Molecule of the Month: Vancomycin

Much of our current arsenal of antibiotics is borrowed from the world's true experts in infection control: bacteria and fungi. These organisms protect themselves with a bewildering collection of exotic chemical weapons, evolved to attack weak points in their competitors. Many of these antibiotic compounds, such as penicillin, attack enzymes, blocking their action and ultimately killing the infecting bacterium. Vancomycin, on the other hand, attacks the thing being built by a bacterial enzyme.

Bacteria build a sturdy cell wall composed of sugar chains crosslinked by short peptides, forming a network called peptidoglycan. This network is built in many steps, laying down the sugar chains and building the peptide connectors. Vancomycin acts near the end of this process. One end of the crosslinking peptide has two alanine amino acids (more specifically, D-alanines, with stereochemistry opposite from the normal L-alanines). To form the crosslink, the final alanine is popped off, and the peptide is attached to a neighboring peptide. As shown here in PDB entry 1fvm , vancomycin binds tightly to this D-alanine-D-alanine peptide, blocking the ability to form the crosslink.

Only some bacteria are susceptible to vancomycin. Bacteria such as Staphylococcus have a thick layer of peptidoglycan that surrounds the cell, and are termed gram positive because of the way this peptidoglycan takes up crystal violet stain when observed in the microscope. Vancomycin is effective for blocking formation of this type of cell wall and is currently used as a last resort antibiotic for persistent infections by these bacteria. Gram negative bacteria such as Escherichia coli, on the other hand, build their peptidoglycan beneath an outer membrane, where it is protected from this stain and from attack by vancomycin. So, smaller antibiotics like penicillin are needed to get inside in these bacteria.

Bacteria become resistant to vancomycin by getting rid of its target. The protein VanA, with the help of two other proteins, adds a lactate group instead of alanine to the end of the peptidoglycan chain. This works just as well for the crosslinking, but is not susceptible to the antibiotic. The structure shown here is VanA from an ancient bacterium, recreated from DNA from 30,000 year old permafrost sediments (PDB entry 3se7 ). Surprisingly, it is very similar to VanA made by modern bacteria, showing that this war of antibiotics and resistance began long before medical science discovered the utility of antibiotics. You can compare the ancient and modern proteins using the Structure Comparison Tool.