Researchers have identified a novel, potent, and specific BCL6 inhibitor that effectively inhibited tumor growth in vitro and in vivo in activated B-cell (ABC) and germinal center B (GCB)-cell–like diffuse large B-cell lymphoma (DLBCL) preclinical models. Mariano G. Cardenas, PhD, a postdoctoral associate in Dr. Ari Melnick’s laboratory at Weill Cornell Medical College, presented details of the new BCL6 inhibitor, FX-1085, in the “Advances in Genetics” oral abstract session at the 2014 ASH Meeting on Lymphoma Biology.
BCL6 is a common oncogene in DLBCLs and inhibition of the interaction between BCL6 and its co-repressors has the potential to kill lymphoma cells. The BTB domain of BCL6 has been identified as a docking site for co-repressor complex proteins. This co-repressor interaction is a critical mediator of BCL6 oncogenic activity, making it a targetable surface.
Using computer-aided drug design, Dr. Melnick’s group and collaborators had previously identified a small molecule, 79-6, that bound to the BCL6-BTB, targeted the interaction of BCL6 and its co-repressors, and had anti-lymphoma activity in mice.
“Our research with 79-6 showed that this interaction could be disrupted with a small molecule inhibitor, but the inhibitor was not extremely potent,” Dr. Cardenas told ASH Clinical News.
To address this issue, Dr. Cardenas and colleagues applied a novel, computer-aided drug design methodology — developed by Alexander MacKerell, PhD, and colleagues — called “site identification by ligand competitive saturation,” or SILCS. SILCS is a method for identifying a molecule’s binding site by simulating its physical movement. In this case, the researchers simulated the physical movement of the 79-6 molecule in an aqueous solution to identify areas on the BCL6-BTB protein’s surface where it would likely bind.
The SILCS process produced a 3-dimensional map of the 79-6 molecule’s probable binding sites, which Dr. Cardenas and colleagues then used to design 35 compounds to test in vitro.
Of these compounds, FX-1085 was identified as the most potent BCL6-inhibitor; analysis showed that it was at least 10 times more effective than 79-6 (the lead compound).
FX-1085 works by disrupting the formation of BCL6-co-repressor complexes, as well as specifically re-activating BCL6 target genes, the investigators explained. They also used RNA sequencing and gene set enrichment analysis to better understand how FX-1085 represses RNA transcription; results showed that treatment with FX-1085 mimicked the gene-expression changes induced by BCL6 depletion.
To confirm the findings of their in vitro tests and assess the specific lymphoma-killing effect of FX-1085, Dr. Cardenas and colleagues added the compound to 12 GCB and ABC-DLBCL cell lines that are BCL6-dependent and four cell lines that are BCL6-independent (as controls). As expected, the FX-1085 drug had a selective inhibitory effect on the BCL6-dependent cell lines, but not in those that do not rely on BCL6 to survive.
Finally, Dr. Cardenas and colleagues conducted an in vivo study of FX-1085 using a xenograft model in SCID mice. The compound was administered at 25 mg/kg and 50 mg/kg per day for 10 days. FX-1085 50 mg/kg induced 95 percent tumor regression in OCI-Ly7 (p=0.0016) and SU-DHL-6 (p=0.0050). In the more aggressive ABC-DLBCL cell line, FX-1085 50 mg/kg induced about 70 percent tumor regression. Notably, there were no treatment-related toxicities to normal tissues.
“FX-1085 is a more potent compound that binds more strongly to the [BCL6-BTB] protein than to the natural ligand and was very potent in vitro, in vivo, and in ex vivo patient samples,” Dr. Cardenas said.
- Cardenas MG. Identification of targetable functional groups on BCL6 dimer allows rational design of potent and selective inhibitors with activity in GCB- and ABC-DLBCLs. Presented at: ASH Meeting on Lymphoma Biology; August 10-13; Colorado Springs, CO.