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3D visualization of the interaction between the native ligand and bioactive compounds with the COX-2 receptor
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July 3, 2024
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December 29, 2024
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Abstract

Inflammation is the defense mechanism of the body against harmful stimuli, such as pathogens, damaged cells, toxic compounds, or irradiation. Javanese cardamom (Amomum compactum) has pharmacological activity that has potential as an anti-inflammatory based on in vitro tests. This study aims to assess the physico-chemical characteristics of bioactive compounds contained in Java cardamom and molecular interactions on cyclooxygenase-2 (COX-2) as a target of inflammatory processes through a computational study. This study used molecular docking and pharmacophore modeling with structure-based drug design principles aimed at simulating how the binding interaction and fit score between bioactive compounds in Java cardamom toward COX-2. In addition, drug-likeness evaluation of the secondary metabolite compounds of Java cardamom was also carried out based on Lipinski rules-of-five and ADMET profiles. Our results demonstrated that trans-nerolidol B from Java cardamom showed the most potential activity against COX-2 based on molecular tethering in the form of Gibbs free energy of -7.11 kcal/mol and inhibition constant of 6.13 μM, as well as its interaction on amino acid residues at HIS75, VAL509, MET508, LEU370, VAL335, TRP373, and pharmacophore hit score of 35.99 in pharmacophore modeling with AUC score of 0.73 and 337 hits. Overall, this study is useful for the future development of Java cardamom and trans-nerolidol B as candidate natural substance-based COX-2 targeted anti-inflammatory agents.

Keywords

Antiradang COX-2 Kapulaga jawa (Amomum compactum) Pemodelan Farmakofor Penambatan Molekuler

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