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Epigenomics Nutritional Insights of Crocus sativus L.: Computational Analysis of Bioactive Molecules Targeting DNA Methyltransferases and Histone Deacetylases
1
Institute for Neuroscience and Medicine (INM-9), Forschungszentrum Jülich, Wilhelm-Johnen-Straße, 52428 Jülich, Germany
2
Department of Neurology, University Hospital Aachen, RWTH Aachen, Pauwelsstraße 30, 52074 Aachen, Germany
3
Department for Sustainability, Italian National Agency for New Technologies, Energy and Sustainable Economic Development (ENEA) Casaccia Research Center, Via Anguillarese 301, 00123 Rome, Italy
*
Authors to whom correspondence should be addressed.
†
The authors contributed equally to this work.
Int. J. Mol. Sci. 2025, 26(15), 7575; https://doi.org/10.3390/ijms26157575 (registering DOI)
Submission received: 18 June 2025
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Revised: 24 July 2025
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Accepted: 2 August 2025
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Published: 5 August 2025
Abstract
Saffron (Crocus sativus L.) contains bioactive compounds with potential health benefits, including modulation of protein function and gene expression. However, their ability to tune the epigenetic machine remains poorly understood. This study employs molecular docking (AutoDock Vina 1.4), dynamics simulations, and MM/PBSA calculations to investigate the interactions between four saffron-derived molecules—crocetin, beta-D-glucosyl trans-crocetin, picrocrocin and safranal—and four epigenetic enzymes—DNMT1, DNMT3a, HDAC2, and SIRT1. Our in silico screening identifies beta-D-glucosyl trans-crocetin, one of the saffron’s crocins, as a potential DNMT1 inhibitor. Along with crocetin, it also shows the ability to inhibit HDAC2 and activate SIRT1. Picrocrocin displays a resveratrol-like ability to activate SIRT1. None of the saffron-derived compounds effectively bind or inhibit DNMT3a. Among the tested molecules, safranal shows no interaction with the selected epigenetic targets. These findings highlight saffron’s nutriepigenomic potential and emphasize the need for functional validation within relevant in vitro and in vivo experimental methodologies.
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MDPI and ACS Style
Piergentili, A.; Saraceni, P.R.; Demurtas, O.C.; Benassi, B.; Arcangeli, C.
Epigenomics Nutritional Insights of Crocus sativus L.: Computational Analysis of Bioactive Molecules Targeting DNA Methyltransferases and Histone Deacetylases. Int. J. Mol. Sci. 2025, 26, 7575.
https://doi.org/10.3390/ijms26157575
AMA Style
Piergentili A, Saraceni PR, Demurtas OC, Benassi B, Arcangeli C.
Epigenomics Nutritional Insights of Crocus sativus L.: Computational Analysis of Bioactive Molecules Targeting DNA Methyltransferases and Histone Deacetylases. International Journal of Molecular Sciences. 2025; 26(15):7575.
https://doi.org/10.3390/ijms26157575
Chicago/Turabian Style
Piergentili, Alessia, Paolo Roberto Saraceni, Olivia Costantina Demurtas, Barbara Benassi, and Caterina Arcangeli.
2025. "Epigenomics Nutritional Insights of Crocus sativus L.: Computational Analysis of Bioactive Molecules Targeting DNA Methyltransferases and Histone Deacetylases" International Journal of Molecular Sciences 26, no. 15: 7575.
https://doi.org/10.3390/ijms26157575
APA Style
Piergentili, A., Saraceni, P. R., Demurtas, O. C., Benassi, B., & Arcangeli, C.
(2025). Epigenomics Nutritional Insights of Crocus sativus L.: Computational Analysis of Bioactive Molecules Targeting DNA Methyltransferases and Histone Deacetylases. International Journal of Molecular Sciences, 26(15), 7575.
https://doi.org/10.3390/ijms26157575
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