Linezolid

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Drug Name

Linezolid is a synthetic antibiotic that is a member of the oxazolidinone class. It inhibits bacterial protein synthesis by binding to the large ribosomal subunit and preventing accurate placement of tRNAs to the A-site. Linezolid is a broad-spectrum drug most commonly used against aerobic gram-positive bacteria including vancomycin-resistant Enterococcus faecium (VRE) and methicillin-resistant Staphylococcus aureus (MRSA) (Wilson et al., 2008).

Table 1. Basic profile of linezolid.

Description Broad-spectrum oxazolidinone antibiotic
Target(s) Ribosome (50S subunit)
Generic Linezolid
Commercial Name Zyvox
Combination Drug(s) N/A
Other Synonyms N/A
IUPAC Name N-[[(5S)-3-(3-fluoro-4-morpholin-4-ylphenyl)-2-oxo-1,3-oxazolidin-5-yl]methyl]acetamide
Ligand Code in PDB ZLD
3D Structure of Linezolid Bound to Target Protein 4wfa (structure of the large ribosomal subunit of Staphylococcus aureus in complex with linezolid)
ATC code J01XX08
RotateHydrogensLabels
Figure 1. 2D and 3D structures of Linezolid (PDB ligand code: ZLD).

Antibiotic Chemistry

The antibacterial features of linezolid can be attributed to many of its chemical properties. It is a hydrophilic drug composed of three aromatic rings and an acetamide group on its tail.

Figure 2. 2D structure of linezolid showing the important functional moieties responsible for antibacterial activity. Structure created using ChemDraw.
Figure 2. 2D structure of linezolid showing the important functional moieties responsible for antibacterial activity. Structure created using ChemDraw.

Drug Information

Table 2. Chemical and physical properties (DrugBank)

Chemical Formula C16H20FN3O4
Molecular Weight 337.35 g/mol
Calculated Predicted Partition Coefficient: cLogP 0.61
Calculated Predicted Aqueous Solubility: cLogS -2.40
Solubility (in water) 1.44 mg/mL
Predicted Topological Polar Surface Area (TPSA) 71.11 Å2

Drug Target

The ribosome is the macromolecular machine on which proteins are synthesized. It is targeted by many classes of US FDA approved antibiotics including oxazolidinones. Linezolid positions itself in the peptidyl transferase center of the 50S ribosomal subunit and makes direct contact with rRNA. It directly interferes with the positioning of tRNAs in the A- and P-site and as a result, prevents peptide bond formation during translation.

Learn more about protein synthesis, and the ribosome.

Drug-Target Complex

Each ribosomal subunit is composed of protein chains and rRNA. X-ray crystallography of the 50S subunit of Staphylococcus aureus bound by linezolid (shown in Figure 3) revealed that the large subunit consists of (Eyal et al., 2015):
* 35 protein chains which are colored in dark blue
* 23S rRNA of 2,923 nucleotides which are colored in cornflower blue
* 5S rRNA of 114 nucleotides which are colored in deep sky blue

Linezolid binds in the peptidyl transferase center in a pocket formed by 23S rRNA residues. In Staphylococcus aureus, the drug is observed to form three hydrogen bonds as well as multiple van der Waals and hydrophobic interactions with the 23S rRNA. The base U2585 forms a hydrogen bond with the morpholino ring, A2451 forms a hydrogen bond with the acetamide group, and G2505 forms a hydrogen bond with the oxazolidinone group. The drug also appears to make van der Waals or hydrophobic interactions with G2061, C2501, U2504, and U2506 (Eyal et al., 2015). All of the interactions between the 23S rRNA and linezolid can be seen in Figure 3.

Figure 3. The binding site of linezolid. The left image shows the 50S ribosomal subunit using the same color scheme as Figure 2. The inset shows the interactions that linezolid makes with the 23S rRNA. The drug is colored in gray, 23S rRNA is colored in blue, and key bases are labeled. Hydrogen bonds are shown in magenta (PDB ID: 4wfa, Eyal et al., 2015).
Figure 3. The binding site of linezolid. The left image shows the 50S ribosomal subunit using the same color scheme as Figure 2. The inset shows the interactions that linezolid makes with the 23S rRNA. The drug is colored in gray, 23S rRNA is colored in blue, and key bases are labeled. Hydrogen bonds are shown in magenta (PDB ID: 4wfa, Eyal et al., 2015).

Upon binding, linezolid causes a significant conformational change in the universally conserved rRNA base U2585. It is located in the peptidyl transferase center and its flexibility is important for the induced-fit binding of tRNAs in the P-site. When linezolid binds, however, it stabilizes U2585 in a fixed conformation through a hydrogen bond. Therefore, since U2585 is no longer flexible and its conformation is significantly altered, the binding of tRNAs is affected. This contributes to the inhibitory action of linezolid (Wilson et al., 2008). The conformational change of U2585 can be seen in Figure 4.

Figure 4. The conformational change of base U2585. The base in the presence of the drug is shown in cornflower blue (PDB ID: 4wfa, Eyal et al., 2015), while the base in the presence of tRNA is shown in tan (PDB ID: 4v5d, Voorhees et al., 2009).
Figure 4. The conformational change of base U2585. The base in the presence of the drug is shown in cornflower blue (PDB ID: 4wfa, Eyal et al., 2015), while the base in the presence of tRNA is shown in tan (PDB ID: 4v5d, Voorhees et al., 2009).

The binding site of linezolid overlaps with the end of the tRNA molecule in the A-site. After translation initiation, the tRNA cannot fully enter the A-site because it is blocked by linezolid. Since it cannot be accommodated by the ribosome, the tRNA is believed to dissociate which prevents the delivery of the amino acid (Wilson et al., 2008). Figure 5 shows the superimposition of two ribosome structures: one with linezolid bound, and one with tRNA molecules bound.

Figure 5. The structure of linezolid bound to the ribosome (PDB ID: 4wfa, Eyal et al., 2015) is superimposed with a structure of tRNAs bound to the ribosome (PDB ID: 4v5d, Voorhees et al., 2009).
Figure 5. The structure of linezolid bound to the ribosome (PDB ID: 4wfa, Eyal et al., 2015) is superimposed with a structure of tRNAs bound to the ribosome (PDB ID: 4v5d, Voorhees et al., 2009).

Pharmacologic Properties and Safety

Table 3. Pharmacokinetics: ADMET of linezolid.

Features Comment(s) Source
Oral Bioavailability (%) ≈100% DrugBank
IC50 0.3 μg/mL in S. aureus (Champney & Miller, 2002)
Ki (μM) N/A N/A
Half-Life (hrs) 4.5-5.5 hours DrugBank
Duration of Action N/A N/A
Absorption Site N/A N/A
Transporter(s) N/A N/A
Metabolism Primarily metabolized though oxidation of the morpholine ring, resulting in two inactive ring-opened metabolites (known as metabolites A and B). FDA
Excretion ≈30% appears in urine as linezolid; ≈40% as metabolite B, ≈10% as metabolite A; ≈6% appears in feces as metabolite B, ≈3% as metabolite A. FDA
AMES Test (Carcinogenic Effect) Probability 0.6839 (non-AMES toxic) DrugBank
hERG Safety Test (Cardiac Effect) Probability 0.7883 (weak inhibitor) DrugBank
Liver Toxicity Instances of liver disease with jaundice have been reported. The drug has been linked to lactic acidosis after 1-8 weeks of treatment. Linezolid is also associated with elevations in serum aminotransferase and alkaline phosphatase levels. LiverTox

Drug Interactions and Side Effects

Before starting treatment with linezolid, patients should inform their healthcare provider if they have any of the following conditions:
* High blood pressure
* Thyrotoxicosis
* Bone marrow suppression or a weak immune system
* Liver or kidney disease
* Diabetes
* Seizures

Table 4. Drug interactions and side effects of linezolid.

Features Comment(s) Source
Total Number of Drug Interactions 468 drugs Drugs.com
Major Drug Interactions 128 drugs (e.g., BCG, typhoid vaccine, cholera vaccine) Drugs.com
Alcohol/Food Interactions Patients should avoid foods or beverages with high amounts of tyramine. Tyramine is a compound produced from the breakdown of the amino acid tyrosine. Foods/beverages with high tyramine levels include aged cheeses, smoked meats, beers, and overripe fruits. FDA
Disease Interactions 12 diseases (major: colitis, bone marrow suppression) Drugs.com
On-Target Side Effects Anemia, chills, dizziness, fast heartbeat, fainting Drugs.com
Off-Target Side Effects Hypertension, severe headache, blurred vision, nausea Drugs.com
CYP Interactions CYP450 3A4 substrate DrugBank

Cases of Clostridium difficile associated diarrhea (CDAD) have been reported with the use of almost all antibacterial drugs, including linezolid, and may vary in severity from mild diarrhea to fatal colitis. CDAD occurs because treatment with antibiotics changes the normal bacterial flora of the colon, which results in an overgrowth of C. difficile (FDA, 2017).

Regulatory Approvals/Commercial

The US FDA approved Zyvox (linezolid) in 2000. It is a member of the oxazolidinones which were the first new class of antibiotics to enter the market in 35 years. It is currently available as a tablet, suspension, and injection. Linezolid has activity against a broad range of gram-positive bacteria. It is often seen as an alternative to vancomycin—linezolid is used to treat serious infections caused by VRE or vancomycin-resistant strains of MRSA. Linezolid is not used to treat gram-negative infections or catheter-related infections (Azzouz & Preuss, 2019).

Off-Target Considerations

Linezolid is also a non-selective, reversible inhibitor of monoamine oxidases (MAO). MAO enzymes catalyze the oxidation of monoamine neurotransmitters including dopamine, serotonin, epinephrine, and norepinephrine. MAO inhibition leads to an increased concentration of these neurotransmitters. MAOs are also important in breaking down monoamines in food, so MAO inhibition in the GI tract leads to high absorption of tyramine which can cause hypertension (Azzouz & Preuss, 2019).

Links

Table 5. Links to learn more about linezolid

Comprehensive Antibiotic Resistance Database (CARD) ARO: 0000072
DrugBank DB00601
Drugs.com https://www.drugs.com/mtm/linezolid-oral-injection.html
FDA – Zyvox https://www.accessdata.fda.gov/drugsatfda_docs/label/2010/021130s022lbl.pdf
LiverTox: National Institutes of Health (NIH) https://www.ncbi.nlm.nih.gov/books/NBK548245/
PubChem CID 441401

Learn about linozolid resistance.

References

Arenz, S., & Wilson, D. (2016). Bacterial protein synthesis as a target for antibiotic inhibition. Cold Spring Harbor Perspectives In Medicine, 6(9), a025361. https://doi.org/10.1101/cshperspect.a025361

Champney, W., & Miller, M. (2002). Linezolid is a specific inhibitor of 50S ribosomal subunit formation in Staphylococcus aureus cells. Current Microbiology, 44(5), 350-356. https://doi.org/10.1007/s00284-001-0023-7

Eyal, Z., Matzov, D., Krupkin, M., Wekselman, I., Paukner, S., Zimmerman, E., Rozenberg, H., Bashan, A., and Yonath, A. (2015). Structural insights into species-specific features of the ribosome from the pathogen Staphylococcus aureus. Proceedings of the National Academy of Sciences of the United States of America, 112(43), E5805–E5814. https://doi.org/10.1073/pnas.1517952112 PDB ID: 4wfa

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., 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/gkw1004

Linezolid – DrugBank. Drugbank.ca. https://www.drugbank.ca/drugs/DB00601

Linezolid. Drugs.com. https://www.drugs.com/mtm/linezolid-oral-injection.html

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

LiverTox - Clinical and Research Information on Drug-Induced Liver Injury. National Institutes of Health. https://www.ncbi.nlm.nih.gov/books/NBK548245/

Voorhees, R. M., Weixlbaumer, A., Loakes, D., Kelley, A. C., & Ramakrishnan, V. (2009). Insights into substrate stabilization from snapshots of the peptidyl transferase center of the intact 70S ribosome. Nature structural & molecular biology, 16(5), 528–533. https://doi.org/10.1038/nsmb.1577 PDB ID: 4v5d

Wilson, D. N., Schluenzen, F., Harms, J. M., Starosta, A. L., Connell, S. R., & Fucini, P. (2008). The oxazolidinone antibiotics perturb the ribosomal peptidyl-transferase center and effect tRNA positioning. Proceedings of the National Academy of Sciences of the United States of America, 105(36), 13339–13344. https://doi.org/10.1073/pnas.0804276105

Zyvox. (2010). Food and Drug Administration. https://www.accessdata.fda.gov/drugsatfda_docs/label/2010/021130s022lbl.pdf

March 2025, Steven Arnold, Helen Gao, Shuchismita Dutta; Reviewed by Dr. Gerard Wright
https://doi.org/10.2210/rcsb_pdb/GH/AMR/drugs/antibiotics/prot-syn/ribo/OXA/linezolid