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| title | chunk | source | category | tags | date_saved | instance |
|---|---|---|---|---|---|---|
| DNA-encoded chemical library | 6/6 | https://en.wikipedia.org/wiki/DNA-encoded_chemical_library | reference | science, encyclopedia | 2026-05-05T10:04:16.238098+00:00 | kb-cron |
Peptide nucleic acids (PNAs) are synthetic oligonucleotides in which the sugar-phosphate backbone of the DNA or RNA is replaced by a neutral N-(2-aminoethyl)-glycine peptide-like backbone . This allows PNAs to hybridize with complementary DNA or RNA with high affinity and specificity, maintaining their ability to be amplified via polymerase chain reaction (PCR). Unlike DNA/RNA, PNAs are able to resist degradation by nucleases and proteases . In a PNA-encoded library system, unique PNA sequences serve as molecular tags that are covalently attached to small molecules that are produced using combinatorial methods that generate large collections of related compounds. These PNA tags act as barcodes that encode the identity of the PNA allowing for downstream identification . PNA libraries are synthesized using solid-phase peptide synthesis (SPPS), allowing library assembly on resin similar to other peptide libraries. This contrasts with DNA-encoded libraries, which often require enzymatic ligation steps and can be limited by the chemical properties of DNA . The neutrality and stability of the PNA backbone means that PNA tags can tolerate conditions that might degrade DNA tags, and the strong hybridization to complementary nucleic acids which allows PNA tags to be decoded wither by direct hybridization or by conversion into DNA, which can then be amplified and analyzed ,. PNA-encoded libraries have been used in several different formats, including microarray hybridization, selection against biological targets, and PCR-based decoding following selection .
=== Barcode-free hit discovery === Böcker, Pomplun, and colleagues developed a barcode-free hit discovery , wherein the small molecules serve as their own identifiers, acting as the ‘barcodes’ themselves. Known as the Self-Encoded Library (SEL) platform, this approach combines tandem mass spectrometry with custom software called COmbinatorial Mass Encoding Decoding Tool (COMET) for automated structure annotation. By removing the need for external tags, such as the bulky DNA sequences used in traditional DNA-encoded libraries (DELs), the platform eliminates potential interference with target binding and expands the range of compatible chemical reactions. The SEL platform enables direct screening of over half a million small molecules in a single experiment. This platform allowed scientists to identify binders for nucleic acid-binding targets like flap endonuclease 1 (FEN1), a DNA-processing enzyme overexpressed in multiple cancer types that was previously inaccessible to traditional DEL screenings. Furthermore, the platform democratizes drug discovery by utilizing standard mass spectrometry facilities and straightforward synthesis techniques that are accessible to smaller academic laboratories . There are some limitations to the SEL platform. Firstly, there is low scaffold diversity within individual libraries, as the chemistry is limited to the structures compatible with the COMET software. Additionally, SEL hits cannot be amplified, so the amount of material for each potential hit must account for the sensitivity limits of the mass spectrometer. Moreover, manual analysis of the proposed candidates and their MS/MS spectra was still necessary to verify structures, which requires laborious technical analysis. To enable larger scale screenings, the software will require more advanced compound filtering and candidate ranking. Overall, this novel system has the potential to discover of inhibitors for challenging enzymatic targets with minimal synthetic effort in a cost-effective, streamlined manner, and become a widespread selection technique in both academic and industry laboratories .
== References ==
== See also == Drug discovery High-throughput screening Combinatorial chemistry DNA sequencing Phage display
== References ==