Vancomycin
Drug Name
Vancomycin is a broad-spectrum glycopeptide antibiotic (Reynolds, 1989) that was originally derived from Streptomyces orientalis. It is effective against gram-positive bacteria and is the drug of choice against methicillin-resistant Staphylococcus aureus infection. Vancomycin acts by binding to bacterial cell wall precursors, thereby interfering with cell wall biosynthesis and causing cell death.
Table 1. Basic drug profile for vancomycin.
| Description | Broad spectrum glycopeptide antibiotic |
| Target | D-Alanyl-D-Alanine residues of the muramyl peptide attached to the NAG-NAM (N-acetylglucosamine-N-acetylmuramic acid) disaccharide subunits of peptidoglycan |
| Generic | Vancomycin |
| Commercial name | Vancocin (capsules), Firvanq (Oral solution), Vancocin HCl (IV) |
| Combination Drugs | N/A |
| Other Synonyms | Diatracin, Vancomycin Hexal, Vancomycin Phosphate, Vanco-saar, VANCO-cell |
| IUPAC Name | (1S,2R,18R,19R,22S,25R,28R,40S)-48-{[(2S,3R,4S,5S,6R)-3-{[(2S,4S,5S,6S)-4-amino-5-hydroxy-4,6-dimethyloxan-2-yl]oxy}-4,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy}-22-(carbamoylmethyl)-5,47-dichloro-2,18,32,35,37-pentahydroxy-19-[(2R)-4-methyl-2-(methylamino)pentanamido]-20,23,26,42,44-pentaoxo-7,13-dioxa-21,24,27,41,43-pentaazaoctacyclo[26.14.2.2³,⁶.2¹⁴,¹⁷.1⁸,¹².1²⁹,³³.0¹⁰,²⁵.0³⁴,³⁹]pentaconta-3,5,8,10,12(48),14,16,29(45),30,32,34,36,38,46,49-pentadecaene-40-carboxylic acid |
| Ligand Code in PDB | PRD_000204 |
| PDB structures | 1AA5 and 1SHO (Structures of vancomycin) 1FVM (Vancomycin in complex with a D-Ala-D-Ala peptide) |
| ATC code | J01XA01 |
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Antibiotic Chemistry
Overall the structure of vancomycin is tricyclic and it contains both carbohydrate and peptide components, which is characteristic of all glycopeptide antibiotics (Pfeiffer, 1981; Reynolds,1989). It has a branched structure formed from a heptapeptide ring attached to a disaccharide via glycosidic bonding (Figure 2), earning it the classification of glycopeptide (Bhattacharjee, 2016). It is a bulky hydrophilic molecule so it is most effective against gram-positive bacteria because it cannot penetrate the outer membranes of most gram-negative bacteria.
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| Figure 2. Structure of vancomycin, consisting of vancosamine (purple) and glucose (pink), two chlorinated ꞵ- hydroxy tyrosine residues (light blue with chlorine in light green), three phenylglycine residues (dark green), an asparagine residue (sea green), and a methyl leucine (yellow). Atom color coding: O - red; N - blue; H - white; C - as specified above. (Pfeiffer, 1981, PDB: 1AA5). |
Drug Information
Table 2. Chemical Properties of vancomycin (PubChem).
| Chemical Information | C66H75Cl2N9O24 |
| Molecular Weight | 1449.265 g/mol |
| Calculated Predicted Partition Coefficient | -3.1 |
| Calculated Predicted Aqueous Solubility | -3.8 |
| Solubility (in water) | >100 mg/mL |
| Predicted Topological Polar Surface Area | 530 Å2 |
Drug Target
Vancomycin is a glycopeptide antibiotic that inhibits peptidoglycan synthesis in gram-positive bacteria (Reynolds,1989). It binds to the C-terminus of the pentapeptide portion of the repeating unit of the cell wall. This pentapeptide forms a crosslink between its penultimate D-Ala residue and a peptide on an adjacent strand (Lovering, Safadi, and Strynadka, 2012).
Learn more about the cell wall biosynthesis and the transpeptidase substrate.
Drug-Target Complex
Most of the clinically used antibiotics bind to the active sites of key enzymes in various biological processes to interfere with their functions. The mechanism of action of vancomycin is different since it binds tightly to the substrate of a transpeptidase - i.e., it binds to the D-alanyl-D-alanine residues of the penta-peptide group in the building block for the bacterial cell wall. As a result, the transpeptidase enzymes (Penicillin-binding proteins or PBP enzymes) are unable to form peptide cross-links between different peptidoglycan strands, weakening the cell wall and rendering the bacterium susceptible to lysis and death (Figure 3). Other glycopeptides like teicoplanin, televancin, and dalbavancin also have the same mechanism of action.
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| Figure 3. Cartoon showing vancomycin interfering with peptidoglycan cross-linking. |
Vancomycin forms five hydrogen bonds with Di-acetyl-Lysine-D-Ala-D-Ala which supports a ligand recognition mechanism (Figure 4). Upon binding, the entrance to the binding pocket of vancomycin narrows because of the extended conformation that the leucine side chain takes (shown in Figure 4b as the right-most hydrogen bond that is formed with the nitrogen of the methylleucine group colored yellow). Experimentally, it is seen that the longer the ligand, the narrower the ligand-binding pocket becomes, thus an induced fit ligand recognition system is suggested as opposed to a simple key and lock recognition system (Nitanai et al., 2009).
Moreover, two additional hydrogen bonds form: one from an oxygen atom in vancomycin to a water molecule, and another from the same water molecule to a nitrogen atom in the Di-acetyl-Lysine-D-Alanyl-D-Alanine ligand (not shown in the figure). This bridge could serve for stabilization and/or ligand recognition (Nitanai et al., 2009). The asparagine side chain may also hold the binding pocket of vancomycin in a suitable conformation for D-Alanyl-D-Alanine to enter; it was observed that the asparagine residue swings out of the way when the peptide enters the binding pocket from the other side (Schäfer, Schneider, and Sheldrick, 1996; Loll et al., 1997).
Through the five-point hydrogen bonding interaction, vancomycin acts as a bulky inhibitor and prevents the final stages of peptidoglycan synthesis from completing by introducing steric hindrance to the D-Ala-D-Ala units involved in transglycosylation (Reynolds,1989). This creates weak points in the peptidoglycan cell wall leaving the bacteria mechanically weak and susceptible to osmotic lysis (Walsh, 1999).
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| Figure 4. a) Structure of vancomycin (stick figure representation) bound to Di-acetyl-Lysine-D-Alanyl-D-Alanine (ball and stick; Atom color coding: C- grey; O - red; N- blue). b) View showing intermolecular hydrogen bonds (blue lines). PDB ID 1fvm, Nitanai et al., 2009. |
Pharmacologic Properties and Safety
- Intravenous (IV) vancomycin is indicated primarily for infections caused by susceptible strains of methicillin and β-lactam resistant Staphylococci.
- Oral vancomycin is indicated primarily for Clostridium difficile associated diarrhea and enterocolitis caused by Staphylococcus aureus; is not effective for other infections
Table 3. Pharmacologic properties and safety table for vancomycin IV and Oral when applicable. Half-life provided is the mean elimination half-life of vancomycin from blood plasma for IV vancomycin only, oral vancomycin data not found. In patients with normal renal function, on average 75% of vancomycin dose is excreted in urine in the first 24 hours
| Feature | Comment | Source |
|---|---|---|
| Oral Bioavailability | Less than 10% | Patel et al., 2024 |
| Intraperitoneal Administration Bioavailability | 60% systemic absorption | DrugBank |
| IC50(µM) | N/A | N/A |
| Ki (µM) | N/A | N/A |
| Half-life (hours) | 6 (range: 4-11) | DrugBank |
| Duration of Action | 24 hours | FDA |
| Absorption Site | Oral: Poorly absorbed in GI IV: Absorbed systemically | DrugBank |
| Transporters | N/A | N/A |
| Metabolism | No apparent metabolism of drug (IV) | FDA |
| Excretion | IV: Mainly excreted through renal glomerular filtration Renal clearance is about 0.048 L/kg/h. Oral: Via feces | FDA |
| AMES Test (Carcinogenic Effect) | Prob =0.5927; Non-AMES toxic | DrugBank |
| hERG Safety Test | Predictor 1: 0.9987 (Weak inhibitor) Predictor 2: 0.8098 (Non inhibitor) | DrugBank |
| Liver Toxicity | IV vancomycin was noted to cause asymptomatic elevations in certain liver enzymes in 1-5% of patients. Cases of hypersensitivity reactions (Stevens-Johnson syndrome, toxic epidermal necrolysis, and DRESS) were seen. Hypersensitivity is more prominent than liver injury | LiverTox |
| Nephrotoxicity | IV: May result in acute kidney injury, with increased risk if preexisting renal impairment or related comorbidities, or combined drug therapy with known nephrotoxicity. Oral: Renal failure or impairment, and elevated blood creatinine has occurred in clinical trials, with increased risk in patients over the age of 65. | FDA |
| Dosing | IV: Recommended 2 grams daily divided into 4 or 2 doses divided every 6 or 12 hours respectively, with concentrations of no more than 5mg/mL at no more than 10mg/min infused, in average adults. Oral: Dosage varies by pathological indicator. | FDA |
Drug Interactions and Side Effects
Table 4. Drug interactions and side effects of vancomycin.
| Features | Comments | Source |
|---|---|---|
| Total Number of Drug Interactions | 161 drugs | Drugs.com |
| Major Drug Interaction(s) | 38 drugs (ex: adefovir, live cholera vaccine, tenofovir) | Drugs.com |
| Alcohol/Food Interaction(s) | No known interactions | Drugs.com |
| Disease Interaction(s) | five disease interactions (Ototoxicity, Renal dysfunction, colitis, neutropenia, GI inflammation) | Drugs.com |
| On-target Side Effects | Nausea, abdominal pain, and hypokalemia | Drugs.com |
| Off-target side effects | Nephrotoxicity, neutropenia, ototoxicity, phlebitis, anaphylaxis | FDA |
Regulatory Approvals/Commercial
Vancomycin was first approved by the US Food and Drug Administration in 1958. At the time, alternative medication was ineffective while word of vancomycin’s success was spreading. However, the same year methicillin, and shortly after cefalotin, were approved as well and vancomycin became a reserved drug due to its perceived toxicity (Levine, 2006).
CutisPharma recently gained approval to launch FIRVANQ on April 2, 2018. FIRVANQ is an oral solution of vancomycin used for the treatment of diarrhea secondary to Clostridium difficile as well as enterocolitis caused by Staphylococcus aureus ("CutisPharma announces FDA approval of FIRVANQ™", 2018). This new availability of oral vancomycin therapy will reduce pharmacists' burden of having to compound the liquid formulations for patient use ("CutisPharma announces FDA approval of FIRVANQ™", 2018).
Links
Table 5: Links to learn more about vancomycin
| Comprehensive Antibiotic Resistance Database (CARD) | ARO: 0000028 |
| DrugBank | DB00512 |
| Drugs.com | https://www.drugs.com/vancomycin.html |
| US FDA | IV Drug Label Oral Drug Label |
| LiverTox: National Institutes of Health (NIH) | https://livertox.nlm.nih.gov/Vancomycin.htm |
| PubChem | 14969 |
Learn about vancomycin resistance.
References
Bhattacharjee, M. (2016) Chemistry of Antibiotics and Related Drugs, pp 88-89. 1st ed. Springer International Publishing, ISBN-10: 3319407449; ISBN-13: 978-3319407449
(2018) CutisPharma announces FDA approval of FIRVANQ™. Cutispharma.com.
Levine, D. (2006). Vancomycin: A History. Clinical Infectious Diseases, 42, S5-S12. https://doi.org/10.1086/491709
Loll, P., Bevivino, A., Korty, B., Axelsen, P. (1997) Simultaneous Recognition of a Carboxylate -Containing Ligand and an Intramolecular Surrogate Ligand in the Crystal Structure of an Asymmetric Vancomycin Dimer. Journal of the American Chemical Society 119:1516-1522. https://pubs.acs.org/doi/10.1021/ja963566p
Lovering, A. L., Safadi, S. S., Strynadka, N. C. (2012). Structural perspective of peptidoglycan biosynthesis and assembly. Annual review of biochemistry, 81, 451–478. https://doi.org/10.1146/annurev-biochem-061809-112742
Nitanai, Y., Kikuchi, T., Kakoi, K., Hanamaki, S., Fujisawa, I., Aoki, K. (2009). Crystal structures of the complexes between vancomycin and cell-wall precursor analogs. Journal of molecular biology, 385, 1422–1432. https://doi.org/10.1016/j.jmb.2008.10.026
Pfeiffer, R. R. (1981) Structural Features of Vancomycin. Reviews of Infectious Diseases, 3, S205-S209. https://doi.org/10.1093/clinids/3.Supplement_2.S205
Reynolds P. E. (1989). Structure, biochemistry and mechanism of action of glycopeptide antibiotics. European journal of clinical microbiology & infectious diseases, 8, 943–950. https://doi.org/10.1007/BF01967563
Schäfer, M., Schneider, T. R., Sheldrick, G. M. (1996). Crystal structure of vancomycin. Structure, 4(12), 1509–1515. https://doi.org/10.1016/s0969-2126(96)00156-6
Walsh C. (1999). Deconstructing vancomycin. Science, 284, 442–443. https://doi.org/10.1126/science.284.5413.442
March 2025, Sameer Ahmad; Reviewed by Dr. Patrick Loll
https://doi.org/10.2210/rcsb_pdb/GH/AMR/drugs/antibiotics/cellwall-biosynth/trpep/gpep-antibiotic/vancomycin
