tumor development

The developmental proteins Hedgehog, Notch and Wnt are key regulators of cell fate, proliferation, migration and differentiation in several tissues. Their related signaling pathways are frequently activated in tumors, and particularly in the rare subpopulation of cancer stem cells. The Wnt signaling pathway is a conserved pathway in animals. Deregulated Wnt signaling has catastrophic consequences for the developing embryo and it is now well appreciated that defective Wnt signaling is a causative factor for a number of pleiotropic human pathologies, including cancer. Hedgehog signaling pathway is linked to tumorigenesis and is aberrantly activated in a variety of cancers. The Notch signaling pathway is a highly conserved cell signaling system present in most animals. It plays an important role in cell-cell communication, and further regulates embryonic development.

MCE designs a unique collection of 654 Wnt/Hedgehog/Notch signaling pathway-related small molecules. Wnt/Hedgehog/Notch Compound Library serves as a useful tool for stem cell research and anti-cancer drug screening.

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

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

MCE carefully prepared a unique collection of 187 ligands for E3 ligase, which have been reported to be used in PROTAC design. MCE E3 ligase ligand library is a useful tool for PROTAC development.

Heat-clearing and detoxification is a specific treatment method in the research of traditional Chinese medicine (TCM), which is clinically used to treat infectious diseases with remarkable effect. Over the past decades, the research of heat-clearing and detoxification treatment has been one of the most active fields of combining traditional Chinese and western medicines, and has made remarkable achievements. Nowadays, the application field of heat-clearing and detoxification traditional Chinese medicine is not only limited to antibacterial and antiviral, but also has made progress in the research fields of anti-inflammatory reaction, anti-endotoxin, anti-peroxidative damage, anti-inflammatory cytokines, enhancement of immune function, protection of cellular organelles, and maintenance of calcium homeostasis. In addition to this, clearing heat and removing toxins has also made significant research progress in non-infectious diseases, for example, in tumors, cardiovascular diseases, renal diseases, blood diseases, geriatrics, and diabetes, all of which have shown good curative effect.

MCE can supply 1,282 monomer component from more than a hundred sources of heat-clearing and detoxification TCM, which can be used in TCM studies, drug development and mechanism-based studies.

Copper is an important co-factor of all biological enzymes, but if the concentration exceeds the threshold of maintaining the homeostasis mechanism, copper will lead to cytotoxicity. This death mechanism has been named "Cuproptosis".

The mechanism of cuproptosis distinct from all other known mechanisms of regulated cell death, including apoptosis, pyroptosis, necroptosis, and ferroptosis.

Copper combine with the lipoylated components of the tricarboxylic acid cycle (TCA), leading to lipoylated protein aggregation and subsequent loss of iron-sulfur cluster proteins, ultimately resulting in protein toxicity stress and cell death. Studies have shown that the necessary factors for cuproptosis include the presence of glutathione, mitochondrial metabolism of galactose and pyruvate, and glutamine metabolism.

Targeted regulation of cuproptosis is a potential choice to treat cancer, rheumatoid arthritis, and other diseases. For example, up-regulation of LIPT1 may inhibit the occurrence and development of tumors by destroying TCA in mitochondria and then inducing cuproptosis.

MCE supplies a unique collection of 446 cuproptosis-related compounds, all of which act on the targets or signaling pathways related to cuproptosis and may have in inhibitory or activated effect on cuproptosis. MCE Cuproptosis Library is a useful tool for drug research related to cancer, rheumatoid arthritis, and other diseases.

PD-1/PD-L1 are key immune checkpoint targets that suppress T-cell-mediated anti-tumor immunity, representing a major focus in cancer immunotherapy. While antibody drugs dominate the clinic, they are limited by administration challenges and immune-related side effects. Small-molecule PD-1/PD-L1 inhibitors, with oral availability, good tissue penetration and low cost, have emerged as a promising next-generation strategy.

A PD-1/PD-L1 lead-like library was built via a five-step virtual screening process. After collecting 8,947 inhibitors from BindingDB and PubChem and filtering by activity and duplicates, AI similarity screening was performed using GeminiMol. Key pharmacophores were extracted from the PPI interface of co-crystal structures, and molecular was screened via a pharmacophore model, effectively enhancing target activity.

Containing 10,000 structurally diverse and drug-like molecules well-matched to the PD-L1 pocket, the library supports virtual docking, high-throughput screening and hit discovery, enabling efficient and rapid development of small-molecule immunotherapies.

With the aging population and increasing competitive pressures, neurodegenerative diseases of the central nervous system (CNS) have become a serious medical challenge in modern society, including Parkinson's disease, Alzheimer's disease, brain tumors, and multiple sclerosis. However, the success rate of CNS drug development remains remarkably low, primarily due to the blood-brain barrier (BBB). The blood-brain barrier (BBB) is a semipermeable barrier structure that surrounds the microvasculature of the CNS. In capillaries, the wedged endothelial cells are tightly packed and wedge-shaped, lining the interior of the vessels to form extensive tight junctions. Along with a range of receptors, transporters, efflux pumps, and other cellular components, this barrier regulates the entry and exit of molecules between the bloodstream and the brain. The intact BBB blocks the passage of most blood-borne substances into the brain, preventing nearly 100% of large-molecule drugs and over 98% of small-molecule drugs from entering. Compared to non-CNS drugs, physicochemical properties such as hydrogen bonds, lipophilicity, and molecular weight significantly influence a compound's ability to cross the BBB. Using artificial intelligence (AI) algorithms to predict BBB permeability, a predicted value greater than 0.75 indicates that the compound has strong potential to cross the BBB, providing a promising starting point for CNS drug discovery.

Protein lactylation, an emerging post-translational modification identified in recent years, plays a critical role in linking cellular metabolic reprogramming, epigenetic regulation, and signaling networks. Based on a systematic framework encompassing lactate metabolism, lactylation, and downstream signaling pathways, this compound library comprehensively targets multiple regulatory layers, including histone modification enzymes (such as p300 and HDACs), key glycolytic enzymes (such as PKM2, LDHA, and GAPDH), transcriptional regulators (such as STAT3, HMGB1, and p53), as well as central signaling pathway nodes including HIF-1α, NF-κB, and PI3K-AKT-mTOR. This integrated design enables a comprehensive representation of the regulatory roles of lactylation across the “metabolism–epigenetics–signaling” axis.

MCE has assembled a collection of 6,182 known bioactive compounds and potential functional molecules, making this library suitable for a wide range of applications, including high-throughput drug screening, inhibitor identification, and mechanistic studies. It can be used to systematically evaluate the functional roles of lactylation in biological processes such as tumor metabolism, immune regulation, and inflammatory responses, and to efficiently identify small-molecule candidates with regulatory potential, thereby facilitating the development of innovative therapeutics targeting the interplay between metabolism and epigenetic regulation.

Neuronal Signaling is involved in the regulation of the mechanisms of the central nervous system (CNS) such as its structure, function, genetics and physiology as well as how this can be applied to understand diseases of the nervous system. Every information processing system in the CNS is composed of neurons and glia, neurons have evolved unique capabilities for intracellular signaling (communication within the cell) and intercellular signaling (communication between cells). G protein-coupled receptors (GPCRs), including 5-HT receptor, histamine receptor, opioid receptor, etc. are the largest class of sensory proteins and are important therapeutic targets in Neuronal Signaling. Besides, Notch signaling, such as β- and γ-secretase, also plays multiple roles in the development of the CNS including regulating neural stem cell (NSC) proliferation, survival, self-renewal and differentiation. GPCR dysfunction caused by receptor mutations and environmental challenges contributes to many neurological diseases. Notch signaling in neurons, glia, and NSCs is also involved in pathological changes that occur in disorders such as stroke, Alzheimer's disease and CNS tumors. Thus, targeting Neuronal Signaling, such as notch signaling and GPCRs, can be used as therapeutic interventions for several different CNS disorders.

MCE designs a unique collection of 3,961 Neuronal Signaling-related compounds that act as a useful tool for the research of neuronal regulation and neuronal diseases.

Carbohydrate metabolism serves as a central hub for energy supply and biosynthesis in living organisms and plays a critical role in the onset and progression of various diseases. In recent years, studies have shown that tumor cells reprogram their energy metabolism through aerobic glycolysis (the Warburg effect) to support rapid proliferation. Immune cells also rely on specific carbohydrate metabolic pathways to regulate their activation and differentiation states, while disorders such as diabetes and metabolic syndrome arise directly from dysregulation of carbohydrate metabolism. In addition, enzymes and key metabolic nodes involved in carbohydrate metabolism have become important targets for drug discovery, and therapeutic strategies targeting glycolysis, the pentose phosphate pathway, and energy metabolism are continuously advancing the treatment of cancer and metabolic diseases. Therefore, systematic analysis of carbohydrate metabolic networks and their associated metabolites is of great significance for elucidating disease mechanisms and developing novel therapeutic approaches.

The MCE Carbohydrate Metabolism Metabolite Library is constructed based on classical carbohydrate metabolic pathways and contains 76 metabolites. It systematically integrates key metabolic networks, including glycolysis, the pentose phosphate pathway, the tricarboxylic acid (TCA) cycle, monosaccharide metabolism, and sugar acid interconversions. The library comprehensively covers core metabolic nodes from glucose uptake and utilization to energy production and biosynthesis, while also incorporating important upstream and downstream intermediates. It enables accurate representation of intracellular metabolic flux dynamics and is well suited for applications such as metabolic flux analysis, target validation, and mechanistic studies. Furthermore, it provides robust support for multi-omics integration and the development of precision intervention strategies.

Oxygen homeostasis regulation is the most fundamental cellular process for adjusting physiological oxygen variations, and its irregularity leads to various human diseases, including cancer. Hypoxia is closely associated with cancer development, and hypoxia/oxygen-sensing signaling plays critical roles in the modulation of cancer progression.

Hypoxia-inducible factor 1 (HIF-1) is a transcription factor that functions as a master regulator of oxygen homeostasis. A variety of HF-1 target genes have been identified thus far which encode proteins that play key roles in critical developmental and physiological processes including angiogenesis/vascular remodeling, erythropoiesis, glucose transport, glycolysis, iron transport, and cell proliferation/survival.

HIF-1 is a heterodimeric transcription factor consisting of a constitutively expressed β-subunit and an oxygen-regulated α-subunit. The unique feature of HIF-1 is the regulation of HIF-1α expression and activity based upon the cellular O₂ concentration. Under normoxic conditions, hydroxylation of HIF-1α on these different proline residues is essential for HIF proteolytic degradation by promoting interaction with the von Hippel-Lindau tumor-suppressor protein (pVHL) through hydrogen bonding to the hydroxyproline-binding pocket in the pVHL β-domain. As oxygen levels decrease, hydroxylation of HIF decreases; HIF-1α then no longer binds pVHL, and becomes stabilized, allowing more of the protein to translocate to the cell’s nucleus, where it acts as a transcription factor, upregulating (often within minutes) the production of proteins that stimulate blood perfusion in tissues and thus tissue oxygenation.

MCE offers a unique collection of 4,317 oxygen sensing related compounds targeting HIF/HIF Prolyl-Hydroxylase, MAPK/ERK, PI3K/AKT signaling pathways, etc. MCE Oxygen Sensing Compound Library is a useful tool to study hypoxia, oxidative stress and discover new anti-cancer drugs.