Structures of BCL-2 in complex with venetoclax reveal the molecular basis of resistance mutations

Abstract

Venetoclax is a first-in-class cancer therapy that interacts with the cellular apoptotic machinery promoting apoptosis. Treatment of patients suffering chronic lymphocytic leukaemia with this BCL-2 antagonist has revealed emergence of a drug-selected BCL-2 mutation (G101V) in some patients failing therapy. To understand the molecular basis of this acquired resistance we describe the crystal structures of venetoclax bound to both BCL-2 and the G101V mutant. The pose of venetoclax in its binding site on BCL-2 reveals small but unexpected differences as compared to published structures of complexes with venetoclax analogues. The G101V mutant complex structure and mutant binding assays reveal that resistance is acquired by a knock-on effect of V101 on an adjacent residue, E152, with venetoclax binding restored by a E152A mutation. This provides a framework for considering analogues of venetoclax that might be effective in combating this mutation.

Multiple BCL2 mutations cooccurring with Gly101Val emerge in chronic lymphocytic leukemia progression on venetoclax

“…BCL2 Asp103Glu was associated with a decrease in affinity for venetoclax of approximately 20-fold compared with the wild-type aspartic acid (Gly101Val showed an ;180-fold reduction 9 ; supplemental Table 2). No reduction was observed for binding to a BIM BH3-only peptide, consistent with previous observations and that BCL2 resistance mutations are selected on the ability to maintain cell survival by binding and sequestering BH3-only proteins (eg, BIM), while selectively reducing affinity for venetoclax 17 (Figure 2A). We then went on to express the Asp103Glu in 2 B-lineage human cell lines: RS4;11 (acute leukemia) and KMS-12-PE (myeloma).…”

Integrating Ligand and Target-Driven Based Virtual Screening Approaches With in vitro Human Cell Line Models and Time-Resolved Fluorescence Resonance Energy Transfer Assay to Identify Novel Hit Compounds Against BCL-2

“…The protein surfaces as well as 2D and 3D ligand interactions between protein and molecules were represented for venetoclax and S55746 in Figure 5 and Figure S5, respectively. Consistent with the previously published data, S55746 bind and fill the pockets P1 to P2, while venetoclax could fill all four pockets on the surface from P1 to P4 (Birkinshaw et al, 2019). When this project was initiated, there was no cocrystallized venetoclaxbound form of the BCL-2.…”

“…When this project was initiated, there was no cocrystallized venetoclaxbound form of the BCL-2. Here, we also checked the binding pose of venetoclax as the crystal structure of BCL-2 bound to venetoclax recently became available (Birkinshaw et al, 2019). A slight difference in binding pose of venetoclax was in the more flexible region of oxane fragment; however, with the rest of the compound, similar amino acid moieties interact by the identical parts of venetoclax in both poses.…”

“…Currently, venetoclax is the only approved drug by the FDA for the treatment of chronic lymphocytic leukemia (CLL), and it is a selective BCL-2 protein inhibitor. Although it has a very high affinity for BCL-2 as shown in various studies performed on different cancer cell lines (Yang et al, 2012) (www.cancerrxgene.org), resistance to this drug has already been observed (Birkinshaw et al, 2019). Hence, it is necessary to suggest new compounds and scaffolds as BCL-2 inhibitors that could be more efficient against mutations on the target structure and have no side effects.…”

Drug Resistance in Non-Hodgkin Lymphomas

“…The disruption of other BCL2 family members, including the upregulation of BCL-XL, loss of BIM, or mutation of BAX were all associated with acquired venetoclax resistance [145][146][147]. Mutations of the BH3 domain of BCL2 gene responsible for venetoclax binding (e.g., G101V and D103Y) were found in CLL patients with acquired resistance to venetoclax therapy [148]. Dynamic changes of lymphoma cells in response to tumor microenvironment were repeatedly associated with venetoclax resistance [145].…”