1
|
Oehler S, Lucaroni L, Migliorini F, Elsayed A, Prati L, Puglioli S, Matasci M, Schira K, Scheuermann J, Yudin D, Jia M, Ban N, Bushnell D, Kornberg R, Cazzamalli S, Neri D, Favalli N, Bassi G. A DNA-encoded chemical library based on chiral 4-amino-proline enables stereospecific isozyme-selective protein recognition. Nat Chem 2023; 15:1431-1443. [PMID: 37400597 DOI: 10.1038/s41557-023-01257-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 05/26/2023] [Indexed: 07/05/2023]
Abstract
DNA-encoded chemical libraries (DELs) consist of large chemical compound collections individually linked to DNA barcodes, facilitating pooled construction and screening. However, screening campaigns often fail if the molecular arrangement of the building blocks is not conducive to an efficient interaction with a protein target. Here we postulated that the use of rigid, compact and stereo-defined central scaffolds for DEL synthesis may facilitate the discovery of very specific ligands capable of discriminating between closely related protein targets. We synthesized a DEL comprising 3,735,936 members, featuring the four stereoisomers of 4-aminopyrrolidine-2-carboxylic acid as central scaffolds. The library was screened in comparative selections against pharmaceutically relevant targets and their closely related protein isoforms. Hit validation results revealed a strong impact of stereochemistry, with large affinity differences between stereoisomers. We identified potent isozyme-selective ligands against multiple protein targets. Some of these hits, specific to tumour-associated antigens, demonstrated tumour-selective targeting in vitro and in vivo. Collectively, constructing DELs with stereo-defined elements contributed to high library productivity and ligand selectivity.
Collapse
Affiliation(s)
| | | | | | - Abdullah Elsayed
- Philochem AG, Otelfingen, Switzerland
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH Zurich), Zurich, Switzerland
| | | | | | | | - Kristina Schira
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH Zurich), Zurich, Switzerland
| | - Jörg Scheuermann
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH Zurich), Zurich, Switzerland
| | - Denis Yudin
- Institute of Molecular Biology and Biophysics, Swiss Federal Institute of Technology (ETH Zurich), Zurich, Switzerland
| | - Min Jia
- Institute of Molecular Biology and Biophysics, Swiss Federal Institute of Technology (ETH Zurich), Zurich, Switzerland
| | - Nenad Ban
- Institute of Molecular Biology and Biophysics, Swiss Federal Institute of Technology (ETH Zurich), Zurich, Switzerland
| | | | - Roger Kornberg
- NeoTX Therapeutics LTD, Stanford, CA, USA
- Department of Structural Biology, Stanford University, Stanford, CA, USA
| | | | - Dario Neri
- Philochem AG, Otelfingen, Switzerland
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH Zurich), Zurich, Switzerland
- Philogen SPA, Siena, Italy
| | | | | |
Collapse
|
2
|
Tian X, Risgaard NA, Löffler PMG, Vogel S. DNA-Programmed Lipid Nanoreactors for Synthesis of Carbohydrate Mimetics by Fusion of Aqueous Sub-attoliter Compartments. J Am Chem Soc 2023; 145:19633-19641. [PMID: 37619973 PMCID: PMC10510321 DOI: 10.1021/jacs.3c04093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Indexed: 08/26/2023]
Abstract
Lipid nanoreactors are biomimetic reaction vessels (nanoreactors) that can host aqueous or membrane-associated chemical and enzymatic reactions. Nanoreactors provide ultra-miniaturization from atto- to zeptoliter volumes per reaction vessel with the major challenge of encoding and spatio-temporal control over reactions at the individual nanoreactor or population level, thereby controlling volumes several orders of magnitude below advanced microfluidic devices. We present DNA-programmed lipid nanoreactors (PLNs) functionalized with lipidated oligonucleotides (LiNAs) that allow programming and encoding of nanoreactor interactions by controlled membrane fusion, exemplified for a set of carbohydrate mimetics with mono- to hexasaccharide azide building blocks connected by click-chemistry. Programmed reactions are initiated by fusion of distinct populations of nanoreactors with individually encapsulated building blocks. A focused library of triazole-linked carbohydrate-Cy5 conjugates formed by strain-promoted azide-alkyne cycloadditions demonstrated LiNA-programmed chemistry, including two-step reaction schemes. The PLN method is developed toward a robust platform for synthesis in confined space employing fully programmable nanoreactors, applicable to multistep synthesis for the generation of combinatorial libraries with subsequent analysis of the molecules formed, based on the addressability of the lipid nanoreactors.
Collapse
Affiliation(s)
- Xinwei Tian
- Department of Physics, Chemistry
and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
| | - Nikolaj Alexander Risgaard
- Department of Physics, Chemistry
and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
| | - Philipp M. G. Löffler
- Department of Physics, Chemistry
and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
| | - Stefan Vogel
- Department of Physics, Chemistry
and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
| |
Collapse
|
3
|
Cui M, Nguyen D, Gaillez MP, Heiden S, Lin W, Thompson M, Reddavide FV, Chen Q, Zhang Y. Trio-pharmacophore DNA-encoded chemical library for simultaneous selection of fragments and linkers. Nat Commun 2023; 14:1481. [PMID: 36932079 PMCID: PMC10023787 DOI: 10.1038/s41467-023-37071-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 02/28/2023] [Indexed: 03/19/2023] Open
Abstract
The split-and-pool method has been widely used to synthesize chemical libraries of a large size for early drug discovery, albeit without the possibility of meaningful quality control. In contrast, a self-assembled DNA-encoded chemical library (DEL) allows us to construct an m x n-member library by mixing an m-member and an n-member pre-purified sub-library. Herein, we report a trio-pharmacophore DEL (T-DEL) of m x l x n members through assembling three pre-purified and validated sub-libraries. The middle sub-library is synthesized using DNA-templated synthesis with different reaction mechanisms and designed as a linkage connecting the fragments displayed on the flanking two sub-libraries. Despite assembling three fragments, the resulting compounds do not exceed the up-to-date standard of molecular weight regarding drug-likeness. We demonstrate the utility of T-DEL in linker optimization for known binding fragments against trypsin and carbonic anhydrase II and by de novo selections against matrix metalloprotease-2 and -9.
Collapse
Affiliation(s)
- Meiying Cui
- B CUBE, Center for Molecular Bioengineering, Technische Universität Dresden, Dresden, Germany
| | | | - Michelle Patino Gaillez
- B CUBE, Center for Molecular Bioengineering, Technische Universität Dresden, Dresden, Germany
| | | | - Weilin Lin
- B CUBE, Center for Molecular Bioengineering, Technische Universität Dresden, Dresden, Germany
| | | | | | - Qinchang Chen
- Research Institute of Intelligent Computing, Zhejiang Lab, Hangzhou, China.
- School of Life Sciences and Technology, Tongji University, Shanghai, China.
| | - Yixin Zhang
- B CUBE, Center for Molecular Bioengineering, Technische Universität Dresden, Dresden, Germany.
| |
Collapse
|
4
|
Dockerill M, Winssinger N. DNA-Encoded Libraries: Towards Harnessing their Full Power with Darwinian Evolution. Angew Chem Int Ed Engl 2023; 62:e202215542. [PMID: 36458812 DOI: 10.1002/anie.202215542] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 11/29/2022] [Accepted: 11/30/2022] [Indexed: 12/05/2022]
Abstract
DNA-encoded library (DEL) technologies are transforming the drug discovery process, enabling the identification of ligands at unprecedented speed and scale. DEL makes use of libraries that are orders of magnitude larger than traditional high-throughput screens. While a DNA tag alludes to a genotype-phenotype connection that is exploitable for molecular evolution, most of the work in the field is performed with libraries where the tag serves as an amplifiable barcode but does not allow "translation" into the synthetic product it is linked to. In this Review, we cover technologies that enable the "translation" of the genetic tag into synthetic molecules, both biochemically and chemically, and explore how it can be used to harness Darwinian evolutionary pressure.
Collapse
Affiliation(s)
- Millicent Dockerill
- Department of Organic Chemistry, NCCR Chemical Biology, Faculty of Sciences, University of Geneva, 1211, Geneva, Switzerland
| | - Nicolas Winssinger
- Department of Organic Chemistry, NCCR Chemical Biology, Faculty of Sciences, University of Geneva, 1211, Geneva, Switzerland
| |
Collapse
|
5
|
Montoya AL, Glavatskikh M, Halverson BJ, Yuen LH, Schüler H, Kireev D, Franzini RM. Combining pharmacophore models derived from DNA-encoded chemical libraries with structure-based exploration to predict Tankyrase 1 inhibitors. Eur J Med Chem 2023; 246:114980. [PMID: 36495630 PMCID: PMC9805525 DOI: 10.1016/j.ejmech.2022.114980] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 11/25/2022] [Accepted: 11/25/2022] [Indexed: 12/03/2022]
Abstract
DNA-encoded chemical libraries (DECLs) interrogate the interactions of a target of interest with vast numbers of molecules. DECLs hence provide abundant information about the chemical ligand space for therapeutic targets, and there is considerable interest in methods for exploiting DECL screening data to predict novel ligands. Here we introduce one such approach and demonstrate its feasibility using the cancer-related poly-(ADP-ribose)transferase tankyrase 1 (TNKS1) as a model target. First, DECL affinity selections resulted in structurally diverse TNKS1 inhibitors with high potency including compound 2 with an IC50 value of 0.8 nM. Additionally, TNKS1 hits from four DECLs were translated into pharmacophore models, which were exploited in combination with docking-based screening to identify TNKS1 ligand candidates in databases of commercially available compounds. This computational strategy afforded TNKS1 inhibitors that are outside the chemical space covered by the DECLs and yielded the drug-like lead compound 12 with an IC50 value of 22 nM. The study further provided insights in the reliability of screening data and the effect of library design on hit compounds. In particular, the study revealed that while in general DECL screening data are in good agreement with off-DNA ligand binding, unpredictable interactions of the DNA-attachment linker with the target protein contribute to the noise in the affinity selection data.
Collapse
Affiliation(s)
- Alba L Montoya
- Department of Medicinal Chemistry, Skaggs College of Pharmacy, University of Utah, 30 S 2000 E, Salt Lake City, UT, 84112, USA.
| | - Marta Glavatskikh
- Center for Integrative Chemical Biology and Drug Discovery, UNC Eshelman School of Pharmacy, 301 Pharmacy Lane, University of North Carolina, Chapel Hill, NC, 27599, USA.
| | - Brayden J Halverson
- Department of Medicinal Chemistry, Skaggs College of Pharmacy, University of Utah, 30 S 2000 E, Salt Lake City, UT, 84112, USA.
| | - Lik Hang Yuen
- Department of Medicinal Chemistry, Skaggs College of Pharmacy, University of Utah, 30 S 2000 E, Salt Lake City, UT, 84112, USA
| | - Herwig Schüler
- Center for Molecular Protein Science, Department of Chemistry, Lund University, 22100, Lund, Sweden.
| | - Dmitri Kireev
- Department of Chemistry, 36 Schlundt Hall, University of Missouri, Columbia, MO, 65211, USA.
| | - Raphael M Franzini
- Department of Medicinal Chemistry, Skaggs College of Pharmacy, University of Utah, 30 S 2000 E, Salt Lake City, UT, 84112, USA; Huntsman Cancer Institute, University of Utah, 2000 Circle of Hope Dr., Salt Lake City, UT, 84112, USA.
| |
Collapse
|
6
|
Ramos De Dios SM, Tiwari VK, McCune CD, Dhokale RA, Berkowitz DB. Biomacromolecule-Assisted Screening for Reaction Discovery and Catalyst Optimization. Chem Rev 2022; 122:13800-13880. [PMID: 35904776 DOI: 10.1021/acs.chemrev.2c00213] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Reaction discovery and catalyst screening lie at the heart of synthetic organic chemistry. While there are efforts at de novo catalyst design using computation/artificial intelligence, at its core, synthetic chemistry is an experimental science. This review overviews biomacromolecule-assisted screening methods and the follow-on elaboration of chemistry so discovered. All three types of biomacromolecules discussed─enzymes, antibodies, and nucleic acids─have been used as "sensors" to provide a readout on product chirality exploiting their native chirality. Enzymatic sensing methods yield both UV-spectrophotometric and visible, colorimetric readouts. Antibody sensors provide direct fluorescent readout upon analyte binding in some cases or provide for cat-ELISA (Enzyme-Linked ImmunoSorbent Assay)-type readouts. DNA biomacromolecule-assisted screening allows for templation to facilitate reaction discovery, driving bimolecular reactions into a pseudo-unimolecular format. In addition, the ability to use DNA-encoded libraries permits the barcoding of reactants. All three types of biomacromolecule-based screens afford high sensitivity and selectivity. Among the chemical transformations discovered by enzymatic screening methods are the first Ni(0)-mediated asymmetric allylic amination and a new thiocyanopalladation/carbocyclization transformation in which both C-SCN and C-C bonds are fashioned sequentially. Cat-ELISA screening has identified new classes of sydnone-alkyne cycloadditions, and DNA-encoded screening has been exploited to uncover interesting oxidative Pd-mediated amido-alkyne/alkene coupling reactions.
Collapse
Affiliation(s)
| | - Virendra K Tiwari
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, United States
| | - Christopher D McCune
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, United States
| | - Ranjeet A Dhokale
- Higuchi Biosciences Center, University of Kansas, Lawrence, Kansas 66047, United States
| | - David B Berkowitz
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, United States
| |
Collapse
|
7
|
Sun J, Nie Q, Fang X, He Z, Zhang G, Li Y, Li Y. Vinyl azide as a synthon for DNA-compatible divergent transformations into N-heterocycles. Org Biomol Chem 2022; 20:5045-5049. [PMID: 35703385 DOI: 10.1039/d2ob00862a] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Inspired by diversity-oriented synthesis, we have developed a series of DNA-compatible transformations utilizing on-DNA vinyl azide as a synthon to forge divergent N-heterocyclic scaffolds. Polysubstituted imidazoles and isoquinolines were efficiently obtained with moderate-to-excellent conversions. Besides, the "one-pot" strategy to prepare in-house on-DNA vinyl azides afforded synthons readily. Results from substrate scope exploration and enzymatic ligation further demonstrate the feasibility of these N-heterocycle syntheses in DNA-encoded chemical library construction.
Collapse
Affiliation(s)
- Jie Sun
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, 401331 Chongqing, P. R. China.
| | - Qigui Nie
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, 401331 Chongqing, P. R. China.
| | - Xianfu Fang
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, 401331 Chongqing, P. R. China.
| | - Zhiwei He
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, 401331 Chongqing, P. R. China.
| | - Gong Zhang
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, 401331 Chongqing, P. R. China. .,Chemical Biology Research Center, School of Pharmaceutical Sciences, Chongqing University, 401331 Chongqing, P. R. China
| | - Yangfeng Li
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, 401331 Chongqing, P. R. China. .,Chemical Biology Research Center, School of Pharmaceutical Sciences, Chongqing University, 401331 Chongqing, P. R. China
| | - Yizhou Li
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, Innovative Drug Research Center, School of Pharmaceutical Sciences, Chongqing University, 401331 Chongqing, P. R. China. .,Chemical Biology Research Center, School of Pharmaceutical Sciences, Chongqing University, 401331 Chongqing, P. R. China.,Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, 400044 Chongqing, P. R. China.,Beijing National Laboratory for Molecular Sciences, 100190 Beijing, P. R. China
| |
Collapse
|
8
|
Li Y, Zhao G, Fan X, Li Y, Zhang G. Switchable DNA-Encoded Chemical Library: Interconversion between Double- and Single-Stranded DNA Formats. Chembiochem 2022; 23:e202200025. [PMID: 35352452 DOI: 10.1002/cbic.202200025] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 03/10/2022] [Indexed: 11/07/2022]
Abstract
DNA-Encoded Chemical Library (DEL) has attracted substantial attention due to the infinite possibility for hit discovery in both pharmaceutical companies and academia. The encoding method is the initial step of DEL construction and one of the cornerstones of DEL applications. Classified by the DNA format, the existing DEL encoding strategies could be categorized into single-stranded DNA-based strategies and double-stranded DNA-based strategies. The two DEL formats have their unique advantages but are usually incompatible with each other. To address this issue, we proposed the concept of interconversion between double- and single-stranded DEL based on the "reversible covalent headpiece (RCHP)" design, which combined maximum robustness of synthesis with extraordinary flexibility of applications in distinct setups. Future opportunities in this field were also proposed to advance DEL technology to a comprehensive drug discovery platform.
Collapse
Affiliation(s)
- Yizhou Li
- Chongqing University, School of Pharmaceutical Sciences, Chongqing College Town, Shapingba, 401331, Chongqing, CHINA
| | - Guixian Zhao
- Chongqing University, School of Pharmaceutical Sciences, CHINA
| | - Xiaohong Fan
- Chongqing University, School of Pharmaceutical Sciences, CHINA
| | - Yangfeng Li
- Chongqing University, School of Pharmaceutical Sciences, CHINA
| | - Gong Zhang
- Chongqing University, School of Pharmaceutical Science, CHINA
| |
Collapse
|
9
|
Shang J, He L, Wang J, Tong A, Xiang Y. In Situ Visualizing Nascent RNA by Exploring DNA-Templated Oxidative Amination of 4-Thiouridine. Bioconjug Chem 2022; 33:164-171. [PMID: 34910465 DOI: 10.1021/acs.bioconjchem.1c00524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Tracking and mapping the nascent RNA molecules in cells is essential for deciphering embryonic development and neuronal differentiation. Here, we utilized 4-thiouridine (s4U) as a metabolic tag to label nascent RNA and developed a fluorescence imaging method based on the DNA-templated oxidative amination (DTOA) reaction of s4U. The DTOA reaction occurred between amine-modified DNA and s4U-containing RNA with high sequence specificity and chemical selectivity. Target nascent mRNAs in HeLa cells, including those encoding green fluorescent proteins (GFPs) and endogenous BAG-1, were thus lit up selectively by DTOA-based fluorescence in situ hybridization (DTOA FISH). We believe the DTOA conjugation chemistry shown in this study could be generally applied to investigate the spatial distribution of nascent transcription dynamics in cellular processes.
Collapse
Affiliation(s)
- Jiachen Shang
- Department of Chemistry, Beijing Key Laboratory for Microanalytical Methods and Instrumentation, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Tsinghua University, Beijing 100084, China
| | - Luo He
- Department of Chemistry, Beijing Key Laboratory for Microanalytical Methods and Instrumentation, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Tsinghua University, Beijing 100084, China
| | - Jingyi Wang
- Department of Chemistry, Beijing Key Laboratory for Microanalytical Methods and Instrumentation, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Tsinghua University, Beijing 100084, China
| | - Aijun Tong
- Department of Chemistry, Beijing Key Laboratory for Microanalytical Methods and Instrumentation, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Tsinghua University, Beijing 100084, China
| | - Yu Xiang
- Department of Chemistry, Beijing Key Laboratory for Microanalytical Methods and Instrumentation, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Tsinghua University, Beijing 100084, China
| |
Collapse
|
10
|
Plais L, Scheuermann J. Macrocyclic DNA-encoded chemical libraries: a historical perspective. RSC Chem Biol 2022; 3:7-17. [PMID: 35128404 PMCID: PMC8729180 DOI: 10.1039/d1cb00161b] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 10/19/2021] [Indexed: 12/25/2022] Open
Abstract
While macrocyclic peptides are extensively researched for therapeutically relevant protein targets, DNA-encoded chemical libraries (DELs) are developed at a quick pace to discover novel small molecule binders. The combination of both fields has been explored since 2004 and the number of macrocyclic peptide DELs is steadily increasing. Macrocycles with high affinity and potency were identified for diverse classes of proteins, revealing DEL's huge potential. By giving a historical perspective, we would like to review the methods which permitted the rise of macrocyclic peptide DELs, describe the different DELs which were created and discuss the achievements and challenges of this emerging field.
Collapse
Affiliation(s)
- Louise Plais
- Department of Chemistry and Applied Biosciences, ETH Zürich (Swiss Federal Institute of Technology) Vladimir-Prelog-Weg 4 CH-8093 Zürich Switzerland
| | - Jörg Scheuermann
- Department of Chemistry and Applied Biosciences, ETH Zürich (Swiss Federal Institute of Technology) Vladimir-Prelog-Weg 4 CH-8093 Zürich Switzerland
| |
Collapse
|
11
|
Second-generation DNA-encoded multiple display on a constant macrocyclic scaffold enabled by an orthogonal protecting group strategy. CHINESE CHEM LETT 2021. [DOI: 10.1016/j.cclet.2021.09.041] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
|
12
|
Gironda-Martínez A, Donckele EJ, Samain F, Neri D. DNA-Encoded Chemical Libraries: A Comprehensive Review with Succesful Stories and Future Challenges. ACS Pharmacol Transl Sci 2021; 4:1265-1279. [PMID: 34423264 PMCID: PMC8369695 DOI: 10.1021/acsptsci.1c00118] [Citation(s) in RCA: 122] [Impact Index Per Article: 40.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Indexed: 12/27/2022]
Abstract
DNA-encoded chemical libraries (DELs) represent a versatile and powerful technology platform for the discovery of small-molecule ligands to protein targets of biological and pharmaceutical interest. DELs are collections of molecules, individually coupled to distinctive DNA tags serving as amplifiable identification barcodes. Thanks to advances in DNA-compatible reactions, selection methodologies, next-generation sequencing, and data analysis, DEL technology allows the construction and screening of libraries of unprecedented size, which has led to the discovery of highly potent ligands, some of which have progressed to clinical trials. In this Review, we present an overview of diverse approaches for the generation and screening of DEL molecular repertoires. Recent success stories are described, detailing how novel ligands were isolated from DEL screening campaigns and were further optimized by medicinal chemistry. The goal of the Review is to capture some of the most recent developments in the field, while also elaborating on future challenges to further improve DEL technology as a therapeutic discovery platform.
Collapse
Affiliation(s)
| | | | - Florent Samain
- Philochem
AG, Libernstrasse 3, CH-8112 Otelfingen, Switzerland
| | - Dario Neri
- Department
of Chemistry and Applied Biosciences, Swiss
Federal Institute of Technology, CH-8093 Zürich, Switzerland
- Philogen
S.p.A, 53100 Siena, Italy
| |
Collapse
|
13
|
Huang Y, Meng L, Nie Q, Zhou Y, Chen L, Yang S, Fung YME, Li X, Huang C, Cao Y, Li Y, Li X. Selection of DNA-encoded chemical libraries against endogenous membrane proteins on live cells. Nat Chem 2020; 13:77-88. [PMID: 33349694 DOI: 10.1038/s41557-020-00605-x] [Citation(s) in RCA: 76] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2019] [Accepted: 11/10/2020] [Indexed: 12/30/2022]
Abstract
Membrane proteins on the cell surface perform a myriad of biological functions; however, ligand discovery for membrane proteins is highly challenging, because a natural cellular environment is often necessary to maintain protein structure and function. DNA-encoded chemical libraries (DELs) have emerged as a powerful technology for ligand discovery, but they are mainly limited to purified proteins. Here we report a method that can specifically label membrane proteins with a DNA tag, and thereby enable target-specific DEL selections against endogenous membrane proteins on live cells without overexpression or any other genetic manipulation. We demonstrate the generality and performance of this method by screening a 30.42-million-compound DEL against the folate receptor, carbonic anhydrase 12 and the epidermal growth factor receptor on live cells, and identify and validate a series of novel ligands for these targets. Given the high therapeutic significance of membrane proteins and their intractability to traditional high-throughput screening approaches, this method has the potential to facilitate membrane-protein-based drug discovery by harnessing the power of DEL.
Collapse
Affiliation(s)
- Yiran Huang
- Department of Chemistry and State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Hong Kong SAR, China
| | - Ling Meng
- Department of Chemistry and State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Hong Kong SAR, China
| | - Qigui Nie
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing, China
| | - Yu Zhou
- Department of Chemistry and State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Hong Kong SAR, China
| | - Langdong Chen
- School of Pharmacy, Second Military Medical University, Shanghai, China
| | - Shilian Yang
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing, China
| | - Yi Man Eva Fung
- Department of Chemistry and State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Hong Kong SAR, China
| | - Xiaomeng Li
- Department of Chemistry and State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Hong Kong SAR, China
| | - Cen Huang
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing, China
| | - Yan Cao
- School of Pharmacy, Second Military Medical University, Shanghai, China.
| | - Yizhou Li
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Chongqing, China. .,Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, China.
| | - Xiaoyu Li
- Department of Chemistry and State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Hong Kong SAR, China. .,Laboratory for Synthetic Chemistry and Chemical Biology of Health@InnoHK, Hong Kong SAR, China.
| |
Collapse
|
14
|
Manicardi A, Cadoni E, Madder A. Visible-light triggered templated ligation on surface using furan-modified PNAs. Chem Sci 2020; 11:11729-11739. [PMID: 34094412 PMCID: PMC8162948 DOI: 10.1039/d0sc04875e] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 10/02/2020] [Indexed: 12/25/2022] Open
Abstract
Oligonucleotide-templated reactions are frequently exploited for target detection in biosensors and for the construction of DNA-based materials and probes in nanotechnology. However, the translation of the specifically used template chemistry from solution to surfaces, with the final aim of achieving highly selective high-throughput systems, has been difficult to reach and therefore, poorly explored. Here, we show the first example of a visible light-triggered templated ligation on a surface, employing furan-modified peptide nucleic acids (PNAs). Tailored photo-oxidation of the pro-reactive furan moiety is ensured by the simultaneous introduction of a weak photosensitizer as well as a nucleophilic moiety in the reacting PNA strand. This allows one to ensure a localized production of singlet oxygen for furan activation, which is not affected by probe dilution or reducing conditions. Simple white light irradiation in combination with target-induced proximity between reactive functionalities upon recognition of a short 22mer DNA or RNA sequence that functions as a template, allows sensitive detection of nucleic acid targets in a 96 well plate format.
Collapse
Affiliation(s)
- Alex Manicardi
- Organic and Biomimetic Chemistry Research Group, Department of Organic and Macromolecular Chemistry, Ghent University Krijgslaan 281-S4 9000 Gent Belgium
| | - Enrico Cadoni
- Organic and Biomimetic Chemistry Research Group, Department of Organic and Macromolecular Chemistry, Ghent University Krijgslaan 281-S4 9000 Gent Belgium
| | - Annemieke Madder
- Organic and Biomimetic Chemistry Research Group, Department of Organic and Macromolecular Chemistry, Ghent University Krijgslaan 281-S4 9000 Gent Belgium
| |
Collapse
|
15
|
Janett E, Diep KL, Fromm KM, Bochet CG. A Simple Reaction for DNA Sensing and Chemical Delivery. ACS Sens 2020; 5:2338-2343. [PMID: 32804492 DOI: 10.1021/acssensors.0c00988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Reactions templated by nucleic acids are currently at the heart of applications in biosensing and drug release. The number of chemical reactions selectively occurring only in the presence of the template, in aqueous solutions, and at room temperature and able to release a chemical moiety is still very limited. Here, we report the use of the p-nitrophenyl carbonate (NPC) as a new reactive moiety for DNA templated reactions releasing a colored reporter by reaction with a simple amine. The easily synthesized p-nitrophenyl carbonate was integrated in an oligonucleotide and showed a very good stability as well as a high reactivity toward amines, without the need for any supplementary reagent, quantitatively releasing the red p-nitrophenolate with a half-life of about 1 h.
Collapse
Affiliation(s)
- Elia Janett
- Department of Chemistry, University of Fribourg, Chemin du Musée 9, CH-1700 Fribourg, Switzerland
| | - Kim-Long Diep
- Department of Chemistry, University of Fribourg, Chemin du Musée 9, CH-1700 Fribourg, Switzerland
| | - Katharina M. Fromm
- Department of Chemistry, University of Fribourg, Chemin du Musée 9, CH-1700 Fribourg, Switzerland
| | - Christian G. Bochet
- Department of Chemistry, University of Fribourg, Chemin du Musée 9, CH-1700 Fribourg, Switzerland
| |
Collapse
|
16
|
Deng Y, Peng J, Xiong F, Song Y, Zhou Y, Zhang J, Lam FS, Xie C, Shen W, Huang Y, Meng L, Li X. Selection of DNA‐Encoded Dynamic Chemical Libraries for Direct Inhibitor Discovery. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202005070] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Yuqing Deng
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry The University of Hong Kong Laboratory for Synthetic Chemistry and Chemical Biology of Health@InnoHK of Innovation and Technology Commission Pokfulam Road Hong Kong SAR China
| | - Jianzhao Peng
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry The University of Hong Kong Laboratory for Synthetic Chemistry and Chemical Biology of Health@InnoHK of Innovation and Technology Commission Pokfulam Road Hong Kong SAR China
- Department of Chemistry Southern University of Science and Technology China 1088 Xueyuan Road Shenzhen China
| | - Feng Xiong
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry The University of Hong Kong Laboratory for Synthetic Chemistry and Chemical Biology of Health@InnoHK of Innovation and Technology Commission Pokfulam Road Hong Kong SAR China
| | - Yinan Song
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry The University of Hong Kong Laboratory for Synthetic Chemistry and Chemical Biology of Health@InnoHK of Innovation and Technology Commission Pokfulam Road Hong Kong SAR China
| | - Yu Zhou
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry The University of Hong Kong Laboratory for Synthetic Chemistry and Chemical Biology of Health@InnoHK of Innovation and Technology Commission Pokfulam Road Hong Kong SAR China
| | - Jianfu Zhang
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry The University of Hong Kong Laboratory for Synthetic Chemistry and Chemical Biology of Health@InnoHK of Innovation and Technology Commission Pokfulam Road Hong Kong SAR China
| | - Fong Sang Lam
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry The University of Hong Kong Laboratory for Synthetic Chemistry and Chemical Biology of Health@InnoHK of Innovation and Technology Commission Pokfulam Road Hong Kong SAR China
| | - Chao Xie
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry The University of Hong Kong Laboratory for Synthetic Chemistry and Chemical Biology of Health@InnoHK of Innovation and Technology Commission Pokfulam Road Hong Kong SAR China
| | - Wenyin Shen
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry The University of Hong Kong Laboratory for Synthetic Chemistry and Chemical Biology of Health@InnoHK of Innovation and Technology Commission Pokfulam Road Hong Kong SAR China
| | - Yiran Huang
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry The University of Hong Kong Laboratory for Synthetic Chemistry and Chemical Biology of Health@InnoHK of Innovation and Technology Commission Pokfulam Road Hong Kong SAR China
| | - Ling Meng
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry The University of Hong Kong Laboratory for Synthetic Chemistry and Chemical Biology of Health@InnoHK of Innovation and Technology Commission Pokfulam Road Hong Kong SAR China
| | - Xiaoyu Li
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry The University of Hong Kong Laboratory for Synthetic Chemistry and Chemical Biology of Health@InnoHK of Innovation and Technology Commission Pokfulam Road Hong Kong SAR China
| |
Collapse
|
17
|
Deng Y, Peng J, Xiong F, Song Y, Zhou Y, Zhang J, Lam FS, Xie C, Shen W, Huang Y, Meng L, Li X. Selection of DNA-Encoded Dynamic Chemical Libraries for Direct Inhibitor Discovery. Angew Chem Int Ed Engl 2020; 59:14965-14972. [PMID: 32436364 DOI: 10.1002/anie.202005070] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 05/18/2020] [Indexed: 11/11/2022]
Abstract
Dynamic combinatorial libraries (DCLs) is a powerful tool for ligand discovery in biomedical research; however, the application of DCLs has been hampered by their low diversity. Recently, the concept of DNA encoding has been employed in DCLs to create DNA-encoded dynamic libraries (DEDLs); however, all current DEDLs are limited to fragment identification, and a challenging process of fragment linking is required after selection. We report an anchor-directed DEDL approach that can identify full ligand structures from large-scale DEDLs. This method is also able to convert unbiased libraries into focused ones targeting specific protein classes. We demonstrated this method by selecting DEDLs against five proteins, and novel inhibitors were identified for all targets. Notably, several selective BD1/BD2 inhibitors were identified from the selections against bromodomain 4 (BRD4), an important anti-cancer drug target. This work may provide a broadly applicable method for inhibitor discovery.
Collapse
Affiliation(s)
- Yuqing Deng
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Laboratory for Synthetic Chemistry and Chemical Biology of Health@InnoHK of Innovation and Technology Commission, Pokfulam Road, Hong Kong SAR, China
| | - Jianzhao Peng
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Laboratory for Synthetic Chemistry and Chemical Biology of Health@InnoHK of Innovation and Technology Commission, Pokfulam Road, Hong Kong SAR, China.,Department of Chemistry, Southern University of Science and Technology China, 1088 Xueyuan Road, Shenzhen, China
| | - Feng Xiong
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Laboratory for Synthetic Chemistry and Chemical Biology of Health@InnoHK of Innovation and Technology Commission, Pokfulam Road, Hong Kong SAR, China
| | - Yinan Song
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Laboratory for Synthetic Chemistry and Chemical Biology of Health@InnoHK of Innovation and Technology Commission, Pokfulam Road, Hong Kong SAR, China
| | - Yu Zhou
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Laboratory for Synthetic Chemistry and Chemical Biology of Health@InnoHK of Innovation and Technology Commission, Pokfulam Road, Hong Kong SAR, China
| | - Jianfu Zhang
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Laboratory for Synthetic Chemistry and Chemical Biology of Health@InnoHK of Innovation and Technology Commission, Pokfulam Road, Hong Kong SAR, China
| | - Fong Sang Lam
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Laboratory for Synthetic Chemistry and Chemical Biology of Health@InnoHK of Innovation and Technology Commission, Pokfulam Road, Hong Kong SAR, China
| | - Chao Xie
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Laboratory for Synthetic Chemistry and Chemical Biology of Health@InnoHK of Innovation and Technology Commission, Pokfulam Road, Hong Kong SAR, China
| | - Wenyin Shen
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Laboratory for Synthetic Chemistry and Chemical Biology of Health@InnoHK of Innovation and Technology Commission, Pokfulam Road, Hong Kong SAR, China
| | - Yiran Huang
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Laboratory for Synthetic Chemistry and Chemical Biology of Health@InnoHK of Innovation and Technology Commission, Pokfulam Road, Hong Kong SAR, China
| | - Ling Meng
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Laboratory for Synthetic Chemistry and Chemical Biology of Health@InnoHK of Innovation and Technology Commission, Pokfulam Road, Hong Kong SAR, China
| | - Xiaoyu Li
- Department of Chemistry and the State Key Laboratory of Synthetic Chemistry, The University of Hong Kong, Laboratory for Synthetic Chemistry and Chemical Biology of Health@InnoHK of Innovation and Technology Commission, Pokfulam Road, Hong Kong SAR, China
| |
Collapse
|
18
|
Bassi G, Favalli N, Oehler S, Martinelli A, Catalano M, Scheuermann J, Neri D. Comparative evaluation of DNA-encoded chemical selections performed using DNA in single-stranded or double-stranded format. Biochem Biophys Res Commun 2020; 533:223-229. [PMID: 32386812 DOI: 10.1016/j.bbrc.2020.04.035] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Accepted: 04/10/2020] [Indexed: 12/23/2022]
Abstract
DNA-encoded chemical libraries (DEL) are increasingly being used for the discovery and optimization of small organic ligands to proteins of biological or pharmaceutical interest. The DNA fragments, that serve as amplifiable identification barcodes for individual compounds in the library, are typically used in double-stranded DNA format. To the best of our knowledge, a direct comparison of DEL selections featuring DNA in either single- or double-stranded DNA format has not yet been reported. In this article, we describe a comparative evaluation of selections with two DEL libraries (named GB-DEL and NF-DEL), based on different chemical designs and produced in both single- and double-stranded DNA format. The libraries were selected in identical conditions against multiple protein targets, revealing comparable and reproducible fingerprints for both types of DNA formats. Surprisingly, selections performed with single-stranded DNA barcodes exhibited improved enrichment factors compared to double-stranded DNA. Using high-affinity ligands to carbonic anhydrase IX as benchmarks for selection performance, we observed an improved selectivity for the NF-DEL library (on average 2-fold higher enrichment factors) in favor of single-stranded DNA. The enrichment factors were even higher for the GB-DEL selections (approximately 5-fold), compared to the same library in double-stranded DNA format. Collectively, these results indicate that DEL libraries can conveniently be synthesized and screened in both single- and double-stranded DNA format, but single-stranded DNA barcodes typically yield enhanced enrichment factors.
Collapse
Affiliation(s)
- Gabriele Bassi
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH Zürich), Vladimir-Prelog-Weg 4, CH-8093, Zürich, Switzerland
| | - Nicholas Favalli
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH Zürich), Vladimir-Prelog-Weg 4, CH-8093, Zürich, Switzerland
| | - Sebastian Oehler
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH Zürich), Vladimir-Prelog-Weg 4, CH-8093, Zürich, Switzerland
| | - Adriano Martinelli
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH Zürich), Vladimir-Prelog-Weg 4, CH-8093, Zürich, Switzerland
| | - Marco Catalano
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH Zürich), Vladimir-Prelog-Weg 4, CH-8093, Zürich, Switzerland
| | - Jörg Scheuermann
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH Zürich), Vladimir-Prelog-Weg 4, CH-8093, Zürich, Switzerland.
| | - Dario Neri
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH Zürich), Vladimir-Prelog-Weg 4, CH-8093, Zürich, Switzerland.
| |
Collapse
|
19
|
Madsen D, Azevedo C, Micco I, Petersen LK, Hansen NJV. An overview of DNA-encoded libraries: A versatile tool for drug discovery. PROGRESS IN MEDICINAL CHEMISTRY 2020; 59:181-249. [PMID: 32362328 DOI: 10.1016/bs.pmch.2020.03.001] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
DNA-encoded libraries (DELs) are collections of small molecules covalently attached to amplifiable DNA tags carrying unique information about the structure of each library member. A combinatorial approach is used to construct the libraries with iterative DNA encoding steps, facilitating tracking of the synthetic history of the attached compounds by DNA sequencing. Various screening protocols have been developed which allow protein target binders to be selected out of pools containing up to billions of different small molecules. The versatile methodology has allowed identification of numerous biologically active compounds and is now increasingly being adopted as a tool for lead discovery campaigns and identification of chemical probes. A great focus in recent years has been on developing DNA compatible chemistries that expand the structural diversity of the small molecule library members in DELs. This chapter provides an overview of the challenges and accomplishments in DEL technology, reviewing the technological aspects of producing and screening DELs with a perspective on opportunities, limitations, and future directions.
Collapse
|
20
|
Yang Z, Kim HJ, Le JT, McLendon C, Bradley KM, Kim MS, Hutter D, Hoshika S, Yaren O, Benner SA. Nucleoside analogs to manage sequence divergence in nucleic acid amplification and SNP detection. Nucleic Acids Res 2019; 46:5902-5910. [PMID: 29800323 PMCID: PMC6159519 DOI: 10.1093/nar/gky392] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Accepted: 05/02/2018] [Indexed: 01/18/2023] Open
Abstract
Described here are the synthesis, enzymology and some applications of a purine nucleoside analog (H) designed to have two tautomeric forms, one complementary to thymidine (T), the other complementary to cytidine (C). The performance of H is compared by various metrics to performances of other 'biversal' analogs that similarly rely on tautomerism to complement both pyrimidines. These include (i) the thermodynamic stability of duplexes that pair these biversals with various standard nucleotides, (ii) the ability of the biversals to support polymerase chain reaction (PCR), (iii) the ability of primers containing biversals to equally amplify targets having polymorphisms in the primer binding site, and (iv) the ability of ligation-based assays to exploit the biversals to detect medically relevant single nucleotide polymorphisms (SNPs) in sequences flanked by medically irrelevant polymorphisms. One advantage of H over the widely used inosine 'universal base' and 'mixed sequence' probes is seen in ligation-based assays to detect SNPs. The need to detect medically relevant SNPs within ambiguous sequences is especially important when probing RNA viruses, which rapidly mutate to create drug resistance, but also suffer neutral drift, the second obstructing simple methods to detect the first. Thus, H is being developed to detect variants of viruses that are rapidly mutating.
Collapse
Affiliation(s)
- Zunyi Yang
- Foundation for Applied Molecular Evolution (FfAME), 13709 Progress Boulevard, Box 7, Alachua, FL 32615, USA.,Firebird Biomolecular Sciences LLC, 13709 Progress Blvd, Box 17, Alachua, FL 32615, USA
| | - Hyo-Joong Kim
- Firebird Biomolecular Sciences LLC, 13709 Progress Blvd, Box 17, Alachua, FL 32615, USA
| | - Jennifer T Le
- Foundation for Applied Molecular Evolution (FfAME), 13709 Progress Boulevard, Box 7, Alachua, FL 32615, USA.,Firebird Biomolecular Sciences LLC, 13709 Progress Blvd, Box 17, Alachua, FL 32615, USA
| | - Chris McLendon
- Foundation for Applied Molecular Evolution (FfAME), 13709 Progress Boulevard, Box 7, Alachua, FL 32615, USA.,Firebird Biomolecular Sciences LLC, 13709 Progress Blvd, Box 17, Alachua, FL 32615, USA
| | - Kevin M Bradley
- Foundation for Applied Molecular Evolution (FfAME), 13709 Progress Boulevard, Box 7, Alachua, FL 32615, USA.,Firebird Biomolecular Sciences LLC, 13709 Progress Blvd, Box 17, Alachua, FL 32615, USA
| | - Myong-Sang Kim
- Firebird Biomolecular Sciences LLC, 13709 Progress Blvd, Box 17, Alachua, FL 32615, USA
| | - Daniel Hutter
- Foundation for Applied Molecular Evolution (FfAME), 13709 Progress Boulevard, Box 7, Alachua, FL 32615, USA.,Firebird Biomolecular Sciences LLC, 13709 Progress Blvd, Box 17, Alachua, FL 32615, USA
| | - Shuichi Hoshika
- Foundation for Applied Molecular Evolution (FfAME), 13709 Progress Boulevard, Box 7, Alachua, FL 32615, USA.,Firebird Biomolecular Sciences LLC, 13709 Progress Blvd, Box 17, Alachua, FL 32615, USA
| | - Ozlem Yaren
- Foundation for Applied Molecular Evolution (FfAME), 13709 Progress Boulevard, Box 7, Alachua, FL 32615, USA
| | - Steven A Benner
- Foundation for Applied Molecular Evolution (FfAME), 13709 Progress Boulevard, Box 7, Alachua, FL 32615, USA.,Firebird Biomolecular Sciences LLC, 13709 Progress Blvd, Box 17, Alachua, FL 32615, USA
| |
Collapse
|
21
|
Potowski M, Kunig VBK, Losch F, Brunschweiger A. Synthesis of DNA-coupled isoquinolones and pyrrolidines by solid phase ytterbium- and silver-mediated imine chemistry. MEDCHEMCOMM 2019; 10:1082-1093. [PMID: 31391880 PMCID: PMC6644566 DOI: 10.1039/c9md00042a] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Accepted: 02/21/2019] [Indexed: 12/16/2022]
Abstract
DNA-encoded libraries of chemically synthesized compounds are an important small molecule screening technology. The synthesis of encoded compounds in solution is currently restricted to a few DNA-compatible and water-tolerant reactions. Encoded compound synthesis of short DNA-barcodes covalently connected to solid supports benefits from a broad range of choices of organic solvents. Here, we show that this encoded chemistry approach allows for the synthesis of DNA-coupled isoquinolones by an Yb(iii)-mediated Castagnoli-Cushman reaction under anhydrous reaction conditions and for the synthesis of highly substituted pyrrolidines by Ag(i)-mediated 1,3-dipolar azomethine ylide cycloaddition. An encoding scheme for these DNA-barcoded compounds based on a DNA hairpin is demonstrated.
Collapse
Affiliation(s)
- Marco Potowski
- Department of Chemistry and Chemical Biology , TU Dortmund University , Otto-Hahn-Str. 6 , 44227 Dortmund , Germany .
| | - Verena B K Kunig
- Department of Chemistry and Chemical Biology , TU Dortmund University , Otto-Hahn-Str. 6 , 44227 Dortmund , Germany .
| | - Florian Losch
- Department of Chemistry and Chemical Biology , TU Dortmund University , Otto-Hahn-Str. 6 , 44227 Dortmund , Germany .
| | - Andreas Brunschweiger
- Department of Chemistry and Chemical Biology , TU Dortmund University , Otto-Hahn-Str. 6 , 44227 Dortmund , Germany .
| |
Collapse
|
22
|
Stress CJ, Sauter B, Schneider LA, Sharpe T, Gillingham D. A DNA-Encoded Chemical Library Incorporating Elements of Natural Macrocycles. Angew Chem Int Ed Engl 2019; 58:9570-9574. [PMID: 30938482 DOI: 10.1002/anie.201902513] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Revised: 04/01/2019] [Indexed: 12/22/2022]
Abstract
Here we show a seven-step chemical synthesis of a DNA-encoded macrocycle library (DEML) on DNA. Inspired by polyketide and mixed peptide-polyketide natural products, the library was designed to incorporate rich backbone diversity. Achieving this diversity, however, comes at the cost of the custom synthesis of bifunctional building block libraries. This study outlines the importance of careful retrosynthetic design in DNA-encoded libraries, while revealing areas where new DNA synthetic methods are needed.
Collapse
Affiliation(s)
- Cedric J Stress
- Department of Chemistry, University of Basel, St. Johanns-Ring 19, CH-4056, Basel, Switzerland
| | - Basilius Sauter
- Department of Chemistry, University of Basel, St. Johanns-Ring 19, CH-4056, Basel, Switzerland
| | - Lukas A Schneider
- Department of Chemistry, University of Basel, St. Johanns-Ring 19, CH-4056, Basel, Switzerland
| | - Timothy Sharpe
- Biophysics Facility, Biozentrum, University of Basel, Klingelbergstrasse 50/70, CH-4056, Basel, Switzerland
| | - Dennis Gillingham
- Department of Chemistry, University of Basel, St. Johanns-Ring 19, CH-4056, Basel, Switzerland
| |
Collapse
|
23
|
Stress CJ, Sauter B, Schneider LA, Sharpe T, Gillingham D. Eine DNA‐kodierte Molekülbibliothek mit Elementen natürlicher Makrocyclen. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201902513] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Cedric J. Stress
- Department ChemieUniversität Basel St. Johanns-Ring 19 4056 Basel Schweiz
| | - Basilius Sauter
- Department ChemieUniversität Basel St. Johanns-Ring 19 4056 Basel Schweiz
| | - Lukas A. Schneider
- Department ChemieUniversität Basel St. Johanns-Ring 19 4056 Basel Schweiz
| | - Timothy Sharpe
- Biophysikalisches InstitutBiozentrumUniversität Basel Klingelbergstrasse 50/70 4056 Basel Schweiz
| | - Dennis Gillingham
- Department ChemieUniversität Basel St. Johanns-Ring 19 4056 Basel Schweiz
| |
Collapse
|
24
|
Zhao G, Huang Y, Zhou Y, Li Y, Li X. Future challenges with DNA-encoded chemical libraries in the drug discovery domain. Expert Opin Drug Discov 2019; 14:735-753. [DOI: 10.1080/17460441.2019.1614559] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Guixian Zhao
- Tumour Targeted Therapy and Chemical Biology Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing, China
| | - Yiran Huang
- Department of Chemistry, The University of Hong Kong, Hong Kong SAR, China
| | - Yu Zhou
- Department of Chemistry, The University of Hong Kong, Hong Kong SAR, China
- Key Laboratory of Chemical Genomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, China
| | - Yizhou Li
- Tumour Targeted Therapy and Chemical Biology Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing, China
| | - Xiaoyu Li
- Department of Chemistry, The University of Hong Kong, Hong Kong SAR, China
| |
Collapse
|
25
|
Hayashi G, Yanase M, Nakatsuka Y, Okamoto A. Simultaneous and Traceless Ligation of Peptide Fragments on DNA Scaffold. Biomacromolecules 2019; 20:1246-1253. [PMID: 30677290 DOI: 10.1021/acs.biomac.8b01655] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Peptide ligation is an indispensable step in the chemical synthesis of target peptides and proteins that are difficult to synthesize at once by a solid-phase synthesis. The ligation reaction is generally conducted with two peptide fragments at a high aqueous concentration to increase the reaction rate; however, this often causes unpredictable aggregation and precipitation of starting or resulting peptides due to their hydrophobicities. Here, we have developed a novel peptide ligation strategy harnessing the two intrinsic characteristics of oligodeoxynucleotides (ODNs), i.e., their hydrophilicity and hybridization ability, which allowed increases in the water solubility of peptides and the reaction kinetics due to the proximity effect, respectively. Peptide-ODN conjugates that can be cleaved to regenerate native peptide sequences were synthesized using novel lysine derivatives containing conjugation handles and photolabile linkers, via solid-phase peptide synthesis and subsequent conjugation to 15-mer ODNs. Two complementary conjugates were applied to carbodiimide-mediated peptide ligation on a DNA scaffold, and the subsequent DNA removal was conducted by photoirradiation in a traceless fashion. This DNA scaffold-assisted ligation resulted in a significant acceleration of the reaction kinetics and enabled ligation of a hydrophobic peptide at a micromolar concentration. On the basis of this chemistry, a simultaneous ligation of three different peptide fragments on two different DNA scaffolds has been conducted for the first time.
Collapse
Affiliation(s)
- Gosuke Hayashi
- Department of Chemistry and Biotechnology , The University of Tokyo , 7-3-1 Hongo, Bunkyo-ku , Tokyo 113-8656 , Japan
| | - Masafumi Yanase
- Department of Chemistry and Biotechnology , The University of Tokyo , 7-3-1 Hongo, Bunkyo-ku , Tokyo 113-8656 , Japan
| | - Yu Nakatsuka
- Department of Chemistry and Biotechnology , The University of Tokyo , 7-3-1 Hongo, Bunkyo-ku , Tokyo 113-8656 , Japan
| | - Akimitsu Okamoto
- Department of Chemistry and Biotechnology , The University of Tokyo , 7-3-1 Hongo, Bunkyo-ku , Tokyo 113-8656 , Japan.,Research Center for Advanced Science and Technology , The University of Tokyo , 4-6-1 Komaba, Meguro-ku , Tokyo 153-8904 , Japan
| |
Collapse
|
26
|
Kolodny G, Li X, Balk S. Addressing Cancer Chemotherapeutic Toxicity, Resistance, and Heterogeneity: Novel Theranostic Use of DNA‐Encoded Small Molecule Libraries. Bioessays 2018; 40:e1800057. [DOI: 10.1002/bies.201800057] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2018] [Revised: 07/08/2018] [Indexed: 11/09/2022]
Affiliation(s)
- Gerald Kolodny
- Beth Israel Deaconess Medical Center − Radiology/Nuclear Medicine and Molecular Imaging330 Brookline AvenueBostonMA02215USA
| | - Xiaoyu Li
- Hong Kong University − ChemistryPokfulam RoadHong Kong
| | - Steven Balk
- Beth Israel Deaconess Medical Center − Medicine330 Brookline AvenueBostonMA02215USA
| |
Collapse
|
27
|
Neri D, Lerner RA. DNA-Encoded Chemical Libraries: A Selection System Based on Endowing Organic Compounds with Amplifiable Information. Annu Rev Biochem 2018; 87:479-502. [PMID: 29328784 PMCID: PMC6080696 DOI: 10.1146/annurev-biochem-062917-012550] [Citation(s) in RCA: 265] [Impact Index Per Article: 44.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The discovery of organic ligands that bind specifically to proteins is a central problem in chemistry, biology, and the biomedical sciences. The encoding of individual organic molecules with distinctive DNA tags, serving as amplifiable identification bar codes, allows the construction and screening of combinatorial libraries of unprecedented size, thus facilitating the discovery of ligands to many different protein targets. Fundamentally, one links powers of genetics and chemical synthesis. After the initial description of DNA-encoded chemical libraries in 1992, several experimental embodiments of the technology have been reduced to practice. This review provides a historical account of important milestones in the development of DNA-encoded chemical libraries, a survey of relevant ongoing research activities, and a glimpse into the future.
Collapse
Affiliation(s)
- Dario Neri
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH Zürich), 8093 Zürich, Switzerland;
| | - Richard A Lerner
- Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, USA;
| |
Collapse
|
28
|
Favalli N, Bassi G, Scheuermann J, Neri D. DNA-encoded chemical libraries - achievements and remaining challenges. FEBS Lett 2018; 592:2168-2180. [PMID: 29683493 PMCID: PMC6126621 DOI: 10.1002/1873-3468.13068] [Citation(s) in RCA: 120] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Revised: 04/11/2018] [Accepted: 04/13/2018] [Indexed: 11/10/2022]
Abstract
DNA-encoded chemical libraries (DECLs) are collections of compounds, individually coupled to DNA tags serving as amplifiable identification barcodes. Since individual compounds can be identified by the associated DNA tag, they can be stored as a mixture, allowing the synthesis and screening of combinatorial libraries of unprecedented size, facilitated by the implementation of split-and-pool synthetic procedures or other experimental methodologies. In this review, we briefly present relevant concepts and technologies, which are required for the implementation and interpretation of screening procedures with DNA-encoded chemical libraries. Moreover, we illustrate some success stories, detailing how novel ligands were discovered from encoded libraries. Finally, we critically review what can realistically be achieved with the technology at the present time, highlighting challenges and opportunities for the future.
Collapse
Affiliation(s)
- Nicholas Favalli
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH Zürich), Vladimir-Prelog-Weg 4, CH-8093 Zürich (Switzerland)
| | - Gabriele Bassi
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH Zürich), Vladimir-Prelog-Weg 4, CH-8093 Zürich (Switzerland)
| | - Jörg Scheuermann
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH Zürich), Vladimir-Prelog-Weg 4, CH-8093 Zürich (Switzerland)
| | - Dario Neri
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH Zürich), Vladimir-Prelog-Weg 4, CH-8093 Zürich (Switzerland)
| |
Collapse
|
29
|
Second-generation DNA-templated macrocycle libraries for the discovery of bioactive small molecules. Nat Chem 2018; 10:704-714. [PMID: 29610462 PMCID: PMC6014893 DOI: 10.1038/s41557-018-0033-8] [Citation(s) in RCA: 133] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Accepted: 02/28/2018] [Indexed: 12/21/2022]
Abstract
DNA-encoded libraries have emerged as a widely used resource for the discovery of bioactive small molecules, and offer substantial advantages compared with conventional small-molecule libraries. Here, we have developed and streamlined multiple fundamental aspects of DNA-encoded and DNA-templated library synthesis methodology, including computational identification and experimental validation of a 20 × 20 × 20 × 80 set of orthogonal codons, chemical and computational tools for enhancing the structural diversity and drug-likeness of library members, a highly efficient polymerase-mediated template library assembly strategy, and library isolation and purification methods. We have integrated these improved methods to produce a second-generation DNA-templated library of 256,000 small-molecule macrocycles with improved drug-like physical properties. In vitro selection of this library for insulin-degrading enzyme affinity resulted in novel insulin-degrading enzyme inhibitors, including one of unusual potency and novel macrocycle stereochemistry (IC50 = 40 nM). Collectively, these developments enable DNA-templated small-molecule libraries to serve as more powerful, accessible, streamlined and cost-effective tools for bioactive small-molecule discovery.
Collapse
|
30
|
Li Y, De Luca R, Cazzamalli S, Pretto F, Bajic D, Scheuermann J, Neri D. Versatile protein recognition by the encoded display of multiple chemical elements on a constant macrocyclic scaffold. Nat Chem 2018; 10:441-448. [PMID: 29556050 PMCID: PMC6044424 DOI: 10.1038/s41557-018-0017-8] [Citation(s) in RCA: 103] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2017] [Accepted: 01/04/2018] [Indexed: 11/09/2022]
Abstract
In nature, specific antibodies can be generated as a result of an adaptive selection and expansion of lymphocytes with suitable protein binding properties. We attempted to mimic antibody-antigen recognition by displaying multiple chemical diversity elements on a defined macrocyclic scaffold. Encoding of the displayed combinations was achieved using distinctive DNA tags, resulting in a library size of 35,393,112. Specific binders could be isolated against a variety of proteins, including carbonic anhydrase IX, horseradish peroxidase, tankyrase 1, human serum albumin, alpha-1 acid glycoprotein, calmodulin, prostate-specific antigen and tumour necrosis factor. Similar to antibodies, the encoded display of multiple chemical elements on a constant scaffold enabled practical applications, such as fluorescence microscopy procedures or the selective in vivo delivery of payloads to tumours. Furthermore, the versatile structure of the scaffold facilitated the generation of protein-specific chemical probes, as illustrated by photo-crosslinking.
Collapse
Affiliation(s)
- Yizhou Li
- Chongqing Key Laboratory of Natural Product Synthesis and Drug Research, School of Pharmaceutical Sciences, Chongqing University, Shapingba, Chongqing, China
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH Zürich), Zürich, Switzerland
| | - Roberto De Luca
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH Zürich), Zürich, Switzerland
| | - Samuele Cazzamalli
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH Zürich), Zürich, Switzerland
| | | | - Davor Bajic
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH Zürich), Zürich, Switzerland
| | - Jörg Scheuermann
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH Zürich), Zürich, Switzerland.
| | - Dario Neri
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH Zürich), Zürich, Switzerland.
| |
Collapse
|
31
|
O’Reilly RK, Turberfield AJ, Wilks TR. The Evolution of DNA-Templated Synthesis as a Tool for Materials Discovery. Acc Chem Res 2017; 50:2496-2509. [PMID: 28915003 PMCID: PMC5746846 DOI: 10.1021/acs.accounts.7b00280] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
![]()
Precise control over reactivity and molecular
structure is a fundamental
goal of the chemical sciences. Billions of years of evolution by natural
selection have resulted in chemical systems capable of information
storage, self-replication, catalysis, capture and production of light,
and even cognition. In all these cases, control over molecular structure
is required to achieve a particular function: without structural control,
function may be impaired, unpredictable, or impossible. The
search for molecules with a desired function is often achieved
by synthesizing a combinatorial library, which contains many or all
possible combinations of a set of chemical building blocks (BBs),
and then screening this library to identify “successful”
structures. The largest libraries made by conventional synthesis are
currently of the order of 108 distinct molecules. To put
this in context, there are 1013 ways of arranging the 21
proteinogenic amino acids in chains up to 10 units long. Given that
we know that a number of these compounds have potent biological activity,
it would be highly desirable to be able to search them all to identify
leads for new drug molecules. Large libraries of oligonucleotides
can be synthesized combinatorially and translated into peptides using
systems based on biological replication such as mRNA display, with
selected molecules identified by DNA sequencing; but these methods
are limited to BBs that are compatible with cellular machinery. In
order to search the vast tracts of chemical space beyond nucleic acids
and natural peptides, an alternative approach is required. DNA-templated
synthesis (DTS) could enable us to meet this challenge.
DTS controls chemical product formation by using the specificity of
DNA hybridization to bring selected reactants into close proximity,
and is capable of the programmed synthesis of many distinct products
in the same reaction vessel. By making use of dynamic, programmable
DNA processes, it is possible to engineer a system that can translate
instructions coded as a sequence of DNA bases into a chemical structure—a
process analogous to the action of the ribosome in living organisms
but with the potential to create a much more chemically diverse set
of products. It is also possible to ensure that each product molecule
is tagged with its identifying DNA sequence. Compound libraries synthesized
in this way can be exposed to selection against suitable targets,
enriching successful molecules. The encoding DNA can then be amplified
using the polymerase chain reaction and decoded by DNA sequencing.
More importantly, the DNA instruction sequences can be mutated and
reused during multiple rounds of amplification, translation, and selection.
In other words, DTS could be used as the foundation for a system of
synthetic molecular evolution, which could allow us to efficiently
search a vast chemical space. This has huge potential to revolutionize
materials discovery—imagine being able to evolve molecules
for light harvesting, or catalysts for CO2 fixation. The field of DTS has developed to the point where a wide variety
of reactions can be performed on a DNA template. Complex architectures
and autonomous “DNA robots” have been implemented for
the controlled assembly of BBs, and these mechanisms have in turn
enabled the one-pot synthesis of large combinatorial libraries. Indeed,
DTS libraries are being exploited by pharmaceutical companies and
have already found their way into drug lead discovery programs. This
Account explores the processes involved in DTS and highlights the
challenges that remain in creating a general system for molecular
discovery by evolution.
Collapse
Affiliation(s)
- Rachel K. O’Reilly
- Department
of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Andrew J. Turberfield
- Clarendon
Laboratory, Department of Physics, University of Oxford, Parks Road, Oxford OX1 3PU, United Kingdom
| | - Thomas R. Wilks
- Department
of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom
| |
Collapse
|
32
|
Škopić MK, Salamon H, Bugain O, Jung K, Gohla A, Doetsch LJ, Dos Santos D, Bhat A, Wagner B, Brunschweiger A. Acid- and Au(i)-mediated synthesis of hexathymidine-DNA-heterocycle chimeras, an efficient entry to DNA-encoded libraries inspired by drug structures. Chem Sci 2017; 8:3356-3361. [PMID: 28507705 PMCID: PMC5416911 DOI: 10.1039/c7sc00455a] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Accepted: 02/27/2017] [Indexed: 11/21/2022] Open
Abstract
Libraries of DNA-tagged compounds are a validated screening technology for drug discovery. They are synthesized through combinatorial iterations of alternated coding and preparative synthesis steps. Thus, large chemical space can be accessed for target-based screening. However, the need to preserve the functionality of the DNA tag severely restricts the choice of chemical methods for library synthesis. Acidic organocatalysts, transition metals, and oxidants furnish diverse drug-like structures from simple starting materials, but cause loss of genetic information by depurination. A hexathymidine oligonucleotide, called "hexT" allows the chemist utilizing these classes of catalysts to access a potentially broad variety of structures in the initial step of library synthesis. We exploited its catalyst tolerance to efficiently synthesize diverse substituted β-carbolines, pyrazolines, and pyrazoles from readily available starting materials as hexT conjugates by acid- and Au(i)-catalysis, respectively. The hexT conjugates were ligated to coding DNA sequences yielding encoded screening libraries inspired by drug structures.
Collapse
Affiliation(s)
- Mateja Klika Škopić
- Department of Chemistry and Chemical Biology , TU Dortmund University , Otto-Hahn-Str. 6 , 44227 Dortmund , Germany .
| | - Hazem Salamon
- Department of Chemistry and Chemical Biology , TU Dortmund University , Otto-Hahn-Str. 6 , 44227 Dortmund , Germany .
| | - Olivia Bugain
- Department of Chemistry and Chemical Biology , TU Dortmund University , Otto-Hahn-Str. 6 , 44227 Dortmund , Germany .
| | - Kathrin Jung
- Department of Chemistry and Chemical Biology , TU Dortmund University , Otto-Hahn-Str. 6 , 44227 Dortmund , Germany .
| | - Anne Gohla
- Department of Chemistry and Chemical Biology , TU Dortmund University , Otto-Hahn-Str. 6 , 44227 Dortmund , Germany .
| | - Lara J Doetsch
- Department of Chemistry and Chemical Biology , TU Dortmund University , Otto-Hahn-Str. 6 , 44227 Dortmund , Germany .
| | - Denise Dos Santos
- Department of Chemistry and Chemical Biology , TU Dortmund University , Otto-Hahn-Str. 6 , 44227 Dortmund , Germany .
| | - Avinash Bhat
- Department of Chemistry and Chemical Biology , TU Dortmund University , Otto-Hahn-Str. 6 , 44227 Dortmund , Germany .
| | - Bernd Wagner
- Department of Chemistry and Chemical Biology , TU Dortmund University , Otto-Hahn-Str. 6 , 44227 Dortmund , Germany .
| | - Andreas Brunschweiger
- Department of Chemistry and Chemical Biology , TU Dortmund University , Otto-Hahn-Str. 6 , 44227 Dortmund , Germany .
| |
Collapse
|
33
|
Klika Škopić M, Willems S, Wagner B, Schieven J, Krause N, Brunschweiger A. Exploration of a Au(i)-mediated three-component reaction for the synthesis of DNA-tagged highly substituted spiroheterocycles. Org Biomol Chem 2017; 15:8648-8654. [DOI: 10.1039/c7ob02347b] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
A gold(i)-mediated reaction to a DNA-tagged spirocycle, and the tolerance of different nucleic acids to the reaction conditions are demonstrated.
Collapse
Affiliation(s)
- Mateja Klika Škopić
- Department of Chemistry and Chemical Biology
- TU Dortmund University
- 44227 Dortmund
- Germany
| | - Suzanne Willems
- Department of Chemistry and Chemical Biology
- TU Dortmund University
- 44227 Dortmund
- Germany
| | - Bernd Wagner
- Department of Chemistry and Chemical Biology
- TU Dortmund University
- 44227 Dortmund
- Germany
| | - Justin Schieven
- Department of Chemistry and Chemical Biology
- TU Dortmund University
- 44227 Dortmund
- Germany
| | - Norbert Krause
- Department of Chemistry and Chemical Biology
- TU Dortmund University
- 44227 Dortmund
- Germany
| | - Andreas Brunschweiger
- Department of Chemistry and Chemical Biology
- TU Dortmund University
- 44227 Dortmund
- Germany
| |
Collapse
|
34
|
Abstract
DNA-encoded chemical library technologies are increasingly being adopted in drug discovery for hit and lead generation. DNA-encoded chemistry enables the exploration of chemical spaces four to five orders of magnitude more deeply than is achievable by traditional high-throughput screening methods. Operation of this technology requires developing a range of capabilities including aqueous synthetic chemistry, building block acquisition, oligonucleotide conjugation, large-scale molecular biological transformations, selection methodologies, PCR, sequencing, sequence data analysis and the analysis of large chemistry spaces. This Review provides an overview of the development and applications of DNA-encoded chemistry, highlighting the challenges and future directions for the use of this technology.
Collapse
|
35
|
Recent advances on the encoding and selection methods of DNA-encoded chemical library. Bioorg Med Chem Lett 2016; 27:361-369. [PMID: 28011218 DOI: 10.1016/j.bmcl.2016.12.025] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Revised: 12/07/2016] [Accepted: 12/08/2016] [Indexed: 11/22/2022]
Abstract
DNA-encoded chemical library (DEL) has emerged as a powerful and versatile tool for ligand discovery in chemical biology research and in drug discovery. Encoding and selection methods are two of the most important technological aspects of DEL that can dictate the performance and utilities of DELs. In this digest, we have summarized recent advances on the encoding and selection strategies of DEL and also discussed the latest developments on DNA-encoded dynamic library, a new frontier in DEL research.
Collapse
|
36
|
Li Y, Gabriele E, Samain F, Favalli N, Sladojevich F, Scheuermann J, Neri D. Optimized Reaction Conditions for Amide Bond Formation in DNA-Encoded Combinatorial Libraries. ACS COMBINATORIAL SCIENCE 2016; 18:438-43. [PMID: 27314981 DOI: 10.1021/acscombsci.6b00058] [Citation(s) in RCA: 92] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
DNA-encoded combinatorial libraries are increasingly being used as tools for the discovery of small organic binding molecules to proteins of biological or pharmaceutical interest. In the majority of cases, synthetic procedures for the formation of DNA-encoded combinatorial libraries incorporate at least one step of amide bond formation between amino-modified DNA and a carboxylic acid. We investigated reaction conditions and established a methodology by using 1-ethyl-3-(3-(dimethylamino)propyl)carbodiimide, 1-hydroxy-7-azabenzotriazole and N,N'-diisopropylethylamine (EDC/HOAt/DIPEA) in combination, which provided conversions greater than 75% for 423/543 (78%) of the carboxylic acids tested. These reaction conditions were efficient with a variety of primary and secondary amines, as well as with various types of amino-modified oligonucleotides. The reaction conditions, which also worked efficiently over a broad range of DNA concentrations and reaction scales, should facilitate the synthesis of novel DNA-encoded combinatorial libraries.
Collapse
Affiliation(s)
- Yizhou Li
- Department
of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH Zürich), Vladimir-Prelog-Weg 3, CH-8093 Zürich, Switzerland
| | - Elena Gabriele
- Department
of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH Zürich), Vladimir-Prelog-Weg 3, CH-8093 Zürich, Switzerland
| | - Florent Samain
- Philochem AG, Libernstrasse 3, 8112 Otelfingen, Switzerland
| | - Nicholas Favalli
- Department
of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH Zürich), Vladimir-Prelog-Weg 3, CH-8093 Zürich, Switzerland
| | | | - Jörg Scheuermann
- Department
of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH Zürich), Vladimir-Prelog-Weg 3, CH-8093 Zürich, Switzerland
| | - Dario Neri
- Department
of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH Zürich), Vladimir-Prelog-Weg 3, CH-8093 Zürich, Switzerland
| |
Collapse
|
37
|
Zimmermann G, Neri D. DNA-encoded chemical libraries: foundations and applications in lead discovery. Drug Discov Today 2016; 21:1828-1834. [PMID: 27477486 DOI: 10.1016/j.drudis.2016.07.013] [Citation(s) in RCA: 98] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Revised: 06/17/2016] [Accepted: 07/23/2016] [Indexed: 12/16/2022]
Abstract
DNA-encoded chemical libraries have emerged as a powerful tool for hit identification in the pharmaceutical industry and in academia. Similar to biological display techniques (such as phage display technology), DNA-encoded chemical libraries contain a link between the displayed chemical building block and an amplifiable genetic barcode on DNA. Using routine procedures, libraries containing millions to billions of compounds can be easily produced within a few weeks. The resulting compound libraries are screened in a single test tube against proteins of pharmaceutical interest and hits can be identified by PCR amplification of DNA barcodes and subsequent high-throughput sequencing.
Collapse
Affiliation(s)
- Gunther Zimmermann
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH Zürich), Vladimir Prelog Weg 1-5/10, CH-8093 Zürich, Switzerland
| | - Dario Neri
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH Zürich), Vladimir Prelog Weg 1-5/10, CH-8093 Zürich, Switzerland.
| |
Collapse
|
38
|
Decurtins W, Wichert M, Franzini RM, Buller F, Stravs MA, Zhang Y, Neri D, Scheuermann J. Automated screening for small organic ligands using DNA-encoded chemical libraries. Nat Protoc 2016; 11:764-80. [PMID: 26985574 DOI: 10.1038/nprot.2016.039] [Citation(s) in RCA: 91] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
DNA-encoded chemical libraries (DECLs) are collections of organic compounds that are individually linked to different oligonucleotides, serving as amplifiable identification barcodes. As all compounds in the library can be identified by their DNA tags, they can be mixed and used in affinity-capture experiments on target proteins of interest. In this protocol, we describe the screening process that allows the identification of the few binding molecules within the multiplicity of library members. First, the automated affinity selection process physically isolates binding library members. Second, the DNA codes of the isolated binders are PCR-amplified and subjected to high-throughput DNA sequencing. Third, the obtained sequencing data are evaluated using a C++ program and the results are displayed using MATLAB software. The resulting selection fingerprints facilitate the discrimination of binding from nonbinding library members. The described procedures allow the identification of small organic ligands to biological targets from a DECL within 10 d.
Collapse
Affiliation(s)
- Willy Decurtins
- Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, Swiss Federal Institute of Technology (ETH Zurich), Zurich, Switzerland
| | - Moreno Wichert
- Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, Swiss Federal Institute of Technology (ETH Zurich), Zurich, Switzerland
| | - Raphael M Franzini
- Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, Swiss Federal Institute of Technology (ETH Zurich), Zurich, Switzerland
| | - Fabian Buller
- Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, Swiss Federal Institute of Technology (ETH Zurich), Zurich, Switzerland
| | - Michael A Stravs
- Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, Swiss Federal Institute of Technology (ETH Zurich), Zurich, Switzerland
| | - Yixin Zhang
- Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, Swiss Federal Institute of Technology (ETH Zurich), Zurich, Switzerland
| | - Dario Neri
- Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, Swiss Federal Institute of Technology (ETH Zurich), Zurich, Switzerland
| | - Jörg Scheuermann
- Department of Chemistry and Applied Biosciences, Institute of Pharmaceutical Sciences, Swiss Federal Institute of Technology (ETH Zurich), Zurich, Switzerland
| |
Collapse
|
39
|
Affiliation(s)
- Raphael M. Franzini
- Department
of Medicinal Chemistry,
College of Pharmacy, University of Utah, 30 S 2000 E, Salt Lake City, Utah 84112, United States
| | - Cassie Randolph
- Department
of Medicinal Chemistry,
College of Pharmacy, University of Utah, 30 S 2000 E, Salt Lake City, Utah 84112, United States
| |
Collapse
|
40
|
Salamon H, Klika Škopić M, Jung K, Bugain O, Brunschweiger A. Chemical Biology Probes from Advanced DNA-encoded Libraries. ACS Chem Biol 2016; 11:296-307. [PMID: 26820267 DOI: 10.1021/acschembio.5b00981] [Citation(s) in RCA: 95] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The identification of bioactive compounds is a crucial step toward development of probes for chemical biology studies. Screening of DNA-encoded small molecule libraries (DELs) has emerged as a validated technology to interrogate vast chemical space. DELs consist of chimeric molecules composed of a low-molecular weight compound that is conjugated to a DNA identifier tag. They are screened as pooled libraries using selection to identify "hits." Screening of DELs has identified numerous bioactive compounds. Some of these molecules were instrumental in gaining a deeper understanding of biological systems. One of the main challenges in the field is the development of synthesis methodology for DELs.
Collapse
Affiliation(s)
- Hazem Salamon
- Faculty of Chemistry and
Chemical Biology, Technical University of Dortmund, Otto-Hahn-Straße
6, D-44227 Dortmund, Germany
| | - Mateja Klika Škopić
- Faculty of Chemistry and
Chemical Biology, Technical University of Dortmund, Otto-Hahn-Straße
6, D-44227 Dortmund, Germany
| | - Kathrin Jung
- Faculty of Chemistry and
Chemical Biology, Technical University of Dortmund, Otto-Hahn-Straße
6, D-44227 Dortmund, Germany
| | - Olivia Bugain
- Faculty of Chemistry and
Chemical Biology, Technical University of Dortmund, Otto-Hahn-Straße
6, D-44227 Dortmund, Germany
| | - Andreas Brunschweiger
- Faculty of Chemistry and
Chemical Biology, Technical University of Dortmund, Otto-Hahn-Straße
6, D-44227 Dortmund, Germany
| |
Collapse
|
41
|
Turkin A, Zhang L, Marcozzi A, Mangel WF, Herrmann A, van Oijen AM. Speeding up biomolecular interactions by molecular sledding. Chem Sci 2016; 7:916-920. [PMID: 26913169 PMCID: PMC4762599 DOI: 10.1039/c5sc03063c] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Accepted: 10/06/2015] [Indexed: 01/30/2023] Open
Abstract
Numerous biological processes involve association of a protein with its binding partner, an event that is preceded by a diffusion-mediated search bringing the two partners together. Often hindered by crowding in biologically relevant environments, three-dimensional diffusion can be slow and result in long bimolecular association times. Similarly, the initial association step between two binding partners often represents a rate-limiting step in biotechnologically relevant reactions. We demonstrate the practical use of an 11-a.a. DNA-interacting peptide derived from adenovirus to reduce the dimensionality of diffusional search processes and speed up associations between biological macromolecules. We functionalise binding partners with the peptide and demonstrate that the ability of the peptide to one-dimensionally diffuse along DNA results in a 20-fold reduction in reaction time. We also show that modifying PCR primers with the peptide sled enables significant acceleration of standard PCR reactions.
Collapse
Affiliation(s)
- Alexander Turkin
- Single-molecule Biophysics , Zernike Institute for Advanced Materials , University of Groningen , Groningen 9747 AG , The Netherlands .
| | - Lei Zhang
- Department of Polymer Chemistry , Zernike Institute for Advanced Materials , University of Groningen , Groningen 9747 AG , The Netherlands .
| | - Alessio Marcozzi
- Department of Polymer Chemistry , Zernike Institute for Advanced Materials , University of Groningen , Groningen 9747 AG , The Netherlands .
| | | | - Andreas Herrmann
- Department of Polymer Chemistry , Zernike Institute for Advanced Materials , University of Groningen , Groningen 9747 AG , The Netherlands .
| | - Antoine M. van Oijen
- Single-molecule Biophysics , Zernike Institute for Advanced Materials , University of Groningen , Groningen 9747 AG , The Netherlands .
| |
Collapse
|
42
|
Chan AI, McGregor LM, Liu DR. Novel selection methods for DNA-encoded chemical libraries. Curr Opin Chem Biol 2015; 26:55-61. [PMID: 25723146 DOI: 10.1016/j.cbpa.2015.02.010] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Revised: 01/31/2015] [Accepted: 02/09/2015] [Indexed: 02/02/2023]
Abstract
Driven by the need for new compounds to serve as biological probes and leads for therapeutic development and the growing accessibility of DNA technologies including high-throughput sequencing, many academic and industrial groups have begun to use DNA-encoded chemical libraries as a source of bioactive small molecules. In this review, we describe the technologies that have enabled the selection of compounds with desired activities from these libraries. These methods exploit the sensitivity of in vitro selection coupled with DNA amplification to overcome some of the limitations and costs associated with conventional screening methods. In addition, we highlight newer techniques with the potential to be applied to the high-throughput evaluation of DNA-encoded chemical libraries.
Collapse
Affiliation(s)
- Alix I Chan
- Department of Chemistry and Chemical Biology and Howard Hughes Medical Institute, Harvard University, 12 Oxford St, Cambridge, MA 02138, United States
| | - Lynn M McGregor
- Department of Chemistry and Chemical Biology and Howard Hughes Medical Institute, Harvard University, 12 Oxford St, Cambridge, MA 02138, United States
| | - David R Liu
- Department of Chemistry and Chemical Biology and Howard Hughes Medical Institute, Harvard University, 12 Oxford St, Cambridge, MA 02138, United States.
| |
Collapse
|
43
|
Li G, Zheng W, Liu Y, Li X. Novel encoding methods for DNA-templated chemical libraries. Curr Opin Chem Biol 2015; 26:25-33. [PMID: 25635927 DOI: 10.1016/j.cbpa.2015.01.004] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Accepted: 01/08/2015] [Indexed: 12/12/2022]
Abstract
Among various types of DNA-encoded chemical libraries, DNA-templated library takes advantage of the sequence-specificity of DNA hybridization, enabling not only highly effective DNA-templated chemical reactions, but also high fidelity in library encoding. This brief review summarizes recent advances that have been made on the encoding strategies for DNA-templated libraries, and it also highlights their respective advantages and limitations for the preparation of DNA-encoded libraries.
Collapse
Affiliation(s)
- Gang Li
- Key Laboratory of Bioorganic Chemistry and Molecular Engineering of the Ministry of Education, Beijing National Laboratory of Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Wenlu Zheng
- Key Laboratory of Chemical Genomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, China
| | - Ying Liu
- Key Laboratory of Bioorganic Chemistry and Molecular Engineering of the Ministry of Education, Beijing National Laboratory of Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Xiaoyu Li
- Key Laboratory of Bioorganic Chemistry and Molecular Engineering of the Ministry of Education, Beijing National Laboratory of Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China; Key Laboratory of Chemical Genomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen 518055, China.
| |
Collapse
|
44
|
Wichert M, Krall N, Decurtins W, Franzini RM, Pretto F, Schneider P, Neri D, Scheuermann J. Dual-display of small molecules enables the discovery of ligand pairs and facilitates affinity maturation. Nat Chem 2015; 7:241-9. [DOI: 10.1038/nchem.2158] [Citation(s) in RCA: 152] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2014] [Accepted: 12/09/2014] [Indexed: 12/22/2022]
|
45
|
Franzini RM, Nauer A, Scheuermann J, Neri D. Interrogating target-specificity by parallel screening of a DNA-encoded chemical library against closely related proteins. Chem Commun (Camb) 2015; 51:8014-6. [DOI: 10.1039/c5cc01230a] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Screening a DNA-encoded chemical library against closely related proteins enabled us to predict target specificity as illustrated for serum albumins from different species.
Collapse
Affiliation(s)
| | - Angela Nauer
- Institute of Pharmaceutical Sciences
- ETH Zürich
- 8093 Zürich
- Switzerland
| | - Jörg Scheuermann
- Institute of Pharmaceutical Sciences
- ETH Zürich
- 8093 Zürich
- Switzerland
| | - Dario Neri
- Institute of Pharmaceutical Sciences
- ETH Zürich
- 8093 Zürich
- Switzerland
| |
Collapse
|
46
|
Franzini RM, Neri D, Scheuermann J. DNA-encoded chemical libraries: advancing beyond conventional small-molecule libraries. Acc Chem Res 2014; 47:1247-55. [PMID: 24673190 DOI: 10.1021/ar400284t] [Citation(s) in RCA: 180] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
DNA-encoded chemical libraries (DECLs) represent a promising tool in drug discovery. DECL technology allows the synthesis and screening of chemical libraries of unprecedented size at moderate costs. In analogy to phage-display technology, where large antibody libraries are displayed on the surface of filamentous phage and are genetically encoded in the phage genome, DECLs feature the display of individual small organic chemical moieties on DNA fragments serving as amplifiable identification barcodes. The DNA-tag facilitates the synthesis and allows the simultaneous screening of very large sets of compounds (up to billions of molecules), because the hit compounds can easily be identified and quantified by PCR-amplification of the DNA-barcode followed by high-throughput DNA sequencing. Several approaches have been used to generate DECLs, differing both in the methods used for library encoding and for the combinatorial assembly of chemical moieties. For example, DECLs can be used for fragment-based drug discovery, displaying a single molecule on DNA or two chemical moieties at the extremities of complementary DNA strands. DECLs can vary substantially in the chemical structures and the library size. While ultralarge libraries containing billions of compounds have been reported containing four or more sets of building blocks, also smaller libraries have been shown to be efficient for ligand discovery. In general, it has been found that the overall library size is a poor predictor for library performance and that the number and diversity of the building blocks are rather important indicators. Smaller libraries consisting of two to three sets of building blocks better fulfill the criteria of drug-likeness and often have higher quality. In this Account, we present advances in the DECL field from proof-of-principle studies to practical applications for drug discovery, both in industry and in academia. DECL technology can yield specific binders to a variety of target proteins and is likely to become a standard tool for pharmaceutical hit discovery, lead expansion, and Chemical Biology research. The introduction of new methodologies for library encoding and for compound synthesis in the presence of DNA is an exciting research field and will crucially contribute to the performance and the propagation of the technology.
Collapse
Affiliation(s)
- Raphael M. Franzini
- Institute of Pharmaceutical
Sciences, Department of Chemistry and Applied Biosciences, ETH Zürich, Wolfgang-Pauli-Strasse 10, 8093 Zürich, Switzerland
| | - Dario Neri
- Institute of Pharmaceutical
Sciences, Department of Chemistry and Applied Biosciences, ETH Zürich, Wolfgang-Pauli-Strasse 10, 8093 Zürich, Switzerland
| | - Jörg Scheuermann
- Institute of Pharmaceutical
Sciences, Department of Chemistry and Applied Biosciences, ETH Zürich, Wolfgang-Pauli-Strasse 10, 8093 Zürich, Switzerland
| |
Collapse
|
47
|
Cao C, Zhao P, Li Z, Chen Z, Huang Y, Bai Y, Li X. A DNA-templated synthesis of encoded small molecules by DNA self-assembly. Chem Commun (Camb) 2014; 50:10997-9. [DOI: 10.1039/c4cc03380a] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Encoded libraries can be prepared by DNA-templated synthesis without any DNA template.
Collapse
Affiliation(s)
- Cheng Cao
- Key Laboratory of Bioorganic Chemistry and Molecular Engineering of the Ministry of Education
- Beijing National Laboratory of Molecular Sciences (BNLMS)
- College of Chemistry and Molecular Engineering
- Peking University
- Beijing, China 100871
| | - Peng Zhao
- Key Laboratory of Bioorganic Chemistry and Molecular Engineering of the Ministry of Education
- Beijing National Laboratory of Molecular Sciences (BNLMS)
- College of Chemistry and Molecular Engineering
- Peking University
- Beijing, China 100871
| | - Ze Li
- Key Laboratory of Bioorganic Chemistry and Molecular Engineering of the Ministry of Education
- Beijing National Laboratory of Molecular Sciences (BNLMS)
- College of Chemistry and Molecular Engineering
- Peking University
- Beijing, China 100871
| | - Zitian Chen
- Biodynamic Optical Imaging Center (BIOPIC) and College of Engineering
- Peking University
- Beijing, China 100871
| | - Yanyi Huang
- Biodynamic Optical Imaging Center (BIOPIC) and College of Engineering
- Peking University
- Beijing, China 100871
| | - Yu Bai
- Key Laboratory of Bioorganic Chemistry and Molecular Engineering of the Ministry of Education
- Beijing National Laboratory of Molecular Sciences (BNLMS)
- College of Chemistry and Molecular Engineering
- Peking University
- Beijing, China 100871
| | - Xiaoyu Li
- Key Laboratory of Bioorganic Chemistry and Molecular Engineering of the Ministry of Education
- Beijing National Laboratory of Molecular Sciences (BNLMS)
- College of Chemistry and Molecular Engineering
- Peking University
- Beijing, China 100871
| |
Collapse
|
48
|
Domaille DW, Cha JN. Aniline-terminated DNA catalyzes rapid DNA–hydrazone formation at physiological pH. Chem Commun (Camb) 2014; 50:3831-3. [DOI: 10.1039/c4cc00292j] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
We integrated aniline organocatalytic hydrazone formation into a DNA-templated variant to increase the rate of DNA–hydrazone formation in a sequence-specific manner. Through systematic optimizations of the aniline organocatalyst, we were able to identify a derivative that is capable of accelerating the rate of DNA–hydrazone formation by more than 85-fold above that of the uncatalyzed variant.
Collapse
Affiliation(s)
- Dylan W. Domaille
- Department of Chemical and Biological Engineering
- University of Colorado Boulder
- , USA
| | - Jennifer N. Cha
- Department of Chemical and Biological Engineering
- University of Colorado Boulder
- , USA
| |
Collapse
|