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Kobashigawa E, Russell S, Zhang MZ, Sinnott EA, Connolly M, Zhang S. RT-QuIC detection of chronic wasting disease prion in platelet samples of white-tailed deer. BMC Vet Res 2024; 20:152. [PMID: 38654224 DOI: 10.1186/s12917-024-04005-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Accepted: 04/04/2024] [Indexed: 04/25/2024] Open
Abstract
BACKGROUND Chronic wasting disease (CWD) is a prion disease of captive and free-ranging cervids. Currently, a definitive diagnosis of CWD relies on immunohistochemistry detection of PrPSc in the obex and retropharyngeal lymph node (RPLN) of the affected cervids. For high-throughput screening of CWD in wild cervids, RPLN samples are tested by ELISA followed by IHC confirmation of positive results. Recently, real-time quacking-induced conversion (RT-QuIC) has been used to detect CWD positivity in various types of samples. To develop a blood RT-QuIC assay suitable for CWD diagnosis, this study evaluated the assay sensitivity and specificity with and without ASR1-based preanalytical enrichment and NaI as the main ionic component in assay buffer. RESULTS A total of 23 platelet samples derived from CWD-positive deer (ELISA + /IHC +) and 30 platelet samples from CWD-negative (ELISA-) deer were tested. The diagnostic sensitivity was 43.48% (NaCl), 65.22% (NaI), 60.87% (NaCl-ASR1) or 82.61% (NaI-ASR1). The diagnostic specificity was 96.67% (NaCl), 100% (NaI), 100% (NaCl-ASR1), or 96.67% (NaI-ASR1). The probability of detecting CWD prion in platelet samples derived from CWD-positive deer was 0.924 (95% CRI: 0.714, 0.989) under NaI-ASR1 experimental condition and 0.530 (95% CRI: 0.156, 0.890) under NaCl alone condition. The rate of amyloid formation (RFA) was greatest under the NaI-ASR1 condition at 10-2 (0.01491, 95% CRI: 0.00675, 0.03384) and 10-3 (0.00629, 95% CRI: 0.00283, 0.01410) sample dilution levels. CONCLUSIONS Incorporation of ASR1-based preanalytical enrichment and NaI as the main ionic component significantly improved the sensitivity of CWD RT-QuIC on deer platelet samples. Blood test by the improved RT-QuIC assay may be used for antemortem and postmortem diagnosis of CWD.
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Affiliation(s)
- Estela Kobashigawa
- Veterinary Medical Diagnostic Laboratory, College of Veterinary Medicine, University of Missouri, 901 E. Campus Loop, Columbia, MO, USA
- Department of Veterinary Pathobiology, College of Veterinary Medicine, University of Missouri, 901 E. Campus Loop, Columbia, MO, USA
| | - Sherri Russell
- Missouri Department of Conservation, 2901 W Truman Blvd, Jefferson City, MO, USA
| | - Michael Z Zhang
- Veterinary Medical Diagnostic Laboratory, College of Veterinary Medicine, University of Missouri, 901 E. Campus Loop, Columbia, MO, USA
- Department of Veterinary Pathobiology, College of Veterinary Medicine, University of Missouri, 901 E. Campus Loop, Columbia, MO, USA
| | - Emily A Sinnott
- Missouri Department of Conservation, 2901 W Truman Blvd, Jefferson City, MO, USA
| | - Michael Connolly
- The Molecular Foundry, Lawrence Berkeley National Laboratory, 67 Cyclotron Rd, Berkeley, CA, USA
| | - Shuping Zhang
- Veterinary Medical Diagnostic Laboratory, College of Veterinary Medicine, University of Missouri, 901 E. Campus Loop, Columbia, MO, USA.
- Department of Veterinary Pathobiology, College of Veterinary Medicine, University of Missouri, 901 E. Campus Loop, Columbia, MO, USA.
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2
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Aquino C, Sarkar M. One Bead-One Compound (OBOC) Peptidomimetic-Encoded Library Synthesis via Split-and-Pool Methods. Methods Mol Biol 2022; 2541:105-120. [PMID: 36083550 DOI: 10.1007/978-1-0716-2545-3_15] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Large structurally diverse peptidomimetic chemical libraries have been very useful tools in chemical biology and drug discovery for the identification of therapeutically important compounds with higher affinity and improved pharmacological properties against different protein targets.Here we describe a simple and general method for the submonomer solid phase synthesis of large one bead-one compound (OBOC) peptidomimetic libraries of structurally diverse compounds that can be encoded by mass or genetic methods.
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3
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Yu B, Li R, Segalman RA. Tuning the Double Gyroid Phase Window in Block Copolymers via Polymer Chain Conformation Near the Interface. Macromolecules 2021. [DOI: 10.1021/acs.macromol.1c00048] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Beihang Yu
- Department of Chemical Engineering, University of California, Santa Barbara, Santa Barbara, California 93106, United States
| | - Ruipeng Li
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, New York 11973, United States
| | - Rachel A. Segalman
- Department of Chemical Engineering, University of California, Santa Barbara, Santa Barbara, California 93106, United States
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4
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Connolly MD, Xuan S, Molchanova N, Zuckermann RN. Submonomer synthesis of sequence defined peptoids with diverse side-chains. Methods Enzymol 2021; 656:241-270. [PMID: 34325788 DOI: 10.1016/bs.mie.2021.04.022] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Peptoids are a diverse family of sequence-defined oligomers of N-substituted glycine monomers, that can be readily accessed by the solid-phase submonomer synthesis method. Due to the versatility and efficiency of this chemistry, and the easy access to hundreds of potential monomers, there is an enormous potential sequence space that can be explored. This has enabled researchers from many different fields to custom-design peptoid sequences tailored to a wide variety of problems in biomedicine, nanoscience and polymer science. Here we provide detailed protocols for the synthesis of peptoids, using optimized protocols that can be performed by non-chemists. The submonomer method is fully compatible with Fmoc-peptide synthesis conditions, so the method is readily automated on existing automated peptide synthesizers using protocols provided here. Although the submonomer synthesis for peptoids is well established, there are special considerations required in order to access many of the most useful and desirable sidechains. Here we provide methods to include most of the amino-acid-like side chains, some of the most important non-natural monomer classes, as well as the creation of peptoid conjugates and peptide-peptoid hybrids.
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Affiliation(s)
- Michael D Connolly
- Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Sunting Xuan
- Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Natalia Molchanova
- Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Ronald N Zuckermann
- Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, United States.
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5
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Davern CM, Lowe BD, Rosfi A, Ison EA, Proulx C. Submonomer synthesis of peptoids containing trans-inducing N-imino- and N-alkylamino-glycines. Chem Sci 2021; 12:8401-8410. [PMID: 34221321 PMCID: PMC8221195 DOI: 10.1039/d1sc00717c] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 05/09/2021] [Indexed: 11/21/2022] Open
Abstract
The use of hydrazones as a new type of submonomer in peptoid synthesis is described, giving access to peptoid monomers that are structure-inducing. A wide range of hydrazones were found to readily react with α-bromoamides in routine solid phase peptoid submonomer synthesis. Conditions to promote a one-pot cleavage of the peptoid from the resin and reduction to the corresponding N-alkylamino side chains were also identified, and both the N-imino- and N-alkylamino glycine residues were found to favor the trans-amide bond geometry by NMR, X-ray crystallography, and computational analyses.
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Affiliation(s)
- Carolynn M Davern
- Department of Chemistry, North Carolina State University Raleigh NC 27695-8204 USA
| | - Brandon D Lowe
- Department of Chemistry, North Carolina State University Raleigh NC 27695-8204 USA
| | - Adam Rosfi
- Department of Chemistry, North Carolina State University Raleigh NC 27695-8204 USA
| | - Elon A Ison
- Department of Chemistry, North Carolina State University Raleigh NC 27695-8204 USA
| | - Caroline Proulx
- Department of Chemistry, North Carolina State University Raleigh NC 27695-8204 USA
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6
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Maresh ME, Zerfas BL, Wuthrich BS, Trader DJ. Identification of a covalent binder to the oncoprotein gankyrin using a NIR-Based OBOC screening method. RSC Adv 2021; 11:12794-12801. [PMID: 35423814 PMCID: PMC8697547 DOI: 10.1039/d0ra10976b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Accepted: 03/23/2021] [Indexed: 11/29/2022] Open
Abstract
Despite huge advancements in the process of synthesizing small molecules as part of one-bead-one-compound (OBOC) libraries, progress lags in the ability to screen these libraries against proteins of interest. Recently, we developed a method to screen OBOC libraries in which a target protein is labeled with a near-infrared (NIR) range fluorophore. The labeled protein incubates with beads of a library in a 96-well plate, then the plate is imaged for fluorescence. Fluorescence intensities produced by the labeled protein binding the bead can be quantitated and provide a basis to rank hits. Here, we present an application of this technique by screening the oncoprotein gankyrin against a 343-member peptoid library. The library was composed of four positions occupied by one of seven amines. In the third position, an amine that facilitates covalent binding via a sulfonyl fluoride moiety was incorporated. After screening for gankyrin binders twice, ten structures showed overlap in the types of amines present at each position. These initial hits were validated with an in-gel fluorescence assay in which the labeled ligands covalently interacted with purified gankyrin. Excitingly, one peptoid was validated from this analysis. This hit was also shown to bind gankyrin in the presence of HEK 293T lysate. Results from this study demonstrate successful use of our screening method to quickly identify quality binders to a target protein of interest.
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Affiliation(s)
- Marianne E Maresh
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University West Lafayette Indiana 47907 USA
| | - Breanna L Zerfas
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University West Lafayette Indiana 47907 USA
| | - Brice S Wuthrich
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University West Lafayette Indiana 47907 USA
| | - Darci J Trader
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University West Lafayette Indiana 47907 USA
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7
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Liu D, Sun J. Thermoresponsive Polypeptoids. Polymers (Basel) 2020; 12:E2973. [PMID: 33322804 PMCID: PMC7763442 DOI: 10.3390/polym12122973] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 12/10/2020] [Accepted: 12/11/2020] [Indexed: 01/02/2023] Open
Abstract
Stimuli-responsive polymers have been widely studied in many applications such as biomedicine, nanotechnology, and catalysis. Temperature is one of the most commonly used external triggers, which can be highly controlled with excellent reversibility. Thermoresponsive polymers exhibiting a reversible phase transition in a controlled manner to temperature are a promising class of smart polymers that have been widely studied. The phase transition behavior can be tuned by polymer architectures, chain-end, and various functional groups. Particularly, thermoresponsive polypeptoid is a type of promising material that has drawn growing interest because of its excellent biocompatibility, biodegradability, and bioactivity. This paper summarizes the recent advances of thermoresponsive polypeptoids, including the synthetic methods and functional groups as well as their applications.
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Affiliation(s)
| | - Jing Sun
- Key Laboratory of Biobased Polymer Materials, Shandong Provincial Education Department, School of Polymer Science and Engineering, Qingdao University of Science and Technology, Qingdao 266042, China;
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8
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Lone A, Arnous A, Hansen PR, Mojsoska B, Jenssen H. Synthesis of Peptoids Containing Multiple Nhtrp and Ntrp Residues: A Comparative Study of Resin, Cleavage Conditions and Submonomer Protection. Front Chem 2020; 8:370. [PMID: 32411678 PMCID: PMC7201050 DOI: 10.3389/fchem.2020.00370] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 04/08/2020] [Indexed: 12/03/2022] Open
Abstract
Peptoids hold status as peptide-mimetics with versatile biological applications due to their proteolytic stability and structural diversity. Among those that have been studied in different biological systems, are peptoids with dominant balanced hydrophobic and charge distribution along the backbone. Tryptophan is an important amino acid found in many biologically active peptides. Tryptophan-like side chains in peptoids allow H-bonding, which is absent from the parent backbone, due to the unique indole ring. Furthermore, the rigid hydrophobic core and flat aromatic system influence the positioning in the hydrocarbon core and allows accommodating tryptophan-like side chains into the interfacial regions of bacterial membranes and causing bacterial membrane damage. Incorporating multiple tryptophan-like side chains in peptoids can be tricky and there is a lack of suitable, synthetic routes established. In this paper, we investigate the synthesis of peptoids rich in Nhtrp and Ntrp residues using different resins, cleavage conditions, and unprotected as well as tert-butyloxycarbonyl-protected amines suitable for automated solid-phase submonomer peptoid synthesis protocols.
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Affiliation(s)
- Abdullah Lone
- Department of Science and Environment, Roskilde University, Roskilde, Denmark.,Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Anis Arnous
- Department of Science and Environment, Roskilde University, Roskilde, Denmark
| | - Paul Robert Hansen
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Biljana Mojsoska
- Department of Science and Environment, Roskilde University, Roskilde, Denmark
| | - Håvard Jenssen
- Department of Science and Environment, Roskilde University, Roskilde, Denmark
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9
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DNA origami protection and molecular interfacing through engineered sequence-defined peptoids. Proc Natl Acad Sci U S A 2020; 117:6339-6348. [PMID: 32165539 PMCID: PMC7104344 DOI: 10.1073/pnas.1919749117] [Citation(s) in RCA: 75] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
DNA nanotechnology provides a structural toolkit for the fabrication of programmable DNA nano-constructs; however, their use in biomedical applications is challenging due the limited structural integrity in complex biological fluids. Here, we report a class of tailorable molecular coatings, peptoids, which can efficiently stabilize three-dimensional wireframed DNA constructs under a variety of biomedically relevant conditions, including magnesium-ion depletion and presence of degrading nuclease. Furthermore, we show that peptoid-coated DNA constructs offer a controllable anticancer drug release and an ability to display functional biomolecules on the DNA surfaces. Our study demonstrates an approach for building multifunctional and environmentally robust DNA-based molecular structures for nanomedicine and biosensing. DNA nanotechnology has established approaches for designing programmable and precisely controlled nanoscale architectures through specific Watson−Crick base-pairing, molecular plasticity, and intermolecular connectivity. In particular, superior control over DNA origami structures could be beneficial for biomedical applications, including biosensing, in vivo imaging, and drug and gene delivery. However, protecting DNA origami structures in complex biological fluids while preserving their structural characteristics remains a major challenge for enabling these applications. Here, we developed a class of structurally well-defined peptoids to protect DNA origamis in ionic and bioactive conditions and systematically explored the effects of peptoid architecture and sequence dependency on DNA origami stability. The applicability of this approach for drug delivery, bioimaging, and cell targeting was also demonstrated. A series of peptoids (PE1–9) with two types of architectures, termed as “brush” and “block,” were built from positively charged monomers and neutral oligo-ethyleneoxy monomers, where certain designs were found to greatly enhance the stability of DNA origami. Through experimental and molecular dynamics studies, we demonstrated the role of sequence-dependent electrostatic interactions of peptoids with the DNA backbone. We showed that octahedral DNA origamis coated with peptoid (PE2) can be used as carriers for anticancer drug and protein, where the peptoid modulated the rate of drug release and prolonged protein stability against proteolytic hydrolysis. Finally, we synthesized two alkyne-modified peptoids (PE8 and PE9), conjugated with fluorophore and antibody, to make stable DNA origamis with imaging and cell-targeting capabilities. Our results demonstrate an approach toward functional and physiologically stable DNA origami for biomedical applications.
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10
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Bordelon T, Bobay B, Murphy A, Reese H, Shanahan C, Odeh F, Broussard A, Kormos C, Menegatti S. Translating antibody-binding peptides into peptoid ligands with improved affinity and stability. J Chromatogr A 2019; 1602:284-299. [DOI: 10.1016/j.chroma.2019.05.047] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 05/03/2019] [Accepted: 05/24/2019] [Indexed: 12/18/2022]
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11
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Ricano A, Captain I, Carter KP, Nell BP, Deblonde GJP, Abergel RJ. Combinatorial design of multimeric chelating peptoids for selective metal coordination. Chem Sci 2019; 10:6834-6843. [PMID: 31391906 PMCID: PMC6657411 DOI: 10.1039/c9sc01068h] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Accepted: 06/05/2019] [Indexed: 12/15/2022] Open
Abstract
The combinatorial synthesis of a new library of tetrameric peptoid ligands is introduced, enabling coordination and characterization of f-block metals.
Current methods for metal chelation are generally based on multidentate organic ligands, which are generated through cumbersome multistep synthetic processes that lack flexibility for systematically varying metal-binding motifs. Octadentate ligands incorporating hydroxypyridinone or catecholamide binding moieties onto a spermine scaffold are known to display some of the highest affinities towards f-elements. Enhancing binding affinity for specific lanthanide or actinide ions however, necessitates ligand architectures that allow for modular and high throughput synthesis. Here we introduce a high-throughput combinatorial library of 16 tetrameric N-substituted glycine oligomers (peptoids) containing hydroxypyridinone or catecholamide chelating units linked via an ethylenediamine bridge and, for comparison, we also synthesized the corresponding mixed ligands derived from the spermine scaffold: 3,4,3-LI(1,2-HOPO)2(CAM)2 and 3,4,3-LI(CAM)2(1,2-HOPO)2. Coordination-based luminescence studies were carried out with Eu3+ and Tb3+ to begin probing the properties of the new ligand architecture and revealed higher sensitization efficiency with the spermine scaffold as well as different spectroscopic features among the structural peptoid isomers. Solution thermodynamic properties of selected ligands revealed different coordination properties between the spermine and peptoid analogues with Eu3+ stability constants log β110 ranging from 28.88 ± 3.45 to 43.97 ± 0.49. The general synthetic strategy presented here paves the way for precision design of new specific and versatile ligands, with a variety of applications tailored towards the use of f-elements, including separations, optical device optimization, and pharmaceutical development.
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Affiliation(s)
- Abel Ricano
- Chemical Sciences Division , Lawrence Berkeley National Laboratory , Berkeley , CA 94720 , USA .
| | - Ilya Captain
- Chemical Sciences Division , Lawrence Berkeley National Laboratory , Berkeley , CA 94720 , USA .
| | - Korey P Carter
- Chemical Sciences Division , Lawrence Berkeley National Laboratory , Berkeley , CA 94720 , USA .
| | - Bryan P Nell
- Chemical Sciences Division , Lawrence Berkeley National Laboratory , Berkeley , CA 94720 , USA .
| | - Gauthier J-P Deblonde
- Chemical Sciences Division , Lawrence Berkeley National Laboratory , Berkeley , CA 94720 , USA .
| | - Rebecca J Abergel
- Chemical Sciences Division , Lawrence Berkeley National Laboratory , Berkeley , CA 94720 , USA . .,Department of Nuclear Engineering , University of California , Berkeley , CA 94720 , USA
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12
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Dickson P, Kodadek T. Chemical composition of DNA-encoded libraries, past present and future. Org Biomol Chem 2019; 17:4676-4688. [PMID: 31017595 PMCID: PMC6520149 DOI: 10.1039/c9ob00581a] [Citation(s) in RCA: 76] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
DNA-encoded libraries represent an exciting and powerful modality for high-throughput screening. In this article, we highlight recent important advances in this field and also suggest some important directions that would make the technology even more powerful.
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Affiliation(s)
- Paige Dickson
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, USA.
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13
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Yu B, Danielsen SPO, Patterson AL, Davidson EC, Segalman RA. Effects of Helical Chain Shape on Lamellae-Forming Block Copolymer Self-Assembly. Macromolecules 2019. [DOI: 10.1021/acs.macromol.9b00211] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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14
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Shu K, Kodadek T. Solid-Phase Synthesis of β-Hydroxy Ketones Via DNA-Compatible Organocatalytic Aldol Reactions. ACS COMBINATORIAL SCIENCE 2018; 20:277-281. [PMID: 29578681 DOI: 10.1021/acscombsci.8b00001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
One-bead one-compound (OBOC) libraries constructed by solid-phase split-and-pool synthesis are a valuable source of protein ligands. Most OBOC libraries are composed of oligoamides, particularly peptides, peptoids, and peptoid-inspired molecules. Further diversification of the chemical space covered by OBOC libraries is desirable. Toward this end, we report here that the proline-catalyzed asymmetric aldol reaction, developed by List and Barbas for solution-phase synthesis, also works well for coupling immobilized aldehydes and soluble ketones. These reaction conditions do not compromise the amplification of DNA by the polymerase chain reaction. Thus, this chemistry should be useful for the construction of novel DNA-encoded OBOC libraries by solid-phase synthesis.
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Affiliation(s)
- Keitou Shu
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, Florida 33458, United States
- Graduate School of Advanced Integrated Studies in Human Survivability, Kyoto University, Sakyo-ku, Kyoto 606-8306, Japan
| | - Thomas Kodadek
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, Florida 33458, United States
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15
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Solid-Phase Synthesis of Azole-Comprising Peptidomimetics and Coordination of a Designed Analog to Zn 2. Molecules 2018; 23:molecules23051035. [PMID: 29710766 PMCID: PMC6102547 DOI: 10.3390/molecules23051035] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Revised: 04/23/2018] [Accepted: 04/26/2018] [Indexed: 12/14/2022] Open
Abstract
Peptidomimetics that can coordinate transition metals have a variety of potential applications as catalysts, sensors, or materials. A new modular peptidomimetic scaffold, the “azole peptoid”, is introduced here. We report methods for the solid-phase synthesis of eleven examples of trimeric N-substituted oligoamides that include oxazole- or thiazole-functionalized backbones. The products prepared comprise a diversity of functionality, including a metal-coordinating terpyridine group. The modular synthetic approach enables ready preparation of analogs for specific applications. To highlight a potential use of this new synthetic scaffold, a trimeric azole peptoid functionalized with a terpyridine residue was prepared and studied. The characteristic 2:1 ligand:metal binding of this terpyridine-functionalized azole peptoid to Zn2+ in aqueous solution was observed. These studies introduce azole peptoids as a useful class of biomimetic molecules for further study and application.
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16
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Shin MK, Hyun YJ, Lee JH, Lim HS. Comparison of Cell Permeability of Cyclic Peptoids and Linear Peptoids. ACS COMBINATORIAL SCIENCE 2018; 20:237-242. [PMID: 29481042 DOI: 10.1021/acscombsci.7b00194] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Cyclic peptoids are emerging as an attractive class of peptidomimetics. Compared to their linear counterparts, cyclic peptoids should have increased conformational rigidity and preorganized structures, enabling them to bind more tightly to target proteins without major entropy penalty. Because cyclic peptoids lack the amide protons in their backbones like linear peptoids, it is perceived that cyclic peptoids are seemingly cell permeable as much as linear peptoids. However, no systematic investigation for cell permeability of cyclic peptoids has been reported yet. Here, we, for the first time, demonstrate that cyclic peptoids are far more cell permeable than linear counterparts irrespective of their size and side chains. This study highlights that cyclic peptoids, along with combinatorial library and high-throughput screening technologies, will serve as a rich source of protein binding molecules, particularly targeting intracellular proteins, given their excellent cell permeability in addition to their conformational rigidity and proteolytic stability.
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Affiliation(s)
- Min-Kyung Shin
- Department of Chemistry and Division of Advanced Material Science, Pohang University of Science and Technology (POSTECH), Pohang 37673, South Korea
| | - Yu-Jung Hyun
- Department of Chemistry and Division of Advanced Material Science, Pohang University of Science and Technology (POSTECH), Pohang 37673, South Korea
| | - Ji Hoon Lee
- New Drug Development Center, Daegu Gyeongbuk Medical Innovation Foundation, Daegu 41061, South Korea
| | - Hyun-Suk Lim
- Department of Chemistry and Division of Advanced Material Science, Pohang University of Science and Technology (POSTECH), Pohang 37673, South Korea
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17
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Sternhagen GL, Gupta S, Zhang Y, John V, Schneider GJ, Zhang D. Solution Self-Assemblies of Sequence-Defined Ionic Peptoid Block Copolymers. J Am Chem Soc 2018; 140:4100-4109. [PMID: 29506382 DOI: 10.1021/jacs.8b00461] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
A series of amphiphilic ionic peptoid block copolymers where the total number (1 or 3) and position of ionic monomers along the polymer chain are precisely controlled have been synthesized by the submonomer method. Upon dissolution in water at pH = 9, the amphiphilic peptoids self-assemble into small spherical micelles having hydrodynamic radius in ∼5-10 nm range and critical micellar concentration (CMC) in the 0.034-0.094 mg/mL range. Small-angle neutron scattering (SANS) analysis of the micellar solutions revealed unprecedented dependence of the micellar structure on the number and position of ionic monomers along the chain. It was found that the micellar aggregation number ( Nagg) and the micellar radius ( Rm) both increase as the ionic monomer is positioned progressively away from the junction of the hydrophilic and hydrophobic segments along the polymer chain. By defining an ionic monomer position number ( n) as the number of monomers between the junction and the ionic monomer, Nagg exhibited a power law dependence on n with an exponent of ∼1/3 and ∼3/10 for the respective singly and triply charged series. By contrast, Rm exhibited a weaker dependence on the ionic monomer position by a power law relationship with an exponent of ∼1/10 and ∼1/20 for the respective singly and triply charged series. Furthermore, Rm was found to scale with Nagg in a power-law relationship with an exponent of 0.32 for the singly charged series, consistent with a weakly charged ionic star-like polymer model in the unscreened regime. This study demonstrated a unique method to precisely tailor the structure of small spherical micelles based on ionic block copolymers by controlling the sequence and position of the ionic monomer.
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Affiliation(s)
- Garrett L Sternhagen
- Department of Chemistry and Macromolecular Studies Group , Louisiana State University , Baton Rouge , Louisiana 70803 , United States
| | - Sudipta Gupta
- Department of Chemistry and Macromolecular Studies Group , Louisiana State University , Baton Rouge , Louisiana 70803 , United States
| | - Yueheng Zhang
- Department of Chemical and Biomolecular Engineering , Tulane University , New Orleans , Louisiana 70118 , United States
| | - Vijay John
- Department of Chemical and Biomolecular Engineering , Tulane University , New Orleans , Louisiana 70118 , United States
| | - Gerald J Schneider
- Department of Chemistry and Macromolecular Studies Group , Louisiana State University , Baton Rouge , Louisiana 70803 , United States.,Department of Physics , Louisiana State University , Baton Rouge , Louisiana 70803 , United States
| | - Donghui Zhang
- Department of Chemistry and Macromolecular Studies Group , Louisiana State University , Baton Rouge , Louisiana 70803 , United States
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18
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Davidson EC, Rosales AM, Patterson AL, Russ B, Yu B, Zuckermann RN, Segalman RA. Impact of Helical Chain Shape in Sequence-Defined Polymers on Polypeptoid Block Copolymer Self-Assembly. Macromolecules 2018. [DOI: 10.1021/acs.macromol.8b00055] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
| | - Adrianne M. Rosales
- Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | | | - Boris Russ
- Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | | | - Ronald N. Zuckermann
- Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
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19
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Ren J, Mann YS, Zhang Y, Browne MD. Synthesis and Mass Spectrometry Analysis of Oligo-peptoids. J Vis Exp 2018. [PMID: 29553518 DOI: 10.3791/56652] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Peptoids are sequence-controlled peptide-mimicking oligomers consisting of N-alkylated glycine units. Among many potential applications, peptoids have been thought of as a type of molecular information storage. Mass spectrometry analysis has been considered the method of choice for sequencing peptoids. Peptoids can be synthesized via solid phase chemistry using a repeating two-step reaction cycle. Here we present a method to manually synthesize oligo-peptoids and to analyze the sequence of the peptoids using tandem mass spectrometry (MS/MS) techniques. The sample peptoid is a nonamer consisting of alternating N-(2-methyloxyethyl)glycine (Nme) and N-(2-phenylethyl)glycine (Npe), as well as an N-(2-aminoethyl)glycine (Nae) at the N-terminus. The sequence formula of the peptoid is Ac-Nae-(Npe-Nme)4-NH2, where Ac is the acetyl group. The synthesis takes place in a commercially available solid-phase reaction vessel. The rink amide resin is used as the solid support to yield the peptoid with an amide group at the C-terminus. The resulting peptoid product is subjected to sequence analysis using a triple-quadrupole mass spectrometer coupled to an electrospray ionization source. The MS/MS measurement produces a spectrum of fragment ions resulting from the dissociation of charged peptoid. The fragment ions are sorted out based on the values of their mass-to-charge ratio (m/z). The m/z values of the fragment ions are compared against the nominal masses of theoretically predicted fragment ions, according to the scheme of peptoid fragmentation. The analysis generates a fragmentation pattern of the charged peptoid. The fragmentation pattern is correlated to the monomer sequence of the neutral peptoid. In this regard, MS analysis reads out the sequence information of the peptoids.
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Affiliation(s)
- Jianhua Ren
- Department of Chemistry, University of the Pacific;
| | | | - Yuntao Zhang
- Department of Chemistry, University of the Pacific
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20
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Tran-Hoang N, Kodadek T. Solid-Phase Synthesis of β-Amino Ketones Via DNA-Compatible Organocatalytic Mannich Reactions. ACS COMBINATORIAL SCIENCE 2018; 20:55-60. [PMID: 29316387 PMCID: PMC7074847 DOI: 10.1021/acscombsci.7b00151] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
One-bead-one-compound (OBOC) libraries constructed by solid-phase split-and-pool synthesis are a valuable source of protein ligands. Most OBOC libraries are comprised of oligoamides, particularly peptides, peptoids, and peptoid-inspired molecules. Further diversification of the chemical space covered by OBOC libraries is desirable. Toward this end, we report here the efficient proline-catalyzed asymmetric Mannich reaction between immobilized aldehydes and soluble ketones and anilines. The reaction conditions do not compromise the amplification of DNA by the PCR. Thus, this chemistry will likely be useful for the construction of novel DNA-encoded libraries by solid-phase synthesis.
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Affiliation(s)
- Nam Tran-Hoang
- Department of Chemistry The Scripps Research Institute 130 Scripps Way, Jupiter, Florida 33458, United States
| | - Thomas Kodadek
- Department of Chemistry The Scripps Research Institute 130 Scripps Way, Jupiter, Florida 33458, United States
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21
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Desai TJ, Toombs JE, Minna JD, Brekken RA, Udugamasooriya DG. Identification of lipid-phosphatidylserine (PS) as the target of unbiasedly selected cancer specific peptide-peptoid hybrid PPS1. Oncotarget 2017; 7:30678-90. [PMID: 27120792 PMCID: PMC5058709 DOI: 10.18632/oncotarget.8929] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Accepted: 03/31/2016] [Indexed: 12/20/2022] Open
Abstract
Phosphatidylserine (PS) is an anionic phospholipid maintained on the inner-leaflet of the cell membrane and is externalized in malignant cells. We previously launched a careful unbiased selection targeting biomolecules (e.g. protein, lipid or carbohydrate) distinct to cancer cells by exploiting HCC4017 lung cancer and HBEC30KT normal epithelial cells derived from the same patient, identifying HCC4017 specific peptide-peptoid hybrid PPS1. In this current study, we identified PS as the target of PPS1. We validated direct PPS1 binding to PS using ELISA-like assays, lipid dot blot and liposome based binding assays. In addition, PPS1 recognized other negatively charged and cancer specific lipids such as phosphatidic acid, phosphatidylinositol and phosphatidylglycerol. PPS1 did not bind to neutral lipids such as phosphatidylethanolamine found in cancer and phosphatidylcholine and sphingomyelin found in normal cells. Further we found that the dimeric version of PPS1 (PPS1D1) displayed strong cytotoxicity towards lung cancer cell lines that externalize PS, but not normal cells. PPS1D1 showed potent single agent anti-tumor activity and enhanced the efficacy of docetaxel in mice bearing H460 lung cancer xenografts. Since PS and anionic phospholipid externalization is common across many cancer types, PPS1 may be an alternative to overcome limitations of protein targeted agents.
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Affiliation(s)
- Tanvi J Desai
- Department of Pharmacological and Pharmaceutical Sciences, University of Houston, Houston, TX 77204, USA
| | - Jason E Toombs
- Hamon Center for Therapeutic Oncology Research, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - John D Minna
- Hamon Center for Therapeutic Oncology Research, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.,Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.,Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.,Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Rolf A Brekken
- Hamon Center for Therapeutic Oncology Research, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.,Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.,Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.,Department of Surgery, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Damith Gomika Udugamasooriya
- Department of Pharmacological and Pharmaceutical Sciences, University of Houston, Houston, TX 77204, USA.,Department of Cancer Systems Imaging, MD Anderson Cancer Center, Houston, TX 77030, USA
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22
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Molchanova N, Hansen PR, Franzyk H. Advances in Development of Antimicrobial Peptidomimetics as Potential Drugs. Molecules 2017; 22:E1430. [PMID: 28850098 PMCID: PMC6151827 DOI: 10.3390/molecules22091430] [Citation(s) in RCA: 181] [Impact Index Per Article: 25.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Revised: 08/18/2017] [Accepted: 08/22/2017] [Indexed: 01/19/2023] Open
Abstract
The rapid emergence of multidrug-resistant pathogens has evolved into a global health problem as current treatment options are failing for infections caused by pan-resistant bacteria. Hence, novel antibiotics are in high demand, and for this reason antimicrobial peptides (AMPs) have attracted considerable interest, since they often show broad-spectrum activity, fast killing and high cell selectivity. However, the therapeutic potential of natural AMPs is limited by their short plasma half-life. Antimicrobial peptidomimetics mimic the structure and biological activity of AMPs, but display extended stability in the presence of biological matrices. In the present review, focus is on the developments reported in the last decade with respect to their design, synthesis, antimicrobial activity, cytotoxic side effects as well as their potential applications as anti-infective agents. Specifically, only peptidomimetics with a modular structure of residues connected via amide linkages will be discussed. These comprise the classes of α-peptoids (N-alkylated glycine oligomers), β-peptoids (N-alkylated β-alanine oligomers), β³-peptides, α/β³-peptides, α-peptide/β-peptoid hybrids, α/γ N-acylated N-aminoethylpeptides (AApeptides), and oligoacyllysines (OAKs). Such peptidomimetics are of particular interest due to their potent antimicrobial activity, versatile design, and convenient optimization via assembly by standard solid-phase procedures.
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Affiliation(s)
- Natalia Molchanova
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Jagtvej 162, DK-2100 Copenhagen, Denmark.
| | - Paul R Hansen
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Jagtvej 162, DK-2100 Copenhagen, Denmark.
| | - Henrik Franzyk
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Jagtvej 162, DK-2100 Copenhagen, Denmark.
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23
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Wu H, An H, Mo SC, Kodadek T. Asymmetric synthesis of vinylogous β-amino acids and their incorporation into mixed backbone oligomers. Org Biomol Chem 2017; 15:3255-3264. [PMID: 28346549 PMCID: PMC7243482 DOI: 10.1039/c7ob00333a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Chiral vinylogous β-amino acids (VBAA) were synthesized using enantioselective Mannich reactions of aldehydes with in situ generated N-carbamoyl imines followed by a Horner-Wadsworth-Emmons reaction. The efficiency with which these units could be incorporated into oligomers with different moieties on the C- and N-terminal sides was established, as was the feasibility of sequencing oligomers containing VBAAs by tandem mass spectrometry. The data show that VBAAs will be useful building blocks for the construction of combinatorial libraries of peptidomimetic compounds.
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Affiliation(s)
- Hao Wu
- Department of Chemistry, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, USA.
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24
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Corson AE, Armstrong SA, Wright ME, McClelland EE, Bicker KL. Discovery and Characterization of a Peptoid with Antifungal Activity against Cryptococcus neoformans. ACS Med Chem Lett 2016; 7:1139-1144. [PMID: 27994753 DOI: 10.1021/acsmedchemlett.6b00338] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Accepted: 10/03/2016] [Indexed: 12/31/2022] Open
Abstract
Studies show there is an increasing rate of fungal infections, especially in immunocompromised patients and treatments for fungal genera, such as Aspergillus, Candida, and Cryptococcus, carry significant cytotoxicity with an increasing prevalence of antifungal resistance. We have previously reported a high-throughput assay for identifying peptoids with antimicrobial properties from combinatorial libraries. Here we report the application of this assay in identifying a peptoid with antifungal properties against Cryptococcus neoformans. Termed AEC5, this peptoid has comparable potency to existing clinical antifungal agents, excellent stability, and minimal cytotoxicity in mammalian cells.
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Affiliation(s)
- Ashley E. Corson
- Department of Chemistry and ‡Department of Biology, Middle Tennessee State University, 1301 East Main Street, Murfreesboro, Tennessee 37132, United States
| | - Scott A. Armstrong
- Department of Chemistry and ‡Department of Biology, Middle Tennessee State University, 1301 East Main Street, Murfreesboro, Tennessee 37132, United States
| | - Matthew E. Wright
- Department of Chemistry and ‡Department of Biology, Middle Tennessee State University, 1301 East Main Street, Murfreesboro, Tennessee 37132, United States
| | | | - Kevin L. Bicker
- Department of Chemistry and ‡Department of Biology, Middle Tennessee State University, 1301 East Main Street, Murfreesboro, Tennessee 37132, United States
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25
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Fu J, Xia A, Qi X. Identification of novel peptoid agonists of fibroblast growth factor receptor using microarray-based screening. MEDCHEMCOMM 2016; 7:1183-1189. [PMID: 27721968 DOI: 10.1039/c6md00121a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Drug development targeting fibroblast growth factor receptors (FGFRs) represents an emerging theme in the field of medicinal chemistry. Considering the fact that most of the currently identified FGFR agonists are long chain peptides with limited stability, the discovery of novel non-peptide FGFR ligands is still highly demanded. A linear one-bead-one-compound peptoid (oligomers of N-substituted glycine units) library with a theoretical diversity of 106 was designed and synthesized. Microarray-based screening led to the identification of four hit sequences 1-4 as FGFR1α ligands, which were further confirmed using both solution-phase and solid-phase binding assays. Western blot results indicated that peptoids 2-4 activated FGFR signaling pathways, resulting in increased levels of p-Akt and p-ERK in different cell lines. Our work discovered novel peptoid ligands as FGFR agonists, shedding new light on FGFR-based drug discovery.
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Affiliation(s)
- Junjie Fu
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, Gainesville, FL, 32610
| | - Amy Xia
- Columbia University, New York, NY 10027
| | - Xin Qi
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, Gainesville, FL, 32610
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26
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Singh J, Lopes D, Gomika Udugamasooriya D. Development of a large peptoid-DOTA combinatorial library. Biopolymers 2016; 106:673-84. [PMID: 27257968 PMCID: PMC5035194 DOI: 10.1002/bip.22883] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Revised: 04/15/2016] [Accepted: 05/31/2016] [Indexed: 01/03/2023]
Abstract
Conventional one-bead one-compound (OBOC) library synthesis is typically used to identify molecules with therapeutic value. The design and synthesis of OBOC libraries that contain molecules with imaging or even potentially therapeutic and diagnostic capacities (e.g. theranostic agents) has been overlooked. The development of a therapeutically active molecule with a built-in imaging component for a certain target is a daunting task, and structure-based rational design might not be the best approach. We hypothesize to develop a combinatorial library with potentially therapeutic and imaging components fused together in each molecule. Such molecules in the library can be used to screen, identify, and validate as direct theranostic candidates against targets of interest. As the first step in achieving that aim, we developed an on-bead library of 153,600 Peptoid-DOTA compounds in which the peptoids are the target-recognizing and potentially therapeutic components and the DOTA is the imaging component. We attached the DOTA scaffold to TentaGel beads using one of the four arms of DOTA, and we built a diversified 6-mer peptoid library on the remaining three arms. We evaluated both the synthesis and the mass spectrometric sequencing capacities of the test compounds and of the final library. The compounds displayed unique ionization patterns including direct breakages of the DOTA scaffold into two units, allowing clear decoding of the sequences. Our approach provides a facile synthesis method for the complete on-bead development of large peptidomimetic-DOTA libraries for screening against biological targets for the identification of potential theranostic agents in the future. © 2016 The Authors. Biopolymers Published by Wiley Periodicals, Inc. Biopolymers (Pept Sci) 106: 673-684, 2016.
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Affiliation(s)
- Jaspal Singh
- Department of Pharmacological and Pharmaceutical Sciences, University of Houston, Houston, TX, 77204
| | - Daniel Lopes
- Advanced Imaging Research Center, UT-Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX, 75390
| | - D Gomika Udugamasooriya
- Department of Pharmacological and Pharmaceutical Sciences, University of Houston, Houston, TX, 77204.
- Department of Cancer Systems Imaging, MD Anderson Cancer Center, 1881 East Road, Houston, TX, 77030-4009.
- Advanced Imaging Research Center, UT-Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX, 75390.
- Department of Biochemistry, UT-Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX, 75390.
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27
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Weller HN, Rubin AE, Moshiri B, Ruediger W, Li WJ, Allen J, Nolfo J, Bertok A, Rosso VW. Development and Commercialization of the MiniBlock Synthesizer Family: A Historical Case Study. ACTA ACUST UNITED AC 2016. [DOI: 10.1016/j.jala.2004.07.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
An internal development project at Bristol-Myers Squibb (BMS) led to invention of a family of organic chemistry synthesis blocks for both parallel synthesis in drug discovery and parallel reaction optimization in pharmaceutical development. The internal demand for these synthesis blocks became so great that the original development team was challenged by the burden of ongoing manufacture, support, and supply chain management. As a result, BMS entered into a unique industry partnership with Mettler-Toledo AutoChem (MT), Newark, DE, formerly Bohdan Automation, to commercialize the reactor blocks and extend the product family, now known as the MiniBlock line. This manuscript describes the initial development drivers, the overall technical design, and the ultimate successful commercialization of the MiniBlock synthesis family.
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Affiliation(s)
- Harold N. Weller
- Bristol-Myers Squibb Company, Princeton, NJ and Mettler-Toledo AutoChem, Inc, Newark, DE
| | - A. Erik Rubin
- Bristol-Myers Squibb Company, Princeton, NJ and Mettler-Toledo AutoChem, Inc, Newark, DE
| | - Ben Moshiri
- Bristol-Myers Squibb Company, Princeton, NJ and Mettler-Toledo AutoChem, Inc, Newark, DE
- EDAX/AMETEk, Mahwah, NJ
| | - Walter Ruediger
- Bristol-Myers Squibb Company, Princeton, NJ and Mettler-Toledo AutoChem, Inc, Newark, DE
| | - Wen-Jeng Li
- Bristol-Myers Squibb Company, Princeton, NJ and Mettler-Toledo AutoChem, Inc, Newark, DE
| | - John Allen
- Bristol-Myers Squibb Company, Princeton, NJ and Mettler-Toledo AutoChem, Inc, Newark, DE
| | - Joseph Nolfo
- Bristol-Myers Squibb Company, Princeton, NJ and Mettler-Toledo AutoChem, Inc, Newark, DE
| | - Alexander Bertok
- Bristol-Myers Squibb Company, Princeton, NJ and Mettler-Toledo AutoChem, Inc, Newark, DE
| | - Victor W. Rosso
- Bristol-Myers Squibb Company, Princeton, NJ and Mettler-Toledo AutoChem, Inc, Newark, DE
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28
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Lee KJ, Lee WS, Yun H, Hyun YJ, Seo CD, Lee CW, Lim HS. Oligomers of N-Substituted β(2)-Homoalanines: Peptoids with Backbone Chirality. Org Lett 2016; 18:3678-81. [PMID: 27404658 DOI: 10.1021/acs.orglett.6b01726] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
A new class of peptoid-based peptidomimetics composed of oligomers of N-substituted β(2)-homoalanines is reported. Design, solid-phase synthesis, and preliminary circular dichroism studies of oligomers of N-alkylated β(2)-homoalanines consisting of up to 8-mers are described.
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Affiliation(s)
- Kang Ju Lee
- Departments of Chemistry and Advanced Material Science, Pohang University of Science and Technology (POSTECH) , Pohang 37673, South Korea
| | - Woo Sirl Lee
- Departments of Chemistry and Advanced Material Science, Pohang University of Science and Technology (POSTECH) , Pohang 37673, South Korea
| | - Hyosuk Yun
- Department of Chemistry, Chonnam National University , Gwangju 61186, South Korea
| | - Yu-Jung Hyun
- Departments of Chemistry and Advanced Material Science, Pohang University of Science and Technology (POSTECH) , Pohang 37673, South Korea
| | - Chang Deok Seo
- Departments of Chemistry and Advanced Material Science, Pohang University of Science and Technology (POSTECH) , Pohang 37673, South Korea
| | - Chul Won Lee
- Department of Chemistry, Chonnam National University , Gwangju 61186, South Korea
| | - Hyun-Suk Lim
- Departments of Chemistry and Advanced Material Science, Pohang University of Science and Technology (POSTECH) , Pohang 37673, South Korea.,Department of Biochemistry and Molecular Biology, Indiana University School of Medicine , Indianapolis, Indiana 46202, United States
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29
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Case A, Desmond A, Lopes D, Dye K, Mapes K, Ruback S, Pop I, Kim JK, Chakravarty P, Smallshaw JE, Pop LM, Vitetta ES. The Immunogenicity of Peptoid-Protein Conjugates. ACTA ACUST UNITED AC 2016; 7. [PMID: 27595050 PMCID: PMC5004597 DOI: 10.4172/2157-7560.1000329] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
We demonstrate that a peptoid composed of five monomers and attached via a maleimide linker to a carrier protein elicits anti-peptoid, anti-linker and anti-carrier antibodies in rabbits. Specific anti-peptoid antibodies were affinity purified and used to reproducibly retrieve three specific peptoid-coupled beads from 20,000 irrelevant peptoid-beads using magnetic screening.
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Affiliation(s)
- Allison Case
- Cancer Immunobiology Center and Department of Immunology, University of Texas Southwestern Medical Center, Dallas, Texas, USA; Department of Bioengineering, The University of Texas at Dallas, Texas, USA
| | - Angela Desmond
- Cancer Immunobiology Center and Department of Immunology, University of Texas Southwestern Medical Center, Dallas, Texas, USA; Department of Pediatrics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, USA
| | - Daniel Lopes
- Cancer Immunobiology Center and Department of Immunology, University of Texas Southwestern Medical Center, Dallas, Texas, USA; Eli Lilly, Indianapolis, Indiana, USA
| | - Kelly Dye
- Cancer Immunobiology Center and Department of Immunology, University of Texas Southwestern Medical Center, Dallas, Texas, USA; School of Medicine, Texas Tech University Health Sciences Center, Lubbock, Texas, USA
| | - Kelly Mapes
- Cancer Immunobiology Center and Department of Immunology, University of Texas Southwestern Medical Center, Dallas, Texas, USA; Green Center for Systems Biology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Stephen Ruback
- Cancer Immunobiology Center and Department of Immunology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Iliodora Pop
- Cancer Immunobiology Center and Department of Immunology, University of Texas Southwestern Medical Center, Dallas, Texas, USA; Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Jiyeun Kate Kim
- Cancer Immunobiology Center and Department of Immunology, University of Texas Southwestern Medical Center, Dallas, Texas, USA; College of Pharmacy, Pusan National University, Busan, Republic of Korea
| | - Pavitra Chakravarty
- Cancer Immunobiology Center and Department of Immunology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Joan E Smallshaw
- Cancer Immunobiology Center and Department of Immunology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Laurentiu M Pop
- Cancer Immunobiology Center and Department of Immunology, University of Texas Southwestern Medical Center, Dallas, Texas, USA; Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Ellen S Vitetta
- Cancer Immunobiology Center and Department of Immunology, University of Texas Southwestern Medical Center, Dallas, Texas, USA; Department of Microbiology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
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30
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Abstract
Parkinson disease (PD) is the second most common neurodegenerative disease. Because dopaminergic neuronal loss begins years before motor symptoms appear, a biomarker for the early identification of the disease is critical for the study of putative neuroprotective therapies. Brain imaging of the nigrostriatal dopamine system has been used as a biomarker for early disease along with cerebrospinal fluid analysis of α-synuclein, but a less costly and relatively non-invasive biomarker would be optimal. We sought to identify an antibody biomarker in the blood of PD patients using a combinatorial peptoid library approach. We examined serum samples from 75 PD patients, 25 de novo PD patients, and 104 normal control subjects in the NINDS Parkinson’s Disease Biomarker Program. We identified a peptoid, PD2, which binds significantly higher levels of IgG3 antibody in PD versus control subjects (P<0.0001) and is 68% accurate in identifying PD. The PD2 peptoid is 84% accurate in identifying de novo PD. Also, IgG3 levels are significantly higher in PD versus control serum (P<0.001). Finally, PD2 levels are positively correlated with the United Parkinson’s Disease Rating Scale score (r=0.457, P<0001), a marker of disease severity. The PD2 peptoid may be useful for the early-stage identification of PD, and serve as an indicator of disease severity. Additional studies are needed to validate this PD biomarker.
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31
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Fisher KJ, Turkett JA, Corson AE, Bicker KL. Peptoid Library Agar Diffusion (PLAD) Assay for the High-Throughput Identification of Antimicrobial Peptoids. ACS COMBINATORIAL SCIENCE 2016; 18:287-91. [PMID: 27186808 DOI: 10.1021/acscombsci.6b00039] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Rapid emergence of antimicrobial resistant organisms necessitates equally rapid methods for the development of new antimicrobial compounds. Of recent interest have been mimics of antimicrobial peptides known as antimicrobial peptoids, which exhibit similar potency to the former but with improved proteolytic stability. Presented herein is a high-throughput method to screen libraries of antimicrobial peptoids immobilized on beads embedded into solid media. Termed the peptoid library agar diffusion (PLAD) assay, this assay allows for individual chemical manipulation of two identical peptoid strands. One strand can be released to diffuse out from a solid support bead and interact with the microorganism during screening. The other strand can be cleaved after screening from beads showing strong antimicrobial activity and analyzed by mass spectrometry to deconvolute the structure of the peptoid. This method was applied to a small library of peptoids to identify an antimicrobial peptoid with modest efficacy against the ESKAPE pathogens.
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Affiliation(s)
- Kevin J. Fisher
- Middle Tennessee State University, Department of
Chemistry, 1301 East Main
Street, Murfreesboro, Tennessee 37132, United States
| | - Jeremy A. Turkett
- Middle Tennessee State University, Department of
Chemistry, 1301 East Main
Street, Murfreesboro, Tennessee 37132, United States
| | - Ashley E. Corson
- Middle Tennessee State University, Department of
Chemistry, 1301 East Main
Street, Murfreesboro, Tennessee 37132, United States
| | - Kevin L. Bicker
- Middle Tennessee State University, Department of
Chemistry, 1301 East Main
Street, Murfreesboro, Tennessee 37132, United States
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32
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Nalband DM, Warner BP, Zahler NH, Kirshenbaum K. Rapid identification of metal-binding peptoid oligomers by on-resin X-ray fluorescence screening. Biopolymers 2016; 102:407-15. [PMID: 25059748 DOI: 10.1002/bip.22528] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Revised: 07/17/2014] [Accepted: 07/18/2014] [Indexed: 12/18/2022]
Abstract
N-Substituted glycine peptoid oligomers have recently attracted attention for their metal binding capabilities. Due to their efficient synthesis on solid phase, peptoids are well suited for generation of compound libraries, followed by screening for molecular recognition and other diverse functional attributes. Ideally, peptoids could be simultaneously screened for binding to a number of metal species. Here, we demonstrate the use of bench-top X-ray fluorescence (XRF) instrumentation to screen rapidly, on solid support, a library of peptoid oligomers incorporating metal-binding functionalities. A subset of the peptoid sequences exhibited significant metal binding capabilities, including a peptoid pentamer and a nonamer that were shown to selectively bind nickel. The binding capabilities were validated by colorimetric assay and by depletion of Ni(2+) ion concentration from solution, establishing bench-top XRF as a rapid, practicable high-throughput screening technique for peptoid oligomers. This protocol will facilitate discovery of metallopeptoids with unique material properties.
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Doran TM, Sarkar M, Kodadek T. Chemical Tools To Monitor and Manipulate Adaptive Immune Responses. J Am Chem Soc 2016; 138:6076-94. [PMID: 27115249 PMCID: PMC5332222 DOI: 10.1021/jacs.6b02954] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Methods to monitor and manipulate the immune system are of enormous clinical interest. For example, the development of vaccines represents one of the earliest and greatest accomplishments of the biomedical research enterprise. More recently, drugs capable of "reawakening" the immune system to cancer have generated enormous excitement. But, much remains to be done. All drugs available today that manipulate the immune system cannot distinguish between "good" and "bad" immune responses and thus drive general and systemic immune suppression or activation. Indeed, with the notable exception of vaccines, our ability to monitor and manipulate antigen-specific immune responses is in its infancy. Achieving this finer level of control would be highly desirable. For example, it might allow the pharmacological editing of pathogenic immune responses without restricting the ability of the immune system to defend against infection. On the diagnostic side, a method to comprehensively monitor the circulating, antigen-specific antibody population could provide a treasure trove of clinically useful biomarkers, since many diseases expose the immune system to characteristic molecules that are deemed foreign and elicit the production of antibodies against them. This Perspective will discuss the state-of-the-art of this area with a focus on what we consider seminal opportunities for the chemistry community to contribute to this important field.
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Affiliation(s)
- Todd M. Doran
- Departments of Chemistry & Cancer Biology, The Scripps Research
Institute, 130 Scripps Way, Jupiter, FL 33458
| | - Mohosin Sarkar
- Departments of Chemistry & Cancer Biology, The Scripps Research
Institute, 130 Scripps Way, Jupiter, FL 33458
| | - Thomas Kodadek
- Departments of Chemistry & Cancer Biology, The Scripps Research
Institute, 130 Scripps Way, Jupiter, FL 33458
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Clark LF, Kodadek T. The Immune System and Neuroinflammation as Potential Sources of Blood-Based Biomarkers for Alzheimer's Disease, Parkinson's Disease, and Huntington's Disease. ACS Chem Neurosci 2016; 7:520-7. [PMID: 27046268 DOI: 10.1021/acschemneuro.6b00042] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Neurodegenerative diseases are characterized by a loss of neurons that leads to cognitive and behavioral dysfunction. Alzheimer's disease (AD) is the most common neurodegenerative disorder affecting millions of people in the United States and worldwide, followed by Parkinson's disease (PD). While some early onset forms of AD and PD are hereditary, the sporadic or late-onset cases are believed to result from lifestyle and environmental factors. On the contrary, Huntington's disease (HD) is a neurodegenerative disease solely caused by mutations in the gene for huntingtin protein. The disease mechanisms at play for all three disorders remain elusive, hampering efforts to develop effective therapeutic interventions. In light of this, the discovery of robust biomarkers is crucial in order to identify people at risk for AD and PD, preferably before symptoms arise. For all three diseases, the identification of biomarkers would not only allow development of treatments but also evaluation and adjustment of these with disease progression. It is now understood that neuroinflammation plays a crucial role in neurodegenerative diseases, along with subsequent immune activation. Therefore, research is actively ongoing to discover and evaluate inflammatory and immune-related biomarkers. Recent progress in this area for AD, PD, and HD is presented here.
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Affiliation(s)
- Lorraine F. Clark
- Departments
of Chemistry
and Cancer Biology, The Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Thomas Kodadek
- Departments
of Chemistry
and Cancer Biology, The Scripps Research Institute, Jupiter, Florida 33458, United States
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35
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Doran TM, Morimoto J, Simanski S, Koesema EJ, Clark LF, Pels K, Stoops SL, Pugliese A, Skyler JS, Kodadek T. Discovery of Phosphorylated Peripherin as a Major Humoral Autoantigen in Type 1 Diabetes Mellitus. Cell Chem Biol 2016; 23:618-628. [PMID: 27185639 DOI: 10.1016/j.chembiol.2016.04.006] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Revised: 04/03/2016] [Accepted: 04/07/2016] [Indexed: 12/21/2022]
Abstract
A major goal in understanding autoimmune diseases is to define the antigens that elicit a self-destructive immune response, but this is a difficult endeavor. In an effort to discover autoantigens associated with type 1 diabetes (T1D), we used epitope surrogate technology that screens combinatorial libraries of synthetic molecules for compounds that could recognize disease-linked autoantibodies and enrich them from serum. Autoantibodies from one patient revealed a highly phosphorylated form of peripherin, a neuroendocrine filament protein, as a candidate T1D antigen. Peripherin antibodies were detected in 72% of donor patient sera. Further analysis revealed that the T1D-associated antibodies only recognized a dimeric conformation of peripherin. These data explain why peripherin was dismissed as an important T1D antigen previously. The discovery of this novel autoantigen would not have been possible using standard methods, such as hybridizing serum antibodies to recombinant protein arrays, highlighting the power of epitope surrogate technology for probing the mechanism of autoimmune diseases.
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Affiliation(s)
- Todd M Doran
- Departments of Chemistry and Cancer Biology, The Scripps Research Institute, Scripps Florida, 130 Scripps Way, Jupiter, FL 33458, USA
| | - Jumpei Morimoto
- Departments of Chemistry and Cancer Biology, The Scripps Research Institute, Scripps Florida, 130 Scripps Way, Jupiter, FL 33458, USA
| | - Scott Simanski
- Departments of Chemistry and Cancer Biology, The Scripps Research Institute, Scripps Florida, 130 Scripps Way, Jupiter, FL 33458, USA
| | - Eric J Koesema
- Departments of Chemistry and Cancer Biology, The Scripps Research Institute, Scripps Florida, 130 Scripps Way, Jupiter, FL 33458, USA
| | - Lorraine F Clark
- Departments of Chemistry and Cancer Biology, The Scripps Research Institute, Scripps Florida, 130 Scripps Way, Jupiter, FL 33458, USA
| | - Kevin Pels
- Departments of Chemistry and Cancer Biology, The Scripps Research Institute, Scripps Florida, 130 Scripps Way, Jupiter, FL 33458, USA
| | - Sydney L Stoops
- Departments of Chemistry and Cancer Biology, The Scripps Research Institute, Scripps Florida, 130 Scripps Way, Jupiter, FL 33458, USA
| | - Alberto Pugliese
- Diabetes Research Institute, Miller School of Medicine, University of Miami, Miami, FL 33136, USA; Division of Endocrinology, Diabetes & Metabolism, Department of Medicine, Miller School of Medicine, University of Miami, Miami, FL 33101, USA; Department of Microbiology and Immunology, Miller School of Medicine, University of Miami, Miami, FL 33101, USA
| | - Jay S Skyler
- Diabetes Research Institute, Miller School of Medicine, University of Miami, Miami, FL 33136, USA; Division of Endocrinology, Diabetes & Metabolism, Department of Medicine, Miller School of Medicine, University of Miami, Miami, FL 33101, USA
| | - Thomas Kodadek
- Departments of Chemistry and Cancer Biology, The Scripps Research Institute, Scripps Florida, 130 Scripps Way, Jupiter, FL 33458, USA.
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36
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Gearhart TL, Montelaro RC, Schurdak ME, Pilcher CD, Rinaldo CR, Kodadek T, Park Y, Islam K, Yurko R, Marques ETA, Burke DS. Selection of a potential diagnostic biomarker for HIV infection from a random library of non-biological synthetic peptoid oligomers. J Immunol Methods 2016; 435:85-9. [PMID: 27182050 PMCID: PMC4947968 DOI: 10.1016/j.jim.2016.05.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Revised: 04/10/2016] [Accepted: 05/02/2016] [Indexed: 12/05/2022]
Abstract
Non-biological synthetic oligomers can serve as ligands for antibodies. We hypothesized that a random combinatorial library of synthetic poly-N-substituted glycine oligomers, or peptoids, could represent a random “shape library” in antigen space, and that some of these peptoids would be recognized by the antigen-binding pocket of disease-specific antibodies. We synthesized and screened a one bead one compound combinatorial library of peptoids, in which each bead displayed an 8-mer peptoid with ten possible different amines at each position (108 theoretical variants). By screening one million peptoid/beads we found 112 (approximately 1 in 10,000) that preferentially bound immunoglobulins from human sera known to be positive for anti-HIV antibodies. Reactive peptoids were then re-synthesized and rigorously evaluated in plate-based ELISAs. Four peptoids showed very good, and one showed excellent, properties for establishing a sero-diagnosis of HIV. These results demonstrate the feasibility of constructing sero-diagnostic assays for infectious diseases from libraries of random molecular shapes. In this study we sought a proof-of-principle that we could identify a potential diagnostic antibody ligand biomarker for an infectious disease in a random combinatorial library of 100 million peptoids. We believe that this is the first evidence that it is possible to develop sero-diagnostic assays – for any infectious disease – based on screening random libraries of non-biological molecular shapes.
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Affiliation(s)
- Tricia L Gearhart
- Center for Vaccine Research, University of Pittsburgh, 3501 Fifth Ave, Pittsburgh, PA, 15261, United States
| | - Ronald C Montelaro
- Center for Vaccine Research, University of Pittsburgh, 3501 Fifth Ave, Pittsburgh, PA, 15261, United States
| | - Mark E Schurdak
- Drug Discovery Institute, University of Pittsburgh, 3501 Fifth Ave, Pittsburgh, PA 15261, United States
| | - Chris D Pilcher
- Center for AIDS Research, University of California, 1001 Potrero Ave, SFGH 80, San Francisco, CA 94110, United States
| | - Charles R Rinaldo
- Graduate School of Public Health, University of Pittsburgh, 130 DeSoto Street, Pittsburgh, PA, United States
| | - Thomas Kodadek
- The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, United States
| | - Yongseok Park
- Graduate School of Public Health, University of Pittsburgh, 130 DeSoto Street, Pittsburgh, PA, United States
| | - Kazi Islam
- Peptide Synthesis Facility, University of Pittsburgh, 300 Technology Drive, Pittsburgh, PA 15219, United States
| | - Raymond Yurko
- Peptide Synthesis Facility, University of Pittsburgh, 300 Technology Drive, Pittsburgh, PA 15219, United States
| | - Ernesto T A Marques
- Center for Vaccine Research, University of Pittsburgh, 3501 Fifth Ave, Pittsburgh, PA, 15261, United States; Graduate School of Public Health, University of Pittsburgh, 130 DeSoto Street, Pittsburgh, PA, United States
| | - Donald S Burke
- Center for Vaccine Research, University of Pittsburgh, 3501 Fifth Ave, Pittsburgh, PA, 15261, United States; Graduate School of Public Health, University of Pittsburgh, 130 DeSoto Street, Pittsburgh, PA, United States.
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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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38
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Sarma BK, Liu X, Kodadek T. Identification of selective covalent inhibitors of platelet activating factor acetylhydrolase 1B2 from the screening of an oxadiazolone-capped peptoid-azapeptoid hybrid library. Bioorg Med Chem 2016; 24:3953-3963. [PMID: 27160052 DOI: 10.1016/j.bmc.2016.04.047] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2015] [Revised: 04/21/2016] [Accepted: 04/22/2016] [Indexed: 12/21/2022]
Abstract
A potent and selective inhibitor of platelet-activating factor acetylhydrolase 1B2 (PAFAH1B2) is described. The compound was derived by improvement of a modest affinity primary hit isolated from the screening of a bead-displayed peptoid-azapeptoid hybrid library tethered to an oxadiazolone 'warhead'. The oxadiazolone moiety of the inhibitors was found to react covalently with the active site serine residue of PAFAH1B2. This screening strategy may be useful for the identification of many selective, covalent inhibitors of serine hydrolases.
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Affiliation(s)
- Bani Kanta Sarma
- Department of Chemistry, School of Natural Sciences, Shiv Nadar University, Dadri, Uttar Pradesh-201314, India
| | - Xiaodan Liu
- Departments of Chemistry, Scripps Research Institute, Scripps Florida, 130 Scripps Way, #3A2, Jupiter, Fl 33458, USA
| | - Thomas Kodadek
- Departments of Chemistry, Scripps Research Institute, Scripps Florida, 130 Scripps Way, #3A2, Jupiter, Fl 33458, USA
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39
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Lim B, Lee J. A Peptoid-Based Fluorescent Sensor for Cyanide Detection. Molecules 2016; 21:339. [PMID: 26978334 PMCID: PMC6273317 DOI: 10.3390/molecules21030339] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Revised: 03/04/2016] [Accepted: 03/07/2016] [Indexed: 01/06/2023] Open
Abstract
Peptoids, N-substituted glycine oligomers, are versatile peptidomimetics with diverse biomedical applications. However, strategies to the development of novel fluorescent peptoids as chemical sensors have not been extensively explored, yet. Here, we synthesized a novel peptoid-based fluorescent probe in which a coumarin moiety was incorporated via copper(I)-catalyzed azide-alkyne cycloaddition reaction. Fluorescence of the newly generated coumarin-peptoid was dramatically quenched upon coordination of the Cu(2+) ion, and the resulting peptoid-Cu(2+) complex exhibited significant Turn-ON fluorescence following the addition of CN(-). The rapid and reversible response, combined with cyanide selectivity of the synthesized peptoid, reflects a multistep photo-process and supports its utility as a new type of CN(-) sensor.
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Affiliation(s)
- Bumhee Lim
- College of Pharmacy, Research Institute of Pharmaceutical Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 151-742, Korea.
| | - Jeeyeon Lee
- College of Pharmacy, Research Institute of Pharmaceutical Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 151-742, Korea.
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40
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Zaman S, Yazdani U, Deng Y, Li W, Gadad BS, Hynan L, Karp D, Roatch N, Schutte C, Nathan Marti C, Hewitson L, German DC. A Search for Blood Biomarkers for Autism: Peptoids. Sci Rep 2016; 6:19164. [PMID: 26764136 PMCID: PMC4725892 DOI: 10.1038/srep19164] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Accepted: 11/12/2015] [Indexed: 12/18/2022] Open
Abstract
Autism spectrum disorder (ASD) is a neurodevelopmental disorder characterized by impairments in social interaction and communication, and restricted, repetitive patterns of behavior. In order to identify individuals with ASD and initiate interventions at the earliest possible age, biomarkers for the disorder are desirable. Research findings have identified widespread changes in the immune system in children with autism, at both systemic and cellular levels. In an attempt to find candidate antibody biomarkers for ASD, highly complex libraries of peptoids (oligo-N-substituted glycines) were screened for compounds that preferentially bind IgG from boys with ASD over typically developing (TD) boys. Unexpectedly, many peptoids were identified that preferentially bound IgG from TD boys. One of these peptoids was studied further and found to bind significantly higher levels (>2-fold) of the IgG1 subtype in serum from TD boys (n = 60) compared to ASD boys (n = 74), as well as compared to older adult males (n = 53). Together these data suggest that ASD boys have reduced levels (>50%) of an IgG1 antibody, which resembles the level found normally with advanced age. In this discovery study, the ASD1 peptoid was 66% accurate in predicting ASD.
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Affiliation(s)
- Sayed Zaman
- Department of Psychiatry, UT Southwestern Medical Center, Dallas TX
| | - Umar Yazdani
- Department of Psychiatry, UT Southwestern Medical Center, Dallas TX
| | - Yan Deng
- Department of Psychiatry, UT Southwestern Medical Center, Dallas TX
| | - Wenhao Li
- Department of Psychiatry, UT Southwestern Medical Center, Dallas TX
| | - Bharathi S Gadad
- Department of Psychiatry, UT Southwestern Medical Center, Dallas TX
| | - Linda Hynan
- Department of Clinical Sciences, UT Southwestern Medical Center, Dallas TX
| | - David Karp
- Department of Internal Medicine, UT Southwestern Medical Center, Dallas TX
| | - Nichole Roatch
- Johnson Center for Child Health and Development, Austin TX
| | - Claire Schutte
- Johnson Center for Child Health and Development, Austin TX
| | | | - Laura Hewitson
- Department of Psychiatry, UT Southwestern Medical Center, Dallas TX.,Johnson Center for Child Health and Development, Austin TX
| | - Dwight C German
- Department of Psychiatry, UT Southwestern Medical Center, Dallas TX
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41
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Doran TM, Gao Y, Simanski S, McEnaney P, Kodadek T. High affinity binding of conformationally constrained synthetic oligomers to an antigen-specific antibody: Discovery of a diagnostically useful synthetic ligand for murine Type 1 diabetes autoantibodies. Bioorg Med Chem Lett 2015; 25:4910-4917. [PMID: 26067174 PMCID: PMC4607566 DOI: 10.1016/j.bmcl.2015.05.046] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2015] [Accepted: 05/18/2015] [Indexed: 10/23/2022]
Abstract
'Antigen surrogates' are synthetic, non-natural molecules that recognize the antigen-binding sites of antibodies. These molecules are of interest as replacements for native antigens as antibody 'capture agents' in ELISA-like assays of potential diagnostic utility, for example when the antibody is indicative of a disease state. Antigen surrogates for disease-related antibodies can be mined from one-bead one-compound (OBOC) libraries by first denuding the library of ligands for antibodies present in the serum of control patients or animals, followed by screening the remainder of the library against serum from individuals with a particular disease of interest. Most of the work in this area has been done with peptoids (oligomers of N-alkylated glycine), which provide antibody ligands with only modest affinity and selectivity. Here, we explore the hypothesis that this is due to the 'floppiness' of the peptoid backbone by creating libraries of peptoid-like molecules that have conformation-restricting structural elements inserted into their backbones. Indeed, we show here that these libraries can provide high affinity and selectivity antigen surrogates and that this much-improved binding is completely dependent on conformational restriction of the oligomer chain.
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Affiliation(s)
- Todd M Doran
- The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, United States
| | - Yu Gao
- The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, United States
| | - Scott Simanski
- The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, United States
| | - Patrick McEnaney
- The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, United States
| | - Thomas Kodadek
- The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, United States.
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42
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Doran TM, Morimoto J, Simanski S, McEnaney PJ, Kodadek T. Reliable diagnosis of murine type 1 diabetes using a panel of autoantigens and "antigen surrogates" mounted onto a liquid array. MOLECULAR BIOSYSTEMS 2015; 11:3156-63. [PMID: 26390856 PMCID: PMC4605892 DOI: 10.1039/c5mb00521c] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Autoantibodies raised against β cell antigens are the most reliable preclinical biomarkers for predicting the imminent onset of type 1 diabetes mellitus (T1DM). The most current detection platforms are technically challenging or are run on clinically esoteric equipment. Here, we present a straightforward approach to detect autoantibody biomarkers that employs highly PEGylated microspheres onto which are mounted various capture agents that include affinity-tagged antigens or small molecule "antigen surrogates." After incubation with small quantities of serum, the bound autoantibodies can be measured using a standard flow cytometer. By multiplexing this assay, we show that a panel of antigen and antigen surrogates reliably predicts hyperglycemia in a mouse model of diabetes without false positives.
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Affiliation(s)
- Todd M Doran
- The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, USA.
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43
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Mendes K, Ndungu JM, Clark LF, Kodadek T. Optimization of the Magnetic Recovery of Hits from One-Bead-One-Compound Library Screens. ACS COMBINATORIAL SCIENCE 2015. [PMID: 26221913 DOI: 10.1021/acscombsci.5b00090] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
On-bead screening of one-bead-one-compound (OBOC) libraries is a useful procedure for the identification of protein ligands. An important aspect of this experiment is the method by which beads that bind the target protein are separated from those that do not. Ideally, such a method would be rapid and convenient and result in the isolation of 100% of the "hits" with no false positives (beads that display compounds that are not good ligands for the target). We introduced a technique in which beads that have bound a labeled target protein can be magnetized, thus allowing their convenient isolation ( Astle et al. Chem. Biol. 2010 , 17 , 38 - 45 ). However, recent work in our laboratory and others has shown that magnetic hit recovery can result in the isolation of large numbers of false positives and has also suggested that many true hit beads are missed. In this study, we employ a well-defined model system to examine the efficiency of various magnetic hit isolation protocols. We show that the choice of reagents and the particular operations employed are critical for optimal results.
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Affiliation(s)
- Kimberly Mendes
- Opko Health, Inc., RF Building, Jupiter, Florida 33458, United States
| | - J. M. Ndungu
- Opko Health, Inc., RF Building, Jupiter, Florida 33458, United States
| | - Lorraine F. Clark
- 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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44
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Trader DJ, Simanski S, Kodadek T. A reversible and highly selective inhibitor of the proteasomal ubiquitin receptor rpn13 is toxic to multiple myeloma cells. J Am Chem Soc 2015; 137:6312-9. [PMID: 25914958 PMCID: PMC4455945 DOI: 10.1021/jacs.5b02069] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The proteasome is a multisubunit complex responsible for most nonlysosomal turnover of proteins in eukaryotic cells. Proteasome inhibitors are of great interest clinically, particularly for the treatment of multiple myeloma (MM). Unfortunately, resistance arises almost inevitably to these active site-targeted drugs. One strategy to overcome this resistance is to inhibit other steps in the protein turnover cascade mediated by the proteasome. Previously, Anchoori et al. identified Rpn13 as the target of an electrophilic compound (RA-190) that was selectively toxic to MM cells (Cancer Cell 2013, 24, 791-805), suggesting that this subunit of the proteasome is also a viable cancer drug target. Here we describe the discovery of the first highly selective, reversible Rpn13 ligands and show that they are also selectively toxic to MM cells. These data strongly support the hypothesis that Rpn13 is a viable target for the development of drugs to treat MM and other cancers.
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Affiliation(s)
- Darci J. Trader
- Departments of Chemistry and Cancer Biology, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458
| | - Scott Simanski
- Departments of Chemistry and Cancer Biology, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458
| | - Thomas Kodadek
- Departments of Chemistry and Cancer Biology, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458
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45
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Structure-activity relationship study of novel peptoids that mimic the structure of antimicrobial peptides. Antimicrob Agents Chemother 2015; 59:4112-20. [PMID: 25941221 DOI: 10.1128/aac.00237-15] [Citation(s) in RCA: 94] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Accepted: 03/15/2015] [Indexed: 11/20/2022] Open
Abstract
The constant emergence of new bacterial strains that resist the effectiveness of marketed antimicrobials has led to an urgent demand for and intensive research on new classes of compounds to combat bacterial infections. Antimicrobial peptoids comprise one group of potential candidates for antimicrobial drug development. The present study highlights a library of 22 cationic amphipathic peptoids designed to target bacteria. All the peptoids share an overall net charge of +4 and are 8 to 9 residues long; however, the hydrophobicity and charge distribution along the abiotic backbone varied, thus allowing an examination of the structure-activity relationship within the library. In addition, the toxicity profiles of all peptoids were assessed in human red blood cells (hRBCs) and HeLa cells, revealing the low toxicity exerted by the majority of the peptoids. The structural optimization also identified two peptoid candidates, 3 and 4, with high selectivity ratios of 4 to 32 and 8 to 64, respectively, and a concentration-dependent bactericidal mode of action against Gram-negative Escherichia coli.
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46
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Pels K, Kodadek T. Solid-phase synthesis of diverse peptide tertiary amides by reductive amination. ACS COMBINATORIAL SCIENCE 2015; 17:152-5. [PMID: 25695359 DOI: 10.1021/acscombsci.5b00007] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The synthesis of libraries of conformationally constrained peptide-like oligomers is an important goal in combinatorial chemistry. In this regard an attractive building block is the N-alkylated peptide, also known as a peptide tertiary amide (PTA). PTAs are conformationally constrained because of allylic 1,3 strain interactions. We report here an improved synthesis of these species on solid supports through the use of reductive amination chemistry using amino acid-terminated, bead-displayed oligomers and diverse aldehydes. The utility of this chemistry is demonstrated by the synthesis of a library of 10,000 mixed peptoid-PTA oligomers.
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Affiliation(s)
- Kevin Pels
- 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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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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Doran TM, Simanski S, Kodadek T. Discovery of native autoantigens via antigen surrogate technology: application to type 1 diabetes. ACS Chem Biol 2015; 10:401-12. [PMID: 25474415 PMCID: PMC4339956 DOI: 10.1021/cb5007618] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2014] [Accepted: 12/04/2014] [Indexed: 01/23/2023]
Abstract
A fundamental goal in understanding the mechanisms of autoimmune disease is the characterization of autoantigens that are targeted by autoreactive antibodies and T cells. Unfortunately, the identification of autoantigens is a difficult problem. We have begun to explore a novel route to the discovery of autoantibody/autoantigen pairs that involves comparative screening of combinatorial libraries of unnatural, synthetic molecules for compounds that bind antibodies present at much higher levels in the serum of individuals with a given autoimmune disease than in the serum of control individuals. We have shown that this approach can yield "antigen surrogates" capable of capturing disease-specific autoantibodies from serum. In this report, we demonstrate that the synthetic antigen surrogates can be used to affinity purify the autoantibodies from serum and that these antibodies can then be used to identify their cognate autoantigen in an appropriate tissue lysate. Specifically, we report the discovery of a peptoid able to bind autoantibodies present in about one-third of nonobese diabetic (NOD) mice. The peptoid-binding autoantibodies were highly enriched through peptoid affinity chromatography and employed to probe mouse pancreatic and brain lysates. This resulted in identification of murine GAD65 as the native autoantigen. GAD65 is a known humoral autoantigen in human type 1 diabetes mellitus (T1DM), but its existence in mice had been controversial. This study demonstrates the potential of this chemical approach for the unbiased identification of autoantigen/autoantibody complexes.
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Affiliation(s)
- Todd M. Doran
- Departments
of Chemistry
& Cancer Biology, The Scripps Research
Institute, 130 Scripps
Way, Jupiter, Florida 33458, United States
| | - Scott Simanski
- Departments
of Chemistry
& Cancer Biology, The Scripps Research
Institute, 130 Scripps
Way, Jupiter, Florida 33458, United States
| | - Thomas Kodadek
- Departments
of Chemistry
& Cancer Biology, The Scripps Research
Institute, 130 Scripps
Way, Jupiter, Florida 33458, United States
| |
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Moon H, Lim HS. Synthesis and screening of small-molecule α-helix mimetic libraries targeting protein–protein interactions. Curr Opin Chem Biol 2015; 24:38-47. [DOI: 10.1016/j.cbpa.2014.10.023] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2014] [Revised: 10/27/2014] [Accepted: 10/28/2014] [Indexed: 12/11/2022]
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50
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The identification of high-affinity G protein-coupled receptor ligands from large combinatorial libraries using multicolor quantum dot-labeled cell-based screening. Future Med Chem 2015; 6:809-23. [PMID: 24941874 DOI: 10.4155/fmc.14.38] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
G protein-coupled receptors (GPCRs), which are involved in virtually every biological process, constitute the largest family of transmembrane receptors. Many top-selling and newly approved drugs target GPCRs. In this review, we aim to recapitulate efforts and progress in combinatorial library-assisted GPCR ligand discovery, particularly focusing on one-bead-one-compound library synthesis and quantum dot-labeled cell-based assays, which both effectively enhance the rapid identification of GPCR ligands with higher affinity and specificity.
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