Risk Elements in Drinking Water of Koya City

Leaves of Annona muricata are commonly used for treating diabetes. This study was conducted to investigate the molecular mechanisms involved in the antidiabetic properties of leaves of Annona muricata. Leaves of Annona muricata were extracted separately with H2O, hydromethanol (50% methanol), methanol, ethylacetate, and n-butanol. Chemical characterization of the extracts was performed by spectrophotometry and Gas chromatography-Mass Spectrometry (GC-MS) techniques. Biological activity was determined by α-amylase inhibition assays and molecular docking. The hydromethanol extract had a total phenolics concentration of 117.00±0.59 µg GAE/mg extract whereas; flavonoids were most abundant in the n-butanol extract accounting for 29.34±8.87 µg QE/mg extract. The n-butanol extract had the best FRAP value of 41.17±0.57 Vit C eqv mM, which was significantly higher than the value of the vitamin C reference. Estimated IC50 for all the extracts did not differ significantly but was significantly higher than the reference compound quercetin. All extracts inhibited α-amylase in vitro albeit significantly lower than acarbose. The hydromethanol extract had the highest inhibitory activity (53.31 ± 0.33%). Furthermore, chemical profiling of the hydromethanol extract revealed the presence of a variety of bioactive compounds. In silico analysis by molecular docking of the compounds identified by GC-MS on α-amylase revealed that the compounds had robust molecular interactions orchestrated by H-bonding and hydrophobic interactions. From the results, it can be concluded that extracts of Annona muricata possess antioxidant phytochemicals that inhibit α-amylase. Therefore, the results justify the use of the plant for the treatment of diabetes.

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Chemical Profile, Antioxidant and Alpha-Amylase Inhibitory Activity of Leaves Extracts of Annona muricata: A Combined In vitro and In silico Study

Letters in Applied NanoBioScience ◽

10.33263/lianbs112.34703479 ◽

2021 ◽

Vol 11 (2) ◽

pp. 3470-3479

Keyword(s):

Molecular Docking ◽

Inhibitory Activity ◽

In Silico ◽

Molecular Mechanisms ◽

Hydrophobic Interactions ◽

In Silico Analysis ◽

Gas Chromatography Mass Spectrometry ◽

Annona Muricata ◽

Butanol Extract

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Antimicrobial Activity and Chemical Characterization of a Non-Polar Extract of Saffron Stamens in Food Matrix

Foods ◽

10.3390/foods10040703 ◽

2021 ◽

Vol 10 (4) ◽

pp. 703

Author(s):

Severino Zara ◽

Giacomo L. Petretto ◽

Alberto Mannu ◽

Giacomo Zara ◽

Marilena Budroni ◽

...

Keyword(s):

Chemical Composition ◽

Fatty Acid Content ◽

Chemical Characterization ◽

Antimicrobial Activities ◽

Added Value ◽

Gas Chromatography Mass Spectrometry ◽

Food Matrix ◽

Bacterial Strains ◽

By Products

The production of saffron spice generates large quantities of plant by-products: over 90% of the plant material collected is discarded, and a consideration fraction of this waste is plant stamens. This work investigated the chemical composition and the antimicrobial activities of the non-polar fraction extracted from four different saffron flower stamens. The chemical composition of ethereal extracts of the saffron stamens was qualitatively assessed by means of gas–chromatography-mass spectrometry (GC-MS) and nuclear magnetic resonance (NMR) analyses. These analyses revealed ethereal extracts to possess a high polyunsaturated fatty acid content. In vitro antibacterial activity of stamen extracts showed no large differences between Gram-positive and Gram-negative bacteria in terms of minimal inhibitory concentration (MIC). In food matrix microbial analysis of the bacterial strains belonging to the main foodborne pathogen species, including Staphylococcus aureus DSM 20231, Escherichia coli DSM 30083, and Listeria monocytogenes DSM 20600, using low-fat UHT milk, revealed a statistically significant reduction in the number of cells (particularly for E. coli and S. aureus with a complete elimination of the population of the two target bacteria following incubation in diethyl ether extracts of saffron stamen (DES) at high concentrations tested, both at 37 °C and 6 °C (for 48 h and 7 days, respectively). A synergic effect was observed when the pathogens were incubated at 6 °C with DES. This work shows these by-products to be excellent sources of bioactive compounds, which could be exploited in high-added-value products, such as food, cosmetics, and drugs.

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Screening marine algae metabolites as high-affinity inhibitors of SARS-CoV-2 main protease (3CLpro): an in silico analysis to identify novel drug candidates to combat COVID-19 pandemic

Applied Biological Chemistry ◽

10.1186/s13765-020-00564-4 ◽

2020 ◽

Vol 63 (1) ◽

Author(s):

Ghazala Muteeb ◽

Adil Alshoaibi ◽

Mohammad Aatif ◽

Md. Tabish Rehman ◽

M. Zuhaib Qayyum

Keyword(s):

Hydrophobic Interactions ◽

In Silico Analysis ◽

Salt Bridge ◽

Competitive Inhibitor ◽

Binding Energies ◽

Dynamics Simulation ◽

In Vivo Studies ◽

Energy Calculation

AbstractThe recent dissemination of SARS-CoV-2 from Wuhan city to all over the world has created a pandemic. COVID-19 has cost many human lives and created an enormous economic burden. Although many drugs/vaccines are in different stages of clinical trials, still none is clinically available. We have screened a marine seaweed database (1110 compounds) against 3CLpro of SARS-CoV-2 using computational approaches. High throughput virtual screening was performed on compounds, and 86 of them with docking score < − 5.000 kcal mol−1 were subjected to standard-precision docking. Based on binding energies (< − 6.000 kcal mol−1), 9 compounds were further shortlisted and subjected to extra-precision docking. Free energy calculation by Prime-MM/GBSA suggested RC002, GA004, and GA006 as the most potent inhibitors of 3CLpro. An analysis of ADMET (Absorption, Distribution, Metabolism, Excretion, and Toxicity) properties of RC002, GA004, and GA006 indicated that only RC002 (callophysin A, from red alga Callophycus oppositifolius) passed Lipinski’s, Veber’s, PAINS and Brenk’s filters and displayed drug-like and lead-like properties. Analysis of 3CLpro-callophysin A complex revealed the involvement of salt bridge, hydrogen bonds, and hydrophobic interactions. callophysin A interacted with the catalytic residues (His41 and Cys145) of 3CLpro; hence it may act as a mechanism-based competitive inhibitor. Docking energy and docking affinity of callophysin A towards 3CLpro was − 8.776 kcal mol−1 and 2.73 × 106 M−1, respectively. Molecular dynamics simulation confirmed the stability of the 3CLpro-callophysin A complex. The findings of this study may serve as the basis for further validation by in vitro and in vivo studies.

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Prediction Mechanism of Nevadensin as Antibacterial Agent against S. sanguinis: In vitro and In silico Studies

Combinatorial Chemistry & High Throughput Screening ◽

10.2174/1386207324666210707104440 ◽

2021 ◽

Vol 24 ◽

Author(s):

Aldina Amalia Nur Shadrina ◽

Yetty Herdiyati ◽

Ika Wiani ◽

Mieke Hemiawati Satari ◽

Dikdik Kurnia

Keyword(s):

Antibacterial Activity ◽

Molecular Docking ◽

Dental Caries ◽

Binding Affinity ◽

In Silico ◽

Antibacterial Agent ◽

In Silico Analysis ◽

Dna Gyrase ◽

Silico Analysis

Background: Streptococcus sanguinis can contribute to tooth demineralization, which can lead to dental caries. Antibiotics used indefinitely to treat dental caries can lead to bacterial resistance. Discovering new antibacterial agents from natural products like Ocimum basilicum will help combat antibiotic resistance. In silico analysis (molecular docking) can help determine the lead compound by studying the molecular interaction between the drug and the target receptor (MurA enzyme and DNA gyrase). It is a potential candidate for antibacterial drug development. Objective: The research objective is to isolate the secondary metabolite of O. basilicum extract that has activity against S. sanguinis through in vitro and in silico analysis. Methods: n-Hexane extract of O. basilicum was purified by combining column chromatography with bioactivity-guided. The in vitro antibacterial activity against S. sanguinis was determined using the disc diffusion and microdilution method, while molecular docking simulation of nevadensin (1) with MurA enzyme and DNA gyrase was performed used PyRx 0.8 program. Results: Nevadensin from O. basilicum was successfully isolated and characterized by spectroscopic methods. This compound showed antibacterial activity against S. sanguinis with MIC and MBC values of 3750 and 15000 μg/mL, respectively. In silico analysis showed that the binding affinity to MurA was -8.5 Kcal/mol, and the binding affinity to DNA gyrase was -6.7 Kcal/mol. The binding of nevadensin-MurA is greater than fosfomycin-MurA. Otherwise, Nevadensin-DNA gyrase has a weaker binding affinity than fluoroquinolone-DNA gyrase and chlorhexidine-DNA gyrase. Conclusion: Nevadensin showed potential as a new natural antibacterial agent by inhibiting the MurA enzyme rather than DNA gyrase.

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Experimental and Computational Insights into Bis-indolylmethane Derivatives as Potent Antimicrobial Agents Inhibiting 2,2-dialkylglycine Decarboxylase

Current Enzyme Inhibition ◽

10.2174/1573408017666210914105731 ◽

2021 ◽

Vol 17 ◽

Author(s):

Dnyaneshwar T. Nagre ◽

Bapu R. Thorat ◽

Suraj N. Mali ◽

Mazhar Farooqui ◽

Brijmohan Agrawal

Keyword(s):

Antimicrobial Agents ◽

In Silico Analysis ◽

Proton Nuclear Magnetic Resonance ◽

Gas Chromatography Mass Spectrometry ◽

Amino Acid Residues ◽

Standard Drug ◽

H Nmr ◽

Highly Active ◽

Dialkylglycine Decarboxylase

Background: A series of bis(indolyl)methanes (3a-3o) have been synthesized using a greener and new approach using the reaction of different substituted aldehydes and indole in the presence of an easily available and biodegradable base such as piperidine in acetic acid at room temperature and characterized with UV (Ultraviolet-visible spectroscopy), Gas chromatography-mass spectrometry (GC-MS), Proton nuclear magnetic resonance (H-NMR), and Fourier transform infrared spectroscopy (FTIR). Methods: All 15 newly synthesized compounds (3a-3o) were subjected to in-vitro anti-microbial activity determination and compared with the known standard drug ciprofloxacin (1-2 µg/mL). Our in-silico analysis on the target protein, pdb id: 1d7u suggested that these analogues would be highly active against bacterial targets and thus, would act as good antimicrobial agents. Results: All 15 newly synthesized compounds (3a-3o) displayed potent activity on various experimental microbial strains (1.0-1.4 µg/mL). Compound, 3k was obtained as the best docked compound against common bacterial target enzyme, (pdb id:1d7u). The standard, Ciprofloxacin, retained the docking score of -111.3 Kcal/mol with similar binding amino acid residues (LYS272 (Pi-cation); ALA A:245 (Pi-sigma); TRP A:138 (Pi-Pi); ALA A:112; and MET A:141 (Pi-alkyl)) as of inbound. Conclusion : We believe that our current study would shed more light on the development of potent bis(indolyl)methanes as antimicrobial agents.

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Molecular docking and pharmacokinetic screening of eucalyptol (1,8 cineole) from eucalyptus essential oil against SARS-CoV-2

Notulae Scientia Biologicae ◽

10.15835/nsb12210711 ◽

2020 ◽

Vol 12 (3) ◽

pp. 536-545

Author(s):

Arun D. SHARMA ◽

Inderjeet KAUR

Keyword(s):

Molecular Docking ◽

Essential Oil ◽

Active Site ◽

In Silico ◽

Hydrophobic Interactions ◽

Rna Virus ◽

In Silico Analysis ◽

Active Site Residues ◽

Virus Family

SARS-CoV-2 (COVID-19), member of corona virus family, is a positive single stranded RNA virus. Due to lack of drugs it is spreading its tentacles across the world. Being associated with cough, fever, and respiratory distress, this disease caused more than 15% mortality worldwide. Mpro/3CLpro has recently been regarded as a suitable target for drug design due to its vital role in virus replication. The current study focused on the inhibitory activity of eucalyptol (1,8 cineole), an essential oil component from eucalyptus oil, against Mpro/3CLprofrom SARS-CoV-2. Till date there is no work is undertaken on in-silico analysis of this compound against Mpro/3CLproof SARS-CoV-2. Molecular docking studies were conducted by using 1-click dock tool and Patchdock analysis. In-silico absorption, distribution, metabolism, excretion and toxicity (ADMET) profile were also studied. The calculated parameters such as docking score indicated effective binding of eucalyptol to COVID-19 Mpro protein. Active site prediction revealed the involvement of active site residues in ligand binding. Interactions results indicated that, Mpro/3CLpro/eucalyptol complexes forms hydrophobic interactions. ADMET studies provided guidelines and mechanistic scope for identification of potent anti-COVID 19 drug. Therefore, eucalyptol may represent potential herbal treatment to act as COVID-19 Mpro/3CLproinhibitor, a finding which must be validated in vivo.

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Identification of Potential Dipeptidyl Peptidase (DPP)-IV Inhibitors among Moringa oleifera Phytochemicals by Virtual Screening, Molecular Docking Analysis, ADME/T-Based Prediction, and In Vitro Analyses

Molecules ◽

10.3390/molecules25010189 ◽

2020 ◽

Vol 25 (1) ◽

pp. 189 ◽

Cited By ~ 5

Author(s):

Yang Yang ◽

Chong-Yin Shi ◽

Jing Xie ◽

Jia-He Dai ◽

Shui-Lian He ◽

...

Keyword(s):

Molecular Docking ◽

Virtual Screening ◽

Moringa Oleifera ◽

Molecular Mechanisms ◽

Dipeptidyl Peptidase ◽

In Vivo Evaluation ◽

Docking Analysis ◽

Dpp Iv ◽

Molecular Docking Analysis

Moringa oleifera Lam. (MO) is called the “Miracle Tree” because of its extensive pharmacological activity. In addition to being an important food, it has also been used for a long time in traditional medicine in Asia for the treatment of chronic diseases such as diabetes and obesity. In this study, by constructing a library of MO phytochemical structures and using Discovery Studio software, compounds were subjected to virtual screening and molecular docking experiments related to their inhibition of dipeptidyl peptidase (DPP-IV), an important target for the treatment of type 2 diabetes. After the four-step screening process, involving screening for drug-like compounds, predicting the absorption, distribution, metabolism, excretion, and toxicity (ADME/T) of pharmacokinetic properties, LibDock heatmap matching analysis, and CDOCKER molecular docking analysis, three MO components that were candidate DPP-IV inhibitors were identified and their docking modes were analyzed. In vitro activity verification showed that all three MO components had certain DPP-IV inhibitory activities, of which O-Ethyl-4-[(α-l-rhamnosyloxy)-benzyl] carbamate (compound 1) had the highest activity (half-maximal inhibitory concentration [IC50] = 798 nM). This study provides a reference for exploring the molecular mechanisms underlying the anti-diabetic activity of MO. The obtained DPP-IV inhibitors could be used for structural optimization and in-depth in vivo evaluation.

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Phosphodiesterase-1 Inhibitory Activity of Two Flavonoids Isolated fromPistacia integerrimaJ. L. Stewart Galls

Evidence-based Complementary and Alternative Medicine ◽

10.1155/2015/506564 ◽

2015 ◽

Vol 2015 ◽

pp. 1-6 ◽

Cited By ~ 10

Author(s):

Abdur Rauf ◽

Muhammad Saleem ◽

Ghias Uddin ◽

Bina S. Siddiqui ◽

Haroon Khan ◽

...

Keyword(s):

Inhibitory Activity ◽

In Silico ◽

Molecular Mechanisms ◽

Methanolic Extract ◽

Chemical Constituents ◽

Folk Medicine ◽

Chemical Characterization ◽

Active Constituents ◽

Isolation And Characterization

Pistacia integerrimais one of twenty species among the genusPistacia. Long horn-shaped galls that develop on this plant are harvested and used in Ayurveda and Indian traditional medicine to make “karkatshringi”, a herbal medicine used for the treatment of asthma and different disorders of respiratory tract. However, until now, the molecular mechanisms of action of “karkatshringi” and its chemical characterization are partially known. This study deals with the isolation and characterization of the active constituents from the methanolic extract ofP. integerrimagalls and it was also oriented to evaluatein vitroandin silicotheir potential enzymatic inhibitory activity against phosphodiesterase-1 (PDE1), a well-known enzyme involved in airway smooth muscle activity and airway inflammation. Our results showed that the methanolic extract ofP. integerrimagalls and some of its active constituents [naringenin (1) and 3,5,7,4′-tetrahydroxy-flavanone (2)] are ablein vitroto inhibit PDE1 activity (59.20 ± 4.95%, 75.90 ± 5.90%, and 65.25 ± 5.25%, resp.) and demonstratein silicoan interesting interaction with this enzymatic site. Taken together, our results add new knowledge of chemical constituents responsible for the biological activity ofP. integerrimaand contextually legitimate the use of this plant in folk medicine.

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Molecular Docking and Drug-Likeness for the Identification of Inhibitory Action of Acetogenins from Annona muricata as Potential Anticancer against Hypoxia Inducible Factor 1 Alpha

Biomedical & Pharmacology Journal ◽

10.13005/bpj/1492 ◽

2018 ◽

Vol 11 (3) ◽

pp. 1301-1307

Author(s):

Supri I. Handayani ◽

Rahmiati Rahmiati ◽

Lisnawati Rahmadi ◽

Rosmalena Rosmalena ◽

Vivitri D. Prasasty

Keyword(s):

Molecular Docking ◽

Hypoxia Inducible Factor ◽

Binding Energies ◽

Binding Modes ◽

Annona Muricata ◽

Chemical Structures ◽

Hypoxia Inducible Factor 1 ◽

Human Cancers

Hypoxia inducible factor 1 alpha (HIF-1α) regulates cell growth and differentiation which is implicated in human cancers. HIF-1α activates its cascade carcinogenesis mechanism in cancer cells. It is well-understood that signaling is initiated by HIF-1α receptor. Overexpression of HIF-1α is associated with several different human cancers, including breast cancer, lung cancer and colon cancer. Thus, HIF-1α becomes potential target of therapeutic approach in developing HIF-1α inhibitors. The aim of this research is to investigate potential inhibitors which are known as Acetogenins (AGEs) isolated from Annona muricata against HIF-1α. In order to achieve this goal, chemical structures of all compounds were retrieved from PubChem database. Molecular docking was performed by AutoDock Vina program and the resulting binding modes were analyzed with AutoDock Tools program. Among all the compounds, murihexocin A showed the best binding modes compared to other two inhibitors based on the lowest binding energies (LBE = -7.9 kcal/mol) as high as gefitinib. This was indicating that murihexocin A has favorable interaction with the essential amino acid residues at catalytic site of HIF-1α. Drug-likeness calculation of AGEs were also performed. These in silico results could be beneficial as a compound model for further studies in-vitro and in-vivo.

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GAS CHROMATOGRAPHY–MASS SPECTROMETRY ANALYSIS, IN VITRO ACTIVITIES, AND IN SILICO MOLECULAR DOCKING OF MAJOR COMPONENTS OF MICHELIA ALBA DC ESSENTIAL OIL AND SCENTED EXTRACTS

Asian Journal of Pharmaceutical and Clinical Research ◽

10.22159/ajpcr.2018.v11i12.29043 ◽

2018 ◽

Vol 11 (12) ◽

pp. 499

Author(s):

Thongchai Khammee ◽

Amornmart Jaratrungtawee ◽

Mayoso Kuno

Keyword(s):

Mass Spectrometry ◽

Gas Chromatography ◽

Molecular Docking ◽

Essential Oil ◽

Binding Energies ◽

Mass Spectrometry Analysis ◽

Gas Chromatography Mass Spectrometry ◽

Spectrometry Analysis ◽

Chromatography Mass Spectrometry

Objective: The essential oil and scented extracts of Michelia alba DC. were analyzed by gas chromatography–mass spectrometry (GC–MS) and investigated for antidiabetic activities in vitro and in silico.Methods: The identification of steam distilled essential oil and scented extracts of M. alba was performed by GC–MS on the Agilent 7890A chromatograph couple with GC-7000 Mass Triple Quadrupole. The extractions have been evaluated the antidiabetic activities by alpha-amylase (α-amylase) assay using starch as substrates. In addition, computational molecular docking analysis of significant components was studied to understanding how selected compounds interacted with α-amylase using AutoDock 4.2.Results: The yields of M. alba of steam distilled essential oil and solvent extractions including hexane, diethyl ether, and dichloromethane were 0.16%, 0.02%, 0.47%, and 0.92%, respectively. GC–MS analysis of essential oil revealed that the main component was monoterpenoids β-linalool (65.03%). Meanwhile, 2-methylbutanoic acid was a primary in hexane extract (36.54%) and dichloromethane extract (33.07%). In the case of ether extract, the primary compound was β-linalool (37.32%) same as in essential oil. The antidiabetic activities evaluation demonstrates that essential oil and scented extracts have shown promising α-amylase inhibition activity. Essential oil from steam distillation revealed the best inhibition potential with a half maximal inhibitory concentration value of 0.67±4.7 mg/ml and their significant components demonstrated negative binding energies, indicating a high affinity to the α-amylase-binding site using molecular docking simulation.Conclusion: Data from this study suggest that essential oil and scented extracts of M. alba DC possess in vitro α-amylase activities and can be used for therapy of diabetes.

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