Expansion of DNA-Encoded Library Hits Using Generative Chemistry and Ultra-Large Compound Catalogs.
| Title: | Expansion of DNA-Encoded Library Hits Using Generative Chemistry and Ultra-Large Compound Catalogs. |
|---|---|
| Authors: | Novy B; UNC Eshelman School of Pharmacy, Center for Integrative Chemical Biology and Drug Discovery, Chemical Biology and Medicinal Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.; Lin SH; UNC Eshelman School of Pharmacy, Center for Integrative Chemical Biology and Drug Discovery, Chemical Biology and Medicinal Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.; Shell DJ; UNC Eshelman School of Pharmacy, Center for Integrative Chemical Biology and Drug Discovery, Chemical Biology and Medicinal Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.; Maxfield T; UNC Eshelman School of Pharmacy, Center for Integrative Chemical Biology and Drug Discovery, Chemical Biology and Medicinal Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.; Merten EM; UNC Eshelman School of Pharmacy, Center for Integrative Chemical Biology and Drug Discovery, Chemical Biology and Medicinal Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.; Wellnitz J; UNC Eshelman School of Pharmacy, Center for Integrative Chemical Biology and Drug Discovery, Chemical Biology and Medicinal Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.; Guduru SKR; UNC Eshelman School of Pharmacy, Center for Integrative Chemical Biology and Drug Discovery, Chemical Biology and Medicinal Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.; Hardy PB; UNC Eshelman School of Pharmacy, Center for Integrative Chemical Biology and Drug Discovery, Chemical Biology and Medicinal Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.; Pearce KH; UNC Eshelman School of Pharmacy, Center for Integrative Chemical Biology and Drug Discovery, Chemical Biology and Medicinal Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.; Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.; Popov KI; UNC Eshelman School of Pharmacy, Center for Integrative Chemical Biology and Drug Discovery, Chemical Biology and Medicinal Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA. |
| Source: | BioRxiv : the preprint server for biology [bioRxiv] 2025 Oct 02. Date of Electronic Publication: 2025 Oct 02. |
| Publication Type: | Journal Article; Preprint |
| Language: | English |
| Journal Info: | Country of Publication: United States NLM ID: 101680187 Publication Model: Electronic Cited Medium: Internet ISSN: 2692-8205 (Electronic) Linking ISSN: 26928205 NLM ISO Abbreviation: bioRxiv Subsets: PubMed not MEDLINE |
| Abstract: | DNA-encoded libraries (DELs) are powerful tools for initial hit identification, yet the combinatorial chemistries and building block choices used in their construction can restrict chemical space coverage and hit drug-likeness, limiting efficient hit expansion. Generative artificial intelligence (AI), by contrast, can in principle explore drug-like chemical space around any given compound, but it often struggles with the synthesizability of generated molecules and requires a set of validated hits to initiate exploration. Here, we present a synergistic methodology that overcomes these mutual limitations by leveraging experimentally validated DEL data to initialize and bias an AI-powered virtual screening pipeline, expanding initial DEL hits with both de novo and purchasable compounds from ultra-large chemical libraries. Using this approach, we identified novel, commercially available hits from the Enamine REAL Space for the chromatin reader protein 53BP1 and validated them in a time-resolved fluorescence resonance energy transfer (TR-FRET) displacement assay. Three compounds demonstrated TR-FRET IC50 values ≤50 μM, while 11 exhibited IC50 values ≤100 μM. Critically, the AI-nominated hits exhibited greater chemical diversity, improved drug-likeness, and were readily purchasable off-the-shelf compared to compounds from the initial DEL selection. This work demonstrates a streamlined platform in which empirical DEL data and generative chemistry models are combined to enable rapid hit expansion from initially screened libraries into diverse, commercially available chemical matter. |
| Competing Interests: | The authors declare no competing financial interest. |
| References: | Molecules. 2020 Feb 22;25(4):. (PMID: 32098353); ACS Chem Biol. 2015 Apr 17;10(4):1072-81. (PMID: 25590533); J Med Chem. 2020 Aug 27;63(16):8857-8866. (PMID: 32525674); J Chem Theory Comput. 2023 Apr 25;19(8):2380-2388. (PMID: 37023332); J Comput Aided Mol Des. 2013 Mar;27(3):221-34. (PMID: 23579614); J Health Econ. 2016 May;47:20-33. (PMID: 26928437); J Med Chem. 2004 Mar 25;47(7):1739-49. (PMID: 15027865); J Med Chem. 2021 May 27;64(10):6730-6744. (PMID: 33955740); SLAS Discov. 2018 Jun;23(5):405-416. (PMID: 29437521); FEBS Lett. 2018 Jun;592(12):2168-2180. (PMID: 29683493); ACS Med Chem Lett. 2018 Apr 17;9(5):408-410. (PMID: 29795750); ACS Comb Sci. 2017 Apr 10;19(4):234-238. (PMID: 28287689); Nat Commun. 2017 Jul 17;8:16081. (PMID: 28714473); J Am Chem Soc. 2019 Apr 3;141(13):5169-5181. (PMID: 30855951); Mol Inform. 2024 Jan;43(1):e202300207. (PMID: 37802967); Nat Chem Biol. 2017 Sep 19;13(10):1053-1056. (PMID: 28926557); Mol Biotechnol. 2011 Mar;47(3):270-85. (PMID: 20865348); Nat Protoc. 2021 Oct;16(10):4799-4832. (PMID: 34561691); Nat Chem Biol. 2010 Mar;6(3):159-161. (PMID: 20154659); Nat Commun. 2024 Sep 5;15(1):7761. (PMID: 39237523); ACS Chem Biol. 2016 Sep 16;11(9):2475-83. (PMID: 27356154); Nat Rev Drug Discov. 2017 Feb;16(2):131-147. (PMID: 27932801); Curr Top Med Chem. 2014;14(16):1923-38. (PMID: 25262799); J Chem Inf Comput Sci. 2004 Nov-Dec;44(6):1912-28. (PMID: 15554660); J Med Chem. 2023 Oct 26;66(20):14133-14149. (PMID: 37782247); ACS Comb Sci. 2019 Feb 11;21(2):75-82. (PMID: 30672692); Br J Pharmacol. 2007 Sep;152(1):53-61. (PMID: 17603542); Curr Opin Chem Biol. 2016 Aug;33:135-41. (PMID: 27348158); Curr Opin Chem Biol. 2017 Jun;38:117-126. (PMID: 28494316); Curr Opin Chem Biol. 2021 Aug;63:132-144. (PMID: 33852996); Chem Rev. 2024 Nov 27;124(22):12551-12572. (PMID: 39508428) |
| Grant Information: | T32 GM148376 United States GM NIGMS NIH HHS |
| Entry Date(s): | Date Created: 20251119 Date Completed: 20251120 Latest Revision: 20251122 |
| Update Code: | 20260130 |
| PubMed Central ID: | PMC12621893 |
| DOI: | 10.1101/2025.09.30.679600 |
| PMID: | 41256572 |
| Database: | MEDLINE |
Journal Article; Preprint