Structure-Activity Relationships and Docking Studies of Hydroxychavicol and Its Analogs as Xanthine Oxidase Inhibitors

Rapid screening of xanthine oxidase inhibitors from Ligusticum wallichii by using xanthine oxidase functionalized magnetic metal-organic framework

In this study, xanthine oxidase was immobilized for the first time using a novel magnetic metal-organic framework material (Fe3O4-SiO2-NH2@MnO2@ZIF-8-NH2). A ligand fishing method was established to rapidly screen XOD inhibitors from Ligusticum wallichii based on the immobilized XOD. Characterization and properties of the immobilized enzyme revealed its excellent stability and reusability. A ligand was screened from Ligusticum wallichii and identified as ligustilide by ultra-high performance liquid chromatography tandem mass spectrometry. The IC50 value of ligustilide was determined to be 27.70 ± 0.13 μM through in vitro inhibition testing. Furthermore, molecular docking verified that ligustilide could bind to amino acid residues at the active site of XOD. This study provides a rapid and effective method for the preliminary screening of XOD inhibitors from complex natural products and has great potential for further discovery of anti-hyperuricemic compounds.

Targeting bone cancer with 4-Allylbenzene-1,2-diol purified from Piper betle L.: an in silico and cytotoxicity scrutiny

Piper betle L., a well-known medicinal plant with rich source of bioactive compounds, is widely used in several therapeutics. The present study was performed to scrutinize the anti-cancer potential of compounds P. betle petiole by means of in silico studies, purification of 4-Allylbenzene-1,2-diol from petioles and assessing its cytotoxicity on bone cancer metastasis. Subsequent to SwissADME screening, 4-Allylbenzene-1,2-diol and Alpha terpineol were chosen for molecular docking together with eighteen approved drugs against fifteen important bone cancer targets accompanied with molecular dynamics simulation studies. 4-Allylbenzene-1,2-diol was found to be multi-targeting, interacted effectively with all targets, particularly exhibited good stability with MMP9 and MMP2 during molecular dynamics simulations and Molecular Mechanics- Generalized Born and Surface Area (MM-GBSA) analysis using Schrodinger. Later, the compound was isolated, purified and the cytotoxicity studies on MG63 bone cancer cell lines confirmed the cytotoxicity nature (75.98% at 100 µg/ml concentration). The results demonstrated the compound as a matrix metalloproteinase inhibitor, and therefore 4-Allylbenzene-1,2-diol may possibly be prescribed in targeted therapy for alleviating the bone cancer metastasis upon further wet lab experimental validations.Communicated by Ramaswamy H. Sarma.

Breynia cernua: Chemical Profiling of Volatile Compounds in the Stem Extract and Its Antioxidant, Antibacterial, Antiplasmodial and Anticancer Activity In Vitro and In Silico

Breynia cernua has been used as an alternative medicine for wounds, smallpox, cervical cancer, and breast cancer. This plant is a potential source of new plant-derived drugs to cure numerous diseases for its multiple therapeutic functions. An in vitro study revealed that the methanol extract of B. cernua (stem) exhibits antioxidant activity according to DPPH and SOD methods, with IC₅₀ values of 33 and 8.13 ppm, respectively. The extract also exerts antibacterial activity against Staphylococcus aureus with minimum bactericidal concentration of 1875 ppm. Further analysis revealed that the extract with a concentration of 1-2 ppm protects erythrocytes from the ring formation stage of Plasmodium falciparum, while the extract with a concentration of 1600 ppm induced apoptosis in the MCF-7 breast cancer cell line. GC-MS analysis showed 45 bioactive compounds consisting of cyclic, alkyl halide, organosulfur, and organoarsenic compounds. Virtual screening via a blind docking approach was conducted to analyze the binding affinity of each metabolite against various target proteins. The results unveiled that two compounds, namely, N-[β-hydroxy-β-[4-[1-adamantyl-6,8-dichloro]quinolyl]ethyl]piperidine and 1,3-phenylene, bis(3-phenylpropenoate), demonstrated the best binding score toward four tested proteins with a binding affinity varying from -8.3 to -10.8 kcal/mol. Site-specific docking analysis showed that the two compounds showed similar binding energy with native ligands. This finding indicated that the two phenolic compounds could be novel antioxidant, antibacterial, antiplasmodial, and anticancer drugs. A thorough analysis by monitoring drug likeness and pharmacokinetics revealed that almost all the identified compounds can be considered as drugs, and they have good solubility, oral bioavailability, and synthetic accessibility. Altogether, the in vitro and in silico analysis suggested that the extract of B. cernua (stem) contains various compounds that might be correlated with its bioactivities.

Design, Synthesis and Structure-Activity Relationship Studies of Protein Kinase CK2 Inhibitors Containing a Purine Scaffold

Protein kinase CK2 (CK2) is involved in the suppression of gene expression, protein synthesis, cell proliferation, and apoptosis, thus making it a target protein for the development of therapeutics toward cancer, nephritis, and coronavirus disease 2019. Using the solvent dipole ordering-based method for virtual screening, we identified and designed new candidate CK2α inhibitors containing purine scaffolds. Virtual docking experiments supported by experimental structure-activity relationship studies identified the importance of the 4-carboxyphenyl group at the 2-position, a carboxamide group at the 6-position, and an electron-rich phenyl group at the 9-position of the purine scaffold. Docking studies based on the crystal structures of CK2α and inhibitor (PDBID: 5B0X) successfully predicted the binding mode of 4-(6-carbamoyl-8-oxo-9-phenyl-8,9-dihydro-7H-purin-2-yl) benzoic acid (11), and the results were used to design stronger small molecule targets for CK2α inhibition. Interaction energy analysis suggested that 11 bound around the hinge region without the water molecule (W1) near Trp176 and Glu81 that is frequently reported in crystal structures of CK2α inhibitor complexes. X-ray crystallographic data for 11 bound to CK2α was in very good agreement with the docking experiments, and consistent with activity. From the structure-activity relationship (SAR) studies presented here, 4-(6-Carbamoyl-9-(4-(dimethylamino)phenyl)-8-oxo-8,9-dihydro-7H-purin-2-yl) benzoic acid (12) was identified as an improved active purine-based CK2α inhibitor with an IC₅₀ of 4.3 µM. These active compounds with an unusual binding mode are expected to inspire new CK2α inhibitors and the development of therapeutics targeting CK2 inhibition.

Interactions of Betel Quid Constituents with Drug Disposition Pathways: An Overview

Global estimates indicate that over 600 million individuals worldwide consume the areca (betel) nut in some form. Nonetheless, its consumption is associated with a myriad of oral and systemic ailments, such as precancerous oral lesions, oropharyngeal cancers, liver toxicity and hepatic carcinoma, cardiovascular distress, and addiction. Users commonly chew slivers of areca nut in a complex consumable preparation called betel quid (BQ). Consequently, the user is exposed to a wide array of chemicals with diverse pharmacokinetic behavior in the body. However, a comprehensive understanding of the metabolic pathways significant to BQ chemicals is lacking. Henceforth, we performed a literature search to identify prominent BQ constituents and examine each chemical's interplay with drug disposition proteins. In total, we uncovered over 20 major chemicals (e.g., arecoline, nicotine, menthol, quercetin, tannic acid) present in the BQ mixture that were substrates, inhibitors, and/or inducers of various phase I (e.g., CYP, FMO, hydrolases) and phase II (e.g., GST, UGT, SULT) drug metabolizing enzymes, along with several transporters (e.g., P-gp, BCRP, MRP). Altogether, over 80 potential interactivities were found. Utilizing this new information, we generated theoretical predictions of drug interactions precipitated by BQ consumption. Data suggests that BQ consumers are at risk for drug interactions (and possible adverse effects) when co-ingesting other substances (multiple therapeutic classes) with overlapping elimination mechanisms. Until now, prediction about interactions is not widely known among BQ consumers and their clinicians. Further research is necessary based on our speculations to elucidate the biological ramifications of specific BQ-induced interactions and to take measures that improve the health of BQ consumers.

Identification of Non-steroidal Aromatase Inhibitors via In silico and In vitro Studies

INTRODUCTION

Breast cancer is the most common cancer affecting women worldwide, including Pakistan. More than half of breast cancer patients have hormone-dependent breast cancer, which is developed due to the over-production of estrogen (the main hormone in breast cancer).

METHOD

The biosynthesis of estrogen is catalyzed by the aromatase enzyme, which thus serves as a target for the treatment of breast cancer. During the current study, biochemical, computational, and STD-NMR methods were employed to identify new aromatase inhibitors. A series of phenyl-3- butene-2-one derivatives 1-9 were synthesized and evaluated for human placental aromatase inhibitory activity. Among them, four compounds 2, 3, 4, and 8 showed a moderate to weak inhibitory activity (IC50 = 22.6 - 47.9 µM), as compared to standard aromatase inhibitory drugs, letrozole (IC50 = 0.0147 ± 1.45 µM), anastrozole (IC50 = 0.0094 ± 0.91 µM), and exemestane (IC50 = 0.2 ± 0.032 µM). Kinetic studies on two moderate inhibitors, 4 and 8, revealed a competitive- and mixed-type of inhibition, respectively.

RESULT

Docking studies on all active compounds indicated their binding adjacent to the heme group and interaction with Met374, a critical residue of aromatase. STD-NMR further highlighted the interactions of these ligands with the aromatase enzyme.

CONCLUSION

STD-NMR-based epitope mapping indicated close proximity of the alkyl chain followed by an aromatic ring with the receptor (aromatase). These compounds were also found to be non-cytotoxic against human fibroblast cells (BJ cells). Thus, the current study has identified new aromatase inhibitors (compounds 4, and 8) for further pre-clinical and clinical research.

In silico Molecular Docking for assessing Anti-fungal Competency of Hydroxychavicol, a Phenolic Compound of Betel Leaf (Piper betle L.) against COVID-19 Associated Maiming Mycotic Infections

Objective: To investigate the inhibitory nature of hydroxychavicol against the Covid-19 associated mycotic infections, the present in silico study was performed in hydroxychavicol with the target Lanosterol 14 alpha demethylase and its competency was compared with four approved anti-fungal drugs. Significance: The corona virus pandemic has drawn stark lines between rich nations and poor, and the occurrence of COVID-19 associated mycotic infections, mucormycosis epidemic stands as the latest manifestation. The increase in resistance in known fungal pathogens to the available anti-fungal drugs and side effects are the important demands that forced to search anti-fungal compounds from medicinal plants as therapeutic alternatives. During the fishing expedition, Piper betle L., gets tremendous attention for its rich source of medicinally important compounds. Among them, hydroxychavicol has the enormous supportive records against microbial growth. Methods: Hydroxychavicol and the chosen drugs were retrieved from the Pubchem database and subjected to ADME analysis. The structure of the target of the chosen COVID-19 associated fungal pathogens was retrieved from PDB and unavailable protein structures were modeled using Swiss Model and validated. Virtual screening (PyRx version 0.8) was performed and the interactions were visualized using BIOVIA Discovery Studio. Results: ADME screening of hydroxychavicol was found to have clear reciprocity with the drug-likeliness nature and the subsequent molecular docking study revealed its good binding affinity towards the target protein suggesting its inhibitory nature. Conclusion: This study offers the possibility of making use of the suppressive nature of hydroxychavicol in the treatment of mycotic infections either exclusively/in synergistic approach.

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.

Natural Chain-Breaking Antioxidants and Their Synthetic Analogs as Modulators of Oxidative Stress

Oxidative stress is associated with the increased production of reactive oxygen species or with a significant decrease in the effectiveness of antioxidant enzymes and nonenzymatic defense. The penetration of oxygen and free radicals in the hydrophobic interior of biological membranes initiates radical disintegration of the hydrocarbon “tails” of the lipids. This process is known as “lipid peroxidation”, and the accumulation of the oxidation products as peroxides and the aldehydes and acids derived from them are often used as a measure of oxidative stress levels. In total, 40 phenolic antioxidants were selected for a comparative study and analysis of their chain-breaking antioxidant activity, and thus as modulators of oxidative stress. This included natural and natural-like ortho-methoxy and ortho-hydroxy phenols, nine of them newly synthesized. Applied experimental and theoretical methods (bulk lipid autoxidation, chemiluminescence, in silico methods such as density functional theory (DFT) and quantitative structure–activity relationship ((Q)SAR) modeling) were used to clarify their structure–activity relationship. Kinetics of non-inhibited and inhibited lipid oxidation in close connection with inhibitor transformation under oxidative stress is considered. Special attention has been paid to chemical reactions resulting in the initiation of free radicals, a key stage of oxidative stress. Effects of substituents in the side chains and in the phenolic ring of hydroxylated phenols and biphenols, and the concentration were discussed.

Optimization of process parameters for the synthesis of silver nanoparticles from Piper betle leaf aqueous extract, and evaluation of their antiphytofungal activity

Biological methods offer eco-friendly and cost-effective alternatives for the synthesis of silver nanoparticles (AgNPs). The present study highlights a green process where AgNPs were synthesized and optimized by using silver nitrate (AgNO₃) and the aqueous extract of Piper betle (Pbet) leaf as the reducing and capping agent. The stable and optimized process for the synthesis of Pbet-AgNPs was exposure of reaction mixture into the sunlight for 40 min, pH 9.0, and 2 mM AgNO₃ using 1:4 diluted Pbet leaf aqueous extract. The optimized Pbet-AgNPs were characterized by UV-visible spectroscopy, high-resolution field emission scanning electron microscopy (FE-SEM), X-ray diffractometry (XRD), and Fourier-transform infrared spectroscopy (FTIR). The prepared Pbet-AgNPs were spherical in shape with size in the range of 6-14 nm. These nanoparticles were stable for 6 months in aqueous solution at room temperature under dark conditions. The biogenic synthesized Pbet-AgNPs are found to have significant antifungal activity against plant pathogenic fungi, Alternaria brassicae and Fusarium solani. Synthesized Pbet-AgNPs potentially reduced the fungal growth in a dose-dependent manner. Microscopic observation of treated mycelium showed that Pbet-AgNPs could disrupt the mycelium cell wall and induce cellular permeability. Protein leakage assay supports these findings. Overall, this study revealed the efficacy of green synthesized AgNPs to control the plant fungal pathogens. Pbet leaves are a rich source of phenolic biomolecule(s). It was hypothesized that these biomolecule(s) mediated metal reduction reactions. In this context, the present work investigates the phytobiomolecule(s) of the aqueous extract of Pbet leaves using high-resolution liquid chromatography-mass spectroscopy (HR-LCMS) method. The analysis revealed that eugenol, chavicol, and hydroxychavicol were present in the Pbet aqueous extract.

Potential Allylpyrocatechol Derivatives as Antibacterial Agent Against Oral Pathogen of S. sanguinis ATCC 10,556 and as Inhibitor of MurA Enzymes: in vitro and in silico Study

BACKGROUND

Streptococcus sanguinis is Gram-positive bacteria that contribute to caries. Many antibacterial agents are resistant against bacteria so that the discovery of new antibacterial agents is a crucial issue. Mechanism of antibacterial agents by disrupting cell wall bacteria is a promising target to be developed. One of the enzymes contributing to the cell wall is MurA enzyme. MurA is an enzyme catalyzing the first step of peptidoglycan biosynthesis in the cell wall formation. Inhibiting MurA is an effective and efficient way to kill the bacteria. Source of bioactive compounds including the antibacterial agent can be found in natural product such as herbal plant. Piper betle L. was reported to contain active antibacterial compounds. However, there is no more information on the antibacterial activity and molecular mechanism of P. betle's compound against S. sanguinis.

PURPOSE

The study aims to identify antibacterial constituents of P. betle L. and evaluate their activities through two different methods including in vitro and in silico analysis.

MATERIALS AND METHODS

The antibacterial agent was purified by bioactivity-guided isolation with combination chromatography methods and the chemical structure was determined by spectroscopic methods. The in vitro antibacterial activity was evaluated by disc diffusion and dilution methods while the in silico study of a compound binds on the MurA was determined using PyRx program.

RESULTS

The antibacterial compound identified as allylpyrocatechol showed inhibitory activity against S. sanguinis with an inhibition zone of 11.85 mm at 1%, together with MIC and MBC values of 39.1 and 78.1 μg/mL, respectively. Prediction for molecular inhibition mechanism of allylpyrocatechols against the MurA presented two allylpyrocatechol derivatives showing binding activity of -5.4, stronger than fosfomycin as a reference with the binding activity of -4.6.

CONCLUSION

Two allylpyrocatechol derivatives were predicted to have a good potency as a novel natural antibacterial agent against S. sanguinis through blocking MurA activity that causes disruption of bacterial cell wall.