Allosteric Small Molecules

By Targets:	Akt (1) Antibiotic (2) Autophagy (2) Bacterial (2) Btk (1) Connective Peptide (1) DNA/RNA Synthesis (1) Endogenous Metabolite (2) FKBP (2) Fungal (2) Glucokinase (1) Hemoglobin (1) HIF/HIF Prolyl-Hydroxylase (1) Interleukin Related (1) mTOR (2) PI3K (1) Protease Activated Receptor (PAR) (1) VEGFR (1)
By Research Areas:	Cancer (7) Cardiovascular Disease (1) Infection (1) Inflammation/Immunology (2) Metabolic Disease (1) Neurological Disease (1)

Targets Recommended: Small Interfering RNA (siRNA) PhosTACs

Cat. No.	Product Name	Target	Research Areas	Chemical Structure

HY-154848

UCL-TRO-1938 3 Publications Verification	PI3K Akt	Cardiovascular Disease Neurological Disease Cancer
UCL-TRO-1938 is a potent small molecule allosteric activator of PI3Kα with an EC₅₀ value of approximately 60 μM. UCL-TRO-1938 can induce cell proliferation and has cardioprotective effects from ischaemia reperfusion injury and enhances nerve regeneration following nerve crush .

HY-123617

AZ8838	Protease Activated Receptor (PAR)	Inflammation/Immunology
AZ8838 is a potent, competitive, allosteric, orally active non-peptide small molecule antagonist of PAR2 with a pK_i of 6.4 for hPAR2 .

HY-148788

Osivelotor GBT-601; GBT-021601	Hemoglobin	Others
Osivelotor is an orally effective small molecule. Osivelotor is an allosteric regulator of deoxyhemoglobin S (HbS). Osivelotor increases the affinity of HbS to oxygen, inhibits HbS polymerization, and thus prevents erythrocyte sickling in the blood. Osivelotor can be used for research of sickle cell disease (SCD) .

HY-159644

Casdatifan AB521	HIF/HIF Prolyl-Hydroxylase VEGFR	Cancer
Casdatifan (AB521) is an orally active and selective allosteric small-molecule inhibitor of hypoxia-inducible factor 2α (HIF-2α). Casdatifan inhibits pro-tumor gene transcription by blocking the heterodimerization of HIF-2α with ARNT, and significantly suppresses tumor growth in clear cell renal cell carcinoma (ccRCC) models either as a monotherapy or in combination with agents such as Zimberelimab (HY-P99109). Casdatifan is applicable for the research of ccRCC .

HY-10219G

Rapamycin Sirolimus; AY-22989; NSC 226080	mTOR FKBP Fungal Autophagy Endogenous Metabolite Antibiotic Bacterial	Infection Cancer
Rapamycin (Sirolimus) (GMP) is Rapamycin (HY-10219) produced by using GMP guidelines. GMP small molecules works appropriately as an auxiliary reagent for cell therapy manufacture. Rapamycin (Sirolimus; AY 22989) is a potent and specific mTOR inhibitor with an IC₅₀ of 0.1 nM in HEK293 cells. Rapamycin binds to FKBP12 and specifically acts as an allosteric inhibitor of mTORC1 . Rapamycin is an autophagy activator, an immunosuppressant .

HY-10219GL

Rapamycin (GMP Like) Sirolimus (GMP Like); AY-22989 (GMP Like); NSC 226080 (GMP Like)	mTOR FKBP Fungal Autophagy Endogenous Metabolite Antibiotic Bacterial	Cancer
Rapamycin (Sirolimus) GMP Like is Rapamycin (HY-10219) produced by using GMP like guidelines. GMP Like small molecules works appropriately as an auxiliary reagent for cell therapy manufacture. Rapamycin (Sirolimus; AY 22989) is a potent and specific mTOR inhibitor with an IC₅₀ of 0.1 nM in HEK293 cells. Rapamycin binds to FKBP12 and specifically acts as an allosteric inhibitor of mTORC1 . Rapamycin is an autophagy activator, an immunosuppressant .

HY-178714

JNJ627	Interleukin Related	Inflammation/Immunology
JNJ627 is a small molecule allosteric inhibitor of IL-17A with a K_D of 92 nM. JNJ627 effectively inhibits the binding of IL-17A and IL-17RA, with an IC₅₀ value of 16 nM. JNJ627 is capable of inhibiting the secretion of G-CSF (granulocyte colony-stimulating factor) caused by IL-17A stimulation. JNJ627 can be used for the study of autoimmune diseases (such as psoriasis) .

HY-141520G

ART558	DNA/RNA Synthesis	Cancer
ART558 (GMP) is ART558 (HY-141520) produced by using GMP guidelines. GMP small molecules works appropriately as an auxiliary reagent for cell therapy manufacture. ART558 is a potent, selective and allosteric DNA polymerase theta (Polθ) inhibitor (IC₅₀=7.9 nM). ART558 elicits BRCA-gene synthetic lethality and DNA damage. ART558 can be used for the research of cancer, such as breast cancer .

HY-162081

BTK-IN-32	Btk	Cancer
BTK-IN-32 (compound C2) is a potent inhibitor of BTK. BTK-IN-32 activates full-length BTK and smaller multidomain BTK fragments instead of the isolated kinase domain .

HY-180913

FQI2-34	Connective Peptide	Cancer
FQI2-34 is an orally active TFCP2 (LSF) small molecule allosteric inhibitor. FQI2-34 directly binds to the LSF protein (K_i = 63 nM), inhibits the oligomerization of LSF, efficiently suppresses the transcriptional activity of LSF (IC₅₀ = 48 nM), and interferes with the SF-DNA interaction. FQI2-34 exhibits significant anti-proliferative activity against Huh7 cells and induces tumor regression in mouse models. FQI2-34 can be used for research on liver cancer .

HY-179419

Glucokinase activator 10	Glucokinase	Metabolic Disease
Glucokinase activator 10, a thiazole-based compound, is a liver-selective and orally active glucokinase activator with an EC₅₀ of 42 nM. Glucokinase activator 10 exhibits significant glucose lowering in acute diet-induced obese mouse oral glucose tolerance (OGTT) test. Glucokinase activator 10 can be used for the study of metabolic disorders .

Cat. No.	Product Name

HY-L170

Allosteric Modulators (AMs) Compound Library	250 compounds
An emerging drug design method is based on the secondary binding site effect, where small molecule drugs are designed to bind to secondary binding sites on target biomolecules rather than primary orthomorphic sites. Successful potential drugs (known as allosteric modulators) will be able to bind to allosteric sites and remotely alter (or modify) the conformation of the main orthosteric binding sites of biological targets. Allosteric modulators (AMs) are ligands of proteins that act through binding sites different from natural (orthosteric) ligand sites. AMs are relatively small, more lipophilic, and more rigid compounds. The binding efficacy of AMs with their targets is often slightly lower. AMs are divided into positive AMs (PAMs) and negative AMs (NAMs). AMs are ideal drug targets because they can fine-tune receptor activity while preserving the spatial and temporal signal transduction characteristics of endogenous ligands, resulting in fewer targeted side effects, improved subtype selectivity, and better promotion of biased signal transduction than normal ligands. MCE designs a unique collection of 250 small allosteric modulators. It is a good tool to be used for research on metabolize, cancer and other diseases.

Allosteric Modulators (AMs) Compound Library

250 compounds

An emerging drug design method is based on the secondary binding site effect, where small molecule drugs are designed to bind to secondary binding sites on target biomolecules rather than primary orthomorphic sites. Successful potential drugs (known as allosteric modulators) will be able to bind to allosteric sites and remotely alter (or modify) the conformation of the main orthosteric binding sites of biological targets. Allosteric modulators (AMs) are ligands of proteins that act through binding sites different from natural (orthosteric) ligand sites. AMs are relatively small, more lipophilic, and more rigid compounds. The binding efficacy of AMs with their targets is often slightly lower. AMs are divided into positive AMs (PAMs) and negative AMs (NAMs). AMs are ideal drug targets because they can fine-tune receptor activity while preserving the spatial and temporal signal transduction characteristics of endogenous ligands, resulting in fewer targeted side effects, improved subtype selectivity, and better promotion of biased signal transduction than normal ligands.

MCE designs a unique collection of 250 small allosteric modulators. It is a good tool to be used for research on metabolize, cancer and other diseases.

HY-L928

GPCR Targeted Diversity Library	7,113 compounds
G protein-coupled receptors (GPCRs) are membrane proteins in humans and one of the most important targets in drug discovery. Approximately 35% of launched drugs are targeted GPCRs, making them a crucial class of targets in drug discovery. The orthosteric site of a GPCR is its endogenous ligand’s (such as neurotransmitters or hormones) binding site. This site plays a central role in signal transduction. Small molecules binding to this site typically contain a protonatable amino group, enabling the formation of salt bridges or hydrogen bonds with acidic residues in the binding pocket. In contrast, the allosteric site does not directly initiate signaling but modulates the signal intensity of the GPCR by altering or stabilizing the conformation of the orthosteric site. Small molecules binding to the allosteric site often contain multiple aromatic rings to occupy hydrophobic pockets and achieve their functional effects. MCE has collected over 7,113 reported bioactive molecules targeting GPCRs, covering Class A, B, and C GPCRs. These small molecules were subjected to AI representation to extract 2D and 3D features. Subsequently, we do screening by AI score based on similarity to identify molecules in diversity library highly similar to the reported bioactive molecules in both 2D and 3D, with a threshold greater than 0.7. Further screening based on cLogP was applied to select molecules with good lipophilicity, which facilitates the binding of small molecules to GPCRs. This diversity library can be widely applied to the discovery of compounds targeting GPCR proteins.

GPCR Targeted Diversity Library

7,113 compounds

G protein-coupled receptors (GPCRs) are membrane proteins in humans and one of the most important targets in drug discovery. Approximately 35% of launched drugs are targeted GPCRs, making them a crucial class of targets in drug discovery.

The orthosteric site of a GPCR is its endogenous ligand’s (such as neurotransmitters or hormones) binding site. This site plays a central role in signal transduction. Small molecules binding to this site typically contain a protonatable amino group, enabling the formation of salt bridges or hydrogen bonds with acidic residues in the binding pocket. In contrast, the allosteric site does not directly initiate signaling but modulates the signal intensity of the GPCR by altering or stabilizing the conformation of the orthosteric site. Small molecules binding to the allosteric site often contain multiple aromatic rings to occupy hydrophobic pockets and achieve their functional effects.

MCE has collected over 7,113 reported bioactive molecules targeting GPCRs, covering Class A, B, and C GPCRs. These small molecules were subjected to AI representation to extract 2D and 3D features. Subsequently, we do screening by AI score based on similarity to identify molecules in diversity library highly similar to the reported bioactive molecules in both 2D and 3D, with a threshold greater than 0.7. Further screening based on cLogP was applied to select molecules with good lipophilicity, which facilitates the binding of small molecules to GPCRs. This diversity library can be widely applied to the discovery of compounds targeting GPCR proteins.

HY-L942

Allosteric Modulator Fragment Library	1802 compounds
In contrast to the high conservation of conventional orthosteric sites, allosteric sites possess structural characteristics of low conservation, high hydrophobicity, weak polarity, confined spatial geometry, and dynamic cryptic properties. There is a significant difference between their core structures and orthosteric pockets — allosteric pockets are mostly dynamic grooves formed by protein conformational changes, subunit interface clefts, or shallow depressions, rather than the rigid "keyhole" structure of orthosteric sites. With looser spatial constraints, allosteric sites have the advantages of high selectivity and low off-target risk, and have become an important direction in new drug discovery. Based on the dynamic, hydrophobic, and narrow-long spatial characteristics of allosteric pockets, MCE has performed targeted modification and screening of fragments. The screening criteria strictly conform to the requirements of allosteric binding: molecular weight is controlled at 120–280 Da (to meet the core needs of small molecules in fragment libraries and high derivatization), hydrogen bond donors (HBD ≤ 2), hydrogen bond acceptors (HBA ≤ 3), polar surface area (PSA = 30–80 Å²), rotatable bonds (≤ 2), moderate hydrophobicity (cLogP = 1–3.5), no strongly ionizable groups, and both appropriate rigidity and conformational flexibility to adapt to the dynamic changes of the pocket. Meanwhile, combined with the results of principal moment of inertia (PMI) analysis, fragments with high 3D diversity were obtained. Such fragments have good shape complementarity with allosteric pockets, ensuring that the fragments can smoothly enter the allosteric pockets and form stable binding, while providing room for subsequent optimization and derivation. This library contains 1,800 structurally diverse fragment molecules with excellent drug-like properties, suitable for allosteric drug development and the design and optimization of allosteric sites. It combines the

Allosteric Modulator Fragment Library

1802 compounds

In contrast to the high conservation of conventional orthosteric sites, allosteric sites possess structural characteristics of low conservation, high hydrophobicity, weak polarity, confined spatial geometry, and dynamic cryptic properties. There is a significant difference between their core structures and orthosteric pockets — allosteric pockets are mostly dynamic grooves formed by protein conformational changes, subunit interface clefts, or shallow depressions, rather than the rigid "keyhole" structure of orthosteric sites. With looser spatial constraints, allosteric sites have the advantages of high selectivity and low off-target risk, and have become an important direction in new drug discovery.

Based on the dynamic, hydrophobic, and narrow-long spatial characteristics of allosteric pockets, MCE has performed targeted modification and screening of fragments. The screening criteria strictly conform to the requirements of allosteric binding: molecular weight is controlled at 120–280 Da (to meet the core needs of small molecules in fragment libraries and high derivatization), hydrogen bond donors (HBD ≤ 2), hydrogen bond acceptors (HBA ≤ 3), polar surface area (PSA = 30–80 Å²), rotatable bonds (≤ 2), moderate hydrophobicity (cLogP = 1–3.5), no strongly ionizable groups, and both appropriate rigidity and conformational flexibility to adapt to the dynamic changes of the pocket. Meanwhile, combined with the results of principal moment of inertia (PMI) analysis, fragments with high 3D diversity were obtained. Such fragments have good shape complementarity with allosteric pockets, ensuring that the fragments can smoothly enter the allosteric pockets and form stable binding, while providing room for subsequent optimization and derivation.

This library contains 1,800 structurally diverse fragment molecules with excellent drug-like properties, suitable for allosteric drug development and the design and optimization of allosteric sites. It combines the

Cat. No.	Product Name	Type

HY-10219G

Rapamycin Sirolimus; AY-22989; NSC 226080	Fluorescent Dyes
Rapamycin (Sirolimus) (GMP) is Rapamycin (HY-10219) produced by using GMP guidelines. GMP small molecules works appropriately as an auxiliary reagent for cell therapy manufacture. Rapamycin (Sirolimus; AY 22989) is a potent and specific mTOR inhibitor with an IC₅₀ of 0.1 nM in HEK293 cells. Rapamycin binds to FKBP12 and specifically acts as an allosteric inhibitor of mTORC1 . Rapamycin is an autophagy activator, an immunosuppressant .

Rapamycin

Sirolimus; AY-22989; NSC 226080

Fluorescent Dyes

Rapamycin (Sirolimus) (GMP) is Rapamycin (HY-10219) produced by using GMP guidelines. GMP small molecules works appropriately as an auxiliary reagent for cell therapy manufacture. Rapamycin (Sirolimus; AY 22989) is a potent and specific mTOR inhibitor with an IC₅₀ of 0.1 nM in HEK293 cells. Rapamycin binds to FKBP12 and specifically acts as an allosteric inhibitor of mTORC1 . Rapamycin is an autophagy activator, an immunosuppressant .

HY-10219GL

Rapamycin (GMP Like) Sirolimus (GMP Like); AY-22989 (GMP Like); NSC 226080 (GMP Like)	Fluorescent Dyes
Rapamycin (Sirolimus) GMP Like is Rapamycin (HY-10219) produced by using GMP like guidelines. GMP Like small molecules works appropriately as an auxiliary reagent for cell therapy manufacture. Rapamycin (Sirolimus; AY 22989) is a potent and specific mTOR inhibitor with an IC₅₀ of 0.1 nM in HEK293 cells. Rapamycin binds to FKBP12 and specifically acts as an allosteric inhibitor of mTORC1 . Rapamycin is an autophagy activator, an immunosuppressant .

Rapamycin (GMP Like)

Sirolimus (GMP Like); AY-22989 (GMP Like); NSC 226080 (GMP Like)

Fluorescent Dyes

Rapamycin (Sirolimus) GMP Like is Rapamycin (HY-10219) produced by using GMP like guidelines. GMP Like small molecules works appropriately as an auxiliary reagent for cell therapy manufacture. Rapamycin (Sirolimus; AY 22989) is a potent and specific mTOR inhibitor with an IC₅₀ of 0.1 nM in HEK293 cells. Rapamycin binds to FKBP12 and specifically acts as an allosteric inhibitor of mTORC1 . Rapamycin is an autophagy activator, an immunosuppressant .

HY-141520G

ART558	Fluorescent Dyes
ART558 (GMP) is ART558 (HY-141520) produced by using GMP guidelines. GMP small molecules works appropriately as an auxiliary reagent for cell therapy manufacture. ART558 is a potent, selective and allosteric DNA polymerase theta (Polθ) inhibitor (IC₅₀=7.9 nM). ART558 elicits BRCA-gene synthetic lethality and DNA damage. ART558 can be used for the research of cancer, such as breast cancer .

ART558

Fluorescent Dyes

ART558 (GMP) is ART558 (HY-141520) produced by using GMP guidelines. GMP small molecules works appropriately as an auxiliary reagent for cell therapy manufacture. ART558 is a potent, selective and allosteric DNA polymerase theta (Polθ) inhibitor (IC₅₀=7.9 nM). ART558 elicits BRCA-gene synthetic lethality and DNA damage. ART558 can be used for the research of cancer, such as breast cancer .

Cat. No.	Product Name	Type

HY-10219G

Rapamycin Sirolimus; AY-22989; NSC 226080	Biochemical Assay Reagents
Rapamycin (Sirolimus) (GMP) is Rapamycin (HY-10219) produced by using GMP guidelines. GMP small molecules works appropriately as an auxiliary reagent for cell therapy manufacture. Rapamycin (Sirolimus; AY 22989) is a potent and specific mTOR inhibitor with an IC₅₀ of 0.1 nM in HEK293 cells. Rapamycin binds to FKBP12 and specifically acts as an allosteric inhibitor of mTORC1 . Rapamycin is an autophagy activator, an immunosuppressant .

Rapamycin

Sirolimus; AY-22989; NSC 226080

Biochemical Assay Reagents

Rapamycin (Sirolimus) (GMP) is Rapamycin (HY-10219) produced by using GMP guidelines. GMP small molecules works appropriately as an auxiliary reagent for cell therapy manufacture. Rapamycin (Sirolimus; AY 22989) is a potent and specific mTOR inhibitor with an IC₅₀ of 0.1 nM in HEK293 cells. Rapamycin binds to FKBP12 and specifically acts as an allosteric inhibitor of mTORC1 . Rapamycin is an autophagy activator, an immunosuppressant .

HY-10219GL

Rapamycin (GMP Like) Sirolimus (GMP Like); AY-22989 (GMP Like); NSC 226080 (GMP Like)	Biochemical Assay Reagents
Rapamycin (Sirolimus) GMP Like is Rapamycin (HY-10219) produced by using GMP like guidelines. GMP Like small molecules works appropriately as an auxiliary reagent for cell therapy manufacture. Rapamycin (Sirolimus; AY 22989) is a potent and specific mTOR inhibitor with an IC₅₀ of 0.1 nM in HEK293 cells. Rapamycin binds to FKBP12 and specifically acts as an allosteric inhibitor of mTORC1 . Rapamycin is an autophagy activator, an immunosuppressant .

Rapamycin (GMP Like)

Sirolimus (GMP Like); AY-22989 (GMP Like); NSC 226080 (GMP Like)

Biochemical Assay Reagents

Rapamycin (Sirolimus) GMP Like is Rapamycin (HY-10219) produced by using GMP like guidelines. GMP Like small molecules works appropriately as an auxiliary reagent for cell therapy manufacture. Rapamycin (Sirolimus; AY 22989) is a potent and specific mTOR inhibitor with an IC₅₀ of 0.1 nM in HEK293 cells. Rapamycin binds to FKBP12 and specifically acts as an allosteric inhibitor of mTORC1 . Rapamycin is an autophagy activator, an immunosuppressant .

HY-141520G

ART558	Biochemical Assay Reagents
ART558 (GMP) is ART558 (HY-141520) produced by using GMP guidelines. GMP small molecules works appropriately as an auxiliary reagent for cell therapy manufacture. ART558 is a potent, selective and allosteric DNA polymerase theta (Polθ) inhibitor (IC₅₀=7.9 nM). ART558 elicits BRCA-gene synthetic lethality and DNA damage. ART558 can be used for the research of cancer, such as breast cancer .

ART558

Biochemical Assay Reagents

ART558 (GMP) is ART558 (HY-141520) produced by using GMP guidelines. GMP small molecules works appropriately as an auxiliary reagent for cell therapy manufacture. ART558 is a potent, selective and allosteric DNA polymerase theta (Polθ) inhibitor (IC₅₀=7.9 nM). ART558 elicits BRCA-gene synthetic lethality and DNA damage. ART558 can be used for the research of cancer, such as breast cancer .

Targets Recommended: Small Interfering RNA (siRNA) PhosTACs

Cat. No.	Product Name	Target	Research Areas	Chemical Structure

HY-10219G

Rapamycin Sirolimus; AY-22989; NSC 226080	mTOR FKBP Fungal Autophagy Endogenous Metabolite Antibiotic Bacterial	Infection Cancer
Rapamycin (Sirolimus) (GMP) is Rapamycin (HY-10219) produced by using GMP guidelines. GMP small molecules works appropriately as an auxiliary reagent for cell therapy manufacture. Rapamycin (Sirolimus; AY 22989) is a potent and specific mTOR inhibitor with an IC₅₀ of 0.1 nM in HEK293 cells. Rapamycin binds to FKBP12 and specifically acts as an allosteric inhibitor of mTORC1 . Rapamycin is an autophagy activator, an immunosuppressant .

HY-141520G

ART558	DNA/RNA Synthesis	Cancer
ART558 (GMP) is ART558 (HY-141520) produced by using GMP guidelines. GMP small molecules works appropriately as an auxiliary reagent for cell therapy manufacture. ART558 is a potent, selective and allosteric DNA polymerase theta (Polθ) inhibitor (IC₅₀=7.9 nM). ART558 elicits BRCA-gene synthetic lethality and DNA damage. ART558 can be used for the research of cancer, such as breast cancer .

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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Screening Libraries

Fluorescent Dyes

Biochemical Assay Reagents

GMP Molecules

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