Fidaxomicin

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Drug Name

Fidaxomicin (also known as lipiarmycin A3) is a natural macrocyclic antibiotic produced as a byproduct of fermentation by Dactylosporangium aurantiacum (Coronelli et al., 1975; Parenti et al., 1975; Sergio et al., 1975). The drug binds to the base of the RNAP clamp, trapping it in an open-clamp state. Fidaxomicin exhibits bactericidal activity against gram-positive bacteria (Boyaci et al., 2018; Srivastava et al., 2011). It has no excellent GI-tract bioavailability and no systemic bioavailbility upon oral dosing. It is used clinically for treatment of Clostridium difficile associated diarrhea.

Table 1. Basic profile of fidaxomicin.

Description Lipairmycin antibiotic
Target(s) RNA polymerase
Generic N/A
Commercial Name Dificid, Dificlir
Combination Drug(s) N/A
Other Synonyms Lipiarmycin A3, tiacumicin B
IUPAC Name [(2R,3S,4S,5S,6R)-6-[[(3E,5E,8S,9E,11S,12R,13E,15E)-12-[(2R,3S,4R,5S)-3,4-dihydroxy-6,6-dimethyl-5-(2-methylpropanoyloxy)oxan-2-yl]oxy-11-ethyl-8-hydroxy-18-[(1R)-1-hydroxyethyl]-9,13,15-trimethyl-2-oxo-1-oxacyclooctadeca-3,5,9,13,15-pentaen-3-yl]methoxy]-4-hydroxy-5-methoxy-2-methyloxan-3-yl] 3,5-dichloro-2-ethyl-4,6-dihydroxybenzoate
Ligand Code in PDB FI8
PDB structure 6fbv (Structure of fidaxomicin bound to its target protein)
ATC Classification A07AA12
RotateHydrogensLabels
Figure 1. 2D and 3D structures of Fidaxomicin (PDB ligand code: FI8).

Antibiotic Chemistry

Fidaxomicin is a macrolide antibiotic that contains an 18-membered lactone ring and four other structural moieties (Hochlowski et al., 2018). Its lactone ring differentiates it from other macrolide drugs, the majority of which are 14-, 15-, and 16-membered macrolides. Unlike most other clinically-relevant macrolides such as erythromycin and azithromycin which bind to bacterial ribosomes, fidaxomicin targets RNAP.

Figure 2. Chemical structure of fidaxomicin. Image created using ChemDraw.
Figure 2. Chemical structure of fidaxomicin. Image created using ChemDraw.

Drug Information

Table 2. Chemical and physical properties (DrugBank).

Chemical Formula C52H74Cl2O18
Molecular Weight 1059.04 g/mol
Calculated Predicted Partition Coefficient: cLogP 5.59
Calculated Predicted Aqueous Solubility: cLogS -4.9
Solubility (in water) 0.0125 mg/mL
Predicted Topological Polar Surface Area (TPSA) 266.66 Å2

Drug Target

The target of fidaxomicin, bacterial RNAP, is composed of five subunits (as seen in Mycobacterium tuberculosis RNAP, PDB ID: 6fbv):
* Two α subunits - α1 and α2, each 347 amino acids (colored lime green and yellow)
* β subunit - 1,178 amino acids (colored sky blue)
* β' subunit - 1,316 amino acids (colored in hot pink)
* ω subunit - 110 amino acids (colored in dim gray)

A key region of RNAP is the ‘clamp.’ During transcription, the RNAP clamp adopts different conformations which are controlled by the ‘switch region’ located at the base. The motions of the clamp are important for loading and retaining DNA in the active-center cleft. Fidaxomicin binds in the switch region which locks the clamp in an open-state conformation, preventing formation of a stable transcription initiation complex. (Boyaci et al., 2018; Lin et al., 2018).

Figure 3. A ribbon representation of RNAP bound by fidaxomicin illustrating the RNAP clamp and switch region (PDB ID: 6fbv, Lin et al., 2018).
Figure 3. A ribbon representation of RNAP bound by fidaxomicin illustrating the RNAP clamp and switch region (PDB ID: 6fbv, Lin et al., 2018).

Drug-Target Complex

Fidaxomicin binds at the base of the RNAP clamp with each of the five structural moieties of the drug interacting with RNAP. The drug makes several van der Waals interactions with RNAP. In the β subunit, I1052, D1094, D1095, V1097, V1100, E1119, and S1120 make van der Waals contacts with the drug. In the βꞋ­ subunit, D57, A85, K86, L324, P326, V328, S338, L405, R412, and Q415 form van der Waals contacts with fidaxomicin. In the σ factor, S338, L423, and D424 make van der Waals contacts with the drug (Lin et al., 2018).

The drug is also observed to form hydrogen bonds with RNAP. Six RNAP residues are involved in making hydrogen bonds with the drug. They are T1096 and K1101 from the β subunit, and R84, R89, E323, and R412 from the βꞋ subunit (Lin et al., 2018). The hydrogen bonds between fidaxomicin and RNAP can be seen in Figure 4.

Figure 4. Interactions between fidaxomicin and RNAP. Hydrogen bonds between fidaxomicin and RNAP residues are shown in dark purple (PDB ID: 6fbv, Lin et al., 2018).
Figure 4. Interactions between fidaxomicin and RNAP. Hydrogen bonds between fidaxomicin and RNAP residues are shown in dark purple (PDB ID: 6fbv, Lin et al., 2018).

Structural and kinetic data reveal that fidaxomicin inhibits transcription by trapping RNAP in an open-conformational state. The cryo-EM structure reveals that RNAP adopts an open-conformational state when bound by fidaxomicin because the interactions that the drug makes with RNAP require elements in the switch region to be in the open state. A superimposition of the cryo-EM structure on a closed-state RNAP reveals a 17° difference in the clamp region. Furthermore, FRET data supports the conclusion that the RNAP clamp remains in the open state during transcription (Lin et al., 2018).

Figure 5. A superimposition of an open clamp RNAP bound by fidaxomicin (PDB ID: 6fbv, Lin et al., 2018) and a closed clamp RNAP (PDB ID: 4g7h, Zhang et al., 2012).
Figure 5. A superimposition of an open clamp RNAP bound by fidaxomicin (PDB ID: 6fbv, Lin et al., 2018) and a closed clamp RNAP (PDB ID: 4g7h, Zhang et al., 2012).

Pharmacologic Properties and Safety

Table 3. Pharmacokinetics: ADMET of fidaxomicin.

Features Comment(s)s Source
Oral Bioavailability (%) 0 DrugBank
IC50 0.3 μM for Escherichia sp.; 8 μM for Mycobacterium sp. (Lin et al., 2018)
Ki (μM) N/A N/A
Half-Life (hrs) 11.7 hours DrugBank
Duration of Action N/A N/A
Absorption Site The drug has minimal systemic absorption DrugBank
Transporter(s) N/A N/A
Metabolism The drug is hydrolyzed by gastric acid and intestinal microsomes into a metabolite DrugBank
Excretion 92% of the dose is excreted in feces as an unchanged drug and metabolites FDA
AMES Test (Carcinogenic Effect) Probability 0.7118 (non-AMES toxic) DrugBank
hERG Safety Test (Cardiac Effect) Probability 0.9875 (weak inhibitor) DrugBank
Liver Toxicity It is an unlikely cause of clinically apparent liver injury and has not been linked to serum enzyme elevations during therapy. LiverTox

Drug Interactions and Side Effects

Table 4. Drug interactions and side effects of fidaxomicin.

Features Comment(s) Source
Total Number of Drug Interactions 61 drugs Drugs.com
Major Drug Interactions 3 drugs (live cholera vaccine, live typhoid vaccine, venetoclax) Drugs.com
Alcohol/Food Interactions No major interactions with alcohol or food Drugs.com
Disease Interactions 1 disease (QT prolongation) Drugs.com
On-Target Side Effects Nausea, abdominal pain, vomiting, diarrhea, dyspepsia, and gastrointestinal hemorrhage. Drugs.com
Off-Target Side Effects N/A N/A
CYP Interactions Metabolism of fidaxomicin is not dependent on cytochrome P450 enzymes FDA

Regulatory Approvals/Commercial

The FDA approved fidaxomicin in 2011 as a treatment for Clostridium difficile infections. The drug is minimally absorbed by the body and has weak activity against the gastrointestinal flora. Fidaxomicin is sold as 200 mg tablets under the brand name Dificid. A 200 mg dose is typically taken twice daily for 10 days. In clinical trials, Dificid was effective in treating C. difficile in 80%-90% of patients.

Links

Table 5: Links to learn more about fidaxomicin

Comprehensive Antibiotic Resistance Database (CARD) ARO: 3001319
DrugBank DB08874
Drugs.com https://www.drugs.com/mtm/fidaxomicin.html
FDA – Dificid https://www.accessdata.fda.gov/drugsatfda_docs/label/2011/201699s000lbl.pdf
LiverTox: National Institutes of Health (NIH) https://www.ncbi.nlm.nih.gov/books/NBK548928/
PubChem ID 46174142

Learn about fidaxomicin resistance.

References

Boyaci, H., Chen, J., Lilic, M., Palka, M., Mooney, R. A., Landick, R., Darst, S. A., & Campbell, E. A. (2018). Fidaxomicin jams Mycobacterium tuberculosis RNA polymerase motions needed for initiation via RbpA contacts. eLife, 7, e34823. https://doi.org/10.7554/elife.34823

Coronelli, C., White, R. J., Lancini, G. C., Parenti, F. (1975) Lipiarmycin, a new antibiotic from Actinoplanes. II. Isolation, chemical, biological and biochemical characterization. J Antibiot (Tokyo). 28(4):253-9. https://doi.org/10.7164/antibiotics.28.253

Dificid. Food and Drug Administration. https://www.accessdata.fda.gov/drugsatfda_docs/label/2011/201699s000lbl.pdf

Fidaxomicin – DrugBank. Drugbank.ca. https://www.drugbank.ca/drugs/DB08874

Fidaxomicin. Drugs.com. https://www.drugs.com/mtm/fidaxomicin.html

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

Lin, W., Das, K., Degen, D., Mazumder, A., Duchi, D., Wang, D., Ebright, Y. W., Ebright, R. Y., Sineva, E., Gigliotti, M., Srivastava, A., Mandal, S., Jiang, Y., Liu, Y., Yin, R., Zhang, Z., Eng, E. T., Thomas, D., Donadio, S., Zhang, H., Zhang, C., Kapanidis, A. N., & Ebright, R. H. (2018). Structural basis of transcription inhibition by fidaxomicin (lipiarmycin A3). Molecular cell, 70(1), 60–71.e15. https://doi.org/10.1016/j.molcel.2018.02.026 PDB IDs: 6fbv

LiverTox – Clinical and Research Information on Drug-Induced Liver Injury. National Institutes of Health. https://www.ncbi.nlm.nih.gov/books/NBK548928/

Parenti, F., Pagani, H., Beretta, G. (1975) Lipiarmycin, a new antibiotic from Actinoplanes. I. Description of the producer strain and fermentation studies. J Antibiot (Tokyo). 28(4):247-52. https://doi.org/10.7164/antibiotics.28.247

Sergio, S., Pirali, G., White, R., Parenti, F. (1975) Lipiarmycin, a new antibiotic from Actinoplanes III. Mechanism of action. J Antibiot (Tokyo). 28(7):543-9. https://doi.org/10.7164/antibiotics.28.543

Srivastava, A., Talaue, M., Liu, S., Degen, D., Ebright, R. Y., Sineva, E., Chakraborty, A., Druzhinin, S. Y., Chatterjee, S., Mukhopadhyay, J., Ebright, Y. W., Zozula, A., Shen, J., Sengupta, S., Niedfeldt, R. R., Xin, C., Kaneko, T., Irschik, H., Jansen, R., Donadio, S., Connell, N., Ebright, R. H. (2011). New target for inhibition of bacterial RNA polymerase: 'switch region'. Current Opinion in Microbiology, 14(5), 532-543. https://doi.org/10.1016/j.mib.2011.07.030

Zhang, Y., Feng, Y., Chatterjee, S., Tuske, S., Ho, M. X., Arnold, E., & Ebright, R. H. (2012). Structural basis of transcription initiation. Science (New York, N.Y.), 338(6110), 1076–1080. https://doi.org/10.1126/science.1227786 PDB ID: 4g7h

March 2025, Steven Arnold, Helen Gao; Reviewed by Dr. Richard Ebright
https://doi.org/10.2210/rcsb_pdb/GH/AMR/drugs/antibiotics/rna-synth/rp/lipiarmycin/fidaxomicin