kinase inhibitors

Kinase is an enzyme that adds phosphate groups to other molecules. This process is known as phosphorylation. Protein phosphorylation is a key aspect in the regulation of a large number of cellular processes including cellular division, metabolism, signal transduction, and so on. There are over 500 kinases encoded by the human genome and it has been estimated that kinases regulate approximately 50% of cellular functions. Kinases are a large group of drug targets in drug discovery. Kinase inhibitors are an important class of drugs that block certain enzymes involved in diseases such as cancer and inflammatory disorders.

Kinase inhibitor library designed by MCE contains 3,849 kinase inhibitors and regulators mainly targeting protein kinases (VEGFR, EGFR, BTK, CDK, Akt, etc.), lipid kinases (PI3K, PI4K, SK, etc.) and carbohydrate kinases (Hexokinase), and is a useful tool for kinase drug discovery and related research.

Kinases is a class of enzymes that adds chemicals called phosphates to other molecules, such as sugars or proteins. Protein phosphorylation serves as a critical regulatory mechanism for numerous cellular processes including cell division, metabolism, and signal transduction, with approximately 50% of cellular functions in humans being regulated by kinase activity. In drug discovery, kinases represent a major category of therapeutic targets, and kinase inhibitors constitute an important class of pharmaceuticals that block the activity of specific disease-associated enzymes, particularly in cancer and inflammatory disorders. Small molecule kinase inhibitors represent one of the fastest-growing drug categories, having received U.S. Food and Drug Administration (FDA) approval for both oncological and non-oncological indications. As of September 2023, over 70 FDA-approved small molecule kinase inhibitors are commercially available.

The MCE Kinase Inhibitor Library Mini contains 270 kinase inhibitors primarily targeting protein kinases (VEGFR, EGFR, BTK, CDK, Akt, etc.), lipid kinases (PI3K, PI4K, SK, etc.), and carbohydrate kinases. This collection includes 1-3 highly specific representative compounds per target, optimized for screening of kinase-related drug targets in pharmaceutical research.

The most prominent mechanism of action of kinase inhibitors is their competition with ATP by binding to the hinge region of the kinase protein. Once the kinase is blocked by an inhibitor, it loses the ability to transfer phosphate groups from ATP to other molecules, resulting in the loss of kinase activity.

The hinge-binding region of kinase inhibitors mimics the interaction pattern between the ATP nucleobase and the kinase. MCE extracted thousands of kinase inhibitors from the ChEMBL database and isolated their molecular fragments. In certain cases, the amino and amide groups on the molecular fragments are crucial for binding in the hinge region. Therefore, we enhanced the diversity of the collected results by adding these two groups to unoccupied positions on the ring system. Subsequently, the fragments were assessed for their hinge region binding ability via docking at distinct kinases, we also applied pharmacophore constraints to ensure interactions with key amino acids in the kinase hinge region, ultimately obtaining kinase-related molecular fragments.

MCE provides over 12,412 kinase fragment molecules that meet the above requirements and are available off the shelf, serving as an effective tool for screening and developing drugs targeting kinases.

Kinases are enzymes that catalyze the addition of phosphate groups to substrate molecules, a process known as phosphorylation. Protein phosphorylation serves as a critical regulatory mechanism for numerous cellular processes, including cell division, metabolism, and signal transduction. The human genome encodes over 500 kinases, which collectively regulate approximately 50% of cellular functions. Due to their pivotal roles, kinases represent one of the most important target classes in drug development.

Kinase inhibitors can selectively block the activity of disease-associated kinases, making them valuable therapeutics for conditions such as cancer and inflammatory diseases. FDA-approved kinase inhibitors have undergone extensive preclinical and clinical studies, demonstrating high bioactivity, favorable safety profiles, and good bioavailability, rendering them suitable for investigating new therapeutic indications.

Protein serine/threonine kinases (PSKs) are protein kinases that use ATP as a high-energy donor molecule to transfer phosphate groups to serine/threonine residues of target protein. As an important signal transduction regulator, serine/threonine kinases can affect the function of target proteins by disrupting enzyme activity or binding of target proteins to other proteins. Serine/threonine kinases are involved in the regulation of immune response, cell proliferation, differentiation, apoptosis and other physiological processes. Serine/threonine kinase inhibitors are an important class of compounds that have been widely studied in cancer, chronic inflammation, autoimmune diseases, aging and other diseases.

MCE designs a unique collection of 2,162 serine/threonine kinase inhibitors, mainly targeting the receptor PKA, Akt, PKC, MAPK/ERK, etc, which is an effective tool for development and research of anti-cancer, anti-chronic inflammatory diseases, anti-autoimmune diseases and anti-aging compounds.

Glycolysis is a series of metabolic processes by which one molecule of glucose is catabolized to two molecules of pyruvate with a net gain of two ATP. Glycolysis takes place in 10 steps and catalyzed by a series of enzyme, such as hexokinase, Glucose-6-phosphate isomerase, Phosphofructokinase, etc. Glycolysis is used by all cells in the body for energy generation.

Most cancer cells exhibit increased glycolysis and use this metabolic pathway for generation of ATP as a main source of their energy supply. This phenomenon is known as the Warburg effect and is considered as one of the most fundamental metabolic alterations during malignant transformation. Because increased aerobic glycolysis is commonly seen in a wide spectrum of human cancers, development of novel glycolytic inhibitors as a new class of anticancer agents is likely to have broad therapeutic applications.

MCE provides a unique collection of 1,258 glycolysis compounds that mainly target hexokinase, glucokinase, enolase, pyruvate kinase, PDHK, etc. MCE Glycolysis Compound Library is a useful tool for glucose metabolism research and anti-cancer drug discovery.

According to reports, most known kinase inhibitors exert their effects through competitive binding in highly conserved ATP pockets. Although genetic techniques such as RNA interference can inactivate specific genes, most kinases are multi domain proteins, each of which has an independent function. Highly selective inhibitors have higher efficiency than non-selective inhibitors, and the selectivity to the target is at least 100 times higher. Therefore, ensuring the validation of targets with the most selective inhibitors is crucial for a more thorough understanding of the pharmacology of the kinase field. The Highly Selective Inhibitors Library contains 6,135 compounds, covering multiple targets and subtypes, such as GPCR protein family, Ion channel, multiple kinases, etc. The Highly Selective Inhibitors Library is an effective tool for screening different phenotypes

Protein tyrosine kinases (PTKs) are key signaling molecules and important drug targets. Two classes of PTKs are present in cells: the transmembrane receptor PTKs (RTKs) and the nonreceptor PTKs. The RTK family includes the receptors for insulin and for many growth factors, such as EGFR, FGFR, PDGFR, VEGFR, and NGFR. RTKs are transmembrane glycoproteins that are activated by the binding of their ligands, and they transduce the extracellular signal to the cytoplasm by phosphorylating tyrosine residues on the receptors themselves (autophosphorylation) and on downstream signaling proteins. Their principal functions of PTKs involve the regulation of multicellular aspects of the organism. Cell to cell signals concerning growth, differentiation, adhesion, motility, and death are frequently transmitted through tyrosine kinases. In humans, tyrosine kinases have been demonstrated to play significant roles in the development of many disease states, including diabetes and cancers.

MCE designs a unique collection of 1,578 compounds that act as a useful tool for PTKs-related drug screening and disease research.

MAPK families play an important role in complex cellular programs like proliferation, differentiation, development, transformation, and apoptosis. In mammalian cells, four MAPK families have been clearly characterized: ERK1/2, C-Jun N-terminal kinse/stress-activated protein kinase (JNK/SAPK) , p38 kinase and ERK5. They respond to different signals. Each MAPK-related cascade consists of three enzymes that are activated in series: a MAPK kinase kinase (MAPKKK), a MAPK kinase (MAPKK) and a MAP kinase (MAPK). MAPK signaling pathways has been implicated in the development of many human diseases including Alzheimer's disease (AD), Parkinson's disease (PD), amyotrophic lateral sclerosis (ALS) and various types of cancers.

MCE designs a unique collection of 1,063 MAPK signaling pathway inhibitors that act as a useful tool for MAPK-related drug screening and disease research.

Adult stem cells are important for tissue homeostasis and regeneration due to their ability to self-renew and generate multiple types of differentiated daughters. Self-renewal is reflected by their capacity to undergo multiple/limitless divisions. Several signaling pathways are involved in self-renewal of stem cells, that is, Notch, Wnt, and Hedgehog pathways or Polycomb family proteins. Recent studies mainly focus on cancer stem cell (CSCs), induced pluripotent stem cell (iPSCs), neural stem cell and maintenance of embryonic stem cell pluripotency. Among them, CSCs have been believed to be responsible for tumor initiation, growth, and recurrence that have implications for cancer therapy.

MCE owns a unique collection of 2,723 compounds that can be used for stem cell regulatory and signaling pathway research.

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

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

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

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

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

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

The blood-brain barrier (BBB) is the complex network of brain microvessels. It protects the brain from the external bloodstream environment and supplies the brain with the required nutrients for normal function. However, blood-brain barrier is also the obstacle to deliver beneficial drugs to treat CNS (central nervous system) diseases or brain tumors, as it has the least permeable capillaries in the entire body due to physical barriers (tight junctions). Therefore, it is crucial to discover drugs which can cross this barrier for the treatment of brain-based diseases, such as Alzheimer’s disease (AD), Parkinson’s disease (PD) and epilepsy.

MCE offers a unique collection of 1,096 compounds with confirmed CNS-Penetrant property. It’s a useful tool for the discovery of drugs used for brain diseases, such as brain tumors, mental disorders, and neurodegenerative diseases.

Nucleoside and nucleotide analogues are synthetic, chemically modified compounds that have been developed to mimic their physiological counterparts in order to exploit cellular metabolism and subsequently be incorporated into DNA and RNA to inhibit cellular division and viral replication. In addition to their incorporation into nucleic acids, nucleoside and nucleotide analogues can interact with and inhibit essential enzymes such as human and viral polymerases (that is, DNA-dependent DNA polymerases, RNA-dependent DNA polymerases or RNA-dependent RNA polymerases), kinases, ribonucleotide reductase, DNA methyltransferases, purine and pyrimidine nucleoside phosphorylase and thymidylate synthase. These actions of nucleoside and nucleotide analogues have potential therapeutic benefits — for example, in the inhibition of cancer cell growth, the inhibition of viral replication as well as other indications.

MCE offers a unique collection of 572 nucleotide compounds including nucleotide, nucleoside and their structural analogues. MCE Nucleotide Compound Library is a useful tool to discover anti-cancer and antiviral drugs for high throughput screening (HTS) and high content screening (HCS).

Protein phosphorylation is a key post-translational modification underlying the regulation of many cellular processes. Phosphatases and kinases contribute to the regulation of protein phosphorylation homeostasis in the cell. This reversible regulation of protein phosphorylation is critical for the proper control of a wide range of cellular activities, including cell cycle, proliferation and differentiation, metabolism, cell-cell interactions, etc.

Protein phosphatases have evolved in separate families that are structurally and mechanistically distinct. Based on substrate specificity and functional diversity, protein phosphatases are classified into two superfamilies: Protein serine/threonine phosphatases and Protein tyrosine phosphatases. Ser/Thr phosphatases are metalloenzymes belonging to two major gene families termed PPP (phosphoprotein phosphatase) and PPM (metal-dependent protein phosphatases), whereas protein tyrosine phosphatases (PTPs) belong to distinct classes of enzymes that utilize a phospho-cysteine enzyme intermediate as a part of their catalytic action.

MCE supplies a unique collection of 175 phosphatase inhibitors that mainly targeting protein tyrosine phosphatases (PTPs) and serine/threonine-specific protein phosphatases. MCE Phosphatase Inhibitor Library is a useful tool for phosphatase drug discovery and related research.

The PI3K/Akt/mTOR pathway controls many cellular processes that are important for the formation and progression of cancer, including apoptosis, transcription, translation, metabolism, angiogenesis, and cell cycle progression. Every major node of this signaling network is activated in a wide range of human tumors. Mechanisms for the pathway activation include activation of receptor tyrosine kinases (RTKs) upstream of PI3K, mutation or amplification of PIK3CA encoding p110α catalytic subunit of PI3K, mutation or loss of PTEN tumor suppressor gene, and mutation or amplification of Akt1. Once the pathway is activated, signaling through Akt can stimulate a series of substrates including mTOR which is involved in protein synthesis. Thus, inhibition of this pathway is an attractive concept for cancer prevention and/or therapy. Currently some mTOR inhibitors are approved for several indications, and there are several novel PI3K/Akt/mTOR inhibitors in clinical trials.

MCE owns a unique collection of 1,049 compounds that can be used for PI3K/Akt/mTOR pathway research. PI3K/Akt/mTOR Compound Library also acts as a useful tool for anti-cancer drug discovery.

Dopamine receptor (DAR), widely distributed in the brain, plays a key role in regulating motor function, motivation, driving force and cognition. The role of DA is mediated by D1-type (D1, D5) and D2-type receptors (D2S, D2L, D3, D4), which are distributed in presynaptic, postsynaptic and extrasynaptic, projection neurons and interneurons. Each receptor has a different function. D1 and D5 receptors couple with G stimulation sites and activate Adenylyl cyclase. The activation of Adenylyl cyclase leads to the production of the second messenger cAMP, which leads to the production of protein kinase A (PKA), which leads to further transcription in the nucleus. D2 to D4 receptors are coupled to G inhibitory sites to inhibit adenylyl cyclase and activate potassium Ion channel. These receptors utilize phosphorylation cascades or direct membrane interactions to affect the functions of voltage-gated and neurotransmitter-gated channels, cytoplasmic enzymes, and transcription factors. Dopamine receptor plays an important role in daily life.

MCE designs a unique collection of 267 small molecules related to dopamine receptor. It is a good tool for screening drugs from nervous system disease.

DEL technology enables the simultaneous screening of millions or billions of compounds in a single tube by covalently linking each small molecule with a unique DNA sequence. Traditional DEL screening primarily focuses on identifying non-covalent binding molecules, where interactions with the target are reversible. In contrast, DNA‑encoded covalent library is an ultra‑high‑throughput screening library developed on the basis of conventional DNA‑encoded library technology. It incorporates controllable electrophilic covalent warheads capable of forming irreversible covalent bonds with amino acid residues at the active sites of target proteins, including Cys, Lys, Ser, Tyr, and others. This covalent binding enhances binding affinity, prolongs residence time at the target site, and has the potential to overcome challenges associated with traditional non-covalent inhibitors, such as drug resistance or off-target effects.

Each compound in the library contains both a binding domain and an electrophilic warhead. It first recognizes and binds to the target through non covalent interactions, and then forms a stable covalent bond with key amino acid residues to achieve irreversible inhibition. This library is specifically designed for the discovery of potent, long lasting, and highly selective covalent inhibitors, particularly for undruggable targets such as kinases, GPCRs, proteases, and mutant oncoproteins. Each molecule is uniquely labeled with a DNA barcode for molecular identification and sequencing decoding.

This library is an advanced and highly diverse collection, consists of 35 independent sub-libraries with a total scaleof 14 million compounds, It incorporates over 14 experimentally validated covalent warheads capable of targeting cysteine, lysine, arginine, aspartic acid and glutamic acid. This library is constructed with diverse drug like core scaffolds and integrated controllable covalent warheads, it features structural diversity, reaction spec

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.