hydrogen bonding interactions

By Targets:	Apoptosis (1) Autophagy (1) Fat Mass and Obesity-associated Protein (FTO) (1) Fluorescent Dye (1) Fungal (2) HDAC (1) Indoleamine 2,3-Dioxygenase (IDO) (1) Keap1-Nrf2 (1) Microtubule/Tubulin (1) Mitochondrial Metabolism (1) Tyrosinase (1)
By Research Areas:	Cancer (2) Infection (2) Inflammation/Immunology (3) Metabolic Disease (1) Neurological Disease (1)

Targets Recommended: Na+/H+ Exchanger (NHE)

Cat. No.	Product Name	Target	Research Areas	Chemical Structure

HY-121930

Coumarin 6H	Fluorescent Dye	Inflammation/Immunology
Coumarin 6H, a Coumarin (Coumarin (HY-N0709)) derivative, is a laser dye. The fluorescence emission of Coumarin 6H can be enhanced by hydrogen bonding interactions .

HY-W127329

12-Hydroxystearic acid	Others	Others
12-Hydroxystearic acid is a structurally simple and cost-effective low molecular weight organogelator, and its metal salts and derivatives find roles in many important applications .

HY-151108

IDO1/TDO-IN-4	Indoleamine 2,3-Dioxygenase (IDO)	Neurological Disease Inflammation/Immunology
IDO1/TDO-IN-4 is a potent IDO1/TDO dual inhibitor, with IC₅₀ values of 3.53 μM (IDO1) and 1.15 μM (TDO). IDO1/TDO-IN-4 forms hydrogen bond with IDO1, and π−π stacking interaction with TDO. IDO1/TDO-IN-4 can be used in the research of depression, and depression-induced infectious, metabolic, and autoimmune disorders .

HY-150579

Keap1-Nrf2-IN-13	Keap1-Nrf2	Inflammation/Immunology Cancer
Keap1-Nrf2-IN-13 is a Keap1-Nrf2 protein–protein interaction (PPI) inhibitor with an IC₅₀ value of 0.15 μM. Keap1-Nrf2-IN-13 has strong binding affinities to the Keap1 protein by forming **hydrogen bond** with the key polar residues (Asn414, Arg415, Arg483, Gln530). Keap1-Nrf2-IN-13 can be used in the research of oxidative stress-related and inflammatory diseases, including pulmonary fibrosis, chronic obstructive pulmonary disorder (COPD) and cancers .

HY-N10219

Dihydroaltenuene B	Tyrosinase Fungal	Infection
Dihydroaltenuene B is a potent mushroom tyrosinase inhibitor with an IC₅₀ of 38.33 µM. Dihydroaltenuene B shows the hydrogen bonding interactions between the 3-OH and 4’-OH and the His244, Met280 and Gly281 residues of tyrosinase .

HY-W127329R

12-Hydroxystearic acid (Standard)	Others	Others
12-Hydroxystearic acid (Standard) is the analytical standard of 12-Hydroxystearic acid. This product is intended for research and analytical applications. 12-Hydroxystearic acid is a structurally simple and cost-effective low molecular weight organogelator, and its metal salts and derivatives find roles in many important applications .

HY-121125

Aucubigenin	Others	Others
Aucubigenin, the aglycone of the iridoid glycoside aucubin, has been characterized through X-ray diffraction analysis. Its crystal structure reveals monoclinic symmetry with specific conformations adopted by its cyclopentane and pyran rings. The study also determined the absolute configurations of both aucubin and aucubigenin. Significant O–H?O hydrogen bonding interactions were observed in the crystal lattices of both compounds, highlighting their structural stability and potential for intermolecular interactions .

HY-156405

FTO-IN-10	Fat Mass and Obesity-associated Protein (FTO) Autophagy	Metabolic Disease
FTO-IN-10 (compound 7) is a potent human demethylase FTO (the fat mass and obesity-associated protein) inhibitor with an IC₅₀ of 4.5 μM. FTO-IN-10 enters the FTO’s structural domain II binding pocket through hydrophobic and hydrogen bonding interactions. FTO-IN-10 induces DNA damage and autophagic cell death in A549 cells .

HY-150772

Tubulin/HDAC-IN-1	Microtubule/Tubulin HDAC Apoptosis Mitochondrial Metabolism	Cancer
Tubulin/HDAC-IN-1 is a dual tubulin and HDAC-IN-1 inhibitor through CH/π interaction with tubulin and hydrogen bond interaction with HDAC8. Tubulin/HDAC-IN-1 inhibits tubulin polymerization and selectively inhibits HDAC8 (IC₅₀: 150 nM). Tubulin/HDAC-IN-1 has cytotoxicity against various human cancer cells, also arrests cell cycle in the G2/M phase and induces cell apoptosis. Tubulin/HDAC-IN-1 can be used in the research of hematologic and solid tumors such as neuroblastoma, leukemia .

HY-146464

Antifungal agent 30	Fungal	Infection
Antifungal agent 30 (compound A18) is a potent antifungal agent. Antifungal agent 30 shows excellent antifungal activity against Candida albicans (CPCC400616) and Aspergillus fumigatus, with MIC of 0.03 and 0.5 μg/mL, respectively. Antifungal agent 30 also shows excellent antifungal activity against fluconazole-resistant strains. The potent antifungal activity of Antifungal agent 30 mainly causes by hydrogen and coordination bond interaction with the CYP51 .

HY-121690

Semotiadil SD-3211	Others	Others
Semotiadil is a novel calcium antagonist whose stereochemical structure was investigated by X-ray crystallography and circular dichroism spectroscopy. X-ray structural analysis was performed using its enantiomeric salts with (S)-(+)-mandelic acid (2); 1 (mandelate salt). The R absolute configuration of 1, which was previously determined by chemical transformation of an optically active synthetic precursor, was directly confirmed by this analysis. Hydrogen bonding, charge repulsion, and hydrophobic interactions that stabilize the crystal structure were observed in the crystals. Circular dichroism spectra of 1 (mandelate salt) and 1 (hydrofuranate salt) in ethanolic solution showed similar spectral patterns. The CD bands of each chromophore were unambiguously assigned, and the conformation of the benzothiazole ring was determined using the optical rotation rule. The X-ray and CD data confirmed the P conformation of the benzothiazole ring and the equatorial position of the 2-phenyl ring in both the crystal and ethanolic solution states. These findings are in good agreement with our previous results on the conformational analysis of 2-arylbenzothiazole derivatives.

Cat. No.	Product Name

HY-L152

F-Fragments Library	5,017 compounds
19F-NMR has proved to be a detection mode in fragment-based drug discovery (FBDD) for studies of protein structure and interactions. 19F shows high sensitivity for NMR detection, and the exquisite sensitivity of 19F chemical shifts and linewidths to ligand binding all make it a valuable approach in FBDD.F (Fluorine) -Fragments can be used for 19F-NMR detection after binding to target proteins, and can be used as an effective 19F-NMR tool for FBDD. MCE designs a unique collection of 5,017 F-fragments, all of which obey a heuristic rule called the “Rule of Three (RO3)”, in which molecular weight ≤300 Da, the number of hydrogen bond donors (H-donors) ≤3, the number of hydrogen bond acceptors (H-acceptors) is ≤3 and cLogP is ≤3. This F-fragments library is an important source of lead-like drugs.

F-Fragments Library

5,017 compounds

19F-NMR has proved to be a detection mode in fragment-based drug discovery (FBDD) for studies of protein structure and interactions. 19F shows high sensitivity for NMR detection, and the exquisite sensitivity of 19F chemical shifts and linewidths to ligand binding all make it a valuable approach in FBDD.F (Fluorine) -Fragments can be used for 19F-NMR detection after binding to target proteins, and can be used as an effective 19F-NMR tool for FBDD.

MCE designs a unique collection of 5,017 F-fragments, all of which obey a heuristic rule called the “Rule of Three (RO3)”, in which molecular weight ≤300 Da, the number of hydrogen bond donors (H-donors) ≤3, the number of hydrogen bond acceptors (H-acceptors) is ≤3 and cLogP is ≤3. This F-fragments library is an important source of lead-like drugs.

HY-L913

Tyrosine Focused Covalent Fragment Library	124 compounds
Recently, significant advancements in tyrosine-targeting electrophiles have primarily occurred in the field of protein-protein interactions (PPIs), where cysteine residues are often underrepresented and novel chemistries are needed to address these interfaces. In this context, tyrosines are frequently more accessible compared to more buried binding sites. Moreover, they are commonly found at "hot spots," which are functional epitopes of PPIs, with 12.3% of the residues consisting of tyrosines. This prevalence is likely due to the hydrophobic nature of tyrosine, its ability to participate in aromatic π-interactions, and its capacity for hydrogen bonding. Beyond PPIs, some progress has also been made in covalent tyrosine targeting in other areas where more commonly addressed side chains are lacking. Even though tyrosine has a slightly lower pKa value compared to the protonated lysine side chain (approximately 10 vs. 10.5 for the unprotected amino acid side chains), significantly less progress has been made in the development of tyrosine-targeted covalent ligands compared to lysine. This is likely due to the reduced flexibility of the tyrosine side chain and the greater steric hindrance of its hydroxy group, which makes it more challenging to adopt suitable reaction geometries. Through careful selection, we constructed a structural filter containing over 110 electrophilic groups. By analyzing the electrophilic fragments selected by the structural filter, we removed any molecules with trivial or undesirable structural features. Ultimately, we obtained 124 fragment molecules which can target tyrosine residue and can be used for fragment-based covalent drug discovery.

Tyrosine Focused Covalent Fragment Library

124 compounds

Recently, significant advancements in tyrosine-targeting electrophiles have primarily occurred in the field of protein-protein interactions (PPIs), where cysteine residues are often underrepresented and novel chemistries are needed to address these interfaces. In this context, tyrosines are frequently more accessible compared to more buried binding sites. Moreover, they are commonly found at "hot spots," which are functional epitopes of PPIs, with 12.3% of the residues consisting of tyrosines. This prevalence is likely due to the hydrophobic nature of tyrosine, its ability to participate in aromatic π-interactions, and its capacity for hydrogen bonding. Beyond PPIs, some progress has also been made in covalent tyrosine targeting in other areas where more commonly addressed side chains are lacking. Even though tyrosine has a slightly lower pKa value compared to the protonated lysine side chain (approximately 10 vs. 10.5 for the unprotected amino acid side chains), significantly less progress has been made in the development of tyrosine-targeted covalent ligands compared to lysine. This is likely due to the reduced flexibility of the tyrosine side chain and the greater steric hindrance of its hydroxy group, which makes it more challenging to adopt suitable reaction geometries.

Through careful selection, we constructed a structural filter containing over 110 electrophilic groups. By analyzing the electrophilic fragments selected by the structural filter, we removed any molecules with trivial or undesirable structural features. Ultimately, we obtained 124 fragment molecules which can target tyrosine residue and can be used for fragment-based covalent drug discovery.

HY-L045

Oxygen Sensing Compound Library	2,691 compounds
Oxygen homeostasis regulation is the most fundamental cellular process for adjusting physiological oxygen variations, and its irregularity leads to various human diseases, including cancer. Hypoxia is closely associated with cancer development, and hypoxia/oxygen-sensing signaling plays critical roles in the modulation of cancer progression. Hypoxia-inducible factor 1 (HIF-1) is a transcription factor that functions as a master regulator of oxygen homeostasis. A variety of HF-1 target genes have been identified thus far which encode proteins that play key roles in critical developmental and physiological processes including angiogenesis/vascular remodeling, erythropoiesis, glucose transport, glycolysis, iron transport, and cell proliferation/survival. HIF-1 is a heterodimeric transcription factor consisting of a constitutively expressed β-subunit and an oxygen-regulated α-subunit. The unique feature of HIF-1 is the regulation of HIF-1α expression and activity based upon the cellular O₂ concentration. Under normoxic conditions, hydroxylation of HIF-1α on these different proline residues is essential for HIF proteolytic degradation by promoting interaction with the von Hippel-Lindau tumor-suppressor protein (pVHL) through hydrogen bonding to the hydroxyproline-binding pocket in the pVHL β-domain. As oxygen levels decrease, hydroxylation of HIF decreases; HIF-1α then no longer binds pVHL, and becomes stabilized, allowing more of the protein to translocate to the cell’s nucleus, where it acts as a transcription factor, upregulating (often within minutes) the production of proteins that stimulate blood perfusion in tissues and thus tissue oxygenation. MCE offers a unique collection of 2,691 oxygen sensing related compounds targeting HIF/HIF Prolyl-Hydroxylase, MAPK/ERK, PI3K/AKT signaling pathways, etc. MCE Oxygen Sensing Compound Library is a useful tool to study hypoxia, oxidative stress and discover new anti-cancer drugs.

Oxygen Sensing Compound Library

2,691 compounds

Oxygen homeostasis regulation is the most fundamental cellular process for adjusting physiological oxygen variations, and its irregularity leads to various human diseases, including cancer. Hypoxia is closely associated with cancer development, and hypoxia/oxygen-sensing signaling plays critical roles in the modulation of cancer progression.

Hypoxia-inducible factor 1 (HIF-1) is a transcription factor that functions as a master regulator of oxygen homeostasis. A variety of HF-1 target genes have been identified thus far which encode proteins that play key roles in critical developmental and physiological processes including angiogenesis/vascular remodeling, erythropoiesis, glucose transport, glycolysis, iron transport, and cell proliferation/survival.

HIF-1 is a heterodimeric transcription factor consisting of a constitutively expressed β-subunit and an oxygen-regulated α-subunit. The unique feature of HIF-1 is the regulation of HIF-1α expression and activity based upon the cellular O₂ concentration. Under normoxic conditions, hydroxylation of HIF-1α on these different proline residues is essential for HIF proteolytic degradation by promoting interaction with the von Hippel-Lindau tumor-suppressor protein (pVHL) through hydrogen bonding to the hydroxyproline-binding pocket in the pVHL β-domain. As oxygen levels decrease, hydroxylation of HIF decreases; HIF-1α then no longer binds pVHL, and becomes stabilized, allowing more of the protein to translocate to the cell’s nucleus, where it acts as a transcription factor, upregulating (often within minutes) the production of proteins that stimulate blood perfusion in tissues and thus tissue oxygenation.

MCE offers a unique collection of 2,691 oxygen sensing related compounds targeting HIF/HIF Prolyl-Hydroxylase, MAPK/ERK, PI3K/AKT signaling pathways, etc. MCE Oxygen Sensing Compound Library is a useful tool to study hypoxia, oxidative stress and discover new anti-cancer drugs.

Cat. No.	Product Name	Type

HY-121930

Coumarin 6H	Fluorescent Dyes/Probes
Coumarin 6H, a Coumarin (Coumarin (HY-N0709)) derivative, is a laser dye. The fluorescence emission of Coumarin 6H can be enhanced by hydrogen bonding interactions .

Cat. No.	Product Name	Category	Target	Chemical Structure

HY-W127329

12-Hydroxystearic acid	Microorganisms Source classification	Others
12-Hydroxystearic acid is a structurally simple and cost-effective low molecular weight organogelator, and its metal salts and derivatives find roles in many important applications .

HY-N10219

Dihydroaltenuene B	Infection Monophenols Microorganisms Classification of Application Fields Source classification Phenols Disease Research Fields	Tyrosinase Fungal
Dihydroaltenuene B is a potent mushroom tyrosinase inhibitor with an IC₅₀ of 38.33 µM. Dihydroaltenuene B shows the hydrogen bonding interactions between the 3-OH and 4’-OH and the His244, Met280 and Gly281 residues of tyrosinase .

HY-W127329R

12-Hydroxystearic acid (Standard)	Microorganisms Source classification	Others
12-Hydroxystearic acid (Standard) is the analytical standard of 12-Hydroxystearic acid. This product is intended for research and analytical applications. 12-Hydroxystearic acid is a structurally simple and cost-effective low molecular weight organogelator, and its metal salts and derivatives find roles in many important applications .

HY-121125

Aucubigenin	Plantaginaceae Structural Classification Iridoids Terpenoids Source classification Plants Pseudolysimachion linariifolium subsp. dilatatum (Nakai & Kitag.) D. Y. Hong	Others
Aucubigenin, the aglycone of the iridoid glycoside aucubin, has been characterized through X-ray diffraction analysis. Its crystal structure reveals monoclinic symmetry with specific conformations adopted by its cyclopentane and pyran rings. The study also determined the absolute configurations of both aucubin and aucubigenin. Significant O–H?O hydrogen bonding interactions were observed in the crystal lattices of both compounds, highlighting their structural stability and potential for intermolecular interactions .

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