Molecular Design: Concepts and Applications

Molecular Objects and Design Objectives
- Molecular geometry and surface
- Molecular properties
- The concept of drug-likeness
- Representing molecules as strings

Receptor-Ligand Interaction
- Thermodynamics of protein-ligand interaction
- QSAR: estimating quantitative structure-activity relationships
- The biophore concept
- Pharmacophores

Creating the Design
- Rational drug design
- Ligand-based design of compound libraries
- Transition state analogs
- de novo design

Virtual Screening
- Similarity searching
- Pharmacophore-based virtual screening
- Molecular docking and scoring
- Structure-based vs. ligand-based design
- Case study 1: design of Kv1.5 ion channel modulators
- Case study 2: virtual screening of a natural-product derived combinatorial library for novel 5-lipoxygenase inhibitors
- Case study 3: scaffold de novo design for cannabinoid-1 (CB-1) receptor ligands

Secondary design constraints and machine learning
- Introduction to Pharmacokinetics
- Prodrugs and bioisosters
- Machine learning methods
- Case study 1: predicting cross-activities of allosteric modulators of metabotropic glutamate receptors (mGluR)
- Case study 2: dopamine D3 antagonists and ACE inhbitors