Crystallography receptor characterization

The problem of characterizing the three-dimensional structure of G-protein-coupled receptors by x-ray crystallography or nuclear magnetic resonance (NMR) has been particularly difficult to solve. The receptors are complicated membrane proteins that are difficult to produce in sufficiently large quantities. When they have been available, it has been difficult to make them form useful... 

As structure and function are intimely related. X-ray crystallography is the most comprehensive technique, which elucides the three-dimensional structure of the molecule. X-ray crystallographic study provides an accurate and complete chemical characterization of the compound. This method has successfully been used for the analysis of such opioid alkaloids as morphine and has evaluated as very precise and even suitable for the research of novelizations of compounds. The use of this method can also help the estimation of the receptor, because compound structure is important in binding to the receptor. 

Conformational restriction is a very powerful method for probing the bioactive conformations of peptides. Small peptides have many flexible torsion angles so that enormous numbers of conformations are possible in solution. For example, a simple tripeptide such as thyrotropin-releasing hormone (TRH 7) (Fig. 15.4) with six flexible bonds could have over 65,000 possible conformations. The number of potential conformers for larger peptides is enormous, and some method is needed to exclude potential conformers. Modem biophysical methods, e.g., X-ray crystallography or isotope edited nuclear magnetic resonance (NMR), (33) can be used to characterize peptide-protein interactions for soluble proteins, but most biophysical methods cannot yet determine the conformation of a ligand bound to constitutive receptors, e.g., G-protein-coupled receptors (34, 35). 

The choice of CADD methods that may be applied to drug design depends highly on the availability of the receptor information. If the receptor structure has been characterized by either high-resolution x-ray crystallography or NMR... 

Once an enzyme or receptor has been identified, ideally it should be isolated and characterized. A three-dimensional structure is very useful and can be determined from X-ray crystallography, NMR or by some other means which may include computer-assisted molecular modeling. The mechanism for the normal catalytic activity of the enzyme should be understood. This includes knowing the natural substrates, any natural inhibitors, and any coenzyme requirements. An i n vitro assay method must be developed to quantitatively test the effectiveness of potential inhibitors. At this point molecular modeling techniques can be used in the design process. 

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