DNA-Encoded Library Synthesis for High-Diversity Screening
Find Innovative SolutionsGenerate Solutions
Solution Overview
Problem
Current methods for synthesizing combinatorial libraries face challenges in producing libraries of sufficient complexity and diversity while efficiently identifying active molecules, as increasing library complexity decreases the concentration of individual members, complicating deconvolution and requiring improved encoding strategies to enhance the discovery of small molecule ligands for biological targets.
Innovation Solution
The development of a compound library synthesis method using a compound of Formula II, where two functional moieties are operably linked to a double-stranded oligonucleotide, allowing for high-fidelity incorporation of oligonucleotide tags and enabling the synthesis of libraries with a large number of copies of each member, facilitating multiple rounds of selection and amplification of encoding oligonucleotides for sequencing.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Quantity of substance
If the number of distinct members within the library is increased to enhance complexity and diversity, then the probability of containing active molecules is improved, but the concentration of any particular library member decreases, complicating identification and deconvolution
Solution Approach 1:
The patent employs DNA encoding where each small molecule is paired with a unique DNA sequence that serves as a molecular barcode. This allows virtual copying of molecular information into the DNA domain, enabling high-throughput sequencing to identify compounds without requiring high concentrations of individual molecules. The DNA copy acts as an information carrier that can be amplified and detected with high sensitivity.
Solution Approach 2:
The patent introduces DNA oligonucleotide tags as an intermediary between the small molecule ligands and the detection system. These DNA tags serve as mediators that bridge the chemical space of diverse compounds with the high-sensitivity detection capabilities of molecular biology techniques, allowing identification even when individual compound concentrations are low.
2Stability of the object's composition
If double stranded DNA constructs are used to encode small molecules, then encoding stability is improved, but problems arise with polymerase reactions and sequencing fidelity, compromising identification accuracy
Solution Approach 1:
The patent employs single-stranded DNA oligonucleotides instead of stable double-stranded constructs. These single-stranded tags are sufficient for their intended function of encoding molecular information during the screening process, and can be easily synthesized and incorporated without the complications of maintaining double-stranded structure. The single-stranded nature avoids polymerase reaction problems while maintaining encoding capability.
Solution Approach 2:
The patent inverts the conventional approach by using single-stranded DNA instead of double-stranded DNA for encoding. This inversion resolves the fidelity problems associated with double-stranded constructs and polymerase reactions, while single-stranded oligonucleotides can still be efficiently synthesized and incorporated into the library members.
3Quantity of substance
If library complexity is increased to improve the probability of finding active molecules, then the diversity of compounds is enhanced, but the time required for synthesis and screening increases
Solution Approach 1:
The patent uses DNA encoding to copy molecular structural information into the nucleic acid domain. This allows parallel synthesis and screening of large numbers of compounds because the DNA tags can be amplified by PCR and detected by high-throughput sequencing, dramatically reducing the time required to analyze complex libraries compared to traditional methods.
Solution Approach 2:
The patent employs a universal DNA encoding scheme that can represent diverse chemical structures using the same four nucleotide bases. This universal language allows different compound classes to be encoded using identical methodologies, enabling standardized high-throughput processing and reducing the time required for library synthesis and analysis across different chemical spaces.
Applied Scientific Principles
This section explains which scientific principles are used to turn an abstract innovation direction into a practical engineering solution.
Function Achieved in This Case
This approach allows for the synthesis of libraries with a high ratio of chemicals to DNA sequences, improving the recognition of affinity binders during screening and enhancing the signal/noise ratio after sequencing, thereby facilitating the identification of active compounds.
Implementation Method 1
a DNA entity identifying a library member can be amplified and characterized using the techniques of molecular biology, such as the polymerase chain reaction
Data Source
Figure 1
Figure 2
Figure 3
AI summary
Methods of producing compounds and combinatorial compound libraries, the compounds and libraries produced via the methods are provided, and methods of using the libraries to identify compounds having a desired property, such as a desired biological activity and the compounds identified using these methods are provided.