How does a bacteriophage enzybiotic target bacteria? Introducing a structural model of bacteriophage PhaxI lytic enzyme

Spurred by the emergence and prevalence of multidrug resistance of human pathogens, there has been aglobal call for novel classes of antibacterials over the last decade. Phages as natural predators of bacteriarespond to this call and have been considered a promising candidate since their discovery. Their lytic enzymesserve for cell wall degradation of the infected bacteria. The natural function of these enzymes, also called'enzybiotics,' can be exploited as powerful enzyme-based antibiotics. These insights have paved the roadtowards the (pre)clinical development of enzybiotics in various trials phases. Due to poor structural andbiochemical characterization, their significant potential as antimicrobials remains unexplored. Verifyingstructural features and enzymatic specificity is crucial for prospective enzyme modification and furtherapplication. Hence, this study aimed to shed light on the ۳D structure, determination of essential amino acidresidues, and assessment of interactions mode with the bacterial cell wall of a novel PhaxI bacteriophageenzybiotic. A computationally aided method determined that this enzybiotic has two domains: The structurewas predicted using the YASARA program and dihedral angles were evaluated by Ramachandran plot with۹۶.۷% residues in the most favored regions. After generating a tautomers library of NAG-NAM-NAGmolecules as a piece of the bacterial cell wall, virtual screening was done with Autodock Vina to determinethe best substrate-enzyme interaction. The stability and binding affinity of the complex were studied usingAMBER ۱۴ forcefield for molecular dynamics simulations for ۱۵۰ ns (۳ × ۵۰ ns) at physiological pH (۷.۴).The predicted enzyme tunnel and essential residues were further confirmed using Dali server andevolutionary structural relationship studies. These results can subsequently lead to discovering new activitiesand modes of action of these enzymes to develop potent and more efficient broad-spectrum antibacterials.

کلیدواژه ها:

Antibiotic resistant ، phage lytic enzymes ، enzybiotics ، homology modeling ، molecular dynamic simulation ، evolutionary relationships