Protease physicochemical properties

Libraries of hundreds to thousands of spatially separate inhibitors have been prepared and screened to identify small molecule inhibitors of the human protease cathepsin D and the essential malarial proteases, plasmepsins I and II. The best inhibitors do not incorporate any amino adds and possess high affinity (Kj<5 nM).1241 Furthermore, these lead compounds were optimized by combinatorial methods for good physicochemical properties and minimal binding to human serum albumin. The optimized inhibitors effectively block cathepsin D-mediated proteolysis in human hippocampyl slices and are currently being used to evaluate the therapeutic potential of cathepsin D inhibition in the treatment of Alzheimer s disease. Additionally, the plasmepsin inhibitors serve as promising leads for the treatment of malaria. 

ProtScale tool of ExPASy computes amino acid scale (physicochemical properties/parameters) and presents the result in a profile plot. Perform ProtScale computations to compare the hydrophobicity/polarity profiles with %buried resi-dues/%accessible residues profiles for human serine protease with the following amino acid sequence. 

Over the last decades, several academic and industrial research programs have been focused on the development and production of appropriate biocompatible formulations that provide enhanced therapeutic performance. Three different strategies can be discerned that are applied separately or in combination (i) addition of excipients to proteins, such as protease inhibitors, penetration or absorption enhancers like bile salts, fatty acids, cyclodextrins or surfactants " (ii) modification of the physicochemical properties of proteins, e.g. by attachment of lipophilic or hydrophilic moieties or (iii) incorporation of proteins into polymeric or liposomal delivery carriers. " A variety of polymeric vectors has been developed and exploited for this purpose, including biodegradable nanoparticles, nanogels, micelles, polymer bioconjugates and soluble nanocomposites. These polymeric carriers are more extensively described in the following sub-sections. 

HX-MS at both whole protein and peptide resolutions offers important insights into a protein s dynamic properties in solution through its physicochemical properties. At peptide resolution, HX-MS describes the relative exchange across different regions of the protein, contingent on the acid-stable protease s fragmentation profile (see Section 6.2.2). If high-resolution structures of the protein are available, the output of an HX-MS experiment can be overlaid on the structural model of the protein and represented by a heat map of the protein of interest. 

An extracellular form and a cell-bound form of pullulanase (mol. wts. 1.26 x 10 and 1.41 x 10 , respectively) from Klebsiella aerogenes have been purified by ion-exchange chromatography, gel filtration, and affinity chromatography. The cell-bound form was also released by proteolysis. Comparisons of their physicochemical properties and amino-acid compositions suggested that the enzymes are derived from the same gene product, which can be cleaved selectively by endogenous or added proteases. 

Calculations of solvation and bitiditig free energy differences between (3S)-tetrahydro-3-fuiyl-Y-((lS,2R0-3-(4-amino-Y-isotbutylbenzenesulfonainido)-l-benzyl-2-hydroxypropyl) carbamate - a potent low molecular weight and orally bioactive inhibitor of tire HlV-1 protease - and its analogues were carried out witii free energy perturbation, SM2/AM1 and SM3/PM3 methods. Results showed how physicochemical properties like aqueous solubilities and bioavailabilities of friese HTV-l protease inhibitors were improved while maintaining their inhibitory potency [92]. 

Jung, S. RA. Murphy L.A. Johnson. Physicochemical and functional properties of soy protein substrates modified by low levels of protease hydrolysis./. Food Sci. 2005, 70, C180-187. 

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