Search Results (11)

The phosphinito–phosphinous acid ligand (PAP) is a singular bidentate-like self-assembled ligand exhibiting dissymmetric but interchangeable electronic properties. This unusual structure has been used for the generation of active palladium hydride through alcohol oxidation. In this paper, we report the first theoretical highlight of the adaptative modulation ability of this ligand within a direct H-abstraction path for Pd and Pt catalyzed alcohol oxidation. A reaction forces study revealed rearrangements in the ligand self-assembling system triggered by a simple proton shift to promote the metal hydride generation via concerted six-center mechanism. We unveil here the peculiar behavior of the phosphinito–phosphinous acid ligand in this catalysis. Full article

Background: Monoamine oxidases (MAO) are flavoenzymes that metabolize a range of brain neurotransmitters, whose dysregulation is closely associated with the development of various neurological disorders. This is why MAOs have been the central target in pharmacological interventions for neurodegeneration for more than 60 years. Still, existing drugs only address symptoms and not the cause of the disease, which underlines the need to develop more efficient inhibitors without adverse effects. Methods: Our drug design strategy relied on docking 25 organic scaffolds to MAO-B, which were extracted from the ChEMBL20 database with the highest cumulative counts of unique member compounds and bioactivity assays. The most promising candidates were substituted with the inactivating propargylamine group, while further affinity adjustment was made by its N-methylation. A total of 46 propargylamines were submitted to the docking and molecular dynamics simulations, while the best binders underwent mechanistic DFT analysis that confirmed the hydride abstraction mechanism of the covalent inhibition reaction. Results: We identified indole-2-propargylamine 4fH and indole-2-N-methylpropargylamine 4fMe as superior MAO-B binders over the clinical drugs rasagiline and selegiline. DFT calculations highlighted 4fMe as more potent over selegiline, evident in a reduced kinetic requirement (ΔΔG^‡ = −2.5 kcal mol⁻¹) and an improved reaction exergonicity (ΔΔG_R = −4.3 kcal mol⁻¹), together with its higher binding affinity, consistently determined by docking (ΔΔG_BIND = −0.1 kcal mol⁻¹) and MM-PBSA analysis (ΔΔG_BIND = −1.5 kcal mol⁻¹). Conclusions: Our findings strongly advocate 4fMe as an excellent drug candidate, whose synthesis and biological evaluation are highly recommended. Also, our results reveal the structural determinants that influenced the affinity and inhibition rates that should cooperate when designing further MAO inhibitors, which are of utmost significance and urgency with the increasing prevalence of brain diseases. Full article

The preparation of bis(3-methylthio-1-azulenyl)phenylmethyl cations and 1,4-phenylenebis[bis(3,6-di-tert-butyl-1-azulenyl)methyl] dications was accomplished by the hydride abstraction of the corresponding hydride derivatives, which were synthesized by the acid-catalyzed condensation of 1-azulenyl methyl sulfide with benzaldehyde and terephthalaldehyde with 2,3-dichloro-5,6-dicyano-1,4-benzoquinone. The intramolecular charge transfer among the azulene ring and the methylium moieties of these cations and dications was investigated by UV–Vis spectroscopy and electrochemical analyses. The pK_R⁺ values of the cations were examined for their thermodynamic stability spectrophotometrically. The voltammetry experiments of these cations revealed their reversible reduction waves on their cyclic voltammograms. Moreover, a notable spectral change of cations was observed by spectroelectrochemistry during electrochemical reduction conditions. Full article

Histamine levels in the human brain are controlled by rather peculiar metabolic pathways. In the first step, histamine is enzymatically methylated at its imidazole N^τ atom, and the produced N-methylhistamine undergoes an oxidative deamination catalyzed by monoamine oxidase B (MAO-B), as is common with other monoaminergic neurotransmitters and neuromodulators of the central nervous system. The fact that histamine requires such a conversion prior to oxidative deamination is intriguing since MAO-B is known to be relatively promiscuous towards monoaminergic substrates; its in-vitro oxidation of N-methylhistamine is about 10 times faster than that for histamine, yet this rather subtle difference appears to be governing the decomposition pathway. This work clarifies the MAO-B selectivity toward histamine and N-methylhistamine by multiscale simulations of the rate-limiting hydride abstraction step for both compounds in the gas phase, in aqueous solution, and in the enzyme, using the established empirical valence bond methodology, assisted by gas-phase density functional theory (DFT) calculations. The computed barriers are in very good agreement with experimental kinetic data, especially for relative trends among systems, thereby reproducing the observed MAO-B selectivity. Simulations clearly demonstrate that solvation effects govern the reactivity, both in aqueous solution as well as in the enzyme although with an opposing effect on the free energy barrier. In the aqueous solution, the transition-state structure involving histamine is better solvated than its methylated analog, leading to a lower barrier for histamine oxidation. In the enzyme, the higher hydrophobicity of N-methylhistamine results in a decreased number of water molecules at the active side, leading to decreased dielectric shielding of the preorganized catalytic electrostatic environment provided by the enzyme. This renders the catalytic environment more efficient for N-methylhistamine, giving rise to a lower barrier relative to histamine. In addition, the transition state involving N-methylhistamine appears to be stabilized by the surrounding nonpolar residues to a larger extent than with unsubstituted histamine, contributing to a lower barrier with the former. Full article

Protoporphyrinogen oxidase (PPO) is a critical enzyme across life as the last common step in the synthesis of many metalloporphyrins. The reaction mechanism of PPO was assessed in silico and the unstructured loop near the binding pocket was investigated. The substrate, intermediates, and product were docked in the catalytic domain of PPO using a modified Autodock method, introducing flexibility in the macrocycles. Sixteen PPO protein sequences across phyla were aligned and analyzed with Phyre2 and ProteinPredict to study the unstructured loop from residue 204–210 in the H. sapiens structure. Docking of the substrate, intermediates, and product all resulted in negative binding energies, though the substrate had a lower energy than the others by 40%. The α-H of C10 was found to be 1.4 angstroms closer to FAD than the β-H, explaining previous reports of the reaction occurring on the meso face of the substrate. A lack of homology in sequence or length in the unstructured loop indicates a lack of function for the protein reaction. This docking study supports a reaction mechanism proposed previously whereby all hydride abstractions occur on the C10 of the tetrapyrrole followed by tautomeric rearrangement to prepare the intermediate for the next reaction. Full article

Monoamine oxidases (MAOs) catalyze the degradation of a very broad range of biogenic and dietary amines including many neurotransmitters in the brain, whose imbalance is extensively linked with the biochemical pathology of various neurological disorders, and are, accordingly, used as primary pharmacological targets to treat these debilitating cognitive diseases. Still, despite this practical significance, the precise molecular mechanism underlying the irreversible MAO inhibition with clinically used propargylamine inhibitors rasagiline and selegiline is still not unambiguously determined, which hinders the rational design of improved inhibitors devoid of side effects current drugs are experiencing. To address this challenge, we present empirical valence bond QM/MM simulations of the rate-limiting step of the MAO inhibition involving the hydride anion transfer from the inhibitor α-carbon onto the N5 atom of the flavin adenin dinucleotide (FAD) cofactor. The proposed mechanism is strongly supported by the obtained free energy profiles, which confirm a higher reactivity of selegiline over rasagiline, while the calculated difference in the activation Gibbs energies of ΔΔG^‡ = 3.1 kcal mol⁻¹ is found to be in very good agreement with that from the measured literature k_inact values that predict a 1.7 kcal mol⁻¹ higher selegiline reactivity. Given the similarity with the hydride transfer mechanism during the MAO catalytic activity, these results verify that both rasagiline and selegiline are mechanism-based irreversible inhibitors and offer guidelines in designing new and improved inhibitors, which are all clinically employed in treating a variety of neuropsychiatric and neurodegenerative conditions. Full article

The main aim of this work is to substantiate the mechanism of 1-propanol oxidation by ozone in aqueous solution when the substrate is present in large excess. Further goals are assessment of the products, their formation yields as well as the kinetic parameters of the considered reaction. The reaction of ozone with 1-propanol in aqueous solution occurs via hydride transfer, H-abstraction and insertion. Of these three mechanisms, the largest share is for hydride transfer. This implies the extraction of an hydride ion from the activated C−H group by O₃ according to reaction: (C₂H₅)(H)(HO)C−H + O₃ → [(C₂H₅)(H)(HO)C⁺ + HO₃⁻]_cage → (C₂H₅)(H)(HO)C⁺ + HO₃⁻. The experimentally determined products and their overall formation yields with respect to ozone are: propionaldehyde—(60 ± 3)%, propionic acid—(27.4 ± 1.0)%, acetaldehyde—(4.9 ± 0.3)%, acetic acid—(0.3 ± 0.1)%, formaldehyde—(1.0 ± 0.1)%, formic acid—(4.6 ± 0.3)%, hydrogen peroxide—(11.1 ± 0.3)% and hydroxyl radical—(9.8 ± 0.3)%. The reaction of ozone with 1-propanol in aqueous media follows a second order kinetics with a reaction rate constant of (0.64 ± 0.02) M⁻¹·s⁻¹ at pH = 7 and 23 °C. The dependence of the second order rate constant on temperature is described by the equation: $ln k_{II}=\left(27.17\pm 0.38\right)–\left(8180\pm 120\right)\times T^{-1}$ , which gives the activation energy, Ea = (68 ± 1) kJ mol⁻¹ and pre-exponential factor, A = (6.3 ± 2.4) × 10¹¹ M⁻¹ s⁻¹. The nature of products, their yields and the kinetic data can be used in water treatment. The fact that the hydride transfer is the main pathway in the 1-propanol/ozone system can probably be transferred on other systems in which the substrate is characterized by C−H active sites only. Full article

Diorganyl[2-(trimethylsilylethynyl)phenyl]silanes 1a–c and methyl-substituted phenylsilanes 1d and 1e were treated with a small amount of trityl tetrakis(pentafluorophenyl)borate (TPFPB) as an initiator in benzene to afford the corresponding benzosiloles (2a–e) in moderate to good yields. However, no reaction was observed for the reaction using [2-(1-hexynyl)phenyl]diisopropylsilane lf. The methyl substituent was tolerated under the reaction conditions and increased the yield of the corresponding benzosilole depending on the substitution position. From the result using 1f, the current reaction was found to require the trimethylsilyl group, which can stabilize intermediary alkenyl carbocations by the β-silyl effect. The current reaction can be considered an intramolecular chain hydrosilylation of alkynylarylsilanes involving silyl cations as chain carriers. Therefore, the silyl cations generated by hydride abstraction from hydrosilanes 1 with the trityl cation causes intramolecular electrophilic addition to the C-C triple bond to form ethenyl cations, which abstract a hydride from 1 to afford benzosiloles 2 with the regeneration of the silyl cations. Full article

Recent studies of Escherichia coli thymidylate synthase (ecTSase) showed that a highly conserved residue, Y209, that is located 8 Å away from the reaction site, plays a key role in the protein’s dynamics. Those crystallographic studies indicated that Y209W mutant is a structurally identical but dynamically altered relative to the wild type (WT) enzyme, and that its turnover catalytic rate governed by a slow hydride-transfer has been affected. The most challenging test of an examination of a fast chemical conversion that precedes the rate-limiting step has been achieved here. The physical nature of both fast and slow C-H bond activations have been compared between the WT and mutant by means of observed and intrinsic kinetic isotope effects (KIEs) and their temperature dependence. The findings indicate that the proton abstraction step has not been altered as much as the hydride transfer step. Additionally, the comparison indicated that other kinetic steps in the TSase catalyzed reaction were substantially affected, including the order of the substrate binding. Enigmatically, although Y209 is H-bonded to 3'-OH of 2'-deoxyuridine-5'-mono­phosphate (dUMP), its altered dynamics is more pronounced on the binding of the remote cofactor, (6R)-N⁵,N¹⁰-methylene-5,6,7,8-tetrahydrofolate (CH₂H₄folate), revealing the importance of long-range dynamics of the enzymatic complex and its catalytic function. Full article

The complex [(κ³-(N,N,O-py₂B(Me)OH)Ru(NCMe)₃]⁺ TfO⁻ (1) is a catalyst for transfer dehydrogenation of alcohols, which was designed to function through a cooperative transition state in which reactivity was split between boron and ruthenium. We show here both stoichiometric and catalytic evidence to support that in the case of alcohol oxidation, the mechanism most likely involves reactivity only at the ruthenium center. Full article

Abstract Cytochrome P-450 (P450) catalyzes a wide variety of chemical reactions; however, its use for in vitro assays has several limitations, the most striking one is the use of the reduced nicotinamide adenine dinucleotide phosphate (NADPH) coenzyme. In this work, the P450 activity using NADP⁺ reduced by an anionic organosiloxane, commonly named silica hydride, was evaluated. The results showed that the reduction of NADP⁺with silica hydride was concentration- and time-dependent. P-450 activity was maintained when NADP⁺ and silica hydride were added during the reaction; however, it was lower than when commercial NADPH was employed. This is due to the ability of silica hydride to reduce P450 iron atom as corroborated by the electronic paramagnetic resonance (EPR). Furthermore, this compound possibly chelates FeII because, in its presence, the P450 affinity for aniline diminishes. However, the P450 activity was the best when NADP⁺ was reduced by silica hydride before the former was added to the reaction. Therefore, this system could be apt for studying biotransformation reactions. Full article