Mechanism of proteases

Polgar, L. (1989) Mechanisms of Protease Action, CRC Press, Boca Raton, Florida... 

With more than 500 members, the proteases constitute one of the largest families of enzymes in the human genome and are an important class of targets for drug discovery. Biochemical assays based on fluorescence readouts are the most frequently used technologies to elaborate the enzymatic mechanisms of proteases and to test the inhibitory potencies of drug-like chemical compounds. These assay formats exist for all classes of proteases and substrate specificities. 

A class of thiazole hydrazide inhibitors of cathepsin K has also been evaluated in references 26 and 27. Similar problems to those described in the preceding paragraph related to enzyme acylation and slow turnover of inhibitor in solution were observed in trying to determine the mechanism of protease inhibition based... 

R. J. Fletteeick, Macromolecular chelation as an improved mechanism of protease inhibition structure of the ecotin-trypsin complex. Embo J. 1994, 13, 1502-1507. 11... 

The reaction mechanism of proteases is to convert the carbonyl group of the target peptide bond into an enzyme-stabilized tetrahedral diol transition state intermediate. This intermediate further collapses to yield the two-peptide products. The enzyme binds the diol intermediate, the specificity being provided by specific contacts for the amino acids side chains PI, P2, P3, PI, P2, P3 (Fig. 1) and so on, with their respective binding sites on the protein (S1, S2, S3, S1, S2, S3 ). 

Figure 25-4 Generalized mechanism of protease catalysis. (Adapted from Chem. Eng. News. Apr. 16, 1979, p. 23.)...

This simple presentation leads to interesting speculation on the pathways preferred by the enzyme. Does the conformational change occurs at the level of the substrate tetrahedral intermediate or at the level of the enzyme s active site residue Obviously rigid bioorganic models are necessary to solve this dilemma. Such models are yet to come but will offer the capacity of defining the enzyme mechanism of proteases from relatively limited conformations of the tetrahedral intermediate. 

Pelmenschikov, V. Siegbahn, P.E.M. (2002). Catalytic Mechanism of Matrix Metalloproteinases Two-Layered Piana, S. Carloni, P. (2000). Conformational flexibility of the catalytic asp dyad in HIV-1 protease an ab initio study on the free enzyme. Proteins Struct, Funct. Genet, Vol. 39, No.l, pp. 26-36 Polgar, L. (1989). Mechanisms of Protease Action, pp 157-182, CRC Press, Inc., Boca Raton, FL Pollack, L. (2011a). SAXS Studies of Ion-Nucleic Acid InteractionsAnnual Review of Biophysics Vol 40,(June 2011),pp 225-242... 

An example of a pseudoirreversible inhibitor has been demonstrated for chymotrypsin (36). This enzyme is a serine protease, and its mechanism of catalysis may be outlined as follows, where or R2 preferentially is a hydrophobic amino acid residue. 

Kraut, J. Serine proteases structure and mechanism of catalysis. Anna. Rev. Biochem. 46 331-358, 1977. 

The release of arachidonate and the synthesis or interconversion of eicosanoids can be initiated by a variety of stimuli, including histamine, hormones such as epinephrine and bradykinin, proteases such as thrombin, and even serum albumin. An important mechanism of arachidonate release and eicosanoid syn-... 

According to their genetic relationship and their biochemical mechanism of action (3-lactamases are divided into enzymes of the serine-protease type containing an active-site serine (molecular class A, C, and D enzymes) and those of the metallo-protease type (molecular class B enzymes), which contain a complex bound zinc ion. 

Proteases (proteinases, peptidases, or proteolytic enzymes) are enzymes that break peptide bonds between amino acids of proteins. The process is called peptide cleavage, a common mechanism of activation or inactivation of enzymes. They use a molecule of water for this, and are thus classified as hydrolases. 

The requirements of protease inhibitors as drugs in terms of potency, pharmacokinetics, and toxicity will vary depending on the nature of the infection and the goals of therapy. At one extreme is treatment of HlV-1, a chroific infection that requires life-long therapy and full suppression of viral replication. At the other extreme is the treatment of human rhinovirus (i.e., the cold virus), where short-term treatment to blunt viremia will likely be sufficient to reduce the unwanted symptoms of a cold. In all cases, viral proteases represent very attractive targets with familiar mechanisms of catalysis that frequently allow for the design of transition state analogs and with distinct specificities from host proteases. 

A general mechanism of resistance is reducing the affinity of the antiretroviral compound for its mutant target protein. Resistance mutations associated with reduced affinity are observed during treatment failure with a fusion inhibitor, nonnucleoside reverse transcriptase inhibitors (NNRTl), integrase inhibitor, and protease inhibitors as reviewed in Chaps. 3,4, 6, and 7 (Hazuda et al. 2007 Hsiou et al. 2001 King et al. 2002 Mink et al. 2005). 

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