Identification of Potential Insect Growth Inhibitor against Aedes aegypti: A Bioinformatics Approach

Abstract

Aedes aegypti is the main vector that transmits viral diseases such as dengue, hemorrhagic dengue, urban yellow fever, zika, and chikungunya. Worldwide, many cases of dengue have been reported in recent years, showing significant growth. The best way to manage diseases transmitted by Aedes aegypti is to control the vector with insecticides, which have already been shown to be toxic to humans; moreover, insects have developed resistance. Thus, the development of new insecticides is considered an emergency. One way to achieve this goal is to apply computational methods based on ligands and target information. In this study, sixteen compounds with acceptable insecticidal activities, with 100% larvicidal activity at low concentrations (2.0 to 0.001 mg·L−1), were selected from the literature. These compounds were used to build up and validate pharmacophore models. Pharmacophore model 6 (AUC = 0.78; BEDROC = 0.6) was used to filter 4793 compounds from the subset of lead-like compounds from the ZINC database; 4142 compounds (dG < 0 kcal/mol) were then aligned to the active site of the juvenile hormone receptor Aedes aegypti (PDB: 5V13), 2240 compounds (LE < −0.40 kcal/mol) were prioritized for molecular docking from the construction of a chitin deacetylase model of Aedes aegypti by the homology modeling of the Bombyx mori species (PDB: 5ZNT), which aligned 1959 compounds (dG < 0 kcal/mol), and 20 compounds (LE < −0.4 kcal/mol) were predicted for pharmacokinetic and toxicological prediction in silico (Preadmet, SwissADMET, and eMolTox programs). Finally, the theoretical routes of compounds M01, M02, M03, M04, and M05 were proposed. Compounds M01−M05 were selected, showing significant differences in pharmacokinetic and toxicological parameters in relation to positive controls and interaction with catalytic residues among key protein sites reported in the literature. For this reason, the molecules investigated here are dual inhibitors of the enzymes chitin synthase and juvenile hormonal protein from insects and humans, characterizing them as potential insecticides against the Aedes aegypti mosquito.

Keywords: Aedes aegypti; insect growth inhibitor; molecular docking; pharmacophore.

Scheme 1

Methodological scheme. First stage (pharmacophore models) > second stage (comparative modeling) and third stage (hierarchical virtual screening—model and coupling).

Figure 1

ROC curve for pharmacophore models. Below the diagonal line, poor models are represented for random selection (AUC < 0.5).

Figure 2

(A)—potent inhibitor (0.001 mg·L⁻¹; QFIT = 84.94); (B)—flucycloxuron (0.05 mg·L⁻¹; QFIT = 58.66), superposed to model pharmacophore 06. Spheres represent H-bond donors (green), H-bond acceptors (magenta) and hydrophobic groups (cyan). The size of spheres varies according to the tolerance radius calculated using GALAHAD^TM. All the distances are measured in angstroms.

Figure 3

Overlap between alpha-carbons of macromolecule 5ZNT (green) and the Bombyx-Aedes model (red); RMSD value 0.396.

Figure 4

Ramachandran, the Bombyx-Aedes Model terrain. The most favorable regions are shown in dark green, neutral in light green, and non-favorable in white; each amino acid residue is marked with different colors, generated by the structure assessment program (https://swissmodel.expasy.org/assess/KGJVtX/01, accessed on 27 June 2021).

Figure 5

Overlays of crystallographic ligand poses in JH3 (in red) with the calculated pose (in blue).

Figure 6

Interaction of selected molecules, in yellow, with the amino acid residues, in green, of the macromolecule 5V13 (juvenile hormone), in green. (A) M01 (ZINC13514543); (B) M02 (ZINC14413017); (C) M03 (ZINC05680928); (D) M04 (ZINC04691148); (E) M05 (ZINC95851150); (F) JH3.

Figure 7

Interactions in the catalytic region around the metal zinc in the 5ZNT protein (A) and the Bombyx-Aedes model (B) and the overlapping of the amino acid residues closest to the zinc metal in the 5ZNT protein (C) and the Bombyx-Aedes model (D).

Figure 8

Interaction between the selected molecules, in yellow, with the amino acid residues, in green, of the macromolecule Bombyx-Aedes model, in green. (A) M01 (ZINC13514543); (B) M02 (ZINC14413017); (C) M03 (ZINC05680928); (D) M04 (ZINC04691148); (E) M05 (ZINC95851150); (F) Zinc Ray.

Figure 9

Promising compounds (A) M01 (ZINC13514543); (B) M02 (ZINC14413017); (C) M03 (ZINC05680928); (D) M04 (ZINC04691148); (E) M05 (ZINC95851150). Source: authors.

Figure 10

The basic chemical structure of benzoylphenylurean compounds consists of three regions for SAR analysis: the benzoyl ring (A), the urea bridge (B), and the aniline (C).

Figure 11

Synthetic route for the preparation of M01. DCM (dichloromethane). Starting material I is commercially available.

Figure 12

Theoretical synthetic route for the preparation of M02. Starting material IV is commercially available.

Figure 13

Alternative synthetic route for the preparation of M02. Starting material VI is commercially available.

Figure 14

Traditional method for the preparation of compound M03. Starting material VIII is commercially available.

Figure 15

Alternative synthetic route for the preparation of compound M03. Starting material IX is commercially available.

Figure 16

Synthetic route for the preparation of MO4. THF (tetrahydrofuran), Potassium hydroxide, Starting material X is commercially available.

Figure 17

Theoretical synthetic route for the preparation of M05. Starting materials XII and XV are commercially available.

Figure 18

The 2D structure of benzoylphenylurean derivatives. R1 and R2 are radicals, and X = methyl or halogens.

Figure 19

Structures of selected training set compounds, with canonical smiles and concentrations ([ ]) with 100% larvicidal activity (mg·L⁻¹). (A)—Compound 01; (B)—Compound 05; (C)—Compound 06; (D)—Compound 07; (E)—Compound 12; (F)—Compound 13; (G)—Compound 16.