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Decoding the therapeutic potential of empon-empon: a bioinformatics expedition unraveling mechanisms against COVID-19 and atherosclerosis

Hasanah et al., International Journal of Applied Pharmaceutics, doi:10.22159/ijap.2024v16i2.50128
Mar 2024  
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Quercetin for COVID-19
22nd treatment shown to reduce risk in July 2021
 
*, now known with p = 0.0031 from 11 studies.
No treatment is 100% effective. Protocols combine complementary and synergistic treatments. * >10% efficacy in meta analysis with ≥3 clinical studies.
4,100+ studies for 60+ treatments. c19early.org
In Silico study of compounds in empon-empon showing that quercetin may be beneficial for treating COVID-19 and atherosclerosis by inhibiting key signaling targets. Authors found that quercetin exhibits strong binding affinity to EP300 and HSP90AA1, which are involved in upregulating profibrotic genes, inflammatory cytokine production, and facilitating viral entry into cells.
In Silico studies predict inhibition of SARS-CoV-2, or minimization of side effects, with quercetin or metabolites via binding to the spike Note A, Alavi, Azmi (B), Chandran, Kandeil, Mandal, Moschovou, Nguyen, Pan, Thapa (B), Şimşek, Mpro Note B, Akinwumi, Alanzi, Ibeh, Kandeil, Mandal, Moschovou, Nguyen, Qin, Rehman, Sekiou (B), Singh, Thapa (B), Wang, Zhang, Shaik, Waqas, Nalban, Irfan, RNA-dependent RNA polymerase Note C, Corbo, PLpro Note D, Ibeh, Zhang, ACE2 Note E, Chandran, Ibeh, Qin, Thapa (B), Şimşek, Alkafaas, TMPRSS2 Note F, Chandran, helicase Note G, Alanzi, Singh (B), endoribonuclease Note H, Alavi, cathepsin L Note I, Ahmed, Wnt-3 Note J, Chandran, FZD Note K, Chandran, LRP6 Note L, Chandran, ezrin Note M, Chellasamy, ADRP Note N, Nguyen, NRP1 Note O, Şimşek, EP300 Note P, Hasanah, PTGS2 Note Q, Qin, HSP90AA1 Note R, Qin, Hasanah, matrix metalloproteinase 9 Note S, Sai Ramesh, IL-6 Note T, Yang, Yang (B), IL-10 Note U, Yang, VEGFA Note V, Yang (B), and RELA Note W, Yang (B) proteins. In Vitro studies demonstrate efficacy in Calu-3 Note X, DiGuilio, A549 Note Y, Yang, HEK293-ACE2+ Note Z, Singh (C), Huh-7 Note AA, Pan, Caco-2 Note AB, Roy, Vero E6 Note AC, Kandeil, El-Megharbel, Roy, mTEC Note AD, Wu, and RAW264.7 Note AE, Wu cells. Animal studies demonstrate efficacy in K18-hACE2 mice Note AF, Aguado, db/db mice Note AG, Wu, Wu (B), BALB/c mice Note AH, Shaker, and rats El-Megharbel (B). Quercetin reduced proinflammatory cytokines and protected lung and kidney tissue against LPS-induced damage in mice Shaker.
Hasanah et al., 7 Mar 2024, peer-reviewed, 5 authors. Contact: arry.yanuar@ui.ac.id.
In Silico studies are an important part of preclinical research, however results may be very different in vivo.
This PaperQuercetinAll
DECODING THE THERAPEUTIC POTENTIAL OF EMPON-EMPON: A BIOINFORMATICS EXPEDITION UNRAVELING MECHANISMS AGAINST COVID-19 AND ATHEROSCLEROSIS
Nur Hasanah, Fadlina Chany Saputri, Alhadi Bustamam, Vannajan Sanghiran Lee, Arry Yanuar
International Journal of Applied Pharmaceutics, doi:10.22159/ijap.2024v16i2.50128
Objective: This study aims to elucidate the main compounds and mechanisms of action of Empon-empon (EE), a traditional Indonesian herb used for treating COVID-19 and atherosclerosis, utilizing an integrated network pharmacology and molecular docking approach. Methods: Active compounds in EE were obtained through the KNApSAcK, screening active compounds using parameters: oral bioavailability (OB) ≥ 30% and drug-likeness (DL) ≥ 0.18. Compound-related target genes were collected from GeneCard, ChemBL, and Traditional Chinese Medicine Systems Pharmacology (TCMSP). Disease targets were obtained from the GeneCard database. The protein-protein interaction (PPI) network was built using STRING and visualized using Cytoscape. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis using ShinyGO. Molecular docking analysis using Autodock Vina in PyRx. Results: We identified 18 main compounds in EE. PPI analysis obtained 5 central EE targets involved in treating COVID-19 and atherosclerosis, namely E1A Binding Protein P300 (EP300), Heat Shock Protein 90 Alpha Family Class A Member 1 (HSP90AA1), SRC Proto-Oncogene (SRC), Estrogen Receptor 1 (ESR1), and RELA Proto-Oncogene (RELA). GO and KEGG analysis illustrated EE's pharmacological effects through pathways in cancer, lipid and atherosclerosis, and PI3K-Akt signaling, including Coronavirus disease. Catechin and quercetin exhibited the strongest binding affinity to EP300; licarin B and delphinidin to HSP90AA1; epicatechin and delphinidin to SRC; galangin and ellagic acid to ESR1; and guaiacin and licarin B to RELA. Conclusion: This research provides a strong foundation regarding the main compound and mechanism action of EE in treating atherosclerosis and COVID-19, suggesting potential as a novel therapeutic agent.
AUTHORS CONTRIBUTIONS The manuscript was written through the contributions of all authors, and all authors have approved the final version. CONFLICT OF INTERESTS The authors declare no conflict of interest.
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Molecular docking analysis using Autodock Vina in PyRx.\n' 'Results: We identified 18 main compounds in EE. PPI analysis obtained 5 central EE targets ' 'involved in treating COVID-19 and atherosclerosis, namely E1A Binding Protein P300 (EP300), ' 'Heat Shock Protein 90 Alpha Family Class A Member 1 (HSP90AA1), SRC Proto-Oncogene (SRC), ' 'Estrogen Receptor 1 (ESR1), and RELA Proto-Oncogene (RELA). GO and KEGG analysis illustrated ' "EE's pharmacological effects through pathways in cancer, lipid and atherosclerosis, and " 'PI3K-Akt signaling, including Coronavirus disease. 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Network pharmacology, ' 'molecular docking and Molecular Dynamics to explore the potential ' 'immunomodulatory mechanisms of deer antler. Int J Mol Sci. ' '2023;24(12):10370. doi: 10.3390/ijms241210370, PMID 37373516.'}, { 'DOI': '10.22159/ijap.2022v14i2.43784', 'doi-asserted-by': 'crossref', 'key': '1180567', 'unstructured': 'Nurhidayah M, Fadilah F, Arsianti A, Bahtiar A. Identification of Fgfr ' 'inhibitor as St2 receptor/interleukin-1 receptor-like 1 inhibitor in ' 'chronic obstructive pulmonary disease due to exposure to E-cigarettes by ' 'network pharmacology and molecular docking prediction. Int J App Pharm. ' '2022;14(2):256-66. doi: 10.22159/ijap.2022v14i2.43784.'}, { 'DOI': '10.22159/ijap.2023v15i5.48416', 'doi-asserted-by': 'crossref', 'key': '1180568', 'unstructured': 'Nahir CF, Putra MY, Wibowo JT, Lee VS, Yanuar A. The potential of ' 'indonesian marine natural product with dual targeting activity through ' 'Sars-Cov-2 3Clpro and PLpro: an in silico studies. Int J App Pharm. ' '2023;15(5):171-80. doi: 10.22159/ijap.2023v15i5.48416.'}, { 'DOI': '10.3389/fphar.2023.1237454', 'doi-asserted-by': 'crossref', 'key': '1180569', 'unstructured': 'Giner-soriano M, Dominguez A, Morros R, Pericas C, Dolores A. ' 'Vilaplana-carnerero C. Narrative Rev. 2023;2:1-14.'}, { 'DOI': '10.1371/journal.pcbi.0030059', 'doi-asserted-by': 'crossref', 'key': '1180570', 'unstructured': 'Yu H, Kim PM, Sprecher E, Trifonov V, Gerstein M. The importance of ' 'bottlenecks in protein networks: correlation with gene essentiality and ' 'expression dynamics. PLoS Comput Biol. 2007;3(4):e59. doi: ' '10.1371/journal.pcbi.0030059, PMID 17447836.'}, { 'DOI': '10.1142/S0219720013410023', 'doi-asserted-by': 'crossref', 'key': '1180571', 'unstructured': 'Li M, Wang JX, Wang H, Pan Y. Identification of essential proteins from ' 'weighted protein-protein interaction networks. J Bioinform Comput Biol. ' '2013;11(3):1341002. doi: 10.1142/S0219720013410023, PMID 23796179.'}, { 'DOI': '10.1371/journal.pone.0195410', 'doi-asserted-by': 'crossref', 'key': '1180572', 'unstructured': 'Zhang X, Xiao W, Hu X. Predicting essential proteins by integrating ' 'orthology, gene expressions, and PPI networks. PLOS ONE. ' '2018;13(4):e0195410. doi: 10.1371/journal.pone.0195410, PMID 29634727.'}, { 'DOI': '10.3390/ijms241512302', 'doi-asserted-by': 'crossref', 'key': '1180573', 'unstructured': 'Rubio K, Molina Herrera A, Perez Gonzalez A, Hernandez Galdamez HV, ' 'Piña-Vazquez C, Araujo Ramos T. EP300 as a molecular integrator of ' 'fibrotic transcriptional programs. Int J Mol Sci. 2023;24(15):1-23. doi: ' '10.3390/ijms241512302, PMID 37569677.'}, { 'DOI': '10.1016/j.biopha.2018.07.132', 'doi-asserted-by': 'crossref', 'key': '1180574', 'unstructured': 'Tao J, Zhang M, Wen Z, Wang B, Zhang L, Ou Y. Inhibition of EP300 and ' 'DDR1 synergistically alleviates pulmonary fibrosis in vitro and in vivo. ' 'Biomed Pharmacother. 2018;106(May):1727-33. doi: ' '10.1016/j.biopha.2018.07.132, PMID 30119248.'}, { 'DOI': '10.4314/tjpr.v19i9.22', 'doi-asserted-by': 'crossref', 'key': '1180575', 'unstructured': 'Liu C, Fan FF, Li XH, Wang WX, Tu Y, Zhang Y. Elucidation of the ' 'mechanisms underlying the anticholecystitis effect of the tibetan ' 'medicine ”Dida” using network pharmacology. Trop J Pharm Res. ' '2020;19(9):1953-61. doi: 10.4314/tjpr.v19i9.22.'}, { 'DOI': '10.1155/2012/502813', 'doi-asserted-by': 'crossref', 'key': '1180576', 'unstructured': 'Kilic A, Mandal K. Heat shock proteins: pathogenic role in ' 'atherosclerosis and potential therapeutic implications. Autoimmune Dis. ' '2012;2012(1):502813. doi: 10.1155/2012/502813, PMID 23304456.'}, { 'DOI': '10.1093/cvr/cvq046', 'doi-asserted-by': 'crossref', 'key': '1180577', 'unstructured': 'Madrigal Matute J, Lopez Franco O, Blanco Colio LM, Munoz Garcia B, ' 'Ramos-Mozo P, Ortega L. Heat shock protein 90 inhibitors attenuate ' 'inflammatory responses in atherosclerosis. Cardiovasc Res. ' '2010;86(2):330-7. doi: 10.1093/cvr/cvq046, PMID 20154064.'}, { 'DOI': '10.3390/ijms22179366', 'doi-asserted-by': 'crossref', 'key': '1180578', 'unstructured': 'Lubkowska A, Pluta W, Stronska A, Lalko A. Role of heat shock proteins ' '(Hsp70 and hsp90) in viral infection. Int J Mol Sci. 2021;22(17). doi: ' '10.3390/ijms22179366, PMID 34502274.'}, { 'DOI': '10.1253/circj.CJ-15-1039', 'doi-asserted-by': 'crossref', 'key': '1180579', 'unstructured': 'Wang JG, Aikawa M. Toll-like receptors and src-family kinases in ' 'atherosclerosis–Focus on macrophages. Circ J. 2015;79(11):2332-4. doi: ' '10.1253/circj.CJ-15-1039, PMID 26467082.'}, { 'DOI': '10.1155/2012/512926', 'doi-asserted-by': 'crossref', 'key': '1180580', 'unstructured': 'Byeon SE, Yi YS, Oh J, Yoo BC, Hong S, Cho JY. The role of Src kinase in ' 'macrophage-mediated inflammatory responses. Mediators Inflamm. ' '2012;2012:512926. doi: 10.1155/2012/512926, PMID 23209344.'}, { 'DOI': '10.7150/ijbs.74864', 'doi-asserted-by': 'crossref', 'key': '1180581', 'unstructured': 'Chen W, Zheng W, Liu S, Su Q, Ding K, Zhang Z. SRC-3 deficiency prevents ' 'atherosclerosis development by decreasing endothelial ICAM-1 expression ' 'to attenuate macrophage recruitment. Int J Biol Sci. ' '2022;18(15):5978-93. doi: 10.7150/ijbs.74864, PMID 36263184.'}, { 'DOI': '10.1038/s41598-022-13585-4', 'doi-asserted-by': 'crossref', 'key': '1180582', 'unstructured': 'Li F, Boon ACM, Michelson AP, Foraker RE, Zhan M, Payne PRO. Estrogen ' 'hormone is an essential sex factor inhibiting inflammation and immune ' 'response in COVID-19. Sci Rep. 2022;12(1):9462. doi: ' 'org/10.1038/s41598-022-13585-4, PMID 35676404.'}, { 'DOI': '10.1111/j.1399-0039.2007.00865.x', 'doi-asserted-by': 'crossref', 'key': '1180583', 'unstructured': 'Hirankarn N, Manonom C, Tangkijvanich P, Poovorawan Y. Association of ' 'interleukin-18 gene polymorphism (−607A/A genotype) with susceptibility ' 'to chronic hepatitis B virus infection. Tissue Antigens. ' '2007;70(2):160-3. doi: 10.1111/j.1399-0039.2007.00865.x, PMID 17610422.'}, { 'DOI': '10.1186/s12906-023-04148-9', 'doi-asserted-by': 'crossref', 'key': '1180584', 'unstructured': 'Xiao W, Xu Y, Baak JP, Dai J, Jing L, Zhu H. Network module analysis and ' 'molecular docking-based study on the mechanism of astragali radix ' 'against non-small cell lung cancer. BMC Complement Med. 2023;23(1):345. ' 'doi: 10.1186/s12906-023-04148-9, PMID 37770919.'}, { 'key': '1180585', 'unstructured': 'Jimi E, Fei Huang CN. NF-κB signaling regulates; 2019. p. 3-11.'}, { 'DOI': '10.1161/CIRCRESAHA.110.233841', 'doi-asserted-by': 'crossref', 'key': '1180586', 'unstructured': 'Cuhlmann S, Van Der Heiden K, Saliba D, Tremoleda JL, Khalil M, Zakkar ' 'M. Disturbed blood flow induces rela expression via c-Jun N-terminal ' 'kinase 1: a novel mode of NF-κB regulation that promotes arterial ' 'inflammation. Circ Res. 2011;108(8):950-9. doi: ' '10.1161/circresaha.110.233841, PMID 21350211.'}], 'reference-count': 43, 'references-count': 43, 'relation': {}, 'resource': {'primary': {'URL': 'https://journals.innovareacademics.in/index.php/ijap/article/view/50128'}}, 'score': 1, 'short-title': [], 'source': 'Crossref', 'subject': ['Pharmaceutical Science'], 'subtitle': [], 'title': 'DECODING THE THERAPEUTIC POTENTIAL OF EMPON-EMPON: A BIOINFORMATICS EXPEDITION UNRAVELING ' 'MECHANISMS AGAINST COVID-19 AND ATHEROSCLEROSIS', 'type': 'journal-article'}
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