Proteases, activity fingerprint

Figure 10.10 Libraries of peptide-like structures containing warheads used to study the activity fingerprint of several proteases...

The i-poly(3HB) depolymerase of R. rubrum is the only i-poly(3HB) depolymerase that has been purified [174]. The enzyme consists of one polypeptide of 30-32 kDa and has a pH and temperature optimum of pH 9 and 55 °C, respectively. A specific activity of 4 mmol released 3-hydroxybutyrate/min x mg protein was determined (at 45 °C). The purified enzyme was inactive with denatured poly(3HB) and had no lipase-, protease-, or esterase activity with p-nitro-phenyl fatty acid esters (2-8 carbon atoms). Native poly(3HO) granules were not hydrolyzed by i-poly(3HB) depolymerase, indicating a high substrate specificity similar to extracellular poly(3HB) depolymerases. Recently, the DNA sequence of the i-poly(3HB) depolymerase of R. eutropha was published (AB07612). Surprisingly, the DNA-deduced amino acid sequence (47.3 kDa) did not contain a lipase box fingerprint. A more detailed investigation of the structure and function of bacterial i-poly(HA) depolymerases will be necessary in future. 

D-QSAR studies demonstrated that there could be more than one way to fit structure-activity data within a QSAR methodology. A receptor-independent 4D-QSAR study identified the hydrophobic nature of a HIV protease receptor site and helped in structural modification to improve the potency of the AHPBA inhibitors [241], A 4D-fingerprint-based QSAR model developed for AHPBA inhibitors of HIV was generated independent of any receptor structure or alignment information [126]. These models exhibited comparable statistical data with CoMFA, CoMSIA and H-QSAR approaches. This study proved that genuine representation of 3D and conformational properties of compounds is possible using this approach. 

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