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Life Sciences Modeling & Simulation

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Structure Based Design

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:
    • Build in drug-like and ADME properties
    • Minimize toxicity
    • Optimize pharmacokinetic profile

Read the Discovery Studio Structure Based Design Datasheet

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