Optimization of a Series of RIPK2 PROTACs

Abstract

Receptor-interacting serine/threonine protein kinase 2 (RIPK2) is an important kinase of the innate immune system. Herein, we describe the optimization of a series of RIPK2 PROTACs which recruit members of the inhibitor of apoptosis (IAP) family of E3 ligases. Our PROTAC optimization strategy focused on reducing the lipophilicity of the early lead which resulted in the identification of analogues with improved solubility and increased human and rat microsomal stability. We identified a range of IAP binders that were successfully incorporated into potent RIPK2 PROTACs with attractive pharmacokinetic profiles. Compound 20 possessed the best overall profile with good solubility, potent degradation of RIPK2, and associated inhibition of TNFα release. A proof-of-concept study utilizing a slow release matrix demonstrated the feasibility of a long-acting parenteral formulation with >1 month duration. This represents an attractive alternative dosing paradigm to oral delivery, especially for chronic diseases where compliance can be challenging.

E3 ligase ligand chemistries: from building blocks to protein degraders

“…The effectiveness of SNIPERs as degraders improved as IAP ligands with higher affinity towards IAPs were incorporated into bifunctional molecules. 71,233,[237][238][239][240][241][242][243][244][245] The first more evident leap in the degradation potency of SNIPERs was achieved by utilising LCL161 (IAP ligand C) as the recruiting ligand. 7,233 In this review, however, we focus on IAP ligands D, E, I, and J, because of synthetic simplicity or availability of reliable synthetic procedures, on target potency, and beneficial physicochemical properties.…”

“…In addition, the exemplified PROTACs in the following sections were also extensively evaluated both in vitro and in vivo. E, I, and J, is given here: bestatin (IAP ligand A), 232,[234][235][236] MV1 (IAP ligand B), 238,239,244 LCL161 (IAP ligand C), 239,240,[243][244][245] IAP ligand F, 71,237 IAP ligand G, 241 IAP ligand H. 242 ligand (IAP ligand D, Fig. 15) is a beneficial IAP recruiter for targeted protein depletion.…”

“…The latter showed very potent in vivo degradation of endogenous RIPK2 and an extended pharmacodynamic efficacy that persisted in the absence of the compound. 241,243 Of note, Example 81 showed efficient RIPK2 depletion despite reduced binding affinity at both cIAP1 and XIAP BIR3 domains. It did, however, possess an increased potency at the BIR2 XIAP domain.…”

“…Consequently, this degrader exhibited a lower propensity to cause cIAP1 autodegradation. 243 For the synthesis of this IAP ligand, a convergent approach was used (Scheme 38). 241 Dipeptide 214 was first prepared by coupling of Boc-N-methyl-L-alanine ( 209) and L-tertleucine methyl ester (210), whereas the substituted pyrrolidine derivative 213 was obtained with 1-tert-butyl 2-methyl (2S,4R)-4hydroxypyrrolidine-1,2-dicarboxylate (211) as starting material.…”

Recent Advances of Degradation Technologies Based on PROTAC Mechanism

“…For example, due to the discovery that immunomodulatory drugs (IMiDs), including thalidomide, lenalidomide and pomalidomide, could act as ligands for the E3 ligase CRBN, a large number of CRBN-based PROTACs were successfully developed to degrade BRD4 [ 13 ], CDK9 [ 14 ], Sirt2 [ 15 ], KRAS G12C [ 16 ], AKT [ 17 ], HDAC6 [ 18 ] and CDK6 [ 19 ]. Similarly, VHL-based PROTACs have successfully degraded ERRα [ 20 ], RIPK2 [ 21 ], HaloTag7 fusion proteins [ 22 ], BRD4 [ 23 ], Smad3 [ 24 ] and RTK [ 25 ], and RNF114-based PROTACs have degraded BRD4 [ 26 ] and BCR-ABL [ 26 , 27 ]; IAP-based PROTACs have degraded RIPK2 [ 28 ], CDK4/6 [ 29 ], Bcl-XL [ 29 ], etc. In more recent years, the explosive growth of PROTACs has indicated that PROTAC is becoming the most popular drug development technology.…”