Gut Microbial Dipeptidyl Peptidase-4 and Associated Prolyl Tripeptidyl Peptidases: A Novel Classification and Response to Inhibitors

In recent decades, microbiome research has progressed profoundly from exploring microbial diversity to uncovering host-microbial-isozymes (HMI). The understanding of the implications for human health of one such HMI, microbially derived dipeptidyl peptidases, remains limited, despite their structural and functional similarities to human DPP-4 (hDPP-4). In humans, hDPP-4 plays a critical role in several vital processes, including glucose metabolism and immune regulation. Moreover, its structure and inhibition have been well studied. In contrast, putative microbial homologs of hDPP-4 lack precise delineation, classification, and nomenclature, limiting the development of targeted therapeutics. Early evidence indicates that microbial homologs of hDPP-4 may not be effectively inhibited by current therapeutics designed for hDPP-4, underscoring the need for novel approaches to target these microbial enzymes. Using a combination of experimental and computational methods, including in vitro screening of activity and hDPP-4 inhibitor assays across selected bacterial strains, this study establishes the landscape of putative microbial homologs of DPP-4 and closely associated prolyl tripeptidyl‐peptidases. We propose a novel classification of microbial DPP-4 enzymes into four distinct classes. These classes are characterized by structural variations at critical residues, which may render them incompatible with current hDPP-4 targeted therapeutics. Computational studies show molecular distinctions between potential microbial homologs and hDPP-4, highlighting variations that would explain the results of in vitro screening of hDPP-4 inhibitors across various microbial species. These findings demonstrate a high diversity of microbial enzymes structurally similar to hDPP-4 and highlight the need to develop personalized microbial-specific DPP-4 therapeutics that accommodate the unique characteristics of microbial enzymes.