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



Vidya Mukund1*, Santosh Kumar Behera2, Afroz Alam1 & Ganji Purnachandra Nagaraju3



1Department of Bioscience and Biotechnology, Banasthali University, Banasthali, RJ, 304 022, India; 2Biomedical Informatics Centre, Regional Medical Research Centre (ICMR), Bhubaneswar 751023, Odisha, India; 3Department of Hematology and Medical Oncology, Winship Cancer Institute, Emory University, Atlanta, GA, 30322, USA



Vidya Mukund- E-mail:; *Corresponding author


Article Type

Research Article



Received October 31, 2018; Accepted November 12, 2018; Published January 31, 2019



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 developing additional druggable NF-κB inhibitors with high potency, specificity and outstanding bioavailability.



Breast cancer, NF-κB, Genistein, Docking



Mukund et al. Bioinformation 15(1): 11-17 (2019)


Edited by

P Kangueane






Biomedical Informatics



This is an Open Access article which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. This is distributed under the terms of the Creative Commons Attribution License.