This is difficult because the outer membrane will prevent most dye-like organic molecules from getting into the cytoplasm of living cells. The free amino group of the DAP moiety of peptidoglycan can, in principle, be labeled with any amine-reactive dye, although such reactive dyes will not react specifically with the cell wall but will also label any protein.

Inhibition of cell wall synthesis in E.coli results in characteristic changes to the cell shape, depending on the target. For example, inhibition of penicillin-binding protein (PBP) 3 results in cell elongation (prior to cell death) because it blocks cell division, whereas inhibition of PBP2 causes the cells to become round because it blocks cell elongation. These phenomena may allow you to follow inhibition in living cells microscopically without having to stain them.

May consider using Permai fluorescence dye.