Molecular targets

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

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 320 molecular glue analogs, and these compounds serve as powerful tools for the research of molecular glues.

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 1,793 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.

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

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 883 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.

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 10,000 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.

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 2,621 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.

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 5,308 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 4,824 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).

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 2,872 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.

Lung cancer is a major global health problem, as it is the leading cause of cancer-related deaths worldwide. Lung cancer is divided into two categories: small cell lung cancer and non-small cell lung cancer (NSCLC). Non-small cell lung cancer accounts for about 85 percent of lung cancers.

As with all cancers, lung cancer may be treated with surgery, chemotherapy, radiation therapy, targeted therapy, immunotherapy or a combination thereof. Targeted therapy is one of the most exciting developments in lung cancer medicine, especially for NSCLC. Extensive genomic characterization of NSCLC has led to the identification of molecular subtypes of NSCLC that are oncogene addicted and exquisitely sensitive to targeted therapies. These include activating mutations in epidermal growth factor receptor (EGFR) and BRAF or echinoderm microtubule-associated protein-like 4 (EML4)-anaplastic lymphoma kinase (ALK) fusions and ROS1 receptor tyrosine kinase fusions. These are important targets for target therapy.

MCE offers a unique collection of 2,355 compounds with identified and potential anti-lung cancer activity. These compounds target lung cancer’s major targets and signaling pathways. MCE anti-lung cancer compound library is a useful tool for anti-lung cancer drugs screening and other related research.

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.

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 5,873 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.

Blood cancers, also called hematologic cancers, occur when abnormal blood cells start growing out of control, interrupting the function of normal blood cells, which fight off infection and produce new blood cells. Most blood cancers start in the bone marrow, which is where blood is produced. There are three main types of blood cancers: leukemia, lymphoma and myeloma, which afflict millions of children and adults every year, and are often deadly.

Some common blood cancer treatments include stem cell transplantation, chemotherapy, radiation therapy, targeted therapy, immunotherapy or a combination thereof. As we begin to understand the key signaling pathways and molecular drivers of malignant transformation in haematological disorders, new treatment strategies will continue to be developed.

MCE offers a unique collection of 3,455 compounds with identified and potential anti-blood cancer activity. These compounds target blood cancer’s major targets and signaling pathways. MCE anti-blood cancer compound library is a useful tool for anti-blood cancer drugs screening and other related 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 305 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.

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 2,882 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.

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 745 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 2,300 high-structurally diverse 'RO3' compliant fragment molecules from large-scale fragment molecules, which can be applied to fragment based 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.

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 372 compounds including peptoid, α-helix mimetics, β-turn/sheets mimetics, etc. This library is an indispensable tool of structure-activity relationships in drug discovery.

Lactic acid metabolism is one of the key metabolic pathways within living organisms. It plays a crucial role not only in cellular energy conversion but is also closely related to a variety of physiological and pathological processes. The production and clearance of lactic acid are important indicators of cellular metabolic balance, and its abnormal regulation may lead to conditions such as lactic acidosis, muscle fatigue, and hereditary metabolic diseases. Moreover, lactic acid is closely related to the malignancy of tumors and is considered a biomarker for malignant tumors and poor prognosis. Lactic acid can serve as a metabolic substrate to support the metabolic needs of tumor cells under hypoxic conditions, and it can also cause acidification of the tumor microenvironment, suppress immune cell function to promote immune evasion, and induce drug resistance in tumor cells. Currently, targeting lactic acid-lactylation and its related metabolic pathways has become a new research avenue for cancer treatment. In-depth exploration of the molecular mechanisms of lactic acid metabolism can help in screening lead compounds that regulate the lactic acid metabolism.

MCE contains 428 small molecule compounds targeting enzymes involved in lactic acid metabolism. This library is of significant value for researching the role of lactate metabolism in the mechanisms of diseases.

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 5,098 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.

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 3,061 cell death compounds, covering multiple targets, such as Apoptosis, Ferroptosis, Pyroptosis, Necroptosis, etc. It is a useful tool for screening cell death 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 23,319 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.

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

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 1,076 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.

Natural products are small molecular compounds that occur in nature and come from any organism, including primary and secondary metabolites. Natural products have potential biological activity and can be used as lead compounds for drug discovery. Nature has been a source of medicines for thousands of years, and a large number of drugs have been isolated from nature, many based on their use in traditional medicine. With the development of compound targets, there is an increasing need to screen for compound diversity. Through ongoing research into natural biodiversity, much of which remains to be exploited, natural products will play a key role in meeting this demand. The Lipinski rule of 5 is used to describe the drug-like properties of a molecule, molecules that adhere to the rule of 5 have higher drug potential. Based on MCE natural product library, MCE selects the molecules that obey the rule of 5, which makes the efficiency of drug screening higher.

MCE designs a unique collection of 2,668 RO5 drug-like natural products, which is an important tool for drug discovery.