{
  "id": "AIBD-0016",
  "title": "Halicin: a deep-learning-identified antibiotic validated in vitro and in mice, with no verified human outcome",
  "summary": "A deep-learning screen identified halicin, active in vitro and in mice and confirmed by other labs; no human outcome.",
  "date_observed": "2020-02-20",
  "date_basis": "unassessed",
  "date_precision": "unassessed",
  "benefit_status": null,
  "source_collection": null,
  "source_entry": null,
  "account": "Jonathan Stokes, Regina Barzilay, James Collins and colleagues at MIT, the Broad Institute, Harvard and McMaster University published in Cell on 20 February 2020. They reported halicin, a molecule identified by a directed-message-passing neural network trained on 2,335 molecules to predict inhibition of E. coli growth. Halicin, originally investigated as a kinase inhibitor for diabetes, is structurally divergent from conventional antibiotics. It reduced Acinetobacter baumannii in a mouse wound model and cleared Clostridioides difficile in a mouse infection model. Independent laboratories at KACST in Riyadh (December 2021) and Central South University in Changsha (September 2022) confirmed antibacterial activity in vitro. The latter also in a mouse abscess model. No clinical use or human trial result appears in any cited source.",
  "category": "general benefit",
  "unexpected": false,
  "purpose": "Built to predict molecules that inhibit bacterial growth and surface antibiotic candidates. Halicin was that purpose.",
  "system": "Directed-message-passing neural network (D-MPNN) for antibacterial activity prediction (Chemprop-style, MIT)",
  "model_version": "Chemprop (directed-message passing neural network)",
  "developer": "Massachusetts Institute of Technology (Collins and Barzilay laboratories) with the Broad Institute",
  "deployer": "MIT / Broad Institute / McMaster University research teams",
  "location": "Cambridge, United States",
  "domain": "Biomedicine / antibiotic discovery",
  "segment": "Academic research",
  "benefit_type": "Improved Knowledge Discovery",
  "taxonomy_note": null,
  "registry_ids": {},
  "ratings": [
    {
      "group": "societal",
      "depth": null,
      "reason": "The sources document in vitro and murine results and independent laboratory confirmation. No individually attributable real-world outcome such as a treated patient or an approved drug."
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    "status": "assessed",
    "statement": "The neural network's prediction selected halicin for testing from compounds not previously recognized as antibiotics. Wet-lab experiments by the authors and later by independent groups confirmed the activity. The outcome so far is a laboratory and animal-model result."
  },
  "evidence": [
    {
      "kind": "peer-reviewed study",
      "citation": "Stokes, J. M. et al. (2020). A Deep Learning Approach to Antibiotic Discovery. Cell 180, 688–702 (PMC8349178).",
      "title": "A deep learning approach to antibiotic discovery",
      "url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC8349178/",
      "date": "2020-02-20",
      "written_by": "makers",
      "quote": "sterilization of 3 out of 4 mice after 72 hr of treatment, and 4 out of 4 mice after 96 hr of treatment."
    },
    {
      "kind": "peer-reviewed study",
      "citation": "Booq, R. Y., Tawfik, E. A., Alfassam, H. A., Alfahad, A. J. and Alyamani, E. J. (2021). Assessment of the Antibacterial Efficacy of Halicin against Pathogenic Bacteria. Antibiotics 10(12), 1480 (PMC8698312).",
      "title": "Assessment of the Antibacterial Efficacy of Halicin against Pathogenic Bacteria",
      "url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC8698312/",
      "date": "2021-12-02",
      "written_by": "independent",
      "quote": "The new antibacterial agent was able to inhibit all tested gram-positive and gram-negative bacterial strains, but in different concentrations—including the A. baumannii multidrug-resistant (MDR) isolate."
    },
    {
      "kind": "peer-reviewed study",
      "citation": "Hussain, Z. et al. (2022). Study on antibacterial effect of halicin (SU3327) against Enterococcus faecalis and Enterococcus faecium. Pathogens and Disease 80(1), ftac037.",
      "title": "Study on antibacterial effect of halicin (SU3327) against Enterococcus faecalis and Enterococcus faecium",
      "url": "https://academic.oup.com/femspd/article/80/1/ftac037/6713948",
      "date": "2022-09-24",
      "written_by": "independent",
      "quote": "the minimum inhibitory concentrations (MIC) of halicin against different strains of Enterococcus faecalis and Enterococcus faecium ranged from 4 to 8 μg/ml."
    }
  ],
  "replication": {
    "produced_by": [
      "A growth-inhibition training set of a few thousand molecules",
      "A message-passing network ranking large chemical libraries",
      "Wet-lab confirmation of predicted actives and animal-model testing"
    ],
    "must_hold": [
      "Predicted compounds must be available for synthesis or purchase",
      "Activity must be confirmed experimentally. A verified real-world outcome would require clinical use"
    ],
    "echoes": [
      {
        "date": "2023-05-25",
        "setting": "Abaucin, a narrow-spectrum anti-Acinetobacter baumannii compound identified by a neural network trained on about 7,500 screened molecules (McMaster and MIT), controlled infection in a mouse wound model; preclinical only",
        "model_version": null,
        "outcome": "recurred",
        "source": "https://www.nature.com/articles/s41589-023-01349-8"
      }
    ]
  },
  "paired_incident": null,
  "headline": "MIT neural network finds halicin, active in vitro and in mice",
  "metric": null,
  "comparator": {
    "against": "vehicle control and the first-line antibiotic metronidazole in a mouse Clostridioides difficile infection model",
    "before": "vehicle or the antibiotic metronidazole (lower clearance rate)",
    "after": "sterilization of 3 out of 4 mice after 72 hr of treatment, and 4 out of 4 mice after 96 hr of treatment",
    "basis": "measured",
    "quote": "Excitingly, we observed that halicin resulted in C. difficile clearance at a greater rate than vehicle or the antibiotic metronidazole (Figure 5F), which is not only a first-line treatment for C. difficile infection, but also the antibiotic most similar to halicin based on Tanimoto score (Figure 2H, Table S2H). Indeed, halicin resulted in sterilization of 3 out of 4 mice after 72 hr of treatment, and 4 out of 4 mice after 96 hr of treatment.",
    "url": "https://pmc.ncbi.nlm.nih.gov/articles/PMC8349178/"
  },
  "later": {
    "status": "persisted",
    "date": "2021-12-02",
    "note": "An independent laboratory at KACST in Riyadh confirmed halicin's in vitro activity against gram-positive and gram-negative strains, including a multidrug-resistant A. baumannii isolate; the compound remains preclinical.",
    "quote": "The new antibacterial agent was able to inhibit all tested gram-positive and gram-negative bacterial strains, but in different concentrations—including the A. baumannii multidrug-resistant (MDR) isolate.",
    "url": "https://europepmc.org/article/PMC/PMC8698312"
  },
  "value": null,
  "developer_country": "United States",
  "deployer_country": "United States",
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    {
      "date": "2026-10-20",
      "change": "Record drafted from the cited sources.",
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      "editor": "AIBD"
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    {
      "date": "2026-10-20",
      "change": "Replaced all three evidence quotes with the sentences as printed in the cited papers, because the Booq quote had been given a subject borrowed from the Discussion and the Hussain and Stokes quotes silently abbreviated or dropped words.",
      "source": "https://pmc.ncbi.nlm.nih.gov/articles/PMC8349178/ ; https://pmc.ncbi.nlm.nih.gov/articles/PMC8698312/ ; https://academic.oup.com/femspd/article/80/1/ftac037/6713948",
      "editor": "AIBD"
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      "change": "Added what happened since from the cited sources.",
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      "change": "Country of the developer and the deployer added from the organization's own site or a registry.",
      "source": "https://en.wikipedia.org/wiki/Massachusetts_Institute_of_Technology; https://en.wikipedia.org/wiki/Massachusetts_Institute_of_Technology",
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      "date": "2026-10-21",
      "change": "Prose pass: a rating reason, account, purpose, the replication conditions, the system's part rewritten in shorter sentences with abbreviations expanded; facts, figures and quotations unchanged.",
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  "confidence": "studied",
  "shade": "high",
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                  "setting": "Abaucin, a narrow-spectrum anti-Acinetobacter baumannii compound identified by a neural network trained on about 7,500 screened molecules (McMaster and MIT), controlled infection in a mouse wound model; preclinical only",
                  "outcome": "recurred",
                  "source": "https://www.nature.com/articles/s41589-023-01349-8"
                }
              ]
            }
          }
        },
        "provenance": {
          "kind": "legacy_record",
          "basis": "Preserved from the existing AIBD record; external sources were not rechecked.",
          "record_fields": [
            "account",
            "replication"
          ],
          "source_refs": []
        },
        "review_state": "record_mapped",
        "coverage": "partial"
      }
    },
    "summary": {
      "total": 91,
      "addressed": 91,
      "known": 31,
      "reviewed": 0,
      "record_mapped": 31,
      "not_assessed": 60,
      "complete": false,
      "by_state": {
        "value_present": 31,
        "not_reported": 0,
        "unresolved": 0,
        "not_assessed": 60,
        "not_applicable": 0,
        "withheld": 0,
        "source_unavailable": 0
      }
    }
  }
}