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Structural insights into the binding mode of flavonols with the active site of Matrix MetalloProteinase-9 through molecular docking and Molecular Dynamic Simulations studies.

Cartilage degradation in rheumatoid arthritis is mediated principally by the collagenases and gelatinases. Gelatinase B (also calledMatrix metalloproteinase 9-MMP-9),is a valid target molecule which is known to participate in cartilage degradation as well as angiogenesis associated with the disease and inhibition of its activity shall prevent cartilage damage and angiogenesis. The focus of this study is to investigate the possibilities of MMP-9 inhibition by flavonol class of bioflavonoids by studying their crucial binding interactions at the active site of MMP 9using molecular docking(Glide XP and QPLD) and further improvisation by post docking MM-GBSA and molecular dynamic (MD) simulations. The results show that flavonols can convincingly bind to active site ofMMP-9 asdemonstrated by their stable interactions at the S1' specificity pocket and favourablebinding energies. Gossypin has emerged as a promising candidate with a docking score of -14.618 kcal/mol, binding energy of -79.97 kcal/mol and a stable MD pattern over 15ns. In addition, interaction mechanisms with respect to catalytic site zinc are also discussed.Further, the drug-like charactersofthe ligands were also analysed using ADME analysis.

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