Comparative analysis of SilA-laccase mediated degradation of ciprofloxacin, norfloxacin and ofloxacin and interpretation of the possible catalytic mechanism

Fluoroquinolones (FQs) are the most commonly used antimicrobial drugs and regardless of their advantages in the healthcare sector, the pollution of these antimicrobial drugs in the environment has big concerns about human and environmental health. The presence of these antibiotic drugs even at the lowest concentrations in the environment has resulted in the emergence and spread of antibiotic resistance. Hence, it is necessary to remediate these pollutants from the environment. Previously alkaline laccase (SilA) from Streptomyces ipomoeae has been demonstrated to show degrading potentials against two of the FQs, Ciprofloxacin (CIP) and Norfloxacin (NOR); however, the molecular mechanism was not elucidated in detail. In this study, we have analyzed the possible molecular catalytic mechanism of FQ degrading SilA-laccase for the degradation of the FQs, CIP, NOR and Ofloxacin (OFL) using three-dimensional protein structure modeling, molecular docking and molecular dynamic (MD) studies. The comparative protein sequence analysis revealed the presence of tetrapeptide conserved catalytic motif, His(102)-X-His(104)-Gly(105). After evaluating the active site of the enzyme in depth using CDD, COACH and S-site tools, we have identified the catalytic triad composed of three conserved amino acid residues, His(102), Val(103) and Tyr(108) with which ligands interacted during the catalysis process. By analyzing the MD trajectories, it is revealed that the highest degradation potential of SilA is for CIP followed by NOR and OFL. Ultimately, this study provides the possible comparative catalytic mechanism for the degradation of CIP, NOR and OFL by the SilA enzyme.Communicated by Ramaswamy H. Sarma

Automated summary

Fluoroquinolones (FQs) are widely used antimicrobial drugs, but their environmental pollution poses significant concerns for human and environmental health. Previous studies have shown that alkaline laccase (SilA) from Streptomyces ipomoeae can degrade Ciprofloxacin (CIP) and Norfloxacin (NOR), but the molecular mechanism was not well understood. In this study, molecular modeling, docking, and molecular dynamic analysis were used to elucidate the catalytic mechanism of SilA-laccase in the degradation of CIP, NOR, and Ofloxacin (OFL). The results identified a conserved tetrapeptide catalytic motif and a catalytic triad composed of three conserved amino acid residues. MD trajectories revealed that SilA exhibited the highest degradation potential for CIP, followed by NOR and OFL. This study provides insights into the comparative catalytic mechanism of SilA enzyme in the degradation of FQs.