Substrate Specificity and Immunological Implications of <i>Cutibacterium acnes</i> Phage Endolysins

<i>Cutibacterium acnes</i> resistance to antibiotics poses a significant challenge in treating acne vulgaris. Bacteriophages offer a promising alternative to overcome this challenge given their specificity. In the current study, 15 bacteriophages were isolated from acne affected volunteers and subjected to whole genome sequencing to characterize their genetic features, diversity and endolysins encoding genes for further structural and functional analysis. Five representative endolysins (CAP 1-1, 6-3, 7-1, 10-3, and 12-3) were chosen for structural and functional analysis after average nucleotide identity (ANI) analysis where 5 different endolysins were categorized. Furthermore, molecular docking studies assessed the binding affinities of endolysins to common peptidoglycan fragments of <i>C. acnes</i> cell wall, identifying variations in the binding interactions as CAP 6-3, 7-1, and 12-3 had greater affinities for the NAG-NAM dimer, while CAP 1-1 and CAP 10-3 interacted preferentially with NAM-L-alanyl-D-isoglutamine (MDP). Residue-level interaction mapping revealed several conserved histidine residues; ASP170 is conserved in peptide-targeting endolysins. These results imply that <i>C. acnes</i> phage (CAP) endolysins may be functionally differentiated into peptide-targeting and glycan-targeting classes based on their substrate-binding preferences, in addition to the traditional classification of endolysins by bond-cleaving activity. Notably, by interfering with NOD2-mediated signaling, MDP binding may increase the potential for modifying host immunological responses. Together, this research offers novel molecular understandings of the substrate selectivity and possible immunomodulatory functions of CAP phage endolysins. These results provide computational insights into substrate specificity and potential immunomodulatory mechanisms of <i>C. acnes</i> phage endolysins therefore experimental validation is necessary to verify their biological and therapeutic significance.