Hygromycin B

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Hygromycin B
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Executive Summary Information

Compound Hygromycin B
Toxicities Cytotoxicity
Mechanisms Binds to the 40S subunit of the 80S ribosome, distorting the ribosomal structure. The compound is generically toxic to all cell types in all species, including bacteria, fungi, and higher eukaryotes.
Comments This compound was selected for the validation of electron cryomicroscopy methods and is optional for more general profiling.

SAFETY WARNING: The powder is highly allergenic, is a lachrymator, and can be fatal if absorbed through the skin. Avoid contact or inhalation. The ears are especially sensitive to this reagent. It is preferable to handle this compound in aqueous solution. Reference

Feedback Contact Gold Compound Working Group (GCWG)
Hygromycin B
Hygromycin B.png
Leadscope Id LS-146953
CAS 31282-04-9
Pathway DBs
Assay DBs
PubChem CID 35766
ChEMBL 1276484
Omics DBs
ToxCast Accepted yes
ToxBank Accepted yes
Toxicities Cytotoxicity

In Vivo Data ? Compound Assessment
Adverse Events ? This material inhibits protein synthesis nonselectively with respect to species and is generally toxic to all cells. Hygromycin b distorts the structure of ribosome in crystal structures.


-Maria A. Borovinskaya, Shinichiro Shoji, Kurt Fredrick, Jamie H.D. Cate. “Structural basis for hygromycin B inhibition of protein biosynthesis”, RNA (2008), 14:1590–1599.
Toxicity Mechanisms ? The compound is species nonselective, and the major toxicity derives from its inhibition of protein synthesis.
Therapeutic Target ? Hygromycin B is an aminoglycoside antibiotic that kills bacteria, fungi and eukaryotic cells by inhibiting protein synthesis.


-McGuire, Pettinger (1953), "Hygromycin I. Preliminary studies on the production and biological activity of a new antibiotic.", Antibiot. Chemother. 3: 1268–1278

It stabilizes the tRNA-ribosomal acceptor site in the 30S subunit of the 70S ribosome, thereby inhibiting translocation and protein synthesis.


-Maria A. Borovinskaya, Shinichiro Shoji, Kurt Fredrick, Jamie H.D. Cate. “Structural basis for hygromycin B inhibition of protein biosynthesis”, RNA (2008), 14:1590–1599

PubMed references

The following resource link will perform a PubMed query for the terms "hygromycin b" and "liver toxicity".
Hygromycin B Search

PK-ADME ? Compound Assessment
PK parameters ? Not prescribed for humans. Administered to animals at 20 umol per kg of feed (0.2 umol / kg animal weight) for control of parasites in the GI tract.
Therapeutic window ? The therapeutic window is increased when the drug is administered orally for treatment of GI parasites due to its low bioavailability.

LD50 = single dose at 6 mg/kg i.p. in rats (12 umol/kg). GuideChem

Effective single i.p. dose vs. murine coronaviral hepatitis is 0.01 umol/kg.


-Georgina Macintyre, Bernadette Curry, Fred Wong, Robert Anderson. “Hygromycin B Therapy of a Murine Coronaviral Hepatitis”, Antimicrob Agents Chemother, 1991: 2125-2127.
Metabolically activated ? No

Omics and IC50 Data ? Compound Assessment
Gene expression profiles known. ?
Proteomics profiles known. ?
Metabonomics profiles known. ?
Fluxomics profiles known. ?
Epigenomics profiles known. ?
Observed IC50 for in vitro cellular efficacy. ? The IC50 for binding to the ribosome is 20 uM. Hygromycin b is normally used at 0.1-1.0 mM concentrations in cell selection experiments.


-Susan M. McGaha and W. Scott Champney. “Hygromycin B Inhibition of Protein Synthesis and Ribosome Biogenesis in Escherichia coli”, Antimicrob Agents Chemother, 2007: 591–596
Observed IC50 for in vitro cellular toxicity studies. ? Same as IC50 for efficacy.

Physical Properties ? Compound Assessment
Accepted and listed within the ToxCast/Tox21 program. ? No - Not included in ToxCast Phase I and II Chemicals List
Substance stability. ? Hygromycin is stable for at least one year at –20°C, three months at room temperature, and at least one month at 37°C. Hygromycin B is sensitive to high concentrations of acid, but short-term exposure to dilute acids can be tolerated. Impurities cause darkening of solutions to dark yellow by oxidation on standing. Sterilize by filtration (not autoclaving).


Soluble in buffer solution at 30 times the in vitro IC50 for toxicity. ? Hydrocholride and disulphate salts soluble at 100 mM in PBS at pH 7.2.
Solubility in DMSO 100 times buffer solubility. ? Normally handled in aqueous solution.
Vessel binding properties. ? Not determined.
Vapor pressure. (Non-volatile) ? Yes. However, the solid is allergenic and can cause organ toxicity if inhaled as a dust.

Authors of this ToxBank wiki page

David Bower
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