@article{MTMT:34627084,
	title = {Rational Design of Antifungal Peptides Based on the γ-Core Motif of a Neosartorya (Aspergillus) fischeri Antifungal Protein to Improve Structural Integrity, Efficacy, and Spectrum},
	url = {https://m2.mtmt.hu/api/publication/34627084},
	author = {Váradi, Györgyi and Bende, Gábor and Borics, Attila and Dán, Kinga and Rákhely, Gábor and Tóth, Gábor and Galgóczi, László Norbert},
	doi = {10.1021/acsomega.3c09377},
	journal-iso = {ACS OMEGA},
	journal = {ACS OMEGA},
	volume = {9},
	unique-id = {34627084},
	issn = {2470-1343},
	year = {2024},
	eissn = {2470-1343},
	pages = {7206-7214},
	orcid-numbers = {Váradi, Györgyi/0000-0001-7907-8908; Rákhely, Gábor/0000-0003-2557-3641; Tóth, Gábor/0000-0002-3604-4385; Galgóczi, László Norbert/0000-0002-6976-8910}
}

@article{MTMT:34575640,
	title = {Expression and purification of the receptor-binding domain of SARS-CoV-2 spike protein in mammalian cells for immunological assays},
	url = {https://m2.mtmt.hu/api/publication/34575640},
	author = {Ábrahám, Edit and Bajusz, Csaba and Marton, Annamária and Borics, Attila and Mdluli, Thandiswa and Pardi, Norbert and Lipinszki, Zoltán},
	doi = {10.1002/2211-5463.13754},
	journal-iso = {FEBS OPEN BIO},
	journal = {FEBS OPEN BIO},
	volume = {14},
	unique-id = {34575640},
	issn = {2211-5463},
	abstract = {The receptor-binding domain (RBD) of the spike glycoprotein of SARS-CoV-2 virus mediates the interaction with the host cell and is required for virus internalization. It is, therefore, the primary target of neutralizing antibodies. The receptor-binding domain soon became the major target for COVID-19 research and the development of diagnostic tools and new-generation vaccines. Here, we provide a detailed protocol for high-yield expression and one-step affinity purification of recombinant RBD from transiently transfected Expi293F cells. Expi293F mammalian cells can be grown to extremely high densities in a specially formulated serum-free medium in suspension cultures, which makes them an excellent tool for secreted protein production. The highly purified RBD is glycosylated, structurally intact, and forms homomeric complexes. With this quick and easy method, we are able to produce large quantities of RBD (80 mg center dot L-1 culture) that we have successfully used in immunological assays to examine antibody titers and seroconversion after mRNA-based vaccination of mice.},
	keywords = {ELISA; protein purification; recombinant rbd; Expi293F mammalian cells; mRNA-LNP vaccination},
	year = {2024},
	eissn = {2211-5463},
	pages = {380-389},
	orcid-numbers = {Lipinszki, Zoltán/0000-0002-2067-0832}
}

@article{MTMT:34043893,
	title = {Hard nut to crack: Solving the disulfide linkage pattern of the Neosartorya (Aspergillus) fischeri antifungal protein 2},
	url = {https://m2.mtmt.hu/api/publication/34043893},
	author = {Váradi, Györgyi and Kele, Zoltán and Czajlik, András and Borics, Attila and Bende, Gábor and Papp, Csaba Gergő and Rákhely, Gábor and Tóth, Gábor and Batta, Gyula and Galgóczi, László Norbert},
	doi = {10.1002/pro.4692},
	journal-iso = {PROTEIN SCI},
	journal = {PROTEIN SCIENCE},
	volume = {32},
	unique-id = {34043893},
	issn = {0961-8368},
	abstract = {As a consequence of the fast resistance spreading, a limited number of drugs are available to treat fungal infections. Therefore, there is an urgent need to develop new antifungal treatment strategies. The features of a disulfide bond-stabilized antifungal protein, NFAP2 secreted by the mold Neosartorya (Aspergillus) fischeri render it to be a promising template for future protein-based antifungal drug design, which requires knowledge about the native disulfide linkage pattern as it is one of the prerequisites for biological activity. However, in the lack of tryptic and chymotryptic proteolytic sites in the ACNCPNNCK sequence, the determination of the disulfide linkage pattern of NFAP2 is not easy with traditional mass spectrometry-based methods. According to in silico predictions working with a preliminary nuclear magnetic resonance (NMR) solution structure, two disulfide isomers of NFAP2 (abbacc and abbcac) were possible. Both were chemically synthesized; and comparative reversed-phase high-performance liquid chromatography, electronic circular dichroism and NMR spectroscopy analyses, and antifungal susceptibility and efficacy tests indicated that the abbcac is the native pattern. This knowledge allowed rational modification of NAFP2 to improve the antifungal efficacy and spectrum through the modulation of the evolutionarily conserved gamma-core region, which is responsible for the activity of several antimicrobial peptides. Disruption of the steric structure of NFAP2 upon gamma-core modification led to the conclusions that this motif may affect the formation of the biologically active three-dimensional structure, and that the gamma-core modulation is not an efficient tool to improve the antifungal efficacy or to change the antifungal spectrum of NFAP2.},
	keywords = {DYNAMICS; PREDICTION; DRUG DESIGN; BONDS; protein structure; ANTIFUNGAL PROTEIN; disulfide linkage pattern},
	year = {2023},
	eissn = {1469-896X},
	orcid-numbers = {Váradi, Györgyi/0000-0001-7907-8908; Kele, Zoltán/0000-0002-4401-0302; Papp, Csaba Gergő/0000-0003-4450-0667; Rákhely, Gábor/0000-0003-2557-3641; Tóth, Gábor/0000-0002-3604-4385; Batta, Gyula/0000-0002-0442-1828; Galgóczi, László Norbert/0000-0002-6976-8910}
}

@article{MTMT:33723346,
	title = {All-Atom Molecular Dynamics Simulations Indicated the Involvement of a Conserved Polar Signaling Channel in the Activation Mechanism of the Type I Cannabinoid Receptor},
	url = {https://m2.mtmt.hu/api/publication/33723346},
	author = {Sarkar, Arijit and Mitra, Argha and Borics, Attila},
	doi = {10.3390/ijms24044232},
	journal-iso = {INT J MOL SCI},
	journal = {INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES},
	volume = {24},
	unique-id = {33723346},
	issn = {1661-6596},
	abstract = {The type I cannabinoid G protein-coupled receptor (CB1, GPCR) is an intensely investigated pharmacological target, owing to its involvement in numerous physiological functions as well as pathological processes such as cancers, neurodegenerative diseases, metabolic disorders and neuropathic pain. In order to develop modern medications that exert their effects through binding to the CB1 receptor, it is essential to understand the structural mechanism of activation of this protein. The pool of atomic resolution experimental structures of GPCRs has been expanding rapidly in the past decade, providing invaluable information about the function of these receptors. According to the current state of the art, the activity of GPCRs involves structurally distinct, dynamically interconverting functional states and the activation is controlled by a cascade of interconnecting conformational switches in the transmembrane domain. A current challenge is to uncover how different functional states are activated and what specific ligand properties are responsible for the selectivity towards those different functional states. Our recent studies of the mu-opioid and beta(2)-adrenergic receptors (MOP and beta(2)AR, respectively) revealed that the orthosteric binding pockets and the intracellular surfaces of these receptors are connected through a channel of highly conserved polar amino acids whose dynamic motions are in high correlation in the agonist- and G protein-bound active states. This and independent literature data led us to hypothesize that, in addition to consecutive conformational transitions, a shift of macroscopic polarization takes place in the transmembrane domain, which is furnished by the rearrangement of polar species through their concerted movements. Here, we examined the CB1 receptor signaling complexes utilizing microsecond scale, all-atom molecular dynamics (MD) simulations in order to see if our previous assumptions could be applied to the CB1 receptor too. Apart from the identification of the previously proposed general features of the activation mechanism, several specific properties of the CB1 have been indicated that could possibly be associated with the signaling profile of this receptor.},
	keywords = {EXPRESSION; MUTATION; BINDING; PROTEIN; SEQUENCE; CB1; signal transduction; CRYSTAL-STRUCTURE; tyrosine; cannabinoid; SIGNALING PATHWAY; GPCR; Arrestin; G protein; Biochemistry & Molecular Biology; ACTIVATION MECHANISM; Helix 8},
	year = {2023},
	eissn = {1422-0067}
}

@article{MTMT:32746161,
	title = {A series of xanthenes inhibiting Rad6 function and Rad6–Rad18 interaction in the PCNA ubiquitination cascade},
	url = {https://m2.mtmt.hu/api/publication/32746161},
	author = {Fenteany, Gabriel and Sharma, Gaurav and Gaur, Paras and Borics, Attila and Wéber, Edit and Kiss, Ernő and Haracska, Lajos},
	doi = {10.1016/j.isci.2022.104053},
	journal-iso = {ISCIENCE},
	journal = {ISCIENCE},
	volume = {25},
	unique-id = {32746161},
	abstract = {Ubiquitination of proliferating cell nuclear antigen (PCNA) triggers pathways of DNA damage tolerance, including mutagenic translesion DNA synthesis, and comprises a cascade of reactions involving the E1 ubiquitin-activating enzyme Uba1, the E2 ubiquitin-conjugating enzyme Rad6, and the E3 ubiquitin ligase Rad18. We report here the discovery of a series of xanthenes that inhibit PCNA ubiquitination, Rad6-ubiquitin thioester formation, and the Rad6-Rad18 interaction. Structure-activity relationship experiments across multiple assays reveal chemical and structural features important for different activities along the pathway to PCNA ubiquitination. The compounds that inhibit these processes are all a subset of the xanthen-3-ones we tested. These small molecules thus represent first-in-class probes of Rad6 function and the association of Rad6 and Rad18, the latter being a new inhibitory activity discovered for a small molecule, in the PCNA ubiquitination cascade and potential therapeutic agents to contain cancer progression.},
	year = {2022},
	eissn = {2589-0042},
	orcid-numbers = {Fenteany, Gabriel/0000-0001-7407-2195; Wéber, Edit/0000-0002-5904-0619; Kiss, Ernő/0000-0002-7344-1750}
}

@article{MTMT:32473848,
	title = {Universal Properties and Specificities of the beta(2)-Adrenergic Receptor-G(s) Protein Complex Activation Mechanism Revealed by All-Atom Molecular Dynamics Simulations},
	url = {https://m2.mtmt.hu/api/publication/32473848},
	author = {Mitra, Argha and Sarkar, Arijit and Borics, Attila},
	doi = {10.3390/ijms221910423},
	journal-iso = {INT J MOL SCI},
	journal = {INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES},
	volume = {22},
	unique-id = {32473848},
	issn = {1661-6596},
	abstract = {G protein-coupled receptors (GPCRs) are transmembrane proteins of high pharmacological relevance. It has been proposed that their activity is linked to structurally distinct, dynamically interconverting functional states and the process of activation relies on an interconnecting network of conformational switches in the transmembrane domain. However, it is yet to be uncovered how ligands with different extents of functional effect exert their actions. According to our recent hypothesis, based on indirect observations and the literature data, the transmission of the external stimulus to the intracellular surface is accompanied by the shift of macroscopic polarization in the transmembrane domain, furnished by concerted movements of highly conserved polar motifs and the rearrangement of polar species. In this follow-up study, we have examined the beta(2)-adrenergic receptor (beta(2)AR) to see if our hypothesis drawn from an extensive study of the mu-opioid receptor (MOP) is fundamental and directly transferable to other class A GPCRs. We have found that there are some general similarities between the two receptors, in agreement with previous studies, and there are some receptor-specific differences that could be associated with different signaling pathways.},
	keywords = {PHOSPHORYLATION; MUTATION; BINDING; SEQUENCE; AGONISTS; signal transduction; CRYSTAL-STRUCTURE; INSIGHTS; GPCR; Adrenergic; Biochemistry & Molecular Biology; ACTIVATION MECHANISM; BETA-2-ADRENERGIC RECEPTOR},
	year = {2021},
	eissn = {1422-0067}
}

@article{MTMT:32048186,
	title = {Correlated Motions of Conserved Polar Motifs Lay out a Plausible Mechanism of G Protein-Coupled Receptor Activation},
	url = {https://m2.mtmt.hu/api/publication/32048186},
	author = {Mitra, Argha and Sarkar, Arijit and Szabó, Márton Richárd and Borics, Attila},
	doi = {10.3390/biom11050670},
	journal-iso = {BIOMOLECULES},
	journal = {BIOMOLECULES},
	volume = {11},
	unique-id = {32048186},
	issn = {2218-273X},
	abstract = {Recent advancements in the field of experimental structural biology have provided high-resolution structures of active and inactive state G protein-coupled receptors (GPCRs), a highly important pharmaceutical target family, but the process of transition between these states is poorly understood. According to the current theory, GPCRs exist in structurally distinct, dynamically interconverting functional states of which populations are shifted upon binding of ligands and intracellular signaling proteins. However, explanation of the activation mechanism, on an entirely structural basis, gets complicated when multiple activation pathways and active receptor states are considered. Our unbiased, atomistic molecular dynamics simulations of the mu opioid receptor (MOP) revealed that transmission of external stimulus to the intracellular surface of the receptor is accompanied by subtle, concerted movements of highly conserved polar amino acid side chains along the 7th transmembrane helix. This may entail the rearrangement of polar species and the shift of macroscopic polarization in the transmembrane domain, triggered by agonist binding. Based on our observations and numerous independent indications, we suggest amending the widely accepted theory that the initiation event of GPCR activation is the shift of macroscopic polarization between the ortho- and allosteric binding pockets and the intracellular G protein-binding interface.},
	year = {2021},
	eissn = {2218-273X},
	orcid-numbers = {Szabó, Márton Richárd/0000-0003-0415-5192}
}

@article{MTMT:31830008,
	title = {Solution Structure, Dynamics, and New Antifungal Aspects of the Cysteine-Rich Miniprotein PAFC},
	url = {https://m2.mtmt.hu/api/publication/31830008},
	author = {Czajlik, András and Holzknecht, Jeanett and Galgóczi, László Norbert and Tóth, Liliána and Poór, Péter and Ördög, Attila and Váradi, Györgyi and Kühbacher, Alexander and Borics, Attila and Tóth, Gábor and Marx, Florentine and Batta, Gyula},
	doi = {10.3390/ijms22031183},
	journal-iso = {INT J MOL SCI},
	journal = {INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES},
	volume = {22},
	unique-id = {31830008},
	issn = {1661-6596},
	abstract = {The genome of Penicillium chrysogenum Q176 contains a gene coding for the 88-amino-acid (aa)-long glycine- and cysteine-rich P. chrysogenum antifungal protein C (PAFC). After maturation, the secreted antifungal miniprotein (MP) comprises 64 aa and shares 80% aa identity with the bubble protein (BP) from Penicillium brevicompactum, which has a published X-ray structure. Our team expressed isotope (15N, 13C)-labeled, recombinant PAFC in high yields, which allowed us to determine the solution structure and molecular dynamics by nuclear magnetic resonance (NMR) experiments. The primary structure of PAFC is dominated by 14 glycines, and therefore, whether the four disulfide bonds can stabilize the fold is challenging. Indeed, unlike the few published solution structures of other antifungal MPs from filamentous ascomycetes, the NMR data indicate that PAFC has shorter secondary structure elements and lacks the typical β-barrel structure, though it has a positively charged cavity and a hydrophobic core around the disulfide bonds. Some parts within the two putative γ-core motifs exhibited enhanced dynamics according to a new disorder index presentation of 15N-NMR relaxation data. Furthermore, we also provided a more detailed insight into the antifungal spectrum of PAFC, with specific emphasis on fungal plant pathogens. Our results suggest that PAFC could be an effective candidate for the development of new antifungal strategies in agriculture.},
	keywords = {DYNAMICS; nuclear magnetic resonance; Plant protection; Penicillium chrysogenum; Solution structure; antifungal protein PAFC; γ-core motif},
	year = {2021},
	eissn = {1422-0067},
	orcid-numbers = {Galgóczi, László Norbert/0000-0002-6976-8910; Tóth, Liliána/0000-0003-1400-6174; Poór, Péter/0000-0002-4539-6358; Ördög, Attila/0000-0002-1867-8237; Váradi, Györgyi/0000-0001-7907-8908; Borics, Attila/0000-0002-6331-3536; Tóth, Gábor/0000-0002-3604-4385; Marx, Florentine/0000-0002-8408-1842; Batta, Gyula/0000-0002-0442-1828}
}

@article{MTMT:31655071,
	title = {Design, Synthesis and Functional Analysis of Cyclic Opioid Peptides with Dmt-Tic Pharmacophore},
	url = {https://m2.mtmt.hu/api/publication/31655071},
	author = {Sarkar, Arijit and Adamska-Bartlomiejczyk, Anna and Piekielna-Ciesielska, Justyna and Wtorek, Karol and Kluczyk, Alicja and Borics, Attila and Janecka, Anna},
	doi = {10.3390/molecules25184260},
	journal-iso = {MOLECULES},
	journal = {MOLECULES},
	volume = {25},
	unique-id = {31655071},
	issn = {1420-3049},
	abstract = {The opioid receptors are members of the G-protein-coupled receptor (GPCR) family and are known to modulate a variety of biological functions, including pain perception. Despite considerable advances, the mechanisms by which opioid agonists and antagonists interact with their receptors and exert their effect are still not completely understood. In this report, six new hybrids of the Dmt-Tic pharmacophore and cyclic peptides, which were shown before to have a high affinity for the mu-opioid receptor (MOR) were synthesized and characterized pharmacologically in calcium mobilization functional assays. All obtained ligands turned out to be selective antagonists of the delta-opioid receptor (DOR) and did not activate or block the MOR. The three-dimensional structural determinants responsible for the DOR antagonist properties of these analogs were further investigated by docking studies. The results indicate that these compounds attach to the DOR in a slightly different orientation with respect to the Dmt-Tic pharmacophore than Dmt-Tic psi[CH2-NH]Phe-Phe-NH2 (DIPP-NH2[psi]), a prototypical DOR antagonist peptide. Key pharmacophoric contacts between the DOR and the ligands were maintained through an analogous spatial arrangement of pharmacophores, which could provide an explanation for the predicted high-affinity binding and the experimentally observed functional properties of the novel synthetic ligands.},
	year = {2020},
	eissn = {1420-3049},
	orcid-numbers = {Kluczyk, Alicja/0000-0003-2943-2782; Borics, Attila/0000-0002-6331-3536}
}

@article{MTMT:31312066,
	title = {Biofungicidal Potential of Neosartorya (Aspergillus) Fischeri Antifungal Protein NFAP and Novel Synthetic γ-Core Peptides},
	url = {https://m2.mtmt.hu/api/publication/31312066},
	author = {Tóth, Liliána and Váradi, Györgyi and Boros, Éva and Borics, Attila and Ficze, Hargita and Nagy, István and Tóth, Gábor and Rákhely, Gábor and Marx, Florentine and Galgóczi, László Norbert},
	doi = {10.3389/fmicb.2020.00820},
	journal-iso = {FRONT MICROBIOL},
	journal = {FRONTIERS IN MICROBIOLOGY},
	volume = {11},
	unique-id = {31312066},
	issn = {1664-302X},
	abstract = {Because of enormous crop losses worldwide due to pesticide-resistant plant pathogenic fungi, there is an increasing demand for the development of novel antifungal strategies in agriculture. Antifungal proteins (APs) and peptides are considered potential biofungicides; however, several factors limit their direct agricultural application, such as the high cost of production, narrow antifungal spectrum, and detrimental effects to plant development and human/animal health. This study evaluated the safety of the application of APs and peptides from the ascomycete Neosartorya fischeri as crop preservatives. The full-length N. fischeri AP (NFAP) and novel rationally designed γ-core peptide derivatives (PDs) γNFAP-opt and γNFAP-optGZ exhibited efficacy by inhibiting the growth of the agriculturally relevant filamentous ascomycetes in vitro. A high positive net charge, however, neither the hydrophilicity nor the primary structure supported the antifungal efficacy of these PDs. Further testing demonstrated that the antifungal activity did not require a conformational change of the β-pleated NFAP or the canonically ordered conformation of the synthetic PDs. Neither hemolysis nor cytotoxicity was observed when the NFAP and γNFAP-opt were applied at antifungally effective concentrations in human cell lines. Similarly, the Medicago truncatula plants that served as toxicity model and were grown from seedlings that were treated with NFAP, γNFAP-opt, or γNFAP-optGZ failed to exhibit morphological aberrations, reduction in primary root length, or the number of lateral roots. Crop protection experiments demonstrated that NFAP and associated antifungal active γ-core PDs were able to protect tomato fruits against the postharvest fungal pathogen Cladosporium herbarum.},
	keywords = {CYTOTOXICITY; Crop protection; Biofungicide; Neosartorya fischeri antifungal protein; γ-core peptides},
	year = {2020},
	eissn = {1664-302X},
	orcid-numbers = {Tóth, Liliána/0000-0003-1400-6174; Váradi, Györgyi/0000-0001-7907-8908; Tóth, Gábor/0000-0002-3604-4385; Rákhely, Gábor/0000-0003-2557-3641; Galgóczi, László Norbert/0000-0002-6976-8910}
}