scholarly journals Molecular docking analysis and evaluation of the antibacterial and antioxidant activities of the constituents of Ocimum cufodontii

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Muhdin Aliye ◽  
Aman Dekebo ◽  
Hailemichael Tesso ◽  
Teshome Abdo ◽  
Rajalakshmanan Eswaramoorthy ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Essential Oil ◽  
Hydrophobic Interactions ◽  
Antioxidant Activities ◽  
Reducing Power ◽  
Principal Component ◽  
Inhibition Zone ◽  
Hexane Extract ◽  
Docking Analysis ◽  
Molecular Docking Analysis

AbstractOcimum cufodontii ((Lanza) A.J.Paton) has been traditionally used in Ethiopia against bacteria. The extracts of the leaves and roots of O. cufodontii after silica gel column chromatography furnished compounds 1–5, compounds 3 and 4 are new natural products. The oil from the hydro-distillation of the leaves, after analyzed with GC–MS, has led to the identification of β-caryophyllene as a principal component, suggesting the essential oil as medicine and spices to enhance the taste of food. The constituents of O. cufodontii were assessed for their antibacterial activity against E. coli, K. pneumonia, S. typhymurium and S. aureus. The best activity was displayed against S. aureus by the hexane extract of the roots, compound 4, and the essential oil with an inhibition zone of 17, 15, and 19 mm, respectively. Molecular docking analysis revealed that compound 1 has better docking efficiency and forms hydrophobic interactions with five amino acids (ARG192, PHE196, GLU185, GLU193, and LYS189). This suggests that the compounds may act as potential inhibitors of DNA gyrase. The constituents were also assessed for their antioxidant activities using DPPH, ferric thicyanate and ferric reducing power assay. The hexane extracts of the roots inhibited the DPPH radical and peroxide formation by 90.5 and 83%, respectively, suggesting the potential of the extract as an antioxidant. Furthermore, the hexane extract of the roots of O. cufodontii exhibited the maximum reducing power compared with the EtOAc and methanol extracts. Hence, the activity displayed herein indicated as the plant has great potential as a remedy for diseases caused by bacteria and radicals.

scholarly journals Free and Bound Phenolics of Buckwheat Varieties: HPLC Characterization, Antioxidant Activity, and Inhibitory Potency towards α-Glucosidase with Molecular Docking Analysis

Antioxidants ◽  
2019 ◽  
Vol 8 (12) ◽  
pp. 606 ◽  
Author(s):  
Huilan Zhu ◽  
Sixin Liu ◽  
Linling Yao ◽  
Lu Wang ◽  
Congfa Li
Keyword(s):  
Molecular Docking ◽  
Antioxidant Activities ◽  
Pearson Correlation ◽  
Principal Component ◽  
Free Form ◽  
Inhibitory Effects ◽  
Docking Analysis ◽  
Free Phenolics ◽  
Bound Phenolics ◽  
Molecular Docking Analysis

Free and bound phenolic fractions from six buckwheat varieties were investigated for their compositions, antioxidant activities, and inhibitory effects on α-glucosidase. The results showed that different buckwheat varieties have significant differences in phenolic/flavonoid contents, and these contents were found in higher quantities in free form than in bound form. HPLC results revealed that rutin, quercetin, and kaempferol-3-O-rutinoside were the most abundant components in free and bound forms, whereas dihydromyricetin was found only in the bound form. Free phenolics showed higher antioxidant activities of DPPH, ABTS+, OH•, and FRAP than those of bound phenolics. Strong inhibitory effects against α-glucosidase by the free/bound phenolic fractions were found in all buckwheat varieties, and free phenolics showed stronger α-glucosidase inhibition than that of the corresponding bound phenolics. More importantly, the main phenolic compounds observed in the buckwheat varieties were subjected to molecular docking analysis to provide insight into their interactions with α-glucosidase. The contributions by individual phenolics to the observed variation was analysed by Pearson correlation coefficient analysis and principal component analysis. The present study provides a comprehensive comparison for the phenolic fractions of buckwheat varieties and identify the main contributors to antioxidant and α-glucosidase inhibitory activity.

scholarly journals Synthesis, in silico molecular docking analysis, pharmacokinetic properties and evaluation of antibacterial and antioxidant activities of fluoroquinolines

BMC Chemistry ◽  
2022 ◽  
Vol 16 (1) ◽  
Author(s):  
Mona Fekadu ◽  
Digafie Zeleke ◽  
Bayan Abdi ◽  
Anuradha Guttula ◽  
Rajalakshmanan Eswaramoorthy ◽  
...  
Keyword(s):  
Molecular Docking ◽  
In Silico ◽  
Antioxidant Activities ◽  
Biological Activities ◽  
Dna Gyrase ◽  
Topoisomerase Iiα ◽  
Docking Analysis ◽  
E Coli ◽  
In Silico Molecular Docking ◽  
Molecular Docking Analysis

Abstract Background Quinolines have demonstrated various biological activities such as antimalarial, antibacterial and anticancer. Hence, compounds with such scaffold have been used as lead in drug development. This project is, therefore, aimed to synthesis and evaluates some biological activities of quinoline analogs. Methods 2-Chloro-7-fluoroquinoline-3-carbaldehydes were synthesized by the application of Vilsmeier–Haack reaction. The chlorine in the fluoroquinoline-3-carbaldehyde was replaced with various nucleophiles. The aldehyde functional group was also converted to carboxylic acid and imine groups using oxidizing agent and various amines, respectively. The structures of the compounds synthesized were characterized by spectroscopic methods. Disc diffusion and DPPH assays were used to evaluate the antibacterial and antioxidant activities, respectively. The in silico molecular docking analysis of the synthesized compounds were done using AutoDock Vina against E. coli DNA Gyrase B and human topoisomerase IIα. The drug likeness properties were assessed using SwissADME and PreADMET. Results Nine novel quinoline derivatives were synthesized in good yields. The in vitro antibacterial activity of the synthesized compounds was beyond 9.3 mm inhibition zone (IZ). Compounds 4, 5, 6, 7, 8, 10, 15, and 16 exhibited activity against E. coli, P. aeruginosa, S. aureus and S. pyogenes with IZ ranging from 7.3 ± 0.67 to 15.3 ± 0.33 mm at 200 μg/mL. Compound 9 displayed IZ against three of the bacterial strains except S. aureus. The IC50 for the radical scavenging activity of the synthesized compounds were from 5.31 to 16.71 μg/mL. The binding affinities of the synthesized compounds were from − 6.1 to − 7.2 kcal/mol against E. coli DNA gyrase B and − 6.8 to − 7.4 kcal/mol against human topoisomerase IIα. All of the synthesized compounds obeyed Lipinski’s rule of five without violation. Conclusion Compounds 4, 5, 6, 7, 8, 10, 15, and 16 displayed activity against Gram positive and Gram negative bacterial strains indicating that these compounds might be used as broad spectrum bactericidal activity. Compound 8 (13.6 ± 0.22 mm) showed better IZ against P. aeruginosa compared with ciprofloxacin (10.0 ± 0.45 mm) demonstrating the potential of this compound as antibacterial agent against this strain. Compounds 5, 6, 7, 8, 9 and 10 showed comparable binding affinities in their in silico molecular docking analysis against E. coli DNA gyrase B. All of the synthesized compounds also obeyed Lipinski’s rule of five without violation which suggests these compounds as antibacterial agents for further study. Compounds 7 and 8 were proved to be a very potent radical scavenger with IC50 values of 5.31 and 5.41 μg/mL, respectively. Compound 5, 6, 8, 10 and 16 had comparable binding affinity against human topoisomerase IIα suggesting these compounds as a possible candidate for anticancer drugs.

scholarly journals Comparative molecular docking analysis of essential oil constituents as elastase inhibitors

2012 ◽  
Vol 8 (10) ◽  
pp. 457-460 ◽  
Author(s):  
Periyasamy Sivamani ◽  
Ganesan Singaravelu ◽  
Venkatesan Thiagarajan ◽  
Tamilarasu Jayalakshmi ◽  
Gopal Ramesh Kumar
Keyword(s):  
Molecular Docking ◽  
Essential Oil ◽  
Docking Analysis ◽  
Molecular Docking Analysis

scholarly journals Cell Growth Stimulation, Cell Cycle Alternation, and Anti-Apoptosis Effects of Bovine Bone Collagen Hydrolysates Derived Peptides on MC3T3-E1 Cells Ex Vivo

Molecules ◽  
2020 ◽  
Vol 25 (10) ◽  
pp. 2305
Author(s):  
Jianing Wang ◽  
Junli Liu ◽  
Yanchuan Guo
Keyword(s):  
Cell Cycle ◽  
Molecular Docking ◽  
Bone Growth ◽  
Hydrophobic Interactions ◽  
Bone Collagen ◽  
Bovine Bone ◽  
Docking Analysis ◽  
Egfr Signaling Pathway ◽  
Collagen Hydrolysates ◽  
Molecular Docking Analysis

Bovine bone collagen hydrolysates promote bone formation through regulating bone growth. However, the peptide sequences within these isolates have not been characterized. In this study, twenty-nine peptides from bovine bone collagen hydrolysates were purified and identified using nano-HPLC-MS-MS and Peak Studio analysis. HHGDQGAPGAVGPAGPRGPAGPSGPAGKDGR (Deamidation) and GPAGANGDRGEAGPAGPAGPAGPR (Deamidation) enhanced cell viability, inhibited apoptosis, and significantly altered the cell cycle of MC3T3-E1 osteoblast cells. These peptides were selected to perform molecular docking analysis to examine the mechanism underlying these bioactivities. Molecular docking analysis showed that these two peptides formed hydrophobic interactions and hydrogen bonds with epidermal growth factor receptor (EGFR) to activate the EGFR-signaling pathway, which may explain their bioactivity. These findings indicate that these and other similar peptides might be candidates for the treatment of osteoporosis.

scholarly journals Potential Role of Colchicine in Combating COVID-19 Cytokine Storm and Its Ability to Inhibit Protease Enzyme of SARS-CoV-2 as Conferred by Molecular Docking Analysis

Medicina ◽  
2021 ◽  
Vol 58 (1) ◽  
pp. 20
Author(s):  
Noha A. Kamel ◽  
Nasser S. M. Ismail ◽  
Ibrahim S. Yahia ◽  
Khaled M. Aboshanab
Keyword(s):  
Molecular Docking ◽  
Hydrophobic Interactions ◽  
Cytokine Storm ◽  
Destructive Effect ◽  
Health Crisis ◽  
Docking Analysis ◽  
Global Pandemic ◽  
Protease Enzyme ◽  
Anti Inflammatory ◽  
Molecular Docking Analysis

Despite the advance in the management of Coronavirus disease 2019 (COVID-19), the global pandemic is still ongoing with a massive health crisis. COVID-19 manifestations may range from mild symptoms to severe life threatening ones. The hallmark of the disease severity is related to the overproduction of pro-inflammatory cytokines manifested as a cytokine storm. Based on its anti-inflammatory activity through interfering with several pro and anti-inflammatory pathways, colchicine had been proposed to reduce the cytokine storm and subsequently improve clinical outcomes. Molecular docking analysis of colchicine against RNA-dependent RNA polymerase (RdRp) and protease enzymes of Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) revealed that colchicine provided a grid-based molecular docking method, C-DOCKER interaction energy 64.26 and 47.53 (Kcal/mol) with protease and RdRp, respectively. This finding indicated higher binding stability for colchicine–protease complexes than the colchicine–RdRp complex with the involvement of seven hydrogen bonds, six hydrogen acceptors with Asn142, Gly143, Ser144, and Glu166 and one hydrogen-bond donors with Cys145 of the protease enzyme. This is in addition to three hydrophobic interactions with His172, Glu166, and Arg188. A good alignment with the reference compound, Boceprevir, indicated high probability of binding to the protease enzyme of SARS-CoV-2. In conclusion, colchicine can ameliorate the destructive effect of the COVID-19 cytokine storm with a strong evidence of antiviral activity by inhibiting the protease enzyme of SARS-CoV-2.

scholarly journals Discovery of 2-Substituted 3-Arylquinoline Derivatives as Potential Anti-Inflammatory Agents Through Inhibition of LPS-Induced Inflammatory Responses in Macrophages

Molecules ◽  
2019 ◽  
Vol 24 (6) ◽  
pp. 1162 ◽  
Author(s):  
Cheng-Yao Yang ◽  
Yung-Li Hung ◽  
Kai-Wei Tang ◽  
Shu-Chi Wang ◽  
Chih-Hua Tseng ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Inflammatory Cytokines ◽  
Inflammatory Responses ◽  
Hydrophobic Interactions ◽  
Activated Macrophages ◽  
Docking Analysis ◽  
Lead Compounds ◽  
Anti Inflammatory ◽  
Molecular Docking Analysis ◽  
Pro Inflammatory Cytokines

We describe herein the preparation of certain 2-substituted 3-arylquinoline derivatives and the evaluation of their anti-inflammatory effects in LPS-activated murine J774A.1 macrophage cells. Among these newly synthesized 2-substituted 3-arylquinoline derivatives, 2-(4-methoxy- benzoyl)-3-(3,4,5-trimethoxyphenyl)quinoline (18a) and 2-(4-fluorobenzoyl)-3-(3,4,5-trimethoxy- phenyl)quinoline (18b) are two of the most active compounds which can inhibit the production of NO at non-cytotoxic concentrations. Our results have also indicated that compounds 18a and 18b significantly decrease the secretion of pro-inflammatory cytokines (TNF-á and IL-6), inhibit the expression of iNOS, suppress the phosphorylation of MAPKs, and attenuate the activity of NF-êB by LPS-activated macrophages. Through molecular docking analysis, we found that 18b could fit into the middle of the TNF-á dimer and form hydrophobic interactions with Leu55, Leu57 chain A and B, Tyr59, Val123 chain B and D, Ile 155. These results suggest that both 18a and 18b are potential lead compounds in inhibiting LPS-induced inflammatory responses. Further structural optimization to discover novel anti-inflammatory agents is ongoing.

scholarly journals HPLC-ESI-qTOF-MS/MS Characterization, Antioxidant Activities and Inhibitory Ability of Digestive Enzymes with Molecular Docking Analysis of Various Parts of Raspberry (Rubus ideaus L.)

Antioxidants ◽  
2019 ◽  
Vol 8 (8) ◽  
pp. 274 ◽  
Author(s):  
Lingfeng Wu ◽  
Yufeng Liu ◽  
Yin Qin ◽  
Lu Wang ◽  
Zhenqiang Wu
Keyword(s):  
Molecular Docking ◽  
Phenolic Compounds ◽  
Digestive Enzymes ◽  
Antioxidant Activities ◽  
Rubus Idaeus ◽  
Total Phenolic ◽  
Dependent Manner ◽  
Inhibitory Effects ◽  
Docking Analysis ◽  
Molecular Docking Analysis

The anti-oxidative phenolic compounds in plant extracts possess multiple pharmacological functions. However, the phenolic characterization and in vitro bio-activities in various parts of raspberry (Rubus idaeus L.) have not been investigated systematically. In the present study, the phenolic profiles of leaves (LE), fruit pulp (FPE), and seed extracts (SE) in raspberry were analyzed by HR-HPLC-ESI-qTOF-MS/MS method, and their antioxidant activities and digestive enzymes inhibitory abilities were also investigated. The molecular docking analysis was used to delineate their inhibition mechanisms toward type II diabetes related digestive enzymes. Regardless of LE, FPE, or SE, 50% methanol was the best solvent for extracting high contents of phenolic compounds, followed by 50% ethanol and 100% methanol. The LE of raspberry displayed the highest total phenolic content (TPC) and total flavonoid content (TFC). A total of nineteen phenolic compounds were identified. The quantitative results showed that gallic acid, ellagic acid, and procyanidin C3 were the major constituents in the three extracts. The various parts extracts of raspberry all exhibited the strong antioxidant activities, especially for LE. Moreover, the powerful inhibitory effects of the three extracts against digestive enzymes (α-glucosidase and α-amylase) were observed. The major phenolic compounds of the three extracts also showed good inhibitory activities of digestive enzyme in a dose-dependent manner. The underlying inhibitory mechanisms of the main phenolic compounds against digestive enzymes were clarified by molecular docking analysis. The present study demonstrated that the various parts of raspberry had strong antioxidant activities and inhibitory effects on digestive enzymes, and can potentially prevent oxidative damage or diabetes-related problems.

scholarly journals Investigation on Chemical Constituents of Foeniculum vulgare Essential Oil and the Molecular Docking Studies of its Components for Possible Matrix Metalloproteinase-13 Inhibition

2020 ◽  
Vol 1 (2) ◽  
pp. 65-71
Author(s):  
Amir Taherkhani ◽  
Zahra Khamverdi ◽  
Mahdi Sayafi ◽  
Shirin Moradkhani
Keyword(s):  
Alzheimer’S Disease ◽  
Alzheimer's Disease ◽  
Molecular Docking ◽  
Essential Oil ◽  
Matrix Metalloproteinase ◽  
Chemical Constituents ◽  
Foeniculum Vulgare ◽  
Docking Analysis ◽  
Matrix Metalloproteinase 13 ◽  
Molecular Docking Analysis

Background: Foeniculum vulgare (Fennel) has a wide range of applications. Previous studies revealed the presence of different compounds in the essential oil (EO) of fennel fruit (FF). Matrix metalloproteinase-13 (MMP-13) participates in several human biological processes including the degradation of extracellular matrix proteins, activation or degradation of some significant regulatory proteins, and tumor cell invasion. Furthermore, the up-regulation of MMP-13 is associated with many disorders such as tooth caries and periodontitis, as well as the degradation of enamel and tissues around the implant and Alzheimer’s disease. Therefore, the aims of the present study were to investigate the compounds of the EO of FF (EOFF) from the Hamedan district, along with performing molecular docking analysis to assess the binding affinity of four compounds originated from F. vulgare with the MMP-13. Finally, the study focused on evaluating the pharmacokinetic and toxicity characteristics of the compounds. Methods: Hydrodistillation method was used for obtaining the EO from FF. Then, gas chromatography-mass spectrometry was applied to identify the components of the EO. Molecular docking analysis was carried out using AutoDock software. Eventually, the pharmacokinetic and toxicity features of compounds were evaluated using bioinformatics webservers. Results: The results revealed the presence of fourteen compounds, among which e-anethole (86.86%), fenchone (743%), estragole (165%), and thymol (1.21%) were the main components. Based on the results, thymol, fenchone, e-anethole, and estragole could potentially bind to the MMP-13 active site, respectively. Conclusion: Regardless of several studies on the chemical constituents of EOFF, the subject has its own pharmacognostical importance. According to computational studies, EOFF has the potential for study on several human disorders such as cancer, tooth decay, and Alzheimer’s disease.

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