Molecular investigation on active compounds in papaya leaves (Carica papaya Linn) as anti-malaria using network pharmacology, molecular docking, clustering-based analysis and molecular dynamics simulation
Malaria remains a significant global health issue. In Indonesia, >400,000 cases of malaria were reported, with the highest prevalence in Papua Province. However, limited access to healthcare services in remote areas and the emergence of resistance to antimalarial drugs pose significant challenges...
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Elsevier
2025-02-01
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| Series: | Phytomedicine Plus |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S2667031324001878 |
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| author | Arwansyah Arwansyah Sitti Rahmawati Siti Nuryanti Yenni Yusuf Hartono Abdur Rahman Arif |
| author_facet | Arwansyah Arwansyah Sitti Rahmawati Siti Nuryanti Yenni Yusuf Hartono Abdur Rahman Arif |
| author_sort | Arwansyah Arwansyah |
| collection | DOAJ |
| description | Malaria remains a significant global health issue. In Indonesia, >400,000 cases of malaria were reported, with the highest prevalence in Papua Province. However, limited access to healthcare services in remote areas and the emergence of resistance to antimalarial drugs pose significant challenges to malaria elimination efforts in Indonesia. Hence, we investigate the active compounds in Carica papaya Linn as potential drugs against malaria using pharmacology combined with several in silico methods. A total of 23 proteins linked to the active compounds and malaria-related targets in human proteins were identified using network analysis. STAT3 protein is the first-degree rank based on network topological analysis, indicating it has a strong correlation with malaria infection. Furthermore, molecular docking was performed on the parasite protein Falcipain-2, revealing that five compounds exhibited higher binding affinities than Artemisinin (control), suggesting their potential as Falcipain-2 inhibitor. The stability of these complexes was further validated using MD simulations, showing no signs of instability in any of the models based on validation metrics. Citroxanthin (model 2) emerged as the most stable complex due to its favorable binding energy score. To confirm Citroxanthin's binding site, re-docking simulations and k-means clustering analysis were conducted. The results indicated that Citroxanthin in cluster 1 occupied a similar binding site as in the initial docking and MD simulation. From the viewpoints of the molecular investigations, including binding site analysis, binding energy, and structural dynamics, Citroxanthin may become a promising drug for treating malaria infections. |
| format | Article |
| id | doaj-art-e7aa52011309487b86f48d5dd92579a8 |
| institution | Kabale University |
| issn | 2667-0313 |
| language | English |
| publishDate | 2025-02-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Phytomedicine Plus |
| spelling | doaj-art-e7aa52011309487b86f48d5dd92579a82025-02-10T04:35:15ZengElsevierPhytomedicine Plus2667-03132025-02-0151100713Molecular investigation on active compounds in papaya leaves (Carica papaya Linn) as anti-malaria using network pharmacology, molecular docking, clustering-based analysis and molecular dynamics simulationArwansyah Arwansyah0Sitti Rahmawati1Siti Nuryanti2Yenni Yusuf3 Hartono4Abdur Rahman Arif5Department of Chemistry Education, Faculty of Teacher Training and Education, Tadulako University, Palu, Indonesia; Corresponding authors.Department of Chemistry Education, Faculty of Teacher Training and Education, Tadulako University, Palu, Indonesia; Corresponding authors.Department of Chemistry Education, Faculty of Teacher Training and Education, Tadulako University, Palu, IndonesiaDepartment of Parasitology, Faculty of Medicine, Hasanuddin University, Makassar, IndonesiaDepartment of Biology, Faculty of Mathematics and Natural Sciences, Universitas Negeri Makassar, IndonesiaDepartment of Chemistry, Faculty of Mathematics and Natural Sciences, Hasanuddin University, Makassar, IndonesiaMalaria remains a significant global health issue. In Indonesia, >400,000 cases of malaria were reported, with the highest prevalence in Papua Province. However, limited access to healthcare services in remote areas and the emergence of resistance to antimalarial drugs pose significant challenges to malaria elimination efforts in Indonesia. Hence, we investigate the active compounds in Carica papaya Linn as potential drugs against malaria using pharmacology combined with several in silico methods. A total of 23 proteins linked to the active compounds and malaria-related targets in human proteins were identified using network analysis. STAT3 protein is the first-degree rank based on network topological analysis, indicating it has a strong correlation with malaria infection. Furthermore, molecular docking was performed on the parasite protein Falcipain-2, revealing that five compounds exhibited higher binding affinities than Artemisinin (control), suggesting their potential as Falcipain-2 inhibitor. The stability of these complexes was further validated using MD simulations, showing no signs of instability in any of the models based on validation metrics. Citroxanthin (model 2) emerged as the most stable complex due to its favorable binding energy score. To confirm Citroxanthin's binding site, re-docking simulations and k-means clustering analysis were conducted. The results indicated that Citroxanthin in cluster 1 occupied a similar binding site as in the initial docking and MD simulation. From the viewpoints of the molecular investigations, including binding site analysis, binding energy, and structural dynamics, Citroxanthin may become a promising drug for treating malaria infections.http://www.sciencedirect.com/science/article/pii/S2667031324001878Anti-malariaLigand-receptor complexNetwork pharmacologyClustering-based analysis |
| spellingShingle | Arwansyah Arwansyah Sitti Rahmawati Siti Nuryanti Yenni Yusuf Hartono Abdur Rahman Arif Molecular investigation on active compounds in papaya leaves (Carica papaya Linn) as anti-malaria using network pharmacology, molecular docking, clustering-based analysis and molecular dynamics simulation Phytomedicine Plus Anti-malaria Ligand-receptor complex Network pharmacology Clustering-based analysis |
| title | Molecular investigation on active compounds in papaya leaves (Carica papaya Linn) as anti-malaria using network pharmacology, molecular docking, clustering-based analysis and molecular dynamics simulation |
| title_full | Molecular investigation on active compounds in papaya leaves (Carica papaya Linn) as anti-malaria using network pharmacology, molecular docking, clustering-based analysis and molecular dynamics simulation |
| title_fullStr | Molecular investigation on active compounds in papaya leaves (Carica papaya Linn) as anti-malaria using network pharmacology, molecular docking, clustering-based analysis and molecular dynamics simulation |
| title_full_unstemmed | Molecular investigation on active compounds in papaya leaves (Carica papaya Linn) as anti-malaria using network pharmacology, molecular docking, clustering-based analysis and molecular dynamics simulation |
| title_short | Molecular investigation on active compounds in papaya leaves (Carica papaya Linn) as anti-malaria using network pharmacology, molecular docking, clustering-based analysis and molecular dynamics simulation |
| title_sort | molecular investigation on active compounds in papaya leaves carica papaya linn as anti malaria using network pharmacology molecular docking clustering based analysis and molecular dynamics simulation |
| topic | Anti-malaria Ligand-receptor complex Network pharmacology Clustering-based analysis |
| url | http://www.sciencedirect.com/science/article/pii/S2667031324001878 |
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