Hygromycin B
[CAS 31282-04-9]

Identification

• Classification: API >> Antibiotics >> Other antibiotics
• Name: Hygromycin B
• Synonyms: O-6-Amino-6-deoxy-L-glycero-D-galacto-heptopyranosylidene-(1-2-3)-o-beta-D-talopyranosyl-(1-5)-2-deoxy-N3-methyl-D-streptamine
• Molecular Formula: C₂₀H₃₇N₃O₁₃
• Molecular Weight: 527.52
• CAS Registry Number: 31282-04-9
• EC Number: 250-545-5
• SMILES: CN[C@H]1C[C@H]([C@@H]([C@H]([C@@H]1O)O[C@H]2[C@@H]3[C@H]([C@H]([C@H](O2)CO)O)OC4(O3)[C@@H]([C@H]([C@H]([C@H](O4)[C@H](CO)N)O)O)O)O)N

Properties

• Density: 1.7±0.1 g/cm³ Calc.^*
• Melting point: 160-180 °C (Expl.)
• Boiling point: 897.6±65.0 °C 760 mmHg (Calc.)^*
• Flash point: 496.7±34.3 °C (Calc.)^*
• Index of refraction: 1.672 (Calc.)^*

^* Calculated using Advanced Chemistry Development (ACD/Labs) Software.

Safety Data

• Hazard Symbols: GHS05;GHS06;GHS07;GHS08 Danger
• Risk Statements: H300+H310+H330-H300-H310-H317-H318-H330-H334
• Safety Statements: P233-P260-P261-P262-P264-P264+P265-P270-P271-P272-P280-P284-P301+P316-P302+P352-P304+P340-P305+P354+P338-P316-P317-P320-P321-P330-P333+P317-P342+P316-P361+P364-P362+P364-P403-P403+P233-P405-P501

Hazard Classification

Hazard	Class	Category Code	Hazard Statement
Acute toxicity	Acute Tox.	2	H300
Respiratory sensitization	Resp. Sens.	1	H334
Serious eye damage	Eye Dam.	1	H318
Acute toxicity	Acute Tox.	2	H330
Acute toxicity	Acute Tox.	2	H310
Skin sensitization	Skin Sens.	1	H317
Acute toxicity	Acute Tox.	1	H330
Acute toxicity	Acute Tox.	1	H310
Eye irritation	Eye Irrit.	2	H319
Acute toxicity	Acute Tox.	4	H332
Acute toxicity	Acute Tox.	1	H300
Skin irritation	Skin Irrit.	2	H315

• Transport Information: UN 3462

Discovery and Applications

Hygromycin B is a naturally occurring aminoglycoside antibiotic produced by certain strains of *Streptomyces hygroscopicus*. It is a complex polyfunctional organic molecule composed of multiple sugar-like rings, amino groups, and hydroxyl substituents, forming a highly polar structure that interacts strongly with biological macromolecules, particularly the ribosome.

Structurally, hygromycin B belongs to the aminoglycoside class, which is characterized by amino-modified sugars linked through glycosidic bonds. The molecule contains a central aminocyclitol core (a sugar-like cyclic polyol containing nitrogen) attached to several amino sugar residues. These structural motifs are heavily functionalized with hydroxyl (–OH) and amino (–NH2 or protonated –NH3+) groups, giving the molecule extensive hydrogen-bonding capacity and high water solubility.

The abundance of hydroxyl groups throughout the structure makes hygromycin B highly polar. These hydroxyl groups can act as both hydrogen-bond donors and acceptors, enabling strong interactions with polar biological environments such as nucleic acids and proteins. The amino groups, which are often protonated under physiological conditions, contribute positive charges that enhance electrostatic interactions with negatively charged biomolecules such as RNA.

A key structural feature of hygromycin B is its conformational rigidity in certain ring systems combined with flexible glycosidic linkages between sugar-like units. This combination allows the molecule to adopt conformations that fit into the binding site of the ribosome, particularly the A-site region of the 30S subunit in prokaryotic ribosomes and the corresponding functional region in eukaryotic ribosomes.

The biological activity of hygromycin B arises from its ability to interfere with protein synthesis. It binds to ribosomal RNA and disrupts the accuracy of translation. Specifically, it inhibits translocation and causes misreading of mRNA during protein synthesis. This leads to the production of abnormal or truncated proteins, ultimately resulting in inhibition of cell growth and cell death at sufficient concentrations.

The mechanism of action is closely related to its structural complementarity with ribosomal RNA. The multiple amino and hydroxyl groups form a network of hydrogen bonds and electrostatic interactions with phosphate groups and nucleotide bases in ribosomal RNA. This strong binding affinity underlies its antibiotic potency.

Because of its potent inhibitory effects on protein synthesis, hygromycin B is also widely used as a selective agent in molecular biology. Cells that express resistance genes (commonly encoding hygromycin phosphotransferase enzymes) can inactivate the antibiotic through phosphorylation, allowing them to survive in its presence. This property makes hygromycin B an important selectable marker in genetic engineering and cell culture experiments.

Physicochemically, hygromycin B is highly hydrophilic due to its dense functionalization with polar groups. It is typically soluble in water but has low permeability through lipid membranes without transport mechanisms, reflecting its charged and polar nature.

Chemically, the molecule is relatively stable under mild conditions, although the glycosidic linkages and amino sugar functionalities can be susceptible to degradation under strong acidic or enzymatic conditions. Its primary mode of chemical activity, however, is not general reactivity but highly specific binding to ribosomal RNA structures.

Overall, hygromycin B is a complex aminoglycoside antibiotic composed of multiple amino sugars and polyhydroxylated ring systems. Its strong binding to ribosomal RNA disrupts protein synthesis, making it both a potent antimicrobial agent and a widely used selection reagent in molecular and cellular biology.

References

2026. Structural and molecular basis of specialized translation mediated by the ribosome mRNA-binding channel. Nature Communications.
DOI: 10.1038/s41467-026-72263-5

2025. Deciphering hygromycin B biosynthetic pathway and D-optimal design for production optimization. World Journal of Microbiology and Biotechnology.
DOI: 10.1007/s11274-025-04364-0

2025. Hygromycin A Treatment of Borrelia burgdorferi –Infected Peromyscus leucopus Suggests Potential as a Reservoir-Targeted Antibiotic. The Journal of Infectious Diseases.
DOI: 10.1093/infdis/jiaf363