Inhibitor binding site

FIGURE 7.3 Diversity of structures that interact with the (a) HIV reverse transcriptase inhibitor binding site [8] and (b) the CCR5 receptor mediating HIV-1 fusion [9],... 

Love RA, Parge HE, Yu X, Hickey MJ, Diehl W, Gao J, Wriggers H, Ekker A, Wang L, Thomson JA, Dragovich PS, Fuhrman SA (2003) Crystallographic identification of a noncompetitive inhibitor binding site on the hepatitis C vims NS5B RNA polymerase enzyme. J Virol 77 7575-7581... 

Tian, G., Ghanekar, S.V., Aharony, D., et al. (2003) The mechanism of y-secretase. Multiple inhibitor binding sites for transition state analog and small molecule inhibitors. J. Biol. Chem., 278, 28968-28975. 

An important issue in analyzing HIV-1 RT is the flexibility of the enzyme. Comparison of structures of unliganded HIV-1 RT and NNRTI-bound HIV-1 RT complexes has shown that the NNIBP is not present in the unliganded form [34,41,43]. This underscores the importance of searching both the unliganded HIV-1 RT and the HIV-1 RT complexes with inhibitors and substrates in order to identify any potential inhibitor-binding sites. 

The groove that extends down from it is highly hydrophobic and was initially assumed to be the inhibitor binding site. Figure prepared using the GRASP program [49]. 

Uncompetitive inhibitors bind only to the enzyme-substrate complex and not to the free enzyme. For example, the substrate binds to the enzyme causing a conformational change which reveals the inhibitor binding site, or it could bind directly to the enzyme-bound substrate. In neither case does the enzyme compete for the same binding site, so the inhibition cannot be overcome by increasing the substrate concentration. Scheme 5.A5.2 below illustrates this uncompetitive behaviour. 

Many lines of evidence indicate that the first committed step in de novo purine nucleotide biosynthesis, production of 5-phosphoribosylamine by glutamine PRPP amidotransfer-ase, is rate-limiting for the entire sequence. Consequently, regulation of this enzyme is probably the most important factor in control of purine synthesis de novo (fig. 23.24). The enzyme is inhibited by purine-5 -nucleotides, but the most inhibitory nucleotides vary with the source of the enzyme. Inhibition constants (A, ) are usually in the range 10-3-10-5 M. The maximum effect of this end-product inhibition is produced by certain combinations of nucleotides (e.g., AMP and GMP) in optimum concentrations and ratios, indicating two kinds of inhibitor binding sites. This is an example of a concerted feedback inhibition. 

Arias, H.R. (1996) Luminal and non-luminal non-competitive inhibitor binding sites on the nicotinic acetylcholine receptor. Molec. Membr. Biol., 13, 1. 

Lorey, S., Stockel-Maschek, A., Faust, J., et al. (2003) Different modes of dipep-tidyl peptidase IV (CD26) inhibition by oligopeptides derived from the N-terminus of HIV-1 Tat indicate at least two inhibitor binding sites. Eur. J. Biochem. 270, 2147-2156. 

Uncompetitive The ES complex at locations other than the catalytic site. Substrate binding modifies the enzyme structure, making an inhibitor-binding site available. Inhibition is not reversed by substrate. Apparent Vmax decreased Km is decreased. 

Similarity of substrate and inhibitor binding sites of enzymes in the crystal and in solution can often be demonstrated by a comparison of NMR and X-ray data, and... 

Several inhibitor binding sites have been identified in GP [4,17-19] ... 

Al-Mawsawi LQ, Fikkert V, Dayam R et al (2006) Discovery of a small-molecule HIV-1 integrase inhibitor-binding site. Proc Nat Acad Sci USA 103 10080-10085... 

Uncompetitive inhibition. The black and gray shaded objects labeled "E" represent enzyme molecules. The light purple objects, labeled "S" represent substrate molecules. The dark purple objects labeled "I" represent inhibitor molecules. The substrate binding site and the inhibitor binding site are represented as separate indentations in the... 

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