Data analysis of molecular dynamics simulation trajectories of β-sitosterol, sonidegib and cholesterol in smoothened protein with the CHARMM36 force field
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Date
2020-09-29
Authors
Mohammad Tasyriq Che Omar
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Publisher
Elsevier
Abstract
Inactivation of smoothened protein (SMO) by the antagonists in SHH-driven cancer types is essential for inhibition of cancer progression. This article presents molecular dynamics (MD) trajectories of water solution of three protein-ligand complexes smoothened-β-sitosterol (SMO-BST), smoothened-sonidegib (SMO-SNG) and smoothened-cholesterol (SMO-CLR) using CHARMM36 and SPC/E water model combination. Additionally, the work presents the topologies and trajectories of GROMACS files that were employed to analyse the protein-ligand interaction types (PyContact) and binding energy calculation (g_mmpbsa). The data demonstrated that equilibrated models of SMO-SNG and SMO-CLR complexes showed crucial residues that almost similar for interaction and contribution energy as previously reported in laboratory setup (in vitro). Initial simulations confirmed the role of ARG451 and TRP535 in the dynamic regulation of SMO. These data then were used as a reference for understanding the molecular dynamics of SMO-BST complex and thus predicted its mechanism of action.
Description
Data were obtained from molecular dynamics simulation ran on Ubuntu 18.4 LTE desktop with GROMACS software version 2018.1
Link to data: https://data.mendeley.com/datasets/v94vzbwzf3/1