Hydrolytic peptides

In many metal ion-assisted hydrolytic peptide bond cleavage reactions, the metal ions, such as Pd, Pt, Cu, Mo, and Ni, are trapped by hydrolyzed products. Because free metal ions that are reactive for peptide bond hydrolysis hardly regenerate, examples for metal ion-catalyzed peptide bond cleavage are Umited. 

Although, as stated above, we wiU mostly focus on hydrolytic systems it is worth discussing oxidation catalysts briefly [8]. Probably the best known of these systems is exemphfied by the antitumor antibiotics belonging to the family of bleomycins (Fig. 6.1) [9]. These molecules may be included in the hst of peptide-based catalysts because of the presence of a small peptide which is involved both in the coordination to the metal ion (essential co-factor for the catalyst) and as a tether for a bisthiazole moiety that ensures interaction with DNA. It has recently been reported that bleomycins will also cleave RNA [10]. With these antibiotics DNA cleavage is known to be selective, preferentially occurring at 5 -GpC-3 and 5 -GpT-3 sequences, and results from metal-dependent oxidation [11]. Thus it is not a cleavage that occurs at the level of a P-O bond as expected for a non-hydrolytic mechanism. 

Fig. 6.5 Possible interaction between the helical dinuclear Zn(ll)-peptide [33] and DNA which leads to hydrolytic cleavage of the phosphate bond. The structure of the Zn(ll)-ATANP complex is shown in the top right-hand corner...

As we have already seen zinc-finger peptides are well-studied polypeptide motifs that have found many applications in synthetic systems, mostly because of their abihty to bind metal ions and interact with oligonucleotides. In this context the report by lima and Crooke [44] of the hydrolytic cleavage by a zinc-finger peptide devoid of any metal ion is a surprising. The system they studied, a 30-amino acid sequence, is based on a catalytic mechanism very similar to that discussed above... 

While catalysis by aspartic proteases involves the direct hydrolytic attack of water on a peptide bond, catalysis... 

In mammalian cells, the two most common forms of covalent modification are partial proteolysis and ph osphorylation. Because cells lack the ability to reunite the two portions of a protein produced by hydrolysis of a peptide bond, proteolysis constitutes an irreversible modification. By contrast, phosphorylation is a reversible modification process. The phosphorylation of proteins on seryl, threonyl, or tyrosyl residues, catalyzed by protein kinases, is thermodynamically spontaneous. Equally spontaneous is the hydrolytic removal of these phosphoryl groups by enzymes called protein phosphatases. 

Burke TR Jr, Smyth M, Nomizu M, Otaka A, Roller PP. Preparation of fluoro- and hydroxy-4-(phosphonomethyl)-D,L-phenylalanine suitably protected for a solid-phase synthesis of peptides containing hydrolytically stable analogues of O-phosphotyrosine. J Org Chem 1993 58 1336-1340. 

Selective cleavage of peptides and proteins is an important procedure in biochemistry and molecular biology. The half-life for the uncatalyzed hydrolysis of amide bonds is 350 500 years at room temperature and pH 4 8. Clearly, efficient methods of cleavage are needed. Despite their great catalytic power and selectivity to sequence, proteinases have some disadvantages. Peptides 420,423,424,426 an(j proteins428 429 can be hydrolytically cleaved near histidine and methionine residues with several palladium(II) aqua complexes, often with catalytic turnover. 

Kostic et al. recently reported the use of various palladium(II) aqua complexes as catalysts for the hydration of nitriles.456 crossrefil. 34 Reactivity of coordination These complexes, some of which are shown in Figure 36, also catalyze hydrolytic cleavage of peptides, decomposition of urea to carbon dioxide and ammonia, and alcoholysis of urea to ammonia and various carbamate esters.420-424, 427,429,456,457 Qggj-jy palladium(II) aqua complexes are versatile catalysts for hydrolytic reactions. Their catalytic properties arise from the presence of labile water or other solvent ligands which can be displaced by a substrate. In many cases the coordinated substrate becomes activated toward nucleophilic additions of water/hydroxide or alcohols. New palladium(II) complexes cis-[Pd(dtod)Cl2] and c - Pd(dtod)(sol)2]2+ contain the bidentate ligand 3,6-dithiaoctane-l,8-diol (dtod) and unidentate ligands, chloride anions, or the solvent (sol) molecules. The latter complex is an efficient catalyst for the hydration and methanolysis of nitriles, reactions shown in Equation (3) 435... 

Figure 36 Complexes catalyzing hydrolytic cleavage of peptides, hydrolysis and alcoholysis of nitriles, decomposition of urea to carbon dioxide and ammonia, and alcoholysis of urea to ammonia and various...

Since kinases are not hydrolytic enzymes, a small molecule-based FRET probe does not seem to be a straight forward solution for this enzyme activity. Nevertheless, quite a number of fluorescent probes based on small substrate peptides have been prepared in... 

Bromocriptine is rapidly and completely metabolised in animals and man. The major components of the urinary metabolites have been identified as 2-bromo-lysergic acid and 2-bro-mo-isolysergic acid. Apart from the hydrolytic cleavage of the amine bond and the isomerization at position 8 of the lysergic acid moiety, a third principal biotransformation pathway consists in the oxidative attack of the molecule at the proline fragment of the peptide part, predominantly at position 8, giving rise to the formation of a number of hydroxylated and further oxidized derivatives of bromocriptine, and in addition of conjugated derivatives thereof. 

As mentioned earlier, by far the largest number of zinc enzymes are involved in hydrolytic reactions, frequently associated with peptide bond cleavage. Carboxypeptidases and ther-molysins are, respectively, exopeptidases, which remove amino acids from the carboxyl terminus of proteins, and endopeptidases, which cleave peptide bonds in the interior of a polypeptide chain. However, they both have almost identical active sites (Figure 12.4) with two His and one Glu ligands to the Zn2+. It appears that the Glu residue can be bound in a mono- or bi-dentate manner. The two classes of enzymes are expected to follow similar reaction mechanisms. 

The finding that the hydrolytic activity of the enzyme is retained after replacement of a tyrosine residue by phenylalanyl challenges the notion that a tyrosine acts as a general acid catalyst in peptide hydrolysis. It has been suggested that either the protonated Glu270 moiety or the zinc-water complex could perform the proton transfer [77]. 

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