Rifampin

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Drug Name

Rifampin is a semisynthetic antibiotic belonging to the rifamycin class. The drug binds within bacterial RNA polymerase and sterically blocks the extension of 2-3 nucleotide RNA products. Rifampin has bactericidal activity against gram-positive and gram-negative bacteria. It is a first-line drug in combination therapy to treat Mycobacterium tuberculosis infections (Campbell et al., 2001).

Table 1. Basic profile of rifampin.

Description Broad-spectrum rifamycin antibiotic
Target(s) RNA polymerase
Generic Rifampin
Commercial Name RIFADIN
Combination Drug(s) Isoniazid, pyrazinamide, ethambutol, streptomycin
Other Synonyms Rifampicin
IUPAC Name [(7S,9E,11S,12R,13S,14R,15R,16R,17S,18S,19E,21Z)-2,15,17,27,29-pentahydroxy-11-methoxy-3,7,12,14,16,18,22-heptamethyl-26-[(E)-(4-methylpiperazin-1-yl)iminomethyl]-6,23-dioxo-8,30-dioxa-24-azatetracyclo[23.3.1.14,7.05,28]triaconta-1(29),2,4,9,19,21,25,27-octaen-13-yl] acetate
Ligand Code in PDB RFP
PDB Structure 5uhb (Structure of Mycobacterium tuberculosis transcription initiation complex in complex with Rifampin)
ATC code J04AB02
RotateHydrogensLabels
Figure 1. 2D and 3D structures of Rifampin (PDB ligand code: RFP).

Antibiotic Chemistry

Rifampin, a semisynthetic derivative of rifamycin, is composed of a naphthol ring fused to an “ansa” bridge. It is a relatively apolar molecule.

Figure 2. Chemical structure of rifampin. Key chemical groups are colored and labeled. Structure created using ChemDraw.
Figure 2. Chemical structure of rifampin. Key chemical groups are colored and labeled. Structure created using ChemDraw.

Drug Information

Table 2. Chemical and physical properties (DrugBank).

Chemical Formula C43H58N4O12
Molecular Weight 822.94 g/mol
Calculated Predicted Partition Coefficient: cLogP 2.7
Calculated Predicted Aqueous Solubility: cLogS -4.8
Solubility (in water) 1.4 mg/mL
Predicted Topological Polar Surface Area (TPSA) 220.15 Å2

Drug Target

Transcription is the process by which an RNA molecule is synthesized from a DNA template by the enzyme RNA polymerase (RNAP). It is targeted by two classes of antibacterial agents: rifamycins, and lipiarmycins. (fidaxomicin). Rifampin binds to a site in the RNAP β subunit immediately adjacent to the RNAP active center and sterically blocks the extension of short RNA products (Ho et al., 2009).

Learn more about transcription and RNAP.

Drug-Target Complex

The target of rifampin, RNAP of Mycobacterium tuberculosis (PDB ID: 5uhb), is composed of five subunits (Lin et al., 2017):
1. Two α subunits (α1 and α2) - each 313 amino acids (colored in dark magenta and orchid)
2. β subunit - 1,119 amino acids (colored in dim gray)
3. βꞋsubunit - 1,525 amino acids (colored in light gray)
4. ω subunit - 91 amino acids (colored in steel blue)
A synthetic DNA scaffold colored in red, was crystallized in this structure.

Figure 3. The left image illustrates a surface view of RNAP bound by rifampin. The inset shows the binding pocket of rifampin in the β subunit (PDB ID: 5uhb, Lin et al., 2017).
Figure 3. The left image illustrates a surface view of RNAP bound by rifampin. The inset shows the binding pocket of rifampin in the β subunit (PDB ID: 5uhb, Lin et al., 2017).

Rifampin binds to a site in the RNAP β subunit immediately adjacent to the RNAP active center. The drug is observed to make hydrogen bonds with protein groups in the β subunit, and van der Waals contacts with hydrophobic residues lining the binding pocket. The first set of interactions involves hydrogen bonds between RNAP and hydroxyl groups in rifampin.
Residues participating in these interactions involve Gln438, Phe439, His451, Arg454, and Ser456 (residue numbers as in M. tuberculosis, PDB ID 5uhb, Figure 4). Moreover, Gln435 forms an hydrogen bond with an oxygen atom in the drug. The next group of interactions involves van der Waals contacts between the naphthol ring of the drug and the β subunit. Residues including Val176, Leu458, Arg465, Asn493, and Ile497 all interact with the naphthol ring. The methyl group at C7 of the ring interacts with Leu436, Gln438, and Gly459. The last set of key interactions are van der Waals contacts between the β subunit and the ansa bridge of the drug. Residues making these interactions include Arg173, Ser437, Asp441, Pro489, Arg613, and His680 (Lin et al., 2017). The set of interactions between rifampin and RNAP can be seen below in Figure 4.

Figure 4. The interactions between rifampin (yellow) and residues of the β subunit. Hydrogen bonds are colored in cyan (PDB ID: 5uhb, Lin et al., 2017).
Figure 4. The interactions between rifampin (yellow) and residues of the β subunit. Hydrogen bonds are colored in cyan (PDB ID: 5uhb, Lin et al., 2017).

Asp441 is vital for the binding of rifampin. The negative charge of Asp441 is important for neutralizing the positive charge of Arg454 which is located about 6 Å away. Since rifampin is apolar, the charge neutralization by Asp441 promotes rifampin binding (Campbell et al., 2001).

Rifampin inhibits RNAP by binding to a site immediately adjacent to the enzyme active center and sterically blocking the extension of short (2-3 nt) RNA products into longer RNA products. When the nascent RNA is 2-3 nucleotides long, its 5’ end clashes with rifampin, preventing the completion of RNA synthesis. Figure 5 shows the clash between rifampin and a 3-nucleotide 5'-OH RNA product.

Figure 5. The blockage of the RNA exit path by rifampin. A three-nucleotide-long RNA segment (green) is shown in a complex with DNA and RNAP. The drug interferes with the 5’ end of the RNA segment as it moves downwards (PDB ID: 5uhb, Lin et al., 2017).
Figure 5. The blockage of the RNA exit path by rifampin. A three-nucleotide-long RNA segment (green) is shown in a complex with DNA and RNAP. The drug interferes with the 5’ end of the RNA segment as it moves downwards (PDB ID: 5uhb, Lin et al., 2017).

Pharmacologic Properties and Safety

Table 3. Pharmacokinetics: ADMET of rifampin.

Features Comment(s) Source
Oral Bioavailability (%) 93%-95% after single dose administration (Xu et al., 2013)
IC50 N/A N/A
Ki (μM) N/A N/A
Half-Life (hrs) 3.35 ± 0.66 DrugBank
Duration of Action ≤ 24 hours Drugs.com
Absorption Site Readily absorbed from the gastrointestinal tract DrugBank
Transporter(s) N/A N/A
Metabolism Primarily metabolized by the liver; rapidly deacetylated DrugBank
Excretion Up to 30% is excreted in the urine, with half of this being an unchanged drug. The rest is eliminated in the bile where it then undergoes progressive deacetylation. FDA
AMES Test (Carcinogenic Effect) Probability 0.5803 (non-AMES toxic) DrugBank
hERG Safety Test (Cardiac Effect) Probability 0.9080 (weak inhibitor) DrugBank
Liver Toxicity It is associated with transient and asymptomatic elevations in serum aminotransferase and bilirubin levels. The drug is also associated with liver injury and acute liver disease. In the treatment of tuberculosis, rifampin is usually given in combination with pyrazinamide and/or isoniazid which are hepatotoxic agents, making it difficult to distinguish LiverTox

Drug Interactions and Side Effects

Before starting treatment with rifampin, patients should inform their healthcare provider if they have an allergy to rifampin, or are taking any HIV/AIDS medications.

Table 4. Drug interactions and side effects of rifampin.

Features Comment(s) Source
Total Number of Drug Interactions 449 drugs Drugs.com
Major Drug Interactions 165 drugs (e.g., warfarin, ketoconazole, telithromycin) Drugs.com
Alcohol/Food Interactions Avoid drinking alcohol while taking rifampin as it may increase the risk of liver damage. The drug is most effective when taken 1 hour before or 2 hours after a meal. Drugs.com
Disease Interactions six diseases (major: colitis, liver disease, porphyria) Drugs.com
On-Target Side Effects Skin rash, fever, swollen glands, flu-like symptoms, and temporary discoloration of teeth, sweat, urine, and saliva Drugs.com
Off-Target Side Effects N/A N/A
CYP Interactions Inducer of CYP 1A2, 2C9, 2C19, and 3A4 LiverTox

Regulatory Approvals/Commercial

In 1957, a research group led by Piero Sensi discovered a new antibiotic which they named rifamycin. It was isolated from cultures of Amycolatopsis rifamycinica. Seven years later in 1965, rifampin was first synthesized and was found to be chemically stable, less toxic to humans, and exhibit activity against a broad spectrum of bacterial species. Rifampin was approved by the U.S. Food and Drug Administration in 1971 but its clinical use was limited to meningococcal carriage and pulmonary tuberculosis (Sensi, 1983).

Today, rifampin is used in the treatment of all forms of tuberculosis and of asymptomatic carriers of meningococci. When used against tuberculosis, rifampin is frequently administered in a three-drug regimen with isoniazid and pyrazinamide. A fourth drug—often streptomycin or ethambutol—is sometimes added. Rifampin is sold as capsules for oral administration and as a powder for solution for intravenous administration.

Links

Table 5. Links to learn more about rifampin

Comprehensive Antibiotic Resistance Database (CARD) ARO: 3000169
DrugBank DB01045
Drugs.com https://www.drugs.com/mtm/rifampin.html
FDA – RIFADIN https://www.accessdata.fda.gov/drugsatfda_docs/label/2010/050420s073,050627s012lbl.pdf
LiverTox: National Institutes of Health (NIH) https://www.ncbi.nlm.nih.gov/books/NBK548314/
PubChem CID 135398735

Learn about rifampin resistance.

References

Campbell, E., Korzheva, N., Mustaev, A., Murakami, K., Nair, S., Goldfarb, A., Darst, S. (2001). Structural mechanism for rifampicin inhibition of bacterial RNA polymerase. Cell, 104(6), 901-912. https://doi.org/10.1016/s0092-8674(01)00286-0

Ho, M., Hudson, B., Das, K., Arnold, E., and Ebright, R. (2009) Structures of RNA polymerase-antibiotic complexes. Curr. Opin. Structl. Biol. 19, 715-723. https://doi.org/10.1016/j.sbi.2009.10.010

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. doi:10.1093/nar/gkw1004

LiverTox – Clinical and Research Information on Drug-induced Liver Injury. National Institutes of Health. https://www.ncbi.nlm.nih.gov/books/NBK548314/

Lin, W., Mandal, S., Degen, D., Liu, Y., Ebright, Y. W., Li, S., Feng, Y., Zhang, Y., Mandal, S., Jiang, Y., Liu, S., Gigliotti, M., Talaue, M., Connell, N., Das, K., Arnold, E., Ebright, R. H. (2017). Structural basis of Mycobacterium tuberculosis transcription and transcription inhibition. Molecular cell, 66(2), 169–179.e8. https://doi.org/10.1016/j.molcel.2017.03.001 PDB IDs: 5uhb, 5uh5

RIFADIN (rifampin capsules USP) and RIFADIN IV (rifampin for injection USP). (2010). Food and Drug Administration. https://www.accessdata.fda.gov/drugsatfda_docs/label/2010/050420s073,050627s012lbl.pdf

Rifampin. Drugs.com. https://www.drugs.com/mtm/rifampin.html

Rifampin – DrugBank. Drugbank.ca. https://www.drugbank.ca/drugs/DB01045

Rifampin. PubChem. https://pubchem.ncbi.nlm.nih.gov/compound/135398735

Sensi, P. (1983). History of the development of rifampin. Clinical Infectious Diseases, 5(Supplement_3), S402-S406. https://doi.org/10.1093/clinids/5.Supplement_3.S402

Xu, J., Jin, H., Zhu, H., Zheng, M., Wang, B., Liu, C., Chen, M., Zhou, L., Zhao, W., Fu, L., Lu, Y. (2013) Oral bioavailability of rifampicin, isoniazid, ethambutol, and pyrazinamide in a 4-drug fixed-dose combination compared with the separate formulations in healthy Chinese male volunteers. Clin Ther. 35(2):161-8. https://doi.org/10.1016/j.clinthera.2013.01.003

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