Structural insight into TNF-α inhibitors through combining pharmacophore-based virtual screening and molecular dynamic simulation

Potential Utilization of Phenolic Acid Compounds as Anti-Inflammatory Agents through TNF-α Convertase Inhibition Mechanisms: A Network Pharmacology, Docking, and Molecular Dynamics Approach

Inflammation is a dysregulated immune response characterized by an excessive release of proinflammatory mediators, such as cytokines and prostanoids, leading to tissue damage and various pathological conditions. Natural compounds, notably phenolic acid phytocompounds from plants, have recently garnered substantial interest as potential therapeutic agents to bolster well-being and combat inflammation recently. Based on previous research, the precise molecular mechanism underlying the anti-inflammatory activity of phenolic acids remains elusive. Therefore, this study aimed to predict the molecular mechanisms underpinning the anti-inflammatory properties of selected phenolic acid phytocompounds through comprehensive network pharmacology, molecular docking, and dynamic simulations. Network pharmacology analysis successfully identified TNF-α convertase as a potential target for anti-inflammatory purposes. Among tested compounds, chlorogenic acid (-6.90 kcal/mol), rosmarinic acid (-6.82 kcal/mol), and ellagic acid (-5.46 kcal/mol) exhibited the strongest binding affinity toward TNF-α convertase. Furthermore, phenolic acid compounds demonstrated molecular binding poses similar to those of the native ligand, indicating their potential as inhibitors of TNF-α convertase. This study provides valuable insights into the molecular mechanisms that drive the anti-inflammatory effects of phenolic compounds, particularly through the suppression of TNF-α production via TNF-α convertase inhibition, thus reinforcing their anti-inflammatory attributes.

Discovery of novel VEGFR2-TK inhibitors by phthalimide pharmacophore based virtual screening, molecular docking, MD simulation and DFT

Currently, numerous potent chemotherapeutic agents are available in the market but most of them show poor pharmacokinetics, lethal effects and drug resistance during their enduring use. The increased cancer cases, deaths and need of better treatment stimulates us to give newer lifesaving anticancer drugs. The phthalimide derivatives are structurally diverse and exert potential anticancer activity. In this regard, the 3D QSAR Pharmacophore model was developed and validated using fifty-eight phthalimide derivatives. The validation parameters corroborated the reliability and statistical robustness of CEASER Hypo 1. Three databases-NCI Open, Drug Bank, and Asinex were submitted to ADMET and drug-like filtering; 117893 drug-like compounds were mapped on CEASER Hypo 1; and 362 hits with IC50 <1 µM were discovered. These hits were docked on VEGFR2-TK, and in the form of results fifteen hits exhibited greater affinity than sorafenib. The top lead ASN 03206926 was subjected for MD simulation (100 ns) and RMSD, Rg, RMSF, number of hydrogen bonds, and SASA verified that the complex was stable, rigid and highly compact. Results demonstrated GLU885, PHE918, CYS919, LYS920, HIS1026, CYS1045, ASP1046 are the essential residues for favourable interactions. The binding free energy calculations support the affinity and stability revealed by docking and MD simulation. The DFT calculations, negative binding energy and lower HOMO-LUMO band gap revealed that the process is spontaneous and ASN 03206926 is very reactive. Following extensive analysis we suggest that the ASN 03206926 might be employed as a new VEGFR2-TK inhibitor for the treatment of breast and VEGFR2-TK associated cancers.Communicated by Ramaswamy H. Sarma.