By Temea Turjaka - Biochemistry Student @ Christ Church College, Oxford
Antibiotics are medicines that help stop infections caused by bacteria. They do this by killing the bacteria or keeping them from reproducing. One way to achieve this is by targeting the process of translation, also known as protein synthesis. Without protein synthesis, bacteria will die because they cannot exist without essential proteins; for example, enzymes, which catalyse every metabolic chemical reaction in the cell, proteins embedded on the cell membrane, receptors, signalling proteins, and tubulin which is part of the cytoskeletal structure of bacteria.
Compounds made by fungi that inhibit bacterial protein synthesis are some of the most effective antibiotics used in modern medicine. Millions of years of coevolution between bacteria and fungi have resulted in fungi producing potent bacterial inhibitors. Antibiotics exploit the structural differences between bacterial and eukaryotic ribosomes in order to preferentially interfere with the function of bacterial ribosomes, hence why humans can take high doses of antibiotics without undue toxicity.
The translational machinery’s complexity makes it vulnerable to disruption in multiple ways. Bacteria require a specific concoction of molecules for protein synthesis: mRNA, aminoacyl transfer RNAs (charged tRNAs that bring amino acids to the ribosome), GTP (guanine equivalent of ATP which is provide the energy for the reactions via the hydrolysis of GTP). There are 3 main stages of translation: initiation, elonation, and termination. There are also 3 main sites on the large ribosomal subunit involved in these steps, including the aminoacyl (A) site, peptidyl (P) site, and exit (E) site.
1. Initiation- small ribosomal subunit combines with mRNA and initiator tRNA, only then does large subunit join
2. Elongation- internal codons are translated in a series of translocation steps
3. Termination- synthesis stops when a stop codon is encountered
Now that the process of translation is better understood, we can move onto how antibiotics target this process.
Macrolides such as clarithromycin, erythromycin and azithromycin are bacteriostatic, meaning the agents prevent the growth of bacteria, thus keeping them in the stationary phase of growth. Macrolides bind to the 50S subunit of the 70S prokaryotic ribosome and prevent the ribosome from moving along the mRNA, thereby inhibiting the elongation of the polypeptide chain. Specific conditions these antibiotics can treat include pneumonia (by targeting the protein synthesis of Legionella or Mycoplasma), peptic ulcers (by targeting H.Pylori), gastrointestinal infections (by targeting the ribosomes of Campylobacter).
Aminoglycosides such as Gentamicin and Tobramycin, inhibit protein synthesis by binding to the A site with high affinity on the 16S rRNA of the 30S subunit. By blocking the most vital site, where aminoacyl tRNAs would normally bind to by bringing amino acids, the building blocks of proteins are not coming into the ribosome. Protein synthesis ceases to happen, therefore aminoglycosides are bactericidal antibiotics that directly kill the bacteria. These antibiotics mainly treat gram-negative bacteria, such as Pseudomonas, Enterobacteria, and other aerobic gram-negative bacteria.
In conclusion, the reason why antibiotics directly or indirectly kill bacteria by targeting the protein synthesis machinery is because: they either cause premature termination of the polypeptide chain, so the primary sequence cannot fold properly into the secondary structure and then tertiary 3D structure and perhaps quaternary structure. If it cannot achieve its stable 3D structure, it will cease to function. Antibiotics can also prevent charged tRNA from entering the A site, therefore amino acids cannot enter the ribosome, and the polypeptide chain cannot be made by peptidyl transferase catalysing the formation of peptide bonds between the protein building blocks.