The molecular modelling of compound 4d was performed with Schrödinger Suite 2015-1 (Schrödinger LLC., New York, NY, USA)39 . The crystal structure of the MEK1 (PDB ID: 3EQF) was downloaded from Protein Data Bank (PDB) and prepared using the Protein Preparation Wizard workflow from Schrödinger Suite, including the optimisation of hydrogen bond network and a short energy minimisation with position restraints on heavy atoms using OPLS_2005 force field. The docking grid was generated according to the initial ligand K252A. Then the target compounds were freely docked into the designated binding site using the standard protocol implemented in Maestro version 10.1 (Schrodinger LLC, Cambridge, MA, USA). Van der Waals (vdW) scaling of 0.8 and partial cut-off of 0.15 were set to soften the potential for non-polar sites, and no constraints were specified. The best docked pose ranked by Glide Score value was recorded, and saved for each ligand. The structures of complexes were analysed for interaction modes, and the binding pose of compound 4d with MEK1 kinase was displayed using Discovery studio 3.5 client.
Suite 2015 1
Manufactured by Schrödinger
Sourced in United States
The Schrödinger Suite 2015-1 is a software package for computational chemistry and drug discovery. It provides a suite of tools for molecular modeling, simulation, and analysis.
Automatically generated - may contain errors
4 protocols using suite 2015 1
1
Molecular Modeling of Compound 4d
2
Molecular Modeling and Docking of Compound 10g
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The molecular modelling of compound 10g was performed with Schrödinger Suite 2015–1 (Schrödinger LLC., New York, NY, USA). The crystal structure of the MEK1 (PDB ID: 3EQF) was downloaded from Protein Data Bank (PDB) and prepared using the Protein Preparation Wizard workflow from Schrödinger Suite, including the optimisation of hydrogen bond network and a short energy minimisation with position restraints on heavy atoms using OPLS_2005 force field. The docking grid was generated according to the initial ligand K252A. Then the target compounds were freely docked into the designated binding site using the standard protocol implemented in Maestro v 10.1 (Schrödinger LLC, Cambridge, MA, USA). Van der Waals (vdW) scaling of 0.8 and partial cut-off of 0.15 were set to soften the potential for non-polar sites, and no constraints were specified. The best docked pose ranked by Glide Score value was recorded, and saved for each ligand. The structures of complexes were analysed for interaction modes, and the binding pose of compound 10g with MEK1 kinase was displayed using Discovery studio 3.5 client.
3
Structure-Based and Ligand-Based Pharmacophore Modeling
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The computational tasks, except MD, were performed on an Intel(R) Core (TM) i5-3210M CPU @ 2.50 GHz processor with a memory of 8.0 GB RAM running on a Linux 64 operating system. Schrödinger suite 2015-1 (Schrödinger, LLC, New York, NY, 2015) was utilized to develop structure-based and ligand-based pharmacophore models and for the screening of publicly free ‘ZINC15’ database. MD simulation was perform using Desmond package on an Intel(R) Xeon(R) CPU E3-1225v5@ 3.30 GHz 3.31 GHz processor, RAM 32.0 GB system with Nvidia ‘Quadro P600’ GPU running on a Linux 64 operating system.
4
Molecular Modeling of Compound 5f
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The molecular modeling of compound 5f was performed with Schrödinger Suite 2015-1 (Schrödinger LLC., New York, NY, USA). The crystal structure of Topo IIα (PDB ID: 5GWK) was downloaded from Protein Data Bank (PDB) and prepared using the Protein Preparation Wizard workflow from Schrödinger Suite, including the optimization of hydrogen bond network and a short energy minimization with position restraints on heavy atoms using OPLS_2005 force field. The docking grid was generated according to the initial ligand etoposide. Then, the target compounds were freely docked into the designated binding site using the standard protocol implemented in Maestro v 10.1 (Schrödinger LLC, Cambridge, MA, USA). Van der Waals (vdW) scaling of 0.8 and partial cut-off of 0.15 were set to soften the potential for non-polar sites, and no constraints were specified. The best docked pose ranked by Glide Score value was recorded and saved for the ligand. The structures of complexes were analyzed for interaction modes, and the binding pose of compound 5f with Topo IIα was displayed using the Discovery Studio 2016 client (Accelrys Software, San Diego, CA, USA).
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