Computational analysis of protein–ligand interactions involving compounds from Acmella oleracea (L.) R.K. Jansen with antitumor relevance

Authors

DOI:

https://doi.org/10.47236/2594-7036.2026.v10.2016

Keywords:

Acmella oleracea, ADMET, Carcinogenesis, In silico screening, Molecular docking, Natural products

Abstract

Natural compound prospection has emerged as a promising strategy for the development of new bioactive agents with potential antitumor applications. In this context, the present study aimed to evaluate, through in silico approaches, the potential of metabolites derived from Acmella oleracea against molecular targets associated with carcinogenesis. A total of 18 compounds from the species were selected and subjected to molecular docking studies using AutoDock Vina against three relevant proteins: PMS2 (1H7U), PI3Kβ (4AJW and 4BFR), and COX-2 (3LN1). Protocol validation was performed by redocking, yielding RMSD values consistent with those reported in the literature. The results indicated that phenolic and glycosylated flavonoid compounds showed the best docking performance, with ligand 2 standing out by exhibiting the lowest estimated binding energy values and favorable interaction patterns across the evaluated targets. Additionally, predictive pharmacokinetic and toxicological (ADMET) assessment revealed that ligand 4 showed the most balanced profile in terms of bioavailability, permeability, and predicted safety. Overall, the findings suggest that the evaluated compounds exhibit relevant in silico potential for interaction with cancer-related targets, with ligand 2 appearing promising from a molecular recognition perspective and ligand 4 from a pharmacokinetic standpoint. These results reinforce the importance of integrated approaches in the prioritization of bioactive candidates and highlight the need for further experimental validation.

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Author Biographies

Vitória Ramos de Moura Santos, Federal Institute of Tocantins

Holds a Bachelor’s Degree in Biological Sciences Teaching from the Araguatins Campus of the Federal Institute of Tocantins. Scholarship holder of the Scientific Initiation Program at the Araguatins Campus of the Federal Institute of Tocantins. Araguatins, Tocantins, Brazil. E-mail address: vimou2101@gmail.com. Orcid: https://orcid.org/0009-0009-9295-9465. Lattes Curriculum: http://lattes.cnpq.br/0438811399069443

Tiago dos Reis Almeida Almeida, Federal Institute of Tocantins

Master in Physical Chemistry from the Institute of Chemistry of São Carlos at the University of São Paulo. Professor of basic, technical, and technological education, working in the Articulated Teaching Center in the field of Chemistry at the Araguatins Campus of the Federal Institute of Tocantins. Araguatins, Tocantins, Brazil. E-mail address: tiago.almeida@ifto.edu.br. Orcid: https://orcid.org/0000-0001-6927-4016. Lattes Curriculum: http://lattes.cnpq.br/5004685012482665

Luana Priscilla Rodrigues Macedo, Federal Institute of Tocantins

Master in Chemistry from the Federal University of Tocantins. Professor of basic, technical, and technological education, working in the Articulated Teaching Center in the field of Chemistry at the Araguatins Campus of the Federal Institute of Tocantins. Araguatins, Tocantins, Brazil. E-mail address: luana.macedo@ifto.edu.br. Orcid: https://orcid.org/0009-0009-6383-5842. Lattes Curriculum: http://lattes.cnpq.br/6475213690096051.

Ana Lívia Ferreira dos Santos, Federal Institute of Tocantins

Holds a Bachelor’s Degree in Biological Sciences Teaching from the Araguatins Campus of the Federal Institute of Tocantins. Scholarship holder of the Scientific Initiation Program at the Araguatins Campus of the Federal Institute of Tocantins. Araguatins, Tocantins, Brazil. E-mail address: ferreiralivia803@gmail.com. Orcid: https://orcid.org/0009-0007-7519-4638. Lattes Curriculum: http://lattes.cnpq.br/0892630091846602

References

AGU, P. C.; AFIUKWA, C. A.; ORJI, O. U.; EZEH, E. M.; OFOKE, I. H.; OGBU, C. O.; UGWUJA, E. I.; AJA, P. M. Molecular docking as a tool for the discovery of molecular targets of nutraceuticals in diseases management. Scientific Reports, [s. l.], v. 13, art. 13398, 2023. DOI: https://doi.org/10.1038/s41598-023-40160-2.

AKTAR, M. A. et al. Pharmacological and phytochemical review of Acmella oleracea: a comprehensive analysis of its therapeutic potential. Discover Applied Sciences, v. 6, n. 1, p. 412, 2024. DOI: https://doi.org/10.1007/s42452-024-06108-5.

APLIN, C. et al. Evolving experimental techniques for structure-based drug design. Journal of Physical Chemistry B, Washington, v. 126, n. 35, p. 6599-6607, 2022. DOI: https://doi.org/10.1021/acs.jpcb.2c04344.

AZAD, I. et al. Updates on drug designing approach through computational strategies: a review. Future Science OA, Londres, v. 9, n. 5, 2023. DOI: https://doi.org/10.2144/fsoa-2022-0085.

BELLUMORI, M. et al. Acmella oleracea (L.) R.K. Jansen: alkylamides and phenolic compounds in aerial parts and roots of in vitro seedlings. Journal of Pharmaceutical and Biomedical Analysis, [s. l.], v. 220, art. 114991, 2022. DOI: https://doi.org/10.1016/j.jpba.2022.114991.

BRAY, F. et al. Global cancer statistics 2022: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185 countries. CA: A Cancer Journal for Clinicians, Hoboken, v. 74, n. 3, p. 229-263, 2024. DOI: https://doi.org/10.3322/caac.21834.

BUCKLEY, M. E.; NDUKWE, A. R. N.; NAIR, P. C.; RANA, S.; FAIRFULL-SMITH, K. E.; GANDHI, N. S. Comparative assessment of docking programs for docking and virtual screening of ribosomal oxazolidinone antibacterial agents. Antibiotics, v. 12, art. 463, 2023. DOI: https://doi.org/10.3390/antibiotics12030463.

CHEN, H. et al. Structure-based design of anticancer drugs based on β-elemene: research foundations and development potential. Journal of Pharmaceutical Analysis, Amsterdã, 2025. DOI: https://doi.org/10.1016/j.jpha.2025.101325.

CREANZA, T. M. et al. Structure-based prediction of hERG-related cardiotoxicity. Journal of Chemical Information and Modeling, [s. l.], v. 62, n. 18, p. 4390-4403, 2022. DOI: https://doi.org/10.1021/acs.jcim.1c00744.

DAINA, A.; MICHIELIN, O.; ZOETE, V. SwissADME: a free web tool to evaluate pharmacokinetics, drug-likeness and medicinal chemistry friendliness of small molecules. Scientific Reports, [s. l.], v. 7, n. 1, p. 42717, 2017. DOI: https://doi.org/10.1038/srep42717.

FROMM, M. F. P-glycoprotein: a defense mechanism limiting oral bioavailability and CNS accumulation of drugs. International Journal of Clinical Pharmacology and Therapeutics, [s. l.], v. 38, n. 2, p. 69-74, 2000. DOI: https://doi.org/10.5414/cpp38069.

GIMENO, A. et al. Minimizing the entropy penalty for ligand binding: lessons from the molecular recognition of the histo blood-group antigens by human Galectin-3. Angewandte Chemie International Edition, Weinheim, v. 58, n. 22, p. 7268-7272, 2019. DOI: https://doi.org/10.1002/anie.201900723.

GU, Y. et al. admetSAR3.0: a comprehensive platform for exploration, prediction and optimization of chemical ADMET properties. Nucleic Acids Research, [s. l.], v. 52, n. W1, p. W432-W438, 2024. DOI: https://doi.org/10.1093/nar/gkae298.

GUARNÉ, A.; JUNOP, M. S.; YANG, W. Structure and function of the N-terminal 40 kDa fragment of human PMS2: a monomeric GHL ATPase. The EMBO Journal, Oxford, v. 20, n. 19, p. 5521-5531, 2001. DOI: https://doi.org/10.1093/emboj/20.19.5521.

HOSACK, T. et al. Drug-induced liver injury: a comprehensive review. Pharmaceuticals, [s. l.], v. 16, n. 5, p. 689, 2023. DOI: https://doi.org/10.1177/17562848231163410.

JERÔNIMO, L. B. et al. Acmella oleracea (L.) R.K. Jansen essential oils: chemical composition, antioxidant, and cytotoxic activities. Biochemical Systematics and Ecology, [s. l.], v. 112, art. 104775, 2024. DOI: 10.1016/j.bse.2023.104775.

JIN, K.; QIAN, C.; LIN, J.; LIU, B. Cyclooxygenase-2–Prostaglandin E2 pathway: a key player in tumor-associated immune cells. Frontiers in Oncology, Lausanne, v. 13, p. 1099811, 2023. DOI: https://doi.org/10.3389/fonc.2023.1099811.

LEE, B.-W. Botany, ethnopharmacology, phytochemistry, and biological activities of Acmella oleracea: a comprehensive review. Molecules, [s. l.], v. 31, n. 4, art. 677, 2026. DOI: 10.3390/molecules31040677.

LI, H. et al. Targeting PI3K family with small-molecule inhibitors in cancer therapy: current clinical status and future directions. Molecular Cancer, Londres, v. 23, n. 1, 2024. DOI: https://doi.org/10.1186/s12943-024-02072-1.

LIPINSKI, C. A. et al. Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. Advanced Drug Delivery Reviews, [s. l.], v. 46, n. 1-3, p. 3-26, 2001. DOI: https://doi.org/10.1016/S0169-409X(00)00129-0.

MA, Z.; AJIBADE, A.; ZOU, X. Docking strategies for predicting protein-ligand interactions and their application to structure-based drug design. Communications in Information and Systems, v. 24, n. 3, p. 199-230, 2024. DOI: https://doi.org/10.4310/cis.241021221101.

MARTIS, E. A. F.; TÉLETCHÉA, S. Ten quick tips to perform meaningful and reproducible molecular docking calculations. PLoS Computational Biology, v. 21, n. 5, p. e1013030, 2025. DOI: https://doi.org/10.1371/journal.pcbi.1013030.

MILLER, E. B. et al. Enabling structure-based drug discovery utilizing predicted models. Cell, Cambridge, v. 187, n. 3, p. 521-525, 2024. DOI: https://doi.org/10.1016/j.cell.2023.12.034.

MIRANDA-FILHO, A. et al. The GLOBOCAN 2022 cancer estimates: data sources, methods, and a snapshot of the cancer burden worldwide. International Journal of Cancer, Hoboken, v. 156, n. 7, 2024. DOI: https://doi.org/10.1002/ijc.35278.

NASCIMENTO, L. E. S. et al. Phytochemical profile of different anatomical parts of jambu (Acmella oleracea (L.) R.K. Jansen): a comparison between hydroponic and conventional cultivation using PCA and cluster analysis. Food Chemistry, [s. l.], v. 327, 2020. DOI: https://doi.org/10.1016/j.foodchem.2020.127393.

ONUFRIEV, A. V.; ALEXOV, E. Protonation and pK changes in protein-ligand binding. Quarterly Reviews of Biophysics, [s. l.], v. 46, n. 2, p. 181-209, 2013. DOI: 10.1017/S0033583513000024.

PATIL, P. A.; KUMBHAR, B. V. Structure based drug design and machine learning approaches for identifying natural inhibitors against the human αβIII tubulin isotype. Scientific Reports, Londres, v. 15, n. 1, 2025. DOI: https://doi.org/10.1038/s41598-025-17708-5.

PINHEIRO, M. S. da S.; MOYSÉS, D. A.; GALUCIO, N. C. R.; SANTOS, W. O.; PINA, J. R. S.; OLIVEIRA, L. C.; SILVA, S. Y. S.; SILVA, S. da C.; FRAZÃO, N. F.; MARINHO, P. S. B.; NOVAIS, A. L. F.; KHAYAT, A. S.; MARINHO, A. M. do R. Cytotoxic and molecular evaluation of spilanthol obtained from Acmella oleracea (L.) R.K. Jansen (jambu) in human gastric cancer cells. Natural Product Research, [s. l.], v. 38, n. 10, p. 1806-1811, 2024. DOI: 10.1080/14786419.2023.2222220.

RAMÍREZ, D.; CABALLERO, J. Is it reliable to take the molecular docking top scoring position as the best solution without considering available structural data? Molecules, Basel, v. 23, n. 5, p. 1038, 2018. DOI: https://doi.org/10.3390/molecules23051038.

SHAMSIAN, S.; SOKOUTI, B.; DASTMALCHI, S. Benchmarking different docking protocols for predicting the binding poses of ligands complexed with cyclooxygenase enzymes. BioImpacts, Tabriz, v. 14, p. 29955, 2023. DOI: https://doi.org/10.34172/bi.2023.29955.

SILVA, R. C. da; SALLET, L. A. P.; SOUSA, K. P. de. Efeitos da amora (Morus spp.) no controle dos sintomas da menopausa: uma revisão integrativa. Revista Sítio Novo, Palmas, v. 9, p. e1687, 2025. DOI: https://doi.org/10.47236/2594-7036.2025.v9.1687.

SILVEIRA, G. E.; BARROSO, M. A. de S. Upcycling de subprodutos da agroindústria da Amazônia e do Cerrado: microrrevisão de tecnologias e impactos socioeconômicos. Revista Sítio Novo, Palmas, v. 10, p. e1896, 2026. DOI: https://doi.org/10.47236/2594-7036.2026.v10.1896.

SUNG, H. et al. Global cancer statistics 2020: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185 countries. CA: A Cancer Journal for Clinicians, Hoboken, v. 71, n. 3, p. 209-249, 2021. DOI: https://doi.org/10.3322/caac.21660.

TROTT, O.; OLSON, A. J. AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. Journal of Computational Chemistry, [s. l.], v. 31, n. 2, p. 455-461, 2010. DOI: https://doi.org/10.1002/jcc.21334.

TRUONG, N. T. H. et al. Effects of chemotherapy agents on circulating leukocyte populations: potential implications for the success of CAR-T cell therapies. Cancers, Basel, v. 13, n. 9, p. 2225, 2021. DOI: https://doi.org/10.3390/cancers13092225.

VEBER, D. F. et al. Molecular properties that influence the oral bioavailability of drug candidates. Journal of Medicinal Chemistry, [s. l.], v. 45, n. 12, p. 2615-2623, 2002. DOI: https://doi.org/10.1021/jm020017n.

VIJAY, U.; RAMESH, M.; DURGADEVI, R. Microbial mutagenicity assay: Ames test. Bio-protocol, [s. l.], v. 8, n. 17, e2997, 2018. DOI: 10.21769/BioProtoc.2763.

VITTORIO, S. et al. Addressing docking pose selection with structure-based deep learning: recent advances, challenges and opportunities. Computational and Structural Biotechnology Journal, v. 23, p. 2141-2151, 2024. DOI: https://doi.org/10.1016/j.csbj.2024.05.024.

WALLERSTEIN, J. et al. Entropy-entropy compensation between the protein, ligand, and solvent degrees of freedom fine-tunes affinity in ligand binding to Galectin-3C. JACS Au, Washington, v. 1, n. 4, p. 484-500, 2021. DOI: https://doi.org/10.1021/jacsau.0c00094.

WINKLER, D. A. Ligand entropy is hard but should not be ignored. Journal of Chemical Information and Modeling, Washington, v. 60, n. 10, p. 4421-4423, 2020. DOI: https://doi.org/10.1021/acs.jcim.0c01146.

YANG, C.; CHEN, E. A.; ZHANG, Y. Protein-ligand docking in the machine-learning era. Molecules, Basel, v. 27, n. 14, p. 4568, 2022. DOI: https://doi.org/10.3390/molecules27144568.

ZEIGER, E. The Ames test and the regulation of chemicals. Mutation Research/Genetic Toxicology and Environmental Mutagenesis, [s. l.], v. 841, p. 43-48, 2019. DOI: 10.1016/j.mrgentox.2019.05.007.

Published

2026-05-26

How to Cite

SANTOS, Vitória Ramos de Moura; ALMEIDA, Tiago dos Reis Almeida; MACEDO, Luana Priscilla Rodrigues; SANTOS, Ana Lívia Ferreira dos. Computational analysis of protein–ligand interactions involving compounds from Acmella oleracea (L.) R.K. Jansen with antitumor relevance. Sítio Novo Magazine, Palmas, v. 10, p. e2016, 2026. DOI: 10.47236/2594-7036.2026.v10.2016. Disponível em: https://sitionovo.ifto.edu.br/index.php/sitionovo/article/view/2016. Acesso em: 28 may. 2026.

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Artigo Científico