molecular recognition

By Targets:	Biochemical Assay Reagents (1) Drug Derivative (2) Drug Intermediate (1) Liposome (4) PKC (1) STING (1) TNF Receptor (1)
By Research Areas:	Cancer (4) Neurological Disease (4)

Targets Recommended: Molecular Glues

Cat. No.	Product Name	Target	Research Areas	Chemical Structure

HY-W014081

Ethyl 3-coumarincarboxylate Ethyl 2-oxo-2H-chromene-3-carboxylate	Drug Derivative	Others
Ethyl 3-coumarincarboxylate is a coumarin derivative. Ethyl 3-coumarincarboxylate can be used as a pseudo-template to give a molecularly imprinted polymer (MIP) that has a fairly specific recognition capability for aflatoxins .

HY-75102

4-Boronobenzoic acid	Biochemical Assay Reagents	Cancer
4-Boronobenzoic acid is an organic compound. 4-Boronobenzoic acid forms reversible cyclic boronate esters with molecules containing cis-vicinal diol structures (such as sialic acid) through the boron atom, achieving molecular recognition and binding. 4-Boronobenzoic acid can be used in research of breast cancer .

HY-P2612A

WP9QY TFA	TNF Receptor	Others Cancer
WP9QY, TNF-a Antagonist, TNF-a Antagonist is a biological active peptide. (This cyclic peptide is designed to mimic the most critical tumor necrosis factor (TNF) recognition loop on TNF receptor I. It prevents interactions of TNF with its receptor. This TNF antagonist is a useful template for the development of small molecular inhibitors to prevent both inflammatory bone destruction and systemic bone loss in rheumatoid arthritis.)

HY-172533

3′,5′-DiOA-dC	STING	Cancer
3’,5’-DiOA-dC is a hydrophobic nucleotide lipid and a ligand for the STING agonist c-di-GMP (CDG). 3’,5’-DiOA-dC can assemble with CDG and form stable cyclic dinucleotide nanoparticles via various supramolecular forces driven by molecular recognition. 3’,5’-DiOA-dC can decrease tumor weight and volume, increase CD8 T cell, neutrophils as well as NK cell counts in tumor microenvironment in combination with CDG. 3’,5’-DiOA-dC also increases the levels of TNF-α and IFN-γ in murine melanoma model .

HY-D2954

BC-PEG-NH2 CLIP-PEG-NH2	Drug Intermediate	Others
BC-PEG-NH2 (CLIP-PEG-NH2) is a chemical building block specifically designed for the CLIP-tag system, featuring enhanced water solubility and reactivity. BC-PEG-NH2 can be used for the synthesis of super-resolution imaging probes .

HY-W114420

3-Methyl-L-tyrosine	PKC Drug Derivative	Cancer
3-Methyl-L-tyrosine is a derivative of L-Tyrosine (HY-N0473). Structurally, 3-Methyl-L-tyrosine features a methyl modification at the third position of the aromatic ring of L-Tyrosine. As a substrate for the protein tyrosine kinase Csk, 3-Methyl-L-tyrosine's relative catalytic efficiency (kcat/Km) is 38% of L-Tyrosine, indicating that the methyl modification impacts the processing efficiency of Gsk significantly. 3-Methyl-L-tyrosine helps to deepen the understanding of Gsk's molecular recognition mechanisms of its substrates, which is crucial for developing specific inhibitors targeting Gsk .

HY-182096C

DSPE-PEG5000-MG1	Liposome	Neurological Disease
DSPE-PEG5000-MG1 is a PEG compound which composed of DSPE and a MG1 peptide (HY-P11315). MG1 peptide is a M1 Microglia-targeting peptide. MG1 peptide can conjugate to anoparticles, crossing the BBB to precisely M1 microglia recognition and achieving controlled release and specific accumulation of drugs through intelligent molecular switching. DSPE-PEG5000-KTP can be used for drug delivery .

HY-182096A

DSPE-PEG2000-MG1	Liposome	Neurological Disease
DSPE-PEG2000-MG1 is a PEG compound which composed of DSPE and a MG1 peptide (HY-P11315). MG1 peptide is a M1 Microglia-targeting peptide. MG1 peptide can conjugate to anoparticles, crossing the BBB to precisely M1 microglia recognition and achieving controlled release and specific accumulation of drugs through intelligent molecular switching. DSPE-PEG2000-KTP can be used for drug delivery .

HY-182096B

DSPE-PEG3400-MG1	Liposome	Neurological Disease
DSPE-PEG3400-MG1 is a PEG compound which composed of DSPE and a MG1 peptide (HY-P11315). MG1 peptide is a M1 Microglia-targeting peptide. MG1 peptide can conjugate to anoparticles, crossing the BBB to precisely M1 microglia recognition and achieving controlled release and specific accumulation of drugs through intelligent molecular switching. DSPE-PEG3400-KTP can be used for drug delivery .

HY-182096

DSPE-PEG1000-MG1	Liposome	Neurological Disease
DSPE-PEG1000-MG1 is a PEG compound which composed of DSPE and a MG1 peptide (HY-P11315). MG1 peptide is a M1 Microglia-targeting peptide. MG1 peptide can conjugate to anoparticles, crossing the BBB to precisely M1 microglia recognition and achieving controlled release and specific accumulation of drugs through intelligent molecular switching. DSPE-PEG1000-KTP can be used for drug delivery .

Cat. No.	Product Name

HY-L934

CRBN Ligand Library	125 compounds
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 125 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.

CRBN Ligand Library

125 compounds

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 125 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.

HY-L237

Pattern Recognition Receptors Library	313 compounds
Pattern Recognition Receptors (PRRs) are a crucial class of protein molecules expressed in cells of the innate immune system. The core function of Pattern Recognition Receptors is to recognize Pathogen-Associated Molecular Patterns (PAMPs) and Damage-Associated Molecular Patterns (DAMPs). Upon recognizing and binding to PAMPs or DAMPs, PRRs rapidly initiate intracellular signaling pathways (such as the NF-κB, IRF, and inflammasome pathways). This triggers the production of inflammatory factors, chemokines, and type I interferons, thereby initiating inflammatory responses to eliminate pathogens or repair damage. PRRs represent the body's first line of defense against infection, and the rapidity and broad specificity of their response are crucial for host survival. However, aberrant activation of PRR signaling is also a cause of many chronic inflammatory diseases, autoimmune disorders, and neurodegenerative diseases. Therefore, precisely regulating PRR activity has become a key therapeutic strategy for these conditions. MCE has cataloged 313 inhibitors targeting key PRRs, such as NLRs, TLRs, C-type Lectin Receptors (CLRs), and cGAS, to support drug discovery efforts for chronic inflammatory diseases.

Pattern Recognition Receptors Library

313 compounds

Pattern Recognition Receptors (PRRs) are a crucial class of protein molecules expressed in cells of the innate immune system. The core function of Pattern Recognition Receptors is to recognize Pathogen-Associated Molecular Patterns (PAMPs) and Damage-Associated Molecular Patterns (DAMPs). Upon recognizing and binding to PAMPs or DAMPs, PRRs rapidly initiate intracellular signaling pathways (such as the NF-κB, IRF, and inflammasome pathways). This triggers the production of inflammatory factors, chemokines, and type I interferons, thereby initiating inflammatory responses to eliminate pathogens or repair damage. PRRs represent the body's first line of defense against infection, and the rapidity and broad specificity of their response are crucial for host survival. However, aberrant activation of PRR signaling is also a cause of many chronic inflammatory diseases, autoimmune disorders, and neurodegenerative diseases. Therefore, precisely regulating PRR activity has become a key therapeutic strategy for these conditions.

MCE has cataloged 313 inhibitors targeting key PRRs, such as NLRs, TLRs, C-type Lectin Receptors (CLRs), and cGAS, to support drug discovery efforts for chronic inflammatory diseases.

HY-L903

3D Diverse Fragment Library	5,278 compounds
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.

3D Diverse Fragment Library

5,278 compounds

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.

HY-L033

Peptidomimetic Library	370 compounds
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.

Peptidomimetic Library

370 compounds

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.

HY-L906

Norepinephrine Transporter (NET) Compound Library	647 compounds
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.

Norepinephrine Transporter (NET) Compound Library

647 compounds

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.

Cat. No.	Product Name	Type

HY-D2954

BC-PEG-NH2 CLIP-PEG-NH2	Fluorescent Dye
BC-PEG-NH2 (CLIP-PEG-NH2) is a chemical building block specifically designed for the CLIP-tag system, featuring enhanced water solubility and reactivity. BC-PEG-NH2 can be used for the synthesis of super-resolution imaging probes .

Cat. No.	Product Name	Type

HY-75102

4-Boronobenzoic acid	Biochemical Assay Reagents
4-Boronobenzoic acid is an organic compound. 4-Boronobenzoic acid forms reversible cyclic boronate esters with molecules containing cis-vicinal diol structures (such as sialic acid) through the boron atom, achieving molecular recognition and binding. 4-Boronobenzoic acid can be used in research of breast cancer .

HY-182096C

DSPE-PEG5000-MG1	Biochemical Assay Reagents
DSPE-PEG5000-MG1 is a PEG compound which composed of DSPE and a MG1 peptide (HY-P11315). MG1 peptide is a M1 Microglia-targeting peptide. MG1 peptide can conjugate to anoparticles, crossing the BBB to precisely M1 microglia recognition and achieving controlled release and specific accumulation of drugs through intelligent molecular switching. DSPE-PEG5000-KTP can be used for drug delivery .

HY-182096A

DSPE-PEG2000-MG1	Biochemical Assay Reagents
DSPE-PEG2000-MG1 is a PEG compound which composed of DSPE and a MG1 peptide (HY-P11315). MG1 peptide is a M1 Microglia-targeting peptide. MG1 peptide can conjugate to anoparticles, crossing the BBB to precisely M1 microglia recognition and achieving controlled release and specific accumulation of drugs through intelligent molecular switching. DSPE-PEG2000-KTP can be used for drug delivery .

HY-182096B

DSPE-PEG3400-MG1	Biochemical Assay Reagents
DSPE-PEG3400-MG1 is a PEG compound which composed of DSPE and a MG1 peptide (HY-P11315). MG1 peptide is a M1 Microglia-targeting peptide. MG1 peptide can conjugate to anoparticles, crossing the BBB to precisely M1 microglia recognition and achieving controlled release and specific accumulation of drugs through intelligent molecular switching. DSPE-PEG3400-KTP can be used for drug delivery .

HY-182096

DSPE-PEG1000-MG1	Biochemical Assay Reagents
DSPE-PEG1000-MG1 is a PEG compound which composed of DSPE and a MG1 peptide (HY-P11315). MG1 peptide is a M1 Microglia-targeting peptide. MG1 peptide can conjugate to anoparticles, crossing the BBB to precisely M1 microglia recognition and achieving controlled release and specific accumulation of drugs through intelligent molecular switching. DSPE-PEG1000-KTP can be used for drug delivery .

Cat. No.	Product Name	Target	Research Area

HY-P2612A

WP9QY TFA	TNF Receptor	Others Cancer
WP9QY, TNF-a Antagonist, TNF-a Antagonist is a biological active peptide. (This cyclic peptide is designed to mimic the most critical tumor necrosis factor (TNF) recognition loop on TNF receptor I. It prevents interactions of TNF with its receptor. This TNF antagonist is a useful template for the development of small molecular inhibitors to prevent both inflammatory bone destruction and systemic bone loss in rheumatoid arthritis.)

MCE Japan Authorized Agent ナミキ商事株式会社コスモ・バイオ株式会社重松貿易株式会社
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