ToxProfiler Method

ToxProfiler1 is a web-based tool that predicts the potential of a chemical to interact with 64 toxicity targets. ToxProfiler provides a complementary computational approach to experimental in vitro screening. It aids in understanding the adverse liability associated with chemicals and provides insights into the underlying mechanisms of toxicity.

ToxProfiler uses a chemical-similarity-based read-across approach to generate toxicity target profiles for query chemicals.1 Chemical similarity between each query compound and a set of reference compounds (target representative set) known to interact with the toxicity target of interest is calculated, and the maximum similarity score (MAX) between them is used to represent the potential of the query to interact with the toxicity target. Figure 1 summarizes the overall workflow of this tool.

Figure 1. ToxProfiler workflow. Users upload query molecules as SMILES which will be screened against reference molecules/target representatives associated with each toxicity target, and the MAX similarity score is used to create a link between the query molecule and the toxicity target.

ToxProfiler has three basic building blocks. They are: 1) a panel of toxicity targets, 2) a set of target representatives or reference compounds, and 3) a suitable chemical similarity approach.

Toxicity targets panel

Figure 2. Protein classes of the 64 toxicity targets. Toxicity targets were grouped into six major protein classes, and the number of targets per class is given.

Toxicity targets represent molecular initiating events in adverse outcome pathways, i.e., chemical interaction with these targets is known to be causally linked with an adverse effect. We used two major sources to create the toxicity targets panel in this work, i.e., the collaborative data published from four major pharmaceutical companies and the U.S. National Tox21 collaborative program.2,3 Our panel includes 64 toxicity targets. Figure 2 shows the different protein classes represented in our toxicity targets panel. A majority of the targets in our panel are G-protein coupled receptors (GPCRs) (24 of 64) followed by nuclear receptors (14 of 64) and ion channels (9 of 64). It should be noted that 44 of the 64 targets are being used in a commercial in vitro safety screening panel such as Eurofins Cerep SafetyScreen44.4

Target representatives/Reference compounds

Figure 3. Number of target representatives per toxicity target.

Target representatives are compounds that are known to interact with these toxicity targets. We used two publicly available and well-recognized reference datasets, DrugBank and the Toxin and Toxin-Target Database, to create the target representative dataset.5,6 After pre-processing, we obtained a final chemical-toxicity target matrix with 2,655 chemicals and 64 toxicity targets. Each row in the matrix is a chemical, and each column is a toxicity target. The matrix has a value of 1 if there is a known interaction between the chemical and target; otherwise, it is 0. Overall, it is a sparse matrix with 1,300 chemicals (49%) interacting with only one target and 407 chemicals interacting with two targets. Forty-three of the 64 targets have more than 50 chemicals as target representatives, 14 targets have between 10 and 50 chemicals as target representatives, and seven targets have between 3 and 10 chemicals as target representatives. Aryl hydrocarbon receptor (AHR), estrogen receptors 1 and 2 (ESR1, ESR2), and pregnane X receptor (NR1I2) have the highest number (≥300) of target representatives (Figure 3). Vasopressin receptor 1A (AVPR1A) and voltage-gated potassium channel protein (KCNQ1) have the lowest number (three) of target representatives.

Chemical similarity approach

Chemical similarity can be calculated based on a 2D or 3D approach. The 2D approach uses atom connectivity/fingerprints. We used Pipeline Pilot extended-connectivity fingerprints with a diameter of four chemical bonds (ECFP4) for 2D similarity calculations. We evaluated the performance of the 2D and 3D approach (ROCS) using external data for 35 targets from ChEMBL. More details of this evaluation analysis can be found in our paper.1 We found the 2D approach to perform better in retrieving actives from inactives for each of the tested targets (Figure 4). Based on this, 2D similarity-based screening approach is implemented in ToxProfiler.

Figure 4. Receiver operating characteristic area under the curve (AUC) values using the 2D and 3D similarity approach across 35 targets in the external validation set. The names of each target are given in Table 1.

TABLE 1. Receiver operating characteristic area under the curve (AUC) values from the 2D and 3D approach across 35 targets in external validation analysis.

NoNAMESYMBOL2D3D%Diff
1D(1A) dopamine receptorDRD10.930.859
2Endothelin-1 receptorEDNRA0.940.7525
3Mu-type opioid receptorOPRM10.840.7217
4Potassium voltage-gated channel subfamily H member 2KCNH20.570.562
5AcetylcholinesteraseACHE0.770.5833
6Prostaglandin G/H synthase 2PTGS20.690.72-4
7Tyrosine-protein kinase LckLCK0.830.5551
8Vascular endothelial growth factor receptor 2KDR0.640.598
9Androgen receptorAR0.700.691
10cAMP-specific 3',5'-cyclic phosphodiesterase 4DPDE4D0.700.3884
11cGMP-inhibited 3',5'-cyclic phosphodiesterase APDE3A0.730.5338
12Sodium-dependent dopamine transporterSLC6A30.790.781
13Alpha-2A adrenergic receptorADRA2A0.680.5036
14D(2) dopamine receptorDRD20.880.7222
15Histamine H1 receptorHRH10.880.5657
16Histamine H2 receptorHRH20.810.40103
17Delta-type opioid receptorOPRD10.800.6719
18Prostaglandin G/H synthase 1PTGS10.570.59-3
19Platelet-derived growth factor receptor betaPDGFRB0.570.4624
20Sodium-dependent serotonin transporterSLC6A40.770.727
21Sodium-dependent noradrenaline transporterSLC6A20.800.7310
22Muscarinic acetylcholine receptor M1CHRM10.810.6721
23Muscarinic acetylcholine receptor M2CHRM20.760.6027
24Amine oxidase [flavin-containing] AMAOA0.600.559
25Voltage-dependent L-type calcium channel alpha-1CCACNA1C0.960.933
265-hydroxytryptamine receptor 3AHTR3A0.840.92-9
27Sodium channel protein type 5 subunit alphaSCN5A0.550.58-5
28Adenosine receptor A2aADORA2A0.720.5629
29Beta-1 adrenergic receptorADRB10.870.37135
30Beta-2 adrenergic receptorADRB20.830.31168
31Cannabinoid receptor 1CNR10.750.6810
32Kappa-type opioid receptorOPRK10.870.6534
335-hydroxytryptamine receptor 2AHTR2A0.860.7515
345-hydroxytryptamine receptor 2BHTR2B0.690.665
35Muscarinic acetylcholine receptor M3CHRM30.830.6234

ToxProfiler

In summary, we used 2,655 chemicals collected from public chemogenomics databases as target representatives to represent 64 toxicity targets and used a 2D similarity approach to compare the similarity between the query molecules with the reference set of molecules. Users can upload query chemicals in SMILES format. Users are also given an option to draw the compound of interest and add it as a query molecule. Users can view all of the results on the ToxProfiler itself or download them for offline analysis.

MAX 2D similarity Tanimoto scores between each query chemical and respective toxicity targets were calculated and converted into Z-score. The Z-score of chemical i for a toxicity target j is given by

(1)

where X,j is the MAX Tanimoto score for chemical i and toxicity target j; μi is the average of MAX Tanimoto score for chemical i across all 64 toxicity targets; and σi is the standard deviation of the MAX Tanimoto score for chemical i across all 64 toxicity targets.

Figure 5. shows the snapshot of output obtained from ToxProfiler. For each query compound, ToxProfiler displays as output its name, structure, and a toxicity targets profile bar. The toxicity targets profile is color-coded based on the similarity to target representatives. Based on the Z-score range 1.96, 1.645-1.96, and <1.645, it is marked in red, yellow, and green, respectively.

Figure 5. Screenshot of a typical result generated from ToxProfiler web tool. Each chemical in the user-uploaded query set is present in each row. The molecular structure of the chemical query is displayed along with a summary of toxicity targets profile and rat oral acute toxicity values. The summary of the toxicity targets profile is present as a bar plot. The red, yellow, and green color in the bar plot represents the number of predicted interactions, potential interactions, and lack of interactions with 64 toxicity targets, respectively.


References

  1. AbdulHameed, M.D.M., Liu, R., Schyman, P., Sachs, D., Xu, Z., Desai, V., Wallqvist, A. (2021) ToxProfiler: Toxicity-target profiler based on chemical similarity. Comput Toxicol 18, 100162.
  2. Bowes, J., Brown, A. J., Hamon, J., Jarolimek, W., Sridhar, A., Waldron, G., and Whitebread, S. (2012) Reducing safety-related drug attrition: the use of in vitro pharmacological profiling. Nat Rev Drug Discov 11, 909-922.
  3. Tice, R. R., Austin, C. P., Kavlock, R. J., and Bucher, J. R. (2013) Improving the human hazard characterization of chemicals: a Tox21 update. Environ Health Perspect 121, 756-765.
  4. https://www.eurofinsdiscoveryservices.com/catalogmanagement/viewitem/SafetyScreen44-Panel-Cerep/P270
  5. Wishart, D. S., Feunang, Y. D., Guo, A. C., Lo, E. J., Marcu, A., Grant, J. R., Sajed, T., Johnson, D., Li, C., Sayeeda, Z., Assempour, N., Iynkkaran, I., Liu, Y., Maciejewski, A., Gale, N., Wilson, A., Chin, L., Cummings, R., Le, D., Pon, A., Knox, C., and Wilson, M. (2018) DrugBank 5.0: a major update to the DrugBank database for 2018. Nucleic Acids Res 46, D1074-D1082.
  6. Wishart, D., Arndt, D., Pon, A., Sajed, T., Guo, A. C., Djoumbou, Y., Knox, C., Wilson, M., Liang, Y., Grant, J., Liu, Y., Goldansaz, S. A., and Rappaport, S. M. (2015) T3DB: the toxic exposome database. Nucleic Acids Res 43, D928-934.

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