1
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Ji D, Feng H, Liew SW, Kwok CK. Modified nucleic acid aptamers: development, characterization, and biological applications. Trends Biotechnol 2023; 41:1360-1384. [PMID: 37302912 DOI: 10.1016/j.tibtech.2023.05.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Revised: 04/30/2023] [Accepted: 05/18/2023] [Indexed: 06/13/2023]
Abstract
Aptamers are single-stranded oligonucleotides that bind to their targets via specific structural interactions. To improve the properties and performance of aptamers, modified nucleotides are incorporated during or after a selection process such as systematic evolution of ligands by exponential enrichment (SELEX). We summarize the latest modified nucleotides and strategies used in modified (mod)-SELEX and post-SELEX to develop modified aptamers, highlight the methods used to characterize aptamer-target interactions, and present recent progress in modified aptamers that recognize different targets. We discuss the challenges and perspectives in further advancing the methodologies and toolsets to accelerate the discovery of modified aptamers, improve the throughput of aptamer-target characterization, and expand the functional diversity and complexity of modified aptamers.
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Affiliation(s)
- Danyang Ji
- Department of Chemistry and State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon Tong, Hong Kong, SAR, China
| | - Hengxin Feng
- Department of Chemistry and State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon Tong, Hong Kong, SAR, China
| | - Shiau Wei Liew
- Department of Chemistry and State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon Tong, Hong Kong, SAR, China
| | - Chun Kit Kwok
- Department of Chemistry and State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon Tong, Hong Kong, SAR, China; Shenzhen Research Institute of City University of Hong Kong, Shenzhen, China.
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2
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Gantz M, Neun S, Medcalf EJ, van Vliet LD, Hollfelder F. Ultrahigh-Throughput Enzyme Engineering and Discovery in In Vitro Compartments. Chem Rev 2023; 123:5571-5611. [PMID: 37126602 PMCID: PMC10176489 DOI: 10.1021/acs.chemrev.2c00910] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Novel and improved biocatalysts are increasingly sourced from libraries via experimental screening. The success of such campaigns is crucially dependent on the number of candidates tested. Water-in-oil emulsion droplets can replace the classical test tube, to provide in vitro compartments as an alternative screening format, containing genotype and phenotype and enabling a readout of function. The scale-down to micrometer droplet diameters and picoliter volumes brings about a >107-fold volume reduction compared to 96-well-plate screening. Droplets made in automated microfluidic devices can be integrated into modular workflows to set up multistep screening protocols involving various detection modes to sort >107 variants a day with kHz frequencies. The repertoire of assays available for droplet screening covers all seven enzyme commission (EC) number classes, setting the stage for widespread use of droplet microfluidics in everyday biochemical experiments. We review the practicalities of adapting droplet screening for enzyme discovery and for detailed kinetic characterization. These new ways of working will not just accelerate discovery experiments currently limited by screening capacity but profoundly change the paradigms we can probe. By interfacing the results of ultrahigh-throughput droplet screening with next-generation sequencing and deep learning, strategies for directed evolution can be implemented, examined, and evaluated.
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Affiliation(s)
- Maximilian Gantz
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Rd, Cambridge CB2 1GA, U.K
| | - Stefanie Neun
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Rd, Cambridge CB2 1GA, U.K
| | - Elliot J Medcalf
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Rd, Cambridge CB2 1GA, U.K
| | - Liisa D van Vliet
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Rd, Cambridge CB2 1GA, U.K
| | - Florian Hollfelder
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Rd, Cambridge CB2 1GA, U.K
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3
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Neun S, van Vliet L, Hollfelder F, Gielen F. High-Throughput Steady-State Enzyme Kinetics Measured in a Parallel Droplet Generation and Absorbance Detection Platform. Anal Chem 2022; 94:16701-16710. [DOI: 10.1021/acs.analchem.2c03164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Affiliation(s)
- Stefanie Neun
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, U.K
| | - Liisa van Vliet
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, U.K
| | - Florian Hollfelder
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, U.K
| | - Fabrice Gielen
- Living Systems Institute and College of Engineering Mathematics and Physical Sciences, University of Exeter, Exeter EX4 4QD, U.K
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4
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Increasing insulin measurement throughput by fluorescence anisotropy imaging immunoassays. Anal Chim Acta 2022; 1212:339942. [DOI: 10.1016/j.aca.2022.339942] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 05/10/2022] [Accepted: 05/11/2022] [Indexed: 01/25/2023]
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5
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Lindenburg LH, Pantelejevs T, Gielen F, Zuazua-Villar P, Butz M, Rees E, Kaminski CF, Downs JA, Hyvönen M, Hollfelder F. Improved RAD51 binders through motif shuffling based on the modularity of BRC repeats. Proc Natl Acad Sci U S A 2021; 118:e2017708118. [PMID: 34772801 PMCID: PMC8727024 DOI: 10.1073/pnas.2017708118] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/10/2021] [Indexed: 01/20/2023] Open
Abstract
Exchanges of protein sequence modules support leaps in function unavailable through point mutations during evolution. Here we study the role of the two RAD51-interacting modules within the eight binding BRC repeats of BRCA2. We created 64 chimeric repeats by shuffling these modules and measured their binding to RAD51. We found that certain shuffled module combinations were stronger binders than any of the module combinations in the natural repeats. Surprisingly, the contribution from the two modules was poorly correlated with affinities of natural repeats, with a weak BRC8 repeat containing the most effective N-terminal module. The binding of the strongest chimera, BRC8-2, to RAD51 was improved by -2.4 kCal/mol compared to the strongest natural repeat, BRC4. A crystal structure of RAD51:BRC8-2 complex shows an improved interface fit and an extended β-hairpin in this repeat. BRC8-2 was shown to function in human cells, preventing the formation of nuclear RAD51 foci after ionizing radiation.
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Affiliation(s)
- Laurens H Lindenburg
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, United Kingdom
| | - Teodors Pantelejevs
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, United Kingdom
| | - Fabrice Gielen
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, United Kingdom
- Living Systems Institute, University of Exeter, Exeter EX4 4QD, United Kingdom
| | - Pedro Zuazua-Villar
- Division of Cancer Biology, The Institute of Cancer Research, London SW3 6JB, United Kingdom
| | - Maren Butz
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, United Kingdom
| | - Eric Rees
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge CB3 0AS, United Kingdom
| | - Clemens F Kaminski
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge CB3 0AS, United Kingdom
| | - Jessica A Downs
- Division of Cancer Biology, The Institute of Cancer Research, London SW3 6JB, United Kingdom
| | - Marko Hyvönen
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, United Kingdom;
| | - Florian Hollfelder
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, United Kingdom;
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6
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Gao Y, Zhao CX, Sainsbury F. Droplet shape control using microfluidics and designer biosurfactants. J Colloid Interface Sci 2021; 584:528-538. [PMID: 33129162 DOI: 10.1016/j.jcis.2020.09.126] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 09/23/2020] [Accepted: 09/30/2020] [Indexed: 11/30/2022]
Abstract
Many uses of emulsion droplets require precise control over droplet size and shape. Here we report a 'shape-memorable' micro-droplet formulation stabilized by a polyethylene glycol (PEG)-modified protein -surfactant, the droplets are stable against coalescence for months and can maintain non-spherical shapes for hours, depending on the surface coverage of PEGylated protein. Monodisperse droplets with aspect ratios ranging from 1.0 to 3.4 were controllably synthesized with a flow-focusing microfluidic device. Mechanical properties of the interfacial protein network were explored to elucidate the mechanism behind the droplet shape conservation phenomenon. Characterization of the protein film revealed that the presence of a PEG layer at interfaces alters the mechanical responses of the protein film, resulting in interfacial networks with improved strength. Taking advantage of the prolonged stabilization of non-spherical droplets, we demonstrate functionalization of the droplet interface with accessible biotins. The stabilization of micro-droplet shape with surface-active proteins that also serve as an anchor for integrating functional moieties, provides a tailorable interface for diverse biomimetic applications.
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Affiliation(s)
- Yuan Gao
- Australian Institute for Bioengineering and Nanotechnology, University of Queensland, St Lucia, QLD 4072, Australia
| | - Chun-Xia Zhao
- Australian Institute for Bioengineering and Nanotechnology, University of Queensland, St Lucia, QLD 4072, Australia.
| | - Frank Sainsbury
- Australian Institute for Bioengineering and Nanotechnology, University of Queensland, St Lucia, QLD 4072, Australia; Centre for Cell Factories and Biopolymers, Griffith Institute for Drug Discovery, Griffith University, Nathan, QLD 4111, Australia; Synthetic Biology Future Science Platform, Commonwealth Scientific and Industrial Research Organization (CSIRO), Brisbane, QLD 4001, Australia.
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7
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Zurek PJ, Hours R, Schell U, Pushpanath A, Hollfelder F. Growth amplification in ultrahigh-throughput microdroplet screening increases sensitivity of clonal enzyme assays and minimizes phenotypic variation. LAB ON A CHIP 2021; 21:163-173. [PMID: 33242058 DOI: 10.1039/d0lc00830c] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Microfluidic ultrahigh-throughput screening of enzyme activities provides information on libraries with millions of variants in a day. Each individual library member is represented by a recombinant single cell, compartmentalised in an emulsion droplet, in which an activity assay is carried out. Key to the success of this approach is the precision and sensitivity of the assay. Assay quality is most profoundly challenged when initially weak, promiscuous activities are to be enhanced in early rounds of directed evolution or when entirely novel catalysts are to be identified from metagenomic sources. Implementation of measures to widen the dynamic range of clonal assays would increase the chances of finding and generating new biocatalysts. Here, we demonstrate that the assay sensitivity and DNA recovery can be improved by orders of magnitude by growth of initially singly compartmentalised cells in microdroplets. Homogeneous cell growth is achieved by continuous oxygenation and recombinant protein expression is regulated by diffusion of an inducer from the oil phase. Reaction conditions are adjusted by directed droplet coalescence to enable full control of buffer composition and kinetic incubation time, creating level playing field conditions for library selections. The clonal amplification multiplies the product readout because more enzyme is produced per compartment. At the same time, phenotypic variation is reduced by measuring monoclonal populations rather than single cells and recovery efficiency is increased. Consequently, this workflow increases the efficiency of lysate-based microfluidic enzyme assays and will make it easier for protein engineers to identify or evolve new enzymes for applications in synthetic and chemical biology.
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Affiliation(s)
- Paul Jannis Zurek
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, CB2 1GA Cambridge, UK.
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8
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Neun S, Zurek PJ, Kaminski TS, Hollfelder F. Ultrahigh throughput screening for enzyme function in droplets. Methods Enzymol 2020; 643:317-343. [PMID: 32896286 DOI: 10.1016/bs.mie.2020.06.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Water-in-oil droplets, made and handled in microfluidic devices, provide a new experimental format, in which ultrahigh throughput experiments can be conducted faster and with minimal reagent consumption. An increasing number of studies have emerged that applied this approach to directed evolution and metagenomic screening of enzyme catalysts. Here, we review the considerations necessary to implement robust workflows, based on choices of device design, detection modes, emulsion formulations and substrates, and scope out which enzyme classes have become amenable to droplet screening.
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Affiliation(s)
- Stefanie Neun
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Paul J Zurek
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Tomasz S Kaminski
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Florian Hollfelder
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom.
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9
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Choi JW, Vasamsetti BMK, Choo J, Kim HY. Analysis of deoxyribonuclease activity by conjugation-free fluorescence polarisation in sub-nanolitre droplets. Analyst 2020; 145:3222-3228. [PMID: 32118224 DOI: 10.1039/c9an02380a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
We report the analysis of deoxyribonuclease (DNase) activity by conjugation-free fluorescence polarisation in a droplet-based microfluidic chip. DNase is a DNA cleaving enzyme and its activity is important in the maintenance of normal cellular functions. Alterations in DNase activity have been implicated as the cause of various cancers and autoimmune diseases. To date, various methods for the analysis of DNase activity have been reported. However, they are not cost effective due to the requirement of large sample volumes and the need for the conjugation of fluorescent dyes. In this study, we have used ethidium bromide (EtBr), a DNA intercalating reagent, as a fluorescent reporter without any prior conjugation or modification of DNA. Degradation of DNA by DNase 1 was monitored at a steady state by making changes in the fluorescence polarisation of EtBr in droplets with a volume of 330 picolitre at a 40 hertz frequency under visible light. Using this technique, we successfully determined the half-maximal inhibitory concentration (IC50) of ethylenediaminetetraacetic acid (EDTA) for the inhibition of DNase 1 activity to be 1.56 ± 0.91 mM.
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Affiliation(s)
- Jae-Won Choi
- Department of Biochemistry, Chungbuk National University, Cheongju 28644, Republic of Korea.
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10
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Cavell AC, Krasecki VK, Li G, Sharma A, Sun H, Thompson MP, Forman CJ, Guo SY, Hickman RJ, Parrish KA, Aspuru-Guzik A, Cronin L, Gianneschi NC, Goldsmith RH. Optical monitoring of polymerizations in droplets with high temporal dynamic range. Chem Sci 2020; 11:2647-2656. [PMID: 34084323 PMCID: PMC8157680 DOI: 10.1039/c9sc05559b] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Accepted: 02/02/2020] [Indexed: 12/23/2022] Open
Abstract
The ability to optically monitor a chemical reaction and generate an in situ readout is an important enabling technology, with applications ranging from the monitoring of reactions in flow, to the critical assessment step for combinatorial screening, to mechanistic studies on single reactant and catalyst molecules. Ideally, such a method would be applicable to many polymers and not require only a specific monomer for readout. It should also be applicable if the reactions are carried out in microdroplet chemical reactors, which offer a route to massive scalability in combinatorial searches. We describe a convenient optical method for monitoring polymerization reactions, fluorescence polarization anisotropy monitoring, and show that it can be applied in a robotically generated microdroplet. Further, we compare our method to an established optical reaction monitoring scheme, the use of Aggregation-Induced Emission (AIE) dyes, and find the two monitoring schemes offer sensitivity to different temporal regimes of the polymerization, meaning that the combination of the two provides an increased temporal dynamic range. Anisotropy is sensitive at early times, suggesting it will be useful for detecting new polymerization "hits" in searches for new reactivity, while the AIE dye responds at longer times, suggesting it will be useful for detecting reactions capable of reaching higher molecular weights.
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Affiliation(s)
- Andrew C Cavell
- Department of Chemistry, University of Wisconsin-Madison 1101 University Avenue Madison WI 53706 USA
| | - Veronica K Krasecki
- Department of Chemistry, University of Wisconsin-Madison 1101 University Avenue Madison WI 53706 USA
| | - Guoping Li
- Department of Chemistry, Northwestern University 2145 Sheridan Road Evanston IL 60208 USA
| | - Abhishek Sharma
- School of Chemistry, University of Glasgow Joseph Black Building, University Avenue Glasgow Scotland G12 8QQ UK
| | - Hao Sun
- Department of Chemistry, Northwestern University 2145 Sheridan Road Evanston IL 60208 USA
| | - Matthew P Thompson
- Department of Chemistry, Northwestern University 2145 Sheridan Road Evanston IL 60208 USA
| | - Christopher J Forman
- Department of Chemistry, Northwestern University 2145 Sheridan Road Evanston IL 60208 USA
| | - Si Yue Guo
- Department of Chemistry, University of Toronto 80 St. George Street Toronto Ontario M5S 3H6 Canada
- Department of Computer Science, University of Toronto 40 St. George Street Toronto Ontario M5S 2E4 Canada
| | - Riley J Hickman
- Department of Chemistry, University of Toronto 80 St. George Street Toronto Ontario M5S 3H6 Canada
- Department of Computer Science, University of Toronto 40 St. George Street Toronto Ontario M5S 2E4 Canada
| | - Katherine A Parrish
- Department of Chemistry, University of Wisconsin-Madison 1101 University Avenue Madison WI 53706 USA
| | - Alán Aspuru-Guzik
- Department of Chemistry, University of Toronto 80 St. George Street Toronto Ontario M5S 3H6 Canada
- Department of Computer Science, University of Toronto 40 St. George Street Toronto Ontario M5S 2E4 Canada
- Canadian Institute for Advanced Research (CIFAR) Senior Fellow Toronto Ontario M5S 1M1 Canada
- CIFAR Artificial Intelligence Chair, Vector Institute Toronto Ontario M5S 1M1 Canada
| | - Leroy Cronin
- School of Chemistry, University of Glasgow Joseph Black Building, University Avenue Glasgow Scotland G12 8QQ UK
| | - Nathan C Gianneschi
- Department of Chemistry, Northwestern University 2145 Sheridan Road Evanston IL 60208 USA
| | - Randall H Goldsmith
- Department of Chemistry, University of Wisconsin-Madison 1101 University Avenue Madison WI 53706 USA
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11
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Hackler AL, FitzGerald FG, Dang VQ, Satz AL, Paegel BM. Off-DNA DNA-Encoded Library Affinity Screening. ACS COMBINATORIAL SCIENCE 2020; 22:25-34. [PMID: 31829554 DOI: 10.1021/acscombsci.9b00153] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
DNA-encoded library (DEL) technology is emerging as a key element of the small molecule discovery toolbox. Conventional DEL screens (i.e., on-DNA screening) interrogate large combinatorial libraries via affinity selection of DNA-tagged library members that are ligands of a purified and immobilized protein target. In these selections, the DNA tags can materially and undesirably influence target binding and, therefore, the experiment outcome. Here, we use a solid-phase DEL and droplet-based microfluidic screening to separate the DEL member from its DNA tag (i.e., off-DNA screening), for subsequent in-droplet laser-induced fluorescence polarization (FP) detection of target binding, obviating DNA tag interference. Using the receptor tyrosine kinase (RTK) discoidin domain receptor 1 (DDR1) as a proof-of-concept target in a droplet-scale competition-binding assay, we screened a 67 100-member solid-phase DEL of drug-like small molecules for competitive ligands of DDR1 and identified several known RTK inhibitor pharmacophores, including azaindole- and quinazolinone-containing monomers. Off-DNA DEL affinity screening with FP detection is potentially amenable to a wide array of target classes, including nucleic acid binding proteins, proteins that are difficult to overexpress and purify, or targets with no known activity assay.
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Affiliation(s)
| | | | | | - Alexander L. Satz
- Roche Pharma Research and Early Development (pRED), Roche Innovation Center Basel Hoffman-La Roche Ltd, Grenzacherstrasse 124, CH-4070 Basel, Switzerland
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12
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van Loo B, Heberlein M, Mair P, Zinchenko A, Schüürmann J, Eenink BDG, Holstein JM, Dilkaute C, Jose J, Hollfelder F, Bornberg-Bauer E. High-Throughput, Lysis-Free Screening for Sulfatase Activity Using Escherichia coli Autodisplay in Microdroplets. ACS Synth Biol 2019; 8:2690-2700. [PMID: 31738524 DOI: 10.1021/acssynbio.9b00274] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Directed evolution of enzymes toward improved catalytic performance has become a powerful tool in protein engineering. To be effective, a directed evolution campaign requires the use of high-throughput screening. In this study we describe the development of an ultra high-throughput lysis-free procedure to screen for improved sulfatase activity by combining microdroplet-based single-variant activity sorting with E. coli autodisplay. For the first step in a 4-step screening procedure, we quantitatively screened >105 variants of the homodimeric arylsulfatase from Silicibacter pomeroyi (SpAS1), displayed on the E. coli cell surface, for improved sulfatase activity using fluorescence activated droplet sorting. Compartmentalization of the fluorescent reaction product with living E. coli cells autodisplaying the sulfatase variants ensured the continuous linkage of genotype and phenotype during droplet sorting and allowed for direct recovery by simple regrowth of the sorted cells. The use of autodisplay on living cells simplified and reduced the degree of liquid handling during all steps in the screening procedure to the single event of simply mixing substrate and cells. The percentage of apparent improved variants was enriched >10-fold as a result of droplet sorting. We ultimately identified 25 SpAS1 variants with improved performance toward 4-nitrophenyl sulfate (up to 6.2-fold) and/or fluorescein disulfate (up to 30-fold). In SpAS1 variants with improved performance toward the bulky fluorescein disulfate, many of the beneficial mutations occur in residues that form hydrogen bonds between α-helices in the C-terminal oligomerization region, suggesting a previously unknown role for the dimer interface in shaping the substrate binding site of SpAS1.
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Affiliation(s)
- Bert van Loo
- Institute for Evolution and Biodiversity, University of Münster, 48149 Münster, Germany
| | - Magdalena Heberlein
- Institute for Evolution and Biodiversity, University of Münster, 48149 Münster, Germany
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, United Kingdom
| | - Philip Mair
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, United Kingdom
| | - Anastasia Zinchenko
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, United Kingdom
| | - Jan Schüürmann
- Institute of Pharmaceutical and Medicinal Chemistry, University of Münster, 48149 Münster, Germany
| | - Bernard D. G. Eenink
- Institute for Evolution and Biodiversity, University of Münster, 48149 Münster, Germany
| | - Josephin M. Holstein
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, United Kingdom
| | - Carina Dilkaute
- Institute of Pharmaceutical and Medicinal Chemistry, University of Münster, 48149 Münster, Germany
| | - Joachim Jose
- Institute of Pharmaceutical and Medicinal Chemistry, University of Münster, 48149 Münster, Germany
| | - Florian Hollfelder
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, United Kingdom
| | - Erich Bornberg-Bauer
- Institute for Evolution and Biodiversity, University of Münster, 48149 Münster, Germany
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13
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Vinegoni C, Feruglio PF, Gryczynski I, Mazitschek R, Weissleder R. Fluorescence anisotropy imaging in drug discovery. Adv Drug Deliv Rev 2019; 151-152:262-288. [PMID: 29410158 PMCID: PMC6072632 DOI: 10.1016/j.addr.2018.01.019] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Revised: 01/29/2018] [Accepted: 01/30/2018] [Indexed: 12/15/2022]
Abstract
Non-invasive measurement of drug-target engagement can provide critical insights in the molecular pharmacology of small molecule drugs. Fluorescence polarization/fluorescence anisotropy measurements are commonly employed in protein/cell screening assays. However, the expansion of such measurements to the in vivo setting has proven difficult until recently. With the advent of high-resolution fluorescence anisotropy microscopy it is now possible to perform kinetic measurements of intracellular drug distribution and target engagement in commonly used mouse models. In this review we discuss the background, current advances and future perspectives in intravital fluorescence anisotropy measurements to derive pharmacokinetic and pharmacodynamic measurements in single cells and whole organs.
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Affiliation(s)
- Claudio Vinegoni
- Center for System Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
| | - Paolo Fumene Feruglio
- Center for System Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA; Department of Neurological, Biomedical and Movement Sciences, University of Verona, Verona, Italy
| | - Ignacy Gryczynski
- University of North Texas Health Science Center, Institute for Molecular Medicine, Fort Worth, TX, United States
| | - Ralph Mazitschek
- Center for System Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Ralph Weissleder
- Center for System Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
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14
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Buryska T, Vasina M, Gielen F, Vanacek P, van Vliet L, Jezek J, Pilat Z, Zemanek P, Damborsky J, Hollfelder F, Prokop Z. Controlled Oil/Water Partitioning of Hydrophobic Substrates Extending the Bioanalytical Applications of Droplet-Based Microfluidics. Anal Chem 2019; 91:10008-10015. [PMID: 31240908 DOI: 10.1021/acs.analchem.9b01839] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Functional annotation of novel proteins lags behind the number of sequences discovered by the next-generation sequencing. The throughput of conventional testing methods is far too low compared to sequencing; thus, experimental alternatives are needed. Microfluidics offer high throughput and reduced sample consumption as a tool to keep up with a sequence-based exploration of protein diversity. The most promising droplet-based systems have a significant limitation: leakage of hydrophobic compounds from water compartments to the carrier prevents their use with hydrophilic reagents. Here, we present a novel approach of substrate delivery into microfluidic droplets and apply it to high-throughput functional characterization of enzymes that convert hydrophobic substrates. Substrate delivery is based on the partitioning of hydrophobic chemicals between the oil and water phases. We applied a controlled distribution of 27 hydrophobic haloalkanes from oil to reaction water droplets to perform substrate specificity screening of eight model enzymes from the haloalkane dehalogenase family. This droplet-on-demand microfluidic system reduces the reaction volume 65 000-times and increases the analysis speed almost 100-fold compared to the classical test tube assay. Additionally, the microfluidic setup enables a convenient analysis of dependences of activity on the temperature in a range of 5 to 90 °C for a set of mesophilic and hyperstable enzyme variants. A high correlation between the microfluidic and test tube data supports the approach robustness. The precision is coupled to a considerable throughput of >20 000 reactions per day and will be especially useful for extending the scope of microfluidic applications for high-throughput analysis of reactions including compounds with limited water solubility.
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Affiliation(s)
- Tomas Buryska
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science , Masaryk University , Kamenice 5 , Brno 625 00 , Czech Republic.,International Clinical Research Center , St. Anne's University Hospital , Pekarska 53 , Brno 656 91 , Czech Republic
| | - Michal Vasina
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science , Masaryk University , Kamenice 5 , Brno 625 00 , Czech Republic.,International Clinical Research Center , St. Anne's University Hospital , Pekarska 53 , Brno 656 91 , Czech Republic
| | - Fabrice Gielen
- Department of Biochemistry , University of Cambridge , 80 Tennis Court Road , Cambridge CB2 1GA , United Kingdom.,Living Systems Institute , University of Exeter , Exeter EX4 4QD , United Kingdom
| | - Pavel Vanacek
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science , Masaryk University , Kamenice 5 , Brno 625 00 , Czech Republic.,International Clinical Research Center , St. Anne's University Hospital , Pekarska 53 , Brno 656 91 , Czech Republic
| | - Liisa van Vliet
- Department of Biochemistry , University of Cambridge , 80 Tennis Court Road , Cambridge CB2 1GA , United Kingdom
| | - Jan Jezek
- Institute of Scientific Instruments, Czech Academy of Sciences , Kralovopolska 147 , Brno 612 64 , Czech Republic
| | - Zdenek Pilat
- Institute of Scientific Instruments, Czech Academy of Sciences , Kralovopolska 147 , Brno 612 64 , Czech Republic
| | - Pavel Zemanek
- Institute of Scientific Instruments, Czech Academy of Sciences , Kralovopolska 147 , Brno 612 64 , Czech Republic
| | - Jiri Damborsky
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science , Masaryk University , Kamenice 5 , Brno 625 00 , Czech Republic.,International Clinical Research Center , St. Anne's University Hospital , Pekarska 53 , Brno 656 91 , Czech Republic
| | - Florian Hollfelder
- Department of Biochemistry , University of Cambridge , 80 Tennis Court Road , Cambridge CB2 1GA , United Kingdom
| | - Zbynek Prokop
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science , Masaryk University , Kamenice 5 , Brno 625 00 , Czech Republic.,International Clinical Research Center , St. Anne's University Hospital , Pekarska 53 , Brno 656 91 , Czech Republic
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15
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Cochrane WG, Malone ML, Dang VQ, Cavett V, Satz AL, Paegel BM. Activity-Based DNA-Encoded Library Screening. ACS COMBINATORIAL SCIENCE 2019; 21:425-435. [PMID: 30884226 DOI: 10.1021/acscombsci.9b00037] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Robotic high-throughput compound screening (HTS) and, increasingly, DNA-encoded library (DEL) screening are driving bioactive chemical matter discovery in the postgenomic era. HTS enables activity-based investigation of highly complex targets using static compound libraries. Conversely, DEL grants efficient access to novel chemical diversity, although screening is limited to affinity-based selections. Here, we describe an integrated droplet-based microfluidic circuit that directly screens solid-phase DELs for activity. An example screen of a 67 100-member library for inhibitors of the phosphodiesterase autotaxin yielded 35 high-priority structures for nanomole-scale synthesis and validation (20 active), guiding candidate selection for synthesis at scale (5/5 compounds with IC50 values of 4-10 μM). We further compared activity-based hits with those of an analogous affinity-based DEL selection. This miniaturized screening platform paves the way toward applying DELs to more complex targets (signaling pathways, cellular response) and represents a distributable approach to small molecule discovery.
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Affiliation(s)
| | | | | | | | - Alexander L. Satz
- Roche Pharma Research and Early Development (pRED) Roche Innovation Center Basel F. Hoffman-La Roche Ltd Grenzacherstrasse 124 CH-4070 Basel Switzerland
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16
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Sotnikov DV, Zherdev AV, Dzantiev BB. Mathematical Modeling of Bioassays. BIOCHEMISTRY (MOSCOW) 2018. [PMID: 29523069 DOI: 10.1134/s0006297917130119] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The high affinity and specificity of biological receptors determine the demand for and the intensive development of analytical systems based on use of these receptors. Therefore, theoretical concepts of the mechanisms of these systems, quantitative parameters of their reactions, and relationships between their characteristics and ligand-receptor interactions have become extremely important. Many mathematical models describing different bioassay formats have been proposed. However, there is almost no information on the comparative characteristics of these models, their assumptions, and predictive insights. In this review we suggested a set of criteria to classify various bioassays and reviewed classical and contemporary publications on these bioassays with special emphasis on immunochemical analysis systems as the most common and in-demand techniques. The possibilities of analytical and numerical modeling are discussed, as well as estimations of the minimum concentrations that may be detected in bioassays and recommendations for the choice of assay conditions.
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Affiliation(s)
- D V Sotnikov
- Bach Institute of Biochemistry, Research Center for Biotechnology, Russian Academy of Sciences, Moscow, 119071, Russia.
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17
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Charmet J, Arosio P, Knowles TP. Microfluidics for Protein Biophysics. J Mol Biol 2018; 430:565-580. [DOI: 10.1016/j.jmb.2017.12.015] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Revised: 12/19/2017] [Accepted: 12/20/2017] [Indexed: 01/09/2023]
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18
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Assays with Detection of Fluorescence Anisotropy: Challenges and Possibilities for Characterizing Ligand Binding to GPCRs. Trends Pharmacol Sci 2018; 39:187-199. [DOI: 10.1016/j.tips.2017.10.004] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Revised: 10/10/2017] [Accepted: 10/10/2017] [Indexed: 01/24/2023]
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19
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Mair P, Gielen F, Hollfelder F. Exploring sequence space in search of functional enzymes using microfluidic droplets. Curr Opin Chem Biol 2017; 37:137-144. [PMID: 28390246 DOI: 10.1016/j.cbpa.2017.02.018] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Revised: 02/08/2017] [Accepted: 02/15/2017] [Indexed: 12/21/2022]
Abstract
Screening of enzyme mutants in monodisperse picoliter compartments, generated at kilohertz speed in microfluidic devices, is coming of age. After a decade of proof-of-principle experiments, workflows have emerged that combine existing microfluidic modules to assay reaction progress quantitatively and yield improved enzymes. Recent examples of the screening of libraries of randomised proteins and from metagenomic sources suggest that this approach is not only faster and cheaper, but solves problems beyond the feasibility scope of current methodologies. The establishment of new assays in this format - so far covering hydrolases, aldolases, polymerases and dehydrogenases - will enable the exploration of sequence space for new catalysts of natural and non-natural chemical transformations.
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Affiliation(s)
- Philip Mair
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| | - Fabrice Gielen
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK; Living Systems Institute, University of Exeter, Stocker Road, Exeter EX4 4QD, UK
| | - Florian Hollfelder
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Cambridge CB2 1GA, UK.
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