American Chemical Society
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Molecular Dynamics and Machine Learning Give Insights on the Flexibility–Activity Relationships in Tyrosine Kinome

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posted on 2023-07-18, 13:07 authored by Sarmistha Majumdar, Francesco Di Palma, Francesca Spyrakis, Sergio Decherchi, Andrea Cavalli
Tyrosine kinases are a subfamily of kinases with critical roles in cellular machinery. Dysregulation of their active or inactive forms is associated with diseases like cancer. This study aimed to holistically understand their flexibility–activity relationships, focusing on pockets and fluctuations. We studied 43 different tyrosine kinases by collecting 120 μs of molecular dynamics simulations, pocket and residue fluctuation analysis, and a complementary machine learning approach. We found that the inactive forms often have increased flexibility, particularly at the DFG motif level. Noteworthy, thanks to these long simulations combined with a decision tree, we identified a semiquantitative fluctuation threshold of the DGF+3 residue over which the kinase has a higher probability to be in the inactive form.