{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,6]],"date-time":"2025-11-06T18:02:33Z","timestamp":1762452153882,"version":"build-2065373602"},"reference-count":62,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2025,9,19]],"date-time":"2025-09-19T00:00:00Z","timestamp":1758240000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"},{"start":{"date-parts":[[2025,9,19]],"date-time":"2025-09-19T00:00:00Z","timestamp":1758240000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"crossref","award":["82304707","82374485"],"award-info":[{"award-number":["82304707","82374485"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"crossref"}]},{"name":"Hubei Provincial Natural Science Foundation of China","award":["2023AFB373"],"award-info":[{"award-number":["2023AFB373"]}]},{"name":"Doctoral Research Initiation Grant of Hubei University of Technology","award":["XJ2022004001"],"award-info":[{"award-number":["XJ2022004001"]}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["J Comput Aided Mol Des"],"published-print":{"date-parts":[[2025,12]]},"DOI":"10.1007\/s10822-025-00662-9","type":"journal-article","created":{"date-parts":[[2025,9,19]],"date-time":"2025-09-19T01:53:14Z","timestamp":1758246794000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Integrated strategy for screening direct Keap1-Nrf2 PPI inhibitors from traditional Chinese medicine: a case study of Achyranthis bidentatae Radix"],"prefix":"10.1007","volume":"39","author":[{"given":"Ban","family":"Chen","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Shuangshuang","family":"Liu","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Huiyin","family":"Xia","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xican","family":"Li","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Rongxin","family":"Cai","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yingqing","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yuchen","family":"Hu","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jiangtao","family":"Su","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2025,9,19]]},"reference":[{"key":"662_CR1","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1038\/s41420-024-02278-8","volume":"11","author":"N Chandimali","year":"2025","unstructured":"Chandimali N, Bak SG, Park EH et al (2025) Free radicals and their impact on health and antioxidant defenses: a review. Cell Death Discov 11:1\u201317. https:\/\/doi.org\/10.1038\/s41420-024-02278-8","journal-title":"Cell Death Discov"},{"key":"662_CR2","doi-asserted-by":"publisher","DOI":"10.1016\/j.mrrev.2021.108365","volume":"787","author":"AW Caliri","year":"2021","unstructured":"Caliri AW, Tommasi S, Besaratinia A (2021) Relationships among smoking, oxidative stress, inflammation, macromolecular damage, and cancer. Mutat Res-Rev Mutat 787:108365. https:\/\/doi.org\/10.1016\/j.mrrev.2021.108365","journal-title":"Mutat Res-Rev Mutat"},{"key":"662_CR3","doi-asserted-by":"publisher","DOI":"10.1016\/j.biopha.2022.113238","volume":"152","author":"D Rotariu","year":"2022","unstructured":"Rotariu D, Babes EE, Tit DM et al (2022) Oxidative stress \u2013 complex pathological issues concerning the hallmark of cardiovascular and metabolic disorders. Biomed Pharmacother 152:113238. https:\/\/doi.org\/10.1016\/j.biopha.2022.113238","journal-title":"Biomed Pharmacother"},{"key":"662_CR4","doi-asserted-by":"publisher","first-page":"609","DOI":"10.1007\/s10522-023-10050-1","volume":"24","author":"MR Chaudhary","year":"2023","unstructured":"Chaudhary MR, Chaudhary S, Sharma Y et al (2023) Aging, oxidative stress and degenerative diseases: mechanisms, complications and emerging therapeutic strategies. Biogerontology 24:609\u2013662. https:\/\/doi.org\/10.1007\/s10522-023-10050-1","journal-title":"Biogerontology"},{"key":"662_CR5","doi-asserted-by":"publisher","DOI":"10.1016\/j.redox.2022.102389","volume":"54","author":"S Liu","year":"2022","unstructured":"Liu S, Pi J, Zhang Q (2022) Signal amplification in the KEAP1-NRF2-ARE antioxidant response pathway. Redox Biol 54:102389. https:\/\/doi.org\/10.1016\/j.redox.2022.102389","journal-title":"Redox Biol"},{"key":"662_CR6","doi-asserted-by":"publisher","first-page":"237","DOI":"10.1002\/med.21925","volume":"43","author":"E Crisman","year":"2023","unstructured":"Crisman E, Duarte P, Dauden E et al (2023) KEAP1-NRF2 protein\u2013protein interaction inhibitors: Design, pharmacological properties and therapeutic potential. Med Res Rev 43:237\u2013287. https:\/\/doi.org\/10.1002\/med.21925","journal-title":"Med Res Rev"},{"key":"662_CR7","doi-asserted-by":"publisher","first-page":"1121","DOI":"10.1021\/jm4017174","volume":"57","author":"C Zhuang","year":"2014","unstructured":"Zhuang C, Narayanapillai S, Zhang W et al (2014) Rapid identification of Keap1\u2013Nrf2 small-molecule inhibitors through structure-based virtual screening and hit-based substructure search. J Med Chem 57:1121\u20131126. https:\/\/doi.org\/10.1021\/jm4017174","journal-title":"J Med Chem"},{"key":"662_CR8","doi-asserted-by":"publisher","first-page":"285","DOI":"10.1016\/j.apsb.2015.05.008","volume":"5","author":"DA Abed","year":"2015","unstructured":"Abed DA, Goldstein M, Albanyan H et al (2015) Discovery of direct inhibitors of Keap1\u2013Nrf2 protein\u2013protein interaction as potential therapeutic and preventive agents. Acta Pharm Sin B 5:285\u2013299. https:\/\/doi.org\/10.1016\/j.apsb.2015.05.008","journal-title":"Acta Pharm Sin B"},{"key":"662_CR9","doi-asserted-by":"publisher","first-page":"2736","DOI":"10.1021\/jm5000529","volume":"57","author":"ZY Jiang","year":"2014","unstructured":"Jiang ZY, Lu MC, Xu L et al (2014) Discovery of potent Keap1\u2013Nrf2 protein\u2013protein interaction inhibitor based on molecular binding determinants analysis. J Med Chem 57:2736\u20132745. https:\/\/doi.org\/10.1021\/jm5000529","journal-title":"J Med Chem"},{"key":"662_CR10","doi-asserted-by":"publisher","first-page":"7420","DOI":"10.1038\/s41598-021-86616-1","volume":"11","author":"Y Shimizu","year":"2021","unstructured":"Shimizu Y, Yonezawa T, Sakamoto J et al (2021) Identification of novel inhibitors of Keap1\/Nrf2 by a promising method combining protein\u2013protein interaction-oriented library and machine learning. Sci Rep 11:7420. https:\/\/doi.org\/10.1038\/s41598-021-86616-1","journal-title":"Sci Rep"},{"key":"662_CR11","doi-asserted-by":"publisher","first-page":"369","DOI":"10.2515\/therapie\/2013064","volume":"68","author":"R Atheymen","year":"2013","unstructured":"Atheymen R, Affes H, Ksouda K et al (2013) Effets ind\u00e9sirables de la sulfasalazine\u202f: discussion de leur m\u00e9canisme et du r\u00f4le de la composante sulfamid\u00e9e. Therapies 68:369\u2013373. https:\/\/doi.org\/10.2515\/therapie\/2013064","journal-title":"Therapies"},{"key":"662_CR12","doi-asserted-by":"publisher","DOI":"10.1016\/j.lfs.2021.120111","volume":"291","author":"AV Ulasov","year":"2022","unstructured":"Ulasov AV, Rosenkranz AA, Georgiev GP et al (2022) Nrf2\/Keap1\/ARE signaling: towards specific regulation. Life Sci 291:120111. https:\/\/doi.org\/10.1016\/j.lfs.2021.120111","journal-title":"Life Sci"},{"key":"662_CR13","doi-asserted-by":"publisher","first-page":"279","DOI":"10.1146\/annurev-pharmtox-052220-104025","volume":"62","author":"L Torrente","year":"2022","unstructured":"Torrente L, DeNicola GM (2022) Targeting NRF2 and its downstream processes: opportunities and challenges. Annu Rev Pharmacol Toxicol 62:279\u2013300. https:\/\/doi.org\/10.1146\/annurev-pharmtox-052220-104025","journal-title":"Annu Rev Pharmacol Toxicol"},{"key":"662_CR14","doi-asserted-by":"publisher","DOI":"10.1016\/j.phymed.2022.154330","volume":"105","author":"Z Pan","year":"2022","unstructured":"Pan Z, He Q, Zeng J et al (2022) Naringenin protects against iron overload-induced osteoarthritis by suppressing oxidative stress. Phytomedicine 105:154330. https:\/\/doi.org\/10.1016\/j.phymed.2022.154330","journal-title":"Phytomedicine"},{"key":"662_CR15","doi-asserted-by":"publisher","first-page":"30","DOI":"10.1186\/s43094-024-00605-5","volume":"10","author":"J Li","year":"2024","unstructured":"Li J, Lv Z (2024) Cordycepin alleviates osteoarthritis by inhibiting chondrocyte ferroptosis via Keap1\/Nrf2 axis. Future J Pharm Sci 10:30. https:\/\/doi.org\/10.1186\/s43094-024-00605-5","journal-title":"Future J Pharm Sci"},{"key":"662_CR16","doi-asserted-by":"publisher","DOI":"10.1016\/j.biopha.2023.116067","volume":"170","author":"L Zhao","year":"2024","unstructured":"Zhao L, Tao X, Wang Q et al (2024) Diosmetin alleviates neuropathic pain by regulating the Keap1\/Nrf2\/NF-\u03baB signaling pathway. Biomed Pharmacother 170:116067. https:\/\/doi.org\/10.1016\/j.biopha.2023.116067","journal-title":"Biomed Pharmacother"},{"key":"662_CR17","doi-asserted-by":"publisher","DOI":"10.1016\/j.biopha.2022.113631","volume":"155","author":"J Chen","year":"2022","unstructured":"Chen J, Zhang J, Chen T et al (2022) Xiaojianzhong decoction attenuates gastric mucosal injury by activating the p62\/Keap1\/Nrf2 signaling pathway to inhibit ferroptosis. Biomed Pharmacother 155:113631. https:\/\/doi.org\/10.1016\/j.biopha.2022.113631","journal-title":"Biomed Pharmacother"},{"key":"662_CR18","doi-asserted-by":"publisher","first-page":"67","DOI":"10.1142\/S0192415X25500041","volume":"53","author":"Y Li","year":"2025","unstructured":"Li Y, Wang X, Li S et al (2025) Therapeutic effects of natural products in the treatment of chronic diseases: the role in regulating KEAP1\u2013NRF2 pathway. Am J Chin Med 53:67\u201396. https:\/\/doi.org\/10.1142\/S0192415X25500041","journal-title":"Am J Chin Med"},{"key":"662_CR19","doi-asserted-by":"publisher","first-page":"930","DOI":"10.1093\/jpp\/rgae012","volume":"76","author":"YR Chen","year":"2024","unstructured":"Chen YR, Niu Y, Zhou HL (2024) Achyranthes bidentata Blume (Amaranthaceae): a review of its botany, traditional uses, phytochemistry, pharmacology, and toxicology. J Pharm Pharmacol 76:930\u2013966. https:\/\/doi.org\/10.1093\/jpp\/rgae012","journal-title":"J Pharm Pharmacol"},{"key":"662_CR20","doi-asserted-by":"publisher","DOI":"10.1016\/j.foodchem.2021.131746","volume":"375","author":"J Yi","year":"2022","unstructured":"Yi J, Li X, Wang S et al (2022) Steam explosion pretreatment of Achyranthis bidentatae radix: modified polysaccharide and its antioxidant activities. Food Chem 375:131746. https:\/\/doi.org\/10.1016\/j.foodchem.2021.131746","journal-title":"Food Chem"},{"key":"662_CR21","doi-asserted-by":"publisher","DOI":"10.1016\/j.phymed.2024.155353","volume":"125","author":"P Guo","year":"2024","unstructured":"Guo P, Zeng M, Liu M et al (2024) Isolation of calenduloside E from Achyranthes bidentata Blume and its effects on LPS\/D-GalN-induced acute liver injury in mice by regulating the AMPK-SIRT3 signaling pathway. Phytomedicine 125:155353. https:\/\/doi.org\/10.1016\/j.phymed.2024.155353","journal-title":"Phytomedicine"},{"key":"662_CR22","doi-asserted-by":"publisher","first-page":"1659","DOI":"10.1002\/pca.3409","volume":"35","author":"B Chen","year":"2024","unstructured":"Chen B, Liu S, Li X et al (2024) Reconstruction of quality marker system for ginkgo folium tablet using UHPLC-Q-orbitrap MS, quantum chemical calculation, network pharmacology, and molecular simulation. Phytochem Anal 35:1659\u20131673. https:\/\/doi.org\/10.1002\/pca.3409","journal-title":"Phytochem Anal"},{"key":"662_CR23","doi-asserted-by":"publisher","first-page":"21146","DOI":"10.1038\/srep21146","volume":"6","author":"Z Liu","year":"2016","unstructured":"Liu Z, Guo F, Wang Y et al (2016) BATMAN-TCM: a bioinformatics analysis tool for molecular mechANism of traditional Chinese medicine. Sci Rep 6:21146. https:\/\/doi.org\/10.1038\/srep21146","journal-title":"Sci Rep"},{"key":"662_CR24","doi-asserted-by":"publisher","first-page":"D1197","DOI":"10.1093\/nar\/gkaa1063","volume":"49","author":"S Fang","year":"2021","unstructured":"Fang S, Dong L, Liu L et al (2021) HERB: a high-throughput experiment- and reference-guided database of traditional Chinese medicine. Nucleic Acids Res 49:D1197\u2013D1206. https:\/\/doi.org\/10.1093\/nar\/gkaa1063","journal-title":"Nucleic Acids Res"},{"key":"662_CR25","doi-asserted-by":"publisher","first-page":"D1110","DOI":"10.1093\/nar\/gky1021","volume":"47","author":"Y Wu","year":"2019","unstructured":"Wu Y, Zhang F, Yang K et al (2019) SymMap: an integrative database of traditional Chinese medicine enhanced by symptom mapping. Nucleic Acids Res 47:D1110\u2013D1117. https:\/\/doi.org\/10.1093\/nar\/gky1021","journal-title":"Nucleic Acids Res"},{"key":"662_CR26","doi-asserted-by":"publisher","first-page":"89","DOI":"10.1186\/s13321-022-00670-z","volume":"14","author":"LX Zhang","year":"2022","unstructured":"Zhang LX, Dong J, Wei H et al (2022) TCMSID: a simplified integrated database for drug discovery from traditional Chinese medicine. J Cheminf 14:89. https:\/\/doi.org\/10.1186\/s13321-022-00670-z","journal-title":"J Cheminf"},{"key":"662_CR27","doi-asserted-by":"publisher","DOI":"10.1186\/1758-2946-6-13","volume":"6","author":"J Ru","year":"2014","unstructured":"Ru J, Li P, Wang J et al (2014) TCMSP: a database of systems pharmacology for drug discovery from herbal medicines. J Cheminf 6:13. https:\/\/doi.org\/10.1186\/1758-2946-6-13","journal-title":"J Cheminf"},{"key":"662_CR28","volume-title":"Pharmacopoeia of the people\u2019s republic of China","author":"Chinese Pharmacopoeia Commission","year":"2020","unstructured":"Chinese Pharmacopoeia Commission (2020) Pharmacopoeia of the people\u2019s republic of China. China Medical Science Press, Beijing"},{"key":"662_CR29","doi-asserted-by":"publisher","first-page":"D1373","DOI":"10.1093\/nar\/gkac956","volume":"51","author":"S Kim","year":"2023","unstructured":"Kim S, Chen J, Cheng T et al (2023) PubChem 2023 update. Nucleic Acids Res 51:D1373\u2013D1380. https:\/\/doi.org\/10.1093\/nar\/gkac956","journal-title":"Nucleic Acids Res"},{"key":"662_CR30","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0294236","volume":"18","author":"D Tang","year":"2023","unstructured":"Tang D, Chen M, Huang X et al (2023) SRplot: a free online platform for data visualization and graphing. PLoS ONE 18:e0294236. https:\/\/doi.org\/10.1371\/journal.pone.0294236","journal-title":"PLoS ONE"},{"key":"662_CR31","doi-asserted-by":"publisher","first-page":"337","DOI":"10.1016\/j.ddtec.2004.11.007","volume":"1","author":"CA Lipinski","year":"2004","unstructured":"Lipinski CA (2004) Lead- and drug-like compounds: the rule-of-five revolution. Drug Discov Today Technol 1:337\u2013341. https:\/\/doi.org\/10.1016\/j.ddtec.2004.11.007","journal-title":"Drug Discov Today Technol"},{"key":"662_CR32","doi-asserted-by":"publisher","first-page":"2726","DOI":"10.1021\/acs.jcim.2c00242","volume":"62","author":"MC Hutter","year":"2022","unstructured":"Hutter MC (2022) Differential multimolecule fingerprint for similarity search\u2500making use of active and inactive compound sets in virtual screening. J Chem Inf Model 62:2726\u20132736. https:\/\/doi.org\/10.1021\/acs.jcim.2c00242","journal-title":"J Chem Inf Model"},{"key":"662_CR33","first-page":"2825","volume":"12","author":"F Pedregosa","year":"2011","unstructured":"Pedregosa F, Varoquaux G, Gramfort A et al (2011) Scikit-learn: machine learning in python. J Mach Learn Res 12:2825\u20132830","journal-title":"J Mach Learn Res"},{"doi-asserted-by":"publisher","unstructured":"Ashari IF, Nugroho ED, Baraku R et al (2023) Analysis of elbow, silhouette, davies-bouldin, calinski-harabasz, and rand-index evaluation on K-means algorithm for classifying flood-affected areas in Jakarta. J Appl Inform Comput 7:95\u2013103. https:\/\/doi.org\/10.30871\/jaic.v7i1.4947","key":"662_CR34","DOI":"10.30871\/jaic.v7i1.4947"},{"key":"662_CR35","doi-asserted-by":"publisher","first-page":"5499","DOI":"10.1021\/acs.jctc.8b00652","volume":"14","author":"H Zhou","year":"2018","unstructured":"Zhou H, Wang F, Tao P (2018) T-distributed stochastic neighbor embedding method with the least information loss for macromolecular simulations. J Chem Theory Comput 14:5499\u20135510. https:\/\/doi.org\/10.1021\/acs.jctc.8b00652","journal-title":"J Chem Theory Comput"},{"key":"662_CR36","doi-asserted-by":"publisher","first-page":"D271","DOI":"10.1093\/nar\/gkw1000","volume":"45","author":"PW Rose","year":"2017","unstructured":"Rose PW, Prli\u0107 A, Altunkaya A et al (2017) The RCSB protein data bank: integrative view of protein, gene and 3D structural information. Nucleic Acids Res 45:D271\u2013D281. https:\/\/doi.org\/10.1093\/nar\/gkw1000","journal-title":"Nucleic Acids Res"},{"key":"662_CR37","doi-asserted-by":"publisher","first-page":"204","DOI":"10.1021\/acs.jcim.9b00778","volume":"60","author":"N Nguyen","year":"2020","unstructured":"Nguyen N, Nguyen T, Pham T et al (2020) Autodock Vina adopts more accurate binding poses but Autodock4 forms better binding affinity. J Chem Inf Model 60:204\u2013211. https:\/\/doi.org\/10.1021\/acs.jcim.9b00778","journal-title":"J Chem Inf Model"},{"key":"662_CR38","doi-asserted-by":"publisher","first-page":"12964","DOI":"10.1039\/C6CP01555G","volume":"18","author":"Z Wang","year":"2016","unstructured":"Wang Z, Sun H, Yao X et al (2016) Comprehensive evaluation of ten docking programs on a diverse set of protein\u2013ligand complexes: the prediction accuracy of sampling power and scoring power. Phys Chem Chem Phys 18:12964\u201312975. https:\/\/doi.org\/10.1039\/C6CP01555G","journal-title":"Phys Chem Chem Phys"},{"key":"662_CR39","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1003571","volume":"10","author":"S Ruiz-Carmona","year":"2014","unstructured":"Ruiz-Carmona S, Alvarez-Garcia D, Foloppe N et al (2014) Rdock: a fast, versatile and open source program for docking ligands to proteins and nucleic acids. PLoS Comput Biol 10:e1003571. https:\/\/doi.org\/10.1371\/journal.pcbi.1003571","journal-title":"PLoS Comput Biol"},{"key":"662_CR40","doi-asserted-by":"publisher","first-page":"1701","DOI":"10.1002\/jcc.20291","volume":"26","author":"D Van Der Spoel","year":"2005","unstructured":"Van Der Spoel D, Lindahl E, Hess B et al (2005) GROMACS: fast, flexible, and free. J Comput Chem 26:1701\u20131718. https:\/\/doi.org\/10.1002\/jcc.20291","journal-title":"J Comput Chem"},{"key":"662_CR41","doi-asserted-by":"publisher","first-page":"580","DOI":"10.1002\/jcc.22885","volume":"33","author":"T Lu","year":"2012","unstructured":"Lu T, Chen F (2012) Multiwfn: a multifunctional wavefunction analyzer. J Comput Chem 33:580\u2013592. https:\/\/doi.org\/10.1002\/jcc.22885","journal-title":"J Comput Chem"},{"key":"662_CR42","doi-asserted-by":"publisher","first-page":"6281","DOI":"10.1021\/acs.jctc.1c00645","volume":"17","author":"MS Vald\u00e9s-Tresanco","year":"2021","unstructured":"Vald\u00e9s-Tresanco MS, Vald\u00e9s-Tresanco ME, Valiente PA et al (2021) Gmx_MMPBSA: a new tool to perform end-state free energy calculations with GROMACS. J Chem Theory Comput 17:6281\u20136291","journal-title":"J Chem Theory Comput"},{"unstructured":"Frisch MJ, Trucks GW, Schlegel HB et al (2016) Gaussian 16 revision C.01","key":"662_CR43"},{"key":"662_CR44","doi-asserted-by":"publisher","first-page":"650","DOI":"10.1063\/1.438955","volume":"72","author":"R Krishnan","year":"1980","unstructured":"Krishnan R, Binkley JS, Seeger R et al (1980) Self-consistent molecular orbital methods. XX. A basis set for correlated wave functions. J Chem Phys 72:650\u2013654. https:\/\/doi.org\/10.1063\/1.438955","journal-title":"J Chem Phys"},{"key":"662_CR45","doi-asserted-by":"publisher","first-page":"11623","DOI":"10.1021\/j100096a001","volume":"98","author":"PJ Stephens","year":"1994","unstructured":"Stephens PJ, Devlin FJ, Chabalowski CF et al (1994) Ab initio calculation of vibrational absorption and circular dichroism spectra using density functional force fields. J Phys Chem 98:11623\u201311627. https:\/\/doi.org\/10.1021\/j100096a001","journal-title":"J Phys Chem"},{"key":"662_CR46","doi-asserted-by":"publisher","DOI":"10.1063\/1.3382344","volume":"132","author":"S Grimme","year":"2010","unstructured":"Grimme S, Antony J, Ehrlich S et al (2010) A consistent and accurate ab initio parametrization of density functional dispersion correction (DFT-D) for the 94 elements H-Pu. J Chem Phys 132:154104. https:\/\/doi.org\/10.1063\/1.3382344","journal-title":"J Chem Phys"},{"key":"662_CR47","doi-asserted-by":"publisher","first-page":"1456","DOI":"10.1002\/jcc.21759","volume":"32","author":"S Grimme","year":"2011","unstructured":"Grimme S, Ehrlich S, Goerigk L (2011) Effect of the damping function in dispersion corrected density functional theory. J Comput Chem 32:1456\u20131465. https:\/\/doi.org\/10.1002\/jcc.21759","journal-title":"J Comput Chem"},{"key":"662_CR48","doi-asserted-by":"publisher","first-page":"215","DOI":"10.1007\/s00214-007-0310-x","volume":"120","author":"Y Zhao","year":"2008","unstructured":"Zhao Y, Truhlar DG (2008) The M06 suite of density functionals for main group thermochemistry, thermochemical kinetics, noncovalent interactions, excited states, and transition elements: two new functionals and systematic testing of four M06-class functionals and 12 other functionals. Theor Chem Acc 120:215\u2013241. https:\/\/doi.org\/10.1007\/s00214-007-0310-x","journal-title":"Theor Chem Acc"},{"key":"662_CR49","doi-asserted-by":"publisher","first-page":"3297","DOI":"10.1039\/B508541A","volume":"7","author":"F Weigend","year":"2005","unstructured":"Weigend F, Ahlrichs R (2005) Balanced basis sets of split valence, triple zeta valence and quadruple zeta valence quality for H to Rn: design and assessment of accuracy. Phys Chem Chem Phys 7:3297\u20133305. https:\/\/doi.org\/10.1039\/B508541A","journal-title":"Phys Chem Chem Phys"},{"key":"662_CR50","doi-asserted-by":"publisher","first-page":"6378","DOI":"10.1021\/jp810292n","volume":"113","author":"AV Marenich","year":"2009","unstructured":"Marenich AV, Cramer CJ, Truhlar DG (2009) Universal solvation model based on solute electron density and on a continuum model of the solvent defined by the bulk dielectric constant and atomic surface tensions. J Phys Chem B 113:6378\u20136396. https:\/\/doi.org\/10.1021\/jp810292n","journal-title":"J Phys Chem B"},{"key":"662_CR51","doi-asserted-by":"publisher","first-page":"33","DOI":"10.1016\/0263-7855(96)00018-5","volume":"14","author":"W Humphrey","year":"1996","unstructured":"Humphrey W, Dalke A, Schulten K (1996) VMD: visual molecular dynamics. J Mol Graphics 14:33\u201338. https:\/\/doi.org\/10.1016\/0263-7855(96)00018-5","journal-title":"J Mol Graphics"},{"key":"662_CR52","doi-asserted-by":"publisher","first-page":"173","DOI":"10.1039\/D2MD00333C","volume":"14","author":"B Chen","year":"2022","unstructured":"Chen B, Su J, Hu Y et al (2022) Antioxidant mechanisms and products of four 4\u2032,5,7-trihydroxyflavonoids with different structural types. RSC Med Chem 14:173\u2013182. https:\/\/doi.org\/10.1039\/D2MD00333C","journal-title":"RSC Med Chem"},{"key":"662_CR53","doi-asserted-by":"publisher","DOI":"10.1016\/j.microc.2023.108938","volume":"191","author":"X Li","year":"2023","unstructured":"Li X, Zeng J, Cai R et al (2023) New UHPLC-Q-orbitrap MS\/MS-based library-comparison method simultaneously distinguishes 22 phytophenol isomers from Desmodium styracifolium. Microchem J 191:108938. https:\/\/doi.org\/10.1016\/j.microc.2023.108938","journal-title":"Microchem J"},{"key":"662_CR54","doi-asserted-by":"publisher","first-page":"22148","DOI":"10.1039\/D3RA04057G","volume":"13","author":"B Chen","year":"2023","unstructured":"Chen B, Ouyang X, Cheng C et al (2023) Bioactive peptides derived from radix angelicae sinensis inhibit ferroptosis in HT22 cells through direct Keap1\u2013Nrf2 PPI inhibition. RSC Adv 13:22148\u201322157. https:\/\/doi.org\/10.1039\/D3RA04057G","journal-title":"RSC Adv"},{"key":"662_CR55","doi-asserted-by":"publisher","first-page":"101","DOI":"10.1016\/j.freeradbiomed.2015.05.034","volume":"88","author":"P Canning","year":"2015","unstructured":"Canning P, Sorrell FJ, Bullock AN (2015) Structural basis of Keap1 interactions with Nrf2. Free Radic Biol Med 88:101\u2013107. https:\/\/doi.org\/10.1016\/j.freeradbiomed.2015.05.034","journal-title":"Free Radic Biol Med"},{"key":"662_CR56","doi-asserted-by":"publisher","first-page":"11","DOI":"10.1021\/acs.jcim.6b00340","volume":"57","author":"F Pereira","year":"2017","unstructured":"Pereira F, Xiao K, Latino DARS et al (2017) Machine learning methods to predict density functional theory B3LYP energies of HOMO and LUMO orbitals. J Chem Inf Model 57:11\u201321. https:\/\/doi.org\/10.1021\/acs.jcim.6b00340","journal-title":"J Chem Inf Model"},{"key":"662_CR57","doi-asserted-by":"publisher","first-page":"2868","DOI":"10.1002\/jcc.26068","volume":"40","author":"S Emamian","year":"2019","unstructured":"Emamian S, Lu T, Kruse H, Emamian H (2019) Exploring nature and predicting strength of hydrogen bonds: a correlation analysis between atoms-in-molecules descriptors, binding energies, and energy components of symmetry-adapted perturbation theory. J Comput Chem 40:2868\u20132881. https:\/\/doi.org\/10.1002\/jcc.26068","journal-title":"J Comput Chem"},{"key":"662_CR58","doi-asserted-by":"publisher","first-page":"2224","DOI":"10.1021\/acs.jcim.8b00266","volume":"58","author":"R Kurczab","year":"2018","unstructured":"Kurczab R, \u015aliwa P, Rataj K et al (2018) Salt bridge in ligand\u2013protein complexes\u2014systematic theoretical and statistical investigations. J Chem Inf Model 58:2224\u20132238. https:\/\/doi.org\/10.1021\/acs.jcim.8b00266","journal-title":"J Chem Inf Model"},{"key":"662_CR59","doi-asserted-by":"publisher","first-page":"1029","DOI":"10.14336\/AD.2023.0817","volume":"15","author":"X An","year":"2024","unstructured":"An X, Wang J, Xu K et al (2024) Perspectives on osteoarthritis treatment with mesenchymal stem cells and radix achyranthis bidentatae. Aging Dis 15:1029\u20131045. https:\/\/doi.org\/10.14336\/AD.2023.0817","journal-title":"Aging Dis"},{"key":"662_CR60","doi-asserted-by":"publisher","DOI":"10.1016\/j.cbi.2019.108901","volume":"315","author":"Y Zhang","year":"2020","unstructured":"Zhang Y, Huang X, Yuan Y et al (2020) Linagliptin protects human chondrogenic ATDC5 cells against advanced glycation end products (AGEs)-induced apoptosis via a mitochondria-dependent pathway. Chem-Biol Interact 315:108901. https:\/\/doi.org\/10.1016\/j.cbi.2019.108901","journal-title":"Chem-Biol Interact"},{"key":"662_CR61","doi-asserted-by":"publisher","DOI":"10.1016\/j.lfs.2020.118192","volume":"258","author":"W Yu","year":"2020","unstructured":"Yu W, Xu Z, Gao Q et al (2020) Protective role of wogonin against cadmium induced testicular toxicity: involvement of antioxidant, anti-inflammatory and anti-apoptotic pathways. Life Sci 258:118192. https:\/\/doi.org\/10.1016\/j.lfs.2020.118192","journal-title":"Life Sci"},{"key":"662_CR62","doi-asserted-by":"publisher","DOI":"10.1155\/2021\/9995342","volume":"2021","author":"X Shi","year":"2021","unstructured":"Shi X, Zhang B, Chu Z et al (2021) Wogonin inhibits cardiac hypertrophy by activating Nrf-2-mediated antioxidant responses. Cardiovasc Ther 2021:9995342. https:\/\/doi.org\/10.1155\/2021\/9995342","journal-title":"Cardiovasc Ther"}],"container-title":["Journal of Computer-Aided Molecular Design"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/s10822-025-00662-9.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1007\/s10822-025-00662-9\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/s10822-025-00662-9.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,11,6]],"date-time":"2025-11-06T17:56:24Z","timestamp":1762451784000},"score":1,"resource":{"primary":{"URL":"https:\/\/link.springer.com\/10.1007\/s10822-025-00662-9"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,9,19]]},"references-count":62,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2025,12]]}},"alternative-id":["662"],"URL":"https:\/\/doi.org\/10.1007\/s10822-025-00662-9","relation":{},"ISSN":["0920-654X","1573-4951"],"issn-type":[{"type":"print","value":"0920-654X"},{"type":"electronic","value":"1573-4951"}],"subject":[],"published":{"date-parts":[[2025,9,19]]},"assertion":[{"value":"25 April 2025","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"31 August 2025","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"19 September 2025","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"The authors declare no competing interests.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Conflict of interest"}}],"article-number":"83"}}