For a long time, targeting DNA was considered only in the context of non-specific and cytotoxic agents. Almost all known to date DNA-interacting drugs pose catastrophic actions to the live cells. Several well-known, previously, and still widely used cancer drugs such as Cisplatin, Doxorubicin, and ethidium bromide are non-selective DNA binders or intercalating compounds. Within the last several years protein-DNA interaction interfaces gained much attention among drug hunters. This area is under investigation and requires intensive research to bring new molecules to the clinic. To meet the growing need for new specific DNA binders, we have created a versatile library combining different approaches and tools.

The library has been plated for most convenient and quick access. Using our DNA focused 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 4.4M 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

Library design

Different DNA structures have been carefully investigated and analyzed: (1) G-quadruplex structures; G-quadruplexes are noncanonical DNA structures that consist of stacked G-tetrads formed by guanine-rich sequences. These structures are stabilized by monovalent cations such as K+ and Na+. G-quadruplexes are commonly found in the promoter regions of oncogenes like MYC and play an important role in regulating gene expression. Understanding the binding of ligands to G-quadruplexes provides insights into potential therapeutic strategies for targeting oncogenes and modulating gene expression. (2) The double helix DNA structure is a fundamental arrangement where two strands of DNA wind around each other. The integrity of DNA double-strands is crucial for the stability and functioning of cells and organisms. DNA double-strand breaks are particularly critical events that can lead to various consequences. They are associated with the development of human syndromes, neurodegenerative diseases, immunodeficiency, and cancer.

To search for potential DNA ligands all available in PDB and in PDBe liganded DNA structures were analyzed. Then the following entries were selected for in silico screening: 5W77, 6JJ0, 7KBW, 5T4W, 6IJW, 7KWK, 5Z80, 6CCW, 6SX3, and 7EL7. The two main approaches, binding types, were used for search of potential ligands:

• Intercalation: ligands insert itself between the stacked DNA bases pairs.
• Binding insight the DNA grove: ligands binds to the DNA groove without significantly disrupting of the DNA structure.

The molecular docking simulations were conducted using the following queries: pharmacophore of H-bond acceptors and H-bond donors, aromatic group, stearic and volume exclusion features. Each pharmacophore model includes both common and specific features, making the binding points specific to each DNA target structure and its corresponding native ligand. Several examples are provided below.

Examples of molecular docking simulation to histone lysine methyltransferases

A. The minor groove (PDB ID 6IJW - left image) involves binding between QCy-DT DNA ligand and 6IJW, ligand should match with three aromatic features.

B. G-quadruplex (PDB ID 6CCW - right image) the pharmacophore model based on the presence of epiberberine intercalated within the G-quadruplex. The ligand should consist of three aromatic parts (F1, F2, and F3) that can stack between the DNA nucleobases G12, G16, A15, and T13.

DNA and its native ligand are colored in grey, docked ligands are shown in yellow.

Drug repurposing is a promising field in drug discovery that identifies new therapeutic opportunities for existing drugs (e.g. Metformin and Raloxifene). High-content screens, new biomarkers, and noninvasive imaging techniques have created new capabilities for pursuing novel indications for approved compounds. Hits from our FDA Approved Drug Collection will provide a significant head start in any drug optimization program.

• Carefully collected and distilled collection of 1 123 FDA approved drugs
• Supported with full bioactivity annotation, pathway indications and all related chemical structure information (structure, CAS, smiles, molecular parameters)
• NMR and HPLC validated to ensure the highest purity
• Supplied in 96, 384 or 1536-well plates, ready for immediate shipping
• Minimal preparation – just peel, dilute & transfer to assay plate

To date no commercially available compound collection covered all drug classes, resulting in complications in combinatorial screening attempts. We collaborated with a group of researchers at CeMM and collected a condensed screening set of 299 small molecules representing the entire target and chemical space of all FDA-approved drugs. The CeMM Library of Unique Drugs (CLOUD) covers prodrugs and active forms at pharmacologically relevant concentrations and is ideally suited for combinatorial studies. Recent publication [1] provides evidences of successful drug repurposing by pairwise compound screening from CLOUD collection in cancer cell viability assay. The findings highlight that refined chemical library CLOUD is a powerful tool for drug repurposing and evaluation of new substances suitable for all high-content and high-throughput assays.

Key features

• Covers all therapeutically significant space of approved drugs.
• Contains prodrugs and active metabolites at pharmacologically relevant concentrations.
• Ideally applicable for combinatorial assays to study new drug combinations.
• Most structurally diverse drug library among commercially available collections.
• Immediately accessible in convenient pre-plated formats with carefully prepared detailed documentation. The library can be also made in any customized ready-to-screen formats.

Examples of drugs in the library

Selection and library evolution scheme

[1] Nature Chemical Biology 13, 771–778 (2017).

Fragment screening usually provides high numbers of hits and is one of the most affordable approaches to start drug discovery. However, subsequent steps involving hit-to-lead optimization may be challenging and require significant resources. It’s even more painful when efforts result in false positives.

We have designed a new fragment library specifically addressing the quality of decision making when evaluating hits. Our High Fidelity Fragment Library features high medchem tractability enabling researchers to grow interesting hits with confidence.

High medchem tractability of this set was achieved through structure review and selection by FBDD experts at Takeda and Carmot Therapeutics. In particular, we would like to thank Dr. Derek Cole, Dr. Dan Erlanson, Dr. David Lawson and Dr. Xiaolun Wang for their involvement in the design of our High Fidelity Fragment Library.

High quality: All compounds selected for this library passed turbidity tests to assure high solubility in water at 1 mM; all aggregators were filtered out. In addition, the fragments in this set were screened by surface plasmon resonance (SPR) to remove any false positive fragments. SPR screening was kindly provided by Dr. Delphine Collin at HarkerBio.

Optimal molecular properties: Fragments in this set all have 9–16 heavy atoms, are moderately complex and have suitable physiochemical and shape profiles.

Our High Fidelity Fragment Library is available for prompt delivery in various formats. The most popular library options are listed below:

Library design

A complex iterative approach has been applied in the design of this library. Fragment selection was made from over 260k Ro3-compliant compounds in Enamine’s stock collection. All industry recommended medchem filters, including PAINS, were applied. Diversity selection was performed using clustering algorithm and manual review of identified clusters to select the most representative structure within each cluster.

All compounds were tested for solubility in water and aggregation by laser nephelometry to remove compounds with solubility issues. The resulting set of fragments was then tested in clean SPR screens to exclude SPR “sticky” compounds.

The selection process and resulting molecular parameters of our High Fidelity Fragment Set are described in the following scheme: