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All Journal Narra J Journal of Bio-molecule Research And Engineering
Rizaldy, Rafli
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Biochemistry, Genetics & Molecular Biology Chemistry Health Professions Immunology & microbiology Medicine & Pharmacology Public Health

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Molecular interaction analysis of ferulic acid (4-hydroxy-3-methoxycinnamic acid) as main bioactive compound from palm oil waste against MCF-7 receptors: An in silico study Herdiansyah, Mochammad A.; Rizaldy, Rafli; Alifiansyah, Mochamad RT.; Fetty, Amelia JT.; Anggraini, Dhea; Agustina, Niken; Alfian, Fariz R.; Setianingsih, Primanita NM.; Elfianah, Verah; Aulia, Halimatus S.; Putra, Justitia ERP.; Ansori, Arif NM.; Kharisma, Viol D.; Jakhmola, Vikash; Purnobasuki, Hery; Pratiwi, Intan A.; Rebezov, Maksim; Shmeleva, Svetlana; Bonkalo, Tatyana; Kovalchuk, Dmitriy F.; Zainul, Rahadian
Narra J Vol. 4 No. 2 (2024): August 2024
Publisher : Narra Sains Indonesia

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.52225/narra.v4i2.775

Abstract

Ferulic acid (4-hydroxy-3-methoxycinnamic acid) is a phytochemical compound that is commonly found in conjugated forms within mono-, di-, polysaccharides and other organic compounds in cell walls of grain, fruits, and vegetables. This compound is highly abundant in the palm oil waste. The aim of the study was to predict the anticancer activity of ferulic acid against the breast cancer cell lines (MCF-7) receptors through a computational analysis. MCF-7 receptors with PDB IDs of 1R5K, 2IOG, 4IV2, 4IW6, 5DUE, 5T92, and 5U2B were selected based on the SMILE similarity of the native ligand. Thereafter, the protein was prepared on Chimera 1.16 and docked with ferulic acid on Autodock Vina 1.2.5. The ligand-protein complex interaction was validated by computing the root mean square fluctuation (RMSF) and radius of gyration (Rg) through molecular dynamic simulation. In addition, an absorption, distribution, metabolism, excretion, and toxicity (ADMET) prediction was performed on ferulic acid using the pkCSM platform. The molecular docking revealed that the ferulic acid could interact with all receptors as indicated by the affinity energy <-5 kcal/mol. The compound had the most optimum interaction with receptor 2IOG (affinity energy=-6.96 kcal/mol), involving hydrophobic interaction (n=12) and polar hydrogen interaction (n=4). The molecular dynamic simulation revealed that the complex had an RMSF of 1.713 Å with a fluctuation of Rg value around 1.000 Å. The ADMET properties of ferulic acid suggested that the compound is an ideal drug candidate. In conclusion, this study suggested that ferulic acid, which can be isolated from palm oil waste, has the potential to interact with MCF-7 receptors.
Semi-empirical study of acetic acid esterification and methyl ester transesterification reactions with Nafion catalyst using PM7 level of theory Alfian, Fariz R.; Faiq, Farly Y.; Rizaldy, Rafli; Haq, Kautsar Ul
Journal of Bio-Molecule Research and Engineering Vol 1 No 2 (2022)
Publisher : Universitas Airlangga

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.20473/jbiome.v1i2.51930

Abstract

Nafion, as a highly acidic catalyst, is appropriate for application in both esterification and transesterification reactions. Nevertheless, its computational efficacy hasn't been explored yet. A semi-empirical approach employing the PM7 theory was utilized to determine the configurations of reactants, transition states, intermediates, and products, along with the energetics of the reactions. The findings indicate that, with Nafion catalysts, a 6-ring complex is formed in both reactions, and the rate-determining step occurs at the initial activation energy. Additionally, a quantum leap in reaction kinetics was observed in the presence of the Nafion catalyst, leading to an accelerated reaction rate.
Co-Authors Agustina, Niken Alfian, Fariz R. Alifiansyah, Mochamad RT. Anggraini, Dhea Ansori, Arif NM. Aulia, Halimatus S. Bonkalo, Tatyana Elfianah, Verah Faiq, Farly Y. Fetty, Amelia JT. Haq, Kautsar Ul Herdiansyah, Mochammad A. Hery Purnobasuki Jakhmola, Vikash Kharisma, Viol D. Kovalchuk, Dmitriy F. Pratiwi, Intan A. Putra, Justitia ERP. Rahadian Zainul Rebezov, Maksim Setianingsih, Primanita NM. Shmeleva, Svetlana