Plazomicin

● Links

Drug Name

Plazomicin is a relatively new or next-generation aminoglycoside, that is used to treat drug-resistant bacteria, including carbapenem-resistant (CRE) and extended-spectrum β-lactamase (ESBL) producing Enterobacteriaceae. It is administered intravenously to treat complicated urinary tract infections and other infections that have limited or no alternative treatment options.

Table 1. Basic profile of plazomicin.

Description Synthetically derived next-generation aminoglycoside
Target(s) Ribosomal 30S subunit
Generic Plazomicin
Commercial Name Zemdri
Combination Drug(s) N/A
Other Synonyms N/A
IUPAC Name (2S)-4-amino-N-[(1R,2S,3S,4R,5S)-5-amino-4-{[(2S,3R)-3-amino-6-{[(2-hydroxyethyl)amino]methyl}-3,4-dihydro-2H-pyran-2-yl]oxy}-2-{[(2R,3R,4R,5R)-3,5-dihydroxy-5-methyl-4-(methylamino)oxan-2-yl]oxy}-3-hydroxycyclohexyl]-2-hydroxybutanamide
Ligand Code in PDB EDS
PDB Structure 7lh5
ATC code J01GB14
RotateHydrogensLabels
Figure 1. 2D and 3D structures of Plazomicin (PDB ligand code: EDS).

Antibiotic Chemistry

Plazomicin was synthesized from a sisomicin and designed to be resistant to the action of a variety of aminoglycoside modifying enzymes (AMEs) commonly found in gram-negative pathogens (Krause et al., 2016). It has the 2-deoxystreptamine ring in its core but the substitutions around the ring are different so that it can not be modified by APH(3')-III, -VI, and -VII phosphotransferases and ANT adenyltransferase (see Figure 2). Modification at the N-1 position sterically hinders the action of the AAC(3) acetyltransferases, ANT(2"), and APH(2") enzymes, while the addition of a hydroxyethyl substituent at the 6' position inhibits the action of the AAC(6') enzymes (Golkar et al., 2021). Plazomicin also lacks hydroxyl groups at the 3′ and 4′ positions, protecting it against the activity of AMEs ANT(4′) and APH(3′).

Learn more about AMEs that act on plazomicin.

Learn about other aminoglycoside modifying enzymes.

Figure 2. The 2D structure of plazomicin is shown with the core deoxystreptamine ring marked with an oval in dashed lines. The action sites of clinically relevant aminoglycoside modifying enzymes (AMEs) are shown - AMEs with a black arrow cannot modify plazomicin, while the colored arrow indicates modification by AMEs. The figure was made with ChemDraw and used information from Golkar et al., 2021.
Figure 2. The 2D structure of plazomicin is shown with the core deoxystreptamine ring marked with an oval in dashed lines. The action sites of clinically relevant aminoglycoside modifying enzymes (AMEs) are shown - AMEs with a black arrow cannot modify plazomicin, while the colored arrow indicates modification by AMEs. The figure was made with ChemDraw and used information from Golkar et al., 2021.

Drug Information

Table 2. Chemical and physical properties (DrugBank).

Chemical Formula C25H48N6O10
Molecular Weight 592.691 g/mol
Calculated Predicted Partition Coefficient: cLogP -2.2
Calculated Predicted Aqueous Solubility: cLogS -1.7
Solubility (in water) 12.3 mg/mL
Predicted Topological Polar Surface Area (TPSA) 269.29 Å2

Drug Target

The ribosome is the macromolecular machine on which proteins are synthesized. It is targeted by many classes of antibiotics approved by the US FDA. Plazomicin positions itself in the decoding center of the 30S ribosomal subunit and makes direct contact with rRNA. It inhibits the accommodation of tRNAs in the A-site, as a result, incorrect amino acids are inserted into nascent polypeptide chains during translation, producing nonfunctional proteins.

Learn more about mRNA decoding, protein synthesis, and ribosomes.

Drug-Target Complex

The structure of Thermus thermophilus ribosome in complex with plazomicin reveals that the antibiotic binds to the 16S ribosomal A site. It interacts vi hydrogen bonds with G1405, C1407, A1408, G1494, U1495, C1496, and G1497 (Figure 3). These interactions in the aminoacyl-tRNA site (A-site) likely interfere with the fidelity of mRNA translation (Golkar et al., 2021).

Figure 3. The binding site of plazomicin and the major interactions of the drug with the ribosome (PDB ID: 7lh5, Golkar et al., 2021).
Figure 3. The binding site of plazomicin and the major interactions of the drug with the ribosome (PDB ID: 7lh5, Golkar et al., 2021).

Pharmacologic Properties and Safety

Table 3. Pharmacokinetics: ADMET of plazomicin.

Features Comment(s) Source
Oral Bioavailability (%) 0 DrugBank
IC50 N/A N/A
Ki (μM) N/A N/A
Half-Life (hrs) 3.5 ± 0.5 hours DrugBank
Duration of Action 24 hours FDA
Absorption Site Rapidly absorbed into the extracellular components of body tissues after injection DrugBank
Transporter(s) Multidrug and toxin extrusion protein 1 (MATE1) and MATE2 DrugBank
Metabolism Plazomicin does not undergo significant metabolism DrugBank
Excretion ~89% of plazomicin is excreted via urine, ~0.2% is excreted via the feces DrugBank
AMES Test (Carcinogenic Effect) N/A N/A
hERG Safety Test (Cardiac Effect) N/A N/A
Liver Toxicity Aminoglycosides are not listed or mentioned in large case series of drug-induced liver disease and acute liver failure. Thus, hepatic injury due to plazomicin is rare if it occurs at all. LiverTox

Drug Interactions and Side Effects

Table 4. Drug interactions and side effects of plazomicin.

Features Comment(s) Source
Total Number of Drug Interactions 185 drugs Drugs.com
Major Drug Interactions 58 drugs (ex: bcg, diatrizoate, furosemide, mannitol) Drugs.com
Alcohol/Food Interactions No major alcohol or food interactions Drugs.com
Disease Interactions Neuromuscular disease (major) Hearing impairment (major) Renal dysfunction (major) Clostridioides difficile-associated diarrhea (CDAD) (major) Hepatic impairment (moderate) Drugs.com
On-Target Side Effects N/A N/A
Off-Target Side Effects Blood in the urine, change in the frequency of urination or amount of urine, difficulty in breathing, drowsiness, increased thirst, loss of appetite, nausea, swelling of the feet or lower legs, vomiting, ototoxicity Drugs.com
CYP Interactions N/A N/A

Links

Table 5. Links to learn more about plazomicin

Comprehensive Antibiotic Resistance Database (CARD) ARO:3003675
DrugBank DB12615
Drugs.com https://www.drugs.com/mtm/plazomicin.html
FDA - Zemdri https://www.accessdata.fda.gov/drugsatfda_docs/label/2018/210303Orig1s000lbl.pdf
LiverTox: National Institutes of Health (NIH) https://www.ncbi.nlm.nih.gov/books/NBK548540/
PubChem CID 42613186

Learn about plazomicin resistance.

References

Golkar, T., Bassenden, A. V., Maiti, K., Arya, D. P., Schmeing, T. M., & Berghuis, A. M. (2021). Structural basis for plazomicin antibiotic action and resistance. Communications biology, 4(1), 1-8. https://doi.org/10.1038/s42003-021-02261-4

Jia, B., Raphenya, A. R., Alcock, B., Waglechner, N., Guo, P., Tsang, K. K., Lago, B. A., Dave, B. M., Pereira, S., Sharma, A. N., Doshi, S., Courtot, M., Lo, R., Williams, L. E., Frye, J. G., Elsayegh, T., Sardar, D. Westman, E. L., Pawlowski, A. C., Johnson, T. A., Brinkman, F. S., Wright, G. D., and McArthur, A. G. (2017) CARD 2017: expansion and model-centric curation of the Comprehensive Antibiotic Resistance Database. Nucleic Acids Research 45, D566-573. https://doi.org/10.1093/nar/gkac920

Krause, K. M., Serio, A. W., Kane, T. R., & Connolly, L. E. (2016). Aminoglycosides: An Overview. Cold Spring Harbor perspectives in medicine, 6(6), a027029. https://doi.org/10.1101/cshperspect.a027029

LiverTox - Clinical and Research Information on Drug-Induced Liver Injury. National Institutes of Health. https://www.ncbi.nlm.nih.gov/books/NBK548540/

Plazomicin. PubChem. https://pubchem.ncbi.nlm.nih.gov/compound/Plazomicin

Plazomicn - DrugBank. Drugbank.ca https://go.drugbank.com/drugs/DB12615

Plazomicin (injection). Drugs.com https://www.drugs.com/mtm/plazomicin.html

Zemdri (plazomicin for injection) (2018) Food and Drug Administration. https://www.accessdata.fda.gov/drugsatfda_docs/label/2018/210303Orig1s000lbl.pdf

March 2025, Helen Gao, Shuchismita Dutta; Reviewed by Drs. Albert Berghuis and Tolou Golkar
https://doi.org/10.2210/rcsb_pdb/GH/AMR/drugs/antibiotics/prot-syn/ribo/AMG/plazomicin