Modelling the elusive conformational activation in kynurenine 3-monooxygenase.

Kynurenine 3-monooxygenase (KMO) regulates the levels of important physiological intermediates in the kynurenine pathway [Guillemin, et al., Journal of Neuroscience, 2007, 27, 12884], which is the major route for L-tryptophan catabolism. Its catalytic activity (hydroxylation) is dependent on the formation of a short-lived intermediate that forms after the reduction of the coenzyme FAD. The reduction takes place fast when the substrate binds to KMO. Crystal structures of the apo form and in complex with an effector inhibitor, which prevents the hydroxylation of the substrate but also stimulates KMO like the substrate, and a competitive inhibitor, which suppresses the substrate hydroxylation, are available for the resting in conformation only. The active out conformational state that enables the reduction of FAD at an exposed location of KMO after its stimulation by an effector, however, was implicated but not resolved experimentally and has remained elusive so far. Molecular dynamics simulations of apo KMO and the inhibitor-KMO complexes are carried out using extensive multi-dimensional umbrella sampling to explore the free-energy surface of the coenzyme FAD's conformational conversion from the in state (buried within the active site) to the out state. This allows a discussion and comparison with the experimental results, which showed a significant increase in the rate of reduction of FAD in the presence of an effector inhibitor and absence of enzymatic function in the presence of a competitive inhibitor [Kim, et al., Cell Chemical Biology, 2018, 25, 426]. The free-energy barriers associated with those conformational changes and structural models for the active out conformation are obtained. The interactions during the conformational changes are determined to identify the influence of the effector.

Chemical accuracy for ligand-receptor binding Gibbs energies through multi-level SQM/QM calculations.

Calculating the Gibbs energies of binding of ligand-receptor systems with a thermochemical accuracy of ± 1 kcal mol-1 is a challenge to computational approaches. After exploration of the conformational space of the host, ligand and their resulting complexes upon coordination by semi-empirical GFN2 MD and meta-MD simulations, the systematic refinement through a multi-level improvement of binding modes in terms of electronic energies and solvation is able to give Gibbs energies of binding of drug molecules to CB[8] and ß-CD macrocyclic receptors with such an accuracy. The accurate treatment of a small number of structures outperforms system-specific force-matching and alchemical transfer model approaches without an extensive sampling and integration.

Aqueous solution and solid-state behaviour of l-homophenylalanine: experiment, modelling, and DFT calculations.

In the present study, the solid-state and aqueous solubility behaviour of l-homophenylalanine (l-Hpa) is explored. Different characterization techniques such as TG, DSC, temperature-resolved PXRD, and hot-stage microscopy were used to investigate basic thermal solid-state characteristics. Solubilities of l-Hpa in water were determined as a function of temperature and pH. Moreover, a thermodynamic model based on perturbation theory (PC-SAFT) is applied to represent the data. In addition, aqueous density data of l-Hpa were measured in a broader temperature range. To model the solubility data as a function of pH, pKa values are needed, which were accessed by employing density functional theory (DFT) calculations. The solid-state investigation did not show a simple melting process of l-Hpa, but a complete decomposition of the prevalent initial solid phase at elevated temperatures approximately above 520 K. This system exhibited extraordinarily low solubilities for an amino acid at all investigated temperatures. While the solubility does not differ from its isoelectric-point value over a wide pH range, it dramatically increases as the pH falls below 2.5 and rises above 9.5. The PC-SAFT model was able to calculate the solubilities as a function of pH and predict the density values.

Pharmacological effects of methysticin and L-sulforaphane through the Nrf2/ARE signaling pathway in MLO-Y4 osteocytes: in vitro study.

BACKGROUND: Oxidative stress plays a crucial role in the pathogenesis of many skeletal diseases by inducing osteocyte death. The transcription factor nuclear factor erythroid 2-related factor 2 (Nrf2) is a master regulator of various antioxidant gene expressions through antioxidant response element (ARE) against cellular oxidative stress and can be induced by various stimulants, including the phytochemicals methysticin (MET) and L-sulforaphane (SFN). This study aimed to establish an osteocyte in vitro model to investigate the pharmacological effects of MET and SFN on the Nrf2/ARE pathway. METHODS: MLO-Y4 murine osteocytes and the stably transduced MLO-Y4-SIN-lenti-ARE reporter gene cell line were used. MET and SFN were used as Nrf2 inducers. The cytotoxicity of MET, SFN, and hydrogen peroxide (H2O2) was evaluated using the CytoTox-Glo™ Assay. Time- and dose-dependent ARE induction was examined by Monoluciferase Assay. The mRNA and protein expressions of Nrf2 target markers, such as heme-oxygenase 1 (Ho-1), NADPH quinone dehydrogenase 1 (Nqo1), and thioredoxin reductase 1 (Txnrd1), were detected by RT-qPCR, Western Blot, and immunofluorescence staining, respectively. Osteogenesis markers, osteopontin, and osteocalcin were compared with and without treatment by immunofluorescence staining. RESULTS: The experimental data showed that MET and SFN induced ARE activity in a time- and dose-dependent manner and increased the mRNA and protein expression of antioxidant markers compared to vehicle-treated controls. The protein expression of osteopontin and osteocalcin in the samples treated with SFN were significantly higher than without treatment, and the number of cell death treated with SFN was significantly lower than without treatment under H2O2-induced stress conditions. CONCLUSIONS: Nrf2 inducers MET and SFN increased the mRNA expression of antioxidant genes through the Nrf2/ARE pathway in osteocytes. Notably, SFN increased the protein expression of osteocyte-associated osteogenic markers and suppressed cell death under H2O2-induced stress condition. Thus, Nrf2 stimulators can exert stress-relieving and osteogenic effects on osteocytes.