{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,1]],"date-time":"2026-09-01T09:16:10Z","timestamp":1788254170459,"version":"build-2803163510"},"reference-count":27,"publisher":"MDPI AG","issue":"17","license":[{"start":{"date-parts":[[2026,9,1]],"date-time":"2026-09-01T00:00:00Z","timestamp":1788220800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["32272237"],"award-info":[{"award-number":["32272237"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"award":["32272237"],"award-info":[{"award-number":["32272237"]}],"id":[{"id":"https:\/\/ror.org\/01h0zpd94","id-type":"ROR","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Molecules"],"abstract":"<jats:p>(1) Background: The mitochondrial permeability transition pore (mPTP) contributes to mitochondrial dysfunction under pathological conditions. Cyclophilin D (CypD), a key regulator of sustained mPTP opening, represents an important molecular target. However, systematic strategies for selecting an appropriate CypD crystal structure for virtual screening and efficiently identifying CypD-binding natural polyphenols remain limited. (2) Methods: Six CypD crystal structures were evaluated by receiver operating characteristic analysis using reported CypD inhibitors and approximately 4000 decoys. The optimal receptor structure was subsequently used to screen 484 dietary polyphenols by molecular docking. Selected top-ranked candidates were further characterized by 15N\u20131H HSQC NMR titration and surface plasmon resonance (SPR). (3) Results: PDB 6R8L exhibited the best virtual-screening performance, particularly in early enrichment. Several polyphenol glucuronides ranked among the top candidates. NMR analysis showed that apigenin 7-glucuronide and luteolin 7-glucuronide induced pronounced chemical shift perturbations at CypD residues F60, M61, I117, and W121, with F60, M61, and W121 located within or near the docking-predicted S1 binding region. SPR independently confirmed direct binding, yielding KD values of 66 \u03bcM and 84 \u03bcM for apigenin 7-glucuronide and luteolin 7-glucuronide, respectively. (4) Conclusions: Integrating systematic receptor evaluation, molecular docking, and complementary NMR and SPR characterization provides a practical workflow for identifying and characterizing natural CypD-binding compounds. Apigenin 7-glucuronide and luteolin 7-glucuronide were identified as micromolar CypD-binding candidates, highlighting polyphenol glucuronides as a chemical class warranting further investigation in CypD ligand discovery.<\/jats:p>","DOI":"10.3390\/molecules31173074","type":"journal-article","created":{"date-parts":[[2026,9,1]],"date-time":"2026-09-01T08:31:13Z","timestamp":1788251473000},"page":"3074","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Structure-Based Screening Identifies Polyphenol Glucuronides as Cyclophilin D Ligands"],"prefix":"10.3390","volume":"31","author":[{"given":"Annan","family":"Wu","sequence":"first","affiliation":[{"name":"College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China"},{"name":"National Engineering Research Center for Fruit & Vegetable Processing, Beijing 100083, China"},{"name":"Beijing Key Laboratory for Food Non-Thermal Processing, Beijing 100083, China"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"investigation","vocabulary":"credit"},{"role":"methodology","vocabulary":"credit"},{"role":"data-curation","vocabulary":"credit"},{"role":"writing-original-draft","vocabulary":"credit"}]},{"given":"Jie","family":"Zhang","sequence":"additional","affiliation":[{"name":"College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China"},{"name":"National Engineering Research Center for Fruit & Vegetable Processing, Beijing 100083, China"},{"name":"Beijing Key Laboratory for Food Non-Thermal Processing, Beijing 100083, China"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"investigation","vocabulary":"credit"},{"role":"data-curation","vocabulary":"credit"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5681-6058","authenticated-orcid":false,"given":"Jing","family":"Zhao","sequence":"additional","affiliation":[{"name":"College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China"},{"name":"National Engineering Research Center for Fruit & Vegetable Processing, Beijing 100083, China"},{"name":"Beijing Key Laboratory for Food Non-Thermal Processing, Beijing 100083, China"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"conceptualization","vocabulary":"credit"},{"role":"investigation","vocabulary":"credit"},{"role":"methodology","vocabulary":"credit"},{"role":"data-curation","vocabulary":"credit"},{"role":"supervision","vocabulary":"credit"},{"role":"project-administration","vocabulary":"credit"},{"role":"writing-review-editing","vocabulary":"credit"},{"role":"funding-acquisition","vocabulary":"credit"}]}],"member":"1968","published-online":{"date-parts":[[2026,9,1]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"50","DOI":"10.1016\/j.tips.2018.11.004","article-title":"Mitochondrial Permeability Transition: A Molecular Lesion with Multiple Drug Targets","volume":"40","author":"Briston","year":"2019","journal-title":"Trends Pharmacol. Sci."},{"key":"ref_2","doi-asserted-by":"crossref","unstructured":"Stauffer, W.T., Goodman, A.Z., and Gallay, P.A. (2024). Cyclophilin Inhibition as a Strategy for the Treatment of Human Disease. Front. Pharmacol., 15.","DOI":"10.3389\/fphar.2024.1417945"},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"1869","DOI":"10.1038\/s41418-023-01187-0","article-title":"Identity, Structure, and Function of the Mitochondrial Permeability Transition Pore: Controversies, Consensus, Recent Advances, and Future Directions","volume":"30","author":"Bernardi","year":"2023","journal-title":"Cell Death Differ."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"523","DOI":"10.1016\/j.freeradbiomed.2020.11.009","article-title":"Physiological Evidence of Mitochondrial Permeability Transition Pore Opening Caused by Lipid Deposition Leading to Hepatic Steatosis in Db\/Db Mice","volume":"162","author":"Li","year":"2021","journal-title":"Free Radic. Biol. Med."},{"key":"ref_5","doi-asserted-by":"crossref","unstructured":"Belosludtsev, K.N., Belosludtseva, N.V., and Dubinin, M.V. (2020). Diabetes Mellitus, Mitochondrial Dysfunction and Ca2+-Dependent Permeability Transition Pore. Int. J. Mol. Sci., 21.","DOI":"10.3390\/ijms21186559"},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"1267","DOI":"10.1016\/j.bbadis.2013.09.003","article-title":"Mitochondrial Permeability Transition Pore Is a Potential Drug Target for Neurodegeneration","volume":"1842","author":"Rao","year":"2014","journal-title":"Biochim. Biophys. Acta Mol. Basis Dis."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"142","DOI":"10.1016\/j.yjmcc.2014.08.015","article-title":"Molecular Identity of the Mitochondrial Permeability Transition Pore and Its Role in Ischemia-Reperfusion Injury","volume":"78","author":"Morciano","year":"2015","journal-title":"J. Mol. Cell. Cardiol."},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"1822","DOI":"10.1002\/med.21892","article-title":"Small-Molecule Inhibitors of Cyclophilin D as Potential Therapeutics in Mitochondria-Related Diseases","volume":"42","author":"Haleckova","year":"2022","journal-title":"Med. Res. Rev."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"1184","DOI":"10.1038\/s41589-022-01116-1","article-title":"Discovery and Molecular Basis of Subtype-Selective Cyclophilin Inhibitors","volume":"18","author":"Peterson","year":"2022","journal-title":"Nat. Chem. Biol."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"23910","DOI":"10.1021\/acs.jmedchem.5c01146","article-title":"Potent Preorganized Pyrazolidine Cyclophilin D Inhibitors Prevent Mitochondrial and Organ Injury in a Mouse Pancreatitis Disease Model","volume":"68","author":"Awais","year":"2025","journal-title":"J. Med. Chem."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"102654","DOI":"10.1016\/j.xcrm.2026.102654","article-title":"A Preclinical Candidate of Cyclophilin D Inhibition Improves Alcohol-Associated Liver Injury","volume":"7","author":"Che","year":"2026","journal-title":"Cell Rep. Med."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"126717","DOI":"10.1016\/j.bmcl.2019.126717","article-title":"Discovery of Novel Cyclophilin D Inhibitors Starting from Three Dimensional Fragments with Millimolar Potencies","volume":"29","author":"Schwarz","year":"2019","journal-title":"Bioorg. Med. Chem. Lett."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"626","DOI":"10.1080\/10408398.2018.1546669","article-title":"Bioactivity of Dietary Polyphenols: The Role of Metabolites","volume":"60","author":"Luca","year":"2020","journal-title":"Crit. Rev. Food Sci. Nutr."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"514","DOI":"10.1039\/C8FO01997E","article-title":"The Effects of Polyphenols and Other Bioactives on Human Health","volume":"10","author":"Fraga","year":"2019","journal-title":"Food Funct."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"2759","DOI":"10.2147\/DDDT.S215358","article-title":"Cerebral Protection of Epigallocatechin Gallate (EGCG) via Preservation of Mitochondrial Function and ERK Inhibition in a Rat Resuscitation Model","volume":"13","author":"Qin","year":"2019","journal-title":"Drug Des. Devel. Ther."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"2532","DOI":"10.1016\/j.bbamem.2013.06.026","article-title":"Mitochondrial Membrane Permeabilisation by Amyloid Aggregates and Protection by Polyphenols","volume":"1828","author":"Camilleri","year":"2013","journal-title":"Biochim. Biophys. Acta Biomembr."},{"key":"ref_17","doi-asserted-by":"crossref","unstructured":"Naoi, M., Wu, Y., Shamoto-Nagai, M., and Maruyama, W. (2019). Mitochondria in Neuroprotection by Phytochemicals: Bioactive Polyphenols Modulate Mitochondrial Apoptosis System, Function and Structure. Int. J. Mol. Sci., 20.","DOI":"10.3390\/ijms20102451"},{"key":"ref_18","doi-asserted-by":"crossref","unstructured":"Wu, A., Zhang, J., Li, Q., Liao, X., Wang, C., and Zhao, J. (2022). (-)-Epigallocatechin-3-Gallate Directly Binds Cyclophilin D: A Potential Mechanism for Mitochondrial Protection. Molecules, 27.","DOI":"10.3390\/molecules27248661"},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"389","DOI":"10.1146\/annurev-biochem-030222-120000","article-title":"The Art and Science of Molecular Docking","volume":"93","author":"Paggi","year":"2024","journal-title":"Annu. Rev. Biochem."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"2534","DOI":"10.1021\/jm049092j","article-title":"Virtual Screening Workflow Development Guided by the \u201cReceiver Operating Characteristic\u201d Curve Approach. Application to High-Throughput Docking on Metabotropic Glutamate Receptor Subtype 4","volume":"48","author":"Triballeau","year":"2005","journal-title":"J. Med. Chem."},{"key":"ref_21","doi-asserted-by":"crossref","unstructured":"Wang, S., Jiang, J.H., Li, R.Y., and Deng, P. (2020). Docking-Based Virtual Screening of T\u03b2R1 Inhibitors: Evaluation of Pose Prediction and Scoring Functions. BMC Chem., 14.","DOI":"10.1186\/s13065-020-00704-3"},{"key":"ref_22","doi-asserted-by":"crossref","unstructured":"Liu, P., Wu, A., Song, Y., and Zhao, J. (2023). Virtual Screening of Soybean Protein Isolate-Binding Phytochemicals and Interaction Characterization. Foods, 12.","DOI":"10.3390\/foods12020272"},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"8915","DOI":"10.1021\/acs.jmedchem.9b00179","article-title":"Hydroxyl Groups in Synthetic and Natural-Product-Derived Therapeutics: A Perspective on a Common Functional Group","volume":"62","author":"Cramer","year":"2019","journal-title":"J. Med. Chem."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"153","DOI":"10.1007\/s10858-022-00402-3","article-title":"The Measurement of Binding Affinities by NMR Chemical Shift Perturbation","volume":"76","author":"Hobbs","year":"2022","journal-title":"J. Biomol. NMR"},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"6582","DOI":"10.1021\/jm300687e","article-title":"Directory of Useful Decoys, Enhanced (DUD-E): Better Ligands and Decoys for Better Benchmarking","volume":"55","author":"Mysinger","year":"2012","journal-title":"J. Med. Chem."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"3891","DOI":"10.1021\/acs.jcim.1c00203","article-title":"AutoDock Vina 1.2.0: New Docking Methods, Expanded Force Field, and Python Bindings","volume":"61","author":"Eberhardt","year":"2021","journal-title":"J. Chem. Inf. Model."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"bap024","DOI":"10.1093\/database\/bap024","article-title":"Phenol-Explorer: An Online Comprehensive Database on Polyphenol Contents in Foods","volume":"2010","author":"Neveu","year":"2010","journal-title":"Database"}],"container-title":["Molecules"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/1420-3049\/31\/17\/3074\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,9,1]],"date-time":"2026-09-01T08:32:07Z","timestamp":1788251527000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/1420-3049\/31\/17\/3074"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,9,1]]},"references-count":27,"journal-issue":{"issue":"17","published-online":{"date-parts":[[2026,9]]}},"alternative-id":["molecules31173074"],"URL":"https:\/\/doi.org\/10.3390\/molecules31173074","relation":{},"ISSN":["1420-3049"],"issn-type":[{"value":"1420-3049","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,9,1]]}}}