RNA Library
Library of compounds capable of binding to RNA
8 960 compounds
The recent substantial progress in RNA biology underscores the importance of RNA in normal and aberrant cellular functions. RNA is essential for transcriptional regulation, translational regulation, protein function, and catalysis, responsibilities that have classically been reserved for proteins. It also highlights the potential of targeting RNA for treatment of a multitude of diseases including bacterial, viral infection and cancer.
We combined different in silico approaches to design optimum compound library focused to target RNA. The library has been plated for most convenient and quick access. Using our RNA targeted library you receive multiple benefits, allowing you to save on time and costs in hit expansion and optimization:
- Analogs and hit samples resupply from dry stock of over 2.6 M compounds.
- Straightforward & low-cost synthesis of follow-up libraries through our REAL Database technology
- Medicinal chemistry support enhanced with on-site broad ADME/T panel
Most popular library formats available for immediate supply
Catalog No.
RNA-8960-Z-0
Compounds
8 960 7 plates
Amount
Up to 300 nL of 2 mM DMSO solutions
Format
1536-well microplates, Cat. No LP-0400, 1280 compounds per plate, 1-4 and 44-48 columns empty
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Catalog No.
RNA-8960-Y-10
Compounds
8 960 28 plates
Amount
10 µL of 10 mM DMSO stock solutions
Format
384-well plates Greiner Cat. No 781280, 320 compounds per plate, first two and last two columns empty
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Catalog No.
RNA-8960-X-50
Compounds
8 960 112 plates
Amount
50 µL of 10 mM DMSO solutions
Format
96-well plates, Greiner Cat. No 650201, round (U) bottom, 80 compounds per plate, 1 & 12 columns empty
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Please request for any other options through our contact form. We will be happy to deliver our library in any convenient for your project formats.
Library Design
RNAs can form well-defined secondary structures, such as double helices, hairpins, bulges, internal loop, stems, which offer structural basis for designing therapeutic agents. These structural features have been taken into account in the design of our RNA Targeted Library. We focused on compounds which bind to RNA, forming interactions with different types of secondary structures.
Examples of the molecules
Reference Set of active compounds has been collected from public sources/databases (ChEMBL, PubChem, Drugs.com and other), then filtered to remove non selective binders and compounds with reactive moieties. Similarity search (chemical fingerprints) was carried out against MedChem filtered Enamine in-stock collection, 2.6 M compounds, to yield subset of 400 molecule.
Pharmacophore search and Shape similarity search were used to enrich the library with new structures that can form same types of interaction as known ligand. Three 3D pharmacophore models were used for in silico screening based on the structure of most known binders. Additionally, substructure search was applied to find molecules bearing common structural moieties and cores known to be important for interaction with RNA (Inforna database was used for substructure selection).
Molecular modeling and Docking
Additionally, we analyzed all recorded in PDB RNA-ligand complexes. Four structures, which represent the most common types RNA-ligand interactions, have been selected for molecular docking and query generations – 1lvj, 1q8n, 4lvy, 6fz0 pdb entries. All query models were validated with the small sets of known active and non active ligands and subsequently corrected.
Example of molecular docking result (6fz0), native ligand is colored in grey, docked hit compounds (Z1723434664) is in yellow.
Example of molecular docking using 1qn8 pdb entry, docked ligand, identified as a hit compounds colored with yellow (Z1135145616).
The library comprises only drug-like compounds and provides an excellent basis for posttranscriptional gene regulation researches, antiviral and antibacterial drug discovery projects.