Recent Advancements in Docking Methodologies

Abstract

Nowadays molecular docking has become an important methodology in CADD (Computer-Aided Drug Design)-assisted drug discovery process. It is an important computational tool widely used to predict binding mode, binding affinity and binding free energy of a protein-ligand complex. The important factors responsible for accurate results in docking studies are correct binding site prediction, use of suitable small-molecule databases, consistent docking pose, high dock score with good MD (Molecular Dynamics), clarity whether the compound is an inhibitor or agonist, etc. However, still there are several limitations which make it difficult to obtain accurate results from docking studies. In this chapter, the main focus is on recent advancements in various aspects of molecular docking such as ligand sampling, protein flexibility, scoring functions, fragment docking, post-processing, docking into homology models and protein-protein docking.

Pharmacological and Nutritional Effects of Natural Coumarins and Their Structure–Activity Relationships

“…[24] Srivastav et al built the regression models of two different variable selection approaches. [25] The HIV-1 IN inhibition activity is predicted by the genetic function approximation and sequential multiple linear regression. The study displayed that two coumarin units linked via an aryl junction were the most important for HIV-1 IN inhibitory activity.…”

“…Presence of nitrogen in compounds 10, 11, and 12 reduced the aromaticity and the value of oil-water partition coefficients (LogP), thus showed low biological activity. [25] The inhibitory effects and the structure-activity relationships of seven coumarins were studied on the replication of HIV-1 RT, HIV-1 PR, and HIV-1 IN. 11-desmethyl-inophyllum B (13) together with its precursor compound-12-carbonyl-11-demethyl-inophyllum B (14) (Figure 5), tricyclic linear intermediate and tricyclic angular intermediates all showed inhibitory effects on HIV-1 PR.…”