database

This library contains about 439,804 natural and synthetic screening compounds. The information in the database includes logP, H-bond donors, H-bond acceptors, rotable bonds.

Cosmetics are complex mixtures formulated through the rational blending and processing of various natural, synthetic, or extracted raw materials. The ingredients used in cosmetics are diverse in type and functionality. Based on their properties and applications, cosmetic ingredients can generally be classified into two main categories: base materials and auxiliary ingredients. The former constitutes the primary component of cosmetics, accounting for a significant proportion in formulations and serving as the key functional substances. Auxiliary ingredients, on the other hand, play roles in shaping the product, ensuring stability, or imparting color, fragrance, and other specific characteristics.Establishing a systematic ingredient database is of great significance for cosmetic research and development. By analyzing the physicochemical properties (such as oil-water partition coefficients and molecular weight distribution), biological activity mechanisms (such as antioxidant pathways and cellular signaling regulation), and compatibility of ingredients, the database can provide precise guidance for formulation design. This approach helps shorten the development cycle of cosmetic/skincare products and reduces trial-and-error costs.

MCE offers 626 types of cosmetic ingredient compounds, including antioxidants, humectants, emulsifiers, film-forming agents, and more.

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 12,373 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.

Animal drug (also veterinary drug) refers to a drug intended for use in the diagnosis, cure, mitigation, treatment, or prevention of disease in animals. Animal Drugs @ FDA is a searchable online database that includes most FDA-approved and conditionally approved animal drugs. The major classes of veterinary drugs include antibiotics, anthelmintics, coccidiostats, nonsteroidal anti-inflammatory drugs, sedatives, corticosteroids, beta-agonists, and anabolic hormones.

MCE has collected 166 FDA-approved veterinary drug compounds for use in scientific research.

Flavor is an expression of smell and taste that is achieved through a variety of chemical processes triggered by molecules. Food flavor is an important attribute of food quality and in some cases determines consumers' food preferences. In addition to playing a key role in taste and smell, flavor molecules can also be involved in regulating metabolism and have an impact on health. In daily life, flavor molecules have absolute application value in food and spices. In scientific research, the study of flavor molecules is helpful to reveal the relationship between food intake and taste perception. Research on the combination behavior of flavor and food components can explore the retention, release and perception of flavor molecules. Most importantly, while exploring multi-sensory flavor perception, the food industry can fully mobilize the enthusiasm of researching new strategies for delicious and healthy food design.

Based on the FlavorDB database, collects and organizes 442 flavor molecules, which can be used in taste perception and other related studies.

Hormones are a class of biologically active substances secreted by endocrine gland cells, which are transported through the circulatory system to various parts of the body, and precisely act on specific target organs or cells, playing a crucial role in regulating the growth, development, metabolism, and reproduction of organisms. The mechanisms of hormone action are diverse and complex. Some hormones (such as corticosteroids, vitamin D, and thyroid hormones) can enter the cell interior and interact with receptors in the nucleus, thereby regulating gene expression and affecting cell function. Other hormones (such as growth hormone and thyrotropin-releasing hormone) bind directly to receptors on the cell surface, exerting their effects by regulating enzyme activity or influencing the state of ion channels. Additionally, hormones play a key role in the study of endocrine and metabolic diseases, and are closely related to the development of diseases such as diabetes and thyroid diseases.

MCE has included 86 human hormone compounds, which is of great significance for the study of human metabolic pathways, and can also be used to build a metabonomics database.

Natural products are small-molecule compounds produced in nature, derived from animals, plants, and microorganisms, including both primary and secondary metabolites. With their structural diversity and favorable biological activities, natural products have long been an important source for drug discovery. Traditional natural product research has often focused on isolating single active components, whereas metabolomics emphasizes a holistic approach—comprehensively detecting all metabolites in a sample and systematically capturing both known and unknown constituents. Consequently, mass spectrometry‑based metabolomics databases have become a key technological support for screening known components and identifying unknown compounds from natural sources.

MCE Mass Spectrometry Natural Product Library contains 4,412 natural products, covering multiple structural classes, including sugars and glycosides, phenylpropanoids, quinones, flavonoids, terpenoids, etc. All compounds have undergone rigorous quality control by LC/MS and other analytical methods, and can serve as high‑purity reference standards for metabolite identification.

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 858 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.

RNA is crucial for the regulation of numerous cellular processes and functions. With the in-depth study of disease mechanisms, processes such as RNA expression, splicing, translation, and stability regulation have become new targets for disease intervention. RNA has provided new therapeutic modalities for metabolic diseases, genetic disorders, and cancer patients, resulting in several innovative drugs.

MCE R&D team collected small molecules targeting RNA from the PDB, R-BIND, ROBIN, and internal database as the positive dataset, and non-targeting RNA small molecules from ROBIN as the negative dataset. Based on the GeminiMol pre-trained model, we encoded the molecules and calculated over 1700 molecular descriptors using Mordred as inputs for the model. Subsequently, we employed 13 deep learning models to learn from the data. All of which yielded good training results, with AUROCs greater than 0.75. Ultimately, we selected the Finetune model to screen HY-L901P, which exhibited the best classification performance, achieving an AUROC of 0.82 and a prediction accuracy of 0.76. We then applied filtering based on StaR rules (with at least two of the following properties: cLogP ≥ 1.5, Molar Refractivity ≥ 4, Relative Polar Surface Area ≤ 0.3) to obtain a library containing approximately 5,000 small molecule compounds targeting RNA. This library serves as a valuable tool for screening small molecules that interact with RNA.

MCE-18 stands for Medicinal Chemistry Evolution 2018, which was first published in Journal of Medicinal Chemistry in 2019 for assessing molecular novelty and three-dimensional complexity. Developed based on Clarivate global pharmaceutical patent database, this descriptor was constructed via big-data analysis covering 28,161 patented lead compounds, 1,370 approved drugs and nearly 30,000 preclinical-to-phase III drug candidates from 23 top pharmaceutical companies worldwide between 1950 and 2018, followed by structural clustering and removal of redundant outdated scaffolds for data denoising. Its scoring system integrates five core structural features including aromatic ring (AR), aliphatic heterocycle (NAR), chiral center (CHIRAL), spiro atom (SPIRO), cyclic and acyclic sp³ carbon ratio together with a quadratic topological correction factor. Breaking the limitations of the single Fsp³ parameter, MCE-18 effectively distinguishes conventional flat aromatic scaffolds from modern 3D-enriched novel chemotypes, overcoming typical drawbacks of traditional compound libraries such as scaffold redundancy, low screening hit rates and poor compatibility with allosteric and PPI-related difficult targets.

This library contains over 37,000 structurally diverse compounds with favorable overall drug-likeness, suitable for high-throughput screening against canonical targets including kinases, GPCRs and proteases as well as challenging allosteric and PPI targets. Compounds comply with the developmental trend of modern novel drug discovery, supporting routine primary screening as well as early hit identification of allosteric modulators and PPI inhibitors, serving as an efficient screening resource for early-stage innovative drug discovery.

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.