The present invention provides methods for the design and identification of novel antimicrobial compounds, and provides antimicrobial compounds identified using these methods. These antimicrobial compounds inhibit the binding of a prokaryotic single-stranded DNA binding protein to a polypeptide that binds to the prokaryotic single-stranded DNA binding protein. In some examples, the prokaryotic single-stranded DNA binding protein is prokaryotic Exonuclease I. In one embodiment, the antimicrobial compound has the structure wherein Y is selected from the group consisting of CH2, O, and NH, R1 is selected from the group consisting of H, F, Cl, Br, and I, R2 is selected from the group consisting of H and CF3, R3 is selected from the group consisting of H and CO2H, R4 is selected from the group consisting of H and OH, and R5 is selected from the group consisting of H, alkoxy, and NO2.