51
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Large-scale DNA Barcode Library Generation for Biomolecule Identification in High-throughput Screens. Sci Rep 2017; 7:13899. [PMID: 29066821 PMCID: PMC5654825 DOI: 10.1038/s41598-017-12825-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Accepted: 09/14/2017] [Indexed: 01/23/2023] Open
Abstract
High-throughput screens allow for the identification of specific biomolecules with characteristics of interest. In barcoded screens, DNA barcodes are linked to target biomolecules in a manner allowing for the target molecules making up a library to be identified by sequencing the DNA barcodes using Next Generation Sequencing. To be useful in experimental settings, the DNA barcodes in a library must satisfy certain constraints related to GC content, homopolymer length, Hamming distance, and blacklisted subsequences. Here we report a novel framework to quickly generate large-scale libraries of DNA barcodes for use in high-throughput screens. We show that our framework dramatically reduces the computation time required to generate large-scale DNA barcode libraries, compared with a naїve approach to DNA barcode library generation. As a proof of concept, we demonstrate that our framework is able to generate a library consisting of one million DNA barcodes for use in a fragment antibody phage display screening experiment. We also report generating a general purpose one billion DNA barcode library, the largest such library yet reported in literature. Our results demonstrate the value of our novel large-scale DNA barcode library generation framework for use in high-throughput screening applications.
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52
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MacConnell AB, Paegel BM. Poisson Statistics of Combinatorial Library Sampling Predict False Discovery Rates of Screening. ACS COMBINATORIAL SCIENCE 2017; 19:524-532. [PMID: 28682059 PMCID: PMC5558193 DOI: 10.1021/acscombsci.7b00061] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
Microfluidic droplet-based
screening of DNA-encoded one-bead-one-compound
combinatorial libraries is a miniaturized, potentially widely distributable
approach to small molecule discovery. In these screens, a microfluidic
circuit distributes library beads into droplets of activity assay
reagent, photochemically cleaves the compound from the bead, then
incubates and sorts the droplets based on assay result for subsequent
DNA sequencing-based hit compound structure elucidation. Pilot experimental
studies revealed that Poisson statistics describe nearly all aspects
of such screens, prompting the development of simulations to understand
system behavior. Monte Carlo screening simulation data showed that
increasing mean library sampling (ε), mean droplet occupancy,
or library hit rate all increase the false discovery rate (FDR). Compounds
identified as hits on k > 1 beads (the replicate k class) were much more likely to be authentic
hits than singletons (k = 1), in agreement with previous
findings. Here, we explain this observation by deriving an equation
for authenticity, which reduces to the product of a library sampling
bias term (exponential in k) and a sampling saturation
term (exponential in ε) setting a threshold that the k-dependent bias must overcome. The equation thus quantitatively
describes why each hit structure’s FDR is based on its k class, and further predicts the feasibility of intentionally
populating droplets with multiple library beads, assaying the micromixtures
for function, and identifying the active members by statistical deconvolution.
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Affiliation(s)
- Andrew B. MacConnell
- Department
of Chemistry and †Doctoral Program in Chemical and Biological
Sciences, The Scripps Research Institute, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Brian M. Paegel
- Department
of Chemistry and †Doctoral Program in Chemical and Biological
Sciences, The Scripps Research Institute, 130 Scripps Way, Jupiter, Florida 33458, United States
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53
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Prioritizing multiple therapeutic targets in parallel using automated DNA-encoded library screening. Nat Commun 2017; 8:16081. [PMID: 28714473 PMCID: PMC5520047 DOI: 10.1038/ncomms16081] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2016] [Accepted: 05/24/2017] [Indexed: 12/18/2022] Open
Abstract
The identification and prioritization of chemically tractable therapeutic targets is a significant challenge in the discovery of new medicines. We have developed a novel method that rapidly screens multiple proteins in parallel using DNA-encoded library technology (ELT). Initial efforts were focused on the efficient discovery of antibacterial leads against 119 targets from Acinetobacter baumannii and Staphylococcus aureus. The success of this effort led to the hypothesis that the relative number of ELT binders alone could be used to assess the ligandability of large sets of proteins. This concept was further explored by screening 42 targets from Mycobacterium tuberculosis. Active chemical series for six targets from our initial effort as well as three chemotypes for DHFR from M. tuberculosis are reported. The findings demonstrate that parallel ELT selections can be used to assess ligandability and highlight opportunities for successful lead and tool discovery. Encoded Library Technology (ELT) has streamlined the identification of chemical ligands for protein targets in drug discovery. Here, the authors optimize the ELT approach to screen multiple proteins in parallel and identify promising targets and antibacterial compounds for S. aureus, A. baumannii and M. tuberculosis.
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54
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Acylated heptapeptide binds albumin with high affinity and application as tag furnishes long-acting peptides. Nat Commun 2017; 8:16092. [PMID: 28714475 PMCID: PMC5520048 DOI: 10.1038/ncomms16092] [Citation(s) in RCA: 92] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Accepted: 05/24/2017] [Indexed: 12/12/2022] Open
Abstract
The rapid renal clearance of peptides in vivo limits this attractive platform for the treatment of a broad range of diseases that require prolonged drug half-lives. An intriguing approach for extending peptide circulation times works through a ‘piggy-back’ strategy in which peptides bind via a ligand to the long-lived serum protein albumin. In accordance with this strategy, we developed an easily synthesized albumin-binding ligand based on a peptide-fatty acid chimera that has a high affinity for human albumin (Kd=39 nM). This ligand prolongs the elimination half-life of cyclic peptides in rats 25-fold to over seven hours. Conjugation to a peptide factor XII inhibitor developed for anti-thrombotic therapy extends the half-life from 13 minutes to over five hours, inhibiting coagulation for eight hours in rabbits. This high-affinity albumin ligand could potentially extend the half-life of peptides in human to several days, substantially broadening the application range of peptides as therapeutics. A major challenge for the application of peptide therapeutics is their short half-life in vivo. Here, the authors design peptide-fatty acid chimeras bearing an engineered linker that promotes albumin binding and allows longer circulation times of therapeutic peptides in animal models.
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55
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Li Y, Zimmermann G, Scheuermann J, Neri D. Quantitative PCR is a Valuable Tool to Monitor the Performance of DNA-Encoded Chemical Library Selections. Chembiochem 2017; 18:848-852. [PMID: 28220596 PMCID: PMC5606288 DOI: 10.1002/cbic.201600626] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Indexed: 01/25/2023]
Abstract
Phage-display libraries and DNA-encoded chemical libraries (DECLs) represent useful tools for the isolation of specific binding molecules from large combinatorial sets of compounds. With both methods, specific binders are recovered at the end of affinity capture procedures by using target proteins of interest immobilized on a solid support. However, although the efficiency of phage-display selections is routinely quantified by counting the phage titer before and after the affinity capture step, no similar quantification procedures have been reported for the characterization of DECL selections. In this article, we describe the potential and limitations of quantitative PCR (qPCR) methods for the evaluation of selection efficiency by using a combinatorial chemical library with more than 35 million compounds. In the experimental conditions chosen for the selections, a quantification of DNA input/recovery over five orders of magnitude could be performed, revealing a successful enrichment of abundant binders, which could be confirmed by DNA sequencing. qPCR provided rapid information about the performance of selections, thus facilitating the optimization of experimental conditions.
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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)
| | - Gunther Zimmermann
- 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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56
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Satz AL, Hochstrasser R, Petersen AC. Analysis of Current DNA Encoded Library Screening Data Indicates Higher False Negative Rates for Numerically Larger Libraries. ACS COMBINATORIAL SCIENCE 2017; 19:234-238. [PMID: 28287689 DOI: 10.1021/acscombsci.7b00023] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
To optimize future DNA-encoded library design, we have attempted to quantify the library size at which the signal becomes undetectable. To accomplish this we (i) have calculated that percent yields of individual library members following a screen range from 0.002 to 1%, (ii) extrapolated that ∼1 million copies per library member are required at the outset of a screen, and (iii) from this extrapolation predict that false negative rates will begin to outweigh the benefit of increased diversity at library sizes >108. The above analysis is based upon a large internal data set comprising multiple screens, targets, and libraries; we also augmented our internal data with all currently available literature data. In theory, high false negative rates may be overcome by employing larger amounts of library; however, we argue that using more than currently reported amounts of library (≫10 nmoles) is impractical. The above conclusions may be generally applicable to other DNA encoded library platforms, particularly those platforms that do not allow for library amplification.
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Affiliation(s)
- Alexander L. Satz
- Roche Pharmaceutical Research
and Early Development (pRED) Roche Innovation Center Basel, F. Hoffmann-La Roche, Ltd., Grenzacherstrasse 124 CH-4070 Basel, Switzerland
| | - Remo Hochstrasser
- Roche Pharmaceutical Research
and Early Development (pRED) Roche Innovation Center Basel, F. Hoffmann-La Roche, Ltd., Grenzacherstrasse 124 CH-4070 Basel, Switzerland
| | - Ann C. Petersen
- Roche Pharmaceutical Research
and Early Development (pRED) Roche Innovation Center Basel, F. Hoffmann-La Roche, Ltd., Grenzacherstrasse 124 CH-4070 Basel, Switzerland
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57
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Velagapudi SP, Luo Y, Tran T, Haniff HS, Nakai Y, Fallahi M, Martinez GJ, Childs-Disney JL, Disney MD. Defining RNA-Small Molecule Affinity Landscapes Enables Design of a Small Molecule Inhibitor of an Oncogenic Noncoding RNA. ACS CENTRAL SCIENCE 2017; 3:205-216. [PMID: 28386598 PMCID: PMC5364451 DOI: 10.1021/acscentsci.7b00009] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Indexed: 05/03/2023]
Abstract
RNA drug targets are pervasive in cells, but methods to design small molecules that target them are sparse. Herein, we report a general approach to score the affinity and selectivity of RNA motif-small molecule interactions identified via selection. Named High Throughput Structure-Activity Relationships Through Sequencing (HiT-StARTS), HiT-StARTS is statistical in nature and compares input nucleic acid sequences to selected library members that bind a ligand via high throughput sequencing. The approach allowed facile definition of the fitness landscape of hundreds of thousands of RNA motif-small molecule binding partners. These results were mined against folded RNAs in the human transcriptome and identified an avid interaction between a small molecule and the Dicer nuclease-processing site in the oncogenic microRNA (miR)-18a hairpin precursor, which is a member of the miR-17-92 cluster. Application of the small molecule, Targapremir-18a, to prostate cancer cells inhibited production of miR-18a from the cluster, de-repressed serine/threonine protein kinase 4 protein (STK4), and triggered apoptosis. Profiling the cellular targets of Targapremir-18a via Chemical Cross-Linking and Isolation by Pull Down (Chem-CLIP), a covalent small molecule-RNA cellular profiling approach, and other studies showed specific binding of the compound to the miR-18a precursor, revealing broadly applicable factors that govern small molecule drugging of noncoding RNAs.
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Affiliation(s)
- Sai Pradeep Velagapudi
- Department
of Chemistry, Informatics Core, and Genomics Core, The Scripps
Research Institute, 130
Scripps Way, Jupiter, Florida 33458, United
States
| | - Yiling Luo
- Department
of Chemistry, Informatics Core, and Genomics Core, The Scripps
Research Institute, 130
Scripps Way, Jupiter, Florida 33458, United
States
| | - Tuan Tran
- Department
of Chemistry, Informatics Core, and Genomics Core, The Scripps
Research Institute, 130
Scripps Way, Jupiter, Florida 33458, United
States
| | - Hafeez S. Haniff
- Department
of Chemistry, Informatics Core, and Genomics Core, The Scripps
Research Institute, 130
Scripps Way, Jupiter, Florida 33458, United
States
| | - Yoshio Nakai
- Department
of Chemistry, Informatics Core, and Genomics Core, The Scripps
Research Institute, 130
Scripps Way, Jupiter, Florida 33458, United
States
| | - Mohammad Fallahi
- Department
of Chemistry, Informatics Core, and Genomics Core, The Scripps
Research Institute, 130
Scripps Way, Jupiter, Florida 33458, United
States
| | - Gustavo J. Martinez
- Department
of Chemistry, Informatics Core, and Genomics Core, The Scripps
Research Institute, 130
Scripps Way, Jupiter, Florida 33458, United
States
| | - Jessica L. Childs-Disney
- Department
of Chemistry, Informatics Core, and Genomics Core, The Scripps
Research Institute, 130
Scripps Way, Jupiter, Florida 33458, United
States
| | - Matthew D. Disney
- Department
of Chemistry, Informatics Core, and Genomics Core, The Scripps
Research Institute, 130
Scripps Way, Jupiter, Florida 33458, United
States
- E-mail:
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58
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Yuen LH, Franzini RM. Stability of Oligonucleotide-Small Molecule Conjugates to DNA-Deprotection Conditions. Bioconjug Chem 2017; 28:1076-1083. [PMID: 28233987 DOI: 10.1021/acs.bioconjchem.7b00005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Oligonucleotide conjugates of small molecules are widely used in chemical biology and have found increasing interest in the context of DNA-encoded chemical libraries for drug discovery. Attachment of molecules to DNA bound to the solid support is an attractive small-molecule conjugation method that permits the use of organic solvents, rigorous reaction conditions, and simple workup. However, the conjugated structures must be resistant to the harsh DNA deprotection/cleavage conditions and the stabilities of building blocks under various deprotection conditions are mostly unexplored. In the present study, we analyzed the stability of 131 structurally diverse fragments that contain amides and amide-like elements during DNA deprotection protocols. Structural features susceptible to decomposition in DNA deprotection conditions were identified and a protocol that enabled the synthesis of DNA conjugates with labile fragments on solid support was identified.
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Affiliation(s)
- Lik Hang Yuen
- Department of Medicinal Chemistry, College of Pharmacy, University of Utah , 30 S 2000 E, Salt Lake City, Utah 84112, United States
| | - Raphael M Franzini
- 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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59
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Zimmermann G, Li Y, Rieder U, Mattarella M, Neri D, Scheuermann J. Hit-Validation Methodologies for Ligands Isolated from DNA-Encoded Chemical Libraries. Chembiochem 2017; 18:853-857. [PMID: 28067010 DOI: 10.1002/cbic.201600637] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Indexed: 01/13/2023]
Abstract
DNA-encoded chemical libraries (DECLs) are large collections of compounds linked to DNA fragments, serving as amplifiable barcodes, which can be screened on target proteins of interest. In typical DECL selections, preferential binders are identified by high-throughput DNA sequencing, by comparing their frequency before and after the affinity capture step. Hits identified in this procedure need to be confirmed, by resynthesis and by performing affinity measurements. In this article we present new methods based on hybridization of oligonucleotide conjugates with fluorescently labeled complementary oligonucleotides; these facilitate the determination of affinity constants and kinetic dissociation constants. The experimental procedures were demonstrated with acetazolamide, a binder to carbonic anhydrase IX with a dissociation constant in the nanomolar range. The detection of binding events was compatible not only with fluorescence polarization methodologies, but also with Alphascreen technology and with microscale thermophoresis.
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Affiliation(s)
- Gunther Zimmermann
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology, ETH Zürich, Vladimir-Prelog-Weg 3, 8093, Zürich, Switzerland
| | - Yizhou Li
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology, ETH Zürich, Vladimir-Prelog-Weg 3, 8093, Zürich, Switzerland
| | - Ulrike Rieder
- Philochem AG, Libernstrasse 3, 8112, Otelfingen, Switzerland
| | | | - Dario Neri
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology, ETH Zürich, Vladimir-Prelog-Weg 3, 8093, Zürich, Switzerland
| | - Jörg Scheuermann
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology, ETH Zürich, Vladimir-Prelog-Weg 3, 8093, Zürich, Switzerland
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60
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Yuen LH, Franzini RM. Achievements, Challenges, and Opportunities in DNA-Encoded Library Research: An Academic Point of View. Chembiochem 2017; 18:829-836. [DOI: 10.1002/cbic.201600567] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Indexed: 12/19/2022]
Affiliation(s)
- Lik Hang Yuen
- Department of Medicinal Chemistry; University of Utah; 30 S 2000 E Salt Lake City UT 84113 USA
| | - Raphael M. Franzini
- Department of Medicinal Chemistry; University of Utah; 30 S 2000 E Salt Lake City UT 84113 USA
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61
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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.
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62
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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.
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63
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Peri-Naor R, Motiei L, Margulies D. Mimicking the Function of Signaling Proteins: Toward Artificial Signal Transduction Therapy. J Vis Exp 2016. [PMID: 27768030 DOI: 10.3791/54396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Signal transduction pathways, which control the response of cells to various environmental signals, are mediated by the function of signaling proteins that interact with each other and activate one other with high specificity. Synthetic agents that mimic the function of these proteins might therefore be used to generate unnatural signal transduction steps and consequently, alter the cell's function. We present guidelines for designing 'chemical transducers' that can induce artificial communication between native proteins. In addition, we present detailed protocols for synthesizing and testing a specific 'transducer', which can induce communication between two unrelated proteins: platelet-derived growth-factor (PDGF) and glutathione-S-transferase (GST). The way by which this unnatural PDGF-GST communication could be used to control the cleavage of an anticancer prodrug is also presented, indicating the potential for using such systems in 'artificial signal transduction therapy'. This work is intended to facilitate developing additional 'transducers' of this class, which may be used to mediate intracellular protein-protein communication and consequently, to induce artificial cell signaling pathways.
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Affiliation(s)
- Ronny Peri-Naor
- Department of Organic Chemistry, Weizmann Institute of Science
| | - Leila Motiei
- Department of Organic Chemistry, Weizmann Institute of Science
| | - David Margulies
- Department of Organic Chemistry, Weizmann Institute of Science;
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64
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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: 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.
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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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65
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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.
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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.
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66
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Abstract
DNA-encoded synthesis can generate vastly diverse screening libraries of arbitrarily complex molecules as long as chemical reaction conditions do not compromise DNA's informational integrity, a fundamental constraint that "DNA-compatible" reaction development does not presently address. We devised DNA-encoded reaction rehearsal, an integrated analysis of reaction yield and impact on DNA, to acquire these key missing data. Magnetic DNA-functionalized sensor beads quantitatively report the % DNA template molecules remaining viable for PCR amplification after exposure to test reaction conditions. Analysis of solid-phase bond forming (e.g., Suzuki-Miyaura cross-coupling, reductive amination) and deprotection reactions (e.g., allyl esters, silyl ethers) guided the definition and optimization of DNA-compatible reaction conditions (>90% yield, >30% viable DNA molecules), most notably in cases that involved known (H(+), Pd) and more obscure (Δ, DMF) hazards to DNA integrity. The data provide an empirical yet mechanistically consistent and predictive framework for designing successful DNA-encoded reaction sequences for combinatorial library synthesis.
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Affiliation(s)
- Marie L. Malone
- Department of Chemistry and ‡Doctoral Program
in Chemical and Biological
Sciences, The Scripps Research Institute 130 Scripps Way Jupiter, Florida 33458, United States
| | - Brian M. Paegel
- Department of Chemistry and ‡Doctoral Program
in Chemical and Biological
Sciences, The Scripps Research Institute 130 Scripps Way Jupiter, Florida 33458, United States
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67
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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.
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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
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68
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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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69
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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: 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.
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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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70
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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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71
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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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72
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Škopić MK, Bugain O, Jung K, Onstein S, Brandherm S, Kalliokoski T, Brunschweiger A. Design and synthesis of DNA-encoded libraries based on a benzodiazepine and a pyrazolopyrimidine scaffold. MEDCHEMCOMM 2016. [DOI: 10.1039/c6md00243a] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
DNA-encoded libraries based on scaffolds functionalized for DNA-compatible chemistry were synthesized by split-and-pool combinatorial chemistry. The library design was aided by a chemoinformatic filtering cascade.
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Affiliation(s)
- M. Klika Škopić
- Faculty of Chemistry and Chemical Biology
- Technical University of Dortmund
- D-44227 Dortmund
- Germany
| | - O. Bugain
- Faculty of Chemistry and Chemical Biology
- Technical University of Dortmund
- D-44227 Dortmund
- Germany
| | - K. Jung
- Faculty of Chemistry and Chemical Biology
- Technical University of Dortmund
- D-44227 Dortmund
- Germany
| | - S. Onstein
- Faculty of Chemistry and Chemical Biology
- Technical University of Dortmund
- D-44227 Dortmund
- Germany
| | - S. Brandherm
- Faculty of Chemistry and Chemical Biology
- Technical University of Dortmund
- D-44227 Dortmund
- Germany
| | | | - A. Brunschweiger
- Faculty of Chemistry and Chemical Biology
- Technical University of Dortmund
- D-44227 Dortmund
- Germany
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73
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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: 34] [Impact Index Per Article: 3.8] [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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74
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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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75
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MacConnell AB, McEnaney PJ, Cavett VJ, Paegel BM. DNA-Encoded Solid-Phase Synthesis: Encoding Language Design and Complex Oligomer Library Synthesis. ACS COMBINATORIAL SCIENCE 2015; 17:518-34. [PMID: 26290177 PMCID: PMC4571006 DOI: 10.1021/acscombsci.5b00106] [Citation(s) in RCA: 109] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
![]()
The
promise of exploiting combinatorial synthesis for small molecule
discovery remains unfulfilled due primarily to the “structure
elucidation problem”: the back-end mass spectrometric analysis
that significantly restricts one-bead-one-compound (OBOC) library
complexity. The very molecular features that confer binding potency
and specificity, such as stereochemistry, regiochemistry, and scaffold
rigidity, are conspicuously absent from most libraries because isomerism
introduces mass redundancy and diverse scaffolds yield uninterpretable
MS fragmentation. Here we present DNA-encoded solid-phase synthesis
(DESPS), comprising parallel compound synthesis in organic solvent
and aqueous enzymatic ligation of unprotected encoding dsDNA oligonucleotides.
Computational encoding language design yielded 148 thermodynamically
optimized sequences with Hamming string distance ≥ 3 and total
read length <100 bases for facile sequencing. Ligation is efficient
(70% yield), specific, and directional over 6 encoding positions.
A series of isomers served as a testbed for DESPS’s utility
in split-and-pool diversification. Single-bead quantitative PCR detected
9 × 104 molecules/bead and sequencing allowed for
elucidation of each compound’s synthetic history. We applied
DESPS to the combinatorial synthesis of a 75 645-member OBOC
library containing scaffold, stereochemical and regiochemical diversity
using mixed-scale resin (160-μm quality control beads and 10-μm
screening beads). Tandem DNA sequencing/MALDI-TOF MS analysis of 19
quality control beads showed excellent agreement (<1 ppt) between
DNA sequence-predicted mass and the observed mass. DESPS synergistically
unites the advantages of solid-phase synthesis and DNA encoding, enabling
single-bead structural elucidation of complex compounds and synthesis
using reactions normally considered incompatible with unprotected
DNA. The widespread availability of inexpensive oligonucleotide synthesis,
enzymes, DNA sequencing, and PCR make implementation of DESPS straightforward,
and may prompt the chemistry community to revisit the synthesis of
more complex and diverse libraries.
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Affiliation(s)
- Andrew B. MacConnell
- Department of Chemistry and ‡Doctoral Program in Chemical and Biological
Sciences, The Scripps Research Institute, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Patrick J. McEnaney
- Department of Chemistry and ‡Doctoral Program in Chemical and Biological
Sciences, The Scripps Research Institute, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Valerie J. Cavett
- Department of Chemistry and ‡Doctoral Program in Chemical and Biological
Sciences, The Scripps Research Institute, 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Brian M. Paegel
- Department of Chemistry and ‡Doctoral Program in Chemical and Biological
Sciences, The Scripps Research Institute, 130 Scripps Way, Jupiter, Florida 33458, United States
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76
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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 COMBINATORIAL SCIENCE 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] [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.
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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
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77
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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] [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
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