Molecular Docking of Azadirachtin in Nuclear Ecdysone Receptor

2019 ◽  
Vol 9 (1) ◽  
pp. 50-57 ◽  
Author(s):  
Daniel Augusto Barra de Oliveira ◽  
Alcedino Venancio da Silva ◽  
Edenilson dos Santos Niculau
Keyword(s):  
Amino Acids ◽  
Molecular Docking ◽  
Growth Inhibition ◽  
Theoretical Calculation ◽  
Molecular Structures ◽  
Ecdysone Receptor ◽  
Interaction Mode ◽  
Natural Insecticide ◽  
Oniom Approach ◽  
Epidemic Diseases

Background: The azadirachtin is a triterpenoid associated with growth inhibition in several kinds of insects which cause epidemic diseases like Dengue, Chikungunya and Malaria. Azadirachtin acts by inhibiting the Ecdysone Receptor (EcR), which is responsible from larvae phase in insects. However, the interaction between the azadirachtin molecule and the Ecdysone Receptor is unknown. In this work, we used the program Dock Thor to generate several azadirachtin conformations inside the EcR binding site. The ten most stable conformations were optimized with the ONIOM approach present in the Gaussian 09 program. The interaction energy was calculated between the azadirachtin molecule and EcR receptor. Theoretical calculation shows that the azadirachtin molecule interacts with the same amino acids present in the ecdysone EcR interaction. These results will be useful to design new EcR inhibitors, which can be used in the control of some diseases based on insect proliferations. Objective: To understand the interaction between the natural insecticide azadirachtin and the Ecdysone Receptor. Methods: A combination of Dock Thor program with QM-MM calculation was used in order to obtain the most favorable molecular structures. Results: The hydrogens bond obtained by Dock Thor Program combined with QM-MM calculation suggest the azadirachtin interact with EcR in the same way that ecdysone molecule. Conclusion: The interaction mode that the molecule azadirachtin inhibits EcR in order to avoid insect proliferation was described.

scholarly journals DESIGN AND MOLECULAR DOCKING STUDIES OF NOVEL ANTIMICROBIAL PEPTIDES USING AUTODOCK MOLECULAR DOCKING SOFTWARE

2017 ◽  
Vol 10 (16) ◽  
pp. 28 ◽  
Author(s):  
Kiranpreet Kaur ◽  
Paranjeet Kaur ◽  
Amit Mittal ◽  
Surendra Kumar Nayak ◽  
Gopal L Khatik
Keyword(s):  
Amino Acids ◽  
Molecular Docking ◽  
Antimicrobial Peptides ◽  
Binding Affinity ◽  
Docking Studies ◽  
Molecular Structures ◽  
Short Chain ◽  
Receptor Protein ◽  
Autodock Vina ◽  
E Coli

Objective: Design of novel antimicrobial peptides and study through the molecular docking.Methods: The molecular structures were drawn in ChemBiodraw ultra and by the help of ChemBiodraw 3D, all structures were energy minimized by theMM2 method and converted to pdbextension file which is readable at the ADT interface. The AutoDock Vina (ADT) 1.5.6 software is used for molecular docking purposes.Results: Eight antimicrobial peptides (AMPs) were designed based on theMP196antimicrobial peptide. Among these KP_03R (FWRWRW-NH2) showed good binding affinity. These peptides also showed the stereochemical influence on affinity toward the3vma protein of E. coli, where AMP with R stereochemistry showed better activity than its opposite stereochemistry.  Conclusion: Novel AMPs were designed by modifications on the MP196 a short chain of amino acids antimicrobial peptides. Molecular docking software was used to determine the binding affinity between drug and receptor protein. Among all the designed peptides KP_03R(FWRWRW-NH2) showed the maximum binding affinity against thepenicillin-binding protein of E.coli and also exhibited stereoselective activity.

Antimyotoxic Activity of Synthetic Peptides Derived from Bothrops atrox Snake Gamma Phospholipase A2 Inhibitor Selected by Virtual Screening

2019 ◽  
Vol 19 (22) ◽  
pp. 1952-1961 ◽  
Author(s):  
J.C. Sobrinho ◽  
A.F. Francisco ◽  
R. Simões-Silva ◽  
A.M. Kayano ◽  
J.J. Alfonso Ruiz Diaz ◽  
...  
Keyword(s):  
Amino Acids ◽  
Molecular Docking ◽  
Synthetic Peptides ◽  
Cell Damage ◽  
Neutralization Assay ◽  
Phospholipase Activity ◽  
Phospholipases A2 ◽  
Catalytically Active ◽  
Bothrops Atrox

Background: Several studies have aimed to identify molecules that inhibit the toxic actions of snake venom phospholipases A2 (PLA2s). Studies carried out with PLA2 inhibitors (PLIs) have been shown to be efficient in this assignment. Objective: This work aimed to analyze the interaction of peptides derived from Bothrops atrox PLIγ (atPLIγ) with a PLA2 and to evaluate the ability of these peptides to reduce phospholipase and myotoxic activities. Methods: Peptides were subjected to molecular docking with a homologous Lys49 PLA2 from B. atrox venom modeled by homology. Phospholipase activity neutralization assay was performed with BthTX-II and different ratios of the peptides. A catalytically active and an inactive PLA2 were purified from the B. atrox venom and used together in the in vitro myotoxic activity neutralization experiments with the peptides. Results: The peptides interacted with amino acids near the PLA2 hydrophobic channel and the loop that would be bound to calcium in Asp49 PLA2. They were able to reduce phospholipase activity and peptides DFCHNV and ATHEE reached the highest reduction levels, being these two peptides the best that also interacted in the in silico experiments. The peptides reduced the myotubes cell damage with a highlight for the DFCHNV peptide, which reduced by about 65%. It has been suggested that myotoxic activity reduction is related to the sites occupied in the PLA2 structure, which could corroborate the results observed in molecular docking. Conclusion: This study should contribute to the investigation of the potential of PLIs to inhibit the toxic effects of PLA2s.

Molecular Docking Analysis of Flavonoid Compounds with Matrix Metalloproteinase-8 for the Identification of Potential Effective Inhibitors

2020 ◽  
Vol 17 ◽  
Author(s):  
Amir Taherkhani ◽  
Athena Orangi ◽  
Shirin Moradkhani ◽  
Zahra Khamverdi
Keyword(s):  
Amino Acids ◽  
Molecular Docking ◽  
Amino Acid ◽  
Matrix Metalloproteinase ◽  
Ligand Binding ◽  
Chronic Inflammation ◽  
Cancer Progression ◽  
Dimensional Structure ◽  
Control Test ◽  
Therapeutic Procedures

Background: Matrix metalloproteinase-8 (MMP-8) participates in degradation of different types of collagens in the extracellular matrix and basement membrane. Up-regulation of the MMP-8 has been demonstrated in many of disorders including cancer development, tooth caries, periodontal/peri-implant soft and hard tissue degeneration, and acute/chronic inflammation. Therefore, MMP-8 has become an encouraging target for therapeutic procedures for scientists. We carried out molecular docking approach to study the binding affinity of 29 flavonoids, as drug candidates, with the MMP-8. Pharmacokinetic and toxicological properties of the compounds were also studied. Moreover, it was attempted to identify the most important amino acids participating in ligand binding based on degree of each of the amino acids in the ligand-amino acid interaction network for MMP-8. Methods: Three-dimensional structure of the protein was gained from the RCSB database (PDB ID: 4QKZ). AutoDock version 4.0 and Cytoscape 3.7.2 were used for molecular docking and network analysis, respectively. Notably, the inhibitor of the protein in the crystalline structure of the 4QKZ was considered as a control test. Pharmacokinetic and toxicological features of compounds were predicted using bioinformatic web tools. Post-docking analyses were performed using BIOVIA Discovery Studio Visualizer version 19.1.0.18287. Results and Discussions: According to results, 24 of the studied compounds considered to be top potential inhibitors for MMP-8 based on their salient estimated free energy of binding and inhibition constant as compared with the control test: Apigenin-7-glucoside, nicotiflorin, luteolin, glabridin, taxifolin, apigenin, licochalcone A, quercetin, isorhamnetin, myricetin, herbacetin, kaemferol, epicatechin, chrysin, amentoflavone, rutin, orientin, epiafzelechin, quercetin-3-rhamnoside, formononetin, isoliquiritigenin, vitexin, catechine, isoquercitrin. Moreover, His-197 was found to be the most important amino acid involved in the ligand binding for the enzyme. Conclusion: The results of the current study could be used in the prevention and therapeutic procedures of a number of disorders such as cancer progression and invasion, oral diseases, and acute/chronic inflammation. Although, in vitro and in vivo tests are inevitable in the future.

Molecular docking studies of tea (Thea sinensis Linn.) polyphenols inhibition pattern with Rat P-glycoprotein

2020 ◽  
Vol 0 (0) ◽  
Author(s):  
Babar Ali ◽  
Qazi Mohammad Sajid Jamal ◽  
Showkat R. Mir ◽  
Saiba Shams ◽  
Mohammad Amjad Kamal
Keyword(s):  
Amino Acids ◽  
Molecular Docking ◽  
Binding Energy ◽  
Oral Administration ◽  
Docking Studies ◽  
Vital Role ◽  
Glycoprotein P ◽  
High Affinity ◽  
P Glycoprotein ◽  
Inhibition Pattern

AbstractSince 3000 B.C., evergreen plant Thea sinensis (Theaceae) is used both as a social and medicinal beverage. Leaves of T. sinensis contain amino acids, vitamins, caffeine, polysaccharides and polyphenols. Most of the natural medicinal actions of tea are due to the availability and abundance of polyphenols mainly catechins. It has also been stated that some catechins were absorbed more rapidly than other compounds after the oral administration of tea and could increase the bio-enhancing activities of anticancer drugs by inhibiting P-glycoprotein (P-gp). The results of the molecular docking showed that polyphenols bind easily to the active P-gp site. All compounds exhibited fluctuating binding affinity ranged from −11.67 to −8.36 kcal/mol. Observed binding energy required for theaflavin to bind to P-gp was lowest (−11.67 kcal/mol). The obtained data that supports all the selected polyphenols inhibited P-gp and therefore may enhance the bioavailability of drugs. This study may play a vital role in finding hotspots in P-gp and eventually may be proved useful in designing compounds with high affinity and specificity to the protein.

scholarly journals Destruxin A Interacts with Aminoacyl tRNA Synthases in Bombyx mori

2021 ◽  
Vol 7 (8) ◽  
pp. 593
Author(s):  
Jingjing Wang ◽  
Alexander Berestetskiy ◽  
Qiongbo Hu
Keyword(s):  
Amino Acids ◽  
Protein Synthesis ◽  
Bombyx Mori ◽  
Metarhizium Anisopliae ◽  
Free Amino ◽  
Molecular Target ◽  
Trna Synthetases ◽  
Interaction Mode ◽  
Aminoacyl Trna Synthetases ◽  
Wide Range

Destruxin A (DA), a hexa-cyclodepsipeptidic mycotoxin produced by the entomopathogenic fungus Metarhizium anisopliae, exhibits insecticidal activities in a wide range of pests and is known as an innate immunity inhibitor. However, its mechanism of action requires further investigation. In this research, the interactions of DA with the six aminoacyl tRNA synthetases (ARSs) of Bombyx mori, BmAlaRS, BmCysRS, BmMetRS, BmValRS, BmIleRS, and BmGluProRS, were analyzed. The six ARSs were expressed and purified. The BLI (biolayer interferometry) results indicated that DA binds these ARSs with the affinity indices (KD) of 10−4 to 10−5 M. The molecular docking suggested a similar interaction mode of DA with ARSs, whereby DA settled into a pocket through hydrogen bonds with Asn, Arg, His, Lys, and Tyr of ARSs. Furthermore, DA treatments decreased the contents of soluble protein and free amino acids in Bm12 cells, which suggested that DA impedes protein synthesis. Lastly, the ARSs in Bm12 cells were all downregulated by DA stress. This study sheds light on exploring and answering the molecular target of DA against target insects.

scholarly journals Multi-scale modeling of electronic spectra of three aromatic amino acids: importance of conformational averaging and explicit solute–solvent interactions

2014 ◽  
Vol 16 (38) ◽  
pp. 20639-20649 ◽  
Author(s):  
Petr Štěpánek ◽  
Petr Bouř
Keyword(s):  
Amino Acids ◽  
Quantum Mechanics ◽  
Molecular Mechanics ◽  
Electronic Spectra ◽  
Aromatic Amino Acids ◽  
Molecular Structures ◽  
Solvent Interactions ◽  
Multi Scale ◽  
Scale Modeling ◽  
Multi Scale Modeling

Electronic spectra provide a wealth of information on molecular structures. We demonstrate a very satisfactory agreement between experimental and modeled spectra, as obtained by combined molecular mechanics/quantum mechanics computations for three aromatic amino acids.

scholarly journals In-silico Investigation of the Interaction between Beta-class Glutathione S-Transferase and Five Antibiotics, namely; Ampicillin, Tetracycline, Chloramphenicol, Ciprofloxacin and Cephalexin

2021 ◽  
Vol 25 (4) ◽  
pp. 497-502
Author(s):  
D. Shehu ◽  
S Danlami ◽  
M. Ya’u ◽  
A. Babandi ◽  
H.M. Yakasai ◽  
...  
Keyword(s):  
Amino Acids ◽  
Antibiotic Resistance ◽  
Molecular Docking ◽  
Binding Site ◽  
Substrate Binding ◽  
Docking Study ◽  
Glutathione S Transferase ◽  
Molecular Docking Study ◽  
Substrate Binding Site ◽  
Glutathione S Transferases

Glutathione s-transferases(GSTs) are enzymes involved in the conjugation and deactivation of various xenobiotics including drugs. Thisin-silico study was undertaken in order to investigate the interaction between beta-class glutathione s-transferase and five selected antibiotics, namely; ampicillin, tetracycline, chloramphenicol, ciprofloxacin and cephalexin using molecular docking study. RaptorX server was used to predict the amino acids involved at the binding sitewhile molecular docking study was employed in order to investigate the binding interactions.RaptorX predicted several amino acids which were different from the ones observed in molecular docking because of the variability in the substrate binding site of GSTs however, all the amino acids predicted by RaptorX were also found to be involved in the GSH binding.Lys107, Phe109, Ser110, Leu113, Trp114, His115 and Arg123, Leu168 were the amino acids involved in the binding of various antibiotics to the substrate binding site of the protein while Ala9, Cys10, Leu32, Tyr51, Val52, Pro53, Glu65 and Ala66were involved in the binding of the co-substrate GSH to the binding site of the protein. The results indicated that all the antibiotics showed a good binding affinity with the beta class GST and are therefore capable of deactivating the drugs. With these, finding a beta class GST inhibitors alongside antibiotics during a treatment of diseases will be of beneficial in the current fight against antibiotic resistance.

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