A series of hybrid compounds were constructed using Marvin Sketch version 1.5.6. These ligand structures were converted into 3D formats and geometrically optimized with OPLS3 using Ligand Preparation Wizard in Schrodinger Small Molecule Drug Discovery Suite 2017-1.
Ligand preparation wizard
Manufactured by Schrödinger
The Ligand Preparation Wizard is a software tool that assists in the preparation and processing of ligand molecules for use in computational chemistry and drug discovery. The tool performs tasks such as structure cleaning, protonation, tautomer generation, and conformer generation to ensure the ligand data is ready for further analysis and simulation.
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2 protocols using ligand preparation wizard
1
Hybrid Compound Generation and Optimization
2
Screening ApoE4-Targeting Compounds Using Glide Docking
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To identify the best candidates in the ChemBridge library that target ApoE4, we used the Glide docking protocol7 (link),8 (link),10 (link). Briefly, the pocket identified as the DNA-binding region of ApoE4 was placed within a docking grid box. The full ChemBridge structural library of ~780,000 compounds were prepared using the Ligand Preparation Wizard from the Schrodinger Small Molecule Drug Discovery Suite. Prepared ligands were initially screened under the HTVS protocol in the Glide docking package. For high-stringency (phase II) docking, we employed high-precision mode within the Glide docking package. Highest-stringency (phase III) screening used the Molecular Mechanics Generalized Born Solvent Accessible (MM-GBSA) protocol from Schrodinger Prime module. All three-dimensional results were analyzed in Maestro and BIOVIA Discovery Studio visualizers.
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