DNA编码化合物库与传统小分子化合物库相比优势分析
DNA序列分析与结构比对

DNA序列分析与结构比对DNA(脱氧核糖核酸)是构成遗传物质的分子,它指导所有生命的形成和发展。
DNA序列是由不同的碱基对组成的排列顺序,而这些碱基对的不同排列顺序,决定了不同的生物体的基因特征。
因此,DNA序列的分析和比对,对于理解生命的机理、诊断和治疗疾病都具有非常重要的意义。
一、DNA序列的分析DNA序列的分析是指对DNA序列进行测序、注释、分类、比对等过程。
DNA测序是一项基础的实验前提,通过它我们可以获取到DNA序列的数据。
DNA注释是将测序数据进行翻译、比对和分类,并以一定的方式存储。
在分类的过程中,我们可以将DNA序列根据不同的类型进行分类,如线粒体DNA、叶绿体DNA和核DNA等等。
我们可以通过对DNA序列的分析,来研究基因,从而探索生命的本质和各种生物体的演化过程。
二、DNA序列的比对DNA序列的比对是将两个DNA序列进行对比,确定其相同和不同之处的过程。
DNA序列的比对可以用于基因检测、病理诊断、动物进化研究等领域。
在DNA序列的比对当中,比对技术是非常核心的一部分。
目前,主要有以下两种DNA序列比对的算法:1、全局比对:通过比对整个DNA序列来确定差异。
全局比对的优点在于比对的结果非常准确,但是由于比对的长度过长,所以计算速度相对较慢。
2、局部比对:主要是针对两个DNA序列中长度较短的区域,进行匹配和比对。
局部比对的优点在于比对速度非常快,但是比对的结果可能仅限于某一段序列,因此需要进行针对性的分析。
三、DNA序列的结构比对DNA序列的结构比对指的是查找DNA序列中的一些结构特征,例如基础对序列、序列的二级结构以及序列的三级结构等。
DNA序列的结构比对可以通过计算序列的折叠情况、组合情况来求出序列的结构差异。
通过比对不同的序列结构,我们可以获得更精确的结构信息,这些信息在疾病预测、治疗和药物设计上具有重要的价值。
在DNA序列的分析和比对中,遗传多样性是非常重要的一部分。
DNA序列的遗传多样性涵盖了种类、强度、频率等多个方面。
dna编码化合物库的流程 -回复

dna编码化合物库的流程-回复DNA编码化合物库的流程是一个重要的研究方法,它能够帮助科学家快速筛选和识别具有特定功能的化合物。
本文将详细介绍DNA编码化合物库的流程,并逐步回答相关问题。
第一步:设计和合成DNA编码化合物库DNA编码化合物库是由一系列化合物组成的,每个化合物都带有一个独一无二的DNA条码序列。
为了设计合成DNA编码化合物库,首先需要确定要研究的化合物类型,并将其化学结构转化为可以编码的DNA序列。
这可以通过合成化学方法实现,例如通过化学反应合成含有特定功能基团的化合物,然后将其与DNA条码连接。
问题1:DNA编码化合物库的设计和合成有哪些关键考虑因素?回答1:在设计和合成DNA编码化合物库时,关键考虑因素包括所需的化合物种类、化合物的结构多样性、DNA条码的长度和序列设计、合成方法的可行性和效率等。
这些因素将直接影响到后续的筛选和识别效果。
第二步:构建DNA编码化合物库在构建DNA编码化合物库时,将合成的DNA编码化合物连接到适当的载体上,这样就可以将各个化合物分开,并将其与对应的DNA条码关联起来。
常用的载体包括DNA微球、DNA纳米粒子和DNA芯片等。
问题2:为什么要将DNA编码化合物连接到载体上?回答2:将DNA编码化合物连接到载体上,从而分离和区分每个化合物,保证每个化合物与其对应的DNA条码联系。
这样一来,当需要特定化合物时,可以通过DNA条码进行定位和识别。
第三步:高通量筛选和识别DNA编码化合物库的优势在于能够进行高通量的筛选和识别。
首先,目标蛋白或其他分子与DNA编码化合物进行相互作用。
然后,使用适当的技术将与目标分子发生相互作用的DNA编码化合物分离出来,并对其进行识别和测序。
问题3:DNA编码化合物库与其他筛选方法相比的优势是什么?回答3:DNA编码化合物库具有高通量、高选择性和高灵敏度的优势。
通过对DNA编码化合物进行筛选和识别,可以同时对大量化合物进行分析,并确定与目标分子相互作用的化合物。
高通量药物筛选技术

高通量药物筛选技术是20 世纪80 年代后期形成的寻找新药的高新技术。
经过十余年的实践,该技术体系不断发展和完善,成为目前寻找新药的重要手段。
高通量药物筛选采用的筛选方法一般是以药物作用靶点为主要对象的细胞和分子水平的筛选模型,根据样品与靶点结合的表现,判断化合物的生物活性。
由于这些筛选方法是在微量条件下进行,同时采用自动化操作系统,可以实现大规模的筛选,因而称为高通量药物筛选。
同一化合物不同模型筛选的活性数据以及由同一模型不同化合物的活性数据归纳出的结构活性关系可以为药物的发现提供极有价值的信息。
在高通量药物筛选中,通过活性数据处理过程确定化合物的药物活性,并为基于信息的药物发现过程准备准确、丰富的资料。
1 高通量药物筛选的基本条件1.1 化合物样品库高通量筛选是一种利用已有的化合物进行的体外随机筛选,因此通过高通量药物筛选发现先导化合物(leading compounds)的有效性取决于化合物样品库中化合物的数量及其质量。
化合物样品的数量是指不同样品的数量,化合物样品的质量主要由化合物结构的多样性决定。
许多活性反应基团(ractive groups)使初筛的假阳性大量增加,剔除这些化合物可以提高化合物样品库的质量。
化合物样品主要有人工合成和从天然产物中分离纯化两个来源。
人工合成又可分为常规化学合成和组合化学合成两种方法。
1.2 高通量药物筛选的自动操作系统自动化操作系统就是实验室自动化站, 其基本功能就是自动连续地完成实验的基本操作, 即①加样;②稀释;③转移;④混合, 其方式包括震荡, 也可以用加样器反复吹洗混合;⑤洗板, 就是用适当的溶剂清洗微板;⑥温孵;⑦检测, 反应体系与一种或多种检测仪器相连, 在反应完成后进行自动检测并自动采集储存数据, 完成整个实验过程。
1.3 高通量药物筛选的数据库管理系统高通量药物筛选的特点是对数以万计的化合物样品进行多模型的筛选与高通量药物筛选相适应的数据库管理系统主要承担4个方面的功能。
dna编码化合物库参数

DNA编码化合物库参数概述DNA编码化合物库是一种用于高通量筛选和发现新的化合物的技术。
它利用DNA条形码标记化合物,使得可以通过DNA测序技术对化合物进行快速、高效的筛选和鉴定。
DNA编码化合物库的参数是指在构建和应用该库时需要考虑的各种因素和参数。
本文将详细介绍DNA编码化合物库的参数,包括化合物标记方法、DNA序列设计、文库构建、测序筛选和数据分析等方面的内容。
化合物标记方法DNA编码化合物库的核心是将化合物与DNA条形码进行关联。
化合物标记方法主要包括两种:化学标记和生物标记。
化学标记化学标记是通过在化合物上引入化学标记基团,将化合物与DNA条形码进行连接。
常用的化学标记方法包括:1.化合物上引入亲核试剂:通过化合物与亲核试剂之间的反应,将化合物与DNA条形码连接起来。
常用的亲核试剂包括氨基、羟基、巯基等。
2.化合物上引入反应性基团:通过化合物上的反应性基团与DNA条形码上的亲核试剂发生反应,将化合物与DNA条形码连接起来。
常用的反应性基团包括异氰酸酯、酸酐、酰氯等。
生物标记生物标记是利用生物学方法将化合物与DNA条形码进行连接。
常用的生物标记方法包括:1.酶标记:将化合物与DNA条形码连接后,利用酶的特异性与亲和试剂结合,实现化合物的标记。
常用的酶包括辣根过氧化物酶(HRP)、碱性磷酸酶(AP)等。
2.生物素标记:将化合物与DNA条形码连接后,利用生物素与亲和试剂结合,实现化合物的标记。
生物素与亲和试剂的结合可以通过生物素-亲和试剂结合系统实现。
DNA序列设计DNA编码化合物库的DNA序列设计是构建该库的关键步骤之一。
合理的DNA序列设计可以提高化合物库的多样性和筛选效率。
DNA序列设计主要包括以下几个方面:条形码长度DNA条形码的长度直接影响化合物库的大小和多样性。
较长的条形码可以提高化合物库的多样性,但也会增加测序和数据分析的复杂度。
通常,DNA条形码的长度在10-20个碱基对之间。
dna编码化合物合成流程

dna编码化合物合成流程英文回答:DNA-Encoded Compound Libraries (DELs)。
DNA-encoded compound libraries (DELs) are collections of small molecules that are each tagged with a unique DNA sequence. This allows for the synthesis of vast libraries of compounds in a single reaction, and for the subsequent screening of these libraries against biological targets.DELs are synthesized using a process called split-and-pool synthesis. In this process, a pool of DNA oligonucleotides is split into multiple smaller pools, and each pool is reacted with a different building block. The pools are then recombined, and the process is repeated until the desired library size is reached.The DNA tags on each compound allow for the tracking and identification of individual compounds. Thisinformation can be used to identify compounds that are active against a particular target, and to optimize the design of new compounds.DELs have several advantages over traditional compound libraries. First, they allow for the synthesis of much larger libraries than is possible with traditional methods. Second, the DNA tags allow for the tracking and identification of individual compounds, which can be used to identify active compounds and to optimize the design of new compounds. Third, DELs can be screened against multiple targets simultaneously, which can help to identify compounds with broad-spectrum activity.DELs are a powerful tool for drug discovery. They allow for the synthesis of vast libraries of compounds, and for the screening of these libraries against multiple targets simultaneously. This can help to identify compounds with broad-spectrum activity, and to optimize the design of new compounds.中文回答:DNA编码化合物库 (DEL)。
DNA条形码技术在植物中的研究现状_闫化学

DNA条形码技术在植物中的研究现状_闫化学DNA条形码技术是一种通过特定的DNA序列来进行物种鉴定的新技术。
它通过鉴定和分析物种的特定DNA序列,实现了对物种的快速、准确和高通量的鉴定。
DNA条形码技术在动物物种鉴定中得到了广泛应用和研究,然而在植物中的研究相对较少。
本文将探讨DNA条形码技术在植物中的研究现状。
DNA条形码技术在植物中的研究主要集中在以下几个方面。
首先,针对植物种的DNA条形码技术的开发与优化是近年来的热门研究课题。
由于植物基因组的复杂性和多样性,传统的DNA条形码技术在植物中存在一定的挑战。
因此,研究人员正在努力开发新的分析方法和技术来解决这些问题。
例如,一些研究者利用多个基因组区域的DNA片段进行分析,以提高物种鉴定的准确性和可靠性。
其次,DNA条形码技术在植物物种识别和系统演化中的应用也是研究的重点之一、通过对植物物种进行DNA条形码分析,可以不仅可以准确鉴定植物物种,还可以研究不同物种之间的亲缘关系和系统发育演化。
例如,研究者通过对植物的DNA条形码序列进行比较和分析,发现了一些植物物种之间的细微差异和演化关系。
这些研究对于植物系统分类和种质资源保护具有重要意义。
此外,DNA条形码技术在植物种群遗传结构和种群进化中的研究也开始引起了研究人员的关注。
通过对植物物种的DNA条形码序列进行比较和分析,可以研究植物种群间的遗传结构、种群演化和迁移。
例如,一些研究结果显示,植物种群的遗传多样性和种群结构与地理环境和栖息地状况密切相关。
这些研究对于了解植物种群演化和种群保护具有重要意义。
总的来说,DNA条形码技术在植物中的研究现状尚处于起步阶段,但已经取得了一些重要的研究成果。
随着技术的进一步发展和完善,相信DNA条形码技术将在植物科研和应用中发挥更大的作用,并为植物物种鉴定、系统演化、遗传结构和商品鉴定等提供更多的研究手段和方法。
几种常见的基因测序技术的优缺点及应用

几种常见的基因测序技术的优缺点及应用发布时间:2014-07-19 来源:毕业论文网随着人类基因组计划的完成,人类对自身遗传信息的了解和掌握有了前所未有的进步。
与此同时,分子水平的基因检测技术平台不断发展和完善,使得基因检测技术得到了迅猛发展,基因检测效率不断提高。
从最初第一代以 Sanger 测序为代表的直接检测技术和以连锁分析为代表的间接测序技术,到 2005 年,以 Illumina 公司的 Solexa技术和 ABI 公司的 SOLiD 技术为标志的新一代测序 (next-generation sequencing,NGS) 的相继出现,测序效率明显提升,时间明显缩短,费用明显降低,基因检测手段有了革命性的变化。
其技术正向着大规模、工业化的方向发展,极大地提高了基因检测的检出率,并扩展了疾病在基因水平的研究范围。
2009 年 3 月,约翰霍普金斯大学的研究人员在《Science》杂志上发表了通过 NGS外显子测序技术,发现了一个新的遗传性胰腺癌的致病基因 PALB2,标志着 NGS 测序技术成功应用于致病基因的鉴定研究。
同年,《Nature》发表了采用 NGS 技术发现罕见弗里曼谢尔登综合征MYH3 致病基因突变和《Nat Genet》发表了遗传疾病米勒综合征致病基因。
此后,通过 NGS 技术,与遗传相关的致病基因不断被发现,NGS 技术已成为里程碑式的进步。
2010 年,《Science》杂志将这一技术评选为当年“十大科学进展”。
近两年,基因检测成为临床诊断和科学研究的热点,得到了突飞猛进和日新月异的发展,越来越多的临床和科研成果不断涌现出来。
同时,基因检测已经从单一的遗传疾病专业范畴扩展到复杂疾病和个体化应用更加广阔的领域,其临床检测范围包括高危疾病的新生儿筛查、遗传疾病的诊断和基因携带的检测以及基因药物检测用于指导个体化用药剂量、选择和药物反应等诸多方面的研究。
目前,基因检测在临床诊断和医学研究的应用正越来越受到医生的普遍重视和引起研究人员的极大的兴趣。
2024北京高三一模生物汇编:生物技术与工程(非选择题)

2024北京高三一模生物汇编生物技术与工程(非选择题)一、非选择题1.(2024北京顺义高三一模)人在衰老过程中某些性状会发生改变,为寻找衰老的原因,科研人员对染色质开展了相关研究。
(1)由图1可知,导致个体衰老的原因包括某些染色质区域,某些DNA 。
(2)DNA甲基化会抑制转录并引发更紧密的染色质结构的形成,推测衰老染色质结构松散会(促进/抑制)基因表达。
(3)科研人员推测:核内DNA断裂后的修复会导致表观遗传信息紊乱或丢失,加速细胞衰老。
为验证该推测,科研人员基于图2原理,利用以下实验材料构建ICE模型鼠。
①Cre酶基因:源自噬菌体,其编码的酶进入细胞核后作用于DNA上的Lx序列,导致两个Lx间的DNA 片段丢失;①I-E核酸酶基因:编码的I-E核酸酶位于细胞核,与诱导剂T、Cre酶形成复合物,切割DNA;①口服诱导剂T:小分子化合物,可诱导Cre酶进细胞核。
请完善技术路线:(4)染色质上的修复蛋白因子可修复受损DNA,通过对ICE小鼠的检测,发现已修复的DNA未发生碱基序列的改变。
通过检测,可知获得的ICE鼠表观遗传信息紊乱;检测细胞的形态结构,可知细胞衰老。
2.(2024北京顺义高三一模)学习以下材料,回答(1)~(5)题。
碳同化途径的工程化改造烟草是转基因研究的模式生物。
烟草的光合速率受RuBP羧化-氧化酶(R酶)催化效率和胞内CO2浓度服制。
R酶由大亚基(RL)和小亚基(RS)组成,RL蛋白和RS蛋白分别由叶绿体rl基因和细胞核rs基因编码,大小亚基在叶绿体中组装形成R酶。
R酶既能催化C5羧化形成C3,也能催化C5氧化为C2,进入线粒体分解为CO2,R酶催化的反应类型取决于其周围的CO2和O2浓度。
玉米等植物已经进化出CCM机制,叶绿体中R酶周围积累CO2以增强羧化和抑制氧化。
研究人员尝试在烟草中替换R酶,并构建CCM 途径。
H+菌是一种自养型细菌。
H+菌的羧基体由多种蛋白构成,蛋白外壳包裹着R酶和碳酸酐酶(CA)。
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DNA-Encoded Chemical Libraries:Advancing beyond Conventional Small-Molecule LibrariesRaphael M.Franzini,Dario Neri,*and Jo r g Scheuermann*Institute of Pharmaceutical Sciences,Department of Chemistry and Applied Biosciences,ETH Zu r ich,Wolfgang-Pauli-Strasse10, 8093Zu r ich,SwitzerlandDNA-barcode followed by high-throughput DNA sequencing.Severalthe methods used for library encoding and for the combinatorialfor fragment-based drug discovery,displaying a single moleculecomplementary DNA strands.the library size.While ultralarge libraries containing billions ofof building blocks,also smaller libraries have been shown to bethe overall library size is a poor predictor for library performancerather important indicators.Smaller libraries consisting of two todrug-likeness and often have higher quality.In this Account,we presentpractical applications for drug discovery,both in industry and intarget proteins and is likely to become a standard tool forBiology research.The introduction of new methodologies for libraryis an exciting researchfield and will crucially contribute to theNA-encoded chemical libraries(DECLs)are collections of organic compounds,individually coupled to oligonu-cleotides or DNA fragments,serving as amplifiable identi-fication barcodes.The embodiment of a“phenotype”(i.e.,an organic small-molecule binder to a target protein of interest) and a“genotype”(i.e.,a DNA sequence that permits the identification of the corresponding phenotypic molecule)is reminiscent of display technologies(e.g.,phage display,1,2yeast display,3mRNA display,4ribosome display,5SELEX6,7),which have been used to generate large combinatorial libraries of biomacromolecules(e.g.,peptides,proteins,antibodies,nucleic acids)and to isolate binders against a variety of target proteins8 [Figure1].In the display technologies mentioned,the nucleic acids code for the biosynthesis of the corresponding polypeptides.These technologies have been expanded to allow for the incorporation of non-natural amino acids,9−11for the formation of cyclic structures,12,13and for modification with chemical moieties.14 For example,the reaction of a small molecule scaffold containing two or three reactive groups with cysteine residues in the polypeptide chain has been applied to generate libraries of peptide bicycles.15By contrast,it is not the transcription/ translation machinery that links the DNA sequence of DECLs to the synthesis of the organic molecule;instead the DNA merely acts as an unambiguous and amplifiable identification tag or contains information for hybridization steps during library synthesis.It is thus possible to construct libraries containing molecules with a substantially lower molecular weight compared with peptide libraries.DECL technology was originally proposed by Lerner and Brenner to allow the construction of peptide libraries on beads that contain oligonucleotide barcodes by means of mutually compatible synthetic routes.16However,it was later shown that the technology could be implemented without the need for Received:November27,2013Published:March28,2014beads,thus allowing the construction of larger libraries and more e fficient screening procedures [Figure 1].17−19The most direct comparators for DECLs are probably conventional libraries of small organic molecules.These libraries can be obtained and screened as sets of individual molecules or as combinatorial mixtures of compounds prepared by split-and-pool methodologies [Figure 1].Conventional small-molecule libraries provide great freedom for selecting the chemical structures of choice,and screening such libraries has provided numerous drug leads.Furthermore,the screening of individual molecules (i.e.,those obtained from various sources or by parallel synthesis strategies)has the potential advantage of being compatible with phenotypic assays.20However,the synthesis and screening of individual molecules is an expensive and complex endeavor,requiring large amounts of target protein,a suitable bioassay,and expensive logistics.Even at large pharmaceutical companies screening campaigns are typically limited to a few hundred thousand compounds.By contrast,the use of combinatorial libraries not encoded by DNA (e.g.,one-bead −one-compound libraries)has met with limited success,because it is extremely di fficult to identify bioactive molecules present at low concentration in a large mixture of compounds.Positional scanning may be another possibility for identifying optimal binders but is mostly limited to peptides and requires a known lead structure.21Several approaches have been proposed for the synthesis and screening of DECLs [Figure 2].One fundamental aspect is the distinction between “single-pharmacophore ”and “dual-pharma-cophore ”chemical libraries,depending on whether a single molecule is coupled to a DNA fragment,or whether two molecules are attached at the adjoining extremities of two complementary DNA strands [Figure 2].This latter technology has also been named “encoded self-assembling chemical libraries ”(ESAC library technology).18For the synthesis of single-pharmacophore chemical libraries,two distinct general approaches are routinely applied.In DNA-programmed synthesis [Figure 2],molecules are assembled on an oligonucleotide strand,which may contain the DNA codes for the identi fication of building blocks.With the help of complementary reactant oligonucleotide derivatives,the oligonucleotide can drive the synthesis by DNA-templated chemical reactions.22Heteroduplex formation increases the local concentration of reagents,which may facilitate chemical reactions,followed by linker cleavage,puri fication,and restoration of the original single-stranded oligonucleotide template carrying the growing chemical structure of interest.17Additionally,the encoding oligonucleotides can be used to cause sequence-de fined localization in speci fic reaction vessels for chemical modi fication.19The use of DNA-templated reactions has the advantage that the high e ffective molarityofFigure parison of di fferent library types.DNA-encoded compound libraries are hybrid-type libraries bringing together bene ficial aspects from conventional small-molecule chemical libraries and display technologies such as phage display.In particular,DNA-encoded chemical libraries combine the unparalleled level of high-throughput of phage display with the chemical space of conventional small-molecule chemicallibraries.Several types of encoded chemical libraries have been described including DNA-encoded beads (one-bead −one-compound libraries),DNA-encoded small-molecule libraries (which are the focus of this Account)and libraries encoding peptides with chemical modi fications and unnatural aminoacids.Figure 2.Basic strategies for the preparation of DNA-encoded small-molecule libraries.Encoded self-assembling chemical (ESAC)libraries are formed by the hybridization of two oligonucleotides displaying two pharmacophores at the adjoining termini.In single-pharmacophore libraries,the encoded compoundis linked toonly one oligonucleotide.Two main preparative approaches are available for the synthesis of single-pharmacophorelibraries.In DNA-programmed synthesis,an initial oligonucleotide template contains the information for the synthesis of the final small-molecule product.The template sequence can be converted,for example,by sequential DNA-templated reactions or by hybridization-based sorting.Alternatively,DNA-recorded synthesis provides libraries by consecutive cycles of chemical reaction and encoding steps.the reagents enables the use of reactions that normally would be incompatible with or low-yielding under standard bioconjugation conditions.A disadvantage of DNA-pro-grammed synthesis is that it requires the preparation of reactive oligonucleotide conjugates,which can be laborious.Further-more,because the DNA code is synthesized prior to compound assembly,the generation and purification of a large set of coding oligonucleotides is necessary.Two designs have been described to overcome this limitation.Researchers at Vipergen have made use of three-way junctions for concomitant compound synthesis and encoding obviating the need for an a priori template.23In a recent report,Li and co-workers have described a method where a universal template is used with inosine stretches,which are promiscuous with respect to base-pairing,and where the sequence tags for the building blocks are added during synthesis.24Alternatively,small organic molecules can be coupled to oligonucleotides using a split-and-pool synthesis approach,sometimes referred to as DNA-recorded synthesis[Figure2].25−28Here,individual molecules are coupled to oligonucleotides carrying distinct short sequences serving as identification barcodes for the corresponding chemical moieties.After successful coupling and purification, encoded compounds are mixed and subsequently divided into aliquots,for a successive round of chemical synthesis with a second set of building blocks followed by elongation of the oligonucleotide codes with corresponding sequences[Figure 2].25−27The chemical coupling step is temporally separated from the DNA-encoding step,which can be performed using partially complementary oligonucleotide strands25or by ligation of double-stranded DNA fragments.27■LIBRARY SIZE AND NUMBER OF BUILDING BLOCKSThe probability of identifying hit compounds depends both on the number of molecules in the library and on their structures. When evaluating libraries,in addition to the total number of compounds also the number of modular building blocks used for synthesis is relevant.Reported DECLs vary substantially with respect to these two descriptors[Figure3].When libraries are built by the assembly of several sets of building blocks, library size grows exponentially with the number of reaction steps.This strategy has enabled the synthesis of compound collections of unprecedented size,including,for example,a library of108peptoid8-mers29or>109organic compounds consisting of four building blocks.30The multistep construction of very large combinatorial libraries may be appealing,yet it also has several limitations.Consecutive reactions tend to increase the average molecular weight of the compounds.As reported by Lipinski,31compounds with a molecular mass of >500Da have an elevated risk of failing in clinical trials,and controlling the molecular mass is an important design consideration for DECLs.Library purity is also a concern when several reaction cycles are applied.DECLs with>4 building blocks have been prepared without purification steps and control over reaction yields,possibly affecting the quality of these libraries.27,29,30To the other extreme,the coupling of single molecules to individual oligonucleotides becomes prohibitively expensive for very large compound collections but may nevertheless be a practical avenue for libraries containing102−103members.32,33Often,the hit discovery potential of DECLs is best achieved with libraries based on two to three sets of building blocks. Even relatively small libraries(103−106compounds)may allow the isolation of useful binding specificities[Table1].For example,a DECL with only30000compounds enabled the discovery of a drug fragment for interleukin-228and a lead expansion library with only4000compounds containing a benzamidine lead structure provided nanomolar inhibitors of serine proteases.34These results suggest that the total compound number in a library is not the only predictor of screening success.Combinatorial libraries of DNA-encoded polypeptides can be very large(i.e.,billions of compounds)but are typically made of the20proteinogenic amino acids and possibly a few unnatural amino acids.15,39High binding affinities can be achieved,but molecules tend to have a high molecular mass.As a consequence,oral administration and targeting of intracellular components remain challenging.DECLs constructed by DNA-templated synthesis methods so far rely on the use of a limited set of reactive oligonucleotide derivatives,which is typically on the order of20−200.38As a consequence,the technology is particularly suited for the construction of small macrocyclic peptides,17but other structures could also be considered.Split-and-pool approaches,where sets of building blocks(often commercially available)can be added to a nascent chemical structure on solid phase or in solution,probably provide the largest versatility in library construction.Intermediates of library synthesis can be purified by HPLC only after thefirst reaction step,and subsequent modifications crucially rely on reactions with high yield and broad substrate specificity.■SUCCESS STORIESThefirst DECLs were spiked with known protein ligands, which were later isolated in selection experiments(Table1, Figure3.Summary of library sizes of representative DNA-encoded small molecule libraries.Libraries are grouped according to the number of building blocks(BB)per compound(1BB,red circles;2BB, purple diamonds;3BB,blue triangles;4BB,green squares;8BB,brown triangles).Dotted lines are curves of the total number of compounds as a function of the number of building blocks for hypothetical libraries consisting of equally sized sets of building blocks.Numbering of libraries:1=Scheuermann et al.;322=Dumelin et al.;333=Mannocci et al.;254=Buller et al.;265=Leimbacher et al.;286=Franzini et al., unpublished;7=Samain et al.unpublished;8=Scheuermann et al., unpublished;9=Buller et al.;3510=Clark et al.;2711=Disch et al.;36 12=Tse et al.;37,3813=Clark et al.;2714=Deng et al.;3015=Wrenn et al.29“proof-of-principle ”),thereby proving both the completeness of library assembly and the principle of selection decoding.17−19Encouraged by such proof-of-principle results,large libraries were constructed,in order to use the technology for de novo selections.27,29,30However,even small libraries can yield novel active compounds.For example,interleukin-2ligands (11),28portable albumin binders (3),33inhibitors of Bcl-xL (8),40and inhibitors of kinases (7)38have been identi fied.GlaxoSmithKline has described several large DECLs based on split-and-pool synthesis and identi fied ligands of pharma-ceutical interest.In 2009,they described the construction of a triazine-based 7million-membered 3-building block library and of a 4-building block library containing 800million compounds.27Potent aurora A kinase inhibitors (4)(IC 50=270nM)andp38MAP kinase inhibitors (5,IC 50=250nM hitcompound from libraryscreening;IC 50=7nM afteroptimization)were reported.27More recently,using librariesof a similar design,containing a central triazine core,the authors reported the isolation of a 30nM ADAMTS-5inhibitor (10).30Moreover,e fficient triazine-based inhibitors have beenTable 1.DNA-Encoded Chemical Libraries inPracticedescribed for soluble epoxide hydrolase(sEH)(13,14),41,42 but the design of the corresponding libraries used for selections has not been disclosed.The same company reported a high-affinity pan-inhibitor of the sirtuin-type histone deacetylase family inhibiting SIRT1(12,IC50=4nM),SIRT2(IC50=1 nM),and SIRT3(IC50=7nM).36Our group used a two-building block library derived from Diels−Alder chemistry26for the de novo discovery of a TNF-αbinder(6,K d=10μM),and a Bcl-xL binder(K d=10μM).43A set of sulfonamide-containing carbonic anhydrase IX inhibitors (IC50=240nM),which were able to recognize the cognate antigen in hypoxic tumor sections,were isolated out of a one million-membered three-building block library.35Other two-building block libraries yielded specific low micromolar binders to Bcl-xL(8,K d=930nM)40and interleukin-2(11,K d=2.5μM).28Philochem and collaborators described a small two-building block“lead-expansion”library,containing the known non-specific serine protease binder benzamidine,from which a high-affinity trypsin binder(9,IC50=3nM)with high specificity could be isolated.34Liu and co-workers were thefirst to report novel binders from a library synthesized by DNA-templated reactions.A library of13824macrocycles was screened against a set of36 proteins and yielded two specific high-affinity inhibitors of Src kinase(7,IC50of680and960nM),as well as low micromolar inhibitors of Pim1,Akt3,MAPKAPK2,and p38-MAPKAP2.38 From the initial Src kinase hit,a nanomolar inhibitor(IC50=99 nM)could be derived by systematically varying amino acid residues.44In addition to libraries displaying conventional small molecules,DNA-or PNA-encoded peptide or peptoid libraries have been built and used for affinity-based screening.45,46 Selections with a100million peptoid library were performed against the SH3domain of Crk,yielding a16μM binder,which was superior to the natural Crk-SH3ligands.29■COMPARISON OF CONVENTIONAL LIBRARIES AND DECLSConventional chemical libraries consist of individual com-pounds,which need to be synthesized,quality-controlled,and screened one by one.The costs for the synthesis,management, and screening of large chemical libraries(e.g.,1million compounds)are enormous.The quality of compounds from commercial sources can also be substandard.47In principle,pools of organic compounds could be screened simultaneously,for example,by affinity capture on a target protein of interest.48However,the procedure is prone to artifacts and typically relies on mass-spectrometric identification of compounds.In general,the screening of combinatorial libraries or of pools of compounds becomes more and more difficult with increasing library size,as the concentration of individual compounds progressively decreases.Similar consid-erations apply also for the“one bead−one compound”approach.Library encoding with a nucleic acid arguably represents the only general avenue for obtaining binding data in a very large compound collection,because the DNA “barcode”provides quantitative information about the ability of individual molecules to interact with the target protein(s)of interest.Indeed,PCR amplification can theoretically detect a single DNA-encoded molecule that survives the selection procedure.Since DECLs are typically constructed by split-and-pool methods,library purity cannot be directly assessed using analytical methods,but only estimated based on representative reaction yields or assessed indirectly by the performance of selection experiments.However,when comparing conventional chemical libraries and DECLs,many features play to the advantage of encoded libraries,as discussed in the following paragraphs.Costs and LogisticsThe cost of reagents for the construction and screening of DECLs can be orders of magnitude lower,compared with conventional libraries.For example,the synthesis of a one-million compound DNA-encoded chemical library consisting of 100×100×100building blocks requires merely the purchase of300oligonucleotides and of300chemical compounds.Once synthesized on nanomole scale,the library is sufficient for thousands of affinity-based selections and can be stored as a compound pool in a normal freezer.Selections need only minute amounts of target protein(i.e.,microgram quantities), do not require expensive robotics,and can be performed in many different screening conditions.Also the decoding steps are inexpensive,in view of the enormous progress made in the field of high-throughput DNA sequencing.25,49,50TimeThe construction of a DNA-encoded chemical library can be much faster compared with the parallel synthesis of individual molecules.While conventional split-and-pool libraries can be rapidly synthesized,they are not compatible with efficient decoding procedures.The synthesis of a typical DECL can be performed in a few months.Once available,multiple targets can be screened in parallel in various experimental conditions, whereas a single conventional high-throughput screening campaign(one molecule at a time)may require days or weeks. Purity and Ease of SynthesisA DECL can be of variable purity,depending on design, execution and reaction schemes.Libraries constructed using multiple reaction cycles tend to have lower purity.As a notable exception,encoded self-assembling chemical(ESAC)libraries enjoy the benefit of being composed of individually purified sublibraries.Not all reactions are compatible with the presence of a DNA moiety,but a large variety of synthetic schemes have been shown to be feasible,including Diels−Alder cyclo-additions,26nucleophilic aromatic substitution,27and the Wittig reaction,17to mention only a few.Most DECLs reported to date contain at least one peptide bond formation step during assembly.The DNA tag may also facilitate synthetic procedures,by ease of separation of products from starting reagents and by facile mass-spectrometric confirmation of reaction product identity.A particular case with respect to library purity is the synthesis of macrocycles using DNA-templated chemistry.A clever design of the reaction strategy enables the purification of the reaction product after each synthesis step.37The Impact of the DNA Moiety of DECLs on Library ScreeningThe presence of DNA on individual compounds typically does not interfere with affinity selection procedures,since double-stranded DNA has a fairly rigid“rod-like”structure,which is conserved for all library members.Furthermore,DNA is typically spaced away from the compounds by aflexible linker of sufficient length,in order to minimize electrostatic effects.Intheory,potential problems could arise when screening for binders to DNA-binding proteins.Indeed,a large excess of herring or salmon sperm DNA is typically used in selection procedures for saturating potential DNA-binding sites.27,51An important feature of DECLs relates to the fact that the linker between compound and DNA points away from the target protein of interest and provides a direct avenue for subsequent chemical modi fication steps (e.g.,increase of compound solubility or attachment of a payload).Solubility and Artifacts DNA also confers high water solubility to otherwise insoluble molecules,thus facilitating selection procedures.Furthermore,individual library members can be used at low (e.g.,femtomolar)concentrations,thus minimizing screening artifacts associated with precipitation or aggregation phenom-ena.Other artifacts may arise from several origins and may be common both to conventional libraries and DECLs,for example,artifacts resulting from target unfolding,lack of purity,or library impurities.However,DNA-encoded libraries can be screened in multiple conditions,thus increasing the chance to identify artifacts.Ease of Screening In analogy to protein-display technologies,DECLs are typically screened by a ffinity-capture selections [Figure 4].A target protein of interest,usually immobilized on a solid support,is incubated with the DECL,and binding compounds are physically separated from nonbinders.Unlike conventional libraries,which need the ad hoc development of dedicated screening methods,DECL selections do not require a bioassay,but only the possibility of implementing an a ffinity capture procedure.Several conditions can be robotically implemented in library selection schemes,varying experimental parameters such as bu ffer composition or stringency of washing.While,in principle,compounds may be found to bind to any accessible site of the target protein,most identi fied hits tend to accommodate in clefts of the target protein,including the active sites of enzymes.Depending on the conditions used for selection the a ffinity of the obtained binders can vary broadly from single-digit nanomolar to high micromolar.Structure −Activity Relationships (SAR)A major bottleneck in small-molecule drug development is the evolution of early hit structures to lead compounds,which often involves the determination of structure −activity relation-ships (SAR)by the synthesis and evaluation of sets of hit-derived compounds.Simple structure −activity patterns may be directly accessible from the relative sequence enrichment of encoded compounds in DECL selection experiments,which would provide valuable information for subsequent medicinal chemistry optimization.In order to provide reliable SAR data,DECLs need to have an adequate level of purity and structural diversity that allow for a meaningful comparison,and further studies will be necessary to reveal the full potential of DECLs for this application.Addressed Chemical SpaceThe chemical space of compounds that can be theoretically synthesized 52vastly exceeds the number of compounds that can be screened,even using DNA-encoding procedures.The main strengths of DECL technology relate to the large number of compounds that can be synthesized and easily screened.However,the modular nature of typical DECL members may cause undesired liabilities for pharmaceutical development,such as suboptimal ligand e fficiency or a di fficult geometric fitinFigure 4.Screening results of DECL selections obtained by high-throughput DNA sequencing.(a)Histogram plots of two selections against a target protein (carbonic anhydrase IX)performed under di fferent selection conditions,depicting library building blocks on the x −y plane and relative frequencies after selection on the z -axis.28(b −d)Examples of fingerprints of selections against three undisclosed target proteins.Enrichment of compounds is given as colored dots,ranging from blue to red.tight protein pockets.These liabilities may be due to the intrinsic nature of chemical reactions used in DECL synthesis. On the other hand,the larger structures of DECL compounds consisting of multiple building blocks may be both an advantage when selecting against large epitopes and a disadvantage when selecting against enzymes and for down-stream medicinal chemistry optimization.A long-term challenge and opportunity for DECL research consists in the development of novel synthetic schemes that are compatible with the creation of large compound libraries whose functional groups are arranged on a small and geometrically defined (rigid)scaffold.Hit-to-Lead DevelopmentA major challenge in drug discovery is the progression of hit compounds to lead structures for pharmaceutical development. Different screening technologies tend to provide different starting points for hit-to-lead development,53and hits from DECLs tend to be large with relatively low ligand efficiencies. Moreover,DNA conjugation may mask potential solubility problems.It is therefore important to take parameters such as drug-likeness and solubility into account already at the design stage.DECL technology can however also be implemented as a tool for hit-to-lead optimization.Lead-expansion libraries may consist of a variable part combined with a known drug fragment for the examined target.For example,a lead-expansion library containing a benzamidine lead provided nanomolar inhibitors of serine proteases.34Furthermore,the obtained structure−affinity information can be helpful for hit-to-lead development.■CHALLENGES AND OPPORTUNITIESDECL technology has advanced during recent years from proof-of-principle experiments to a potent method for pharmaceutical hit discovery.The possibility of preparing libraries with sizes previously unconceivable for small-molecule collections,together with efficient screening protocols,makes DECL a very promising technology for pharmaceutical research.However,further advances are required in order to establish DECLs as routine tools for drug discovery.A major challenge remains associated with the need to expand library size while preserving the drug-likeness of compounds and library purity.For this aim,it will be necessary to identify and optimize chemical reactions that are compatible with DNA and which provide access to structurally diverse building blocks. These reactions must then be implemented in library design schemes,which privilege structural compactness of the encoded compounds.Furthermore,the development of novel ap-proaches for library purification and for quality control will be of great significance.Several approaches to DECL technology have been conceived and successfully applied to the discovery of protein binders.Until now,however,binders to a relatively small set of target proteins have been reported[Table1].Moreover,little is known about the impact of library design and experimental factors on the successful(or unsuccessful)use of DECLs.More systematic studies are needed in order to gain statistical information on the performance of DECLs in pharmaceutical hit discovery.Structural details of library synthesis are sometimes not disclosed in publications,which hinders a comparative evaluation of different DECL approaches and different library designs.Some companies active in thefield do not publish at all.In time,a comparative evaluation of the performance of different libraries on the same protein targets will shed light on general chemical rules,which are important for selection success.It is very well possible that different classes of protein targets may be best screened with different types of libraries and that no single“all-purpose”library exists. In summary,DECLs have been established as an emerging tool for drug discovery,with a promising potential for hit discovery and lead expansion.Encoded libraries may provide structural information of broad utility to several areas of Medicinal Chemistry research,including fragment-based drug discovery.54,55DECLs are having an increasing impact on the drug discovery process not only in the pharmaceutical industry but also in academia,which can(for thefirst time)afford the construction and screening of libraries containing millions of compounds.Undoubtedly,encoded libraries will remain an active area of research,in which inventiveness in library construction and selection schemes may bear fruit not only for drug discovery applications but also for the study of biological processes.■AUTHOR INFORMATIONCorresponding Authors*E-mail:dario.neri@pharma.ethz.ch.*E-mail:joerg.scheuermann@pharma.ethz.ch.NotesThe authors declare the following competingfinancial interest(s):RF consults for Philochem,DN is a co-founder and shareholder of Philochem and JS is a board member of Philochem.BiographiesDr.Raphael M.Franzini has received his Master degree in Chemistry from EPF Lausanne(Switzerland).He then obtained his Ph.D.in Chemistry from Stanford University working on DNA-templated fluorescence detection of nucleic acids under the guidance of Prof.Eric Kool.He continued as an SNF postdoctoral researcher at Stanford University in the groups of Profs.Matthew Bogyo and Eric Kool.In 2012,he joined the group of Prof.Dario Neri at ETH Zurich as a VPFW-ETH postdoctoral fellow.In the group of Prof.Neri,he has advanced the development,synthesis,and application of DNA-encoded small-molecule libraries.Prof.Dr.Dario Neri studied Chemistry at the Scuola Normale Superiore of Pisa(Italy)and obtained his Ph.D.at the ETH Zurich (Switzerland)under the guidance of professor Kurt Wu t hrich.After postdoctoral research with Sir Gregory Winter at the Medical Research Council,Cambridge(U.K.),in1996,he returned to the ETH Zu r ich as a professor.His research focuses on strategies for the targeted delivery of therapeutic effectors to sites of disease and the development of DNA-encoded chemical libraries.He is cofounder of Philogen SpA,an Italian−Swiss biotech company,which has brought several antibody drugs into clinical development programs.Dr.Jo r g Scheuermann studied Chemistry at the Ruprecht-Karls-University Heidelberg(Germany)and ETH Zurich(Switzerland). During his Ph.D.study in the group of professor Neri at the ETH Zurich,he worked on the identification of novel binding molecules to markers of angiogenesis.Together with Dario Neri,he co-developed DNA-encoded self-assembling chemical(ESAC)libraries.He is currently working on his habilitation in thefield of DNA-encoded chemical libraries and targeted cytotoxics and their application in drug discovery and development.。