Prediction and Prioritisation of Novel Anthelmintic Candidates from Public Databases Using Deep Learning and Available Bioactivity Data Sets
Abstract
1. Introduction
2. Results
2.1. Modelling Approach
2.2. Data Curation and Establishment of Publicly Accessible Database
2.3. Feature Generation, Model Architecture, and Training
2.4. In Silico Screening and Post-Processing
2.5. Clustering of Compounds with Predicted Nematocidal Activity
2.6. Selection of Molecules for Experimental Evaluation
2.7. Experimental Evaluation of Molecules with Predicted Bioactivity Against H. contortus
3. Discussion
3.1. Harnessing Existing In-House and Literature Data to Apply Machine Learning Methodologies
3.2. Prediction and Prioritisation of Novel Compounds with Nematocidal Properties and Assessment of Potential Leads
4. Materials and Methods
4.1. Small-Molecule Bioactivity Data
4.2. Model
4.3. Input Features
4.4. Hyperparameter Tuning
4.5. In Silico Screening of ZINC Database
4.6. Clustering of Compounds with Predicted Nematocidal Activity
4.7. Post-Processing and Prioritisation
4.8. Assay to Evaluate Bioactivity of Prioritised Compounds
4.9. Method to Assess Cytotoxicity of Prioritised Compounds
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Activity Label | Wiggle Index | Viability | Reduction | EC50 | MIC75 |
---|---|---|---|---|---|
active | x < 0.25 | x < 20% | x > 80% | x < 50 µM | x < 1 µg/mL |
weakly active | 0.25 ≤ x < 0.5 | 20% ≤ x < 50% | 80% ≥ x > 50% | 50 µM ≤ x < 100 µM | 1 µg/mL ≤ x < 10 µg/mL |
none | 0.5 ≤ x | 50% ≤ x | 50% ≥ x | 100 µM ≤ x | 10 µg/mL ≤ x |
Library/Compound Family | N | Reference |
---|---|---|
Open Scaffolds | 14,464 | [26] |
Pathogen Box | 400 | [61] |
1-methyl-1H-pyrazole-5-carboxamides | 64 | [64] |
Tolfenpyrad derivatives | 57 | [65] |
pyrrolidine-oxadiazoles | 57 | [66] |
1-methyl-1H-pyrazole-5-carboxamides | 30 | [67] |
Monepantel derivatives | 28 | [68] |
Tetrahydroquinoxalines | 1 | [69] |
Selenophenes, thiophenes | 12 | [70] |
Diarylamidines | 6 | [71] |
Milbemycine derivatives | 4 | [72] |
Anthelmintics (rafoxanide, naphthalophos, nitroxynil, disophenol) | 4 | [16] |
Phosphoethanolamine methyltransferases inhibitors | 3 | [73] |
p-amino-phenethyl-m-trifluoromethylphenyl piperazine | 3 | [74] |
Anthelmintics (derquantel, abamectin) | 2 | [75] |
Anthelmintics (abamectin, benzimidazole) | 2 | [76] |
Fromiamycalin, halaminol A | 2 | [77] |
Anthelmintic (closantel) | 1 | [78] |
Phenothiazine | 1 | [79] |
Deguelin | 1 | [27] |
Anthelmintic (eprinomectin) | 1 | [80] |
Anthelmintic (albendazole, monepantel, morantel, moxidectin, thiabendazole) | 5 | in-house data |
Total | 15,162 |
Label | Training | Test | Total | |||
---|---|---|---|---|---|---|
# | Fraction | # | Fraction | # | Fraction | |
None | 11,005 | 0.902 | 2643 | 0.894 | 13,648 | 0.900 |
Weakly active | 1081 | 0.089 | 272 | 0.092 | 1353 | 0.089 |
Active | 121 | 0.010 | 40 | 0.014 | 161 | 0.011 |
(Combined active) | 1202 | 0.098 | 314 | 0.106 | 1516 | 0.100 |
Total | 12,207 | 0.81 | 2955 | 0.19 | 15,162 | 1.0 |
Tested Models | Best Model Performance on Test Set | |||||
---|---|---|---|---|---|---|
Series | No of Models | n_hidden | dim_hidden | dim_hidden | Precision ‘Active’ | Recall ‘Active’ |
series_1001 | 39 | 1 | 5–195 | 100 | 0.816 | 0.756 |
series_1002 | 19 | 2 | 5–95/5 | 75/5 | 0.825 | 0.805 |
series_1003 | 9 | 2 | 100–900/10 | 500/10 | 0.821 | 0.780 |
series_1004 | 9 | 2 | 100–900/50 | 600/50 | 0.811 | 0.732 |
series_2001 | 39 | 1 | 5–195 | 185 | 0.789 | 0.732 |
Predicted Bioactivity Against H. contortus | |||
---|---|---|---|
No of Compounds | Active | Weakly Active | None |
14,154,291 | 174,539 | 12,922 | 13,966,830 |
1.2% | 0.09% | 98.7% |
Compound | Structure | Larval Motility IC50 μM a (MI; %) | Larval Development IC50 μM a (MI; %) | Abnormal Phenotype b (Exhibited at 50 µM; %) |
---|---|---|---|---|
1 | 6.2 ± 0.3 (50) | >50 | Cur, Evi (20) | |
2 | 1.8 ± 1.4 (53) | >50 | nil | |
3 | 7.9 ± 1.9 (54) | 37.1 (100) | Evi (80) | |
4 | 5.8 ± 4.1 (90) | >50 | nil | |
5 | 37.5 ± 2.5 (65) | >50 | nil | |
6 | 7.4 ± 9.4 (100) | 23.6 (100) | Evi (100) | |
7 | 2.1 ± 3.5 (70) | >50 | nil | |
8 | 0.8 ± 1.6 (42) | >50 | nil | |
9 | 4.1 ± 21.4 (46) | >50 | nil | |
10 | 0.8 ± 1.2 (50) | >50 | nil | |
Monepantel | 0.2 ± 0.002 (100) | 0.4 (100) | Coi (100) | |
Moxidectin | 0.8 ± 0.4 (75) | 45.0 (100) | nil |
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Taki, A.C.; Kapp, L.; Hall, R.S.; Byrne, J.J.; Sleebs, B.E.; Chang, B.C.H.; Gasser, R.B.; Hofmann, A. Prediction and Prioritisation of Novel Anthelmintic Candidates from Public Databases Using Deep Learning and Available Bioactivity Data Sets. Int. J. Mol. Sci. 2025, 26, 3134. https://doi.org/10.3390/ijms26073134
Taki AC, Kapp L, Hall RS, Byrne JJ, Sleebs BE, Chang BCH, Gasser RB, Hofmann A. Prediction and Prioritisation of Novel Anthelmintic Candidates from Public Databases Using Deep Learning and Available Bioactivity Data Sets. International Journal of Molecular Sciences. 2025; 26(7):3134. https://doi.org/10.3390/ijms26073134
Chicago/Turabian StyleTaki, Aya C., Louis Kapp, Ross S. Hall, Joseph J. Byrne, Brad E. Sleebs, Bill C. H. Chang, Robin B. Gasser, and Andreas Hofmann. 2025. "Prediction and Prioritisation of Novel Anthelmintic Candidates from Public Databases Using Deep Learning and Available Bioactivity Data Sets" International Journal of Molecular Sciences 26, no. 7: 3134. https://doi.org/10.3390/ijms26073134
APA StyleTaki, A. C., Kapp, L., Hall, R. S., Byrne, J. J., Sleebs, B. E., Chang, B. C. H., Gasser, R. B., & Hofmann, A. (2025). Prediction and Prioritisation of Novel Anthelmintic Candidates from Public Databases Using Deep Learning and Available Bioactivity Data Sets. International Journal of Molecular Sciences, 26(7), 3134. https://doi.org/10.3390/ijms26073134