Aspartic acid proteases

Signals of apoptosis lead to the activation of a family of intracellular cysteinyl aspartic acid proteases (caspases see Section 3.3) to play a pivotal role in the initiation and execution of apoptosis induced by various stimuli. Fourteen caspases in mammalian cell have been identified (W13). 

Fig. 1.10. Statine pharmacophore library targeting aspartic acid proteases (reprinted ( adapted or in part ) with permission from Journal of the American Chemical Society. Copyright 2001 American Chemical Society).

Substrates for hepatic metabolism include insulin, glucagon, and t-PAs [89,90]. For insulin, an acidic endopeptidase (termed endosomal acidic insulinase ) appears to mediate internalized insulin proteolysis at a number of sites [91]. Specifically, the endosomal activity results from cathepsin D, an aspartic acid protease [92]. Similarly, proteolysis of glucagon has also been attributed to membrane-bound forms ofcathepsins B and D [93]. 

Characterization of HIV-1 protease as a member of the aspartic acid protease family provided the rationale for most of the efforts to design inhibitors (Kohl et al, 1988 Krausslich et al., 1988 Navia et al., 1989 Pearl and Taylor, 1987). Previous efforts to develop therapeutically useful inhibitors of the mechanistically related enzyme renin had demonstrated that potent inhibitors could be prepared by replacing the scissile amide bond of a substrate analogue with a nonhydrolyzable isostere to mimic the tetrahedral intermediate or transition state involved in amide hydrolysis (Greenlee, 1990). Although several dipeptide isosteres have been used to successfully generate highly potent HIV-1 protease inhibitors, a relatively small number have resulted in compounds that reached clinical development. 

Caspase 8 Cysteinyl aspartic acid-protease 8 FLICE, FADD-like Ice, Mach-1, Mch5... 

Caspase 9 cysteinyl aspartic acid-protease-9 ICE-LAP6, Mch6, Apaf-3... 

Caspase 3 Cysteinyl aspartic acid-protease-3 CPP32, Yama, Apopain, SCA-1, LICE... 

Caspase 10 Cysteinyl aspartic acid-protease-10 Mch4, FLICE-2... 

Figure 1.18 Left Piperidine-derived inhibitors (top) were shown to inhibit aspartic acid proteases by bridging the two catalytically active aspartate residues (bottom). Based on this finding [99, 100], together with the knowledge of the cyclohexanone-based active site-spanning cysteine protease inhibitors [96-98], novel cyclic warheads against aspartic acid proteases can be designed as target family-directed privileged structures [3, 101],...

Caspase-14 MICE Cysteinyl aspartic acid-protease-14, also known as MICE. Overexpression of MICE induces apoptosis... 

LaPointe CF, Taylor RK. 2000. The type 4 prepilin peptidases comprise a novel family of aspartic acid proteases. J. Biol. Chem. 275 1502-10... 

As the names already imply, the amino acids serine, cysteine and aspartic acid play an essential role in the catalytic site of the respective enzymes. Modification or blocking of these amino acid residues leads to complete inactivation of these enzymes. The serine proteases have a pH optimum at alkaline pH, the cysteine proteases show maximum activity at more neutral pH, whereas the aspartic acid proteases exhibit optimal activity at acidic pH. The metalloproteases contain an essential metal atom in their active site, usually zinc. They have optimal activity at neutral pH. 

Several examples have appeared in the literature in which this linker has been employed in combinatorial chemistry strategies. Thus, it has been used in a Pd-mediated three-component coupling strategy for the solid-phase synthesis of tropane derivatives [46], in the solid-phase synthesis of aspartic acid protease inhibitors [47], in the attachment of cholic acid as a template for a combinatorial approach [48] and, more recently, in the solid-phase synthesis of pyrrolidines via 2-aza allyl anion cycloadditions with alkenes [49]. 

Keywords Alzheimer s disease- Aspartic acid protease- BACE-1- Fragment-based drug discovery- Structure-based design... 

BACE-1 is a membrane-anchored aspartic acid protease that is localized to the acidic compartments of endosomes and lysosomes in the CNS and has an optimal enzymatic activity at around pH 5. As a consequence, a BACE-1 inhibitor needs to be able to cross the blood-brain barrier and to have a significant non-protein bound fraction in order to reach the active site of the enzyme. This makes traditional aspartic protease inhibitors, which typically are large and peptidic, unsuitable as BACE-1 inhibitors. Moreover, the BACE-1 active site is extended, shallow and hydrophilic (Fig. 2) [99]. Therefore, the development of potent, selective, orally active, and brain penetrant low MW compounds has been a big challenge for the pharmaceutical industry [101, 102],... 

Fig. 2 BACE-1 characteristics. The overall fold of BACE-1 is typical for an aspartic acid protease, consisting of an N- and C-terminal lobe with the substrate binding site located in a crevice between the two lobes [99, 100], A flexible hairpin, called the flap (Yellow see-through surface), partially covers the active site of BACE-1 and can adopt many different conformations as a result of inhibitor binding. In the center of the active site are the two aspartic acid residues orange and inset) that are involved in the enzymatic reaction... 

We have used a highly structure-driven approach composed of fragment-based NMR screening, X-ray crystallography, and structure-assisted chemistry to develop a first-in-class clinical candidate as a potential proof-of-concept for the inhibition of BACE-1 in AD. Crucial to this achievement was the initial identification of a ligand-efficient isothiourea fragment and its X-ray crystal structure, which revealed an extensive H-bond network with the two active site aspartates. This interaction was unprecedented in the aspartic acid protease field when we discovered it several... 

The human immunodeficiency virus protease (HIV-PR), an aspartic acid protease, is involved in the processing of viral polyproteins and is therefore essential for the production of new infectious virions. This enzyme is one of the best-characterized macromolecules from the vantage of drug design, with several hundred crystal structures determined to date. Protein crystallography has contributed in many... 

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