Simulation of the interaction of the enzyme Fumarate reductase with Nizatidine and comparison with the inhibitory effect some Yarrow compounds of the plant to enhance the effects of Metronidazole on Helicobacter pylori in Insilico
Subject Areas :
khadijeh
tavakoli hafshejani
1
(باشگاه پژوهشگران جوان ونخبگان، دانشگاه آزاد اسلامی واحد شهرکرد، شهرکرد ایران)
ali
kazemi babahydari
2
(chemistry,factualy,islamic azad university shahrekord,shahrekird iran)
afsaneh
nikkhah
3
(Payam Noor University of Taft)
Keywords: Fumarate reductase, docking, Nizatidine, Helicobacter pylori, Yarrow compound, molecular dynamics,
Abstract :
Helicobacter pylorus is a spiral-shaped bacterium that is Microaerophilic and gastric ulcer and gastritis is still a major factor. Fumarat reductase (FRD), a key enzyme in the anaerobic respiration Helicobacter pylori. Recently, the effect of some medications, including drug nizatidine inhibit FRD activity in H. pylori has been shown to inhibit cell growth and leads to cell death The aim of this study was to compare the antimicrobial effects of compounds on enzyme FRD yarrow plant molecular docking and molecular dynamics simulations are used. For this purpose, three-dimensional structure of compounds taken yarrow and optimized with Gaussian software and how to connect the components (energy connection) FRD enzyme was determined after modeling three-dimensional structure of the enzyme with the application Mdlr (Modeller10.14) and to evaluate and compare the results of yarrow compounds bind to the enzyme FRD of Nizatidine drug that has proven its effectiveness on FRD were used in docking studies and then yarrow compounds, three compounds had the highest binding energy for molecular dynamics simulations on FRD were selected enzymes. Complex molecular dynamics simulations using the best connection from docking were obtained after 10 nanoseconds of simulation showed that the calculated root mean square displacement (RMSD) fumarate reductase enzyme backbone of the entire simulation is almost homogenous. Indicating that the enzyme was stable during the simulation; Calculation distance of the center of gravity low thymol also stated that the distance between the three combined to better the enzyme's effect.
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