Survival tactics: A study on the substrate-binding protein SapA-mediated defense mechanism of non-typeable Haemophilus influenzae against human antimicrobial peptides.

Non-typeable Haemophilus influenzae (NTHi) is an opportunistic pathogen that causes several respiratory diseases. It employs the Sap (sensitivity to antimicrobial peptide) transporter to achieve resistance against the human antimicrobial peptides (hAMPs). In H. influenzae, the Sap system comprises six subunits, SapABCDFZ, akin to the canonical ATP-binding cassette (ABC) importers. The subunit HiSapA, which plays a role in the substrate binding, has been reported to capture hAMPs such as LL-37 and β-defensins. However, the substrate types and their binding mechanism(s) by HiSapA have not been fully understood. In this study, attempts were made to fill such gaps using in silico approaches. The results of this study suggest that five hAMPs, hBD-2, hBD-3, hNP-1, hNP-4, and hLL-37 can bind to HiSapA with a binding energy ranging from -24.03 to -78.55 kcal mol. Further, specific sequence motifs, RRYKQ of hBD-2, PKEEQ of hBD-3, RRYGT of hNP-1, RLVFCR of hNP-4, and LGDFFR of hLL-37, present in the hAMPs, were identified as crucial for HiSapA interaction. In addition, an analysis of the conformational changes and variations in the volumes of the binding-site pocket suggested that there is an increase (from 823 Åto 2095 Å) upon hAMPs binding to HiSapA, indicating its binding mechanism is similar to the previously proposed mechanism, viz. "Venus Flytrap", known for SBPs of ABC importers. In summary, the findings of this study can be utilized for structure-based drug development.