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pharmacophore model

" in MedChemExpress (MCE) Product Catalog:

By Targets:	Apoptosis (1) Bacterial (1) Btk (1) Caspase (1) EGFR (1) GABA Receptor (1) HDAC (1) IKK (1) NAMPT (1) Opioid Receptor (2) PD-1/PD-L1 (1) RAR/RXR (1)
By Research Areas:	Cancer (8) Infection (1) Inflammation/Immunology (2) Neurological Disease (3)

Inhibitors & Agonists

Screening Libraries

Peptides

Cat. No.	Product Name	Target	Research Areas	Chemical Structure

HY-100982

(E) -4-Hydroxycrotonic acid trans-4-Hydroxycrotonic acid; trans-γ-Hydroxycrotonic acid; T‐HCA	GABA Receptor	Neurological Disease
(E)-4-Hydroxycrotonic acid (T-HCA) is a high-affinity ligand for GHB binding sites, with a k_i value of 1.1 μM. The introduction of diaryl substituents into (E)-4-Hydroxycrotonic acid significantly enhances its affinity for GHB binding sites, with k_i values ranging from 0.023 to 0.075 μM. (E)-4-Hydroxycrotonic acid holds promise for optimizing GHB ligand structures and assisting in the development of effective three-dimensional pharmacophore models .

HY-P3223A

Biphalin acetate	Opioid Receptor	Neurological Disease
Biphalin acetate, a BBB-penetrable opioid peptide analog, contains two active enkephalin pharmacophores.Biphalin acetate has high affinity for opioid receptors. Biphalin acetate shows analgesic effect in acute, neuropathic, and chronic animal pain models. Biphalin acetate is also an antiviral, antiproliferative, anti-inflammatory, and neuroprotective agent .

HY-111135

IKK2-IN-3	IKK	Inflammation/Immunology Cancer
IKK2-IN-3 is an IKK2 inhibitor with an IC₅₀ value of 0.075 μM. IKK2-IN-3 can be used for the research of cancer, rheumatoid arthritis, chronic obstructive pulmonary disease (COPD) .

HY-161518

PD-1/PD-L1-IN-44	PD-1/PD-L1	Cancer
PD-1/PD-L1-IN-44 (Compound 22) selectively inhibits PD-1/PD-L1 proteins (IC₅₀=1.21 nM). PD-1/PD-L1-IN-44 inhibits tumor growth without toxicity in animal models and increases CD8 ⁺ cell infiltration .

HY-P3223

Biphalin TFA	Opioid Receptor	Neurological Disease
Biphalin TFA, a BBB-penetrable opioid peptide analog, contains two active enkephalin pharmacophores. Biphalin TFA has high affinity for opioid receptors. Biphalin TFA shows analgesic effect in acute, neuropathic, and chronic animal pain models. Biphalin TFA is also an antiviral, antiproliferative, anti-inflammatory, and neuroprotective agent .

HY-147756

Nampt-IN-7	NAMPT	Cancer
Nampt-IN-7 (compound GF8) is a potent NAMPT inhibitor, with an IC₅₀ of 7.31 μM. Nampt-IN-7 also displays cytotoxic activity against human HepG2 hepatocellular carcinoma cell line with an IC₅₀ of 24.28 μM .

HY-117093

H8-A5	HDAC	Cancer
H8-A5 is a novel human histone deacetylase 8 (HDAC8) inhibitor. A highly specific ZBG-based pharmacophore model was developed by incorporating a custom zinc-binding group (ZBG) feature. Pharmacophore-based virtual screening identified three novel HDAC8 inhibitors with low micromolar IC50 values (1.8-1.9 μM). Further studies showed that H8-A5 was more selective for HDAC8 than HDAC1/4 and exhibited antiproliferative activity in MDA-MB-231 cancer cells. Molecular docking and molecular dynamics studies showed that H8-A5 could bind to HDAC8, providing a good starting point for the development of HDAC8 inhibitors for cancer treatment.

HY-172826

Anti-MRSA agent 26	Bacterial	Infection
Anti-MRSA agent 26 is a potent anti-MRSA agent with MIC <0.015 μg/mL. Anti-MRSA agent 26 has superior activity against a broad range of Gram-positive pathogens and shows no cytotoxicity in three mammalian cell lines (Caco-2, DU-145 and MDCKII MDR1 cells) at 10 μM. Anti-MRSA agent 26 has a robust TAP pharmacophore and an excellent antibacterial activity in Staphylococcus aureus skin infection mice model .

HY-172160

HER2-IN-21	EGFR	Cancer
HER2-IN-21 (compound 657994) is a human epidermal growth factor receptor 2 (HER2) inhibitor, with an IC₅₀ of 3.85 μM .

HY-119574

GW0791	RAR/RXR	Cancer
GW0791 (Compound 3) is an RXRα agonist with an EC₅₀ of 5 nM. GW0791 can be used for cancer research .

HY-179699

Procaspase-3 activator 1	Caspase Apoptosis	Cancer
Procaspase-3 activator 1 is a potent procaspase-3 activator. Procaspase-3 activator directly activates procaspase-3 through zinc chelation, thereby inducing apoptosis and inhibiting cancer cell proliferation. Procaspase-3 activator 1 can be used for the research of non-small cell lung cancer (NSCLC) and melanoma .

HY-148584

BTK-IN-21	Btk	Inflammation/Immunology Cancer
BTK-IN-21 (Compound 12) is a BTK inhibitor with an IC₅₀ of 33 nM. BTK-IN-21 can be used for research in cancer and autoimmunity therapies .

Cat. No.	Product Name

HY-L923

Ion Channel Lead-like Compound Library	9000 compounds
Ion channels are key proteins on the cell membrane that regulate the flow of ions across membranes. They participate in nearly all physiological processes, including nerve conduction, muscle contraction, heart rhythm, and pain perception. Abnormalities in their function can lead to various serious diseases such as arrhythmia, epilepsy, hypertension, neuropathic pain, and cancer. Therefore, ion channels are highly valuable drug targets—over 15% of approved drugs target ion channels currently, demonstrating their irreplaceable therapeutic value in cardiovascular, neurological, and analgesic fields. MCE has collected a library of over 5,000 reported ion channel-related bioactive compounds targeting major sites such as Na+ channels, K+ channels, Ca2+ channels, GABA receptors, iGluRs, and others. Using AI models, these compounds are characterized through both 2D representations (molecular fingerprints, pharmacophores) and 3D representations (3D conformation) to screen for a collection of lead-like compounds highly similar to known active molecules. Additionally, an hERG channel prediction algorithm integrating XGB and ISE mapping strategy is employed to assess and exclude potential cardiotoxicity in the library.. This step significantly reduces safety risks in subsequent screenings, particularly for ion channel drug development related to cardiovascular systems (e.g., Nav1.5, Cav1.2), effectively minimizing failures due to hERG inhibition and serving as a valuable tool for ion channel drug screening.

Ion Channel Lead-like Compound Library

9000 compounds

Ion channels are key proteins on the cell membrane that regulate the flow of ions across membranes. They participate in nearly all physiological processes, including nerve conduction, muscle contraction, heart rhythm, and pain perception. Abnormalities in their function can lead to various serious diseases such as arrhythmia, epilepsy, hypertension, neuropathic pain, and cancer. Therefore, ion channels are highly valuable drug targets—over 15% of approved drugs target ion channels currently, demonstrating their irreplaceable therapeutic value in cardiovascular, neurological, and analgesic fields.

MCE has collected a library of over 5,000 reported ion channel-related bioactive compounds targeting major sites such as Na+ channels, K+ channels, Ca2+ channels, GABA receptors, iGluRs, and others. Using AI models, these compounds are characterized through both 2D representations (molecular fingerprints, pharmacophores) and 3D representations (3D conformation) to screen for a collection of lead-like compounds highly similar to known active molecules. Additionally, an hERG channel prediction algorithm integrating XGB and ISE mapping strategy is employed to assess and exclude potential cardiotoxicity in the library.. This step significantly reduces safety risks in subsequent screenings, particularly for ion channel drug development related to cardiovascular systems (e.g., Nav1.5, Cav1.2), effectively minimizing failures due to hERG inhibition and serving as a valuable tool for ion channel drug screening.

Cat. No.	Product Name	Target	Research Area

HY-P3223A

Biphalin acetate	Opioid Receptor	Neurological Disease
Biphalin acetate, a BBB-penetrable opioid peptide analog, contains two active enkephalin pharmacophores.Biphalin acetate has high affinity for opioid receptors. Biphalin acetate shows analgesic effect in acute, neuropathic, and chronic animal pain models. Biphalin acetate is also an antiviral, antiproliferative, anti-inflammatory, and neuroprotective agent .

HY-P3223

Biphalin TFA	Opioid Receptor	Neurological Disease
Biphalin TFA, a BBB-penetrable opioid peptide analog, contains two active enkephalin pharmacophores. Biphalin TFA has high affinity for opioid receptors. Biphalin TFA shows analgesic effect in acute, neuropathic, and chronic animal pain models. Biphalin TFA is also an antiviral, antiproliferative, anti-inflammatory, and neuroprotective agent .

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BODIPY 493/503 purchased from MedChemExpress. Usage Cited in: Nat Commun. 2025 Feb 1;16(1):1241. [Abstract]

MedchemExpress Validation 01

Western blot analysis of extracts from THP-1(lane 2(20μg), Jurkat (lane 3(20μg) and NIH3T3(lane 4(20μg) using FOXO1A (HY-P80132) Rabbit mAb. Proteins were transferred to a PVDF membrane and blocked with 5% non-fat milk in TBST for 2 hour at room temperature. The primary antibody (1/1000) and Loading control antibody (Beta Actin, HY-P80438, 1/10000) was used in 5% non-fat milk in TBST at 4°C overnight. Goat Anti-Mouse/Rabbit IgG-HRP Secondary Antibody (1/10000) was used for 1 hour at room temperature. Western blot analysis of extracts from THP-1(lane 2(20μg), Jurkat (lane 3(20μg) and NIH3T3(lane 4(20μg) using FOXO1A (HY-P80132) Rabbit mAb. Proteins were transferred to a PVDF membrane and blocked with 5% non-fat milk in TBST for 2 hour at room temperature. The primary antibody (1/1000) and Loading control antibody (Beta Actin, HY-P80438, 1/10000) was used in 5% non-fat milk in TBST at 4°C overnight. Goat Anti-Mouse/Rabbit IgG-HRP Secondary Antibody (1/10000) was used for 1 hour at room temperature. Western blot analysis of extracts from THP-1(lane 2(20μg), Jurkat (lane 3(20μg) and NIH3T3(lane 4(20μg) using FOXO1A (HY-P80132) Rabbit mAb. Proteins were transferred to a PVDF membrane and blocked with 5% non-fat milk in TBST for 2 hour at room temperature. The primary antibody (1/1000) and Loading control antibody (Beta Actin, HY-P80438, 1/10000) was used in 5% non-fat milk in TBST at 4°C overnight. Goat Anti-Mouse/Rabbit IgG-HRP Secondary Antibody (1/10000) was used for 1 hour at room temperature.

BODIPY 493/503 purchased from MedChemExpress. Usage Cited in: Nat Commun. 2025 Feb 1;16(1):1241. [Abstract]

MedchemExpress Validation 01

MedchemExpress Validation 03

Western blot analysis of extracts from THP-1(lane 2(20μg), Jurkat (lane 3(20μg) and NIH3T3(lane 4(20μg) using FOXO1A (HY-P80132) Rabbit mAb. Proteins were transferred

MedchemExpress Validation 04

MedchemExpress Validation

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