Common Structural Features Their Role and the Utility for Drug Design

The structural descriptions of the various domains of the nonreceptor and receptor tyrosine kinases highlight their roles in the regulation of the kinase activity. There are general themes that span the two groups, such as kinases in which autoinhibition involves the positioning of the A-loop such that the substrate binding site is blocked (e.g., Abl, IRK, IGF-1R, MuSK, FLT3, KIT, Met, FGFR), in which case the DFG motif is usually displaced rendering the kinase inactive, and yet others for which helix C is displaced by intereactions (or the lack of interactions) with other domains or with cellular proteins (cSrc, FAK, Btk, Met, EphB2, EphA2, Tie2). There are also themes restricted to each family such as the assembled inactive state involving SH3 and SH2 domains of nonreceptor PTKs (cSrc, Hck, Abl) and variations of these themes involving the same domains to help activate the kinase (e.g.,

Csk). A binding site for the myristate regulatory element in Abl is also found in cSrc where it is used by the unphosphorylated C-terminal tail. The receptor PTKs have regions such as JM domains (e.g., cKit, FLT-3, IRK, EphB2) and/or C-terminal tails (e.g., Tie, VEGFR) to regulate their activity. Many of these regulatory regions, in both families of kinases, are also involved in downstream signaling.

Each of the structures provides detailed information about intereactions of residues that stabilize or destabilize certain conformations. Many small-molecule PTK inhibitors have up till now been targeted against the well-conserved ATP binding site in the active conformation (77), exploiting subtle differences in this region to attain specificity. The most obvious example of this is the gatekeeping residue for the so-called selectivity pocket (Thr315 in Abl kinase, Thr670 in cKit, Phe654 in MuSK, Leu1157 in Met). When this residue is small, inhibitors can be designed that reach past this side chain into a hydrophobic pocket. These inhibitors will not bind to kinases with a large side chain in this position. Others have tried to target other regions of the kinase such as the substrate binding site (e.g., ref. 78). The development of a drug targeted against Abl kinase showed that an extremely high degree of selectivity can be obtained by inhibiting the unique inactive conformation of the kinase domain (79). Differences in the regulatory mechanisms, as summarized above for many of the known kinase structures, mean that they can have very different inactive conformations, resulting in binding sites that are unique for the kinase in question (Fig. 9). Such conformational differences can also be caused by local sequence differences, and even by residues outside the binding sites. Perhaps the best example of this is the effect of mutants of Abl kinase that do not contact the ligand, that do not lie in regulatory elements, but still cause insensitivity to Gleevec (55). In the Gleevec case, targeting of the inactive conformation led to the selection of resistant mutants in patients that were treated in the late stages of CML. This is because of the fact that the inhibitor contacts residues that are not important for the binding of the cofactor or for the catalytic function of the enzyme as a whole. This does not invalidate the approach of targeting an inactive conformation because Gleevec is a very successful drug in the majority of CML patients.

In summary, structural studies of inhibitors in complex with the kinase domain are very useful for discovering possible determinants of selectivity in addition to optimizing potency.

Diabetes 2

Diabetes 2

Diabetes is a disease that affects the way your body uses food. Normally, your body converts sugars, starches and other foods into a form of sugar called glucose. Your body uses glucose for fuel. The cells receive the glucose through the bloodstream. They then use insulin a hormone made by the pancreas to absorb the glucose, convert it into energy, and either use it or store it for later use. Learn more...

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