In vitro and in silico characterization of Crocatin A from red betel leaves: targeting DNA gyrase B and DNA ligase of Enterococcus faecalis with ADMET-based druglikeness analysis

Dental caries is a disease of tooth tissue that can lead to complications, with Enterococcus faecalis being one of the Gram-positive bacteria that plays a crucial role in the infection process. Red betel leaves (Piper crocatum Ruiz & Pav.) are known to contain various phytochemicals; however, the antibacterial potential of Crocatin A, one of its isolated compounds, against E. faecalis and its molecular targets has not been previously reported. This study hypothesized that Crocatin A exhibits antibacterial activity against E. faecalis and has the potential to inhibit DNA gyrase B and DNA ligase, which are essential enzymes in DNA replication. Crocatin A was isolated from P. crocatum via column chromatography and characterized using infrared (IR) spectroscopy, nuclear magnetic resonance (NMR) spectroscopy, and mass spectrometry. In vitro assays were carried out using the Kirby-Bauer disk diffusion method at concentrations of 1, 2, and 5%, as well as the microdilution method. Antibacterial activity was further analyzed in silico to predict binding affinity toward DNA gyrase B and DNA ligase, along with the evaluation of ADMET properties. The results demonstrated that Crocatin A produced concentration-dependent inhibition zones and exhibited a minimum inhibitory concentration (MIC) of 1250 µg/mL. In silico studies revealed binding energies of -6.34 kcal/mol for DNA gyrase B and - 5.77 kcal/mol for DNA ligase. In summary, Crocatin A showed moderate inhibition zones in vitro, although its MIC and MBC activities remain weak. In silico screening suggested possible binding interactions with DNA gyrase B and DNA ligase. Given the preliminary nature of these findings and the methodological limitations of the study, further validation is required to confirm its antibacterial potential.