1
|
Shkil DO, Muhamedzhanova AA, Petrov PI, Skorb EV, Aliev TA, Steshin IS, Tumanov AV, Kislinskiy AS, Fedorov MV. Expanding Predictive Capacities in Toxicology: Insights from Hackathon-Enhanced Data and Model Aggregation. Molecules 2024; 29:1826. [PMID: 38675645 PMCID: PMC11055041 DOI: 10.3390/molecules29081826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 04/11/2024] [Accepted: 04/15/2024] [Indexed: 04/28/2024] Open
Abstract
In the realm of predictive toxicology for small molecules, the applicability domain of QSAR models is often limited by the coverage of the chemical space in the training set. Consequently, classical models fail to provide reliable predictions for wide classes of molecules. However, the emergence of innovative data collection methods such as intensive hackathons have promise to quickly expand the available chemical space for model construction. Combined with algorithmic refinement methods, these tools can address the challenges of toxicity prediction, enhancing both the robustness and applicability of the corresponding models. This study aimed to investigate the roles of gradient boosting and strategic data aggregation in enhancing the predictivity ability of models for the toxicity of small organic molecules. We focused on evaluating the impact of incorporating fragment features and expanding the chemical space, facilitated by a comprehensive dataset procured in an open hackathon. We used gradient boosting techniques, accounting for critical features such as the structural fragments or functional groups often associated with manifestations of toxicity.
Collapse
Affiliation(s)
- Dmitrii O. Shkil
- Syntelly LLC, Moscow 121205, Russia; (A.A.M.); (I.S.S.); (A.V.T.); (A.S.K.)
- Moscow Institute of Physics and Technology, Moscow 141700, Russia
| | | | | | - Ekaterina V. Skorb
- Infochemistry Scientific Center, ITMO University, Saint-Petersburg 191002, Russia; (E.V.S.); (T.A.A.)
| | - Timur A. Aliev
- Infochemistry Scientific Center, ITMO University, Saint-Petersburg 191002, Russia; (E.V.S.); (T.A.A.)
| | - Ilya S. Steshin
- Syntelly LLC, Moscow 121205, Russia; (A.A.M.); (I.S.S.); (A.V.T.); (A.S.K.)
| | | | | | - Maxim V. Fedorov
- Kharkevich Institute for Information Transmission Problems of Russian Academy of Sciences, Moscow 127994, Russia
| |
Collapse
|
2
|
Raman NV, Dubey A, van Donk E, von Elert E, Lürling M, Fernandes TV, de Senerpont Domis LN. Understanding the differential impacts of two antidepressants on locomotion of freshwater snails (Lymnaea stagnalis). ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:12406-12421. [PMID: 38233708 PMCID: PMC10869440 DOI: 10.1007/s11356-024-31914-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 01/03/2024] [Indexed: 01/19/2024]
Abstract
There is growing evidence of negative impacts of antidepressants on behavior of aquatic non-target organisms. Accurate environmental risk assessment requires an understanding of whether antidepressants with similar modes of action have consistent negative impacts. Here, we tested the effect of acute exposure to two antidepressants, fluoxetine and venlafaxine (0-50 µg/L), on the behavior of non-target organism, i.e., freshwater pond snail, Lymnaea stagnalis. As compounds interact with chemical cues in the aquatic ecosystems, we also tested whether the effects altered in the presence of bile extract containing 5α-cyprinol sulfate (5α-CPS), a characterized kairomone of a natural predator, common carp (Cyprinus carpio). Behavior was studied using automated tracking and analysis of various locomotion parameters of L. stagnalis. Our results suggest that there are differences in the effects on locomotion upon exposure to venlafaxine and fluoxetine. We found strong evidence for a non-monotonic dose response on venlafaxine exposure, whereas fluoxetine only showed weak evidence of altered locomotion for a specific concentration. Combined exposure to compounds and 5α-CPS reduced the intensity of effects observed in the absence of 5α-CPS, possibly due to reduced bioavailability of the compounds. The results highlight the need for acknowledging different mechanisms of action among antidepressants while investigating their environmental risks. In addition, our results underline the importance of reporting non-significant effects and acknowledging individual variation in behavior for environmental risk assessment.
Collapse
Affiliation(s)
- Nandini Vasantha Raman
- Department of Aquatic Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB, Wageningen, The Netherlands
| | - Asmita Dubey
- Department of Aquatic Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB, Wageningen, The Netherlands.
- Department of Aquatic Ecology and Water Quality Management, Wageningen University & Research, P.O. Box 47, 6708 PB, Wageningen, The Netherlands.
| | - Ellen van Donk
- Department of Aquatic Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB, Wageningen, The Netherlands
- Department of Environmental Biology, University of Utrecht, Utrecht, The Netherlands
| | - Eric von Elert
- Aquatic Chemical Ecology, Biocenter, Institute of Zoology, University of Cologne, Cologne, Germany
| | - Miquel Lürling
- Department of Aquatic Ecology and Water Quality Management, Wageningen University & Research, P.O. Box 47, 6708 PB, Wageningen, The Netherlands
| | - Tânia V Fernandes
- Department of Aquatic Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB, Wageningen, The Netherlands
| | - Lisette N de Senerpont Domis
- Department of Aquatic Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB, Wageningen, The Netherlands
- Department of Aquatic Ecology and Water Quality Management, Wageningen University & Research, P.O. Box 47, 6708 PB, Wageningen, The Netherlands
- Department of Pervasive Systems, EEMCS, University of Twente & Department of Water Resources, ITC, University of Twente, Enschede, The Netherlands
| |
Collapse
|
3
|
Guimarães B, Römbke J, Amorim MJB. On the importance of longer-term exposure to stressors - A critical review and proposal for multigenerational testing in standard soil invertebrates. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 854:158680. [PMID: 36108845 DOI: 10.1016/j.scitotenv.2022.158680] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 09/05/2022] [Accepted: 09/07/2022] [Indexed: 06/15/2023]
Abstract
Standard laboratory tests to describe the impact of stressors (most notably: chemicals) on organisms offer a good compromise between feasibility and outcome, i.e., they should be reproducible and provide robust results. However, these tests may underestimate the potential effects of prolonged exposures, particularly for persistent contaminants. Within the last years, we have observed an increase in studies aiming to target prolonged exposure, e.g., via an extended test duration or by multigenerational (MG) exposure. Seemingly, both reduced and increased impacts have been observed in these studies, but it is also clear that no unique test setup was used, and test designs vary widely among studies. To better describe long term effects, MG is a highly relevant aspect which deserves more consideration at various testing and assessment levels. Therefore, we conducted a literature review focusing on available studies performed with soil invertebrates, exposed to stressors for periods longer than in standard laboratory tests, i.e., full life cycle tests, as well as extensions to standard and MG tests. So far, it has been recommended that such studies should cover more than one generation, but this statement is probably too vague. In this contribution, we summarize and critically discuss the information provided in the literature, and we provide suggestions for future research. The currently available test results from long-term studies have produced clear evidence to recommend the implementation of long-term tests in existing regulatory testing requirements (e.g., for pesticides), in particular for persistent substances and also for delayed effects. Consequently, we recommend the inclusion of such longer exposure test designs (e.g., as annexes) in current OECD and ISO guidelines. However, when doing so, the long-term test designs proposed so far have to be critically adapted for a selected set of representative soil invertebrate test species.
Collapse
Affiliation(s)
- B Guimarães
- University of Aveiro, Department of Biology & CESAM, 3810-193 Aveiro, Portugal
| | - J Römbke
- ECT Oekotoxikologie GmbH, Boettgerstr. 2-14, D-65439 Flörsheim, Germany
| | - M J B Amorim
- University of Aveiro, Department of Biology & CESAM, 3810-193 Aveiro, Portugal.
| |
Collapse
|
4
|
Barascou L, Sene D, Le Conte Y, Alaux C. Pesticide risk assessment: honeybee workers are not all equal regarding the risk posed by exposure to pesticides. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:90328-90337. [PMID: 35864404 DOI: 10.1007/s11356-022-21969-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 07/07/2022] [Indexed: 06/15/2023]
Abstract
Toxicological studies in honeybees have long shown that a single pesticide dose or concentration does not necessarily induce a single response. Inter-individual differences in pesticide sensitivity and/or the level of exposure (e.g., ingestion of pesticide-contaminated matrices) may explain this variability in risk posed by a pesticide. Therefore, to better inform pesticide risk assessment for honeybees, we studied the risk posed by pesticides to two behavioral castes, nurse, and forager bees, which are largely represented within colonies and which exhibit large differences in their physiological backgrounds. For that purpose, we determined the sensitivity of nurses and foragers to azoxystrobin (fungicide) and sulfoxaflor (insecticide) upon acute or chronic exposure. Azoxystrobin was found to be weakly toxic to both types of bees. However, foragers were more sensitive to sulfoxaflor than nurses upon acute and chronic exposure. This phenomenon was not explained by better sulfoxaflor metabolization in nurses, but rather by differences in body weight (nurses being 1.6 times heavier than foragers). Foragers consistently consumed more sugar syrup than nurses, and this increased consumption was even more pronounced with pesticide-contaminated syrup (at specific concentrations). Altogether, the stronger susceptibility and exposure of foragers to sulfoxaflor contributed to increases of 2 and tenfold for the acute and chronic risk quotients, respectively, compared to nurses. In conclusion, to increase the safety margin and avoid an under-estimation of the risk posed by insecticides to honeybees, we recommend systematically including forager bees in regulatory tests.
Collapse
Affiliation(s)
| | - Deborah Sene
- INRAE, Abeilles Et Environnement, Avignon, France
| | | | - Cedric Alaux
- INRAE, Abeilles Et Environnement, Avignon, France.
| |
Collapse
|
5
|
Radwan MA, Gad AF. Insights into the ecotoxicological perturbations induced by the biocide Abamectin in the white snail, Theba pisana. JOURNAL OF ENVIRONMENTAL SCIENCE AND HEALTH. PART. B, PESTICIDES, FOOD CONTAMINANTS, AND AGRICULTURAL WASTES 2022; 57:201-210. [PMID: 35193456 DOI: 10.1080/03601234.2022.2044708] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Abamectin (avermectin B1, ABM) has been widely used as a biocide in agriculture, veterinary and medicine around the world. Yet, there is still a lack of knowledge about the ecotoxicological effects of ABM. In this study, we investigated the acute toxicity and sub-lethal (20% and 60% LD50) biochemical responses of ABM on the non-target land snail, Theba pisana. Mortality of snails increased with the dose increase, resulting 48 h- LD50 value of 1.048 µg/snail. The biochemical results showed a decrease in glycogen content and lipids for two sub-lethal doses after all time intervals, whereas increased the level of total proteins after exposure to 60% LD50 ABM. Overall, the tested sub-lethal doses significantly decreased the total energy reserves. ABM-exposure to snails elevated γ-Glutamyl transferase and Lactate dehydrogenase activities at all-time intervals. A significant increase of Glutathione-S-transferase activity was also recorded in snails exposed to 20% and 60% LD50 after 7 days and all time intervals, respectively. However, ABM inhibited the activity of Aspartate aminotransferase and Alanine aminotransferase after 7 days of exposure. Our investigation provides new insights into the disturbances of energy reserves and enzyme activities in T. pisana that are sensitive and may be used as biomarkers for assessing ABM toxicity.
Collapse
Affiliation(s)
- Mohamed A Radwan
- Department of Pesticide Chemistry and Technology, Faculty of Agriculture, University of Alexandria, Alexandria, Egypt
| | - Amira F Gad
- Department of Animal Pests, Plant Protection Research Institute, Agricultural Research Center, Alexandria, Egypt
| |
Collapse
|