small-molecule ligand

Proteolysis-targeting chimera (PROTAC) has been developed to be a useful technology for targeted protein degradation. PROTACs consist of a ligand for E3 ligase (E3 ligase binder), a linker and a ligand (mostly small-molecule inhibitor) for protein of interest（target binder）. Upon binding to the target protein, the PROTACs can recruit E3 for target protein ubiquitination, which is subjected to proteasome-mediated degradation.

Although there are more than 600 E3 ubiquitin ligases, only several with small molecule ligands have been used for designing PROTACs, including Skp1-Cullin-F box complex containing Hrt1 (SCF), Von Hippel-Lindau tumor suppressor (VHL), Cereblon (CRBN), inhibitor of apoptosis proteins (IAPs), and mouse double minute 2 homolog (MDM2).

MCE carefully prepared a unique collection of 174 ligands for E3 ligase, which have been reported to be used in PROTAC design. MCE E3 ligase ligand library is a useful tool for PROTAC development.

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 125 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.

Proteolysis-targeting chimera (PROTAC) has been developed to be a useful technology for targeted protein degradation. PROTACs consist of a ligand for E3 ligase (E3 ligase binder), a linker and a ligand (mostly small-molecule inhibitor) for protein of interest（target binder）. Upon binding to the target protein, the PROTACs can recruit E3 for target protein ubiquitination, which is subjected to proteasome-mediated degradation. Therefore, PROTACs execute their functions by degrading the target proteins rather than inhibiting them, which has a great superiority in overcoming resistance caused by target mutation or overexpression. To date, PROTAC technology has been applied to a variety of targets, including AR, ER, BTK, BET, and BCR-ABL to overcome resistance.

MCE carefully prepared a unique collection of 94 ligands for target proteins, which have been reported to be used in PROTAC design. MCE Target Protein Ligand Library is a useful tool for PROTAC development.

POI (Protein of Interest) refers to the target protein, namely the disease-causing protein or key functional protein that undergoes degradation or functional modulation in molecular glue-mediated processes. The Molecular Glue POI Library consists of a series of fragments that can specifically bind to different types of POIs. As key components of molecular glues, these ligands form stable interactions with target proteins, laying the foundation for molecular glues to induce the interaction between POIs and E3 ubiquitin ligases. The covered POIs include various types such as cancer-associated GSPT1, androgen receptors, and abnormally aggregated proteins linked to neurodegenerative diseases.

This fragment library can be applied to the screening and optimization of targeted protein degraders. By screening ligands with high affinity and strong selectivity for specific POIs from the library, core structures can be identified to develop novel molecular glues. For instance, optimization of ligands targeting GSPT1 has yielded molecular glue degraders with enhanced degradation activity. Since many POIs are difficult to drug due to the lack of traditional small-molecule binding pockets, some ligands in the POI Ligand Library can modulate such POIs by inducing protein-protein interactions, thereby further expanding the scope of drug discovery for undruggable targets.

MCE has compiled a POI Fragment Library comprising thousands of POI fragments with molecular weights ranging from 150 to 400. This compound library can be widely applied in Molecular Glue research and development.

G protein-coupled receptors (GPCRs) are membrane proteins in humans and one of the most important targets in drug discovery. Approximately 35% of launched drugs are targeted GPCRs, making them a crucial class of targets in drug discovery.

The orthosteric site of a GPCR is its endogenous ligand’s (such as neurotransmitters or hormones) binding site. This site plays a central role in signal transduction. Small molecules binding to this site typically contain a protonatable amino group, enabling the formation of salt bridges or hydrogen bonds with acidic residues in the binding pocket. In contrast, the allosteric site does not directly initiate signaling but modulates the signal intensity of the GPCR by altering or stabilizing the conformation of the orthosteric site. Small molecules binding to the allosteric site often contain multiple aromatic rings to occupy hydrophobic pockets and achieve their functional effects.

MCE has collected over 7,113 reported bioactive molecules targeting GPCRs, covering Class A, B, and C GPCRs. These small molecules were subjected to AI representation to extract 2D and 3D features. Subsequently, we do screening by AI score based on similarity to identify molecules in diversity library highly similar to the reported bioactive molecules in both 2D and 3D, with a threshold greater than 0.7. Further screening based on cLogP was applied to select molecules with good lipophilicity, which facilitates the binding of small molecules to GPCRs. This diversity library can be widely applied to the discovery of compounds targeting GPCR proteins.

Targeted Protein Degradation (TPD) is a novel and promising approach to drug development. It shows great potential for targeting proteins traditionally considered "undruggable" due to the lack of enzymatic function and absence of binding sites by tagging them for degradation or recruiting natural degradation mechanisms.

Molecular glues are a type of small-molecule degraders that primarily induce novel interactions between E3 ubiquitin ligases and target proteins, forming ternary complexes that lead to protein ubiquitination and subsequent proteasomal degradation. Compared with PROTACs, molecular glues generally have lower molecular weights, higher cell permeability, and better drug-like properties. Additionally, the design of molecular glues is relatively simple, without the requirements for complex linkers and ligand optimization. As a result, molecular glues have gradually emerged as a promising therapeutic approach for various diseases.

Multiple types of molecular glues have been reported previously. Analysis of co-crystal complex structures reveals that CRBN-related molecular glues are more versatile. Therefore, MCE researchers select active molecules related to these targets as probes for artificial intelligence (AI) screening.Subsequently, molecular docking technology was used to verify whether the screened molecules retained the key pharmacophore features. Ultimately, we obtained 317 molecular glue analogs, and these compounds serve as powerful tools for the research of molecular glues.

An emerging drug design method is based on the secondary binding site effect, where small molecule drugs are designed to bind to secondary binding sites on target biomolecules rather than primary orthomorphic sites. Successful potential drugs (known as allosteric modulators) will be able to bind to allosteric sites and remotely alter (or modify) the conformation of the main orthosteric binding sites of biological targets. Allosteric modulators (AMs) are ligands of proteins that act through binding sites different from natural (orthosteric) ligand sites. AMs are relatively small, more lipophilic, and more rigid compounds. The binding efficacy of AMs with their targets is often slightly lower. AMs are divided into positive AMs (PAMs) and negative AMs (NAMs). AMs are ideal drug targets because they can fine-tune receptor activity while preserving the spatial and temporal signal transduction characteristics of endogenous ligands, resulting in fewer targeted side effects, improved subtype selectivity, and better promotion of biased signal transduction than normal ligands.

MCE designs a unique collection of 250 small allosteric modulators. It is a good tool to be used for research on metabolize, cancer and other diseases.

Covalent inhibitors are small molecules that can bind specifically to target proteins through covalent bonds and inhibit their biological functions. Although for a long time, covalent targeting has been playing a subordinate role in drug discovery, with an increasing number of reports on successful clinical applications of such drugs, the potential of these agents is now being acknowledged.

Covalent ligands rely on reactive groups (“warheads”), and new warheads are key to expanding the scope of covalent modalities. Through careful selection, we constructed a structural filter containing over 110 electrophilic groups. By analyzing the electrophilic fragments selected by the structural filter, we removed any molecules with trivial or undesirable structural features. Ultimately, we obtained 8,900 fragment molecules with covalent modification potential, which can target various reactive amino acid residues and can be used for fragment-based covalent drug discovery.

Ion channel is a membrane-binding enzyme whose catalytic site is an ion conduction pore, which is opened and closed in response to specific environmental stimuli (voltage, ligand concentration, membrane tension, temperature, etc.). Ion channel provide pores for the passive diffusion of ions on the biofilm. Due to their high selectivity for ion, ion channel are generally classified as sodium (Na⁺ ), potassium (K⁺ ), calcium (Ca²⁺ ), chloride (Cl^- ), and non-specific cation channel. Ion channel is an important contributor to cell signal transduction and homeostasis. In addition to electrical signal transduction, ion channel also have many functions: regulating vascular smooth muscle contraction, maintaining normal cell volume, regulating glandular secretion, protein kinase activation, etc. Therefore, dysfunction of ion channel can lead to many diseases, and its mechanism research is particularly important.

MCE designs a unique collection of 1,679 small molecules related to ion channel, mainly targeting Na⁺ channel, K⁺ channel, Ca²⁺ channel, GABA receptor, iGluR, etc. It is an essential tool for research of cardiovascular diseases, Nervous system diseases and other diseases.