@article{MTMT:34377793,
	title = {Target-ligand binding affinity from single point enthalpy calculation and elemental composition},
	url = {https://m2.mtmt.hu/api/publication/34377793},
	author = {Szél, Viktor and Zsidó, Balázs Zoltán and Jeszenői, Norbert and Hetényi, Csaba},
	doi = {10.1039/d3cp04483a},
	journal-iso = {PHYS CHEM CHEM PHYS},
	journal = {PHYSICAL CHEMISTRY CHEMICAL PHYSICS},
	volume = {25},
	unique-id = {34377793},
	issn = {1463-9076},
	abstract = {Reliable target-ligand binding thermodynamics data are essential for successful drug design and molecular engineering projects. Besides experimental methods, a number of theoretical approaches have been introduced for the generation of binding thermodynamics data. However, available approaches often neglect electronic effects or explicit water molecules influencing target-ligand interactions. To handle electronic effects within a reasonable time frame, we introduce a fast calculator QMH-L using a single target-ligand complex structure pre-optimized at the molecular mechanics level. QMH-L is composed of the semi-empirical quantum mechanics calculation of binding enthalpy with predicted explicit water molecules at the complex interface, and a simple descriptor based on the elemental composition of the ligand. QMH-L estimates the target-ligand binding free energy with a root mean square error (RMSE) of 0.94 kcal mol-1. The calculations also provide binding enthalpy values and they were compared with experimental binding thermodynamics data collected from the most reliable isothermal titration calorimetry studies of systems including various protein targets and challenging, large peptide ligands with a molecular weight of up to 2-3 thousand. The single point enthalpy calculations of QMH-L require modest computational resources and are based on short runs with open source and/or free software like Gromacs, Mopac, MobyWat, and Fragmenter. QMH-L can be applied for fast, automated scoring of drug candidates during a virtual screen, enthalpic engineering of new ligands or thermodynamic explanation of complex interactions.},
	year = {2023},
	eissn = {1463-9084},
	pages = {31714-31725},
	orcid-numbers = {Jeszenői, Norbert/0000-0002-6472-5807}
}

@misc{MTMT:34192396,
	title = {The Role of Water in Material Design: Improved Models for Molecular and Quantum Mechanical Simulations},
	url = {https://m2.mtmt.hu/api/publication/34192396},
	author = {Hetényi, Csaba and Zsidó, Balázs Zoltán and Börzsei, Rita and Szél, Viktor},
	unique-id = {34192396},
	year = {2023}
}

@misc{MTMT:34192188,
	title = {Optimization of Drug-Target Interactions Using Fast Pharmacoinformatics Protocols},
	url = {https://m2.mtmt.hu/api/publication/34192188},
	author = {Hetényi, Csaba and Szél, Viktor and Zsidó, Balázs Zoltán and Börzsei, Rita},
	unique-id = {34192188},
	year = {2023}
}

@article{MTMT:34167335,
	title = {Construction of Histone-Protein Complex Structures by Peptide Growing},
	url = {https://m2.mtmt.hu/api/publication/34167335},
	author = {Zsidó, Balázs Zoltán and Bayarsaikhan, Bayartsetseg and Börzsei, Rita and Hetényi, Csaba},
	doi = {10.3390/ijms241813831},
	journal-iso = {INT J MOL SCI},
	journal = {INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES},
	volume = {24},
	unique-id = {34167335},
	issn = {1661-6596},
	abstract = {The structures of histone complexes are master keys to epigenetics. Linear histone peptide tails often bind to shallow pockets of reader proteins via weak interactions, rendering their structure determination challenging. In the present study, a new protocol, PepGrow, is introduced. PepGrow uses docked histone fragments as seeds and grows the full peptide tails in the reader-binding pocket, producing atomic-resolution structures of histone-reader complexes. PepGrow is able to handle the flexibility of histone peptides, and it is demonstrated to be more efficient than linking pre-docked peptide fragments. The new protocol combines the advantages of popular program packages and allows fast generation of solution structures. AutoDock, a force-field-based program, is used to supply the docked peptide fragments used as structural seeds, and the building algorithm of Modeller is adopted and tested as a peptide growing engine. The performance of PepGrow is compared to ten other docking methods, and it is concluded that in situ growing of a ligand from a seed is a viable strategy for the production of complex structures of histone peptides at atomic resolution.},
	keywords = {PEPTIDE; LIGAND; FRAGMENT; Docking; Histone; Growing},
	year = {2023},
	eissn = {1422-0067}
}

@article{MTMT:34153929,
	title = {Inhibition of xanthine oxidase-catalyzed xanthine and 6-mercaptopurine oxidation by luteolin, naringenin, myricetin, ampelopsin and their conjugated metabolites.},
	url = {https://m2.mtmt.hu/api/publication/34153929},
	author = {Balázs, Orsolya and Dombi, Ágnes and Zsidó, Balázs Zoltán and Hetényi, Csaba and Valentová, Kateřina and Vida, Róbert György and Poór, Miklós},
	doi = {10.1016/j.biopha.2023.115548},
	journal-iso = {BIOMED PHARMACOTHER},
	journal = {BIOMEDICINE & PHARMACOTHERAPY},
	volume = {167},
	unique-id = {34153929},
	issn = {0753-3322},
	abstract = {Luteolin, naringenin, myricetin, and ampelopsin are abundant flavonoids in nature, and several dietary supplements also contain them at very high doses. After the peroral intake, flavonoids go through extensive presystemic biotransformation; therefore, typically their sulfate/glucuronic acid conjugates reach high concentrations in the circulation. Xanthine oxidase (XO) enzyme is involved in uric acid production, and it also takes part in the elimination of certain drugs (e.g., 6-mercaptopurine). The inhibitory effects of flavonoid aglycones on XO have been widely studied; however, only limited data are available regarding their sulfate and glucuronic acid conjugates. In this study, we examined the impacts of luteolin, naringenin, myricetin, ampelopsin, and their sulfate/glucuronide derivatives on XO-catalyzed xanthine and 6-mercaptopurine oxidations employing in vitro enzyme incubation assays and molecular modeling studies. Our major results/conclusions are the following: (1) Sulfate metabolites were stronger while glucuronic acid derivatives were weaker inhibitors of XO compared to the parent flavonoids. (2) Naringenin, ampelopsin, and their metabolites were weak inhibitors of the enzyme. (3) Luteolin, myricetin, and their sulfates were highly potent inhibitors of XO, and the glucuronides of luteolin showed moderate inhibitory impacts. (4) Conjugated metabolites of luteolin and myricetin can be involved in the inhibitory effects of these flavonoids on XO enzyme.},
	keywords = {xanthine oxidase; myricetin; luteolin; naringenin; ampelopsin; Flavonoid conjugates},
	year = {2023},
	eissn = {1950-6007},
	orcid-numbers = {Vida, Róbert György/0000-0003-1176-0251}
}

@article{MTMT:34073753,
	title = {The Advances and Limitations of the Determination and Applications of Water Structure in Molecular Engineering},
	url = {https://m2.mtmt.hu/api/publication/34073753},
	author = {Zsidó, Balázs Zoltán and Bayarsaikhan, Bayartsetseg and Börzsei, Rita and Szél, Viktor and Mohos, Violetta Karolin and Hetényi, Csaba},
	doi = {10.3390/ijms241411784},
	journal-iso = {INT J MOL SCI},
	journal = {INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES},
	volume = {24},
	unique-id = {34073753},
	issn = {1661-6596},
	abstract = {Water is a key actor of various processes of nature and, therefore, molecular engineering has to take the structural and energetic consequences of hydration into account. While the present review focuses on the target–ligand interactions in drug design, with a focus on biomolecules, these methods and applications can be easily adapted to other fields of the molecular engineering of molecular complexes, including solid hydrates. The review starts with the problems and solutions of the determination of water structures. The experimental approaches and theoretical calculations are summarized, including conceptual classifications. The implementations and applications of water models are featured for the calculation of the binding thermodynamics and computational ligand docking. It is concluded that theoretical approaches not only reproduce or complete experimental water structures, but also provide key information on the contribution of individual water molecules and are indispensable tools in molecular engineering.},
	year = {2023},
	eissn = {1422-0067},
	orcid-numbers = {Mohos, Violetta Karolin/0000-0001-6248-060X}
}

@article{MTMT:34006433,
	title = {Elucidation of the binding mode of organic polysulfides on the human TRPA1 receptor},
	url = {https://m2.mtmt.hu/api/publication/34006433},
	author = {Nemes, Balázs and László, Szabolcs and Zsidó, Balázs Zoltán and Hetényi, Csaba and Fehér, Ádám and Papp, Ferenc and Varga, Zoltán and Szőke, Éva and Sándor, Zoltán and Pintér, Erika},
	doi = {10.3389/fphys.2023.1180896},
	journal-iso = {FRONT PHYSIOL},
	journal = {FRONTIERS IN PHYSIOLOGY},
	volume = {14},
	unique-id = {34006433},
	abstract = {Introduction: Previous studies have established that endogenous inorganic polysulfides have significant biological actions activating the Transient Receptor Potential Ankyrin 1 (TRPA1) receptor. Organic polysulfides exert similar effects, but they are much more stable molecules, therefore these compounds are more suitable as drugs. In this study, we aimed to better understand the mechanism of action of organic polysulfides by identification of their binding site on the TRPA1 receptor.},
	year = {2023},
	eissn = {1664-042X},
	orcid-numbers = {Pintér, Erika/0000-0001-9898-632X}
}

@article{MTMT:33811185,
	title = {Serum albumin binding studies on antiproliferative cyclic C5-curcuminoid derivatives using spectroscopic methods and molecular modelling},
	url = {https://m2.mtmt.hu/api/publication/33811185},
	author = {Tyukodi, Levente and Zsidó, Balázs Zoltán and Hetényi, Csaba and Kőszegi, Tamás and Huber, Imre and Rozmer, Zsuzsanna},
	doi = {10.1016/j.molstruc.2023.135761},
	journal-iso = {J MOL STRUCT},
	journal = {JOURNAL OF MOLECULAR STRUCTURE},
	volume = {1287},
	unique-id = {33811185},
	issn = {0022-2860},
	year = {2023},
	eissn = {1872-8014},
	orcid-numbers = {Tyukodi, Levente/0000-0002-8983-1876; Huber, Imre/0000-0003-0217-0188}
}

@article{MTMT:33777591,
	title = {Interaction of Fumonisin B1, N-Palmitoyl-Fumonisin B1, 5-O-Palmitoyl-Fumonisin B1, and Fumonisin B4 Mycotoxins with Human Serum Albumin and Their Toxic Impacts on Zebrafish Embryos},
	url = {https://m2.mtmt.hu/api/publication/33777591},
	author = {Csenki, Zsolt Imre and Bartók, Tibor and Bock, Illés and Horváth, Levente and Lemli, Beáta and Zsidó, Balázs Zoltán and Angeli, Cserne and Hetényi, Csaba and Szabó, István and Urbányi, Béla and Kovács, Melinda and Poór, Miklós},
	doi = {10.3390/biom13050755},
	journal-iso = {BIOMOLECULES},
	journal = {BIOMOLECULES},
	volume = {13},
	unique-id = {33777591},
	issn = {2218-273X},
	keywords = {human serum albumin; Fumonisin B1; ZEBRAFISH EMBRYOS; N-palmitoyl-fumonisin B; 5-O-palmitoyl-fumonisin B1; fumonisin B4},
	year = {2023},
	eissn = {2218-273X},
	orcid-numbers = {Lemli, Beáta/0000-0001-8903-1337; Szabó, István/0000-0002-3954-799X; Kovács, Melinda/0000-0001-5988-3934}
}

@article{MTMT:33722503,
	title = {Probing the Interactions of 31 Mycotoxins with Xanthine Oxidase: Alternariol, Alternariol-3-Sulfate, and α-Zearalenol Are Allosteric Inhibitors of the Enzyme},
	url = {https://m2.mtmt.hu/api/publication/33722503},
	author = {Balázs, Orsolya and Dombi, Ágnes and Zsidó, Balázs Zoltán and Hetényi, Csaba and Vida, Róbert György and Poór, Miklós},
	doi = {10.3390/toxins15040250},
	journal-iso = {TOXINS},
	journal = {TOXINS},
	volume = {15},
	unique-id = {33722503},
	issn = {2072-6651},
	year = {2023},
	eissn = {2072-6651},
	orcid-numbers = {Vida, Róbert György/0000-0003-1176-0251}
}