{
  "abstract": "Background. The AcrAB-TolC system is the principal constitutive efflux pump of Escherichia coli and an attractive adjuvant target. Virtual screening campaigns against its distal binding pocket have been published without the retrospective validation standard elsewhere in the field. This study asked whether such a benchmark can be built from the published literature. Methods. Compounds reported as AcrB inhibitors were filtered against an independent reproducibility screen and assigned to a binding site by the strongest structural or mutational evidence available. Property-matched decoys, a library-representative background and a class of reported-but-non-reproducing inhibitors served as negatives. A pilot docking screen against the hydrophobic trap of 5ENQ was re-analysed under the curated labels, with areas under the receiver-operating-characteristic curve reported with analytic and bootstrap confidence intervals. Two controls were pre-specified: a wrong-site control, and a ligand-only ablation deleting the receptor entirely. Results. Of 49 compounds reported as AcrB inhibitors, 38 have been independently retested and 17 reproduced; 13 maps to the distal pocket and 5 have a co-crystal there. Two barriers follow. With 5 actives the 95% interval cannot be narrower than ±0.26; reaching a conventional ±0.06 would require 94 actives, while raising the decoy ratio from 40:1 to 500:1 narrows the interval by 0.8%. More seriously, the ligand-only ablation reached 1.000 against a docking area of 0.707: deleting the receptor improved performance. 4 of the 5 co-crystal actives are analogues spanning 2 scaffolds, with a median pairwise ECFP4 similarity of 0.574 against 0.077 to the negatives; every active–active pair lies above the decoy-exclusion threshold of 0.35 and every active–negative pair below it. Conclusions. A retrospective docking benchmark for the AcrB distal pocket cannot currently be built. The first barrier is quantitative and yields to more confirmed inhibitors of any kind; the second is qualitative and yields only to inhibitors that are chemically unlike one another. Screening against this pocket therefore proceeds unvalidated and cannot be validated until structurally diverse confirmed inhibitors exist, which is a medicinal-chemistry result rather than a computational one. The curated compound table, the metrics implementation with its unit tests and the analysis notebook are released.",
  "abstract_shown": true,
  "affiliations": [
    "Faculty of Health Sciences",
    "Bahçeşehir Cyprus University"
  ],
  "article_type": null,
  "arxiv": null,
  "author_total": 1,
  "authors": [
    {
      "affs": [
        0,
        1
      ],
      "name": "Ibrahim Ibrahim Shuaibu",
      "orcid": "0000-0003-1103-3150"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/d0nhetnfesqxg.bib",
  "cited_by": 0,
  "doi": "10.26434/chemrxiv.15009731/v1",
  "fulltext_url": null,
  "id": "d0nhetnfesqxg",
  "issns": [],
  "landing_url": "https://chemrxiv.org/doi/full/10.26434/chemrxiv.15009731/v1",
  "language": null,
  "licence": "CC-BY",
  "licence_label": "CC BY",
  "licence_source": "journal",
  "licence_url": "https://creativecommons.org/licenses/by/4.0/",
  "metadata_licence": null,
  "native_subjects": [
    [
      "openalex",
      "1703|Computational Drug Discovery Methods"
    ]
  ],
  "openalex": "W7215082315",
  "pdf_url": "https://chemrxiv.org/doi/pdf/10.26434/chemrxiv.15009731/v1",
  "pmcid": null,
  "pmid": null,
  "published": "2026-10-01",
  "publisher": "American Chemical Society (ACS)",
  "ris": "https://research.draconitic.com/paper/d0nhetnfesqxg.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T12:17:21Z",
      "native_id": "10.26434/chemrxiv.15009731",
      "source": "chemrxiv",
      "url": "https://chemrxiv.org/doi/full/10.26434/chemrxiv.15009731/v1"
    }
  ],
  "subjects": [
    {
      "field": "chemistry",
      "origin": "source:chemrxiv",
      "subfield": "general"
    }
  ],
  "title": "Two barriers to benchmarking structure-based virtual screening against the AcrB efflux pump: a sample-size ceiling and an identifiability failure",
  "title_text": "Two barriers to benchmarking structure-based virtual screening against the AcrB efflux pump: a sample-size ceiling and an identifiability failure",
  "type": "preprint",
  "updated_at": "2026-10-30T12:17:21Z",
  "url": "https://research.draconitic.com/paper/d0nhetnfesqxg",
  "venue": "ChemRxiv",
  "versions": []
}