Introduction Prostate cancer is one of the leading causes of cancer-related death in men worldwide. Current treatment options are limited to traditional chemotherapy, surgery, radiation, or hormone therapy, which often have unwanted side effects. There is a need to develop safer molecules that attenuate tumour progression without adversely affecting the overall quality of life. We report the in vitro activity of a novel, synthetic, small molecule, with potential to be a lead candidate for the treatment of prostate cancer. Methods A library of novel small molecule inhibitors was developed through rational drug design. A pyrrolo-pyrimidine derivative (MSU-1001) was identified as a potential lead molecule. Prostate and colon cancer cell lines (LNCap, HT-29, and HCT-8) were obtained from the American Type Culture Collection (ATCC). Cells were incubated with various concentrations of MSU-1001 for 72 h. Growth inhibition was determined colorimetrically on a plate-reader using a 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) reduction assay. Findings Colon cancer cell lines HCT-8 and HT-29 were used in conjunction with the androgen-sensitive human prostate adenocarcinoma cell line, LNCaP, to investigate the specificity of MSU-1001 on tumour type. Among the library of compounds tested, MSU-1001 was pursued based on its anti-proliferative activity in LNCaP cells. Addition of MSU-1001 to LNCaP cells resulted in a dose-dependent inhibition of proliferation (GI 50 = 161 nM) with a near-complete inhibition of cell growth noted at 10 μM. By contrast, GI 50 of gemcitabine was more than 6-fold higher (GI 50 = 1.21 μM) in LNCaP cells. Additionally, GI 50 of MSU-1001 in HCT-8 and HT-29 was 1.8 and 8.7 μM, respectively, indicating relative specificity of MSU-1001 against prostate cancer. Interpretation These data show the therapeutic potential of MSU-1001 in prostate cancer. Combination studies of MSU-1001 with testosterone, 17 β -estradiol, and dehydroepiandro-stenone in androgen-sensitive and insensitive prostate cancer cell lines are currently ongoing.