Liang Xu
Professor, Department of Molecular Biosciences
University of Kansas

 

 

Fragment-based discovery of chemical probes for RNA-binding protein Musashi-2 (2017-18)

This project relates to the discovery of chemical probes as tools for functional study of a protein critical for cancer initiation and progression. The discovery from this project may be further studied as potential leads for cancer drug discovery, with the ultimate goal of developing the best compound as a whole new class of molecular cancer therapy.

The RNA-binding protein Musashi-2 (MSI2), long considered as a regulator of stem and progenitor cell characteristics, has recently been found to be over-expressed in many types of cancer. MSI2 maintains cancer stem cell populations and regulates cancer invasion, metastasis and development of more aggressive cancer phenotypes, including drug resistance by mediating mRNA stability and translation of proteins operating in essential oncogenic signaling pathways. MSI2 is a promising target for cancer. So far there is limited success on small molecules that directly inhibit MSI2-RNA interaction. RBPs such as MSI2 are considered “undruggable” due to the lack of a well-defined binding pocket for target RNA. We have set up fluorescence polarization (FP) and surface plasmon resonance (SPR) assays for initial screening of a fragment library, and obtained one class of promising MSI2 fragments. However, to make active conjugates, more classes of fragments binding to different sites of the MSI2 RNA-binding pocket are needed. We propose, in the current pilot project, to further screen a larger fragment library to obtain more chemically diverse fragment hits, for subsequent conjugation of active fragments. Our hypothesis for the overall project is that small molecule compounds that disrupt MSI2-RNA binding will block the MSI2 function, leading to translation of target genes that are critical for inhibiting cancer cell growth and progression. Two Specific Aims are proposed: Aim 1, STD-NMR screening of fragment libraries; Aim 2, Validation of hit fragments with binding assays and their anti-tumor activity in cancer cells and target validation.

The success of this one year pilot project will provide us with strong preliminary data and materials enabling us to apply for NIH grants to make chemical conjugates, with structure-based rational design (Docking with NMR/ crystallography data). Our long-term objective is to discover potent and specific chemical probes for delineating the functional roles of MSI2 in cancer initiation and progression, and provide promising hit compounds to further development as novel molecular therapeutics targeting the oncogenic MSI2 protein.

Fragment-based drug discovery for inhibitors of RNA-binding protein HuR (2014-15)

Our objective is to use fragment-based drug discovery to identify novel small molecule inhibitors targeting RNA binding protein HuR, as new chemical probes and eventually novel molecular cancer therapy that inhibit cancer with HuR overexpression. Successfully carried out, the data and hits obtained will enable us to seek out partners for further drug discovery and development studies. We will obtain a few validated hits for further lead optimization and development as a whole new class of molecular cancer therapeutics that inhibit specific protein-HuR interaction required for cancer cell survival and proliferation.

The RNA-binding protein Hu antigen R (HuR) is a member of the embryonic lethal abnormal vision (ELAV) family that binds to adenine- and uridine-rich elements (ARE) located in the 3’- or 5’-untranslated region (UTR). The elevated expression of HuR has been characterized in cancers of brain, ovaries, colon, breast, pancreas and lung. HuR promotes tumorigenesis by interacting with a subset of mRNAs that encode proteins implicated in different tumor process including cell proliferation, cell survival, angiogenesis, invasion, and metastasis. These findings suggest that HuR is a promising therapeutic target for cancer.

So far there is limited success on small molecules that directly inhibit HuR-ARE interaction. RBPs such as HuR are considered “undruggable” due to the lack of a well-defined binding pocket for target RNA. The X-ray crystallography of protein HuR with ARE oligo shows that the RNA-binding pocket of HuR is a long narrow grove, and our existing hit compounds appears only occupy a portion of the pocket. Therefore, the Fragment Based Drug Discovery (FBDD) strategy is suitable to find small molecule compounds binding to the two end of the long narrow RNA-binding pocket, then link the two to make long linear molecule with better affinity and specificity, which is the goal of the current proposal. Our hypothesis is that small molecule compounds that disrupt the HuR-ARE binding will block HuR function, leading to decay and reduced translation of mRNAs of the target genes critical for cancer cell survival and proliferation.

Two goals are proposed: first, Fragment Library Screening for small molecules that disrupt the HuR interaction with AREs of target mRNAs; Second, Active fragments conjugation and analysis of anti-tumor activity, target validation, and mechanism of action. Our long-term objective is to discover potent and specific chemical probes for delineating the functional roles of HuR in cancer initiation and progression, and provide promising hit compounds to further develop novel molecular therapeutics targeting the oncogenic HuR protein. This project fits the scientific theme of COBRE-PSF. FBDD is a new direction of our research on HuRinhibitors. Successfully carried out, this project will discover novel small molecule disruptors of HuR-RNA interaction, which potently inhibit cancer cells dependent on Wnt/Notch signaling and Bcl-2/Mcl-1/XIAP for cell proliferation/survival. The data and validated hits obtained will enable us to pursue additional structureactivity relationships analysis and lead optimization, aiming to generate a new class of molecular cancer therapeutics that will inhibit specific protein-RNA interactions required for cancer cell survival and progression.