Molecular docking and spectral shift supported toxicity profile of metaldehyde mollucide and the toxicity-reducing effects of bitter melon extract

Allium cepa as a Toxicogenetic Investigational Tool for Plant Extracts: A Systematic Review

Toxicological studies are important to investigate the genotoxic effects of various substances. Allium cepa can be used as test model for this purpose. This review summarizes the scope and applications for this A. cepa test model. For this, an up-to-date (April 2023) literature search was made in the Science Direct, PubMed, and Web of Science databases to find published evidence on studies performed using A. cepa as a test model. Out of 3,748 studies, 74 fit the inclusion criteria. The results showed that the use of the test model A. cepa contributed considerably to measuring the toxicological potential of plant extracts, proving the efficacy of the test as a potent bioindicator of toxic effects. In addition, 27 studies used more than one test system to verify the toxicological potential of extracts and fractions. Studies have shown that the A. cepa model has the potential to replace other test systems that make use of animals and cell cultures, besides having other advantages such as low cost, ease of execution, and good conditions for the observation of chromosomes. In conclusion, the A. cepa test can be considered one of the potential biomonitoring systems in toxicological studies of crude extracts.

Direct and indirect toxicity mechanisms of the natural insecticide azadirachtin based on in-silico interactions with tubulin, topoisomerase and DNA

Natural pesticides, which attract attention with safe properties, pose a threat to many non-target organisms, so their toxic effects should be studied extensively. In this study, the toxic effects of Azadirachtin, a natural insecticide derived from Azadirachta indica, were investigated by in-vivo and in-silico methods. In-vivo toxic effects were determined using the Allium test and bulbs were treated with 5 mg/L (0.5x EC50), 10 mg/L (EC50), and 20 mg/L (2xEC50) Azadirachtin. In the groups treated with Azadirachtin, there was a decline in germination-related parameters and accordingly growth was delayed. This regression may be related to oxidative stress in the plant, and the increase in malondialdehyde and proline levels in Azadirachtin-applied groups confirms oxidative stress. Azadirachtin toxicity increased dose-dependently and the most significant toxic effect was observed in the group administered 20 mg/L Azadirachtin. In this group, the mitotic index decreased by 43.4% and sticky chromosomes, vagrant chromosomes and fragments were detected at rates of 83.1 ± 4.01, 72.7 ± 3.46 and 65.1 ± 3.51, respectively. By comet analysis, it was determined that Azadirachtin caused DNA fragmentation, and tail DNA, which was 0.10 ± 0.32% in the control group, increased to 34.5 ± 1.35% in the Azadirachtin -treated groups. These cytotoxic and genotoxic effects of Azadirachtin may be due to direct interaction with macromolecules as well as induced oxidative stress. Azadirachtin has been found to interact in-silico with alpha-tubulin, beta-tubulin, topoisomerase I and II, and various DNA sequences. Possible deteriorations in macromolecular structure and functions as a result of these interactions may cause cytotoxic and genotoxic effects. These results suggest that natural insecticides may also be unreliable for non-target organisms, and the toxic effects of compounds presented as "natural" should also be investigated.

A comprehensive analysis of royal jelly protection against cypermethrin-induced toxicity in the model organism Allium cepa L., employing spectral shift and molecular docking approaches

In this study, the toxicity of the pesticide cypermethrin and the protective properties of royal jelly against this toxicity were investigated using Allium cepa L., a model organism. Toxicity was evaluated using 6 mg/L cypermethrin, while royal jelly (250 mg/L and 500 mg/L) was used in combination with cypermethrin to test the protective effect. To comprehend toxicity and protective impact, growth, genotoxicity, biochemical, comet assay and anatomical parameters were employed. Royal jelly had no harmful effects when applied alone. On the other hand, following exposure to cypermethrin, there was a reduction in weight increase, root elongation, rooting percentage, mitotic index (MI), and chlorophyll a and b. Cypermethrin elevated the frequencies of micronucleus (MN) and chromosomal aberrations (CAs), levels of proline and malondialdehyde (MDA), and the activity rates of the enzymes catalase (CAT) and superoxide dismutase (SOD). A spectral change in the DNA spectrum indicated that the interaction of cypermethrin with DNA was one of the reasons for its genotoxicity, and molecular docking investigations suggested that tubulins, histones, and topoisomerases might also interact with this pesticide. Cypermethrin also triggered some critical meristematic cell damage in the root tissue. At the same time, DNA tail results obtained from the comet assay revealed that cypermethrin caused DNA fragmentation. When royal jelly was applied together with cypermethrin, all negatively affected parameters due to the toxicity of cypermethrin were substantially restored. However, even at the maximum studied dose of 500 mg/L of royal jelly, this restoration did not reach the levels of the control group. Thus, the toxicity of cypermethrin and the protective function of royal jelly against this toxicity in A. cepa, the model organism studied, were determined by using many different approaches. Royal jelly is a reliable, well-known and easily accessible protective functional food candidate against the harmful effects of hazardous substances such as pesticides.

LC-MS/MS, GC-MS and molecular docking analysis for phytochemical fingerprint and bioactivity of Beta vulgaris L

The plants that we consume in our daily diet and use as a risk preventer against many diseases have many biological and pharmacological activities. In this study, the phytochemical fingerprint and biological activities of Beta vulgaris L. leaf extract, which are widely consumed in the Black Sea region, were investigated. The leaf parts of the plant were dried in an oven at 35 °C and then ground into powder. The main constituents in B. vulgaris were identified by LC-MS/MS and GC-MS analyses. Phenolic content, betaxanthin and betacyanin levels were investigated in the extracts obtained using three different solvents. The biological activity of the extract was investigated by anti-microbial, anti-mutagenic, anti-proliferative and anti-diabetic activity tests. Anti-diabetic activity was investigated by in vitro enzyme inhibition and in-silico molecular docking was performed to confirm this activity. In the LC-MS analysis of B. vulgaris extract, a major proportion of p_coumaric acid, vannilin, protecatechuic aldehyde and sesamol were detected, while the major essential oils determined by GC-MS analysis were hexahydrofarnesyl acetone and phytol. Among the solvents used, the highest extraction efficiency of 2.4% was obtained in methanol extraction, and 36.2 mg of GAE/g phenolic substance, 5.1 mg/L betacyanin and 4.05 mg/L betaxanthin were determined in the methanol extract. Beta vulgaris, which exhibited broad-spectrum anti-microbial activity by forming a zone of inhibition against all tested bacteria, exhibited anti-mutagenic activity in the range of 35.9-61.8% against various chromosomal abnormalities. Beta vulgaris extract, which did not exhibit mutagenic, sub-lethal or lethal effects, exhibited anti-proliferative activity by reducing proliferation in Allium root tip cells by 21.7%. 50 mg/mL B. vulgaris extract caused 58.9% and 55.9% inhibition of α-amylase and α-glucosidase activity, respectively. The interactions of coumaric acid, vanniline, hexahydrofarnesyl acetone and phytol, which are major compounds in phytochemical content, with α-amylase and α-glucosidase were investigated by in silico molecular docking and interactions between molecules via various amino acids were determined. Binding energies between the tested compounds and α-amylase were obtained in the range of - 4.3 kcal/mol and - 6.1 kcal/mol, while for α-glucosidase it was obtained in the range of - 3.7 kcal/mol and - 5.7 kcal/mol. The biological activities of B. vulgaris are closely related to the active compounds it contains, and therefore studies investigating the phytochemical contents of plants are very important. Safe and non-toxic plant extracts can help reduce the risk of various diseases, such as diabetes, and serve as an alternative or complement to current pharmaceutical practices.

Deep neural network and molecular docking supported toxicity profile of prometryn

In this study, the versatile toxicity profile of prometryn herbicide on Allium cepa was investigated. In this context, 4 different groups were formed. While the control group was treated with distilled water, Groups II, III and IV were treated with 200 mg/L, 400 mg/L and 800 mg/L prometryn, respectively. After 72 h of germination, cytogenetic, biochemical, physiological and anatomical changes were investigated. As a result increase in malondialdehyde levels, decrease in glutathione level, changes in superoxide dismutase and catalase activities in root tip cells show that prometryn causes oxidative stress. The decrease in mitotic index values and the increase in the frequency of micronucleus and chromosomal abnormalities observed after prometryn treatment indicate genotoxic effects. The genotoxic effects may be due to the induced oxidative stress as well as the promethryn-DNA interaction. Molecular docking analyses revealed that prometryn interacts with various bases in DNA. As a result of the Comet assay, exposure to prometryn was found to cause DNA fragmentation. In physiological parameters final weight, germination percentage and root length decreased by 23.8%, 59.1% and 87.3%, respectively, in the 800 mg/L prometryn applied group. Deep neural network (DNN) model was optimized to predict the effects of different doses of prometryn on 4 different endpoints: micronucleus, mitotic index, chromosomal abnormalities and DNA Damage. The predicted data was found to be very similar to the actual data. The performance of the model was evaluated using MAE, MAPE, RMSE and R2, and these metrics indicate that the model performed well. Overall, the findings of this study suggest that the DNN model developed here is a valuable tool for predicting genotoxicity biomarkers in response to the application doses of prometryn, and has the potential to contribute to the development of safer and more sustainable agricultural practices.

A scoping review of recent advances in the application of comet assay to Allium cepa roots

The comet assay is a sensitive method for the evaluation of DNA damages and DNA repair capacity at single-cell level. Allium cepa is a well-established plant model for toxicological studies. The aim of this scoping review was to investigate the recent application of the comet assay in Allium cepa root cells to assess the genotoxicity. To explore the literature a search was performed selecting articles published between January 2015 and February 2023 from Web of Science, PubMed, and Scopus databases using the combined search terms "Comet assay" and "Allium cepa". All the original articles that applied the comet assay to Allium cepa root cells were included. Of the 334 records initially found, 79 articles were identified as meeting the inclusion criteria. Some studies reported results for two or more toxicants. In these cases, the data for each toxicant were treated separately. Thus, the number of analyzed toxicants (such as chemicals, new materials, and environmental matrices) was higher than the number of selected papers and reached 90. The current use of the Allium-comet assay seems to be directed towards two types of approach: the direct study of the genotoxicity of compounds, mainly biocides (20% of analyzed compounds) and nano- and microparticles (17%), and assessing a treatment's ability to reduce or eliminate genotoxicity of known genotoxicants (19%). Although the genotoxicity identified by the Allium-comet assay is only one piece of a larger puzzle, this method could be considered a useful tool for screening the genotoxic potential of compounds released into the environment.

Potential toxicity assessment of mycotoxin fusaric acid with the spectral shift profile on DNA

In this study, the multiple toxicities induced by three different doses (1, 5, and 10 μM) of fusaric acid (FA), a mycotoxin, was investigated with Allium test. Physiological (percent germination, root number, root length, and weight gain), cytogenetic (micronucleus = MN, chromosomal abnormalities = CAs, and mitotic index = MI), biochemical (proline level, malondialdehyde = MDA level, catalase = CAT activity, and superoxide dismutase = SOD activity), and anatomical parameters were used as indicators of toxicity. Allium cepa L. bulbs were divided into four groups as one control and three applications. The bulbs in the control group were germinated with tap water for 7 days, and the bulbs in the treatment groups were germinated with three different doses of FA for 7 days. As a result, FA exposure caused a decrease in all physiological parameters examined at all three doses. Besides, all FA doses caused a decrease in MI and an increase in the frequency of MN and the number of CAs. FA promoted CAs such as nucleus with vacuoles, nucleus buds, irregular mitosis, bridge, and misdirection in root meristem cells. DNA and FA interactions, which are the possible causes of genotoxic effects, were examined by spectral analysis, and FA could interact with DNA through intercalation, causing bathochromic and hypochromic shifts in the spectrum. FA also causes toxicity by inducing oxidative stress in cells, confirming this; dose-related increases in root MDA and proline levels were measured as a result of FA exposure. In the root SOD and CAT enzyme activities, increases up to 5 μM doses and decreases at 10 μM doses were measured. FA exposure induced anatomical damage such as necrosis, epidermis cell damage, flattened cell nucleus, thickening of the cortex cell wall, and unclear vascular tissue in root tip meristem cells. As a result, FA caused a comprehensive toxicity by showing an inhibitory effect in A. cepa test material, and the Allium test was a very useful test in determining this toxicity.

Qualitative and quantitative phytochemical screening of Nerium oleander L. extracts associated with toxicity profile

In this study, phytochemical analysis and toxicity profile of leaf and flower extracts of Nerium oleander L. species collected from Giresun province (Turkey) were investigated. In phytochemical analyzes, the cardiac glycoside, alkaloid, saponin and tannin contents of the extracts were analyzed qualitatively and quantitatively. The physiological effects of extracts were determined by examining root elongation, weight gain and germination rates. Biochemical effects were determined by measuring the levels of malondialdehyde (MDA), glutathione (GSH), superoxide dismutase (SOD) and catalase (CAT), which are indicators of oxidative stress. Cytotoxic and genotoxic effects were investigated by mitotic index (MI), micronucleus (MN) and chromosomal abnormality (CA) tests. N. oleander leaf and flower extract applications caused significant decreases in the physiological parameters of Allium bulbs. SOD and CAT activity in root tip cells increased significantly after the application of leaf extract compared to the control group. Similar changes were observed in the application of flower extract, but these increases were found to be at a lower level compared to the increases induced by the leaf extract. An increase in MDA levels and a decrease in GSH levels were observed in groups treated with leaf and flower extracts. These changes show that the extracts cause deterioration in antioxidant/oxidant balance. It was determined that the extracts, which caused a decrease in MI rates and an increase in MN and CAs frequencies, showed the most prominent cytotoxic and genotoxic effects at 250 μg/mL doses. These toxic effects were associated with the phytochemical content of the extracts, and it was thought that cardiac glycosides and alkaloids, whose presence were detected in qualitative and quantitative analyzes, may play an important role in toxicity. Studies investigating the therapeutic properties of plants as well as their toxic effects are insufficient, which leads to the fact that plants exhibiting potential toxicity are not well known. Therefore, this study will lead many studies on the toxicity profile of the phytochemical contents of plants. Therefore, this study will draw attention to the investigation of the toxicity profile and phytochemical contents of plants and will lead to similar studies.

Screening the toxicity profile and genotoxicity mechanism of excess manganese confirmed by spectral shift

In this study, the toxicity induced by excessive doses of manganese (MnCl2), which is one of the essential trace elements for the continuation of the metabolic activities of the organisms, was investigated with the help of the Allium test. Toxicity was investigated by using physiological (percent germination, root length, weight gain), cytogenetic [mitotic index (MI), micronucleus (MN), chromosomal abnormalities (CAs)], biochemical [malondialdehyde (MDA), superoxide dismutase (SOD) catalase (CAT)] and anatomical (root tip meristematic cell damage) parameters. Allium cepa L. bulbs were divided into four groups as one control and three treatments. The control group was germinated with tap water, and the treatment groups were germinated with 250, 500 and 1000 µM doses of MnCl2. The germination process was continued for 72 h without interruption. At the end of the period, the root tips were collected, washed in distilled water and made ready for microscopic and spectrophotometric analyzes with the help of routine preparation techniques. As a result, the highest germination percentage, root length, weight gain and MI, and the lowest MN frequency, CAs numbers, MDA level, SOD and CAT enzyme activities were determined in the control group (group I). MnCl2 exposure caused a decrease in physiological parameter values and an increase in cytogenetic (except MI) and biochemical parameter values, depending on the dose. MnCl2 exposure induced MN and CAs such as fragment, sticky chromosome, vagrant chromosome, unequal distribution of chromatin and bridge. This genotoxic effect of MnCl2 was associated with DNA-MnCl2 interaction, and this interaction was also confirmed by bathochromic and hypochromic shifts in spectral analysis. Anatomical damages such as epidermis cell damage, flattened cell nucleus, cortex cell damage and cortex cell wall thickening were observed after MnCl2 treatment. As a result, it has been determined that excessive doses of the trace element Mn cause physiological, cytogenetic, biochemical and anatomical toxicity and A. cepa test material is a reliable bio-indicator in determining this toxicity.

Spectroscopic contribution to glyphosate toxicity profile and the remedial effects of Momordica charantia

In this study, the glyphosate toxicity and the toxicity-reducing role of bitter melon extract (Bmex) (Momordica charantia L.) were investigated in Allium cepa L. test material. The toxicity of glyphosate and protective role of Bmex were investigated with the help of physiological (germination, root elongation and weight gain), cytogenetic (mitotic index-MI, micronucleus-MN and chromosomal abnormalities-CAs), biochemical (malondialdehyde-MDA, superoxide dismutase-SOD and catalase-CAT) and anatomical (root meristem cell damage) parameters. The genotoxicity mechanism of glyphosate was elucidated by spectral analysis. A. cepa bulbs were divided into six groups as one control and five applications. Tap water was applied to the bulbs in the control group for 72 h. Glyphosate (500 mg/L) and two different doses of Bmex (350 and 700 mg/L) were applied to the bulbs in the treatment group for 72 h. At the end of the period, the germinated bulbs were prepared for experimental analyses, measurements and observations by applying routine preparation procedures. As a result, glyphosate administration caused a significant (p < 0.05) decrease in all selected physiological parameter values, and significant (p < 0.05) increases in the number of cytogenetic parameters (except MI), the levels of biochemical parameters and the severity of anatomical damage. Glyphosate promoted CAs such as fragment, sticky chromosome, bridge and unequal distribution of chromatin in root tip meristem cells. By spectral analysis, it was determined that glyphosate interacts directly with DNA and causes genotoxicity. It also caused anatomical damages such as epidermis cell damage, cortex cell damage, flattened cell nucleus, binuclear cell and irregular vascular tissue in root tip meristem cells. Co-administration of glyphosate with Bmex at two different doses (350 and 700 mg/L) reduced the toxicity of glyphosate and led to significant (p < 0.05) improvements in the values of all parameters examined. It was determined that this improvement was even more pronounced at 700 mg/L dose of Bmex. As a result, it was determined that glyphosate herbicide caused multi-dimensional toxicity in A. cepa test material, and Bmex reduced the effects of this toxicity due to its antioxidant properties. Therefore, glyphosate dose ranges need to be reconsidered, especially considering non-target organisms in agricultural applications. In addition, antioxidant products such as Bmex should be included in the daily diet in order to reduce the toxic effects of environmental agents such as pesticides.