Docking studies: &lt;i&gt;In silico&lt;/i&gt; phosphodiesterase inhibitory activity of commercially available flavonoids

Arumugam Madeswaran,Kuppusamy Asokkumar,Varadharajan Subhadradevi,Thirumalaisamy Sivashanmugam,Muthuswamy Umamaheswari,Puliyath Jagannath

doi:10.3329/bjp.v7i1.10595

Docking studies: <i>In silico</i> phosphodiesterase inhibitory activity of commercially available flavonoids

Arumugam Madeswaran, Kuppusamy Asokkumar + Show 4 more

Open Access

https://doi.org/10.3329/bjp.v7i1.10595

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Abstract

The objective of the current study is to evaluate the phosphodiesterase inhibitory activity of flavonoids using in silico docking studies. In silico docking studies were carried out using AutoDock 4.2, based on the Lamarckian genetic algorithm principle. The results showed that all the selected flavonoids showed binding energy ranging between -7.50 kcal/mol to -6.61 kcal/mol when compared with that of the standard (-4.77 kcal/mol). Inhibition constant (3.17 µM to 14.36 µM) and intermolecular energy (-9.29 kcal/mol to -8.70 kcal/mol) of the ligands also coincide with the binding energy. All the selected flavonoids contributed better phosphodiesterase inhibitory activity because of its structural parameters. Benzopyran ring in the flavonoids are majorly contributed its activity. These molecular docking analyses could lead to the further development of potent phosphodiesterase inhibitors for the treatment of inflammatory diseases.

Highlights

Docking is finding the binding ability of two interacting molecules with known structures
Its default search function is based on Lamarckian Genetic Algorithm (LGA), a hybrid genetic algorithm with local optimization that uses a parameterized free-energy scoring function to estimate the binding energy
Python 2.7- language was downloaded from www.python.com, Cygwin c:\program and Python 2.5 were simultaneously downloaded from www.cygwin.com, Molecular graphics laboratory (MGL) tools and AutoDock 4.2 was downloaded from www.scripps.edu, Discovery studio visualizer 2.5.5 was downloaded from www.accelerys.com, Molecular orbital package (MOPAC), ChemSketch was downloaded from www.acdlabs.com

Summary

Introduction

Docking is finding the binding ability of two interacting molecules with known structures. In the field of molecular modeling, docking is a method which predicts the preferred orientation of one molecule to a second when bound to each other to form a stable complex (Sandeep et al, 2011). The use of computers to predict the binding of libraries of small molecules to known target structures is an increasingly important component in the drug discovery process (Koppen, 2009). Docking of small molecules in the receptor binding site and estimation of binding affinity of the complex is a vital part of structure based drug design (Cosconati et al, 2010; Seeliger and Groot, 2010)

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Results