Abstract
DNA-encoded combinatorial libraries (DECLs) represent an exciting new technology for high-throughput screening, significantly increasing its capacity and cost–effectiveness. Historically, DECLs have been the domain of specialized academic groups and industry; however, there has recently been a shift toward more drug discovery academic centers and institutes adopting this technology. Key to this development has been the simplification, characterization and standardization of various DECL subprotocols, such as library design, affinity screening and data analysis of hits. This review examines the feasibility of implementing DECL screening technology as a first-time user, particularly in academia, exploring the some important considerations for this, and outlines some applications of the technology that academia could contribute to the field.
Papers of special note have been highlighted as: • of interest; •• of considerable interest
References
- 1. . Genome editing with CRISPR–Cas nucleases, base editors, transposases and prime editors. Nat. Biotechnol. 38, 824–844 (2020).
- 2. . Molecular-imaging pioneers scoop Nobel. Nature. 550(7675), 167 (2017).
- 3. . DNA-encoded chemistry: enabling the deeper sampling of chemical space. Nat. Rev. Drug Discov. 16, 131 (2017).
- 4. . Encoded combinatorial chemistry. Proc. Natl. Acad. Sci. U. S. A. 89(12), 5381–5383 (1992).
- 5. Discovery of 1-(1,3,5-triazin-2-yl)piperidine-4-carboxamides as inhibitors of soluble epoxide hydrolase. Bioorganic Med. Chem. Lett. 23(12), 3584–3588 (2013).
- 6. DNA-encoded library screening identifies benzo[b][1,4]oxazepin-4-ones as highly potent and monoselective receptor interacting protein 1 kinase inhibitors. J. Med. Chem. 59(5), 2163–2178 (2016).
- 7. Discovering drugs with DNA-encoded library technology: from concept to clinic with an inhibitor of soluble epoxide hydrolase. ChemBioChem. 18(9), 837–842 (2017). •• A powerful example of DECL technology leading to a clinical drug candidate.
- 8. . Achievements, challenges, and opportunities in DNA-encoded library research: an academic point of view. ChemBioChem. 18(9), 829–836 (2017).
- 9. . Adopting new technology: barriers and breakthroughs. Pharm. Exec. 39(5), (2019). https://www.pharmexec.com/view/adopting-new-technology-barriers-and-breakthroughs
- 10. DNA encoded libraries: a visitor's guide. 60, 268–280 (2020).
- 11. . Recent achievements and current trajectories of diversity-oriented synthesis. Curr. Opin. Chem. Biol. 56, 1–9 (2020).
- 12. . DNA-encoded library screening as core platform technology in drug discovery: its synthetic method development and applications in DEL synthesis. J. Med. Chem. 63(13), 6578–6599 (2020).
- 13. . Synthetic ligands discovered by in vitro selection. J. Am. Chem. Soc. 129(43), 13137–13143 (2007).
- 14. . DNA display II. Genetic manipulation of combinatorial chemistry libraries for small-molecule evolution. PLoS Biol. 2(7), (2004).
- 15. DNA-templated organic synthesis and selection of a library of macrocycles. Science (80-.). 305(5690), 1601–1605 (2004).
- 16. . Encoded self-assembling chemical libraries. Nat. Biotechnol. 22(5), 568–574 (2004).
- 17. A yoctoliter-scale DNA reactor for small-molecule evolution. J. Am. Chem. Soc. 131(3), 1322–1327 (2009).
- 18. Comparative evaluation of DNA-encoded chemical selections performed using DNA in single-stranded or double-stranded format. Biochem. Biophys. Res. Commun. (2020).
- 19. . Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. Adv. Drug Deliv. Rev. 23, 3–25 (1997).
- 20. . Chemical space of DNA-encoded libraries: Miniperspective. J. Med. Chem. 59(14), 6629–6644 (2016).
- 21. Chapter Four – an overview of DNA-encoded libraries: a versatile tool for drug discovery. In: Progress in Medicinal Chemistry. Witty DRCox B (Eds). Elsevier, 181–249 (2020).
- 22. Design, synthesis and selection of DNA-encoded small-molecule libraries. Nat. Chem. Biol. 5(9), 647–654 (2009).
- 23. Automated screening for small organic ligands using DNA-encoded chemical libraries. Nat. Protoc. 11(4), 764–780 (2016). •• A recent detailed protocol of how to perform an affinity screen of a DECL, with specific details to run the quantification of the sequencing data also.
- 24. . Foundations of a DNA-encoded library (DEL). In: A Handbook for DNA-Encoded Chemistry. Goodnow RA Jr (Ed.). Wiley, 99–121 (2014).
- 25. . Molecular complexity and fragment-based drug discovery: ten years on. Curr. Opin. Chem. Biol. 15(4), 489–496 (2011).
- 26. . Molecular complexity and its impact on the probability of finding leads for drug discovery. J. Chem. Inf. Comput. Sci. 41(3), 856–864 (2001).
- 27. . Properties guiding drug- and lead-likeness. Mol. Drug Prop. Chapter 17, 439–461 (2007). https://onlinelibrary.wiley.com/doi/abs/10.1002/9783527621286.ch17
- 28. . The design of leadlike combinatorial libraries. Angew. Chemie Int. Ed. 38(24), 3743–3748 (1999).
- 29. . What do you get from DNA-encoded libraries? ACS Med. Chem. Lett. 8(5), 408–410 (2018).
- 30. Discovery of a first-in-class receptor interacting protein 1 (RIP1) kinase specific clinical candidate (GSK2982772) for the treatment of inflammatory diseases. J. Med. Chem. 60(4), 1247–1261 (2017).
- 31. Novel autotaxin inhibitor for the treatment of idiopathic pulmonary fibrosis: a clinical candidate discovered using DNA-encoded chemistry. J. Med. Chem. 63(14), 7840–7856 (2020).
- 32. A DNA-encoded library of chemical compounds based on common scaffolding structures reveals the impact of ligand geometry on protein recognition. ChemMedChem. 13(13), 1303–1307 (2018).
- 33. TEAD-YAP interaction inhibitors and MDM2 binders from DNA-encoded indole-focused Ugi-peptidomimetics. Angew. Chemie Int. Ed. 59, 20338–20342 (2020).
- 34. . On the magnitude of the chelate effect for the recognition of proteins by pharmacophores scaffolded by self-assembling oligonucleotides. Chem. Biol. 13(2), 225–231 (2006).
- 35. Dual-display of small molecules enables the discovery of ligand pairs and facilitates affinity maturation. Nat. Chem. 7(3), 241–249 (2015).
- 36. Discovery of potent thrombin inhibitors from a protease-focused DNA-encoded chemical library. Proc. Natl Acad. Sci. USA 117(29), 16782–16789 (2020).
- 37. A focused DNA-encoded chemical library for the discovery of inhibitors of NAD+-dependent enzymes. J. Am. Chem. Soc. 141(13), 5169–5181 (2019).
- 38. Design and construction of a focused DNA-encoded library for multivalent chromatin reader proteins. Molecules. 25(4), 1–12 (2020).
- 39. Optimization of ligands using focused DNA-encoded libraries to develop a selective, cell-permeable CBX8 chromodomain inhibitor. ACS Chem. Biol. 15(1), 112–131 (2020).
- 40. Robustness of in vitro selection assays of DNA-encoded peptidomimetic ligands to CBX7 and CBX8. SLAS Discov. 23(5), 417–428 (2018).
- 41. Selective fragments for the CREBBP bromodomain identified from an encoded self-assembly chemical library. Chem Med Chem.
doi: 10.1002/cmdc.202000528 (2020). - 42. Selection of DNA-encoded dynamic chemical libraries for direct inhibitor discovery. Angew. Chemie – Int. Ed. 59, 14965–14972 (2020).
- 43. . Kinetic target-guided synthesis in drug discovery and chemical biology: a comprehensive facts and figures survey. Future Med. Chem. 8(4), 381–404 (2016).
- 44. . DNA barcoding a complete matrix of stereoisomeric small molecules. J. Am. Chem. Soc. 141(26), 10225–10235 (2019).
- 45. Synthesis of a bicyclic azetidine with in vivo antimalarial activity enabled by stereospecific, directed C(sp3)-H arylation. J. Am. Chem. Soc. 139(32), 11300–11306 (2017).
- 46. . Approaches to the design of combinatorial libraries. Chemom. Intell. Lab. Syst. 48(1), 1–20 (1999).
- 47. . Designing DNA encoded libraries of diverse products in a focused property space. J. Chem. Inf. Model. 59(11), 4645–4653 (2019).
- 48. New modalities for challenging targets in drug discovery. Angew. Chem. Int. Ed. Angew. Chem. 56, 10294–10323 (2016).
- 49. . Lead generation: enabling a mode-of-action centric paradigm new modalities, technologies, and partnerships in probe and lead generation: enabling a mode-of-action centric paradigm. J. Med. Chem. 60(21), 9004–9029 (2018).
- 50. Cyclic peptide design. In: Methods in Molecular Biology 2001. Goetz G (Ed.). Humana Press, Springer Nature, NY, USA, 273–284 (2019).
- 51. . Second-generation DNA-templated macrocycle libraries for the discovery of bioactive small molecules. Nat. Chem. 10(7), 704–714 (2018).
- 52. . DNA-encoded combinatorial library of macrocyclic peptoids. Bioconjug. Chem. 30(11), 2931–2938 (2019).
- 53. Functionality-independent DNA encoding of complex natural products. Angew. Chemie – Int. Ed. 58(27), 9254–9261 (2019).
- 54. . Chemistry: chemical con artists foil drug discovery. Nature 513(7519), 481–483 (2014).
- 55. Selection of small molecules that bind to and activate the insulin receptor from a DNA-encoded library of natural products. iScience 23(6), 101197 (2020).
- 56. . Solid-phase synthesis of DNA-encoded libraries: via an ‘aldehyde explosion’ strategy. Chem. Commun. 56(34), 4656–4659 (2020).
- 57. The Impact of variable selection coverage on detection of ligands from a DNA-encoded library screen. SLAS Discov. 25(5), 515–522 (2020).
- 58. Interaction-dependent PCR: identification of ligand-target pairs from libraries of ligands and libraries of targets in a single solution-phase experiment. J. Am. Chem. Soc. 132(44), 15522–15524 (2010).
- 59. . Identification of ligand-target pairs from combined libraries of small molecules and unpurified protein targets in cell lysates. J. Am. Chem. Soc. 136(8), 3264–3270 (2014).
- 60. Selection of DNA-encoded small molecule libraries against unmodified and non-immobilized protein targets. Angew. Chemie - Int. Ed. 53(38), 10056–10059 (2014).
- 61. Method for making an enriched library.
US10513700B2 (2013). - 62. . Fidelity by design: Yoctoreactor and binder trap enrichment for small-molecule DNA-encoded libraries and drug discovery. Curr. Opin. Chem. Biol. 26, 62–71 (2015).
- 63. Novel p38α MAP kinase inhibitors identified from yoctoReactor DNA-encoded small molecule library. Medchemcomm. 7(7), 1332–1339 (2016).
- 64. . Selection of smart small-molecule ligands: the proof of principle. Anal. Chem. 81(1), 490–494 (2009).
- 65. . Predicting efficiency of NECEEM-based partitioning of protein binders from nonbinders in DNA-encoded libraries. Electrophoresis. 39(23), 2991–2996 (2018).
- 66. Predicting Electrophoretic Mobility of Protein-Ligand Complexes for Ligands from DNA-Encoded Libraries of Small Molecules. Anal. Chem. 88(10), 5498–5506 (2016).
- 67. . Encoded library technologies as integrated lead finding platforms for drug discovery. Molecules 24(8), 1–22 (2019).
- 68. . DNA-encoded solid-phase synthesis: encoding language design and complex oligomer library synthesis. ACS Comb. Sci. 17(9), 518–534 (2015).
- 69. . An integrated microfluidic processor for DNA-encoded combinatorial library functional screening. ACS Comb. Sci. 19(3), 181–192 (2017).
- 70. . HvSABR: photochemical dose–response bead screening in droplets. Anal. Chem. 88(5), 2904–2911 (2016).
- 71. Investigation and identification of functional post-translational modification sites associated with drug binding and protein-protein interactions. BMC Syst. Biol. 11(Suppl. 7), (2017).
- 72. Cell-based selection expands the utility of DNA-encoded small-molecule library technology to cell surface drug targets: identification of novel antagonists of the NK3 tachykinin receptor. ACS Comb. Sci. 17(12), 722–731 (2015).
- 73. . Selecting a DNA-encoded chemical library against non-immobilized proteins using a ‘ligate-cross-link-purify’ strategy. Bioconjug. Chem. 28(9), 2293–2301 (2017).
- 74. . Polymerase-extension-based selection method for dna-encoded chemical libraries against nonimmobilized protein targets. ACS Comb. Sci. 21(5), 345–349 (2019).
- 75. . Crosslinking of DNA-linked ligands to target proteins for enrichment from DNA-encoded libraries. Medchemcomm. 7(10), 2020–2027 (2016).
- 76. Ideal-filter capillary electrophoresis (IFCE) facilitates the one-step selection of aptamers. Angew. Chemie Int. Ed. 58(9), 2739–2743 (2019).
- 77. . Empirical predictor of conditions that support ideal-filter capillary electrophoresis. Electrophoresis. 41, 1225–1229 (2020).
- 78. . A DNA-assisted immunoassay for enzyme activity: via a DNA-linked, activity-based probe. Chem. Commun. 53(68), 9474–9477 (2017). • The first example of DECL technology being used for identification of irreversible activity-based probes.
- 79. Off-DNA DNA-encoded library affinity screening. ACS Comb. Sci. 22(1), 25–34 (2020).
- 80. Activity-based DNA-encoded library screening. ACS Comb. Sci. 21(5), 425–435 (2019).
- 81. Selection of DNA-encoded libraries to protein targets within and on living cells. J. Am. Chem. Soc. 141(43), 17057–17061 (2019). •• The first example of DECL screening for intracellular targets, allowing target protein affinity to be measured in a more physiological context.
- 82. . DELs Inside Cells. Trends Pharmacol. Sci. 41(4), 225–227 (2020).
- 83. Novel nucleic acid binding small molecules discovered using DNA-encoded chemistry. Molecules. 24(10), 1–14 (2019).
- 84. Accurate whole human genome sequencing using reversible terminator chemistry. Nature. 456(7218), 53–59 (2008).
- 85. High-throughput sequencing for the identification of binding molecules from DNA-encoded chemical libraries. Bioorganic Med. Chem. Lett. 20(14), 4188–4192 (2010).
- 86. . Applications of metagenomics in microbial bioremediation of pollutants. In: Microbial Diversity in the Genomic Era Das SDash HR (Eds). Academic Press, Elsevier, London, UK, 459–477 (2019).
- 87. On-DNA hit validation methodologies for ligands identified from DNA-encoded chemical libraries. Biochem. Biophys. Res. Commun. https://doi.org/10.1016/j.bbrc.2020.04.03 (2020).
- 88. . Analysis of current DNA encoded library screening data indicates higher false negative rates for numerically larger libraries. ACS Comb. Sci. 19(4), 234–238 (2017).
- 89. Quantitative assessment of affinity selection performance by Using DNA-Encoded Chemical Libraries. ChemBioChem. 20(7), 955–962 (2019).
- 90. Exploring the lower limit of individual DNA-encoded library molecules in selection. SLAS Discov. 25(5), 523–529 (2020).
- 91. Design of an automated reagent-dispensing system for reaction screening and validation with DNA-tagged substrates. ACS Comb. Sci. 22(3), 101–108 (2020).
- 92. High fidelity Suzuki-Miyaura coupling for the synthesis of DNA encoded libraries enabled by micelle forming surfactants. Bioconjug. Chem. 31(1), 149–155 (2020).
- 93. Quantitative comparison of enrichment from DNA-encoded chemical library selections. ACS Comb. Sci. 21(2), 75–82 (2019).
- 94. . Randomness in DNA encoded library selection data can be modeled for more reliable enrichment calculation. SLAS Discov. 23(5), 405–416 (2018).
- 95. . Poisson statistics of combinatorial library sampling predict false discovery rates of screening. ACS Comb. Sci. 19(8), 524–532 (2017).
- 96. A method for estimating binding affinity from primary DEL selection data. Biochem. Biophys. Res. Commun. 533(2), 249–255 (2020).
- 97. A simple method for determining compound affinity and chemical yield from DNA-encoded library selections. Biochem. Biophys. Res. Commun. 527(1), 250–256 (2020).
- 98. . Denoising DNA encoded library screens with sparse learning. ACS Comb. Sci. 8, 410–421 (2020).
- 99. . UMI-tools: modeling sequencing errors in Unique Molecular Identifiers to improve quantification accuracy. Genome Res. 27(3), 491–499 (2017).
- 100. tagFinder: a novel tag analysis methodology that enables detection of molecules from DNA-encoded chemical libraries. SLAS Discov. 23(5), 397–404 (2018).
- 101. Machine learning on DNA-encoded libraries: a new paradigm for hit finding. 63(16), 8857–8866 (2020). • An application of machine learning the DECL to leverage their data to predict new hit scaffolds.
- 102. Application of encoded library technology (ELT) to a protein-protein interaction target: discovery of a potent class of integrin lymphocyte function-associated antigen 1 (LFA-1) antagonists. Bioorganic Med. Chem. 22(7), 2353–2365 (2014).
- 103. Structure based design of non-natural peptidic macrocyclic Mcl-1 inhibitors. ACS Med. Chem. Lett. 8(2), 239–244 (2017).
- 104. . SICLOPPS cyclic peptide libraries in drug discovery. Curr. Opin. Chem. Biol. 38, 30–35 (2017).
- 105. Plexium company website. https://plexium.com/
- 106. . Targeted protein degradation: expanding the toolbox. Nat. Rev. Drug Discov. 18(12), 949–963 (2019).
- 107. . Targeted protein degradation by PROTACs. Pharmacol. Ther. 174, 138–144 (2017).
- 108. Discovery of highly potent and efficient PROTAC degraders of androgen receptor (AR) by employing weak binding affinity VHL E3 ligase ligands. J. Med. Chem. 62(24), 11218–11231 (2019).
- 109. Abstract 981: degradation of immuno-oncology targets via proprietary PROTAC platform integrating DNA-encoded library technology and rational drug design. Cancer Res. 79(Suppl. 13), 981–981 (2019).
- 110. Affinity selection-mass spectrometry screening techniques for small molecule drug discovery. Curr. Opin. Chem. Biol. 11(5), 518–526 (2007).
- 111. Ultra-large chemical libraries for the discovery of high-affinity peptide binders. Nat. Commun. 11, 3183 (2020).