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Access to the complete human genome sequence as well as to the complete sequences of pathogenic organisms provides information that can result in an avalanche of therapeutic targets. Structure-based design is one of the first techniques to be used in drug design. Structure based design refers specifically to finding and complementing the 3D structure (binding and/or active site) of a target molecule such as a receptor protein. The aim of this review is to give an outline of studies in the field of structure based drug design that has helped in the discovery process of new drugs. The emphasis will be on comparative/homology modeling.

Abstract:With the Entamoeba genome essentially complete, the organism can be studied from a whole genome standpoint. The understanding of cellular mechanisms and interactions between cellular components is instrumental to the development of new effective drugs and vaccines. Metabolic pathway analysis is becoming increasingly important for assessing inherent network properties in reconstructed biochemical reaction networks. Metabolic pathways illustrate how proteins work in concert to produce cellular compounds or to transmit information at different levels. Identification of drug targets in E. histolytica through metabolic pathway analysis promises to be a novel approach in this direction. This article focuses on the identification of drug targets by subjecting the Entamoeba genome to BLAST with the e-value inclusion threshold set to 0.005 and choke point analysis. A total of 86.9 percent of proposed drug targets with biological evidence are chokepoint reactions in Entamoeba genome database.

The chemokine receptor CXCR4 is the receptor for several chemokines and major co-receptor for X4 human immunodeficiency virus type-1 strains entry into cell. A three-dimensional model of human CXCR4 was developed by homology modeling using the high-resolution bovine rhodopsin structure as template. Interactions between CXCR4 and flavonoids were investigated using in silico docking studies. The results underscore the potential of these compounds that they may become important new antiviral drugs to combat AIDS. It is worth mentioning also that apart from these existing flavonoids, there are many new compounds that may also be useful as topical agents to inactivate virus, or may act as adjuvants with other antiviral drugs.

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Coprocessing of the petroleum vacuum residue (XVR) with polystyrene, polypropylene, and Bakelite has been undertaken in a batch reactor under isothermal conditions at atmospheric pressure. The liquids obtained by coprocessing have been characterized by Fourier transform infrared spectroscopy, 1 H nuclear magnetic resonance (NMR), 13 C NMR, gel permeation chromatography (GPC), inductively coupled argon plasma, and gas chromatography analyses. The main aim of the characterization of the liquid products was to find out the molecular weight distributions as well as the determination of average structural parameters. The GPC analysis showed that the liquids derived from XVR are quite complex, containing a complex range of products. The liquid products obtained from coprocessing showed that there is an interaction of reacting species when they are cracked together. It is also interesting that the liquid products obtained from coprocessing with plastics contained less than 1 ppm of Ni and V. The detailed results obtained are reported.

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