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Drug and Chemical Toxicology

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In silico evaluation of multispecies toxicity of


natural compounds

Sripriya N., Ranjith Kumar M., Ashwin Karthick N., Bhuvaneswari S. & Udaya
Prakash N. K.

To cite this article: Sripriya N., Ranjith Kumar M., Ashwin Karthick N., Bhuvaneswari S. & Udaya
Prakash N. K. (2019): In�silico evaluation of multispecies toxicity of natural compounds, Drug and
Chemical Toxicology, DOI: 10.1080/01480545.2019.1614023

To link to this article: https://doi.org/10.1080/01480545.2019.1614023

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Published online: 21 May 2019.

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DRUG AND CHEMICAL TOXICOLOGY
https://doi.org/10.1080/01480545.2019.1614023

RESEARCH ARTICLE

In silico evaluation of multispecies toxicity of natural compounds


Sripriya N.a, Ranjith Kumar M.a, Ashwin Karthick N.a, Bhuvaneswari S.b and Udaya Prakash N. K.c
a
R and D, Marina Labs, Chennai, India; bDepartment of Botany, Bharathi Women’s College, Chennai, India; cDepartment of Biotechnology,
Vels Institute of Science, Technology and Advanced Studies, Chennai, India

ABSTRACT ARTICLE HISTORY


Natural compounds are widely explored in industries, as a lead compound. Evaluating their toxicity is Received 14 January 2019
of utmost importance, as they may cause other side effects. The major hassles in evaluating the toxicity Revised 20 April 2019
of compounds through in vivo and in vitro methods such as time, money, workforce, and use of animal Accepted 25 April 2019
models can be overcome by computational methods. Quantitative structure–activity relationship
KEYWORDS
(QSAR) models predict the toxicity from the structure of a compound. In the present study, the metha- Natural compounds; GC-MS;
nolic extracts of three plants, namely, Carissa carandas, Canthium angustifolium, and Epiphyllum oxype- QSAR; TEST; toxicity
talum, were subjected to Gas Chromatography-Mass Spectrometry (GC-MS), in which 27 different
compounds were identified. The compounds were evaluated for their toxicity through QSAR-Toxicity
Estimation Software Tool (TEST) against multispecies – Daphnia magna, Pimephales promelas,
Tetrahymena pyriformis, and rat (Oral). The study revealed that the order of toxicity of the natural com-
pounds was D. magna > T. pyriformis > P. promelas > Rat (Oral). All the compounds were non-bioac-
cummulative, while most of them were developmental toxicants. Only one compound (Dasycarpidan-1-
methanol, acetate (ester)) was a mutagen. Further studies of the compounds on in vivo models are rec-
ommended after in silico analysis, for exploration in different industries.

Introduction physiochemical properties of the compound (Barratt 2000).


Quantitative structure activity relationships (QSARs) are math-
Plant and plant products have revolutionized the modern
ematical models used for predicting structure relative activ-
world with a market size of 62 billion dollars. Most of the
ities of the compound (Kar and Roy 2010).
countries use medicinal plants in therapeutics for cardiovas-
Toxicity of various compounds such as phenols
cular diseases, inflammation disorders and cancer. Industries
(Duchowicz et al. 2008), pesticides (Basant et al. 2015), food
isolate the active components of medicinal plants to utilize
chemicals (Valerio et al. 2007), industrial chemicals (Alves
in their product formulation. In food and cosmetic industries,
et al. 2018), narcotic chemicals (Aruoja et al. 2014), and
plants are used for their antioxidant and antimicrobial prop-
organic chemicals (Singh et al. 2014) have been predicted
erties. Further, pharmacological industries utilize medicinal
using QSAR models previously. However, studies on toxicity
plants as an agent for drug synthesis. However, safety and
of natural compounds from plants are scarce. In the present
efficacy are the major factors that hinder the utilization of
study, three plants, namely, Canthium angustifolium, Carissa
plants before they reach the market (Harrison 2016).
carandas, and Epiphyllum oxypetalum, are subjected to GC-MS
Transformation of plant compounds to the development of
analysis and further evaluated for their toxicity through the
drugs or other finished products necessarily requires know-
in silico method.
ledge on the toxicity of the compounds. About one-third of
the products developed fail due to preclinical toxicity and
adverse drug reactions (Hornberg et al. 2014). The major has- Materials and methods
sles in evaluating the toxicity of compounds through in vivo
Weed collection, extraction, and GC-MS analysis
and in vitro methods are time, money and workforce (Lei
et al. 2017). Toxicity assessment through computational The leaves of Canthium angustifolium (Rubiaceae), Carissa car-
methods provides knowledge on chemicals lacking experi- andas (Apocynaceae), and Epiphyllum oxypetalum (Cactaceae)
mental data and aids in screening of chemicals for early drug were collected from Tiruvananthapuram of Kerala state in
development (Jordan et al. 2010). Additionally, these meth- India. The collected healthy leaves were dried under shade,
ods serve as an alternate to toxicity studies on animal mod- pulverized, and extracted with methanol at a ratio of 1:10
els. In silico prediction methods determine the activity of a (w/v) by cold percolation method. The methanolic extract
chemical in any given biological system based on the was analyzed by Gas Chromatography-Mass spectrometry

CONTACT Udaya Prakash N. K. nkudayaprakash@gmail.com Department of Biotechnology, School of Life Sciences, Vels Institute of Science, Technology
and Advanced Studies, Pallavaram, Chennai, India
Supplemental data for this article can be accessed here.
ß 2019 Informa UK Limited, trading as Taylor & Francis Group
2 SRIPRIYA N. ET AL.

Figure 1. GC-MS spectrum of (a) C. angustifolium, (b) C. carandas, and (c) E. oxypetalum.

(Agilent Technologies, Palo Alto, CA) and the compounds mammalian toxicity scales (Category X: Extreme toxicity; A:
detected were identified with the mass spectral database of Very high toxicity; B: High toxicity; C: Moderate toxicity; and
NIST, USA. D: Low toxicity) according to Agency for Toxic Substances
and Disease Registry (ATSDR). In addition, the bioaccumula-
tion factor (BF), developmental toxicity (DT), and mutagenic-
Endpoints for toxicity prediction by QSAR-TEST
ity of the compounds were also studied. The prediction of
The compounds identified through GC-MS analysis were eval- bioaccummulation factor through QSAR-TEST was based on
uated for their toxicity using QSAR – Toxicity Estimation the data compiled from Dimitrov et al. (2005), Arnot and
Software Tool (TEST), Version 4.2 (Martin 2016). The end- Gobas (2006), EURAS bioconcentration factor (BCF) Gold
points for the analysis were Daphnia magna (LC50-48 h), Standard Database, and Zhao et al. (2008). The developmen-
Pimephales promelas (LC50-96 h), Tetrahymena pyriformis tal toxicity was predicted based on the data from Arena et al.
(IGC50-48 h), and Oral rat (LD50). The toxicity values predicted (2004), Sussman et al. (2003), Briggs et al. (2012), and
for the compounds were correlated with aquatic toxicity and (Shepard and Lemire, 2004). Based on the response of
DRUG AND CHEMICAL TOXICOLOGY 3

compounds to Ames test, the mutagenicity of the com- values predicted for the compounds against D. magna,
pounds was predicted using the data set established by T. pyriformis, P. promelas, and rat are presented in Table 1.
Hansen et al. (2009). Different methods were employed to High bioaccumulation factor was recorded from the com-
evaluate the toxicity, such as Hierarchial clustering, single pounds of E. oxypetalum – C21, C23, and C22, with their val-
model, group contribution, nearest neighbor, and consensus, ues 981.97, 507, and 475.83, respectively. This was followed
as applicable for each of the endpoint. Hierarchical clustering, by C17 (130.9) and C15 (109.77) from C. carandas. The BF val-
single model, group contribution, food and drug administra- ues for all the other compounds were less than 100.
tion (FDA), and nearest neighbor models were employed to Among the compounds studied, 15 compounds were
predict the bioaccumulation factor and the toxicity against D. developmental toxicants and 10 (C2, C4, C5, C6, C9, C10, C11,
magna and P. promelas. The toxicity was predicted against T. C13, C18, and C24) were nontoxicants. Of the toxicants, four
pyriformis through hierarchical clustering, group contribution, compounds were from C. angustifolium (C1, C3, C7, and C8)
FDA, and nearest neighbor models. Hierarchical clustering, and four from C. carandas (C12, C14, C16, and C17). Among
FDA, and nearest neighbor models were used to predict the the compounds detected from E. oxypetalum, C18 and C24
mutagenicity and toxicity of the compounds against rat were developmental nontoxicants, while C19–C23, C25, and
(oral). The developmental toxicity of the compounds was pre- C26 were toxicants. Dasycarpidan-1-methanol, acetate (ester)
dicted through hierarchical clustering, single model, FDA, and was the only compound that was predicted to be a mutagen,
nearest neighbor models. The consensus method was chosen while all other compounds were non-mutagens. The bio-
for the present study, as it takes into consideration of all the accumulation factor, developmental toxicity and mutagenec-
ity of the compounds studied are represented in Table 2.
above stated models for the prediction of toxicity.

Results Discussion
The current study predicts the toxicity of natural compounds
Analysis by GC-MS revealed the presence of 10 compounds
detected in the methanolic extract of C. angustifolium, C. car-
in C. angustifolium (C1–C10); 9 in C. carandas (C10–C18), and
andas, and E. oxypetalum, against different end points using
10 in E. oxypetalum (C18–C27). The GC-MS chromatograms of
QSAR-TEST.
the three plants are presented in Figure 1. The isolated com-
The pharmacological activities of these plants have been
pounds were labeled as C1 to C27 (Table 1).
documented (Dhar et al. 1974, Hegde et al. 2009, Upendra
Among the 27 compounds studied, four compounds, i.e.,
and Khandelwal 2012, Dandekar et al. 2015, Kaunda and
C21, C22, C23, and C27 detected in the extract of E. oxypeta-
Zhang 2017). However, studies on their toxicity are scarce.
lum were predicted to possess extreme toxicity (Category X)
Hence, evaluation of their toxicity may provide information
based on their LC50 (mg/L) recorded against the plankton –
on further use of the natural compounds in differ-
D. magna. Very high toxicity (Category A) was recorded for
ent industries.
the compounds C4, C5, C6, C9, C12, C17, and C18. The com-
To relate the physiochemical properties to biological activ-
pounds C2, C3, C7, C10, C11, C13–C16, C19, C20, C24, and ity, relevant descriptors called molecular descriptors (MD) are
C26 were predicted to possess high toxicity (Category B). used. The relevance of molecular descriptors in toxicity pre-
Against T. pyriformis, the compounds C4, C6, C9, C12, and diction depends on the endpoints, concerned biological sys-
C15 showed extreme toxicity. The compounds C5, C10, C11, tem and class of chemicals (Balls et al. 2012). More than 2000
C14, C17, C18, C19, and C24 recorded very high toxicity while molecular descriptors such as molecular volume, shape,
C2, C3, C7, C13, and C20 were highly toxic. The toxicity was dipole moment, the number of atoms, steric effect, refractiv-
categorized based on the IGC50 recorded against ity, dissociation constant, electronegativity, octanol/water par-
T. pyriformis. tition coefficient can be generated and used for in silico
The compounds C6, C12, C15, C21, C22, and C23 were predictions (Hansch 1993, Todeschini and Consonni 2008).
predicted to possess extreme toxicity, with their LC50 values One such tool in evaluating the toxicity of any compound is
less than 0.1 mg/L against P. promelas. The compounds C2, Toxicity Evaluation Software Tool (TEST), which integrates
C3, C5, C7, C9, C10, C14, C16, C18, and C24 showed very and predicts the toxicity based on the compound’s toxic
high toxicity, whereas C1, C4, C8, C11, C13, C17, C19, C20, mechanism and critical structural similarities. Thus, the multi-
and C26 were predicted to possess LC50 in the range species toxicity of natural compounds was evaluated using
1–4.69 mg/L and hence, categorized in Category B (high tox- QSAR-TEST in this study.
icity) of the toxicity scale. With the advent of QSAR prediction systems, the accuracy
The compounds C1 &andC8 from C. angustifolium exhib- of toxicity evaluation of natural compounds can be improved
ited moderate toxicity against the rat model, with the significantly. The applicability domain in a QSAR model
respective LD50 values of 11.43 and 31.12 mg/kg. Low toxicity defines the physicochemical, structural, or biological informa-
was predicted in the compounds C3 (from C. angustifolium), tion of compounds (Balls et al. 2012). The applicability
C22, C23, and C26 (from E. oxypetalum). All the compounds domain of hierarchical clustering, single model, and group
detected in the extract of C. carandas possessed LD50 above contribution models is based on the model ellipsoid, Rmax,
500 mg/kg, thus classified as nontoxic against rat, according and fragment constraints. In addition to model ellipsoid and
to the mammalian toxicity scale of ATSDR, EPA. The toxicity fragment constraints, the cosine similarity coefficient and
4

Table 1. Predicted toxicity values and category of natural compounds against D. magna, T. pyriformis, P. promelas, and rat.
D. magna T. pyriformis P. promelas Rat
LC50 IGC50 LC50 LD50
Compound ID Plant Name of the compound (mg/L) Category (mg/L) Category (mg/L) Category (mg/kg) Category
C1 C. angustifolium Carda-4,20(22)-dienolide, 3-[(6-deoxy-3-O- N/A N/A N/A N/A 3.64 B 11.43 C
SRIPRIYA N. ET AL.

methyl-a-L-mannopyranosyl)oxy]-14-hydroxy-
, (3a)-
C2 Chloromethyl 2-chloroundecanoate 2.61 B 1.20 B 0.75 A 1602.62 NT
C3 Dasycarpidan-1-methanol, acetate (ester) 1.32 B 3.24 B 0.23 A 286.89 D
C4 Octadecanoic acid, 9,10-dichloro-, methyl ester 0.47 A 0.07 X 1.77 B 830.49 NT
C5 9-Octadecenoic acid (Z)-, methyl ester 0.74 A 0.28 A 0.57 A 15,279.68 NT
C6 Oleic acid, eicosyl ester 0.79 A 0.0011 X 0.0352 X 28,662.33 NT
C7 4-Piperidineacetic acid, 1-acetyl-5-ethyl-2-[3-(2- 5.93 B 5.37 B 0.14 A N/A N/A
hydroxyethyl)-1H-indol-2-yl]-a-methyl-,
methyl ester
C8 Sarreroside N/A N/A N/A N/A 1.47 B 31.12 C
C9 Docosanedioic acid, dimethyl ester 0.95 A 0.0996 X 0.14 A 20,476.93 NT
C10 C. angustifolium; Hexadecanoic acid, methyl ester 1.78 B 0.56 A 0.36 A 15,356.82 NT
C. carandas
C11 C. carandas 9-Octadecenoic acid (Z)-, 2-hydroxy-1- 1.14 B 0.80 A 4.69 B 13,511.72 NT
(hydroxymethyl)ethyl ester
C12 Hexadecanoic acid, 1-(hydroxymethyl)-1,2- 0.24 A 0.0112 X 0.0083 X 21,073.39 NT
ethanediyl ester
C13 n-Hexadecanoic acid 4.58 B 1.28 B 1.31 B 13,454.34 NT
C14 Oleic acid 1.16 B 0.37 A 0.14 A 12,911.86 NT
C15 17-Pentatriacontene 5.28 B 0.0018 X 0.0011 X 7505.29 NT
C16 Pregnan-18-oic acid, 20-hydroxy-, (5a)- 7.84 B N/A N/A 0.40 A 8231.46 NT
C17 3,7,11,15-Tetramethyl-2-hexadecen-1-ol 0.37 A 0.12 A 1 B 7554.77 NT
C18 C. carandas; 10-Octadecenoic acid, methyl ester 0.72 A 0.28 A 0.57 A 15,263.11 NT
E. oxypetalum
C19 E. oxypetalum 1,2-Benzenedicarboxylic acid, butyl octyl ester 3.98 B 0.52 A 1.21 B 15,853.27 NT
C20 1,2-Benzenedicarboxylic acid, mono(2- 2.68 B 5.24 B 3.53 B 6782.54 NT
ethylhexyl) ester
C21 Cyclopropanebutanoic acid,2-[(2-[(2-[(2- 0.03 X N/A N/A 0.0062 X 2002.69 NT
pentylcyclopropyl)methyl]
cyclopropyl)methyl]cyclopropyl)methyl]-,
methyl ester
C22 17-(1,5-Dimethylhexyl)-10,13-dimethyl-3- 0.0153 X N/A N/A 0.0019 X 427.05 D
styrylhexadecahydrocyclopenta(a)
phenanthren-2-one
C23 Ergosteryl acetate 0.0229 X N/A N/A 0.0249 X 112.26 D
C24 Ethanol, 2-(9-octadecenyloxy)-, (Z)- 1.13 B 0.19 A 0.97 A 10,547.27 NT
C25 Glycine, N-[(3a,5a,7a,12a)-24-oxo-3,7,12- N/A N/A N/A N/A N/A N/A 559.75 NT
tris[(trimethylsilyl)oxy]cholan-24-yl]-,
methyl ester
C26 (5a)Pregnane-3,20a-diol, 14a,18a-[4-methyl-3- 6.35 B N/A N/A 3.35 B 485.26 D
oxo-(1-oxa-4-azabutane-1,4-diyl)]-, diacetate
C27 Rhodopin 0.0000881 X N/A N/A N/A N/A N/A N/A
X: Extreme toxicity; A: very high toxicity; B: high toxicity; C: moderate toxicity; D: low toxicity; NT: nontoxic; N/A: not applicable.
Table 2. Predicted values of bioaccumulation factor, developmental toxicity, and mutagenicity of natural compounds.
Developmental toxicity Mutagenicity
Bioaccumulation
Compound ID Plant Name of the compound factor Value Result Value Result
C1 C. angustifolium Carda-4,20(22)-dienolide, 3-[(6-deoxy-3-O-methyl-a-L- N/A 0.60 T 0.03 
mannopyranosyl)oxy]-14-hydroxy-, (3a)-
C2 Chloromethyl 2-chloroundecanoate 44.61 0.42 NT 0.28 
C3 Dasycarpidan-1-methanol, acetate (ester) 57.87 0.85 T 0.69 þ
C4 Octadecanoic acid, 9,10-dichloro-, methyl ester 45.54 0.44 NT 0.33 
C5 9-Octadecenoic acid (Z)-, methyl ester 77.58 0.47 NT 0.11 
C6 Oleic acid, eicosyl ester 33.44 0.43 NT 0.14 
C7 4-Piperidineacetic acid, 1-acetyl-5-ethyl-2-[3-(2- 11.78 0.80 T 0.13 
hydroxyethyl)-1H-indol-2-yl]-a-methyl-,
methyl ester
C8 Sarreroside N/A 0.70 T 0.10 
C9 Docosanedioic acid, dimethyl ester 24.74 0.44 NT 0.17 
C10 C. angustifolium; Hexadecanoic acid, methyl ester 44.45 0.44 NT 0.02 
C. carandas
C11 C. carandas 9-Octadecenoic acid (Z)-, 2-hydroxy-1- 12.21 0.49 NT 0.29 
(hydroxymethyl)ethyl ester
C12 Hexadecanoic acid, 1-(hydroxymethyl)-1,2- 9.11 0.61 T 0.18 
ethanediyl ester
C13 n-Hexadecanoic acid 29.05 0.27 NT 0.04 
C14 Oleic acid 16.55 0.51 T 0.01 
C15 17-Pentatriacontene 109.77 N/A N/A 0.01 
C16 Pregnan-18-oic acid, 20-hydroxy-, (5a)- 27.32 1.02 T 0.25 
C17 3,7,11,15-Tetramethyl-2-hexadecen-1-ol 130.90 0.61 T 0.05 
C18 C. carandas; 10-Octadecenoic acid, methyl ester 77.55 0.43 NT 0.11 
E. oxypetalum
C19 E. oxypetalum 1,2-Benzenedicarboxylic acid, butyl octyl ester 17.82 0.54 T 0.03 
C20 1,2-Benzenedicarboxylic acid, mono(2- 9.40 0.78 T 0.02 
ethylhexyl) ester
C21 Cyclopropanebutanoic acid,2-[(2-[(2-[(2- 981.97 0.64 T 0.40 
pentylcyclopropyl)methyl]cyclopropyl)methyl]
cyclopropyl)methyl]-, methyl ester
C22 17-(1,5-Dimethylhexyl)-10,13-dimethyl-3- 475.83 0.94 T 0.18 
styrylhexadecahydrocyclopenta(a)phenanthren-
2-one
C23 Ergosteryl acetate 507 0.90 T 0.09 
C24 Ethanol, 2-(9-octadecenyloxy)-, (Z)- 42.20 0.40 NT 0.12 
C25 Glycine, N-[(3a,5a,7a,12a)-24-oxo-3,7,12- 13.73 0.52 T 0.09 
tris[(trimethylsilyl)oxy]cholan-24-yl]-, methyl ester
C26 (5a)Pregnane-3,20a-diol, 14a,18a-[4-methyl-3-oxo-(1- 10.53 0.77 T 0.29 
oxa-4-azabutane-1,4-diyl)]-, diacetate
C27 Rhodopin N/A N/A N/A 0.05 
T: toxicant; NT: nontoxicant; N/A: not applicable; : negative; þ: positive.
DRUG AND CHEMICAL TOXICOLOGY
5
6 SRIPRIYA N. ET AL.

cross validation coefficient are considered for the FDA model. constituents (Nelson and Kursar 1999, Williamson 2001).
In the nearest neighbor model, the major applicability However, the exact mechanism of drug action largely relies
domain is the cosine similarity coefficient. The consensus on experimental and clinical evidence. In silico studies pro-
model includes the applicability domains that are valid for vide insights on the interactions of the constituents of phyto-
the respective models. Only the activity of molecules falling medicines and their toxicity. The toxicity of natural
within the applicability domain of the model can be pre- compounds from plants has previously been documented by
dicted. In the present study, toxicity prediction by consensus the same authors (Prakash et al. 2014, Udayaprakash et al.
model is presented, since the model takes an average esti- 2014). Evaluation of toxicity through in silico models over-
mates from multiple models and compensates the limitations comes the consumption of time, money, and workforce
of the individual models. Individual models use different involved in screening of drug targets during preclinical stud-
descriptors and statistical methods to model different aspects ies. Additionally, the use of animals for toxicity estimation
of the toxicological effects. The toxicity could not be pre- can be limited through in silico studies. In the present study,
dicted through consensus model for few of the compounds the toxicity of individual compounds present in the plants –
in the present study, due to the non-applicability of two or C. angustifolium, C. carandas, and E. oxypetalum was eval-
more QSAR models. The predicted toxicity values for each of uated through QSAR-TEST. Further studies on the interactions
the endpoints, molecular descriptors and number of similar between the compounds of the respective plants through in
chemicals studied through different models are provided in silico tools such as docking are recommended prior to in
the supplementary material (Tables S1–S7). From the results vivo studies.
of the present study, it could be noted that the plant com-
pounds had high toxicity for lower organisms which grad-
ually decreased with higher order of organisms in the order, Disclosure statement
D. magna > T. pyriformis > P. promelas > Rat (Oral).
No potential conflict of interest was reported by the authors.
Bioaccumulation factor is the ratio of the concentration of
a chemical in fish due to absorption via the respiratory sur-
face with respect to water at steady state. In general, a com- Funding
pound is termed bioaccummulative, if its BF value is greater
This research was supported by internal fund of R & D, Marina Labs,
than 2000 and very bioaccummulative if its value is greater Chennai [Grant no. ML-2015-RD002].
than 5000 (Burden et al. 2014). In the present study, the bio-
accumulation factor for all the compounds was less than
2000, and hence, non-bioaccummulative in nature. References
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