Molecular docking, molecular dynamics, MM/PBSA approaches and bioactivity studies of nepetanudoside B isolated from endemic Nepeta aristata.

Nepetanudoside B (NNB) was isolated from aerial parts of endemic Nepeta aristata crude extract (CH3OH-CHCl3) using silica gel (n-hexane, methanol, ethyl acetate, and dichlorometane, respectively) and sephadex LH-20 (65% Methanol-35% Chloroform) column chromatographies. Preparative-HPLC was used to purify NNB after activity-guided isolation of methanol sub-fractions with enzyme inhibitory and DNA protective properties. The NNB was determined using 1H,13C, COSY, HSQC, HMBC, and LC-MS/MS. The study compared the effects of NNB with conventional drugs in terms of its ability to inhibit enzymes such as urease, α-amylase, carbonic anhydrase (CA), lipase, α-glucosidase, and tyrosinase, as well as its ability to protect DNA. Enzyme kinetic and molecular docking were also used to evaluate this. NNB exhibited the best inhibitory activity on urease (1.28 ± 0.00 µg/mL), lipase (5.83 ± 0.10 µg/mL), BChE (3.73 ± 0.46 µg/mL), tyrosinase (7.39 ± 0.00 µg/mL), α-glucosidase (10.95 ± 0.00 µg/mL), α-amylase (22.11 ± 1.03 µg/mL) and AChE (25.68 ± 3.32 µg/mL), respectively. NNB has higher MolDock scores with binding energy in α-glucosidase (-233) and BChE (-8.90 kcal/mol). In enzyme kinetics studies, it was determined that urease, AChE, α-glucosidase, lipase, and CA were non-competitive , while BChE and tyrosinase were competitive inhibition mechanisms. Their Ki values were calculated as 0.09, 0.24, 0.09, 0.10, 0.08, 0.05, and 0.07 mM, respectively. Molecular dynamics simulation studies were performed for the interactions of NNB-BChE with MM/PBSA binding free energey RMSD, RMSF, Rg, SASA, and also the number of hydrogen bonds was calculated. The suitability and effectiveness of NNB have been proven in the food and pharmaceutical industries. The NNB molecule may lead to development studies as a BChE inhibitor.Communicated by Ramaswamy H. Sarma.

DNA protection, molecular docking, antioxidant, antibacterial, enzyme inhibition, and enzyme kinetic studies for parietin, isolated from Xanthoria parietina (L.) Th. Fr.

Parietin was isolated from Xanthoria parietina (L.) Th. Fr.' (methanol:chloroform) extract, using a silica column. 13 C NMR and 1H NMR were used to confirm the structure of the isolated parietin. For the first time, parietin was investigated for its antioxidant, antibacterial and DNA protective activities. Molecular docking was carried out to determine the binding affinity and interactions between the enzymes and our molecule. Inhibition and kinetic mechanism studies for the action of the enzymes were performed too. Parietin exhibited high metal chelating activity. The MIC values of parietin were sufficient to inhibit different bacterial strains; E. coli, P. aeruginosa, K. pneumoniae and S. aureus. Molecular docking applications exhibited that acetylcholinesterase (AChE), butyrylcholinesterase (BChE), lipase, and tyrosinase have high potential for binding with the parietin. Especially, the parietin's highest binding affinity was recorded with AChE and tyrosinase. These results were confirmed by the inhibition and kinetics results, where, parietin observed a potent inhibition with an IC50 values between 0.013-0.003 µM. Moreover, parietin acts' as a non-competitive inhibitor against AChE, BChE, and lipase, and as a competitive inhibitor against tyrosinase with a high rate of inhibition stability. The promising biological properties of parietin revealed its effectiveness in terms of suitability in the food and pharmaceutical industries.Communicated by Ramaswamy H. Sarma.

DNA protection, molecular docking, enzyme inhibition and enzyme kinetic studies of 1,5,9-epideoxyloganic acid isolated from Nepeta aristata with bio-guided fractionation.

1,5,9-epideoxyloganic acid (ELA) was isolated from the aerial parts of endemic Nepeta aristata Boiss Et Kotschy Ex Boiss crude extract (methanol:chloroform) using silica gel (hexane, chloroform, ethyl acetate, and methanol) and sephadex LH-20 (65% methanol-35% chloroform) columns. Activity-guided isolation was performed on methanol sub-fractions with DNA protection and enzyme inhibitory activities, and then the ELA was purified by prep-HPLC. The ELA structure, bio-guided isolate, was determined via 1H NMR, 13C NMR, and MS spectrometry. ELA's enzyme inhibition and DNA protection activities were investigated and compared with standard drugs. The inhibition capacity of ELA against acetylcholinesterase (AChE), butyrylcholinesterase (BChE), urease, carbonic anhydrase (CA), α-glucosidase, α-amylase, lipase, and tyrosinase enzymes was evaluated by kinetic and molecular docking results. The ELA displayed the best inhibitory activity on AChE, BChE, α-glucosidase, urease, α-amylase, and tyrosinase with IC50 values of 2.53 ± 0.27, 3.75 ± 0.11, 3.98 ± 0.07, 4.40 ± 0.01, 6.43 ± 0.54 and 7.39 ± 0.00 µg/mL, respectively. ELA acted as a competitive inhibitor against BChE and α-glucosidase and a non-competitive inhibitor against AChE. The ELA's binding affinity values on AChE, BChE, and α-glucosidase were -7.70, -8.50, and -8.30 kcal/mol, respectively. DNA protection activity of the ELA molecule was determined as 57.53% for form I and 53.57% for form II. In conclusion, the inhibitory activity of ELA demonstrated its effectiveness in terms of its suitability in the pharmaceutical industry.Communicated by Ramaswamy H. Sarma.

Determination of antioxidant, DNA protection, enzyme inhibition potential and molecular docking studies of a biomarker ursolic acid in Nepeta species.

Ursolic acid (UA), which has many biological properties such as anti-cancer, anti-inflammatory and antioxidant, and regulates some pharmacological processes, has been isolated from the flowers, leaves, berries and fruits of many plant species. In this work, UA was purified from the methanol-chloroform crude extract of Nepeta species (N. aristata, N. baytopii, N. italica, N. trachonitica, N. stenantha) using a silica gel column with chloroform or ethyl acetate solvents via bioactivity-guided isolation. The most active sub-fractions were determined under bioactivities using antioxidant and DNA protection activities and enzyme inhibitions. UA was purified from these fractions and its structure was elucidated by NMR spectroscopy techniques. The highest amount of UA was found in N. stenantha (8.53 mg UA/g), while the lowest amount of UA was found in N. trachonitica (1.92 mg UA/g). The bioactivities of UA were evaluated with antioxidant and DNA protection activities, enzyme inhibitions, kinetics and interactions. The inhibition values (IC50) of α-amylase, α-glucosidase, urease, CA, tyrosinase, lipase, AChE, and BChE were determined between 5.08 and 181.96 µM. In contrast, Ki values of enzyme inhibition kinetics were observed between 0.04 and 0.20 mM. In addition, Ki values of these enzymes for enzyme-UA interactions were calculated as 0.38, 0.86, 0.45, 1.01, 0.23, 0.41, 0.01 and 2.24 µM, respectively. It is supported that UA can be widely used as a good antioxidant against oxidative damage, an effective DNA protector against genetic diseases, and a suitable inhibitor for metabolizing enzymes.Communicated by Ramaswamy H. Sarma.

Kinetic Studies, Antioxidant Activities, Enzyme Inhibition Properties and Molecular Docking of 1,3-Dihydro-1,3-Dioxoisoindole Derivatives.

The acid catalyzed hydrolysis of the N-(p-substitutedphenyl) phthalimides in three different acids was investigated at 50.0±0.1°C. Two different antioxidant activity tests as DPPH• and ABTS•+ scavenging activities, and three various enzyme inhibition activity tests as urease, acetylcholinesterase (AChE), and butyrylcholinesterase (BChE) inhibition activities, were applied. Compound 3c (2.03 µg/mL ) has higher antioxidant activity than other compounds and standards according to DPPH test. In AChE assay, compounds 3a and 3b (13.13 and 9.59 µg/mL) has higher enzyme inhibition activity than the standard Galantamine (14.37 µg/mL). In BChE and urease tests, all compounds (6.84-13.60 and 10.49-17.73 µg/mL) have higher enzyme inhibition activity than the standard Galantamine (49.40 µg/mL) and thiourea (26.19 µg/mL), respectively. The molecule interaction for each of the three compounds with the active sites of AChE, BChE, and urease enzymes was examined via molecular docking simulations.

Evaluation of Bioactivities, Phenolic and Metal Content of Ten Wild Edible Mushrooms from Western Black Sea Region of Turkey.

In this study, we investigated the phenolic profile, metal concentrations, and antioxidant and antimicrobial activities of edible mushrooms collected from Sinop, Turkey: Amanita caesarea, Boletus edulis, Grifola frondosa, Hydnum repandum, Lactarius deliciosus, L. piperatus, L. volemus, Laetiporus sulphureus, Pleurotus ostreatus, and Ramaria flava. The mycochemical contents of R. flava, L. sulphureus, A. caesarea, L. deliciosus, and B. edulis were high. The cobalt (Co), cadmium (Cd), nickel (Ni), and lead (Pb) contents of mushrooms were between < 0.54 and 8.97 ppm. L. deliciosus had effective total antioxidant activity (7990 µmol α-tocopherol eq./g), ABTS·+ (2,2'-azino-bis-(3-ethylbenzthiazoline-6-sulphonic acid)) scavenging activity scavenging activity (EC50:7.87 µg/mL), and free-radical scavenging activity (EC50: 0.018 µg/mL) due to high levels of phenol, flavonoid, ß-carotene, and lycopene. B. edulis demonstrated strong reducing power (A0.5: 11.89 µg/mL), inhibition of linoleic acid peroxidation (EC50:0.0016 µg/mL), and H2O2 scavenging activity (EC50: 0.28 µg/mL). A. caesarea and R. flava showed the best metal chelating activity (EC50:44.31 µg/mL) and superoxide anion scavenging activity (EC50:0.18 µg/mL), respectively. Inhibition zone values of A. caesarea extract were detected between 8.1 and 27.1 mm for B. cereus. Our results show that mushrooms are promising dietary sources for natural prevention of many infectious diseases and that they act as antioxidant agents.

Phytochemical Constituents, ChEs and Urease Inhibitions, Antiproliferative and Antioxidant Properties of Elaeagnus umbellata Thunb.

AIM AND OBJECTIVE: Due to the common ethnopharmacological used or scientifically examined biochemical properties, Elaeagnaceae family, Elaeagnus umbellate (Thunb.) (EU, Guz yemisi) was worth investigating. MATERIALS AND METHODS: In this investigation, we revealed antioxidant, antiproliferative and enzyme inhibition activities of the water, methanol, ethanol, acetone, ethyl acetate and hexane extracts of EU as well as the contents of their phenolic, flavonoid, anthocyanin, ascorbic acid, lycopene and ß- carotene. The antioxidant activity was screened by total antioxidant (phosphomolybdenum), inhibition of linoleic acid peroxidation, reducing power, 2-deoxyribose degradation assay, H2O2 scavenging and metal chelating activities of the samples were tested in vitro. Additionally, the scavenging activities of the extracts were determined against 1,1-diphenyl-2-picrylhydrazyl (DPPH˙), 2,2-azino-bis(3-ethylbenzothiazloine-6-sulfonicacid (ABTS˙+), superoxide anion and peroxide radicals. The samples were determined for their inhibitory activities against urease, acetylcholinesterase (AChE) and butyrylcholinesterase (BuChE). In vitro, antiproliferative activities of six different extracts were tested using the xCELLigence system against HeLa and HT29 cell lines. RESULTS: The antioxidant activities of the extracts were found higher than standard antioxidants. The water extracts of fruit and leaf showed the best antioxidant activity. In inhibition assays of urease, AChE and BuChE, all extracts exhibited remarkable inhibition potential. Ethyl acetate extracts, especially, showed better inhibition capacity. It was found that the antioxidant activities of the extracts presented consistently with their chemical contents. The antiproliferative activities of leaf extracts were more effective than the fruit extracts. The chromatographic methods were applied to the different solvents to analyses phenolic secondery metabolites. It was found that fumaric acid, 4- hydroxybenzoic acid, rutin and quercetin-3-ß-D-glucoside, neohesperidin, hesperidin determined to have higher contents all the extracts. CONCLUSION: EU can be suggested as a potential natural source of antioxidants appropriate for utilization in nutritional/pharmaceutical fields.