Serine protease active site

Figure 15. 3- and 4-point multiple pharmacophore overlaps for the thrombin ligand MQPA and the serine protease active-site derived pharmacophores the left-side arrow indicates the incorrect indication of factor Xa selectivity from the 3-point figures, and the right-side arrow the observed activity and the increased resolution of selectivity using the 4-point relative pharmacophores. 

Eco is a powerful tool for defining the active sites of serine protease due to the extended substrate-like interaction that it makes with the protease. The three-dimensional structure of a complex with eco has many advantages that a structure of a protease alone or bound to a small molecule inhibitor does not have. Eco can be used to take a molecular impression of the serine protease active site and reveal features that determine substrate preference. These features are used to design specific inhibitors with therapeutic prospects. Often, a small molecule inhibitor is used to define a protease active site cleft, but the resulting structures have particular drawbacks. Typically, a small molecule inhibitor lacks the prime side interac-... 

H-bond acceptor (C=0), acid (COj), base (NH and lipophilic (aromatic CH). Figure 4.7 illustrates the contours and the atoms which were added (with associated pharmacophore features) for the Factor Xa serine protease active site. 

Zhou GW, Guo J, Huang W, Hetterick, RJ, Scanlan TS. Crystal stracture of a catalytic antibody with a serine protease active site. Science 1994 265(5175) 1059-1064. 

Phosphonates (Fig. 8) and sulfonates represent a third class of covalent irreversible inhibitors. These inhibitors adopt a stable tetrahedral geometry and are covalently bound transition-state analogs. They often have a peptide-like specificity element, and the electrophilicity of the leaving groups can be modified to mne the reactivity of the inhibitor. These inhibitors are specific for serine proteases, because the serine protease active site has a well-defined oxyanion hole, which stabilizes the transition-state mimic. 

Figure 3 Schematic views of the H-bond network in m2unmalian serine proteases active site (a) and of the aulduct with the intermediate of the enzymatic rea tion (b). In (b) the double arrow symbol refers to the a putative low-barrier H-bond. (Reproduced with permission from ref.citepapersp, Copyright 1999 Wiley.)...

B 200 93,000 Contains serine protease active site of C3bBb... 

C4a C4b C2 25 110,000 Amino terminal residues, anaphylatoxin (weak), increases vascular permeability and causes mast cell degranulation C4b contains a thioester bond that can attach C4b can attach covalently to target cells. Forms a complex with C2, allowing Cls to cleave C2 Contains serine protease active site of C4b2a, which... 

Bachovchin, W.W. (2001) Contributions of NMR spectroscopy to the study of hydrogen bonds in serine protease active sites, Magn. Resort Chem. 39, S199-S213. 

Serine proteases Active site serine in a Digestion and blood clotting ... 

G. W. Zhou, J. Guo, W. Huang, R. J. Fletterick, and T. S. Scanlan, Science, 265,1059 (1994). Crystal Structure of a Catalytic Antibody with a Serine Protease Active Site. 

Catalytic antibodies are capable of catalyzing reactions normally carried out by enzymes, albeit usually with much lower efficiency. Interestingly, an x-ray crystallographic analysis of the structure of a catalytic antibody that mimics chorismate mutase showed that it uses essentially the same mechanism to carry out the reaction (45), A similar finding was made for a catalytic antibody with a serine protease active site (46), Both of these observations are fascinating because while enzymes evolved over millions of years, the catalytic antibodies were generated in only a matter of weeks. 

The carboxy-terminal region in apolipoprotein (a) closely resembles the protease domain in plasminogen [eight amino acid substitutions, nine amino acid deletions, and one insertion in apo(a) relative to plasminogen, with 94% overall nucleotide sequence identity] (G28). The most important difference is the substitution of arginine by serine in the site responsible for proteolytic activity (position 4308) (G28). As a result, Lp(a) has no protease activity towards substrates for plasmin (J3). Salonen (SI) reported a serine-protease activity of Lp(a) towards fibronectin, a glycoprotein present in connective tissue matrices. 

Peptide a-oxo acids 1 (R4=H), a-oxo esters 1 (R4= alkyl or substituted alkyl), and a-oxo-amides 2 (R5=R6=H, alkyl, substituted alkyl, aryl, and/or heteroaryl) are potent reversible inhibitors for cysteine and serine proteases (Scheme 1).[1 9 Their inhibitory potency is the result of their enhanced electrophilic a-carbonyl functional group that can better compete with the substrate in the formation of a tetrahedral adduct with the cysteine or serine residue at the protease active site. In the case of peptide a-oxo esters and a-oxoamides, the extension in PI and beyond gives the inhibitors additional interactions with the protease at the corresponding sites. 

A schematic of the structure of the thrombin molecule is presented in Figure 2. The important binding sites on the surface of the thrombin molecule include the catalytic site and two exosites (anionic and apolar) or substrate recognition sites. Whereas the catalytic site is responsible for the serine protease activity, the separate substrate recognition sites are involved in the binding of heparin, fibrinogen, and thrombomodulin (6). These sites serve as targets for the direct thrombin inhibitors,... 

Figure 1 Diagram of a protease active site. A protease cieaves a peptide at the scissiie bond, and has a number of specificity subsites, which determine protease specificity. Substrates bind to a protease with their non-prime residues on the N-terminai side of the scissiie bond and their prime-side residues C-terminal to the scissiie bond. The cataiytic residues determine the ciass of protease. Serine, cysteine, and threonine proteases hydroiyze a peptide bond via a covalent acyl-enzyme intermediate, and aspartic, giutamic and metaiioproteases activate a water moiecuie to hydroiyze the peptide bond in a non-covalent manner.

Figure 7.17. Convergent Evolntion of Protease Active Sites. The relative positions of the three key residues shown are nearly identical in the active sites of the serine proteases chymotrypsin and subtilisin.

Cls 34 85,000 activity (Clra), active site-containing chain (Clr Proenzyme to serine protease activates C2 and C4 to... 

The protease/esterase inhibitor diisopropyl phosphofluoridate (LFP) was shown to block the cleavage of poliovirus polyprotein (7) This implicates a protease with a serine-containing active site. 

Sequences have been determined for plasminogen and bovine Factor XII, and they are not homologous with the other serine proteases. The amino-terminal sequence of Factor XII is homologous, however, with the active site of several naturally occurring protease inhibitors (11). 

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