Molecule-receptor binding

After an alignment of a set of molecules known to bind to the same receptor a comparative molecular field analysis CoMFA) makes it possible to determine and visuahze molecular interaction regions involved in hgand-receptor binding [51]. Further on, statistical methods such as partial least squares regression PLS) are applied to search for a correlation between CoMFA descriptors and biological activity. The CoMFA descriptors have been one of the most widely used set of descriptors. However, their apex has been reached. 

Figure 5.27 Schematic representation of a model for the conformational change of hemagglutinin that at low pH brings the fusion peptide to the same end of the molecule as the receptor binding site. The fusion peptide (purple) is at the end of heUx A about 100 A away from the receptor binding site in the high pH form. In the low pH fragment this region of helix A has moved about 100 A towards the area where the receptor binding sites are expected to be in the intact hemagglutinin molecule. (Adapted from D. Stuart, Nature 371 19-20, 1994.)...

Figure 13.20 Ribbon diagram of the structure of a 1 2 complex between the human growth hormone and the extracellular domains of two receptor molecules. The two receptor molecules (blue) bind the hormone (red) with essentially the same loop regions (yellow).

These structural key descriptors incorporate a remarkable amount of pertinent molecular arrangements covering each type of interaction involved in ligand-receptor bindings [26]. Since every structure in a database is represented by one or more of the 960 key codes available in ISIS, suppose that two molecules include respectively A and B key codes, then the Tanimoto coefficient is given by ... 

Association constant, the ratio of the rate of onset of a molecule to a receptor binding site and the rate of... 

Ligand, a molecule that binds to a biological receptor. 

A basic concept in receptor pharmacology is the idea of orthosteric and allosteric interaction. Orthosteric interaction occurs when two molecules compete for a single binding domain on the receptor. With allosteric interactions two molecules each have their own binding domain on the receptor and the two interact through effects on the protein (conformational change). Tims, with orthosteric interactions only one molecule may occupy the receptor at any one instant whereas with allosteric interactions both molecules can bind to the receptor at the same time. There are implications for... 

The Src-homology 2 (SH2) domain is a protein domain of roughly 100 amino acids found in many signaling molecules. It binds to phosphorylated tyrosines, in particular peptide sequences on activated receptor tyrosine kinases or docking proteins. By recognizing specific phosphorylated tyrosines, these small domains serve as modules that enable the proteins that contain them to bind to activated receptor tyrosine kinases or other intracellular signaling proteins that have been transiently phosphorylated on tyrosines. 

The ability of PO to interact with the acetyl residues of chitin allows us to compare them with monovalent lectins (i.e. extensins) which when binding with hemicellulose are only affected in a medium with a high ionic strength (Brownleader et al., 2006). As a rule, POs are bound with the plant cell wall and act as its modifiers. Some POs can form complexes with an extensin of cell walls (Brownleader et al., 2006). Consequently, chitin-specific sites that are capable of interacting with polysaccharides exist in the molecules of PO, and these sites can resemble the membrane receptor binding sites or else be similar to the domains of heparinbinding proteins (Kim et al., 2001). 

A widely used 3-D QSAR method that makes use of PLS is comparative molecular field analysis (CoMFA), in which a probe atom is used to calculate the steric and electronic fields at numerous points in a 3D lattice within which the molecules have been aligned. Poso et al. [56] used the technique to model the binding of coumarins to cytochrome P450 2A5, with similar results to those obtained by Bravi and Wikel [55]. Shi et al. [57] used it to model the estrogen receptor binding of a large diverse set of compounds, and Cavalli et al. [58] used it to develop a pharmacophore for hERG potassium... 

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