How Antibiotics Work: Penicillin and Beyond

Before the 1940s, a scratch that became infected, a case of pneumonia or a difficult childbirth could easily be fatal. Antibiotics changed that, and they remain one of the most important achievements of chemistry and medicine. An antibiotic has a difficult job: it must kill or stop the growth of bacteria living inside the human body while leaving human cells unharmed. The trick is chemistry: targeting molecules and processes that bacteria have and we don’t, or that differ enough between us to be hit selectively.

Selective toxicity

The key principle is selective toxicity: harming the microbe far more than the host. Bacteria are prokaryotes, and their cells differ from human (eukaryotic) cells in several important ways:

• bacteria have a cell wall made of peptidoglycan; human cells have no cell wall at all;
• bacterial ribosomes (called 70S) differ in structure from human cytoplasmic ribosomes (80S);
• bacteria use somewhat different enzymes to copy and package their DNA;
• many bacteria must make their own folic acid, while humans get it from food;
• bacterial membranes have a different lipid composition.

Each of these differences is a potential target. Antibiotics that kill bacteria are called bactericidal; those that stop them multiplying, letting the immune system finish the job, are bacteriostatic.

Target 1: the cell wall

Why the wall matters

Bacteria live in environments where water tends to rush into their cells by osmosis. Their cell wall resists the resulting pressure, like a corset around the cell membrane. It’s made of peptidoglycan: long chains of sugars (see carbohydrates) cross-linked by short peptide bridges into a mesh. The final cross-linking step is carried out by enzymes called transpeptidases (also known as penicillin-binding proteins).

β-Lactam antibiotics

The β-lactams include penicillins, cephalosporins and carbapenems. They all contain a β-lactam ring: a four-membered ring made of three carbon atoms and one nitrogen, with a C=O group, in which the nitrogen is bonded to the carbonyl carbon (an amide).

A four-membered ring is highly strained: its bond angles of about 90° are far from the normal ~109° or ~120°, so the ring is eager to open. In a penicillin, the β-lactam ring is also fused to a second ring, which prevents the normal resonance stabilisation of the amide and makes the carbonyl carbon especially reactive.

The β-lactam ring resembles the end of the peptide that transpeptidase normally cross-links. The enzyme’s active-site serine attacks the β-lactam carbonyl, the strained ring opens, and the antibiotic ends up covalently bonded to the enzyme. The enzyme is permanently inactivated: an irreversible inhibitor (see competitive vs non-competitive inhibition).

Without cross-links, growing bacteria build weak walls, and they burst. Human cells have no peptidoglycan and no transpeptidase, which is why penicillins are generally so safe (though some people are allergic to them). The history of penicillin is told in penicillin: discovery and chemistry.

Glycopeptides

Vancomycin also blocks cell-wall building, but by a different method: it binds tightly to the ends of the peptide chains themselves, through five hydrogen bonds, physically blocking the enzymes. It’s an important antibiotic for serious infections caused by resistant bacteria.

Target 2: the ribosome (protein synthesis)

Bacteria must constantly make proteins, using their ribosomes (see transcription and translation). Several antibiotic families bind bacterial ribosomes more strongly than human ones:

• Tetracyclines block transfer RNA from binding to the ribosome’s A site.
• Macrolides (such as erythromycin, clarithromycin and azithromycin) block the tunnel through which the new protein chain leaves the ribosome.
• Aminoglycosides (such as gentamicin) cause the ribosome to misread messenger RNA, producing faulty proteins.

Because human mitochondria have ribosomes similar to bacterial ones (mitochondria are descended from bacteria), some of these drugs can cause side effects, such as hearing damage with aminoglycosides.

Target 3: DNA replication

Quinolones and fluoroquinolones (such as ciprofloxacin) inhibit bacterial DNA gyrase and topoisomerase IV, enzymes that relieve the twisting of DNA during copying (see DNA replication: the chemistry). The enzymes get stuck halfway through cutting DNA, leaving broken strands that kill the bacterium. Human cells use different topoisomerases that the drugs affect much less.

Target 4: folic acid synthesis

Bacteria must make folic acid (a B vitamin) from scratch, starting from a small molecule called para-aminobenzoic acid (PABA). Humans can’t make folic acid and get it from their diet.

• Sulfonamides (“sulfa drugs”), the first widely used synthetic antibacterial drugs from the 1930s, have a shape similar to PABA. They act as competitive inhibitors of the enzyme that uses PABA.
• Trimethoprim blocks a later enzyme in the same pathway.

Used together, they block two steps of one pathway, which is more effective and makes resistance less likely. Folate’s importance for making DNA bases is explained in vitamins.

Target 5: membranes

A few antibiotics, such as polymyxins (colistin), act like detergents on the outer membranes of certain bacteria. They’re used as a last resort because they can also damage human kidney cells.

Why antibiotics don’t work on viruses

Viruses have no cell wall, no ribosomes of their own and no metabolism; they hijack the host cell’s machinery. Antibiotics have nothing to target, so they’re useless against colds, flu and COVID-19. Using them for viral infections doesn’t help the patient and encourages antibiotic resistance. Viral infections are treated with antiviral drugs, which target viral enzymes, or prevented with vaccines (see the chemistry of mRNA vaccines).

The chemistry of resistance

Bacteria reproduce quickly, and mutations or genes swapped between bacteria can give them resistance. The main chemical strategies:

1. Destroying the antibiotic. Enzymes called β-lactamases hydrolyse the β-lactam ring before it can reach its target, inactivating penicillins and related drugs. To counter this, some medicines combine a β-lactam with a β-lactamase inhibitor, such as clavulanic acid in co-amoxiclav: the inhibitor sacrifices itself by binding the β-lactamase.
2. Changing the target. MRSA (methicillin-resistant Staphylococcus aureus) makes an altered transpeptidase that β-lactams bind poorly. Vancomycin-resistant bacteria change the peptide ends so vancomycin forms one fewer hydrogen bond, reducing binding about a thousandfold.
3. Pumping the drug out. Efflux pumps in the bacterial membrane expel antibiotics before they reach effective concentrations.
4. Blocking entry. Changing the pores in the outer membrane so the drug can’t get in.

Antimicrobial resistance is now a major global health threat. Using antibiotics only when needed, completing prescribed courses as directed, preventing infections and developing new antibiotics are all part of the response.

Key takeaways

• Antibiotics rely on selective toxicity: hitting targets bacteria have and human cells lack or have in a different form.
• Main targets: cell walls (β-lactams, vancomycin), ribosomes (tetracyclines, macrolides, aminoglycosides), DNA gyrase (quinolones), folate synthesis (sulfonamides, trimethoprim) and membranes (polymyxins).
• β-Lactams work because their strained four-membered ring acylates the transpeptidase’s serine, irreversibly blocking cell-wall cross-linking.
• Antibiotics don’t work on viruses.
• Resistance comes from β-lactamases, altered targets, efflux pumps and reduced entry. For the story that started it all, see penicillin.