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Maikhunthod B, Chaipayang S, Jittmittraphap A, Thippornchai N, Boonchuen P, Tittabutr P, Eumkeb G, Sabuakham S, Rungrotmongkol T, Mahalapbutr P, Leaungwutiwong P, Teaumroong N, Tanthanuch W. Exploring the therapeutic potential of Thai medicinal plants: in vitro screening and in silico docking of phytoconstituents for novel anti-SARS-CoV-2 agents. BMC Complement Med Ther 2024; 24:274. [PMID: 39030504 PMCID: PMC11264683 DOI: 10.1186/s12906-024-04586-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2023] [Accepted: 07/10/2024] [Indexed: 07/21/2024] Open
Abstract
BACKGROUND The high virulence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), responsible for coronavirus disease 2019 (COVID-19), has triggered global health and economic concerns. The absence of specific antiviral treatments and the side effects of repurposed drugs present persistent challenges. This study explored a promising antiviral herbal extract against SARS-CoV-2 from selected Thai medicinal plants based on in vitro efficacy and evaluated its antiviral lead compounds by molecular docking. METHODS Twenty-two different ethanolic-aqueous crude extracts (CEs) were rapidly screened for their potential activity against porcine epidemic diarrhea virus (PEDV) as a surrogate using a plaque reduction assay. Extracts achieving ≥ 70% anti-PEDV efficacy proceeded to the anti-SARS-CoV-2 activity test using a 50% tissue culture infectious dose method in Vero E6 cells. Molnupiravir and extract-free media served as positive and negative controls, respectively. Potent CEs underwent water/ethyl acetate fractionation to enhance antiviral efficacy, and the fractions were tested for anti-SARS-CoV-2 performance. The fraction with the highest antiviral potency was identified using liquid chromatography-high-resolution mass spectrometry (LC-HRMS). Molecular docking analyses of these compounds against the main protease (Mpro) of SARS-CoV-2 (6LU7) were performed to identify antiviral lead molecules. The top three hits were further evaluated for their conformational stability in the docked complex using molecular dynamics (MD) simulation. RESULTS The water fraction of mulberry (Morus alba Linn.) leaf CE (WF-MLCE) exhibited the most potent anti-SARS-CoV-2 efficacy with low cytotoxicity profile (CC50 of ~ 0.7 mg/mL), achieving 99.92% in pre-entry mode and 99.88% in postinfection treatment mode at 0.25 mg/mL. Flavonoids and conjugates were the predominant compounds identified in WF-MLCE. Molecular docking scores of several flavonoids against SARS-CoV-2 Mpro demonstrated their superior antiviral potency compared to molnupiravir. Remarkably, myricetin-3-O-β-D-galactopyranoside, maragrol B, and quercetin 3-O-robinobioside exhibited binding energies of ~ - 9 kcal/mol. The stability of each ligand-protein complex of these compounds with the Mpro system showed stability during MD simulation. These three molecules were pronounced as antiviral leads of WF-MLCE. Given the low cytotoxicity and high antiviral potency of WF-MLCE, it holds promise as a candidate for future therapeutic development for COVID-19 treatment, especially considering its economic and pharmacological advantages.
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Affiliation(s)
- Bussayarat Maikhunthod
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima, 30000, Thailand
| | - Sukanya Chaipayang
- Synchrotron Light Research Institute (Public Organization), Nakhon Ratchasima, 30000, Thailand
| | - Akanitt Jittmittraphap
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, 10400, Thailand
| | - Narin Thippornchai
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, 10400, Thailand
| | - Pakpoom Boonchuen
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima, 30000, Thailand
| | - Panlada Tittabutr
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima, 30000, Thailand
| | - Griangsak Eumkeb
- School of Preclinical Sciences, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima, 30000, Thailand
| | - Sahachai Sabuakham
- Department of Biochemistry, Center for Translational Medicine, Faculty of Medicine, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Thanyada Rungrotmongkol
- Program in Bioinformatics and Computational Biology, Graduate School, Chulalongkorn University, Bangkok, 10330, Thailand
- Center of Excellence in Structural and Computational Biology, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Panupong Mahalapbutr
- Department of Biochemistry, Center for Translational Medicine, Faculty of Medicine, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Pornsawan Leaungwutiwong
- Department of Microbiology and Immunology, Faculty of Tropical Medicine, Mahidol University, Bangkok, 10400, Thailand
| | - Neung Teaumroong
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima, 30000, Thailand.
| | - Waraporn Tanthanuch
- Synchrotron Light Research Institute (Public Organization), Nakhon Ratchasima, 30000, Thailand.
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Gayathri K, Abhinand P, Gayathri V, Prasanna Lakshmi V, Chamundeeswari D, Jiang L, Tian Z, Malathi N. Computational analysis of phytocompounds in Centella asiatica for its antifibrotic and drug-likeness properties - Herb to drug study. Heliyon 2024; 10:e33762. [PMID: 39027607 PMCID: PMC11255509 DOI: 10.1016/j.heliyon.2024.e33762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 06/24/2024] [Accepted: 06/26/2024] [Indexed: 07/20/2024] Open
Abstract
Oral submucous fibrosis (OSMF) is a potentially malignant disorder with no permanent cure that affects the quality of life due to trismus. Computational pharmacology has accelerated the discovery of drug candidates for the treatment of incurable diseases. The present study aimed to screen the compounds of the miracle herb Centella asiatica with drug-likeness properties based on the absorption, distribution, metabolism, and excretion (ADME) properties. The pharmacological actions of these screened compounds against OSMF were identified by network pharmacology, gene ontology, pathway enrichment analysis, molecular docking, and simulation. Fifteen drug-like ligands were identified after virtual screening viz; asiatic acid, kaempferol, quercetin, luteolin, apigenin, bayogenin, gallic acid, isothankunic acid, madecassic acid, madasiatic acid, arjunolic acid, terminolic acid, catechin, epicatechin, and nobiletin. 850 potential targets were predicted for the ligands, which were analyzed against 354 proteins associated with OSMF. Compound pathway analysis and disease pathway analysis identified 53 common proteins. The GO enrichment analysis identified 472 biological process terms, 76 molecular function terms, and 44 cellular component terms. Pathway enrichment analysis predicted 142 KEGG pathways, 35 Biocarta pathways, and 236 Reactome pathways for the target proteins. The analysis revealed that the herb targets crucial events of fibrosis such as inflammation, oxidative stress, apoptosis, collagen deposition, and epithelial-mesenchymal transition. The common 53 proteins were used for protein-protein interaction (PPI) network analysis, which revealed 4 key proteins interacting with the phytocompounds viz; transforming growth factor-β1 (TGF-β1), mothers against decapentaplegic-3 (SMAD-3), mitogen-activated protein kinase-1 (MAPK-1) and proto-oncogene tyrosine-protein kinase (SRC). Molecular docking revealed that all ligands had a good binding affinity to the target proteins. Bayogenin had the highest binding affinity towards MAPK-1 (-9.7 kcal/mol), followed by isothankunic acid towards SRC protein (-9.3 kcal/mol). Madasiatic acid had the highest binding affinity to SMAD-3 (-7.6 kcal/mol) and TGF-β1 (-7.1 kcal/mol). Molecular dynamics simulation demonstrated stable ligand protein interactions of bayogenin and MAPK complex, isothankunic acid and SRC complex. This in silico study is the first to identify potential phytochemicals present in Centella asiatica and their target molecules, which might be responsible for reversing OSMF.
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Affiliation(s)
- K. Gayathri
- Faculty of Biomedical Sciences, Sri Ramachandra Institute of Higher Education and Research, Porur, Chennai, 600116, India
- Department of Oral Pathology and Microbiology, Sri Ramachandra Dental College, Sri Ramachandra Institute of Higher Education and Research, Porur, Chennai, 600116, India
| | - P.A. Abhinand
- Department of Bioinformatics, Faculty of Engineering and Technology, Sri Ramachandra Institute of Higher Education & Research, Porur, Chennai, 600116, India
| | - V. Gayathri
- Centre for Toxicology and Developmental Research, Sri Ramachandra Institute of Higher Education and Research, Porur, Chennai, 600116, India
| | - V. Prasanna Lakshmi
- Department of Bioinformatics, Faculty of Engineering and Technology, Sri Ramachandra Institute of Higher Education & Research, Porur, Chennai, 600116, India
| | - D. Chamundeeswari
- Faculty of Pharmacy, Meenakshi Academy of Higher Education and Research, Chennai, India
| | - Li Jiang
- Department of Oral Pathology, The Ninth People's Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - Zhen Tian
- Department of Oral Pathology, The Ninth People's Hospital, Shanghai Jiao Tong University, Shanghai, China
| | - N. Malathi
- Department of Oral Pathology and Microbiology, Sri Ramachandra Dental College, Sri Ramachandra Institute of Higher Education and Research, Porur, Chennai, 600116, India
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Supandi S, Wulandari MS, Samsul E, Azminah A, Purwoko RY, Herman H, Kuncoro H, Ibrahim A, Silfi Ambarwati NS, Rosmalena R, Azizah RN, Paramita S, Ahmad I. Dipeptidyl peptidase IV inhibition of phytocompounds from Artocarpus champeden (Lour.) Stokes: In silico molecular docking study and ADME-Tox prediction approach. J Adv Pharm Technol Res 2022; 13:207-215. [PMID: 35935696 PMCID: PMC9355056 DOI: 10.4103/japtr.japtr_376_22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Revised: 05/18/2022] [Accepted: 05/23/2022] [Indexed: 11/04/2022] Open
Abstract
The present study examines the potential activity prediction based on free binding energy (ΔG) and interaction confirmation of phytocompounds from Artocarpus champeden (Lour.) Stokes with macromolecule protein receptor of dipeptidyl peptidase IV (DPP-IV) using in silico molecular docking studies and physicochemical and pharmacokinetic properties (ADME-Tox) prediction approaches. The active subsites of the DPP-IV receptor macromolecule protein Protein Data Bank (ID: 1 × 70) were docked using Autodock v4.2.6 (100 docking runs). A grid box of 52 × 28 × 26 Å points spaced by 0.37 Å was centered on the active site of x = 40.926 Å; y = 50.522 Å; z = 35.031 Å. For ADME-Tox prediction, Swiss ADME online-based application programs were used. The results show that 12 pythocompounds from A. champeden have the potential as DPP-IV inhibitors based on ΔG value and interaction conformation. There are five pythocompounds with lower ΔG values and inhibition constants than the native ligand and seven pythocompounds with ΔG values and inhibition constants close to the native ligand. The 12 compounds form an interaction conformation at the active subsites of the DPP-IV receptor. At the same time, the results of the ADME-Tox prediction analysis showed that the 12 compounds had different physicochemical and pharmacokinetic properties.
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Affiliation(s)
- Supandi Supandi
- Department of Pharmaceutical Analysis, Faculty of Pharmacy and Science, Universitas Muhammadiyah Prof. Dr. HAMKA, South Jakarta, Indonesia
| | - Mesy Savira Wulandari
- Department of Pharmaceutical Sciences, Faculty of Pharmacy, Universitas Mulawarman, Samarinda, East Kalimantan, Indonesia
| | - Erwin Samsul
- Department of Pharmaceutical Sciences, Faculty of Pharmacy, Universitas Mulawarman, Samarinda, East Kalimantan, Indonesia
| | - Azminah Azminah
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Surabaya, Surabaya, Indonesia
| | - Reza Yuridian Purwoko
- Research Center for Pre-Clinical and Clinical Medicine, Indonesian Research and Innovation Agency, East Jakarta, Jakarta, Indonesia
| | - Herman Herman
- Department of Pharmaceutical Sciences, Faculty of Pharmacy, Universitas Mulawarman, Samarinda, East Kalimantan, Indonesia
| | - Hadi Kuncoro
- Department of Pharmaceutical Sciences, Faculty of Pharmacy, Universitas Mulawarman, Samarinda, East Kalimantan, Indonesia
| | - Arsyik Ibrahim
- Department of Pharmaceutical Sciences, Faculty of Pharmacy, Universitas Mulawarman, Samarinda, East Kalimantan, Indonesia
| | - Neneng Siti Silfi Ambarwati
- Department of Cosmetology, Engineering Faculty, Universitas Negeri Jakarta, East Jakarta, Jakarta, Indonesia
| | - Rosmalena Rosmalena
- Department of Medical Chemistry, Faculty of Medicine, Universitas Indonesia, South Jakarta, Indonesia
| | - Rizqi Nur Azizah
- Laboratory of Biopharmacy and Pharmacology, Faculty of Pharmacy, Universitas Muslim Indonesia, Makassar, South Sulawesi, Indonesia
| | - Swandari Paramita
- Department of Community Medicine, Faculty of Medicine, and Research Center of Natural Products from Tropical Rainforest, Universitas Mulawarman, Samarinda, East Kalimantan, Indonesia
| | - Islamudin Ahmad
- Department of Pharmaceutical Sciences, Faculty of Pharmacy, Universitas Mulawarman, Samarinda, East Kalimantan, Indonesia,Address for correspondence: Dr. Islamudin Ahmad, Jl. Kuaro Gn. Kelua, Samarinda 75119 East Kalimantan, Indonesia. E-mail:
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Erratum: In silico identification of natural products from Centella asiatica as severe acute respiratory syndrome-coronavirus 2 main protease inhibitor. J Adv Pharm Technol Res 2021; 12:435. [PMID: 34820322 PMCID: PMC8588924 DOI: 10.4103/2231-4040.328640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
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