Ligand Design for RIPK2-targeting PROTAC^®

The receptor-interacting protein kinase 2 (RIPK2) is linked to the pathogen pathway and autophagic activation. Recently, a great effort has been made by Creative Biolabs to develop new ligands for inducing RIPK2 protein degradation by proteolysis targeting chimera (PROTAC^®) technology. With the comprehensive advanced platforms, Creative Biolabs provides global clients with ligand design services for RIPK2-targeting PROTAC^® discovery to meet the novel drug discovery goals.

Fig.1 Model of PROTAC^®-induced degradation and PROTAC^® examples. (Bondeson, 2015)

Introduction of RIPK2

RIPK2 is an intracellular serine/threonine/tyrosine kinase, a key signaling partner, and an obligate kinase for nucleotide-binding oligomerization domain-containing protein 2 (NOD2). Thus, RIPK2 represents an attractive target to probe the pathological roles of the NOD2 pathway. RIKP2 has a C-terminal caspase-activation-and-recruitment (CARD) domain perceiving the upstream activation signal, and an N-terminal kinase domain that could dimerize and phosphorylate other downstream factors. The loss of RIPK2 gene has been demonstrated to result in the inability of cells to carry out mitophagy, leading to enhanced mitochondrial production of superoxide/reactive oxygen species and accumulation of damaged mitochondria that will trigger a caspase 1-dependent inflammasome activation. Besides, RIKP2 is also involved in NOD1/2-independent signaling events, such as autophagy and neuronal activation. Loss-of-function mutations in RIP2 are associated with autoimmune diseases such as Crohn’s disease and lupus.

Fig.2 Schematic for domain organization of NOD1/2, RIPK2, and NOD2-RIPK2 signaling.

Ligand Design Services for RIPK2

Since RIPK2 plays a vital role in the innate immune response and the production of inflammatory cytokines, ligands of RIPK2 are of great interest for the treatment of inflammatory diseases. To search for selective RIPK2 ligands with strong binding capacity, Creative Biolabs employs virtual library screening (VLS) with millions of commercial compounds and structure-based design strategies to develop various ligands such as engineered antibodies, peptides and small molecule inhibitors targeting RIPK2 and evaluate its effects of RIPK2 in various in vitro and in vivo assays.

Besides, other screening strategies are also used by Creative Biolabs to identify novel protein ligands. Our strategies include but not limited to the methods used in fragment-based hit identification such as nuclear magnetic resonance (NMR), surface plasmon resonance (SPR), thermal shift and affinity-based hit identification such as DNA-encoded libraries of small molecules and small-molecule microarrays. Because these technologies do not rely on enzymatic inhibition, they may facilitate the discovery of ligands for protein targets that are “undruggable” by current small-molecule means. Although these ligands may not be intrinsically biologically active, their incorporation into PROTAC^® molecules would allow the modulation of proteins for which identification of functional inhibitors has proved difficult.

Fig.3 Intercepting inflammation with RIPK2 inhibitors.

Key Benefits

• Diverse RPIK2 inhibitors and RIPK2-targeting peptides.
• Capable of specifically reducing RIPK2 levels by >90% at nanomolar concentrations when acting as target ligand in PTORAC development.
• Possessing good levels of selectivity.
• Possessing both sufficient target binding affinity and a solvent-exposed position for the introduction of the linker moiety.
• Broad tissue distribution in PTORAC development.

PROTAC^®s are viable and useful tools that employ the ubiquitin-protease system to target a protein and induce its degradation. As a first-class supplier in molecular discovery, Creative Biolabs has been recognized as a long-term expert in successfully developing chimeric degraders for protein degradation. If you are interested in our ligand design services for RIPK2-targeting PROTAC^®, please feel free to contact us for more information.

Reference

1. Bondeson, D. P.; et al. Catalytic in vivo protein knockdown by small-molecule PROTAC^®s. Nature chemical biology. 2015, 11(8): 611.