ligand discovery

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.

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.

Membrane receptors, also known cell surface receptors or transmembrane receptors, are transmembrane proteins embedded into the plasma membrane which play an essential role in maintaining communication between the internal processes within the cell and various types of extracellular signals. They act in cell signaling by receiving (binding to) extracellular molecules, which are also called ligands. These extracellular molecules include hormones, cytokines, growth factors, neurotransmitters, lipophilic signaling molecules such as prostaglandins, and cell recognition molecules.

There are three kinds of membrane receptors: ion channel-linked receptors, enzyme-linked receptors and G-protein-linked receptors. They play important roles in keeping human normal physiologic processes. GPCRs and ion channels are important drug targets in drug discovery.

MCE provides a unique collection of 6,917 compounds targeting a variety of membrane receptors. MCE Membrane reeptor-targeted Compound Library can be used for membrane receptor-focused screening and drug discovery.

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.

Sodium channels conduct sodium ions (Na+) through a cell's plasma membrane that are the source of excitatory currents for the nervous system and muscle. Na channels are classified according to the trigger that opens the channel for such ions, i.e. either a voltage-change (Voltage-gated, voltage-sensitive, or voltage-dependent sodium channel also called VGSCs or Nav channel) or a binding of a substance (a ligand) to the channel (ligand-gated sodium channels). Dysfunction in voltage-gated sodium channels correlates with neurological and cardiac diseases, including epilepsy, myopathies, pain and cardiac arrhythmias. Sodium channel blockers are used in the treatment of cardiac arrhythmia, pain and convulsion.

MCE offers a unique collection of 191 sodium channel blocker and antagonists, all of which have the identified inhibitory effect on sodium channels. MCE Sodium Channel Blocker Library can be used for neurological and cardiac diseases drug discovery and sodium channel research.

GABA receptors are a class of receptors that respond to the neurotransmitter gamma-aminobutyric acid (GABA), the chief inhibitory neurotransmitter in the vertebrate central nervous system. There are two classes of GABA receptors: GABAA and GABAB. GABAA receptors are ligand-gated ion channels (also known as ionotropic receptors), whereas GABAB receptors are G protein-coupled receptors (also known asmetabotropic receptors). GABA receptors are significant drug targets in the treatment of neuropsychiatric disorders such as epilepsy, insomnia, and anxiety, as well as in anesthesia in surgical operations.

MCE offers a unique collection of 211 GABA receptors inhibitors and activators, which is an efficient tool for neuropsychiatric disorders drugs discovery.

PROTACs (Proteolysis-targeting chimeras) is a class of molecules that utilize ubiquitin-proteasome system (UPS) to ubiquitinate and degrade target proteins. The PROTACs molecule consists of two ligands joined by a linker. The one-to-one interaction between PROTACs and target proteins determines the high efficiency of PROTACs, making it a potential molecule for targeted protein degradation (TPD) therapy.

MCE supplies a unique collection of 512 PROTACs that effectively degrade target proteins with more powerful screening capability. MCE PROTAC Library is a useful tool for signal pathway research, protein degradation therapy research, drug discovery and drug repurposing, etc.

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.

Neurotransmitter (NT) receptors, also known as neuroreceptors, are a broadly diverse group of membrane proteins that bind neurotransmitters for neuronal signaling. There are two major types of neurotransmitter receptors: ionotropic and metabotropic. Ionotropic receptors are ligand-gated ion channels, meaning that the receptor protein includes both a neurotransmitter binding site and an ion channel. The binding of a neurotransmitter molecule (the ligand) to the binding site induces a conformational change in the receptor structure, which opens, or gates, the ion channel. The term “metabotropic receptors” is typically used to refer to transmembrane G-protein-coupled receptors. Metabotropic receptors trigger second messenger-mediated effects within cells after neurotransmitter binding.

In some neurological diseases, the neurotransmitter receptor itself appears to be the target of the disease process. Many neuroactive drugs act by modifying neurotransmitter receptors. A better understanding of neurotransmitter receptor changes in disease may lead to improvements in therapy.

MCE designs a unique collection of 2,526 compounds targeting a variety of neurotransmitter receptors. MCE Neurotransmitter Receptor Compound Library is a useful tool for neurological diseases drug discovery.

19F-NMR has proved to be a detection mode in fragment-based drug discovery (FBDD) for studies of protein structure and interactions. 19F shows high sensitivity for NMR detection, and the exquisite sensitivity of 19F chemical shifts and linewidths to ligand binding all make it a valuable approach in FBDD.F (Fluorine) -Fragments can be used for 19F-NMR detection after binding to target proteins, and can be used as an effective 19F-NMR tool for FBDD.

MCE designs a unique collection of 5,134 F-fragments, all of which obey a heuristic rule called the “Rule of Three (RO3)”, in which molecular weight ≤300 Da, the number of hydrogen bond donors (H-donors) ≤3, the number of hydrogen bond acceptors (H-acceptors) is ≤3 and cLogP is ≤3. This F-fragments library is an important source of lead-like drugs.

5-HT receptors, also called Serotonin receptors, are a group of G protein-coupled receptors (GPCRs) and ligand-gated ion channels (LGICs) found in the central and peripheral nervous systems. These receptors are now classified into seven families, 5-HT1–7, comprising a total of 14 structurally and pharmacologically distinct mammalian 5-HT receptor subtypes. The 5-HT receptors influence various biological and neurological processes such as aggression, anxiety, appetite, cognition, learning, memory, mood, nausea, sleep, andthermoregulation. The serotonin receptors are the target of a variety of pharmaceutical drugs, including many antidepressants, antipsychotics, anorectics, antiemetics, gastroprokinetic agents, antimigraine agents, hallucinogens, and entactogens.

MCE 5-HT Receptor Compound Library consists of 414 5-HT receptor inhibitors and activators, which can be used for neuropsychiatric disorders drugs discovery.

In modern drug discovery and chemical biology research, the azide group (-N₃) is an important functional moiety that is widely used in click chemistry, biomolecular labeling, drug delivery systems, and prodrug design due to its unique reactivity and bioorthogonality.

The MCE Azide Structural Compound Library contains 37 compounds featuring -N₃ functional groups. It is designed for the construction of click chemistry reaction systems and the subsequent development of functional molecules. This library enables the rapid assembly of targeting ligands, linkers, and functional molecular modules, thereby accelerating PROTAC assembly, optimization of antibody-drug conjugate (ADC) linkers, and the development of biological labeling probes. In addition, the high reaction selectivity and excellent biocompatibility of the azide group allow it to maintain stable reactivity even in complex biological environments, improving controllability and efficiency in drug design. It serves as an indispensable molecular tool in modern medicinal chemistry and chemical biology research.

Owing to the high conservation of orthosteric sites, conventional orthosteric drugs frequently suffer from poor subtype selectivity, off-target toxicity, and drug resistance, severely restricting their clinical application. In contrast, allosteric sites feature low conservation, high hydrophobicity, weak polarity, confined spatial geometry, and dynamic cryptic properties. These characteristics endow allosteric modulators with distinct advantages including high selectivity, functional tunability, and improved safety, making allosteric therapy a key direction in modern drug discovery.

MCE has curated nearly 1,000 structurally disclosed clinical-stage allosteric modulators. By analyzing allosteric protein–ligand complex structures from the PDB database, we extracted core pharmacophores and privileged scaffolds. Adopting a rational design strategy of “scaffold derivation + allosteric physicochemical filtering”, we performed secondary screening on the derived compounds strictly following the optimal physicochemical principles for allosteric binding based on universal allosteric pocket properties: molecular weight 300–500 Da, HBD ≤ 3, HBA = 3–8, PSA = 70–120 Ų, rotatable bonds ≤ 6, highly rigid scaffolds, cLogP = 1.0–3.8, and no strongly ionizable groups. The selected compounds exhibit high rigidity and shape complementarity, making them well-suited for targeting shallow, dynamic, and hydrophobic-dominated allosteric pockets.

This allosteric modulator library contains 4,315 structurally diverse, lead-like compounds dedicated to allosteric drug development, allosteric site targeting, and allosteric modulator screening. It is suitable for kinases, GPCRs, and other important drug targets. All compounds are analogs of clinical-stage allosteric modulators with a similarity score > 0.6, combining excellent druggability and allosteric binding potential. It provides a highly efficient tool for early-stage allosteric drug discovery.

Lysine is the second most common target residue used in the design of TCIs and related covalent ligands. Its appeal lies in its abundance in human proteins, which is approximately three times higher than that of cysteine (5.8% vs. 1.9%). This significantly increases the number of proteins suitable for covalent targeting, especially given that many human proteins lack ligandable cysteine residues. Moreover, it has been suggested that functional lysines have a lower probability of being replaced by mutation, as they often play a crucial role in catalysis by acting as bases or nucleophiles. Additionally, lysines are essential for maintaining the structural integrity of proteins and for regulating post-translational modifications (PTMs). Consequently, targeting lysine has garnered significant interest in recent years.

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 445 fragment molecules which can target lysine residue and can be used for fragment-based covalent drug discovery.

Protein protein interactions (PPI) have pivotal roles in life processes. The studies showed that aberrant PPI are associated with various diseases, including cancer, infectious diseases, and neurodegenerative diseases. The classic drug targets are usually enzymes, ion channels, or receptors, the PPI indicate new potential therapeutic targets. Therefore, targeting PPI is a new direction in treating diseases and an essential strategy for the development of new drugs.

However, the design of modulators targeting PPI still faces tremendous challenges, such the difficult PPI interfaces for the drug design, lack of ligands reference, lack of guidance rules for the PPI modulators development and high-resolution PPI proteins structures.

With the development of high-throughput technology, high-throughput screening is also gradually used for the identification of PPI inhibitors, but the compound library used for conventional target screening is not very effective in screening PPI inhibitors. To improve screening efficiency, MCE carefully selected 797 PPI inhibitors and mainly targeting MDM2-p53, Keap1-Nrf2, PD-1/PD-L1, Myc-Max, etc. MCE Protein-protein Interaction Inhibitor Library is a useful tool for PPI drug discovery and related research.

Recently, significant advancements in tyrosine-targeting electrophiles have primarily occurred in the field of protein-protein interactions (PPIs), where cysteine residues are often underrepresented and novel chemistries are needed to address these interfaces. In this context, tyrosines are frequently more accessible compared to more buried binding sites. Moreover, they are commonly found at "hot spots," which are functional epitopes of PPIs, with 12.3% of the residues consisting of tyrosines. This prevalence is likely due to the hydrophobic nature of tyrosine, its ability to participate in aromatic π-interactions, and its capacity for hydrogen bonding. Beyond PPIs, some progress has also been made in covalent tyrosine targeting in other areas where more commonly addressed side chains are lacking. Even though tyrosine has a slightly lower pKa value compared to the protonated lysine side chain (approximately 10 vs. 10.5 for the unprotected amino acid side chains), significantly less progress has been made in the development of tyrosine-targeted covalent ligands compared to lysine. This is likely due to the reduced flexibility of the tyrosine side chain and the greater steric hindrance of its hydroxy group, which makes it more challenging to adopt suitable reaction geometries.

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 124 fragment molecules which can target tyrosine residue and can be used for fragment-based covalent drug discovery.