Protein-ligand binding interactions

In all the treatments of enzyme-inhibitor interactions that we have discussed so far, we assumed that the inhibitor concentration required to achieve 50% inhibition is far in excess of the concentration of enzyme in the reaction mixture. The concentration of inhibitor that is sequestered in formation of the El complex is therefore a very small fraction of the total inhibitor concentration added to the reaction. Hence one may ignore this minor perturbation and safely assume that the concentration of free inhibitor is well approximated by the total concentration of inhibitor (i.e, [7]f [/]T). This is a typical assumption that holds for most protein-ligand binding interactions, as discussed in Copeland (2000) and in Appendix 2. 

Euture improvements of the methods presented here will include modifications that enable determination of the thermodynamic parameters of protein-ligand binding interactions. Eor example, ALIS-based Kd or off-rate measurements at varying temperatures could yield useful relationships between chemical structures and binding thermodynamics. Ready access to such information, especially for targets that otherwise require complex bioassays for their study, could posi-... 

Powell, K.D. Ghaemmaghami, S. Wang, M.Z. Ma, L Oas, T.G. Fitzgerald, M.C. A general mass spectrometry-based assay for the quantitation of protein—ligand binding interactions in solution. 

Deng et al. [18] recently described an approach to representing and analyzing 3D protein-ligand binding interactions. The Structural Interaction Fingerprint (SIFt see also Chapter 10) method represents a ligand by the interactions it un-... 

Deng, Z., Chuaqui, C., Singh, J., Structural interaction fingerprint (SI Ft) A novel method for analyzing three-dimensional protein-ligand binding interactions. J. Med. Chem. 2004, 47, 337-344. 

Novel Method for Analyzing Three-Dimensional Protein-Ligand Binding Interactions, J. Med. Chem. 2004, 47, 337-344. 

Fig. 3.3 The raw data output of ITC is transformed to show the heat exchange at each injection (kcal mol of injectant), obtained by integration of the area of each spike in the raw data output, as a function of the molar ratio of the protein-ligand binding interaction. The curve is then computer-generated as the best fit to either a one-site or multi-site binding model.

Structural interaction fingerprint (SIFt) a novel method for analyzing three-dimensional protein—ligand binding interactions. Joumol of Medicinal Chemistry, 47, 337—344. 

---