Bispecific Estrogen Receptor α Degraders Incorporating Novel Binders Identified Using DNA-Encoded Chemical Library Screening

Abstract

Bispecific degraders (PROTACs) of ERα are expected to be advantageous over current inhibitors of ERα signaling (aromatase inhibitors/SERMs/SERDs) used to treat ER+ breast cancer. Information from DNA-encoded chemical library (DECL) screening provides a method to identify novel PROTAC binding features as the linker positioning, and binding elements are determined directly from the screen. After screening ∼120 billion DNA-encoded molecules with ERα WT and 3 gain-of-function (GOF) mutants, with and without estradiol to identify features that enrich ERα competitively, the off-DNA synthesized small molecule exemplar 7 exhibited nanomolar ERα binding, antagonism, and degradation. Click chemistry synthesis on an alkyne E3 ligase engagers panel and an azide variant of 7 rapidly generated bispecific nanomolar degraders of ERα, with PROTACs 18 and 21 inhibiting ER+ MCF7 tumor growth in a mouse xenograft model of breast cancer. This study validates this approach toward identifying novel bispecific degrader leads from DECL screening with minimal optimization.

Chemistries of bifunctional PROTAC degraders

“…25), which had a DC 50 of 37 nM for the degradation of ERα. 228 AstraZeneca company designed ERα degrader 181 with AZD9496 as the ligand of ERα protein, but its degradation activity on ERα protein was slightly worse than that of ERD-308 . 112 Interestingly, the ERα protein degraders reported above were all designed based on VH032 as an E3 ligase ligand.…”

Proteolysis-targeting chimaeras (PROTACs) as pharmacological tools and therapeutic agents: advances and future challenges

“…described many IAP-based PROTACs targeting ERα. 105 The representative compound PROTAC 69 ( Table 17 ) was less efficient in degrading ERα proteins compared to the reported IAP-based PROTACs, which had not been studied much by the authors.…”

“…identified some novel ERα binding agents that were efficiently integrated into VHL-involved PROTACs, exhibiting nanomolar ERα DC 50 values in ER + cells, while showing no effect in ER- cells. 105 The representative compounds PROTAC 61 and PROTAC 62 ( Table 16 ) showed no off-target effects in normal immortalised mammary cells. In addition, PROTAC 61 and PROTAC 62 exhibited properties suitable for in vivo application and efficacy in ERα-dependent xenograft models.…”

Discovery of small molecule ligands for the von Hippel-Lindau (VHL) E3 ligase and their use as inhibitors and PROTAC degraders

“…39), with nanomolar DC 50 values and suppression of CDK6 levels for up to 96 h. In a recent approach to develop novel oestrogen receptor a (ERa) degraders, an ERa antagonist derived from DNA-encoded chemical library screening followed by off-DNA hit optimisation has been incorporated into a series of PROTAC molecules featuring CRBN, VHL and IAP binders with different linkage vectors as E3 ligase recruiting moieties. 181 Using the Huisgen 1,3-dipolar cycloaddition, commonly referred to as click reaction, the azide-functionalised ERa binder was coupled with E3 ligase binders featuring PEG linkers of different length terminated with an alkyne functionality. The VHL-based PROTACs of both the amide-linked and phenoxy-linked series induced ERa degradation at sub-micromolar level in multiple cell lines, with compounds 96 and 97 (Fig.…”