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Ren J, Tian Y, Hossain E, Ho JS, Mann YS, Zhang Y, Browne MD, Connolly MD, Zuckermann RN. Mass spectrometry studies of the fragmentation patterns and mechanisms of protonated peptoids. Biopolymers 2020; 111:e23358. [DOI: 10.1002/bip.23358] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Revised: 05/02/2020] [Accepted: 05/04/2020] [Indexed: 12/28/2022]
Affiliation(s)
- Jianhua Ren
- Department of Chemistry University of the Pacific Stockton CA, U.S.A. USA
| | - Yuan Tian
- Department of Chemistry University of the Pacific Stockton CA, U.S.A. USA
| | - Ekram Hossain
- Department of Chemistry University of the Pacific Stockton CA, U.S.A. USA
| | - Joshua S. Ho
- Department of Chemistry University of the Pacific Stockton CA, U.S.A. USA
| | - Yadwinder S. Mann
- Department of Chemistry University of the Pacific Stockton CA, U.S.A. USA
| | - Yuntao Zhang
- Department of Chemistry University of the Pacific Stockton CA, U.S.A. USA
| | - Michael D. Browne
- Department of Chemistry University of the Pacific Stockton CA, U.S.A. USA
| | - Michael D. Connolly
- The Molecular Foundry Lawrence Berkeley National Laboratory Berkeley CA, U.S.A. USA
| | - Ronald N. Zuckermann
- The Molecular Foundry Lawrence Berkeley National Laboratory Berkeley CA, U.S.A. USA
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Culf AS. Peptoids as tools and sensors. Biopolymers 2019; 110:e23285. [PMID: 31070792 DOI: 10.1002/bip.23285] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 04/09/2019] [Accepted: 04/15/2019] [Indexed: 12/19/2022]
Abstract
A review of molecular tools and sensors assembled on N-substituted glycine, or α-peptoid, oligomers between 2013 and November 2018 with the following sections: (a) Peptoids as crystal growth modifiers, (b) Peptoids as catalysts, (c) Ion and molecule sequestration and transport, (d) Peptoid sensors, (e) Macromolecule recognition, (f) Cellular transporters, (g) Medical imaging, (h) Future direction and (i) Summary and outlook. Peptoids are a promising class of peptide mimic making them an excellent platform for functional molecule preparation. Attributes of peptoid oligomers include: (a) the ease of precise sequence definition and mono-dispersity; (b) access to a vast chemical space within simple and repeating chemical preparative steps and (c) thermal, chemical and biological stability all lending support for their application in a number of areas, with some that have been realised to date. The peptoid tool and sensor examples selected have realised practical utility. They serve to illustrate the rapidity of new insight that can generate in many disparate areas of science and technology, enabling the quick assembly of design criteria for efficient peptoid molecular tools and sensors.
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Affiliation(s)
- Adrian S Culf
- Sussex Research Laboratories, Inc., Ottawa, Ontario, Canada
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Perret G, Boschetti E. Aptamer affinity ligands in protein chromatography. Biochimie 2017; 145:98-112. [PMID: 29054800 DOI: 10.1016/j.biochi.2017.10.008] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2017] [Accepted: 10/12/2017] [Indexed: 02/07/2023]
Abstract
The present review deals with the place of single chain oligonucleotide ligands (aptamers) in affinity chromatography applied to proteins. Aptamers are not the only affinity ligands available but they represent an emerging and highly promising route that advantageously competes with antibodies in immunopurification processes. A historical background of affinity chromatography from the beginning of the discipline to the most recent outcomes is first presented. Then the focus is centered on aptamers which represent the last step so far to the long quest for affinity ligands associating very high specificity, availability and strong stability against most harsh cleaning agents required in chromatography. Then technologies of ligand selection from large libraries followed by the most appropriate chemical grafting approaches are described and supported by a number of bibliographic references. Experimental results assembled from relevant published paper are reported; they are selected by their practical applicability and potential use at large scale. The review concludes with specific remarks and future developments that are expected in the near future to turn this technology into a large acceptance for preparative applications.
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Gopalakrishnan R, Frolov AI, Knerr L, Drury WJ, Valeur E. Therapeutic Potential of Foldamers: From Chemical Biology Tools To Drug Candidates? J Med Chem 2016; 59:9599-9621. [PMID: 27362955 DOI: 10.1021/acs.jmedchem.6b00376] [Citation(s) in RCA: 121] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Over the past decade, foldamers have progressively emerged as useful architectures to mimic secondary structures of proteins. Peptidic foldamers, consisting of various amino acid based backbones, have been the most studied from a therapeutic perspective, while polyaromatic foldamers have barely evolved from their nascency and remain perplexing for medicinal chemists due to their poor drug-like nature. Despite these limitations, this compound class may still offer opportunities to study challenging targets or provide chemical biology tools. The potential of foldamer drug candidates reaching the clinic is still a stretch. Nevertheless, advances in the field have demonstrated their potential for the discovery of next generation therapeutics. In this perspective, the current knowledge of foldamers is reviewed in a drug discovery context. Recent advances in the early phases of drug discovery including hit finding, target validation, and optimization and molecular modeling are discussed. In addition, challenges and focus areas are debated and gaps highlighted.
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Affiliation(s)
- Ranganath Gopalakrishnan
- Cardiovascular and Metabolic Diseases, Innovative Medicines and Early Development Biotech Unit, AstraZeneca , Pepparedsleden 1, Mölndal, 431 83, Sweden.,AstraZeneca MPI Satellite Unit, Department of Chemical Biology, Max Planck Institute of Molecular Physiology , Dortmund 44202, Germany
| | - Andrey I Frolov
- Cardiovascular and Metabolic Diseases, Innovative Medicines and Early Development Biotech Unit, AstraZeneca , Pepparedsleden 1, Mölndal, 431 83, Sweden
| | - Laurent Knerr
- Cardiovascular and Metabolic Diseases, Innovative Medicines and Early Development Biotech Unit, AstraZeneca , Pepparedsleden 1, Mölndal, 431 83, Sweden
| | - William J Drury
- Cardiovascular and Metabolic Diseases, Innovative Medicines and Early Development Biotech Unit, AstraZeneca , Pepparedsleden 1, Mölndal, 431 83, Sweden
| | - Eric Valeur
- Cardiovascular and Metabolic Diseases, Innovative Medicines and Early Development Biotech Unit, AstraZeneca , Pepparedsleden 1, Mölndal, 431 83, Sweden
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Ren J, Tian Y, Hossain E, Connolly MD. Fragmentation Patterns and Mechanisms of Singly and Doubly Protonated Peptoids Studied by Collision Induced Dissociation. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2016; 27:646-661. [PMID: 26832347 DOI: 10.1007/s13361-016-1341-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2015] [Revised: 01/07/2016] [Accepted: 01/09/2016] [Indexed: 06/05/2023]
Abstract
Peptoids are peptide-mimicking oligomers consisting of N-alkylated glycine units. The fragmentation patterns for six singly and doubly protonated model peptoids were studied via collision-induced dissociation tandem mass spectrometry. The experiments were carried out on a triple quadrupole mass spectrometer with an electrospray ionization source. Both singly and doubly protonated peptoids were found to fragment mainly at the backbone amide bonds to produce peptoid B-type N-terminal fragment ions and Y-type C-terminal fragment ions. However, the relative abundances of B- versus Y-ions were significantly different. The singly protonated peptoids fragmented by producing highly abundant Y-ions and lesser abundant B-ions. The Y-ion formation mechanism was studied through calculating the energetics of truncated peptoid fragment ions using density functional theory and by controlled experiments. The results indicated that Y-ions were likely formed by transferring a proton from the C-H bond of the N-terminal fragments to the secondary amine of the C-terminal fragments. This proton transfer is energetically favored, and is in accord with the observation of abundant Y-ions. The calculations also indicated that doubly protonated peptoids would fragment at an amide bond close to the N-terminus to yield a high abundance of low-mass B-ions and high-mass Y-ions. The results of this study provide further understanding of the mechanisms of peptoid fragmentation and, therefore, are a valuable guide for de novo sequencing of peptoid libraries synthesized via combinatorial chemistry. Graphical Abstract ᅟ.
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Affiliation(s)
- Jianhua Ren
- Department of Chemistry, University of the Pacific, 3601 Pacific Avenue, Stockton, CA, 95211, USA.
| | - Yuan Tian
- Department of Chemistry, University of the Pacific, 3601 Pacific Avenue, Stockton, CA, 95211, USA
| | - Ekram Hossain
- Department of Chemistry, University of the Pacific, 3601 Pacific Avenue, Stockton, CA, 95211, USA
| | - Michael D Connolly
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
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Corredor M, Bonet R, Moure A, Domingo C, Bujons J, Alfonso I, Pérez Y, Messeguer À. Cationic Peptides and Peptidomimetics Bind Glycosaminoglycans as Potential Sema3A Pathway Inhibitors. Biophys J 2016; 110:1291-303. [PMID: 27028639 PMCID: PMC4816699 DOI: 10.1016/j.bpj.2016.01.033] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Revised: 01/29/2016] [Accepted: 01/29/2016] [Indexed: 12/28/2022] Open
Abstract
Semaphorin3A (Sema3A) is a vertebrate-secreted protein that was initially characterized as a repulsive-guidance cue. Semaphorins have crucial roles in several diseases; therefore, the development of Sema3A inhibitors is of therapeutic interest. Sema3A interacts with glycosaminoglycans (GAGs), presumably through its C-terminal basic region. We used different biophysical techniques (i.e., NMR, surface plasmon resonance, isothermal titration calorimetry, fluorescence, and UV-visible spectroscopy) to characterize the binding of two Sema3A C-terminus-derived basic peptides (FS2 and NFS3) to heparin and chondroitin sulfate A. We found that these peptides bind to both GAGs with affinities in the low-micromolar range. On the other hand, a peptoid named SICHI (semaphorin-induced chemorepulsion inhibitor), which is positively charged at physiological pH, was first identified by our group as being able to block Sema3A chemorepulsion and growth-cone collapse in axons at the extracellular level. To elucidate the direct target for the reported SICHI inhibitory effect in the Sema3A signaling pathway, we looked first to the protein-protein interaction between secreted Sema3A and the Nrp1 receptor. However, our results show that SICHI does not bind directly to the Sema3A sema domain or to Nrp1 extracellular domains. We evaluated a new, to our knowledge, hypothesis, according to which SICHI binds to GAGs, thereby perturbing the Sema3A-GAG interaction. By using the above-mentioned techniques, we observed that SICHI binds to GAGs and competes with Sema3A C-terminus-derived basic peptides for binding to GAGs. These data support the ability of SICHI to block the biologically relevant interaction between Sema3A and GAGs, thus revealing SICHI as a new, to our knowledge, class of inhibitors that target the GAG-protein interaction.
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Affiliation(s)
- Miriam Corredor
- Departamento de Química Biológica y Modelización Molecular, Instituto de Química Avanzada de Catalunya, IQAC-CSIC, Barcelona, Spain
| | - Roman Bonet
- Departamento de Química Biológica y Modelización Molecular, Instituto de Química Avanzada de Catalunya, IQAC-CSIC, Barcelona, Spain
| | - Alejandra Moure
- Departamento de Química Biológica y Modelización Molecular, Instituto de Química Avanzada de Catalunya, IQAC-CSIC, Barcelona, Spain
| | - Cecilia Domingo
- Departamento de Química Biológica y Modelización Molecular, Instituto de Química Avanzada de Catalunya, IQAC-CSIC, Barcelona, Spain
| | - Jordi Bujons
- Departamento de Química Biológica y Modelización Molecular, Instituto de Química Avanzada de Catalunya, IQAC-CSIC, Barcelona, Spain
| | - Ignacio Alfonso
- Departamento de Química Biológica y Modelización Molecular, Instituto de Química Avanzada de Catalunya, IQAC-CSIC, Barcelona, Spain
| | - Yolanda Pérez
- Servicio de Resonancia Magnética Nuclear, Instituto de Química Avanzada de Catalunya, IQAC-CSIC, Barcelona, Spain.
| | - Àngel Messeguer
- Departamento de Química Biológica y Modelización Molecular, Instituto de Química Avanzada de Catalunya, IQAC-CSIC, Barcelona, Spain.
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Bolt HL, Cobb SL. A practical method for the synthesis of peptoids containing both lysine-type and arginine-type monomers. Org Biomol Chem 2016; 14:1211-5. [DOI: 10.1039/c5ob02279g] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
A practical synthetic procedure to synthesise linear and cyclic peptoids containing both arginine- and lysine-type residues within the same sequence has been developed. The methodology utilises orthogonal N-Boc and N-Dde protection, pyrazole-1-carboxamide as a guanidinylation reagent and is compatible with the sub-monomer method.
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Affiliation(s)
- H. L. Bolt
- Department of Chemistry
- Durham University
- Durham
- UK
| | - S. L. Cobb
- Department of Chemistry
- Durham University
- Durham
- UK
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Perret G, Santambien P, Boschetti E. The quest for affinity chromatography ligands: are the molecular libraries the right source? J Sep Sci 2015; 38:2559-72. [DOI: 10.1002/jssc.201500285] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Revised: 04/26/2015] [Accepted: 05/10/2015] [Indexed: 12/15/2022]
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