Structure-based virtual screening of highly potent inhibitors of the nematode chitinase CeCht1

Abstract

Nematode chitinases play vital roles in various physiological processes, including egg hatching, larva moulting, and reproduction. Small-molecule inhibitors of nematode chitinases have potential applications for controlling nematode pests. On the basis of the crystal structure of Ce Cht1, a representative chitinase indispensable to the eggshell chitin degradation of the model nematode Caenorhabditis elegans , we have discovered a series of novel inhibitors bearing a ( R )-3,4-diphenyl-4,5-dihydropyrrolo[3,4- c ]pyrazol-6(2 H )-one scaffold by hierarchical virtual screening. The crystal structures of Ce Cht1 complexed with two of these inhibitors clearly elucidated their interactions with the enzyme active site. Based on the inhibitory mechanism, several analogues with improved inhibitory activities were identified, among which the compound PP28 exhibited the most potent activity with a K i value of 0.18 μM. This work provides the structural basis for the development of novel nematode chitinase inhibitors.

Discovery of novel inhibitors targeting nematode chitinase CeCht1: Virtual screening, biological evaluation, and molecular dynamics simulation

“…Firstly, in order to improve the screening efficiency, the pesticide-likeness rules ( Hao et al, 2011 ) were used to reasonably reduce the number of compounds and this yielded 3176361 molecules. Then, the reported co-crystal structure of Ce Cht1 with PP7 (PDB ID: 6LE8) ( Chen W. et al, 2021 ) was selected as the template to generate the pharmacophore model in MOE. We focused on the H-bonding and hydrophobic interactions between ligand and residues Glu179, Trp138, and Trp394 at −1 and +1 subsists of Ce Cht1.…”

“…The complex crystal structure of Ce Cht1 (PDB ID: 6LE8) ( Chen W. et al, 2021 ) was selected as the template to generate a pharmacophore model. The protein ligand interaction fingerprints (PLIF) tool in MOE was used to establish a pharmacophore model.…”

“…Downregulation of Bursaphelenchus xylophilus chitinase ( Bx Cht1) led to hatching delay and spawning decrease ( Ju et al, 2016 ). Accordingly, nematode chitinase may serve as a potential target for the development of novel nematicides ( Chen W. et al, 2021 ; Chen Q. et al, 2021 ).…”

“…However, the development of chitinase inhibitors for nematicides is rarely mentioned. Only few nematode chitinase inhibitors have been reported, including allosamidin ( Arnold et al, 1993 ), β- carboline ( Gooyit et al, 2015 ), closantel ( Gloeckner et al, 2010 ), 4-hydroxy-1,2,3-triazoles ( Pippione et al, 2015 ), benzothiazoles (BP) ( Chen Q. et al, 2021 ), and dihydropyrrolopyrazoles (PP) ( Chen W. et al, 2021 ) ( Figure 1 ). Among these inhibitors, allosamidin, carbolines, closantel, and 4-hydroxy-1,2,3-triazoles were reported to have good inhibitory effect on animal parasitic nematodes (e.g., Heligmosomoides polygyrus , Brugia malayi , Onchocerca volvulus ).…”

“…Benzothiazoles (BP) and dihydropyrrolopyrazole (PP) were recently found by Yang’s group to have excellent inhibitory potency against the model nematode Caenorhabditis elegans . Furthermore, the crystal structures of Caenorhabditis elegans chitinase Ce Cht1 and Ce Cht1-inhibitor complexes were obtained by Yang’s group ( Chen W. et al, 2021 ; Chen Q. et al, 2021 ). The results showed that Ce Cht1 consists of a signal peptide, a catalytic domain, and two chitin-binding modules.…”