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Identification of Potential Small Molecule Binding Pockets in p38α MAP kinase

P. Gomez-Gutierrez, J. Rubio-Martinez, J. J. Perez.
J. Chem. Inf. Model., 57 (2017) 2566.

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Searching binding pockets using molecular dynamics.

Given the essential role played by protein kinases in regulating cellular pathways, their dysregulation can result in the onset and/or progression of various human diseases. Structural analysis of diverse protein kinases suggests that these proteins exhibit a remarkable plasticity. The present work reports the results of a in silico screening study aimed at identifying novel prospective allosteric binding sites in the paradigmatic p38α MAP kinase. The process was carried out using a protein ensemble generated from a 6 μs accelerated molecular dynamics. The procedure permitted to identify diverse allosteric sites of p38α already described in the literature including the DFG pocket, the lipid binding pocket, the DEF site, the docking groove, the CD and ED sites, the backside site as well as a novel site recently reported: the A-loop regulatory site. Furthermore, the study also permitted to identify ten novel prospective allosteric sites.


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