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Encoded combinatorial chemistry.

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Brenner, S, Lerner, R A·1992·Proceedings of the National Academy of Sciences

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Abstract

The diversity of chemical synthesis and the power of genetics are linked to provide a powerful, versatile method for drug screening. A process of alternating parallel combinatorial synthesis is used to encode individual members of a large library of chemicals with unique nucleotide sequences. After the chemical entity is bound to a target, the genetic tag can be amplified by replication and utilized for enrichment of the bound molecules by serial hybridization to a subset of the library. The nature of the chemical structure bound to the receptor is decoded by sequencing the nucleotide tag.

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Recent advances in DNA-encoded dynamic libraries
Shi, B., Zhou, Y., & Li, X. (2022) · RSC Chemical Biology · doi:10.1039/d2cb00007e · Cited by 28
PUNCH: An Evolutionary Algorithm for Optimizing Bit Set Selection
Ruben, A. J., Freeland, S. J., & Landweber, L. F. (2002) · Lecture notes in computer science · doi:10.1007/3-540-48017-x_14 · Cited by 27
“Though many papers have proposed the use of combinatorial constraints on the composition of a set of DNA code words [1, 2, 4, 5 , 6, 7, 8, 11, 12, 13, 21, 22, 26, 29, 30, 31], currently no method exists for finding the “best” bit set.”
Background
Quantitative PCR is a Valuable Tool to Monitor the Performance of DNA‐Encoded Chemical Library Selections
Li, Y., Zimmermann, G., Scheuermann, J., & Neri, D. (2017) · ChemBioChem · doi:10.1002/cbic.201600626 · Cited by 27
Selective Discovery of GPCR Ligands within DNA-Encoded Chemical Libraries Derived from Natural Products: A Case Study on Antagonists of Angiotensin II Type I Receptor
Liang, Q., He, J., Zhao, X., Xue, Y., Zuo, H., Ru, X., Jin, Y., Wang, J., Li, Q., & Zhao, X. (2021) · Journal of Medicinal Chemistry · doi:10.1021/acs.jmedchem.1c00123 · Cited by 27
Design and applications of modified oligonucleotides
Gallo, M. L., Montserrat, J. M., & Iribarren, A. M. (2003) · Brazilian Journal of Medical and Biological Research · doi:10.1590/s0100-879x2003000200001 · Cited by 27
“This idea has been used by Brenner and Lerner (31) to develop a versatile method named encoded”
Method
Design, synthesis and use of binary encoded synthetic chemical libraries
Baldwin, J. J. (1996) · Molecular Diversity · doi:10.1007/bf01718704 · Cited by 27
Agonist Discovery for Membrane Proteins on Live Cells by Using DNA-encoded Libraries
Huang, Y., Hou, R., Lam, F. S., Jia, Y., Zhou, Y., He, X., Li, G., Xiong, F., Cao, Y. W., Wang, D., et al. (2024) · Journal of the American Chemical Society · doi:10.1021/jacs.4c08624 · Cited by 26
Translation of the copper/bipyridine-promoted Petasis reaction to solid phase-coupled DNA for encoded library synthesis
Potowski, M., Esken, R., & Brunschweiger, A. (2020) · Bioorganic & Medicinal Chemistry · doi:10.1016/j.bmc.2020.115441 · Cited by 26
Comparative evaluation of DNA-encoded chemical selections performed using DNA in single-stranded or double-stranded format
Bassi, G., Favalli, N., Oehler, S., Martinelli, A. L., Catalano, M., Scheuermann, J., & Neri, D. (2020) · Biochemical and Biophysical Research Communications · doi:10.1016/j.bbrc.2020.04.035 · Cited by 26
Design and Development of a Technology Platform for DNA-Encoded Library Production and Affinity Selection
Castañón, J., Román, J. P., Jessop, T. C., de Blas, J., & Haro, R. (2018) · SLAS DISCOVERY · doi:10.1177/2472555217752091 · Cited by 26
Synthetic Compound Libraries Displayed on the Surface of Encoded Bacteriophage
Woiwode, T. F., Haggerty, J. E., Katz, R., Gallop, M. A., Barrett, R. W., Dower, W. J., & Cwirla, S. E. (2003) · Chemistry & Biology · doi:10.1016/j.chembiol.2003.08.005 · Cited by 26
Palladium-Mediated C–N Coupling of DNA-Conjugated (Hetero)aryl Halides with Aliphatic and (Hetero)aromatic Amines
Chheda, P. R., Simmons, N., Schuman, D. P., & Shi, Z. (2022) · Organic Letters · doi:10.1021/acs.orglett.2c01175 · Cited by 25
Control of the antitumour activity and specificity of CAR T cells via organic adapters covalently tethering the CAR to tumour cells
Stepanov, A. V., Xie, J., Zhu, Q., Shen, Z., Su, W., Kuai, L., Söll, R., Rader, C. M., Shaver, G., Douthit, L., et al. (2023) · Nature Biomedical Engineering · doi:10.1038/s41551-023-01102-5 · Cited by 26
“We synthesized bifunctional adapter molecules that linked the selected cancer-targeting compounds obtained from DNA-encoded libraries (DELs) 39 to the 1,3-diketone hapten and used 38C2 as universal CAR.”
Self-citation
Libraries of 2,3,4,6,7,11b-Hexahydro-1H-pyrido[2,1-a]isoquinolin-2-amine Derivatives via a Multicomponent Assembly Process/1,3-Dipolar Cycloaddition Strategy
Granger, B. A., Kaneda, K., & Martin, S. F. (2011) · ACS Combinatorial Science · doi:10.1021/co2001636 · Cited by 25
Techniques for Molecular Imaging Probe Design
Reynolds, F., & Kelly, K. A. (2011) · Molecular Imaging · doi:10.2310/7290.2011.00003 · Cited by 24
Universal strategies for the DNA-encoding of libraries of small molecules using the chemical ligation of oligonucleotide tags
Litovchick, A., Clark, M., & Keefe, A. D. (2014) · Artificial DNA PNA & XNA · doi:10.4161/adna.27896 · Cited by 25
“This ligation is efficient as indicated in Figure 2B with conversions exceeding 90% and the conjugate of (1) and (4) was synthesized with a yield exceeding 80% and an observed deconvoluted MW of 15,819 Da (calculated MW 15,813 Da).”
BackgroundMethodInfluential
Use of a cell-based, lawn format assay to rapidly screen a 442,368 bead-based peptide library
Jayawickreme, C. K., Sauls, H. R., Bolio, N., Ruan, J., Moyer, M. B., Burkhart, W., Marron, B. E., Rimele, T. J., & Shaffer, J. (1999) · Journal of Pharmacological and Toxicological Methods · doi:10.1016/s1056-8719(00)00083-6 · Cited by 25
Binary Encoding of Compound Libraries
Eckes, P. (1994) · Angewandte Chemie International Edition in English · doi:10.1002/anie.199415731 · Cited by 25
The Art of DNA Strings: Sixteen Years of DNA Coding TheoryPreprint
Limbachiya, D., Rao, B., & Gupta, M. K. (2016) · arXiv (Cornell University) · doi:10.48550/arxiv.1607.00266 · Cited by 42
“IONS OF DNA CODES DNA codes are used in various technologies like DNA computing [1], surface based DNA computation [90]–[93], DNA Microarray technology [94], Molecular barcodes for chemical libraries [95], DNA nanostructures [96], [97], DNA origami Page 10 of 19 [10], data encrytption [98], [99] [100]–[102], data stor…”
Method
Highly Parallel Translation of DNA Sequences into Small Molecules
Weisinger, R. M., Wrenn, S. J., & Harbury, P. B. (2012) · PLoS ONE · doi:10.1371/journal.pone.0028056 · Cited by 24
“Tagging small molecules with DNA, as suggested by Lerner and Brenner in 1992, [22] allows complex chemical mixtures to be subjected to selection in bulk for binding to a target.”
Background
A Strategy for the Synthesis of Sulfonamides on DNA
Liu, W., Deng, W., Sun, S., Yu, C., Su, X., Wu, A., Yuan, Y., Ma, Z., Li, K., Yang, H., et al. (2019) · Organic Letters · doi:10.1021/acs.orglett.9b03843 · Cited by 24
Identification of isoform/domain-selective fragments from the selection of DNA-encoded dynamic library
Zhou, Y., Shen, W., Peng, J., Deng, Y., & Li, X. (2021) · Bioorganic & Medicinal Chemistry · doi:10.1016/j.bmc.2021.116328 · Cited by 24
Metal‐Free and Open‐Air Arylation Reactions of Diaryliodonium Salts for DNA‐Encoded Library Synthesis
Xu, H., Tan, T., Zhang, Y., Wang, Y., Pan, K., Yao, Y., Zhang, S., Gu, Y., Chen, W., Li, J., et al. (2022) · Advanced Science · doi:10.1002/advs.202202790 · Cited by 24
Microelectronic Morphogenesis: Smart Materials with Electronics Assembling into Artificial Organisms
McCaskill, J. S., Karnaushenko, D., Zhu, M., & Schmidt, O. G. (2023) · Advanced Materials · doi:10.1002/adma.202306344 · Cited by 24

Authors: Brenner, S., & Lerner, R. A.
Affiliations: Scripps Research Institute (US)
ORCID: Lerner, R A
Venue: Proceedings of the National Academy of Sciences
Publisher: National Academy of Sciences
Published: 1992-06-15
Volume: 89
Issue: 12
Pages: 5381-5383
ISSN: 0027-8424 (ISSN-L)
1091-6490
DOI: 10.1073/pnas.89.12.5381
PMC: PMC49295
OpenAlex: W2017423606
Cited by: 1,014
References: 9
Citations by year: 2026: 60 · 2025: 77 · 2024: 71 · 2023: 73 · 2022: 87 · 2021: 72 · 2020: 52 · 2019: 55 · 2018: 30 · 2017: 32 · 2016: 25 · 2015: 24 · 2014: 13 · 2013: 9 · 2012: 8
FWCI: 8.46
Type: journal article
Language: en
Open access: green
europepmc.org
Locations: Proceedings of the National Academy of Sciences (publishedVersion)
Europe PMC (PubMed Central) (publishedVersion)
PubMed Central (publishedVersion)
PubMed (publishedVersion)
Topics: Physical Sciences › Chemistry › Organic Chemistry › Chemical Synthesis and Analysis
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › DNA and Nucleic Acid Chemistry
Physical Sciences › Chemistry › Organic Chemistry › Click Chemistry and Applications
Keywords: drug screening, gene tagging, ligand-receptor binding
MeSH terms: Amino Acid Sequence, Base Sequence, Molecular Sequence Data, Peptides, Restriction Mapping, Drug Design, Polymerase Chain Reaction, Databases, Factual

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