In vitro and in silico investingation of antimicrobial activity of essential oils from two Pastinaca sativa subspecies

Abstract

INTRODUCTION: Cultivated parsnip (Pastinaca sativa subsp. sativa L., Apiaceae) root is a well-known vegetable, common ingredient of soups, stews, salads, casseroles etc. Besides, its leaves and young shoots can be added to soups and fruits are used as a condiment. Furthermore, young shoots of wild-growing parsnips, e.g. P. sativa subsp. urens (Req. ex Godr.) Čelak., are consumed pickled or in salads or soups and it is considered that their essential oil acts as a natural preservative.

OBJECTIVES: To investigate and compare the antimicrobial activity of the essential oils obtained from the roots, leaves, stems, flowers and fruits of cultivated P. sativa subsp. sativa and wild-growing P. sativa subsp. urens collected in Serbia. Furthermore, the most active essential oil constituents (against the most susceptible microorganisms) were predicted in silico.

METHOD / DESIGN: Minimum inhibitory concentrations (MICs) and minimum bactericidal/fungicidal concentrations (MBCs/MFCs) of the essential oils (isolated by hydrodistillation using Clevenger-type apparatus) were determined by microdilution method against three Gram-positive bacteria: Staphylococcus aureus ATCC 11632, Bacillus cereus clinical isolate and Listeria monocytogenes NCTC 7973, three Gram-negative bacteria: Escherichia coli ATCC 25922, Salmonella Typhimurium ATCC 13311 and Enterobacter cloacae ATCC 35030, three Candida standard strains: C. albicans ATCC 10231, C. tropicalis ATCC 750 and C. parapsilosis ATCC 22019, and three Candida isolates from oral cavity: C. albicans 475/15, C. krusei H1/16 and C. glabrata 4/6/15. Pharmacokinetic properties of the compounds present in at least one oil in the quantity ≥ 1% (determined by GC-FID and GC-MS) were initially evaluated using SwissADME web tool and molecular docking was performed using AutoDock Vina 1.1.2 (interactions were visualized using Discovery Studio Visualizer 2019).

RESULTS: All the investigated essential oils of the two Pastinaca sativa subspecies were able to reduce the growth of different tested Candida strains (MIC range 0.25-2 mg/mL; MFC range 0.5-4 mg/mL). The most promising activity was observed for both root oils (MIC range 0.25-1 mg/mL; MFC range 0.5-2 mg/mL). Among investigated Candida strains, C. parapsilosis strain was the most sensitive to these essential oils (MIC range 0.25-1 mg/mL; MFC range 0.5-2 mg/mL). The antibacterial activity of the tested essential oils was lower compared to their anticandidal potential (MIC range 1-4 mg/mL; MBC range 2-8 mg/mL). Thirty compounds were present in at least one oil in the quantity ≥ 1%. Estimation of pharmacokinetic properties using SwissADME tool suggested that 23 of these compounds are inhibitors of some of the cytochrome P450 system isoenzymes. This fact led to assumption that they could also act against fungal sterol 14α-demethylase (CYP51), which is a common target of antifungal drugs (e.g., ketoconazole). Thus, the compounds (3D structures downloaded from PubChem) were docked to the active site of this enzyme (downloaded from Protein Data Bank, PDB code 5TZ1). The highest affinities were predicted for sesquiterpenes caryophyllene oxide, (E)-caryophyllene, germacrene D, α-copaene, β-bourbonene and δ-cadinene (free binding energies from -9.4 to -8.7 kcal/mol; ketoconazole -11.6 kcal/mol). These compounds were present in somewhat lower quantities in the essential oils (≤ 9.9%). For dominant compounds of the tested essential oils, e.g. myristicin, γ-palmitolactone and octyl butanoate a bit lower affinities were predicted (free binding energies from -7.3 to -5.8 kcal/mol). Tested compounds mostly docked near the heme of the enzyme and formed hydrophobic interactions with the amino acid residues of the active site. According to SwissADME tool, four of five most active compounds have low absorption from gastrointestinal tract and higher skin permeation value, while caryophyllene oxide and three dominant compounds have high absorption and lower skin permeation value (similarly to ketoconazole).

CONCLUSIONS: Investigated parsnips represent sources of essential oils and compounds with anticandidal activity.