Synthesis and Evaluation of Anti-Inflammatory and Anti-Nociceptive Potential of Novel Acyl Hydrazone Derivatives of Ketoprofen using DFT, Virtual Screening, MD Simulation and Binding Free Energy Calculations
Muhammad Zubair, Muhammad Waqar, Ashraf Ullah Khan, Aishma Khattak, Nadia Bibi, Kaleem Ullah, Amir Zeb, Amin Ullah, Mumtaz Ali · Journal of Computational Biophysics and Chemistry · 2025
In this study, the ketoprofen derivatives were evaluated against inflammation and nociception using comprehensive computational methods. These derivatives were synthesized by modifying the structure of ketoprofen, a well-known NSAID (nonsteroidal anti-inflammatory drug) used clinically for the management of pain and inflammation. The virtual screening was performed to predict the binding affinities of the ketoprofen-based acyl hydrazone derivatives with key inflammatory and pain-related targets including cyclooxygenase-2 (COX-2), Transient Receptor Potential menthol-8 (TRPV1), c-Jun N-terminal Kinase-3 (JNK3), Extracellular Receptor Kinase (ERK) and Purinergic Receptor Type Y1 (P2Y1) to obtain the top hits. The virtual screening studies revealed the top hits such as COMP2, COMP10, COMP16 and COMP17 against the target protein. Based on the virtual screening, Molecular Dynamic (MD) simulation was performed on the top hits for 50 ns by using parameters like Root Mean Square Fluctuations (RMSF), Root Mean Square Deviation (RMSD), Radius of Gyration (RoG), Solvent Accessible Surface Area (SASA) and hydrogen bonds. The three complexes showed significantly lowered RMSD value and hence, the complexes remained stable throughout the simulation. For binding free energy, Molecular, Mechanics-Poison Boltzmann Surface Area (MM-PBSA) and Molecular Mechanics-Generalized Born Surface Area (MM-GBSA) were performed after MD simulation for the analysis of stability in the context of energy. The MM-PBSA and MM-GBSA evaluation showed overall energy of the system remains negative and indicates favorable binding interaction and hence, stability of the complexes. Furthermore, the per-residue decomposition was carried out to evaluate each amino acid involved in the ligand–protein interaction, and highest contributing amino acid in terms of energy involved in the ligand–protein interactions. The binding free energy calculation was succeeded by Density Functional Theory (DFT) analysis to evaluate the Highest Occupied Molecular Orbital (HOMO), Lowest Unoccupied Molecular Orbital (LUMO) and the HOMO-LUMO gap. In conclusion, the four compounds showed significant activity against pain and inflammation based on the computational analysis; however, to employ it clinically further analysis will be required.