Rational Design of a Potential New Nematicide Targeting Chitin Deacetylase

Abstract

In a previously published study, the authors devised a molecular topology QSAR (quantitative structure-activity relationship) approach to detect novel fungicides acting as inhibitors of chitin deacetylase (CDA). Several of the chosen compounds exhibited noteworthy activity. Due to the close relationship between chitin-related proteins present in fungi and other chitin-containing plant-parasitic species, the authors decided to test these molecules against nematodes, based on their negative impact on agriculture. From an overall of 20 fungal CDA inhibitors, six showed to be active against Caenorhabditis elegans. These experimental results made it possible to develop two new molecular topology-based QSAR algorithms for the rational design of potential nematicides with CDA inhibitor activity for crop protection. Linear discriminant analysis was employed to create the two algorithms, one for identifying the chemo-mathematical pattern of commercial nematicides and the other for identifying nematicides with activity on CDA. After creating and validating the QSAR models, the authors screened several natural and synthetic compound databases, searching for alternatives to current nematicides. Finally one compound, the N2-(dimethylsulfamoyl)-N-{2-[(2-methyl-2-propanyl)sulfanyl]ethyl}-N2-phenylglycinamide or nematode chitin deacetylase inhibitor, was selected as the best candidate and was further investigated both in silico, through molecular docking and molecular dynamic simulations, and in vitro, through specific experimental assays. The molecule shows favorable binding behavior on the catalytic pocket of C. elegans CDA and the experimental assays confirm potential nematicide activity.

Keywords: Caenorhabditis elegans; QSAR; chitin deacetylase; molecular topology; nematicide.

Figure 1

Workflow of the QSAR strategy developed for the identification of new potential nematicides with CDA inhibitory activity.

Figure 2

Nematicidal effect of the three most active compounds against C. elegans. The life cycle of C. elegans is also included. See Table S1 for details.

Figure 3

Example of topological active and inactive chemical structures for the training set, with respective MATS5c and GATS3c values.

Figure 4

Discriminant function 1 (DF₁) nematicidal distribution diagram (NDD). Blue peaks represent the nematicides’ CDA inhibitors distribution, while orange peaks represent the inactive.

Figure 5

Discriminant function 2 (DF₂) nematicidal distribution diagram (NDD). Blue peaks represent the nematicides’ CDA inhibitor distribution, while orange peaks are the inactive.

Figure 6

Example of commercial nematicides with their respective topological and topo-chemical descriptor values.

Figure 7

Chemical structure and topo-chemical descriptors of the potential nematicide with CDA inhibitory activity selected by the QSAR strategy.

Figure 8

Proposed binding sites for CDA of C. elegans using the SiteMap tool from Schrödinger.

Figure 9

Left image shows the top-ranked binding mode of NCDI in C. elegans, while the right image depicts the detailed 3D interactions between the docked ligand and the protein.

Figure 10

RMSD values of the Cα atoms of the CDA C. elegans in complex with NCDI, computed from the trajectory range 25–45 ns during MD simulations (represented by the blue lines). The RMSD values of the ligand’s heavy atoms, after being superimposed to the Cα atoms of the protein through least-squares-fit, are also depicted in purple.

Figure 11

Protein–ligand interactions monitored throughout the MD simulation (simulation period of 25–45 ns). Hydrogen bonds are shown in green, water-mediated hydrogen bonds in blue and hydrophobic interactions in purple.

Figure 12

Specific atom-level interactions between NCDI and the residues of CDA C. elegans. Only interactions that occur for more than 30.0% of the simulation time within the selected trajectory range (25.0–45.0 ns) are depicted.

Figure 13

Oxidative burst measurement triggered by NCDI in C. elegans N2 by using the ROS indicator dihydrorhodamine-123 (DHR-123). Whisker plot showing the fluorescence intensity of C. elegans mitochondria, stained with DHR123 after treatment with 0.6 mM Fluopyram, 1 mM NCDI and 1.5% Acetone. Whiskers’ plot shows all measurements (green dots), medians (black line), and minimum and maximum (whiskers ends). Data sets passed Shapiro-Wilk test for normality (P > 0.05) and were compared using a parametric two-tailed Student′s t test with Welch’s correction.* P = 0.0122; **** P < 0.0001.

Figure 14

Effect of NCDI on C. elegans N2 lifecycle development. The impact of 0.6 mM fluopyram, 1 mM NCDI, and 1.5% acetone was assessed on the life cycle of C. elegans N2. This evaluation involved direct counting of various stages of the life cycle over a five-day duration.