Antimicrobial resistance is rising at an alarming rate. The methylerythritol phosphate (MEP) pathway is a metabolic pathway that produces the isoprenoids isopentyl pyrophosphate (IPP) and dimethylallyl pyrophosphate (DMAPP). Notably, the MEP pathway is present in bacteria and not mammals, which made the enzymes of the MEP pathway attractive targets for discovering new anti-infective agents due to reduced chances of off-target interactions leading to side effects. The biophysical properties of 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase (IspD) and 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase (IspE) were determined to aid discovery of novel inhibitors. Thermal shift screening was used as an initial filter to narrow down a library of compounds with thermal shifts greater than 1° C., which could indicate binding to the IspD and IspE enzymes. Follow-up studies were performed using isothermal titration calorimetry and enzymatic inhibition assays. Results from these studies have revealed compounds with high micromolar inhibition of both IspD from Escherichia coli and IspE from Burkholderia thailandensis. The hit compounds are used for future development of more potent IspD and IspE inhibitors.