Rationally designed BCL6 inhibitors target activated B cell diffuse large B cell lymphoma
Mariano G. Cardenas, … , Alexander D. MacKerell Jr., Ari M. Melnick
Mariano G. Cardenas, … , Alexander D. MacKerell Jr., Ari M. Melnick
Published August 2, 2016
Citation Information: J Clin Invest. 2016;126(9):3351-3362. https://doi.org/10.1172/JCI85795.
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Research Article Oncology

Rationally designed BCL6 inhibitors target activated B cell diffuse large B cell lymphoma

Abstract

Diffuse large B cell lymphomas (DLBCLs) arise from proliferating B cells transiting different stages of the germinal center reaction. In activated B cell DLBCLs (ABC-DLBCLs), a class of DLBCLs that respond poorly to current therapies, chromosomal translocations and amplification lead to constitutive expression of the B cell lymphoma 6 (BCL6) oncogene. The role of BCL6 in maintaining these lymphomas has not been investigated. Here, we designed small-molecule inhibitors that display higher affinity for BCL6 than its endogenous corepressor ligands to evaluate their therapeutic efficacy for targeting ABC-DLBCL. We used an in silico drug design functional-group mapping approach called SILCS to create a specific BCL6 inhibitor called FX1 that has 10-fold greater potency than endogenous corepressors and binds an essential region of the BCL6 lateral groove. FX1 disrupted formation of the BCL6 repression complex, reactivated BCL6 target genes, and mimicked the phenotype of mice engineered to express BCL6 with corepressor binding site mutations. Low doses of FX1 induced regression of established tumors in mice bearing DLBCL xenografts. Furthermore, FX1 suppressed ABC-DLBCL cells in vitro and in vivo, as well as primary human ABC-DLBCL specimens ex vivo. These findings indicate that ABC-DLBCL is a BCL6-dependent disease that can be targeted by rationally designed inhibitors that exceed the binding affinity of natural BCL6 ligands.

Authors

Mariano G. Cardenas, Wenbo Yu, Wendy Beguelin, Matthew R. Teater, Huimin Geng, Rebecca L. Goldstein, Erin Oswald, Katerina Hatzi, Shao-Ning Yang, Joanna Cohen, Rita Shaknovich, Kenno Vanommeslaeghe, Huimin Cheng, Dongdong Liang, Hyo Je Cho, Joshua Abbott, Wayne Tam, Wei Du, John P. Leonard, Olivier Elemento, Leandro Cerchietti, Tomasz Cierpicki, Fengtian Xue, Alexander D. MacKerell Jr., Ari M. Melnick

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Figure 1

Identification and characterization of FX1 as a BCL6 BTB inhibitor.

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Identification and characterization of FX1 as a BCL6 BTB inhibitor. (A) ...
(A) SILCS FragMaps overlaid on the apo BCL6 BTB domain with the aromatic (purple), aliphatic (green), hydrogen bond donor (blue) and acceptor (red), and charged acceptor (orange) maps. (B and C) Superposition of the SILCS FragMaps with 79-6 alone (B) and with FX1 and 79-6 in complex with BCL6 BTB (C). (D) Comparison of the affinity of the natural ligand SMRT peptide and the small molecules 79-6 and FX1 to BCL6 BTB domains determined by microscale thermophoresis (MST; n = 3 independent experiments; error bars represent the SD). (E) Comparison of the MST results of SMRT and FX1 interaction with the BTB domains of BCL6 or LRF. Results represent mean ± SD of 3 independent experiments. (F) Luciferase reporter assays showing activity of 79-6 or FX1 as compared with vehicle against the repressor activity of a GAL4DBD-BCL6BTB fusion construct compared with the GAL4DBD alone. The y axis represents the relative percentage of repression mediated by the fusion protein in the presence of vehicle, set as 100%. Bars represent mean ± SD of 3 independent experiments. (*P < 0.05, **P < 0.005, t test.) (G) Heteronuclear single quantum coherence spectrum of 250 μM BCL6 BTB with 5% DMSO (red) is superimposed onto the spectrum of BTB with 500 μM FX1 (blue). Residues that experience the most significant chemical shift perturbation are labeled. (H) A graphical representation of the BCL6 BTB domain homodimer based on Protein Data Bank (PDB) structure 1R2B is shown, indicating residues perturbed upon binding of FX1 in magenta.