In Silico Prediction of the Toxic Potential of Lupeol - Chemical

Jun 27, 2017 - Lupeol is a natural triterpenoid found in many plant species such as mango. This compound is the principal active component of many tra...
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In Silico Prediction of the Toxic Potential of Lupeol Manuel A. Ruiz-Rodríguez,*,†,‡ Angelo Vedani,‡ Ana L. Flores-Mireles,§ Manuel H. Cháirez-Ramírez,† José A. Gallegos-Infante,† and Rubén F. González-Laredo*,† †

Department of Chemical and Biochemical Engineering, Tecnológico Nacional de México-Instituto Tecnológico de Durango, Boulevard Felipe Pescador 1830 Ote., 34080 Durango, México ‡ Department of Pharmaceutical Sciences, University of Basel, Klingelbergstrasse 50, 4056 Basel, Switzerland § Department of Molecular Microbiology and Center for Women’s Infectious Disease Research, Washington University School of Medicine, Saint Louis, Missouri 63110-1093, United States ABSTRACT: Lupeol is a natural triterpenoid found in many plant species such as mango. This compound is the principal active component of many traditional herbal medicines. In the past decade, a considerable number of publications dealt with lupeol and its analogues due to the interest in their pharmacological activities against cancer, inflammation, arthritis, diabetes, and heart disease. To identify further potential applications of lupeol and its analogues, it is necessary to investigate their mechanisms of action, particularly their interaction with off-target proteins that may trigger adverse effects or toxicity. In this study, we simulated and quantified the interaction of lupeol and 11 of its analogues toward a series of 16 proteins known or suspected to trigger adverse effects employing the VirtualToxLab. This software provides a thermodynamic estimate of the binding affinity, and the results were challenged by molecular-dynamics simulations, which allow probing the kinetic stability of the underlying protein−ligand complexes. Our results indicate that there is a moderate toxic potential for lupeol and some of its analogues, by targeting and binding to nuclear receptors involved in fertility, which could trigger undesired adverse effects.



INTRODUCTION Lupeol and its analogues are triterpenes found in a diversity of vegetables and fruits. For instance, lupeol is found in mangoes, cabbage, green pepper, strawberry, olives, and grapes.1,2 Interestingly, this group of compounds is the active component in many plants used in traditional medicine by native cultures in North America, Japan, China, Latin America, and Caribbean islands.2−4 Importantly, it has been shown that lupeol and its analogues display therapeutic properties against cancer, inflammation, arthritis, diabetes, and heart disease. Therefore, these compounds have raised interest as drugs to treat such conditions.5 In some cases, it has been possible to determinate their action mechanism against these diseases. Lupeol is a multitarget agent that affects different protein receptors depending on the disease that is treated with this compound. In the case of inflammation, lupeol affects the molecular pathways of the nuclear factor kappa B(NFκB), cFLIP, Fas, Kras, phosphatidylinositol-3-kinase PI3K/Akt, and Wnt/β-catenin in a variety of cells.6 In cancer treatments, lupeol inhibits DNA topoisomerase II, protein kinases, and serine proteases, causing the death of cancer cells.7,8 Lupeol has also been reported to inhibit growth in melanoma and leukemia cells and inhibit tumor promotion in mouse skin by modulating various signaling pathways.9−11 The topical application of lupeol at 200 μg/animal has been reported to prevent DNA strand breaks in mice skin caused by 7,12-dimethylbenz[a]anthracene (DMBA).12 Furthermore, in © 2017 American Chemical Society

skin mouse models, lupeol has inhibited the genotoxicity effect of benzo[a]pyrene (B[a]P), which is a binding mutagen. Additionally, lupeol was able to significantly decrease B[a]P-induced clastogenicity by pretreating mice with lupeol [1 mg/animal] for 7 days prior to B[a]P administration.13 Many studies have focused on understanding the properties of lupeol and its analogues such as determination of phytochemical properties, synthesis and biological activity using mice, dogs, and cancer cell lines as test models to find promising applications to cure diseases. However, prior to their potential application in humans, it is necessary to establish if they might trigger undesired effects. Traditionally, initial bioassays are performed using mouse models, but these experiments are both laborious and expensive with the inconvenience that results may not simply be translated to humans.14,15 Therefore, to better understand the toxicological effects of a new drug, it is necessary to develop new approaches to overcome these problems. Computational approaches for in silico toxicology determinations turn into an efficient alternative to predict drug−protein interactions without the aforementioned drawbacks. One of these new tools is VirtualToxLab (cf. http://www. virtualtoxlab.org), which is an in silico concept for estimating the toxic potential: endocrine and metabolic disruption, aspects Received: March 11, 2017 Published: June 27, 2017 1562

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Figure 1. Chemical structures of lupeol and its investigated analogues. using the Aquarius software (cf. ref 18: Figure 3, left). Then a similar protocol with allowance for induced fit was employed at the protein (cf. ref 18: Figure 3, center) using Alignator23 and Cheetah.18,24 In a next step, the change in free energy, ΔG, of the small molecule when binding from the aqueous environment to the protein was estimated.18 Finally, the toxic potential of lupeol and its analogues were determined using VirtualToxLab. The technology and mathematical models underlying in VirtualToxLab have been recently described in detail18 and shall, therefore, only be briefly summarized in this document. VirtualToxLab is based on a client−server protocol and consists of a graphical user interface (building and uploading compounds, downloading, and visualizing results) that calculates the toxic potential (TP) and binding affinity (IC50 values) of a chemical compound in base to the values of quantitative structure−activity relationship (QSAR) and multiple docking with 16 protein susceptible to trigger adverse effects from chemical compounds. The philosophy underlying the VirtualToxLab is to estimate the toxic potential of a compound through the normalized individual binding affinities toward a series of protein models known or suspected to trigger adverse effects. In addition, the standard deviation of the predictions, the predictive power of the individual models and the underlying protein superfamilies are considered. Then the compound−protein interaction is adjusted and compared by statistical relative importance using the standard deviation of the individual predictions and the quality of the subjacent models (e.g., the number of modeled structures and the range of activity covered). An extended description of the mathematical models used in VitualToxLab is described by Vedani et al.18 The TP is based only in thermodynamic properties and does not consider adsorption, disruption, metabolism, and elimination properties (ADME). A very low value of TP does not necessary indicate that a compound is safe to use. This value only indicates a low statistical probability that this compound can trigger an adverse effect on the basis of the chemical compound submitted to VirtualToxLab can bond to one or more of the tested proteins. The values of TP may range from 0.0 (none) to 1.0 (extreme). The toxic potential is a nonlinear complex function that should not be overestimated but interpreted as a toxic alert. Besides the results of toxic potential, the program provides the calculations of the concentration that can inhibit one of the proteins used as reference in the VirtualToxLab.

of carcinogenicity and cardiotoxicity of drugs, chemicals and natural products.16−20 This software calculates the toxic potential (TP), which is defined in this document as the ability to trigger adverse effects in base of an automated protocol that simulates and quantifies the binding affinities of small molecules toward a series of 16 proteins, known or suspected to trigger adverse effects. The binding affinity is defined as the attraction between a ligand (chemical compound tested) and one of the 16 proteins suspected to trigger adverse effects. This union is quantified considering covalent and noncovalent bonds, intermolecular interactions such as hydrogen bonding, electrostatic interactions, hydrophobic, and van der Waals forces. Among these proteins, there are 10 nuclear receptors (androgen, estrogen α, estrogen β, glucocorticoid, liver X, mineralocorticoid, peroxisome proliferator-activated receptor γ, progesterone, thyroid α, thyroid β), four members of the cytochrome P450 enzyme family (1A2, 2C9, 2D6, 3A4), a cytosolic transcription factor (aryl hydrocarbon receptor), and a potassium ion channel (hERG). In this study, we simulated and quantified the interaction of lupeol and 11 of its analogues toward the 16 proteins currently included in the VirtualToxLab. As the simulations are conducted at the atomic level, this allows for a mechanistic interpretation of the underlying binding modes. This protocol is independent from any training data and makes the approach universal with respect to the applicability domain. Moreover, the platform provides individual binding affinities and an estimate for the overall toxic potential.21



MATERIALS AND METHODS

The three-dimensional structures of lupeol and 11 of its analogues were constructed and energy-minimized using the BioX software.22 The chemical structures of all investigated compounds are shown in Figure 1. In a first step, the configuration of a compound (position, orientation, conformation) in aqueous solution was sampled and quantified 1563

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113.00 not binding 19000.00

4880.00

not binding not binding

Only proteins with the highest TP value were modeled by molecular dynamics (MD) to determine the stability of the protein−compound relationship for 10 ns. The MD simulations were carried out employing Desmond25 as embedded in the VirtualDesignLab.26 A force field OPLS3 was set to 10 ns during the MD simulations, at constant pressure and temperature MTK and considering water as solvent. The visualization of the results was performed using visual molecular dynamics (VMD).27 To assess the physicochemical properties of the investigated compounds, we employed the QikProp software28 accessible through the VirtualDesignLab.26 For a complementary assessment of the investigated compound’s harmful feature, we have employed thirdparty software components: Toxtree29 based on the Cramer rules,30 MolInspiration31 based on a molecular-fragment database,32 and Lazar (end points, carcinogenesis-rodents, and mutagenesis-Salmonella typhimurium)33 using structure−activity relationships.34 All the calculations were done using a Linux server of 1024 nodes.

not binding not binding 1630.00

“Not binding” refers to a binding affinity >100 μM.

4660.00 3880.00 methylbetulinate

17400.00 98.40

34700.00

820.00

244.00

RESULTS AND DISCUSSION The binding affinities of lupeol and its analogues were determined against all 16 target proteins currently embedded in this platform (Table 1). Our results suggested that nuclear receptors were the primary targets, showing that the highest affinities were toward androgen (AR), the glucocorticoid (GR), the progesterone (PR), and estrogen receptors (ER). The estimated toxic potential ranged from 0.377 (low) to 0.569 (moderate) as represented in Figure 2. The results from MD simulations showed the lead compound. Lupeol was the most active compound presenting PR-, ER-, and AhR-binding affinities in nanomolar concentrations (see Table 1). Lupeol binds most strongly not only to the PR (24.30 nM) and the ERα (67.90 nM), but also to the aryl hydrocarbon receptor (AhR: 419 nM) and the mineralocorticoid receptor (MR: 696 nM). The affinities of other targets were greater than 1.0 μM. Kinetic stability of lupeol-PR and -ER complexes was determined according to results shown in Figure 3 (PR) and Figure 4 (ERα). In both ligand−protein complexes, the ligand is stabilized through weak intermolecular interactions due to the lipophilic feature of lupeol bearing just a single hydroxyl group, which confers the hydrogen-bond accepting or donating properties of the ligand. At the lupeol− PR complex, a strong hydrogen bond is formed with Thr894, while at the ERα, the interaction is formed with Glu353. The main interactions are, therefore, formed with aliphatic and aromatic amino-acid side chains lining the binding pocket. The 30-hydroxylated derivative of lupenone displays a remarkable binding affinity (31.4 nM) toward the AR and appears to be kinetically stable (Figure 5). The interaction is stabilized by hydrophobic interactions through two hydrogen bonds with Asn705 and Gln711. In the case of betulin, the results indicate a strong and kinetically stable binding with the glucocorticoid receptor (GR: 15.3 nM) (Figure 6). This compound is stabilized through three hydrogen bonds with Asn564, Arg611, and Cys736 residues along with hydrophobic interactions. Particularly, the interaction of the extra hydroxyl group (C28), compared to lupeol, appears to create a stronger binding. On the other hand, the interaction with Arg611 is kinetically labile (Figure 7: center), which appears to reduce the binding affinity by, possibly, a factor of 5−10. Some analogues of lupeol displayed a moderate binding affinity toward the aryl hydrocarbon receptor (AhR), among them betulinic acid amide had the lowest IC50 with 131 nM. While the MD simulation suggests a stable ligand−protein

a

8130.00

44900.00 5280.00 66.50 238.00

not binding 22900.00

52100.00 1370.00 1120.00 lupeol-30-aldehyde

not binding 31000.00

3650.00 70600.00 2910.00

82.10

1150.00

1690.00

39.60

6660.00

1840.00

1900.00

6760.00

3160.00 9640.00 2470.00

8890.00

3280.00

12000.00

21300.00

3270.00

5550.00

lupeol acetate

12000.00 1430.00

5750.00

1400.00 2490.00

24.30

5790.00

2980.00

10900.00

696.00 5320.00

9170.00 138.00

144.00 1330.00

2020.00 4770.00

502.00 67.90 7300.00

5100.00 not binding 8170.00

not binding 5670.00 419.00

1670.00

4660.00 3150.00 lupeol

63600.00 58100.00 131.00

8610.00 7130.00 lupenone

3170.00

not binding

14100.00 2350.00 22.00

7650.00 47300.00

10800.00

4590.00 46200.00

100.00 5110.00

10500.00 71700.00

26.50 30.20 326.00 82.70

74900.00 not binding not binding not binding 20700.00 2770.00

5490.00 1240.00

betulonic acid

12100.00 not binding 860.00

7080.00

betulinic acid amide

6680.00

1300.00 not binding not binding

527.00 20.60

384.00

335.00

1810.00 586.00

36600.00 17500.00

3530.00 81.40 1820.00 344.00

not binding 42700.00 3450.00 3540.00

68.90 21400.00 5060.00 306.00

not binding not binding 61300.00

13800.00 643.00 betulinic acid

not binding 1890.00 414.00

6790.00

betulin aldehyde

2760.00

15900.00

5980.00 441.00

36.30

2520.00

1240.00 1310.00

48.10 8190.00

27500.00 469.00

35.30 64.80 1820.00

not binding 15.30 213.00

47.50 1490.00

17900.00 2550.00

2910.00 19800.00 58800.00

not binding 3720.00 3810.00 56.90 betulin

365.00 31.40 30-hydroxylupeol

TRβ TRα PR PPARγ

not binding not binding 0.97

MR LXR

356.00 11.90

hERG GR ERβ

not binding 6.37 0.30

ERα CYP3A4

412.00 4850.00

CYP2D6 CYP2C9 CYP1A2

not binding 15400.00 6090.00

AhR AR

2.87

molecule

30-hydroxylupenone

Table 1. Binding Affinities (IC50 Nanomolar) of Investigated Compounds against All 16 Target Proteins in the VirtualToxLab16−18a

not binding not binding

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Figure 2. Toxic potential of the 12 investigated compounds as computed with the VirtualToxLab.16,18

Figure 3. Left: binding of lupeol to the progesterone receptor. The ligand and key amino-acid residues are shown in licorice; the protein is depicted by its inner surface (colored by z-depth). Hydrophobic residues are shown in space-filling mode (brown) and water molecules represented by blue beads. Hydrogen bonds are indicated by yellow dashed lines. The image was generated employing the VMD software.27 Right: structure of lupeol oriented as in the left image.

Figure 4. Left: binding of lupeol to the estrogen receptor α. The ligand and key amino-acid residues are shown in licorice; the protein is depicted by its inner surface (colored by z-depth). Hydrophobic residues are shown in space-filling mode (brown) and water molecules represented by blue beads. Hydrogen bonds are indicated by yellow dashed lines. The image was generated employing the VMD software.27 Right: structure of lupeol oriented as in the left image.

complex, the lack of a hydrogen-bond acceptor for the aliphatic hydroxyl group of betulinic acid amide (Figure 7) would reduce the binding affinity by a factor of 5−10, leading to a moderate binding of the AhR and therefore to a smaller carcinogenic potential. 30-Hydroxylupenone displays a computed binding affinity of 485 nM toward cytochrome P450−2D6 (2D6), which might trigger a metabolic response, for example, drug−drug interactions.35 Apart from the interaction with the FeIII ion, the hydroxyl group is stabilized by two hydrogen bonds with Gln244 and Ser304, respectively. The MD simulation underlines the stability of the protein−ligand complex (Figure 8). Computational assessment of a compound’s biological activity or toxicity should always be discussed along with its ADME properties (adsorption, distribution, metabolism, elimination) and bioavailability as a prerequisite for understanding its potential beneficial or undesired effects.18 The physicochemical properties of the investigated compounds were assessed by the

QikProp software28 accessible through the VirtualDesignLab (Table 2).16 All compounds had a similar molecular weight (425−470) but significantly different lipophilic properties (log P: 4.6−7.8). They are not very soluble in water (log S: 5.1−8.9) but are orally bioavailable (94−100%) and can penetrate cell membranes (Caco permeability: 310−4400). Their polar surface area ranges from 20−62 Å2. They might also penetrate the blood-brain barrier (MDCK permeability: 190−2500; but log BB: −0.50−0.12). In conclusion, all compounds could be present at considerable concentrations in the systemic circulation, which might trigger adverse effects. The results for the compounds discussed above are given in Table 3. Calculations with ToxTree showed low estimated toxicity for lupeol and its analogues, while MolInspiration showed probabilities of binding nuclear receptors between 0.72 (lupeol) to 0.93 (betulinic acid). The results from ToxTree would seem rather unexpected, particularly when compared with results from MolInspiration, but the former software is based on rather 1565

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Figure 5. Left: binding of 30-hydroxylupenone to the androgen receptor. The ligand and key amino-acid residues are shown in licorice; the protein is depicted by its inner surface (colored by z-depth). Hydrophobic residues are shown in space-filling mode (brown) and water molecules represented by blue beads. Hydrogen bonds are indicated by yellow dashed lines. The image was generated employing the VMD software.27 Right: structure of 30-hydroxylupenone oriented as in the left image.

Figure 7. Left: binding of betulinic acid amide to the aryl hydrocarbon receptor. The ligand and key amino-acid residues are shown in licorice; the protein is depicted by its inner surface (colored by z-depth). Hydrophobic residues are shown in space-filling mode (brown) and water molecules represented by blue beads. Hydrogen bonds are indicated by yellow dashed lines. The image was generated employing the VMD software.27 Right: structure of betulinic acid amide oriented as in the left image.

Figure 6. Left: binding of betulin to the glucocorticoid receptor. The ligand and key amino-acid residues are shown in licorice; the protein is depicted by its inner surface (colored by z-depth). Hydrophobic residues are shown in space-filling mode (brown) and water molecules represented by blue beads. Hydrogen bonds are indicated by yellow dashed lines. The image was generated employing the VMD software.27 Right: structure of betulin oriented as in the left image.

Figure 8. Left: binding of 30-hydroxylupenone to CYP450 2D6. The ligand, the heme, and key amino-acid residues are shown in licorice; the protein is depicted by its inner surface (colored by z-depth). The FeIII ion is represented as a pink sphere. Hydrophobic residues are shown in space-filling mode (brown) and water molecules represented by blue beads. Hydrogen bonds are indicated by yellow dashed lines. The image was generated employing the VMD software.27 Right: structure of 30-hydroxylupenone oriented as in the left image.

simple rules,29 for example, the occurrence of more than one aromatic ring, the presence of a substituted aromatic ring or any atom other than C, H, O, N, or divalent S. If none of these conditions is met, a low probability results (denoted as “−” in Table 3). In MolInspiration, the most interesting value is the probability to bind a nuclear receptor, which is indeed preeminent for all investigated compounds, and is in agreement with the results obtained from the VirtualToxLab. There is consensus with respect to bind the hERG ion channel, which was not observed in both methods. MolInspiration, which includes more enzymes than the four CYP450 entities currently employed in the VirtualToxLab, weights slightly higher the binding of enzymes. In addition, the results from MolInspiration suggest that lupeol and its analogues are somewhat susceptible to attack and possibly to degradation by proteases. Over the years, numerous specialized QSAR-based tools have been and are still being actively developed; some of them have

been settled to determine the toxicity of man-made chemicals. One of those tools to which VirtualToxLab could be compared is ToxCast (http://www.epa.gov/ncct/toxcast/).36−39 This tool uses QSAR models for ER and AR to evaluate chemicals for potential endocrine disruption. Some advantages of ToxCast is that besides the QSAR models, it uses decision forest (DF) models to give a backup to its results and does not rely only on the QSAR information to determine if a chemical compound could be harmful. VirtualToxLab does not use DF models but to give a backup to its results, the compound−protein interaction is adjusted and compared by statistical relative importance (weight toxic potential wTP) using the standard deviation of the individual predictions and the quality of the subjacent models. Besides, VirtualToxLab does the calculations of toxic potential using the 1566

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Chemical Research in Toxicology Table 2. Physicochemical Properties of Selected Compounds Employed in This Studya compound

MW [g/Mol]b

log Pc

log Sd

log BBe

oral abs [%]f

Caco perm [nm/sec]g

MDCK perm [nm/sec]h

PSA [Å2]i

lupeol lupeol acetate 30-hydroxylupeol lupeol-30-aldehyde lupenone 30-hydroxylupenone betulin betulinic acid betulinic acid amide betulin aldehyde betulonic acid methylbetulinate

427 469 443 441 425 441 443 457 456 441 455 470

7.0 7.8 5.7 5.9 6.9 5.8 5.8 6.1 4.6 5.9 6.1 6.5

−7.8 −8.9 −6.6 −7.6 −7.6 −6.9 −6.6 −6.5 −5.1 −6.7 −6.8 −7.4

0.12 0.08 −0.40 −0.50 0.18 −0.37 −0.35 −0.40 −0.45 −0.27 −0.38 −0.10

100 100 100 100 100 100 100 94 100 100 94 100

4400 4200 1600 1300 4300 1500 1800 334 620 1800 310 3000

2500 2300 820 660 2400 790 950 190 560 950 176 1600

20 34 42 52 25 47 40 57 62 47 63 47

Preferred values are given in square brackets. For details, see ref 28. bMW: molecular weight {MW | 130 ≤ MW ≤ 725}. clog P: predicted octanol/water partition coefficient {log P | −2.0 ≤ log P ≤ + 6.5}. dlog S: predicted aqueous solubility in mol/dm3 {log S | −6.5 ≤ log S ≤ −0.5}. e log BB: predicted brain/blood partition coefficient {−3.0 ≤ log BB ≤ −1.2}. fOral abs: predicted human oral absorption on a 0 to 100% scale {80% is high}. gCaco perm: predicted apparent Caco-2 cell permeability in nm/s {500 is great}. hMDCK perm: predicted apparent MDCK cell permeability in nm/s {500 is great}. iPSA: polar surface area {PSA | 7 ≤ PSA ≤ 200}. a

Table 3. Consensus Scoring Employing ToxTree,29 MolInspiration,31 and Lazar33 ToxTree: General HarmfulnessLow (−), Intermediate (+), High (++) compound

ToxTree

MI/NRLa

MI/ICMb

MI/PIc

MI/EId

Laz/Care

Laz/Mutf

lupeol lupeol acetate 30-hydroxylupeol lupeol-30-aldehyde lupenone 30-hydroxylupenone betulin betulinic acid betulinic acid amide betulin aldehyde betulonic acid methylbetulinate

− − − − − − − − − − − −

0.76 0.72 0.80 0.87 0.75 0.74 0.85 0.93 0.80 0.79 0.88 0.83

0.10 0.08 0.06 0.13 −0.01 −0.04 −0.04 0.03 0.01 0.03 −0.06 0.02

0.19 0.10 0.16 0.24 0.01 0.05 0.09 0.14 0.18 0.19 0.04 0.10

0.45 0.44 0.55 0.61 0.41 0.46 0.51 0.55 0.53 0.53 0.47 0.46

3 3 3 3 4 3 3 3 3 3 3 3

0 0 0 0 0 0 0 0 0 0 0 0

MI/NRL: MolInspirationprobability to bind to a nuclear receptor {range | −1.0 ≤ range ≤ +1.0}. bMI/ICM: MolInspirationprobability to modulate an ion channel {range | −1.0 ≤ range ≤ +1.0}. cMI/PI: MolInspirationprobability to inhibit a protease {range | −1.0 ≤ range ≤ +1.0}. d MI/EI: MolInspirationprobability to inhibit an enzyme {range | −1.0 ≤ range ≤ +1.0}. eLaz/Car: Lazarcarcinogenicity {six tests: range | 0 ≤ range ≤ 6}. fLaz/Mut: Lazarmutagenicity {two tests: range | 0 ≤ range ≤ 2.} a

Although VirtualToxLab employs a sophisticated protocol to assess the toxic potential of chemical compounds, both falsepositive and false-negative results may occur. False-negative results are more frequent as the technology tests “only” 16 pathways that may eventually trigger a toxic response, while many more adverse mechanisms exist.18 Another source for underestimating a compound’s harmful feature is associated with the fact that exhaustive sampling of ligand binding to a macromolecular target is not possible at the currently available computing capabilities. In such case, the correct binding mode might be unidentified, particularly for large and very flexible molecules. The need for validation of the VirtualToxLab calculations by MD simulations arises from the fact that the Monte Carlo sampling technology employed in the VirtualToxLab (i.e., software Cheetah18,24) computes a thermodynamic value for a compound’s strength to bind a given target protein. While this is a necessary condition for binding, it is not sufficient as the ligand−protein interaction must be stable over a reasonable period of time to trigger an (e.g., agonistic) effect. This kinetic aspect (i.e., the time-dependent stability of a ligand−protein complex)

results from QSAR toward 16 proteins susceptible of triggering adverse effects, while ToxCast performance calculations of QSAR are only on AR and ER. Unfortunately, there were not available results of ToxCast for lupeol and its analogues to be compared with the results obtained from VirtualToxLab in this study. Computing time is another aspect to consider when discussing an in silico study. In our case, it ranged from 41−66 (CPU) hours. Considering that VirtualToxLab is able of parallel computing, the time needed to determine TP of bigger molecules could be a limiting factor, since at present time the software runs in a Linux server of 1024 nodes. Exhaustive sampling would imply a hundred times longer protocol, which is currently not feasible. Even then, it could not be guaranteed that the correct binding was identified, as induced fit adaptation of the protein conformation to the ligand’s topology might still not be properly addressed. False-positive results may occur when underestimating a compound’s desolvation energy, which in turn, leads to too high binding affinities. Thermodynamically feasible but kinetically unstable, binding modes are typically detected by MD simulations. 1567

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Chemical Research in Toxicology Table 4. Toxicity Reported for Lupeol and Its Analogues compound

dose tested

model

via of administration

administration time (days)

adverse effects

refs

lupeol lupeol lupeol lupeol lupeol lupeol

50 mg/kg 200 mg/kg 2000 mg/kg 2 mg/animal 2 g/kg 50 mg/kg

mice mice mice mice mice rats

oral oral oral cutaneous oral oral

none none none none none none

18 1 14 2 4 15

lupeol lupeol lupeol lupeol

100 mg/kg 50 μmol/L 2 mg/animal 50 μM

oral medium injection medium

none none none none

7 2 30 2

lupeol lupeol lupeol lupeol lupeol lupeol lupeol lupeol lupeol lupeol

medium oral oral oral oral medium topical oral intratumoral intratumoral injection

none none none none none none none none none none

3 4 7 10 3 1 0.6 28 21 1

58 60 54 61, 62 64 65 1 59 66 67

mice rats rats mice rats rats mice

oral oral intratumoral oral oral injected injected

none none none none none none none

1 15 21 18 3 14 28

68 53, 63 66 50 64 43 69

betulin betulin betulin betulin betulin betulin betulin betulin betulin

80 μmol/L 10 mg/kg 100 mg/kg 50 mg/kg 150 mg/kg 50 μg/L 1.5 mg/animal 50 mg/kg 35 mg/kg 0.75−1.5 mg/tumor site 0.5−3 g/kg 50 mg/kg 35 mg/kg 50 mg/kg 150 mg/kg 3000 mg/kg 540 mg/kg; mouse 300 mg/kg 5 and 10 μM 42 μM 5.12 ug/mL 5% 15.34 μM 500 mg/kg 10 μM 50 μM

mice human pac cell mice human pancreatic adenocarcinoma cells melanoma cells rats rats rats rats human melanoma cells mice rats rats dogs

49 50 41 51 52 53, 57, 59, 63 54 55 40 56

dogs humans cells humans cells porcine chondrocytes mice human cancer cells mice mice liver cells hamster cells

injected medium medium medium topical medium oral medium medium

28 4 3 7 21 4 28 1 2

69 70 71 72 73 74 42 75 76

betulin

50 μM

mice cells

medium

2

76

betulinic acid

100 mg/kg

77

500 mg/kg 13.10 μM 5 μM 20 mg/kg

oral (chosen dose was the maximum reachable with selected solvent) oral medium medium topical

3

betulinic acid betulinic acid betulinic acid 30-hydroxy lupenone

human cells (cancer) in mice mice human cancer cells mice liver cells mice

none none none none none none none none none (one derivate of betulin showed toxicity) none (one derivate of betulin showed toxicity) none none none none none

28 4 1 0.2

78 74 75 35

lupeol lupeol linolate lupeol linolate lupeol linolate lupeol linolate betulin betulin

interactions. It is for this reason that some harmful ADME properties studied in vitro are not possible to compare directly with the results from VirtualToxLab. Reports on levels tested of lupeol and its analogs have been concentrated in Table 4. Until now, there are no reports on lupeol toxicity even at concentrations as higher as 2 g/kg animal, which is puzzling considering that these compounds have shown cytotoxic effects against cancer cells by inhibiting topoisomerase, a vital enzyme in cellular replication. The administration of lupeol did not show mortality, no matter if lupeol and its analogs were administrated by intravenous,

can be assessed through MD simulations. The time span for which a MD simulation should be conducted is debatable; in this study we used a reasonable span time of 10−8 s (10 ns), which allows to safely monitor the stability of key ligand−protein interactions (e.g., hydrogen bonds) as well as the response of the protein to ligand binding (induced fit). Simulations at longer times (e.g., 100 ns) could be desired but are not reasonable considering actual hardware limitations and computing times.16−18 The toxic potential calculated by VirtualToxLab of lupeol or its analogues is based in the protein−chemical compound 1568

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cutaneous, or oral ways. The maximum administration time for lupeol was 30 days in intravenous doses at 2 mg/animal without reporting mortality or toxicity effects in mice.40 This may suggest that these compounds are not toxic in animals at doses as high as 500, 2000, and 3000 mg/kg for betulinic acid,41 lupeol,42 and betulin,43 respectively. Saleem et al.2 showed that lupeol docks with the human androgen receptor using a computer docking-ligand model. This was further confirmed in vitro where lupeol interacted with the estrogen-receptor alfa (ERα) causing its expression in MDA-MB-231 breast cancer cells.44 Gupta et al.45 reported a 100% reduction on fertility of albino rats after the application of lupeol acetate. Likewise, traditional healers of Chhattisgarh in India use an extract from Echinops echinatus for the treatment of sexual disorders, also a paste prepared by mixing the root bark powder with the juice of Datura stramonium and Blumea lacera leaves is used to avoid premature ejaculation.46 Additionally, male rats treated with Echinops echinatus extracts, which contain high concentration of lupeol, reduced the level of testosterone and the testicular weight.47 These reports on lupeol and its analogues present interactions with protein receptors related with fertility, which corroborates our results were lupeol interacted with the estrogen-receptor alfa (ERα). Another possible adverse effect reported on lupeol that was not tested with VirtualToxLab is that lupeol is a competitive inhibitor of trypsin and chymotrypsin (Ki values 22 and 8 μM, respectively),48 indicating that chymotrypsin could be an interesting enzyme to be included as a protein model of VirtualToxLab. In conclusion, our studies have shown that lupeol and its analogues do not display a high toxic potential and binding to nuclear receptors according to VitrtualToxLab and other computer programs used in this report (possibly, with the exception of MolInspiration). However, lupeol and its analogues bind toward the ERα receptor, which could generate adverse effects; therefore, this would be considered when new research is directed in the use of lupeol and its analogues as potential new drugs to treat illnesses. Adverse effects might be triggered via diverse mechanisms, but only few of them have been simulated in this study. In contrast to classic synthetic drugs, natural products often display a complex topology complemented with a larger number of hydrogen-bond functionalities. Therefore, it is less likely that they meet other (off-) targets binding patterns than rather simple chemotherapeutic compounds. Instead, the unique configuration of natural compounds might privilege them to trigger more complex agonistic mechanisms.



Article

ACKNOWLEDGMENTS

This article is dedicated to the memory of our dear friend and coauthor Prof. Dr. Angelo Vedani (1951−2016). Authors gratefully acknowledge the software support from the Biographics Laboratory 3R and the invaluable technical assistance of Dr. Martin Smieško and team. Manuscript revision and suggestions from Joseph J. Karchesy and Jeffrey R. Bacon are recognized.



ABBREVIATIONS 1A2, cytochrome P450−1A2; 2C9, cytochrome P450−2C9; 2D6, cytochrome P450−2D6; 3A4, cytochrome P450−3A4; ADME, adsorption, disruption, metabolism, and elimination properties; AhR, aryl hydrocarbon receptor; AR, androgen receptor; Arg611, arginine 611; Asn564, asparagine 564; Asn705, asparagine 705; B(NFκB), nuclear factor kappa beta; B[a]P, benzo[a]pyrene; C28, carbon atom number 28; Caco, cancer coli (epithelial cell line); cFLIP, cellular FLICE-like inhibitory protein; CYP450, cytochrome P450; Cys736, cysteine 736; DF, decision forest; DMBA, 7,12-dimethylbenz[a]anthracene; Erα, estrogen alpha receptor; Fas, Fas cell surface death receptor; Gln244, glutamine 244; Gln711, glutamine 711; Glu353, glutamic acid 353; GR, glucocorticoide receptor; hERG, human ether-à-go-go-related gene K(+) ion channel; IC50, half maximal inhibitory concentration; Kras, Kras protein; LXR, liver-X receptor; MD, molecular dynamics; MDA-MB-231, M. D. Anderson Cancer Center-MB-231 (Human breast cancer cell line); MDCK, Madin-Darby canine kidney (epithelial cell line); MR, mineralocorticoid receptor; MTK, Martyna, Tobias, and Klein: constant pressure and temperature conditions; OPLS3, optimized potentials for liquid simulations 3; PI3K/Akt, phosphatidylinositol-3-kinase; PPARγ, peroxisome proliferator-activated receptor gamma; PR, progesterone receptor; QSAR, quantitative structure− activity relationship; Ser304, serine 304; Thr894, threonine 894; TP, toxic potential; TRα, thyroid receptor alpha; TRβ, thyroid receptor beta; VMD, visual molecular dynamics; Wnt/ β-catenin, Wnt/β-Catenin (signaling pathway)



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AUTHOR INFORMATION

Corresponding Authors

*E-mail: [email protected]. Phone: +52(618)8185402 ext 113 and +52(618)8405954. *E-mail: [email protected]. Phone: +52(618)8405954. ORCID

Rubén F. González-Laredo: 0000-0001-6329-1413 Funding

M.A.R.-R. gratefully acknowledges a graduate-student scholarship from the Mexican Science and Technology Council (CONACyT) and financial support from the University of Basel. Notes

The authors declare no competing financial interest. 1569

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