Predictive mutagenesis of prolyl endopeptidase from non-pathogenic acidophilic bacteria for gliadin catalysis

Abstract

The enzyme prolyl endopeptidase is a member of serine peptidase group belonging to the MEROPS peptidase family S9 of clan SC. It is popularly known for its preferential cleavage of small peptides usually 30 amino acid long at the carboxyl end of proline residues. This characteristic cleavage property makes prolyl endopeptidase a therapeutic in treating gluten allergy which is triggered by 33 amino acid long (gliadin α-2) or 26 amino acid long peptides rich in proline and glutamine residues. Digestion of gliadin peptides to a length lesser than 9 amino acids can impede an autoimmune response and thus gluten sensitivity in genetically susceptible individuals. To address this issue, we have investigated the prolyl endopeptidase interactions with gliadin peptide by docking studies. Based on the docking exercises, interacting residues of endopeptidase can be further subjected to introduction of in silico mutations. A series of favourable mutations sites such as N477, I478, N483 and A682 in human PEP corresponding to which sites A548, G549, A555 and I737 have been identified respectively in Candidatus sulfotelmatobacter sp. sbA7, a non-pathogenic acidophilic human PEP homolog. Simulation of single substitution mutation at site A548 was tested capable to catalyse complete digestion of immunogenic gliadin α-2 peptide.