Ampicillin

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Drug Name

Ampicillin is a semi-synthetic derivative of penicillin that belongs in the β-lactam class. It is used to treat a variety of infections by both gram-positive and gram-negative bacteria, and even anaerobes.

Table 1. Basic profile of ampicillin.

Description Orally active broad-spectrum antibiotic
Target(s) Penicillin-binding proteins (PBPs)
Generic Ampicillin for injection
Commercial Name Omnipen, Omnipen-N, Principen, Totacillin-N
Combination Drug(s) may be combined with Sulbactam
Other Synonyms ABPC, Ampicilina, Ampicillinum, Ampicillin acid, Ampicilline, AP
IUPAC Name (2R,4S)-2-[(1R)-1-{[(2R)-2-amino-2-phenylacetyl]amino}-2-oxoethyl]-5,5-dimethyl-1,3-thiazolidine-4-carboxylic acid
Ligand Code in PDB AIC (closed form) AIX (open form)
PDB structures 6KGW (Mycobacterium tuberculosis PBP3 bound to ampicillin)
ATC code J01CA01
RotateHydrogensLabels
Figure 1. 2D and 3D structures of Ampicillin (PDB ligand code: AIC).

Drug Information

Table 2. Chemical and physical properties (DrugBank).

Chemical Formula C16H21N3O4S
Molecular Weight 351.42 g/mol
Calculated Predicted Partition Coefficient: cLogP 0.88
Calculated Predicted Aqueous Solubility: cLogS -2.8
Solubility (in water) 0.605 mg/mL
Predicted Topological Polar Surface Area (TPSA) 112.73 Å2

Antibiotic Chemistry

Ampicillin (Figure 2) is a penicillin β-lactam antibiotic with in vitro activity against gram-positive and gram-negative aerobic and anaerobic bacteria. It has the characteristic structural features of all penicillins, including a β-lactam ring (shown in pink) and a thiazolidine ring (shown in orange). The two methyl groups at position 2, and an amide group at position 4 (with sulfur being at position 1) allows it to remain stable against hydrolysis by a variety of β-lactamases, including penicillinases, and cephalosporinases and extended-spectrum β-lactamases.

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

Drug Target

Ampicillin disrupts cell wall biosynthesis in bacteria by inhibiting enzymes known as penicillin-binding proteins (PBPs). This name originates from the ability of penicillin and other β-lactam antibiotics to bind to these proteins. Some of these PBP enzymes catalyze the final steps of the peptidoglycan synthesis pathway, which include polymerizing glycan strands and then cross-linking adjacent chains to form the characteristic mesh structure of peptidoglycan. Other PBPs regulate peptidoglycan recycling and cell wall remodeling. Peptidoglycan, which is a polymer consisting of amino acids (peptido-) and sugars (-glycan), is the major component of the bacterial cell wall, and its mesh-like structure provides the cell wall with structure and rigidity. Inhibition of the PBPs responsible for cross-linking results in a severely weakened cell wall, which then causes bacterial cell lysis and death. However, inhibition of PBPs involved only in peptidoglycan remodeling is non-lethal to the bacteria.

Learn more about PBPs.

One target of ampicillin is PBP6, but since PBP6 is responsible for cell wall remodeling and is not essential to the survival of the bacteria, it will not be discussed in detail here. Explore the structure of E. coli PBP6 bound to ampicillin 3ITA.

Instead, the target of ampicillin, PBP3 of Mycobacterium tuberculosis, will be discussed here. While PBP3 of other bacteria are involved in peptidoglycan synthesis, the PBP3 of Mycobacterium tuberculosis specifically is a DD-transpeptidase, an essential protein that forms a ternary complex with other cell-division proteins. Inhibition of this protein prevents the bacteria from forming filamentous cells and replicating (Lu et al., 2020). This enzyme has two domains (Lu et al,, 2020):
1. C-terminal Transpeptidase Domain
2. N-terminal Domain

The active site, where ampicillin binds, is located in the C-terminal transpeptidase domain, which is made of two subdomains, the α and β subdomains (Figure 3). The active site is sandwiched between these two subdomains. Three conserved motifs are conserved at this active site, which will be discussed in the next section. The antibiotic reacts with the Ser386 nucleophile to form an acyl-enzyme covalent complex (Figure 3). As the β-lactam blocks the Ser386 residue, the natural peptide substrate can no longer access the active site of PBP3. Thus, ampicillin inactivates the enzyme and prevents the enzyme from functioning.

Figure 3. Ribbon representation of PBP3 bound to ampicillin (color-coded atomic stick figure: C-spring green, N-blue, O-red, S-yellow). The inset shows the covalent linkage that forms between ampicillin and Ser386 (color-coded atomic stick figure: C-gold, O-red). (PDB ID: 6KGW; Lu et al., 2020).
Figure 3. Ribbon representation of PBP3 bound to ampicillin (color-coded atomic stick figure: C-spring green, N-blue, O-red, S-yellow). The inset shows the covalent linkage that forms between ampicillin and Ser386 (color-coded atomic stick figure: C-gold, O-red). (PDB ID: 6KGW; Lu et al., 2020).

Drug-Target Complex

In the apo structure of PBP3 of Mycobacterium tuberculosis, three conserved motifs are found in the active site (Lu et al., 2020). The first motif is known as the SXXK motif, also found in β-lactamases. It contains nucleophilic Ser386 and Lys389, which is important in acid/base catalysis. The second conserved motif is SXN, containing Ser441 and Asn443. The third conserved motif is KT/SG, made of Lys592, Thr593, Gly594, and Thr595. These motifs form an extensive active-site cleft that not only accomodates natural polypeptide substrates that allow the bacteria to perform normally, but also is the target site for ampicillin (Figure 4a).

Figure 3 compares the active site of the apoenzyme structure of PBP3 with the ampicillin-bound structure. In the active site, The C-3 carboxylate group of ampicillin is stabilized by hydrogen bonds with Thr593 and Thr595. The hydrophobic C2 dimethyl groups of the thiazolidine ring are stabilized by Ala424, Trp425, and Thr578 side chains. The C6 amino side chain group forms hydrogen bonds with Asn443 and Gln597. These interactions stabilize the drug in the active site (Figure 4b)

Figure 4. (a) Ribbon representation of the active site in the apoenzyme structure of PBP3 (PDB ID: 6kgh; Lu et al., 2020). (b) Ribbon representation of the PBP3 active site after ampicillin binding (PDB ID: 6kgw; Lu et al., 2010). Color-coded atomic stick figure: C-khaki, O-red, N-blue.
Figure 4. (a) Ribbon representation of the active site in the apoenzyme structure of PBP3 (PDB ID: 6kgh; Lu et al., 2020). (b) Ribbon representation of the PBP3 active site after ampicillin binding (PDB ID: 6kgw; Lu et al., 2010). Color-coded atomic stick figure: C-khaki, O-red, N-blue.

Pharmacologic Properties and Safety

Table 3. Pharmacokinetics: ADMET of ampicillin.

Features Comment(s) Source
Oral Bioavailability (%) 39–54% (Bolme et al., 1976)
IC50 2.0 ± 0.2 µM (for binding to PBP1a in Acinetobacter baumannii); 3.0 ± 1.0 µM (for binding to PBP3 in Acinetobacter baumannii) (Papp-Wallace, 2012)
Ki (µM) N/A N/A
Half-life (hrs) 1 to 1.5 hours PubChem
Duration of Action 6- 8 hours LiverTox
Absorption Site N/A N/A
Transporter(s) N/A N/A
Metabolism N/A N/A
Excretion Ampicillin is excreted in the urine largely unchanged FDA
AMES Test (Carcinogenic Effect) Non-carcinogenic Drugbank
hERG Safety Test (Cardiac Effect) Weak inhibitor Drugbank
Liver Toxicity Instances of liver injury occur in less than 1 in 100,000 people. The onset of liver injury can occur after the antibiotic is stopped, though there is a rapid recovery after withdrawal. Usually, the cause of liver injury with ampicillin use is hypersensitivity or allergy. LiverTox

Drug Interactions and Side Effects

Table 4. Drug interactions and side effects of ampicillin.

Features Comment(s) Source
Total Number of Drug Interactions 50 drugs Drugs.com
Major Drug Interaction(s) bcg (Tice BCG, Tice BCG Vaccine), cholera vaccine, live, methotrexate, typhoid vaccine, live Drugs.com
Alcohol/Food Interaction(s) Food interaction (moderate), Hypertension (moderate) Drugs.com
Disease Interaction(s) Clostridioides difficile-associated diarrhea (major), Mononucleosis (moderate), Patients with heart disease on sodium restriction diet (moderate)Renal dysfunction (moderate), Hemodialysis (moderate) Drugs.com
On-target Side Effects Pain at injection site after intramuscular administration, phlebitis at intravenous administration Drugs.com
Off-target Side Effects Nausea, vomiting, diarrhea, rash, anaphylaxis, headache, weakness, dizziness, fever, muscular aches Drugs.com
CYP Interactions None DrugBank

Links

Table 5. Links to learn more about ampicillin

Comprehensive Antibiotic Resistance Database (CARD) ARO:3000637
DrugBank https://go.drugbank.com/drugs/DB00415
Drugs.com https://www.drugs.com/mtm/ampicillin.html
FDA - Ampicillin for Injection https://www.fda.gov/media/127633/download
LiverTox: National Institutes of Health (NIH) https://www.ncbi.nlm.nih.gov/books/NBK547894/
PubChem CID 6249

Learn about ampicillin resistance.

References

Ampicillin - DrugBank. Drugbank.ca https://go.drugbank.com/drugs/DB00415

Ampicillin for injection. Food and Drug Administration. https://www.fda.gov/media/127633/download

Ampicillin. PubChem. https://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=6249

Ampicillin. Drugs.com https://www.drugs.com/mtm/ampicillin.html

Bolme, P., Dahlström, B., Diding, N. Å., Flink, O., Paalzow, L. (1976). Ampicillin: Comparison of bioavailability and pharmacokinetics after oral and intravenous administration of three brands. European Journal of Clinical Pharmacology, 10(3), 237-243. https://doi.org/10.1007/BF00558335

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

Lu, Z., Wang, H., Zhang, A., Liu, X., Zhou, W., Yang, C., Guddat, L., Yang, H., Schofield, C. J., Rao, Z. (2020) Structures of Mycobacterium tuberculosis Penicillin-Binding Protein 3 in Complex with Five β-Lactam Antibiotics Reveal Mechanism of Inactivation. Mol Pharmacol., 97, 287-294. https://doi.org/10.1124/mol.119.118042

Papp-Wallace, K. M., Senkfor, B., Gatta, J., Chai, W., Taracila, M. A., Shanmugasundaram, V., Han, S., Zaniewski, R. P., Lacey, B. M., Tomaras, A. P., Skalweit, M. J., Harris, M. E., Rice, L. B., Buynak, J. D., Bonomo, R. A. (2012) Early insights into the interactions of different β-lactam antibiotics and β-lactamase inhibitors against soluble forms of Acinetobacter baumannii PBP1a and Acinetobacter sp. PBP3. Antimicrob Agents Chemother., 56, 5687-92. https://doi.org/10.1128/aac.01027-12

March 2025, Helen Gao, Shuchismita Dutta; Reviewed by Dr. Andrew Lovering
https://doi.org/10.2210/rcsb_pdb/GH/AMR/drugs/antibiotics/cellwall-biosynth/pbp/blm/ampicillin