Structure-Activity Relationship of Xanthones as Inhibitors of Xanthine Oxidase

A consensual machine-learning-assisted QSAR model for effective bioactivity prediction of xanthine oxidase inhibitors using molecular fingerprints

Xanthine oxidase inhibitors (XOIs) have been widely studied due to the promising potential as safe and effective therapeutics in hyperuricemia and gout. Currently, available XOI molecules have been developed from different experiments but they are with the wide structure diversity and significant varying bioactivities. So it is of great practical significance to present a consensual QSAR model for effective bioactivity prediction of XOIs based on a systematic compiling of these XOIs across different experiments. In this work, 249 XOIs belonging to 16 scaffolds were collected and were integrated into a consensual dataset by introducing the concept of IC50 values relative to allopurinol (RIC50). Here, extended connectivity fingerprints (ECFPs) were employed to represent XOI molecules. By performing effective feature selection by machine-learning method, 54 crucial fingerprints were indicated to be valuable for predicting the inhibitory potency (IP) of XOIs. The optimal predictor yields the promising performance by different cross-validation tests. Besides, an external validation of 43 XOIs and a case study on febuxostat also provide satisfactory results, indicating the powerful generalization of our predictor. Here, the predictor was interpreted by shapely additive explanation (SHAP) method which revealed several important substructures by mapping the featured fingerprints to molecular structures. Then, 15 new molecules were designed and predicted by our predictor to show superior IP than febuxostat. Finally, molecular docking simulation was performed to gain a deep insight into molecular binding mode with xanthine oxidase (XO) enzyme, showing that molecules with selenazole moiety, cyano group and isopropyl group tended to yield higher IP. The absorption, distribution, metabolism, excretion and toxicity (ADMET) prediction results further enhanced the potential of these novel XOIs as drug candidates. Overall, this work presents a QSAR model for accurate prediction of IP of XOIs, and is expected to provide new insights for further structure-guided design of novel XOIs.

Identification of natural xanthine oxidase inhibitors: Virtual screening, anti-xanthine oxidase activity, and interaction mechanism

Xanthine oxidase (XO) is a crucial target for hyperuricemia treatment(s). Naturally occurred XO inhibitors with minimal toxicity and high efficacy have attracted researchers' attention. With the goal of quickly identifying natural XO inhibitors, an integrated computational screening strategy was constructed by molecular docking and calculating the free energy of binding. Twenty-seven hits were achieved from a database containing 19,377 natural molecules. This includes fourteen known XO inhibitors and four firstly-reported inhibitors (isolicoflavonol, 5,7-dihydroxycoumarin, parvifolol D and clauszoline M, IC50 < 40 μM). Iolicoflavonol (hit 8, IC50 = 8.45 ± 0.68 μM) and 5,7-dihydroxycoumarin (hit 25, IC50 = 10.91 ± 0.71 μM) displayed the great potency as mixed-type inhibitors. Docking study and molecular dynamics simulation revealed that both hits could interact with XO's primarily active site residues ARG880, MOS1328, and ASN768 of XO. Fluorescence spectroscopy studies showed that hit 8 bound to the active cavity region of XO, causing changes in XO's conformation and hydrophobicity. Hits 8 and 25 exhibit favorable Absorption, Distribution, Metabolism, and Excretion (ADME) properties. Additionally, no cytotoxicity against human liver cells was observed at their median inhibition concentrations against XO. Therefore, the present study offers isolicoflavonol and 5,7-dihydroxycoumarin with the potential to be disease-modifying agents for hyperuricemia.

Comparative phytochemical studies on the roots of Polygala azizsancarii and P. peshmenii and neuroprotective activities of the two xanthones

Six known sucrose mono-, di- and triesters and five xanthone derivatives were isolated from the roots of Polygala peshmenii Eren, Parolly, Raus & Kürschner which is a narrow species endemic to Türkiye. Among the xanthones, 1,7-dihydroxy-2,3-methylenedioxy-5,6-dimethoxy-xanthone is an undescribed compound isolated for the first time from a natural source. The studies on the roots of P. azizsancarii Dönmez have resulted in the isolation of four known compounds including sucrose mono-, di- and triesters. The structures of the sucrose esters and xanthones isolated from P. azizsancarii and P. peshmenii were established by spectroscopic methods, including 1D-NMR (¹H NMR, ¹³C NMR, DEPT-135), 2D-NMR (COSY, NOESY, HSQC, HMBC). Neuroprotective activities of two xanthones, 1,3,6-trihydroxy-2,5,7-trimethoxyxanthone and 3-O-β-D-glucopyranosyloxy-1,6-dihydroxy-2,5,7-trimethoxyxanthone isolated from the roots of P. azizsancarii were evaluated in vitro using in a cellular model of Alzheimer's disease. SKNAS human neuroblastoma cells were used in the study and treated with different consecrations of Aβ₂₅₋₃₅ oligomer for up to 48 h. Cell viability was evaluated using MTT assay. The distribution of β-amyloid, α-synuclein, tau, JAK2, STAT3, caspase 3 and BMP-2 were investigated using indirect immunoperoxidase staining. Our results suggested that both xanthones control tau aggregation with no effect on β-amyloid plaque formation. In addition, for neuronal pathophysiology in AD cell model, decreased distributions of JAK/STAT3 and BMP2 signaling pathways were demonstrated, therefore they play a role in the protective effect on neurons in neurodegenerative disease. A significant decrease in caspase 3 immunoreactivity was detected after the administration of both compounds in AD cells. Therefore, both compounds control neuronal pathophysiology and rescue cell death in AD disease.

Xanthones and Xanthone O-β-D-glucosides from the Roots of Polygala azizsancarii Dönmez

Nine xanthone derivatives (1-9) were isolated from the roots of Polygala azizsancarii, which is a narrow endemic species for the flora of Türkiye. Based on all of the evidence, the structures of 1-9 were established as two previously undescribed xanthone O-glucosides, 3-O-β-D-glucopyranosyloxy-1,6-dihydroxy-2,5,7-trimethoxyxanthone (1), 3-O-β-D-glucopyranosyloxy-1,6-dihydroxy-2,7-dimethoxyxanthone (2), and seven previously described xanthones, 1,3,6-trihydroxy-2,5,7-trimethoxyxanthone (3), 1,3,6-trihydroxy-2,7-dimethoxyxanthone (4), 1,2,3,4,7-pentamethoxyxanthone (5), 1,3-dihydroxy-2,5,6,7-tetramethoxyxanthone (6), 1,3-dihydroxy-4,7-dimethoxyxanthone (7), 1,7-dihydroxy-3-methoxyxanthone (8), 1,7-dihydroxy-2,3-methylenedioxy-xanthone (9). The structures of the compounds were determined by spectroscopic methods, including 1D-NMR (1H NMR, 13C NMR, DEPT-135), 2D-NMR (COSY, NOESY, HSQC, HMBC, INADEQUATE), and HRMS. The solid-state structures of 1-4, including the absolute configurations of the stereogenic carbons of the sugar moiety in 1 and 2, were established by X-ray crystal-structure analyses. For the newly described compounds, the trivial names sancarosides A (1) and B (2) are proposed.

A multiscale screening strategy for the identification of novel xanthine oxidase inhibitors based on the pharmacological features of febuxostat analogues

Two compounds as potential XOI hits were identified by a novel screening strategy based on the pharmacophores of well-known scaffolds.

Exploration of Novel Xanthine Oxidase Inhibitors Based on 1,6-Dihydropyrimidine-5-Carboxylic Acids by an Integrated in Silico Study

Xanthine oxidase (XO) is an important target for the effective treatment of hyperuricemia-associated diseases. A series of novel 2-substituted 6-oxo-1,6-dihydropyrimidine-5-carboxylic acids (ODCs) as XO inhibitors (XOIs) with remarkable activities have been reported recently. To better understand the key pharmacological characteristics of these XOIs and explore more hit compounds, in the present study, the three-dimensional quantitative structure-activity relationship (3D-QSAR), molecular docking, pharmacophore modeling, and molecular dynamics (MD) studies were performed on 46 ODCs. The constructed 3D-QSAR models exhibited reliable predictability with satisfactory validation parameters, including q2 = 0.897, R2 = 0.983, rpred2 = 0.948 in a CoMFA model, and q2 = 0.922, R2 = 0.990, rpred2 = 0.840 in a CoMSIA model. Docking and MD simulations further gave insights into the binding modes of these ODCs with the XO protein. The results indicated that key residues Glu802, Arg880, Asn768, Thr1010, Phe914, and Phe1009 could interact with ODCs by hydrogen bonds, π-π stackings, or hydrophobic interactions, which might be significant for the activity of these XOIs. Four potential hits were virtually screened out using the constructed pharmacophore model in combination with molecular dockings and ADME predictions. The four hits were also found to be relatively stable in the binding pocket by MD simulations. The results in this study might provide effective information for the design and development of novel XOIs.

Natural Products and Extracts as Xantine Oxidase Inhibitors - A Hope for Gout Disease?

Xanthine oxidase (EC 1.17.3.2) (XO) is one of the main enzymatic sources that create reactive oxygen species (ROS) in the living system. It is a dehydrogenase enzyme that performs electron transfer to nicotinamide adenine dinucleotide (NAD+), while oxidizing hypoxanthin, which is an intermediate compound in purine catabolism, first to xanthine and then to uric acid. XO turns into an oxidant enzyme that oxidizes thiol groups under certain stress conditions in the tissue. The last metabolic step, in which hypoxanthin turns into uric acid, is catalyzed by XO. Uric acid, considered a waste product, can cause kidney stones and gouty-type arthritis as it is crystallized, when present in high concentrations. Thus, XO inhibitors are one of the drug classes used against gout, a purine metabolism disease that causes urate crystal storage in the joint and its surroundings caused by hyperuricemia. Urate-lowering therapy includes XO inhibitors that reduce uric acid production as well as uricosuric drugs that increase urea excretion. Current drugs that obstruct uric acid synthesis through XO inhibition are allopurinol, febuxostat, and uricase. However, since the side effects, safety and tolerability problems of some current gout medications still exist, intensive research is ongoing to look for new, effective, and safer XO inhibitors of natural or synthetic origins for the treatment of the disease. In the present review, we aimed to assess in detail XO inhibitory capacities of pure natural compounds along with the extracts from plants and other natural sources via screening Pubmed, Web of Science (WoS), Scopus, and Google Academic. The data pointed out to the fact that natural products, particularly phenolics such as flavonoids (quercetin, apigenin, and scutellarein), tannins (agrimoniin and ellagitannin), chalcones (melanoxethin), triterpenes (ginsenoside Rd and ursolic acid), stilbenes (resveratrol and piceatannol), alkaloids (berberin and palmatin) have a great potential for new XO inhibitors capable of use against gout disease. In addition, not only plants but other biological sources such as microfungi, macrofungi, lichens, insects (silk worms, ants, etc) seem to be the promising sources of novel XO inhibitors.

Anti-Tumor Xanthones from Garcinia nujiangensis Suppress Proliferation, and Induce Apoptosis via PARP, PI3K/AKT/mTOR, and MAPK/ERK Signaling Pathways in Human Ovarian Cancers Cells

BACKGROUND

Ovarian cancer (OC) is a serious public health concern in the world. It is important to develop novel drugs to inhibit OC.

PURPOSE

This study investigated the isolation, elucidation, efficiency, molecular docking, and pharmaceutical mechanisms of xanthones isolated from Garcinia nujiangensis.

METHODS

Xanthones were isolated, and purified by different chromatography, including silica gel, reversed-phase silica gel (ODS-C18), and semipreparative HPLC, then identified by analysis of their spectral data. Three xanthones were estimated for their efficiency on the human OC cells HEY and ES-2. 2 was found to be the most potent cytotoxic xanthones of those tested. Further, its mechanisms of action were explored by molecular docking, cell apoptosis, and Western blotting analysis.

RESULTS

Bioassay-guided fractionation of the fruits of Garcinia nujiangensis led to the separation of a new xanthone named nujiangexanthone G (1) and two known xanthones. Among these, isojacareubin (2) exhibited the most potent cytotoxic compound against the HEY and ES-2 cell lines. The analysis of Western blot suggested that 2 inhibited OC via regulating the PARP, PI3K/AKT/mTOR, and ERK/MAPK signal pathways in the HEY cell lines.

CONCLUSION

In conclusion, isojacareubin (2) might be a potential drug for the treatment of OC.

A review on the phytopharmacological studies of the genus Polygala

ETHNOPHARMACOLOGICAL RELEVANCE

The genus Polygala, the most representative genus of the Polygalaceae family, comprises more than 600 species from all over the world of which around 40 are distributed in China, some of them, being used in the Traditional Chinese Medicine system.

AIM OF THE REVIEW

We intend to discuss the current knowledge about the traditional uses, and the newest phytochemical and pharmacological achievements with tentative elucidation of the mechanism of action on the genus Polygala covering the period 2013-2019 to provide a scientific support to the traditional uses, and to critically analyze the reported studies to obtain new insights for further researches.

MATERIALS AND METHODS

The data were systematically collected from the scientific electronic data bases including SciFinder, Scopus, Elsevier, PubMed and Google Scholar.

RESULTS

This literature overview reported several traditional uses of different species of Polygala, mainly against wounds, inflammation, cardiovascular and central nervous system disorders. P. altomontana, P caudata, P. flavescens, P. glomerata, P. japonica, P. molluginifolia, P. sibirica, P. tenuifolia are the main species which have been studied in the last few years. Phytochemical studies showed that they contain triterpene saponins, triterpenes, terpenoids, xanthones, flavonoids, coumarins, oligosaccharide esters, styryl-pyrones, benzophenones, and polysaccharides. Pharmacological in vitro and in vivo studies and proposal of the mechanisms of action indicated that pure constituents and extracts of Polygala ssp exhibited significant anti-inflammatory, neuroprotective, antiischemic, antidepressant, sedative, analgesic, antiatherosclerosis, antitumor and enzyme inhibitory properties.

CONCLUSION

This review on traditional uses and phytopharmacological potential of the genus Polygala revealed updated insights which can be explored for further mechanism-based pharmacological activities and structure/activity relationships studies and a better comprehension of the development of Chinese medicine preparations. However some pharmacological studies showed several gaps such as incomplete methodologies and ambiguous findings. More high scientific quality preclinical studies with pharmacokinetic considerations will be required in the future to assess the traditional uses of some species of this genus. This might lead to efficacy and safety issues in clinical trials and to potential medicinal applications.

Intestinal Absorption Profile of Three Polygala Oligosaccharide Esters in Polygalae Radix and the Effects of Other Components in Polygalae Radix on Their Absorption

Oligosaccharide esters, which are among the main active components of Polygalae Radix (PR), demonstrate significant pharmacological activities in the human nervous system. In our previous research, some other constituents in PR were able to improve the bioavailability of oligosaccharide esters such as sibiricose A5 (SA5), sibiricose A6 (SA6), and 3,6'-disinapoyl sucrose (DISS), but the related components and their underlying mechanisms remain unknown. The present study aimed to investigate the intestinal absorptive profile of SA5, SA6, and DISS and the absorptive behavior influenced by the coadministration of polygalaxanthone III and total saponins of PR (TS) using an in vitro everted rat gut sac model, along with the possible mechanisms that may influence absorption. The results showed that TS could significantly enhance the absorption of SA5, SA6, and DISS monomers. Verapamil, a P-glycoprotein inhibitor, was able to elevate the absorption of SA5 and SA6, and an absorption experiment using Rho123 led us to conclude that TS influenced the absorption of SA5 and SA6 in a manner similar to that of a P-glycoprotein inhibitor. Sodium caprate, a paracellular absorption enhancer, was found to increase the absorption of SA5, SA6, and DISS. Results showed that the absorption mechanisms of SA5 and SA6 may combine active transport with paracellular passive penetration, while DISS's absorption was dominated by paracellular passive penetration. However, the relationship between polygala saponins and the absorption of SA5, SA6, and DISS by paracellular passive penetration remain to be examined. This is the direction of our future research.

In Silico and 3D QSAR Studies of Natural Based Derivatives as Xanthine Oxidase Inhibitors

BACKGROUND

A large number of disorders and their symptoms emerge from deficiency or overproduction of specific metabolites has drawn the attention for the discovery of new therapeutic agents for the treatment of disorders. Various approaches such as computational drug design have provided the new methodology for the selection and evaluation of target protein and the lead compound mechanistically. For instance, the overproduction of xanthine oxidase causes the accumulation of uric acid which can prompt gout.

OBJECTIVE

In the present study we critically discussed the various techniques such as 3-D QSAR and molecular docking for the study of the natural based xanthine oxidase inhibitors with their mechanistic insight into the interaction of xanthine oxidase and various natural leads.

CONCLUSION

The computational studies of deferent natural compounds were discussed as a result the flavonoids, anthraquinones, xanthones shown the remarkable inhibitory potential for xanthine oxidase inhibition moreover the flavonoids such as hesperidin and rutin were found as promising candidates for further exploration.