Protease stability is a pivotal consideration in the development of peptide-based drugs. Improving the bioavailability of pharmacologically active peptides requires in-depth investigation into the noncovalent interactions between the protease and the peptide substrate under consideration.
To this end, different strategies such as the use of unnatural building blocks and fluorinated amino acids have become standard approaches in protein engineering. The incorporation of fluorine into amino acids has attracted much interest in recent years due to the unique stereoelectronic properties of fluorine, which have already proven useful in the development of therapeutically active small molecules. In this manner, the current thesis presents data on the systematic investigation of the influence of side chain fluorination on proteolytic stability of peptide sequences that are based on ideal protease substrates. Several model peptides were designed according to the specificities of serine and aspartic proteases; three different control sequences were modified by introducing either 2-aminobutyric acid
(Abu) or one of its fluorinated derivatives at the P2, P1'or P2' positions. Through the use of an RP-HPLC assay with fluorescence detection, the proteolytic stabilities of these peptides toward α-chymotrypsin, pepsin, elastase, proteinase K and human blood plasma proteases were determined. Molecular modeling was used to support the interpretation of the structure-activity relationship based on the analysis of potential ligand-enzyme interactions. In all cases, increases and decreases in proteolytic stability were observed for the different isolated enzymes and the human blood plasma, and these effects depend upon the particular peptide sequence, the fluorine content of the side chain, and the position of substitution relative to the cleavage site. Interestingly, in some cases fluorination leads to dramatic improvements in resistance to degradation: namely, TfeGly and DfeGly at the P2’ position with pepsin; DfeGly at the P2 position with chymotrypsin; TfeGly and DfeGly at the P2 and P2’ positions with proteinase K; and TfeGly at the P2 and P1’ positions with elastase. Our observations indicate that although the fluorination of peptide substrates does not always have predictable effects on proteolytic stability, this strategy for developing more bioavailable peptide therapies is promising; in particular, part of this thesis was devoted to establishing an analytical approach for the identification of fluorinated peptide-based HIV-1 entry inhibitors.
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