Structure-Based Design (SBD) and the related Fragment-Based Design (FBD) are well established strategies in the rational development of small molecule drugs. Knowledge of how a small molecule binds into a protein affords considerable advantages, both in terms of prioritizing compounds for early stage screening, through to optimizing potency and selectivity. Discovery Studio delivers a comprehensive, scalable portfolio of scientific tools, tailored to support and assist SBD and FBD strategies from hit discovery through to late-stage lead optimization.
Prepare macromolecule structures for SBD
Analyze and prepare 3D structure models (e.g., PDB, X-ray structure, homology model)
Predict residue ionization states at pH
Identify and study putative ligand binding sites
Prepare ligands
Clean up and calculate 3D coordinates
Generate ligand conformations
Filter ligands based on molecular properties, or undesirable groups
Hit Identification and optimization
Perform virtual screening on ligands and fragments using pharmacophore or docking models
Profile and prioritize screening hits
Optimizing potency and target specificity
Perform in situ lead optimization using classical medicinal chemistry reaction transformations and commercially-available reagents
Scaffold-hop or perform R-group substitutions in situ using molecular fragments derived from commercially-available compounds
Extend the reach of your SBD project easily with additional design tools: