Targeting the Tumour-Specific Spliceosome Through In Silico Virtual Screening for Discovery of New SF3B1 Small Molecule Inhibitors

Background: The coding (exon) and noncoding (intron) eukaryotic genes are expressed as precursor messenger RNA (premRNA). mRNA splicing defines the process by which introns are excised from premRNA and flanking exons are ligated together. This process is catalyzed by the spliceosome in which combination of small nuclear ribonucleoproteins (U1, U2, U4, U5, U6) forms a spliceosome. The SF3B1 protein is a core component of the U2 snRNP that binds to the branch site and facilitate RNA splicing. Recent studies have identified mutations and dysregulation of in SF3B1 activities in subsets of human cancers including chronic lymphocytic leukemias (CLLs), uveal melanomas, pancreatic cancers and breast cancers. Despite promising in vivo results indicating the potential of spliceosome modulators in targeting the refractory breast cancers, the preclinical and clinical development of such modulators will take several years to complete. Aim: In the current study, we sought to identify new SF3B1 modulators using massive virtual screening of FDA-approved drugs or novel agents for drug repurposing. Methods: A total of 3000 compounds were screened and the hits were identified based on the binding free energy (kcal/mol) of the molecules to the predicted binding sites. Of the 90 hits, vitamin D3 and its analogs (calcipotriol and calcitriol) were identified as a putative SF3B1 modulators. Results: Further in vitro testing revealed that vitamin D3 and its analogs induced significant mRNA misplicing and tumor-specific cell death in MCF7 and MDA-MB-468. Further analyses revealed that vitamin D3 and its analogs significantly reduce SF3B1 protein expression with no changes in its mRNA expression. Conclusion: These results suggest that vitamin D3 and its analogs might interact with SF3B1 to induce protein degradation rather than transcriptional activation.