ArticlePloS one2024
Phenolic compounds of Theobroma cacao L. show potential against dengue RdRp protease enzyme inhibition by In-silico docking, DFT study, MD simulation and MMGBSA calculation.
Article in PloS one, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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7 citing papers in PubMed, 17 citations in OpenAlex.
- Decoding antidengue serotype-3 (DENV-3) mechanism of natural glycosides fromOpen veterinary journal · 2026Article
- Conformational dynamics and binding free energy analyses unveil a stable flavonoid inhibitor of dengue virus NS5 polymerase.Scientific reports · 2026Article
- Repurposing of natural products for spinocerebellar ataxia type 3 using integrated network pharmacology and in silico approaches.Scientific reports · 2026Article
- Identification of potent inhibitors of potential VEGFR2: a graph neural network-based virtual screening andJournal of enzyme inhibition and medicinal chemistry · 2025Article
- One Health Approach in the Era of Emerging Viruses: The Challenge of Usutu Virus.International journal of molecular sciences · 2025Review
- Therapeutic potential inhibitor for dipeptidyl peptidase IV in diabetic type 2: in silico approaches.3 Biotech · 2025Article
- Investigate the binding of pesticides with the TLR4 receptor protein found in mammals and zebrafish using molecular docking and molecular dynamics simulations.Scientific reports · 2024Article
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Authors and funding
9 authors at 4 institutions in 3 countries.
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No grant is acknowledged in the PubMed record.
Abstract
backgroundCurrently, there is no antiviral medication for dengue, a potentially fatal tropical infectious illness spread by two mosquito species, Aedes aegypti and Aedes albopictus. The RdRp protease of dengue virus is a potential therapeutic target. This study focused on the in silico drug discovery of RdRp protease inhibitors.
methodsTo assess the potential inhibitory activity of 29 phenolic acids from Theobroma cacao L. against DENV3-NS5 RdRp, a range of computational methods were employed. These included docking, drug-likeness analysis, ADMET prediction, density functional theory (DFT) calculations, and molecular dynamics (MD) simulations. The aim of these studies was to confirm the stability of the ligand-protein complex and the binding pose identified during the docking experiment.
resultsTwenty-one compounds were found to have possible inhibitory activities against DENV according to the docking data, and they had a binding affinity of ≥-37.417 kcal/mol for DENV3- enzyme as compared to the reference compound panduratin A. Additionally, the drug-likeness investigation produced four hit compounds that were subjected to ADMET screening to obtain the lead compound, catechin. Based on ELUMO, EHOMO, and band energy gap, the DFT calculations showed strong electronegetivity, favouravle global softness and chemical reactivity with considerable intra-molecular charge transfer between electron-donor to electron-acceptor groups for catechin. The MD simulation result also demonstrated favourable RMSD, RMSF, SASA and H-bonds in at the binding pocket of DENV3-NS5 RdRp for catechin as compared to panduratin A.
conclusionAccording to the present findings, catechin showed high binding affinity and sufficient drug-like properties with the appropriate ADMET profiles. Moreover, DFT and MD studies further supported the drug-like action of catechin as a potential therapeutic candidate. Therefore, further in vitro and in vivo research on cocoa and its phytochemical catechin should be taken into consideration to develop as a potential DENV inhibitor.
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