Home Unraveling the therapeutic potential of Bombax ceiba roots: A comprehensive study of chemical composition, heavy metal content, antibacterial activity, and in silico analysis
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Unraveling the therapeutic potential of Bombax ceiba roots: A comprehensive study of chemical composition, heavy metal content, antibacterial activity, and in silico analysis

  • Ali Alrabie EMAIL logo , Mohammed ALSaeedy , Arwa Al-Adhreai , Inas Al-Qadsy , Abdel-Basit Al-Odayni , Waseem Sharaf Saeed , Ahmed Hasan and Mazahar Farooqui
Published/Copyright: December 25, 2023
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Open Chemistry
From the journal Open Chemistry Volume 21 Issue 1

Abstract

This study sought to assess the heavy metal content, phytochemical composition, antibacterial activity, and absorption, distribution, metabolism, and excretion (ADME) properties of Bombax ceiba L. tree. The heavy metal content of the plant roots was determined using inductively coupled plasma-mass spectrometry technique, and it was found that only Cr, Mn, Fe, and Ni concentrations were above the permissible limits for edible plants. Gas chromatography-mass spectrometry analysis identified 11 phytochemicals in the aqueous extract of the plant. Both in vitro and in silico confirmed the extract’s antibacterial efficacy. The aqueous extract showed significant antibacterial activity, with minimal inhibition concentration values of 125 µg/mL against Escherichia coli, Staphylococcus aureus, and Streptococcus pyogenes. Among the 11 identified compounds, 1,8-Dioxa-5-thiaoctane,8-(9-borabicyclo[3,3,1]non-9-yl)-3-(9 borabicyclo[3,3,1]non-9-yloxy)-1-phenyl- showed the highest docking score (−8.31 kcal/mol) when docked into the active site of E. coli MenB protein (PDB id: 3t88). It formed four hydrogen bonds with GLY86, GLY85, GLY132, and GLY133. Furthermore, the identified compounds were analyzed for ADME properties, most of them showed very good pharmacokinetic properties and did not violate Lipinski’s Rule of Five. Additional research is required to determine the medicinal potential of the compounds that have antibacterial activity.

Graphical abstract

Keywords: Bombax ceiba ; GC-MS analysis; antibacterial activity; molecular docking; ADME properties

1 Introduction

From ancient Ayurvedic and Chinese medicine to cutting-edge pharmaceutical research, medicinal plants have played a critical role in improving treatment options [1]. Finding novel medication candidates and learning more about the medicinal uses of this plant are both possible outcomes of this research. Therefore, it is crucial for researchers, medical practitioners, and the general public to have an understanding of the properties and applications of medicinal plants.

Bombax is a genus of trees in the mallow family (Malvaceae) that is native to tropical and subtropical regions of Africa, Asia, and the Americas. Large, beautiful flowers that bloom throughout the dry season and tall, straight trunks are the trees’ distinguishing features [2]. There exist approximately 20 species of Bombax trees, many of which are commonly known as kapok trees or silk-cotton trees. Some of the most well-known species include Bombax ceiba, which is a versatile and important tree that has a range of cultural, medicinal, and commercial uses [3].

Both the tree’s bark and leaves have been used to alleviate symptoms of asthma and other breathing problems. The sap from the tree has been used topically to treat wounds, boils, and other skin infections. The bark and leaves are also used in poultices for these purposes. The root bark of Bombax ceiba was traditionally used for the treatment of gastrointestinal ailments, including conditions such as diarrhoea, dysentery, and intestinal worm infestations. The bark of the tree has been used to treat cardiovascular conditions, such as high blood pressure and heart disease. The bark and leaves of the tree have been used as a natural pain reliever for various conditions, such as headaches and joint pain [4,5].

Bombax ceiba has been noted for a number of different biological effects, including its antioxidant activity [6], anti-inflammatory activity [7], antimicrobial activity [8], anticancer activity [9], and antidiabetic activity [10]. Flavonoids are just one of several compounds extracted and identified from Bombax ceiba such as kaempferol and quercetin, and their glycosides have been identified in the leaves, flowers, and bark of Bombax ceiba; sterols, such as stigmasterol and sitosterol, have been identified in the seeds; alkaloids, such as hordenine, have been isolated from the roots. Bombax ceiba produces a diverse range of phytochemicals that can vary depending on various factors; it is essential to screen this plant regularly and continuously to ensure the quality and consistency of the plant-based remedy [11]. In order to detect and quantify the individual phytochemicals contained in the plant, regular screening and analysis utilizing advanced analytical techniques is required. Additionally, these techniques can be used to ensure the safety and efficacy of the plant by detecting the presence of potentially harmful compounds such as heavy metals or pesticides. To the best of our knowledge, the heavy metal content of Bombax ceiba has not been reported, and little has been reported about the phytochemical composition of the roots of this plant. This study can help provide insightful information in these regards.

2 Experimental

2.1 Chemicals and reagents

In this study, HNO3 (37%), H2O2 (30%), and ultrapure water of 18 MΩ were used for inductively coupled plasma-mass spectrometry (ICP-MS) analysis.

2.2 Collection of plant material

The roots of Bombax ceiba L. were procured from a local herbalist trading in the Aurangabad market, which was collected from the Aurangabad district. Herbarium of the Botany Department, Maulana Azad College, Aurangabad, received the plant’s authentication certificate from Dr. Rafiuddin Naser (Voucher no. mach 01270). The powdered plant roots were sealed in a glass container for later use.

2.3 Preparation of extract

In order to make an aqueous extract from the roots of Bombax ceiba, the roots were first ground into a coarse powder, and then, they were added to a 1-L round-bottom flask that already contained 500 mL of deionized water. In the following 3 h, the mixture was reflux-heated to boiling point using a heating mantle. After that, the mixture went through a filtering process, and for solvent removal from the filtrate, a rotary vacuum evaporator was used. We weighed the extracted material and put it in an amber bottle to keep it fresh for later.

2.4 ICP-MS analysis

Approximately 0.1 g of Martynia annua seed powder was digested with a mixture of 7 mL of HNO3 (37%) and 1.0 mL of H2O2 (30%) using a microwave digestor (Anton Paar Multiwave 300 system) [12]. The sample was held for 25 min, with zero ramp time at 400 W, and then retained for 30 min, five ramp time at 500 W. After cooling for at least 1 h, the sample solutions were then filtered and diluted to 100 mL with Milli-Q water (18 MΩ). Blanks were prepared to ensure that the sample was not contaminated. To determine the heavy metal content of the plant seed powder, ICP-MS was used (ICP-MS; iCAP Q, Thermo Fisher Scientific, USA) [13]. The following were typical ICP-MS spectrometer working conditions: The plasma RF forward power was 1548.6 W, the sample uptake time was 30 s, the cool flow read back was 13.67 L/min, the nebulizer flow was 1.0180 L/min, 10 s of integration time resulted in an auxiliary flow rate of 0.796 L/min, the peristaltic pump speed was 40 rpm, the sampler and skimmer cones were Ni, and the analysis mode was eQuant.

2.4.1 Quality control and assurance

In order to prevent any contamination, the laboratory glassware and apparatus were carefully cleaned by soaking them in 20% HNO3 for 24 h and then washing them many times with Mili-Q water. Ultrapure water of 18 MΩ purified with a Mili-Q system (Millipore, St. Louis, MI, USA) was used to prepare standards, diluted samples, and blanks. The external calibration solution was made using a standard certified multi-elements solution to ensure the analytical method’s accuracy. A stock solution of 1,000 ng/mL was prepared from a 30-multi-element standard solution at a concentration of 10 µg/mL (PerkinElmer Inc, USA). A series of standard calibration solutions (5, 10, 20, 50, and 100 ng/mL), were then prepared by dilution of the stock solution with 0.15 M of HNO3 for ordinary use. For each calculated concentration, the calibration curve shows good linearity, with correlation coefficients (r) greater than 0.999. In order to ensure the accuracy of the ICP-MS data throughout the study, as a quality control measure between each analysis run, standard solutions are used (ten samples per batch). The acceptable range was set at 95–104%. It is possible to examine many different kinds of samples using ICP-MS, a sensitive element analysis technique. The resultant complex matrices can influence the physical properties. Reducing matrix-generated physical interferences and compensating for instrumental drift and sample-to-calibration standard variations are two of the many benefits of using internal standards [14,15]. At a concentration of 25 µg/L, Yttrium (Y) or Rhodium (Rh) served as the internal standard for the analysis. Y was used for low-mass elements like Co, Zn, Cr, and Cu, while Rh was used for high-mass elements like Pb and Cd. A tune solution (BICAP) containing 1.0 µg/L of each element in 2% HNO3 and 0.5% HCl was utilized for performance validation and instrument tuning.

2.5 Gas Chromatography-Mass Spectrometry (GC-MS) analysis

A Thermo Scientific TSQ-800 GS-MS equipment attached to a TG-5-MS silica capillary column (dimensions 30 m, 0.25 mm, film thickness 0.25 m) was used to analyze phytoconstituents. GC had a 35-min running time. The carrier gas employed was helium, flowing at a rate of 1 mL/min. For 2 min, the oven temperature was held at 60°C before being programmed to rise to 280°C at a rate of 5°C/min and held there for 10 min. The injector port, ion source, and detector temperature were set at 250, 260, and 280°C, respectively. A scan range of 50–700 (m/z) was used for the mass spectrometric detector, which was run in electron impact ionization mode at a fragment of 70 eV. NIST Library’s database was utilized to identify the components’ names, molecular weights, and structural characteristics [16].

2.6 Antibacterial activity

The Broth-dilution method was used to determine MIC (minimal inhibition concentration) of the methanol extract of Bombax ceiba roots. Staphylococcus aureus (MTCC96) and Streptococcus pyogenes (MTCC442) were obtained from Microcare Laboratory in Surat as Gram-positive strains, and Escherichia coli (MTCC443) and Pseudomonas aeruginosa (MTCC1688). Subculturing the control tube with a medium suitable for the test microorganism’s development, and then incubating it at 37°C for a full 24 h, yields the results. Both the extract and the drug were concentrated in a stock solution of 2,000 µg/mL. A series of dilutions were made of the extract for both primary and secondary testing. Extract concentrations of 1,000, 500, and 250 µg/mL were employed for the primary testing. Those bacteria against which the extract was determined to be effective in the primary test were the subjects of the secondary test. Concentrations of 200, 100, 50, 25, 12.5, and 6.25 µg/mL were obtained by diluting the extract that showed activity in the primary evaluation. The concentration of the extract is validated by recording the MIC of the control microorganism. The MIC is the lowest concentration at which a zone of inhibition of at least 99% is seen. The extract’s MIC was compared to that of the standard antibiotic ampicillin [17].

2.7 Molecular docking

Based on the literature references, the crystal structures of Escherichia coli Murd ligase (PDB ID: 5A5E) [18] were retrieved from the RSCB protein data bank. The preparation of proteins involved removing water molecules and ligands with the help of MOE software was done. Standard protocol was used for energy minimization (Amber10, EHT) and to set the protonation. The site finder module of MOE was used to assign the active site of proteins [19]. The selected phytochemical (ligands) structures were drawn with ChemDraw professional 15.0(PerkinElmer, Inc.), and then, ligands were prepared by Protonation, application of partial charges, and minimization of energy. After ligand preparation, all ligands were saved in a single database. The induced-fit protocol was applied where the Triangle Matcher method was used to place ligand confirmations in the site and then ranked using the London ΔG scoring function [20].

2.8 Absorption, distribution, metabolism, and excretion (ADME) study

ADME properties of compounds from Bombax ceiba aqueous extract via GC-MS were carried out via SwissADME (http://www.swissadme.ch/).

2.9 Statistical analysis

A total of three replicates were conducted for the heavy metal analysis and biological evaluation of the extract. The presented results were mean ± SD (Standard Deviation), and the graphs were drawn using Graphpad Prim9 software.

3 Results and discussion

3.1 ICP-MS analysis

The results of the ICP-MS analysis of Bombax ceiba roots, as presented in Table 1, demonstrate that this plant has accumulated toxic levels of some heavy metals such as Cr, Mn, Fe, and Ni, which are above the permissible limits established by the Food and Agriculture Organization/World Health Organization (FAO/WHO) for edible plants. Ni is a trace element necessary for many cellular reactions and metabolic functions. It is an essential cofactor for numerous enzymes involved in the metabolism of glucose, amino acids, and lipids [21]. Nickel also helps regulate blood sugar levels by contributing to the pancreas’ ability to produce the hormone insulin. Cr is a transition metal that plays a crucial role in various biological functions, including glucose metabolism and insulin function [22]. Cr has been shown to activate several enzymes involved in glucose metabolisms, such as insulin receptor kinase and glucose transporters. It is required for the proper configuration of RNA molecules. Research has linked insufficient Cr consumption to an elevated danger of acquiring type 2 diabetes mellitus, decreased glucose tolerance, and insulin resistance.

Table 1

Concentration (mg/kg) of heavy metals in Bombax ceiba roots

S. no. Element symbol Concentration (mg/kg) Permissible limits in medicinal plants (mg/kg)
1 Cr 4.72 ± 0.03
2 Mn 17.07 ± 0.29
3 Fe 641.52 ± 4.86
4 Co 0.48 ± 0.01
5 Ni 7.04 ± 0.39
6 Cu 7.09 ± 0.16 20 (China) 150 (Singapore)
7 Zn 16.37 ± 0.13
8 As 0.09 ± 0.005 3
9 Cd 0.04 ± 0.002 0.3
10 Pb 1.51 ± 0.03 10

Enzyme activation, bone growth, and immune response modulation are just a few of the many physiological activities that rely on manganese, an essential element. Many enzymes require it as a cofactor, including those that metabolize carbohydrates, amino acids, and cholesterol; generate energy; and control oxidative stress [23]. However, excessive levels of Mn in the body can be toxic, causing neurological disorders, such as Parkinson’s disease, and other health problems. Iron is an essential micronutrient required for various physiological processes in plants and animals. The production of hemoglobin, the protein that carries oxygen throughout the body, depends on it. The production of hemoglobin, the protein that carries oxygen throughout the body, depends on it [24]. Anemia, in which the blood is unable to transport enough oxygen to the tissues, can develop as a result of an iron deficit. Anemia, in which the blood is unable to transport enough oxygen to the tissues, can develop as a result of an iron deficit. However, the excessive accumulation of iron in plants can be toxic and may lead to oxidative stress, which can damage cellular components such as lipids, proteins, and nucleic acids. However, the levels of other heavy metals such as Co, Zn, and Cu were within the acceptable limits set by FAO/WHO for edible plants. The permissible limits for Cu in medicinal plants vary among different nations, with China and Singapore permitting 20 and 150 mg/kg, respectively. The concentration of Cu in Bombax ceiba roots was found to be 7.09 mg/kg, which is within the permissible limits for both countries. This finding suggests that Bombax ceiba can be used safely for medicinal purposes, especially in China and Singapore, without any significant risk of toxicity from Cu.

Heavy metals such as Pb, As, and Cd are highly poisonous and have no beneficial role in the human body. As a result, many countries have set maximum allowable levels for these metals in raw herbal material. Cd, As, and Pb levels in herbal material cannot exceed 0.3, 3, and 10 mg/kg, respectively, in India. As for the other two heavy metals, Cd (0.04 mg/kg), As (0.09 mg/kg), and Pb (1.51 mg/kg) in Bombax ceiba roots were all determined to be well within the AYUSH allowed limits. The results of this study are in agreement with other studies that have reported the presence of heavy metals in medicinal plants. Some therapeutic herbs in Turkey were found to contain Cr, Mn, Fe, and Ni, according to a study conducted by Karahan [25]. Some Eritrean medicinal herbs have been found to contain traces of heavy metals like chromium, lead, zinc, mercury, and copper, according to a study by Sium et al. [26].

3.2 GC-MS analysis

Eleven compounds were identified from the GC-MS analysis of the aqueous extract of Bombax ceiba roots. The chromatogram is presented in Figure 1 while the phytochemical name with their retention time (RT), molecular formula, and peak area % are presented in Table 2, and the structure of phytochemicals is presented in Figure 2. The following phytochemicals were present in the GC-MS analysis carried out on the aqueous extract of Bombax ceiba roots: A1- 5,8,11.14-Eicosatetraenoic acid, phenylmethyl ester, (all-z)-, A2- 4-benzyloxy-N-methylamphetamine, A3- 1,3.5-pentanetriol,3-methyl-, A4- alpha-d-glucopyranoside, methyl 2-(acetylamino)-2-deoxy-3-O-(trimethylsilyl)-,cyclic methylboronate, A5- Z,Z,Z-4,6,9-nonadecatriene (organic compound), A6- 2,5-octadecadiynoic acid, methyl ester, A7- 9,12,15-octadecatrienoic acid, 2,3-bis[(trimethylsilyl)oxy]propyl ester, (Z,Z,Z)-, A8- cis-5,8,11,14,17-eicosapentaenoic acid, A9- 1,8-dioxa-5-thiaoctane,8-(9-borabicyclo[3,3,1]non-9-yl)-3-(9-borabicyclo[3,3,1]non-9-yloxy)-1-phenyl-, A10- 1-monolinoleoylglycerol trimethylsilyl ether, and A11- perhydrocyclopropa[e]azulene-4,5,6-triol, 1,1,4,6-tetramethyl.

Figure 1 GC-MS chromatogram of aqueous extract of Bombax ceiba roots.
Figure 1

GC-MS chromatogram of aqueous extract of Bombax ceiba roots.

Table 2

Phytochemicals identified in aqueous extract of Bombax ceiba roots

Code RT (min) Peak area% Molecular formula Probable compound name
A1 3.25 12.79 C27H38O2 5,8,11.14-Eicosatetraenoic acid,phenylmethyl ester,(all-z)-
A2 3.87 17.12 C17H21NO 4-benzyloxy-N-methylamphetamine
A3 6.09 1.56 C6H14O3 1,3.5-pentanetriol,3-methyl-
A4 21.78 0.41 C13H26BNO6Si Alpha-d-Glucopyranoside, methyl 2-(acetylamino)-2-deoxy-3-O-(trimethylsilyl)-,cyclic methylboronate
A5 22.76 18.04 C19H34 Z,Z,Z-4,6,9-Nonadecatriene
A6 23.15 1.37 C19H30O2 2,5-Octadecadiynoic acid, methyl ester
A7 24.42 0.39 C27H52O4Si2 9,12,15-Octadecatrienoic acid, 2,3-bis[(trimethylsilyl)oxy]propyl ester, (Z,Z,Z)-
A8 24.84 0.33 C20H30O2 cis-5,8,11,14,17-Eicosapentaenoic acid
A9 25.02 0.43 C27H42B2O3S 1,8-Dioxa-5-thiaoctane,8-(9-borabicyclo[3,3,1]non-9-yl)-3-(9-borabicyclo[3,3,1]non-9-yloxy)-1-phenyl-
A10 25.58 0.51 C27H56O4Si2 1-Monolinoleoylglycerol trimethylsilyl ether
A11 25.72 0.43 C15H26O3 Perhydrocyclopropa[e]azulene-4,5,6-triol, 1,1,4,6-tetramethyl
Figure 2 The structures of identified compounds by GC-MS analysis.
Figure 2

The structures of identified compounds by GC-MS analysis.

Among the identified bioactive compounds, Z,Z,Z-4,6,9-nonadecatriene has the highest peak area % which has been reported to have antioxidant activity [27]. 5,8,11.14-Eicosatetraenoic acid, phenylmethyl ester, (all-z)- has cardioprotective [28]. 2,5-Octadecadiynoic acid, methyl ester has anti-inflammatory activity [29]. 9,12,15-Octadecatrienoic acid, 2,3-bis[(trimethylsilyl)oxy]propyl ester, (Z,Z,Z)- has anticancer and hepatoprotective properties [30]. Cis-5,8,11,14,17-Eicosapentaenoic acid has antidiabetic, anti-cancer effects, anti-allergy, and cerebrovascular protection properties [31]. 1-Aside from its diuretic properties, monolinoleoylglycerol trimethylsilyl ether has antibacterial, anti-inflammatory, anti-arthritic, anti-asthmatic, and antioxidant properties as well [32,33]. Perhydrocyclopropa [e]azulene-4,5,6-triol, 1,1,4,6-tetramethyl has anti-inflammatory activity [34]. The novelty of this study lies in the identification of eleven bioactive compounds in the aqueous extract of Bombax ceiba roots; while previous studies have investigated the phytochemical composition and biological activities of other parts such as bark, leaves, and flowers, to our knowledge, this is the first report of the specific bioactive compounds in the roots of the plant. This information may be useful in developing new therapeutic agents or natural products derived from Bombax ceiba. It could also provide further insight into the biological activities and potential health benefits of the plant.

3.3 Antibacterial activity

The results suggest that the aqueous extract of Bombax ceiba has a potent antimicrobial effect against E.coli, S. aureus, and S. pyogenes, with an MIC value of 125 µg/mL, while it exhibited a slightly lower efficacy against P. aeruginosa, with an MIC value of 200 µg/mL. In contrast, the drug ampicillin had a MIC value of 100 µg/mL against E.coli and S. pyogenes, but exhibited no effect against S. aureus and P. aeruginosa (Table 3 and Figure 3).

Table 3

MIC values of extract and drug against selected microorganisms

S. no. Microorganisms MIC of extract (µg/mL) MIC of ampicillin (µg/mL)
1 E. coli (MTCC443) 125 100
2 P. aeruginosa (MTCC1688) 200 —
3 S. aureus (MTCC96) 125 250
4 S. pyogenes MTCC442 125 100
Figure 3 Graph of antibacterial activity of extract.
Figure 3

Graph of antibacterial activity of extract.

This confirms what has been found in earlier research on the antibacterial properties of natural products. For instance, a study by Digge et al. [35] investigated the antibacterial activity of the aqueous stem bark extract of Bombax ceiba, against drug-resistant strains of bacteria and found that the plant extracts had potent antibacterial effects against a range of bacterial pathogens. Our previous study [36] evaluated the antibacterial activity of the methanol extract of this plant against drug-resistant strains including S. aureus and E.coli and found that Bombax ceiba extract showed the highest inhibition activity against S. aureus with an MIC value of 100 µg/mL.

The observed difference in efficacy between Bombax ceiba extract and ampicillin against S. aureus and P. aeruginosa can be attributed to the differences in their mode of action. Ampicillin is an antibiotic that falls under the category of β-lactam antibiotics. It works by attaching to penicillin-binding proteins and preventing them from facilitating bacterial cell wall construction (PBPs) [37]. However, some bacterial strains, including S. aureus, have developed resistance to β-lactam antibiotics through various mechanisms, such as the production of β-lactamases or changes in PBPs Cantón et al. [38]. In contrast, tannins, flavonoids, and alkaloids, all of which have been demonstrated to have antibacterial activities, are likely responsible for Bombax ceiba extract’s antimicrobial activity.

3.4 Molecular docking

The given molecular docking results represent the interaction of 11 compounds obtained from the aqueous extract of Bombax ceiba roots with the active site of E. coli Mure ligase (PDB id: 5A5E), along with ampicillin. Mure ligase is an enzyme in E. coli involved in bacterial cell wall biosynthesis. One of its functions is to facilitate the assembly of peptidoglycan, an essential component of bacterial cell walls, by establishing peptide connections between N-acetylmuramic acid (MurNAc) and L-alanine. A number of natural products have been identified as inhibitors of MurD ligase. These compounds bind to the enzyme and disrupt its activity, inhibiting cell wall biosynthesis. The docking score quantifies the affinity between the ligand and the protein; a higher score signifies a more robust connection.

Table 4 summarizes the docking scores, bond distance, RMSD, E, and interaction type. Docking scores for the discovered compounds varied from −4.4 to −8.14 kcal/mol, indicating high docking affinity. These high docking score values indicate that the compounds have a favorable interaction with the protein’s active site, the compounds A1, A6, A7, A8, A9, and A10 demonstrated better binding affinity (docking score of −6.32 to −8.14 kcal/mol) against E. coli Mure ligase than the standard drug, ampicillin (6.15 kcal/mol). The highest docking score (−8.14 kcal/mol) was recorded by compound A7. This binding affinity was stabilized by two hydrogen bonds (Figure 4, A7) with amino acid residues LYS115 & LYS319 at distances of 2.84 and 3.32 Å, respectively. The second-best docking score (−7.57 kcal/mol) was recorded by compound A10. This compound formed three hydrogen bonds (Figure 4, A10) with amino acid residues LYS319 & LYS115. Compound 1 (Figure 4, A1) formed only one H-bond with LYS319 while compound 6 (Figure 4, A6) formed two H-bonds with ARG302. Two hydrogen bonds and two ionic bonds were formed between compound 8 and SER160, LYS198, LYS115 (Figure 4, A8) whereas compounds 9 formed one H-bond and one Pi-cation (Figure 4, A9) with LYS319 and TYR187. Compounds 2, 3, 4, 5, and 11 displayed lower docking scores than ampicillin. Overall, the study provides useful insights into the potential inhibitory activity of various compounds against E. coli Mure ligase.

Table 4

Molecular docking results of identified phytochemicals

Compound code Docking score (Kcal/mol) Amino acid residue Type of bond E (Kcal/mol) Bond length (Å)
A1 −6.32 LYS319 H-acceptor −2.2 2.79
A2 −5.05 GLU423 H-donor −2.1 3.20
GLU423 H-donor −2.5 3.17
GLU423 Ionic −3.3 3.20
GLU423 Ionic −3.4 3.17
SER159 Pi-H −0.6 3.69
A3 −4.4 LYS115 H-acceptor −0.5 2.98
LYS198 H-acceptor −0.5 3.30
A4 −5.46 TYR187 H-acceptor −12.8 2.87
A5 −5.44 − − − −
A6 −6.33 ARG302 H-acceptor −3.1 2.99
ARG302 H-acceptor −1.1 3.05
A7 −8.14 LYS115 H-acceptor −7.2 2.84
LYS319 H-acceptor −0.7 3.32
A8 −6.44 SER160 H-acceptor −5.6 2.94
LYS198 H-acceptor −1.8 3.24
LYS115 Ionic −5.7 2.83
LYS198 Ionic −3.0 3.24
A9 −6.61 LYS319 H-acceptor −2.8 4.12
TYR187 Pi-cation −1.1 4.36
A10 −7.57 LYS319 H-acceptor −1.5 3.17
LYS115 H-acceptor −4.7 3.03
LYS319 H-acceptor −1.1 3.02
A11 −4.82 SER160 H-acceptor −1.5 3.23
LYS115 H-acceptor −5.5 2.97
Ampicillin −6.15 ASN322 H-acceptor −2.6 3.28
LYS115 H-acceptor −5.5 2.78
SER160 H-acceptor −1.1 3.30
LYS198 H-acceptor −2.0 3.33
Figure 4 Molecular docking results diagram of phytochemicals docked into 5A5E, A9: 1,8-Dioxa-5-thiaoctane,8-(9-borabicyclo[3,3,1]non-9-yl)-3-(9-borabicyclo[3,3,1]non-9-yloxy)-1-phenyl-; A10: 1-Monolinoleoylglycerol trimethylsilyl ether; A6: 2,5-Octadecadiynoic acid,methyl ester; A1: 5,8,11.14-Eicosatetraenoic acid, phenylmethyl ester,(all-z)-; A7: 9,12,15-Octadecatrienoic acid, 2,3-bis[(trimethylsilyl)oxy]propyl ester, (Z,Z,Z)-; A8: cis-5,8,11,14,17-Eicosapentaenoic acid.
Figure 4 Molecular docking results diagram of phytochemicals docked into 5A5E, A9: 1,8-Dioxa-5-thiaoctane,8-(9-borabicyclo[3,3,1]non-9-yl)-3-(9-borabicyclo[3,3,1]non-9-yloxy)-1-phenyl-; A10: 1-Monolinoleoylglycerol trimethylsilyl ether; A6: 2,5-Octadecadiynoic acid,methyl ester; A1: 5,8,11.14-Eicosatetraenoic acid, phenylmethyl ester,(all-z)-; A7: 9,12,15-Octadecatrienoic acid, 2,3-bis[(trimethylsilyl)oxy]propyl ester, (Z,Z,Z)-; A8: cis-5,8,11,14,17-Eicosapentaenoic acid.
Figure 4

Molecular docking results diagram of phytochemicals docked into 5A5E, A9: 1,8-Dioxa-5-thiaoctane,8-(9-borabicyclo[3,3,1]non-9-yl)-3-(9-borabicyclo[3,3,1]non-9-yloxy)-1-phenyl-; A10: 1-Monolinoleoylglycerol trimethylsilyl ether; A6: 2,5-Octadecadiynoic acid,methyl ester; A1: 5,8,11.14-Eicosatetraenoic acid, phenylmethyl ester,(all-z)-; A7: 9,12,15-Octadecatrienoic acid, 2,3-bis[(trimethylsilyl)oxy]propyl ester, (Z,Z,Z)-; A8: cis-5,8,11,14,17-Eicosapentaenoic acid.

3.5 ADME study

In this study, the ADME characteristics of the compounds were evaluated using in silico methods. The results of these evaluations are presented in (Tables 5 and 6). One of the parameters used to estimate the drug transport properties of the compounds is the topological polar surface area (TPSA), which is the sum of the surface areas of the polar atoms in the molecule. Generally, a lower TPSA value suggests that the compound is more likely to be transported across biological barriers.

Table 5

Physicochemical, Lipophilicity, and water solubility properties of phytochemicals

S. no. Physicochemical properties Lipophilicity Water solubility
MW (g/mol) Fsp3 RB HBA HBD TPSA (Å2) XLog P o/w Log S (ESOL)
A1 394.59 0.44 17 2 0 26.30 8.11 −6.43
A2 255.35 0.29 6 2 1 21.26 3.82 −3.90
A3 134.17 1.00 4 3 3 60.69 −0.86 0.13
A4 331.25 0.92 5 6 1 75.25 0.88 −2.12
A5 262.47 0.68 13 0 0 0.00 8.45 −5.93
A6 290.44 0.74 11 2 0 26.30 7.65 −5.73
A7 496.87 0.74 21 4 0 44.76 8.84 −7.10
A8 302.45 0.45 13 2 1 37.30 6.29 −4.82
A9 468.31 0.78 11 3 0 52.99 7.88 −7.12
A10 500.90 0.89 23 4 0 44.76 10.21 −7.86
A11 254.37 1.00 0 3 3 60.69 1.35 −2.27
Table 6

Pharmacokinetics and drug-likeness properties of phytochemicals

Code Pharmacokinetics Drug-likeness
GI BBB P-gp Lipinski rule Bioavailability score
A1 Low No No Yes 0.55
A2 High Yes No Yes 0.55
A3 High No No Yes 0.55
A4 High No Yes Yes 0.55
A5 Low No No Yes 0.55
A6 High Yes No Yes 0.55
A7 Low No Yes Yes 0.55
A8 High No No Yes 0.85
A9 Low No Yes Yes 0.55
A10 Low No No No 0.17
A11 High Yes Yes Yes 0.55

It was observed that the TPSA values for most of the compounds in the study were within the acceptable range of 20–130 Å2. This indicates that the compounds may have favorable transport properties and could potentially be developed into drug candidates. Lipophilicity is a crucial factor to consider when describing a drug’s effects on the human body. The ability of a medication to penetrate a given tissue is quantified by its LogP value, only compounds A1, A5, A6, A7, A8, A9, and A10 are lipophilic and poorly or moderately soluble in water since their XLogP values are higher than the Muegge filter’s allowable range (XLogP < 5) whereas other are within this range. Lipinski’s Rule of 5 (RO5) is a widely used set of criteria in drug development that helps to evaluate whether a drug candidate is likely to be orally active. The rule was developed by Dr. Christopher Lipinski in 1997, based on the analysis of the physicochemical properties of a large number of drugs. The rule defines four criteria that a drug candidate should meet in order to be considered drug-like and have a good chance of success in development: (1) molecular weight less than 500 Da, (2) no more than five hydrogen bond donors, (3) no more than 10 hydrogen bond acceptors, and (4) a partition coefficient (logP) of less than 5. Violation of any one of these criteria can indicate that a drug candidate may have poor oral bioavailability, solubility, or may not effectively reach the intended target. Bioavailability is a crucial parameter in drug development, as it determines how much of the drug is absorbed into the bloodstream and reaches the target site. If a drug has low bioavailability, to reach therapeutic levels, it may be necessary to take high doses or take them frequently, which raises the possibility of toxicity and side effects.

In the given scenario, compound A10 violated two of Lipinski’s RO5 criteria and had a low bioavailability score of 0.17, indicating that it may have poor oral bioavailability and may not be an effective drug candidate. On the other hand, the other compounds did not violate Lipinski’s RO5 criteria and had high bioavailability scores, indicating that they are more likely to be orally active and may have better chances of success in drug development. The solubility of a medication is a critical factor in its absorption and distribution in the body. Poor solubility can lead to inadequate absorption, particularly when administered orally, resulting in poor therapeutic outcomes. Water solubility, as measured by the logarithm of solubility (log S), is a critical parameter that influences a compound’s distribution and absorption properties. While most compounds are soluble in water, some, such as compounds A1, A7, A9, and A10, have been shown to be very poorly soluble. These compounds may not be suitable for administration via transdermal routes due to their negative skin permeability values. Skin permeability is a critical component of both oral and transdermal drug administration. In oral medications, it helps to recognize accidental skin contact, which can cause adverse drug reactions. In transdermal drugs, it is crucial for permeating the skin and achieving therapeutic outcomes (Figure 5).

Figure 5 Bioavailability radar of identified phytochemicals, A1: 5,8,11.14-eicosatetraenoic acid, phenylmethyl ester,(all-z)-, A2: 4-benzyloxy-N-methylamphetamine, A3: 1,3.5-pentanetriol,3-methyl-, A4: alpha-d-glucopyranoside, methyl 2-(acetylamino)-2-deoxy-3-O-(trimethylsilyl)-,cyclic methylboronate, A5: Z,Z,Z-4,6,9-nonadecatriene, A6: 2,5-octadecadiynoic acid,methyl ester, A7: 9,12,15-octadecatrienoic acid, 2,3-bis[(trimethylsilyl)oxy]propyl ester, (Z,Z,Z)-, A8: cis-5,8,11,14,17-eicosapentaenoic acid, A9: 1,8-dioxa-5-thiaoctane,8-(9-borabicyclo[3,3,1]non-9-yl)-3-(9-borabicyclo[3,3,1]non-9-yloxy)-1-phenyl-, A10: 1-monolinoleoylglycerol trimethylsilyl ether, A11: perhydrocyclopropa[e]azulene-4,5,6-triol, 1,1,4,6-tetramethyl.
Figure 5

Bioavailability radar of identified phytochemicals, A1: 5,8,11.14-eicosatetraenoic acid, phenylmethyl ester,(all-z)-, A2: 4-benzyloxy-N-methylamphetamine, A3: 1,3.5-pentanetriol,3-methyl-, A4: alpha-d-glucopyranoside, methyl 2-(acetylamino)-2-deoxy-3-O-(trimethylsilyl)-,cyclic methylboronate, A5: Z,Z,Z-4,6,9-nonadecatriene, A6: 2,5-octadecadiynoic acid,methyl ester, A7: 9,12,15-octadecatrienoic acid, 2,3-bis[(trimethylsilyl)oxy]propyl ester, (Z,Z,Z)-, A8: cis-5,8,11,14,17-eicosapentaenoic acid, A9: 1,8-dioxa-5-thiaoctane,8-(9-borabicyclo[3,3,1]non-9-yl)-3-(9-borabicyclo[3,3,1]non-9-yloxy)-1-phenyl-, A10: 1-monolinoleoylglycerol trimethylsilyl ether, A11: perhydrocyclopropa[e]azulene-4,5,6-triol, 1,1,4,6-tetramethyl.

The blood–brain barrier (BBB) is a selectively permeable membrane that separates the brain from the blood circulation, and it plays a crucial role in regulating the transport of molecules into and out of the brain. The BBB limits the entry of potentially harmful substances into the brain, but it also prevents the entry of therapeutic drugs into the brain, which can hinder the treatment of various brain disorders. Compounds A2, A6, and A11 have a strong ability to cross the BBB, while other compounds have a poor ability, as demonstrated in the Boiled-egg image ([Figure 6] Yolk). Permeability glycoprotein (P-gp) plays an important function in preventing xenobiotic damage to the central nervous system. P-gp is expressed exclusively in some tumor cells, which ultimately results in tumors that are resistant to several drugs; all compounds were non-substrate for the P-gp (red dots) except compounds A4, A7, A9, and A11 (substrate) (blue dots) as shown in boiled-egg image (Figure 6). More than 50% of compounds had high gastrointestinal absorption (GI) characteristics (white area) in boiled-egg image except for compounds A1, A5, A7, A9, and A10.

Figure 6 Boiled-egg image of identified phytochemicals.
Figure 6

Boiled-egg image of identified phytochemicals.

4 Conclusions

This study provides valuable information on the heavy metal content, phytochemical composition, antibacterial activity, and ADME properties of the Bombax ceiba L. tree. The heavy metal concentrations in the plant roots were within the acceptable range for medicinal plants, and the aqueous extract exhibited significant antibacterial activity against E. coli, S. aureus, and S. pyogenes. The identified compounds in the extract were also found to have good pharmacokinetic properties and did not violate Lipinski’s Rule of Five. These results indicate that Bombax ceiba L. could be a promising source of antibacterial compounds with favorable pharmacokinetics features, which warrants further investigation into its medicinal applications.

Acknowledgments

The authors would like to extend their sincere appreciation to the Researchers Supporting Project number (RSPD2023R703), King Saud University, Riyadh, Saudi Arabia.

  1. Funding information: The work was financially supported by Researchers Supporting Project number (RSPD2023R703), King Saud University, Riyadh, Saudi Arabia.

  2. Author contributions: Ali Alrabie, Mohammed ALSaeedy, Mazahar Farooqui – conceptualization; Ali Alrabie, Abdel-Basit Al-Odayni, Waseem Sharaf Saeed – data curation; Ali Alrabie, Arwa Al-Adhreai, Ahmed Hasan, Inas Al-Qadsy – formal analysis; Abdel-Basit Al-Odayni – funding acquisition; Ali Alrabie and Mazahar Farooqui – investigation; Ali Alrabie – methodology; Mazahar Faroqui – project administration; Ali Alrabie, Arwa Al-Adhreai, Mazahar Farooqui– resources; Ali Alrabie – software; Mazahar Farooqui – supervision; Abdel-Basit Al-Odayni, Waseem Sharaf Saeed– validation; Inas Al-Qadsy– visualization; Ali Alrabie– writing – original draft; Ali Alrabie, Abdel-Basit Al-Odayni, Waseem Sharaf Saeed – review and editing.

  3. Conflict of interest: We have no conflicts of interest to report.

  4. Ethical approval: Neither humans nor animals are involved in the research in any way.

  5. Data availability statement: This published publication contains all of the data gathered or analyzed during this study.

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Received: 2023-10-14
Revised: 2023-12-10
Accepted: 2023-12-11
Published Online: 2023-12-25

© 2023 the author(s), published by De Gruyter

This work is licensed under the Creative Commons Attribution 4.0 International License.

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https://doi.org/10.1515/chem-2023-0179
Keywords for this article
Bombax ceiba; GC-MS analysis; antibacterial activity; molecular docking; ADME properties
Creative Commons
BY 4.0

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