Fragment-Based Ligand Designing

  • Shashank P. Katiyar
  • Vidhi Malik
  • Anjani Kumari
  • Kamya Singh
  • Durai Sundar
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1762)

Abstract

Fragment-based drug design strategies have been used in drug discovery since it was first demonstrated using experimental structural biology techniques such as nuclear magnetic resonance (NMR) and X-ray crystallography. The underlying idea is that existing or new chemical entities with known desirable properties may serve both as tool compounds and as starting points for hit-to-lead expansion. Despite the recent advancements, there remain challenges to overcome, such as assembly of the synthetically feasible structures, development of scoring functions to correlate structure and their activities, and fine tuning of the promising molecules. This chapter first covers the theoretical background needed to understand the concepts and the challenges related to the field of study, followed by the description of important protocols and related software. Case studies are presented to demonstrate practical applications.

Key words

3D QSAR De novo Fragment growing Fragment linking High-throughput screening Ligand-based drug design Structure-based drug design 

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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2018

Authors and Affiliations

  • Shashank P. Katiyar
    • 1
  • Vidhi Malik
    • 1
  • Anjani Kumari
    • 1
  • Kamya Singh
    • 1
  • Durai Sundar
    • 1
  1. 1.Department of Biochemical Engineering and Biotechnology, DBT-AIST International Laboratory for Advanced Biomedicine (DAILAB)Indian Institute of Technology DelhiNew DelhiIndia

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