Discovery of Novel Lin28 Inhibitors to Suppress Cancer Cell Stemness

SIMPLE SUMMARY: Cancer cells gaining stem cell gene signatures has been deemed as the root of cancers. Blocking the driver genes that control cancer stemness will lead to effective tumor suppression. Lin28 is a stemness driver gene that exerts its tumor-promoting activity through its RNA binding capability. Here, we analyzed the protein structure of Lin28 and discovered several chemicals that can block Lin28 RNA-binding activity. The identified Lin28 inhibitors strongly block the cancer cell stemness features, indicating that these chemicals may be further developed into clinically used drugs for cancer patients. ABSTRACT: Lin28 is a pluripotency factor that regulates cancer cell stem-like phenotypes to promote cancer development and therapy-resistant tumor progression. It acts through its cold shock domain and zinc knuckle domain (ZKD) to interact with the Let-7 pre-microRNA and block Let-7 biosynthesis. Chemical inhibition of Lin28 from interacting with Let-7 presents a therapeutic strategy for cancer therapy. Herein, we present the computer-aided development of small molecules by in silico screening 18 million compounds from the ZINC20 library, followed by the biological validation of 163 predicted compounds to confirm 15 new Lin28 inhibitors. We report three lead compounds, Ln7, Ln15, and Ln115, that target the ZKD of both Lin28A and Lin28B isoforms and block Lin28 from binding Let-7. They restore Let-7 expression and suppress tumor oncogenes such as SOX2 in cancer cells and show strong inhibitory effects on cancer cell stem-like phenotypes. However, minimal impacts of these compounds were observed on Lin28-negative cells, confirming the on-target effects of these compounds. We conclude from this study the discovery of several new Lin28 inhibitors as promising candidate compounds that warrant further drug development into potential anticancer therapies.