Binding energies of riboflavin coenzyme B 12 containing enzyme complex by AScore scoring function of ArgusLab. By analyzing the docking results we hypothesized that riboflavin might have inhibitory activity against cobalamin coenzymes. Author information Copyright and License information Disclaimer. For each rotation, torsions are created and poses conformations are generated during the docking process [ 11 ]. View at Google Scholar P. Animal cells contain at least nine cdkss; four of which, Cdk1, 2, 3, and 4, are directly involved in cell cycle regulation. 
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Docking of riboflavin into enzyme diol dehydratase [ 14 ]. These were the structures of enzymes from three major enzyme families with bound coenzyme B This depends on the interaction of the functional groups of riboflavin with those amino acid residues of B 12 enzymes that are present in the active site cavity or take part in enzyme catalysis indirectly. Riboflavin and protein binding sites are shown in element colors in wireframe and thick stick models, respectively, whereas cyanocobalamin is represented in pink color in thick stick.
J Chem Inf Comput Sci. View at Google Scholar P. After the preparation of the protein and ligand, molecular docking studies were performed by ArgusLab 4.
Journal of Computational Medicine
By analyzing the docking results we hypothesized that riboflavin might have inhibitory activity against cobalamin coenzymes.
Journal of Computational Medicine.
Chemistry of neem bitter principles. Inhibitor TAR is seen in green color in thick stick. Crystal structure of cyclin dependent kinase 2.
Leaf decoction is effective against septic wounds, boils, and ulcers. The fact that riboflavin participates in energy-based metabolic reactions may play an important role in enzyme catalysis argus,ab depends on a delicate energy balance for different reaction pathways.
The structure and reactivity of B 12 derivatives and structural aspects of their interactions with proteins and nucleotides are crucial for the efficient catalysis by the important B 12 -dependent enzymes [ 1 ].
They catalyze enzymatic reactions which involve the making and breaking of the C—Co bond of these cofactors. Computer-based molecular modeling aims to speed up drug discoveries by predicting potential effectiveness of ligand-protein interactions prior to laborious experiments and costly preclinical trials.
The docking results of riboflavin with each of the individual enzymes are as follows. Numerous software packages have been developed with the implementation of various molecular docking algorithms based on different search methods [ 10 ].
All the compounds selected for the study are considered as orally safe compounds. Table 1 Compounds of Azadirachta indica and their molecular structures.
Annu Rev Cell Dev Biol. ArgusLab, Azadirachta indica, cancer, cyclin-dependent kinase, docking.
Another hydrogen bond was formed between the nitrogen atom N1 of riboflavin and NH of amino acid Thr at aruslab distance of 2.
A spacing of 0.
BBCU - ArgusLab
The cdk function has been remarkably well conserved during evolution. Therefore, the docked position and conformation of riboflavin revealed that the compound may inhibit the usual catalytic process of the enzyme by altering the conformational change in the nucleotide base, which plays an important role in initiating the Co—C bond cleavage and thus hinders the continuous progress of radical reactions.
The identification of genes that are mutated has been a central aim of cancer research since the advent of recombinant DNA technology. Support Center Support Center. The results indicate a significant inhibitory effect of riboflavin on the catalysis of B 12 -dependent enzymes.
The hydrogen locations are not specified by the X-ray structure but these are necessary to improve the hydrogen bond geometries, at the same time maintaining the protein conformation very close to that observed in the crystallographic model. Results and Plaanria Minimized structure of riboflavin is given in Figure 1.
It is possible, for example, for yeast cells to proliferate normally when their gene for arguzlab is replaced with the human one. Docking of riboflavin into enzyme glutamate mutase [ 13 ].
The number of hydrogen atoms is indicated in light green color. Binding energies of riboflavin coenzyme B 12 containing enzyme complex by AScore scoring function of ArgusLab.
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