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Results for "

hydrophobic cores

" in MedChemExpress (MCE) Product Catalog:

By Targets:	Biochemical Assay Reagents (3) Endogenous Metabolite (2) Environmental Pollutants (1) Fluorescent Dye (1) HBV (3) Liposome (1) Reference Standards (1) α-synuclein (2)
By Research Areas:	Cancer (1) Infection (3) Metabolic Disease (2) Neurological Disease (2)

Inhibitors & Agonists

Screening Libraries

Fluorescent Dyes

Biochemical Assay Reagents

Peptides

Natural
Products

Cat. No.	Product Name	Target	Research Areas	Chemical Structure

HY-147255

Canocapavir ZM-H1505R	HBV	Infection
Canocapavir (ZM-H1505R) is an orally active HBV core protein-targeting antiviral agent. Canocapavir binds to the hydrophobic pocket at the dimer-dimer interface of HBV core protein (HBc), stimulating intracellular accumulation of nonfunctional HBV capsids, disrupting viral replication. Canocapavir interferes with the interaction between HBc and HBV large surface protein, resulting in diminished production of empty virionsis. Canocapavir can be used for the research of hepatitis B virus (HBV) infection .

HY-117401

5-Dodecanoylaminofluorescein	Fluorescent Dye	Others
5-Dodecanoylaminofluorescein is an amphipathic (amphoteric) fluorescent probe (Ex/Em = 485 nm/515-535 nm), which consists of a hydrophilic fluorescein core and a hydrophobic dodecanoyl group (C12 fatty acid chain) linked by an amide bond. 5-Dodecanoylaminofluorescein is mainly used as an interface-localized radical trapping/indicator probe. Dodecanoylaminofluorescein can be used for the determination of the antioxidant properties of emulsions, or can serve as a lipophilic drug model for the study of passive skin penetration when encapsulated in tyrosine-derived nanospheres .

HY-W010514

trans-Cyclohexane-1,2-diol	Endogenous Metabolite	Metabolic Disease
trans-Cyclohexane-1,2-diol (TCHD) is a transient dilator of the nuclear pore complex (NPC). By interacting with the hydrophobic core (FG nucleoporin) of the NPC, trans-Cyclohexane-1,2-diol can disrupt the NPC structure and reversibly increase the permeability of the nuclear pore, allowing macromolecules larger than 40 kDa (such as plasmid DNA) to enter the cell nucleus by passive diffusion, thereby enhancing the nuclear import efficiency of non-viral vectors. trans-Cyclohexane-1,2-diol can improve the efficiency of in vitro electrotransfection or lipid-mediated gene transfection, especially significantly increasing gene expression in differentiated airway epithelial cells .

HY-W040217

MEGA-10 N-Oxodecyl meglumine; Decanoyl N-methylglucamide	Environmental Pollutants Biochemical Assay Reagents	Others
MEGA-10 (N-Oxodecyl meglumine) is a nonionic sugar-based surfactant. MEGA-10 sequesters n-alkylbenzenes into its hydrophobic core via micelle formation as a solubilizer .

HY-P4704A

α-Synuclein (61-95) (human) TFA	α-synuclein	Neurological Disease
α-Synuclein (61-95) (human) TFA is the hydrophobic core region of α-synuclein, and induces neuronal cell death. α-Synuclein (61-95) (human) TFA can be used for research of neurodegenerative diseases, including Alzheimer’s disease (AD) and Parkinson’s disease (PD) .

HY-130908

11-Maleimidoundecanoic acid	Biochemical Assay Reagents	Cancer
11-Maleimidoundecanoic acid is a maleimide-containing hydrophobic core former. 11-Maleimidoundecanoic acid forms a hydrophobic core via maleimide-thiol coupling with cysteine residues on polypeptides, enabling stable loading and controllable release of Doxorubicin (HY-15142A). 11-Maleimidoundecanoic acid can be used for the research of breast cancer .

HY-P4704

α-Synuclein (61-95) (human)	α-synuclein	Neurological Disease
α-Synuclein (61-95) (human) is the hydrophobic core region of α-synuclein, and induces neuronal cell death. α-Synuclein (61-95) (human) can be used for research of neurodegenerative diseases, including Alzheimer’s disease (AD) and Parkinson’s disease (PD) .

HY-W440898

DSPE-PEG5000-SH	Biochemical Assay Reagents	Others
DSPE-PEG5000-SH is a polyPEG attached DSPE molecule. The lipid tails allow formation of lipid bilayer in water and can be used to solubilize hydrophobic drugs while the hydrophilic core can encapsulate therapeutic agents, such as nuclein acid (mRNA/DNA), protein or peptide.

HY-147255A

(S)-Canocapavir (S)-ZM-H1505R	HBV	Infection
(S)-Canocapavir is the isomer of Canocapavir (HY-147255A). Canocapavir (ZM-H1505R) is an orally active HBV core protein-targeting antiviral agent. Canocapavir binds to the hydrophobic pocket at the dimer-dimer interface of HBV core protein (HBc), stimulating intracellular accumulation of nonfunctional HBV capsids, disrupting viral replication. Canocapavir interferes with the interaction between HBc and HBV large surface protein, resulting in diminished production of empty virionsis. Canocapavir can be used for the research of hepatitis B virus (HBV) infection .

HY-W440901

DSPE-PEG5000-SPDP	Liposome	Others
DSPE-PEG5000-SPDP is an amphiphilic polyPEG which forms lipid bilayer in water. It can be used to encapsualte therapeutic agents. The core can encapsulate hydrophilic nutrients, such as protein/peptide and mRNA/DNA/siRNA etc. while the lipid bilayer can solubilize hydrophobic drugs, such as doxorubicin, curcumin etc. The SPDP moiety can react with thiol molecule to form a disulfide bond.

HY-173121

KR019	HBV	Infection
KR019 is a potent HBV capsid assembly modulator, exhibits potent antiviral activity in HBV-replicating cells. KR019 binds to the hydrophobic pocket at the core protein dimer-dimer interface, misdirecting capsid assembly into genome-free capsids and thereby inhibiting viral replication .

HY-W010514R

trans-Cyclohexane-1,2-diol (Standard)	Endogenous Metabolite Reference Standards	Metabolic Disease
trans-Cyclohexane-1,2-diol (Standard) is the analytical standard of trans-Cyclohexane-1,2-diol (HY-W010514). This product is intended for research and analytical applications. trans-Cyclohexane-1,2-diol (TCHD) is a transient dilator of the nuclear pore complex (NPC). By interacting with the hydrophobic core (FG nucleoporin) of the NPC, trans-Cyclohexane-1,2-diol can disrupt the NPC structure and reversibly increase the permeability of the nuclear pore, allowing macromolecules larger than 40 kDa (such as plasmid DNA) to enter the cell nucleus by passive diffusion, thereby enhancing the nuclear import efficiency of non-viral vectors. trans-Cyclohexane-1,2-diol can improve the efficiency of in vitro electrotransfection or lipid-mediated gene transfection, especially significantly increasing gene expression in differentiated airway epithelial cells .

Cat. No.	Product Name

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

HY-L941

Allosteric Modulator Lead‑like Compound Library	4315 compounds
Owing to the high conservation of orthosteric sites, conventional orthosteric drugs frequently suffer from poor subtype selectivity, off-target toxicity, and drug resistance, severely restricting their clinical application. In contrast, allosteric sites feature low conservation, high hydrophobicity, weak polarity, confined spatial geometry, and dynamic cryptic properties. These characteristics endow allosteric modulators with distinct advantages including high selectivity, functional tunability, and improved safety, making allosteric therapy a key direction in modern drug discovery. MCE has curated nearly 1,000 structurally disclosed clinical-stage allosteric modulators. By analyzing allosteric protein–ligand complex structures from the PDB database, we extracted core pharmacophores and privileged scaffolds. Adopting a rational design strategy of “scaffold derivation + allosteric physicochemical filtering”, we performed secondary screening on the derived compounds strictly following the optimal physicochemical principles for allosteric binding based on universal allosteric pocket properties: molecular weight 300–500 Da, HBD ≤ 3, HBA = 3–8, PSA = 70–120 Å², rotatable bonds ≤ 6, highly rigid scaffolds, cLogP = 1.0–3.8, and no strongly ionizable groups. The selected compounds exhibit high rigidity and shape complementarity, making them well-suited for targeting shallow, dynamic, and hydrophobic-dominated allosteric pockets. This allosteric modulator library contains 4,315 structurally diverse, lead-like compounds dedicated to allosteric drug development, allosteric site targeting, and allosteric modulator screening. It is suitable for kinases, GPCRs, and other important drug targets. All compounds are analogs of clinical-stage allosteric modulators with a similarity score > 0.6, combining excellent druggability and allosteric binding potential. It provides a highly efficient tool for early-stage allosteric drug discovery.

Allosteric Modulator Lead‑like Compound Library

4315 compounds

Owing to the high conservation of orthosteric sites, conventional orthosteric drugs frequently suffer from poor subtype selectivity, off-target toxicity, and drug resistance, severely restricting their clinical application. In contrast, allosteric sites feature low conservation, high hydrophobicity, weak polarity, confined spatial geometry, and dynamic cryptic properties. These characteristics endow allosteric modulators with distinct advantages including high selectivity, functional tunability, and improved safety, making allosteric therapy a key direction in modern drug discovery.

MCE has curated nearly 1,000 structurally disclosed clinical-stage allosteric modulators. By analyzing allosteric protein–ligand complex structures from the PDB database, we extracted core pharmacophores and privileged scaffolds. Adopting a rational design strategy of “scaffold derivation + allosteric physicochemical filtering”, we performed secondary screening on the derived compounds strictly following the optimal physicochemical principles for allosteric binding based on universal allosteric pocket properties: molecular weight 300–500 Da, HBD ≤ 3, HBA = 3–8, PSA = 70–120 Å², rotatable bonds ≤ 6, highly rigid scaffolds, cLogP = 1.0–3.8, and no strongly ionizable groups. The selected compounds exhibit high rigidity and shape complementarity, making them well-suited for targeting shallow, dynamic, and hydrophobic-dominated allosteric pockets.

This allosteric modulator library contains 4,315 structurally diverse, lead-like compounds dedicated to allosteric drug development, allosteric site targeting, and allosteric modulator screening. It is suitable for kinases, GPCRs, and other important drug targets. All compounds are analogs of clinical-stage allosteric modulators with a similarity score > 0.6, combining excellent druggability and allosteric binding potential. It provides a highly efficient tool for early-stage allosteric drug discovery.

Cat. No.	Product Name	Type

HY-117401

5-Dodecanoylaminofluorescein	Fluorescent Dyes
5-Dodecanoylaminofluorescein is an amphipathic (amphoteric) fluorescent probe (Ex/Em = 485 nm/515-535 nm), which consists of a hydrophilic fluorescein core and a hydrophobic dodecanoyl group (C12 fatty acid chain) linked by an amide bond. 5-Dodecanoylaminofluorescein is mainly used as an interface-localized radical trapping/indicator probe. Dodecanoylaminofluorescein can be used for the determination of the antioxidant properties of emulsions, or can serve as a lipophilic drug model for the study of passive skin penetration when encapsulated in tyrosine-derived nanospheres .

5-Dodecanoylaminofluorescein

Fluorescent Dyes

5-Dodecanoylaminofluorescein is an amphipathic (amphoteric) fluorescent probe (Ex/Em = 485 nm/515-535 nm), which consists of a hydrophilic fluorescein core and a hydrophobic dodecanoyl group (C12 fatty acid chain) linked by an amide bond. 5-Dodecanoylaminofluorescein is mainly used as an interface-localized radical trapping/indicator probe. Dodecanoylaminofluorescein can be used for the determination of the antioxidant properties of emulsions, or can serve as a lipophilic drug model for the study of passive skin penetration when encapsulated in tyrosine-derived nanospheres .

Cat. No.	Product Name	Type

HY-W040217

MEGA-10 N-Oxodecyl meglumine; Decanoyl N-methylglucamide	Biochemical Assay Reagents
MEGA-10 (N-Oxodecyl meglumine) is a nonionic sugar-based surfactant. MEGA-10 sequesters n-alkylbenzenes into its hydrophobic core via micelle formation as a solubilizer .

HY-W440898

DSPE-PEG5000-SH	Biochemical Assay Reagents
DSPE-PEG5000-SH is a polyPEG attached DSPE molecule. The lipid tails allow formation of lipid bilayer in water and can be used to solubilize hydrophobic drugs while the hydrophilic core can encapsulate therapeutic agents, such as nuclein acid (mRNA/DNA), protein or peptide.

HY-W440901

DSPE-PEG5000-SPDP	Biochemical Assay Reagents
DSPE-PEG5000-SPDP is an amphiphilic polyPEG which forms lipid bilayer in water. It can be used to encapsualte therapeutic agents. The core can encapsulate hydrophilic nutrients, such as protein/peptide and mRNA/DNA/siRNA etc. while the lipid bilayer can solubilize hydrophobic drugs, such as doxorubicin, curcumin etc. The SPDP moiety can react with thiol molecule to form a disulfide bond.

Cat. No.	Product Name	Target	Research Area

HY-P4704A

α-Synuclein (61-95) (human) TFA	α-synuclein	Neurological Disease
α-Synuclein (61-95) (human) TFA is the hydrophobic core region of α-synuclein, and induces neuronal cell death. α-Synuclein (61-95) (human) TFA can be used for research of neurodegenerative diseases, including Alzheimer’s disease (AD) and Parkinson’s disease (PD) .

HY-P4704

α-Synuclein (61-95) (human)	α-synuclein	Neurological Disease
α-Synuclein (61-95) (human) is the hydrophobic core region of α-synuclein, and induces neuronal cell death. α-Synuclein (61-95) (human) can be used for research of neurodegenerative diseases, including Alzheimer’s disease (AD) and Parkinson’s disease (PD) .

HY-P10567

Pip6a	Peptides	Others
Pip6a is an arginine-rich cell-penetrating peptide. Pip6a has the ability to deliver associated cargoes across the plasma and endosomal membranes and is stable to serum proteolysis. Pip6a is composed of a hydrophobic core region flanked on each side by arginine-rich domains containing β-alanine and aminohexanoyl spacers. Pip6a-conjugated morpholino phosphorodiamidate oligomer (PMO) dramatically enhanced antisense oligonucleotide (ASO) delivery into striated muscles of myotonic dystrophy (DM1) mice .

Cat. No.	Product Name	Category	Target	Chemical Structure

HY-W010514

trans-Cyclohexane-1,2-diol	Natural Products Classification of Application Fields Metabolic Disease Endogenous metabolite Disease Research Fields Source Classification	Endogenous Metabolite
trans-Cyclohexane-1,2-diol (TCHD) is a transient dilator of the nuclear pore complex (NPC). By interacting with the hydrophobic core (FG nucleoporin) of the NPC, trans-Cyclohexane-1,2-diol can disrupt the NPC structure and reversibly increase the permeability of the nuclear pore, allowing macromolecules larger than 40 kDa (such as plasmid DNA) to enter the cell nucleus by passive diffusion, thereby enhancing the nuclear import efficiency of non-viral vectors. trans-Cyclohexane-1,2-diol can improve the efficiency of in vitro electrotransfection or lipid-mediated gene transfection, especially significantly increasing gene expression in differentiated airway epithelial cells .

HY-W010514R

trans-Cyclohexane-1,2-diol (Standard)	Structural Classification Natural Products Endogenous metabolite Source Classification	Endogenous Metabolite Reference Standards
trans-Cyclohexane-1,2-diol (Standard) is the analytical standard of trans-Cyclohexane-1,2-diol (HY-W010514). This product is intended for research and analytical applications. trans-Cyclohexane-1,2-diol (TCHD) is a transient dilator of the nuclear pore complex (NPC). By interacting with the hydrophobic core (FG nucleoporin) of the NPC, trans-Cyclohexane-1,2-diol can disrupt the NPC structure and reversibly increase the permeability of the nuclear pore, allowing macromolecules larger than 40 kDa (such as plasmid DNA) to enter the cell nucleus by passive diffusion, thereby enhancing the nuclear import efficiency of non-viral vectors. trans-Cyclohexane-1,2-diol can improve the efficiency of in vitro electrotransfection or lipid-mediated gene transfection, especially significantly increasing gene expression in differentiated airway epithelial cells .

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hydrophobic cores

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