DNA编码化合物库技术用于药物筛选的策略进展Strategy advance of DNA encoded compound library technology for drug screening
张颖,戚敏钰,王冬尧,王彦婷,吕狄亚,曹岩
ZHANG Ying,QI Minyu,WANG Dongyao,WANG Yanting,LYU Diya,CAO Yan
摘要(Abstract):
目的 综述DNA编码化合物库(DNA encoded compound library, DEL)技术用于药物筛选的策略进展。方法 检索国内外相关文献,根据筛选体系的不同对DEL筛选策略进行分类阐述。结果 DEL技术主要包括文库的构建、化合物的筛选和命中解码与重构化合物三个部分。其中,化合物的筛选技术作为DEL技术的中心环节已成为近年来的热门话题。为了扩增DEL技术应用的靶标范围,DEL筛选体系从最初的固相逐步发展成为液相,靶标体系从纯化蛋白逐步扩展到细胞裂解液和活细胞。近年来,DEL技术相继与多种现代技术联用,从基于亲和力的结合筛选转变到生化活性筛选,提高了筛选结果的准确性。结论 DEL筛选具有广阔的技术前景,研究者们正在为DEL筛选进行进一步的研究,预计未来能够继续取得更多实质性突破,用于更多药物的发现。
Objective To summarize the strategies of DNA-encoded compound library(DEL) technology for drug screening.Methods Relevant domestic and international literatures were searched, and DEL screening strategies were categorized and elaborated according to the different screening strategy.Results The DEL technology mainly included three parts: library construction, compound screening, and hit decoding and reconstitution.The technology of compounds had been a hot research topic in recent years.In order to expand the target scope of DEL screening strategies application, the initial solid-phase of the DEL screening system was developed to liquid-phase, and the target was gradually extended from purified proteins to cell lysates and even live cells.In recent years, various modern technologies were combined with DEL technology, and the affinity-based binding screening were converted to the biochemical activity screening.Conclusion DEL technology has a broad prospect, and many research groups and commercial companies are currently conducting further research for DEL screening.It is believed that more breakthroughs in DEL technology and more implementations in drug discovery will be achieved in the future.
关键词(KeyWords):
DEL;药物筛选;亲和力筛选;生化活性筛选
DEL;drug screening;affinity selection;biochemical activity selection
基金项目(Foundation): 国家自然科学基金资助项目(82174092/H3219);; 上海市科委资助项目(21ZR1483000);; 上海市浦江计划资助项目(21PJD083)
作者(Author):
张颖,戚敏钰,王冬尧,王彦婷,吕狄亚,曹岩
ZHANG Ying,QI Minyu,WANG Dongyao,WANG Yanting,LYU Diya,CAO Yan
DOI: 10.14066/j.cnki.cn21-1349/r.2022.0100
参考文献(References):
- [1] BRENNER S,LERNER R A.Encoded combinatorial chemistry[J].Proc Natl Acad Sci U S A,1992,89(12):5381-5383.
- [2] COCHRANE W G,MALONE M L,DANG V Q,et al.Activity-based DNA-encoded library screening[J].ACS Comb Sci,2019,21(5):425-435.
- [3] SHI Y,WU Y R,YU J Q,et al.DNA-encoded libraries (DELs):a review of on-DNA chemistries and their output[J].RSC Adv,2021,11(4):2359-2376.
- [4] GIRONDA-MARTíNEZ A,DONCKELE E J,SAMAIN F,et al.DNA-encoded chemical libraries:a comprehensive review with succesful stories and future challenges[J].ACS Pharmacol Transl Sci,2021,4(4):1265-1279.
- [5] CHEN Q,CHENG X,ZHANG L,et al.Exploring the lower limit of individual DNA-encoded library molecules in selection[J].SLAS Discov,2020,25(5):523-529.
- [6] LI JY,HUANG H.Development of DNA-compatible Suzuki-Miyaura reaction in aqueous media[J].Bioconjug Chem,2018,29(11):3841-3846.
- [7] GARTNER Z J,KANAN M W,LIU D R.Expanding the reaction scope of DNA-templated synthesis[J].Angew Chem,2002,114(10):1874-1878.
- [8] FAVALLI N,BASSI G,ZANETTI T,et al.Screening of copper and palladium-mediated reactions compatible with DNA-encoded chemical libraries[J].Helv Chim Acta,2019,102(4):e1900033.
- [9] XIONG H,GU Y,ZHANG S,et al.Iridium-catalyzed C-H amidation of s-tetrazines[J].Chem Comm,2020,56(34):4692-4695.
- [10] VOUGIOUKALAKIS G C,GRUBBS R H.Ruthenium-based heterocyclic carbene-coordinated olefin metathesis catalysts[J].Chem Soc Rev,2010,110(3):1746-1787.
- [11] AN Y L,LI K,SHEN Y,et al.DNA compatible intermolecular Wittig Olefination for the construction of α,β-unsaturated carbonyl compounds[J].Org Lett,2020,22(10):3931-3935.
- [12] WANG J,LUNDBERG H,ASAI S,et al.Kinetically guided radical-based synthesis of C(sp(3))-C(sp(3)) linkages on DNA[J].Proc Natl Acad Sci U S A,2018,115(28):e6404-e6410.
- [13] K?LMEL D K,LOACH R P,KNAUBER T,et al.Employing photoredox catalysis for DNA-encoded chemistry:decarboxylative alkylation of α-amino acids[J].Chem Med Chem,2018,13(20):2159-2165.
- [14] BELYANSKAYA S L,DING Y,CALLAHAN J F,et al.Discovering drugs with DNA-encoded library technology:from concept to clinic with an inhibitor of soluble epoxide hydrolase[J].Chem Bio Chem,2017,18(9):837-842.
- [15] MCGREGOR L M,JAIN T,LIU D R.Identification of ligand-target pairs from combined libraries of small molecules and unpurified protein targets in cell lysates[J].J Am Chem Soc,2014,136(8):3264-3270.
- [16] CAI B,KIM D,AKHAND S,et al.Selection of DNA-encoded libraries to protein targets within and on living cells[J].J Am Chem Soc,2019,141(43):17057-17061.
- [17] WATSON R O,BELL S L,MACDUFF D A,et al.The cytosolic sensor cGAS detects Mycobacterium tuberculosis DNA to induce type I interferons and activate autophagy[J].Cell Host Microbe,2015,17(6):811-819.
- [18] SANNINO A,GABRIELE E,BIGATTI M,et al.Quantitative assessment of affinity selection performance by using DNA-encoded chemical libraries[J].Chem Bio Chem,2019,20(7):955-962.
- [19] NIELSEN J,BRENNER S,JANDA K D.Synthetic methods for the implementation of encoded combinatorial chemistry[J].J Am Chem Soc,1993,115(21):9812-9813.
- [20] NERI D,LERNER R A.DNA-encoded chemical libraries:a selection system based on endowing organic compounds with amplifiable information[J].Annu Rev Biochem,2018,87:479-502.
- [21] MüLLER K,GOMBERT F O,MANNING U,et al.Rapid identification of phosphopeptide ligands for SH2 domains:screening of peptide libraries by fluorescence-activated bead sorting[J].J Biol Chem,1996,271(28):16500-16505.
- [22] HUANG Y,LI X.Recent advances on the selection methods of DNA-encoded libraries[J].Chem Bio Chem,2021,22(14):2384-2397.
- [23] KLEINER R E,DUMELIN C E,TIU G C,et al.In vitro selection of a DNA-templated small-molecule library reveals a class of macrocyclic kinase inhibitors[J].J Am Chem Soc,2010,132(33):11779-11791.
- [24] KIM D,SUN Y,XIE D,et al.Application of a substrate-mediated selection with c-Src tyrosine kinase to a DNA-encoded chemical library[J].Molecules,2019,24(15):2764.
- [25] BULLER F,STEINER M,FREY K,et al.Selection of carbonic anhydrase IX inhibitors from one million DNA-encoded compounds[J].ACS Chem Biol,2011,6(4):336-344.
- [26] DOYON J B,SNYDER T M,LIU D R.Highly sensitive in vitro selections for DNA-linked synthetic small molecules with protein binding affinity and specificity[J].J Am Chem Soc,2003,125(41):12372-12373.
- [27] ZIMMERMANN G,RIEDER U,BAJIC D,et al.A specific and covalent JNK-1 ligand selected from an encoded self-assembling chemical library[J].Chemistry (Weinheim an der Bergstrasse,Germany),2017,23(34):8152-8155.
- [28] XIN Q,YAN T,XINXIN L.Methods and techniques of capillary electrophoresis for drug screening[J].Chin J Chromatogr,2020,38(10):1170.
- [29] KOCHMANN S,LE A T,HILI R,et al.Predicting efficiency of NECEEM-based partitioning of protein binders from nonbinders in DNA-encoded libraries[J].Electrophoresis,2018,39(23):2991-2996.
- [30] PETERSEN L,BLAKSKJ?R P,CHAIKUAD A,et al.Novel p38α MAP kinase inhibitors identified from yocto-reactor DNA-encoded small molecule library[J].Med Chem Comm,2016,7(7):1332-1339.
- [31] PETERSEN L K,CHRISTENSEN A B,ANDERSEN J,et al.Screening of DNA-encoded small molecule libraries inside a living cell[J].J Am Chem Soc,2021,143(7):2751-2756.
- [32] MCGREGOR L M,GORIN D J,DUMELIN C E,et al.Interaction-dependent PCR:identification of ligand-target pairs from libraries of ligands and libraries of targets in a single solution-phase experiment[J].J Am Chem Soc,2010,132(44):15522-15524.
- [33] ZHANG J,PENG J,HUANG Y,et al.Identification of histone deacetylase (HDAC)-associated proteins with DNA-programmed affinity labeling[J].Angew Chem,2020,132(40):17678-17685.
- [34] SHI B,DENG Y,LI X.Polymerase-extension-based selection method for DNA-encoded chemical libraries against nonimmobilized protein targets[J].ACS Comb Sci,2019,21(5):345-349.
- [35] BROWN D G,BROWN G A,CENTRELLA P,et al.Agonists and antagonists of protease-activated receptor 2 discovered within a DNA-encoded chemical library using mutational stabilization of the target[J].Slas Discov,2018,23(5):429-436.
- [36] SONG Y,LI X.Evolution of the selection methods of DNA-encoded chemical libraries[J].Acc Chem Res,2021,54(17):3491-3503.
- [37] KODADEK T,PACIARONI N G,BALZARINI M,et al.Beyond protein binding:recent advances in screening DNA-encoded libraries[J].Chem Commun (Camb),2019,55(89):13330-13341.
- [38] SVENSEN N,DíAZ-MOCHóN J J,BRADLEY M.Encoded peptide libraries and the discovery of new cell binding ligands[J].Chem Comm,2011,47(27):7638-7640.
- [39] HUANG Y,MENG L,NIE Q,et al.Selection of DNA-encoded chemical libraries against endogenous membrane proteins on live cells[J].Nat Chem,2021,13(1):77-88.
- [40] PETERSEN L K,CHRISTENSEN A B,ANDERSEN J,et al.Screening of DNA-encoded small molecule libraries inside a living cell[J].J Am Chem Soc,2021,143(7):2751-2756.
- [41] GOODNOW R A,DUMELIN C E,KEEFE A D.DNA-encoded chemistry:enabling the deeper sampling of chemical space[J].Nat Rev Drug Discov,2017,16(2):131-147.
- [42] MACCONNELL A B,MCENANEY P J,CAVETT V J,et al.DNA-encoded solid-phase synthesis:encoding language design and complex oligomer library synthesis[J].ACS Comb Sci,2015,17(9):518-534.
- [43] ANNA S L,BONTOUX N,STONE H A.Formation of dispersions using “flow focusing” in microchannels[J].Appl Phys Lett,2003,82(3):364-366.
- [44] HACKLER A L,FITZGERALD F G,DANG V Q,et al.Off-DNA DNA-Encoded Library Affinity Screening[J].ACS Comb Sci,2020,22(1):25-34.
- [45] LEE S A,GREGOR D,CLAUDIO Z.Small molecule screening cellular assay using modified beads:WO,2020212439[P].2020-10-22.
- [46] WILLIAMS D H,WOOD S R,THOMPSON N.Microbeads for tagless encoded chemical library screening:WO,2020084084[P].2020-04-30.
- [47] FRANKLIN R J,MICHAEL V N,KANDASWAMY J,et al.Oligonucleotide encoded chemical libraries:WO,2019060830[P].2019-03-28.
- [48] SATZ A L,KUAI L,PENG X.Selections and screenings of DNA-encoded chemical libraries against enzyme and cellular targets[J].Bioorg Med Chem Lett,2021,39:127851.
- [49] HUANG Y,LI Y,LI X.Strategies for developing DNA-encoded libraries beyond binding assays[J].Nat Chem,2022,14(2):129-140.