1
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Bąchor R. Peptidyl-Resin Substrates as a Tool in the Analysis of Caspase Activity. Molecules 2022; 27:molecules27134107. [PMID: 35807352 PMCID: PMC9268085 DOI: 10.3390/molecules27134107] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 06/22/2022] [Accepted: 06/23/2022] [Indexed: 02/04/2023] Open
Abstract
Caspases, proteolytic enzymes belonging to the group of cysteine proteases, play a crucial role in apoptosis. Understanding their activity and substrate specificity is extremely important. Fluorescence-based approaches, including fluorogenic substrates, are generally used to confirm cleavage preferences. Here we present a new method of substrate specificity and activity analysis based on the application of fix-charge tagged peptides located on the resin. The proteolysis of peptide bond on the resin, occurring even with low efficiency, results in the formation of N-terminal fragments of model peptide containing ionization enhancers in the form of quaternary ammonium groups, allowing for ultrasensitive and reliable analysis by LC-MS/MS. The possibility of application of the proposed solution was tested through the analysis of substrate specificity and activity of caspase 3 or 7. The obtained results confirm the known substrate specificity of executioner caspases. Our solution also allowed us to observe that caspases can hydrolyze peptides shorter than those presented to date in the scientific literature.
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Affiliation(s)
- Remigiusz Bąchor
- Faculty of Chemistry, University of Wroclaw, F. Joliot-Curie 14, 50-383 Wrocław, Poland
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2
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Veni, Vidi, Vici: Immobilized Peptide-Based Conjugates as Tools for Capture, Analysis, and Transformation. CHEMOSENSORS 2022. [DOI: 10.3390/chemosensors10010031] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Analysis of peptide biomarkers of pathological states of the organism is often a serious challenge, due to a very complex composition of the cell and insufficient sensitivity of the current analytical methods (including mass spectrometry). One of the possible ways to overcome this problem is sample enrichment by capturing the selected components using a specific solid support. Another option is increasing the detectability of the desired compound by its selective tagging. Appropriately modified and immobilized peptides can be used for these purposes. In addition, they find application in studying the specificity and activity of proteolytic enzymes. Immobilized heterocyclic peptide conjugates may serve as metal ligands, to form complexes used as catalysts or analytical markers. In this review, we describe various applications of immobilized peptides, including selective capturing of cysteine-containing peptides, tagging of the carbonyl compounds to increase the sensitivity of their detection, enrichment of biological samples in deoxyfructosylated peptides, and fishing out of tyrosine–containing peptides by the formation of azo bond. Moreover, the use of the one-bead-one-compound peptide library for the analysis of substrate specificity and activity of caspases is described. Furthermore, the evolution of immobilization from the solid support used in peptide synthesis to nanocarriers is presented. Taken together, the examples presented here demonstrate immobilized peptides as a multifunctional tool, which can be successfully used to solve multiple analytical problems.
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3
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Abstract
Collagen is the most abundant protein in humans and the major component of human skin. Collagen mimetic peptides (CMPs) can anneal to damaged collagen in vitro and in vivo. A duplex of CMPs was envisioned as a macromolecular mimic for damaged collagen. The duplex was synthesized on a solid support from the amino groups of a lysine residue and by using olefin metathesis to link the N termini. The resulting cyclic peptide, which is a monomer in solution, binds to CMPs to form a triple helix. Among these, CMPs that are engineered to avoid the formation of homotrimers but preorganized to adopt the conformation of a collagen strand exhibit enhanced association. Thus, this cyclic peptide enables the assessment of CMPs for utility in annealing to damaged collagen. Such CMPs have potential use in the diagnosis and treatment of fibrotic diseases and wounds.
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Affiliation(s)
| | - I Caglar Tanrikulu
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Jesús M Dones
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Ronald T Raines
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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4
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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: 25] [Impact Index Per Article: 6.3] [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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5
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Pei D, Kubi GA. Developments with bead-based screening for novel drug discovery. Expert Opin Drug Discov 2019; 14:1097-1102. [PMID: 31335229 PMCID: PMC7301614 DOI: 10.1080/17460441.2019.1647164] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Accepted: 07/19/2019] [Indexed: 01/24/2023]
Abstract
Introduction: Combinatorial chemistry provides a cost-effective method for rapid discovery of drug hits/leads. The one-bead-one-compound (OBOC) library method is in principle ideally suited for this application, because it permits a large number of structurally diverse compounds to be rapidly synthesized and simultaneously screened for binding to a target of interest. However, application of OBOC libraries in drug discovery has encountered significant technical challenges. Areas covered: This Special Report covers the challenges associated with first-generation OBOC libraries (difficulty in structural identification of non-peptidic hits, screening biases and high false positive rates, and poor scalability). It also covers the many strategies developed over the past two decades to overcome these challenges. Expert opinion: With most of the technical challenges now overcome and the advent of powerful intracellular delivery technologies, OBOC libraries of metabolically stable and conformationally rigidified molecules (macrocyclic peptides and peptidomimetics, rigidified acyclic oligomers, and D-peptides) can be routinely synthesized and screened to discover initial hits against previously undruggable targets such as intracellular protein-protein interactions. On the other hand, further developments are still needed to expand the utility of the OBOC method to non-peptidic chemical scaffolds.
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Affiliation(s)
- Dehua Pei
- Department of Chemistry and Biochemistry, The Ohio State University, 484 West 12th Avenue, Columbus, OH 43210, USA
| | - George Appiah Kubi
- Department of Chemistry and Biochemistry, The Ohio State University, 484 West 12th Avenue, Columbus, OH 43210, USA
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6
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Pérez-Pi I, Evans DA, Horrocks MH, Pham NT, Dolt KS, Koszela J, Kunath T, Auer M. α-Synuclein-Confocal Nanoscanning (ASYN-CONA), a Bead-Based Assay for Detecting Early-Stage α-Synuclein Aggregation. Anal Chem 2019; 91:5582-5590. [PMID: 30964656 PMCID: PMC6534341 DOI: 10.1021/acs.analchem.8b03842] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
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α-Synuclein
fibrils are considered a hallmark of Parkinson’s
disease and other synucleinopathies. However, small oligomers that
formed during the early stages of α-synuclein aggregation are
thought to be the main toxic species causing disease. The formation
of α-synuclein oligomers has proven difficult to follow, because
of the heterogeneity and transient nature of the species formed. Here,
a novel bead-based aggregation assay for monitoring the earliest stages
of α-synuclein oligomerization, α-Synuclein–Confocal
Nanoscanning (ASYN-CONA), is presented. The α-synuclein A91C
single cysteine mutant is modified with a trifunctional chemical tag,
which allows simultaneous fluorescent labeling with a green dye (tetramethylrhodamine,
TMR) and attachment to microbeads. Beads with bound TMR-labeled α-synuclein
are then incubated with a red dye (Cy5)-labeled variant of α-synuclein
A91C, and EtOH (20%) to induce aggregation. Aggregation is detected
by confocal scanning imaging, below the equatorial plane of the beads,
which is known as the CONA technique. On-bead TMR-labeled α-synuclein
and aggregated Cy5-labeled α-synuclein from the solution are
quantitatively monitored in parallel by detection of fluorescent halos
or “rings”. α-Synuclein on-bead oligomerization
results in a linear increase of red bead ring fluorescence intensity
over a period of 5 h. Total internal reflection fluorescence microscopy
was performed on oligomers cleaved from the beads, and it revealed
that (i) oligomers are sufficiently stable in solution to investigate
their composition, consisting of 6 ± 1 monomer units, and (ii)
oligomers containing a mean of 15 monomers bind Thioflavin-T. Various
known inhibitors of α-synuclein aggregation were used to validate
the ASYN-CONA assay for drug screening. Baicalein, curcumin, and rifampicin
showed concentration-dependent inhibition of the α-synuclein
aggregation and the IC50 (the concentration of the compound
at which the maxiumum intensity was reduced by one-half) were calculated.
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Affiliation(s)
- Irene Pérez-Pi
- School of Biological Sciences and Edinburgh Medical School: Biomedical Sciences , University of Edinburgh , The King's Buildings, Edinburgh EH9 3BF , United Kingdom
| | - David A Evans
- School of Biological Sciences and Edinburgh Medical School: Biomedical Sciences , University of Edinburgh , The King's Buildings, Edinburgh EH9 3BF , United Kingdom
| | - Mathew H Horrocks
- EaStCHEM School of Chemistry , University of Edinburgh , Edinburgh EH9 3FJ , United Kingdom.,UK Dementia Research Institute , University of Edinburgh , Chancellor's Building, Edinburgh Medical School , Edinburgh EH16 4SB , United Kingdom
| | - Nhan T Pham
- School of Biological Sciences and Edinburgh Medical School: Biomedical Sciences , University of Edinburgh , The King's Buildings, Edinburgh EH9 3BF , United Kingdom
| | - Karamjit S Dolt
- MRC Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences , The University of Edinburgh , Edinburgh EH16 4UU , United Kingdom
| | - Joanna Koszela
- School of Biological Sciences and Edinburgh Medical School: Biomedical Sciences , University of Edinburgh , The King's Buildings, Edinburgh EH9 3BF , United Kingdom
| | - Tilo Kunath
- MRC Centre for Regenerative Medicine, Institute for Stem Cell Research, School of Biological Sciences , The University of Edinburgh , Edinburgh EH16 4UU , United Kingdom
| | - Manfred Auer
- School of Biological Sciences and Edinburgh Medical School: Biomedical Sciences , University of Edinburgh , The King's Buildings, Edinburgh EH9 3BF , United Kingdom
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7
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8
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Koszela J, Pham NT, Evans D, Mann S, Perez-Pi I, Shave S, Ceccarelli DFJ, Sicheri F, Tyers M, Auer M. Real-time tracking of complex ubiquitination cascades using a fluorescent confocal on-bead assay. BMC Biol 2018; 16:88. [PMID: 30097011 PMCID: PMC6086040 DOI: 10.1186/s12915-018-0554-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Accepted: 07/24/2018] [Indexed: 12/05/2022] Open
Abstract
BACKGROUND The ubiquitin-proteasome system (UPS) controls the stability, localization and/or activity of the proteome. However, the identification and characterization of complex individual ubiquitination cascades and their modulators remains a challenge. Here, we report a broadly applicable, multiplexed, miniaturized on-bead technique for real-time monitoring of various ubiquitination-related enzymatic activities. The assay, termed UPS-confocal fluorescence nanoscanning (UPS-CONA), employs a substrate of interest immobilized on a micro-bead and a fluorescently labeled ubiquitin which, upon enzymatic conjugation to the substrate, is quantitatively detected on the bead periphery by confocal imaging. RESULTS UPS-CONA is suitable for studying individual enzymatic activities, including various E1, E2, and HECT-type E3 enzymes, and for monitoring multi-step reactions within ubiquitination cascades in a single experimental compartment. We demonstrate the power of the UPS-CONA technique by simultaneously following ubiquitin transfer from Ube1 through Ube2L3 to E6AP. We applied this multi-step setup to investigate the selectivity of five ubiquitination inhibitors reportedly targeting different classes of ubiquitination enzymes. Using UPS-CONA, we have identified a new activity of a small molecule E2 inhibitor, BAY 11-7082, and of a HECT E3 inhibitor, heclin, towards the Ube1 enzyme. CONCLUSIONS As a sensitive, quantitative, flexible, and reagent-efficient method with a straightforward protocol, UPS-CONA constitutes a powerful tool for interrogation of ubiquitination-related enzymatic pathways and their chemical modulators, and is readily scalable for large experiments.
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Affiliation(s)
- Joanna Koszela
- Institute of Quantitative Biology, Biochemistry and Biotechnology, School of Biological Sciences, University of Edinburgh, C H Waddington Building, 3.07, Max Born Crescent, Edinburgh, EH9 3BF UK
| | - Nhan T. Pham
- Institute of Quantitative Biology, Biochemistry and Biotechnology, School of Biological Sciences, University of Edinburgh, C H Waddington Building, 3.07, Max Born Crescent, Edinburgh, EH9 3BF UK
| | - David Evans
- Institute of Quantitative Biology, Biochemistry and Biotechnology, School of Biological Sciences, University of Edinburgh, C H Waddington Building, 3.07, Max Born Crescent, Edinburgh, EH9 3BF UK
| | - Stefan Mann
- Institute of Quantitative Biology, Biochemistry and Biotechnology, School of Biological Sciences, University of Edinburgh, C H Waddington Building, 3.07, Max Born Crescent, Edinburgh, EH9 3BF UK
| | - Irene Perez-Pi
- Institute of Quantitative Biology, Biochemistry and Biotechnology, School of Biological Sciences, University of Edinburgh, C H Waddington Building, 3.07, Max Born Crescent, Edinburgh, EH9 3BF UK
| | - Steven Shave
- Institute of Quantitative Biology, Biochemistry and Biotechnology, School of Biological Sciences, University of Edinburgh, C H Waddington Building, 3.07, Max Born Crescent, Edinburgh, EH9 3BF UK
| | - Derek F. J. Ceccarelli
- The Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Room 1090, Toronto, Ontario M5G 1X5 Canada
| | - Frank Sicheri
- The Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, 600 University Avenue, Room 1090, Toronto, Ontario M5G 1X5 Canada
| | - Mike Tyers
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, Québec H3C 3J7 Canada
| | - Manfred Auer
- Institute of Quantitative Biology, Biochemistry and Biotechnology, School of Biological Sciences, University of Edinburgh, C H Waddington Building, 3.07, Max Born Crescent, Edinburgh, EH9 3BF UK
- Biomedical Sciences, Medical School, University of Edinburgh, C H Waddington Building, 3.07, Max Born Crescent, Edinburgh, EH9 3BF UK
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9
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Komnatnyy VV, Nielsen TE, Qvortrup K. Bead-based screening in chemical biology and drug discovery. Chem Commun (Camb) 2018; 54:6759-6771. [PMID: 29888365 DOI: 10.1039/c8cc02486c] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
High-throughput screening is an important component of the drug discovery process. The screening of libraries containing hundreds of thousands of compounds requires assays amenable to miniaturisation and automization. Combinatorial chemistry holds a unique promise to deliver structurally diverse libraries for early drug discovery. Among the various library forms, the one-bead-one-compound (OBOC) library, where each bead carries many copies of a single compound, holds the greatest potential for the rapid identification of novel hits against emerging drug targets. However, this potential has not yet been fully realized due to a number of technical obstacles. In this feature article, we review the progress that has been made in bead-based library screening and its application to the discovery of bioactive compounds. We identify the key challenges of this approach and highlight key steps needed for making a greater impact in the field.
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Affiliation(s)
- Vitaly V Komnatnyy
- Department of Chemistry, Technical University of Denmark, DK-2800 Kgs, Lyngby, Denmark.
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10
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Abstract
Chemical methods have enabled the total synthesis of protein molecules of ever-increasing size and complexity. However, methods to engineer synthetic proteins comprising noncanonical amino acids have not kept pace, even though this capability would be a distinct advantage of the total synthesis approach to protein science. In this work, we report a platform for protein engineering based on the screening of synthetic one-bead one-compound protein libraries. Screening throughput approaching that of cell surface display was achieved by a combination of magnetic bead enrichment, flow cytometry analysis of on-bead screens, and high-throughput MS/MS-based sequencing of identified active compounds. Direct screening of a synthetic protein library by these methods resulted in the de novo discovery of mirror-image miniprotein-based binders to a ∼150-kDa protein target, a task that would be difficult or impossible by other means.
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11
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Tang Y, Thillier Y, Liu R, Li X, Lam KS, Gao T. Single-Bead Quantification of Peptide Loading Distribution for One-Bead One-Compound Library Synthesis Using Confocal Raman Spectroscopy. Anal Chem 2017; 89:7000-7008. [PMID: 28530391 DOI: 10.1021/acs.analchem.7b00516] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
We report an analytical method to determine peptide loading of "one-bead one-compound" (OBOC) combinatorial peptide libraries at single-bead level. The quantification is based on a linear relationship between the amount of N-terminal amino groups on individual peptide beads and the intensity of Raman signal obtained from a specifically designed reporter labeled on amino groups. Confocal Raman spectroscopy was employed to characterize peptide loading of beads with defined peptide sequences and from OBOC combinatorial peptide libraries. Although amine loading of blank TentaGel beads was found to be uniform, peptide loading among beads of OBOC peptide libraries varied substantially, particularly for those libraries with long sequences. Construction of OBOC libraries can be monitored with this novel analytical technique so that synthetic conditions can be optimized for the preparation of high-quality OBOC peptide libraries. As the variability of peptide loading of individual library beads can significantly influence the screening results, quantitative information obtained by this method will allow us to gain insight into the complexity and challenge of OBOC library synthesis and screening.
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Affiliation(s)
- Yuchen Tang
- College of Chemistry, Central China Normal University , Wuhan 430079, China.,China Key Laboratory of Pesticide and Chemical Biology of Ministry of Education, Wuhan 430079, China.,Department of Biochemistry and Molecular Medicine, University of California at Davis , Sacramento, California 95817, United States
| | - Yann Thillier
- Department of Biochemistry and Molecular Medicine, University of California at Davis , Sacramento, California 95817, United States
| | - Ruiwu Liu
- Department of Biochemistry and Molecular Medicine, University of California at Davis , Sacramento, California 95817, United States
| | - Xiaocen Li
- Department of Biochemistry and Molecular Medicine, University of California at Davis , Sacramento, California 95817, United States
| | - Kit S Lam
- Department of Biochemistry and Molecular Medicine, University of California at Davis , Sacramento, California 95817, United States
| | - Tingjuan Gao
- College of Chemistry, Central China Normal University , Wuhan 430079, China.,China Key Laboratory of Pesticide and Chemical Biology of Ministry of Education, Wuhan 430079, China
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12
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Satz AL. Simulated Screens of DNA Encoded Libraries: The Potential Influence of Chemical Synthesis Fidelity on Interpretation of Structure-Activity Relationships. ACS COMBINATORIAL SCIENCE 2016; 18:415-24. [PMID: 27116029 DOI: 10.1021/acscombsci.6b00001] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Simulated screening of DNA encoded libraries indicates that the presence of truncated byproducts complicates the relationship between library member enrichment and equilibrium association constant (these truncates result from incomplete chemical reactions during library synthesis). Further, simulations indicate that some patterns observed in reported experimental data may result from the presence of truncated byproducts in the library mixture and not structure-activity relationships. Potential experimental methods of minimizing the presence of truncates are assessed via simulation; the relationship between enrichment and equilibrium association constant for libraries of differing purities is investigated. Data aggregation techniques are demonstrated that allow for more accurate analysis of screening results, in particular when the screened library contains significant quantities of truncates.
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Affiliation(s)
- Alexander L. Satz
- Roche Innovation Center Basel, Grenzacherstrasse
124, 4070 Basel, Switzerland
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13
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Heusermann W, Ludin B, Pham NT, Auer M, Weidemann T, Hintersteiner M. A Wide-Field Fluorescence Microscope Extension for Ultrafast Screening of One-Bead One-Compound Libraries Using a Spectral Image Subtraction Approach. ACS COMBINATORIAL SCIENCE 2016; 18:209-19. [PMID: 27057765 DOI: 10.1021/acscombsci.5b00175] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The increasing involvement of academic institutions and biotech companies in drug discovery calls for cost-effective methods to identify new bioactive molecules. Affinity-based on-bead screening of combinatorial one-bead one-compound libraries combines a split-mix synthesis design with a simple protein binding assay operating directly at the bead matrix. However, one bottleneck for academic scale on-bead screening is the unavailability of a cheap, automated, and robust screening platform that still provides a quantitative signal related to the amount of target protein binding to individual beads for hit bead ranking. Wide-field fluorescence microscopy has long been considered unsuitable due to significant broad spectrum autofluorescence of the library beads in conjunction with low detection sensitivity. Herein, we demonstrate how such a standard microscope equipped with LED-based excitation and a modern CMOS camera can be successfully used for selecting hit beads. We show that the autofluorescence issue can be overcome by an optical image subtraction approach that yields excellent signal-to-noise ratios for the detection of bead-associated target proteins. A polymer capillary attached to a semiautomated bead-picking device allows the operator to efficiently isolate individual hit beads in less than 20 s. The system can be used for ultrafast screening of >200,000 bead-bound compounds in 1.5 h, thereby making high-throughput screening accessible to a wider group within the scientific community.
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Affiliation(s)
- Wolf Heusermann
- IMCF
Biozentrum, Universität Basel, Klingelbergstrasse 50/70, 4056 Basel, Switzerland
| | - Beat Ludin
- Life Imaging Services, Efringerstrasse
79, 4057 Basel, Switzerland
| | - Nhan T Pham
- School
of Biological Sciences and School of Biomedical Sciences, University of Edinburgh, CH Waddington Building, Max Born Crescent, The King's
Buildings, Edinburgh, EH9
3BF, United Kingdom
| | - Manfred Auer
- School
of Biological Sciences and School of Biomedical Sciences, University of Edinburgh, CH Waddington Building, Max Born Crescent, The King's
Buildings, Edinburgh, EH9
3BF, United Kingdom
| | - Thomas Weidemann
- Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
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14
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Kodadek T, McEnaney PJ. Towards vast libraries of scaffold-diverse, conformationally constrained oligomers. Chem Commun (Camb) 2016; 52:6038-59. [PMID: 26996593 PMCID: PMC4846527 DOI: 10.1039/c6cc00617e] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
There is great interest in the development of probe molecules and drug leads that would bind tightly and selectively to protein surfaces that are difficult to target with traditional molecules, such as those involved in protein-protein interactions. The currently available evidence suggests that this will require molecules that are larger and have quite different chemical properties than typical Lipinski-compliant molecules that target enzyme active sites. We describe here efforts to develop vast libraries of conformationally constrained oligomers as a potentially rich source of these molecules.
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Affiliation(s)
- Thomas Kodadek
- Departments of Chemistry and Cancer Biology, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, USA.
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15
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Qvortrup K, Nielsen TE. In-Bead Screening of Hydroxamic Acids for the Identification of HDAC Inhibitors. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201511308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Katrine Qvortrup
- Department of Chemistry; Technical University of Denmark; Kgs. Lyngby 2800 Denmark
| | - Thomas E. Nielsen
- Department of Chemistry; Technical University of Denmark; Kgs. Lyngby 2800 Denmark
- Singapore Centre on Environmental Life Sciences Engineering; Nanyang Technological University; 637551 Singapore Singapore
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16
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Qvortrup K, Nielsen TE. In-Bead Screening of Hydroxamic Acids for the Identification of HDAC Inhibitors. Angew Chem Int Ed Engl 2016; 55:4472-5. [DOI: 10.1002/anie.201511308] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2015] [Revised: 02/02/2016] [Indexed: 12/26/2022]
Affiliation(s)
- Katrine Qvortrup
- Department of Chemistry; Technical University of Denmark; Kgs. Lyngby 2800 Denmark
| | - Thomas E. Nielsen
- Department of Chemistry; Technical University of Denmark; Kgs. Lyngby 2800 Denmark
- Singapore Centre on Environmental Life Sciences Engineering; Nanyang Technological University; 637551 Singapore Singapore
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17
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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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18
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Gao Y, Kodadek T. Direct comparison of linear and macrocyclic compound libraries as a source of protein ligands. ACS COMBINATORIAL SCIENCE 2015; 17:190-5. [PMID: 25623285 PMCID: PMC4356041 DOI: 10.1021/co500161c] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
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There has been much discussion of
the potential desirability of
macrocyclic molecules for the development of tool compounds and drug
leads. But there is little experimental data comparing otherwise equivalent
macrocyclic and linear compound libraries as a source of protein ligands.
In this Letter, we probe this point in the context of peptoid libraries.
Bead-displayed libraries of macrocyclic and linear peptoids containing
four variable positions and 0–2 fixed residues, to vary the
ring size, were screened against streptavidin and the affinity of
every hit for the target was measured. The data show that macrocyclization
is advantageous, but only when the ring contains 17 atoms, not 20
or 23 atoms. This technology will be useful for conducting direct
comparisons between many different types of chemical libraries to
determine their relative utility as a source of protein ligands.
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Affiliation(s)
- Yu Gao
- Departments of Chemistry
and Cancer Biology, The Scripps Research Institute, 130 Scripps
Way, Jupiter, Florida 33458, United States
| | - Thomas Kodadek
- Departments of Chemistry
and Cancer Biology, The Scripps Research Institute, 130 Scripps
Way, Jupiter, Florida 33458, United States
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19
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Doran TM, Gao Y, Mendes K, Dean S, Simanski S, Kodadek T. Utility of redundant combinatorial libraries in distinguishing high and low quality screening hits. ACS COMBINATORIAL SCIENCE 2014; 16:259-70. [PMID: 24749624 PMCID: PMC4053090 DOI: 10.1021/co500030f] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
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Large
one-bead one-compound (OBOC) combinatorial libraries can
be constructed relatively easily by solid-phase split and pool synthesis.
The use of resins with hydrophilic surfaces, such as TentaGel, allows
the beads to be used directly in screens for compounds that bind selectively
to labeled proteins, nucleic acids, or other biomolecules. However,
we have found that this method, while useful, has a high false positive
rate. In other words, beads that are scored as hits often display
compounds that prove to be poor ligands for the target of interest
when they are resynthesized and carried through validation trials.
This results in a significant waste of time and resources in cases
where putative hits cannot be validated without resynthesis. Here,
we report that this problem can be largely eliminated through the
use of redundant OBOC libraries, where more than one bead displaying
the same compound is present in the screen. We show that compounds
isolated more than once are likely to be high quality ligands for
the target of interest, whereas compounds isolated only once have
a much higher likelihood of being poor ligands. While the use of redundant
libraries does limit the number of unique compounds that can be screened
at one time in this format, the overall savings in time, effort, and
materials makes this a more efficient route to the isolation of useful
ligands for biomolecules.
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Affiliation(s)
- Todd M. Doran
- Departments
of Chemistry and Cancer Biology, The Scripps Research Institute, 130
Scripps Way, Jupiter, Florida 33458, United States
| | - Yu Gao
- Departments
of Chemistry and Cancer Biology, The Scripps Research Institute, 130
Scripps Way, Jupiter, Florida 33458, United States
| | - Kimberly Mendes
- OPKO Health, Inc., 555 Heritage
Drive, Jupiter, Florida 33458, United States
| | - Sonja Dean
- OPKO Health, Inc., 555 Heritage
Drive, Jupiter, Florida 33458, United States
| | - Scott Simanski
- Departments
of Chemistry and Cancer Biology, The Scripps Research Institute, 130
Scripps Way, Jupiter, Florida 33458, United States
| | - Thomas Kodadek
- Departments
of Chemistry and Cancer Biology, The Scripps Research Institute, 130
Scripps Way, Jupiter, Florida 33458, United States
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20
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Hintersteiner M, Auer M. A two-channel detection method for autofluorescence correction and efficient on-bead screening of one-bead one-compound combinatorial libraries using the COPAS fluorescence activated bead sorting system. Methods Appl Fluoresc 2013; 1:017001. [PMID: 29148437 DOI: 10.1088/2050-6120/1/1/017001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
One-bead one-compound combinatorial library beads exhibit varying levels of autofluorescence after solid phase combinatorial synthesis. Very often this causes significant problems for automated on-bead screening using TentaGel beads and fluorescently labeled target proteins. Herein, we present a method to overcome this limitation when fluorescence activated bead sorting is used as the screening method. We have equipped the COPAS bead sorting instrument with a high-speed profiling unit and developed a spectral autofluorescence correction method. The correction method is based on a simple algebraic operation using the fluorescence data from two detection channels and is applied on-the-fly in order to reliably identify hit beads by COPAS bead sorting. Our method provides a practical tool for the fast and efficient isolation of hit beads from one-bead one-compound library screens using either fluorescently labeled target proteins or biotinylated target proteins. This method makes hit bead identification easier and more reliable. It reduces false positives and eliminates the need for time-consuming pre-sorting of library beads in order to remove autofluorescent beads.
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