Mechanism of action of antibiotics – Part II

Puromycin:

Puromycin is a structural analogue of the 3′ end of aminoacyl- tRNA, but differs from tRNA as the aminoacyl residue is linked via an amide bond rather than an ester bond. Puromycin, like aminoacyl-tRNA, binds to the A site of the ribosome peptidyl-transferase center. When the A site is occupied by puromycin, peptidyl transferase links the peptide residues of the peptidyl-tRNA in the ribosomal P site covalently to puromycin. Since the amide bond cannot be hydrolyze by the ribosome, no further peptidyl transfer takes place, and the peptidyl-puromycin complex falls off the ribosome. Puromycin concentrations should be high to inhibit translation completely, because (a) the of puromycin bind with ribosome by weak bonds (b) single ribosome is able to transfer several puromycin molecules to peptidyl-puromycin, and (c) once peptidyl-puromycin has fallen off the ribosome, it does not bind again thatswhy no further antibacterial activity.

Actinomycin D:

Actinomycin D is a molecule that consists of a chromophore (fenoxazone ring) attached to two identical cyclic pentapeptides, it favors guanine-cytosine pairs and is therefore inserted between the G-C steps. Hydrogen bonds are established between the guanine 2-amino group and the carbonyl oxygen of threonine, and also between the guanine N-3 atom and the NH group of the same threonine residue, helping to stabilize the actinomycin-DNA complex. The proline, sarcosine and methylvaline residues of the pentapeptide side chain are involved in further hydrophobic interactions with the DNA minor groove. The formation of this stable actinomycin-DNA complex prevents the unwinding of the double helix which leads to inhibition of the DNA-dependent (this prevents DNA from acting as a template for RNA synthesis) RNA polymerase activity and hence transcription. Actinomycin D does not bind to single stranded DNA/RNA and at low concentration it does not affect DNA replication. As this antibiotic does not directly affect the translation rocess, protein synthesis can continue from the preexisting mRNA. Actinmycin D works with both in prokaryotes and eukaryotes.

Vancomycin:

Vancomycin is a branched tricyclic glycosylated nonribosomal peptide. Vancomycin acts by inhibiting the second stage of cell wall synthesis in susceptible bacteria. Peptidoglycan layer of the cell wall is rigid due to its highly cross-linked structure. During the synthesis of the peptidoglycan layer of bacteria vancomycin prevents incorporation of new building blocks of peptidoglycan i.e., N-acetylmuramic acid (NAM)- and N-acetylglucosamine (NAG)-peptide subunits from being incorporated into the peptidoglycan matrix; which forms the major structural component of Gram-positive cell walls. The large hydrophilic molecule is able to form hydrogen bond interactions with the terminal D-alanyl-D-alanine moieties of the NAM/NAG-peptides. This binding of vancomycin to the D-Ala-D Ala prevents the incorporation of the NAM/NAG-peptide subunits into the peptidoglycan matrix.Reformation of the peptide cross links occurs by the enzyme transpeptidase. Vancomycin after binding to the building blocks (i.e. NAG and NAM) of the peptidoglycan prevents the transpeptidase from acting on these new formed blocks and thus prevents cross-linking of the peptidoglycan layer. By doing so, vancomycin makes the peptidoglycan layer less rigid and more permeable. This causes cellular contents of the bacteria to leak out and eventually death of the bacteria.