pharmacophore

The most prominent mechanism of action of kinase inhibitors is their competition with ATP by binding to the hinge region of the kinase protein. Once the kinase is blocked by an inhibitor, it loses the ability to transfer phosphate groups from ATP to other molecules, resulting in the loss of kinase activity.

The hinge-binding region of kinase inhibitors mimics the interaction pattern between the ATP nucleobase and the kinase. MCE extracted thousands of kinase inhibitors from the ChEMBL database and isolated their molecular fragments. In certain cases, the amino and amide groups on the molecular fragments are crucial for binding in the hinge region. Therefore, we enhanced the diversity of the collected results by adding these two groups to unoccupied positions on the ring system. Subsequently, the fragments were assessed for their hinge region binding ability via docking at distinct kinases, we also applied pharmacophore constraints to ensure interactions with key amino acids in the kinase hinge region, ultimately obtaining kinase-related molecular fragments.

MCE provides over 12,412 kinase fragment molecules that meet the above requirements and are available off the shelf, serving as an effective tool for screening and developing drugs targeting kinases.

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.

“BioDesign” approach incorporates key structural features of known pharmacologically relevant natural products (e.g. alkaloids and other secondary metabolites) into synthetically feasible medicinal chemistry scaffolds. In order to identify the privileged pharmacophores, ring systems and linkers, we have carried out statistical analysis of structural features of natural products, marketed drugs, and drug candidates.

Saturated, fused ring, spiro, and bridged systems with a tendency towards multiple chiral centers are highly privileged among natural products and marketed drugs yet these structures are very poorly represented in commercial libraries. This library addressed this market need by incorporating these privileged elements into the design of novel synthetic molecules with high molecular framework diversity, multiple stereogenic centers (≥2), and degree of saturation (Fsp3 > 0.5).

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 370 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.

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.

Ion channels are key proteins on the cell membrane that regulate the flow of ions across membranes. They participate in nearly all physiological processes, including nerve conduction, muscle contraction, heart rhythm, and pain perception. Abnormalities in their function can lead to various serious diseases such as arrhythmia, epilepsy, hypertension, neuropathic pain, and cancer. Therefore, ion channels are highly valuable drug targets—over 15% of approved drugs target ion channels currently, demonstrating their irreplaceable therapeutic value in cardiovascular, neurological, and analgesic fields.

MCE has collected a library of over 5,000 reported ion channel-related bioactive compounds targeting major sites such as Na+ channels, K+ channels, Ca2+ channels, GABA receptors, iGluRs, and others. Using AI models, these compounds are characterized through both 2D representations (molecular fingerprints, pharmacophores) and 3D representations (3D conformation) to screen for a collection of lead-like compounds highly similar to known active molecules. Additionally, an hERG channel prediction algorithm integrating XGB and ISE mapping strategy is employed to assess and exclude potential cardiotoxicity in the library.. This step significantly reduces safety risks in subsequent screenings, particularly for ion channel drug development related to cardiovascular systems (e.g., Nav1.5, Cav1.2), effectively minimizing failures due to hERG inhibition and serving as a valuable tool for ion channel drug screening.

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.