• HIMA VYSHNAVI A. M. Computational Chemistry Group (CCG), Amrita Molecular Modeling And Synthesis Research Lab, Amrita School of Engineering, Coimbatore, Amrita Vishwa Vidyapeetham, India, 641112
  • P. K. KRISHNAN NAMBOORI Computational Chemistry Group (CCG), Amrita Molecular Modeling And Synthesis Research Lab, Amrita School of Engineering, Coimbatore, Amrita Vishwa Vidyapeetham, India, 641112



Breast Cancer, Drug action, Homology modeling, Pharmacogenomic model, Side effect, Variation


Objective: The proneness of disease, as well as drug action and side effects, vary from person to person. This may be due to individual variations in the genome. The individual variation demands the need to design a population-specific 'predictive, preventive, participatory and personalized (p4)' pharmacogenomics drug molecule. The present work aims at designing a pharmacogenomic model for breast cancer to explain the individual variation in the proneness of the diseases and susceptibility towards drug action.

Methods: The drug action and side effects of drugs were analyzed from clinical trial reports. The genes responsible for the drug action and the genes responsible for side effects have been identified and included in the variation analysis. The pharmacogenomic gene models have been designed by inducing population-specific genetic variations within the gene sequence. The 3D structures of the 'variation-specific' protein models have been generated by 'homology modelling.' These models have been used further for docking studies with the known drug molecules. The kinetic stability of the protein-ligand complexes obtained out of docking studies has been studied by the molecular dynamic simulation.

Results: By the interaction studies and the computational analysis using the 'population-specific protein models,' the drug molecule, Capecitabine showed the highest binding affinity (–6.30kcal/mol) with the African population, Paclitaxel was found to be the most interacting with the European population with a binding affinity of–9.5603 kcal/mol, and Lapatinib is found to be the most suitable ligand for the American population with a binding affinity of–6.90 kcal/mol. These observations agree with the clinical trial data found in the 'ClinTrial database'.

Conclusion: The designed models are found to be suitable for representing the respective population-specific target models. The interaction studies of known drug molecules with these population-specific target models correspond to the observations in the 'ClinTrial database.'


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