Overview

This first systematic treatment of the concept and practice of scaffold hopping shows the tricks of the trade and provides invaluable guidance for the reader's own projects.

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 part describes the most common tools and methods for ...
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Scaffold Hopping in Medicinal Chemistry

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Overview

This first systematic treatment of the concept and practice of scaffold hopping shows the tricks of the trade and provides invaluable guidance for the reader's own projects.

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 part describes the most common tools and methods for scaffold hopping, whether topological, shape-based or structure-based. Methods such as CATS, Feature Trees, Feature Point Pharmacophores (FEPOPS), and SkelGen are discussed among many others. 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.
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Product Details

Meet the Author

Nathan Brown is the Head of the In Silico Medicinal Chemistry Group within the Cancer Therapeutics Unit at The Institute of Cancer Research in Sutton (UK). He conducted his doctoral research with Prof. Peter Willett at the University of Sheffield, before moving to Amsterdam (The Netherlands) for a Marie Curie fellowship in collaboration with Prof. Johann Gasteiger. This was followed by a Presidential fellowship at Novartis in Basel (Switzerland). Dr. Brown has published in a wide range of areas of computational chemistry, most notably de novo design and molecular descriptors.

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Table of Contents

INTRODUCTION TO SCAFFOLD HOPPING
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
CATS vectors
Reduced graphs
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)
FEPOPS
ParaFit
XED Forcefields and Fieldstere
Ultrafast shape recognition (USR)

PHARMACOPHORE AND STRUCTURE-BASED METHODS
SkelGen
Molecular interaction fingerprints
ReCore
SHOP

SCAFFOLD HOPPING CASE STUDIES
JAK2 inhibitors mGluR5 inhibitors
Phosphatase inhibitors

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