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Oct 26, 2025
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Nov 13, 2025
Published
Nov 19, 2025
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Abstract

Pseudomonas aeruginosa is an opportunistic pathogen whose virulence is largely mediated by Exotoxin A and LasB (elastase), making them promising anti-virulence drug targets. This study aimed to evaluate the inhibitory potential of natural compounds against these two key proteins using an in silico approach. Pharmacophore-based virtual screening of HerbalDB compounds was performed by LigandScout software, followed by molecular docking using AutoDockTools-1.5.7 against Exotoxin A (PDB ID: 1AER) and LasB (PDB ID: 1U4G). Native ligands and co-crystallized inhibitors were used as docking controls to validate binding accuracy. Among the screened compounds, Epicatechin-(4β-6)-epicatechin-(4β-8)-catechin exhibited the strongest binding affinity to Exotoxin A (ΔG = −10.72 kcal·mol⁻¹), while Carpaine showed the highest affinity for LasB (ΔG = −8.91 kcal·mol⁻¹). The predicted interactions involved hydrogen bonds and hydrophobic interactions with active-site residues, comparable to the native inhibitors. Furthermore, ADMET analysis indicated favorable pharmacokinetic and drug-likeness properties. These findings suggest that selected natural compounds possess potential dual inhibitory activity against Exotoxin A and LasB, warranting further experimental validation as anti-virulence candidates for controlling P. aeruginosa infections.

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Fariska AB, Linda Erlina, Ade Arsianti, Aryo Tedjo. In Silico Evaluation of Natural Compounds as Dual Inhibitors of Exotoxin A and LasB (Elastase) Virulence Proteins in Pseudomonas aeruginosa. EKSAKTA [Internet]. 2025 Nov. 19 [cited 2025 Nov. 19];26(04):480-99. Available from: https://eksakta.ppj.unp.ac.id/index.php/eksakta/article/view/631

References

  1. [1] Sathe, N., Beech, P., Croft, L., Suphioglu, C., Kapat, A., & Athan, E. (2023). Pseudomonas aeruginosa: Infections and novel approaches to treatment “Knowing the enemy” the threat of Pseudomonas aeruginosa and exploring novel approaches to treatment. Infectious medicine, 2(3), 178-194.
  2. [2] Reynolds, D., & Kollef, M. (2021). The epidemiology and pathogenesis and treatment of Pseudomonas aeruginosa infections: an update. Drugs, 81(18), 2117-2131.
  3. [3] Jørgensen, R., Merrill, A. R., Yates, S. P., Marquez, V. E., Schwan, A. L., Boesen, T., & Andersen, G. R. (2005). Exotoxin A–eEF2 complex structure indicates ADP ribosylation by ribosome mimicry. Nature, 436(7053), 979-984.
  4. [4] Casilag, F., Lorenz, A., Krueger, J., Klawonn, F., Weiss, S., & Häussler, S. (2016). The LasB elastase of Pseudomonas aeruginosa acts in concert with alkaline protease AprA to prevent flagellin-mediated immune recognition. Infection and immunity, 84(1), 162-171.
  5. [5] Qin, S., Xiao, W., Zhou, C., Pu, Q., Deng, X., Lan, L., ... & Wu, M. (2022). Pseudomonas aeruginosa: pathogenesis, virulence factors, antibiotic resistance, interaction with host, technology advances and emerging therapeutics. Signal transduction and targeted therapy, 7(1), 199.
  6. [6] Konstantinovic, J., Kany, A. M., Alhayek, A., Abdelsamie, A. S., Sikandar, A., Voos, K., ... & Hirsch, A. K. (2023). Inhibitors of the elastase LasB for the treatment of Pseudomonas aeruginosa lung infections. ACS central science, 9(12), 2205-2215.
  7. [7] Chandrasekaran, B., Agrawal, N., & Kaushik, S. (2019). Pharmacophore development.
  8. [8] Wolber, G., Seidel, T., Bendix, F., & Langer, T. (2008). Molecule-pharmacophore superpositioning and pattern matching in computational drug design. Drug discovery today, 13(1-2), 23-29.
  9. [9] Yanuar, A., Mun'im, A., Lagho, A. B. A., Syahdi, R. R., Rahmat, M., & Suhartanto, H. (2011). Medicinal plants database and three dimensional structure of the chemical compounds from medicinal plants in Indonesia. arXiv preprint arXiv:1111.7183.
  10. [10] Li, M., Dyda, F., Benhar, I., Pastan, I., & Davies, D. R. (1996). Crystal structure of the catalytic domain of Pseudomonas exotoxin A complexed with a nicotinamide adenine dinucleotide analog: implications for the activation process and for ADP ribosylation. Proceedings of the National Academy of Sciences, 93(14), 6902-6906.
  11. [11] Izzaty RE, Astuti B, Cholimah N. (2018) Full wwPDB X-ray Structure Validation Report. Angew Chemie Int Ed. 6(11), 951–952. 1967;7(2018):5–24.
  12. [12] Tintori, C., Corradi, V., Magnani, M., Manetti, F., & Botta, M. (2008). Targets looking for drugs: a multistep computational protocol for the development of structure-based pharmacophores and their applications for hit discovery. Journal of chemical information and modeling, 48(11), 2166-2179.
  13. [13] Sanders, M. P., McGuire, R., Roumen, L., de Esch, I. J., de Vlieg, J., Klomp, J. P., & de Graaf, C. (2012). From the protein's perspective: the benefits and challenges of protein structure-based pharmacophore modeling. MedChemComm, 3(1), 28-38.
  14. [14] Martínez-Rosell, G., Giorgino, T., & De Fabritiis, G. (2017). PlayMolecule ProteinPrepare: a web application for protein preparation for molecular dynamics simulations. Journal of chemical information and modeling, 57(7), 1511-1516.
  15. [15] Dolinsky, T. J., Czodrowski, P., Li, H., Nielsen, J. E., Jensen, J. H., Klebe, G., & Baker, N. A. (2007). PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Nucleic acids research, 35(suppl_2), W522-W525.
  16. [16] Naqvi, A. A., Mohammad, T., Hasan, G. M., & Hassan, M. I. (2018). Advancements in docking and molecular dynamics simulations towards ligand-receptor interactions and structure-function relationships. Current topics in medicinal chemistry, 18(20), 1755-1768.
  17. [17] Ban, T., Ohue, M., & Akiyama, Y. (2018). Multiple grid arrangement improves ligand docking with unknown binding sites: Application to the inverse docking problem. Computational biology and chemistry, 73, 139-146.
  18. [18] Hubbard, R. E., & Haider, M. K. (2010). Hydrogen bonds in proteins: role and strength. Encyclopedia of life sciences, 1, 1-6.
  19. [19] Kusuma, S. A. F., Manan, W. S., & Budiman, F. A. J. A. R. (2017). Inhibitory effect of red piper betel leaf ethanol extract (Piper crocatum Ruiz and Pav.) against Trichomonas vaginalis trophozoites in vitro. Asian J. Pharm. Clin. Res, 10, 311-314.
  20. [20] Kusuma, S. A. F., Zuhrotun, A., & Meidina, F. B. (2016). Antibacterial spectrum of ethanol extract of Indonesian red piper betel leaf (Piper crocatum Ruiz & Pav) against Staphylococcus species. Int J Pharma Sci Res, 7(11), 448-452.
  21. [21] Damayanti, S., & Ibrahim, S. (2018). Interaction binding study of dimethylamylamine with functional monomers to design a molecular imprinted polymer for doping analysis. Journal of Applied Pharmaceutical Science, 8(10), 025-031.
  22. [22] Cadenas Jiménez, I., Badía Tejero, A. M., López-Causapé, C., Morosini, M. I., Portillo-Calderón, I., Machado, M., ... & Gudiol, C. (2025). Molecular epidemiology and antimicrobial resistance profiles of Pseudomonas aeruginosa causing bloodstream infections in neutropenic cancer patients. Frontiers in Microbiology, 16, 1681506.
  23. [23] Li, D., Zhang, L., Liang, J., Deng, W., Wei, Q., & Wang, K. (2021). Biofilm formation by Pseudomonas aeruginosa in a novel septic arthritis model. Frontiers in cellular and infection microbiology, 11, 724113.
  24. [24] Pope, C. N., Schlenk, D., & Baud, F. J. (2020). History and basic concepts of toxicology. In An Introduction to Interdisciplinary Toxicology (pp. 3-15). Academic Press.
  25. [25] Pollastri, M. P. (2010). Overview on the Rule of Five. Current protocols in pharmacology, 49(1), 9-12.
  26. [26] Adiga, R. A. M. A. (2019). Molecular Docking of Hyrtimomine AK from Marine Sponge Hyrtios Spp. as Anticancer Target of Phosphoinositide-dependent Kinase 1. Asian J. Pharm. Clin. Res, 12, 130-135.
  27. [27] Teng, F., Wang, L., Wen, J., Tian, Z., Wang, G., & Peng, L. (2025). Epicatechin gallate and its analogues interact with sortase A and β-lactamase to suppress Staphylococcus aureus virulence. Frontiers in Cellular and Infection Microbiology, 15, 1537564.
  28. [28] Wilson JW. (2020). Bacterial pathogens. Cancer Treat Res.161:91–128.
  29. [29] Karbasizade, V., Dehghan, P., Sichani, M. M., Shahanipoor, K., Sepahvand, S., Jafari, R., & Yousefian, R. (2017). Evaluation of three plant extracts against biofilm formation and expression of quorum sensing regulated virulence factors in Pseudomonas aeruginosa. Pakistan Journal of pharmaceutical sciences, 30.
  30. [30] Shen, M., Tian, S., Li, Y., Li, Q., Xu, X., Wang, J., & Hou, T. (2012). Drug-likeness analysis of traditional Chinese medicines: 1. property distributions of drug-like compounds, non-drug-like compounds and natural compounds from traditional Chinese medicines. Journal of cheminformatics, 4(1), 31.