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Leguizamon SC, Scott TF. Mimicking DNA Functions with Abiotic, Sequence-Defined Polymers. POLYM REV 2021. [DOI: 10.1080/15583724.2021.2014519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Samuel C. Leguizamon
- Department of Chemical Engineering, University of Michigan, Ann Arbor, Michigan, USA
| | - Timothy F. Scott
- Department of Chemical Engineering, Monash University, Clayton, VIC, Australia
- Department of Materials Science and Engineering, Monash University, Clayton, VIC, Australia
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2
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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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Reese HR, Shanahan CC, Proulx C, Menegatti S. Peptide science: A "rule model" for new generations of peptidomimetics. Acta Biomater 2020; 102:35-74. [PMID: 31698048 DOI: 10.1016/j.actbio.2019.10.045] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2019] [Revised: 10/17/2019] [Accepted: 10/30/2019] [Indexed: 02/07/2023]
Abstract
Peptides have been heavily investigated for their biocompatible and bioactive properties. Though a wide array of functionalities can be introduced by varying the amino acid sequence or by structural constraints, properties such as proteolytic stability, catalytic activity, and phase behavior in solution are difficult or impossible to impart upon naturally occurring α-L-peptides. To this end, sequence-controlled peptidomimetics exhibit new folds, morphologies, and chemical modifications that create new structures and functions. The study of these new classes of polymers, especially α-peptoids, has been highly influenced by the analysis, computational, and design techniques developed for peptides. This review examines techniques to determine primary, secondary, and tertiary structure of peptides, and how they have been adapted to investigate peptoid structure. Computational models developed for peptides have been modified to predict the morphologies of peptoids and have increased in accuracy in recent years. The combination of in vitro and in silico techniques have led to secondary and tertiary structure design principles that mirror those for peptides. We then examine several important developments in peptoid applications inspired by peptides such as pharmaceuticals, catalysis, and protein-binding. A brief survey of alternative backbone structures and research investigating these peptidomimetics shows how the advancement of peptide and peptoid science has influenced the growth of numerous fields of study. As peptide, peptoid, and other peptidomimetic studies continue to advance, we will expect to see higher throughput structural analyses, greater computational accuracy and functionality, and wider application space that can improve human health, solve environmental challenges, and meet industrial needs. STATEMENT OF SIGNIFICANCE: Many historical, chemical, and functional relations draw a thread connecting peptides to their recent cognates, the "peptidomimetics". This review presents a comprehensive survey of this field by highlighting the width and relevance of these familial connections. In the first section, we examine the experimental and computational techniques originally developed for peptides and their morphing into a broader analytical and predictive toolbox. The second section presents an excursus of the structures and properties of prominent peptidomimetics, and how the expansion of the chemical and structural diversity has returned new exciting properties. The third section presents an overview of technological applications and new families of peptidomimetics. As the field grows, new compounds emerge with clear potential in medicine and advanced manufacturing.
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Halin E, Hoyas S, Lemaur V, De Winter J, Laurent S, Connolly MD, Zuckermann RN, Cornil J, Gerbaux P. Backbone Cleavages of Protonated Peptoids upon Collision-Induced Dissociation: Competitive and Consecutive B-Y and A 1-Y X Reactions. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2019; 30:2726-2740. [PMID: 31755045 DOI: 10.1007/s13361-019-02342-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Revised: 09/11/2019] [Accepted: 09/11/2019] [Indexed: 06/10/2023]
Abstract
Mass spectrometric techniques and more particularly collision-induced dissociation (CID) experiments represent a powerful method for the determination of the primary sequence of (bio)molecules. However, the knowledge of the ion fragmentation patterns say the dissociation reaction mechanisms is a prerequisite to reconstitute the sequence based on fragment ions. Previous papers proposed that protonated peptoids dissociate following an oxazolone-ring mechanism starting from the O-protonation species and leading to high mass Y sequence ions. Here we revisit this backbone cleavage mechanism by performing CID and ion mobility experiments, together with computational chemistry, on tailor-made peptoids. We demonstrated that the B/Y cleavages of collisionally activated O-protonated peptoids must involve the amide nitrogen protonated structures as the dissociating species, mimicking the CID behavior of protonated peptides. Upon the nucleophilic attack of the oxygen atom of the N-terminal adjacent carbonyl group on the carbonyl carbon atom of the protonated amide, the peptoid ions directly dissociate to form an ion-neutral complex associating an oxazolone ion to the neutral truncated peptoid residue. Dissociation of the ion/neutral complex predominantly produces Y ions due to the high proton affinity of the secondary amide function characteristic of truncated peptoids. Whereas the production of Yx ions from acetylated peptoids also involves the B/Y pathway, the observation of abundant Yx ions from non-acetylated peptoid ions is shown in the present study to arise from an A1-Yx mechanism. The consecutive and competitive characters of the A1-Yx and the B/Y mechanisms are also investigated by drift time-aligned CID experiments.
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Affiliation(s)
- Emilie Halin
- Organic Synthesis & Mass Spectrometry Laboratory, Interdisciplinary Center for Mass Spectrometry (CISMa), Center of Innovation and Research in Materials and Polymers (CIRMAP), University of Mons - UMONS, 23 Place du Parc, 7000, Mons, Belgium
- Department of General, Organic Biomedical Chemistry, NMR and Molecular Imaging Laboratory, University of Mons - UMONS, 23 Place du Parc, 7000, Mons, Belgium
| | - Sébastien Hoyas
- Organic Synthesis & Mass Spectrometry Laboratory, Interdisciplinary Center for Mass Spectrometry (CISMa), Center of Innovation and Research in Materials and Polymers (CIRMAP), University of Mons - UMONS, 23 Place du Parc, 7000, Mons, Belgium
- Laboratory for Chemistry of Novel Materials, Center of Innovation and Research in Materials and Polymers, Research Institute for Science and Engineering of Materials, University of Mons, UMONS, 23 Place du Parc, 7000, Mons, Belgium
| | - Vincent Lemaur
- Laboratory for Chemistry of Novel Materials, Center of Innovation and Research in Materials and Polymers, Research Institute for Science and Engineering of Materials, University of Mons, UMONS, 23 Place du Parc, 7000, Mons, Belgium
| | - Julien De Winter
- Organic Synthesis & Mass Spectrometry Laboratory, Interdisciplinary Center for Mass Spectrometry (CISMa), Center of Innovation and Research in Materials and Polymers (CIRMAP), University of Mons - UMONS, 23 Place du Parc, 7000, Mons, Belgium
| | - Sophie Laurent
- Department of General, Organic Biomedical Chemistry, NMR and Molecular Imaging Laboratory, University of Mons - UMONS, 23 Place du Parc, 7000, Mons, Belgium
| | - Michael D Connolly
- Molecular Foundry, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Ronald N Zuckermann
- Molecular Foundry, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Jérôme Cornil
- Laboratory for Chemistry of Novel Materials, Center of Innovation and Research in Materials and Polymers, Research Institute for Science and Engineering of Materials, University of Mons, UMONS, 23 Place du Parc, 7000, Mons, Belgium
| | - Pascal Gerbaux
- Organic Synthesis & Mass Spectrometry Laboratory, Interdisciplinary Center for Mass Spectrometry (CISMa), Center of Innovation and Research in Materials and Polymers (CIRMAP), University of Mons - UMONS, 23 Place du Parc, 7000, Mons, Belgium.
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5
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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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6
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Mutlu H, Lutz JF. Reading Polymers: Sequencing of Natural and Synthetic Macromolecules. Angew Chem Int Ed Engl 2014; 53:13010-9. [DOI: 10.1002/anie.201406766] [Citation(s) in RCA: 120] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Revised: 07/24/2014] [Indexed: 11/07/2022]
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Mutlu H, Lutz JF. “Lesen” von Polymeren: Die Sequenzierung natürlicher und synthetischer Makromoleküle. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201406766] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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8
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Bogdanov B, Zhao X, Robinson DB, Ren J. Electron capture dissociation studies of the fragmentation patterns of doubly protonated and mixed protonated-sodiated peptoids. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2014; 25:1202-1216. [PMID: 24845348 DOI: 10.1007/s13361-014-0869-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2013] [Revised: 02/09/2014] [Accepted: 02/14/2014] [Indexed: 06/03/2023]
Abstract
The fragmentation patterns of a group of doubly protonated ([P + 2H](2+)) and mixed protonated-sodiated ([P + H + Na](2+)) peptide-mimicking oligomers, known as peptoids, have been studied using electron capturing dissociation (ECD) tandem mass spectrometry techniques. For all the peptoids studied, the primary backbone fragmentation occurred at the N-Cα bonds. The N-terminal fragment ions, the C-ions (protonated) and the C'-ions (sodiated) were observed universally for all the peptoids regardless of the types of charge carrier. The C-terminal ions varied depending on the type of charge carrier. The doubly protonated peptoids with at least one basic residue located at a position other than the N-terminus fragmented by producing the Z(•)-series of ions. In addition, most doubly protonated peptoids also produced the Y-series of ions with notable abundances. The mixed protonated-sodiated peptoids fragmented by yielding the Z(•)'-series of ions in addition to the C'-series. Chelation between the sodium cation and the amide groups of the peptoid chain might be an important factor that could stabilize both the N-terminal and the C-terminal fragment ions. Regardless of the types of the charge carrier, one notable fragmentation for all the peptoids was the elimination of a benzylic radical from the odd-electron positive ions of the protonated peptoids ([P + 2H](•+)) and the sodiated peptoids ([P + H + Na](•+)). The study showed potential utility of using the ECD technique for sequencing of peptoid libraries generated by combinatorial chemistry.
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Affiliation(s)
- Bogdan Bogdanov
- Department of Chemistry, University of the Pacific, Stockton, CA, 95211, USA
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Sarkar M, Pascal BD, Steckler C, Aquino C, Micalizio GC, Kodadek T, Chalmers MJ. Decoding split and pool combinatorial libraries with electron-transfer dissociation tandem mass spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2013; 24:1026-36. [PMID: 23636859 PMCID: PMC4455952 DOI: 10.1007/s13361-013-0633-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2013] [Revised: 03/25/2013] [Accepted: 03/28/2013] [Indexed: 05/03/2023]
Abstract
Screening of bead-based split and pool combinatorial chemistry libraries is a powerful approach to aid the discovery of new chemical compounds able to interact with, and modulate the activities of, protein targets of interest. Split and pool synthesis provides for large and well diversified chemical libraries, in this case comprised of oligomers generated from a well-defined starting set. At the end of the synthesis, each bead in the library displays many copies of a unique oligomer sequence. Because the sequence of the oligomer is not known at the time of screening, methods for decoding of the sequence of each screening "hit" are essential. Here we describe an electron-transfer dissociation (ETD) based tandem mass spectrometry approach for the decoding of mass-encoded split and pool libraries. We demonstrate that the newly described "chiral oligomers of pentenoic amides (COPAs)" yield non-sequence-specific product ions upon collisional activated dissociation; however, complete sequence information can be obtained with ETD. To aid in the decoding of libraries from MS and MS/MS data, we have incorporated (79)Br/(81)Br isotope "tags" to differentiate N- and C-terminal product ions. In addition, we have created "Hit-Find," a software program that allows users to generate libraries in silico. The user can then search all possible members of the chemical library for those that fall within a user-defined mass error.
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Affiliation(s)
- Mohosin Sarkar
- Department of Chemistry, The Scripps Research Institute, Scripps Florida, Jupiter, FL 33458, USA
- Department of Cancer Biology, The Scripps Research Institute, Scripps Florida, Jupiter, FL 33458, USA
| | - Bruce D. Pascal
- TRI Informatics, The Scripps Research Institute, Scripps Florida, Jupiter, FL 33458, USA
- Mass Spectrometry and Proteomics, The Scripps Research Institute, Scripps Florida, Jupiter, FL 33458, USA
| | - Caitlin Steckler
- Mass Spectrometry and Proteomics, The Scripps Research Institute, Scripps Florida, Jupiter, FL 33458, USA
| | - Claudio Aquino
- Department of Chemistry, The Scripps Research Institute, Scripps Florida, Jupiter, FL 33458, USA
| | - Glenn C. Micalizio
- Department of Chemistry, The Scripps Research Institute, Scripps Florida, Jupiter, FL 33458, USA
| | - Thomas Kodadek
- Department of Chemistry, The Scripps Research Institute, Scripps Florida, Jupiter, FL 33458, USA
- Department of Cancer Biology, The Scripps Research Institute, Scripps Florida, Jupiter, FL 33458, USA
| | - Michael J. Chalmers
- Mass Spectrometry and Proteomics, The Scripps Research Institute, Scripps Florida, Jupiter, FL 33458, USA
- Molecular Therapeutics, The Scripps Research Institute, Scripps Florida, Jupiter, FL 33458, USA
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Quan Q, Hao Q, Song T, Siu CK, Chu IK. Mechanistic investigation of phosphate ester bond cleavages of glycylphosphoserinyltryptophan radical cations under low-energy collision-induced dissociation. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2013; 24:554-562. [PMID: 23516067 DOI: 10.1007/s13361-013-0597-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2012] [Revised: 02/18/2013] [Accepted: 02/21/2013] [Indexed: 06/01/2023]
Abstract
Under the conditions of low-energy collision-induced dissociation (CID), the canonical glycylphosphoserinyltryptophan radical cation having its radical located on the side chain of the tryptophan residue ([G(p)SW](•+)) fragments differently from its tautomer with the radical initially generated on the α-carbon atom of the glycine residue ([G(•)(p)SW](+)). The dissociation of [G(•)(p)SW](+) is dominated by the neutral loss of H3PO4 (98 Da), with backbone cleavage forming the [b2 - H](•+)/y1(+) pair as the minor products. In contrast, for [G(p)SW](•+), competitive cleavages along the peptide backbone, such as the formation of [G(p)SW - CO2](•+) and the [c2 + 2H](+)/[z(1) - H](•+) pair, significantly suppress the loss of neutral H3PO4. In this study, we used density functional theory (DFT) to examine the mechanisms for the tautomerizations of [G(•)(p)SW](+) and [G(p)SW](•+) and their dissociation pathways. Our results suggest that the dissociation reactions of these two peptide radical cations are more efficient than their tautomerizations, as supported by Rice-Ramsperger-Kassel-Marcus (RRKM) modeling. We also propose that the loss of H3PO4 from both of these two radical cationic tautomers is preferentially charge-driven, similar to the analogous dissociations of even-electron protonated peptides. The distonic radical cationic character of [G(•)(p)SW](+) results in its charge being more mobile, thereby favoring charge-driven loss of H3PO4; in contrast, radical-driven pathways are more competitive during the CID of [G(p)SW](•+).
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Affiliation(s)
- Quan Quan
- Department of Chemistry, University of Hong Kong, Hong Kong, China
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Kong RPW, Quan Q, Hao Q, Lai CK, Siu CK, Chu IK. Formation and dissociation of phosphorylated peptide radical cations. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2012; 23:2094-2101. [PMID: 22968907 PMCID: PMC3514703 DOI: 10.1007/s13361-012-0479-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/03/2012] [Revised: 08/14/2012] [Accepted: 08/14/2012] [Indexed: 06/01/2023]
Abstract
In this study, we generated phosphoserine- and phosphothreonine-containing peptide radical cations through low-energy collision-induced dissociation (CID) of the ternary metal-ligand phosphorylated peptide complexes [Cu(II)(terpy)(p)M](·2+) and [Co(III)(salen)(p)M](·+) [(p)M: phosphorylated angiotensin III derivative; terpy: 2,2':6',2''-terpyridine; salen: N,N'-ethylenebis(salicylideneiminato)]. Subsequent CID of the phosphorylated peptide radical cations ((p)M(·+)) revealed fascinating gas-phase radical chemistry, yielding (1) charge-directed b- and y-type product ions, (2) radical-driven product ions through cleavages of peptide backbones and side chains, and (3) different degrees of formation of [M - H(3)PO(4)](·+) species through phosphate ester bond cleavage. The CID spectra of the (p)M(·+) species and their non-phosphorylated analogues featured fragment ions of similar sequence, suggesting that the phosphoryl group did not play a significant role in the fragmentation of the peptide backbone or side chain. The extent of neutral H(3)PO(4) loss was influenced by the peptide sequence and the initial sites of the charge and radical. A preliminary density functional theory study, at the B3LYP 6-311++G(d,p) level of theory, of the neutral loss of H(3)PO(4) from a prototypical model--N-acetylphosphorylserine methylamide--revealed several factors governing the elimination of neutral phosphoryl groups through charge- and radical-induced mechanisms.
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Affiliation(s)
- Ricky P. W. Kong
- Department of Chemistry, University of Hong Kong, Hong Kong, China
| | - Quan Quan
- Department of Chemistry, University of Hong Kong, Hong Kong, China
| | - Qiang Hao
- Department of Biology and Chemistry, City University of Hong Kong, Hong Kong, China
| | - Cheuk-Kuen Lai
- Department of Chemistry, University of Hong Kong, Hong Kong, China
| | - Chi-Kit Siu
- Department of Biology and Chemistry, City University of Hong Kong, Hong Kong, China
| | - Ivan K. Chu
- Department of Chemistry, University of Hong Kong, Hong Kong, China
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Sarma BK, Kodadek T. Submonomer synthesis of a hybrid peptoid-azapeptoid library. ACS COMBINATORIAL SCIENCE 2012; 14:558-64. [PMID: 22958123 DOI: 10.1021/co3000852] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We recently reported efficient conditions for the synthesis of N-azapeptoid libraries via the typical submonomer strategy of peptoid synthesis but that substitutes N-acyl hydrazides for primary amines as submonomers. Unfortunately, this approach is not applicable to the synthesis of mixed azapeptoid-peptoid libraries. When an oligomer containing an N-terminal side chain derived from an acyl hydrazide is bromoacetylated and treated with a primary amine, a chain-terminating intramolecular ring-closure to form an oxadiazinone competes with the desired displacement of the bromide by the amine. Here we overcome this limitation and demonstrate that a hybrid peptoid-azapeptoid library derived from primary amines, acyl hydrazides, carbazates, and semicarbazides can be made efficiently using standard peptoid submonomer chemistry. We find that the unwanted, chain-terminating cyclization reaction is competitive with chain extension only when aryl acyl hydrazides are present. Alkyl or heteroaromatic acyl hydrazides do not cyclize under the conditions used for peptoid-azapeptoid synthesis. We also find that carbazates and semicarbazides work well for chain extension. Using primary amines, acyl hydrazides, carbazates, and semicarbazides as submonomers, a high-quality one bead one compound library of tetramers suitable for screening against protein targets was made by split and pool synthesis.
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Affiliation(s)
- Bani Kanta Sarma
- Departments of Chemistry and Cancer Biology, The Scripps Research Institute, Scripps Florida, 130
Scripps Way, #3A2, Jupiter, Florida 33458, United States
| | - Thomas Kodadek
- Departments of Chemistry and Cancer Biology, The Scripps Research Institute, Scripps Florida, 130
Scripps Way, #3A2, Jupiter, Florida 33458, United States
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Abstract
The use of acyl hydrazides as peptoid sub-monomers is investigated. We demonstrate here that azapeptoids derived entirely from acyl hydrazides can be made conveniently and efficiently using standard peptoid sub-monomer chemistry. Structural studies reveal that the main chain amide bond in these molecules predominantly adopts a trans conformation. A high-quality one bead one compound library of tetramers was made by split and pool synthesis and we found that the identity of the molecule on a single bead could be determined by tandem MALDI mass spectrometry.
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Affiliation(s)
- Bani Kanta Sarma
- Departments of Chemistry and Cancer Biology, Scripps Research Institute, Scripps Florida, 130 Scripps Way, #3A2, Jupiter, FL 33458
| | - Muhammed Yousufuddin
- Center for Nanostructured Materials University of Texas at Arlington, Arlington, TX 76019
| | - Thomas Kodadek
- Departments of Chemistry and Cancer Biology, Scripps Research Institute, Scripps Florida, 130 Scripps Way, #3A2, Jupiter, FL 33458
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Thakkar A, Cohen AS, Connolly MD, Zuckermann RN, Pei D. High-throughput sequencing of peptoids and peptide-peptoid hybrids by partial edman degradation and mass spectrometry. ACTA ACUST UNITED AC 2010; 11:294-302. [PMID: 19154119 DOI: 10.1021/cc8001734] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
A method for the rapid sequence determination of peptoids [oligo(N-substituted glycines)] and peptide-peptoid hybrids selected from one-bead-one-compound combinatorial libraries has been developed. In this method, beads carrying unique peptoid (or peptide-peptoid) sequences were subjected to multiple cycles of partial Edman degradation (PED) by treatment with a 1:3 (mol/mol) mixture of phenyl isothiocyanate (PITC) and 9-fluorenylmethyl chloroformate (Fmoc-Cl) to generate a series of N-terminal truncation products for each resin-bound peptoid. After PED, the Fmoc group was removed from the N-terminus and any reacted side chains via piperidine treatment. The resulting mixture of the full-length peptoid and its truncation products was analyzed by matrix-assisted laser desorption ionization (MALDI) mass spectrometry, to reveal the sequence of the full-length peptoid. With a slight modification, the method was also effective in the sequence determination of peptide-peptoid hybrids. This rapid, high-throughput, sensitive, and inexpensive sequencing method should greatly expand the utility of combinatorial peptoid libraries in biomedical and materials research.
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Affiliation(s)
- Amit Thakkar
- Department of Chemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, USA
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Culf AS, Ouellette RJ. Solid-phase synthesis of N-substituted glycine oligomers (alpha-peptoids) and derivatives. Molecules 2010; 15:5282-335. [PMID: 20714299 PMCID: PMC6257730 DOI: 10.3390/molecules15085282] [Citation(s) in RCA: 139] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2010] [Revised: 07/14/2010] [Accepted: 08/02/2010] [Indexed: 12/02/2022] Open
Abstract
Peptoids (N-substituted polyglycines and extended peptoids with variant backbone amino-acid monomer units) are oligomeric synthetic polymers that are becoming a valuable molecular tool in the biosciences. Of particular interest are their applications to the exploration of peptoid secondary structures and drug design. Major advantages of peptoids as research and pharmaceutical tools include the ease and economy of synthesis, highly variable backbone and side-chain chemistry possibilities. At the same time, peptoids have been demonstrated as highly active in biological systems while resistant to proteolytic decay. This review with 227 references considers the solid-phase synthetic aspects of peptoid preparation and utilization up to 2010 from the instigation, by R. N. Zuckermann et al., of peptoid chemistry in 1992.
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Affiliation(s)
- Adrian S Culf
- Atlantic Cancer Research Institute, Moncton, NB, Canada.
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Abstract
Peptidomimetic oligomers and foldamers have received considerable attention for over a decade, with beta-peptides and the so-called peptoids (N-alkylglycine oligomers) representing prominent examples of such architectures. Lately, hybrid or mixed backbones consisting of both alpha- and beta-amino acids (alpha/beta-peptides) have been investigated in some detail as well. The present Minireview is a survey of the literature concerning hybrid structures of alpha-amino acids and peptoids, including beta-peptoids (N-alkyl-beta-alanine oligomers), and is intended to give an overview of this area of research within the field of peptidomimetic science.
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Affiliation(s)
- Christian A Olsen
- Department of Medicinal Chemistry, University of Copenhagen, Universitetsparken 2, Copenhagen, 2100 Denmark.
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17
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Paulick MG, Hart KM, Brinner KM, Tjandra M, Charych DH, Zuckermann RN. Cleavable Hydrophilic Linker for One-Bead-One-Compound Sequencing of Oligomer Libraries by Tandem Mass Spectrometry. ACTA ACUST UNITED AC 2006; 8:417-26. [PMID: 16677012 DOI: 10.1021/cc0501460] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We have developed a method for the rapid and unambiguous identification of sequences of hit compounds from one-bead-one-compound combinatorial libraries of peptide and peptoid ligands. The approach uses a cleavable linker that is hydrophilic to help reduce nonspecific binding to biological samples and allows for the attachment of a halogen tag, which greatly facilitates post-screening sequencing by tandem mass spectrometry (MS/MS). The linker is based on a tartaric acid unit, which, upon cleavage from resin, generates a C-terminal aldehyde. This aldehyde can then be derivatized with a bromine-containing amino-oxy compound that serves as an isotope tag for subsequent MS/MS analysis of y-ion fragments. We have applied this linker and method to the syntheses of a number of peptoids that vary in sequence and length and have also demonstrated single-bead sequencing of a peptoid pentamer. The linker is also shown to have very low levels of nonspecific binding to proteins.
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Gronert S, Li KH, Horiuchi M. Manipulating the fragmentation patterns of phosphopeptides via gas-phase boron derivatization: determining phosphorylation sites in peptides with multiple serines. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2005; 16:1905-14. [PMID: 16242953 DOI: 10.1016/j.jasms.2005.07.018] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2005] [Revised: 07/12/2005] [Accepted: 07/14/2005] [Indexed: 05/05/2023]
Abstract
Trivalent boron species readily react with protonated phosphopeptides to give addition products with the loss of boron ligands. In the present study, trimethoxyborane (TMB), diisopropoxymethylborane (DIPM), and diethylmethoxyborane (DEMB) were allowed to react with four phosphopeptides, VsSF, LSsF, LsGASA, and VSGAsA (lower-case s indicates phosphoserine). Each of the phosphopeptides contains one serine that is phosphorylated and one that is not. Under collision-activated dissociation (CAD) conditions, the boron-derivatized peptides give fragmentation patterns that differ significantly from that of the protonated phosphopeptide. The patterns vary, depending on the number of labile (i.e., alkoxy) ligands on the boron. In general, boron derivatization increases the yield of phosphate-containing sequence ions, but dramatic effects are only seen with certain reagent/peptide combinations. However, the suite of reagents provides a means of altering and increasing the information content of phosphopeptide CAD spectra.
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Affiliation(s)
- Scott Gronert
- Department of Chemistry and Biochemistry, San Francisco State University, CA 94132, USA.
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19
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Current awareness. JOURNAL OF MASS SPECTROMETRY : JMS 2002; 37:345-356. [PMID: 11921378 DOI: 10.1002/jms.250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
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