Protein-inhibitor interactions

Bode W, Huber R. Structural basis of the endoproteinase-protein inhibitor interaction. Biochim. Biophys. Acta 2000 1477 241-252. 

The capability to communicate 3D structural studies with the chemists and other researchers has evolved significantly [80]. Today in our laboratories, the use of a 3D projection room has advanced the HIV-1 protease inhibitor design to a team effort, in which creative design ideas can be discussed within a group in an extremely productive manner, while visualizing the protein/inhibitor interactions. 

Krystek S, Stouch T, Novotny J. Affinity and specificity of serine endopeptidase-protein inhibitor interactions. Empirical free energy calculations based on X-ray crystallographic structures. J Mol Biol 1993 234 661-679. 

S. Krystek, T. Stouch, and J. Novotny, ]. Mol. Biol., 234,661 0 993). Affinity and Specificity of Serine Endopeptidase-Protein Inhibitor Interactions Empirical Free Energy Calculations Based on X-Ray Crystallographic Structures. 

PIAS (protein inhibitors of activated STATs) proteins were first discovered in yeast-two-hybrid screens as interacting molecules with STAT transcription factors. The mammalian family consists ofthe founding member PIAS3, which was described as a repressor of STAT3, and three additional members, PIAS1, PIASy (also known as PIAS4), and PIASx (also known as... 

Cavalli A, Greco G, Novellino E, Recanatini M. Linking CoMFA and protein homology models of enzyme-inhibitor interactions an application to nonsteroidal aromatase inhibitors. Bioorg Med Chem 2000 8 2771-80. 

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. 

Table 9 gives some cases where the rotational strengths of absorption bands have been measured in metalloproteins. At the present time these changes are not used to diagnose the nature of the ligands of the metal but rather they have been used to follow minor changes at the metal when substrates or inhibitors interact with the metals. The sensitivity of CD and MCD measurements to very small changes in the metal environment make them very attractive for protein/metal complex studies. 

In a previous work, using D-fructose pyran- and furan- forms as inhibitors of D-fructose transport in CHO (Chinese Hamsters Ovary)-GLUT5 cells, Rollin, Holman and co-workers established that both ring forms were tolerated. The approach used was to block each hydroxyl function with allylic ether it was concluded that two sites, 0-2 (pyranose and furanose) and 0-6 (furanose) could be modified and addressed a visualization of vital interactions with the protein. These interactions were considered to occur because the D-fructofuranose form is relatively symmetrical for that reason, the binding site can arise either in anomeric center side or on the other side of the molecule. Hence D-fructopyranose appears to present to GLUT5 transporter by hydroxyl 3, 4, 5 recognition (Fig. 3). 

Other enzyme-substrate or inhibitor interaction studies80 82 have been addressed, using a combination of STD and trNOE NMR experiments, in order to collect details on the substrate bound conformation (ligand perspective). In other cases, the availability of a labelled protein receptor83 have permitted to follow the induced chemical shift variations of the protein resonances upon ligand addition to the NMR tube by HSQC methods (protein perspective). 

There are at least two factors that could influence the turnover rate, the site of metabolism (hot spot) and the affinity of a compound toward these enzymes the protein/ligand (substrate or inhibitor) interaction and the chemical reactivity of the compound towards oxidation. Because of the interaction of the protein with the potential ligand, certain atoms of the compound could be exposed to the heme group, and depending on the chemical nature of these moieties the oxidative reaction will take place at different rates, for example celecoxib is metabolized by CYP2C9 at the... 

Vucic, D., W. J. Kaiser, and L. K. Miller, Inhibitor of apoptosis proteins physically interact with and block apoptosis induced by Drosophila proteins HID and GRIM. Mol Cell Biol, 1998, 18(6), 3300-9. 

Some inhibitors interact very slowly with the enzyme protein, and onset of inhibition thus exhibits time-dependence. These inhibitors are generally referred to as slow-binding inhibitors, and as slow tight-binding inhihitors if the potency of inhibition is extremely high. Analysis of these inhibitory mechanisms is complex because binding and dissociation rate constants may be determined in addition to values. Indeed, a complete analysis may require extensive use of specialized computer software, and the complexities of such analyses preclude their discussion in this chapter. However, the reader is directed to several publications from Morrison s laboratory if a slow-binding mechanism is suspected for an inhibitor of interest (Morrison, 1982 Morrison and Stone, 1985 Sculley and Morrison, 1986 Morrison and Walsh, 1988). 

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