Molecular docking analysis of nuclear factor-κB and genistein interaction in the context of breast cancer

Bioinformation
Vidya MukundGanji Purnachandra Nagaraju

Abstract

Nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB) is a transcription factor and it contributes to breast cancer growth and metastasis. Hence, NF-κB is considered as a target for anti-breast cancer drugs. NF-κB was retrieved from the UniProtKB Data Base with UniProt ID P19838, its energy was minimized and subjected to molecular dynamic simulations using Gromacs v5.0.7 software with GROMOS96 43A1 force field implementing the steepest descent algorithm. The structure of genistein was retrieved from NCBI PubChem database in .sdf format and convert to .pdb format. The genistein compound was docked into the active site of NF-κB proteins with AutoDock tools 1.5. The genistein compound displayed the best binding energies at -6.29 (NF-κB) kcal/mol correspondingly. The binding interactions of this compound with the active site of NF-κB proteins suggested that amino acid residues (Lys52, Ser243, Asp274, Lys, 275) might play a key role in anti-breast cancer activity. Genistein also inhibited the translocation and expression of NF-κB in the nucleus of both breast cancer cell lines. These findings might increase our understanding of the molecular and functional role of NF-κB in breast cancer. It could also help in develo...Continue Reading

Citations

Nov 2, 2019·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Prakash ThangavelRossana C Zepeda
May 7, 2020·Redox Biology·M C Gomez-CabreraJ Viña
Sep 18, 2021·Molecular Nutrition & Food Research·Maria Elisa Caetano-SilvaRodney W Johnson

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Methods Mentioned

BETA
x-ray crystallography
PCA

Software Mentioned

LigPlot
BIOVIA Discovery Studio
bSiteFinder
GROMACS VMD
GROMACS
LigPlot +
GROMOS96
ProQ
GalxySite
PyMOL

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