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

Mochammad A. Herdiansyah; Rafli Rizaldy; Mochamad RT. Alifiansyah; Amelia JT. Fetty; Dhea Anggraini; Niken  Agustina; Fariz R.  Alfian; Primanita NM.  Setianingsih; Verah  Elfianah; Halimatus S.  Aulia; Justitia ERP.  Putra; Arif NM. Ansori; Viol D.  Kharisma; Vikash  Jakhmola; Hery Purnobasuki; Intan A.  Pratiwi; Maksim  Rebezov; Svetlana  Shmeleva; Tatyana  Bonkalo; Dmitriy F.  Kovalchuk; Rahadian Zainul

doi:10.52225/narra.v4i2.775

Authors

Mochammad A. Herdiansyah Department of Biology, Faculty of Science and Technology, Universitas Airlangga, Surabaya, Indonesia https://orcid.org/0009-0006-9383-6203
Rafli Rizaldy Department of Chemistry, Faculty of Science and Technology, Universitas Airlangga, Surabaya, Indonesia
Mochamad RT. Alifiansyah Department of Pharmaceutical, Faculty of Pharmacy, Universitas Airlangga, Surabaya, Indonesia
Amelia JT. Fetty Department of Chemistry, Faculty of Science and Technology, Universitas Airlangga, Surabaya, Indonesia https://orcid.org/0009-0003-9940-2682
Dhea Anggraini Department of Practical Pharmacy, Faculty of Pharmacy, Universitas Airlangga, Surabaya, Indonesia
Niken Agustina Department of Chemistry, Faculty of Science and Technology, Universitas Airlangga, Surabaya, Indonesia
Fariz R. Alfian Department of Chemistry, Faculty of Science and Technology, Universitas Airlangga, Surabaya, Indonesia https://orcid.org/0009-0009-0346-2458
Primanita NM. Setianingsih Department of Biology, Faculty of Science and Technology, Universitas Airlangga, Surabaya, Indonesia https://orcid.org/0009-0006-8237-084X
Verah Elfianah Department of Biology, Faculty of Science and Technology, Universitas Airlangga, Surabaya, Indonesia https://orcid.org/0009-0004-1309-068X
Halimatus S. Aulia Department of Biology, Faculty of Science and Technology, Universitas Airlangga, Surabaya, Indonesia https://orcid.org/0009-0004-3721-9935
Justitia ERP. Putra Department of Biology, Faculty of Science and Technology, Universitas Airlangga, Surabaya, Indonesia
Arif NM. Ansori Postgraduate School, Universitas Airlangga, Surabaya, Indonesia; Uttaranchal Institute of Pharmaceutical Sciences, Uttaranchal University, Dehradun, India; Virtual Research Center for Bioinformatics and Biotechnology, Surabaya, Indonesia https://orcid.org/0000-0002-1279-3904
Viol D. Kharisma Department of Biology, Faculty of Science and Technology, Universitas Airlangga, Surabaya, Indonesia; Virtual Research Center for Bioinformatics and Biotechnology, Surabaya, Indonesia
Vikash Jakhmola Uttaranchal Institute of Pharmaceutical Sciences, Uttaranchal University, Dehradun, India https://orcid.org/0000-0002-8108-006X
Hery Purnobasuki Department of Biology, Faculty of Science and Technology, Universitas Airlangga, Surabaya, Indonesia https://orcid.org/0000-0002-0562-2058
Intan A. Pratiwi Department of Biology, Faculty of Science and Technology, Universitas Airlangga, Surabaya, Indonesia https://orcid.org/0000-0003-0362-5113
Maksim Rebezov Department of Scientific Research, V. M. Gorbatov Federal Research Center for Food Systems, Moscow, Russian Federation; Faculty of Biotechnology and Food Engineering, Ural State Agrarian University, Yekaterinburg, Russian Federation https://orcid.org/0000-0003-0857-5143
Svetlana Shmeleva Moscow State University of Technologies and Management (The First Cossack University), Moscow, Russian Federation
Tatyana Bonkalo Research Institute for Healthcare Organization and Medical Management, Moscow Healthcare Department, Moscow, Russian Federation; Kuban State University, Krasnodar, Russian Federation
Dmitriy F. Kovalchuk Kuban State University, Krasnodar, Russian Federation
Rahadian Zainul Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Negeri Padang, Padang, Indonesia; Center for Advanced Material Processing, Artificial Intelligence, and Biophysic Informatics (CAMPBIOTICS), Universitas Negeri Padang, Padang, Indonesia https://orcid.org/0000-0002-3740-3597

DOI:

https://doi.org/10.52225/narra.v4i2.775

Keywords:

ADMET properties, cancer, ferulic acid, in silico, medicine

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.