to trap particular analytes. A higher level of structural control can be achieved by foldamers, which are macromolecules that can attain well-defined conformation in solution. By increasing control over the three-dimensional structure, we can improve the selectivity of polymer materials, which is one of the crucial requirements for sensors. Here, we discuss various examples of polymer gels and foldamer-based sensor systems. We have classified and described applied polymer materials and used sensing techniques. Finally, we deliberated the necessity and potential of further exploration of the field towards the increased selectivity of sensory devices. © 2022 by the authors. Licensee MDPI, Basel, Switzerland.}, keywords = {FOLDAMERS; FOLDAMERS; diagnosis; MACROMOLECULES; quality control; Hydrogels; Hydrogels; Crosslinking; Gels; POLYMER GELS; POLYMER GELS; Analytes; STRUCTURAL DYNAMICS; Functional polymers; Physical changes; SENSING APPLICATIONS; Biosensing; Biosensing; Polymer materials; Sensing; Surrounding environment; Polymer hydrogels; Chemical change}, year = {2022}, eissn = {2073-4360} } @article{MTMT:33305100, title = {Two consecutive aza-amino acids in peptides promote stable beta-turn formation in water}, url = {https://m2.mtmt.hu/api/publication/33305100}, author = {Shi, Chenghui and Correia, Isabelle and Tonali, Nicolo and Ongeri, Sandrine and Lequin, Olivier}, doi = {10.1039/d2ob01225a}, journal-iso = {ORG BIOMOL CHEM}, journal = {ORGANIC & BIOMOLECULAR CHEMISTRY}, volume = {20}, unique-id = {33305100}, issn = {1477-0520}, abstract = {Studies on the synthetic methodologies and the structural propensity of peptides containing consecutive aza-amino acids are still in their infancy. Here, details of the synthesis and conformational analysis of tripeptides containing two consecutive aza-amino acids are provided. The demonstration that the type I beta-turn folding is induced, even in aqueous media, by the introduction of one or two lateral chains on the diaza-peptide unit is of particular importance for the design of peptidomimetics of biological interest.}, year = {2022}, eissn = {1477-0539}, pages = {8430-8437} } @article{MTMT:33305101, title = {Helix-Stabilized Cell-Penetrating Peptides for Delivery of Antisense Morpholino Oligomers: Relationships among Helicity, Cellular Uptake, and Antisense Activity}, url = {https://m2.mtmt.hu/api/publication/33305101}, author = {Takada, Hiroyuki and Tsuchiya, Keisuke and Demizu, Yosuke}, doi = {10.1021/acs.bioconjchem.2c00199}, journal-iso = {BIOCONJUGATE CHEM}, journal = {BIOCONJUGATE CHEMISTRY}, volume = {33}, unique-id = {33305101}, issn = {1043-1802}, abstract = {The secondary structures of cell-penetrating peptides (CPPs) influence their properties including their cell membrane permeability, tolerability to proteases, and intracellular distribution. Herein, we developed helix-stabilized arginine-rich peptides containing alpha,alpha-disubstituted alpha-amino acids and their conjugates with antisense phosphorodiamidate morpholino oligomers (PMOs), to investigate the relationships among the helicity of the peptides, cellular uptake, and antisense activity of the peptide-conjugated PMOs. We demonstrated that helical CPPs can efficiently deliver the conjugated PMO into cells compared with nonhelical CPPs and that their antisense activities are synergistically enhanced in the presence of an endosomolytic reagent or an endosomal escape domain peptide.}, year = {2022}, eissn = {1520-4812}, pages = {1311-1318}, orcid-numbers = {Takada, Hiroyuki/0000-0001-6650-7902; Demizu, Yosuke/0000-0001-7521-4861} } @article{MTMT:33305102, title = {Helical Foldamers and Stapled Peptides as New Modalities in Drug Discovery: Modulators of Protein-Protein Interactions}, url = {https://m2.mtmt.hu/api/publication/33305102}, author = {Tsuchiya, Keisuke and Kurohara, Takashi and Fukuhara, Kiyoshi and Misawa, Takashi and Demizu, Yosuke}, doi = {10.3390/pr10050924}, journal-iso = {PROCESSES}, journal = {PROCESSES}, volume = {10}, unique-id = {33305102}, issn = {2227-9717}, abstract = {A "foldamer" is an artificial oligomeric molecule with a regular secondary or tertiary structure consisting of various building blocks. A "stapled peptide" is a peptide with stabilized secondary structures, in particular, helical structures by intramolecular covalent side-chain cross-linking. Helical foldamers and stapled peptides are potential drug candidates that can target protein-protein interactions because they enable multipoint molecular recognition, which is difficult to achieve with low-molecular-weight compounds. This mini-review describes a variety of peptide-based foldamers and stapled peptides with a view to their applications in drug discovery, including our recent progress.}, keywords = {FOLDAMERS; DRUG DISCOVERY; Helical structure; Building Blocks; MODALITY; Protein-protein interaction}, year = {2022}, eissn = {2227-9717}, orcid-numbers = {Kurohara, Takashi/0000-0003-4228-3478; Fukuhara, Kiyoshi/0000-0001-9677-7911; Demizu, Yosuke/0000-0001-7521-4861} } @{MTMT:32695479, title = {Cell-Penetrating Peptides}, url = {https://m2.mtmt.hu/api/publication/32695479}, author = {Zorko, M. and Langel, Ü.}, booktitle = {Vaccine Design}, doi = {10.1007/978-1-0716-1752-6_1}, volume = {2383}, unique-id = {32695479}, abstract = {In this introductory chapter, we first define cell-penetrating peptides (CPPs), give short overview of CPP history and discuss several aspects of CPP classification. Next section is devoted to the mechanism of CPP penetration into the cells, where direct and endocytic internalization of CPP is explained. Kinetics of internalization is discussed more extensively, since this topic is not discussed in other chapters of this book. At the end of this section some features of the thermodynamics of CPP interaction with the membrane is also presented. Finally, we present different cargoes that can be transferred into the cells by CPPs and briefly discuss the effect of cargo on the rate and efficiency of penetration into the cells. © 2022, The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.}, keywords = {metabolism; MECHANISMS; ENDOCYTOSIS; KINETICS; KINETICS; KINETICS; THERMODYNAMICS; physical chemistry; antiinfective agent; carrier protein; protein interaction; enhancer region; cell penetrating peptide; cell penetrating peptide; Cell-penetrating peptides; direct translocation; internalization (cell); endocytic uptake; CPP classes}, year = {2022}, pages = {3-32} } @article{MTMT:32367953, title = {Ribosomal Synthesis of Macrocyclic Peptides with beta(2)- and beta(2,3)-Homo-Amino Acids for the Development of Natural Product-Like Combinatorial Libraries}, url = {https://m2.mtmt.hu/api/publication/32367953}, author = {Adaligil, Emel and Song, Aimin and Hallenbeck, Kenneth K. and Cunningham, Christian N. and Fairbrother, Wayne J.}, doi = {10.1021/acschembio.1c00062}, journal-iso = {ACS CHEM BIOL}, journal = {ACS CHEMICAL BIOLOGY}, volume = {16}, unique-id = {32367953}, issn = {1554-8929}, abstract = {The development of large, natural-product-like, combinatorial macrocyclic peptide libraries is essential in the quest to develop therapeutics for "undruggable" cellular targets. Herein we report the ribosomal synthesis of macrocyclic peptides containing one or more beta(2)-homo-amino acids (beta(2)haa) to enable their incorporation into mRNA display-based selection libraries. We confirmed the compatibility of 14 beta(2)-homo-amino acids, (S)- and (R)-stereochemistry, for single incorporation into a macrocyclic peptide with low to high translation efficiency. Interestingly, N-methylation of the backbone amide of beta(2)haa prevented the incorporation of this amino acid subclass by the ribosome. Additionally, we designed and incorporated several alpha,beta-disubstituted beta(2,3)-homo-amino acids (beta(2,3)haa) with different R-groups on the alpha- and beta-carbons of the same amino acid. Incorporation of these beta(2,3)haa enables increased diversity in a single position of a macrocyclic peptide without significantly increasing the overall molecular weight, which is an important consideration for passive cell permeability. We also successfully incorporated multiple (S)-beta(2)hAla into a single macrocycle with other non-proteinogenic amino acids, confirming that this class of beta-amino acid is suitable for development of large scale macrocyclic peptide libraries.}, year = {2021}, eissn = {1554-8937}, pages = {1011-1018} } @article{MTMT:32370554, title = {Fluorinated Triazole Foldamers: Folded or Extended Conformational Preferences}, url = {https://m2.mtmt.hu/api/publication/32370554}, author = {Laxio Arenas, Jose and Xu, Yaochun and Milcent, Thierry and Van Heijenoort, Carine and Giraud, Francois and Ha-Duong, Tap and Crousse, Benoit and Ongeri, Sandrine}, doi = {10.1002/cplu.202000791}, journal-iso = {CHEMPLUSCHEM}, journal = {CHEMPLUSCHEM}, volume = {86}, unique-id = {32370554}, issn = {2192-6506}, abstract = {Fluorinated peptidomimetic foldamers are still in their infancy. We report here the easy access to fluorinated triazolamers based on 2-amino-3,3,3-trifluoropropyl-1,4-triazolyl acetic acid (CF3-1,4-Tz) and on aminomethyl-1,4-triazolyl-difluoroacetic acid (1,4-Tz-CF2). Both CF3-1,4-Tz and 1,4-Tz-CF2 amino acids were efficiently prepared by copper(I)-catalyzed Huisgen 1,3-dipolar cycloaddition. Their conformational preferences were studied by 2D NMR analyses and molecular dynamic simulations. Foldamers based on CF3-1,4-Tz amino acids are capable of adopting short multi-stranded beta-sheet-like structures that are maintained by electrostatic interactions between the triazole proton and N2 atom of neighboring subunits. On the contrary, foldamers based on 1,4-Tz-CF2 units adopt elongated beta-strand-like structures, stabilized by electrostatic interaction between fluorine atoms and their neighboring protons.}, keywords = {FOLDAMERS; conformational analysis; PEPTIDOMIMETICS; fluorine; noncovalent interactions}, year = {2021}, eissn = {2192-6506}, pages = {241-251}, orcid-numbers = {Ha-Duong, Tap/0000-0002-0847-2948; Ongeri, Sandrine/0000-0002-2118-7324} } @article{MTMT:32370559, title = {Cell-Penetrating Peptides Derived from Animal Venoms and Toxins}, url = {https://m2.mtmt.hu/api/publication/32370559}, author = {Radis-Baptista, Gandhi}, doi = {10.3390/toxins13020147}, journal-iso = {TOXINS}, journal = {TOXINS}, volume = {13}, unique-id = {32370559}, issn = {2072-6651}, abstract = {Cell-penetrating peptides (CPPs) comprise a class of short polypeptides that possess the ability to selectively interact with the cytoplasmic membrane of certain cell types, translocate across plasma membranes and accumulate in the cell cytoplasm, organelles (e.g., the nucleus and mitochondria) and other subcellular compartments. CPPs are either of natural origin or de novo designed and synthesized from segments and patches of larger proteins or designed by algorithms. With such intrinsic properties, along with membrane permeation, translocation and cellular uptake properties, CPPs can intracellularly convey diverse substances and nanomaterials, such as hydrophilic organic compounds and drugs, macromolecules (nucleic acids and proteins), nanoparticles (nanocrystals and polyplexes), metals and radionuclides, which can be covalently attached via CPP N- and C-terminals or through preparation of CPP complexes. A cumulative number of studies on animal toxins, primarily isolated from the venom of arthropods and snakes, have revealed the cell-penetrating activities of venom peptides and toxins, which can be harnessed for application in biomedicine and pharmaceutical biotechnology. In this review, I aimed to collate examples of peptides from animal venoms and toxic secretions that possess the ability to penetrate diverse types of cells. These venom CPPs have been chemically or structurally modified to enhance cell selectivity, bioavailability and a range of target applications. Herein, examples are listed and discussed, including cysteine-stabilized and linear, alpha-helical peptides, with cationic and amphipathic character, from the venom of insects (e.g., melittin, anoplin, mastoparans), arachnids (latarcin, lycosin, chlorotoxin, maurocalcine/imperatoxin homologs and wasabi receptor toxin), fish (pardaxins), amphibian (bombesin) and snakes (crotamine and cathelicidins).}, keywords = {CELLULAR UPTAKE; cell-penetrating peptide; peptide design; Venom peptide; peptide engineering; arachnid venom peptide; insect venom peptide; snake venom peptide; peptide chemical modification; peptide carrier}, year = {2021}, eissn = {2072-6651} } @article{MTMT:32370557, title = {Peptoid-phthalocyanine architectures with different grafting positions: Synthetic strategy and photoproperties}, url = {https://m2.mtmt.hu/api/publication/32370557}, author = {Rzeigui, Maha and Sahin, Zeynel and Roy, Olivier and Kucuk, Tugba and Goler, Omer and Atilla, Devrim and Khiari, Jameleddine and Dumoulin, Fabienne and Taillefumier, Claude}, doi = {10.1016/j.dyepig.2020.109095}, journal-iso = {DYES PIGMENTS}, journal = {DYES AND PIGMENTS}, volume = {189}, unique-id = {32370557}, issn = {0143-7208}, abstract = {A monoazido Zn phthalocyanine has been grafted onto three different alkynyl-functionalized peptoid helices using copper-catalyzed azide-alkyne cycloaddition, demonstrating the feasibility of such conjugates. Their photoproperties have been examined relatively to the spatial geometry induced by the peptoid helix.}, keywords = {CONJUGATE; HELIX; Phthalocyanine; Peptoid}, year = {2021}, eissn = {1873-3743}, orcid-numbers = {Dumoulin, Fabienne/0000-0002-0388-8338} } @article{MTMT:31957074, title = {Helical Antimicrobial Peptide Foldamers Containing Non-proteinogenic Amino Acids}, url = {https://m2.mtmt.hu/api/publication/31957074}, author = {Yokoo, H. and Hirano, M. and Misawa, T. and Demizu, Y.}, doi = {10.1002/cmdc.202000940}, journal-iso = {CHEMMEDCHEM}, journal = {CHEMMEDCHEM}, volume = {16}, unique-id = {31957074}, issn = {1860-7179}, abstract = {Antimicrobial peptides (AMPs) are potential novel therapeutic drugs against microbial infections. Most AMPs function by disrupting microbial membranes because of their amphipathic properties and ordered secondary structures. In this minireview, we describe recent efforts to develop helical AMP foldamers containing non-proteinogenic amino acids, such as α,α-disubstituted α-amino acids, β-amino acids, γ-amino acids, side-chain stapling and N-alkyl glycines. © 2021 Wiley-VCH GmbH}, keywords = {FOLDAMERS; ANTIMICROBIAL PEPTIDES; Gram-negative bacteria; Gram-Positive Bacteria; non-proteinogenic amino acids; helixes}, year = {2021}, eissn = {1860-7187}, pages = {1226-1233} } @article{MTMT:32695481, title = {A twist in the road less traveled: The AMBER ff15ipq-m force field for protein mimetics}, url = {https://m2.mtmt.hu/api/publication/32695481}, author = {Bogetti, A.T. and Piston, H.E. and Leung, J.M.G. and Cabalteja, C.C. and Yang, D.T. and Degrave, A.J. and Debiec, K.T. and Cerutti, D.S. and Case, D.A. and Horne, W.S. and Chong, L.T.}, doi = {10.1063/5.0019054}, journal-iso = {J CHEM PHYS}, journal = {JOURNAL OF CHEMICAL PHYSICS}, volume = {153}, unique-id = {32695481}, issn = {0021-9606}, abstract = {We present a new force field, AMBER ff15ipq-m, for simulations of protein mimetics in applications from therapeutics to biomaterials. This force field is an expansion of the AMBER ff15ipq force field that was developed for canonical proteins and enables the modeling of four classes of artificial backbone units that are commonly used alongside natural α residues in blended or "heterogeneous"backbones: chirality-reversed D-α-residues, the Cα-methylated α-residue Aib, homologated β-residues (β3) bearing proteinogenic side chains, and two cyclic β residues (βcyc; APC and ACPC). The ff15ipq-m force field includes 472 unique atomic charges and 148 unique torsion terms. Consistent with the AMBER IPolQ lineage of force fields, the charges were derived using the Implicitly Polarized Charge (IPolQ) scheme in the presence of explicit solvent. To our knowledge, no general force field reported to date models the combination of artificial building blocks examined here. In addition, we have derived Karplus coefficients for the calculation of backbone amide J-coupling constants for β3Ala and ACPC β residues. The AMBER ff15ipq-m force field reproduces experimentally observed J-coupling constants in simple tetrapeptides and maintains the expected conformational propensities in reported structures of proteins/peptides containing the artificial building blocks of interest - all on the μs timescale. These encouraging results demonstrate the power and robustness of the IPolQ lineage of force fields in modeling the structure and dynamics of natural proteins as well as mimetics with protein-inspired artificial backbones in atomic detail. © 2020 Author(s).}, keywords = {PROTEINS; AMIDES; AMBER; Building blockes; protein mimetics; Structure and dynamics; Natural proteins; Proteins/Peptides; Explicit solvents; General force; Proteinogenic side chains}, year = {2020}, eissn = {1089-7690} } @article{MTMT:31385327, title = {Unique β‐Turn Peptoid Structures and Their Application as Asymmetric Catalysts}, url = {https://m2.mtmt.hu/api/publication/31385327}, author = {Darapaneni, Chandra Mohan and Ghosh, Pritam and Ghosh, Totan and Maayan, Galia}, doi = {10.1002/chem.202000595}, journal-iso = {CHEM-EUR J}, journal = {CHEMISTRY-A EUROPEAN JOURNAL}, volume = {26}, unique-id = {31385327}, issn = {0947-6539}, keywords = {PEPTIDES; FOLDAMERS; PROLINE; PEPTOIDS; beta-turn}, year = {2020}, eissn = {1521-3765}, pages = {9573-9579} } @article{MTMT:30933404, title = {FoldamerDB: a database of peptidic foldamers}, url = {https://m2.mtmt.hu/api/publication/30933404}, author = {Nizami, Bilal and Bereczki-Szakál, Dorottya and Varró, Nikolett and El Battioui, Kamal and Udyavara Nagaraj, Vignesh and Szigyártó, Imola Csilla and Mándity, István and Beke-Somfai, Tamás}, doi = {10.1093/nar/gkz993}, journal-iso = {NUCLEIC ACIDS RES}, journal = {NUCLEIC ACIDS RESEARCH}, volume = {48}, unique-id = {30933404}, issn = {0305-1048}, year = {2020}, eissn = {1362-4962}, pages = {D1122-D1128}, orcid-numbers = {Bereczki-Szakál, Dorottya/0000-0003-3037-0515; Varró, Nikolett/0000-0003-4161-9021; Mándity, István/0000-0003-2865-6143} } @article{MTMT:31385284, title = {Ultra-large chemical libraries for the discovery of high-affinity peptide binders}, url = {https://m2.mtmt.hu/api/publication/31385284}, author = {Quartararo, Anthony J. and Gates, Zachary P. and Somsen, Bente A. and Hartrampf, Nina and Ye, Xiyun and Shimada, Arisa and Kajihara, Yasuhiro and Ottmann, Christian and Pentelute, Bradley L.}, doi = {10.1038/s41467-020-16920-3}, journal-iso = {NAT COMMUN}, journal = {NATURE COMMUNICATIONS}, volume = {11}, unique-id = {31385284}, issn = {2041-1723}, year = {2020}, eissn = {2041-1723} } @article{MTMT:31385319, title = {A Resin-Bound Peptoid as a Recyclable Heterogeneous Catalyst for Oxidation Reactions}, url = {https://m2.mtmt.hu/api/publication/31385319}, author = {Stamatin, Yekaterina and Maayan, Galia}, doi = {10.1002/ejoc.201901739}, journal-iso = {EUR J ORG CHEM}, journal = {EUROPEAN JOURNAL OF ORGANIC CHEMISTRY}, volume = {2020}, unique-id = {31385319}, issn = {1434-193X}, year = {2020}, eissn = {1099-0690}, pages = {3147-3152} } @article{MTMT:31355941, title = {Membrane Active Janus-Oligomers of β 3 -Peptides}, url = {https://m2.mtmt.hu/api/publication/31355941}, author = {Szigyártó, Imola Csilla and Mihály, Judith and Wacha, András Ferenc and Bogdán, Dóra and Juhász, Tünde and Kohut, Gergely and Schlosser, Gitta (Vácziné) and Zsila, Ferenc and Urlacher, Vlada and Varga, Zoltán and Fulop, Ferenc and Bóta, Attila and Mándity, István and Beke-Somfai, Tamás}, doi = {10.1039/d0sc01344g}, journal-iso = {CHEM SCI}, journal = {CHEMICAL SCIENCE}, volume = {11}, unique-id = {31355941}, issn = {2041-6520}, abstract = {Self-assembling peptides offer a versatile set of tools for bottom-up construction of supramolecular biomaterials. Among these compounds, non-natural peptidic foldamers experience increased focus due to their structural variability and lower sensitivity to enzymatic degradation. However, very little is known about their membrane properties and complex oligomeric assemblies - key areas for biomedical and technological applications. Here we designed short, acyclic beta(3)-peptide sequences with alternating amino acid stereoisomers to obtain non-helical molecules having hydrophilic charged residues on one side, and hydrophobic residues on the other side, with the N-terminus preventing formation of infinite fibrils. Our results indicate that these beta-peptides form small oligomers both in water and in lipid bilayers and are stabilized by intermolecular hydrogen bonds. In the presence of model membranes, they either prefer the headgroup regions or they insert between the lipid chains. Molecular dynamics (MD) simulations suggest the formation of two-layered bundles with their side chains facing opposite directions when compared in water and in model membranes. Analysis of the MD calculations showed hydrogen bonds inside each layer, however, not between the layers, indicating a dynamic assembly. Moreover, the aqueous form of these oligomers can host fluorescent probes as well as a hydrophobic molecule similarly toe.g.lipid transfer proteins. For the tested, peptides the mixed chirality pattern resulted in similar assemblies despite sequential differences. Based on this, it is hoped that the presented molecular framework will inspire similar oligomers with diverse functionality.}, year = {2020}, eissn = {2041-6539}, pages = {6868-6881}, orcid-numbers = {Wacha, András Ferenc/0000-0002-9609-0893; Bogdán, Dóra/0000-0003-4455-8914; Kohut, Gergely/0000-0002-6139-5136; Schlosser, Gitta (Vácziné)/0000-0002-7637-7133; Varga, Zoltán/0000-0002-5741-2669; Mándity, István/0000-0003-2865-6143} } @article{MTMT:31385325, title = {De Novo Design of Cell‐penetrating Foldamers}, url = {https://m2.mtmt.hu/api/publication/31385325}, author = {Yokoo, Hidetomo and Misawa, Takashi and Demizu, Yosuke}, doi = {10.1002/tcr.202000047}, journal-iso = {CHEM REC}, journal = {CHEMICAL RECORD}, volume = {20}, unique-id = {31385325}, issn = {1527-8999}, year = {2020}, eissn = {1528-0691}, pages = {912-921} } @article{MTMT:30452963, title = {Imidazolidinone-Tethered alpha-Hydrazidopeptides - Synthesis and Conformational Investigation}, url = {https://m2.mtmt.hu/api/publication/30452963}, author = {Amabili, Paolo and Calvaresi, Matteo and Martelli, Gianluca and Orena, Mario and Rinaldi, Samuele and Sgolastra, Federica}, doi = {10.1002/ejoc.201801427}, journal-iso = {EUR J ORG CHEM}, journal = {EUROPEAN JOURNAL OF ORGANIC CHEMISTRY}, volume = {2019}, unique-id = {30452963}, issn = {1434-193X}, abstract = {N-alpha-acylated beta(2,3)-3-azapeptides, or alpha-hydrazidopeptides, of different lengths were synthesized starting from a conformationally restricted imidazolidinone-tethered monomer. The preferential conformations of the oligomers were investigated by NMR and CD spectroscopy, supported by computational analysis. The experimental data clearly confirmed the tendency of these alpha-hydrazidopeptides to fold into a zig-zag (Z8) 8-helix conformation, whose stability is length-dependent, stabilized by the C=O(i)center dot center dot center dot H-N(i + 2) and N(i)center dot center dot center dot H-N(i + 1) intramolecular H-bonding pattern, as well as by non-standard C=O center dot center dot center dot H-C hydrogen bonds.}, keywords = {SECONDARY STRUCTURE; FOLDAMERS; molecular dynamics; Hydrogen bonds; Peptide mimics}, year = {2019}, eissn = {1099-0690}, pages = {907-917} } @article{MTMT:30989814, title = {A study of the cis-trans isomerization preference of N-alkylated peptides containing phosphorus in the side chain and backbone}, url = {https://m2.mtmt.hu/api/publication/30989814}, author = {de la Torre, Alexander F. and Ali, Akbar and Concepcion, Odette and Montero-Alejo, Ana L. and Muniz, Francisco M. and Jimenez, Claudio A. and Belmar, Julio and Luis Velazquez-Libera, Jose and Hernandez-Rodriguez, Erix W. and Caballero, Julio}, doi = {10.1039/c9nj02234a}, journal-iso = {NEW J CHEM}, journal = {NEW JOURNAL OF CHEMISTRY}, volume = {43}, unique-id = {30989814}, issn = {1144-0546}, abstract = {The current work provides a study on the cis-trans isomerization behaviour of N-alkylated peptides decorated with phosphonate ester groups. A Ugi four-component reaction was chosen for the synthesis of N-alkylated peptides, where almost only the cis isomer was detected when the phosphonate ester group was incorporated as an amine component in the side chain. However, the phosphonate ester group inserted in the backbone, as an isocyanide component, leads preferably to the trans isomer of this kind of peptides. The diverse behaviour of cis-trans isomerization has been explained via spectroscopic nuclear magnetic resonance analysis and computational calculations.}, year = {2019}, eissn = {1369-9261}, pages = {12804-12813}, orcid-numbers = {Ali, Akbar/0000-0002-2914-0934; Belmar, Julio/0000-0002-0414-7902; Hernandez-Rodriguez, Erix W./0000-0002-9231-7552; Caballero, Julio/0000-0003-0182-1444} } @article{MTMT:30465244, title = {Novel Materials From the Supramolecular Self-Assembly of Short Helical beta(3)-Peptide Foldamers}, url = {https://m2.mtmt.hu/api/publication/30465244}, author = {Kulkarni, Ketav and Habila, Nathan and Del Borgo, Mark P. and Aguilar, Marie-Isabel}, doi = {10.3389/fchem.2019.00070}, journal-iso = {FRONT CHEM}, journal = {FRONTIERS IN CHEMISTRY}, volume = {7}, unique-id = {30465244}, issn = {2296-2646}, abstract = {Self-assembly is the spontaneous organization of small components into higher-order structures facilitated by the collective balance of non-covalent interactions. Peptide-based self-assembly systems exploit the ability of peptides to adopt distinct secondary structures and have been used to produce a range of well-defined nanostructures, such as nanotubes, nanofibres, nanoribbons, nanospheres, nanotapes, and nanorods. While most of these systems involve self-assembly of alpha-peptides, more recently beta-peptides have also been reported to undergo supramolecular self-assembly, and have been used to produce materials-such as hydrogels-that are tailored for applications in tissue engineering, cell culture and drug delivery. This review provides an overview of self-assembled peptide nanostructures obtained via the supramolecular self-assembly of short beta-peptide foldamers with a specific focus on N-acetyl-beta(3)-peptides and their applications as bio- and nanomaterials.}, keywords = {Biomaterials; BETA-PEPTIDE; supramolecular selfassembly; peptide materials; beta-amino acid containing peptides}, year = {2019}, eissn = {2296-2646} } @article{MTMT:31385316, title = {Solid-Phase Insertion of N-mercaptoalkylglycine Residues into Peptides}, url = {https://m2.mtmt.hu/api/publication/31385316}, author = {Mourtas, Spyridon and Gatos, Dimitrios and Barlos, Kleomenis}, doi = {10.3390/molecules24234261}, journal-iso = {MOLECULES}, journal = {MOLECULES}, volume = {24}, unique-id = {31385316}, issn = {1420-3049}, year = {2019}, eissn = {1420-3049} } @article{MTMT:30435771, title = {α/β-Chimera peptide synthesis with cyclic β-sugar amino acids: the efficient coupling protocol}, url = {https://m2.mtmt.hu/api/publication/30435771}, author = {Nagy, Adrienn and Goldschmidt Gőz, Viktória and Pintér, István and Farkas, Viktor and Perczel, András}, doi = {10.1007/s00726-019-02702-9}, journal-iso = {AMINO ACIDS}, journal = {AMINO ACIDS}, volume = {51}, unique-id = {30435771}, issn = {0939-4451}, abstract = {The synthesis of α/β-chimeras comprises peptide bond formation from α- to β-, from β- to β-, and from β- to α-amino acid residues. The fine-tuned solid phase synthesis of –GXXG– chimera peptides containing the simplest achiral α-amino acid glycine and two cyclic SAAs of different ring size [X denoting cyclic β-Sugar Amino Acids (β-SAA)] is reported, variants containing Fmoc–RibAFU(ip)–OH a furanoid-, and Fmoc–GlcAPU(Me)–OH a pyranoid-type structural “Lego-element”. Systematic search for the best coupling strategy with both H–β-SAA–OHs is described, including the comparison of the different coupling reagents and conditions. Selecting the optimal reagent (from commonly used PyBOP, HATU and HOBt) was assisted by time-resolved 1H-NMR: formation and stability of the Fmoc protected active esters were compared. We found that PyBOP is the best choice for successfully coupling both H–β-SAA–OH prototypes. The present comparative results open a reasonable route for building efficiently various –β-SAA– containing homo- and heterooligomers.}, year = {2019}, eissn = {1438-2199}, pages = {669-678}, orcid-numbers = {Farkas, Viktor/0000-0002-8815-2783; Perczel, András/0000-0003-1252-6416} } @article{MTMT:30989813, title = {Cell-Penetrating Peptide Foldamers: Drug-Delivery Tools}, url = {https://m2.mtmt.hu/api/publication/30989813}, author = {Oba, Makoto}, doi = {10.1002/cbic.201900204}, journal-iso = {CHEMBIOCHEM}, journal = {CHEMBIOCHEM}, volume = {20}, unique-id = {30989813}, issn = {1439-4227}, abstract = {Highly efficient drug-delivery tools for membrane-impermeable compounds, proteins, and nucleic acids in living cells are useful in the fields of chemical biology and drug discovery, and such tools have been widely studied. One strategy in the development of novel drug-delivery tools is to utilize cell-penetrating peptide (CPP) foldamers. CPP foldamers are folded oligopeptides that possess cell membrane permeability. In recent decades, a wide variety of CPP foldamers have been reported by many groups. Herein, CPP foldamers are introduced and discussed from the viewpoints of component monomers (amino acids) and their application as drug-delivery tools.}, keywords = {FOLDAMERS; Drug delivery; helical structures; Cell-penetrating peptides; oligoamides}, year = {2019}, eissn = {1439-7633}, pages = {2041-2045}, orcid-numbers = {Oba, Makoto/0000-0002-3691-3608} } @article{MTMT:30706666, title = {Pharmacological targeting of α-synuclein and TPPP/p25 in Parkinson's disease. challenges and opportunities in a Nutshell.}, url = {https://m2.mtmt.hu/api/publication/30706666}, author = {Oláh, Judit and Ovádi, Judit}, doi = {10.1002/1873-3468.13464}, journal-iso = {FEBS LETT}, journal = {FEBS LETTERS}, volume = {593}, unique-id = {30706666}, issn = {0014-5793}, abstract = {With the aging of population, neurological disorders, and especially disorders involving defects in protein conformation (also known as proteopathies) pose a serious socio-economic problem. So far there is no effective treatment for most proteopathies, including Parkinson's disease (PD). The mechanism underlying PD pathogenesis is largely unknown, and the hallmark proteins, α-synuclein (SYN) and Tubulin Polymerization Promoting Protein (TPPP/p25) are challenging drug targets. These proteins are intrinsically disordered with high conformational plasticity, and have diverse physiological and pathological functions. In the healthy brain, SYN and TPPP/p25 occur in neurons and oligodendrocytes, respectively; however, in PD and multiple system atrophy, they are co-enriched and co-localized in both cell types, thereby marking pathogenesis. Although large inclusions appear at a late disease stage, small, soluble assemblies of SYN promoted by TPPP/p25 are pathogenic. In the light of these issues, we propose a new innovative strategy for the validation of a specific drug target based upon the identification of contact surfaces of the pathological SYN-TPPP/p25 complex that may lead to the development of peptidomimetic foldamers suitable for pharmaceutical intervention. This article is protected by copyright. All rights reserved.}, keywords = {PARKINSONISM; Drug target; TPPP/P25; α-synuclein; moonlighting protein; Unstructured protein; innovative strategy}, year = {2019}, eissn = {1873-3468}, pages = {1641-1653} } @article{MTMT:30367943, title = {A facile on-bead method for fully symmetric tetra-substituted DOTA derivatizations using peptoid moieties}, url = {https://m2.mtmt.hu/api/publication/30367943}, author = {Rustagi, V. and Gomika, Udugamasooriya D.}, doi = {10.1002/bip.23249}, journal-iso = {BIOPOLYMERS}, journal = {BIOPOLYMERS}, volume = {110}, unique-id = {30367943}, issn = {0006-3525}, year = {2019}, eissn = {1097-0282} } @article{MTMT:32695486, title = {Chemoenzymatic synthesis of nitrogen polymers with biomedical applications catalyzed by lipases}, url = {https://m2.mtmt.hu/api/publication/32695486}, author = {Baldessari, A. and Liñares, G.G.}, doi = {10.1007/978-1-4939-8672-9_20}, journal-iso = {METHODS MOL BIOL}, journal = {METHODS IN MOLECULAR BIOLOGY}, volume = {1835}, unique-id = {32695486}, issn = {1064-3745}, abstract = {The application of Candida antarctica lipase B as catalyst in the synthesis of two examples of nitrogen polymers is described. Firstly, we report a novel linear polyamidoamine oligomer, obtained by polymerization of ethyl acrylate and N-methyl-1,3-diaminopropane, catalyzed by Candida antarctica lipase B immobilized on polypropylene. The second part of the chapter describes an efficient route for the synthesis of a novel β-peptoid oligomer with hydroxyalkyl pendant groups in the nitrogen atom, through the polymerization of ethyl N-(2-hydroxyethyl)-β-alaninate catalyzed by Candida antarctica lipase B physically adsorbed within a macroporous poly(methyl methacrylate-co-butyl methacrylate) resin. Moreover, two derivatives of the β-peptoid oligomer were prepared: by acetylation and by grafting polycaprolactone. This last process was performed through ring-opening polymerization of caprolactone from the β-peptoid pendant hydroxyl groups and afforded a brush copolymer. The products were blended with polycaprolactone to make films by solvent casting. The inclusion of the acyl derivatives of the β-peptoid to polycaprolactone affected the morphology of the film yielding micro- and nanostructured patterns. The obtained products showed biomedical applications. © Springer Science+Business Media, LLC, part of Springer Nature 2018.}, keywords = {POLYMERIZATION; POLYPROPYLENE; CATALYSIS; CATALYSIS; Chemistry; Nitrogen; Nitrogen; Nitrogen; Molecular weight; nonhuman; POLYMERS; POLYMER; POLYMER; Acetylation; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization; scanning electron microscopy; synthesis; Polyamine; unclassified drug; ultraviolet radiation; aqueous solution; molecular structure; chemical structure; biomaterial; Magnetic Resonance Spectroscopy; CATALYST; LIPASE; lipase B; Candida antarctica; ring opening; Polyamines; Biocompatible Materials; Oligomer; Burkholderia cepacia; triacylglycerol lipase; triacylglycerol lipase; proton nuclear magnetic resonance; Nuclear magnetic resonance spectroscopy; Michael addition; biocompatibility; carbon nuclear magnetic resonance; enzyme synthesis; Lipases; matrix assisted laser desorption ionization time of flight mass spectrometry; Polycaprolactone; polyamidoamine; polyamidoamine; Chemistry Techniques, Synthetic; AMINOLYSIS; matrix-assisted laser desorption-ionization mass spectrometry; Aza-Michael addition and aminolysis reactions; Nitrogen polymers; Poly[N-(2-hydroxyethyl)-β-propylamide-g-polycaprolactone]; 1,3 propanediamine; acrylic acid ethyl ester; n methyl 1,3 diaminopropane}, year = {2018}, eissn = {1940-6029}, pages = {359-376} } @article{MTMT:30452964, title = {Exploring the Conformation of Mixed Cis-Trans alpha,beta-Oligopeptoids: A Joint Experimental and Computational Study}, url = {https://m2.mtmt.hu/api/publication/30452964}, author = {Dumonteil, Geoffrey and Bhattacharjee, Nicholus and Angelici, Gaetano and Roy, Olivier and Faure, Sophie and Jouffret, Laurent and Jolibois, Franck and Perrin, Lionel and Taillefumier, Claude}, doi = {10.1021/acs.joc.8b00606}, journal-iso = {J ORG CHEM}, journal = {JOURNAL OF ORGANIC CHEMISTRY}, volume = {83}, unique-id = {30452964}, issn = {0022-3263}, abstract = {The synthesis and conformational preferences of a set of new synthetic foldamers that combine both the alpha,beta-peptoid backbone and side chains that alternately promote cis- and trans-amide bond geometries have been achieved and addressed jointly by experiment and molecular modeling. Four sequence patterns were thus designed and referred to as cis-beta-trans-alpha, cis-alpha-trans-beta, trans-beta-cis-alpha, and trans-alpha-cis-beta. alpha- and beta NtBu monomers were used to enforce cis-amide bond geometries and alpha- and beta NPh monomers to promote trans-amides. NOESY and molecular modeling reveal that the trans-alpha-cis-beta and cis-beta-trans-alpha tetramers show a similar pattern of intramolecular weak interactions. The same holds for the cis-alpha-trans-beta and trans-beta-cis-alpha tetramers, but the interactions are different in nature than those identified in the trans-acis-beta-based oligomers. Interestingly, the trans-alpha-cis-beta peptoid architecture allows establishment of a larger amount of structure-stabilizing intramolecular interactions.}, year = {2018}, eissn = {1520-6904}, pages = {6382-6396}, orcid-numbers = {Dumonteil, Geoffrey/0000-0002-7386-6281; Roy, Olivier/0000-0002-7238-8708} } @article{MTMT:27609771, title = {Fabrication of cationic nanostructures from short self-assembling amphiphilic mixed alpha/beta-pentapeptide: Potential candidates for drug delivery, gene delivery, and antimicrobial applications}, url = {https://m2.mtmt.hu/api/publication/27609771}, author = {Goel, Rahul and Garg, Charu and Gautam, Hemant Kumar and Sharma, Ashwani Kumar and Kumar, Pradeep and Gupta, Alka}, doi = {10.1016/j.ijbiomac.2018.01.079}, journal-iso = {INT J BIOL MACROMOL}, journal = {INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES}, volume = {111}, unique-id = {27609771}, issn = {0141-8130}, abstract = {The present article describes designing and fabrication of nanostructures from a mixed a/β-pentapeptide, Lys-βAla-βAla-Lys-βAla, which majorly contains non-natural β-alanine residues in the backbone with two a-lysine residues at 1- and 4-positions. The amphiphilic pentapeptide showed the ability to self-assemble into cationic nanovesicles in an aqueous solution The average size of peptide nanostructures was found to be ~270 nm with a very high cationic charge of ~+40 mV. TEM micrographs revealed the average size of the same nanostructures ~80 nm bearing vesicular morphol. CD and FTIR spectroscopic studies on self-assembled pentapeptide hinted at random coil conformation which was also correlated with conformational search program using Hyper Chem 8.0. The pentapeptide nanostructures were then tested for encapsulation of hydrophobic model drug moieties, L-Dopa, and curcumin. Transfection efficiency of the generated cationic nanostructures was evaluated on HEK293 cells and compared the results with those obtained in the presence of chloroquine. The cytotoxicity assay performed using MTT depicted ~75-80% cell viability. The obtained nanostructures also gave pos. results against both Gram-neg. and Gram-pos. bacterial strains. Altogether the results advocate the promising potential of the pentapeptide foldamer, H-Lys-βAla-βAla-Lys-βAla-OEt, for drug and gene delivery applications along with the antimicrobial activity.}, keywords = {Drug delivery; GENE DELIVERY; Antimicrobial peptides (AMPs); β-Peptide; Pseudomonas Escherichia cationic nanostructure fabrication pentapeptide antimicrobial morphol; Amphiphilic foldamers; Self-assembling cationic nanostructures}, year = {2018}, eissn = {1879-0003}, pages = {880-893}, orcid-numbers = {Goel, Rahul/0000-0002-4388-602X} } @article{MTMT:27592892, title = {Selectivity Modulation and Structure of alpha/aza-beta(3) Cyclic Antimicrobial Peptides}, url = {https://m2.mtmt.hu/api/publication/27592892}, author = {Laurencin, Mathieu and Simon, Matthieu and Fleury, Yannick and Baudy-Floc'h, Michele and Bondon, Arnaud and Legrand, Baptiste}, doi = {10.1002/chem.201800152}, journal-iso = {CHEM-EUR J}, journal = {CHEMISTRY-A EUROPEAN JOURNAL}, volume = {24}, unique-id = {27592892}, issn = {0947-6539}, year = {2018}, eissn = {1521-3765}, pages = {6191-6201} } @article{MTMT:27592715, title = {Conformationally Programmable Chiral Foldamers with Compact and Extended Domains Controlled by Monomer Structure}, url = {https://m2.mtmt.hu/api/publication/27592715}, author = {Lockhart, Zachariah and Knipe, Peter C}, doi = {10.1002/anie.201802822}, journal-iso = {ANGEW CHEM INT EDIT}, journal = {ANGEWANDTE CHEMIE-INTERNATIONAL EDITION}, volume = {57}, unique-id = {27592715}, issn = {1433-7851}, year = {2018}, eissn = {1521-3773}, pages = {8478-8482}, orcid-numbers = {Lockhart, Zachariah/0000-0002-4409-0269} } @article{MTMT:30452965, title = {Cell Penetration Profiling Using the Chloroalkane Penetration Assay}, url = {https://m2.mtmt.hu/api/publication/30452965}, author = {Peraro, Leila and Deprey, Kirsten L. and Moser, Matthew K. and Zou, Zhongju and Ball, Haydn L. and Levine, Beth and Kritzer, Joshua A.}, doi = {10.1021/jacs.8b06144}, journal-iso = {J AM CHEM SOC}, journal = {JOURNAL OF THE AMERICAN CHEMICAL SOCIETY}, volume = {140}, unique-id = {30452965}, issn = {0002-7863}, abstract = {Biotherapeutics are a promising class of molecules in drug discovery, but they are often limited to extracellular targets due to their poor cell penetration. High throughput cell penetration assays are required for the optimization of biotherapeutics for enhanced cell penetration. We developed a HaloTag-based assay called the chloroalkane penetration assay (CAPA), which is quantitative, high throughput, and compartment-specific. We demonstrate the ability of CAPA to profile extent of cytosolic penetration with respect to concentration, presence of serum, temperature, and time. We also used CAPA to investigate structure penetration relationships for bioactive stapled peptides and peptides fused to cell-penetrating sequences. CAPA is not only limited to measuring cytosolic penetration. Using a cell line where HaloTag is localized to the nucleus, we show quantitative measurement of nuclear penetration. Going forward, CAPA will be a valuable method for measuring and optimizing the cell penetration of biotherapeutics.}, year = {2018}, eissn = {1520-5126}, pages = {11360-11369} } @article{MTMT:30452966, title = {Promising Antibiofilm Activity of Peptidomimetics}, url = {https://m2.mtmt.hu/api/publication/30452966}, author = {Von Borowski, Rafael Gomes and Baggio Gnoatto, Simone Cristina and Macedo, Alexandre Jose and Gillet, Reynald}, doi = {10.3389/fmicb.2018.02157}, journal-iso = {FRONT MICROBIOL}, journal = {FRONTIERS IN MICROBIOLOGY}, volume = {9}, unique-id = {30452966}, issn = {1664-302X}, abstract = {Pathogenic biofilms are a global health care concern, as they can cause extensive antibiotic resistance, morbidity, mortality, and thereby substantial economic loss. Scientific efforts have been made over the past few decades, but so far there is no effective treatment targeting the bacteria in biofilms. Antimicrobial peptidomimetics have been proposed as promising potential anti-biofilm agents. Indeed, these structurally enhanced molecules can mimic the action of peptides but are not susceptible to proteolysis or immunogenicity, the characteristic limitations of natural peptides. Here, we provide insights into antibiofilm peptidomimetic strategies and molecular targets, and discuss the design of two major peptidomimetics classes: AApeptides (N-acylated-N-aminoethyl-substituted peptides) and peptoids (N-substituted glycine units). In particular, we present details of their structural diversity and discuss the possible improvements that can be implemented in order to develop antibiofilm drug alternatives.}, keywords = {PEPTIDES; PEPTIDOMIMETICS; Biofilm; Antibiotic resistance; PEPTOIDS; AApeptides}, year = {2018}, eissn = {1664-302X} } @article{MTMT:27336862, title = {A Systematic Review of Antiamyloidogenic and Metal-Chelating Peptoids: Two Structural Motifs for the Treatment of Alzheimer's Disease}, url = {https://m2.mtmt.hu/api/publication/27336862}, author = {Young, Sherri C}, doi = {10.3390/molecules23020296}, journal-iso = {MOLECULES}, journal = {MOLECULES}, volume = {23}, unique-id = {27336862}, issn = {1420-3049}, year = {2018}, eissn = {1420-3049} } @article{MTMT:26581834, title = {Unique Functional Materials Derived from beta-Amino Acid Oligomers}, url = {https://m2.mtmt.hu/api/publication/26581834}, author = {Del Borgo, Mark P and Kulkarni, Ketav and Aguilar, Marie-Isabel}, doi = {10.1071/CH16511}, journal-iso = {AUST J CHEM}, journal = {AUSTRALIAN JOURNAL OF CHEMISTRY}, volume = {70}, unique-id = {26581834}, issn = {0004-9425}, year = {2017}, eissn = {1445-0038}, pages = {126-129} } @{MTMT:32695488, title = {Pore- and Channel-Forming Peptides and Their Mimetics}, url = {https://m2.mtmt.hu/api/publication/32695488}, author = {Garcia-Fandiño, R. and Calvelo, M. and Granja, J.R.}, booktitle = {Comprehensive Supramolecular Chemistry II}, doi = {10.1016/B978-0-12-409547-2.12546-6}, volume = {4}, unique-id = {32695488}, abstract = {Membrane channels are transmembrane-spanning structures that have an internal cavity that allow the migration of different ions and molecules. Inspired by the natural systems, chemists have created a variety of synthetic mimicries. Frequently, self-assembling methods were used to prepare the complex structure of these molecular channels. Although initially these synthetic assemblies were based on peptides, later, they were evolved to other structures facilitating the formation of channels. In this article, we review the most relevant strategies used for the preparation of relevant channel- forming architectures. © 2017 Elsevier Ltd. All rights reserved.}, keywords = {PEPTIDES; MEMBRANE; CHANNELS; FOLDAMERS; self-assembling; cyclic peptides}, year = {2017}, pages = {539-573} } @mastersthesis{MTMT:3268249, title = {Molecular mimicry of conformationally diverse β-sheets by using α/β-peptide foldamers}, url = {https://m2.mtmt.hu/api/publication/3268249}, author = {Hegedüs, Zsófia}, doi = {10.14232/phd.3201}, publisher = {SZTE}, unique-id = {3268249}, year = {2017}, orcid-numbers = {Hegedüs, Zsófia/0000-0002-5546-8167} } @article{MTMT:27100853, title = {The relevance of the relative configuration in the folding of hybrid peptides containing beta-cyclobutane amino acids and gamma-amino-L-proline residues}, url = {https://m2.mtmt.hu/api/publication/27100853}, author = {Ilia, Ona and Antonio, Olivares Jose and Nolis, Pau and Ortuno, Rosa M}, doi = {10.1016/j.tet.2017.09.011}, journal-iso = {TETRAHEDRON}, journal = {TETRAHEDRON}, volume = {73}, unique-id = {27100853}, issn = {0040-4020}, year = {2017}, eissn = {1464-5416}, pages = {6286-6295} } @article{MTMT:26581831, title = {-Aminoxy Peptoids: A Unique Peptoid Backbone with a Preference for cis-Amide Bonds}, url = {https://m2.mtmt.hu/api/publication/26581831}, author = {Krieger, Viktoria and Ciglia, Emanuele and Thoma, Roland and Vasylyeva, Vera and Frieg, Benedikt and Amadeu, Nader de Sousa and Kurz, Thomas and Janiak, Christoph and Gohlke, Holger and Hansen, Finn K}, doi = {10.1002/chem.201605100}, journal-iso = {CHEM-EUR J}, journal = {CHEMISTRY-A EUROPEAN JOURNAL}, volume = {23}, unique-id = {26581831}, issn = {0947-6539}, year = {2017}, eissn = {1521-3765}, pages = {3699-3707} } @article{MTMT:26934093, title = {Targeting Apolipoprotein E/Amyloid beta Binding by Peptoid CPO_A beta 17-21 P Ameliorates Alzheimer's Disease Related Pathology and Cognitive Decline}, url = {https://m2.mtmt.hu/api/publication/26934093}, author = {Liu, Shan and Park, Shinae and Allington, Grant and Prelli, Frances and Sun, Yanjie and Marta-Ariza, Mitchell and Scholtzova, Henrieta and Biswas, Goutam and Brown, Bernard and Verghese, Philip B and Mehta, Pankaj D and Kwon, Yong-Uk and Wisniewski, Thomas}, doi = {10.1038/s41598-017-08604-8}, journal-iso = {SCI REP}, journal = {SCIENTIFIC REPORTS}, volume = {7}, unique-id = {26934093}, issn = {2045-2322}, year = {2017}, eissn = {2045-2322}, orcid-numbers = {Wisniewski, Thomas/0000-0002-3379-8966} } @article{MTMT:3266869, title = {Homochirality of beta-Peptides: A Significant Biomimetic Property of Unnatural Systems}, url = {https://m2.mtmt.hu/api/publication/3266869}, author = {Mándity, István and Nekkaa, Imane and Paragi, Gábor and Fülöp, Ferenc}, doi = {10.1002/open.201700078}, journal-iso = {CHEMISTRYOPEN}, journal = {CHEMISTRYOPEN}, volume = {6}, unique-id = {3266869}, issn = {2191-1363}, abstract = {Homochirality, an interesting phenomenon of life, is mainly an unresolved problem and was thought to be a property of living matter. Herein, we show that artificial beta-peptides have the tendency toward homochiral diastereoselective chain elongation. Chain-length-dependent stereochemical discrimination was investigated in the synthesis of foldamers with various side chains and secondary structures. It was found that there is a strong tendency toward the synthesis of homochiral oligomers. The size of the side chain drastically influenced the selectivity of the stereodiscriminative chain-elongation reaction. It is noteworthy that water as the co-solvent increases the selectivity. Such behavior is a novel fundamental biomimetic property of foldamers with a potential of future industrial application.}, keywords = {AMINO-ACIDS; ORIGIN; DESIGN; SECONDARY STRUCTURE; FOLDAMERS; CONFIGURATION; Chemistry; CHIRALITY; diastereoselectivity; asymmetric autocatalysis; CORRELATION-ENERGY; BETA-PEPTIDE; foldamer; CHIRAL MOLECULE; homochiralty}, year = {2017}, eissn = {2191-1363}, pages = {492-496}, orcid-numbers = {Mándity, István/0000-0003-2865-6143; Paragi, Gábor/0000-0001-5408-1748; Fülöp, Ferenc/0000-0003-1066-5287} } @article{MTMT:27106717, title = {Rational Design and Synthesis of Post-Functionalizable Peptide Foldamers as Helical Templates}, url = {https://m2.mtmt.hu/api/publication/27106717}, author = {Misawa, Takashi and Kanda, Yasunari and Demizu, Yosuke}, doi = {10.1021/acs.bioconjchem.7b00621}, journal-iso = {BIOCONJUGATE CHEM}, journal = {BIOCONJUGATE CHEMISTRY}, volume = {28}, unique-id = {27106717}, issn = {1043-1802}, year = {2017}, eissn = {1520-4812}, pages = {3029-3035}, orcid-numbers = {Demizu, Yosuke/0000-0001-7521-4861} } @article{MTMT:3134571, title = {C-3 epimers of sugar amino acids as foldameric building blocks: improved synthesis, useful derivatives, coupling strategies}, url = {https://m2.mtmt.hu/api/publication/3134571}, author = {Nagy, Adrienn and Csordás, Barbara and Zsoldos-Mády, Virág and Pintér, István and Farkas, Viktor and Perczel, András}, doi = {10.1007/s00726-016-2346-5}, journal-iso = {AMINO ACIDS}, journal = {AMINO ACIDS}, volume = {49}, unique-id = {3134571}, issn = {0939-4451}, abstract = {To obtain key sugar derivatives for making homooligomeric foldamers or α/β-chimera peptides, economic and multigram scale synthetic methods were to be developed. Though described in the literature, the cost-effective making of both 3-amino-3-deoxy-ribofuranuronic acid (H–t X–OH) and its C-3 epimeric stereoisomer, the 3-amino-3-deoxy-xylofuranuronic acid (H–c X–OH) from d-glucose is described here. The present synthetic route elaborated is (1) appropriate for large-scale synthesis; (2) reagent costs reduced (e.g. by a factor of 400); (3) yields optimized are ~80% or higher for all six consecutive steps concluding –t X– or –c X– and (4) reaction times shortened. Thus, a new synthetic route step-by-step optimized for yield, cost, time and purification is given both for d-xylo and d-ribo-amino-furanuronic acids using sustainable chemistry (e.g. less chromatography with organic solvents; using continuous-flow reactor). Our study encompasses necessary building blocks (e.g. –X–OMe, –X–OiPr, –X–NHMe, Fmoc–X–OH) and key coupling reactions making –Aaa–t X–Aaa– or –Aaa–t X–t X–Aaa– type “inserts”. Completed for both stereoisomers of X, including the newly synthesized Fmoc–c X–OH, producing longer oligomers for drug design and discovery is more of a reality than a wish.}, year = {2017}, eissn = {1438-2199}, pages = {223-240}, orcid-numbers = {Farkas, Viktor/0000-0002-8815-2783; Perczel, András/0000-0003-1252-6416} } @article{MTMT:26581830, title = {Reversible Stereoselective Folding/Unfolding Fueled by the Interplay of Photoisomerism and Hydrogen Bonding}, url = {https://m2.mtmt.hu/api/publication/26581830}, author = {Opie, Christopher R and Kumagai, Naoya and Shibasaki, Masakatsu}, doi = {10.1002/anie.201610279}, journal-iso = {ANGEW CHEM INT EDIT}, journal = {ANGEWANDTE CHEMIE-INTERNATIONAL EDITION}, volume = {56}, unique-id = {26581830}, issn = {1433-7851}, year = {2017}, eissn = {1521-3773}, pages = {3349-3353} } @article{MTMT:26581832, title = {Controlling the Helix Handedness of alpha alpha beta-Peptide Foldamers through Sequence Shifting}, url = {https://m2.mtmt.hu/api/publication/26581832}, author = {Szefczyk, Monika and Weglarz-Tomczak, Ewelina and Fortuna, Paulina and Krzyszton, Agnieszka and Rudzinska-Szostak, Ewa and Berlicki, Lukasz}, doi = {10.1002/anie.201610154}, journal-iso = {ANGEW CHEM INT EDIT}, journal = {ANGEWANDTE CHEMIE-INTERNATIONAL EDITION}, volume = {56}, unique-id = {26581832}, issn = {1433-7851}, year = {2017}, eissn = {1521-3773}, pages = {2087-2091} } @article{MTMT:3098290, title = {Origin of problems related to Staudinger reduction in carbopeptoid syntheses}, url = {https://m2.mtmt.hu/api/publication/3098290}, author = {Csordás, Barbara and Nagy, Adrienn and Harmat, Veronika and Zsoldos-Mády, Virág and Leveles, Ibolya and Pintér, István and Farkas, Viktor and Perczel, András}, doi = {10.1007/s00726-016-2289-x}, journal-iso = {AMINO ACIDS}, journal = {AMINO ACIDS}, volume = {48}, unique-id = {3098290}, issn = {0939-4451}, abstract = {We report the solid phase synthesis of –GG-X-GG– type α/β-carbopeptoids incorporating RibAFU(ip) (1a, tX) or XylAFU(ip) (2a, cX) sugar amino acids. Though coupling efficacy is moderate, both the lengthier synthetic route using Fmoc derivative (e.g., Fmoc-RibAFU(ip)-OH) and the azido derivative (e.g., N3-RibAFU(ip)-OH) via Staudinger reaction with nBu3P can be successfully applied. Both X-ray diffraction, 1H- and 31P-NMR, and theoretical (QM) data support and explain why the application of Ph3P as Staudinger reagent is “ineffective” in the case of a cis stereoisomer, if cX is attached to the preceding residue with a peptide (–CONH–) bond. The failure of the polypeptide chain elongation with N3-cX originates from the “coincidence” of a steric crowdedness and an electronic effect disabling the mandatory nucleophilic attack during the hydrolysis of a quasi penta-coordinated triphenylphosphinimine. Nevertheless, the synthesis of the above α/β-chimera peptides as completed now by a new pathway via 1,2-O-isopropylidene-3-azido-3-deoxy-ribo- and -xylo-furanuronic acid (H-RibAFU(ip)-OH 1a and H-XylAFU(ip)-OH 2a) coupled with N-protected α-amino acids on solid phase could serve as useful examples and starting points of further synthetic efforts. © 2016 Springer-Verlag Wien}, keywords = {STAUDINGER REACTION; Iminophosphorane; Sugar amino acids; Carbopeptoids}, year = {2016}, eissn = {1438-2199}, pages = {2619-2633}, orcid-numbers = {Harmat, Veronika/0000-0002-1866-9904; Farkas, Viktor/0000-0002-8815-2783; Perczel, András/0000-0003-1252-6416} } @article{MTMT:26277737, title = {Molecular Engineering of the Peptoid Nanosheet Hydrophobic Core}, url = {https://m2.mtmt.hu/api/publication/26277737}, author = {Ellen, J Robertson and Caroline, Proulx and Jessica, K Su and Rita, L Garcia and Stan, Yoo and Eric, M Nehls and Michael, D Connolly and Laudann, Taravati and Ronald, N Zuckermann}, doi = {10.1021/acs.langmuir.6b02735}, journal-iso = {LANGMUIR}, journal = {LANGMUIR}, volume = {32}, unique-id = {26277737}, issn = {0743-7463}, year = {2016}, eissn = {1520-5827}, pages = {11946-11957} } @article{MTMT:26276180, title = {Structure–Rheology Relationship in Nanosheet-Forming Peptoid Monolayers}, url = {https://m2.mtmt.hu/api/publication/26276180}, author = {Ellen, J Robertson and Eric, Michael Nehls and Ronald, N Zuckermann}, doi = {10.1021/acs.langmuir.6b02736}, journal-iso = {LANGMUIR}, journal = {LANGMUIR}, volume = {32}, unique-id = {26276180}, issn = {0743-7463}, year = {2016}, eissn = {1520-5827}, pages = {12146-12158} } @article{MTMT:26393033, title = {Therapeutic Potential of Foldamers: From Chemical Biology Tools To Drug Candidates?}, url = {https://m2.mtmt.hu/api/publication/26393033}, author = {Gopalakrishnan, Ranganath and Frolov, Andrey I and Knerr, Laurent and Drury, William J III and Valeur, Eric}, doi = {10.1021/acs.jmedchem.6b00376}, journal-iso = {J MED CHEM}, journal = {JOURNAL OF MEDICINAL CHEMISTRY}, volume = {59}, unique-id = {26393033}, issn = {0022-2623}, year = {2016}, eissn = {1520-4804}, pages = {9599-9621} } @article{MTMT:25447776, title = {Peptide-based inhibitors of protein-protein interactions}, url = {https://m2.mtmt.hu/api/publication/25447776}, author = {Wojcik, Paulina and Berlicki, Lukasz}, doi = {10.1016/j.bmcl.2015.12.084}, journal-iso = {BIOORG MED CHEM LETT}, journal = {BIOORGANIC & MEDICINAL CHEMISTRY LETTERS}, volume = {26}, unique-id = {25447776}, issn = {0960-894X}, year = {2016}, eissn = {1464-3405}, pages = {707-713} }