Structural insights into the discrepant synergistic activity of Codlemone and (Z)‐8‐dodecenol towards Grapholita molesta pheromones

Abstract

BACKGROUND Insect pheromone synergists have been widely used to produce potent pheromone products for environment‐friendly pest control. Codlemone (Cod) and (Z)‐8‐dodecenol (Dod) are two major Grapholita molesta pheromone synergists, with Cod having greater synergism and affinity for G. molesta pheromone binding protein 2 (GmolPBP2). Uncovering structural information key to the different binding affinity of Cod and Dod to GmolPBP2 would gain insights into what causes their synergy activity discrepancy. RESULTS Binding modes of the two synergists in the binding pocket of GmolPBP2 were analyzed and compared by molecular dynamics‐based approaches. Although Cod and Dod were stabilized in a similar hydrophobic pocket, their interaction details with GmolPBP2 were divergent due to the extra double bond (C10═C11) in Cod. The C10═C11 improved the hydrophobic interactions of Cod with around residues. Such hydrophobic interaction improvement was also reflected in the raised importance of Phe11 in the GmolPBP2‐Cod interaction. Not only that, the increased hydrophobic forces introduced by the C10═C11 changed the CH2–OH orientation in the GmolPBP2‐Cod complex, which improved the H‐bond interaction. Electrostatic complementarity analysis further indicated the positive role of C10═C11 in optimizing GmolPBP2‐Cod interaction. CONCLUSION The C10═C11 is thought to contribute greatly to Cod's stronger synergy as a group key to the higher GmolPBP2‐affinity, based on which the improvement directions for Cod and Dod were addressed as well. Our findings will aid in the development and optimization of more effective pheromone synergists, resulting in more effective pheromone‐based pest management.

Identifying the Key Role of Plutella xylostella General Odorant Binding Protein 2 in Perceiving a Larval Attractant, (E,E)-2,6-Farnesol

“…As reported by Liu et al (2022), the presence of C�C in the aliphatic chain is in favor of the formation of enhanced hydrophobic interactions. 52 Thus, the C�C in farnesol is thought to contribute greatly to farnesol's high affinity for PxylGOBP2. In former reports, the residue Phe is often determined as an important hydrophobic contributor in OBP-odorant interaction.…”

“…In former reports, the residue Phe is often determined as an important hydrophobic contributor in OBP-odorant interaction. 12,52,53 In the PxylGOBP2-farnesol complex, two Phe residues (F33 and F118) formed hydrophobic interactions with farnesol, but only F118 was identified as a key residue; this may be associated with the distance of F33 and F118 to farnesol. Besides hydrophobic interactions, electrostatic interactions in the PxylGOBP2-farnesol complex are also considerable.…”

The chemosensory protein 1 contributes to indoxacarb resistance in Plutella xylostella(L.)

“…A 25000 ps molecular dynamics (MD) simulation of the PxCSP1‐Ind complex was conducted using the Amber12 package 40 . The whole process of MD simulations was similar to that in our former reports 42,47–49 . To prepare for MD simulations, free energy of the PxCSP1‐Ind complex was successively minimized by the steepest descent method (5000 steps) and the conjugated gradient method (5000 steps).…”

“…40 The whole process of MD simulations was similar to that in our former reports. 42,[47][48][49] To prepare for MD simulations, free energy of the PxCSP1-Ind complex was successively minimized by the steepest descent method (5000 steps) and the conjugated gradient method (5000 steps). Parameters and charges of Ind in the PxCSP1-Ind complex were set by the GAFF and semiempirical with bond charge correction (AM1-BCC) method in Amber12.…”

“…The MM-PBSA method in Amber12 was used to perform perresidue free energy decomposition of the PxCSP1-Ind. 55 According to our former reports, 47,56 the binding free energy of each residue in the PxCSP1-Ind system was estimated from three aspects: total free energy contribution, backbone free energy contribution, sidechain free energy contribution. Each aspect of free energy contribution was further decomposed into three energy items: van der Waals energy, electrostatic energy, and polar solvation energy.…”