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Design of Drugs by Filtering Through ADMET, Physicochemical and Ligand-Target Flexibility Properties

  • Marlet Martínez-Archundia
  • Martiniano Bello
  • Jose Correa-Basurto
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1824)

Abstract

There is a synergistic interaction between medicinal chemistry, chemoinformatics, and bioinformatics. The last one includes analyses of sequences as well as structural analysis which employ computational techniques such as docking studies and molecular dynamics (MD) simulations. Over the last years these techniques have allowed the development of new accurate computational tools for drug design. As a result, there have been an increased number of publications where computational methods such as pharmacophore modeling, de novo drug design, evaluation of physicochemical properties, and analysis of ADMET (absorption, distribution, metabolism, excretion, and toxicity) properties have been quite useful for eliminating the compounds with poor physicochemical or toxicological properties. Furthermore, using MD simulations and docking analysis, it is possible to estimate the binding energy of the protein-ligand complexes by using scoring functions, as well as to structurally depict the binding pose of the compounds on proteins, in order to select the best evaluated compounds for subsequent synthetizing and evaluation through biological assays. In this work, we describe some computational tools that have been used for structure-based drug design of new compounds that target histone deacetylases (HDACs), which are known to be potential targets in cancer and parasitic diseases.

Key words

Histone deacetylases Rational drug design ADMET properties Pharmacophore modeling Docking analysis Molecular dynamics simulations 

Notes

Acknowledgments

This work was supported by CONACYT Mexico (CB-254600 and PDCPN-782), SIP20160204, COFAA-SIP/IPN COFAASIP/IPN and Centro de Nanociencias y Micro y Nanotecnologías del IPN, México, and CYTED: 214RT0482.

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Copyright information

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

Authors and Affiliations

  • Marlet Martínez-Archundia
    • 1
  • Martiniano Bello
    • 1
  • Jose Correa-Basurto
    • 1
  1. 1.Laboratorio de Modelado Molecular, Bioinformática y Diseño de Fármacos, de la Escuela Superior de MedicinaInstituto Politécnico Nacional, Plan de San Luis y Díaz Mirón s/n, Col. Casco de Santo Tomas, Delegación Miguel Hidalgo, C.P.Ciudad de MéxicoMexico

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