Molecular docking and molecular dynamics studies r

Authors: Rituparna Bhattacharjee Arpita Devi Seema Mishra

Publish Date: 2015/09/29

Volume: 21, Issue: 10, Pages: 272-

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Abstract

Glioblastoma GBM a malignant form of brain tumor has a high mortality rate GRP78 one of the HSP70 protein family members is overexpressed in GBM GRP78 is the key chaperone protein involved in the unfolded protein response Upregulated GRP78 expression in cancer cells inhibits apoptosis and promotes chemoresistance GRP78 has an ATPase domain a substratebinding domain and a linker region ATPcompetitive inhibitors such as EGCG and OSU03012 inhibit GRP78 activity and reduce its expression in GBM However there is a lack of structural data on the binding modes of these inhibitors to GRP78 ATPase domain Further the mode of selectivity of these inhibitors toward GRP78 also is unknown Toward this end molecular docking was performed with AutoDock Vina and confirmation obtained by docking using ROSIE The stability and MMPBSA binding energy of GRP78inhibitor complexes as well as energetic contribution of individual residues was analyzed by 50 ns molecular dynamics run with GROMACS MSA by ClustalW2 identified unique amino acid residues in the ATPase domain of GRP78 which were different from the residues present in other HSP70 proteins Important and unique amino acid residues of GRP78 such as Ile61 Glu293 Arg297 and Arg367 played a major role in the intermolecular interactions with these inhibitors The interactions with unique residues of GRP78 as compared with those of HSP701A provided the basis for selectivity It was found that the binding affinity and specificity/selectivity of EGCG toward GRP78 was higher than that toward HSP701A and selectivity was even better than OSU03012 OSU03012 was predicted to bind to GRP78 Analyses from MD runs showed tight binding and stability of complexes and the highest number of hydrogen bonds during the trajectory runs were comparable to those found in the docking studies Energetic contribution of individual inhibitorinteracting residues showed that energy values of Ile61 and Glu293 were among the most negative These studies are to the best of our knowledge the first studies characterizing EGCG and OSU03012 interactions with GRP78 on a structural basis and provide a significant insight into their binding modes selectivity and structural stability

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