@article{MTMT:32234787, title = {A computationally designed beta-amino acid-containing miniprotein}, url = {https://m2.mtmt.hu/api/publication/32234787}, author = {Bejger, Magdalena and Fortuna, Paulina and Drewniak-Switalska, Magda and Plewka, Jacek and Rypniewski, Wojciech and Berlicki, Lukasz}, doi = {10.1039/d1cc02192c}, journal-iso = {CHEM COMMUN}, journal = {CHEMICAL COMMUNICATIONS}, volume = {57}, unique-id = {32234787}, issn = {1359-7345}, abstract = {A new miniprotein built from three helices, including one structure based on the alpha alpha beta alpha alpha alpha beta sequence pattern was developed. Its crystal structure revealed a compact conformation with a well-packed hydrophobic core of unprecedented structure. The miniprotein formed dimers that were stabilized by the interaction of their hydrophobic surfaces.}, year = {2021}, eissn = {1364-548X}, pages = {6015-6018}, orcid-numbers = {Bejger, Magdalena/0000-0003-1660-9745; Fortuna, Paulina/0000-0003-4617-798X; Plewka, Jacek/0000-0002-0307-0907; Rypniewski, Wojciech/0000-0002-6097-5518; Berlicki, Lukasz/0000-0003-0318-4944} } @article{MTMT:32000365, title = {Constrained beta-amino acid-containing miniproteins dagger}, url = {https://m2.mtmt.hu/api/publication/32000365}, author = {Drewniak-switalska, Magda and Barycza, Barbara and Rudzinska-Szostak, Ewa and Morawiak, Pawel and Berlicki, Lukasz}, doi = {10.1039/d1ob00309g}, journal-iso = {ORG BIOMOL CHEM}, journal = {ORGANIC & BIOMOLECULAR CHEMISTRY}, volume = {21}, unique-id = {32000365}, issn = {1477-0520}, abstract = {The construction of beta-amino acid-containing peptides that fold to tertiary structures in solution remains challenging. Two model miniproteins, namely, Trp-cage and FSD, were scanned using a constrained beta-amino acid in order to evaluate its impact on the folding process. Relationships between forces stabilizing the miniprotein structure and conformational stability of analogues were found. The possibility of a significant increase of the conformational stability of the studied miniproteins by substitution with the beta-amino acid at the terminus of a helix is shown. On the basis of these results, beta-amino acid containing-peptide analogs with helical fragments substantially altered by the incorporation of several constrained beta-amino acids were designed, synthesized and evaluated with respect to their structure and stability. The smallest known beta-amino acid-containing peptide with a well-defined tertiary structure is described.}, year = {2021}, eissn = {1477-0539}, pages = {4272-4278}, orcid-numbers = {Rudzinska-Szostak, Ewa/0000-0001-7583-9829; Berlicki, Lukasz/0000-0003-0318-4944} } @article{MTMT:32000366, title = {Systematic 'foldamerization' of peptide inhibiting p53-MDM2/X interactions by the incorporation of trans- or cis-2-aminocyclopentanecarboxylic acid residues}, url = {https://m2.mtmt.hu/api/publication/32000366}, author = {Fortuna, Paulina and Twarda-Clapa, Aleksandra and Skalniak, Lukasz and Ozga, Katarzyna and Holak, Tad A. and Berlicki, Lukasz}, doi = {10.1016/j.ejmech.2020.112814}, journal-iso = {EUR J MED CHEM}, journal = {EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY}, volume = {208}, unique-id = {32000366}, issn = {0223-5234}, abstract = {A 'foldamerization' strategy for the discovery of biologically active peptide is evaluated using as an example the peptides that inhibit the p53-MDM2/X interactions. Application of a peptide scan with two constrained beta-residue of trans and cis stereochemistry indicated a substitution pattern that leads to active molecules with enhanced conformational stability and high resistance to proteolysis. This procedure led to the discovery of a peptide that showed subnanomolar inhibition of the p53-MDM2 interaction (K-i = 0.4 nM) with resistance to proteolysis enhanced by ca. two orders of magnitude. Crystallographic analysis and molecular modelling allowed for understanding of these peptide-protein interactions at the molecular level. (c) 2020 Elsevier Masson SAS. All rights reserved.}, keywords = {AFFINITY; NEUROPEPTIDE-Y; BETA-PEPTIDES; STABILITY; DE-NOVO DESIGN; crystal structure; Circular Dichroism; Protein-protein interaction; foldamer; GLP-1 RECEPTOR; Cell penetration; ALPHA-HELIX MIMICRY; PEPTOID FOLDAMERS}, year = {2020}, eissn = {1768-3254}, orcid-numbers = {Twarda-Clapa, Aleksandra/0000-0003-2532-5672; Ozga, Katarzyna/0000-0002-2837-283X; Berlicki, Lukasz/0000-0003-0318-4944} } @article{MTMT:30452990, title = {Helix-loop-helix peptide foldamers and their use in the construction of hydrolase mimetics}, url = {https://m2.mtmt.hu/api/publication/30452990}, author = {Drewniak, Magda and Weglarz-Tomczak, Ewelina and Ozga, Katarzyna and Rudzinska-Szostak, Ewa and Macegoniuk, Katarzyna and Tomczak, Jakub M. and Bejger, Magdalena and Rypniewski, Wojciech and Berlicki, Lukasz}, doi = {10.1016/j.bioorg.2018.07.012}, journal-iso = {BIOORG CHEM}, journal = {BIOORGANIC CHEMISTRY}, volume = {81}, unique-id = {30452990}, issn = {0045-2068}, abstract = {De novo designed helix-loop-helix peptide foldamers containing cis-2-aminocyclopentanecarboxylic acid residues were evaluated for their conformational stability and possible use in enzyme mimetic development. The correlation between hydrogen bond network size and conformational stability was demonstrated through CD and NMR spectroscopies. Molecules incorporating a Cys/His/Glu triad exhibited enzyme-like hydrolytic activity.}, keywords = {PEPTIDES; CONFORMATION; CATALYSIS; FOLDAMERS; Circular Dichroism; nuclear magnetic resonance}, year = {2018}, eissn = {1090-2120}, pages = {356-361}, orcid-numbers = {Bejger, Magdalena/0000-0003-1660-9745; Rypniewski, Wojciech/0000-0002-6097-5518; Berlicki, Lukasz/0000-0003-0318-4944} } @article{MTMT:3399101, title = {Peripheral cyclic β-amino acids balance the stability and edge-protection of β-sandwiches}, url = {https://m2.mtmt.hu/api/publication/3399101}, author = {Olajos, Gábor and Hetényi, Anasztázia and Wéber, Edit and Szögi, Titanilla and Fülöp, Lívia and Martinek, Tamás}, doi = {10.1039/c8ob01322e}, journal-iso = {ORG BIOMOL CHEM}, journal = {ORGANIC & BIOMOLECULAR CHEMISTRY}, volume = {16}, unique-id = {3399101}, issn = {1477-0520}, abstract = {Engineering water-soluble stand-alone beta-sandwich mimetics is a current challenge because of the difficulties associated with tailoring long-range interactions. In this work, single cis-(1R,2S)-2-aminocyclohexanecarboxylic acid mutations were introduced into the edge strands of the eight-stranded beta-sandwich mimetic structures from the betabellin family. Temperature-dependent NMR and CD measurements, together with thermodynamic analyses, demonstrated that the modified peripheral strands exhibited an irregular and partially disordered structure but were able to exert sufficient shielding on the hydrophobic core to retain the predominantly beta-sandwich structure. Although the frustrated interactions decreased the free energy of unfolding, the temperature of the maximum stabilities increased to or remained at physiologically relevant temperatures. We found that the irregular peripheral strands were able to prevent edge-to-edge association and fibril formation in the aggregation-prone model. These findings establish a beta-sandwich stabilization and aggregation inhibition approach, which does not interfere with the pillars of the peptide bond or change the net charge of the peptide.}, keywords = {INHIBITORS; SECONDARY STRUCTURE; DE-NOVO DESIGN; HEAT-CAPACITY; ALPHA/BETA-PEPTIDES; protein–protein interactions; SHEET PROTEIN; FOLDING THERMODYNAMICS; GAMMA-PEPTIDES}, year = {2018}, eissn = {1477-0539}, pages = {5492-5499}, orcid-numbers = {Olajos, Gábor/0000-0002-2479-4891; Hetényi, Anasztázia/0000-0001-8080-6992; Wéber, Edit/0000-0002-5904-0619; Szögi, Titanilla/0000-0002-9854-7340; Fülöp, Lívia/0000-0002-8010-0129; Martinek, Tamás/0000-0003-3168-8066} } @mastersthesis{MTMT:33541002, title = {Monoterpénvázas β-és γ-aminosavszármazékok és 3-amino-1, 2-diolok sztereoszelektív szintézise és alkalmazásai}, url = {https://m2.mtmt.hu/api/publication/33541002}, author = {Szakonyi, Zsolt}, publisher = {SZTE}, unique-id = {33541002}, year = {2018}, orcid-numbers = {Szakonyi, Zsolt/0000-0003-2432-8409} } @{MTMT:3129878, title = {Molecular Recognition Using Foldamers}, url = {https://m2.mtmt.hu/api/publication/3129878}, author = {Hegedüs, Zsófia and Martinek, Tamás}, booktitle = {Comprehensive Supramolecular Chemistry II}, doi = {10.1016/B978-0-12-409547-2.12547-8}, unique-id = {3129878}, abstract = {Self-organizing polymers (foldamers) that are capable of controlled molecular recognition are extensively investigated in supramolecular chemistry. The predictable shape and the modular synthesis of foldamers make them excellent tools with which to design and construct complementary interaction surfaces required for molecular recognition. The appropriate choice of monomeric unit patterns can lead to oligomers that recognize diverse interaction partners: cavities for small-molecule entrapment or the projection of functional groups from a well-defined scaffold to mimic complex structures such as protein surfaces. The construction of foldamers for protein recognition is a very attractive strategy for medicinal chemistry applications with promising results. In this article, foldamers that recognize small molecules, biomacromolecules, and membranes will be addressed with a brief general review of the structures and design strategies. © 2017 Elsevier Ltd. All rights reserved.}, keywords = {PEPTIDES; SECONDARY STRUCTURE; HELIX; FOLDAMERS; Nucleic Acids; SHEET; protein–protein interactions; protein mimetics; β-Peptides; Aromatic oligoamides; PEPTOIDS; oligoureas; Azapeptides; Membrane-interacting foldamers; Molecular capsules}, year = {2017}, pages = {511-537}, orcid-numbers = {Hegedüs, Zsófia/0000-0002-5546-8167; Martinek, Tamás/0000-0003-3168-8066} } @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} } @book{MTMT:3129870, title = {Comprehensive Supramolecular Chemistry II}, url = {https://m2.mtmt.hu/api/publication/3129870}, isbn = {9780128031995}, editor = {Jerry, Atwood and George, W. Gokel and Len, Barbour}, publisher = {Elsevier B.V.}, unique-id = {3129870}, abstract = {Comprehensive Supramolecular Chemistry II, Second Edition, Nine Volume Set is a ‘one-stop shop’ that covers supramolecular chemistry, a field that originated from the work of researchers in organic, inorganic and physical chemistry, with some biological influence. The original edition was structured to reflect, in part, the origin of the field. However, in the past two decades, the field has changed a great deal as reflected in this new work that covers the general principles of supramolecular chemistry and molecular recognition, experimental and computational methods in supramolecular chemistry, supramolecular receptors, dynamic supramolecular chemistry, supramolecular engineering, crystallographic (engineered) assemblies, sensors, imaging agents, devices and the latest in nanotechnology. Each section begins with an introduction by an expert in the field, who offers an initial perspective on the development of the field. Each article begins with outlining basic concepts before moving on to more advanced material.}, year = {2017} } @article{MTMT:3239373, title = {Predictable Conformational Diversity in Foldamers of Sugar Amino Acids}, url = {https://m2.mtmt.hu/api/publication/3239373}, author = {Karancsiné Menyhárd, Dóra and Hudaky, I and Jákli, Imre and Juhasz, G and Perczel, András}, doi = {10.1021/acs.jcim.6b00488}, journal-iso = {J CHEM INF MODEL}, journal = {JOURNAL OF CHEMICAL INFORMATION AND MODELING}, volume = {57}, unique-id = {3239373}, issn = {1549-9596}, abstract = {A systematic conformational search was carried out for monomers and homohexamers of furanoid beta-amino, acids: cis-(S,R) and trans-(S,S) stereoisomers of aminocyclopentane carboxylic acid (ACPC), two different.aniinofuranuronic acids (AFU(alpha) and AFU(beta)), their isopropylidene derivatives (AFU(ip)), and the key intermediate beta-aminotetrahydrofurancarboxylic acid (ATFC). The stereochemistry of the building blocks was chosen to match that of the natural sugar amino acid (xylose and ribose) precursors (XylAFU and RibAFU). The results show that hexamera of cis-furanoid beta-amino acids show great variability: while hydrophobic.cyclopentane (cis-ACPC)(6) and hydrophilic (XylAFU(alpha/beta))(6) foldamers favor two different zigzagged conformation as hexaMers, the backbone fold turns into a helix in the case of (cis-ATFC)(6) (10 -helix) and (XylAFU(ip))(6) (14 -helix). Trans stereochemistry resulted in hexamers exclusively with the right-handed, helix conformation, (H-12(P))(6), regardless of their polarity. We found that the preferred.oligomeric structure of XylAFU(alpha/beta) is conformationally compatible 'with beta-pleated sheets, while that of the trans/(S,S) units matches with alpha-helices of proteins.}, keywords = {DERIVATIVES; RECOGNITION; DESIGN; SECONDARY STRUCTURE; BETA-PEPTIDES; HELIX; OLIGOMERS; STRUCTURAL-CHARACTERIZATION; ALPHA/BETA-PEPTIDE FOLDAMERS; GLP-1 RECEPTOR}, year = {2017}, eissn = {1549-960X}, pages = {757-768}, orcid-numbers = {Karancsiné Menyhárd, Dóra/0000-0002-0095-5531; Perczel, András/0000-0003-1252-6416} } @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:25792592, title = {Towards "bionic'' proteins: replacement of continuous sequences from HIF-1 alpha with proteomimetics to create functional p300 binding HIF-1 alpha mimics}, url = {https://m2.mtmt.hu/api/publication/25792592}, author = {Burslem, George M and Kyle, Hannah F and Breeze, Alexander L and Edwards, Thomas A and Nelson, Adam and Warriner, Stuart L and Wilson, Andrew J}, doi = {10.1039/c6cc01812b}, journal-iso = {CHEM COMMUN}, journal = {CHEMICAL COMMUNICATIONS}, volume = {52}, unique-id = {25792592}, issn = {1359-7345}, year = {2016}, eissn = {1364-548X}, pages = {5421-5424} } @article{MTMT:2993079, title = {Foldameric probes for membrane interactions by induced β-sheet folding}, url = {https://m2.mtmt.hu/api/publication/2993079}, author = {Hegedüs, Zsófia and Makra, Ildikó and Imre, Norbert and Hetényi, Anasztázia and Mándity, István and Monostori, Éva and Martinek, Tamás}, doi = {10.1039/C5CC09257D}, journal-iso = {CHEM COMMUN}, journal = {CHEMICAL COMMUNICATIONS}, volume = {52}, unique-id = {2993079}, issn = {1359-7345}, abstract = {Design strategies were devised for alpha/beta-peptide foldameric analogues of the antiangiogenic anginex with the goal of mimicking the diverse structural features from the unordered conformation to a folded beta-sheet in response to membrane interactions. Structure-activity relationships were investigated in the light of different beta-sheet folding levels.}, keywords = {PROTEIN; ACID; DESIGN; SECONDARY STRUCTURE; ANGIOGENESIS; CIRCULAR-DICHROISM; Practical guide; HAIRPIN; PEPTIDE ANGINEX}, year = {2016}, eissn = {1364-548X}, pages = {1891-1894}, orcid-numbers = {Hegedüs, Zsófia/0000-0002-5546-8167; Hetényi, Anasztázia/0000-0001-8080-6992; Mándity, István/0000-0003-2865-6143; Monostori, Éva/0000-0002-7442-3562; Martinek, Tamás/0000-0003-3168-8066} } @article{MTMT:25792590, title = {Stereopositional Outcome in the Packing of Dissimilar Aromatics in Designed -Hairpins}, url = {https://m2.mtmt.hu/api/publication/25792590}, author = {Makwana, Kamlesh Madhusudan and Mahalakshmi, Radhakrishnan}, doi = {10.1002/chem.201504428}, journal-iso = {CHEM-EUR J}, journal = {CHEMISTRY-A EUROPEAN JOURNAL}, volume = {22}, unique-id = {25792590}, issn = {0947-6539}, year = {2016}, eissn = {1521-3765}, pages = {4147-4156} } @article{MTMT:2993085, title = {An overview of peptide and peptoid foldamers in medicinal chemistry}, url = {https://m2.mtmt.hu/api/publication/2993085}, author = {Mándity, István and Fülöp, Ferenc}, doi = {10.1517/17460441.2015.1076790}, journal-iso = {EXPERT OPIN DRUG DIS}, journal = {EXPERT OPINION ON DRUG DISCOVERY}, volume = {10}, unique-id = {2993085}, issn = {1746-0441}, year = {2015}, eissn = {1746-045X}, pages = {1163-1177}, orcid-numbers = {Mándity, István/0000-0003-2865-6143; Fülöp, Ferenc/0000-0003-1066-5287} }