- Assessment of Tractable Cysteines for Covalent Targeting by Screening Covalent Fragments
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Targeted covalent inhibition and the use of irreversible chemical probes are important strategies in chemical biology and drug discovery. To date, the availability and reactivity of cysteine residues amenable for covalent targeting have been evaluated by proteomic and computational tools. Herein, we present a toolbox of fragments containing a 3,5-bis(trifluoromethyl)phenyl core that was equipped with chemically diverse electrophilic warheads showing a range of reactivities. We characterized the library members for their reactivity, aqueous stability and specificity for nucleophilic amino acids. By screening this library against a set of enzymes amenable for covalent inhibition, we showed that this approach experimentally characterized the accessibility and reactivity of targeted cysteines. Interesting covalent fragment hits were obtained for all investigated cysteine-containing enzymes.
- Petri, László,ábrányi-Balogh, Péter,Tímea, Imre,Pálfy, Gyula,Perczel, András,Knez, Damijan,Hrast, Martina,Gobec, Martina,Sosi?, Izidor,Nyíri, Kinga,Vértessy, Beáta G.,J?nsch, Niklas,Desczyk, Charlotte,Meyer-Almes, Franz-Josef,Ogris, Iza,Goli? Grdadolnik, Simona,Iacovino, Luca Giacinto,Binda, Claudia,Gobec, Stanislav,Keser?, Gy?rgy M.
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p. 743 - 753
(2020/11/30)
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- An electrophilic warhead library for mapping the reactivity and accessibility of tractable cysteines in protein kinases
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Targeted covalent inhibitors represent a viable strategy to block protein kinases involved in different disease pathologies. Although a number of computational protocols have been published for identifying druggable cysteines, experimental approaches are limited for mapping the reactivity and accessibility of these residues. Here, we present a ligand based approach using a toolbox of fragment-sized molecules with identical scaffold but equipped with diverse covalent warheads. Our library represents a unique opportunity for the efficient integration of warhead-optimization and target-validation into the covalent drug development process. Screening this probe kit against multiple kinases could experimentally characterize the accessibility and reactivity of the targeted cysteines and helped to identify suitable warheads for designed covalent inhibitors. The usefulness of this approach has been confirmed retrospectively on Janus kinase 3 (JAK3). Furthermore, representing a prospective validation, we identified Maternal embryonic leucine zipper kinase (MELK), as a tractable covalent target. Covalently labelling and biochemical inhibition of MELK would suggest an alternative covalent strategy for MELK inhibitor programs.
- Petri, László,Egyed, Attila,Bajusz, Dávid,Imre, Tímea,Hetényi, Anasztázia,Martinek, Tamás,ábrányi-Balogh, Péter,Keser?, Gy?rgy M.
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supporting information
(2020/09/22)
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- Comparative reactivity analysis of small-molecule thiol surrogates
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Targeted covalent inhibitors represent an increasingly popular approach to modulate challenging drug targets. Since covalent and non-covalent interactions are both contributing to the affinity of these compounds, evaluation of their reactivity is a key-step to find feasible warheads. There are well-established HPLC- and NMR-based kinetic assays to tackle this task, however, they use a variety of cysteine-surrogates including cysteamine, cysteine or acetyl-cysteine and GSH. The diverse nature of the thiol sources often makes the results incomparable that prevents compiling a comprehensive knowledge base for the design of covalent inhibitors. To evaluate kinetic measurements from different sources we performed a comparative analysis of the different thiol surrogates against a designed set of electrophilic fragments equipped with a range of warheads. Our study included seven different thiol models and 13 warheads resulting in a reactivity matrix analysed thoroughly. We found that the reactivity profile might be significantly different for various thiol models. Comparing the different warheads, we concluded that – in addition to its human relevance - glutathione (GSH) provided the best estimate of reactivity with highest number of true positives identified.
- ábrányi-Balogh, Péter,Imre, Tímea,Keser?, Gy?rgy Miklós,Petri, László,Varga, Petra Regina
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- Gadolinium(III)-Based Dual 1H/19F Magnetic Resonance Imaging Probes
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We present two novel octadentate cyclen-based ligands bearing one (L1) or two (L2) phenylacetamide pendants with two CF3 groups either at positions 3 and 5 (L1) or 4 (L2). The corresponding Gd3+
- Pujales-Paradela, Rosa,Savi?, Tanja,Esteban-Gómez, David,Angelovski, Goran,Carniato, Fabio,Botta, Mauro,Platas-Iglesias, Carlos
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p. 4782 - 4792
(2019/03/07)
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- Reinforced Ni(II)-cyclam derivatives as dual 1H/19F MRI probes
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Reinforced cross-bridged Ni2+-cyclam complexes were functionalised with pendant arms containing both amide protons and CF3 groups that lead to a dual 1H/19F response. The resulting complexes possess very high in
- Pujales-Paradela, Rosa,Savi?, Tanja,Brandariz, Isabel,Pérez-Lourido, Paulo,Angelovski, Goran,Esteban-Gómez, David,Platas-Iglesias, Carlos
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supporting information
p. 4115 - 4118
(2019/07/16)
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- Design, synthesis, and SAR of novel 2-glycinamide cyclohexyl sulfonamide derivatives against botrytis cinerea
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N-(2-trifluoromethyl-4-chlorophenyl)-2-oxocyclohexyl sulfonamide (chesulfamide) is in the limelight as a novel fungicide, and has fungicidal activity against Botrytis cinerea. For exploring more novel structures, 33 new compounds were synthesized by N-alkylation and acid–amine coupling reactions with chesulfamide as the core moiety, and their structures were characterized and established by 1H-NMR, 13C-NMR, MS, and elemental analysis. The structure of (1R,2S)-2-(2-(N-(4-chloro-2-trifluoromethylphenyl)sulfamoyl)-cyclohexylamino)-N-(2-trifluoromethylphenyl) acetamide (II-19) was defined by X-ray single crystal diffraction. The in vivo and in vitro fungicidal activities against B. cinerea were evaluated. The bioassay results of mycelial growth demonstrated that most compounds exhibited excellent inhibitory activity against B. cinerea at 50 μg mL?1, and 7 compounds showed lower EC50 values than boscalid (EC50 = 4.46 μg mL?1) against B. cinerea (CY-09). In cucumber pot experiment, the inhibitory rates of four compounds (II-4, II-5, II-12, and II-13) against B. cinerea were 90.48, 93.45, 92.86, and 91.07, which were better than cyprodinil (88.69%), the best performing of all controls. In tomato pot experiment, the control efficacy of two analogs (II-8 and II-15) were 87.98 and 87.97% at 200 μg mL?1, which were significantly higher than boscalid (78.10%). Most compounds have an excellent fungicidal effect on B. cinerea, with potential as a lead compound for developing new pesticides.
- Cai, Nan,Liu, Caixiu,Feng, Zhihui,Li, Xinghai,Qi, Zhiqiu,Ji, Mingshan,Qin, Peiwen,Ahmed, Wasim,Cui, Zining
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- 1,3-dimethyl-7-substituted-quinazolinyl-2,4-diones, and synthesis method and application thereof
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The invention discloses 1,3-dimethyl-7-substituted-quinazolinyl-2,4-diones. The structural general formula of the compounds is disclosed in the specification, wherein R1 is hydrogen or ethyl; and R2 is a benzene ring, benzene ring derivative, heterocyclic ring or aliphatic hydrocarbon. Part of compounds have favorable inhibiting activities for Candida albicans, Aspergillus flavus, Torula histolytica and Aspergillus fumigatus. The compounds have obvious inhibiting activities for chitin synthetase, have favorable antibacterial effects, and can be used for preparing drugs for anti-pathogenic microorganisms.
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Paragraph 0056; 0057; 0058; 0059; 0060; 0083; 0084
(2017/07/31)
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- Design, synthesis and SAR exploration of tri-substituted 1,2,4-triazoles as inhibitors of the annexin A2-S100A10 protein interaction
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Recent target validation studies have shown that inhibition of the protein interaction between annexin A2 and the S100A10 protein may have potential therapeutic benefits in cancer. Virtual screening identified certain 3,4,5-trisubstituted 4H-1,2,4-triazoles as moderately potent inhibitors of this interaction. A series of analogues were synthesized based on the 1,2,4-triazole scaffold and were evaluated for inhibition of the annexin A2-S100A10 protein interaction in competitive binding assays. 2-[(5-{[(4,6-Dimethylpyrimidin-2-yl)sulfanyl]methyl}-4-(furan-2-ylmethyl)-4H-1,2,4-triazol-3-yl)sulfanyl]-N-[4-(propan-2-yl)phenyl]acetamide (36) showed improved potency and was shown to disrupt the native complex between annexin A2 and S100A10.
- Reddy, Tummala R.K.,Li, Chan,Guo, Xiaoxia,Fischer, Peter M.,Dekker, Lodewijk V.
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p. 5378 - 5391
(2014/12/11)
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- Development of novel ferulic acid derivatives as potent histone deacetylase inhibitors
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Histone deacetylase inhibitors (HDACIs) offer a promising strategy for cancer therapy. The discovery of potent ferulic acid-based HDACIs with hydroxamic acid or 2-aminobenzamide group as zinc binding group was reported. The halogeno-acetanilide was introduced as novel surface recognition moiety (SRM). The majority of title compounds displayed potent HDAC inhibitory activity. In particular, FA6 and FA16 exhibited significant enzymatic inhibitory activities, with IC50 values of 3.94 and 2.82 μM, respectively. Furthermore, these compounds showed moderate antiproliferative activity against a panel of human cancer cells. FA17 displayed promising profile as an antitumor candidate. The results indicated that these ferulic acid derivatives could serve as promising lead compounds for further optimization.
- Wang, Fang,Lu, Wen,Zhang, Tao,Dong, Jinyun,Gao, Hongping,Li, Pengfei,Wang, Sicen,Zhang, Jie
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p. 6973 - 6980
(2013/11/06)
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- Synthesis and cytotoxic evaluation of some new phthalazinylpiperazine derivatives
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A new series of 1,4-disubstituted phthalazinylpiperazine derivatives 7a-f, 12a-f and 20a-f were designed and synthesized in order to develop potent and selective antitumor agents. The target compounds were screened for their cytotoxic activities against A549, HT-29 and MDA-MB-231 cancer cell lines in vitro. Among them, compounds 7a-f exhibited excellent selectivity for MDA-MB-231 with IC50 values ranging from 0.013 μM to 0.079 μM. The most promising compound, 7e (IC50 = 2.19 μM, 2.19 μM, 0.013 μM), was 9.3, 10, and 4.9 × 103 times more active than vatalanib (IC50 = 20.27 μM, 21.96 μM, 63.90 μM), respectively. A new series of 1,4-disubstituted phthalazinylpiperazine derivatives 7a-f, 12a-f and 20a-f were designed and synthesized, and their cytotoxic activities against A549, HT-29 and MDA-MB-231 cancer cell lines in vitro were compared to that of vatalanib.
- Liu, Yajing,Zhang, Shulan,Li, Ye,Wang, Jianqiang,Song, Yu,Gong, Ping
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experimental part
p. 287 - 293
(2012/07/01)
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- Small-Molecule Choline Kinase Inhibitors as Anti-Cancer Therapeutics
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Small molecule choline kinase inhibitors having the following formula: are provided herein. Also provided herein are pharmaceutical compositions containing Formula I compounds, together with methods of treating cancer, methods of inhibiting choline kinase enzymatic activity, and methods of treating tumors by administering an effective amount of a Formula I compound.
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Page/Page column 22; 27-28
(2011/10/31)
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- Synthesis, biological evaluation and molecular modeling studies of N-aryl-2-arylthioacetamides as non-nucleoside HIV-1 reverse transcriptase inhibitors
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A series of N-aryl-2-arylthioacetamide derivatives (2-4) designed as non-nucleoside reverse transcriptase inhibitors was synthesized and evaluated for their inhibitory activity against HIV-1 (IIIB) replication in MT-4 cell cultures. The compounds 2-4 were
- Xiaohe, Zhu,Yu, Qin,Hong, Yan,Xiuqing, Song,Rugang, Zhong
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experimental part
p. 330 - 339
(2011/12/22)
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- BICYCLIC PYRIMIDINE DERIVATIVES AS CALCIUM CHANNEL BLOCKERS
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Methods and compounds effective in ameliorating conditions characterized by unwanted calcium channel activity, particularly unwanted T-type calcium channel activity are disclosed. Specifically, a series of compounds containing thienopyrimidine or oxoquinazoline derivatives are disclosed of the general formula (1) or formula (2) where X is a linker and Y is an aromatic moiety or N(R5)(R6).
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- BENZENESULFONYL COMPOUNDS AND THE USE THEROF
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The invention relates to pyrrolidinyl, piperidinyl, and hexahydroazepinyl compounds of Formula I: and pharmaceutically acceptable salts, prodrugs, or solvates thereof, wherein R1, R2, Z and m are defined as set forth in the specifica
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Page/Page column 66-67
(2008/12/04)
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- BENZENESULFONAMIDE COMPOUNDS AND THEIR USE AS BLOCKERS OF CALCIUM CHANNELS
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The invention relates to piperidinyl and hexahydroazepinyl compounds of Formula (I): and pharmaceutically acceptable salts, prodrugs, or solvates thereof, wherein R1-R3, Z and q are defined as set forth in the specification. The inve
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Page/Page column 179-180
(2010/11/28)
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