Molecular Dynamic Screening Sesquiterpenoid Pogostemon Herba as Suggested Cyclooxygenase Inhibitor

Abstract

Objective:Virtual molecular dynamic sesquiterpenoid Pogostemon Herba (CID56928117, CID94275, CID107152, and CID519743) have screening as cyclooxygenase (COX-1/COX-2) selective inhibitor.Methods:Molecular interaction studies sesquiterpenoid compounds with COX-1 and COX-2 were using the molecular docking tools by Hex 8.0 and interactions were further visualized using by Discovery Studio Client 3.5 software tool and Virtual Molecular Dynamic 1.9.1 software. The binding energy calculation of molecular dynamic interaction was calculated by AMBER12 software.Result:The analysis of the sesquiterpenoid compounds showed that CID56928117, CID94275, CID107152, and CID519743 have suggested as inhibitor of COX-1 and COX-2.Conclusion:Collectively, the scoring binding energy calculation (with PBSA Model Solvent) sesquiterpenoid compounds: CID519743 had suggested as candidate for non-selective inhibitor; CID56928117 and CID94275 had suggested as candidate for a selective COX-1 inhibitor; and CID107152 had suggested as candidate for a selective COX-2 inhibitor.

Anti-Apoptotic Activity of Anthocyanins has Potential to inhibit Caspase-3 Signaling

“…Furthermore, petunidin-3-O-glucoside-caspase-3 complex also has highest van der Waals interaction and also has one covalent bond in Asn141, which the binding energy of the complex was -287.8 cal/mol. The van der Waals interaction, electrostatic and covalent bond affected the energy binding of the protein-ligand complex [32,[36][37][38]. Therefore, based on the interaction type, energy score and binding regions, cyanidin-3-O-glucoside, delphinidin-3-O-glucoside, pelargonidin-3-O-glucoside and peonidin-3-O-glucoside are more potent as anti-apoptotic through caspase-3 inhibition.…”

Virtual Screening of Sesquiterpenoid Pogostemon herba as Predicted Cyclooxygenase Inhibitor

“…Also, sesquiterpenoid alcohols, including alpha-Patchouli alcohol isomers (CID442384, CID521903, CID6432585, CID3080622, CID10955174, and CID56928117) as 3D-SDF format. Then, its energy was minimized which files were converted to 3D-PDB format by Open Babel 2.3.1 in Hex 8.0 as the ligands prepared for virtual screening [6,8,11,31]. The structures of studied ligands are shown in Figure 4.…”

“…The time step of the free MD simulations was 2 fs with a cut-off of 9°A for the non-bonded interaction, and SHAKE was employed to keep all bonds involving hydrogen atoms rigid. Calculation of binding energy was administered using this equation: 8,[33][34][35][36][37]. We were using AMBER12 software and Virtual Molecular Dynamics 1.9.1 to simulate the most possible native complex structure of sesquiterpenoid/ sesquiterpenoid alcohol (CID94275, CID107152, CID519743, CID442384, CID521903, CID6432585, CID3080622, CID10955174, and CID56928117), respectively, that binds with COX-1 and COX-2 in molecular dynamic with MM-PBSA Model Solvent.…”

“…MMPBSA has always been considered as a proper method to compare binding energies of similar ligands. MMPBSA measures the binding free energy based on thermodynamic cycle in which molecular mechanical energy and the continuum solvent approaches are simultaneously used [6,8,33,38]. The calculation of binding free energy is computed as:…”

“…As the demand on this computational method keeps increasing, people expected a fast and reliable method. Another application used in this study was molecular complexes investigation [3,[6][7][8][9][10][11]. Previous studies have shown that dynamic molecular-generated conformations play considerable role in the identification of novel hit compounds because structural rearrangements obtained from molecular dynamic show novel-targetable areas.…”