Computational Study of Natural Compounds in Melon Fruit ( Cucumis melo L. ‘GMP’) as Inhibitor of Epidermal Growth Factor Receptor Protein

Abstract

'GMP' melon is a breeding cultivar that has a bitter taste and fragrant aroma. The bitter taste character indicates the presence of potential natural compounds that can be used as anti-cancer. This study aims to reveal the natural compounds of 'GMP' melon and its use as an anti-cancer computationally. Experimenting with the content of natural compounds in 'GMP' melon with fruit extraction at medium maturity level and analyzed using Liquid Chromatography-Mass Spectrometry. The probable potential of natural compounds was predicted by PASS online. Analysis computationally of natural compounds potency using specific docking of EGFR protein with AutoDock Vina program from PyRx software. Visualization of docking results using Biovia Discovery Studio and comparing binding affinity values. The screening results showed 'GMP' melon had 42 potential natural compounds that passed RO5 screening out of 63 detected metabolites. Based on PASS online, the antioxidant compound group is predicted to have direct activity as a kinase inhibitor, while the cucurbitacin compound group is expected to have antineoplastic activity associated with lung cancer. The docking results show 9 potential natural compound candidates that have a lower binding affinity value than the native ligand (17.7 kcal/mol), namely Quercetin (-8.9 kcal/mol), Cucurbitacin B (-8.5 kcal/mol), Kaempferol (-8.5 kcal/mol), Naringenin (-8.5 kcal/mol), Isorhamnetin (-8.4 kcal/mol), Cucurbitacin I (-8.4 kcal/mol), Catechin (-8.3 kcal/mol), Isocucurbitacin R (-8.3 kcal/mol)), and Cucurbitacin R (-8.2 kcal/mol).