Mechanisms of Macromolecular Protease Inhibitors

Graduate Group in Biophysics, University of California-San Francisco, San Francisco, CA 94143-2240, USA.
ChemBioChem (Impact Factor: 3.09). 11/2010; 11(17):2341-6. DOI: 10.1002/cbic.201000442
Source: PubMed


Relatively few design principles underlie the inhibition mechanisms of macromolecular protease inhibitors. These inhibitors tend to compete with substrate binding either through direct competition or deformation of the protease active site; they gain potency and specificity by burying a large surface area and through contacts with specific exosites. Protein engineering has allowed both potency and specificity to be modified.

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Available from: Charles S Craik
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    • "Although the majority of cysteine protease inhibitors binds into the active site and blocks the access to their target protease, they do not bind in a strictly substrate-like manner (Laskowski & Kato, 1980; Farady & Craik, 2010). Instead, they interact with the cysteine protease subsites and catalytic residues in a non-catalytically competent manner (Farady & Craik, 2010). This view is based upon the observation that static Xray cysteine proteases structures, several in free form and complexed to inhibitors (mainly covalent inhibitors), show little differences in their conformation, as measured by the deviation of backbone dihedral angles (Laskowski & Qasim, 2000; Ratia et al., 2008; Gaspari, Varnai, Szappanos & Perczel, 2010). "
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    ABSTRACT: The major cysteine protease of Trypanosoma cruzi, cruzain (CRZ), has been described as a therapeutic target for Chagas' disease, which affects millions of people worldwide. Thus, a series of CRZ inhibitors has been studied, including a new competitive inhibitor, Nequimed176 (NEQ176). Nevertheless, the structural and dynamic basis for CRZ inhibition remains unclear. Hoping to contribute to this ever-growing understanding of timescale dynamics in the CRZ inhibition mechanism, we have performed the first study using 100 ns molecular dynamics (MD) simulations of two CRZ systems in an aqueous solvent under pH 5.5: CRZ in the apo form (ligand free) and CRZ complexed to NEQ176. According to the MD simulations, the enzyme adopts an open conformation in the apo form and a closed conformation in the NEQ176-CRZ complex. We also suggest that this closed conformation is related to the hydrogen-bonding interactions between NEQ176 and CRZ, which occurs through key residues, mainly Gly66, Met68, Asn69, and Leu160. In addition, the cross-correlation analysis shows evidence of the correlated motions among Ala110-Asp140, Leu160-Gly189, and Glu190-Gly215 sub-domains, as well as, the movements related to Ala1-Thr59 and Asp60-Pro90 regions seem to be crucial for CRZ activity.
    Full-text · Article · Sep 2015 · Journal of biomolecular Structure & Dynamics
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    • "Recently, the Kunitz-type serine protease inhibitor HAI-2 (hepatocyte growth factor activator inhibitor type 2) has been shown to inhibit the proteolytic activity of MT-2 [9]. Since Kunitz-type inhibitors bind to their target proteases in a substrate-like manner [10], HAI-2 can also be considered to bear a processing site attacked by MT-2. For instance, Kunitz domain I exhibited two critical Arg residues which might be recognized by MT-2. "
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    ABSTRACT: Human matriptase-2 is an enzyme that belongs to the family of type II transmembrane serine proteases. So far there is a limited knowledge regarding its specificity and protein substrate(s). One of the identified natural substrates is hemojuvelin, a protein involved in the control of iron homeostasis. In this work, we describe the synthesis and evaluation of internal quenched substrates using a combinatorial approach. The iterative deconvolution of two libraries to define the specificity of matriptase-2 yielded to the identification of the substrate ABZ-Ile-Arg-Ala-Arg-Ser-Ala-Gly-Tyr(3-NO2)-NH2 with a kcat/Km value of 4.5×10(5) M(-1)×s(-1), i.e. the highest specificity constant reported so far for matriptase-2.
    Full-text · Article · Oct 2013 · Biochimie
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    • "Considering eleven mammalian species (Figure 3), methionine is always present at this position except in mouse. Moreover methionine in this position (P1 position of RCL region) has been demonstrated to be involved in the interaction of AAT with its substrates, the proteases [26,27]. Different phylogeny studies of the serpin superfamily showed the importance of the amino acid composition of the RCL region to determine the ability to bind protease and non protease ligand [1,28]. "
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