Background
The Food and Agricultural Organization (FAO) enlists citrus as one of the most important crops with reference to annual production across the globe [
1]. Citrus fruits are being used since ancient times for management of several health related problems including scurvy, common cold, menstrual irregularities, myocardial infarction, coronary artery disease and high blood cholesterol due to strong antioxidant potential [
2,
3]. Citrus fruits and peel are considered as rich source of diverse flavonoids, polyphenolic compounds, carboxylic acids, vitamin C and amino acids [
4,
5]. Amongst all
Citrus bergamia (Rutaceae,
C. bergemia) has gained great attraction from researchers because of its peculiar health benefits [
6].
C bergemia is native to Italy and Spain however it is cultivated throughout the world [
7]. The geographical and botanical origins of this particular fruit are still uncertain [
8].
Bergamot contains essential oils in peel and flowers that has largely been used in medical, food, cosmetics, perfumes, and confectionary industry [
3]. The essential oils (EOs) are complex mixtures of chemical compounds, each having a unique intense odor, and are located in different parts of the plants including seeds, fruits, stems, leaves, roots, and flowers [
9]. The EOs are the secondary metabolites formed as a result of plant defensive mechanisms through the involvement of enzymes [
10]. It has been emphasized that EOs are the final terpenoid products produced in plants as a result of enzymes like terpene synthase [
11]. Numerous studies have reported the therapeutic potential of the EOs including antimicrobial, anticancer, and antioxidant properties. Being an antimicrobial moiety, EOs are also used to preserve food items [
12]. Bergemia essential oil (BEO) is traditionally used for the treatment of parasitic infections, sore throat, tonsillitis, wound healing, hyperhidrosis, vaginal pruritis, leucorrhoea, skin and mouth infections, gonococcal infections, urinary tract and respiratory tract infections [
13].
Oral complications including dental abscess, gingivitis, dental caries and periodontitis are mainly due to oral bacterial infections [
14,
15]. These infections are main reason for global health burden ($442 billion) [
16] and considered serious since these can lead to cancer and death in worst conditions [
17]. It has been estimated that a huge population (3.5 billion) of the world is currently effected by oral diseases untreated dental caries is one of the most common non-communicable disease [
14]. The treatment failures and development of antibiotic resistance [
18] has and the importance of natural origin antimicrobials motivated us to explore the effect of the bergemia flower essential oil (BFEO) effect against oral microorganisms. The core aim of the study was to investigate BFEO against oral pathogens using in silico and in vitro models.
Methods
Plant material and isolation of essential oil
The fresh flowers of Citrus bergemia were collected with consent from farm house in Paharpur area (District D.I.Khan, KPK, Pakistan) and authenticated by Dr. Zain Ul Abedene (Taxonomist in Institute of Biosciences, Gomal University D.I.Khan, Pakistan). The collected flowers (50 g) were stored at -40 °C for essential oil extraction in clevenger- type apparatus to isolated essential oil using hydro-distillation. The anhydrous sodium sulphate (anhydrous) was used for drying of collected essential oil and removal of water. Finally, essential oil was stored at 4 °C.
Microbial strains and growth media
The clinical strains were isolated from dental plaque of female diabetic patients with the help of Dentist. Strains were transferred to lab and purifications, isolation of strains was performed using differential media including EMB (eosin methylene blue) agar, Mackonkey agar and congo red agar. The strains were identified by 16S rRNA as Bacillus chungangensis, Bacillus paramycoides, Bacillus chungangensis, Paenibacillus dendritiformis, Staphylococos aureus and Staphylococus epidermidis. Standard bacterial strains were E.coli (ATCC 25922), Staphylococcus aureus (ATCC 33862), Klebsiella pneumoniae (ATCC BAA-1705). Biomarker strains included Chromobacterium violaceum (DSM 30191). Growth and differential media used during the investigation including Lauria bertani (LB), BHIA (brain heart infusion agar), tryptic soya broth (TSB) were purchased from Hi Media (India) while Mackonkey agar and eosin methylene blue agar was purchased from (Oxoid, UK).
GC–MS analysis
Essential oil component analysis was accomplished by means of GCMS (Shimadzu GC 2010, Japan) having installed, auto sampler (AOC-20i autosampler) and suitable capillary column (dimensions 30 m × 0.25 mm id, 0.25 μm film thickness, a DB-5 MS column). System oven temperature was set (initially at 45–90 °C) with a rise rate of 2 °C (per min), then increase from 91 to 240 °C with a rise rate of 3 °C (per min). Finally achieved temperature (240 °C) was set constant for 5 min. The temperature of injector (240 °C) and detector (280 °C) was kept constant at set temperatures. For loading the sample, an aliquot of essential oil was (0.5 μL) was injected and Helium (1 ml/min) was used as a carrier gas. GCMS component analysis and identification was accomplished on a GCMS-QP 2010 Plus (Shimadzu, Japan) system operating in EI mode (electron ionization mode) at 70 eV. Mass units were monitored from 35 to 500 AMU. The NIST mass spectral library and compound mix (including limonene, carvacrol, thymol, α-pinene, β-pinene, β-myrcene and sabinene) was used for identification of compounds [
19].
Drug likeness, PASS and bioavailability (Lipinski properties)
On relative abundance basis, following major compounds were further chosen for drug likeness and bioavailability and PASS including 1,6-Octadien-3-ol,3,7-dimethyl(linalool) (
1) L-limonene (
2);
p-menth-1-ol,8-ol (
3); aromadendrine (
4); β-myrcene (
5) and β-pinene (
6). The Lipinski properties [
20], bioavailability and PASS analysis were performed using molinspiration tool [
21] SWISS ADME [
22,
23] and ways2 drugs tool [
24].
Molecular docking
For Molecular docking studies, the X-ray crystallographic structures of the transcriptional regulators LasR (2UV0), PqsE (2Q0J) [
25] and quorum sensing regulators CviR (3QP5) [
26] were obtained from the Protein Data Bank (PDB). The active site dimensions for each protein were recorded by using their co-crystallized ligands respectively. Then, the water molecules and co-crystallized ligand were removed and hydrogen atoms and charges were added. The SDF format for 3D structures of all the phyto-constituents were downloaded from Pubchem database and PDB files were generated in Accelrys DS Visualizer 2.0 (Accelrys Software Inc., 2012). The molecular docking was performed using Lamarckian Genetic Algorithm embedded in AutoDock v 4.2. [
27]. A total number of 63 different poses were generated and clustered according to their RMSD values. Each cluster was carefully visualized in Discovery Studio Visualizer [
28] and putative binding modes were selected accordingly. Best docked structures based on the binding energy scores (ΔG) were chosen for further analyses. The hydrogen bonding and hydrophobic interactions between ligand and protein were calculated by Accelrys DS Visualizer 2.0 [
29].
Violacin inhibition assay
A modified method [
34] was adopted for violacein inhibition assay. A 24 h old culture (200 μL of
C. violaceum (OD = 0.4 OD at 600 nm) was loaded to sterilized microtiter plates containing various concentrations of compounds (1–4 mg/mL). The plates were incubated at 30 °C for 24 h and witnessed for the decrease in violacin pigment production by taking absorbance at 585 nm. The percentage inhibition was calculated by following the formula:
$$\mathrm{Violacein\ inhibition\ \% }= (1-\mathrm{ Absorbance\ of\ sample }/\mathrm{Absorbance\ of\ control }\times 100)$$
Statistical analysis
All biological activity experiments were performed in three independent experiments data was expressed as ± SD. One way ANOVA followed by post-hoc Tukey test with p < 0.05.
Discussions
Citrus bergemia is an important medicinal plant, whose several parts has usage in traditional medicinal systems including Italian, Greece and Chinese [
35]. Generally, essential oil from peel of
C. bergemia is known for anti-inflammatory, antibacterial anticancer, antidiabetic anti-viral properties [
36,
37]. We explored flower essential of this plant against oral pathogens, since prevalence rate of such infections is too high [
38] and existing therapies (antibiotics) have become resistant. The prevalence rate of such infections is too high in developing countries [
39], thus there exists a great potential for new alternative treatments. To best of our knowledge, this is first report exploring potential of
C. bergemia against oral pathogens.
Component analysis in GC–MS revealed several monoterpenoids including linalool (1,6-Octadien-3-ol,3,7-dimethyl), limonene,
p-menth-1-ol, 8-ol, aromadendrene, sabinene, β-pinene and β-myrcene, that is comparably diverse in reference to peel essential oil, since several monoterpenoids were discovered from peels including limonene, linalool and β-pinene [
40]. The monoterpenes, due to their small M.wt. and specific chemical structures are capable of producing several biological activities [
41]. Further, these are categorized as “GRAS” i.e. generally recognized as safe with respect to human health and environment [
42]. Thus these can be used as potential therapeutic agents in infection control.
Online computational tools have become a tool of prime importance in drug discovery these days. These tool are based on several algorithms, that enable simulation with reference to targets, and thus provide a prediction with high probability [
43]. We investigated major components for their druglikeness, bioavailability and possible antimicrobial targets. As explained earlier, all major components followed lipinski’s rule of five however as light deviations from drug likeness scores were noticed. However, they were minor and may have a little effect on drug bioavailability. Never the less, in limonene, β-myrcin and β-pinene the number of H-bond donors and acceptors were zero, that indicate a limited or no bond formation with target amino acids, thus limiting the biological activity and polarity imbalance that may effect permeability and drug solubility [
44]. The pharmacokinetic spectrum analysis revealed that except aromdendrene, all drugs may cross the blood brain barrier and therefore may have effect on CNS. This could possibly be reason that essential oils are effectively used in aromatherapy [
45]. Likewise, all parameters of tested compounds followed the cut points of bioavailability radar and therefore regarded as molecules with agreeable bioavailability. cytochrome p450 enzyme in liver are very important for drug metabolism and ADMET analysis indicated that most of tested drug molecules were neither substrate nor enzymes for such enzymes, that show lower metabolism in liver [
46]. Once the initial drug likeness and bioavailability parameters checking, we investigated possible antimicrobial potential using PASS analysis. The prediction of activity spectrum of substances is an important tool that indicates probability of possible biological activity [
24] that was antimicrobial potential in this case. A high confidence interval in PASS results indicated a good possible antimicrobial activity.
Oxidative stress is a key marker that leads to several diseases including bacterial infections [
47]. Several investigations have shown higher oxidative stress in several bacterial infections, that is possibly due to altered metabolic pathways and generation of reactive oxidation products (ROS) during bacterial infections [
48].
C. bergemia essential oil showed high phenolic contents and it was obvious that it may have strong antioxidant activities [
49], as evident from DPPH, H
2O
2 and FRAP assays. The essential oils are mainly consisted up of monoterpenoids that participate in a oxidative chemical reaction by react through H atom and inhibition of free radicals chain in reaction [
50]. Further compounds with strong antioxidant activity may have strong antimicrobial properties [
51].
The
C. bergemia essential oil presented significant inhibition of resistant strains, that showed potential of this essential oil against oral pathogens. Interestingly the MIC of standard strains against
C. bergemia was several fold higher. The strong antimicrobial activity was attributed to presence of monoterpenes, that may interacted synergistically. Studies have shown that monoterpenoids due to their lipophilic nature are mainly partitioned from an aqueous phase into bacterial membrane structures [
52]. This partitioning effect leads to increase in membrane permeability, destruction of membrane bound structures, interference with ion transport and bacterial cell membrane expansion [
53]. Our experiment using congo red assay confirmed that all tested strains were biofilm producers, and thus we investigated
C. bergemia essential oil for their potential biofilm activities. It was observed that
C. bergemia showed a significant inhibition of biofilms produced by tested strains by block cell–cell signaling mechanism (quorum sensing) in a dose dependent manner. Bacterial biofilms are includes a matrix of extracellular polymeric substances, that limit the activity of antimicrobial agents to kill bacteria and their permeability to reach target site [
54], that leads to antimicrobial resistance. Investigators have shown that monoterpenoids mainly inhibit biofilm formation at early stage by inhibiting formation of flagella [
55] blocking biosynthesis of poly-n-acetylglucosamine polymers biosynthesis, that are major elements of bacterial biofilm and quorum sensing [
56].
Publisher’s Note
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.