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Xia B, Summerfield JD. High-Throughput Binder Confirmation (HTBC). Methods Mol Biol 2022; 2541:207-214. [PMID: 36083559 DOI: 10.1007/978-1-0716-2545-3_24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
In this chapter, we describe a DEL "recipe" approach to hit confirmation using on-DNA cleavable linkers which can be followed by direct AS-MS evaluation and identification of binder(s) from the released small-molecule mixture. When coupled with automation, this platform creates opportunity for enabling an even higher-throughput binder confirmation (HTBC) platform to allow full interrogation of selections results. Two on-DNA cleavable strategies of releasing small molecules from DNA are reported herein.
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Affiliation(s)
- Bing Xia
- Encoded Library Technologies/NCE Molecular Discovery, R&D Medicinal Science and Technology, GlaxoSmithKline, Cambridge, MA, USA
| | - Jennifer D Summerfield
- Encoded Library Technologies/NCE Molecular Discovery, R&D Medicinal Science and Technology, GlaxoSmithKline, Cambridge, MA, USA.
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Ratnayake AS, Flanagan ME, Foley TL, Hultgren SL, Bellenger J, Montgomery JI, Lall MS, Liu B, Ryder T, Kölmel DK, Shavnya A, Feng X, Lefker B, Byrnes LJ, Sahasrabudhe PV, Farley KA, Chen S, Wan J. Toward the assembly and characterization of an encoded library hit confirmation platform: Bead-Assisted Ligand Isolation Mass Spectrometry (BALI-MS). Bioorg Med Chem 2021; 41:116205. [PMID: 34000509 DOI: 10.1016/j.bmc.2021.116205] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 04/27/2021] [Accepted: 04/28/2021] [Indexed: 12/15/2022]
Abstract
The ability to predict chemical structure from DNA sequence has to date been a necessary cornerstone of DNA-encoded library technology. DNA-encoded libraries (DELs) are typically screened by immobilized affinity selection and enriched library members are identified by counting the number of times an individual compound's sequence is observed in the resultant dataset. Those with high signal reads (DEL hits) are subsequently followed up through off-DNA synthesis of the predicted small molecule structures. However, hits followed-up in this manner often fail to translate to confirmed ligands. To address this low conversion rate of DEL hits to off-DNA ligands, we have developed an approach that eliminates the reliance on chemical structure prediction from DNA sequence. Here we describe our method of combining non-combinatorial resynthesis on-DNA following library procedures as a rapid means to assess the probable molecules attached to the DNA barcode. Furthermore, we apply our Bead-Assisted Ligand Isolation Mass Spectrometry (BALI-MS) technique to identify the true binders found within the mixtures of on-DNA synthesis products. Finally, we describe a Normalized Enrichment (NE) metric that allows for the quantitative assessment of affinity selection in these studies. We exemplify how this combined approach enables the identification of putative hit matter against a clinically relevant therapeutic target bisphosphoglycerate mutase, BPGM.
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Affiliation(s)
- Anokha S Ratnayake
- Pfizer Worldwide Research and Development, Eastern Point Road, Groton, CT 06340, United States.
| | - Mark E Flanagan
- Pfizer Worldwide Research and Development, Eastern Point Road, Groton, CT 06340, United States.
| | - Timothy L Foley
- Pfizer Worldwide Research and Development, Eastern Point Road, Groton, CT 06340, United States.
| | - Scott L Hultgren
- Pfizer Worldwide Research and Development, Eastern Point Road, Groton, CT 06340, United States.
| | - Justin Bellenger
- Pfizer Worldwide Research and Development, Eastern Point Road, Groton, CT 06340, United States.
| | - Justin I Montgomery
- Pfizer Worldwide Research and Development, Eastern Point Road, Groton, CT 06340, United States.
| | - Manjinder S Lall
- Pfizer Worldwide Research and Development, Eastern Point Road, Groton, CT 06340, United States.
| | - Bo Liu
- Pfizer Worldwide Research and Development, Eastern Point Road, Groton, CT 06340, United States.
| | - Tim Ryder
- Pfizer Worldwide Research and Development, Eastern Point Road, Groton, CT 06340, United States.
| | - Dominik K Kölmel
- Pfizer Worldwide Research and Development, Eastern Point Road, Groton, CT 06340, United States.
| | - Andre Shavnya
- Pfizer Worldwide Research and Development, Eastern Point Road, Groton, CT 06340, United States.
| | - Xidong Feng
- Pfizer Worldwide Research and Development, Eastern Point Road, Groton, CT 06340, United States.
| | - Bruce Lefker
- Lefker Biopharma Consulting LLC, Arlington, MA 02474 United States.
| | - Laura J Byrnes
- Pfizer Worldwide Research and Development, Eastern Point Road, Groton, CT 06340, United States.
| | - Parag V Sahasrabudhe
- Pfizer Worldwide Research and Development, Eastern Point Road, Groton, CT 06340, United States.
| | - Kathleen A Farley
- Pfizer Worldwide Research and Development, Eastern Point Road, Groton, CT 06340, United States.
| | - Shi Chen
- HitGen Inc., Shuangliu District, Chengdu, China.
| | - Jinqiao Wan
- HitGen Inc., Shuangliu District, Chengdu, China.
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