51
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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: 87] [Impact Index Per Article: 10.9] [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.
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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
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52
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Satz AL. Simulated Screens of DNA Encoded Libraries: The Potential Influence of Chemical Synthesis Fidelity on Interpretation of Structure-Activity Relationships. ACS COMBINATORIAL SCIENCE 2016; 18:415-24. [PMID: 27116029 DOI: 10.1021/acscombsci.6b00001] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Simulated screening of DNA encoded libraries indicates that the presence of truncated byproducts complicates the relationship between library member enrichment and equilibrium association constant (these truncates result from incomplete chemical reactions during library synthesis). Further, simulations indicate that some patterns observed in reported experimental data may result from the presence of truncated byproducts in the library mixture and not structure-activity relationships. Potential experimental methods of minimizing the presence of truncates are assessed via simulation; the relationship between enrichment and equilibrium association constant for libraries of differing purities is investigated. Data aggregation techniques are demonstrated that allow for more accurate analysis of screening results, in particular when the screened library contains significant quantities of truncates.
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Affiliation(s)
- Alexander L. Satz
- Roche Innovation Center Basel, Grenzacherstrasse
124, 4070 Basel, Switzerland
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53
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Octa-1,7-diene-4,5-diamine Derivatives: Useful Intermediates for the Stereoselective Synthesis of Nitrogen Heterocycles and Ligands for Asymmetric Catalysis. European J Org Chem 2016. [DOI: 10.1002/ejoc.201600310] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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54
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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
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55
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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: 94] [Impact Index Per Article: 11.8] [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.
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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
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56
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Tahara YK, Obinata S, Kanyiva KS, Shibata T, Mándi A, Taniguchi T, Monde K. Enantioselective Synthesis of Aminoindan Carboxylic Acid Derivatives by the Catalytic Intramolecular [2+2+2] Cycloaddition of Amino-Acid-Tethered Triynes. European J Org Chem 2016. [DOI: 10.1002/ejoc.201501612] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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57
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Tian X, Basarab GS, Selmi N, Kogej T, Zhang Y, Clark M, Goodnow Jr. RA. Development and design of the tertiary amino effect reaction for DNA-encoded library synthesis. MEDCHEMCOMM 2016. [DOI: 10.1039/c6md00088f] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The tertiary amino effect reaction was explored and developed for application to DNA-encoded library synthesis.
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Affiliation(s)
| | - Gregory S. Basarab
- AstraZeneca Infection
- Innovative Medicines and Early Development Biotech Unit
- Waltham
- USA
- Department of Chemistry
| | - Nidhal Selmi
- AstraZeneca Discovery Sciences
- Innovative Medicines and Early Development
- Biotech Unity
- SE-431 83 Mölndal
- Sweden
| | - Thierry Kogej
- AstraZeneca Discovery Sciences
- Innovative Medicines and Early Development
- Biotech Unity
- SE-431 83 Mölndal
- Sweden
| | | | | | - Robert A. Goodnow Jr.
- AstraZeneca Discovery Sciences
- Innovative Medicines and Early Development Biotech Unit
- Waltham
- USA
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58
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Zambaldo C, Daguer JP, Saarbach J, Barluenga S, Winssinger N. Screening for covalent inhibitors using DNA-display of small molecule libraries functionalized with cysteine reactive moieties. MEDCHEMCOMM 2016. [DOI: 10.1039/c6md00242k] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Discriminating between non-covalent and covalent inhibitors with SDS wash in microarray-based screen.
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Affiliation(s)
- C. Zambaldo
- Department of Organic Chemistry
- NCCR Chemical Biology
- University of Geneva
- Switzerland
| | - J.-P. Daguer
- Department of Organic Chemistry
- NCCR Chemical Biology
- University of Geneva
- Switzerland
| | - J. Saarbach
- Department of Organic Chemistry
- NCCR Chemical Biology
- University of Geneva
- Switzerland
| | - S. Barluenga
- Department of Organic Chemistry
- NCCR Chemical Biology
- University of Geneva
- Switzerland
| | - N. Winssinger
- Department of Organic Chemistry
- NCCR Chemical Biology
- University of Geneva
- Switzerland
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59
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Abstract
Analysis of physical properties and structural diversity of 57 molecules derived from screening 5–16 DNA encoded libraries against two protein targets. DNA encoded library size is not predictive of productivity.
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Affiliation(s)
- Oliv Eidam
- Roche Pharmaceutical Research and Early Development (pRED)
- Roche Innovation Center Basel
- F. Hoffmann-La Roche Ltd
- CH-4070 Basel
- Switzerland
| | - Alexander L. Satz
- Roche Pharmaceutical Research and Early Development (pRED)
- Roche Innovation Center Basel
- F. Hoffmann-La Roche Ltd
- CH-4070 Basel
- Switzerland
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60
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Arico-Muendel CC. From haystack to needle: finding value with DNA encoded library technology at GSK. MEDCHEMCOMM 2016. [DOI: 10.1039/c6md00341a] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Innovation incubation: DNA encoded library technology (ELT) was invented in academia and biotech, but came of age in a big pharma environment.
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61
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Wu Z, Graybill TL, Zeng X, Platchek M, Zhang J, Bodmer VQ, Wisnoski DD, Deng J, Coppo FT, Yao G, Tamburino A, Scavello G, Franklin GJ, Mataruse S, Bedard KL, Ding Y, Chai J, Summerfield J, Centrella PA, Messer JA, Pope AJ, Israel DI. Cell-Based Selection Expands the Utility of DNA-Encoded Small-Molecule Library Technology to Cell Surface Drug Targets: Identification of Novel Antagonists of the NK3 Tachykinin Receptor. ACS COMBINATORIAL SCIENCE 2015; 17:722-31. [PMID: 26562224 DOI: 10.1021/acscombsci.5b00124] [Citation(s) in RCA: 90] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
DNA-encoded small-molecule library technology has recently emerged as a new paradigm for identifying ligands against drug targets. To date, this technology has been used with soluble protein targets that are produced and used in a purified state. Here, we describe a cell-based method for identifying small-molecule ligands from DNA-encoded libraries against integral membrane protein targets. We use this method to identify novel, potent, and specific inhibitors of NK3, a member of the tachykinin family of G-protein coupled receptors (GPCRs). The method is simple and broadly applicable to other GPCRs and integral membrane proteins. We have extended the application of DNA-encoded library technology to membrane-associated targets and demonstrate the feasibility of selecting DNA-tagged, small-molecule ligands from complex combinatorial libraries against targets in a heterogeneous milieu, such as the surface of a cell.
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Affiliation(s)
- Zining Wu
- Molecular
Discovery Research, GlaxoSmithKline, Collegeville, Pennsylvania 19426, United States
| | - Todd L. Graybill
- Molecular
Discovery Research, GlaxoSmithKline, Collegeville, Pennsylvania 19426, United States
| | - Xin Zeng
- Molecular
Discovery Research, GlaxoSmithKline, Collegeville, Pennsylvania 19426, United States
| | - Michael Platchek
- Molecular
Discovery Research, GlaxoSmithKline, Collegeville, Pennsylvania 19426, United States
| | - Jean Zhang
- Molecular
Discovery Research, GlaxoSmithKline, Waltham, Massachusetts 02451, United States
| | - Vera Q. Bodmer
- Molecular
Discovery Research, GlaxoSmithKline, Collegeville, Pennsylvania 19426, United States
| | - David D. Wisnoski
- Molecular
Discovery Research, GlaxoSmithKline, Collegeville, Pennsylvania 19426, United States
| | - Jianghe Deng
- Molecular
Discovery Research, GlaxoSmithKline, Collegeville, Pennsylvania 19426, United States
| | - Frank T. Coppo
- Molecular
Discovery Research, GlaxoSmithKline, Collegeville, Pennsylvania 19426, United States
| | - Gang Yao
- Molecular
Discovery Research, GlaxoSmithKline, Waltham, Massachusetts 02451, United States
| | - Alex Tamburino
- Molecular
Discovery Research, GlaxoSmithKline, Waltham, Massachusetts 02451, United States
| | - Genaro Scavello
- Molecular
Discovery Research, GlaxoSmithKline, Collegeville, Pennsylvania 19426, United States
| | - G. Joseph Franklin
- Molecular
Discovery Research, GlaxoSmithKline, Waltham, Massachusetts 02451, United States
| | - Sibongile Mataruse
- Molecular
Discovery Research, GlaxoSmithKline, Waltham, Massachusetts 02451, United States
| | - Katie L. Bedard
- Molecular
Discovery Research, GlaxoSmithKline, Waltham, Massachusetts 02451, United States
| | - Yun Ding
- Molecular
Discovery Research, GlaxoSmithKline, Waltham, Massachusetts 02451, United States
| | - Jing Chai
- Molecular
Discovery Research, GlaxoSmithKline, Waltham, Massachusetts 02451, United States
| | - Jennifer Summerfield
- Molecular
Discovery Research, GlaxoSmithKline, Waltham, Massachusetts 02451, United States
| | - Paolo A. Centrella
- Molecular
Discovery Research, GlaxoSmithKline, Waltham, Massachusetts 02451, United States
| | - Jeffrey A. Messer
- Molecular
Discovery Research, GlaxoSmithKline, Waltham, Massachusetts 02451, United States
| | - Andrew J. Pope
- Molecular
Discovery Research, GlaxoSmithKline, Collegeville, Pennsylvania 19426, United States
| | - David I. Israel
- Molecular
Discovery Research, GlaxoSmithKline, Waltham, Massachusetts 02451, United States
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62
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Novel PTP1B inhibitors identified by DNA display of fragment pairs. Bioorg Med Chem Lett 2015; 26:1080-1085. [PMID: 26691757 DOI: 10.1016/j.bmcl.2015.11.102] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Revised: 11/27/2015] [Accepted: 11/28/2015] [Indexed: 12/15/2022]
Abstract
DNA display of PNA-encoded libraries was used to pair fragments containing different phosphotyrosine surrogates with diverse triazoles. Microarray-based screening of the combinatorially paired fragment sets (62,500 combinations) against a prototypical phosphatase, PTP1B, was used to identify the fittest fragments. A focused library (10,000 members) covalently pairing identified fragments with linkers of different length and geometry was synthesized. Screening of the focused library against PTP1B and closely related TCPTP revealed orthogonal inhibitors. The selectivity of the identified inhibitors for PTP1B versus TCPT was confirmed by enzymatic inhibition assay.
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63
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Abstract
Modulation of protein-protein interactions (PPIs) is becoming increasingly important in drug discovery and chemical biology. While a few years ago this 'target class' was deemed to be largely undruggable an impressing number of publications and success stories now show that targeting PPIs with small, drug-like molecules indeed is a feasible approach. Here, we summarize the current state of small-molecule inhibition and stabilization of PPIs and review the active molecules from a structural and medicinal chemistry angle, especially focusing on the key examples of iNOS, LFA-1 and 14-3-3.
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64
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Satz AL. DNA Encoded Library Selections and Insights Provided by Computational Simulations. ACS Chem Biol 2015; 10:2237-45. [PMID: 26176408 DOI: 10.1021/acschembio.5b00378] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
DNA encoded library (DEL) technology allows for rapid generation of extremely large numbers of small molecules and is often used to find novel chemical starting points for pharmaceutically relevant proteins. DEL selection output consists of a list of small-molecule structures and enrichment levels. It is widely presumed that molecules with greater enrichment will have larger equilibrium association constants, and follow-up efforts are triaged accordingly. Herein we describe a simple mathematical model used to simulate DEL selections. Simulations predict that enrichment levels will correlate poorly with equilibrium association constants when selections use high concentrations of protein or lower quality DELs (high variance in final product synthetic yields). A potentially superior technique is demonstrated to qualitatively assess equilibrium association constants directly from sequencing data. This technique requires conducting selections over a range of protein concentrations, so that the influence of synthetic yield can be accounted for.
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Affiliation(s)
- Alexander L. Satz
- Roche Innovation Center Basel, Grenzacherstrasse
124, Basel 4070, Switzerland
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65
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Li G, Zheng W, Chen Z, Zhou Y, Liu Y, Yang J, Huang Y, Li X. Design, preparation, and selection of DNA-encoded dynamic libraries. Chem Sci 2015; 6:7097-7104. [PMID: 28757982 PMCID: PMC5510007 DOI: 10.1039/c5sc02467f] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Accepted: 09/09/2015] [Indexed: 01/10/2023] Open
Abstract
We report a method for the preparation and selection of DNA-encoded dynamic libraries (DEDLs). The library is composed of two sets of DNA-linked small molecules that are under dynamic exchange through DNA hybridization. Addition of the protein target shifted the equilibrium, favouring the assembly of high affinity bivalent binders. Notably, we introduced a novel locking mechanism to stop the dynamic exchange and "freeze" the equilibrium, thereby enabling downstream hit isolation and decoding by PCR amplification and DNA sequencing. Our DEDL approach has circumvented the limitation of library size and realized the analysis and selection of large dynamic libraries. In addition, this method also eliminates the requirement for modified and immobilized target proteins.
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Affiliation(s)
- Gang 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 .
| | - Wenlu Zheng
- Key Laboratory of Chemical Genomics , School of Chemical Biology and Biotechnology , Peking University Shenzhen Graduate School , Shenzhen , China 518055
| | - Zitian Chen
- Biodynamic Optical Imaging Centre (BIOPIC) and College of Engineering , Peking University , Beijing , China 100871
| | - Yu Zhou
- Key Laboratory of Chemical Genomics , School of Chemical Biology and Biotechnology , Peking University Shenzhen Graduate School , Shenzhen , China 518055
| | - Yu Liu
- 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 .
| | - Junrui Yang
- Biodynamic Optical Imaging Centre (BIOPIC) and College of Engineering , Peking University , Beijing , China 100871
| | - Yanyi Huang
- Biodynamic Optical Imaging Centre (BIOPIC) and College of 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 . .,Key Laboratory of Chemical Genomics , School of Chemical Biology and Biotechnology , Peking University Shenzhen Graduate School , Shenzhen , China 518055
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66
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Litovchick A, Clark MA, Keefe AD. Universal strategies for the DNA-encoding of libraries of small molecules using the chemical ligation of oligonucleotide tags. ARTIFICIAL DNA, PNA & XNA 2015; 5:e27896. [PMID: 25483841 PMCID: PMC4014522 DOI: 10.4161/adna.27896] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
The affinity-mediated selection of large libraries of DNA-encoded small molecules is increasingly being used to initiate drug discovery programs. We present universal methods for the encoding of such libraries using the chemical ligation of oligonucleotides. These methods may be used to record the chemical history of individual library members during combinatorial synthesis processes. We demonstrate three different chemical ligation methods as examples of information recording processes (writing) for such libraries and two different cDNA-generation methods as examples of information retrieval processes (reading) from such libraries. The example writing methods include uncatalyzed and Cu(I)-catalyzed alkyne-azide cycloadditions and a novel photochemical thymidine-psoralen cycloaddition. The first reading method “relay primer-dependent bypass” utilizes a relay primer that hybridizes across a chemical ligation junction embedded in a fixed-sequence and is extended at its 3′-terminus prior to ligation to adjacent oligonucleotides. The second reading method “repeat-dependent bypass” utilizes chemical ligation junctions that are flanked by repeated sequences. The upstream repeat is copied prior to a rearrangement event during which the 3′-terminus of the cDNA hybridizes to the downstream repeat and polymerization continues. In principle these reading methods may be used with any ligation chemistry and offer universal strategies for the encoding (writing) and interpretation (reading) of DNA-encoded chemical libraries.
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67
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Ding Y, O’Keefe H, DeLorey JL, Israel DI, Messer JA, Chiu CH, Skinner SR, Matico RE, Murray-Thompson MF, Li F, Clark MA, Cuozzo JW, Arico-Muendel C, Morgan BA. Discovery of Potent and Selective Inhibitors for ADAMTS-4 through DNA-Encoded Library Technology (ELT). ACS Med Chem Lett 2015; 6:888-93. [PMID: 26288689 DOI: 10.1021/acsmedchemlett.5b00138] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2015] [Accepted: 07/07/2015] [Indexed: 12/12/2022] Open
Abstract
The aggrecan degrading metalloprotease ADAMTS-4 has been identified as a novel therapeutic target for osteoarthritis. Here, we use DNA-encoded Library Technology (ELT) to identify novel ADAMTS-4 inhibitors from a DNA-encoded triazine library by affinity selection. Structure-activity relationship studies based on the selection information led to the identification of potent and highly selective inhibitors. For example, 4-(((4-(6,7-dimethoxy-3,4-dihydroisoquinolin-2(1H)-yl)-6-(((4-methylpiperazin-1-yl)methyl)amino)-1,3,5-triazin-2-yl)amino)methyl)-N-ethyl-N-(m-tolyl)benzamide has IC50 of 10 nM against ADAMTS-4, with >1000-fold selectivity over ADAMT-5, MMP-13, TACE, and ADAMTS-13. These inhibitors have no obvious zinc ligand functionality.
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Affiliation(s)
- Yun Ding
- Platform Technology & Science, GlaxoSmithKline, ELT-Boston, 830 Winter Street, Waltham, Massachusetts 02451, United States
| | - Heather O’Keefe
- Platform Technology & Science, GlaxoSmithKline, ELT-Boston, 830 Winter Street, Waltham, Massachusetts 02451, United States
| | - Jennifer L. DeLorey
- Tedor Pharma, Inc., 400 Highland Corporate Drive, Cumberland, Rhode Island 02864, United States
| | - David I. Israel
- Platform Technology & Science, GlaxoSmithKline, ELT-Boston, 830 Winter Street, Waltham, Massachusetts 02451, United States
| | - Jeffrey A. Messer
- Platform Technology & Science, GlaxoSmithKline, ELT-Boston, 830 Winter Street, Waltham, Massachusetts 02451, United States
| | - Cynthia H. Chiu
- Platform Technology & Science, GlaxoSmithKline, ELT-Boston, 830 Winter Street, Waltham, Massachusetts 02451, United States
| | - Steven R. Skinner
- Platform Technology & Science, GlaxoSmithKline, ELT-Boston, 830 Winter Street, Waltham, Massachusetts 02451, United States
| | - Rosalie E. Matico
- Biological
Reagent and Assay Development, GlaxoSmithKline, 709 Swedeland Road, King of Prussia, Pennsylvania 19406, United States
| | - Monique F. Murray-Thompson
- Biological
Reagent and Assay Development, GlaxoSmithKline, 709 Swedeland Road, King of Prussia, Pennsylvania 19406, United States
| | - Fan Li
- Tufts Healthcare Institute, 136 Harrison Avenue, Boston, Massachusetts 02111, United States
| | - Matthew A. Clark
- X-Chem, Inc., 100 Beaver Street, Waltham, Massachusetts 02453, United States
| | - John W. Cuozzo
- X-Chem, Inc., 100 Beaver Street, Waltham, Massachusetts 02453, United States
| | - Christopher Arico-Muendel
- Platform Technology & Science, GlaxoSmithKline, ELT-Boston, 830 Winter Street, Waltham, Massachusetts 02451, United States
| | - Barry A. Morgan
- Center for Drug Discovery, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, United States
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68
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Deng H, Zhou J, Sundersingh FS, Summerfield J, Somers D, Messer JA, Satz AL, Ancellin N, Arico-Muendel CC, (Sargent) Bedard KL, Beljean A, Belyanskaya SL, Bingham R, Smith SE, Boursier E, Carter P, Centrella PA, Clark MA, Chung CW, Davie CP, Delorey JL, Ding Y, Franklin GJ, Grady LC, Herry K, Hobbs C, Kollmann CS, Morgan BA, (Pothier) Kaushansky LJ, Zhou Q. Discovery, SAR, and X-ray Binding Mode Study of BCATm Inhibitors from a Novel DNA-Encoded Library. ACS Med Chem Lett 2015; 6:919-24. [PMID: 26288694 DOI: 10.1021/acsmedchemlett.5b00179] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Accepted: 07/21/2015] [Indexed: 12/27/2022] Open
Abstract
As a potential target for obesity, human BCATm was screened against more than 14 billion DNA encoded compounds of distinct scaffolds followed by off-DNA synthesis and activity confirmation. As a consequence, several series of BCATm inhibitors were discovered. One representative compound (R)-3-((1-(5-bromothiophene-2-carbonyl)pyrrolidin-3-yl)oxy)-N-methyl-2'-(methylsulfonamido)-[1,1'-biphenyl]-4-carboxamide (15e) from a novel compound library synthesized via on-DNA Suzuki-Miyaura cross-coupling showed BCATm inhibitory activity with IC50 = 2.0 μM. A protein crystal structure of 15e revealed that it binds to BCATm within the catalytic site adjacent to the PLP cofactor. The identification of this novel inhibitor series plus the establishment of a BCATm protein structure provided a good starting point for future structure-based discovery of BCATm inhibitors.
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Affiliation(s)
- Hongfeng Deng
- Platform
Technology and Science, GlaxoSmithKline, 830 Winter Street, Waltham, Massachusetts 02451, United States
| | - Jingye Zhou
- Platform
Technology and Science, GlaxoSmithKline, 830 Winter Street, Waltham, Massachusetts 02451, United States
| | - Flora S. Sundersingh
- Platform
Technology and Science, GlaxoSmithKline, 830 Winter Street, Waltham, Massachusetts 02451, United States
| | - Jennifer Summerfield
- Platform
Technology and Science, GlaxoSmithKline, 830 Winter Street, Waltham, Massachusetts 02451, United States
| | - Don Somers
- Medicines
Research Centre, GlaxoSmithKline, Gunnels Wood Road, Stevenage, Herts SG1 2NY, U.K
| | - Jeffrey A. Messer
- Platform
Technology and Science, GlaxoSmithKline, 830 Winter Street, Waltham, Massachusetts 02451, United States
| | - Alexander L. Satz
- Platform
Technology and Science, GlaxoSmithKline, 830 Winter Street, Waltham, Massachusetts 02451, United States
| | - Nicolas Ancellin
- Centre
de Recherche, GlaxoSmithKline, Les Ulis, 25,27 Avenue du Québec, 91140 Villebon sur Yvette, France
| | - Christopher C. Arico-Muendel
- Platform
Technology and Science, GlaxoSmithKline, 830 Winter Street, Waltham, Massachusetts 02451, United States
| | - Katie L. (Sargent) Bedard
- Platform
Technology and Science, GlaxoSmithKline, 830 Winter Street, Waltham, Massachusetts 02451, United States
| | - Arthur Beljean
- Medicines
Research Centre, GlaxoSmithKline, Gunnels Wood Road, Stevenage, Herts SG1 2NY, U.K
| | - Svetlana L. Belyanskaya
- Platform
Technology and Science, GlaxoSmithKline, 830 Winter Street, Waltham, Massachusetts 02451, United States
| | - Ryan Bingham
- Medicines
Research Centre, GlaxoSmithKline, Gunnels Wood Road, Stevenage, Herts SG1 2NY, U.K
| | - Sarah E. Smith
- Medicines
Research Centre, GlaxoSmithKline, Gunnels Wood Road, Stevenage, Herts SG1 2NY, U.K
| | - Eric Boursier
- Centre
de Recherche, GlaxoSmithKline, Les Ulis, 25,27 Avenue du Québec, 91140 Villebon sur Yvette, France
| | - Paul Carter
- Medicines
Research Centre, GlaxoSmithKline, Gunnels Wood Road, Stevenage, Herts SG1 2NY, U.K
| | - Paolo A. Centrella
- Platform
Technology and Science, GlaxoSmithKline, 830 Winter Street, Waltham, Massachusetts 02451, United States
| | - Matthew A. Clark
- Platform
Technology and Science, GlaxoSmithKline, 830 Winter Street, Waltham, Massachusetts 02451, United States
| | - Chun-wa Chung
- Medicines
Research Centre, GlaxoSmithKline, Gunnels Wood Road, Stevenage, Herts SG1 2NY, U.K
| | - Christopher P. Davie
- Platform
Technology and Science, GlaxoSmithKline, 830 Winter Street, Waltham, Massachusetts 02451, United States
| | - Jennifer L. Delorey
- Platform
Technology and Science, GlaxoSmithKline, 830 Winter Street, Waltham, Massachusetts 02451, United States
| | - Yun Ding
- Platform
Technology and Science, GlaxoSmithKline, 830 Winter Street, Waltham, Massachusetts 02451, United States
| | - G. Joseph Franklin
- Platform
Technology and Science, GlaxoSmithKline, 830 Winter Street, Waltham, Massachusetts 02451, United States
| | - LaShadric C. Grady
- Platform
Technology and Science, GlaxoSmithKline, 830 Winter Street, Waltham, Massachusetts 02451, United States
| | - Kenny Herry
- Centre
de Recherche, GlaxoSmithKline, Les Ulis, 25,27 Avenue du Québec, 91140 Villebon sur Yvette, France
| | - Clare Hobbs
- Medicines
Research Centre, GlaxoSmithKline, Gunnels Wood Road, Stevenage, Herts SG1 2NY, U.K
| | - Christopher S. Kollmann
- Platform
Technology and Science, GlaxoSmithKline, 830 Winter Street, Waltham, Massachusetts 02451, United States
| | - Barry A. Morgan
- Platform
Technology and Science, GlaxoSmithKline, 830 Winter Street, Waltham, Massachusetts 02451, United States
| | | | - Quan Zhou
- Chemistry
Department, Brandeis University, Waltham, Massachusetts 02453, United States
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69
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Welzenbach K, Mancuso RV, Krähenbühl S, Weitz-Schmidt G. A novel multi-parameter assay to dissect the pharmacological effects of different modes of integrin αLβ2 inhibition in whole blood. Br J Pharmacol 2015. [PMID: 26224111 DOI: 10.1111/bph.13256] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND AND PURPOSE The integrin αLβ2 plays central roles in leukocyte adhesion and T cell activation, rendering αLβ2 an attractive therapeutic target. Compounds with different modes of αLβ2 inhibition are in development, currently. Consequently, there is a foreseeable need for bedside assays, which allow assessment of the different effects of diverse types of αLβ2 inhibitors in the peripheral blood of treated patients. EXPERIMENTAL APPROACH Here, we describe a flow cytometry-based technology that simultaneously quantitates αLβ2 conformational change upon inhibitor binding, αLβ2 expression and T cell activation at the single-cell level in human blood. Two classes of allosteric low MW inhibitors, designated α I and α/β I allosteric αLβ2 inhibitors, were investigated. The first application revealed intriguing inhibitor class-specific profiles. KEY RESULTS Half-maximal inhibition of T cell activation was associated with 80% epitope loss induced by α I allosteric inhibitors and with 40% epitope gain induced by α/β I allosteric inhibitors. This differential establishes that inhibitor-induced αLβ2 epitope changes do not directly predict the effect on T cell activation. Moreover, we show here for the first time that α/β I allosteric inhibitors, in contrast to α I allosteric inhibitors, provoked partial downmodulation of αLβ2, revealing a novel property of this inhibitor class. CONCLUSIONS AND IMPLICATIONS The multi-parameter whole blood αLβ2 assay described here may enable therapeutic monitoring of αLβ2 inhibitors in patients' blood. The assay dissects differential effect profiles of different classes of αLβ2 inhibitors.
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Affiliation(s)
- Karl Welzenbach
- Novartis Pharma AG, Novartis Institutes of Biomedical Research, Basel, Switzerland
| | - Riccardo V Mancuso
- Division of Clinical Pharmacology and Toxicology, University Hospital, Basel, Switzerland
| | - Stephan Krähenbühl
- Division of Clinical Pharmacology and Toxicology, University Hospital, Basel, Switzerland
| | - Gabriele Weitz-Schmidt
- Novartis Pharma AG, Novartis Institutes of Biomedical Research, Basel, Switzerland.,AlloCyte Pharmaceuticals AG, Basel, Switzerland
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70
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Satz AL, Cai J, Chen Y, Goodnow R, Gruber F, Kowalczyk A, Petersen A, Naderi-Oboodi G, Orzechowski L, Strebel Q. DNA Compatible Multistep Synthesis and Applications to DNA Encoded Libraries. Bioconjug Chem 2015; 26:1623-32. [DOI: 10.1021/acs.bioconjchem.5b00239] [Citation(s) in RCA: 141] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
| | - Jianping Cai
- Roche Innovation Center, Basel 4070, Switzerland
| | - Yi Chen
- Hoffmann-La Roche, Inc., Nutley, New Jersey 07110, United States
| | - Robert Goodnow
- Hoffmann-La Roche, Inc., Nutley, New Jersey 07110, United States
| | - Felix Gruber
- Roche Innovation Center, Basel 4070, Switzerland
| | | | - Ann Petersen
- Roche Innovation Center, Basel 4070, Switzerland
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71
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Encoded Library Synthesis Using Chemical Ligation and the Discovery of sEH Inhibitors from a 334-Million Member Library. Sci Rep 2015; 5:10916. [PMID: 26061191 PMCID: PMC4603778 DOI: 10.1038/srep10916] [Citation(s) in RCA: 88] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2015] [Accepted: 04/21/2015] [Indexed: 11/08/2022] Open
Abstract
A chemical ligation method for construction of DNA-encoded small-molecule libraries has been developed. Taking advantage of the ability of the Klenow fragment of DNA polymerase to accept templates with triazole linkages in place of phosphodiesters, we have designed a strategy for chemically ligating oligonucleotide tags using cycloaddition chemistry. We have utilized this strategy in the construction and selection of a small molecule library, and successfully identified inhibitors of the enzyme soluble epoxide hydrolase.
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72
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Yang H, Medeiros PF, Raha K, Elkins P, Lind KE, Lehr R, Adams ND, Burgess JL, Schmidt SJ, Knight SD, Auger KR, Schaber MD, Franklin GJ, Ding Y, DeLorey JL, Centrella PA, Mataruse S, Skinner SR, Clark MA, Cuozzo JW, Evindar G. Discovery of a Potent Class of PI3Kα Inhibitors with Unique Binding Mode via Encoded Library Technology (ELT). ACS Med Chem Lett 2015; 6:531-6. [PMID: 26005528 PMCID: PMC4434457 DOI: 10.1021/acsmedchemlett.5b00025] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Accepted: 03/20/2015] [Indexed: 01/05/2023] Open
Abstract
In the search of PI3K p110α wild type and H1047R mutant selective small molecule leads, an encoded library technology (ELT) campaign against the desired target proteins was performed which led to the discovery of a selective chemotype for PI3K isoforms from a three-cycle DNA encoded library. An X-ray crystal structure of a representative inhibitor from this chemotype demonstrated a unique binding mode in the p110α protein.
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Affiliation(s)
- Hongfang Yang
- MDR (Molecular Discovery Research) Boston,
Platform Technology and Science, GlaxoSmithKline, 830 Winter Street, Waltham, Massachusetts 02451, United States
| | - Patricia F. Medeiros
- MDR (Molecular Discovery Research) Boston,
Platform Technology and Science, GlaxoSmithKline, 830 Winter Street, Waltham, Massachusetts 02451, United States
| | | | | | - Kenneth E. Lind
- MDR (Molecular Discovery Research) Boston,
Platform Technology and Science, GlaxoSmithKline, 830 Winter Street, Waltham, Massachusetts 02451, United States
| | | | | | | | | | | | | | | | - G. Joseph Franklin
- MDR (Molecular Discovery Research) Boston,
Platform Technology and Science, GlaxoSmithKline, 830 Winter Street, Waltham, Massachusetts 02451, United States
| | - Yun Ding
- MDR (Molecular Discovery Research) Boston,
Platform Technology and Science, GlaxoSmithKline, 830 Winter Street, Waltham, Massachusetts 02451, United States
| | - Jennifer L. DeLorey
- MDR (Molecular Discovery Research) Boston,
Platform Technology and Science, GlaxoSmithKline, 830 Winter Street, Waltham, Massachusetts 02451, United States
| | - Paolo A. Centrella
- MDR (Molecular Discovery Research) Boston,
Platform Technology and Science, GlaxoSmithKline, 830 Winter Street, Waltham, Massachusetts 02451, United States
| | - Sibongile Mataruse
- MDR (Molecular Discovery Research) Boston,
Platform Technology and Science, GlaxoSmithKline, 830 Winter Street, Waltham, Massachusetts 02451, United States
| | - Steven R. Skinner
- MDR (Molecular Discovery Research) Boston,
Platform Technology and Science, GlaxoSmithKline, 830 Winter Street, Waltham, Massachusetts 02451, United States
| | - Matthew A. Clark
- MDR (Molecular Discovery Research) Boston,
Platform Technology and Science, GlaxoSmithKline, 830 Winter Street, Waltham, Massachusetts 02451, United States
| | - John W. Cuozzo
- MDR (Molecular Discovery Research) Boston,
Platform Technology and Science, GlaxoSmithKline, 830 Winter Street, Waltham, Massachusetts 02451, United States
| | - Ghotas Evindar
- MDR (Molecular Discovery Research) Boston,
Platform Technology and Science, GlaxoSmithKline, 830 Winter Street, Waltham, Massachusetts 02451, United States
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73
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Keefe AD, Clark MA, Hupp CD, Litovchick A, Zhang Y. Chemical ligation methods for the tagging of DNA-encoded chemical libraries. Curr Opin Chem Biol 2015; 26:80-8. [PMID: 25756406 DOI: 10.1016/j.cbpa.2015.02.015] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Revised: 02/17/2015] [Accepted: 02/18/2015] [Indexed: 11/28/2022]
Abstract
The generation of DNA-encoded chemical libraries requires the unimolecular association of multiple encoding oligonucleotides with encoded chemical entities during combinatorial synthesis processes. This has traditionally been achieved using enzymatic ligation. We discuss a range of chemical ligation methods that provide alternatives to enzymatic ligation. These chemical ligation methods include the generation of modified internucleotide linkages that support polymerase translocation and other modified linkages that while not supporting the translocation of polymerases can also be used to generate individual cDNA molecules containing encoded chemical information specifying individual library members. We also describe which of these approaches have been successfully utilized for the preparation of DNA-encoded chemical libraries and those that were subsequently used for the discovery of inhibitors.
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Affiliation(s)
- Anthony D Keefe
- X-Chem Pharmaceuticals, 100 Beaver Street, Waltham, MA 02453, USA.
| | - Matthew A Clark
- X-Chem Pharmaceuticals, 100 Beaver Street, Waltham, MA 02453, USA
| | | | | | - Ying Zhang
- X-Chem Pharmaceuticals, 100 Beaver Street, Waltham, MA 02453, USA
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74
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Blakskjaer P, Heitner T, Hansen NJV. Fidelity by design: Yoctoreactor and binder trap enrichment for small-molecule DNA-encoded libraries and drug discovery. Curr Opin Chem Biol 2015; 26:62-71. [PMID: 25732963 DOI: 10.1016/j.cbpa.2015.02.003] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Revised: 01/13/2015] [Accepted: 02/02/2015] [Indexed: 01/26/2023]
Abstract
DNA-encoded small-molecule library (DEL) technology allows vast drug-like small molecule libraries to be efficiently synthesized in a combinatorial fashion and screened in a single tube method for binding, with an assay readout empowered by advances in next generation sequencing technology. This approach has increasingly been applied as a viable technology for the identification of small-molecule modulators to protein targets and as precursors to drugs in the past decade. Several strategies for producing and for screening DELs have been devised by both academic and industrial institutions. This review highlights some of the most significant and recent strategies along with important results. A special focus on the production of high fidelity DEL technologies with the ability to eliminate screening noise and false positives is included: using a DNA junction called the Yoctoreactor, building blocks (BBs) are spatially confined at the center of the junction facilitating both the chemical reaction between BBs and encoding of the synthetic route. A screening method, known as binder trap enrichment, permits DELs to be screened robustly in a homogeneous manner delivering clean data sets and potent hits for even the most challenging targets.
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Affiliation(s)
| | - Tara Heitner
- Vipergen ApS, Gammel Kongevej 23A, 1610 Copenhagen V, Denmark
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75
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Franzini RM, Ekblad T, Zhong N, Wichert M, Decurtins W, Nauer A, Zimmermann M, Samain F, Scheuermann J, Brown PJ, Hall J, Gräslund S, Schüler H, Neri D. Identification of Structure-Activity Relationships from Screening a Structurally Compact DNA-Encoded Chemical Library. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201410736] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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76
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Franzini RM, Ekblad T, Zhong N, Wichert M, Decurtins W, Nauer A, Zimmermann M, Samain F, Scheuermann J, Brown PJ, Hall J, Gräslund S, Schüler H, Neri D. Identification of Structure-Activity Relationships from Screening a Structurally Compact DNA-Encoded Chemical Library. Angew Chem Int Ed Engl 2015; 54:3927-31. [DOI: 10.1002/anie.201410736] [Citation(s) in RCA: 78] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2014] [Indexed: 11/10/2022]
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77
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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.
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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
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