Toxoplasma gondii
and
Cryptosporidium parvum
are protozoan parasites that are highly prevalent and opportunistically infect humans worldwide, but for which completely effective and safe medications are lacking. Herein, we synthesized a series of novel small molecules bearing the diacyl urea scaffold and related structures, and screened them for
in vitro
cytotoxicity and antiparasitic activity against
T. gondii
and
C. parvum
. We identified one compound (GMG-1-09), and four compounds (JS-1-09, JS-2-20, JS-2-35 and JS-2-49) with efficacy against
C. parvum
and
T. gondii
, respectively, at low micromolar concentrations and showed appreciable selectivity in human host cells. Among the four compounds with efficacy against
T. gondii
, JS-1-09 representing the diacyl urea scaffold was the most effective, with an anti-
Toxoplasma
IC
50
concentration (1.21 μM) that was nearly 53-fold lower than its cytotoxicity IC
50
concentration, indicating that this compound has a good selectivity index. The other three compounds (JS-2-20, JS-2-35 and JS-2-49) were structurally more divergent from JS-1-09 as they represent the acyl urea and acyl carbamate scaffold. This appeared to correlate with their anti-
Toxoplasma
activity, suggesting that these compounds’ potency can likely be enhanced by selective structural modifications. One compound, GMG-1-09 representing acyl carbamate scaffold, depicted
in vitro
efficacy against
C. parvum
with an IC
50
concentration (32.24 μM) that was 14-fold lower than its cytotoxicity IC
50
concentration in a human intestinal cell line. Together, our studies unveil a series of novel synthetic acyl/diacyl urea and acyl carbamate scaffold-based small molecule compounds with micromolar activity against
T. gondii
and
C. parvum
that can be explored further for the development of the much-needed novel anti-protozoal drugs.