A molecular docking and dynamics study to screen phytochemicals that target mutant thymidine phosphorylase for colon cancer therapy

Thymidine phosphorylase (TYPH) is an enzyme involved in pyrimidine catabolism and its mutation is associated with chemoresistance of colon cancer to 5-fluorouracil (5-FU) treatment. Here we have analysed the most destabilized mutation of TYPH protein at glycosyltransferase domain where isoleucine alter to alanine at position 214(I214A) that linked to the onset of colon cancer. This study aims to conduct virtual screening of phytochemicals to find novel compounds against mutated TYPH protein. The in silico study aimed to predict the physicochemical properties of phytochemicals and their binding performance with mutated TYPH compared to 5-FU. From the screened phytochemicals, berbamine showed the best binding affinity (-7.2 kcal/mol) with mutant TYPH protein as compared to 5-FU. For further confirmations, the dynamics properties of native, mutant, and docked complex of I214A mutant with berbamine systems were studied through molecular dynamics simulations with a trajectory of 100ns. From root mean square fluctuation, radius of gyration, number of hydrogen bonds, principal component analysis, and free energy landscape, we predicted that the I214A mutant lost its compactness, however, on complex formation with berbamine it gained its compactness. MM/PBSA and molecular docking studies confirmed that berbamine could show potential inhibitory effects against the mutant model of TYPH. Our finding may open the door for its experimental validation and may take as a potential therapeutic against colon cancer treatment in near future.

Automated summary

In this study, the binding performance of berbamine, a phytochemical, with mutated TYPH protein was predicted using computational and molecular dynamics simulations. The results suggest that berbamine could be a potential therapeutic agent for colon cancer treatment.