1
|
Herdiansyah MA, Rizaldy R, Alifiansyah MRT, Fetty AJT, Anggraini D, Agustina N, Alfian FR, Setianingsih PNM, Elfianah V, Aulia HS, Putra JERP, Ansori ANM, Kharisma VD, Jakhmola V, Purnobasuki H, Pratiwi IA, Rebezov M, Shmeleva S, Bonkalo T, Kovalchuk DF, Zainul R. 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. NARRA J 2024; 4:e775. [PMID: 39280296 PMCID: PMC11391962 DOI: 10.52225/narra.v4i2.775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Accepted: 07/14/2024] [Indexed: 09/18/2024]
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 Simplified Molecular Input Line Entry System (SMILES) 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.
Collapse
Affiliation(s)
- Mochammad A. Herdiansyah
- Department of Biology, Faculty of Science and Technology, Universitas Airlangga, Surabaya, Indonesia
| | - Rafli Rizaldy
- Department of Chemistry, Faculty of Science and Technology, Universitas Airlangga, Surabaya, Indonesia
| | | | - Amelia JT. Fetty
- Department of Chemistry, Faculty of Science and Technology, Universitas Airlangga, Surabaya, Indonesia
| | - 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
| | | | - Verah Elfianah
- Department of Biology, Faculty of Science and Technology, Universitas Airlangga, Surabaya, Indonesia
| | - Halimatus S. Aulia
- Department of Biology, Faculty of Science and Technology, Universitas Airlangga, Surabaya, Indonesia
| | - 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
| | - 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
| | - Hery Purnobasuki
- Department of Biology, Faculty of Science and Technology, Universitas Airlangga, Surabaya, Indonesia
| | - Intan A. Pratiwi
- Department of Biology, Faculty of Science and Technology, Universitas Airlangga, Surabaya, Indonesia
| | - 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
| | - 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
| | | | - 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
| |
Collapse
|
2
|
Jarab AS, Abu Heshmeh SR, Al Meslamani AZ. Biosimilars as antivirals: opportunities and challenges. Expert Rev Anti Infect Ther 2024; 22:273-275. [PMID: 38288681 DOI: 10.1080/14787210.2024.2313064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 01/29/2024] [Indexed: 02/02/2024]
Affiliation(s)
- Anan S Jarab
- College of Pharmacy, Al Ain University, Abu Dhabi, United Arab Emirates
- AAU Health and Biomedical Research Center, Al Ain University, Abu Dhabi, United Arab Emirates
- College of Pharmacy, Jordan University of Science and Technology, Jordan
| | | | - Ahmad Z Al Meslamani
- College of Pharmacy, Al Ain University, Abu Dhabi, United Arab Emirates
- AAU Health and Biomedical Research Center, Al Ain University, Abu Dhabi, United Arab Emirates
| |
Collapse
|
3
|
Arman M, Alam S, Maruf RA, Shams Z, Islam MN. Molecular modeling of some commercially available antiviral drugs and their derivatives against SARS-CoV-2 infection. NARRA J 2024; 4:e319. [PMID: 38798846 PMCID: PMC11125382 DOI: 10.52225/narra.v4i1.319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 02/07/2024] [Indexed: 05/29/2024]
Abstract
Numerous prior studies have identified therapeutic targets that could effectively combat severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, including the angiotensin-converting enzyme 2 (ACE2) receptor, RNA-dependent RNA polymerase (RdRp), and Main protease (Mpro). In parallel, antiviral compounds like abacavir, acyclovir, adefovir, amantadine, amprenavir, darunavir, didanosine, oseltamivir, penciclovir, and tenofovir are under investigation for their potential in drug repurposing to address this infection. The aim of the study was to determine the effect of modifying the functional groups of the aforementioned antivirals in silico. Using the genetic optimization for ligand docking algorithm on software Maestro (version 11.1), the modified antivirals were docked onto ACE2 receptor, RdRp, and Mpro. Using QuickProp (Maestro v11.1), PASS (prediction of activity spectra for the substances), and altogether with SwissADME, the ADMET (absorption, distribution, metabolism, excretion, and toxicity) of the modified antivirals, as well as their bioavailability and the predicted activity spectra, were determined. Discovery studio software was used to undertake post-docking analysis. Among the 10 antivirals, N(CH3)2 derivative of darunavir, N(CH3)2 derivative of amprenavir and NCH3 derivative of darunavir exhibited best binding affinities with ACE2 receptor (docking scores: -10.333, -9.527 and -9.695 kJ/mol, respectively). Moreover, NCH3 derivative of abacavir (-6.506 kJ/mol), NO2 derivative of didanosine (-6.877 kJ/mol), NCH3 derivative of darunavir (-7.618 kJ/mol) exerted promising affinity to Mpro. In conclusion, the results of the in silico screenings can serve as a useful information for future experimental works.
Collapse
Affiliation(s)
- Mohammad Arman
- Department of Pharmacy, State University of Bangladesh, Dhaka, Bangladesh
- Department of Pharmacy, International Islamic University Chittagong, Chittagong, Bangladesh
| | - Safaet Alam
- Pharmaceutical Sciences Research Division, Bangladesh Council of Scientific and Industrial Research (BCSIR), Dhaka, Bangladesh
- Department of Pharmaceutical Technology, Faculty of Pharmacy, University of Dhaka, Dhaka, Bangladesh
| | - Rifat A. Maruf
- Department of Pharmacy, State University of Bangladesh, Dhaka, Bangladesh
- Department of Pharmacy, International Islamic University Chittagong, Chittagong, Bangladesh
| | - Ziaus Shams
- Department of Pharmacy, State University of Bangladesh, Dhaka, Bangladesh
- Department of Pharmacy, International Islamic University Chittagong, Chittagong, Bangladesh
| | - Mohammad N. Islam
- Department of Pharmacy, State University of Bangladesh, Dhaka, Bangladesh
| |
Collapse
|