BLC6

May 2023

B-cell lymphoma 6 (BCL6)

B-cell lymphoma 6 protein (BCL6) is a transcriptional factor that regulates the differentiation and proliferation of lymphocytes, making it an attractive therapeutic target for cancer and autoimmune diseases.  

The function of BCL6 is to bind and repress target genes. To do this, it requires binding to other proteins (BCOR and NCOR), which act as co-repressors. Therefore, disrupting the protein-protein interactions between BCL6 and its co-repressor proteins is a promising strategy for designing new drugs. Some BCL6-targeting inhibitors and degraders have been developed by pharma (Boehringer Ingelheim, GSK, Janssen), but their passage into clinics is still lacking. 

Recently, scientists reported an interesting shape complementarity, structure-based approach, to develop a new, highly potent chemical series of BCL6 inhibitors.

From the structural analysis of BCL6 in complex with the previously studied inhibitor 2, they noticed the presence of a hydrophobic subpocket next to the binding site (Image 1). They decided to expand the molecule in that direction, to fill this space.  

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Image 1. 3D structure of BCL6 bound to inhibitor 2 (blue, PDB: 7OKH). The hydrophobic pocket close to position-3 in the ligand is indicated. The molecular surface of the pocket is colored by hydrophobicity index, with green indicating high hydrophobicity. The picture is produced with the 3decision® software. 

Unfortunately, the simple addition of a substituent at the 3-position proved to be an unsuccessful strategy: the ligand flipped and exposed the newly added chemical moiety towards the solvent, with a loss of 4 times in potency. Therefore, they decided to proceed with the addition of a fused ring system, aiming to constrain the substituent at the 3-position. 

The substitution with a 7-membered ring preserved the original potency, but no significant activity in cells was observed, likely due to the low permeability of the compound. Therefore, they looked for new strategies to further optimize the ligand. The x-ray crystal structure showed that compound 7 did not align closely to the pocket surface but was sitting on top of it (Image 2). This was probably caused by the repulsions between the lactone oxygen and the backbone carbonyl of Cys53. This structural insight led them to decide to modify the position of the oxygen in the ring, to produce ligand 9a. The crystal structure confirmed that such change was crucial: in this case, the ligand adopted a different conformation, that matched much more the shape of the pocket. This translated into a significant increase in cellular activity.

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Image 2. On the left: overlay of the ligand poses. Ligand 7 (purple, PDB: 7Q7T) sits on top of the pocket, with the lactone oxygen (pointed by the blue arrow) away from the molecular surface of BCL6 (mesh, hydrophobicity index colored), while ligand 9a (white, PDB: 7Q7U) adopts a conformation that fills the space of the pocket. On the right: 2D structures of ligands 7 and 9a, with indication of the lactone oxygen. The picture is produced with the 3decision® software. 

They exploited the same approach for further modifying the molecule: they added a cyclopropyl substituent (Image 3A) and two fluorine atoms (Image 3B), to fill the available space around the ligand. Overall, their optimization led to a 300-fold increase in potency, and high cellular activity, without the addition of any strong polar interactions, but only based on protein-ligand shape complementarity. 

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Image 3. Substitution with a cyclopropyl two fluorine atoms (PDB: 7Q7R) increase the shape complementarity of ligand-protein surface. The molecular surfaces of BCL6 (solid, light purple) and of ligand 1 were calculated by the 3decision® software. 

In this study, the knowledge of the structure and geometry of the pocket drove the drug design, with an infrequently exploited shape-complementarity approach, leading to a final 300-fold improvement in activity.  

Reference:

Davis OA, Cheung KJ, Brennan A, Lloyd MG, Rodrigues MJ, Pierrat OA, Collie GW, Le Bihan YV, Huckvale R, Harnden AC, Varela A, Bright MD, Eve P, Hayes A, Henley AT, Carter MD, McAndrew PC, Talbot R, Burke R, van Montfort RLM, Raynaud FI, Rossanese OW, Meniconi M, Bellenie BR, Hoelder S. Optimizing Shape Complementarity Enables the Discovery of Potent Tricyclic BCL6 Inhibitors. J Med Chem. 2022 Jun 23;65(12):8169-8190. doi: 10.1021/acs.jmedchem.1c02174. Epub 2022 Jun 3. PMID: 35657291; PMCID: PMC9234963.