scholarly journals Binding Energy Calculation of Patchouli Alcohol Isomer Cyclooxygenase Complexes Suggested as COX-1/COX-2 Selective Inhibitor

2014 ◽  
Vol 2014 ◽  
pp. 1-12 ◽  
Author(s):  
Sentot Joko Raharjo ◽  
Chanif Mahdi ◽  
Nurdiana Nurdiana ◽  
Takheshi Kikuchi ◽  
Fatchiyah Fatchiyah

To understand the structural features that dictate the selectivity of the two isoforms of the prostaglandin H2 synthase (PGHS/COX), the three-dimensional (3D) structure of COX-1/COX-2 was assessed by means of binding energy calculation of virtual molecular dynamic with using ligand alpha-Patchouli alcohol isomers. Molecular interaction studies with COX-1 and COX-2 were done using the molecular docking tools by Hex 8.0. Interactions were further visualized by using Discovery Studio Client 3.5 software tool. The binding energy of molecular interaction was calculated by AMBER12 and Virtual Molecular Dynamic 1.9.1 software. The analysis of the alpha-Patchouli alcohol isomer compounds showed that all alpha-Patchouli alcohol isomers were suggested as inhibitor of COX-1 and COX-2. Collectively, the scoring binding energy calculation (with PBSA Model Solvent) of alpha-Patchouli alcohol isomer compounds (CID442384, CID6432585, CID3080622, CID10955174, and CID56928117) was suggested as candidate for a selective COX-1 inhibitor and CID521903 as nonselective COX-1/COX-2.

Food Research ◽  
2020 ◽  
Vol 4 (3) ◽  
pp. 780-785
Author(s):  
Y.T. Wijaya ◽  
A. Yulandi ◽  
A.W. Gunawan ◽  
Yanti

Inflammatory markers such as cyclooxygenase (COX)-2, inducible nitric oxide synthase (iNOS), myeloperoxidase (MPO), and prostaglandin (PEG) are widely known as major targets in discovering natural anti-inflammatory drugs for the treatment of inflammationrelated diseases. Non-steroidal anti-inflammatory drugs (NSAIDs) such as ibuprofen and aspirin are mostly used at present, however, some NSAIDS have been reported to cause gastrointestinal side effect due to ligand-protein interaction. Molecular docking is a promising tool to study such modes of interaction. In this study, we evaluated the potential use of anthocyanin and ternatin flavonoids as natural anti-inflammatory agents for treatment of inflammatory-related diseases using in silico molecular docking assay. Automated docking study using Protein-Ligand ANT System (PLANTS) and AutoDock Vina was performed with various ligand molecules, including ibuprofen, anthocyanin, and ternatin against the protein crystal structures of COX-1, COX-2, iNOS, and MPO. The in silico data demonstrated that ibuprofen bound effectively to the active site of COX-1 and MPO with minimum binding energy, yet the compound required more energy to bind the active site of COX-2. Ternatin flavonoid was bound to COX-2 and iNOS with minimum binding energy. In terms of binding energy, anthocyanin flavonoid was found to be effective for inhibiting COX-1, COX-2, and iNOS. These results suggested that anthocyanin and ternatin flavonoids may potentially be developed as anti-inflammatory drug candidate for the treatment of inflammatory-related diseases.


2021 ◽  
Vol 1080 (1) ◽  
pp. 012012
Author(s):  
Shivani Rana ◽  
Sanjib Kabi ◽  
Kamakhya Prakash Misra ◽  
Saikat Chattopadhyay

2011 ◽  
Vol 2011 ◽  
pp. 1-11 ◽  
Author(s):  
E. V. Orlenko ◽  
T. S. Orlova ◽  
F. E. Orlenko ◽  
G. G. Zegrya

A new methodology of binding energy calculation with respect to different spin arrangements for a multiatomic electron system is developed from the first principle in the frame of the exchange perturbation theory (EPT). We developed EPT formalism in the general form of the Rayleigh-Srchödinger expansion with a symmetric Hamiltonian, taking into account an exchange and nonadditive contributions of a superexchange interaction. The expressions of all corrections to the energy and wave function were reduced to the nonsymmetric Hamiltonian form. The EPT method is extended for the case of degeneracy in the total spin of a system. As an example of the application of the developed EPT formalism for the degeneracy case, spin arrangements were considered for the key –O– (: Mn3+ or Mn4+) fragments in manganites. In –O– for La1/3Ca2/3MnO3 are in good agreement the obtained estimations of Heisenberg parameter and binding energy with the available experimental data.


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