GC/MS analysis and computational evaluation of C. cinerea EO constituents for colorectal cancer: Molecular docking, dynamics, and quantum chemical insights into Cis-Verbenyl acetate

Abstract

The essential oil of Cotula cinerea was subjected to gas chromatography-mass spectrometry (GC-MS) analysis, leading to the identification of 31 chemical constituents. The major compounds were selected for comprehensive computational investigations to explore their potential anti-colorectal cancer activity. Among the identified constituents, cis-verbenyl acetate (CVA) exhibited the most favorable binding affinities across a panel of fifteen protein targets implicated in colorectal cancer. Notably, Tankyrase1 (PDB ID: 4OA7) and Tankyrase2 (PDB ID: 4UFU) emerged as the most promising targets, with docking scores of -9.49 and -8.46 kcal/mol, respectively. Molecular dynamics simulations conducted over 300 nanoseconds demonstrated the structural stability and sustained interactions of the CVA-protein complexes, characterized by low root mean square deviation (RMSD) values and limited conformational fluctuations. These findings were corroborated by molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) calculations, which revealed highly favorable binding free energies, particularly in the CVA- TNKS2 complex (ΔGtotal = -45.64 kcal/mol). In silico ADMET profiling indicated high oral bioavailability and low predicted toxicity for CVA compared to native ligands. Furthermore, density functional theory (DFT) analysis provided insight into the electronic properties of CVA, revealing a stable electronic configuration, suitable frontier molecular orbital energies, and a well-distributed electrostatic potential surface. Thermodynamic evaluations supported its chemical stability, showing a consistent increase in entropy, enthalpy, and heat capacity with rising temperature. Collectively, these computational findings suggest that CVA is a thermodynamically stable, pharmacokinetically favorable, and potentially bioactive compound with dual-target affinity against colorectal cancer-related proteins, meriting further experimental validation.