{
  "abstract": "Pituitary adenylate cyclase-activating peptide 38 (PACAP-38) is a vasoactive peptide that is attracting attention as a potential target for next-generation migraine treatments. Antibodies against PACAP-38 have recently shown promising results as a ligand trap medicine in clinical trials. In this study, we investigated the de novo design of miniproteins to evaluate the potential for developing a medium-molecular-weight drug that binds to PACAP-38. Using Bindcraft, we designed binders against PACAP-38 and identified ICLIST-2, a 63-residue peptide with affinity for PACAP-38 (KD = 26.5 nM). Furthermore, by alanine scanning and structural analysis of ICLIST-2, we determined residues that were suitable for further optimization using ProteinMPNN. This resulted in the design of ICLIST-11, which incorporates nine amino acid substitutions relative to ICLIST-2, resulting in a KD of 4.51 nM. Interaction analysis based on a structural model suggested that three mutations in ICLIST-11 may be important for enhancing affinity. Moreover, ICLIST-11 exhibits a Tm value that is 14 {degrees}C higher, and MD simulations suggest that the substitution of three residues with hydrophobic residues (E30F, M31L, and R54W) is one reason for this. In cell-based functional assays, ICLIST-11 demonstrated potent, concentration-dependent neutralizing activity against PACAP-38-induced PAC1R activation (IC50 = 10.6 nM), significantly outperforming the parental ICLIST-2. Taken together, these results provide a framework for protein drug discovery targeting PACAP-38.",
  "abstract_shown": true,
  "affiliations": [
    "Imperial College London"
  ],
  "article_type": "New results",
  "arxiv": null,
  "author_total": 4,
  "authors": [
    {
      "affs": [
        0
      ],
      "name": "H. Yamaguchi"
    },
    {
      "name": "S. Suzuki"
    },
    {
      "name": "Y. Fujiyoshi"
    },
    {
      "name": "M. Isalan"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/64sagz20v2e2m.bib",
  "cited_by": 0,
  "doi": "10.64898/2026.10.30.763049",
  "fulltext_url": "https://www.biorxiv.org/content/10.64898/2026.10.30.763049v1.full",
  "id": "64sagz20v2e2m",
  "issns": [],
  "landing_url": "https://www.biorxiv.org/content/10.64898/2026.10.30.763049v1",
  "language": null,
  "licence": "CC-BY",
  "licence_label": "CC BY",
  "licence_source": "article",
  "licence_url": "https://creativecommons.org/licenses/by/4.0/",
  "metadata_licence": null,
  "native_subjects": [
    [
      "biorxiv",
      "bioengineering"
    ]
  ],
  "openalex": null,
  "pdf_url": "https://www.biorxiv.org/content/10.64898/2026.10.30.763049v1.full.pdf",
  "pmcid": null,
  "pmid": null,
  "published": "2026-10-30",
  "publisher": null,
  "ris": "https://research.draconitic.com/paper/64sagz20v2e2m.ris",
  "sources": [
    {
      "first_seen": "2026-11-03T00:20:41Z",
      "native_id": "10.64898/2026.10.30.763049",
      "source": "biorxiv",
      "url": "https://www.biorxiv.org/content/10.64898/2026.10.30.763049v1"
    }
  ],
  "subjects": [
    {
      "field": "biology",
      "origin": "biorxiv:bioengineering",
      "subfield": "systems-synthetic"
    }
  ],
  "title": "De novo design of mini-proteins as specific binders to PACAP-38, a key mediator of migraine",
  "title_text": "De novo design of mini-proteins as specific binders to PACAP-38, a key mediator of migraine",
  "type": "preprint",
  "updated_at": "2026-11-04T00:21:11Z",
  "url": "https://research.draconitic.com/paper/64sagz20v2e2m",
  "venue": "bioRxiv",
  "versions": []
}