Comparing sequence and structure of falcipains and human homologs at prodomain and catalytic active site for malarial peptide-based inhibitor design

Falcipains are major cysteine proteases of Plasmodium falciparum essential in hemoglobin digestion. Several inhibitors blocking their activity have been identified, yet none of them has been approved for malaria treatment. For selective therapeutic targeting of these plasmodial proteases, identification of sequence and structure differences with homologous human cathepsins is necessary. The protein substrate processing activity of these proteases is tightly controlled in space and time via a prodomain segment occluding the active site making it inaccessible. Here, we utilised in silico approaches to determine sequence and structure variations between the prodomain regions of plasmodial proteins and human cathepsins. Hot spot residues, key for maintaining structural integrity of the prodomains as well as conferring their inhibitory activity, were identified via residue interaction analysis. Information gathered was used to design short peptides able to mimic the prodomain activity on plasmodial proteases whilst showing selectivity on human cathepsins. Inhibitory potency was highly dependent on peptide amino acid composition and length. Our current results show that despite the conserved structural and catalytic mechanism of human cathepsins and plasmodial proteases, significant differences between the two groups exist and may be valuable in the development of novel antimalarial peptide inhibitors.