Insights into the recognition mechanism of shark-derived single-domain antibodies with high affinity and specificity targeting fluoroquinolones.

ABSTRACT: In this study, we investigated the molecular recognition mechanisms of shark-derived single-domain antibodies (ssdAbs) targeting fluoroquinolones using an integrated approach that combines in silico homologous modeling, molecular dynamics simulations, molecular docking, and alanine scanning mutagenesis. Three ssdAbs-2E6, 1N9, and 1O17-specific to enrofloxacin, norfloxacin, and ofloxacin, respectively, were selected based on previous work. Through AlphaFold2 and GalaxyWEB, the protein structures of these ssdAbs were predicted and optimized, followed by molecular dynamics simulations to emulate realistic protein behavior in a solvent environment. Molecular docking, alanine scanning mutagenesis, and subsequent verifications identified 30N and 93W of 2E6; 30N, 89R, 98Y, and 99D of 1N9; 100W an

SUBMITTER: Liu C 

PROVIDER: S-EPMC12102038 | biostudies-literature | 2025 May

REPOSITORIES: biostudies-literature