Binding analysis of HDAC2 and metavert was performed using SBGIRD software32 (link). The X-ray crystal structure coordinates for human HDAC2 in complex with Saha (PDB 4LXZ)33 (link) was retrieved from the RCSB Protein Data Bank (PDB) and prepared with the Protein Preparation Wizard in MAESTRO v9.2 (Schrodinger, Inc. San Diego, CA). The optimized protein structure was then subjected to all-atom constrained energy minimization using the IMPREF module of MAESTRO v9.2 with OPLS-2005 force field (Schrodinger, Inc.). The prepared HDAC2 structure was used for the molecular docking simulations. The prepared Saha and metavert molecules were docked flexibly utilizing GLIDE v5.7 standard precision (SP) and GLIDE extra precision (XP) scoring functions34 (link) using standard protocols. The best docking positions were selected based on the total binding energy and the number of contacts.
Protein preparation wizard in maestro v9
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The Protein Preparation Wizard in MAESTRO v9.2 is a tool designed to facilitate the preparation of protein structures for computational analysis. It provides a step-by-step process to optimize the protein structure, including tasks such as adding missing atoms, assigning bond orders, and handling water molecules. The wizard aims to prepare the protein structure in a format suitable for further computational studies.
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Lab products found in correlation
2 protocols using protein preparation wizard in maestro v9
1
HDAC2 Binding Analysis with Metavert
2
Docking p38α MAPK Inhibitors: Ensemble-based Approach
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In our previous work we identified the 1BL7–2EWA ensemble as a good model for docking p38α MAPK inhibitors containing the 4-fluorophenyl and 4-pyridyl ring substituents.[15] (link) Therefore, this model was used to dock designed ligands.
The designed ligands suggested for p38α MAPK inhibition were built in ChemBioDraw Ultra 12.0 (CambridgeSoft) and prepared using LigPrep v2.4 (Schrödinger) to convert the two-dimensional structures to their respective three-dimensional structures.
The 1BL7[7a] (link) and 2EWA[20] crystal structures were downloaded from the Protein Data Bank (PDB)[21] (link) and prepared using the Protein Preparation Wizard in Maestro v9.2 (Schrödinger) for the addition of hydrogens and assignment of bond orders and partial charges. Prime v2.2 (Schrödinger) added side chains to residues with missing atoms. Each protein was refined using exhaustive sampling and minimisations were conducted only on the newly added hydrogens.
Docking into both the 1BL7 and 2EWA crystal structures was conducted using the Glide v5.6 (Schrödinger) extra precision (XP) method. For the ensemble analysis, the glidescores of best conformation of each ligand were taken from each crystal structure and averaged. The compounds were re-ranked based on the ensemble score (see Supporting Information).
The designed ligands suggested for p38α MAPK inhibition were built in ChemBioDraw Ultra 12.0 (CambridgeSoft) and prepared using LigPrep v2.4 (Schrödinger) to convert the two-dimensional structures to their respective three-dimensional structures.
The 1BL7[7a] (link) and 2EWA[20] crystal structures were downloaded from the Protein Data Bank (PDB)[21] (link) and prepared using the Protein Preparation Wizard in Maestro v9.2 (Schrödinger) for the addition of hydrogens and assignment of bond orders and partial charges. Prime v2.2 (Schrödinger) added side chains to residues with missing atoms. Each protein was refined using exhaustive sampling and minimisations were conducted only on the newly added hydrogens.
Docking into both the 1BL7 and 2EWA crystal structures was conducted using the Glide v5.6 (Schrödinger) extra precision (XP) method. For the ensemble analysis, the glidescores of best conformation of each ligand were taken from each crystal structure and averaged. The compounds were re-ranked based on the ensemble score (see Supporting Information).
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