@article{MTMT:33712712, title = {Structural Adaptation of the Single-Stranded DNA-Binding Protein C-Terminal to DNA Metabolizing Partners Guides Inhibitor Design}, url = {https://m2.mtmt.hu/api/publication/33712712}, author = {Tököli, Attila and Bodnár, Brigitta and Bogár, Ferenc and Paragi, Gábor and Hetényi, Anasztázia and Bartus, Éva and Wéber, Edit and Hegedüs, Zsófia and Szabó, Zoltán and Kecskeméti, Gábor and Szakonyi, Gerda and Martinek, Tamás}, doi = {10.3390/pharmaceutics15041032}, journal-iso = {PHARMACEUTICS}, journal = {PHARMACEUTICS}, volume = {15}, unique-id = {33712712}, issn = {1999-4923}, abstract = {Single-stranded DNA-binding protein (SSB) is a bacterial interaction hub and an appealing target for antimicrobial therapy. Understanding the structural adaptation of the disordered SSB C-terminus (SSB-Ct) to DNA metabolizing enzymes (e.g., ExoI and RecO) is essential for designing high-affinity SSB mimetic inhibitors. Molecular dynamics simulations revealed the transient interactions of SSB-Ct with two hot spots on ExoI and RecO. The residual flexibility of the peptide–protein complexes allows adaptive molecular recognition. Scanning with non-canonical amino acids revealed that modifications at both termini of SSB-Ct could increase the affinity, supporting the two-hot-spot binding model. Combining unnatural amino acid substitutions on both segments of the peptide resulted in enthalpy-enhanced affinity, accompanied by enthalpy–entropy compensation, as determined by isothermal calorimetry. NMR data and molecular modeling confirmed the reduced flexibility of the improved affinity complexes. Our results highlight that the SSB-Ct mimetics bind to the DNA metabolizing targets through the hot spots, interacting with both of segments of the ligands.}, year = {2023}, eissn = {1999-4923}, orcid-numbers = {Tököli, Attila/0000-0001-8413-3182; Bogár, Ferenc/0000-0002-0611-1452; Paragi, Gábor/0000-0001-5408-1748; Hetényi, Anasztázia/0000-0001-8080-6992; Bartus, Éva/0000-0001-9976-6978; Wéber, Edit/0000-0002-5904-0619; Hegedüs, Zsófia/0000-0002-5546-8167; Szabó, Zoltán/0000-0001-8278-8038; Kecskeméti, Gábor/0000-0002-5584-6869; Szakonyi, Gerda/0000-0002-4366-4283; Martinek, Tamás/0000-0003-3168-8066} } @article{MTMT:33597958, title = {Improved Metal-Free Approach for the Synthesis of Protected Thiol Containing Thymidine Nucleoside Phosphoramidite and Its Application for the Synthesis of Ligatable Oligonucleotide Conjugates}, url = {https://m2.mtmt.hu/api/publication/33597958}, author = {Kupihár, Zoltán and Ferenc, Györgyi and Petrovicz, Vencel László and Fáy, Viktória R. and Kovács, Lajos and Martinek, Tamás and Hegedüs, Zsófia}, doi = {10.3390/pharmaceutics15010248}, journal-iso = {PHARMACEUTICS}, journal = {PHARMACEUTICS}, volume = {15}, unique-id = {33597958}, issn = {1999-4923}, abstract = {Oligonucleotide conjugates are versatile scaffolds that can be applied in DNA-based screening platforms and ligand display or as therapeutics. Several different chemical approaches are available for functionalizing oligonucleotides, which are often carried out on the 5′ or 3′ end. Modifying oligonucleotides in the middle of the sequence opens the possibility to ligate the conjugates and create DNA strands bearing multiple different ligands. Our goal was to establish a complete workflow that can be applied for such purposes from monomer synthesis to templated ligation. To achieve this, a monomer is required with an orthogonal functional group that can be incorporated internally into the oligonucleotide sequence. This is followed by conjugation with different molecules and ligation with the help of a complementary template. Here, we show the synthesis and the application of a thiol-modified thymidine nucleoside phosphoramidite to prepare ligatable oligonucleotide conjugates. The conjugations were performed both in solution and on solid phase, resulting in conjugates that can be assembled into multivalent oligonucleotides decorated with tissue-targeting peptides using templated ligation.}, year = {2023}, eissn = {1999-4923}, orcid-numbers = {Kupihár, Zoltán/0000-0001-5499-7617; Ferenc, Györgyi/0000-0002-3456-319X; Petrovicz, Vencel László/0000-0002-5437-2462; Kovács, Lajos/0000-0002-0331-3980; Martinek, Tamás/0000-0003-3168-8066; Hegedüs, Zsófia/0000-0002-5546-8167} } @article{MTMT:32783557, title = {Understanding p300-transcription factor interactions using sequence variation and hybridization}, url = {https://m2.mtmt.hu/api/publication/32783557}, author = {Hobor, Fruzsina and Hegedüs, Zsófia and Ibarra, Amaurys Avila and Petrovicz, Vencel László and Bartlett, Gail and Sessions, Richard Barry and Wilson, Andrew and Edwards, Thomas A}, doi = {10.1039/D2CB00026A}, journal-iso = {RSC CHEM BIOL}, journal = {RSC CHEMICAL BIOLOGY}, volume = {3}, unique-id = {32783557}, year = {2022}, eissn = {2633-0679}, pages = {592-603}, orcid-numbers = {Hegedüs, Zsófia/0000-0002-5546-8167; Petrovicz, Vencel László/0000-0002-5437-2462} } @article{MTMT:32783554, title = {Towards identification of protein–protein interaction stabilizers via inhibitory peptide-fragment hybrids using templated fragment ligation}, url = {https://m2.mtmt.hu/api/publication/32783554}, author = {Srdanović, Sonja and Hegedüs, Zsófia and Warriner, Stuart L. and Wilson, Andrew J.}, doi = {10.1039/D2CB00025C}, journal-iso = {RSC CHEM BIOL}, journal = {RSC CHEMICAL BIOLOGY}, volume = {3}, unique-id = {32783554}, year = {2022}, eissn = {2633-0679}, pages = {546-550}, orcid-numbers = {Hegedüs, Zsófia/0000-0002-5546-8167; Wilson, Andrew J./0000-0001-9852-6366} } @article{MTMT:32006750, title = {Query-guided protein–protein interaction inhibitor discovery}, url = {https://m2.mtmt.hu/api/publication/32006750}, author = {Celis, Sergio and Hobor, Fruzsina and James, Thomas and Bartlett, Gail J. and Ibarra, Amaurys A. and Shoemark, Deborah K. and Hegedüs, Zsófia and Hetherington, Kristina and Woolfson, Derek N. and Sessions, Richard B. and Edwards, Thomas A. and Andrews, David M. and Nelson, Adam and Wilson, Andrew J.}, doi = {10.1039/D1SC00023C}, journal-iso = {CHEM SCI}, journal = {CHEMICAL SCIENCE}, volume = {12}, unique-id = {32006750}, issn = {2041-6520}, year = {2021}, eissn = {2041-6539}, pages = {4753-4762}, orcid-numbers = {Celis, Sergio/0000-0001-8177-2472; Hobor, Fruzsina/0000-0002-0768-3292; James, Thomas/0000-0002-9728-9482; Bartlett, Gail J./0000-0002-9932-2960; Shoemark, Deborah K./0000-0002-1240-8463; Hegedüs, Zsófia/0000-0002-5546-8167; Woolfson, Derek N./0000-0002-0394-3202; Sessions, Richard B./0000-0003-0320-0895; Edwards, Thomas A./0000-0002-1467-3674; Andrews, David M./0000-0002-6716-6270; Nelson, Adam/0000-0003-3886-363X; Wilson, Andrew J./0000-0001-9852-6366} } @article{MTMT:31868515, title = {Identification of β-strand mediated protein–protein interaction inhibitors using ligand-directed fragment ligation}, url = {https://m2.mtmt.hu/api/publication/31868515}, author = {Hegedüs, Zsófia and Hóbor, Fruzsina and Shoemark, Deborah K. and Celis, Sergio and Lian, Lu-Yun and Trinh, Chi H. and Sessions, Richard B. and Edwards, Thomas A. and Wilson, Andrew J.}, doi = {10.1039/D0SC05694D}, journal-iso = {CHEM SCI}, journal = {CHEMICAL SCIENCE}, volume = {12}, unique-id = {31868515}, issn = {2041-6520}, abstract = {beta-Strand mediated protein-protein interactions (PPIs) represent underexploited targets for chemical probe development despite representing a significant proportion of known and therapeutically relevant PPI targets. beta-Strand mimicry is challenging given that both amino acid side-chains and backbone hydrogen-bonds are typically required for molecular recognition, yet these are oriented along perpendicular vectors. This paper describes an alternative approach, using GKAP/SHANK1 PDZ as a model and dynamic ligation screening to identify small-molecule replacements for tranches of peptide sequence. A peptide truncation of GKAP functionalized at the N- and C-termini with acylhydrazone groups was used as an anchor. Reversible acylhydrazone bond exchange with a library of aldehyde fragments in the presence of the protein as template and in situ screening using a fluorescence anisotropy (FA) assay identified peptide hybrid hits with comparable affinity to the GKAP peptide binding sequence. Identified hits were validated using FA, ITC, NMR and X-ray crystallography to confirm selective inhibition of the target PDZ-mediated PPI and mode of binding. These analyses together with molecular dynamics simulations demonstrated the ligands make transient interactions with an unoccupied basic patch through electrostatic interactions, establishing proof-of-concept that this unbiased approach to ligand discovery represents a powerful addition to the armory of tools that can be used to identify PPI modulators.}, year = {2021}, eissn = {2041-6539}, pages = {2286-2293}, orcid-numbers = {Hegedüs, Zsófia/0000-0002-5546-8167; Hóbor, Fruzsina/0000-0002-0768-3292; Shoemark, Deborah K./0000-0002-1240-8463; Celis, Sergio/0000-0001-8177-2472; Lian, Lu-Yun/0000-0001-9481-749X; Trinh, Chi H./0000-0002-5087-5011; Sessions, Richard B./0000-0003-0320-0895; Edwards, Thomas A./0000-0002-1467-3674; Wilson, Andrew J./0000-0001-9852-6366} } @article{MTMT:31502481, title = {Stapled Peptides as HIF-1 alpha/p300 Inhibitors: Helicity Enhancement in the Bound State Increases Inhibitory Potency}, url = {https://m2.mtmt.hu/api/publication/31502481}, author = {Hetherington, Kristina and Hegedüs, Zsófia and Edwards, Thomas A. and Sessions, Richard B. and Nelson, Adam and Wilson, Andrew J.}, doi = {10.1002/chem.202000417}, journal-iso = {CHEM-EUR J}, journal = {CHEMISTRY-A EUROPEAN JOURNAL}, volume = {26}, unique-id = {31502481}, issn = {0947-6539}, abstract = {Protein-protein interactions (PPIs) control virtually all cellular processes and have thus emerged as potential targets for development of molecular therapeutics. Peptide-based inhibitors of PPIs are attractive given that they offer recognition potency and selectivity features that are ideal for function, yet, they do not predominantly populate the bioactive conformation, frequently suffer from poor cellular uptake and are easily degraded, for example, by proteases. The constraint of peptides in a bioactive conformation has emerged as a promising strategy to mitigate against these liabilities. In this work, using peptides derived from hypoxia-inducible factor 1 (HIF-1 alpha) together with dibromomaleimide stapling, we identify constrained peptide inhibitors of the HIF-1 alpha/p300 interaction that are more potent than their unconstrained sequences. Contrary to expectation, the increased potency does not correlate with an increased population of an alpha-helical conformation in the unbound state as demonstrated by experimental circular dichroism analysis. Rather, the ability of the peptide to adopt a bioactive alpha-helical conformation in the p300 bound state is better supported in the constrained variant as demonstrated by molecular dynamics simulations and circular dichroism difference spectra.}, keywords = {Oncology; PEPTIDOMIMETICS; protein–protein interactions; chemical biology; stapled peptides}, year = {2020}, eissn = {1521-3765}, pages = {7638-7646}, orcid-numbers = {Hegedüs, Zsófia/0000-0002-5546-8167} } @article{MTMT:31371344, title = {DPP-4 Cleaves alpha/beta-Peptide Bonds: Substrate Specificity and Half-Lives}, url = {https://m2.mtmt.hu/api/publication/31371344}, author = {Turalic, Amila and Dedibegovic, Jasmina and Hegedüs, Zsófia and Martinek, Tamás}, doi = {10.1002/cbic.202000050}, journal-iso = {CHEMBIOCHEM}, journal = {CHEMBIOCHEM}, volume = {21}, unique-id = {31371344}, issn = {1439-4227}, abstract = {The incorporation of beta-amino acids into a peptide sequence has gained particular attention as beta- and alpha/beta-peptides have shown remarkable proteolytic stability, even after a single homologation at the scissile bond. Several peptidases have been shown to cleave such bonds with high specificity but at a much slower rate compared to alpha-peptide bonds. In this study, a series of analogs of dipeptidyl peptidase-4 (DPP-4) substrate inhibitors were synthesized in order to investigate whether beta-amino acid homologation at the scissile bond could be a valid approach to improving peptide stability towards DPP-4 degradation. DPP-4 cleaved the alpha/beta-peptide bond after the N-terminal penultimate Pro with a broad specificity and retained full activity regardless of the beta(3)-amino acid side chain and peptide length. Significantly improved half-lives were observed for beta(3)Ile-containing peptides. Replacing the penultimate Pro with a conformationally constrained Pro mimetic led to proteolytic resistance. DPP-4 cleavage of alpha/beta-peptide bonds with a broad promiscuity represents a new insight into the stability of peptide analogs containing beta-amino acids as such analogs were thought to be stable towards enzymatic degradation.}, year = {2020}, eissn = {1439-7633}, pages = {2060-2066}, orcid-numbers = {Hegedüs, Zsófia/0000-0002-5546-8167; Martinek, Tamás/0000-0003-3168-8066} } @article{MTMT:31025406, title = {Predicting and Experimentally Validating Hot-Spot Residues at Protein-Protein Interfaces}, url = {https://m2.mtmt.hu/api/publication/31025406}, author = {Ibarra, Amaurys A. and Bartlett, Gail J. and Hegedüs, Zsófia and Dutt, Som and Hobor, Fruzsina and Horner, Katherine A. and Hetherington, Kristina and Spence, Kirstin and Nelson, Adam and Edwards, Thomas A. and Woolfson, Derek N. and Sessions, Richard B. and Wilson, Andrew J.}, doi = {10.1021/acschembio.9b00560}, journal-iso = {ACS CHEM BIOL}, journal = {ACS CHEMICAL BIOLOGY}, volume = {14}, unique-id = {31025406}, issn = {1554-8929}, abstract = {Protein-protein interactions (PPIs) are vital to all biological processes. These interactions are often dynamic, sometimes transient, typically occur over large topographically shallow protein surfaces, and can exhibit a broad range of affinities. Considerable progress has been made in determining PPI structures. However, given the above properties, understanding the key determinants of their thermodynamic stability remains a challenge in chemical biology. An improved ability to identify and engineer PPIs would advance understanding of biological mechanisms and mutant phenotypes and also provide a firmer foundation for inhibitor design. In silico prediction of PPI hot-spot amino acids using computational alanine scanning (CAS) offers a rapid approach for predicting key residues that drive protein-protein association. This can be applied to all known PPI structures; however there is a trade-off between throughput and accuracy. Here we describe a comparative analysis of multiple CAS methods, which highlights effective approaches to improve the accuracy of predicting hot-spot residues. Alongside this, we introduce a new method, BUDE Alanine Scanning, which can be applied to single structures from crystallography and to structural ensembles from NMR or molecular dynamics data. The comparative analyses facilitate accurate prediction of hot-spots that we validate experimentally with three diverse targets: NOXA-B/MCL-1 (an alpha-helix-mediated PPI), SIMS/SUMO, and GKAP/SHANK-PDZ (both beta-strand-mediated interactions). Finally, the approach is applied to the accurate prediction of hot-spot residues at a topographically novel Affimer/BCL-x(L) protein-protein interface.}, year = {2019}, eissn = {1554-8937}, pages = {2252-2263}, orcid-numbers = {Hegedüs, Zsófia/0000-0002-5546-8167} } @article{MTMT:30609649, title = {Recognition of ASF1 by Using Hydrocarbon-Constrained Peptides.}, url = {https://m2.mtmt.hu/api/publication/30609649}, author = {Bakail, May and Rodriguez-Marin, Silvia and Hegedüs, Zsófia and Perrin, Marie E. and Ochsenbein, Francoise and Wilson, Andrew J.}, doi = {10.1002/cbic.201800633}, journal-iso = {CHEMBIOCHEM}, journal = {CHEMBIOCHEM}, volume = {20}, unique-id = {30609649}, issn = {1439-4227}, abstract = {Inhibiting the histone H3-ASF1 (anti-silencing function 1) protein-protein interaction (PPI) represents a potential approach for treating numerous cancers. As an α-helix-mediated PPI, constraining the key histone H3 helix (residues 118-135) is a strategy through which chem. probes might be elaborated to test this hypothesis. In this work, variant H3118-135 peptides bearing pentenylglycine residues at the i and i+4 positions were constrained by olefin metathesis. Biophys. analyses revealed that promotion of a bioactive helical conformation depends on the position at which the constraint is introduced, but that the potency of binding towards ASF1 is unaffected by the constraint and instead that enthalpy-entropy compensation occurs. [on SciFinder(R)]}, year = {2019}, eissn = {1439-7633}, pages = {891-895}, orcid-numbers = {Hegedüs, Zsófia/0000-0002-5546-8167} }