{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,28]],"date-time":"2026-07-28T15:02:34Z","timestamp":1785250954942,"version":"3.55.0"},"reference-count":51,"publisher":"American Chemical Society (ACS)","issue":"29","license":[{"start":{"date-parts":[[2026,7,13]],"date-time":"2026-07-13T00:00:00Z","timestamp":1783900800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100003359","name":"Generalitat Valenciana","doi-asserted-by":"publisher","award":["PROMETEO CIPROM\/2021\/079"],"award-info":[{"award-number":["PROMETEO CIPROM\/2021\/079"]}],"id":[{"id":"10.13039\/501100003359","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100014440","name":"Ministerio de Ciencia, Innovaci?n y Universidades","doi-asserted-by":"publisher","award":["PID2020- 117742GBI00\/AEI\/10.13039\/501100011033"],"award-info":[{"award-number":["PID2020- 117742GBI00\/AEI\/10.13039\/501100011033"]}],"id":[{"id":"10.13039\/100014440","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100007515","name":"Universidad de Valladolid","doi-asserted-by":"publisher","award":["PID2020-117742GBI00\/AEI\/10.13039\/501100011033"],"award-info":[{"award-number":["PID2020-117742GBI00\/AEI\/10.13039\/501100011033"]}],"id":[{"id":"10.13039\/501100007515","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,7,28]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Immunomodulatory drugs such as thalidomide and its derivatives act as molecular glues by binding to the E3 ligase substrate receptor cereblon (CRBN) and promoting the selective recruitment and degradation of specific neosubstrates. Despite extensive structural and experimental characterization, the molecular origin of ligand-induced neosubstrate selectivity remains incompletely understood. Here, we present a comparative computational study of ternary CRBN\u2013ligand\u2013neosubstrate complexes involving two biologically relevant neosubstrates, IKZF1 and SALL4, and five thalidomide derivatives displaying distinct experimental selectivity profiles. Using molecular dynamics simulations and thermodynamic integration calculations, we analyze ligand binding poses, CRBN\u2013ligand interactions, and protein\u2013protein contacts within the ternary complexes. Our results show that all ligands bind CRBN through a conserved interaction network within the thalidomide-binding domain, while direct and persistent ligand\u2013neosubstrate contacts are not observed for the most stable binding modes. Moreover, the CRBN\u2013neosubstrate interaction patterns remain largely unchanged across ligands, and calculated relative binding free energies do not reproduce experimentally observed selectivity trends. These findings suggest that ligand-induced selectivity cannot be explained solely by static interaction patterns in the ternary complex and point to the importance of additional factors, such as CRBN conformational dynamics and kinetic effects, in controlling neosubstrate recruitment.<\/jats:p>","DOI":"10.1021\/acsomega.6c06210","type":"journal-article","created":{"date-parts":[[2026,7,13]],"date-time":"2026-07-13T14:28:01Z","timestamp":1783952881000},"page":"44515-44525","source":"Crossref","is-referenced-by-count":0,"title":["Binding Modes of\nThalidomide Derivatives in Cereblon\u2013Neosubstrate\nComplexes Revealed by Molecular Dynamics and Free Energy Calculations"],"prefix":"10.1021","volume":"11","author":[{"given":"Vero\u0301nica","family":"Marti\u0301n","sequence":"first","affiliation":[{"name":"Universidad de Valladolid , , ,","place":["Valladolid, Spain, 47011"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4331-2322","authenticated-orcid":true,"given":"Milorad","family":"Andjelkovic","sequence":"additional","affiliation":[{"name":"Universitat de Vale\u0300ncia , , ,","place":["Burjassot, Spain, 46100"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Carmen","family":"Barrientos","sequence":"additional","affiliation":[{"name":"Universidad de Valladolid , , ,","place":["Valladolid, Spain, 47011"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1992-935X","authenticated-orcid":true,"given":"Iker","family":"Leon","sequence":"additional","affiliation":[{"name":"Universidad de Valladolid , , ,","place":["Valladolid, Spain, 47011"]},{"name":"Universidad de Valladolid , , ,","place":["Valladolid, Spain, 47011"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6995-1838","authenticated-orcid":true,"given":"In\u0303aki","family":"Tun\u0303o\u0301n","sequence":"additional","affiliation":[{"name":"Universitat de Vale\u0300ncia , , ,","place":["Burjassot, Spain, 46100"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"316","published-online":{"date-parts":[[2026,7,13]]},"reference":[{"key":"2026072810105026100_cit1","doi-asserted-by":"publisher","first-page":"683","DOI":"10.3109\/10428194.2012.728597","article-title":"Molecular Mechanism of Action of\nImmune-Modulatory Drugs Thalidomide, Lenalidomide and Pomalidomide\nin Multiple Myeloma","volume":"54","author":"Zhu","year":"2013","journal-title":"Leuk. Lymphoma"},{"key":"2026072810105026100_cit2","doi-asserted-by":"publisher","first-page":"505","DOI":"10.1007\/s40265-017-0689-1","article-title":"Immunomodulatory Drugs in Multiple\nMyeloma: Mechanisms\nof Action and Clinical Experience","volume":"77","author":"Holstein","year":"2017","journal-title":"Drugs"},{"key":"2026072810105026100_cit3","doi-asserted-by":"publisher","first-page":"189","DOI":"10.2183\/pjab.96.016","article-title":"Molecular Mechanisms\nof Thalidomide and Its Derivatives","volume":"96","author":"Ito","year":"2020","journal-title":"Proc. Jpn.\nAcad. Series B: Phys. Biol. Sci. Jpn. Acad."},{"issue":"1","key":"2026072810105026100_cit4","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1093\/toxsci\/kfr088","article-title":"Thalidomide: The Tragedy of Birth Defects and the Effective\nTreatment of Disease","volume":"122","author":"Kim","year":"2011","journal-title":"Toxicol. Sci."},{"key":"2026072810105026100_cit5","doi-asserted-by":"publisher","first-page":"140","DOI":"10.1002\/bdrc.21096","article-title":"Thalidomide-Induced\nTeratogenesis: History and Mechanisms","volume":"105","author":"Vargesson","year":"2015","journal-title":"Birth\nDefects Res C Embryo Today: Rev."},{"key":"2026072810105026100_cit6","doi-asserted-by":"publisher","first-page":"110114","DOI":"10.1016\/j.biopha.2020.110114","article-title":"Recent Advances in\nthe Molecular Mechanism of Thalidomide Teratogenicity","volume":"127","author":"Gao","year":"2020","journal-title":"Biomed. Pharmacother."},{"key":"2026072810105026100_cit7","doi-asserted-by":"publisher","first-page":"1345","DOI":"10.1126\/science.1177319","article-title":"Identification of a\nPrimary Target of Thalidomide Teratogenicity","volume":"327","author":"Ito","year":"2010","journal-title":"Science 1979"},{"issue":"1","key":"2026072810105026100_cit8","doi-asserted-by":"publisher","first-page":"8885","DOI":"10.1038\/s41467-024-52871-9","article-title":"Design of\na Cereblon Construct for\nCrystallographic and Biophysical Studies of Protein Degraders","volume":"15","author":"Kroupova","year":"2024","journal-title":"Nat. Commun."},{"key":"2026072810105026100_cit9","doi-asserted-by":"crossref","unstructured":"Watson, E. R.; Novick, S.; Matyskiela, M. E.; Chamberlain, P. P.; de la Pen\u0303a, A. H.; Zhu, J.; Tran, E.; Griffin, P. R.; Wertz, I. E.; Lander, G. C.\n          Molecular Glue\nCELMoD Compounds Are Regulators of Cereblon Conformation.  Science, 2022, 378, 549.10.1126\/science.add7574.","DOI":"10.1126\/science.add7574"},{"issue":"1","key":"2026072810105026100_cit10","doi-asserted-by":"publisher","first-page":"1294","DOI":"10.1038\/s41598-018-19202-7","article-title":"Structural\nBasis of Thalidomide Enantiomer Binding to Cereblon","volume":"8","author":"Mori","year":"2018","journal-title":"Sci. Rep."},{"key":"2026072810105026100_cit11","doi-asserted-by":"publisher","first-page":"6234","DOI":"10.1039\/d2cs00116k","article-title":"Discovery of CRBN as a Target of\nThalidomide: A Breakthrough for Progress in the Development of Protein\nDegraders","volume":"51","author":"Yamamoto","year":"2022","journal-title":"Chem. Soc. Rev."},{"key":"2026072810105026100_cit12","doi-asserted-by":"publisher","first-page":"308","DOI":"10.1038\/s41392-024-02004-x","article-title":"Targeted Protein Degradation:\nAdvances in Drug Discovery and Clinical Practice","volume":"9","author":"Zhong","year":"2024","journal-title":"Signal Transduction Targeted Ther."},{"issue":"25","key":"2026072810105026100_cit13","doi-asserted-by":"publisher","first-page":"11519","DOI":"10.1039\/D5SC01371B","article-title":"The Contribution\nof Cyclic Imide Stereoisomers on Cereblon-Dependent Activity","volume":"16","author":"Amako","year":"2025","journal-title":"Chem. Sci."},{"issue":"1","key":"2026072810105026100_cit14","doi-asserted-by":"publisher","first-page":"4578","DOI":"10.1038\/s41467-020-18488-4","article-title":"Structural\nBases of IMiD Selectivity That Emerges by 5-Hydroxythalidomide","volume":"11","author":"Furihata","year":"2020","journal-title":"Nat. Commun."},{"issue":"3","key":"2026072810105026100_cit15","doi-asserted-by":"publisher","first-page":"501","DOI":"10.1039\/D2MD00347C","article-title":"Structural\nRationalization of GSPT1 and IKZF1 Degradation\nby Thalidomide Molecular Glue Derivatives","volume":"14","author":"Nowak","year":"2023","journal-title":"RSC\nMed. Chem."},{"issue":"1","key":"2026072810105026100_cit16","doi-asserted-by":"publisher","first-page":"4683","DOI":"10.1038\/s41467-023-40385-9","article-title":"Lenalidomide Derivatives\nand Proteolysis-Targeting Chimeras for Controlling Neosubstrate Degradation","volume":"14","author":"Yamanaka","year":"2023","journal-title":"Nat. Commun."},{"issue":"7611","key":"2026072810105026100_cit17","doi-asserted-by":"publisher","first-page":"252","DOI":"10.1038\/nature18611","article-title":"A Novel Cereblon Modulator Recruits\nGSPT1 to the CRL4 CRBN Ubiquitin Ligase","volume":"535","author":"Matyskiela","year":"2016","journal-title":"Nature"},{"issue":"7597","key":"2026072810105026100_cit18","doi-asserted-by":"publisher","first-page":"127","DOI":"10.1038\/nature16979","article-title":"Structural\nBasis of Lenalidomide-Induced\nCK1\u03b1 Degradation by the CRL4 CRBN Ubiquitin Ligase","volume":"532","author":"Petzold","year":"2016","journal-title":"Nature"},{"issue":"10","key":"2026072810105026100_cit19","doi-asserted-by":"publisher","first-page":"1034","DOI":"10.1038\/ni.2709","article-title":"Fingerprinting Ikaros","volume":"14","author":"Gounari","year":"2013","journal-title":"Nat. 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Immunol."},{"key":"2026072810105026100_cit23","doi-asserted-by":"publisher","first-page":"111","DOI":"10.1016\/j.gene.2016.02.019","article-title":"SALL4, the Missing Link between Stem\nCells, Development and Cancer","volume":"584","author":"Tatetsu","year":"2016","journal-title":"Gene"},{"key":"2026072810105026100_cit24","doi-asserted-by":"publisher","first-page":"55","DOI":"10.1016\/j.canlet.2014.11.037","article-title":"SALL4: An\nEmerging Cancer Biomarker and Target","volume":"357","author":"Zhang","year":"2015","journal-title":"Cancer\nLett."},{"key":"2026072810105026100_cit25","doi-asserted-by":"publisher","DOI":"10.1002\/jcla.24927","article-title":"The New Advance of\nSALL4 in Cancer: Function, Regulation,\nand Implication","volume":"37","author":"Abouelnazar","year":"2023","journal-title":"J. Clin. Lab. Anal."},{"key":"2026072810105026100_cit26","doi-asserted-by":"publisher","first-page":"771","DOI":"10.4161\/cc.10.5.14829","article-title":"Understanding PLZF: Two Transcriptional Targets, REDD1\nand Smooth Muscle \u03b1-Actin, Define New Questions in Growth Control,\nSenescence, Self-Renewal and Tumor Suppression","volume":"10","author":"Kolesnichenko","year":"2011","journal-title":"Cell Cycle"},{"issue":"4","key":"2026072810105026100_cit27","doi-asserted-by":"publisher","DOI":"10.15252\/embj.2020105375","article-title":"Thalidomide and Its\nMetabolite 5-hydroxythalidomide Induce Teratogenicity via the Cereblon\nNeosubstrate PLZF","volume":"40","author":"Yamanaka","year":"2021","journal-title":"EMBO J."},{"issue":"9","key":"2026072810105026100_cit28","doi-asserted-by":"publisher","first-page":"6037","DOI":"10.1021\/acs.jmedchem.2c01692","article-title":"Lenalidomide\nStabilizes Protein-Protein Complexes by Turning Labile Intermolecular\nH-Bonds into Robust Interactions","volume":"66","author":"Min\u0303arro-Lleonar","year":"2023","journal-title":"J. Med. Chem."},{"issue":"8","key":"2026072810105026100_cit29","doi-asserted-by":"publisher","first-page":"2382","DOI":"10.1021\/acs.jcim.2c01386","article-title":"On Ternary Complex Stability in Protein\nDegradation: In Silico Molecular Glue Binding Affinity Calculations","volume":"63","author":"Weiss","year":"2023","journal-title":"J. Chem. Inf. Model."},{"issue":"11","key":"2026072810105026100_cit30","doi-asserted-by":"publisher","first-page":"5712","DOI":"10.1021\/acs.jctc.5c00064","article-title":"Quantifying\nCooperativity\nthrough Binding Free Energies in Molecular Glue Degraders","volume":"21","author":"Dudas","year":"2025","journal-title":"J. Chem. Theory Comput."},{"issue":"6414","key":"2026072810105026100_cit31","doi-asserted-by":"publisher","DOI":"10.1126\/science.aat0572","article-title":"Defining\nthe Human C2H2 Zinc Finger Degrome Targeted by Thalidomide Analogs\nthrough CRBN","volume":"362","author":"Sievers","year":"2018","journal-title":"Science (1979)"},{"issue":"4","key":"2026072810105026100_cit32","doi-asserted-by":"publisher","first-page":"319","DOI":"10.1038\/s41594-020-0405-9","article-title":"Crystal\nStructure of the SALL4\u2013Pomalidomide\u2013Cereblon\u2013DDB1\nComplex","volume":"27","author":"Matyskiela","year":"2020","journal-title":"Nat. Struct. Mol. Biol."},{"key":"2026072810105026100_cit33","article-title":"Maestro Schro\u0308dinger, 2018-3","year":"2018"},{"key":"2026072810105026100_cit34","unstructured":"Berman, H. M.; Westbrook, J.; Feng, Z.; Gilliland, G.; Bhat, T. N.; Weissig, H.; Shindyalov, I. N.; Bourne, P. E.\n          The Protein Data Bank.  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Chem."},{"issue":"5","key":"2026072810105026100_cit50","doi-asserted-by":"publisher","first-page":"1542","DOI":"10.1021\/ct200909j","article-title":"Routine Microsecond\nMolecular Dynamics Simulations\nwith AMBER on GPUs. 1. Generalized Born","volume":"8","author":"Go\u0308tz","year":"2012","journal-title":"J.\nChem. Theory Comput."},{"issue":"9","key":"2026072810105026100_cit51","doi-asserted-by":"publisher","first-page":"4611","DOI":"10.1021\/acsomega.9b04233","article-title":"Fast, Accurate, and Reliable Protocols for Routine Calculations of\nProtein-Ligand Binding Affinities in Drug Design Projects Using AMBER\nGPU-TI with Ff14SB\/GAFF","volume":"5","author":"He","year":"2020","journal-title":"ACS Omega"}],"container-title":["ACS Omega"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/pubs.acs.org\/doi\/pdf\/10.1021\/acsomega.6c06210","content-type":"application\/pdf","content-version":"vor","intended-application":"unspecified"},{"URL":"https:\/\/pubs.acs.org\/acsodf\/article-pdf\/11\/29\/44515\/65892233\/acsomega.6c06210.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/pubs.acs.org\/acsodf\/article-pdf\/11\/29\/44515\/65892233\/acsomega.6c06210.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,7,28]],"date-time":"2026-07-28T14:40:03Z","timestamp":1785249603000},"score":1,"resource":{"primary":{"URL":"https:\/\/pubs.acs.org\/acsodf\/article\/11\/29\/44515\/5207497\/Binding-Modes-of-Thalidomide-Derivatives-in"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,7,13]]},"references-count":51,"journal-issue":{"issue":"29","published-online":{"date-parts":[[2026,7,13]]},"published-print":{"date-parts":[[2026,7,28]]}},"URL":"https:\/\/doi.org\/10.1021\/acsomega.6c06210","relation":{},"ISSN":["2470-1343"],"issn-type":[{"value":"2470-1343","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,7,13]]}}}