Molecular Docking Technique to Understand Enzyme-Ligand Interactions

Molecular Docking Technique to Understand Enzyme-Ligand Interactions

Kailas Dashrath Sonawane (Shivaji University, India) and Maruti Jayram Dhanavade (Shivaji University, India)
DOI: 10.4018/978-1-5225-0115-2.ch010
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Abstract

Molecular docking has advanced to such an extent that one can rapidly and accurately identify pharmaceutically useful lead compounds. It is being used routinely to understand molecular interactions between enzyme and ligand molecules. Several computational approaches are combined with experimental work to investigate molecular mechanisms in detail at the atomic level. Molecular docking method is also useful to investigate proper orientation and interactions between receptor and ligand. In this chapter we have discussed protein-protein approach to understand interactions between enzyme and amyloid beta (Aß) peptide. The Aß peptide is a causative agent of Alzheimer's disease. The Aß peptides can be cleaved specifically by several enzymes. Their interactions with Aß peptide and specific enzyme can be investigated using molecular docking. Thus, the molecular information obtained from docking studies might be useful to design new therapeutic approaches in treatment of Alzheimer's as well as several other diseases.
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Introduction

Molecular docking has become a useful technique in structure-based drug design (Sousa, 2006). We can predict the preferred orientation of receptor and ligand bound to each other to form a stable complex (Lengauer & Rarey, 2006). The molecular docking is a multistep process which starts with the representation followed by docking algorithms to identify best matched conformation to receptor structure. The docking algorithms complemented by scoring functions which is used for evaluation of interactions between ligand and receptor based on shape and electrostatic complementarities (Kitchen, et al., 2004). The two main features of molecular docking technique are conformation search algorithm and scoring function estimates the binding affinity between molecules. There are three types of docking such as protein-protein (Sonawane & Barage, 2004; Tseng, et al., 2007; Barage, et al., 2014), protein-ligand (Jalkute, et al., 2014; Jalkute, et al., 2015) and DNA-protein (Parulekar, et al., 2013) which may apply depending upon the receptors and ligands used in the docking experiments. There are two types of docking approaches used such as rigid docking and flexible docking. In rigid docking approach both the protein and ligand are considered as rigid bodies whereas in the flexible-ligand docking, receptor and ligand kept flexible. Most of the molecular docking programs treat protein as a rigid molecule and ligand as a flexible molecule. For molecular docking studies several docking programs such as AutoDock (Morris, et al., 2009), HEX (Macindoe, et al., 2010), PatchDock (Duhovny, et al., 2002; Schneidman-Duhovny, et al., 2005), Ludi (Böhm, et al., 1992), Glide (Halgren, et al., 2004), etc. are being used with appropriate docking algorithms and scoring functions.

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