QSAR prediction of inhibition of aldose reductase for flavonoids

Resonance structure contributions, flexibility, and frontier molecular orbitals (HOMO-LUMO) of pelargonidin, cyanidin, and delphinidin throughout the conformational space: application to antioxidant and antimutagenic activities

This research refers to the study and understanding of the conformational space of the positive-charged anthocyanidin structures in relation with the known chemical reactivities and bioactivities of these compounds. Therefore, the planar (P) and nonplanar (Z) conformers of the three hydroxylated anthocyanidins pelargonidin, cyanidin, and delphinidin were analyzed throughout the conformational space at the B3LYP/6-311 ++ G** level of theory. The outcome displayed eleven new conformers for pelargonidin, fifty-four for cyanidin, and thirty-one for delphinidin. Positive-charged quinoidal structures showed a significant statistical weight in the conformational space, thus coexisting simultaneously with other resonance structures, such that under certain reaction conditions, the anthocyanidins behave as positive-charged quinoidal structures instead of oxonium salts. The calculations of the permanent dipole moment and the polarizability showed relationships with the quantity and arrangement of hydroxyls in the structure. In addition, theoretical calculations were used to analyze the frontier molecular orbitals (HOMO-LUMO) of the three anthocyanidins. The novel conception of this work lies in the fact that dipole moment, polarizability, and HOMO-LUMO values were related to the reactivity/bioactivity of these three anthocyanidins. HOMO-LUMO energy gaps were useful to explain the antioxidant activity, while the percent atom contributions to HOMO were appropriate to demonstrate the antimutagenic activity as enzyme inhibitors, as well as the steric and electrostatic requirements to form the pharmacophore. Delphinidin was the strongest antioxidant anthocyanidin, and pelargonidin the best anthocyanidin with antimutagenic activity.

Antisteatotic and antioxidant activities of Thymbra spicata L. extracts in hepatic and endothelial cells as in vitro models of non-alcoholic fatty liver disease

ETHNOPHARMACOLOGICAL RELEVANCE

Thymbra spicata, a member of the Lamiaceae family, is native to eastern Mediterranean area. Leaves of this plant are rich in phenolic compounds and are a popular remedy of traditional medicine in Lebanon to prevent and/or counteract hyperlipidemia and hyperglycemia.

AIM OF THE STUDY

To evaluate the antisteatotic and antioxidant activities of extracts from leaves of Thymbra spicata L. using in vitro models of non-alcoholic fatty liver disease (NAFLD), a leading cause of liver-related morbidity and mortality worldwide, for whom no effective treatments are still available.

MATERIALS AND METHODS

Two different extracts from Thymbra spicata L. aerial parts were prepared using water (TW) or ethanol (TE) as solvent. Their chemical composition was characterized by gas and liquid chromatography coupled with mass spectrometry. Both extracts were tested on cultured hepatic and endothelial cells treated to mimic in vitro a multisistemic pathology such as NAFLD. We assayed the effects on lipid accumulation, free radical production, lipid peroxidation, cell migration.

RESULTS

Both the total phenolic and the total flavonoid contents were higher in the ethanolic extract. Rosmarinic acid was the most abundant polyphenol in TW, while TE was richer in carvacrol. Our findings demonstrated that both extracts ameliorated lipid accumulation, oxidative stress and inflammation in the NAFLD cellular models. However, the aqueous extract was more effective to reduce hepatic steatosis, and the ethanolic extract had higheranti-oxidant potential and wound healing activity.

CONCLUSIONS

T. spicata extracts could be promising bioactive products to develop natural therapeutic agents or dietary supplements to treat NAFLD and obesity-related metabolic disease. Our findings suggest that while the ethanolic extract might be used in preventing endothelium dysfunction, the aqueous extract would act better as lipid-lowering agent.

Computational Molecular Modeling of Pin1 Inhibition Activity of Quinazoline, Benzophenone, and Pyrimidine Derivatives

Pin1 (peptidyl-prolyl cis-trans isomerase NIMA-interacting 1) is directly involved in cancer cell-cycle regulation because it catalyses the cis-trans isomerization of prolyl amide bonds in proteins. In this sense, a modeling evaluation of the inhibition of Pin1 using quinazoline, benzophenone, and pyrimidine derivatives was performed by using multilinear, random forest, SMOreg, and IBK regression algorithms on a dataset of 51 molecules, which was divided randomly in 78% for the training and 22% for the test set. Topological descriptors were used as independent variables and the biological activity (pIC50) as a dependent variable. The most robust individual model contained 9 features, and its predictive capability was statistically validated by the correlation coefficient for adjusting, 10-fold cross validation, test set, and bootstrapping with values of 0.910, 0.819, 0.841, and 0.803, respectively. In order to improve the prediction of the pIC50 values, the aggregation of the individual models was performed through the construction of an ensemble, and the most robust one was constructed by two individual models (LR3 and RF1) by applying the IBK algorithm, and a substantial improvement in predictive performance is reflected in the values of R2ADJ = 0.982, Q2CV = 0.962, and Q2EXT = 0.918. Mean square errors <0.165 and good fitting between calculated and experimental pIC50 values suggest a robustness on the prediction of pIC50. Regarding the docking simulation, a binding affinity between the molecules and the active site for the Pin1 inhibition into the protein (3jyj) was estimated through the calculation of the binding free energy (BE), with values in the range of −5.55 to −8.00 kcal/mol, implying a stabilizing interaction molecule receptor. The ligand interaction diagrams between the drugs and amino acid in the binding site for the three most active compounds denoted a good wrapper of these organic compounds into the protein mainly by polar amino acids.

Preferential adsorption of flavonoids from peanut shell by amino-modified Fe3 O4 nanoparticles (MNP-NH2 )

BACKGROUND

The highly selective capture of individual components of complex systems such as Chinese medicine extracts is a great challenge. With the rapid development of nanoscience, magnetic materials have attracted increased attention as suitable candidates for use in drug transport vehicles.

RESULTS

In this work, amino-modified Fe₃ O₄ nanoparticles (MNP-NH₂ ) have been synthesized and successfully used to selectively isolate luteolin, a type of flavonoid, from peanut shell, coupled with high-performance liquid chromatography. MNP-NH₂ were characterized by transmission electron microscopy, scanning electron microscopy, Fourier transform infrared spectroscopy and vibrating sample magnetometer analysis, which showed that the amino functional groups were successfully bound to the surface of the magnetic particles. Adsorption of six different flavonoids by MNP-NH₂ showed that the mechanism of adsorption was related to the number of ortho-phenolic hydroxyl groups. The optimized adsorption conditions were extraction for 40 min at 30 °C by single-factor experiments and the final elution conditions were determined to be 5 mL of 20% glacial acetic acid (methanol:water = 60:40) and ultrasonication for 40 min by L9 (3⁴ ) orthogonal test.

CONCLUSION

Based on these findings, we first created a method for separating luteolin from peanut shell extract by MNP-NH₂ . This newly developed magnetic method of extracting chemical compounds from herbal foodstuffs and medicines provides new ideas for the utilization of a cash crop. © 2018 Society of Chemical Industry.

Construction of explicit models to correlate the structure and the inhibitory activity of aldose reductase: Flavonoids and sulfonyl-pyridazinones as inhibitors

The correlation between binding energies and bioactivities is the core of structure-based computer-aided drug design. However, many models to address this correlation are still strongly system-dependent at current stage. We constructed two explicit models to correlate the binding energies with the inhibitory activities of flavonoids and sulfonyl-pyridazinones as inhibitors of aldose reductase. The introduction of multiple complex states comprised of protein, coenzyme, substrate, and inhibitor can remarkably improve the correlation coefficients, compared with that using single complex state. Recombination of energy terms from complex structures and molecular descriptors of inhibitors can further improve the correlation. The explicit models provide correlation coefficients of 0.90 and 0.92 for flavonoids and sulfonyl-pyridazinones, respectively. These models also steadily present the contribution from each energy term and the favorite of protein-inhibitor complex states. Meanwhile, we also observed that some inhibitors can accommodate alternative sites out of the conserved binding pocket at the presence/absence of coenzyme and substrate. It is responsible for the remarkable change in the binding energies and thus significantly influences the correlation between the structures and the inhibitory activities. Overall, this work presents a rational way to construct reliable explicit models through the combination of multiple physically accessible complex states, even though each of them only bears marginal information related to their activities.

A flavonoid fraction purified from Rutaceae aurantiae (Daflon(R)) inhibiting AGE formation, reduces urinary albumin clearance and corrects hypoalbuminemia in normotensive and hypertensive diabetic rats

AIM

Advanced glycation endproducts (AGEs) have been shown to contribute to alteration of glomerular permselectivity to proteins in diabetes. Oxidative stress is required for AGE formation. Therefore we studied the effect of an antioxidant micronized purified flavonoid fraction (MPFF, Daflon(R) 500 mg), on urinary albumin clearance in diabetic rats.

METHODS

Hyperglycaemia was induced by streptozotocin 55 mg/kg IM at days 0 and 7 in normotensive Wistar rats (NWR, diabetes duration 5 months) or hypertensive Wistar Kyoto rats (SHR, diabetes duration 2 months). MPFF was administered at 300 mg/kg/day, from day -2 until sacrifice.

RESULTS

After 5 months of diabetes in NWR, MPFF reduced albumin clearance from 729±92 to 392±60 nl/min/kg, p<0.01, and restored albuminemia from 20.4±0.9 to 24.0±1 g/l, p<0.05; albumin fractional clearance was significantly diminished in the flavonoid-treated diabetic rats (0.360±0.037‰ versus 1.335±0.430‰ in the diabetic controls, p<0.001); MPFF did not significantly modify blood glucose and plasma fructosamine levels. After 2 months of diabetes in SHR, MPFF reduced albumin clearance from 243±121 to 101±47 nl/min/kg, p<0.05, and restored albuminemia from 21.1±1.6 to 26.7±2.2 g/l (p<0.05); MPFF also decreased plasma fluorescence characteristic of AGEs (p<0.02). Besides hesperetin, a main metabolite of MPFF recovered in plasma, inhibited in vitro the formation of the crosslinking AGE pentosidine in collagen incubated with high glucose (p<0.001).

CONCLUSION

Our results confirm the role of glycoxidative stress in diabetic nephropathy. MPFF might be useful as complementary treatment for preventing diabetic microangiopathy.

Flavones: an important scaffold for medicinal chemistry

Flavones have antioxidant, anti-proliferative, anti-tumor, anti-microbial, estrogenic, acetyl cholinesterase, anti-inflammatory activities and are also used in cancer, cardiovascular disease, neurodegenerative disorders, etc. Also, flavonoids are found to have an effect on several mammalian enzymes like protein kinases that regulate multiple cell signaling pathways and alterations in multiple cellular signaling pathways are frequently found in many diseases. Flavones have been an indispensable anchor for the development of new therapeutic agents. The majority of metabolic diseases are speculated to originate from oxidative stress, and it is therefore significant that recent studies have shown the positive effect of flavones on diseases related to oxidative stress. Due to the wide range of biological activities of flavones, their structure-activity relationships have generated interest among medicinal chemists. The outstanding development of flavones derivatives in diverse diseases in very short span of time proves its magnitude for medicinal chemistry research. The present review gives detail about the structural requirement of flavone derivatives for various pharmacological activities. This information may provide an opportunity to scientists of medicinal chemistry discipline to design selective, optimize as well as poly-functional flavone derivatives for the treatment of multi-factorial diseases.

Anti-enterovirus 71 effects of chrysin and its phosphate ester

Enterovirus 71 (EV71) can cause severe disease and even lead to death in children, and an effective antiviral drug is currently unavailable. The anti-EV71 effect of chrysin (5,7-dihydroxyflavone), a natural flavonoid commonly found in many plants, was tested in this report. By using the predicting program Autodock 4.0 and an in vitro protease inhibition assay, we found that chrysin could suppress viral 3Cpro activity. Replication of viral RNA and production of viral capsid protein and the infectious virion were strongly inhibited by chrysin, without noticeable cytotoxicity. Cytopathic effects on cells were also prevented. Diisopropyl chrysin-7-yl phosphate (CPI), the phosphate ester for chrysin, was generated through a simplified Atheron-Todd reaction to achieve stronger anti-viral activity. CPI was also able to bind with and inhibit viral 3Cpro activity in vitro. As expected, CPI demonstrated more potent antiviral activity against EV71.

Retrospective group fusion similarity search based on eROCE evaluation metric

In this study, a simple evaluation metric, denoted as eROCE was proposed to measure the early enrichment of predictive methods. We demonstrated the superior robustness of eROCE compared to other known metrics throughout several active to inactive ratios ranging from 1:10 to 1:1000. Group fusion similarity search was investigated by varying 16 similarity coefficients, five molecular representations (binary and non-binary) and two group fusion rules using two reference structure set sizes. We used a dataset of 3478 actives and 43,938 inactive molecules and the enrichment was analyzed by means of eROCE. This retrospective study provides optimal similarity search parameters in the case of ALDH1A1 inhibitors.

Kinetics and molecular docking studies of kaempferol and its prenylated derivatives as aldose reductase inhibitors

Aldose reductase inhibitors (ARIs) suppressing the hyperglycemia-induced polyol pathway have been provided as potential therapeutic candidates in the treatment and prevention of diabetic complications. Based upon structure-activity relationships of desmethylanhydroicaritin (1) and sophoflavescenol (2) as promising ARIs, 3,4'-dihydroxy flavonols with a prenyl or lavandulyl group at the C-8 position and a hydroxyl or methoxy group at the C-5 position are important for aldose reductase (AR) inhibition. In order to prove the above results, a combination of computational prediction and enzyme kinetics has begun to emerge as an effective screening technique for the potential. In the present study, we predicted the 3D structure of AR in rat and human using a docking algorithm to simulate binding between AR and prenylated flavonoids (1 and 2) and kaempferol (3) and scrutinized the reversible inhibition of AR by these ARIs. Docking simulation results of 1-3 demonstrated negative binding energies (Autodock 4.0=-9.11 to -7.64 kcal/mol; Fred 2.0=-79.54 to -51.84 kcal/mol) and an additional hydrogen bond through Phe122 and Trp219, in addition to the previously proposed interaction of AR and phenolics through Trp20, Tyr48, His110, and Trp111 residues, indicating that the presence of 8-prenyl and 5-methyl groups might potentiate tighter binding to the active site of the enzyme and more effective AR inhibitors. Moreover, types of AR inhibition were different depending on the presence or absence of the 8-prenyl group, in that 1 and 2 are mixed inhibitors with respective Ki values of 0.69 μM and 0.94 μM, while 3 showed noncompetitive inhibition with a Ki value of 4.65 μM. The present study suggests that an effective strategy for screening potential ARIs could be established by predicting 3D structural conformation of prenylated flavonoids and the orientation within the enzyme as well as by simultaneously determining the mode of enzyme inhibition.

Consensus ranking approach to understanding the underlying mechanism with QSAR

Constructing a highly predictive model and exploiting the underlying mechanism associated with a specific property of chemicals are the two main goals of quantitative structure-activity relationship analysis (QSAR). However, the latter has long been carried out as a byproduct of model construction. Here we confirmed for the first time in this study that conventional descriptor selection methods designed to develop a best predictive model are likely not suitable for mechanistic analysis, i.e., the selected descriptors strongly depended on the selection of chemicals in the training sets. As an alternative, a consensus ranking protocol was proposed to select a robust descriptor set for mechanistic analysis, which can successfully overcome the above shortcoming. Moreover, the consistently inferior model performance using descriptors selected for mechanistic analysis suggested the irreplaceable role of model development in achieving models with the best predictive capability.

3D-QSAR (CoMFA and CoMSIA) and pharmacophore (GALAHAD) studies on the differential inhibition of aldose reductase by flavonoid compounds

Inhibitory activities of flavonoid derivatives against aldose reductase (AR) enzyme were modelled by using CoMFA, CoMSIA and GALAHAD methods. CoMFA and CoMSIA methods were used for deriving quantitative structure-activity relationship (QSAR) models. All QSAR models were trained with 55 compounds, after which they were evaluated for predictive ability with additional 14 compounds. The best CoMFA model included both steric and electrostatic fields, meanwhile, the best CoMSIA model included steric, hydrophobic and H-bond acceptor fields. These models had a good predictive quality according to both internal and external validation criteria. On the other hand, GALAHAD was used for deriving a 3D pharmacophore model. Twelve active compounds were used for deriving this model. The obtained model included hydrophobe, hydrogen bond acceptor and hydrogen bond donor features; it was able to identify the active AR inhibitors from the remaining compounds. These in silico tools might be useful in the rational design of new AR inhibitors.