Maternal embryonic leucine zipper kinase (MELK) has been implicated in various cellular processes and is highly upregulated in diverse cancers, then it is thought to be a promising anticancer target. 3-Anilino-1H-pyrazolo[3,4-b]pyridine scaffold was identified as a novel scaffold for MELK kinase inhibitors in high throughput screening (HTS). From exploration for structure–activity relationship (SAR) studies mainly by the modification of the 3 (C3), and 5-positions (C5), 4-(4-methylpiperazin-1-yl)-N-{5-[1-(piperidin-4-yl)-1H-pyrazol-4-yl]-1H-pyrazolo[3,4-b]pyridin-3-yl}benzamide (21a) was found to exhibit good activity (IC50 = 0.15 μM) on MELK as a lead in early state.