Virtual Screening for HIV Protease Inhibitors Using a Novel Database Filtering Procedure

Identification of Potential Inhibitors of Cathepsin-B using Shape & Pharmacophore-based Virtual Screening, Molecular Docking and Explicit Water Thermodynamics

Lysosome has been long understood as a vital digestive organelle. Increasing reports indicate that the lysosome also plays a crucial role in the pathogenesis of a variety of neurodegenerative diseases, including Huntington's disease, Alzheimer's disease, Parkinson's disease and amyotrophic lateral sclerosis. Abnormal protein degradation and deposition stimulated by lysosomal dysfunction may cause age-related neurodegeneration. Enormous efforts have been devoted to the development of effective therapeutics against Alzheimer's disease, the most debilitating neurodegenerative disease. Endopeptidase activity of the Cathepsin-B is associated with the pathological processes. Work presented here focuses on identification of new inhibitors against Cathepsin-B protein using diverse computational approaches together. The inhibitors identified were further tested for in-vitro activity using enzyme based assay method. The identified inhibitors provided interesting understanding on how the water thermodynamic properties along with hydrophobic, steric, electronic, and structural requirements contribute to cathepsin-B inhibitory activity. These water thermodynamic studies, may further be used in computer aided drug discovery pipeline to design and predict more potent derivatives of various scaffolds as cathepsin-B inhibitors.

Molecular Docking: From Lock and Key to Combination Lock

Accurate modeling of protein ligand binding is an important step in structure-based drug design, is a useful starting point for finding new lead compounds or drug candidates. The 'Lock and Key' concept of protein-ligand binding has dominated descriptions of these interactions, and has been effectively translated to computational molecular docking approaches. In turn, molecular docking can reveal key elements in protein-ligand interactions-thereby enabling design of potent small molecule inhibitors directed against specific targets. However, accurate predictions of binding pose and energetic remain challenging problems. The last decade has witnessed more sophisticated molecular docking approaches to modeling protein-ligand binding and energetics. However, the complexities that confront accurate modeling of binding phenomena remain formidable. Subtle recognition and discrimination patterns governed by three-dimensional features and microenvironments of the active site play vital roles in consolidating the key intermolecular interactions that mediates ligand binding. Herein, we briefly review contemporary approaches and suggest that future approaches treat protein-ligand docking problems in the context of a 'combination lock' system.