Structure

MCE 5K Scaffold Library consists of 5,000 lead-like compounds. Each compound represents one unique scaffold. All compounds are compatible with Lipinski’s rule (Rule of 5) with multiple characteristics such as calculated good solubility (-3.2 < logP < 5), oral bioavailability (RotB <= 10), drug transportability (PSA < 120). Compounds contained within the library have been screened to remove any inappropriate chemical structures, avoiding “false hits”. The sufficient diverse of compound structure makes this library a powerful tool for drug screening.

Glycomimetics are designed to mimic the structure of natural carbohydrates and modulate their disease-related functions. Macrocyclic glycomimetics are an extremely interesting class of glycomimetics as they occupy space between small and macro molecules. Macrocyclic glycomimetics are mostly represented by naturally occurring molecules derived from marine microorganisms and bacterial or fungal metabolites.

Quinone compounds are a significant class of natural products featuring a conjugated quinone structure, widely distributed in plants, fungi, and microorganisms. Based on their core structures, they can be primarily categorized into benzoquinones, naphthoquinones, phenanthrenequinones, and anthraquinones, among others. This structural diversity endows quinone compounds with a broad spectrum of pharmacological activities, making them key components in traditional Chinese medicine (such as rhubarb, Lithospermum erythrorhizon, and Salvia miltiorrhiza). Modern research has confirmed that their activities encompass anti-tumor, anti-inflammatory, antibacterial, antiviral, antiplatelet aggregation, and neuroprotective effects, among others, establishing them as an important source for drug development.

MCE designs a unique collection of 89 quinones that all come from natural products. MCE Quinones Library is a useful tool for drug discovery that can be used for high throughput screening (HTS) and high content screening (HCS).

Protein protein interactions (PPI) have pivotal roles in life processes. The studies showed that aberrant PPI are associated with various diseases. 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.

The PPI Library comprises molecules of various sizes, frameworks, and shapes ranging from fragment-like entities to macrocyclic derivatives designed as secondary structure mimetics or as epitope mimetics. The designs cover β-turn / loop mimetics and α-helix mimetics. Since helices present at the interface in 62% of all protein-protein interactions. This library focused on designs including mimics with the substitution geometry of an a-helices, as well as designs that mimic the location of “hot-spot” side chains in helix-mediated PPIs.

Heterocyclic compounds are cyclic organic compounds which contain at least one hetero atom, the most common heteroatoms are nitrogen, oxygen ,and sulfur. Heterocycles are common in biology, featuring a wide range of structures from enzyme co-factors to amino acids and proteins. On the one hand, heterocycles are common structural units in approved drugs and in medicinal chemistry targets in the drug discovery process. In addition, heterocycles have been found as a key structure in medical chemistry and also they are frequently found in large percent of biomolecules such as vitamins, natural products ,and biologically active compounds including antifungal, anti-inflammatory, antibacterial, antioxidant, antiallergic, anti-HIV, antidiabetic, anticancer activity.

MCE offers a unique collection of 6,445 heterocyclic compounds which can be used for drug discovery for high throughput screening (HTS) and high content screening (HCS). MCE heterocyclic compound library is critical for drug discovery and development.

The cytoskeleton is responsible for contraction, cell motility, movement of organelles and vesicles through the cytoplasm, cytokinesis, intracellular signal transduction, and many other functions that are essential for cellular homeostasis and survival. It accomplishes these tasks through three basic structures: F-actin, microtubules, and intermediate filaments (IFs). The cytoskeleton is a dynamic structure where the three major filaments and tubules are under the influence of proteins that regulate their length, state of polymerization, and level of cross-linking. Since cytoskeleton is involved in virtually all cellular processes, cytoskeletal protein aberrations are the underlying reason for many pathological phenotypes, including several cardiovascular disease syndromes, neurodegeneration, cancer, liver cirrhosis, pulmonary fibrosis, and blistering skin diseases.

MCE designs a unique collection of 2,114 cytoskeleton-related compounds mainly focusing on the key targets in the cytoskeleton signal pathway and can be used in the research of cytoskeleton signal pathway and related diseases.

Designed to maximize efficiency in hit discovery and optimization, this compound library is built on a foundation of diverse Bemis-Murcko scaffolds, with each scaffold is represented by two specifically derived molecules. This strategy ensures broad chemical space through scaffold diversity while enabling preliminary functional group exploration. This approach provides early structure-activity relationship (SAR) insights for every scaffold, making it a valuable tool for accelerating drug discovery.

The rising prevalence of multidrug-resistant and extensively drug-resistant bacteria, combined with emerging resistance mechanisms and the limitations of existing antibacterial drugs, creates an urgent need for novel antibacterial agents. Antibacterial compound libraries serve as key tools to support antibacterial drug screening and development.

This library features structurally diverse compounds, including small-molecule scaffolds and natural product derivatives, and exhibits diverse antibacterial mechanisms of action. For example, these compounds exert antibacterial effects by disrupting bacterial cell structures, interfering with bacterial metabolic processes, and inhibiting nucleic acid synthesis. The derivation of scaffold structures enhances their activity against drug-resistant bacteria and their selectivity against different types of bacteria. This library can be used for the high-throughput screening of novel antibacterial drug candidates and the identification of potent compounds against drug-resistant and multidrug-resistant bacteria. Additionally, it provides a reference for compound structural modification, enabling further in-depth research on the structure-activity relationships(SARs) of antibacterial drugs. It can also be applied to the exploration of bacterial resistance mechanisms and reversal strategies, as well as the discovery of antibacterial molecules that inhibit efflux pumps and restore drug susceptibility.

The library contains 10855 structurally diverse drug-like compounds. Its core compound sources include analogs of known antifungal active moleculeswith a similarity score of ≥ 0.6. MCE has collected more than 1900 antibacterial molecules. All screened compounds conform to lead-like physicochemical properties, providing valuable support for the research and development of novel antibacterial drugs.

Liposomes are spherical or multilayered spherical vesicles formed by the self-assembly of diacyl chain phospholipids (lipid bilayers) in aqueous solutions, which can be made from natural or synthetic phospholipids and exhibit good biocompatibility and low toxicity. They can serve as delivery carriers for various bioactive substances (such as drugs, proteins, nucleic acids, etc.) and are widely used in biomedical and chemical research. The main advantages of liposomes include 1) Protective effect: Their bilayer structure can protect encapsulated molecules from enzymatic degradation, oxidation, and other influences, extending stability and activity; 2) Active targeting: Surface modifications enable active targeting, enhancing the concentration of drugs or molecules in specific tissues or cells; 3) Customizability: The composition and structure of liposomes can be adjusted according to needs, such as altering phospholipid types or adding targeting ligands. These properties make liposomes highly valuable in developing novel drug delivery systems, serving as nucleic acid carriers for gene transfection, studying cellular uptake mechanisms and drug release kinetics, as well as developing functional food additives to improve the bioavailability of nutritional components.

MCE contains 192 liposome compounds, which is a good tool for lipidomic-related studies.

Epigenetics refers to changes in phenotype that are not rooted in DNA sequence. Many types of epigenetic processes have been identified, including DNA methylation, alteration in the structure of histone proteins and gene regulation by small noncoding microRNAs. Modification of DNA, protein, or RNA, resulting in changes to the function and/or regulation of these molecules, without altering their primary sequences, reveals the complexities of cellular differentiation, embryology, the regulation of gene expression, aging, cancer, and other diseases.

MCE provide a unique collection of 1,915 epigenetics-related compounds that can be used in the research of the related diseases.

Natural products are an attractive source with varied structures that exhibit potent biological activities, and desirable pharmacological profiles. The core scaffold of a natural product can also provide a biologically validated framework upon which to display diverse functional groups. Inspired by bioactive natural products, natural product-like compounds, occupying the same chemical space, are ideally suited to explore and to facilitate understanding of biological pathways.

MCE provides a unique collection of 45 natural product-like compounds that are structurally like Steroids, Tannins, Flavonoids, Quinones, Isoquinolines, etc. This library is an important source of lead compounds for drug discovery.

Dipeptide compounds have attracted extensive attention in drug discovery and life science research due to their simple structures, ease of modification, and favorable biocompatibility. As small peptides composed of two amino acids, dipeptides exhibit diverse biological activities, including anti-inflammatory, antioxidant, antimicrobial, anticancer, and immunomodulatory effects, showing significant application potential in metabolic disorders, neurological diseases, and cancer research. Compared with traditional small molecules, dipeptide compounds possess favorable target-binding properties and high structural plasticity, making them valuable tools for drug screening and mechanism studies.

The MCE Dipeptide Compound Library contains 0 dipeptide compounds and can be applied to peptide drug discovery and development.

The discovery of hit molecule is a cornerstone of drug development. Among the diverse tools available, DNA-encoded libraries have emerged a revolutionary platform for high-throughput screening. Compared with traditional HTS, DEL features shorter screening processes, lower costs, simpler assays, and larger library capacities.

DEL Construction utilizes split-and-pool synthesis, a combinatorial chemistry approach that involves iterative splitting, reaction, and pooling. This strategy enables rapid, exponential assembly of fragments in minimal steps without the need for individual compound synthesis andassoicicated isolation or purification steps, thus greatly reducing overall costs. The technology enables simultaneous affinity screeningof massive compound collections to target proteins in a single step. By coupling chemical structures with unique DNA barcodes, each compound is tagged with a distinct DNA sequence for convenient tracking and decoding.DELs readily enable the construction and efficient screening of libraries containing millions to billions of compounds. As a result, DEL screening combines the dual advantages of high efficiency and low cost, making DEL a transformative technology in modern drug discovery.

The DEL kit consists of 50 independent libraries with a total scale of 100 billion compounds. It is constructed through stepwise combinatorial chemistry strategies involving 2-, 3-, and 4-round synthesis. By employing diverse scaffolds and flexible linking strategies, it encompasses various ring systems, linear frameworks, and heterocyclic structures. Screening can be achieved solely through affinity, independent of target-specific activity detection methods. This library is suitable for DEL screening against a wide range of targets.

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 67 polysaccharides that can be used in biomedical studies.

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 164 boronic acid compounds. It is a good tool to be used for research on cancer and other diseases.

Human metabolism is an integral part of cellular function that reflects individual differences in health, disease, diet, and lifestyle. Many health conditions such as obesity, diabetes, hypertension, heart disease, and cancer are associated with abnormal metabolic states. In the pathological state of the human body, metabolic pathways are significantly altered, resulting in aberrant levels of intermediates or end-products that can be viewed as potential diagnostic biomarkers or even therapeutic targets. Therefore, detection, identification and quantification of human metabolites are very important for drug metabolism research in drug development.

MCE offers a unique collection of 6,664 human metabolites, including endogenous metabolites and exogenous metabolites, covering multiple structure types, such as lipids, amino acids, nucleic acids, carbohydrates, organic acids, biogenic amines, vitamins,. MCE Human Metabolites Library is a helpful tool for studying the relationship between diseases and metabolism.

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.

Antibiotics are types of antimicrobial products used for the treatment and prevention of bacterial infections. Antibiotics can kill or inhibit bacterial growth. Although the target of an antibiotic is bacteria, some antibiotics also attack fungi and protozoans. However, antibiotics rarely have an effect on viruses. The major mechanism underlying antibiotics is the inhibition or regulation of enzymes involved in cell wall biosynthesis, nucleic acid metabolism and repair, protein synthesis, or disruption of membrane structure. Many of these cellular functions targeted by antibiotics are most active in multiplying cells. Since there is often overlap in these functions between prokaryotic bacterial cells and eukaryotic mammalian cells, it is not surprising that some antibiotics have also been found to be useful as anticancer agents.

MCE supplies a unique collection of 756 antibiotics, including penicillins, cephalosporins, tetracyclines, macrolides, etc. MCE Antibiotics Library is a useful tool for anti-bacterial or anti-cancer drugs discovery.

Fibrosis is a kind of repair response to long-term tissue damage, which is mainly manifested by excessive deposition of extracellular matrix (ECM) and scar formation. Myofibroblasts are the main generating cells of extracellular matrix, and their activation process is related to various pathological mechanisms including Oxidative stress, chronic inflammation and cytokine secretion. Fibrosis can occur in many organs, such as kidneys, liver, heart, lungs, etc. Continuous fibrosis can lead to the destruction of the normal structure of tissues and organs, and if not controlled in time, may cause organ failure or even life-threatening.

MCE contains 2,390 compounds targeting ant-fibrosis targets such as TGF-β, PI3K, Wnt, MMP, etc. These compounds have clear or potential anti-fibrosis activity and can be used for mechanism research and drug screening of fibrosis diseases.

“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) 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.

In contrast to the high conservation of conventional orthosteric sites, allosteric sites possess structural characteristics of low conservation, high hydrophobicity, weak polarity, confined spatial geometry, and dynamic cryptic properties. There is a significant difference between their core structures and orthosteric pockets — allosteric pockets are mostly dynamic grooves formed by protein conformational changes, subunit interface clefts, or shallow depressions, rather than the rigid "keyhole" structure of orthosteric sites. With looser spatial constraints, allosteric sites have the advantages of high selectivity and low off-target risk, and have become an important direction in new drug discovery.

Based on the dynamic, hydrophobic, and narrow-long spatial characteristics of allosteric pockets, MCE has performed targeted modification and screening of fragments. The screening criteria strictly conform to the requirements of allosteric binding: molecular weight is controlled at 120–280 Da (to meet the core needs of small molecules in fragment libraries and high derivatization), hydrogen bond donors (HBD ≤ 2), hydrogen bond acceptors (HBA ≤ 3), polar surface area (PSA = 30–80 Ų), rotatable bonds (≤ 2), moderate hydrophobicity (cLogP = 1–3.5), no strongly ionizable groups, and both appropriate rigidity and conformational flexibility to adapt to the dynamic changes of the pocket. Meanwhile, combined with the results of principal moment of inertia (PMI) analysis, fragments with high 3D diversity were obtained. Such fragments have good shape complementarity with allosteric pockets, ensuring that the fragments can smoothly enter the allosteric pockets and form stable binding, while providing room for subsequent optimization and derivation.

This library contains 1,800 structurally diverse fragment molecules with excellent drug-like properties, suitable for allosteric drug development and the design and optimization of allosteric sites. It combines the

At the forefront of innovative drug discovery, every medicinal chemist faces the challenge of rapidly identifying high-quality hit compounds from vast repositories of chemical resources.

The MCE Natural Product Diversity Scaffold Library is the result of a streamlined optimization process built upon our existing natural product collection. Adhering to the rigorous selection principle of "retaining only one representative compound per BMS scaffold", we have concentrated the diversity of thousands of compounds into a high-value, low-redundancy core set containing 2,272 compounds. All compounds are derived from natural sources, inheriting their inherent advantages of structural complexity and drug-likeness. By eliminating redundancy, the library size is significantly reduced without any compromise to chemical diversity. This approach effectively lowers the cost and time required for primary screening while simplifying downstream data analysis and structure-activity relationship (SAR) studies.

Flavonoids are an important class of natural products; particularly, they belong to a class of plant secondary metabolites having a polyphenolic structure, widely found in fruits, vegetables and certain beverages. Flavonoids can be subdivided into different subgroups depending on the carbon of the C ring on which the B ring is attached and the degree of unsaturation and oxidation of the C ring. These subgroups are: flavones, flavonols, flavanones, flavanonols, flavanols or catechins, anthocyanins and chalcones. Flavonoids are now considered as an indispensable component in a variety of nutraceutical, pharmaceutical, medicinal and cosmetic applications. This is attributed to their anti-oxidative, anti-inflammatory, anti-mutagenic and anti-carcinogenic properties coupled with their capacity to modulate key cellular enzyme function. Naturally occurring flavonoids are known to have biological activities for use as drugs, for example, in diseases like cancer, Alzheimer’s disease (AD), atherosclerosis, etc.

MCE offers a unique collection of 568 natural flavonoid compounds which is a useful tool for drug discovery as an important source of lead compounds.

A histone modification, a covalent post-translational modification (PTM) to histone proteins, includes methylation, phosphorylation, acetylation, ubiquitylation, and sumoylation, etc. In general, histone modifications are catalyzed by specific enzymes that act predominantly at the histone N-terminal tails involving amino acids such as lysine or arginine, as well as serine, threonine, tyrosine, etc. The PTMs made to histones can impact gene expression by altering chromatin structure or recruiting histone modifiers. Histone modifications act in diverse biological processes such as transcriptional activation/inactivation, chromosome packaging, and DNA damage/repair. Deregulation of histone modification contributes to many diseases, including cancer and autoimmune diseases.

MCE owns a unique collection of 895 bioactive compounds targeting Epigenetic Reader Domain, HDAC, Histone Acetyltransferase, Histone Demethylase, Histone Methyltransferase, Sirtuin, etc. Histone Modification Research Compound Library is a useful tool for histone modification research and drug screening.

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 5,124 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.

DNA is prone to numerous forms of damage that can injure cells and impair fitness. Cells have developed an array of mechanisms to repair these injuries. Proliferating cells are especially vulnerable to DNA damage due to the added demands of cellular growth and division. Cell cycle checkpoints represent integral components of DNA repair that coordinate cooperation between the machinery of the cell cycle and several biochemical pathways that respond to damage and restore DNA structure. By delaying progression through the cell cycle, checkpoints provide more time for repair before the critical phases of DNA replication, when the genome is replicated, and of mitosis, when the genome is segregated. Loss or attenuation of checkpoint function may increase spontaneous and induced gene mutations and chromosomal aberrations by reducing the efficiency of DNA repair.

MCE owns a unique collection of 3,275 cell cycle/DNA damage-related compounds which can be used in the research of the same.

Cyclic peptides are polypeptide chains taking cyclic ring structure, which exhibit diverse biological activities, such as antibacterial activity, immunosuppressive activity and anti-tumor activity. Cyclic peptides, with the features of good binding affinity, target selectivity and low toxicity, show great success as therapeutics. Multiple cyclic peptides are currently in clinical use, for examples, gramicidin and tyrocidine with bactericidal activity, cyclosporin A with immunosuppressive activity, and vancomycin with antibacterial activity. Furthermore, cyclic peptides usually have the sufficient size and a balanced conformational flexibility/rigidity for binding to flat protein-protein interaction (PPI) interfaces, which have potential to develop PPI drugs.

MCE offers a unique collection of 96 cyclic peptides, all of which have good bioactivities. MCE Cyclic Peptide Library is a powerful tool for drug discovery and PPI inhibitor screening.

Natural products are an attractive source with varied structures that exhibit potent biological activities, and desirable pharmacological profiles. The core scaffold of a natural product can also provide a biologically validated framework upon which to display diverse functional groups. Inspired by bioactive natural products, natural product-like compounds, occupying the same chemical space, are ideally suited to explore and to facilitate understanding of biological pathways.

MCE 10K Natural Product-like Compound Library consists of 10,000 natural product-like compounds. Each compound has scaffold of natural products or Tanimoto coefficient >0.6 with natural products. The natural-likeness scoring of these compounds is >-2. What’s more, compounds in the library are drug-like and readily available for re-supply, making it a powerful tool for new drug research and development. It can be widely applied in high-throughput screening (HTS) and high-content screening (HCS).

Natural products are an attractive source with varied structures that exhibit potent biological activities, and desirable pharmacological profiles. The core scaffold of a natural product can also provide a biologically validated framework upon which to display diverse functional groups. Inspired by bioactive natural products, natural product-like compounds, occupying the same chemical space, are ideally suited to explore and to facilitate understanding of biological pathways.

MCE 5K Natural Product-like Compound Library consists of 5,000 natural product-like compounds. Each compound has scaffold of natural products or Tanimoto coefficient >0.6 with natural products. The natural-likeness scoring of these compounds is >-2. What’s more, compounds in the library are drug-like and readily available for re-supply, making it a powerful tool for new drug research and development. It can be widely applied in high-throughput screening (HTS) and high-content screening (HCS).

The high rates of morbidity and mortality caused by fungal infections are associated with the current limited antifungal arsenal and the high toxicity of the compounds. Additionally, identifying novel drug targets is challenging because there are many similarities between fungal and human cells. The most common antifungal targets include fungal RNA synthesis and cell wall and membrane components, though new antifungal targets are being investigated. Nonetheless, fungi have developed resistance mechanisms, such as overexpression of efflux pump proteins, overexpression and changes in drug targets and biofilm formation, emphasizing the importance of discovering new antifungal drugs and therapies. Due to the limited antifungal arsenal, researchers have sought to improve treatment via different approaches, such as the combination of antifungal drugs, development of new formulations for antifungal agents and modifications to the chemical structures of traditional antifungals, etc.

MCE offers a unique collection of 537 compounds with validated antifungal activities. MCE antifungal compound library is an effective tool for drug repurposing screening, combination screening and biological investigation.

Extracellular vesicles (EVs) are small membrane binding structures that are released from cells into the surrounding environment and play a crucial role in mediating and regulating intercellular communication related to physiological and pathological processes. EVs are lipid membrane vesicles composed of proteins, lipids, and nucleic acids. EVs can be divided into several types based on their source, such as extracellular vesicles, microcapsules, and apoptotic vesicles. The size range of exosomes is 30-150nm, which are endocrine in multi vesicular endosomes (MVEs); microvesicles (50-1000nm) are secreted directly through extracellular interactions, thereby releasing plasma membrane vesicles. In contrast, apoptotic bodies are usually larger, ranging in size from 1 to 5 μ m. This is generated during programmed cell death. EV plays a crucial role in transmitting information between cells and influencing the behavior and function of receptor cells.

MCE designs a unique collection of 634 small molecules related to extracellular vesicles (EVs). It is a good tool to be used for research on metabolize, cancer and other diseases.

The immune system is a host defense system comprising many biological structures and processes within an organism that protects against disease. To function properly, an immune system must detect a wide variety of agents, known as pathogens, from viruses to parasitic worms, and distinguish them from the organism's own healthy tissue. Inflammation is also the body's attempt at self-protection to remove harmful stimuli and begin the healing process. It’s part of the body's immune response. The immune system recognizes damaged cells, irritants, and pathogens, and inflammation begins the healing process. Inflammatory abnormalities are a large group of disorders that underlie a vast variety of human diseases. The immune system is often involved with inflammatory disorders, demonstrated in both allergic reactions and some myopathies, with many immune system disorders resulting in abnormal inflammation.

MCE designs a unique collection of 7,742 compounds that are useful tool for Immunology/Inflammation research or autoimmune inflammatory diseases drug discovery.

COVID-19 poses a serious threat to people's health, and it is urgent to develop drugs to treat COVID-19 quickly. The screening of anti-COVID-19 drugs by using the clinical and approved compounds can greatly shorten the research and development cycle. In addition, the virtual screening technology can effectively narrow the scope of screening and improve the screening efficiency in the pre-screening of new drugs.

Taking advantage of our virtual screening, we conduct virtual screening of approved compound library and clinical compound library based on the 3CL protease (PDB ID: 6LU7), Spike Glycoprotein (PDB ID: 6VSB), NSP15 (PDB ID: 6VWW), RDRP, PLPro and ACE2 (Angiotensin Converting Enzyme 2) structure. We design a unique collection of 1,383 compounds which may have anti-COVID-19 activity. Anti-COVID-19 Compound Library will be a powerful tool for screening new anti-COVID-19 activity drugs.

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 2,463 compounds targeting a variety of neurotransmitter receptors. MCE Neurotransmitter Receptor Compound Library is a useful tool for neurological diseases drug discovery.

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.

Oceans cover more than 70% of the Earth’s surface and host a huge species diversity. Marine organisms are considered the most recent source of bioactive natural products after terrestrial plants and nonmarine microorganisms. Marine biological sources are taxonomically diverse and include sponges, tunicates, corals, mollusks, fungi, and sediment-derived bacteria.

Marine organisms can produce a plethora of small molecules with novel chemical structures and potent biological properties, being a rich source for the discovery of pharmacologically active compounds, already with several marine-derived agents approved as drugs. Ziconotide, a peptide originally discovered in a tropical cone snail, was the first marine-derived compound to be approved in the United States in December 2004 for the treatment of pain. Then, in October 2007, Trabectedin became the first marine anticancer drug to be approved in the European Union.

MCE offers a unique collection of 61 marine-sourced natural products which can be used for drug discovery for high throughput screening (HTS) and high content screening (HCS). MCE marine-sourced natural product library is an important source for drug discovery and development.

Lipids are important energy storage substances in the human body. They are involved in the regulation of cell structure and function, as well as signaling pathways and gene expression. Abnormal lipid levels in tissues or their dysregulation can lead to various diseases. These include obesity, type 2 diabetes, non-alcoholic fatty liver disease, neurodegenerative diseases, infections, and cancer. Therefore, maintaining normal levels of lipid metabolism is critical to overall health.

One of the key features of cancer is aberrant lipid metabolism. This includes alterations in lipid uptake, lipid desaturation, neolipogenesis, lipid droplets, and fatty acid oxidation in cancer cells. These changes all contribute to cellular survival in an ever-changing microenvironment. They do this by modulating feed-forward oncogenic signals and key oncogenic functions. Additionally, they affect oxidative stress, other types of stress, immune responses, and intercellular communication. Alterations in lipid metabolism have a strong impact on the properties of cancer stem cells. This includes aspects such as self-renewal, differentiation, invasion, metastasis, drug sensitivity, and resistance. Furthermore, these alterations also modulate T cell responses.

MCE can offer 145 metabolites of lipid metabolism pathways, which can be used for drug screening in cancer, immune-based diseases, metabolic diseases, and other diseases.

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 767 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.

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 118 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.

Drug-induced liver injury (DILI; also known as drug-induced hepatotoxicity) is caused by medications (prescription or OTC), herbal and dietary supplements (HDS), or other xenobiotics that result in abnormalities in liver tests or in hepatic dysfunction that cannot be explained by other causes. Drugs are an important cause of liver injury. Drug-induced hepatic injury is the most common reason cited for withdrawal of an approved drug.

DILI is thought to occur via several different mechanisms. Among these are direct impairment of the structural (e.g., mitochondrial dysfunction) and functional integrity of the liver; production of a metabolite that alters hepatocellular structure and function; production of a reactive drug metabolite that binds to hepatic proteins to produce new antigenic drug-protein adducts, which are targeted by hosts’ defenses (the hapten hypothesis); and initiation of a systemic hypersensitivity response (i.e., drug allergy) that damages the liver.

MCE Drug-induced Liver Injury (DILI) Compound Library contains a unique collection of 641 hepatotoxicity causing compounds and is a powerful tool to research DILI and other drug toxicities. This library can be used to understand the mechanisms of DILI, identify biomarkers for early DILI prediction, and allow timely recognition during drug development, thus finally achieving successful DILI prevention and assessment in the pre-marketing phase.

The RNA-targeted bioactive compound library is a high-quality collection of small molecules specifically designed and curated to target RNA structures and functions. It is widely applied in cutting-edge drug discovery and life science research. Unlike traditional strategies that focus on protein targets, RNA-targeted compounds can directly modulate various functional RNA molecules by influencing their splicing, translation, stability, or structural conformation, thereby enabling precise intervention in key biological processes. In the field of drug development, these compounds provide a novel approach to addressing previously “undruggable” targets and have demonstrated significant potential in areas such as oncology, antiviral therapies, and neurodegenerative diseases. For example, by targeting disease-associated RNA structural domains or regulating the aberrant expression of non-coding RNAs, these compounds can effectively inhibit disease progression or restore normal cellular function. In mechanistic studies, RNA-targeted compounds serve as valuable chemical biology tools to elucidate the roles of RNA in gene expression regulation, cellular signaling pathways, and disease development.

The MCE RNA-targeted bioactive compound library contains 854 compounds, sourced from databases such as TargetRX Atlas and R-BIND. The library features excellent structural diversity and biological activity, making it suitable for high-throughput screening (HTS), target validation, phenotypic screening, and lead compound discovery. It represents a valuable resource for RNA-related research and innovative drug development.

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.