Metabolites profiling in tomato (Solanum lycopersicum) plants on foliar application of nano-copper micronutrient formulation – A molecular docking and dynamics simulation approach

This study presents the synthesis, physicochemical characterization, and biological assessment of a Nano-Copper Micronutrient liquid formulation, focusing on its influence on tomato leaf metabolism and molecular interactions. The Nano-Copper formulation characterized using FTIR, which displayed distinct peaks at 3269 cm −1 , 2179 cm −1 , 2156 cm −1 , 2014 cm −1 , 1622 cm −1 , 1401 cm −1 , 1100 cm −1 and 516 cm −1 . TEM imaging confirmed spherical nanoparticles of Cu ranging from 45 to 55 nm and XPS analysis of the Nano-Copper shows two peaks at 933.5 eV and 953.0 eV corresponding to Cu2p3/2 and Cu2p1/2. DLS measurement indicated an average particle diameter of 53.7 nm with a PDI of 0.223; and the zeta potential value of − 17.4 mV suggested stable dispersion and surface charge. Tomato leaf samples from the control (T1–0.5% CuSO 4 foliar application) and Nano-Copper Micronutrient applications (T2–0.1% Nano-Copper Micronutrient Foliar application, T3–0.2% Nano-Copper Micronutrient Foliar Application) were examined through GC–MS metabolite profiling, identifying 26 compounds in T1, 34 compounds in T2 and 21 compounds in T3 respectively, with the highest metabolic diversity recorded under T2 (0.1% Foliar application of Nano-Copper Micronutrient). Metabolite–protein interaction networks were constructed using the STITCH database and accordingly selected metabolites such as 2-hydroxy-2-methyl-butanedioic acid and 2-methyl-butanoic acid were docked with target proteins including Succinyl-CoA ligase and electron transfer flavoprotein alpha respectively. Subsequent molecular dynamics (MD) simulations confirmed stable complexes, with RMSD values around 5.0 Å for proteins, 5–5.5 Å for ligands, RMSF mostly between 1 and 3 Å, and dominant hydrogen bonding or water bridge interactions between key amino acids and ligand residues. • Physicochemical Characterization (FTIR, TEM, XPS, PSA & Zeta potential, pH, Viscosity and Electrophoretic mobility) of Nano-Copper Micronutrient Liquid Formulation. • Metabolite Extraction to Assess the Effect of Nano-Copper Micronutrient's Foliar Application in Tomato ( Solanum lycopersicum ) crop field. • Molecular modeling and docking studies of Nano-Copper Micronutrient induced metabolites-protein complex in Tomato to decipher the variable metabolomics. • Molecular Dynamics Simulation of Succinyl-CoA ligase [ADP-forming] protein complex with 2-hydroxy-2-methyl-butanedioic acid (S) (metabolite ligand) and Electron transfer flavoprotein subunit alpha complex with 2-methyl-butanoic acid (metabolite ligand) induced in tomato crop on Nano-Copper Micronutrient Application.