DNA-Encoded Solid-Phase Synthesis: Encoding Language Design and Complex Oligomer Library Synthesis

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• 作者：Andrew B. MacConnell ; Patrick J. McEnaney ; Valerie J. Cavett ; Brian M. Paegel
• 刊名：ACS Combinatorial Science
• 出版年：2015
• 出版时间：September 14, 2015
• 年：2015
• 卷：17
• 期：9
• 页码：518-534
• 全文大小：683K
• ISSN：2156-8944

文摘

The promise of exploiting combinatorial synthesis for small molecule discovery remains unfulfilled due primarily to the 鈥渟tructure elucidation problem鈥? the back-end mass spectrometric analysis that significantly restricts one-bead-one-compound (OBOC) library complexity. The very molecular features that confer binding potency and specificity, such as stereochemistry, regiochemistry, and scaffold rigidity, are conspicuously absent from most libraries because isomerism introduces mass redundancy and diverse scaffolds yield uninterpretable MS fragmentation. Here we present DNA-encoded solid-phase synthesis (DESPS), comprising parallel compound synthesis in organic solvent and aqueous enzymatic ligation of unprotected encoding dsDNA oligonucleotides. Computational encoding language design yielded 148 thermodynamically optimized sequences with Hamming string distance 鈮?3 and total read length <100 bases for facile sequencing. Ligation is efficient (70% yield), specific, and directional over 6 encoding positions. A series of isomers served as a testbed for DESPS鈥檚 utility in split-and-pool diversification. Single-bead quantitative PCR detected 9 脳 10⁴ molecules/bead and sequencing allowed for elucidation of each compound鈥檚 synthetic history. We applied DESPS to the combinatorial synthesis of a 75鈥?45-member OBOC library containing scaffold, stereochemical and regiochemical diversity using mixed-scale resin (160-渭m quality control beads and 10-渭m screening beads). Tandem DNA sequencing/MALDI-TOF MS analysis of 19 quality control beads showed excellent agreement (<1 ppt) between DNA sequence-predicted mass and the observed mass. DESPS synergistically unites the advantages of solid-phase synthesis and DNA encoding, enabling single-bead structural elucidation of complex compounds and synthesis using reactions normally considered incompatible with unprotected DNA. The widespread availability of inexpensive oligonucleotide synthesis, enzymes, DNA sequencing, and PCR make implementation of DESPS straightforward, and may prompt the chemistry community to revisit the synthesis of more complex and diverse libraries.