TY - JOUR AU - Tököli, Attila AU - Bodnár, Brigitta AU - Bogár, Ferenc AU - Paragi, Gábor AU - Hetényi, Anasztázia AU - Bartus, Éva AU - Wéber, Edit AU - Hegedüs, Zsófia AU - Szabó, Zoltán AU - Kecskeméti, Gábor AU - Szakonyi, Gerda AU - Martinek, Tamás TI - Structural Adaptation of the Single-Stranded DNA-Binding Protein C-Terminal to DNA Metabolizing Partners Guides Inhibitor Design JF - PHARMACEUTICS J2 - PHARMACEUTICS VL - 15 PY - 2023 IS - 4 PG - 17 SN - 1999-4923 DO - 10.3390/pharmaceutics15041032 UR - https://m2.mtmt.hu/api/publication/33712712 ID - 33712712 N1 - Department of Medical Chemistry, University of Szeged, Szeged, H6720, Hungary ELKH-SZTE Biomimetic Systems Research Group, Eötvös Loránd Research Network (ELKH), Szeged, H6720, Hungary Institute of Physics, University of Pécs, Pécs, H7624, Hungary Department of Theoretical Physics, University of Szeged, Szeged, H6720, Hungary Institute of Pharmaceutical Analysis, University of Szeged, Szeged, H6720, Hungary Export Date: 8 September 2023 Correspondence Address: Martinek, T.A.; Department of Medical Chemistry, Hungary; email: martinek.tamas@med.u-szeged.hu AB - 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. LA - English DB - MTMT ER - TY - JOUR AU - Kupihár, Zoltán AU - Ferenc, Györgyi AU - Petrovicz, Vencel László AU - Fáy, Viktória R. AU - Kovács, Lajos AU - Martinek, Tamás AU - Hegedüs, Zsófia TI - Improved Metal-Free Approach for the Synthesis of Protected Thiol Containing Thymidine Nucleoside Phosphoramidite and Its Application for the Synthesis of Ligatable Oligonucleotide Conjugates JF - PHARMACEUTICS J2 - PHARMACEUTICS VL - 15 PY - 2023 IS - 1 PG - 16 SN - 1999-4923 DO - 10.3390/pharmaceutics15010248 UR - https://m2.mtmt.hu/api/publication/33597958 ID - 33597958 N1 - Funding Agency and Grant Number: National Research, Development and Innovation Office of Hungary [NKFIH PD 135324, K 128801, K 134754]; Ministry of Innovation and Technology of Hungary through the National Research, Development and Innovation Fund [TKP2021-EGA-32] Funding text: This work received funding from the National Research, Development and Innovation Office of Hungary-NKFIH PD 135324 (Z.H.), K 128801 (L.K.) and K 134754 (T.A.M.). Support by the Ministry of Innovation and Technology of Hungary through the National Research, Development and Innovation Fund (TKP2021-EGA-32) is acknowledged. AB - 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. LA - English DB - MTMT ER - TY - JOUR AU - Hobor, Fruzsina AU - Hegedüs, Zsófia AU - Ibarra, Amaurys Avila AU - Petrovicz, Vencel László AU - Bartlett, Gail AU - Sessions, Richard Barry AU - Wilson, Andrew AU - Edwards, Thomas A TI - Understanding p300-transcription factor interactions using sequence variation and hybridization JF - RSC CHEMICAL BIOLOGY J2 - RSC CHEM BIOL VL - 3 PY - 2022 IS - 5 SP - 592 EP - 603 PG - 12 SN - 2633-0679 DO - 10.1039/D2CB00026A UR - https://m2.mtmt.hu/api/publication/32783557 ID - 32783557 LA - English DB - MTMT ER - TY - JOUR AU - Srdanović, Sonja AU - Hegedüs, Zsófia AU - Warriner, Stuart L. AU - Wilson, Andrew J. TI - Towards identification of protein–protein interaction stabilizers via inhibitory peptide-fragment hybrids using templated fragment ligation JF - RSC CHEMICAL BIOLOGY J2 - RSC CHEM BIOL VL - 3 PY - 2022 IS - 5 SP - 546 EP - 550 PG - 5 SN - 2633-0679 DO - 10.1039/D2CB00025C UR - https://m2.mtmt.hu/api/publication/32783554 ID - 32783554 LA - English DB - MTMT ER - TY - JOUR AU - Celis, Sergio AU - Hobor, Fruzsina AU - James, Thomas AU - Bartlett, Gail J. AU - Ibarra, Amaurys A. AU - Shoemark, Deborah K. AU - Hegedüs, Zsófia AU - Hetherington, Kristina AU - Woolfson, Derek N. AU - Sessions, Richard B. AU - Edwards, Thomas A. AU - Andrews, David M. AU - Nelson, Adam AU - Wilson, Andrew J. TI - Query-guided protein–protein interaction inhibitor discovery JF - CHEMICAL SCIENCE J2 - CHEM SCI VL - 12 PY - 2021 IS - 13 SP - 4753 EP - 4762 PG - 10 SN - 2041-6520 DO - 10.1039/D1SC00023C UR - https://m2.mtmt.hu/api/publication/32006750 ID - 32006750 LA - English DB - MTMT ER - TY - JOUR AU - Hegedüs, Zsófia AU - Hóbor, Fruzsina AU - Shoemark, Deborah K. AU - Celis, Sergio AU - Lian, Lu-Yun AU - Trinh, Chi H. AU - Sessions, Richard B. AU - Edwards, Thomas A. AU - Wilson, Andrew J. TI - Identification of β-strand mediated protein–protein interaction inhibitors using ligand-directed fragment ligation JF - CHEMICAL SCIENCE J2 - CHEM SCI VL - 12 PY - 2021 IS - 6 SP - 2286 EP - 2293 PG - 8 SN - 2041-6520 DO - 10.1039/D0SC05694D UR - https://m2.mtmt.hu/api/publication/31868515 ID - 31868515 AB - 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. LA - English DB - MTMT ER - TY - JOUR AU - Hetherington, Kristina AU - Hegedüs, Zsófia AU - Edwards, Thomas A. AU - Sessions, Richard B. AU - Nelson, Adam AU - Wilson, Andrew J. TI - Stapled Peptides as HIF-1 alpha/p300 Inhibitors: Helicity Enhancement in the Bound State Increases Inhibitory Potency JF - CHEMISTRY-A EUROPEAN JOURNAL J2 - CHEM-EUR J VL - 26 PY - 2020 IS - 34 SP - 7638 EP - 7646 PG - 9 SN - 0947-6539 DO - 10.1002/chem.202000417 UR - https://m2.mtmt.hu/api/publication/31502481 ID - 31502481 N1 - School of Chemistry, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, United Kingdom Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, United Kingdom School of Molecular and Cellular Biology, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, United Kingdom School of Biochemistry, University of Bristol, Medical Sciences Building, University Walk, Bristol, BS8 1TD, United Kingdom BrisSynBio, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol, BS8 1TQ, United Kingdom Cited By :8 Export Date: 24 February 2023 CODEN: CEUJE Correspondence Address: Wilson, A.J.; School of Chemistry, Woodhouse Lane, United Kingdom; email: a.j.wilson@leeds.ac.uk Correspondence Address: Wilson, A.J.; Astbury Centre for Structural Molecular Biology, Woodhouse Lane, United Kingdom; email: a.j.wilson@leeds.ac.uk Chemicals/CAS: E1A-Associated p300 Protein; EP300 protein, human; HIF1A protein, human; Hypoxia-Inducible Factor 1, alpha Subunit; Peptides Funding details: Wellcome Trust, WT, 094232/Z/10/Z, 097827/Z/11/A, EP/N025652/1, WT094232MA Funding details: Engineering and Physical Sciences Research Council, EPSRC, EP/KO39292/1, EP/N013573/1 Funding text 1: A.J.W., R.B.S., A.N. and T.A.E. conceived and designed the research programme, K.H., Z.H. and R.B.S. designed studies and performed research. The manuscript was written by K.H. and A.J.W. with contributions from all authors. K.H. prepared figures. This work was supported by the EPSRC (EP/N013573/1, EP/KO39292/1), and The Wellcome Trust (097827/Z/11/A, WT094232MA, 094232/Z/10/Z). A.N. holds an EPSRC Fellowship (EP/N025652/1). AB - 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. LA - English DB - MTMT ER - TY - JOUR AU - Turalic, Amila AU - Dedibegovic, Jasmina AU - Hegedüs, Zsófia AU - Martinek, Tamás TI - DPP-4 Cleaves alpha/beta-Peptide Bonds: Substrate Specificity and Half-Lives JF - CHEMBIOCHEM J2 - CHEMBIOCHEM VL - 21 PY - 2020 IS - 14 SP - 2060 EP - 2066 PG - 7 SN - 1439-4227 DO - 10.1002/cbic.202000050 UR - https://m2.mtmt.hu/api/publication/31371344 ID - 31371344 N1 - Department of Pharmaceutical Analysis, University of Sarajevo, Faculty of Pharmacy, Zmaja od Bosne 8, Sarajevo, 71 000, Bosnia and Herzegovina Department of Medical Chemistry, University of Szeged, Faculty of Medicine, 8 Dóm tér, Szeged, 6720, Hungary MTA-SZTE Biomimetic Systems Research Group, University of Szeged, Dóm tér 8, Szeged, 6720, Hungary Cited By :2 Export Date: 8 September 2023 CODEN: CBCHF Correspondence Address: Hegedüs, Z.; Department of Medical Chemistry, 8 Dóm tér, Hungary; email: hegedus.zsofia@med.u-szeged.hu Correspondence Address: Martinek, T.A.; Department of Medical Chemistry, 8 Dóm tér, Hungary; email: martinek.tamas@med.u-szeged.hu Correspondence Address: Martinek, T.A.; MTA-SZTE Biomimetic Systems Research Group, Dóm tér 8, Hungary; email: martinek.tamas@med.u-szeged.hu AB - 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. LA - English DB - MTMT ER - TY - JOUR AU - Ibarra, Amaurys A. AU - Bartlett, Gail J. AU - Hegedüs, Zsófia AU - Dutt, Som AU - Hobor, Fruzsina AU - Horner, Katherine A. AU - Hetherington, Kristina AU - Spence, Kirstin AU - Nelson, Adam AU - Edwards, Thomas A. AU - Woolfson, Derek N. AU - Sessions, Richard B. AU - Wilson, Andrew J. TI - Predicting and Experimentally Validating Hot-Spot Residues at Protein-Protein Interfaces JF - ACS CHEMICAL BIOLOGY J2 - ACS CHEM BIOL VL - 14 PY - 2019 IS - 10 SP - 2252 EP - 2263 PG - 12 SN - 1554-8929 DO - 10.1021/acschembio.9b00560 UR - https://m2.mtmt.hu/api/publication/31025406 ID - 31025406 AB - 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. LA - English DB - MTMT ER - TY - JOUR AU - Bakail, May AU - Rodriguez-Marin, Silvia AU - Hegedüs, Zsófia AU - Perrin, Marie E. AU - Ochsenbein, Francoise AU - Wilson, Andrew J. TI - Recognition of ASF1 by Using Hydrocarbon-Constrained Peptides. JF - CHEMBIOCHEM J2 - CHEMBIOCHEM VL - 20 PY - 2019 IS - 7 SP - 891 EP - 895 PG - 5 SN - 1439-4227 DO - 10.1002/cbic.201800633 UR - https://m2.mtmt.hu/api/publication/30609649 ID - 30609649 N1 - CAPLUS AN 2019:290706(Journal) AB - 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)] LA - English DB - MTMT ER -