Identification of Less Harmful Pesticides against Honey Bees: Shape-Based Similarity Analysis

: The high concentration of pesticide residues existing in vegetation, crops, and various edible products and the prolonged exposure to them can harm human life and contribute to the disappearance of honey bees, and several avian and animal species. The honey bees (Apis mellif-era), which are efficient pollinators in addition to honey producers, are also considered important non-target test species for the terrestrial toxicity assessment of chemicals. In this context, using thiacloprid and acetamiprid as queries, we performed a 3D similarity search to select new potential products with less harmful effects against bees. For a similarity search, a small dataset of 302 compounds with pesticide activity, compiled from the literature, was used. The first 10 compounds were selected and structurally analyzed according to the TanimotoCombo metrics, and compared with each of these two queries, which is known to be effective, easily metabolized, and less toxic for bees. This approach came as a forward step in the research of pesticide ecotoxicological risk assessment for the evaluation of their potential impact on the pollinator insects and the environment.


Introduction
Neonicotinoids are the most commonly used insecticides for pest control. The main problems associated with the use of these insecticides, alone or in combination with other factors, are related to their negative impact against many species of insects including bees. Additionally, the application mode of insecticides (e.g., direct spray, soil and seed application, etc.) plays a key role in their impact against pollinators. Honeybees are considered the most successful and commercially valuable pollinators due to their pollination functions, maintenance of biodiversity in natural ecosystems as well as the commercial products delivered such as honey, propolis, etc. This negative neonicotinoid impact on bees has been extremely studied because the effect at different doses is still not fully understood [1]. Honeybees can be envisaged as very vulnerable to pesticides because their genome has fewer genes compared to other insects [2]. The exposure to neonicotinoids can influence the flying and the foraging ability, reproduction, and pollination for many useful insects including honeybees [3]. In particular, they affect bees by forgetting the locations of flowers or even hives, and also by increasing the fertility of queens or bumblebees [3]. In this context, the strategy of designing new neonicotinoids by modifying existing structures may be an effective way to overcome this harmful influence against pollinators.
Theoretical methods (QSAR, linear and nonlinear regression techniques, molecular docking, 2D and 3D similarity search, etc.) [5][6][7] applied in cheminformatics to discover new drugs have also been successfully employed to predict novel insecticides and pesticides with less polluting and toxic effects to fill data gaps and to reduce toxicity testing on animals. In the current work, thiacloprids and acetamiprids were used as template molecules in the 3D similarity analysis accomplished with ROCS (Rapid Overlay of Chemical Structures) [8,9] from the OpenEye package. The main goal is to find novel compounds, similar to template molecules, which are easy to metabolize and less toxic for bees.
The lowest energy conformers for thiacloprid and acetamiprid were also generated with Omega. The BIOVIA Discovery Studio facilities were used for structure visualization and picture delivery ( Figure 1).  [8,9]. ROCS, a shape comparison application, is faster and more useful in handling the large conformer databases. This tool offers alignment and scoring of a database engaging thirteen similarity coefficients. The resulted aligned molecules are ordered by a TanimotoCombo ranking score (as the default option).

Results and Discussion
A 3D overlay with ROCS has a great advantage as it allows for optimal visualization of overlapping compounds, which leads to a better understanding of their similarity. The ROCS principles are based on the Gaussian function, which is widely used to represent shape and molecular volume.
In this light, several highly occupied regions corresponding to the pyridine ring and a yliden-cyanamide group of both template molecules were identified ( Figure 2). These regions appear to have multiple hydrogen binding abilities. The pyridine ring of thiacloprids and acetamiprids and the thiazolidine ring of thiacloprid may be involved in пп or п-σ hydrophobic bonds. As can be seen in Figure 2, the compounds prioritized by ROCS follow the same trend as the query compounds. This trend is in line with the high ShapeTanimoto similarity values (Figure 3), and implicitly the shapes (Figure 2) displayed by all the prioritized compounds.
As can be observed from Figure 3, the 3D coefficients calculated with ROCS for all ten prioritized compounds against each of the two queries showed values greater than 1.2 for TanimotoCombo, greater than 0.8 for ShapeTanimoto, and greater than 1.2 for ComboScore [27,28]. These high values indicate a very good similarity between the selected compounds and acetamiprid and thiacloprid, respectively. Four out of ten prioritized ROCS compounds, highlighted with circles in Figure 3, were considered to have a good profile through a comparison with each of the two queries.
2-Chloro-5-(4,5-dihydroimidazol-1-ylmethyl)pyridine, I,(green circles) was the second compound prioritized by thiacloprid and the seventh by acetamiprid.   The computed pharmacokinetic proprieties of the selected four compounds and the two queries are listed in Table 1. These were performed with a freely accessible web server pkCSM (http://biosig.unimelb.edu.au/pkcsm/ (accessed on 28 September 2020)). The pkCSM program affords a fast and easy method to the early assessment of compounds [29]. Regarding the CNS (central nervous system) permeability, it could be observed that all four selected compounds showed logPS values lower than −3, being considered unable to penetrate the CNS of insects. . For a given compound: a logBB > 0.3 is considered to readily cross the blood-brain barrier while molecules with logBB < −1 are poorly distributed to the brains, a MRTD of less than or equal to 0.477 log(mg/kg/day) is considered low, and high if greater than 0.477 log(mg/kg/day), a LC50 value below 0.5 mM (logLC50 < −0.3) is regarded as high acute toxicity, a pIGC50 (negative logarithm of the concentration required to inhibit 50% growth in log ug/L) is predicted, while a value >−0.5 log ug/L is considered toxic. Compounds with a logPS > −2 are considered to penetrate the central nervous system (CNS), while those with logPS < −3 are considered as unable to penetrate the CNS.

Data Availability Statement:
The data presented in this study are available on request from the corresponding author.