@article{MTMT:34718013, title = {Boronic acid inhibitors of penicillin-binding protein 1b: serine and lysine labelling agents}, url = {https://m2.mtmt.hu/api/publication/34718013}, author = {Kollár, Levente and Grabrijan, Katarina and Hrast Rambaher, Martina and Bozovičar, Krištof and Imre, Tímea and Ferenczy, György and Gobec, Stanislav and Keserű, György Miklós}, doi = {10.1080/14756366.2024.2305833}, journal-iso = {J ENZYM INHIB MED CH}, journal = {JOURNAL OF ENZYME INHIBITION AND MEDICINAL CHEMISTRY}, volume = {39}, unique-id = {34718013}, issn = {1475-6366}, year = {2024}, eissn = {1475-6374}, orcid-numbers = {Ferenczy, György/0000-0002-5771-4616} } @{MTMT:34535308, title = {Free Energy Calculations in Covalent Drug Design}, url = {https://m2.mtmt.hu/api/publication/34535308}, author = {Mihalovits, Levente Márk and Ferenczy, György and Keserű, György Miklós}, booktitle = {Computational Drug Discovery}, doi = {10.1002/9783527840748.ch23}, unique-id = {34535308}, year = {2024}, pages = {561-578}, orcid-numbers = {Mihalovits, Levente Márk/0000-0003-1022-3294; Ferenczy, György/0000-0002-5771-4616} } @article{MTMT:34223252, title = {Molecular Mechanism of Labelling Functional Cysteines by Heterocyclic Thiones}, url = {https://m2.mtmt.hu/api/publication/34223252}, author = {Mihalovits, Levente Márk and Kollár, Levente and Bajusz, Dávid and Knez, Damijan and Bozovičar, Krištof and Imre, Timea and Ferenczy, György and Gobec, Stanislav and Keserű, György Miklós}, doi = {10.1002/cphc.202300596}, journal-iso = {CHEMPHYSCHEM}, journal = {CHEMPHYSCHEM: A EUROPEAN JOURNAL OF CHEMICAL PHYSICS AND PHYSICAL CHEMISTRY}, volume = {25}, unique-id = {34223252}, issn = {1439-4235}, abstract = {Heterocyclic thiones have recently been identified as reversible covalent warheads, consistent with their mild electrophilic nature. Little is known so far about their mechanism of action in labelling nucleophilic sidechains, especially cysteines. The vast number of tractable cysteines promotes a wide range of target proteins to examine; however, our focus was put on functional cysteines. We chose the main protease of SARS‐CoV‐2 harboring Cys145 at the active site that is a structurally characterized and clinically validated target of covalent inhibitors. We screened an in‐house, cysteine‐targeting covalent inhibitor library which resulted in several covalent fragment hits with benzoxazole, benzothiazole and benzimidazole cores. Thione derivatives and Michael acceptors were selected for further investigations with the objective of exploring the mechanism of inhibition of the thiones and using the thoroughly characterized Michael acceptors for benchmarking our studies. Classical and hybrid quantum mechanical/molecular mechanical (QM/MM) molecular dynamics simulations were carried out that revealed a new mechanism of covalent cysteine labelling by thione derivatives, which was supported by QM and free energy calculations and by a wide range of experimental results. Our study shows that the molecular recognition step plays a crucial role in the overall binding of both sets of molecules.}, year = {2024}, eissn = {1439-7641}, orcid-numbers = {Mihalovits, Levente Márk/0000-0003-1022-3294; Bajusz, Dávid/0000-0003-4277-9481; Ferenczy, György/0000-0002-5771-4616} } @article{MTMT:33298396, title = {Next-Generation Heterocyclic Electrophiles as Small-Molecule Covalent MurA Inhibitors}, url = {https://m2.mtmt.hu/api/publication/33298396}, author = {Ábrányi-Balogh, Péter and Keeley, Aaron and Ferenczy, György and Petri, László and Imre, Timea and Grabrijan, Katarina and Hrast, Martina and Knez, Damijan and Ilaš, Janez and Gobec, Stanislav and Keserű, György Miklós}, doi = {10.3390/ph15121484}, journal-iso = {PHARMACEUTICALS-BASE}, journal = {PHARMACEUTICALS}, volume = {15}, unique-id = {33298396}, abstract = {Heterocyclic electrophiles as small covalent fragments showed promising inhibitory activity on the antibacterial target MurA (UDP-N-acetylglucosamine 1-carboxyvinyltransferase, EC:2.5.1.7). Here, we report the second generation of heterocyclic electrophiles: the quaternized analogue of the heterocyclic covalent fragment library with improved reactivity and MurA inhibitory potency. Quantum chemical reaction barrier calculations, GSH (L-glutathione) reactivity assay, and thrombin counter screen were also used to demonstrate and explain the improved reactivity and selectivity of the N-methylated heterocycles and to compare the two generations of heterocyclic electrophiles.}, year = {2022}, eissn = {1424-8247}, orcid-numbers = {Ferenczy, György/0000-0002-5771-4616; Hrast, Martina/0000-0003-0488-2445; Knez, Damijan/0000-0001-9917-1384; Ilaš, Janez/0000-0002-0124-0474; Gobec, Stanislav/0000-0002-9678-3083} } @article{MTMT:32830244, title = {Contribution of hydrophobic interactions to protein mechanical stability}, url = {https://m2.mtmt.hu/api/publication/32830244}, author = {Ferenczy, György and Kellermayer, Miklós}, doi = {10.1016/j.csbj.2022.04.025}, journal-iso = {CSBJ}, journal = {COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL}, volume = {20}, unique-id = {32830244}, issn = {2001-0370}, year = {2022}, eissn = {2001-0370}, pages = {1946-1956}, orcid-numbers = {Ferenczy, György/0000-0002-5771-4616; Kellermayer, Miklós/0000-0002-5553-6553} } @article{MTMT:32668322, title = {The Structure-Derived Mechanism of Box H/ACA Pseudouridine Synthase Offers a Plausible Paradigm for Programmable RNA Editing}, url = {https://m2.mtmt.hu/api/publication/32668322}, author = {Kiss, Dóra Judit and Oláh, Julianna and Tóth, Gergely János and Varga, Máté and Stirling, András and Karancsiné Menyhárd, Dóra and Ferenczy, György}, doi = {10.1021/acscatal.1c04870}, journal-iso = {ACS CATAL}, journal = {ACS CATALYSIS}, volume = {12}, unique-id = {32668322}, issn = {2155-5435}, year = {2022}, eissn = {2155-5435}, pages = {2756-2769}, orcid-numbers = {Tóth, Gergely János/0000-0002-5146-5700; Varga, Máté/0000-0003-4289-1705; Karancsiné Menyhárd, Dóra/0000-0002-0095-5531; Ferenczy, György/0000-0002-5771-4616} } @article{MTMT:32298744, title = {The role of quantum chemistry in covalent inhibitor design}, url = {https://m2.mtmt.hu/api/publication/32298744}, author = {Mihalovits, Levente Márk and Ferenczy, György and Keserű, György Miklós}, doi = {10.1002/qua.26768}, journal-iso = {INT J QUANTUM CHEM}, journal = {INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY}, volume = {122}, unique-id = {32298744}, issn = {0020-7608}, abstract = {The recent ascent of targeted covalent inhibitors (TCI) in drug discovery brings new opportunities and challenges to quantum chemical reactivity calculations supporting discovery efforts. TCIs typically form a covalent bond with the targeted nucleophilic amino acid side chain. Their reactivity that can be both computed and experimentally measured is therefore one of the key factors in determining inhibitory potency. Calculation of relevant quantum chemical descriptors and corresponding reaction barriers of model reactions represent efficient ways to predict intrinsic reactivities of covalent ligands. A more comprehensive description of covalent ligand binding is offered by mixed quantum mechanical/molecular mechanical (QM/MM) potentials. Reaction mechanisms can be investigated by the exploration of the potential energy surface as a function of suitable reaction coordinates, and free energy surfaces can also be calculated with molecular dynamics based simulations. Here we review the methodological aspects and discuss applications with primary focus on high-end QM/MM simulations to illustrate the current status of quantum chemical support to covalent inhibitor design. Available QM approaches are suitable to identify likely reaction mechanisms and rate determining steps in the binding of covalent inhibitors. The efficient QM/MM prediction of ligand reactivities complemented with the computational description of the recognition step makes these computations highly useful in covalent drug discovery.}, keywords = {MOLECULAR MECHANICS; REACTIVITY; quantum mechanics; free energy; Targeted covalent inhibitors; reaction barrier}, year = {2022}, eissn = {1097-461X}, orcid-numbers = {Mihalovits, Levente Márk/0000-0003-1022-3294; Ferenczy, György/0000-0002-5771-4616} } @article{MTMT:33543903, title = {A kovalens enziminhibíció számításos kémiai jellemzése}, url = {https://m2.mtmt.hu/api/publication/33543903}, author = {Mihalovits, Levente Márk and Ferenczy, György and Keserű, György Miklós}, doi = {10.24100/MKF.2022.03-4.150}, journal-iso = {MAGY KÉM FOLY KÉM KÖZL}, journal = {MAGYAR KÉMIAI FOLYÓIRAT - KÉMIAI KÖZLEMÉNYEK (1997-)}, volume = {128}, unique-id = {33543903}, issn = {1418-9933}, year = {2022}, eissn = {1418-8600}, pages = {150-156}, orcid-numbers = {Mihalovits, Levente Márk/0000-0003-1022-3294; Ferenczy, György/0000-0002-5771-4616} } @article{MTMT:32544488, title = {Fragment-Sized and Bidentate (Immuno)Proteasome Inhibitors Derived from Cysteine and Threonine Targeting Warheads}, url = {https://m2.mtmt.hu/api/publication/32544488}, author = {Kollár, Levente and Gobec, Martina and Proj, Matic and Smrdel, Lara and Knez, Damijan and Imre, Timea and Gömöry, Ágnes and Petri, László and Ábrányi-Balogh, Péter and Csányi, Dorottya and Ferenczy, György and Gobec, Stanislav and Sosič, Izidor and Keserű, György Miklós}, doi = {10.3390/cells10123431}, journal-iso = {CELLS-BASEL}, journal = {CELLS}, volume = {10}, unique-id = {32544488}, year = {2021}, eissn = {2073-4409}, orcid-numbers = {Kollár, Levente/0000-0001-9679-3735; Proj, Matic/0000-0003-4043-9686; Knez, Damijan/0000-0001-9917-1384; Gömöry, Ágnes/0000-0001-5216-0135; Ferenczy, György/0000-0002-5771-4616; Gobec, Stanislav/0000-0002-9678-3083; Sosič, Izidor/0000-0002-3370-4587} } @article{MTMT:32129052, title = {Virtual Screening and Biochemical Testing of Borocycles as Immunoproteasome Inhibitors}, url = {https://m2.mtmt.hu/api/publication/32129052}, author = {Kollár, Levente and Ferenczy, György and Proj, Matic and Gobec, Martina and Gobec, Stanislav and Sosič, Izidor and Keserű, György Miklós}, doi = {10.3311/PPch.17202}, journal-iso = {PERIOD POLYTECH CHEM ENG}, journal = {PERIODICA POLYTECHNICA-CHEMICAL ENGINEERING}, volume = {65}, unique-id = {32129052}, issn = {0324-5853}, year = {2021}, eissn = {1587-3765}, pages = {292-298}, orcid-numbers = {Ferenczy, György/0000-0002-5771-4616} } @article{MTMT:31984014, title = {Discovery of selective fragment-sized immunoproteasome inhibitors}, url = {https://m2.mtmt.hu/api/publication/31984014}, author = {Kollár, Levente and Gobec, Martina and Szilágyi, Bence and Proj, Matic and Knez, Damijan and Ábrányi-Balogh, Péter and Petri, László and Imre, Timea and Bajusz, Dávid and Ferenczy, György and Gobec, Stanislav and Keserű, György Miklós and Sosič, Izidor}, doi = {10.1016/j.ejmech.2021.113455}, journal-iso = {EUR J MED CHEM}, journal = {EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY}, volume = {219}, unique-id = {31984014}, issn = {0223-5234}, year = {2021}, eissn = {1768-3254}, orcid-numbers = {Bajusz, Dávid/0000-0003-4277-9481; Ferenczy, György/0000-0002-5771-4616; Gobec, Stanislav/0000-0002-9678-3083} } @article{MTMT:32298742, title = {Mechanistic and thermodynamic characterization of oxathiazolones as potent and selective covalent immunoproteasome inhibitors}, url = {https://m2.mtmt.hu/api/publication/32298742}, author = {Mihalovits, Levente Márk and Ferenczy, György and Keserű, György Miklós}, doi = {10.1016/j.csbj.2021.08.008}, journal-iso = {CSBJ}, journal = {COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL}, volume = {19}, unique-id = {32298742}, issn = {2001-0370}, abstract = {The ubiquitin-proteasome system is responsible for the degradation of proteins and plays a critical role in key cellular processes. While the constitutive proteasome (cPS) is expressed in all eukaryotic cells, the immunoproteasome (iPS) is primarily induced during disease processes, and its inhibition is beneficial in the treatment of cancer, autoimmune disorders and neurodegenerative diseases. Oxathiazolones were reported to selectively inhibit iPS over cPS, and the inhibitory activity of several oxathiazolones against iPS was experimentally determined. However, the detailed mechanism of the chemical reaction leading to irreversible iPS inhibition and the key selectivity drivers are unknown, and separate characterization of the noncovalent and covalent inhibition steps is not available for several compounds. Here, we investigate the chemical reaction between oxathiazolones and the Thr1 residue of iPS by quantum mechanics/ molecular mechanics (QM/MM) simulations to establish a plausible reaction mechanism and to determine the rate-determining step of covalent complex formation. The modelled binding mode and reaction mechanism are in line with the selective inhibition of iPS versus cPS by oxathiazolones. The k(inact )value of several ligands was estimated by constructing the potential of mean force of the rate-determining step by QM/MM simulations coupled with umbrella sampling. The equilibrium constant K-i of the noncovalent complex formation was evaluated by classical force field-based thermodynamic integration. The calculated K-i and kinact values made it possible to analyse the contribution of the noncovalent and covalent steps to the overall inhibitory activity. Compounds with similar intrinsic reactivities exhibit varying selectivities for iPS versus cPS owing to subtle differences in the binding modes that slightly affect K-i, the noncovalent affinity, and importantly alter k(inact), the covalent reactivity of the bound compounds. A detailed understanding of the inhibitory mechanism of oxathiazolones is useful in designing iPS selective inhibitors with improved drug-like properties. (C) 2021 The Author(s). Published by Elsevier B.V. on behalf of Research Network of Computational and Structural Biotechnology.}, keywords = {molecular dynamics; free energy calculation; Immunoproteasome; covalent inhibition; Covalent drug discovery; Oxathiazolones; QM/MM potential}, year = {2021}, eissn = {2001-0370}, pages = {4486-4496}, orcid-numbers = {Mihalovits, Levente Márk/0000-0003-1022-3294; Ferenczy, György/0000-0002-5771-4616} } @article{MTMT:31698584, title = {Allosteric Molecular Switches in Metabotropic Glutamate Receptors}, url = {https://m2.mtmt.hu/api/publication/31698584}, author = {Orgován, Zoltán and Ferenczy, György and Keserű, György Miklós}, doi = {10.1002/cmdc.202000444}, journal-iso = {CHEMMEDCHEM}, journal = {CHEMMEDCHEM}, volume = {16}, unique-id = {31698584}, issn = {1860-7179}, abstract = {Metabotropic glutamate receptors (mGlu) are class C G protein-coupled receptors of eight subtypes that are omnipresently expressed in the central nervous system. mGlus have relevance in several psychiatric and neurological disorders, therefore they raise considerable interest as drug targets. Allosteric modulators of mGlus offer advantages over orthosteric ligands owing to their increased potential to achieve subtype selectivity, and this has prompted discovery programs that have produced a large number of reported allosteric mGlu ligands. However, the optimization of allosteric ligands into drug candidates has proved to be challenging owing to induced-fit effects, flat or steep structure-activity relationships and unexpected changes in theirpharmacology. Subtle structural changes identified as molecular switches might modulate the functional activity of allosteric ligands. Here we review these switches discovered in the metabotropic glutamate receptor family..}, keywords = {METABOTROPIC GLUTAMATE RECEPTORS; Allosteric modulation; MOLECULAR SWITCHES; GPCRs; water networks}, year = {2021}, eissn = {1860-7187}, pages = {81-93}, orcid-numbers = {Ferenczy, György/0000-0002-5771-4616} } @article{MTMT:31997741, title = {Binding Mode Prediction and Virtual Screening Applications by Covalent Docking}, url = {https://m2.mtmt.hu/api/publication/31997741}, author = {Scarpino, Andrea and Ferenczy, György and Keserű, György Miklós}, doi = {10.1007/978-1-0716-1209-5_4}, journal-iso = {METHODS MOL BIOL}, journal = {METHODS IN MOLECULAR BIOLOGY}, volume = {2266}, unique-id = {31997741}, issn = {1064-3745}, abstract = {The mechanism of action of covalent drugs involves the formation of a bond between their electrophilic warhead group and a nucleophilic residue of the protein target. The recent advances in covalent drug discovery have accelerated the development of computational tools for the design and characterization of covalent binders. Covalent docking algorithms can predict the binding mode of covalent ligands by modeling the bonds and interactions formed at the reaction site. Their scoring functions can estimate the relative binding affinity of ligands towards the target of interest, thus allowing virtual screening of compound libraries. However, most of the scoring schemes have no specific terms for the bond formation, and therefore it prevents the direct comparison of warheads with different intrinsic reactivity. Herein, we describe a protocol for the binding mode prediction of covalent ligands, a typical virtual screening of compound sets with a single warhead chemistry, and an alternative approach to screen libraries that include various warhead types, as applied in recently validated studies. © 2021, Springer Science+Business Media, LLC, part of Springer Nature.}, year = {2021}, eissn = {1940-6029}, pages = {73-88}, orcid-numbers = {Ferenczy, György/0000-0002-5771-4616} } @article{MTMT:31848994, title = {WIDOCK: a reactive docking protocol for virtual screening of covalent inhibitors}, url = {https://m2.mtmt.hu/api/publication/31848994}, author = {Scarpino, Andrea and Petri, László and Knez, Damijan and Imre, Timea and Ábrányi-Balogh, Péter and Ferenczy, György and Gobec, Stanislav and Keserű, György Miklós}, doi = {10.1007/s10822-020-00371-5}, journal-iso = {J COMPUT AID MOL DES}, journal = {JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN}, volume = {35}, unique-id = {31848994}, issn = {0920-654X}, year = {2021}, eissn = {1573-4951}, pages = {223-244}, orcid-numbers = {Ferenczy, György/0000-0002-5771-4616; Keserű, György Miklós/0000-0003-1039-7809} } @article{MTMT:31021220, title = {Thermodynamic profiling for fragment-based lead discovery and optimization}, url = {https://m2.mtmt.hu/api/publication/31021220}, author = {Ferenczy, György and Keserű, György Miklós}, doi = {10.1080/17460441.2020.1691166}, journal-iso = {EXPERT OPIN DRUG DIS}, journal = {EXPERT OPINION ON DRUG DISCOVERY}, volume = {15}, unique-id = {31021220}, issn = {1746-0441}, abstract = {Introduction: The enthalpic and entropic components of the ligand-protein binding free energy reflect the type and quality of the interactions and relate to the physicochemical properties of the ligands. These findings have significance in medicinal chemistry optimizations since they suggest that the thermodynamic profiling of the binding may help monitor and control the unfavorable size and hydrophobicity increase typically accompanying affinity improvements and leading to suboptimal pharmacokinetic properties. Areas covered: This review describes the ligand-protein binding event in terms of elementary steps, their associated interactions, and their enthalpic and entropic consequences. The relationships among the breaking and forming interactions, the binding thermodynamic profile, and the physicochemical properties of the ligands are also discussed. Expert opinion: Analysis of the size dependence of available affinity and favorable enthalpy highlights the limitation of the simultaneous optimization of these quantities. Indeed, moderate, rather than very high affinities can be conciliated with favorable physicochemical and pharmacokinetic profiles as it is supported by the affinity range of historical oral drugs. Although thermodynamic quantities are not suitable endpoints for medicinal chemistry optimizations owing to the complexity of the binding thermodynamics, thermodynamic profiling together with structural studies can be advantageously used to understand the details of the binding process and to optimize it.}, keywords = {Binding thermodynamics; fragment optimization; enthalpy driven optimization; entropy driven optimization; fragment binding}, year = {2020}, eissn = {1746-045X}, pages = {117-129}, orcid-numbers = {Ferenczy, György/0000-0002-5771-4616} } @article{MTMT:30834454, title = {Allosteric activation of metabotropic glutamate receptor 5}, url = {https://m2.mtmt.hu/api/publication/30834454}, author = {Jójárt, Balázs and Orgován, Zoltán and Márki, Árpád and Pándy-Szekeres, Gáspár and Ferenczy, György and Keserű, György Miklós}, doi = {10.1080/07391102.2019.1638302}, journal-iso = {J BIOMOL STRUCT DYN}, journal = {JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS}, volume = {38}, unique-id = {30834454}, issn = {0739-1102}, year = {2020}, eissn = {1538-0254}, pages = {2624-2632}, orcid-numbers = {Márki, Árpád/0000-0002-6056-8891; Ferenczy, György/0000-0002-5771-4616} } @article{MTMT:31799316, title = {Affinity and Selectivity Assessment of Covalent Inhibitors by Free Energy Calculations}, url = {https://m2.mtmt.hu/api/publication/31799316}, author = {Mihalovits, Levente Márk and Ferenczy, György and Keserű, György Miklós}, doi = {10.1021/acs.jcim.0c00834}, journal-iso = {J CHEM INF MODEL}, journal = {JOURNAL OF CHEMICAL INFORMATION AND MODELING}, volume = {60}, unique-id = {31799316}, issn = {1549-9596}, year = {2020}, eissn = {1549-960X}, pages = {6579-6594}, orcid-numbers = {Mihalovits, Levente Márk/0000-0003-1022-3294; Ferenczy, György/0000-0002-5771-4616} } @article{MTMT:31817108, title = {Covalent Docking in Drug Discovery: Scope and Limitations}, url = {https://m2.mtmt.hu/api/publication/31817108}, author = {Scarpino, Andrea and Ferenczy, György and Keserű, György Miklós}, doi = {10.2174/1381612824999201105164942}, journal-iso = {CURR PHARM DESIGN}, journal = {CURRENT PHARMACEUTICAL DESIGN}, volume = {26}, unique-id = {31817108}, issn = {1381-6128}, year = {2020}, eissn = {1873-4286}, pages = {5684-5699}, orcid-numbers = {Scarpino, Andrea/0000-0003-3287-6210; Ferenczy, György/0000-0002-5771-4616; Keserű, György Miklós/0000-0003-1039-7809} } @article{MTMT:30334026, title = {Structure-Based Optimization Strategies for G Protein-Coupled Receptor (GPCR) Allosteric Modulators: A Case Study from Analyses of New Metabotropic Glutamate Receptor 5 (mGlu 5 ) X-ray Structures}, url = {https://m2.mtmt.hu/api/publication/30334026}, author = {Christopher, John A. and Orgován, Zoltán and Congreve, Miles and Doré, Andrew S. and Errey, James C. and Marshall, Fiona H. and Mason, Jonathan S. and Okrasa, Krzysztof and Rucktooa, Prakash and Serrano-Vega, Maria J. and Ferenczy, György and Keserű, György Miklós}, doi = {10.1021/acs.jmedchem.7b01722}, journal-iso = {J MED CHEM}, journal = {JOURNAL OF MEDICINAL CHEMISTRY}, volume = {62}, unique-id = {30334026}, issn = {0022-2623}, year = {2019}, eissn = {1520-4804}, pages = {207-222}, orcid-numbers = {Ferenczy, György/0000-0002-5771-4616} }