Propolis bioactive compounds as potential topical agents for atopic dermatitis: an in silico pharmacokinetic screening and molecular docking study
Abstract
Background: Atopic dermatitis (AD) is a common chronic inflammatory skin disease. Current treatments, including corticosteroids and calcineurin inhibitors, are effective but limited by long-term adverse effects. Propolis possesses antimicrobial, anti-inflammatory, antioxidant, and immunomodulatory properties. This study evaluated propolis bioactive compounds as topical therapeutic candidates for AD using molecular docking analysis.
Methods: Bioactive compounds from propolis were screened for pharmacokinetic and ADMET properties relevant to topical application. Molecular docking was performed against key protein targets implicated in AD pathogenesis to evaluate binding affinities and interaction profiles versus reference ligands.
Results: A total of 31 compounds fulfilled the pharmacokinetic and toxicity criteria for topical use. Tschimgin showed the strongest affinity toward secretory phospholipase A₂ (ΔG = −8.00 kcal/mol; Ki = 1.37 µM) and favorable binding to FK506-binding protein 12 (ΔG = −7.88 kcal/mol; Ki = 1.68 µM), suggesting multitarget potential. Suberosin showed the highest affinity toward PDE4 (ΔG = −6.86 kcal/mol; Ki = 9.35 µM), exceeding the reference drug roflumilast (ΔG = −6.47 kcal/mol; Ki = 18.06 µM).
Conclusion: These findings suggest propolis contains bioactive compounds relevant to multiple AD-associated targets. Tschimgin and suberosin may serve as lead compounds for developing safer topical therapies, pending further in vitro and in vivo validation.
References
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22. Rammali S, Idir A, Aherkou M, Ciobică A, Kamal FZ, Aalaoui M El, et al. In vitro and computational investigation of antioxidant and anticancer properties of Streptomyces coeruleofuscus SCJ extract on MDA-MB-468 triple-negative breast cancer cells. Sci Rep. 2024;14. https://doi.org/10.1038/s41598-024-76200-8
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27. Jeziorkowska R, Sysa-Jedrzejowska A, Samochocki PZ. Topical steroid therapy in atopic dermatitis in theory and practice. Postepy Dermatol Alergol. 2015;32: 162-166. https://doi.org/10.5114/pdia.2014.40962
28. Gutierres PG, Pereira DR, Vieira NL, Arantes LF, Silva NJ, Torres-Bonilla KA, et al. Action of Varespladib (LY-315920), a Phospholipase A2 Inhibitor, on the Enzymatic, Coagulant and Haemorrhagic Activities of Lachesis muta rhombeata (South-American Bushmaster) Venom. Front Pharmacol. 2022;12. https://doi.org/10.3389/fphar.2021.812295
29. Yasuda H, Fukusumi Y, Ivanov V, Zhang Y, Kawachi H. Tacrolimus ameliorates podocyte injury by restoring FK506 binding protein 12 (FKBP12) at actin cytoskeleton. FASEB Journal. 2021;35. https://doi.org/10.1096/fj.202101052R
30. Simpson EL, Eichenfield LF, Alonso-Llamazares J, Draelos ZD, Ferris LK, Forman SB, et al. Roflumilast Cream, 0.15%, for Atopic Dermatitis in Adults and Children: INTEGUMENT-1 and INTEGUMENT-2 Randomized Clinical Trials. JAMA Dermatol. 2024;160. https://doi.org/10.1001/jamadermatol.2024.3121
31. BIOVIA DS. Discovery Studio Visualizer. San Diego: Dassault Systèmes; 2021.
32. Andrýsková N, Motyčka J, Babincová M, Babinec P, Šimaljaková M. Computational Design of a Novel Dithranol-Salicylic Acid Antipsoriatic Prodrug for Esterase-Activated Topical Drug Delivery. Applied Sciences. 2024;14. https://doi.org/10.3390/app14031094
33. Lim JY, Gew LT, Tang YQ. Biocomputational-mediated screening and molecular docking platforms for discovery of coumarin-derived antimelanogenesis agents. Dermatologica Sinica. 2023;41: 8-17. https://doi.org/10.4103/ds.DS-D-22-00087
34. Herbig ME, Evers DH, Gorissen S, Köllmer M. Rational Design of Topical Semi-Solid Dosage Forms-How Far Are We? Pharmaceutics. 2023;15. https://doi.org/10.3390/pharmaceutics15071822
35. Auli WN, Husniati H, Suprahman NY, Fauziyya R, Sarmoko S, Ashari A, et al. Study of Gnetum gnemon metabolites as potential anti-breast and prostate cancer by metabolomic and molecular docking. J Appl Pharm Sci. 2024;14: 120-130. https://doi.org/10.7324/JAPS.2024.170723
36. Khachatryan H, Matevosyan M, Harutyunyan V, Gevorgyan S, Shavina A, Tirosyan I, et al. Computational evaluation and benchmark study of 342 crystallographic holo-structures of SARS-CoV-2 Mpro enzyme. Sci Rep. 2024;14: 1-14. https://doi.org/10.1038/s41598-024-65228-5
37. Shah M, Patel M, Shah M, Patel M, Prajapati M. Computational transformation in drug discovery: A comprehensive study on molecular docking and quantitative structure activity relationship (QSAR). Intelligent Pharmacy. KeAi Publishing Communications Ltd.; 2024. pp. 589-595. https://doi.org/10.1016/j.ipha.2024.03.001
38. Chibuye B, Singh I Sen, Chimuka L, Maseka KK. In silico and ADMET molecular analysis targeted to discover novel anti-inflammatory drug candidates as COX-2 inhibitors from specific metabolites of Diospyros batokana (Ebenaceae). Biochem Biophys Rep. 2024;39. https://doi.org/10.1016/j.bbrep.2024.101758
39. Yamamoto K, Miki Y, Sato M, Taketomi Y, Nishito Y, Taya C, et al. The role of group IIF-secreted phospholipase A2 in epidermal homeostasis and hyperplasia. Journal of Experimental Medicine. 2015;212: 1901-1919. https://doi.org/10.1084/jem.20141904
40. Murakami M, Yamamoto K, Taketomi Y. Phospholipase A2 in skin biology: new insights from gene-manipulated mice and lipidomics. Inflamm Regen. 2018;38: 31. https://doi.org/10.1186/s41232-018-0089-2
41. Park YJ, Yoo SA, Kim M, Kim WU. The Role of Calcium-Calcineurin-NFAT Signaling Pathway in Health and Autoimmune Diseases. Front Immunol. 2020;11: 1-14. https://doi.org/10.3389/fimmu.2020.00195
42. Jo KA, Park S-Y, Choi K, Lee D-H, Kim JY. Comparing the Effects of Korean and Brazilian Propolis on Anti‐Atopic Dermatitis and the Related Mechanisms Through In Silico and In Vitro Analyses. J Food Biochem. 2024;2024. https://doi.org/10.1155/2024/1845999
43. Cheng L, Wang J, Wang Y, Li J, Yang W. Network Pharmacology and Experimental Validation Reveal Therapeutic Potential of Propolis in UV-Induced Allergic Dermatitis. Foods. 2025;14: 996. https://doi.org/10.3390/foods14060996
44. Han J-T, Zhu Y, Pan D-B, Xue H-X, Wang S, Peng Y, et al. Discovery of pentapeptide-inhibitor hits targeting FKBP51 by combining computational modeling and X-ray crystallography. Comput Struct Biotechnol J. 2021;19: 4079-4091. https://doi.org/10.1016/j.csbj.2021.07.015
45. Beken B, Serttas R, Yazicioglu M, Turkekul K, Erdogan S. Quercetin Improves Inflammation, Oxidative Stress, and Impaired Wound Healing in Atopic Dermatitis Model of Human Keratinocytes. Pediatr Allergy Immunol Pulmonol. 2020;33: 69-79. https://doi.org/10.1089/ped.2019.1137
46. Ahn SS, Lee YH, Yeo H, Lee Y, Min DS, Lim Y, et al. Effect of 6,7-dimethoxy-2,2-dimethyl-2H-chromene (agerarin) on the recovery of filaggrin expression through targeting of Janus kinases in the inflammatory skin. J Food Drug Anal. 2020;28. https://doi.org/10.38212/2224-6614.1178
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48. Zheng R, Ren Y, Liu X, He C, Liu H, Wang Y, et al. Exogenous drug-induced mouse models of atopic dermatitis. Cytokine Growth Factor Rev. 2024;77: 104-116. https://doi.org/10.1016/j.cytogfr.2024.01.003
2. Pinto LM, Chiricozzi A, Calabrese L, Mannino M, Peris K. Novel Therapeutic Strategies in the Topical Treatment of Atopic Dermatitis. Pharmaceutics. 2022;14. https://doi.org/10.3390/pharmaceutics14122767
3. Khan SA, Wu Y, Li ASM, Fu XQ, Yu ZL. Network pharmacology and molecular docking-based prediction of active compounds and mechanisms of action of Cnidii Fructus in treating atopic dermatitis. BMC Complement Med Ther. 2022;22. https://doi.org/10.1186/s12906-022-03734-7
4. Courtney A, Su JC. The Psychology of Atopic Dermatitis. Journal of Clinical Medicine. Multidisciplinary Digital Publishing Institute (MDPI); 2024. https://doi.org/10.3390/jcm13061602
5. Yang H, Wang J, Zhang X, Zhang Y, Qin ZL, Wang H, et al. Application of Topical Phosphodiesterase 4 Inhibitors in Mild to Moderate Atopic Dermatitis: A Systematic Review and Meta-analysis. JAMA Dermatol. 2019;155: 585-593. https://doi.org/10.1001/jamadermatol.2019.0008
6. Meledathu S, Naidu MP, Brunner PM. Update on atopic dermatitis. Journal of Allergy and Clinical Immunology. Elsevier Inc.; 2025. pp. 1124-1132. https://doi.org/10.1016/j.jaci.2025.01.013
7. Martin BA, Lemos CN, Dalmolin LF, Arruda C, Brait ÍSC, de Souza Cazarim M, et al. A new approach to atopic dermatitis control with low-concentration propolis-loaded cold cream. Pharmaceutics. 2021;13. https://doi.org/10.3390/pharmaceutics13091346
8. Shin N, Jung N, Lee SE, Kong D, Kim NG, Kook MG, et al. Pimecrolimus interferes the therapeutic efficacy of human mesenchymal stem cells in atopic dermatitis by regulating NFAT-COX2 signaling. Stem Cell Res Ther. 2021;12: 1-16. https://doi.org/10.1186/s13287-021-02547-8
9. Tang L, Gao J, Li X, Cao X, Zhou B. Molecular Mechanisms of Luteolin Against Atopic Dermatitis Based on Network Pharmacology and in vivo Experimental Validation. Drug Des Devel Ther. 2022;16: 4205-4221. https://doi.org/10.2147/DDDT.S387893
10. Frazier W, Bhardwaj N. Atopic Dermatitis: Diagnosis and Treatment. Am Fam Physician. 2020;101: 590-598.
11. Pasupuleti VR, Sammugam L, Ramesh N, Gan SH. Honey, Propolis, and Royal Jelly: A Comprehensive Review of Their Biological Actions and Health Benefits. Oxid Med Cell Longev. 2017;2017. https://doi.org/10.1155/2017/1259510
12. Salatino A, Salatino MLF, Negri G. How diverse is the chemistry and plant origin of Brazilian propolis? Apidologie. 2021;52: 1075-1097. https://doi.org/10.1007/s13592-021-00889-z
13. Yanti EN, Kustiawan PM. Study of Indonesian Stingless Bee Propolis Potential as Antioxidant: A Review. Jurnal Farmasi Sains dan Praktis. 2023; 261-269. https://doi.org/10.31603/pharmacy.v9i3.7105
14. Kustiawan PM, Luthfi CFMM, Dewi SR, Pratiwi J, Aisyiyah NM, Nugraha ASD, et al. Phytochemical Analysis and Anti-Inflammatory Activity of The Combination of Trigona apicalis propolis Extract and Honey. Borneo Journal of Pharmacy. 2023;6: 125-132. https://doi.org/10.33084/bjop.v6i2.4696
15. Zulhendri F, Lesmana R, Tandean S, Christoper A, Chandrasekaran K, Irsyam I, et al. Recent Update on the Anti-Inflammatory Activities of Propolis. Molecules. 2022;27. https://doi.org/10.3390/molecules27238473
16. Liew KY, Kamise NI, Ong HM, Aw Yong PY, Islam F, Tan JW, et al. Anti-Allergic Properties of Propolis: Evidence From Preclinical and Clinical Studies. Front Pharmacol. 2022;12. https://doi.org/10.3389/fphar.2021.785371
17. Roney M, Mohd Aluwi MFF. The importance of in-silico studies in drug discovery. Intelligent Pharmacy. 2024;2: 578-579. https://doi.org/10.1016/j.ipha.2024.01.010
18. Kim S, Chen J, Cheng T, Gindulyte A, He J, He S, et al. PubChem 2025 update. Nucleic Acids Res. 2025;53: D1516-D1525. https://doi.org/10.1093/nar/gkae1059
19. Pires DEV, Blundell TL, Ascher DB. pkCSM: Predicting small-molecule pharmacokinetic and toxicity properties using graph-based signatures. J Med Chem. 2015;58: 4066-4072. https://doi.org/10.1021/acs.jmedchem.5b00104
20. de Souza MM, Gini ALR, Moura JA, Scarim CB, Chin CM, dos Santos JL. Prodrug Approach as a Strategy to Enhance Drug Permeability. Pharmaceuticals. Multidisciplinary Digital Publishing Institute (MDPI); 2025. https://doi.org/10.3390/ph18030297
21. Abbas M, Alanzi AR, Sahibzada KI, Nawaz M, Fatima G, Wei DQ. Identification of novel inhibitors targeting Mycobacterium abscessus InhA through virtual screening, docking, and molecular dynamic simulations. Sci Rep. 2025;15. https://doi.org/10.1038/s41598-025-97513-2
22. Rammali S, Idir A, Aherkou M, Ciobică A, Kamal FZ, Aalaoui M El, et al. In vitro and computational investigation of antioxidant and anticancer properties of Streptomyces coeruleofuscus SCJ extract on MDA-MB-468 triple-negative breast cancer cells. Sci Rep. 2024;14. https://doi.org/10.1038/s41598-024-76200-8
23. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, et al. The Protein Data Bank. Nucleic Acids Res. 2000;28. https://doi.org/10.1093/nar/28.1.235
24. Hasyim DM, Musfiroh I, Hendra R, Fakih TM, Ikram NKK, Muchtaridi M. In Silico Approaches for the Discovery of Novel Pyrazoline Benzenesulfonamide Derivatives as Anti-Breast Cancer Agents Against Estrogen Receptor Alpha (ERα). Applied Sciences. 2025;15: 8444. https://doi.org/10.3390/app15158444
25. Morris GM, Ruth H, Lindstrom W, Sanner MF, Belew RK, Goodsell DS, et al. Software news and updates AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility. J Comput Chem. 2009;30: 2785-2791. https://doi.org/10.1002/jcc.21256
26. Saputro AH, Amelia T, Mahardhika AB, Widyawaruyanti A, Wahyuni TS, Permanasari AA, et al. Alpha-mangostin, piperine and beta-sitosterol as hepatitis C antivirus (HCV): In silico and in vitro studies. Heliyon. 2023;9. https://doi.org/10.1016/j.heliyon.2023.e20141
27. Jeziorkowska R, Sysa-Jedrzejowska A, Samochocki PZ. Topical steroid therapy in atopic dermatitis in theory and practice. Postepy Dermatol Alergol. 2015;32: 162-166. https://doi.org/10.5114/pdia.2014.40962
28. Gutierres PG, Pereira DR, Vieira NL, Arantes LF, Silva NJ, Torres-Bonilla KA, et al. Action of Varespladib (LY-315920), a Phospholipase A2 Inhibitor, on the Enzymatic, Coagulant and Haemorrhagic Activities of Lachesis muta rhombeata (South-American Bushmaster) Venom. Front Pharmacol. 2022;12. https://doi.org/10.3389/fphar.2021.812295
29. Yasuda H, Fukusumi Y, Ivanov V, Zhang Y, Kawachi H. Tacrolimus ameliorates podocyte injury by restoring FK506 binding protein 12 (FKBP12) at actin cytoskeleton. FASEB Journal. 2021;35. https://doi.org/10.1096/fj.202101052R
30. Simpson EL, Eichenfield LF, Alonso-Llamazares J, Draelos ZD, Ferris LK, Forman SB, et al. Roflumilast Cream, 0.15%, for Atopic Dermatitis in Adults and Children: INTEGUMENT-1 and INTEGUMENT-2 Randomized Clinical Trials. JAMA Dermatol. 2024;160. https://doi.org/10.1001/jamadermatol.2024.3121
31. BIOVIA DS. Discovery Studio Visualizer. San Diego: Dassault Systèmes; 2021.
32. Andrýsková N, Motyčka J, Babincová M, Babinec P, Šimaljaková M. Computational Design of a Novel Dithranol-Salicylic Acid Antipsoriatic Prodrug for Esterase-Activated Topical Drug Delivery. Applied Sciences. 2024;14. https://doi.org/10.3390/app14031094
33. Lim JY, Gew LT, Tang YQ. Biocomputational-mediated screening and molecular docking platforms for discovery of coumarin-derived antimelanogenesis agents. Dermatologica Sinica. 2023;41: 8-17. https://doi.org/10.4103/ds.DS-D-22-00087
34. Herbig ME, Evers DH, Gorissen S, Köllmer M. Rational Design of Topical Semi-Solid Dosage Forms-How Far Are We? Pharmaceutics. 2023;15. https://doi.org/10.3390/pharmaceutics15071822
35. Auli WN, Husniati H, Suprahman NY, Fauziyya R, Sarmoko S, Ashari A, et al. Study of Gnetum gnemon metabolites as potential anti-breast and prostate cancer by metabolomic and molecular docking. J Appl Pharm Sci. 2024;14: 120-130. https://doi.org/10.7324/JAPS.2024.170723
36. Khachatryan H, Matevosyan M, Harutyunyan V, Gevorgyan S, Shavina A, Tirosyan I, et al. Computational evaluation and benchmark study of 342 crystallographic holo-structures of SARS-CoV-2 Mpro enzyme. Sci Rep. 2024;14: 1-14. https://doi.org/10.1038/s41598-024-65228-5
37. Shah M, Patel M, Shah M, Patel M, Prajapati M. Computational transformation in drug discovery: A comprehensive study on molecular docking and quantitative structure activity relationship (QSAR). Intelligent Pharmacy. KeAi Publishing Communications Ltd.; 2024. pp. 589-595. https://doi.org/10.1016/j.ipha.2024.03.001
38. Chibuye B, Singh I Sen, Chimuka L, Maseka KK. In silico and ADMET molecular analysis targeted to discover novel anti-inflammatory drug candidates as COX-2 inhibitors from specific metabolites of Diospyros batokana (Ebenaceae). Biochem Biophys Rep. 2024;39. https://doi.org/10.1016/j.bbrep.2024.101758
39. Yamamoto K, Miki Y, Sato M, Taketomi Y, Nishito Y, Taya C, et al. The role of group IIF-secreted phospholipase A2 in epidermal homeostasis and hyperplasia. Journal of Experimental Medicine. 2015;212: 1901-1919. https://doi.org/10.1084/jem.20141904
40. Murakami M, Yamamoto K, Taketomi Y. Phospholipase A2 in skin biology: new insights from gene-manipulated mice and lipidomics. Inflamm Regen. 2018;38: 31. https://doi.org/10.1186/s41232-018-0089-2
41. Park YJ, Yoo SA, Kim M, Kim WU. The Role of Calcium-Calcineurin-NFAT Signaling Pathway in Health and Autoimmune Diseases. Front Immunol. 2020;11: 1-14. https://doi.org/10.3389/fimmu.2020.00195
42. Jo KA, Park S-Y, Choi K, Lee D-H, Kim JY. Comparing the Effects of Korean and Brazilian Propolis on Anti‐Atopic Dermatitis and the Related Mechanisms Through In Silico and In Vitro Analyses. J Food Biochem. 2024;2024. https://doi.org/10.1155/2024/1845999
43. Cheng L, Wang J, Wang Y, Li J, Yang W. Network Pharmacology and Experimental Validation Reveal Therapeutic Potential of Propolis in UV-Induced Allergic Dermatitis. Foods. 2025;14: 996. https://doi.org/10.3390/foods14060996
44. Han J-T, Zhu Y, Pan D-B, Xue H-X, Wang S, Peng Y, et al. Discovery of pentapeptide-inhibitor hits targeting FKBP51 by combining computational modeling and X-ray crystallography. Comput Struct Biotechnol J. 2021;19: 4079-4091. https://doi.org/10.1016/j.csbj.2021.07.015
45. Beken B, Serttas R, Yazicioglu M, Turkekul K, Erdogan S. Quercetin Improves Inflammation, Oxidative Stress, and Impaired Wound Healing in Atopic Dermatitis Model of Human Keratinocytes. Pediatr Allergy Immunol Pulmonol. 2020;33: 69-79. https://doi.org/10.1089/ped.2019.1137
46. Ahn SS, Lee YH, Yeo H, Lee Y, Min DS, Lim Y, et al. Effect of 6,7-dimethoxy-2,2-dimethyl-2H-chromene (agerarin) on the recovery of filaggrin expression through targeting of Janus kinases in the inflammatory skin. J Food Drug Anal. 2020;28. https://doi.org/10.38212/2224-6614.1178
47. Mohd Kasim VNK, Noble SM, Liew KY, Tan JW, Israf DA, Tham CL. Management of Atopic Dermatitis Via Oral and Topical Administration of Herbs in Murine Model: A Systematic Review. Front Pharmacol. 2022;13. https://doi.org/10.3389/fphar.2022.785782
48. Zheng R, Ren Y, Liu X, He C, Liu H, Wang Y, et al. Exogenous drug-induced mouse models of atopic dermatitis. Cytokine Growth Factor Rev. 2024;77: 104-116. https://doi.org/10.1016/j.cytogfr.2024.01.003
Published
2026-06-09
How to Cite
NURNAHARI, Naura et al.
Propolis bioactive compounds as potential topical agents for atopic dermatitis: an in silico pharmacokinetic screening and molecular docking study.
Acta Pharmaciae Indonesia : Acta Pharm Indo, [S.l.], v. 13, n. 2, p. 17894, june 2026.
ISSN 2621-4520.
Available at: <https://jos.unsoed.ac.id/index.php/api/article/view/17894>. Date accessed: 20 aug. 2026.
doi: https://doi.org/10.20884/1.api.2025.13.2.17894.
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This work is licensed under a Creative Commons Attribution 4.0 International License.
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