molecular recognition

CRBN, namely cereblon, is the substrate recognition subunit of the E3 ubiquitin ligase complex in the ubiquitin-proteasome system. A CRBN ligand library refers to a collection of numerous fragments that can specifically bind to the CRBN protein.

These ligands are mostly designed based on validated CRBN-binding warheads and modified through AI-driven molecular generation optimization systems. They not only include classic lenalidomide-derived structures but also cover novel non-lenalidomide scaffolds. After drug-likeness filtering, these ligands exhibit structural diversity and favorable druggable properties. They can be further optimized and modified to facilitate the development of novel molecular glue degraders, accelerate the discovery of molecular glues that induce interactions between CRBN and new substrate proteins, and enable the exploration of novel CRBN substrates for identifying previously unknown CRBN-binding proteins.

MCE compiles 122 fragments that can specifically bind to the CRBN protein, with molecular weights ranging from 200 to 500. Compounds developed based on the library ligands target multiple disease targets such as cancer and autoimmune diseases, further advancing the development of Molecular Glues and PROTACs therapeutic agents.

Pattern Recognition Receptors (PRRs) are a crucial class of protein molecules expressed in cells of the innate immune system. The core function of Pattern Recognition Receptors is to recognize Pathogen-Associated Molecular Patterns (PAMPs) and Damage-Associated Molecular Patterns (DAMPs). Upon recognizing and binding to PAMPs or DAMPs, PRRs rapidly initiate intracellular signaling pathways (such as the NF-κB, IRF, and inflammasome pathways). This triggers the production of inflammatory factors, chemokines, and type I interferons, thereby initiating inflammatory responses to eliminate pathogens or repair damage. PRRs represent the body's first line of defense against infection, and the rapidity and broad specificity of their response are crucial for host survival. However, aberrant activation of PRR signaling is also a cause of many chronic inflammatory diseases, autoimmune disorders, and neurodegenerative diseases. Therefore, precisely regulating PRR activity has become a key therapeutic strategy for these conditions.

MCE has cataloged 327 inhibitors targeting key PRRs, such as NLRs, TLRs, C-type Lectin Receptors (CLRs), and cGAS, to support drug discovery efforts for chronic inflammatory diseases.

Fragment-based drug discovery (FBDD) is well suited for discovering both drug leads and chemical probes of protein function. 3-dimensionality (3D) diversity is pivotal because the molecular shape is one of the most important factors in molecular recognition by a biomolecule. There is a developing appreciation that 3D fragments could offer opportunities that are not provided by 2D fragments.

MCE 3D Diverse Fragment Library consists of 5,400 non-flat fragment-like molecules (average Fsp3 value 0.58). More than 4,700 fragment compounds contain at least one chiral center in the structure. The key concepts that underlie the library design were 3D shape, structural diversity, reactive functionality and fragment-like. This 3D Diverse Fragment Library brings higher fragment hit optimization and increases the likelihood to find innovative hits in FBDD.

Peptidomimetics are compounds whose essential elements (pharmacophore) mimic a natural peptide or protein in 3D space and which retain the ability to interact with the biological target and produce the same biological effect. Peptidomimetics are designed to circumvent some of the problems associated with a natural peptide: e.g. stability against proteolysis (duration of activity) and poor bioavailability. Certain other properties, such as receptor selectivity or potency, often can be substantially improved. The design and synthesis of peptidomimetics are most important because of the dominant position peptide and protein-protein interactions play in molecular recognition and signaling, especially in living systems. Hence mimics have great potential in drug discovery.

MCE Peptidomimetic Library contains 371 compounds including peptoid, α-helix mimetics, β-turn/sheets mimetics, etc. This library is an indispensable tool of structure-activity relationships in drug discovery.

On May 15, 2024, "Dimerization and antidepressant recognition at noradrenaline transporter" was published online by Nature. The research findings were an effort from Shanghai Institute of Materia Medica, Chinese Academy of Sciences. This study unraveled the important neural system target - the noradrenaline transporter (NET), obtaining the binding modes of human NET homodimers with the natural substrate norepinephrine (NE) and six selective antidepressants. It laid an important theoretical foundation for understanding the physiological regulation mechanisms of NET and other monoamine transporters.

The Norepinephrine Transporter (NET) Compound Library is obtained by computer-aided virtual screening based on the HY-L901 compound library . The specific screening process includes molecular docking screening, key pharmacophore screening, and CNS-MPO screening, which can be used for new drug discovery targeting the noradrenaline transporter.