Molecular Modeling Approaches to Investigate Essential Oils (Volatile Compounds) Interacting with Molecular Targets

Abstract

“Molecular modeling” can also be alternatively expressed as “CADD” (Computer-aided drug design) or “CAMD” (computer assisted molecular design), etc. (Yu and Mackerell, Methods Mol Biol 1520:85-106. 2017). This technique can simply be defined as a range of computerized methods useful to analyze molecules or molecular systems or to predict biological activity based on theoretical chemistry principles and experimental data. Therefore, in this chapter, we will cover various molecular modeling methods used to investigate, among other things, naturally occurring compounds that are capable of interacting with molecular targets of pharmacological importance. Here we will address methodologies such as: SAR, QSAR, molecular docking, molecular dynamics simulations and methods used to calculate the affinity energy in protein-ligand complexes. In addition, we will also devote a portion of the chapter to demonstrate how these methods can be used to investigate the interaction of fixed and volatile compounds with molecular targets.