ADMET analysis of phyto-components of Syzygium cumini seeds and Allium cepa peels

Abstract

Background

The inedible wastes generated from vegetables and fruits are one of the sources of environmental pollution if not utilized or disposed-off in a proper way. Research is focused on the utilization of these wastes as potential resources rather than undesirable and unwanted products in order to avoid contamination of natural resources. Syzygium cumini (black plum) seeds and Allium cepa (onion) peels were studied. These wastes were fermented and phyto-components of these wastes were determined by gas chromatography mass spectrometry (GCMS). The phyto-components were examined for their pharmacokinetics properties like drug-likeness and toxicity. The open source softwares, DruLiTo and VEGA QSAR, were used to perform the aforementioned study.

Result

GCMS: Twenty phyto-components were identified by performing GCMS analysis of the methanol extracts of fermented Syzygium cumini seeds and fermented Allium cepa peels.

DruLiTo: Four phyto-components each from the methanol extracts of Syzygium cumini seeds and Allium cepa peels followed all the drug-likeness rules.

VEGA QSAR: Six phyto-components of methanol extract of fermented Syzygium cumini seeds were identified as non-mutagenic whereas nine phyto-components of methanol extract of fermented Allium cepa peels were non-mutagenic.

Collectively two phyto-components of methanol extracts of Syzygium cumini seeds and four phyto-components of methanol extracts of Allium cepa possess the pharmacokinetic properties.

Conclusion

The phyto-components predicted to be drug-like and non-mutagenic can be further studied as ligands for bacterial and cancerous targets by the means of in-silico docking approach/techniques. The exploration carries supportive data for future examinations that can lead to their therapeutic use.

Background

Since ancient time, Syzygium cumini seeds are used to treat several diseases. Extracts of Syzygium cumini seed contains flavonoids, alkaloids, glycosides, triterpenoids, steroids, saponins, and tannins [1]. Allium cepa peel possesses alkaloids, tannins, flavanoids, phenolic flavanoids, carbohydrates, steroids, cardiac glycosides and phlobatannins. Fermented Allium cepa peel extracts are reported to possess antioxidant potential [2].

Currently, pharmaceutical industry faces large attrition rates of preclinical and clinical candidates due to toxicity or lag of optimal pharmacokinetics properties, resulting in high costs and increased timelines for the drug discovery process [3].

To be a functional as a drug, the molecule must reach its target in the body in adequate concentration and stay there in a bioactive form until the expected biological events occur. Poor pharmacokinetic properties are one of the main reasons for terminating the development of drug candidates. Computed physicochemical properties associated with compounds that have good oral bioavailability, less or no toxicity and optimum values of physicochemical properties are key parameters for the drug discovery [4, 5]. Drug development involves valuation of absorption, distribution, metabolism, excretion (ADME) and toxicity (Tox) earlier in the discovery process, at a stage when more number of compounds are taken into consideration [6].

ADME/Tox was performed virtually to know the pharmacokinetic or drug-likeness property and mutagenicity of components obtained from the gas chromatography mass spectrometry analysis by open source software DruLiTo and VEGA QSAR [7, 8].

DruLiTo is an open source virtual Drug Likeness Tool available from http://www.niper.gov.in/pi_dev_tools/DruLiToWeb/DruLiTo_index.html [9]. DruLito calculates the basic pharmacokinetic properties like the molecular weight (Mw), partition coefficient (logP), octanol-water partition coefficient (AlogP), H-bond acceptor (HBA), H-bond donor (HBD), total polar surface area (TPSA), atom molar refractivity (AMR), number of rotatable bonds (nRB), rotatable bond count (RC), number of rigid bonds (nRigidB) and number of hydrogen bonds (nHB) [9]. Calculations with DruLiTo are dependent on various drug-likeness rules, namely Lipinski’s rule, Veber’s rule, the BBB rule and quantitative estimate of the drug-likeness (QED). Taking these rules and restrictions into account, DruLito allows one to determine substances that fulfil required parameters and enables their application in further research [6].

The toxicity of molecules was predicted by VEGA QSAR. VEGA QSAR is a freely available in silico model provided by VEGAHUB and can be downloaded from www.vegahub.eu/portfolio-item/vega-qsar [8]. Predictive toxicology is using models to predict biological endpoints for toxicity, without making real experiments. “Structure-Activity Relationship” (SAR) is based on the concept that the biological activity of a chemical can be linked to its molecular structure. When quantified, this relationship is known as “QSAR”. A QSAR model makes use of existing experimental toxicity data for a series of chemicals to build a model that relates experimentally observed toxicity with molecular descriptors in order to predict the toxicity of further chemicals. VEGA is an open source software that offers many models for study of properties such as persistence, LogP, carcinogenicity, mutagenicity, skin sensitization. The input can be given in different standard formats used in the chemical domain, including SMILES and SDF (Structure Data Format) files [10]. Regarding mutagenicity, 85% reproducibility is reported while conducting in-vivo test [8].

Amongst the four VEGA models for mutagenicity, the CAESAR 2.1.13 model is more accurate, sensitive and specific [11]. Mutagenicity (Ames test) model (CAESAR) 2.1.13 provides a qualitative prediction of mutagenicity on Salmonella typhimurium [12].

Methods

Inedible food waste

Syzygium cumini and Allium cepa were bought from local fruit and vegetable market, Surat, Gujarat, India. Their authentication was carried out by botanist Dr. Bimal S. Desai. The voucher specimens were deposited at herbarium of Navsari Agriculture University, Navsari (Syzygium cumini—Voucher no. HSK/BPBSCI/JAMUN/2017-18/01-04; Allium cepa—Voucher no. HSK/BPBSCI/ONION/2017-18/01-04). The seeds of Syzygium cumini and peels of Allium cepa were washed several times with tap water and were shade dried until constant weight was obtained. After drying the seeds and peels were powered using electric blender and stored until further use.

Fermentation

The method [13] is used with slight modification. Erlenmeyer flask (250 mL), containing 10-g Syzygium cumini seeds powder and 100-mL water, was sterilized at 121 °C for 1 h. After sterilization, the flask was allowed to cool to room temperature and inoculated with Saccharomyces cerevisiae. The inoculated flasks were statically incubated at 30 °C for 5 days. Same protocol was followed for fermentation of Allium cepa peels.

Extraction

After fermentation, 100 mL of methanol was added to the flask and extraction was performed at room temperature in shaking condition for 24 h. The extraction mixture was filtered through a Whatman No. 1 filter paper [13] and allowed to evaporate in preweighed glassware. After evaporation, the extracted material is dissolved in methanol to obtain a desired concentration.

Gas chromatography mass spectroscopy

The gas chromatography mass spectroscopy (GCMS) was performed by Agilent 7890 coupled to JeolAccuTOF GCV, USA.

Make of GC: Agilent 7890; FID detector.

Make of MS: Model – JeolAccuTOF GCV, USA; EI/CI source; time of flight analyser; Mass range: 10–2000 amu, mass resolution: 6000.

Operation conditions:

Ionization mode: EI+; Ionization volt: 70 eV

Column specification: length—30 m, thickness—0.25 μm, internal diameter—25 mm

Helium was used as carrier gas at a flow rate of 1 mL/min.

The temperature raised from 70 °C up to 280 °C with the rate of 8 °C per min rise in temperature.

The analysis was carried out at Sophisticated Analytical Instrument Facility, Indian Institute of Technology, Bombay. The outcomes of mass spectra were compared with those stored in spectrometer database of National Institute of Standards and Technology Mass Spectral Database (NIST-MS). The Kovats retention index of each compound was also confirmed.

The Structure Data Format and canonical SMILES of the compounds identified by GCMS were downloaded from PUBCHEM.

ADME/Tox analysis

The compounds identified by GCMS were virtually scrutinized for their drug-like property (ADME) and mutagenicity (Tox) by using open source tool DruLiTo and software VEGA QSAR.

DruLiTo

Four filters of DruLiTo namely Lipinski’s rule, Veber rule, BBB rule and Quantitative Estimate of Drug-likeness (QED) were used to study ADME profile [7] of compounds obtained from the GCMS results of fermented methanol extracts of Syzygium cumini seeds and Allium cepa peels.

Structure Data Format (SDF) of compounds was used as input.

The threshold values of the filters were kept default and are described below:

Lipinski’s rule:

Molecular weight	≤ 500
LogP	≤ 5
H- bond donor	≤ 5
H- bond acceptor	≤ 10

Veber rule:

Rotable bond	≤ 10
Polar surface area	≤ 140

BBB rule:

Molecular weight	≤ 400
H-bond	≤ 8
Number of acids	≤ 0

QED:

Weighted QED	≥ 0.5
Unweighted QED	≥ 0.5

VEGA QSAR

VEGA QSAR was used for the qualitative prediction of mutagenicity (Ames test – CAESAR 2.1.13) of the compounds identified by GCMS, where canonical SMILES were used as input.

Results

Gas chromatography mass spectrometry

GCMS analysis of methanol extracts of fermented Syzygium cumini seeds and fermented Allium cepa peels was carried out at IIT SAIF, Bombay. Ten compounds from each extract were identified. The chromatograms are given in Figs. 1 and 2. The compounds identified are listed in Tables 1 and 2.

Fig. 1

GCMS chromatogram of methanol extract of fermented Syzygium cumini seeds

Fig. 2

GCMS chromatogram of methanol extract of fermented Allium cepa peels

Table 1 Compounds identified in the GCMS analysis of methanol extract of fermented Syzygium cumini seeds

Table 2 Compounds identified in the GCMS analysis of methanol extract of fermented Allium cepa peels

ADME/Tox analysis

ADME/Tox analysis of phyto-components identified by GCMS analysis was carried out by DruLiTo and VEGA QSAR.

DruLiTo

The molecular characteristics of phyto-components of extracts of fermented Syzygium cumini seeds and fermented Allium cepa peels determined by DruLiTo are shown in Tables 3 and 4 respectively.

Table 3 Characteristics of compounds identified from GCMS analysis of fermented Syzygium cumini seeds methanol extracts

Table 4 Characteristics of compounds identified from GCMS analysis of fermented Allium cepa peel methanolic extracts

Various drug-likeness rules like Lipinski’s rule, Veber rule, BBB likeness rule and Quantitative estimate (QED) of drug-likeness are employed. Each rule functions according to a set threshold value for abovementioned characteristics. The results are noted in Tables 5 and 6.

Table 5 Drug-likeness property of compounds of fermented Syzygium cumini seed methanolic extract

Table 6 Drug-likeness property of compounds of fermented Allium cepa peels methanolic extract

The result of Table 5 shows that four compounds with codes SC1, SC3, SC7 and SC10 follow all the drug-likeness rules.

It is apparent from Table 6 that the compounds with codes AC1, AC2, AC6 and AC8 follow all the drug-likeness rules.

VEGA QSAR

VEGA QSAR helped to virtually study the mutagenic behaviour of the compounds identified by GCMS. The results obtained are the predicted values which may help in reducing the wet lab efforts. If the compound has already been studied, the results is denoted as “experimentally proven” and for rest of compound it is denoted as “prediction”. Ames test – CAESAR 2.1.13 model was used to qualitatively predict mutagenicity of test compounds. The results are noted in Tables 7 and 8.

Table 7 Mutagenic property of compounds of fermented Syzygium cumini seed methanolic extract

Table 8 Mutagenic property of compounds of fermented Allium cepa peel methanolic extract

Out of ten compounds from methanol extract of fermented Syzygium cumini seeds, six compounds were identified as non-mutagenic. Of these six non-mutagenic compounds, two are experimentally proven to be non-mutagenic viz. SC4 and SC5.

The results noted in Table 8 show that nine compounds of methanol extract of fermented Allium cepa peels are non-mutagenic; amongst them, AC2, AC3, AC4 and AC6 are experimentally proven to be non-mutagenic.

Collectively on analysing the results of ADME/Tox, it was observed that there are compounds which justify drug-likeness rules but are mutagenic and vice versa. But there are compounds which fulfil both criteria. SC3, SC7, AC1, AC2, AC6 and AC8 are the molecules that obey the ADME/Tox analysis prediction. AC2 and AC6 are experimentally proven to be non-mutagenic.

Discussion

Amongst the parameters of DruLiTo, LogP is a key parameter that determines the environmental fate and hydrophobicity of test moiety. Hydrophobicity of the molecule is responsible for its absorption, bioavailability, interaction with a receptor, metabolism and toxicity [14]. If the molecule has AlogP value less than five, then it is prioritized as drug-like molecule. Restrictions for using the HBA, HBD, logP and Mw were postulated by Lipinski et al. [15]; fulfilment of Lipinski’s rule approves of molecule being orally administrable. TPSA parameter is used to know the behaviour of polar atoms in a molecule that predicts the absorption and transportation of test molecule [16].

Twenty components were identified from gas chromatography mass spectrometry of methanol extracts of fermented Syzygium cumini seeds and fermented Allium cepa peels. Virtual prediction of these components for their drug-like property (tool used: DruLiTo) and mutagenicity (software used: VEGA QSAR) conveys that:

• (a) There are four components from each extract that possess drug-like property based on their molecular characteristics.

• (b) Six components of fermented Syzygium cumini seed methanol extract and nine components of fermented Allium cepa peel methanol extract are non-mutagenic. Six of these fifteen components are experimentally proven to be non-mutagenic.

Some of the compounds, which were identified by GCMS, are at present used for medicinal and therapeutic purposes. Their uses are mentioned below.

SC2—Oxetane, 2, 4-dimethyl-, trans-

Taxol possessing oxetane ring is used in cancer therapy. Oxetanocin A was first isolated from Bacillus megaterium and inhibits in vivo replication of HIV. Oxetanes being more polar are used as replacement groups to block metabolically vulnerable methylene sites. And also they are stable and not prone to enzymatic attack. Oxetane improves the binding affinity of 1,25-dihydroxyvitamin D3 analogues for bovine thymus D3 receptors [17].

SC3—Ethanamine,2-methoxy-

On condensation of ethanamine,2-methoxy- with salicylaldehyde derivatives, the derivatives obtained possess antioxidant and anticancer activity against gastric cancer cell lines [18].

SC5—Glycerin

Glycerin has tonic, wound healing, immune boosting, protective, antiseptic, antibacterial, hypo allergic and soothing properties [19].

SC8—Benzene-1,2,3-triol

This compound is used as topical agent to treat psoriasis, leprosy, eczema, and destroy lupus. It is also used as eye drops in chronic cases of conjunctivitis [20].

AC2—2,3-Butanediol

The 2,3-Butanediol is commonly known as dimethyl ethylene glycol. The polyethylene glycols are used as laxatives. They are attached to various protein medications, to allow slower clearance of the carried proteins from the blood. Gene therapy vectors like viruses can be coated with these gylcols in order to shield them from immune system [21, 22].

AC4—Monoethanolamine

The monoethanolamine is used for therapeutic neurolysis of nerves or ganglia to provide relief in chronic pain caused in certain conditions such as inoperable cancers and trigeminal neuralgia [23].

AC6—1,2-Benzenediol

1,2-Benzenediol is commonly known as catechol, which is used as precursor to pesticides, flavours and fragrances. It is employed in medicine as expectorant [24].

AC7—Cyclohexan-1,4,5-triol-3-one-1-carboxylic acid

This compound is precursor to tyrosine, 3-phenylalanine, tryptophan, vitamin K and folate [25].

Conclusion

From the collective analysis of predicted drug-like property and mutagenicity of the components of these two fermented waste extracts, it is deduced that:

Ethanamine, 2-methoxy- and hydroperoxide, 1-methylpentyl from methanolic extract of fermented Syzygium cumini seeds and Selenolo[2,3-b]pyridine, 3-methyl-, 2,3-butanediol, 1,2-benzenediol and ethaneperoxoic acid, 1-cyano-1-[2-(2-phenyl-1,3-dioxolan-2-yl)ethyl] pentyl ester from fermented methanol extract of Allium cepa peels exhibit drug-like properties and are also non-mutagenic. These compounds predicted to be drug-like and non-mutagenic can be further studied as ligands for bacterial and cancerous targets by the means of in silico docking techniques. The findings can lead to their use in diseases like multi-drug resistant bacterial diseases, oxidative stress and cancer.