TY - JOUR AU - Péczka, Nikolett AU - Orgován, Zoltán AU - Ábrányi-Balogh, Péter AU - Keserű, György Miklós TI - Electrophilic warheads in covalent drug discovery: an overview JF - EXPERT OPINION ON DRUG DISCOVERY J2 - EXPERT OPIN DRUG DIS VL - 17 PY - 2022 IS - 4 SP - 413 EP - 422 PG - 10 SN - 1746-0441 DO - 10.1080/17460441.2022.2034783 UR - https://m2.mtmt.hu/api/publication/32756662 ID - 32756662 N1 - CAplus AN 2022:310212; MEDLINE PMID: 35129005 (Journal; General Review; Article); LA - English DB - MTMT ER - TY - JOUR AU - Kollár, Levente AU - Gobec, Martina AU - Proj, Matic AU - Smrdel, Lara AU - Knez, Damijan AU - Imre, Timea AU - Gömöry, Ágnes AU - Petri, László AU - Ábrányi-Balogh, Péter AU - Csányi, Dorottya AU - Ferenczy, György AU - Gobec, Stanislav AU - Sosič, Izidor AU - Keserű, György Miklós TI - Fragment-Sized and Bidentate (Immuno)Proteasome Inhibitors Derived from Cysteine and Threonine Targeting Warheads JF - CELLS J2 - CELLS-BASEL VL - 10 PY - 2021 IS - 12 PG - 19 SN - 2073-4409 DO - 10.3390/cells10123431 UR - https://m2.mtmt.hu/api/publication/32544488 ID - 32544488 N1 - Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Magyar tudósok krt. 2, Budapest, H-1117, Hungary Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, Ljubljana, SI-1000, Slovenia MS Metabolomics Research Group, Research Centre for Natural Sciences, Magyar tudósok krt. 2, Budapest, H-1117, Hungary MS Proteomics Research Group, Research Centre for Natural Sciences, Magyar tudósok krt. 2, Budapest, H-1117, Hungary Export Date: 27 May 2022 Correspondence Address: Sosič, I.; Faculty of Pharmacy, Aškerčeva cesta 7, Slovenia; email: izidor.sosic@ffa.uni-lj.si Correspondence Address: Keserű, G.M.; Medicinal Chemistry Research Group, Magyar tudósok krt. 2, Hungary; email: keseru.gyorgy@ttk.hu AB - Constitutive- and immunoproteasomes are part of the ubiquitin–proteasome system (UPS), which is responsible for the protein homeostasis. Selective inhibition of the immunoproteasome offers opportunities for the treatment of numerous diseases, including inflammation, autoimmune diseases, and hematologic malignancies. Although several inhibitors have been reported, selective nonpeptidic inhibitors are sparse. Here, we describe two series of compounds that target both proteasomes. First, benzoxazole-2-carbonitriles as fragment-sized covalent immunoproteasome inhibitors are reported. Systematic substituent scans around the fragment core of benzoxazole-2-carbonitrile led to compounds with single digit micromolar inhibition of the β5i subunit. Experimental and computational reactivity studies revealed that the substituents do not affect the covalent reactivity of the carbonitrile warhead, but mainly influence the non-covalent recognition. Considering the small size of the inhibitors, this finding emphasizes the importance of the non-covalent recognition step in the covalent mechanism of action. As a follow-up series, bidentate inhibitors are disclosed, in which electrophilic heterocyclic fragments, i.e., 2-vinylthiazole, benzoxazole-2-carbonitrile, and benzimidazole-2-carbonitrile were linked to threonine-targeting (R)-boroleucine moieties. These compounds were designed to bind both the Thr1 and β5i-subunit-specific residue Cys48. However, inhibitory activities against (immuno)proteasome subunits showed that bidentate compounds inhibit the β5, β5i, β1, and β1i subunits with submicromolar to low-micromolar IC50 values. Inhibitory assays against unrelated enzymes showed that compounds from both series are selective for proteasomes. The presented nonpeptidic and covalent derivatives are suitable hit compounds for the development of either β5i-selective immunoproteasome inhibitors or compounds targeting multiple subunits of both proteasomes. LA - English DB - MTMT ER - TY - JOUR AU - Petri, László AU - Szijj, Péter A. AU - Kelemen, Ádám AU - Imre, Timea AU - Gömöry, Ágnes AU - Lee, Maximillian T. W. AU - Hegedűs, Krisztina AU - Ábrányi-Balogh, Péter AU - Chudasama, Vijay AU - Keserű, György Miklós TI - Cysteine specific bioconjugation with benzyl isothiocyanates JF - RSC ADVANCES J2 - RSC ADV VL - 10 PY - 2020 IS - 25 SP - 14928 EP - 14936 PG - 9 SN - 2046-2069 DO - 10.1039/D0RA02934C UR - https://m2.mtmt.hu/api/publication/31294506 ID - 31294506 N1 - Funding Agency and Grant Number: National Office of Research, Development and Innovation [2018-1.3.1-VKE-2018-00032, NKFIH PD124598]; Wellcome TrustWellcome TrustEuropean Commission; Hungarian Ministry for Innovation and Technology Funding text: This work has been supported by the National Office of Research, Development and Innovation (2018-1.3.1-VKE-2018-00032, NKFIH PD124598). We gratefully acknowledge the spectrophotometry measurements to Denes Sovari and the 15N-HSQC NMR measurements to Gyula Palfy and Andras Perczel. We gratefully acknowledge the Wellcome Trust for funding P. S. The flow cytometry facility is operated in ELTE Thematic Excellence Programme supported by the Hungarian Ministry for Innovation and Technology. LA - English DB - MTMT ER - TY - JOUR AU - Scarpino, Andrea AU - Ferenczy, György AU - Keserű, György Miklós TI - Comparative Evaluation of Covalent Docking Tools JF - JOURNAL OF CHEMICAL INFORMATION AND MODELING J2 - J CHEM INF MODEL VL - 58 PY - 2018 IS - 7 SP - 1441 EP - 1458 PG - 18 SN - 1549-9596 DO - 10.1021/acs.jcim.8b00228 UR - https://m2.mtmt.hu/api/publication/3401463 ID - 3401463 AB - Increased interest in covalent drug discovery led to the development of computer programs predicting binding mode and affinity of covalent inhibitors. Here we compare the performance of six covalent docking tools, AutoDock4, CovDock, FITTED, GOLD, ICM-Pro, and MOE, for reproducing experimental binding modes in an unprecedently large and diverse set of covalent complexes. It was found that 40-60% of the top scoring ligand poses are within 2.0 Å RMSD from the experimental binding mode. This rate showed program dependent increase and achieved 50-90% when the best RMSD among the top ten scoring poses was considered. This performance is comparable to that of noncovalent docking tools and therefore suggests that anchoring the ligand does not necessarily improve the accuracy of the prediction. The effect of various ligand and protein features on the docking performance was investigated. At the level of warhead chemistry, higher success rate was found for Michael additions, nucleophilic additions and nucleophilic substitutions than for ring opening reactions and disulfide formation. Increasing ligand size and flexibility generally affects pose predictions unfavorably, although AutoDock4, FITTED, and ICM-Pro were found to be less sensitive up to 35 heavy atoms. Increasing the accessibility of the target cysteine tends to result in improved binding mode predictions. Docking programs show protein dependent performance suggesting a target-dependent choice of the optimal docking tool. It was found that noncovalent docking into Cys/Ala mutated proteins by ICM-Pro and Glide reproduced experimental binding modes with only slightly lower performance and at a significantly lower computational expense than covalent docking did. Overall, our results highlight the key factors influencing the docking performance of the investigated tools and they give guidelines for selecting the optimal combination of warheads, ligands, and tools for the system investigated. Results also identify the most important aspects to be considered for developing improved protocols for docking and virtual screening of covalent ligands. Copyright © 2018 American Chemical Society. LA - English DB - MTMT ER -