Theoretical study of the molecular structure and intramolecular proton transfer in benzohydroxamic acid

Synthesis and HDAC inhibitory activity of pyrimidine-based hydroxamic acids

Histone deacetylases (HDACs) play an essential role in the transcriptional regulation of cells through the deacetylation of nuclear histone and non-histone proteins and are promising therapeutic targets for the treatment of various diseases. Here, the synthesis of new compounds in which a hydroxamic acid residue is attached to differently substituted pyrimidine rings via a methylene group bridge of varying length as potential HDAC inhibitors is described. The target compounds were obtained by alkylation of 2-(alkylthio)pyrimidin-4(3H)-ones with ethyl 2-bromoethanoate, ethyl 4-bromobutanoate, or methyl 6-bromohexanoate followed by aminolysis of the obtained esters with hydroxylamine. Oxidation of the 2-methylthio group to the methylsulfonyl group and following treatment with amines resulted in the formation of the corresponding 2-amino-substituted derivatives, the ester group of which reacted with hydroxylamine to give the corresponding hydroxamic acids. The synthesized hydroxamic acids were tested as inhibitors of the HDAC4 and HDAC8 isoforms. Among the synthesized pyrimidine-based hydroxamic acids N-hydroxy-6-[6-methyl-2-(methylthio)-5-propylpyrimidin-4-yloxy]hexanamide was found to be the most potent inhibitor of both the HDAC4 and HDAC8 isoforms, with an IC50 of 16.6 µM and 1.2 µM, respectively.

Synthesis and amide imidic prototropic tautomerization in thiophene-2-carbohydrazide: XRD, DFT/HSA-computation, DNA-docking, TG and isoconversional kinetics via FWO and KAS models

Thiophene-2-carbohydrazide as a novel small-molecule amide tautomer has been synthesized with an acceptable yield under microwave radiation (MW) conditions. The amide imidic thiophene-2-carbohydrazide prototropic tautomerization via single proton intramigration was computed using the DFT B3LYP/6-311G(d,p) level of theory. The endo-isomer amide structure of thiophene-2-carbohydrazide was proved by XRD and is considered to be the kinetically favored isomer. The DFT-structure parameters were compared to their corresponding XRD-experimental parameters. Several H-bond interactions were detected in the crystal lattice experimentally using the XRD-packing model then correlated to MEP and HSA calculations. The manual and calculated electronic parameters such as, frontier molecular orbital energies, excitation energy, absorption, dipole moment, DOS, GRD quantum parameters and TD-SCF/B3LYP were DFT computed. The thiophene-2-carbohydrazide isomers together with their prototropic (E)/(Z)-thiophene-2-carbohydrazonic acid tautomers were docked against 1BNA DNA. FWO and KAS isoconversional kinetic methods were applied, and the thermal behavior and estimated E_a–α relations were determined.

Thiophene-2-carbohydrazide as a novel small-molecule amide tautomer has been synthesized with an acceptable yield under microwave radiation (MW) conditions.

Medium effect on the α-effect for nucleophilic substitution reactions of p-nitrophenyl acetate with benzohydroxamates and m-chlorophenoxide in DMSO–H2O mixtures as contrasts with MeCN–H2O mixtures: comparing two very different polar aprotic solvent components

A kinetic study is reported on nucleophilic substitution reactions of p-nitrophenyl acetate (1a) with three α-effect nucleophiles, benzohydroxamate (BHA–), p-methylbenzohydroxamate (MBHA–), and p-methyl-N-methylbenzohydroxamate (M2BHA–), and a reference nucleophile, m-chlorophenoxide (m-ClPhO–), in DMSO–H2O mixtures of varying compositions at 25.0 ± 0.1 °C. Second-order rate constants for the reactions with BHA– and MBHA– decrease upon addition of DMSO to the reaction medium up to 60 mol % DMSO and then increase thereafter only a little. In contrast, M2BHA– and m-ClPhO– become much more reactive as the DMSO content in the medium increases. Such contrasting medium effects on reactivity are consistent with the report that hydroxamic acids behave as OH acids in H2O but as NH acids in dipolar aprotic solvents (e.g., DMSO and MeCN). It has been concluded that BHA– and MBHA– form an equilibrium of a reactive form I with less reactive species II in DMSO–H2O mixtures and the position of the equilibrium is dependent on solvent compositions. BHA– and MBHA– exhibit the α-effect in H2O but not in in 90 mol % DMSO. In contrast, the α-effect yielded by M2BHA– increases steeply up to 70 mol % DMSO and then levels off thereafter.

New Insights into the Configurations of Lead(II)-Benzohydroxamic Acid Coordination Compounds in Aqueous Solution: A Combined Experimental and Computational Study

Novel collector lead(II)-benzohydroxamic acid (Pb(II)–BHA) complexes in aqueous solution were characterized by using experimental approaches, including Ultraviolet-visible (UV-Vis) spectroscopy and electrospray ionization-mass spectrometry (ESI-MS), as well as first-principle density functional theory (DFT) calculations with consideration for solvation effects. The Job plot delineated that a single coordinated Pb(BHA)+ should be formed first, and that the higher coordination number complexes can be formed subsequently. Moreover, the Pb(II)–BHA species can aggregate with each other to form complicated structures, such as Pb(BHA)2 or highly complicated complexes. ESI-MS results validated the existence of Pb-(BHA)n=1,2 under different solution pH values. Further, the first-principles calculations suggested that Pb(BHA)+ should be the most stable structure, and the Pb atom in Pb(BHA)+ will act as an active site to attack nucleophiles. These findings are meaningful to further illustrate the adsorption mechanism of Pb(II)–BHA complexes, and are helpful for developing new reagents in mineral processing.