Molecular

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.

Targeted protein degradation(TPD) is a novel and promising approach to new drug discovery and development. It shows great potential for treating diseases with “undruggable” pathogenic protein targets and for overcoming drug resistance. Molecular glues and PROTACs are both targeted protein degraders that have attracted the most attention.

Molecular glues are small molecular degraders that mainly induce novel interaction between an E3 ligase and a target protein to form a ternary complex, leading to protein ubiquitination and subsequent proteasome degradation. Compared with PROTACs, molecular glues generally possess more favorable drug-like properties, such as lower MW, higher cell permeability, and better oral absorption. Molecular glues are emerging as a promising new therapeutic strategy.

MCE supplies a unique collection of 105 molecular glues which target various proteins. MCE Molecular Glue Compound Library is a useful tool to conduct scientific research and disease mechanism study.

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.

Molecular Glue Virtual Library is constructed using generative AI technology, integrating the structural features, activity data of known molecular glues, and interaction information of ternary complexes (target protein-E3-molecular glue). Endowed with structural novelty, drug-likeness, diversity and synthesizability, it is applicable to molecular glue-based AI drug screening and large-scale virtual screening.

MCE builds this library based on high-quality molecular building blocks by virtue of robust computing power, coupled with rigorous reaction rules and optimized compound generation strategies. To ensure library quality, molecules with high synthetic difficulty, poor drug-likeness, PAINS and other undesirable molecules are excluded first. Subsequently, scaffold-based compound analysis is performed to screen drug-like diverse molecules for synthesizability evaluation; those with excessively high synthetic difficulty are removed, ultimately forming a large-scale molecular glue virtual library with structural diversity, synthesizability and drug-likeness.

Compounds in the library can be synthesized in only 1-2 chemical reaction steps. With MCE’s experienced chemical synthesis team, custom synthesis of different scales from milligram to kilogram can be easily achieved to meet diverse customer needs.

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.

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.

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 5,123 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.

Fragment-based drug discovery (FBDD) is well suited for discovering both drug leads and chemical probes of protein function; it can cover broad swaths of chemical space and allows the use of creative chemistry. Fragment-based drug discovery is well-established in industry and has resulted in a variety of drugs entering clinical trials, with two, vemurafenib and venetoclax, already approved. FBDD also has key attractions for academia. Notably, it is able to tackle difficult or novel targets for which no chemical matter may be found in existing HTS collections.

MCE designs a unique collection of 23,342 fragment compounds, 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 library is an important source of lead-like drugs.

“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).

Fragment-based drug discovery (FBDD) offers a strategic advantage by categorizing fragment hits according to their functional groups. This approach facilitates both the further optimization of these hits and the rational design of larger compounds through fragment combination. The amine functional group plays a vital role in drug development, as evidenced by its presence in many marketed drugs like Galantamine, Tacrine, and Rivastigmine. It is instrumental in enhancing solubility, improving bioavailability, and ensuring shelf-life stability—all critical factors for drug efficacy.

MCE offers a collection of 19,532 amine fragments for drug discovery. All of these compounds adhere to the Rule of Three (RO3) criteria for drug-likeness, which MCE offers a collection of 19,532 amine fragments for drug discovery, all of which stipulates a molecular weight ≤ 300 Da, ≤ 3 hydrogen bond donors, ≤ 3 hydrogen bond acceptors, and a cLogP ≤ 3.

Boric acid is a stable and usually non-toxic group widely used in modern synthesis to form C-C and C-heteroatom bonds. Boric acid exhibits exquisite reversible coordination characteristics and can be explored as a molecular construction tool, with specific mechanisms for controlling the structure and biological characteristics of bioconjugates. Boric acid has various activities, such as anticancer, antibacterial, and antiviral activities. In drugs, boric acid mainly exists in the form of arylboronic acid. In addition to this form, heterocycles containing boric acid, such as pyridine, pyrrole, and indole derivatives, are also very useful in pharmaceutical chemistry. Molecular modification by introducing boric acid groups into bioactive molecules has been shown to alter selectivity, physicochemical, and pharmacokinetic characteristics, and improve existing activity.

MCE designs a unique collection of 163 boronic acid compounds. It is a good tool to be used for research on cancer and other 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.

Metabolomics, positioned as the systemic characterization of small-molecule metabolites within biological systems, has emerged as an indispensable analytical platform in both fundamental research and translational applications across plant sciences, microbial biotechnology, and biomedical investigations. Functioning as a critical component in multi-omics integration, this discipline deciphers the intricate molecular networks operating downstream of genomic, transcriptomic, and proteomic regulation, thereby capturing the dynamic biochemical phenotype closest to organismal functionality. The metabolome, comprising endogenous compounds with molecular weights typically below 1500 Da, serves as the functional readout of cellular processes and environmental interactions, where perturbations in metabolic networks are frequently implicated in disease pathogenesis. Such unique attributes have propelled metabolomics into a pivotal role in pharmacological research, particularly in target deconvolution, pharmacodynamic assessment, and mechanistic elucidation of pathological processes.

MCE can provide 5,923 mass spectrometry human metabolites that can be used for metabolite identification and quantification, functional cell detection and phenotypic screening of mass spectrometry.

Natural products are small molecules produced naturally by any organism including primary and secondary metabolites. Natural sources may lead to basic research on potential bioactive components for commercial development as lead compounds in drug discovery.

Nature has been a source of medicinal agents for thousands of years, and an impressive number of modern drugs have been isolated from natural sources, many based on their use in traditional medicine. With the development of new molecular targets, there is an increasing demand for novel molecular diversity for screening. Natural products will play a crucial role in meeting this demand through the continued investigation of world’s bio-diversity, much of which remains unexplored.

MCE provides a unique collection of 4,974 natural compounds that contain Saccharides and Glycosides, Phenylpropanoids, Quinones, Flavonoids, Terpenoids and Glycosides, Steroids, Alkaloid, Phenols, Acids and Aldehydes. Natural Product Library is a useful tool for drug discovery that can be used for high throughput screening (HTS) and high content screening (HCS).

Gastric Cancer (GC) is one of the most common malignant tumors in the world, ranking fourth in mortality rate globally. Because the early symptoms of stomach neoplasm are usually not obvious, are diagnosed with gastric cancer at terminal stage, and the relative survival rate within 5 years is very low. With the further understanding of the molecular characteristics of stomach neoplasm, many therapeutic targets for gastric cancer have been identified, and molecular targeted therapies such as CTLA-4, HER2 and immune checkpoint inhibitors have made rapid progress. Although survival rates for patients with gastric neoplasm have improved over the past few decades, the prognosis is still worrying. Therefore, there is an urgent need for new drugs to treat gastric cancer.

MCE designs a unique collection of 1,122 small molecules with definite or potential anti-gastric cancer activity, which is an important tool for studying the pathological mechanism of stomach neoplasm and developing drugs for stomach neoplasm.

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

Natural products are small molecules produced naturally by any organism including primary and secondary metabolites. Natural sources may lead to basic research on potential bioactive components for commercial development as lead compounds in drug discovery.

Nature has been a source of medicinal agents for thousands of years, and an impressive number of modern drugs have been isolated from natural sources, many based on their use in traditional medicine. With the development of new molecular targets, there is an increasing demand for novel molecular diversity for screening. Natural products will play a crucial role in meeting this demand through the continued investigation of world’s bio-diversity, much of which remains unexplored.

MCE provides a unique collection of 6,181 natural compounds that contains Saccharides and Glycosides, Phenylpropanoids, Quinones, Flavonoids, Terpenoids and Glycosides, Steroids, Alkaloid, Phenols, Acids and Aldehydes. Natural Product Library Plus, with more powerful screening capability, further complements Natural Product Library (HY-L021) by adding some compounds with low solubility or solution stability (Part B) to this library. All those supplementary are supplied in powder form.

Unnatural amino acids (UAAs), also referred to as non-canonical amino acids (ncAAs) or non-proteinogenic amino acids, are a class of amino acids that are distinct from the 20 standard natural amino acids. They can be obtained through chemical synthesis, biosynthesis, and other approaches, with structural diversity far exceeding that of natural amino acids. UAAs are mainly including naturally occurring non-canonical amino acids, chemically synthesized amino acids, and biosynthetic amino acids, which provide a molecular basis for protein function design.

UAAs exhibit significant value in multiple fields. They can optimize the pharmacokinetic properties of peptide drugs and peptidomimetics, modify enzyme functions and endow them with new biological activities, thereby overcoming the limitations of traditional peptide drugs and expanding the chemical space . Meanwhile, UAAs can serve as molecular probes to analyze protein-protein interactions and investigate the regulatory mechanisms of protein functions.

MCE has compiled a UAAs Fragment Library comprising nearly a thousand unnatural amino acid fragments with extensive coverage of chemical space and enhanced structural diversity. This compound library can be widely applied in peptide synthesis, drug design, and protein engineering.

Cyclic peptide library have advantages such as high affinity, high selectivity, and suitability for targeting protein–protein interactions. Through DEL synthesis technology, the library size can achieve hundreds of millions. DEL cyclic peptide library have advantages like low cost andhigh screeing efficiency, making them valuable for discovering lead compounds against challenging drug targets.

This cyclic peptide library is constructed with unnatural amino acids as building block, synthesized through DNA-compatible chemical reactions. Each cyclic peptide consist of six amino acids and constrained conformations such as side-chain cross-linking, disulfide bonds, and macrocyclization. These cyclic peptides exhibit significantly improved stability and druggability compared with linear peptides, filling the gap between small molecules and macromolecular biologics. Each cyclic peptide is uniquely conjugated to a DNA barcode sequence for molecular identification and sequencing decoding.

MCE’s cyclic peptide library has8 independent sub-libraries, with a total molecular diversity of 1.2 billion. It is constructed via multi-round combinatorial assembly of building blocks and diverse cyclization strategies, facilitating the discovery of cyclic peptide leads for undruggable targets.

Pesticide is a single substance or mixture that can be used to prevent, mitigate, iminate pests or as a plant conditioner, defoliant or desiccant. In recent years, scientists have proposed the concept of "Molecules to Ecosystems", bringing the concept of molecular biology to understand the impact of pesticides, degradation and relationship with the environment or organisms. MCE integrates effective compounds approved as pesticides by agencies such as the Environmental Protection Agency (EPA), China Pesticide Information Network and some insecticidal compounds with potential for agricultural applications.

MCE can provide a library of 518 pesticide compounds that are tool compounds for relevant research.

In drug discovery and development (R&D) area, target binding and druggability optimization are core processes. Among these attributes, high solubility is critical for a compound to achieve druggability, as it directly impacts the progress of drug R&D. Superior solubility ensures the rapid dissolution and uniform distribution of drug molecules in vivo, thereby enhancing bioavailability and effectively mitigating issues such as suboptimal efficacy, increased dosage requirements, or exacerbated toxic and side effects arising from insufficient solubility.

From the perspective of medicinal chemistry, high-solubility drug fragments serve as high-quality "molecular building blocks". Based on these fragments, lead compounds with potential druggability can be rapidly screened out, which significantly shortens the drug R&D cycle and reduces R&D costs. Meanwhile, the high-solubility drug fragment library can provide diverse options for drug development in different therapeutic areas, offer solutions for the solubility defects of existing clinical drugs, and facilitate the development of novel, highly effective targeted drugs with higher bioavailability and better safety profiles.

MCE has collected and compiled 2,527 experimentally validated small-molecule fragments with high solubility. These fragments can be directly used for drug molecular design, providing high-quality pre-validated solubility fragments that significantly improve the efficiency of lead compound screening and accelerate the progress of drug R&D.

Agonistic drugs activate or stimulate their receptors, triggering responses that increase or decrease cell activity. The highly selective activators can act on specific biological or molecular targets, while non-selective activators may interfere with multiple targets or targets simultaneously. The highly selective activators reduce the likelihood of these non-specific effects by targeting specific targets, making research more precise and reliable. The Highly Selective Activators Library contains 2,083 compounds, covering multiple targets and subtypes, such as GPCR protein family, Ion channel, multiple kinases, etc. The Highly Selective Activators Library is an effective tool for screening different phenotypes.

Breast cancer is the most frequent cancer among women, impacting 2.1 million women each year, and also causes the greatest number of cancer-related deaths among women. Surgery is usually the first type of treatment for breast cancer, which is usually followed by chemotherapy or radiotherapy or, in some cases, hormone or targeted therapies, especially for metastatic breast cancer (MBC).

Breast cancer is a heterogeneous disease, which is categorized into 3 major subtypes based on the presence or absence of molecular markers for estrogen or progesterone receptors and human epidermal growth factor 2 (ERBB2; formerly HER2): hormone receptor positive/ERBB2 negative (70% of patients), ERBB2 positive (15%-20%), and triple-negative (tumors lacking all 3 standard molecular markers; 15%). Different intrinsic subtypes exhibit different tumor behavior with different prognoses, and may require specific targeted therapies to maximize treatment effectiveness. Otherwise, some signaling pathways also play important roles in the development of breast cancer, such as NF-κB Signaling Pathway, TGF-beta Signaling Pathway, PI3K/AKT/mTOR signaling pathway and Notch Signaling Pathway. These signaling pathways offer ideal targets for development of new targeted therapies for breast cancer.

MCE supplies a unique collection of 3,181 compounds with identified and potential anti-breast cancer activity. MCE Anti-Breast Cancer Compound Library is a useful tool for anti-breast cancer drugs screening.

Epigenetics involves heritable phenotypic changes that occur without alterations to the underlying DNA sequence. Key mechanisms include DNA methylation, histone modifications, and regulation by small non-coding RNAs such as microRNAs. By modifying DNA, histones, or RNA—while leaving their primary sequences intact—these processes influence molecular function and regulation, thereby playing critical roles in cellular differentiation, embryonic development, gene expression control, aging, and diseases such as cancer.

MCE provide a unique collection of 297 epigenetics-related compounds. For each regulatory target and its subtype, 3 to 5 highly specific representative compounds have been retained, which can be used in epigenetic and related disease research.

Methylation is an epigenetic modification mechanism that involves adding methyl groups to molecules such as DNA and histones, which can alter gene expression without changing the DNA sequence. This process is catalyzed by enzymes such as DNA methyltransferases (DNMTs) and histone methyltransferases (HMTs), and can be reversed by demethylases. The balance of methylation and demethylation is crucial for maintaining cellular function and genomic stability. Abnormal regulation of methylation may lead to a variety of diseases, including cancer, neurological disorders, and developmental abnormalities. A deep understanding of the molecular mechanisms of methylation metabolism is essential for developing therapeutic strategies for diseases associated with methylation dysregulation.

MCE contains 338 compounds targeting methylation/demethylation enzymes, which is of significant value for studying the pathways of methylation metabolism and exploring their mechanisms of action in diseases.

Drug development is both expensive and time-consuming, with approximately one-third of drug discontinuations caused by severe adverse drug reactions (ADRs). Among these, drug-induced cardiotoxicity (DICT) is one of the primary reasons for late-stage clinical drug failures and market withdrawals. To date, cardiotoxicity has been observed in multiple drug classes, such as anticancer drugs, antipsychotics, antidepressants, antibiotics, and neurodegenerative disease medications. To reduce cardiac ADRs, it is crucial to determine the clinical relevance of DICT to treatment, elucidate the underlying molecular mechanisms, identify reliable biomarkers, and develop new diagnostic and therapeutic approaches.

MCE offers 258 cardiotoxicity compounds, including some FDA-approved drugs as well as inhibitors/blockers of the hERG potassium channel.

ASINEX has elaborated a library of diverse macrocycles using an effective tool box of synthetic methods. The resulting scaffolds are novel, tremendously diverse, medchem-relevant, macrocyclic frameworks.

Macrocyles tend to be larger than traditional screening molecules which make them perfect discovery tools for targets with shallow or extended binding sites. At the same time, their unique character based on restricted flexibility and ability to form intra-molecular hydrogen bonds allows for design approaches effectively optimizing properties such asaqueous solubility and membrane permeability. Many of these macrocycles have been tested for aqueous and DMSO solubility with cut-offs applied at 10 mM in DMSO and 50 µM in PBS (pH 7.4) followed by PAMPA permeability assay.

Cancer is one of the leading causes of mortality amongst world’s population, in which prostate cancer (PCa) is one of the most encountered malignancies among men. Several molecular mechanisms are involved in prostate cancer development and progression. These include common survival factors in prostate cancer (IGF-1), growth factors (TGF-α, EGF), Wnt, Hedgehog, NF-κB, and mTOR and other signaling pathways. These provide potential therapeutic target in prostate cancer treatment.

MCE offers a unique collection of 3,419 compounds with identified and potential anti-prostate cancer activity. MCE Anti-Prostate Cancer Compound Library is a useful tool for anti-prostate cancer drugs screening and other related research.

Polysaccharides are long chains of carbohydrate molecules, consisting of multiple smaller monosaccharides. Polysaccharides are found mainly in natural sources such as plants, microorganisms, algae and animals. Polysaccharides have a large number of active functional groups, different chemical compositions and different molecular weight ranges, which determines their diversity in nature and structure. Also in the field of medical research, polysaccharides act as a class of functional compounds and thus play a role. For example, nanocarrier construction, immunomodulation and vaccine development, new strategies for antitumor therapy, tissue regeneration engineering applications and disease diagnosis. With the advancement of glycomics and synthetic biotechnology, human beings are moving from “knowing polysaccharides” to “designing polysaccharides”, which will provide innovative solutions for materials science, precision medicine and sustainable development.

MCE offers 68 polysaccharides that can be used in biomedical studies.

Animal disease models are used in a variety of settings in basic research, such as studies on mechanisms of disease progression and evaluation new drugs. Animal models can be broadly classified into five categories: 1) experimental, 2) spontaneous, 3) negative, 4) orphan, 5) genetically engineered. Experimental models, which are induced artificially in the laboratory, are most common. Some small molecular compounds are usually used as inducers for animal models, such as Ceruletide for inflammatory model, Azoxymethane for tumor model. These inducers are useful tool in building animal models.

MCE offers a unique collection of 50 animal model inducers, involving inflammatory model, tumor model, nervous disease model, etc. MCE Animal Disease Model library is a powerful tool for the establishment of animal disease models.

A protease (also called a peptidase, proteinase, or proteolytic enzyme) is an enzyme that catalyzes proteolysis, breaking down proteins into smaller polypeptides or single amino acids, and spurring the formation of new protein products. Proteases play important roles in regulating multiple biological processes in all living organisms, such as regulating the fate, localization, and activity of many proteins, modulating protein-protein interactions, creating new bioactive molecules, contributing to the processing of cellular information, and generating, transducing, and amplifying molecular signals.

Proteases are important targets in drug discovery. Some protease inhibitors are often used as anti-virus drugs and anti-cancer drugs. MCE offers a unique collection of 927 protease inhibitors. MCE Protease Inhibitor Library is critical for drug discovery and development.

Fragment-based drug development (FBDD) is a strategy for drug discovery that can be applied both academically and commercially to enhance the identification of some non-drug targets. Fragment-based drug development has identified low molecular weight molecules (<300 Da) capable of binding to related macromolecules. These fragments can cover a wide chemical space and are easy to optimize later. Currently, several fragment-based drugs have entered clinical trials, of which two drugs, Vemurafenib and Venetoclax, have been approved for marketing.

Based on Tanimoto coefficient, MCE uses similarity algorithm to carefully select 2,253 high-structurally diverse 'RO3' compliant fragment molecules from large-scale fragment molecules, which can be applied to fragment based drug development.

The MCE 1K Drug Fragment Library consists of 1,366 drug fragments. These drug fragments are derived from 2,946 FDA-approved drug molecules, and fragments from one drug can appear in other drugs, so these fragments are somewhat correlated with good PK/PD properties. Fragment-based screening can reserve enough chemical space for subsequent structural optimization. This compound library is an essential tool for drug screening based on FBDD (Fragment-Based Drug Discovery).

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.

Targeted cancer therapies are drugs or other substances that block the growth and spread of cancer by interfering with specific molecular targets that are involved in the growth, progression, and spread of cancer.

There are several different types of targeted therapy. The most common types are small-molecule drugs and monoclonal antibodies. Small-molecule drugs are small enough to enter cells easily, so they are used for targets that are inside cells, while monoclonal antibodies are usually used for targets that are located outside the cells. Because of high specificity, low side effect and potent anticancer activity, targeted therapy has become the mainstream of new anti-tumor drugs. Various targeted therapies have been approved by FDA and used in the treatment of diseases.

MCE carefully collects a unique of 108 targeted therapy drugs used in cancer treatment. MCE Targeted therapy drug library is a useful tool for the research of targeted therapy.

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.

Macrocyclic compounds (≥12-atom cyclic small molecules/peptides) have unique physicochemical properties. They form preorganized conformations with high binding affinity/selectivity, target traditional small-molecule-inaccessible proteins, and bridge small-molecule drugs and biological agents. As key protein phosphorylation enzymes, kinases are linked to tumors, COPD, etc., and are critical therapeutic targets. Traditional small-molecule kinase inhibitors lack selectivity, causing off-target toxicity, low bioavailability, and acquired resistance. Macrocycles’ semi-rigid structure restricts conformations, boosts binding selectivity, optimizes pharmacokinetics, and makes macrocyclization a core kinase inhibitor optimization strategy.

Thousands of bioactive macrocycles were curated from ChEMBL. Via Transformer, macrocyclization was converted into a chemical language translation task, enabling end-to-end macrocycle generation from linear precursors with simplified inputs. Macformer achieves efficient, automated linear molecule macrocyclization via deep learning; generated macrocycles have diversity, novelty, biocompatibility, and cover broader chemical space.

MCE collected thousands of marketed/clinical kinase inhibitors, using their fragments for macrocyclization to generate derivatives. After evaluating synthetic accessibility and physicochemical properties, a million-scale virtual macrocyclic library was built for kinase-related virtual and AI-driven screening.

Macrocyclic compounds (≥12-atom cyclic small molecules/peptides) have unique physicochemical properties. They form preorganized conformations with high binding affinity/selectivity, target traditional small-molecule-inaccessible proteins, and bridge small-molecule drugs and biological agents. As key protein phosphorylation enzymes, kinases are linked to tumors, COPD, etc., and are critical therapeutic targets. Traditional small-molecule kinase inhibitors lack selectivity, causing off-target toxicity, low bioavailability, and acquired resistance. Macrocycles’ semi-rigid structure restricts conformations, boosts binding selectivity, optimizes pharmacokinetics, and makes macrocyclization a core kinase inhibitor optimization strategy.

Thousands of bioactive macrocycles were curated from ChEMBL. Via Transformer, macrocyclization was converted into a chemical language translation task, enabling end-to-end macrocycle generation from linear precursors with simplified inputs. Macformer achieves efficient, automated linear molecule macrocyclization via deep learning; generated macrocycles have diversity, novelty, biocompatibility, and cover broader chemical space.

MCE collected thousands of marketed/clinical kinase inhibitors, using their fragments for macrocyclization to generate derivatives. After evaluating synthetic accessibility and physicochemical properties, a million-scale virtual macrocyclic library was built for kinase-related virtual and AI-driven screening.

The TCA cycle (tricarboxylic acid cycle)—is also known as the Krebs cycle or the citric acid cycle (CAC). The TCA cycle is a series of chemical reactions that release stored energy through the oxidation of acetyl-CoA in carbohydrates, fats, and proteins.

For decades, the TCA cycle has been considered as the central pathway for cell oxidative phosphorylation to produce energy and biosynthesis. Research shows that TCA cycle is associated with many diseases, especially cancer. In colon carcinoma, liver cancer and other cancers, there are mutations that lead to the imbalance of TCA cycle metabolites, indicating that TCA cycle may be related to the occurrence of cancer. Understanding the role and molecular mechanism of TCA cycle in inhibiting or promoting cancer progression will promote the development of new metabolite-based cancer treatment methods in the future.

MCE supplies a unique collection of 26 key intermediates of the TCA cycle, which can be utilized for TCA-related research and metabolomics identification studies.

Cell death plays a crucial role in the development of the body and the maintenance of internal balance to prevent the development of diseases. According to the regulation of the involved processes, cell death can be defined as programmed and non-programmed death. Programmed cell death (PCD) can be divided into lytic cell death and nonlytic cell death, mainly including apoptosis, necrotic apoptosis and Pyroptosis. Non-Programmed cell death (Non-PCD) generally refers to necrosis. In stark contrast to Accidental Cell Death (ACD), Regulatory Cell Death (RCD) relies on specialized molecular mechanisms. Cell death includes internal apoptosis, external apoptosis, necrotic apoptosis, ferroptosis, pyroptosis, lysosome-dependent cell death, etc.

MCE designs a unique collection of 3,640 cell death compounds, covering multiple targets, such as Apoptosis, Ferroptosis, Pyroptosis, Necroptosis, etc. It is a useful tool for screening cell death drugs.

Metabolomics is the large-scale study of cellular metabolic complement, with proven utility in both basic and applied studies of plants, microorganisms, and mammals. As an important tool for the study of complex biological systems, metabolomics monitors the complex molecular networks that exist in the natural flow of information from genes to mRNA and proteins to organisms. The metabolome is composed of biomolecules that most closely resemble the phenotype of an organism, and changes in its composition can easily lead to the production of diseases. Therefore, metabolomics has received much attention in drug target discovery, drug response and translational research of disease mechanisms. Mass spectrometry-based metabolomics methods can simultaneously detect and quantify thousands of metabolite signatures, thereby characterizing the pathophysiological mechanisms of various biomedical symptoms.

MCE can provide 664 mass spectrometry human endogenous metabolites that can be used for metabolite identification and quantification, functional cell detection and phenotypic screening of mass spectrometry.

The TCA cycle (tricarboxylic acid cycle)—is also known as the Krebs cycle or the citric acid cycle (CAC). The TCA cycle is a series of chemical reactions that release stored energy through the oxidation of acetyl-CoA in carbohydrates, fats, and proteins.

For decades, the TCA cycle has been considered as the central pathway for cell oxidative phosphorylation to produce energy and biosynthesis. Research shows that TCA cycle is associated with many diseases, especially cancer. In colon carcinoma, liver cancer and other cancers, there are mutations that lead to the imbalance of TCA cycle metabolites, indicating that TCA cycle may be related to the occurrence of cancer. Understanding the role and molecular mechanism of TCA cycle in inhibiting or promoting cancer progression will promote the development of new metabolite-based cancer treatment methods in the future.

MCE supplies a unique collection of 72 compounds related to the TCA cycle. MCE TCA Cycle Compound Library is a useful tool for the TCA cycle related research and anti-cancer drug development.

Kidneys are one of the vital organs in the human body. Due to their exposure to higher concentrations of circulating drugs or metabolites, they are highly susceptible to drug-induced renal injury (DIRI). According to statistics, drug-induced kidney injury accounts for approximately 20% of nephrotoxicity reports and can lead to acute kidney injury (AKI), chronic kidney disease (CKD), or even end-stage renal disease (ESRD). Early detection of drug nephrotoxicity is crucial for preventing irreversible kidney damage. Research into its mechanisms can help optimize clinical medication by adjusting dosages or avoiding combinations of nephrotoxic drugs. Additionally, predicting drug-induced nephrotoxicity in early drug development can reduce the risk of late-stage R&D failure.

MCE offers 158 nephrotoxicity compounds that have been clearly reported by the FDA to be associated with kidney injury. This library can be used for studying molecular mechanisms of nephrotoxicity or developing novel biomarkers.

Cysteine proteases (CPs), a key enzyme family regulating physiological metabolism and mediating pathological processes (such as abnormal bone resorption, tumour invasion, and pathogen infection), represent a core therapeutic target for developing specific inhibitors in disease intervention. Currently reported CP inhibitors primarily achieve their inhibitory function by precisely binding to CP active pockets (e.g., S1-S4 non-primed regions or S1'-S2' primed regions) and forming covalent/non-covalent interactions with the active site cysteine residues, providing clear structural references for the development of novel inhibitors.

This compound library, designed based on the core strategy of "similarity-based known active structures", contains over 200 cysteine protease inhibitors. Leveraging AI-driven molecular screening technology, it retains the critical pharmacological and shape features of reported CP inhibitors, serving as a specialized tool for efficiently discovering novel cysteine protease inhibitors.

Neurodegenerative diseases are incurable and life-threatening conditions that result in progressive degeneration and/or death of nerve cells. Some common neurodegenerative diseases include Alzheimer’s Disease (AD), Parkinson’s Disease (PD), Motor Neuron Disease (MND), Huntington’s Disease (HD), Spino-Cerebellar Ataxia (SCA), Spinal Muscular Atrophy (SMA), and Amyotrophic Lateral Sclerosis (ALS). Because the pathophysiology of neurodegenerative disorders is generally poorly understood, it is difficult to identify promising molecular targets and validate them. At the same time, about 85% of the drugs fail in clinical trials. Therefore, validating new targets and discovering new drugs to mitigate neurodegenerative disorders is need of the hour.

MCE offers a unique collection of 3,545 compounds with anti-Neurodegenerative Diseases activities or targeting the unique targets of neurodegenerative diseases. MCE Neurodegenerative Disease-related Compound Library is a useful tool for exploring the mechanism of neurodegenerative diseases and discovering new drugs for neurodegenerative diseases.

Cytokines are a kind of low molecular soluble proteins synthesized and secreted by immunogen, mitogen or other factors. They have functions of regulating innate and adaptive immune responses, promoting hematopoiesis, stimulating cell activation, proliferation and differentiation. The process of releasing a large number of cytokines is also called “Cytokine storm”, which can cause damage to many tissues and organs in the body. Cytokine is involved in the pathogenesis of many human diseases, including cancer, diabetes, chronic inflammatory diseases and so on. Cytokine inhibitors are a class of essential compounds that act by directly inhibiting the synthesis and release of cytokine or blocking the binding of cytokine to their receptors. Cytokine inhibitors are important compounds for the study of tumor and autoimmune diseases.

MCE designs a unique collection of 1,332 cytokine inhibitors, mainly targeting the receptor interleukin (IL), colony-stimulating factor (CSF), interferon (IFN), tumor necrosis factor (TNF), growth factor (GF) and chemokine, which is an effective tool for development and research of anti-cancer, anti-chronic inflammatory diseases and anti-autoimmune diseases compounds.