{
  "abstract": "This study reports a series of CRBN molecular glues that selectively induce proteasomal degradation of VAV1, a hematopoietic-specific signaling protein and key target in hematological malignancies and autoimmune diseases. Using unbiased global proteomics, we identify phenyl-glutarimide derivatives (e.g., NGT-201-12) as effective VAV1 degraders that engage its C-terminal SH3 domain (SH3-2). We elucidate a non-canonical RT-loop degron (RDxS motif, residues 796-799) in SH3-2, distinct from previously characterized G-loop degrons, supported by the physics- and AI-driven GluePlex workflow and site-directed mutagenesis. Applying Free Energy Perturbation (FEP) to predicted ternary structures yields cooperativity metrics that correlate with degradation potency, overcoming limitations of standard docking and enabling prospective ranking of analogs-even from weak initial binders. We further show that conformational restriction via halogen substitution (e.g., NGT-201-18) potentiates degradation, a principle rationalized by DFT calculations, while comprehensive SAR studies chart a roadmap for next-generation degraders. Dose-response proteomics confirms VAV1 as the primary target and reveals LIMD1, bearing a canonical G-loop, as an off-target, showing that one glue can engage disparate degrons. These findings expand the landscape of CRBN neosubstrate recognition and offer a therapeutic strategy for targeting VAV1.",
  "abstract_shown": true,
  "affiliations": [
    "The Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas, USA. hanfeng.lin@bcm.edu.",
    "Center for NextGen Therapeutics, Baylor College of Medicine, Houston, Texas, USA. hanfeng.lin@bcm.edu.",
    "Graduate School of Biomedical Sciences, Baylor College of Medicine, Houston, Texas, USA. hanfeng.lin@bcm.edu.",
    "The Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas, USA.",
    "Center for NextGen Therapeutics, Baylor College of Medicine, Houston, Texas, USA.",
    "Graduate School of Biomedical Sciences, Baylor College of Medicine, Houston, Texas, USA.",
    "Thermo Fisher Scientific, San Jose, California, USA.",
    "YDS Pharmatech, Inc., Albany, New York, USA.",
    "SandboxAQ, Palo Alto, California, USA.",
    "Receptor.AI Inc., 223 Concord Turnpike, Cambridge, Massachusetts, USA.",
    "The Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas, USA. wangj@bcm.edu.",
    "Center for NextGen Therapeutics, Baylor College of Medicine, Houston, Texas, USA. wangj@bcm.edu.",
    "Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas, USA. wangj@bcm.edu."
  ],
  "article_type": "research article",
  "arxiv": null,
  "author_total": 15,
  "authors": [
    {
      "affs": [
        0,
        1,
        2
      ],
      "name": "Hanfeng Lin",
      "orcid": "0000-0002-3172-5616"
    },
    {
      "affs": [
        3,
        4
      ],
      "name": "Xin Yu",
      "orcid": "0000-0003-1986-9040"
    },
    {
      "affs": [
        3,
        4,
        5
      ],
      "name": "Haiyang Zheng"
    },
    {
      "affs": [
        3,
        4
      ],
      "name": "Ran Cheng"
    },
    {
      "affs": [
        3,
        4
      ],
      "name": "Min Zhang"
    },
    {
      "affs": [
        3,
        4
      ],
      "name": "Xiaoli Qi"
    },
    {
      "affs": [
        6
      ],
      "name": "Yen-Yu Yang"
    },
    {
      "affs": [
        7
      ],
      "name": "Shengmin Zhou"
    },
    {
      "affs": [
        8
      ],
      "name": "Rui Qi"
    },
    {
      "affs": [
        8
      ],
      "name": "Ly Le"
    },
    {
      "affs": [
        8
      ],
      "name": "Andrea Bortolato"
    },
    {
      "affs": [
        9
      ],
      "name": "Semen Yesylevskyy"
    },
    {
      "affs": [
        9
      ],
      "name": "Alan Nafiiev"
    },
    {
      "affs": [
        7
      ],
      "name": "Xing Che",
      "orcid": "0000-0002-7427-9038"
    },
    {
      "affs": [
        10,
        11,
        12
      ],
      "name": "Jin Wang",
      "orcid": "0000-0003-3625-7919"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/2jdhdn3cpqhaf.bib",
  "cited_by": 5,
  "doi": "10.1038/s41467-026-77657-z",
  "fulltext_url": "https://europepmc.org/articles/PMC13661599",
  "id": "2jdhdn3cpqhaf",
  "issns": [
    "2041-1723"
  ],
  "landing_url": "https://europepmc.org/article/MED/42869914",
  "language": "eng",
  "licence": "CC-BY-NC-ND",
  "licence_label": "CC BY-NC-ND",
  "licence_source": "article",
  "licence_url": "https://creativecommons.org/licenses/by-nc-nd/4.0/",
  "metadata_licence": null,
  "native_subjects": [
    [
      "openalex",
      "1312|Protein Degradation and Inhibitors"
    ]
  ],
  "openalex": "W7212404409",
  "pdf_url": "https://europepmc.org/articles/PMC13661599?pdf=render",
  "pmcid": "PMC13661599",
  "pmid": "42869914",
  "published": "2026-09-12",
  "publisher": null,
  "ris": "https://research.draconitic.com/paper/2jdhdn3cpqhaf.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T12:19:18Z",
      "native_id": "MED:42869914",
      "source": "europepmc",
      "url": "https://europepmc.org/article/MED/42869914"
    }
  ],
  "subjects": [
    {
      "field": "biochemistry",
      "origin": "openalex:1312|Protein Degradation and Inhibitors",
      "subfield": "molecular-biology"
    }
  ],
  "title": "Leveraging high-throughput proteomics and AI-based protein folding to accelerate VAV1 molecular glue discovery.",
  "title_text": "Leveraging high-throughput proteomics and AI-based protein folding to accelerate VAV1 molecular glue discovery.",
  "type": "peer-reviewed",
  "updated_at": "2026-10-30T12:19:18Z",
  "url": "https://research.draconitic.com/paper/2jdhdn3cpqhaf",
  "venue": "Nature communications",
  "versions": []
}