{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,1]],"date-time":"2026-07-01T04:17:58Z","timestamp":1782879478399,"version":"3.54.5"},"reference-count":44,"publisher":"MDPI AG","issue":"6","license":[{"start":{"date-parts":[[2026,6,22]],"date-time":"2026-06-22T00:00:00Z","timestamp":1782086400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Pharmaceuticals"],"abstract":"<jats:p>Background\/Objectives: First-generation CDK4\/6 inhibitors (palbociclib, ribociclib, abemaciclib) target the conserved ATP-binding pocket of CDK4 and, despite clinical success, are limited by acquired resistance and insufficient exploration of alternative regulatory sites. This study aimed to identify a putative allosteric small-molecule candidate at the CDK4 \u03b1E-helix\u2013Cyclin D1 \u03b11-helix protein\u2013protein interaction (PPI) interface within the CDK4\/Cyclin D1\/p21 ternary complex using RapidFunnel-AI, a decision-interpretable virtual-screening pipeline. Methods: Starting from 50,000 ChEMBL 33 molecules, the pipeline sequentially applied a Q-Fold\/RapidFunnel topological Tanimoto scan based on clinical CDK4\/6 inhibitor motifs, fragment-level electronic-property enrichment, ADMET\/PAINS filtering, dry Vina-GPU docking, hydration-mediated AutoDock-GPU (Version 1.6) docking, explicit-solvent molecular dynamics, contact-retention analysis, and MM-GBSA energy decomposition. The Q-Fold Thermo-Core surrogate model provided fragment-level enrichment, predicting the HOMO\u2013LUMO gap (R2 = 0.93) and isotropic polarizability (R2 = 0.98) on QM9. Candidate selection did not rely on the lowest docking or MM-GBSA score alone, but on pose persistence, contact continuity, and energy-component consistency. Results: The workflow reduced the initial library to 43 topologically prioritized candidates, 25 ADMET\/PAINS-filtered ligands, and 9 docking-derived complexes for MD validation. Ligand_020 emerged as the only candidate that preserved a persistent binding mode at Site 2 during a 500 ns simulation\u2014an interface engagement reproduced across three independent 500 ns replicates with no full dissociation in any replicate\u2014with a protein C\u03b1 RMSD of 2.88 \u00b1 0.32 \u00c5, a ligand heavy-atom RMSD of 3.56 \u00b1 0.28 \u00c5, and a van der Waals-dominated MM-GBSA profile (\u0394Gbind = \u221228.23 \u00b1 3.57 kcal\/mol). In contrast, palbociclib and ribociclib, forcibly placed at Site 2 as negative controls, lost most initial contacts within 5 ns and tended to detach despite more favorable MM-GBSA values. Conclusions: These results suggest that single-score docking or MM-GBSA ranking can generate false positives at shallow PPI interfaces. By integrating AI-assisted prioritization, multipocket docking, explicit-solvent MD, contact-retention analysis, and energy-component consistency, RapidFunnel-AI nominated Ligand_020 as an experimentally testable putative allosteric hit targeting the CDK4\/Cyclin D1 interface, offering a reusable platform for PPI-focused oncological drug discovery.<\/jats:p>","DOI":"10.3390\/ph19060970","type":"journal-article","created":{"date-parts":[[2026,7,1]],"date-time":"2026-07-01T03:06:34Z","timestamp":1782875194000},"page":"970","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["AI-Assisted Identification of a Putative Allosteric Ligand Targeting the CDK4\/Cyclin D1 Protein\u2013Protein Interface"],"prefix":"10.3390","volume":"19","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-1406-0915","authenticated-orcid":false,"given":"Bar\u0131\u015f","family":"Kurt","sequence":"first","affiliation":[{"name":"Department of Chemistry, Mus Alparslan University, 49250 Mu\u015f, T\u00fcrkiye"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,6,22]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"153","DOI":"10.1038\/nrc2602","article-title":"Cell Cycle, CDKs and Cancer: A Changing Paradigm","volume":"9","author":"Malumbres","year":"2009","journal-title":"Nat. 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