Molecular Docking, Molecular Dynamic Simulation and ADME of Some Plant Extracts and their Effects on COVID-19 Patients

Abstract

With the spread of media reports about the discovery of "innovative" drugs that could treat people infected with the virus, the World Health Organization rushed to refute such claim on February 6, 2020, stressing that there are no known effective treatments. This opened the door to alternative means of preventing the killer virus. One of these methods is to use medicinal plants with antiviral properties, such as garlic and Nigella sativa. These medicinal herbs have the advantage of containing effective anti-viral compounds. Molecular docking is a method for predicting the preferred binding location of one molecule, known as a ligand, to a second, known as a receptor. 3 Receptors are 3D protein structures that are usually published in the protein data bank. When the 3D structure of the test protein is not available, homology modeling is used instead. Docking is a computational method that has become a popular drug discovery tool, particularly in academic settings, due to its low cost and perceived ease of use. 4,5 The first crucial component of molecular techniques is the searching algorithm, and the second is the scoring function. These two components collaborate to identify the most stable binding conformation between the two partners. The searching algorithm component is in charge of exploring the searching space by making systematic adjustments to the orientation and conformation of the molecule. 6 Many searching algorithms have been developed to look for a more stable compound between the two partners within the conformational space. The scoring function, on the other hand, evaluates or, as the name implies, scores the ligand conformations generated by the search method. The searching function may appear overwhelming at first glance, but it is only the sum of the basic bonding and non-bonding characteristics of the two molecules that comprise the complex.