Antibiofilm and antibacterial effects of Nigella sativa extract against Streptococcus mutans predicting the role of fatty acids composition: in vitro, CLSM and in silico studies

Purpose: To investigate the antibiofilm and antibacterial properties of Nigella sativa seed aqueous extract (NSE) against Streptococcus (S.) mutans. Methods: Chemical analysis of aqueous extract powder of Nigella sativa seeds was carried out using gas chromatography–mass spectrometry (GC-MS). S. mutans biofilm removal by NSE and chlorhexidine (CHX) mouthwash was evaluated using crystal violet (CV) assay. Ten extracted human teeth were sectioned to obtain 12 enamel specimens. Enamel specimens were coated by artificial saliva with bovine serum albumin, and then inoculated by S. mutans for biofilm formation. Enamel specimens were divided into four groups [positive biofilm control (without treatment), negative biofilm control (without bacteria), NSE and CHX biofilm treatment groups]. Acridine orange/propidium iodide assay was used for vital/dead biofilm staining. Confocal laser scanning microscopy (CLSM) biofilm images were digitally analyzed to calculate vital/dead stains relative fluorescence (RF) and estimate biofilm thicknesses. Molecular docking (MD) of interaction between long chain fatty acids (FAs) of NSE and MurA enzyme (PDB: 1UAE) was performed. Results: GC-MS revealed high concentration of long chain FAs (linoleic, oleic and palmitic acids). NSE and CHX groups showed significantly the highest red (dead) RF. NSE caused the highest reduction in biofilm thickness. NSE and CHX presented the minimum absorbance in CV assay. MD predicted a high binding affinity between FAs ligands and MurA receptors (Arg371, Arg331, Asn23, Lys22), with maximum affinity to linoleic acid (–98.07 kcal/mol). Conclusion: NSE showed antibacterial effect against S. mutans biofilm comparable to that of CHX, with a higher biofilm removal effect. NSE is expected to have a MurA enzyme inhibitory effect.