DNA-Encoded Solid-Phase Synthesis: Encoding Language Design and Complex Oligomer Library Synthesis.
DNA-Encoded Solid-Phase Synthesis: Encoding Language Design and Complex Oligomer Library Synthesis.
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DOI：
10.1021/acscombsci.5b00106
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发表时间：
2015-09-14
影响因子：
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通讯作者：
Paegel BM
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文献类型：
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作者：
MacConnell AB;McEnaney PJ;Cavett VJ;Paegel BM
利用组合合成用于小分子发现的前景仍然未实现，主要是由于“结构阐明问题”：后端质谱分析显著限制了一珠一化合物（OBOC）文库的复杂性。赋予结合效力和特异性的分子特征，如立体化学、区域化学和支架刚性，在大多数文库中明显不存在，因为异构性引入了质量冗余，并且不同的支架产生不可解释的MS片段化。在这里，我们提出了DNA编码的固相合成（DESPS），包括在有机溶剂中的平行化合物合成和无保护的编码dsDNA寡核苷酸的水酶促连接。计算编码语言设计产生了148个经化学优化的序列，其中汉明串距离≥ 3，总读取长度<100个碱基，便于测序。连接是有效的（70%产率），特异性，和方向超过6个编码位置。一系列同分异构体作为DESPS在拆分和合并多样化中的效用的试验平台。单珠定量PCR检测到9 × 104个分子/珠，测序允许阐明每种化合物的合成历史。我们应用DESPS组合合成了一个包含支架、立体化学和区域化学多样性的75645个成员的OBOC文库，使用混合规模的树脂（160 μm质量控制珠和10 μm筛选珠）。对19个质量控制珠的串联DNA测序/MALDI-TOF MS分析显示DNA序列预测质量与观察质量之间具有极好的一致性（<1 ppt）。DESPS协同地结合了固相合成和DNA编码的优点，使复杂化合物的单珠结构解析和使用通常被认为与未保护的DNA不相容的反应的合成成为可能。廉价的寡核苷酸合成、酶、DNA测序和PCR的广泛可用性使得DESPS的实施简单明了，并且可能促使化学界重新审视更复杂和多样化的文库的合成。
The promise of exploiting combinatorial synthesis for small molecule discovery remains unfulfilled due primarily to the “structure elucidation problem”: 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 ≥ 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’s utility in split-and-pool diversification. Single-bead quantitative PCR detected 9 × 104 molecules/bead and sequencing allowed for elucidation of each compound’s synthetic history. We applied DESPS to the combinatorial synthesis of a 75 645-member OBOC library containing scaffold, stereochemical and regiochemical diversity using mixed-scale resin (160-μm quality control beads and 10-μm 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.