Protein synthesis is a complex, multi-step process involving many enzymes as well as conformational alignment. However, the majority of antibiotics that block bacterial protein synthesis interfere with the processes at the 30S subunit or 50S subunit of the 70S bacterial ribosome. The aminoacyl-tRNA synthetases that activate each amino acid required for peptide synthesis are not antibiotic targets. Instead, the primary steps in the process that are attacked are (1) the formation of the 30S initiation complex (made up of mRNA, the 30S ribosomal subunit, and formyl-methionyl-transfer RNA), (2) the formation of the 70S ribosome by the 30S initiation complex and the 50S ribosome, and (3) the elongation process of assembling amino acids into a polypeptide.
Tetracyclines, including doxycycline, prevent the binding of aminoacyl-tRNA by blocking the A (aminoacyl) site of the 30S ribosome. They are capable of inhibiting protein synthesis in both 70S and 80S (eukaryotic) ribosomes, but they preferentially bind to bacterial ribosomes due to structural differences in RNA subunits. Additionally, tetracyclines are effective against bacteria by exploiting the bacterial transport system and increasing the concentration of the antibiotic within the cell to be significantly higher than the environmental concentration.
Aminoglycoside antibiotics have an affinity for the 30S ribosome subunit. Streptomycin, one of the most commonly used aminoglycosides, interferes with the creation of the 30S initiation complex. Kanamycin and tobramycin also bind to the 30S ribosome and block the formation of the larger 70S initiation complex.
Erythromycin, a macrolide, binds to the 23S rRNA component of the 50S ribosome and interferes with the assembly of 50S subunits. Erythromycin, roxithromycin, and clarithromycin all prevent elongation at the transpeptidation step of synthesis by blocking the 50S polypeptide export tunnel. Elongation is prematurely terminated after a small peptide has been formed, but cannot move past the macrolide roadblock.
Peptidyl transferase is a key enzyme involved in translocation, the final step in the peptide elongation cycle. Lincomycin and clindamycin are specific inhibitors of peptidyl transferase, while macrolides do not directly inhibit the enzyme. Puromycin does not inhibit the enzymatic process, but instead competes by acting as an analog of the 3′-terminal end of aminoacyl-tRNA, disrupting synthesis and causing premature chain termination.
Hygromycin B is an aminoglycoside that specifically binds to a single site within the 30S subunit in a region that contains the A, P, and E sites of tRNA. It has been theorized that this binding distorts the ribosomal A site and may be the cause of hygromycin B’s ability to induce misreading of aminoacyl-tRNAs as well as prevent the translocation of peptide elongation.