SI Pocket

The deep hydrophobic SI pockets are very similar in all three proteins. All residues are conserved except for an A190S mutation in trypsin vhich makes its pocket smaller and slightly more hydrophilic. While this is reflected by the pseudo-contour fields, the authors doubt that this difference can be exploited to design selective ligands. 

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A virtual screen of 10,000 primary amine fragments against dipeptidyl peptidase IV (a diabetes target) identified a number of hits, as determined by bioassay screening at 100 pM, e.g. 6 [21]. An X-ray structure of this fragment confirmed the predicted binding mode in the Si pocket and inspired a structure-based hypothesis that eventually led to identification of a potent series of DPP-IV inhibitors [22],... 

Fig. 19.7 Three possible orientations of the ligand HUB093 within the SI pocket of the enzyme peptide deformylase. Heavy atoms of the protein are coloured according to secondary chemical shift effects caused by the ring current...

Besides the synthetic inhibitors, a variety of natural compounds is known to inhibit the CP. One of these natural inhibitors, lactacystin, was discovered by its ability to induce neurite outgrowth in a murine neuroblastoma cell line. Incubation of cells in the presence of radioactive lactacystin leads to the labelling of the yS5 subunit (Fenteany et al. 1995) and to irreversible inhibition of the CP. As shown by X-ray analysis, the inhibitor is covalently attached to subunit fS5 by an ester bond with the N-terminal ThrlO (Groll et al. 1997) (see Figure 10.7A). The subunit selectivity of lactacystin can be attributed to its dimethyl group, which mimics a valine or a leucine side chain and closely interacts with Met45 in the hydrophobic SI pocket of subunit j85. 

Fig. 10.7. Inh ibitor binding to individual active sites of the yeast 20S proteasome. The inhibitors lactacystin (A), epoxomicin (B) and TMC95A (C) are colored green and are shown in stereo mode together with their unbiased electron densities. The active-site Thrl is highlighted in black. (A) Covalent binding of the Streptomyces metabolite lactacystin to the active site of 5. The SI pockets of the active subunits and differ from that of 5 and are not suitably constructed to bind the inhibitor. As discussed in the text, Met45 (black), which is located at the bottom of the 5-Sl pocket, makes the difference for inhibitor...

Maignan, S., Guilloteau, J.-P., Choi-Sledeski, Y.M., Becker, M.R., and Ewing, W.R. Molecular stmctures of human factor xa complexed with ketopiperazine inhibitors preference for a neutral group in the SI pocket./. Med. Chem. 2003, 46, 685-690. 

The volumes of the SI pockets vary greatly. Matrilysin has the smallest SI pocket at 111 A3. The fibroblast collagenase pocket is not much larger at... 

Not all structure-based design experiments are successful. Attempts to displace the arginine residue that caps the SI pocket of HFC by forming a salt link with carboxylate or hydroxyl moiety were unsuccessful [42]. However, these failed attempts offer some redeeming features in the refinement of parameters that can be used to evaluate the energetic potentials for displacing buried water molecules as well as the inherent desolvation energies for polar compounds. 

In both cases the acids are much more selective for Factor Xa over thrombin. An initial modeling study using a homology-built Factor Xa structure proposed a fit of DX9065a to Factor Xa in which the amidinoaryl group occupies the SI pocket and the acetimidoyl group is directed out of the S4 pocket [60]. 

Molecular modeling fit of compound 2 with the arylamidino group positioned in the SI pocket and the acetimino group in the S4 cation-7t site [69]. 

Lys switch in antistasin. This may be due to Ala190 in the SI pocket of FXa, which... 

G. DeSantis, X. Shang, and J. B. Jones, Toward tailoring the specificity of the SI pocket of subtilisin B. lentus chemical modification of mutant enzymes as a... 

The serine proteases are a dass of proteolytic enzyme (they catalyze the hydrolysis of either ester or peptide bonds in proteins) that require an active site residue for covalent catalysis. The active site residue, the catalytic Ser-195, is particularly activated by hydrogen-bonding interactions with His-57 and Asp-102. Crystal structures show that Ser-195, His-57, and Asp-102 are dose in space. Together these three residues, which are located in the substrate binding (SI) pocket, form the famed catalytic triad of the serine proteases. In humans and mammals serine proteases perform many important functions, especially the digestion of dietary protein, in the blood-dotting cascade, and in the complement system ... 

Tab. 5.1.1. Effect of active-site glycosylation at the artificial cysteine166 at the base of the primary specificity Si pocket on the substrate tolerance of subtilisin (according to ref. [1 7b], with permission from the Royal Society of Chemistry).3... 

Thrombin is the pivotal trypsin-like protease for the regulation of thrombosis and hemostasis. Thrombin hydrolyzes its natural substrates by recognition of the Pro-Arg motif in the apolar S2- and the primary specificity SI pocket [42]. The molecular structure of the thrombin-CtA complex (Figure 1.11) showed that CtA was bound to the active site of the enzyme. The arginine side chain formed an electrostatic interaction with Aspl89, located at the bottom of the SI binding pocket. 

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