Characterisation of chemosensory proteins in Rhynchophorus ferrugineus using structural bioinformatics approaches

Abstract

Rhynchophorus ferrugineus, commonly known as red palm weevil, is a highly invasive pest that affects coconuts, dates, and oil palms globally, causing significant economic losses. The weevil’s chemosensory system detects host volatiles and releases aggregation pheromones, such as ferrugineol, to attract others and facilitate mass infestation. Current pest control relies on semiochemicals, such as ferrugineol and ethyl acetate, as attractants, alongside plant-based repellents like peppermint oil. However, these methods are limited by environmental variability, chemical degradation, and reduced long-term efficacy. Furthermore, inadequate knowledge of R. ferrugineus chemosensory pathways and the absence of three-dimensional (3D) protein structures hinder targeted molecular approaches. To address these limitations, this study employed structural bioinformatics approaches to identify the chemosensory protein sequences of R. ferrugineus and construct high-quality 3D structures using machine learning-based prediction tools; to determine the stable conformations of the apo-form of chemosensory proteins using molecular dynamics (MD) simulations; to screen and

identify potential chemical cues interacting with shortlisted proteins using high- throughput docking techniques; to determine the stability of interactions between

shortlisted protein–chemical cue complexes via MD simulations. A total of 338 R. ferrugineus chemosensory proteins were identified and successfully modelled into high-confidence 3D protein structures. Three representative proteins, RferOR18148, RferOrco, and RferGR64, were selected based on their structural stability assessed through MD simulations in a POPC (1-palmitoyl-2-oleoylphosphatidylcholine) membrane. High-throughput virtual screening was performed using reported ligands and 15,641 compounds from the ZINC20 database. The 20 top-ranked ligand-receptor complexes underwent short 5ns MD screening followed by 100ns production simulations for detailed energetic and dynamic analyses. Eight ligands demonstrated enhanced binding affinity and favourable interaction profiles with their respective receptors, outperforming known compounds. Among these, ZINC000000156132 and ZINC000075284253 displayed attractant- and repellent-like behaviour for RferOR18148, while ZINC000000386233 and ZINC000575624118 exhibited high binding stability to RferOrco and RferGR64. Fluorinated compounds mimicked natural chemical cues, whereas aromatic compounds contributed favourable receptor interactions. These environmentally safe ligands have potential to modulate insect behaviour, supporting sustainable pest management. This study establishes three reference structures representing the odorant and gustatory receptor families in R. ferrugineus, advancing understanding of its chemosensory mechanisms and providing candidates to improve pheromone-based trapping and eco-friendly infestation control.