Small Molecule Docking from Theoretical Structural Models

  • Eva Maria Novoa
  • Lluis Ribas de Pouplana
  • Modesto Orozco
Chapter
First Online:
Part of the Biological and Medical Physics, Biomedical Engineering book series (BIOMEDICAL)

Abstract

Structural approaches to rational drug design rely on the basic assumption that pharmacological activity requires, as necessary but not sufficient condition, the binding of a drug to one or several cellular targets, proteins in most cases. The traditional paradigm assumes that drugs that interact only with a single cellular target are specific and accordingly have little secondary effects, while promiscuous molecules are more likely to generate undesirable side effects. However, current examples indicate that often efficient drugs are able to interact with several biological targets [1] and in fact some dirty drugs, such as chlorpromazine, dextromethorphan, and ibogaine exhibit desired pharmacological properties [2]. These considerations highlight the tremendous difficulty of designing small molecules that both have satisfactory ADME properties and the ability of interacting with a limited set of target proteins with a high affinity, avoiding at the same time undesirable interactions with other proteins. In this complex and challenging scenario, computer simulations emerge as the basic tool to guide medicinal chemists during the drug discovery process.

Keywords

Binding Mode Root Mean Square Deviation Homology Model Virtual Screening Docking Program 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.
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Copyright information

© Springer Science+Business Media, LLC 2012

Authors and Affiliations

  • Eva Maria Novoa
    • 1
    • 2
  • Lluis Ribas de Pouplana
    • 2
    • 3
  • Modesto Orozco
    • 1
    • 3
    • 4
  1. 1.Joint IRB-BSC Research Program in Computational Biology, Barcelona Supercomputing Center and Institute for Research in Biomedicine, IRBBarcelonaSpain
  2. 2.Cell and Developmental BiologyInstitute for Research in BiomedicineBarcelonaSpain
  3. 3.Institució Catalana per la Recerca i Estudis AvançatsBarcelonaSpain
  4. 4.Structural Bioinformatics Node Instituto Nacional de BioinformáticaInstitute of Research in BiomedicineBarcelonaSpain

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