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Practices in Molecular Docking and Structure-Based Virtual Screening

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Book cover Computational Drug Discovery and Design

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1762))

Abstract

Drug discovery has evolved significantly over the past two decades. Progress in key areas such as molecular and structural biology has contributed to the elucidation of the three-dimensional structure and function of a wide range of biological molecules of therapeutic interest. In this context, the integration of experimental techniques, such as X-ray crystallography, and computational methods, such as molecular docking, has promoted the emergence of several areas in drug discovery, such as structure-based drug design (SBDD). SBDD strategies have been broadly used to identify, predict and optimize the activity of small molecules toward a molecular target and have contributed to major scientific breakthroughs in pharmaceutical R&D. This chapter outlines molecular docking and structure-based virtual screening (SBVS) protocols used to predict the interaction of small molecules with the phosphatidylinositol-bisphosphate-kinase PI3Kδ, which is a molecular target for hematological diseases. A detailed description of the molecular docking and SBVS procedures and an evaluation of the results are provided.

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Acknowledgments

We gratefully acknowledge financial support from the State of Sao Paulo Research Foundation (FAPESP, Fundação de Amparo à Pesquisa do Estado de São Paulo), grants 2015/13667-9, 2013/25658-9, and 2013/07600-3.

Author information

Authors and Affiliations

  1. Departamento de Físico-Química, Universidade Estadual de Campinas (UNICAMP), Campinas, SP, Brazil

    Ricardo N. dos Santos

  2. Laboratório de Química Medicinal e Computacional, Centro de Pesquisa e Inovação em Biodiversidade e Fármacos, Instituto de Física de São Carlos, Universidade de São Paulo (USP), São Carlos, SP, Brazil

    Leonardo G. Ferreira & Adriano D. Andricopulo

Authors
  1. Ricardo N. dos Santos
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  2. Leonardo G. Ferreira
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  3. Adriano D. Andricopulo
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Corresponding authors

Correspondence to Leonardo G. Ferreira or Adriano D. Andricopulo .

Editor information

Editors and Affiliations

  1. Department of Basic and Applied Sciences, Dayananda Sagar University, Bangalore, KA, India

    Mohini Gore

  2. Department of Biotechnology, Shivaji University, Kolhapur, MH, India

    Umesh B. Jagtap

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dos Santos, R.N., Ferreira, L.G., Andricopulo, A.D. (2018). Practices in Molecular Docking and Structure-Based Virtual Screening. In: Gore, M., Jagtap, U. (eds) Computational Drug Discovery and Design. Methods in Molecular Biology, vol 1762. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-7756-7_3

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  • DOI: https://doi.org/10.1007/978-1-4939-7756-7_3

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-7755-0

  • Online ISBN: 978-1-4939-7756-7

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