NCE (Year 4)

For Milestone 1, we have successfully completed aa second focused screen of derivative compounds based on 6 leads in the first round. The fragment-based screen is currently in validation for structure-activity relationships (SAR; collaboration with Dr. Paul Workman, ICR, London). The proof-of-concept analysis for Milestone 2, and demonstration of specific interaction in the BCL6 lateral grove has been completed at the end of month 36 of this grant. Using computer-aided drug design (CADD), Dr. Melnick’s group and collaborators had previously identified a small molecule, 79-6, that bound to the BCL6-BTB domain. Thereby, 79-6 targeted the interaction of BCL6 and its co-repressors NCOR, BCOR and SMRT, and restored expression of BCL6 targets in leukemia cells, including Arf and p53. One caveat of the 79-6 compound that was identified by validation studies in Dr. Workman’s laboratory included the low degree of cell penetration and short half-life of the compound. To address these caveats, Dr. Cardenas applied a novel, CADD-based methodology based on “site identification by ligand competitive saturation” (SILCS). SILCS is a method for identifying a molecule’s binding site by simulating its physical movement. In this case, SILCS simulated the physical movement of 79-6 tool compound in solution to map the exact interaction interface between 79-6 and the BCL6 lateral groove. Thereby, SILCS produced a 3-dimensional map of the 79-6 molecule’s probable binding sites, which was then used to design 35 compounds to test in vitro. The new lead compound emerging from Dr. Melnick’s SILCS screen, FX-1085, is approximately 30-fold more effective than 79-6 and is now being validated in our studies on AML and ALL samples (Milestone 3). Results from this collaboration indicates that FX-1085 robustly prevents the formation of complexes between BCL6 and its co-repressors NCOR, BCOR and SMRT and, hence, re-activates BCL6 target genes, including Arf and p53. In the past six months (6-12 of the NCE), we have performed experiments to validate activity of BCL6 inhibition in vivo for the treatment of xenografted Ph+ ALL cells, MLL-rearranged ALL and RAS-driven acute leukemias.