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The first section serves as an introduction to the topic by describing the concept of scaffolds, their discovery, diversity and representation, and their importance for finding new chemical entities. The following parts contain a general description as well as case studies of the most common tools and methods for scaffold hopping, whether topological, shape-based or structure-based. The final part contains three fully documented real-world examples of successful drug development projects by scaffold hopping that illustrate the benefits of the approach for medicinal chemistry.
While most of the case studies are taken from medicinal chemistry, chemical and structural biologists will also benefit greatly from the insights presented here.
Table of Contents
Identifying and representing scaffolds
Markush structures and chemical patents
Diversity of scaffolds from natural products
Scaffold diversity in medicinal chemistry space
Exploring virtual scaffold spaces
TOPOLOGICAL METHODS FOR SCAFFOLD HOPPING
Feature trees (FTrees)
Extended connectivity fingerprints (ECFP)
Maximum common substructure determination in MedChem Studio
SHAPE-BASED METHODS FOR SCAFFOLD HOPPING
Radial distribution function codes
Rapid overlay of chemical structures (ROCS)
XED Forcefields and Fieldstere
Ultrafast shape recognition (USR)
PHARMACOPHORE AND STRUCTURE-BASED METHODS
Molecular interaction fingerprints
SCAFFOLD HOPPING CASE STUDIES