1
|
Gironda-Martínez A, Gorre ÉMD, Prati L, Gosalbes JF, Dakhel S, Cazzamalli S, Samain F, Donckele EJ, Neri D. Identification and Validation of New Interleukin-2 Ligands Using DNA-Encoded Libraries. J Med Chem 2021; 64:17496-17510. [PMID: 34821503 DOI: 10.1021/acs.jmedchem.1c01693] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Interleukin-2 (IL2) is a pro-inflammatory cytokine that plays a crucial role in immunity, which is increasingly being used for therapeutic applications. There is growing interest in developing IL2-based therapeutics which do not interact with the alpha subunit of the IL2 receptor (CD25) as this protein is primarily found on immunosuppressive regulatory T cells (Tregs). Screenings of a new DNA-encoded library, comprising 669,240 members, provided a novel series of IL2 ligands, subsequently optimized by medicinal chemistry. One of these molecules (compound 18) bound to IL2 with a dissociation constant of 0.34 μM was able to form a kinetically stable complex with IL2 in size-exclusion chromatography and recognized the CD25-binding site as evidenced by competition experiments with the NARA1 antibody. Compound 18 and other members of the series may represent the starting point for the discovery of potent small-molecule modulators of IL2 activity, abrogating the binding to CD25.
Collapse
Affiliation(s)
| | - Émile M D Gorre
- Philochem AG, Libernstrasse 3, CH-8112 Otelfingen, Switzerland
| | - Luca Prati
- Philochem AG, Libernstrasse 3, CH-8112 Otelfingen, Switzerland
| | | | - Sheila Dakhel
- Philochem AG, Libernstrasse 3, CH-8112 Otelfingen, Switzerland
| | | | - Florent Samain
- Philochem AG, Libernstrasse 3, CH-8112 Otelfingen, Switzerland
| | | | - Dario Neri
- Philochem AG, Libernstrasse 3, CH-8112 Otelfingen, Switzerland.,Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology (ETH Zürich), Vladimir-Prelog-Weg 3, CH-8093 Zürich, Switzerland.,Philogen S.p.A, 53100 Siena, Italy
| |
Collapse
|
2
|
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: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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
|
3
|
Oehler S, Catalano M, Scapozza I, Bigatti M, Bassi G, Favalli N, Mortensen MR, Samain F, Scheuermann J, Neri D. Cover Feature: Affinity Selections of DNA‐Encoded Chemical Libraries on Carbonic Anhydrase IX‐Expressing Tumor Cells Reveal a Dependence on Ligand Valence (Chem. Eur. J. 35/2021). Chemistry 2021. [DOI: 10.1002/chem.202101855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Sebastian Oehler
- Department of Chemistry and Applied Biosciences ETH Zürich Vladimir-Prelog-Weg 3 8093 Zürich Switzerland
| | - Marco Catalano
- Department of Chemistry and Applied Biosciences ETH Zürich Vladimir-Prelog-Weg 3 8093 Zürich Switzerland
| | - Ilario Scapozza
- Department of Chemistry and Applied Biosciences ETH Zürich Vladimir-Prelog-Weg 3 8093 Zürich Switzerland
| | | | - Gabriele Bassi
- Department of Chemistry and Applied Biosciences ETH Zürich Vladimir-Prelog-Weg 3 8093 Zürich Switzerland
| | - Nicholas Favalli
- Department of Chemistry and Applied Biosciences ETH Zürich Vladimir-Prelog-Weg 3 8093 Zürich Switzerland
| | - Michael R. Mortensen
- Department of Chemistry and Applied Biosciences ETH Zürich Vladimir-Prelog-Weg 3 8093 Zürich Switzerland
| | - Florent Samain
- Philochem AG Libernstrasse 3 8112 Otelfingen Switzerland
| | - Jörg Scheuermann
- Department of Chemistry and Applied Biosciences ETH Zürich Vladimir-Prelog-Weg 3 8093 Zürich Switzerland
| | - Dario Neri
- Philochem AG Libernstrasse 3 8112 Otelfingen Switzerland
| |
Collapse
|
4
|
Oehler S, Catalano M, Scapozza I, Bigatti M, Bassi G, Favalli N, Mortensen MR, Samain F, Scheuermann J, Neri D. Affinity Selections of DNA-Encoded Chemical Libraries on Carbonic Anhydrase IX-Expressing Tumor Cells Reveal a Dependence on Ligand Valence. Chemistry 2021; 27:8985-8993. [PMID: 33905156 DOI: 10.1002/chem.202100816] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Indexed: 12/19/2022]
Abstract
DNA-encoded chemical libraries are typically screened against purified protein targets. Recently, cell-based selections with encoded chemical libraries have been described, commonly revealing suboptimal performance due to insufficient recovery of binding molecules. We used carbonic anhydrase IX (CAIX)-expressing tumor cells as a model system to optimize selection procedures with code-specific quantitative polymerase chain reaction (qPCR) as selection readout. Salt concentration and performing PCR on cell suspension had the biggest impact on selection performance, leading to 15-fold enrichment factors for high-affinity monovalent CAIX binders (acetazolamide; KD =8.7 nM). Surprisingly, the homobivalent display of acetazolamide at the extremities of both complementary DNA strands led to a substantial improvement of both ligand recovery and enrichment factors (above 100-fold). The optimized procedures were used for selections with a DNA-encoded chemical library comprising 1 million members against tumor cell lines expressing CAIX, leading to a preferential recovery of known and new ligands against this validated tumor-associated target. This work may facilitate future affinity selections on cells against target proteins which might be difficult to express otherwise.
Collapse
Affiliation(s)
- Sebastian Oehler
- Department of Chemistry and Applied Biosciences ETH Zürich, Vladimir-Prelog-Weg 3, 8093, Zürich, Switzerland
| | - Marco Catalano
- Department of Chemistry and Applied Biosciences ETH Zürich, Vladimir-Prelog-Weg 3, 8093, Zürich, Switzerland
| | - Ilario Scapozza
- Department of Chemistry and Applied Biosciences ETH Zürich, Vladimir-Prelog-Weg 3, 8093, Zürich, Switzerland
| | - Martina Bigatti
- Philochem AG, Libernstrasse 3, 8112, Otelfingen, Switzerland
| | - Gabriele Bassi
- Department of Chemistry and Applied Biosciences ETH Zürich, Vladimir-Prelog-Weg 3, 8093, Zürich, Switzerland
| | - Nicholas Favalli
- Department of Chemistry and Applied Biosciences ETH Zürich, Vladimir-Prelog-Weg 3, 8093, Zürich, Switzerland
| | - Michael R Mortensen
- Department of Chemistry and Applied Biosciences ETH Zürich, Vladimir-Prelog-Weg 3, 8093, Zürich, Switzerland
| | - Florent Samain
- Philochem AG, Libernstrasse 3, 8112, Otelfingen, Switzerland
| | - Jörg Scheuermann
- Department of Chemistry and Applied Biosciences ETH Zürich, Vladimir-Prelog-Weg 3, 8093, Zürich, Switzerland
| | - Dario Neri
- Philochem AG, Libernstrasse 3, 8112, Otelfingen, Switzerland
| |
Collapse
|
5
|
Prati L, Bigatti M, Donckele EJ, Neri D, Samain F. On-DNA hit validation methodologies for ligands identified from DNA-encoded chemical libraries. Biochem Biophys Res Commun 2020; 533:235-240. [DOI: 10.1016/j.bbrc.2020.04.030] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 03/04/2020] [Accepted: 04/06/2020] [Indexed: 01/16/2023]
|
6
|
Sannino A, Gironda-Martínez A, Gorre ÉMD, Prati L, Piazzi J, Scheuermann J, Neri D, Donckele EJ, Samain F. Critical Evaluation of Photo-cross-linking Parameters for the Implementation of Efficient DNA-Encoded Chemical Library Selections. ACS Comb Sci 2020; 22:204-212. [PMID: 32109359 DOI: 10.1021/acscombsci.0c00023] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The growing importance of DNA-encoded chemical libraries (DECLs) as tools for the discovery of protein binders has sparked an interest for the development of efficient screening methodologies, capable of discriminating between high- and medium-affinity ligands. Here, we present a systematic investigation of selection methodologies, featuring a library displayed on single-stranded DNA, which could be hybridized to a complementary oligonucleotide carrying a diazirine photoreactive group. Model experiments, performed using ligands of different affinity to carbonic anhydrase IX, revealed a recovery of preferential binders up to 10%, which was mainly limited by the highly reactive nature of carbene intermediates generated during the photo-cross-linking process. Ligands featuring acetazolamide or p-phenylsulfonamide exhibited a higher recovery compared to their counterparts based on 3-sulfamoyl benzoic acid, which had a lower affinity toward the target. A systematic evaluation of experimental parameters revealed conditions that were ideally suited for library screening, which were used for the screening of a combinatorial DECL library, featuring 669 240 combinations of two sets of building blocks. Compared to conventional affinity capture procedures on protein immobilized on solid supports, photo-cross-linking provided a better discrimination of low-affinity CAIX ligands over the background signal and therefore can be used as a tandem methodology with the affinity capture procedures.
Collapse
Affiliation(s)
| | | | | | - Luca Prati
- Philochem AG, 8112 Otelfingen, Switzerland
| | | | - Jörg Scheuermann
- Institute of Pharmaceutical Sciences, ETH Zürich, 8093 Zürich, Switzerland
| | - Dario Neri
- Institute of Pharmaceutical Sciences, ETH Zürich, 8093 Zürich, Switzerland
| | | | | |
Collapse
|
7
|
Gironda-Martínez A, Neri D, Samain F, Donckele EJ. DNA-Compatible Diazo-Transfer Reaction in Aqueous Media Suitable for DNA-Encoded Chemical Library Synthesis. Org Lett 2019; 21:9555-9558. [DOI: 10.1021/acs.orglett.9b03726] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
| | - Dario Neri
- 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, CH-8112 Otelfingen, Switzerland
| | | |
Collapse
|
8
|
Sannino A, Gabriele E, Bigatti M, Mulatto S, Piazzi J, Scheuermann J, Neri D, Donckele EJ, Samain F. Quantitative Assessment of Affinity Selection Performance by Using DNA‐Encoded Chemical Libraries. Chembiochem 2019; 20:955-962. [DOI: 10.1002/cbic.201800766] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Indexed: 12/14/2022]
Affiliation(s)
| | - Elena Gabriele
- Philochem AG Libernstrasse 3 8112 Otelfingen Switzerland
| | | | - Sara Mulatto
- Philochem AG Libernstrasse 3 8112 Otelfingen Switzerland
| | - Jacopo Piazzi
- Philochem AG Libernstrasse 3 8112 Otelfingen Switzerland
| | - Jörg Scheuermann
- Department of Chemistry and Applied BiosciencesSwiss Federal Institute of Technology (ETH Zürich) Vladimir-Prelog-Weg 3 8093 Zürich Switzerland
| | - Dario Neri
- Department of Chemistry and Applied BiosciencesSwiss Federal Institute of Technology (ETH Zürich) Vladimir-Prelog-Weg 3 8093 Zürich Switzerland
| | | | - Florent Samain
- Philochem AG Libernstrasse 3 8112 Otelfingen Switzerland
| |
Collapse
|
9
|
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 Comb Sci 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] [What about the content of this article? (0)] [Affiliation(s)] [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
|
10
|
Franzini RM, Biendl S, Mikutis G, Samain F, Scheuermann J, Neri D. "Cap-and-Catch" Purification for Enhancing the Quality of Libraries of DNA Conjugates. ACS Comb Sci 2015; 17:393-8. [PMID: 26083096 DOI: 10.1021/acscombsci.5b00072] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The potential of DNA-encoded combinatorial libraries (DECLs) as tools for hit discovery crucially relies on the availability of methods for their synthesis at acceptable purity and quality. Incomplete reactions in the presence of DNA can noticeably affect the purity of DECLs and methods to selectively remove unreacted oligonucleotide-based starting products would likely enhance the quality of DECL screening results. We describe an approach to selectively remove unreacted oligonucleotide starting products from reaction mixtures and demonstrate its applicability in the context of acylation of amino-modified DNA. Following an amide bond forming reaction, we treat unreacted amino-modified DNAs with biotinylating reagents and isolate the corresponding biotinylated oligonucleotides from the reaction mixture by affinity capture on streptavidin-coated sepharose. This approach, which yields the desired DNA-conjugate at enhanced purity, can be applied both to reactions performed in solution and to procedures in which DNA is immobilized on an anion exchange solid support.
Collapse
Affiliation(s)
- Raphael M. Franzini
- Institute
of Pharmaceutical Sciences, ETH Zürich Vladimir-Prelog-Weg 3, 8093 Zürich, Switzerland
| | - Stefan Biendl
- Institute
of Pharmaceutical Sciences, ETH Zürich Vladimir-Prelog-Weg 3, 8093 Zürich, Switzerland
| | | | - Florent Samain
- Philochem AG, Libernstrasse 3, 8112 Otelfingen, Switzerland
| | - Jörg Scheuermann
- Institute
of Pharmaceutical Sciences, ETH Zürich Vladimir-Prelog-Weg 3, 8093 Zürich, Switzerland
| | - Dario Neri
- Institute
of Pharmaceutical Sciences, ETH Zürich Vladimir-Prelog-Weg 3, 8093 Zürich, Switzerland
| |
Collapse
|
11
|
Samain F, Ekblad T, Mikutis G, Zhong N, Zimmermann M, Nauer A, Bajic D, Decurtins W, Scheuermann J, Brown PJ, Hall J, Gräslund S, Schüler H, Neri D, Franzini RM. Tankyrase 1 Inhibitors with Drug-like Properties Identified by Screening a DNA-Encoded Chemical Library. J Med Chem 2015; 58:5143-9. [DOI: 10.1021/acs.jmedchem.5b00432] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Florent Samain
- Philochem AG, Libernstrasse 3, 8112 Otelfingen, Switzerland
| | - Torun Ekblad
- Department
of Medical Biochemistry and Biophysics, Karolinska Institutet, Scheeles väg 2, 17177 Stockholm, Sweden
| | | | - Nan Zhong
- Structural
Genomics Consortium, University of Toronto, 101 College Street, Toronto, Ontario M5G 1L7, Canada
| | - Mauro Zimmermann
- Institute
of Pharmaceutical Sciences, ETH Zürich, Vladimir-Prelog-Weg 1-5, 8093 Zürich, Switzerland
| | - Angela Nauer
- Institute
of Pharmaceutical Sciences, ETH Zürich, Vladimir-Prelog-Weg 1-5, 8093 Zürich, Switzerland
- Philochem AG, Libernstrasse 3, 8112 Otelfingen, Switzerland
| | - Davor Bajic
- Institute
of Pharmaceutical Sciences, ETH Zürich, Vladimir-Prelog-Weg 1-5, 8093 Zürich, Switzerland
| | - Willy Decurtins
- Institute
of Pharmaceutical Sciences, ETH Zürich, Vladimir-Prelog-Weg 1-5, 8093 Zürich, Switzerland
| | - Jörg Scheuermann
- Institute
of Pharmaceutical Sciences, ETH Zürich, Vladimir-Prelog-Weg 1-5, 8093 Zürich, Switzerland
| | - Peter J. Brown
- Structural
Genomics Consortium, University of Toronto, 101 College Street, Toronto, Ontario M5G 1L7, Canada
| | - Jonathan Hall
- Institute
of Pharmaceutical Sciences, ETH Zürich, Vladimir-Prelog-Weg 1-5, 8093 Zürich, Switzerland
| | - Susanne Gräslund
- Structural
Genomics Consortium, University of Toronto, 101 College Street, Toronto, Ontario M5G 1L7, Canada
| | - Herwig Schüler
- Department
of Medical Biochemistry and Biophysics, Karolinska Institutet, Scheeles väg 2, 17177 Stockholm, Sweden
| | - Dario Neri
- Institute
of Pharmaceutical Sciences, ETH Zürich, Vladimir-Prelog-Weg 1-5, 8093 Zürich, Switzerland
| | - Raphael M. Franzini
- Institute
of Pharmaceutical Sciences, ETH Zürich, Vladimir-Prelog-Weg 1-5, 8093 Zürich, Switzerland
| |
Collapse
|
12
|
Samain F, Casi G. Small targeted cytotoxics from DNA-encoded chemical libraries. Curr Opin Chem Biol 2015; 26:72-9. [DOI: 10.1016/j.cbpa.2015.02.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Revised: 01/23/2015] [Accepted: 02/09/2015] [Indexed: 01/09/2023]
|
13
|
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] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
|
14
|
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] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2014] [Indexed: 11/10/2022]
|
15
|
Franzini RM, Samain F, Abd Elrahman M, Mikutis G, Nauer A, Zimmermann M, Scheuermann J, Hall J, Neri D. Systematic evaluation and optimization of modification reactions of oligonucleotides with amines and carboxylic acids for the synthesis of DNA-encoded chemical libraries. Bioconjug Chem 2014; 25:1453-61. [PMID: 25061844 DOI: 10.1021/bc500212n] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
DNA-encoded chemical libraries are collections of small molecules, attached to DNA fragments serving as identification barcodes, which can be screened against multiple protein targets, thus facilitating the drug discovery process. The preparation of large DNA-encoded chemical libraries crucially depends on the availability of robust synthetic methods, which enable the efficient conjugation to oligonucleotides of structurally diverse building blocks, sharing a common reactive group. Reactions of DNA derivatives with amines and/or carboxylic acids are particularly attractive for the synthesis of encoded libraries, in view of the very large number of building blocks that are commercially available. However, systematic studies on these reactions in the presence of DNA have not been reported so far. We first investigated conditions for the coupling of primary amines to oligonucleotides, using either a nucleophilic attack on chloroacetamide derivatives or a reductive amination on aldehyde-modified DNA. While both methods could be used for the production of secondary amines, the reductive amination approach was generally associated with higher yields and better purity. In a second endeavor, we optimized conditions for the coupling of a diverse set of 501 carboxylic acids to DNA derivatives, carrying primary and secondary amine functions. The coupling efficiency was generally higher for primary amines, compared to secondary amine substituents, but varied considerably depending on the structure of the acids and on the synthetic methods used. Optimal reaction conditions could be found for certain sets of compounds (with conversions >80%), but multiple reaction schemes are needed when assembling large libraries with highly diverse building blocks. The reactions and experimental conditions presented in this article should facilitate the synthesis of future DNA-encoded chemical libraries, while outlining the synthetic challenges that remain to be overcome.
Collapse
Affiliation(s)
- Raphael M Franzini
- Institute of Pharmaceutical Sciences , ETH Zürich, Vladimir-Prelog Weg 1-5/10, 8093 Zürich, Switzerland
| | | | | | | | | | | | | | | | | |
Collapse
|
16
|
|
17
|
Nussbaumer AL, Samain F, Malinovskii VL, Häner R. Supramolecular polymerization of oligopyrenotides--control by single, natural nucleotides. Org Biomol Chem 2012; 10:4891-8. [PMID: 22610059 DOI: 10.1039/c2ob25320h] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Amphiphilic heptapyrenotides (Py(7)) assemble into supramolecular polymers. Here we present a comprehensive spectroscopic study of aggregates and co-aggregates of the non-chiral Py(7) and its mono- or di-substituted nucleotide analogs (Py(7)-N and N-Py(7)-N'). The data show that the formation of supramolecular polymers from oligopyrenotides is highly sensitive to the nature of the attached, chiral auxiliary. A single natural nucleotide may be sufficient for the fine tuning of the aggregates' properties by changing the mechanism of aggregation from an isodesmic to a nucleation-elongation process, which results in a high degree of amplification of chirality in the formed supramolecular polymers. Watson-Crick complementarity does not play a significant role, since co-aggregates of oligomers modified with complementary nucleotides show no signs of supramolecular polymerization. Depending on the nucleotide, the helical sense of the polymers is shifted to an M-helix or a P-helix. The findings demonstrate the value of oligopyrenotides as oligomeric building blocks for the generation of optically active supramolecular polymers.
Collapse
Affiliation(s)
- Alina L Nussbaumer
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
| | | | | | | |
Collapse
|
18
|
|
19
|
Koo CK, Wang S, Gaur RL, Samain F, Banaei N, Kool ET. Fluorescent DNA chemosensors: identification of bacterial species by their volatile metabolites. Chem Commun (Camb) 2011; 47:11435-7. [PMID: 21935547 DOI: 10.1039/c1cc14871k] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Polyfluorophores built on a DNA scaffold (ODFs) were synthesized and tested for fluorescence responses to the volatiles from M. tuberculosis, E. coli and P. putida in closed Petri dishes. Two sensors in a pattern-based response could distinguish the bacterial strains accurately, suggesting the use of ODFs in rapid identification of infectious agents.
Collapse
Affiliation(s)
- Chi-Kin Koo
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
| | | | | | | | | | | |
Collapse
|
20
|
Affiliation(s)
- Florent Samain
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
| | | | | | | |
Collapse
|
21
|
|
22
|
Samain F, Dai N, Kool ET. Differentiating a diverse range of volatile organic compounds with polyfluorophore sensors built on a DNA scaffold. Chemistry 2010; 17:174-83. [PMID: 21207614 DOI: 10.1002/chem.201002836] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2010] [Indexed: 11/07/2022]
Abstract
Oligodeoxyfluorosides (ODFs) are short DNA-like oligomers in which DNA bases are replaced with fluorophores. A preliminary study reported that some sequences of ODFs were able to respond to a few organic small molecules in the vapor phase, giving a change in fluorescence. Here, we follow up on this finding by investigating a larger range of volatile organic analytes, and a considerably larger set of sensors. A library of tetramer ODFs of 2401 different sequences was prepared by using combinatorial methods, and was screened in air for fluorescence responses to a set of ten different volatile organics, including multiple aromatic and aliphatic compounds, acids and bases, varied functional groups, and closely related structures. Nineteen responding sensors were selected and characterized. These sensors were cross-screened against all ten analytes, and responses were measured qualitatively (by changes in color and intensity) and quantitatively (by measuring ΔR, ΔG, and ΔB values averaged over five to six sensor beads; R=red, G=green, B=blue). The results show that sensor responses were diverse, with a single sensor responding differently to as many as eight of the ten analytes; multiple classes of responses were seen, including quenching, lighting-up, and varied shifts in wavelength. Responses were strong, with raw ΔR, ΔG, and ΔB values of as high as >200 on a 256-unit scale and unamplified changes in many cases apparent to the naked eye. Sensors were identified that could distinguish clearly between even very closely related compounds such as acrolein and acrylonitrile. Statistical methods were applied to select a small set of four sensors that, as a pattern response, could distinguish between all ten analytes with high confidence. Sequence analysis of the full set of sensors suggested that sequence/order of the monomer components, and not merely composition, was highly important in the responses.
Collapse
Affiliation(s)
- Florent Samain
- Department of Chemistry, Stanford University, Stanford, CA 94305-5080, USA
| | | | | |
Collapse
|
23
|
|
24
|
Huang CH, Parish A, Samain F, Garo F, Häner R, Morrow JR. Binding of Europium(III) to a Non-Nucleosidic Phenanthroline Linker in DNA. Bioconjug Chem 2010; 21:476-82. [DOI: 10.1021/bc900386w] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Ching-Hui Huang
- Department of Chemistry, 526 Natural Sciences Complex, University at Buffalo, State University of New York, Amherst, New York 14260-3000, and Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland
| | - Austin Parish
- Department of Chemistry, 526 Natural Sciences Complex, University at Buffalo, State University of New York, Amherst, New York 14260-3000, and Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland
| | - Florent Samain
- Department of Chemistry, 526 Natural Sciences Complex, University at Buffalo, State University of New York, Amherst, New York 14260-3000, and Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland
| | - Florian Garo
- Department of Chemistry, 526 Natural Sciences Complex, University at Buffalo, State University of New York, Amherst, New York 14260-3000, and Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland
| | - Robert Häner
- Department of Chemistry, 526 Natural Sciences Complex, University at Buffalo, State University of New York, Amherst, New York 14260-3000, and Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland
| | - Janet R. Morrow
- Department of Chemistry, 526 Natural Sciences Complex, University at Buffalo, State University of New York, Amherst, New York 14260-3000, and Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland
| |
Collapse
|
25
|
Galievsky VA, Malinovskii VL, Stasheuski AS, Samain F, Zachariasse KA, Häner R, Chirvony VS. Photophysical characterization of oligopyrene modules for DNA-based nanosystems. Photochem Photobiol Sci 2009; 8:1448-54. [PMID: 19789815 DOI: 10.1039/b9pp00016j] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The photophysics of free pyrenedicarboxamide (Py-DCA) in solution as well as of single-stranded and double-stranded oligonucleotides (ss and ds ONs) containing 1-7 pyrene building blocks per strand were studied by steady-state and time-resolved fluorescence spectroscopy. It was found that the fluorescence quantum yield Phi(F) of free Py-DCA chromophore in solution is rather high (Phi(F) = 0.44). However, after incorporation of the chromophore into a ss ON the monomeric chromophore fluorescence is quenched more than 40-fold due to electron-transfer reactions with ON bases. An increase of the number n of neighboring pyrenes in an ON results in Phi(F) growth up to 0.25 at n = 6. Starting from n = 2, all fluorescence belongs mainly to excimer formed by pyrene chromophores. Sections composed of multiple pyrenes may be considered as robust functional entities that may serve as independent modules in DNA-based, functional nano-architectures.
Collapse
Affiliation(s)
- Victor A Galievsky
- B.I. Stepanov's Institute of Physics, National Academy of Sciences of Belarus, Nezavisimosti ave. 68, 220072, Minsk, Belarus
| | | | | | | | | | | | | |
Collapse
|
26
|
Abstract
The self-organization of oligopyrene foldamers is described. Bi- and tri-segmental oligomers composed of nucleotides and non-nucleosidic, achiral pyrene monomers form double-stranded helical structures, as shown by absorbance, fluorescence, and CD spectroscopy. The mixed nature of alternating aromatic and phosphate groups ensures water solubility which, in turn, favors folding of the aromatic units. Pyrene molecules also assemble though interstrand stacking interactions. Structural organization of the pyrene units is an intrinsic property of the oligoaryl part and takes place independently from the sequence of the attached DNA. Chirality transfer from DNA to the pyrene segment leads to formation of a double helix, in which neighboring pyrene units are, in the present case, twisted in a right-handed manner. Pyrene helicity is most pronounced in a bi-segmental chimera, in which a DNA stem is present only at one end of the pyrene section.
Collapse
Affiliation(s)
- Robert Häner
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland.
| | | | | |
Collapse
|
27
|
Samain F, Malinovskii VL, Langenegger SM, Häner R. Spectroscopic properties of pyrene-containing DNA mimics. Bioorg Med Chem 2008; 16:27-33. [PMID: 17512737 DOI: 10.1016/j.bmc.2007.04.052] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2006] [Revised: 10/16/2006] [Accepted: 04/27/2007] [Indexed: 11/27/2022]
Abstract
DNA mimics containing non-nucleosidic pyrene building blocks are described. The modified oligomers form stable hybrids, although a slight reduction in hybrid stability is observed in comparison to the unmodified DNA duplex. The nature of the interaction between the pyrene residues in single and double stranded oligomers is analyzed spectroscopically. Intra- and interstrand stacking interactions of pyrenes are monitored by UV-absorbance as well as fluorescence spectroscopy. Excimer formation is observed in both single and double strands. In general, intrastrand excimers show fluorescence emission at shorter wavelengths (approx. 5-10 nm) than excimers formed by interstrand interactions. The existence of two different forms of excimers (intra- vs. interstrand) is also revealed in temperature dependent UV-absorbance spectra.
Collapse
Affiliation(s)
- Florent Samain
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
| | | | | | | |
Collapse
|
28
|
Malinovskii V, Samain F, Häner R. Inside Cover: Helical Arrangement of Interstrand Stacked Pyrenes in a DNA Framework (Angew. Chem. Int. Ed. 24/2007). Angew Chem Int Ed Engl 2007. [DOI: 10.1002/anie.200790108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
|
29
|
Malinovskii V, Samain F, Häner R. Innentitelbild: Helical Arrangement of Interstrand Stacked Pyrenes in a DNA Framework (Angew. Chem. 24/2007). Angew Chem Int Ed Engl 2007. [DOI: 10.1002/ange.200790108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
|
30
|
Affiliation(s)
- Vladimir L Malinovskii
- Departement für Chemie und Biochemie, Universität Bern, Freiestrasse 3, 3012 Bern, Switzerland
| | | | | |
Collapse
|
31
|
|
32
|
Abstract
The purpose of this study was to evaluate the frequency of skin changes among 100 patients from the Hepatogastroenterology Department of the University Hospital, Strasbourg, France who were hepatitis C virus-positive (HCV) and HIV-negative. Their clinical data were compared to those of 50 HCV-, and HIV-negative patients from the same Department, who suffered from various liver diseases. Psoriasis, rosacea, seborrheic dermatitis, cherry angiomas, spider nevus and skin cancers were noted in similar proportions in the two groups. In 15% of HCV-positive patients vs. 4% of controls, chronic pruritus was noted (p < 0.05). In 9 HCV-positive patients, pruritus was not related to itching dermatosis, and only 2 of these patients had mild cholestasis. Four cases of lichen planus vs. 0 in the control group were recorded. The virological data of patients with pruritus or lichen planus were not different than those of the rest of the group. Our findings indicate that systematic skin check-up in HCV-positive patients is valuable.
Collapse
Affiliation(s)
- B Cribier
- Department of Dermatology, University Hospital, Strasbourg, France
| | | | | | | | | |
Collapse
|