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RNA,interaction

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By Targets:	Apoptosis (2) ATP Synthase (1) c-Myc (1) DNA Alkylator/Crosslinker (1) DNA/RNA Synthesis (3) Endonuclease (1) HuR (1) IGF-1R (1) Insulin Receptor (1) TGF-beta/Smad (1)
By Research Areas:	Cancer (6) Infection (1) Inflammation/Immunology (1) Metabolic Disease (1) Neurological Disease (2)

Inhibitors & Agonists

Screening Libraries

Natural
Products

Cat. No.	Product Name	Target	Research Areas	Chemical Structure

HY-175238

KI-DX-014	ATP Synthase DNA/RNA Synthesis	Neurological Disease Cancer
KI-DX-014 is a DDX21 inhibitor with high RNA-binding inhibitory activity (IC₅₀ of 3.31 μM). KI-DX-014 targets DDX21’s intrinsically disordered C-terminal domain, inhibits DDX21-structured RNA interaction, modulates DDX21’s RNA-dependent ATPase activity, and disrupts DDX21 biomolecular condensate formation. KI-DX-014 attenuates in vitro P-TEFb release from the 7SK snRNP complex, suppresses P-TEFb-dependent RNA polymerase II CTD phosphorylation, and induces developmental defects in zebrafish embryos. KI-DX-014 acts as a chemical probe for dissecting DDX21 functions in normal physiology and disease states. KI-DX-014 can be used for cancers and neurodegenerative disorders research .

HY-124447

BTYNB	IGF-1R c-Myc Apoptosis TGF-beta/Smad	Cancer
BTYNB is a structure-specific nucleic acid binder and IGF2BP1 inhibitor (with an IC₅₀ of 5 μM against hBTYNB). BTYNB disrupts the *IGF2BP1-RNA* interaction and blocks its binding to oncogenic mRNAs such as c-Myc, MDM2, PD-L1. BTYNB completely blocks the INHBA-Smad2/3 pathway, disrupts the MYCN/IGF2BP1 loop, and thereby induces apoptosis and cell cycle arrest, effectively inhibiting the proliferation and survival of cancer cells. In addition, BTYNB acts as an immune activator and tumor microenvironment modulator, enhances T cell-mediated tumor killing, and produces significant synergistic effects with inhibitors of PD-1, BRD and BIRC5. BTYNB can be used in relevant research on various malignant tumors including ovarian cancer, neuroblastoma, leukemia and melanoma .

HY-119734

Gossypolone	DNA/RNA Synthesis	Cancer
Gossypolone is an RNA-binding protein Musashi-1 inhibitor with a K_i of 12 nM. Gossypolone disrupts the Musashi-numb RNA interaction and directly binds to the RBD1 of MSI1 protein. Gossypolone can be used for the research of cancer .

HY-139059

ERD03 1 Publications Verification	DNA Alkylator/Crosslinker	Neurological Disease
ERD03 is a potent disruptor of the EXOSC3-RNA interaction, with a K_d of 17±7 μM . ERD03 induces PCH1B-like phenotype in zebrafish embryo and can be used for neurological disorder disease research .

HY-124844

Azaphilone-9 AZA-9	HuR	Cancer
Azaphilone-9 (AZA-9) is an inhibitor of HuR-ARE RNA interaction (IC₅₀=1.2 μM) by binding RNA-binding protein Hu antigen R (HuR). The HuR-RNA interactions stabilize many oncogenic mRNAs in tumors. Thus Azaphilone-9 potentially inhibit cancer cell growth and progression .

HY-164910

AHL-Pu-2	DNA/RNA Synthesis	Metabolic Disease Inflammation/Immunology
AHL-Pu-2 is the clickable electrophilic purine. AHL-Pu-2 can be used to directly quantify protein-RNA interactions on proteins through photoaffinity competition with 4-thiouridine (4SU)-labeled RNA in cells .

HY-W240322

PSF-IN-1	Apoptosis	Cancer
PSF-IN-1 (Compound No.10-3) is a RNA-binding protein (PSF) inhibitor and can effectively inhibit the PSF-RNA interaction (IC₅₀: 2.2 pM). PSF-IN-1 can increase histone acetylation, inhibit tumor cell proliferation and induce apoptosis. PSF-IN-1 has antitumor activity .

HY-181666

Z971169476	Insulin Receptor	Cancer
Z971169476 is a sulfonamide-based protein-RNA interaction inhibitor targeting the KH34 region of insulin-like growth factor 2 mRNA binding protein 2 (IGF2BP2/IMP2) .

HY-N17251

Cusculine FAC21	Endonuclease	Infection
Cusculine (FAC21) is an oropouche virus (OROV) endonuclease inhibitor with an IC₅₀ of 1.4 μM. Cusculine strongly interacts with OROV endonuclease, possibly limiting viral RNA interaction with other proteins, intercalates into double-stranded RNA (a viral replication intermediate), and efficiently inhibits OROV viral replication in vitro. Cusculine can be used for the research of oropouche fever .

Cat. No.	Product Name

HY-L917

RNA Binding Library	5,619 compounds
RNA is crucial for the regulation of numerous cellular processes and functions. With the in-depth study of disease mechanisms, processes such as RNA expression, splicing, translation, and stability regulation have become new targets for disease intervention. RNA has provided new therapeutic modalities for metabolic diseases, genetic disorders, and cancer patients, resulting in several innovative drugs. MCE R&D team collected small molecules targeting RNA from the PDB, R-BIND, ROBIN, and internal database as the positive dataset, and non-targeting RNA small molecules from ROBIN as the negative dataset. Based on the GeminiMol pre-trained model, we encoded the molecules and calculated over 1700 molecular descriptors using Mordred as inputs for the model. Subsequently, we employed 13 deep learning models to learn from the data. All of which yielded good training results, with AUROCs greater than 0.75. Ultimately, we selected the Finetune model to screen HY-L901P, which exhibited the best classification performance, achieving an AUROC of 0.82 and a prediction accuracy of 0.76. We then applied filtering based on StaR rules (with at least two of the following properties: cLogP ≥ 1.5, Molar Refractivity ≥ 4, Relative Polar Surface Area ≤ 0.3) to obtain a library containing approximately 5,000 small molecule compounds targeting RNA. This library serves as a valuable tool for screening small molecules that interact with RNA.

RNA Binding Library

5,619 compounds

RNA is crucial for the regulation of numerous cellular processes and functions. With the in-depth study of disease mechanisms, processes such as RNA expression, splicing, translation, and stability regulation have become new targets for disease intervention. RNA has provided new therapeutic modalities for metabolic diseases, genetic disorders, and cancer patients, resulting in several innovative drugs.

MCE R&D team collected small molecules targeting RNA from the PDB, R-BIND, ROBIN, and internal database as the positive dataset, and non-targeting RNA small molecules from ROBIN as the negative dataset. Based on the GeminiMol pre-trained model, we encoded the molecules and calculated over 1700 molecular descriptors using Mordred as inputs for the model. Subsequently, we employed 13 deep learning models to learn from the data. All of which yielded good training results, with AUROCs greater than 0.75. Ultimately, we selected the Finetune model to screen HY-L901P, which exhibited the best classification performance, achieving an AUROC of 0.82 and a prediction accuracy of 0.76. We then applied filtering based on StaR rules (with at least two of the following properties: cLogP ≥ 1.5, Molar Refractivity ≥ 4, Relative Polar Surface Area ≤ 0.3) to obtain a library containing approximately 5,000 small molecule compounds targeting RNA. This library serves as a valuable tool for screening small molecules that interact with RNA.

Cat. No.	Product Name	Category	Target	Chemical Structure

HY-N17251

Cusculine FAC21	Structural Classification Alkaloids Rutaceae Acridone Alkaloids Plants Angostura paniculata Source Classification	Endonuclease
Cusculine (FAC21) is an oropouche virus (OROV) endonuclease inhibitor with an IC₅₀ of 1.4 μM. Cusculine strongly interacts with OROV endonuclease, possibly limiting viral RNA interaction with other proteins, intercalates into double-stranded RNA (a viral replication intermediate), and efficiently inhibits OROV viral replication in vitro. Cusculine can be used for the research of oropouche fever .

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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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RNA,interaction

Inhibitors & Agonists

Screening Libraries

NaturalProducts

Natural
Products