TY - JOUR AU - Bejger, Magdalena AU - Fortuna, Paulina AU - Drewniak-Switalska, Magda AU - Plewka, Jacek AU - Rypniewski, Wojciech AU - Berlicki, Lukasz TI - A computationally designed beta-amino acid-containing miniprotein JF - CHEMICAL COMMUNICATIONS J2 - CHEM COMMUN VL - 57 PY - 2021 IS - 49 SP - 6015 EP - 6018 PG - 4 SN - 1359-7345 DO - 10.1039/d1cc02192c UR - https://m2.mtmt.hu/api/publication/32234787 ID - 32234787 N1 - Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, Poznań, 61-704, Poland Department of Bioorganic Chemistry Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, Wrocław, 50-370, Poland Department of Medical Biochemistry, Wrocław Medical University, Pausteura 1, Wroclaw, 50-368, Poland Faculty of Chemistry, Jagiellonian Univeristy, Gronostajowa 2, Kraków, 30-387, Poland Export Date: 1 October 2021 CODEN: CHCOF Correspondence Address: Berlicki, Ł.; Department of Bioorganic Chemistry Wrocław University of Science and Technology, Poland; email: lukasz.berlicki@pwr.edu.pl Chemicals/CAS: amino acid, 65072-01-7; protein, 67254-75-5; Amino Acids; Proteins Funding details: Narodowe Centrum Nauki, NCN, DEC-2016/21/B/ST5/00269 Funding text 1: This work was financially supported by the National Science Centre, Poland (Grant no. DEC-2016/21/B/ST5/00269 to Ł. B.). The X-ray crystallographic data were collected on beamline P13, which is operated by EMBL Hamburg at the PETRA III storage ring. The SAXS experiments were performed on beamline BM29 at the European Synchrotron Radiation Facility (ESRF, Grenoble, France). We are grateful to Dr Petra Pernot and Anton Popov at the ESRF for assistance in using beamline BM29. AB - 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. LA - English DB - MTMT ER - TY - JOUR AU - Drewniak-switalska, Magda AU - Barycza, Barbara AU - Rudzinska-Szostak, Ewa AU - Morawiak, Pawel AU - Berlicki, Lukasz TI - Constrained beta-amino acid-containing miniproteins dagger JF - ORGANIC & BIOMOLECULAR CHEMISTRY J2 - ORG BIOMOL CHEM VL - 21 PY - 2021 IS - 19 SP - 4272 EP - 4278 PG - 7 SN - 1477-0520 DO - 10.1039/d1ob00309g UR - https://m2.mtmt.hu/api/publication/32000365 ID - 32000365 N1 - Funding Agency and Grant Number: National Science Centre, PolandNational Science Centre, Poland [2016/21/B/ST5/00269] Funding text: The work was financially supported by the National Science Centre, Poland (grant no. 2016/21/B/ST5/00269). AB - 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. LA - English DB - MTMT ER - TY - JOUR AU - Fortuna, Paulina AU - Twarda-Clapa, Aleksandra AU - Skalniak, Lukasz AU - Ozga, Katarzyna AU - Holak, Tad A. AU - Berlicki, Lukasz TI - Systematic 'foldamerization' of peptide inhibiting p53-MDM2/X interactions by the incorporation of trans- or cis-2-aminocyclopentanecarboxylic acid residues JF - EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY J2 - EUR J MED CHEM VL - 208 PY - 2020 PG - 8 SN - 0223-5234 DO - 10.1016/j.ejmech.2020.112814 UR - https://m2.mtmt.hu/api/publication/32000366 ID - 32000366 N1 - Funding Agency and Grant Number: National Science Centre, PolandNational Science Centre, Poland [DEC-2013/10/E/ST5/00625, UMO-2014/12/W/NZ1/00457]; TEAM TECH CORE FACILITY from the Foundation for Polish Science [2017-4/6]; project CALIPSOplus from the EU Framework Programme for Research and Innovation HORIZON 2020 [730872] Funding text: The work was financed by the National Science Centre, Poland, Grant No. DEC-2013/10/E/ST5/00625 (to L.B.) and UMO-2014/12/W/NZ1/00457 (to T.A.H.). Pictures were prepared using the Discovery Studio package (BIOVIA) used under a Polish countrywide license. The use of software resources (BIOVIA Discovery Studio program package) of the Wroclaw Centre for Networking and Supercomputing is also kindly acknowledged. We acknowledge the MCB Structural Biology Core Facility (supported by the TEAM TECH CORE FACILITY/2017-4/6 grant from the Foundation for Polish Science) for valuable support. The research leading to this result has been supported by the project CALIPSOplus under the Grant Agreement 730872 from the EU Framework Programme for Research and Innovation HORIZON 2020. AB - 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. LA - English DB - MTMT ER - TY - JOUR AU - Drewniak, Magda AU - Weglarz-Tomczak, Ewelina AU - Ozga, Katarzyna AU - Rudzinska-Szostak, Ewa AU - Macegoniuk, Katarzyna AU - Tomczak, Jakub M. AU - Bejger, Magdalena AU - Rypniewski, Wojciech AU - Berlicki, Lukasz TI - Helix-loop-helix peptide foldamers and their use in the construction of hydrolase mimetics JF - BIOORGANIC CHEMISTRY J2 - BIOORG CHEM VL - 81 PY - 2018 SP - 356 EP - 361 PG - 6 SN - 0045-2068 DO - 10.1016/j.bioorg.2018.07.012 UR - https://m2.mtmt.hu/api/publication/30452990 ID - 30452990 N1 - Funding Agency and Grant Number: National Science Centre, PolandNational Science Centre, Poland [DEC-2013/10/E/ST5/00625] Funding text: The work was financed by the National Science Centre, Poland (Grant No. DEC-2013/10/E/ST5/00625). AB - 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. LA - English DB - MTMT ER - TY - JOUR AU - Olajos, Gábor AU - Hetényi, Anasztázia AU - Wéber, Edit AU - Szögi, Titanilla AU - Fülöp, Lívia AU - Martinek, Tamás TI - Peripheral cyclic β-amino acids balance the stability and edge-protection of β-sandwiches JF - ORGANIC & BIOMOLECULAR CHEMISTRY J2 - ORG BIOMOL CHEM VL - 16 PY - 2018 IS - 30 SP - 5492 EP - 5499 PG - 8 SN - 1477-0520 DO - 10.1039/c8ob01322e UR - https://m2.mtmt.hu/api/publication/3399101 ID - 3399101 N1 - Funding text: This work was supported by the Hungarian Academy of Sciences, Lendulet program (LP-2011-009) and GINOP-2.3.3-15-2016-00010. E. W. thanks the Postdoctoral Fellowship Program 2014 of the Hungarian Academy of Sciences. AB - 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. LA - English DB - MTMT ER - TY - THES AU - Szakonyi, Zsolt TI - Monoterpénvázas β-és γ-aminosavszármazékok és 3-amino-1, 2-diolok sztereoszelektív szintézise és alkalmazásai PB - Szegedi Tudományegyetem (SZTE) PY - 2018 UR - https://m2.mtmt.hu/api/publication/33541002 ID - 33541002 LA - Hungarian DB - MTMT ER - TY - CHAP AU - Hegedüs, Zsófia AU - Martinek, Tamás ED - Jerry, Atwood ED - George, W. Gokel ED - Len, Barbour TI - Molecular Recognition Using Foldamers T2 - Comprehensive Supramolecular Chemistry II PB - Elsevier CY - Oxford SN - 9780128031988 T3 - Reference Module in Chemistry, Molecular Sciences and Chemical Engineering PY - 2017 SP - 511 EP - 537 PG - 27 DO - 10.1016/B978-0-12-409547-2.12547-8 UR - https://m2.mtmt.hu/api/publication/3129878 ID - 3129878 AB - 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. LA - English DB - MTMT ER - TY - THES AU - Hegedüs, Zsófia TI - Molecular mimicry of conformationally diverse β-sheets by using α/β-peptide foldamers PB - Szegedi Tudományegyetem (SZTE) PY - 2017 SP - 54 DO - 10.14232/phd.3201 UR - https://m2.mtmt.hu/api/publication/3268249 ID - 3268249 LA - English DB - MTMT ER - TY - BOOK ED - Jerry, Atwood ED - George, W. Gokel ED - Len, Barbour TI - Comprehensive Supramolecular Chemistry II T3 - Reference Module in Chemistry, Molecular Sciences and Chemical Engineering ET - 2 PB - Elsevier CY - Oxford PY - 2017 SP - 4568 SN - 9780128031988 UR - https://m2.mtmt.hu/api/publication/3129870 ID - 3129870 AB - 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. LA - English DB - MTMT ER - TY - JOUR AU - Karancsiné Menyhárd, Dóra AU - Hudaky, I AU - Jákli, Imre AU - Juhasz, G AU - Perczel, András TI - Predictable Conformational Diversity in Foldamers of Sugar Amino Acids JF - JOURNAL OF CHEMICAL INFORMATION AND MODELING J2 - J CHEM INF MODEL VL - 57 PY - 2017 IS - 4 SP - 757 EP - 768 PG - 12 SN - 1549-9596 DO - 10.1021/acs.jcim.6b00488 UR - https://m2.mtmt.hu/api/publication/3239373 ID - 3239373 N1 - Funding Agency and Grant Number: Hungarian National Science Fund (OTKA)Orszagos Tudomanyos Kutatasi Alapprogramok (OTKA) [NK101072, K116305] Funding text: This work was supported by grants from the Hungarian National Science Fund (OTKA) (NK101072 and K116305). AB - 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. LA - English DB - MTMT ER - TY - JOUR AU - Szefczyk, Monika AU - Weglarz-Tomczak, Ewelina AU - Fortuna, Paulina AU - Krzyszton, Agnieszka AU - Rudzinska-Szostak, Ewa AU - Berlicki, Lukasz TI - Controlling the Helix Handedness of alpha alpha beta-Peptide Foldamers through Sequence Shifting JF - ANGEWANDTE CHEMIE-INTERNATIONAL EDITION J2 - ANGEW CHEM INT EDIT VL - 56 PY - 2017 IS - 8 SP - 2087 EP - 2091 PG - 5 SN - 1433-7851 DO - 10.1002/anie.201610154 UR - https://m2.mtmt.hu/api/publication/26581832 ID - 26581832 LA - English DB - MTMT ER - TY - JOUR AU - Burslem, George M AU - Kyle, Hannah F AU - Breeze, Alexander L AU - Edwards, Thomas A AU - Nelson, Adam AU - Warriner, Stuart L AU - Wilson, Andrew J TI - Towards "bionic'' proteins: replacement of continuous sequences from HIF-1 alpha with proteomimetics to create functional p300 binding HIF-1 alpha mimics JF - CHEMICAL COMMUNICATIONS J2 - CHEM COMMUN VL - 52 PY - 2016 IS - 31 SP - 5421 EP - 5424 PG - 4 SN - 1359-7345 DO - 10.1039/c6cc01812b UR - https://m2.mtmt.hu/api/publication/25792592 ID - 25792592 N1 - Funding Agency and Grant Number: AstraZenecaAstraZeneca; EPSRCUK Research & Innovation (UKRI)Engineering & Physical Sciences Research Council (EPSRC); European Research CouncilEuropean Research Council (ERC)European Commission [ERC-StG-240324, ERC-PoC 632207]; Biotechnology and Biological Sciences Research CouncilUK Research & Innovation (UKRI)Biotechnology and Biological Sciences Research Council (BBSRC) [BB/L015056/1] Funding Source: researchfish Funding text: We thank AstraZeneca and EPSRC for PhD studentships (G. M. B. and H. F. K.) and the European Research Council [ERC-StG-240324, and ERC-PoC 632207] for support. LA - English DB - MTMT ER - TY - JOUR AU - Hegedüs, Zsófia AU - Makra, Ildikó AU - Imre, Norbert AU - Hetényi, Anasztázia AU - Mándity, István AU - Monostori, Éva AU - Martinek, Tamás TI - Foldameric probes for membrane interactions by induced β-sheet folding JF - CHEMICAL COMMUNICATIONS J2 - CHEM COMMUN VL - 52 PY - 2016 IS - 9 SP - 1891 EP - 1894 PG - 4 SN - 1359-7345 DO - 10.1039/C5CC09257D UR - https://m2.mtmt.hu/api/publication/2993079 ID - 2993079 N1 - Funding Agency and Grant Number: Hungarian Academy of Sciences; Lendulet program [LP-2011-009]; [TAMOP-4.2.6-14/1]\n Funding text: This work was supported by the Hungarian Academy of Sciences, Lendulet program (LP-2011-009) and TAMOP-4.2.6-14/1. Csaba Vizler is gratefully acknowledged for providing the bEND.3 cell line.\n Funding Agency and Grant Number: Hungarian Academy of Sciences; Lendulet program [LP-2011-009]; [TAMOP-4.2.6-14/1] Funding text: This work was supported by the Hungarian Academy of Sciences, Lendulet program (LP-2011-009) and TAMOP-4.2.6-14/1. Csaba Vizler is gratefully acknowledged for providing the bEND.3 cell line. Funding Agency and Grant Number: Hungarian Academy of SciencesHungarian Academy of Sciences; Lendulet program [LP-2011-009]; [TAMOP-4.2.6-14/1] Funding text: This work was supported by the Hungarian Academy of Sciences, Lendulet program (LP-2011-009) and TAMOP-4.2.6-14/1. Csaba Vizler is gratefully acknowledged for providing the bEND.3 cell line. AB - 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. LA - English DB - MTMT ER - TY - JOUR AU - Makwana, Kamlesh Madhusudan AU - Mahalakshmi, Radhakrishnan TI - Stereopositional Outcome in the Packing of Dissimilar Aromatics in Designed -Hairpins JF - CHEMISTRY-A EUROPEAN JOURNAL J2 - CHEM-EUR J VL - 22 PY - 2016 IS - 12 SP - 4147 EP - 4156 PG - 10 SN - 0947-6539 DO - 10.1002/chem.201504428 UR - https://m2.mtmt.hu/api/publication/25792590 ID - 25792590 N1 - Funding Agency and Grant Number: University Grants Commission, Govt. of IndiaUniversity Grants Commission, India Funding text: K.M.M. acknowledges the University Grants Commission, Govt. of India, for a senior research fellowship. R.M. is a Wellcome Trust/DBT India Alliance Intermediate Fellow. This work is supported by intramural funds. The authors declare no conflict of interest. LA - English DB - MTMT ER - TY - JOUR AU - Mándity, István AU - Fülöp, Ferenc TI - An overview of peptide and peptoid foldamers in medicinal chemistry JF - EXPERT OPINION ON DRUG DISCOVERY J2 - EXPERT OPIN DRUG DIS VL - 10 PY - 2015 IS - 11 SP - 1163 EP - 1177 PG - 15 SN - 1746-0441 DO - 10.1517/17460441.2015.1076790 UR - https://m2.mtmt.hu/api/publication/2993085 ID - 2993085 LA - English DB - MTMT ER -