1
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Roper NJ, Campbell ADG, Waddell PG, Brown AK, Ermanis K, Armstrong RJ. A stereodivergent multicomponent approach for the synthesis of C-N atropisomeric peptide analogues. Chem Sci 2024:d4sc04700a. [PMID: 39323517 PMCID: PMC11418089 DOI: 10.1039/d4sc04700a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2024] [Accepted: 09/15/2024] [Indexed: 09/27/2024] Open
Abstract
A four-component Ugi reaction is described for the stereoselective synthesis of novel C-N atropisomeric peptide analogues. Using this approach, a combination of simple, readily available starting materials (ortho-substituted anilines, aldehydes, carboxylic acids and isocyanides) could be combined to access complex products possessing both central and axial chirality in up to 92% yield and >95 : 5 d.r. Variation of the reaction temperature enabled the development of stereodivergent reactions capable of selectively targeting either diastereoisomer of a desired product from a single set of starting materials with high levels of stereocontrol. Detailed experimental and computational studies have been performed to probe the reaction mechanism and stereochemical outcome of these reactions. Preliminary studies show that novel atropisomeric scaffolds prepared using this method display inhibitory activity against M. tuberculosis with a significant difference in activity observed between different atropisomers.
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Affiliation(s)
- Natalie J Roper
- School of Natural and Environmental Sciences, Newcastle University Newcastle Upon Tyne NE1 7RU UK
| | - Aaron D G Campbell
- School of Natural and Environmental Sciences, Newcastle University Newcastle Upon Tyne NE1 7RU UK
| | - Paul G Waddell
- School of Natural and Environmental Sciences, Newcastle University Newcastle Upon Tyne NE1 7RU UK
| | - Alistair K Brown
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University Newcastle Upon Tyne NE2 4HH UK
| | - Kristaps Ermanis
- School of Chemistry, University of Nottingham, University Park Nottingham NG7 2RD UK
| | - Roly J Armstrong
- School of Natural and Environmental Sciences, Newcastle University Newcastle Upon Tyne NE1 7RU UK
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2
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Ansari S, Knipe PC. Atropisomeric Foldamers. Chempluschem 2024; 89:e202400218. [PMID: 38683695 DOI: 10.1002/cplu.202400218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 04/29/2024] [Accepted: 04/29/2024] [Indexed: 05/02/2024]
Abstract
This concept article explores the emerging role of atropisomerism in foldamer chemistry, a field focussed on oligomers that adopt well-defined conformations through non-covalent interactions. Atropisomerism introduces a novel dimension to foldamer design by restricting rotational freedom around single bonds to dictate molecular shape with precision. Despite the prevalence of atropisomeric bonds in organic synthesis, their application within foldamers remains underexplored. Here, we discuss key developments in both backbone and sidechain atropisomerism, and suggest future directions for atropisomeric foldamers in the context of a recent surge in atropselective synthetic methods. We propose that judicious use of atropisomerism may serve as a transformative tool in the construction of shape-defined macromolecules.
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Affiliation(s)
- Saima Ansari
- School of Chemistry and Chemical Engineering, Queen's University Belfast David Keir Building, Stranmillis Road, Belfast, BT9 5AG, UK
| | - Peter C Knipe
- School of Chemistry and Chemical Engineering, Queen's University Belfast David Keir Building, Stranmillis Road, Belfast, BT9 5AG, UK
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3
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Jiang TY, Ke YT, Wu YJ, Yao QJ, Shi BF. Pd(II)-Catalyzed atroposelective C-H olefination: synthesis of enantioenriched N-aryl peptoid atropisomers. Chem Commun (Camb) 2023; 59:13518-13521. [PMID: 37886838 DOI: 10.1039/d3cc04425d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2023]
Abstract
Herein, we reported the synthesis of enantioenriched N-aryl peptoid atropisomers via Pd(II)-catalyzed atroposelective C-H olefination using the easily accessible L-pyroglutamic acid (L-pGlu-OH) as the chiral ligand. A series of optically active N-aryl peptoid atropisomers were obtained in synthetically useful yields with high enantioselectivities.
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Affiliation(s)
- Tian-Yu Jiang
- Department of Chemistry, Zhejiang University, Hangzhou, Zhejiang, 310027, China.
| | - Yi-Ting Ke
- Department of Chemistry, Zhejiang University, Hangzhou, Zhejiang, 310027, China.
| | - Yong-Jie Wu
- Department of Chemistry, Zhejiang University, Hangzhou, Zhejiang, 310027, China.
| | - Qi-Jun Yao
- Department of Chemistry, Zhejiang University, Hangzhou, Zhejiang, 310027, China.
| | - Bing-Feng Shi
- Department of Chemistry, Zhejiang University, Hangzhou, Zhejiang, 310027, China.
- School of Biotechnology and Health Sciences, Wuyi University, Jiangmen, Guangdong 529020, China
- Green Catalysis Center, College of Chemistry, Zhengzhou University, Zhengzhou 450001, China
- College of Biological, Chemical Science and Engineering, Jiaxing University, Jiaxing 314001, China
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4
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Eastwood JRB, Weisberg EI, Katz D, Zuckermann RN, Kirshenbaum K. Guidelines for designing peptoid structures: Insights from the
Peptoid Data Bank. Pept Sci (Hoboken) 2023. [DOI: 10.1002/pep2.24307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/11/2023]
Affiliation(s)
| | | | - Dana Katz
- Department of Chemistry New York University New York New York USA
| | | | - Kent Kirshenbaum
- Department of Chemistry New York University New York New York USA
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5
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Purushotham M, Paul B, Govindachar DM, Singh AK, Periyasamy G, Peter SC. Ortho-halogen effects: n→π* interactions, halogen bonding, and deciphering chiral attributes in N-aryl glycine peptoid foldamers. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.133276] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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6
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Eastwood JRB, Jiang L, Bonneau R, Kirshenbaum K, Renfrew PD. Evaluating the Conformations and Dynamics of Peptoid Macrocycles. J Phys Chem B 2022; 126:5161-5174. [PMID: 35820178 DOI: 10.1021/acs.jpcb.2c01669] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Peptoid macrocycles are versatile and chemically diverse peptidomimetic oligomers. However, the conformations and dynamics of these macrocycles have not been evaluated comprehensively and require extensive further investigation. Recent studies indicate that two degrees of freedom, and four distinct conformations, adequately describe the behavior of each monomer backbone unit in most peptoid oligomers. On the basis of this insight, we conducted molecular dynamics simulations of model macrocycles using an exhaustive set of idealized possible starting conformations. Simulations of various sizes of peptoid macrocycles yielded a limited set of populated conformations. In addition to reproducing all relevant experimentally determined conformations, the simulations accurately predicted a cyclo-octamer conformation for which we now present the first experimental observation. Sets of three adjacent dihedral angles (ϕi, ψi, ωi+1) exhibited correlated crankshaft motions over the course of simulation for peptoid macrocycles of six residues and larger. These correlated motions may occur in the form of an inversion of one amide bond and the concerted rotation of the preceding ϕ and ψ angles to their mirror-image conformation, a variation on "crankshaft flip" motions studied in polymers and peptides. The energy landscape of these peptoid macrocycles can be described as a network of conformations interconnected by transformations of individual crankshaft flips. For macrocycles of up to eight residues, our mapping of the landscape is essentially complete.
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Affiliation(s)
- James R B Eastwood
- Department of Chemistry, New York University, New York, New York 10003, United States
| | - Linhai Jiang
- Department of Chemistry, New York University, New York, New York 10003, United States
| | - Richard Bonneau
- Center for Data Science, New York University, New York, New York 10011, United States.,Center for Computational Biology, Flatiron Institute, New York, New York 10010 United States
| | - Kent Kirshenbaum
- Department of Chemistry, New York University, New York, New York 10003, United States
| | - P Douglas Renfrew
- Center for Computational Biology, Flatiron Institute, New York, New York 10010 United States
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7
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Jia ZS, Wu YJ, Yao QJ, Xu XT, Zhang K, Shi BF. Pd(II)-Catalyzed Atroposelective C-H Allylation: Synthesis of Enantioenriched N-Aryl Peptoid Atropisomers. Org Lett 2021; 24:304-308. [PMID: 34964649 DOI: 10.1021/acs.orglett.1c03967] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A Pd-catalyzed atroposelective C-H allylation with 1,1-disubstituted alkenes was developed for the synthesis of enantioenriched N-aryl peptoid atropisomers via β-H elimination using commercially available and inexpensive L-pGlu-OH as a chiral ligand. Exclusive allylic selectivity was achieved. Additionally, a series of enantioenriched N-aryl peptoid atropisomers were obtained in synthetically useful yields with excellent enantioselectivities (up to 90% yield and 97% ee).
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Affiliation(s)
- Zhen-Sheng Jia
- School of Biotechnology and Health Sciences, Wuyi University, Jiangmen, Guangdong 529020, China
| | - Yong-Jie Wu
- Department of Chemistry, Zhejiang University, Hangzhou, Zhejiang 310027, China
| | - Qi-Jun Yao
- Department of Chemistry, Zhejiang University, Hangzhou, Zhejiang 310027, China
| | - Xue-Tao Xu
- School of Biotechnology and Health Sciences, Wuyi University, Jiangmen, Guangdong 529020, China
| | - Kun Zhang
- School of Biotechnology and Health Sciences, Wuyi University, Jiangmen, Guangdong 529020, China
| | - Bing-Feng Shi
- Department of Chemistry, Zhejiang University, Hangzhou, Zhejiang 310027, China.,Green Catalysis Center, College of Chemistry, Zhengzhou University, Zhengzhou, Henan 450001, China.,School of Chemistry and Chemical Engineering, Henan Normal University, Xinxiang, Henan 453007, China
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8
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Yang B, Yang J, Zhang J. Synthesis of Axially Chiral Anilides Enabled by a Palladium/
Ming‐Phos‐Catalyzed
Desymmetric Sonogashira Reaction. CHINESE J CHEM 2021. [DOI: 10.1002/cjoc.202100621] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Bin Yang
- Department of Chemistry, Fudan University 2005 Songhu Road Shanghai 200438 China
| | - Junfeng Yang
- Department of Chemistry, Fudan University 2005 Songhu Road Shanghai 200438 China
| | - Junliang Zhang
- Department of Chemistry, Fudan University 2005 Songhu Road Shanghai 200438 China
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9
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Wu YJ, Xie PP, Zhou G, Yao QJ, Hong X, Shi BF. Atroposelective synthesis of N-aryl peptoid atropisomers via a palladium(ii)-catalyzed asymmetric C-H alkynylation strategy. Chem Sci 2021; 12:9391-9397. [PMID: 34349912 PMCID: PMC8278962 DOI: 10.1039/d1sc01130h] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 06/01/2021] [Indexed: 12/15/2022] Open
Abstract
The introduction of chirality into peptoids is an important strategy to determine a discrete and robust secondary structure. However, the lack of an efficient strategy for the synthesis of structurally diverse chiral peptoids has hampered the studies. Herein, we report the efficient synthesis of a wide variety of N-aryl peptoid atropisomers in good yields with excellent enantioselectivities (up to 99% yield and 99% ee) by palladium-catalyzed asymmetric C–H alkynylation. The inexpensive and commercially available l-pyroglutamic acid was used as an efficient chiral ligand. The exceptional compatibility of the C–H alkynylation with various peptoid oligomers renders this procedure valuable for peptoid modifications. Computational studies suggested that the amino acid ligand distortion controls the enantioselectivity in the Pd/l-pGlu-catalyzed C–H bond activation step. The introduction of chirality into peptoids is an important strategy to determine a discrete and robust secondary structure.![]()
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Affiliation(s)
- Yong-Jie Wu
- Center of Chemistry for Frontier Technologies, Department of Chemistry, Zhejiang University Hangzhou 310027 China
| | - Pei-Pei Xie
- Center of Chemistry for Frontier Technologies, Department of Chemistry, Zhejiang University Hangzhou 310027 China
| | - Gang Zhou
- Center of Chemistry for Frontier Technologies, Department of Chemistry, Zhejiang University Hangzhou 310027 China
| | - Qi-Jun Yao
- Center of Chemistry for Frontier Technologies, Department of Chemistry, Zhejiang University Hangzhou 310027 China
| | - Xin Hong
- Center of Chemistry for Frontier Technologies, Department of Chemistry, Zhejiang University Hangzhou 310027 China
| | - Bing-Feng Shi
- Center of Chemistry for Frontier Technologies, Department of Chemistry, Zhejiang University Hangzhou 310027 China .,Green Catalysis Center, and College of Chemistry, Zhengzhou University Zhengzhou 450001 China
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10
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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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11
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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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12
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Palai BB, Sharma NK. N-Arylated peptide: troponyl residue influences the structure and conformation of N-troponylated-(di/tri)-peptides. CrystEngComm 2021. [DOI: 10.1039/d0ce01386b] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
N-arylated peptides as peptoids influence the structural and conformational changes of small peptides that lead to unique foldamers, even in di-/tri-peptides.
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Affiliation(s)
- Bibhuti Bhusana Palai
- School of Chemical Sciences
- National Institute of Science Education and Research (NISER)-Bhubaneswar
- Jatni Campus
- Bhubaneswar
- India
| | - Nagendra K. Sharma
- School of Chemical Sciences
- National Institute of Science Education and Research (NISER)-Bhubaneswar
- Jatni Campus
- Bhubaneswar
- India
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13
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Xuan S, Zuckermann RN. Engineering the atomic structure of sequence-defined peptoid polymers and their assemblies. POLYMER 2020. [DOI: 10.1016/j.polymer.2020.122691] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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14
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Li D, Wang S, Ge S, Dong S, Feng X. Asymmetric Synthesis of Axially Chiral Anilides via Organocatalytic Atroposelective N-Acylation. Org Lett 2020; 22:5331-5336. [DOI: 10.1021/acs.orglett.0c01581] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Dawei Li
- Key Laboratory of Green Chemistry & Technology, Ministry of Education, College of Chemistry, Sichuan University, Chengdu 610064, China
| | - Sijing Wang
- Key Laboratory of Green Chemistry & Technology, Ministry of Education, College of Chemistry, Sichuan University, Chengdu 610064, China
| | - Shulin Ge
- Key Laboratory of Green Chemistry & Technology, Ministry of Education, College of Chemistry, Sichuan University, Chengdu 610064, China
| | - Shunxi Dong
- Key Laboratory of Green Chemistry & Technology, Ministry of Education, College of Chemistry, Sichuan University, Chengdu 610064, China
| | - Xiaoming Feng
- Key Laboratory of Green Chemistry & Technology, Ministry of Education, College of Chemistry, Sichuan University, Chengdu 610064, China
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15
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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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16
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D'Amato A, Pierri G, Tedesco C, Della Sala G, Izzo I, Costabile C, De Riccardis F. Reverse Turn and Loop Secondary Structures in Stereodefined Cyclic Peptoid Scaffolds. J Org Chem 2019; 84:10911-10928. [PMID: 31339718 DOI: 10.1021/acs.joc.9b01509] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Controlling the network of intramolecular interactions encoded by Nα-chiral side chains and the equilibria between cis- and trans-amide junctions in cyclic peptoid architectures constitutes a significant challenge for the construction of stable reverse turn and loop structures. In this contribution, we reveal, with the support of NMR spectroscopy, single-crystal X-ray crystallography and density functional theory calculations, the relevant noncovalent interactions stabilizing tri-, tetra-, hexa-, and octameric cyclic peptoids (as free hosts and host-guest complexes) with strategically positioned N-(S)-(1-phenylethyl)/N-benzyl side chains, and how these interactions influence the backbone topological order. With the help of theoretical models and spectroscopic/diffractometric studies, we disclose new γ-/β-turn and loop structures present in α-peptoid-based macrocycles and classify them according ϕ, ψ, and ω torsion angles. In our endeavor to characterize emergent secondary structures, we solved the solid-state structure of the largest metallated cyclic peptoid ever reported, characterized by an unprecedented alternated cis/trans amide bond linkage. Overall, our results indicate that molecules endowed with different elements of asymmetry (central and conformational) provide new architectural elements of facile atroposelective construction and broad conformational stability as the minimalist scaffold for novel stereodefined peptidomimetic foldamers and topologically biased libraries necessary for future application of peptoids in all fields of science.
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Affiliation(s)
- Assunta D'Amato
- Department of Chemistry and Biology "A. Zambelli" , University of Salerno , Via Giovanni Paolo II, 132 , Fisciano , Salerno 84084 Italy
| | - Giovanni Pierri
- Department of Chemistry and Biology "A. Zambelli" , University of Salerno , Via Giovanni Paolo II, 132 , Fisciano , Salerno 84084 Italy
| | - Consiglia Tedesco
- Department of Chemistry and Biology "A. Zambelli" , University of Salerno , Via Giovanni Paolo II, 132 , Fisciano , Salerno 84084 Italy
| | - Giorgio Della Sala
- Department of Chemistry and Biology "A. Zambelli" , University of Salerno , Via Giovanni Paolo II, 132 , Fisciano , Salerno 84084 Italy
| | - Irene Izzo
- Department of Chemistry and Biology "A. Zambelli" , University of Salerno , Via Giovanni Paolo II, 132 , Fisciano , Salerno 84084 Italy
| | - Chiara Costabile
- Department of Chemistry and Biology "A. Zambelli" , University of Salerno , Via Giovanni Paolo II, 132 , Fisciano , Salerno 84084 Italy
| | - Francesco De Riccardis
- Department of Chemistry and Biology "A. Zambelli" , University of Salerno , Via Giovanni Paolo II, 132 , Fisciano , Salerno 84084 Italy
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17
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Spencer RK, Butterfoss GL, Edison JR, Eastwood JR, Whitelam S, Kirshenbaum K, Zuckermann RN. Stereochemistry of polypeptoid chain configurations. Biopolymers 2019; 110:e23266. [DOI: 10.1002/bip.23266] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Revised: 01/31/2019] [Accepted: 02/05/2019] [Indexed: 12/13/2022]
Affiliation(s)
- Ryan K. Spencer
- Department of Chemistry University of California Irvine California
- Department of Chemical Engineering & Materials Science University of California Irvine California
| | - Glenn L. Butterfoss
- Center for Genomics and Systems Biology New York University Abu Dhabi Abu Dhabi United Arab Emirates
| | - John R. Edison
- Martin A Fisher School of Physics Brandeis University Waltham Massachusetts
- Molecular Foundry Lawrence Berkeley National Laboratory Berkeley California
| | | | - Stephen Whitelam
- Molecular Foundry Lawrence Berkeley National Laboratory Berkeley California
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18
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Li SL, Yang C, Wu Q, Zheng HL, Li X, Cheng JP. Atroposelective Catalytic Asymmetric Allylic Alkylation Reaction for Axially Chiral Anilides with Achiral Morita-Baylis-Hillman Carbonates. J Am Chem Soc 2018; 140:12836-12843. [PMID: 30226765 DOI: 10.1021/jacs.8b06014] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
A highly efficient method to access axially chiral anilides through asymmetric allylic alkylation reaction with achiral Morita-Baylis-Hillman carbonates by using a biscinchona alkaloid catalyst was reported. Through the atroposelective approach, a broad range of axially chiral anilide products with different acyl groups, such as substituted phenyl, naphthyl, alkyl, enyl, styryl, and benzyl, were generated with very good yields, moderate to excellent cis: trans ratios, and good to excellent enantioselectivities. The reaction can be scaled up, and the synthetic utility of axially chiral anilides was proved by transformations. Moreover, the linear free energy relationship analysis was introduced to investigate the reaction.
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Affiliation(s)
- Shou-Lei Li
- State Key Laboratory of Elemento-Organic Chemistry, Collaborative Innovation Center of Chemical Science and Engineering, College of Chemistry , Nankai University , Tianjin 300071 , P. R. China
| | - Chen Yang
- State Key Laboratory of Elemento-Organic Chemistry, Collaborative Innovation Center of Chemical Science and Engineering, College of Chemistry , Nankai University , Tianjin 300071 , P. R. China
| | - Quan Wu
- State Key Laboratory of Elemento-Organic Chemistry, Collaborative Innovation Center of Chemical Science and Engineering, College of Chemistry , Nankai University , Tianjin 300071 , P. R. China
| | - Han-Liang Zheng
- State Key Laboratory of Elemento-Organic Chemistry, Collaborative Innovation Center of Chemical Science and Engineering, College of Chemistry , Nankai University , Tianjin 300071 , P. R. China
| | - Xin Li
- State Key Laboratory of Elemento-Organic Chemistry, Collaborative Innovation Center of Chemical Science and Engineering, College of Chemistry , Nankai University , Tianjin 300071 , P. R. China
| | - Jin-Pei Cheng
- State Key Laboratory of Elemento-Organic Chemistry, Collaborative Innovation Center of Chemical Science and Engineering, College of Chemistry , Nankai University , Tianjin 300071 , P. R. China
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19
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D'Amato A, Schettini R, Della Sala G, Costabile C, Tedesco C, Izzo I, De Riccardis F. Conformational isomerism in cyclic peptoids and its specification. Org Biomol Chem 2017; 15:9932-9942. [DOI: 10.1039/c7ob02643a] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Conformational chirality is an emerging and neglected property of rigid cyclic peptoids determining structural, catalytic, and biological properties. The present contribution analyzes its impact and sets the configurational rules to define it.
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Affiliation(s)
- A. D'Amato
- Department of Chemistry and Biology “A. Zambelli”
- University of Salerno
- Fisciano
- Italy
| | - R. Schettini
- Department of Chemistry and Biology “A. Zambelli”
- University of Salerno
- Fisciano
- Italy
| | - G. Della Sala
- Department of Chemistry and Biology “A. Zambelli”
- University of Salerno
- Fisciano
- Italy
| | - C. Costabile
- Department of Chemistry and Biology “A. Zambelli”
- University of Salerno
- Fisciano
- Italy
| | - C. Tedesco
- Department of Chemistry and Biology “A. Zambelli”
- University of Salerno
- Fisciano
- Italy
| | - I. Izzo
- Department of Chemistry and Biology “A. Zambelli”
- University of Salerno
- Fisciano
- Italy
| | - F. De Riccardis
- Department of Chemistry and Biology “A. Zambelli”
- University of Salerno
- Fisciano
- Italy
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20
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Baskin M, Maayan G. A rationally designed metal-binding helical peptoid for selective recognition processes. Chem Sci 2016; 7:2809-2820. [PMID: 28660058 PMCID: PMC5477017 DOI: 10.1039/c5sc04358a] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2015] [Accepted: 01/08/2016] [Indexed: 12/13/2022] Open
Abstract
A helical peptoid bearing two distinct metal binding ligands at positions i and i+3 (Helix HQT i+3) enables the selective recognition of one or two metal ions depending on its environment, thus mimicking the unique recognition abilities of natural biopolymers.
Metal-binding biopolymers play a significant role in processes, such as regulation, recognition and catalysis, due to their high affinity towards specific metal ions, which they bind selectively from the cellular pool. Many enzymes can bind two or more metal ions, each at a specific binding site, to enable efficient cooperative function. Imitating these recognition abilities might lead to the production of biomimetic materials such as unique chelators and catalysts. Herein, we report a rationally designed helical peptoid bearing two distinct metal binding ligands at positions i and i + 3 (Helix HQT i + 3), which enables the selective recognition of one or two metal ions depending on its environment. Using various spectroscopic techniques, we describe (1) the selective intramolecular binding of Cu2+ and its extraction from a mixture of neighboring metal ions in high concentrations, and (2) the selective intermolecular binding of two different metal ions, including the pair Cu2+ and Zn2+, one at each binding site, for the generation of hetero-bimetallic peptoid duplexes. Thorough analysis and comparison between the spectroscopic data and association constants of the metal complexes formed by Helix HQT i + 3 and those formed by non-helical peptoids, or helical peptoids in which the two metal binding ligands are not pre-organized, revealed that the unique recognition processes performed by Helix HQT i + 3 are controlled by both the sequence and the structure of the peptoid.
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Affiliation(s)
- Maria Baskin
- Schulich Faculty of Chemistry , Technion-Israel Institute of Technology , Technion City , Hailfa 32000 , Israel .
| | - Galia Maayan
- Schulich Faculty of Chemistry , Technion-Israel Institute of Technology , Technion City , Hailfa 32000 , Israel .
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21
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Mazzanti A, Chiarucci M, Prati L, Bentley KW, Wolf C. Computational and DNMR Analysis of the Conformational Isomers and Stereodynamics of Secondary 2,2′-Bisanilides. J Org Chem 2015; 81:89-99. [DOI: 10.1021/acs.joc.5b02330] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Andrea Mazzanti
- Department
of Industrial Chemistry “Toso Montanari”, University of Bologna, Viale Risorgimento 4, I-40136 Bologna, Italy
| | - Michel Chiarucci
- Department
of Industrial Chemistry “Toso Montanari”, University of Bologna, Viale Risorgimento 4, I-40136 Bologna, Italy
| | - Luca Prati
- Department
of Industrial Chemistry “Toso Montanari”, University of Bologna, Viale Risorgimento 4, I-40136 Bologna, Italy
| | - Keith W. Bentley
- Department
of Chemistry, Georgetown University, Washington, DC 20057, United States
| | - Christian Wolf
- Department
of Chemistry, Georgetown University, Washington, DC 20057, United States
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22
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Knight AS, Zhou EY, Francis MB, Zuckermann RN. Sequence Programmable Peptoid Polymers for Diverse Materials Applications. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2015; 27:5665-5691. [PMID: 25855478 DOI: 10.1002/adma.201500275] [Citation(s) in RCA: 170] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2015] [Revised: 02/13/2015] [Indexed: 06/04/2023]
Abstract
Polymer sequence programmability is required for the diverse structures and complex properties that are achieved by native biological polymers, but efforts towards controlling the sequence of synthetic polymers are, by comparison, still in their infancy. Traditional polymers provide robust and chemically diverse materials, but synthetic control over their monomer sequences is limited. The modular and step-wise synthesis of peptoid polymers, on the other hand, allows for precise control over the monomer sequences, affording opportunities for these chains to fold into well-defined nanostructures. Hundreds of different side chains have been incorporated into peptoid polymers using efficient reaction chemistry, allowing for a seemingly infinite variety of possible synthetically accessible polymer sequences. Combinatorial discovery techniques have allowed the identification of functional polymers within large libraries of peptoids, and newly developed theoretical modeling tools specifically adapted for peptoids enable the future design of polymers with desired functions. Work towards controlling the three-dimensional structure of peptoids, from the conformation of the amide bond to the formation of protein-like tertiary structure, has and will continue to enable the construction of tunable and innovative nanomaterials that bridge the gap between natural and synthetic polymers.
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Affiliation(s)
- Abigail S Knight
- UC Berkeley Chemistry Department, Latimer Hall, Berkeley, CA, 94720, USA
| | - Effie Y Zhou
- UC Berkeley Chemistry Department, Latimer Hall, Berkeley, CA, 94720, USA
| | - Matthew B Francis
- UC Berkeley Chemistry Department, Latimer Hall, Berkeley, CA, 94720, USA
- The Molecular Foundry Lawrence Berkeley National Lab, 1 Cyclotron Road, Berkeley, CA, 94720, USA
| | - Ronald N Zuckermann
- The Molecular Foundry Lawrence Berkeley National Lab, 1 Cyclotron Road, Berkeley, CA, 94720, USA
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23
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Lindamulage De Silva A, Risso V, Jean M, Giorgi M, Monnier V, Naubron JV, Vanthuyne N, Farran D, Roussel C. A forgotten chiral spiro compound revisited: 3,3'-dimethyl-3H,3'H-2,2'-spirobi[[1,3]benzothiazole]. Chirality 2015; 27:716-21. [PMID: 26415851 DOI: 10.1002/chir.22492] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2015] [Revised: 07/06/2015] [Accepted: 07/09/2015] [Indexed: 11/09/2022]
Abstract
The title compound was obtained as a side product during dimerization-oxidation steps of the carbene generated from N-methylbenzothiazolium iodide. Chromatography on (S,S)-Whelk O1 column showed on cooling a typical plateau shape chromatogram indicating an exchange between two enantiomers on the column. The thermal barrier to racemization was determined (85 kJ.mol(-1) at 10 °C) by dynamic high-performance liquid chromatography (DHPLC).The absolute configuration of the first (M) and second eluted (P) enantiomers on the (S, S)-Whelk O1 column was established by comparing the reconstructed circular dichroism (CD) spectra from the CD detector signal and the calculated CD spectrum of the (P) enantiomer. Mass spectrometry revealed that 3,3'-dimethyl-3H,3'H-2,2'-spirobi[[1,3]benzothiazole] can be viewed as a masked thiophenate attached to a benzothiazolium framework.
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Affiliation(s)
| | - Vesna Risso
- Aix Marseille Université, Centrale Marseille, CNRS, iSm2 UMR 7313, 13397, Marseille, France
| | - Marion Jean
- Aix Marseille Université, Centrale Marseille, CNRS, iSm2 UMR 7313, 13397, Marseille, France
| | - Michel Giorgi
- Spectropôle, Aix Marseille Université, Marseille, France
| | | | | | - Nicolas Vanthuyne
- Aix Marseille Université, Centrale Marseille, CNRS, iSm2 UMR 7313, 13397, Marseille, France
| | - Daniel Farran
- Aix Marseille Université, Centrale Marseille, CNRS, iSm2 UMR 7313, 13397, Marseille, France
| | - Christian Roussel
- Aix Marseille Université, Centrale Marseille, CNRS, iSm2 UMR 7313, 13397, Marseille, France
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24
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Baskin M, Maayan G. Water-soluble chiral metallopeptoids. Biopolymers 2015; 104:577-84. [DOI: 10.1002/bip.22675] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Revised: 04/19/2015] [Accepted: 05/04/2015] [Indexed: 01/09/2023]
Affiliation(s)
- Maria Baskin
- Schulich Faculty of Chemistry; Technion-Israel Institute of Technology; Haifa 32000 Israel
| | - Galia Maayan
- Schulich Faculty of Chemistry; Technion-Israel Institute of Technology; Haifa 32000 Israel
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25
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Shibukawa M, Miyake A, Eda S, Saito S. Determination of the cis–trans Isomerization Barriers of l-Alanyl-l-proline in Aqueous Solutions and at Water/Hydrophobic Interfaces by On-Line Temperature-Jump Relaxation HPLC and Dynamic On-Column Reaction HPLC. Anal Chem 2015; 87:9280-7. [DOI: 10.1021/acs.analchem.5b02488] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Masami Shibukawa
- Graduate School of Science
and Technology, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama 338-8570, Japan
| | - Ayaka Miyake
- Graduate School of Science
and Technology, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama 338-8570, Japan
| | - Sayaka Eda
- Graduate School of Science
and Technology, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama 338-8570, Japan
| | - Shingo Saito
- Graduate School of Science
and Technology, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama 338-8570, Japan
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26
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Proulx C, Yoo S, Connolly MD, Zuckermann RN. Accelerated Submonomer Solid-Phase Synthesis of Peptoids Incorporating Multiple Substituted N-Aryl Glycine Monomers. J Org Chem 2015; 80:10490-7. [DOI: 10.1021/acs.joc.5b01449] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Caroline Proulx
- The Molecular Foundry, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, United States
| | - Stan Yoo
- The Molecular Foundry, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, United States
| | - Michael D. Connolly
- The Molecular Foundry, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, United States
| | - Ronald N. Zuckermann
- The Molecular Foundry, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, United States
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27
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Kaniraj PJ, Maayan G. A Facile Strategy for the Construction of Cyclic Peptoids under Microwave Irradiation through a Simple Substitution Reaction. Org Lett 2015; 17:2110-3. [PMID: 25868085 DOI: 10.1021/acs.orglett.5b00696] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
We describe a fast and efficient side chain-to-tail cyclization of N-substituted glycine oligomers, peptoids, on a solid support and under microwave irradiation. We demonstrate that cyclic peptoids varied in their ring size and side chains can be synthesized by a bond formation between a chloropropyl group placed anywhere along the sequence and the secondary amine at the N-terminus. This SN2 reaction leads to the formation of a new C-N bond using only one reagent (a base).
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Affiliation(s)
- Prathap Jeya Kaniraj
- Schulich Faculty of Chemistry, Technion - Israel Institute of Technology, Haifa, 32000, Israel
| | - G Maayan
- Schulich Faculty of Chemistry, Technion - Israel Institute of Technology, Haifa, 32000, Israel
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28
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Salvador CEM, Pieber B, Neu PM, Torvisco A, Kleber Z Andrade C, Kappe CO. A sequential Ugi multicomponent/Cu-catalyzed azide-alkyne cycloaddition approach for the continuous flow generation of cyclic peptoids. J Org Chem 2015; 80:4590-602. [PMID: 25842982 DOI: 10.1021/acs.joc.5b00445] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The development of a continuous flow multistep strategy for the synthesis of linear peptoids and their subsequent macrocyclization via Click chemistry is described. The central transformation of this process is an Ugi four-component reaction generating the peptidomimetic core structure. In order to avoid exposure to the often toxic and malodorous isocyanide building blocks, the continuous approach was telescoped by the dehydration of the corresponding formamide. In a concurrent operation, the highly energetic azide moiety required for the subsequent intramolecular copper-catalyzed azide-alkyne cycloaddition (Click reaction) was installed by nucleophilic substitution from a bromide precursor. All steps yielding to the linear core structures can be conveniently coupled without the need for purification steps resulting in a single process generating the desired peptidomimetics in good to excellent yields within a 25 min reaction time. The following macrocyclization was realized in a coil reactor made of copper without any additional additive. A careful process intensification study demonstrated that this transformation occurs quantitatively within 25 min at 140 °C. Depending on the resulting ring strain, either a dimeric or a monomeric form of the cyclic product was obtained.
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Affiliation(s)
- Carlos Eduardo M Salvador
- †Institute of Chemistry, University of Graz, Heinrichstrasse 28, A-8010 Graz, Austria.,‡Laboratório de Química Metodológica e Orgânica Sintética, Instituto de Química, Universidade de Brasília, Campus Universitário Darcy Ribeiro, C.P. 4478, 70904-970, Brasília-DF, Brazil
| | - Bartholomäus Pieber
- †Institute of Chemistry, University of Graz, Heinrichstrasse 28, A-8010 Graz, Austria
| | - Philipp M Neu
- †Institute of Chemistry, University of Graz, Heinrichstrasse 28, A-8010 Graz, Austria
| | - Ana Torvisco
- §Institute of Inorganic Chemistry, Graz University of Technology, Stremayrgasse 9, A-8010 Graz, Austria
| | - Carlos Kleber Z Andrade
- ‡Laboratório de Química Metodológica e Orgânica Sintética, Instituto de Química, Universidade de Brasília, Campus Universitário Darcy Ribeiro, C.P. 4478, 70904-970, Brasília-DF, Brazil
| | - C Oliver Kappe
- †Institute of Chemistry, University of Graz, Heinrichstrasse 28, A-8010 Graz, Austria
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29
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Crisma M, De Zotti M, Formaggio F, Peggion C, Moretto A, Toniolo C. Handedness preference and switching of peptide helices. Part II: Helices based on noncodedα-amino acids. J Pept Sci 2015; 21:148-77. [DOI: 10.1002/psc.2743] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Revised: 12/19/2014] [Accepted: 12/19/2014] [Indexed: 12/27/2022]
Affiliation(s)
| | - Marta De Zotti
- Department of Chemistry; University of Padova; Padova Italy
| | - Fernando Formaggio
- ICB; Padova Unit; CNR Padova Italy
- Department of Chemistry; University of Padova; Padova Italy
| | | | - Alessandro Moretto
- ICB; Padova Unit; CNR Padova Italy
- Department of Chemistry; University of Padova; Padova Italy
| | - Claudio Toniolo
- ICB; Padova Unit; CNR Padova Italy
- Department of Chemistry; University of Padova; Padova Italy
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30
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Urbani M, Torres T. Tautomerism and Atropisomerism in Free-Base (meso)-Strapped Porphyrins: Static and Dynamic Aspects. Chemistry 2014; 20:16337-49. [DOI: 10.1002/chem.201403881] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2014] [Indexed: 11/12/2022]
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31
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Gao Y, Kodadek T. Split-and-pool synthesis and characterization of peptide tertiary amide library. J Vis Exp 2014:e51299. [PMID: 24998250 DOI: 10.3791/51299] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Peptidomimetics are great sources of protein ligands. The oligomeric nature of these compounds enables us to access large synthetic libraries on solid phase by using combinatorial chemistry. One of the most well studied classes of peptidomimetics is peptoids. Peptoids are easy to synthesize and have been shown to be proteolysis-resistant and cell-permeable. Over the past decade, many useful protein ligands have been identified through screening of peptoid libraries. However, most of the ligands identified from peptoid libraries do not display high affinity, with rare exceptions. This may be due, in part, to the lack of chiral centers and conformational constraints in peptoid molecules. Recently, we described a new synthetic route to access peptide tertiary amides (PTAs). PTAs are a superfamily of peptidomimetics that include but are not limited to peptides, peptoids and N-methylated peptides. With side chains on both α-carbon and main chain nitrogen atoms, the conformation of these molecules are greatly constrained by sterical hindrance and allylic 1,3 strain. (Figure 1) Our study suggests that these PTA molecules are highly structured in solution and can be used to identify protein ligands. We believe that these molecules can be a future source of high-affinity protein ligands. Here we describe the synthetic method combining the power of both split-and-pool and sub-monomer strategies to synthesize a sample one-bead one-compound (OBOC) library of PTAs.
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Affiliation(s)
- Yu Gao
- Scripps Florida, The Scripps Research Institute
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32
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Abstract
In cyclic alpha-peptoids, inter-annular CH⋯OC hydrogen bonds provide face to face or side by side arrangement of macrocycles mimicking the beta-sheet secondary structure in proteins. Side chains may promote the formation of peptoid nanotubes, acting as pillars among neighbouring macrocycles.
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Affiliation(s)
- Consiglia Tedesco
- Dipartimento di Chimica e Biologia
- Università degli Studi di Salerno
- I-84084 Fisciano, Italy
- Nano_MATES Research Center
- Università degli Studi di Salerno
| | - Loredana Erra
- Dipartimento di Chimica e Biologia
- Università degli Studi di Salerno
- I-84084 Fisciano, Italy
| | - Irene Izzo
- Dipartimento di Chimica e Biologia
- Università degli Studi di Salerno
- I-84084 Fisciano, Italy
| | - Francesco De Riccardis
- Dipartimento di Chimica e Biologia
- Università degli Studi di Salerno
- I-84084 Fisciano, Italy
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33
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Liu K, Wu X, Kan SBJ, Shirakawa S, Maruoka K. Phase-Transfer-Catalyzed Asymmetric Synthesis of Axially Chiral Anilides. Chem Asian J 2013; 8:3214-21. [DOI: 10.1002/asia.201301036] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2013] [Indexed: 11/06/2022]
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34
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Luxenhofer R, Fetsch C, Grossmann A. Polypeptoids: A perfect match for molecular definition and macromolecular engineering? ACTA ACUST UNITED AC 2013. [DOI: 10.1002/pola.26687] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Robert Luxenhofer
- Functional Polymer Materials; Chair of Chemical Technology of Materials Synthesis; Department of Chemistry and Pharmacy, Julius-Maximilian, University of Würzburg; 97070 Würzburg Germany
| | - Corinna Fetsch
- Functional Polymer Materials; Chair of Chemical Technology of Materials Synthesis; Department of Chemistry and Pharmacy, Julius-Maximilian, University of Würzburg; 97070 Würzburg Germany
| | - Arlett Grossmann
- Professur für Makromolekulare Chemie; Department Chemie; Technische Universität Dresden; 01062 Dresden Germany
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35
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Roy O, Caumes C, Esvan Y, Didierjean C, Faure S, Taillefumier C. The tert-Butyl Side Chain: A Powerful Means to Lock Peptoid Amide Bonds in the Cis Conformation. Org Lett 2013; 15:2246-9. [DOI: 10.1021/ol400820y] [Citation(s) in RCA: 81] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- O. Roy
- Clermont Université, Université Blaise Pascal, Institut de Chimie de Clermont-Ferrand, BP 10448, F-63000 Clermont-Ferrand, France, CNRS, UMR 6296, ICCF, BP 80026, F-63171 Aubière, France, and CRM2, Equipe Biocristallographie, UMR 7036 CNRS-UL, Faculté des Sciences et Techniques, Université de Lorraine, BP 239, 54506 Vandoeuvre-lès-Nancy, France
| | - C. Caumes
- Clermont Université, Université Blaise Pascal, Institut de Chimie de Clermont-Ferrand, BP 10448, F-63000 Clermont-Ferrand, France, CNRS, UMR 6296, ICCF, BP 80026, F-63171 Aubière, France, and CRM2, Equipe Biocristallographie, UMR 7036 CNRS-UL, Faculté des Sciences et Techniques, Université de Lorraine, BP 239, 54506 Vandoeuvre-lès-Nancy, France
| | - Y. Esvan
- Clermont Université, Université Blaise Pascal, Institut de Chimie de Clermont-Ferrand, BP 10448, F-63000 Clermont-Ferrand, France, CNRS, UMR 6296, ICCF, BP 80026, F-63171 Aubière, France, and CRM2, Equipe Biocristallographie, UMR 7036 CNRS-UL, Faculté des Sciences et Techniques, Université de Lorraine, BP 239, 54506 Vandoeuvre-lès-Nancy, France
| | - C. Didierjean
- Clermont Université, Université Blaise Pascal, Institut de Chimie de Clermont-Ferrand, BP 10448, F-63000 Clermont-Ferrand, France, CNRS, UMR 6296, ICCF, BP 80026, F-63171 Aubière, France, and CRM2, Equipe Biocristallographie, UMR 7036 CNRS-UL, Faculté des Sciences et Techniques, Université de Lorraine, BP 239, 54506 Vandoeuvre-lès-Nancy, France
| | - S. Faure
- Clermont Université, Université Blaise Pascal, Institut de Chimie de Clermont-Ferrand, BP 10448, F-63000 Clermont-Ferrand, France, CNRS, UMR 6296, ICCF, BP 80026, F-63171 Aubière, France, and CRM2, Equipe Biocristallographie, UMR 7036 CNRS-UL, Faculté des Sciences et Techniques, Université de Lorraine, BP 239, 54506 Vandoeuvre-lès-Nancy, France
| | - C. Taillefumier
- Clermont Université, Université Blaise Pascal, Institut de Chimie de Clermont-Ferrand, BP 10448, F-63000 Clermont-Ferrand, France, CNRS, UMR 6296, ICCF, BP 80026, F-63171 Aubière, France, and CRM2, Equipe Biocristallographie, UMR 7036 CNRS-UL, Faculté des Sciences et Techniques, Université de Lorraine, BP 239, 54506 Vandoeuvre-lès-Nancy, France
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36
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Crapster JA, Guzei IA, Blackwell HE. A peptoid ribbon secondary structure. Angew Chem Int Ed Engl 2013; 52:5079-84. [PMID: 23576308 DOI: 10.1002/anie.201208630] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2012] [Revised: 01/02/2013] [Indexed: 01/02/2023]
Affiliation(s)
- J Aaron Crapster
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706-1322, USA
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37
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38
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Laursen JS, Engel-Andreasen J, Fristrup P, Harris P, Olsen CA. Cis-trans amide bond rotamers in β-peptoids and peptoids: evaluation of stereoelectronic effects in backbone and side chains. J Am Chem Soc 2013; 135:2835-44. [PMID: 23343406 DOI: 10.1021/ja312532x] [Citation(s) in RCA: 114] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Non-natural peptide analogs have significant potential for the development of new materials and pharmacologically active ligands. One such architecture, the β-peptoids (N-alkyl-β-alanines), has found use in a variety of biologically active compounds but has been sparsely studied with respect to folding propensity. Thus, we here report an investigation of the effect of structural variations on the cis-trans amide bond rotamer equilibria in a selection of monomer model systems. In addition to various side chain effects, which correlated well with previous studies of α-peptoids, we present the synthesis and investigation of cis-trans isomerism in the first examples of peptoids and β-peptoids containing thioamide bonds as well as trifluoroacetylated peptoids and β-peptoids. These systems revealed an increase in the preference for cis-amides as compared to their parent compounds and thus provide novel strategies for affecting the folding of peptoid constructs. By using NMR spectroscopy, X-ray crystallographic analysis, and density functional theory calculations, we present evidence for the presence of thioamide-aromatic interactions through C(sp(2))-H···S(amide) hydrogen bonding, which stabilize certain peptoid conformations.
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Affiliation(s)
- Jonas S Laursen
- Department of Chemistry, Technical University of Denmark, Kemitorvet 207, DK-2800, Kongens Lyngby, Denmark
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De novo structure prediction and experimental characterization of folded peptoid oligomers. Proc Natl Acad Sci U S A 2012; 109:14320-5. [PMID: 22908242 DOI: 10.1073/pnas.1209945109] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Peptoid molecules are biomimetic oligomers that can fold into unique three-dimensional structures. As part of an effort to advance computational design of folded oligomers, we present blind-structure predictions for three peptoid sequences using a combination of Replica Exchange Molecular Dynamics (REMD) simulation and Quantum Mechanical refinement. We correctly predicted the structure of a N-aryl peptoid trimer to within 0.2 Å rmsd-backbone and a cyclic peptoid nonamer to an accuracy of 1.0 Å rmsd-backbone. X-ray crystallographic structures are presented for a linear N-alkyl peptoid trimer and for the cyclic peptoid nonamer. The peptoid macrocycle structure features a combination of cis and trans backbone amides, significant nonplanarity of the amide bonds, and a unique "basket" arrangement of (S)-N(1-phenylethyl) side chains encompassing a bound ethanol molecule. REMD simulations of the peptoid trimers reveal that well folded peptoids can exhibit funnel-like conformational free energy landscapes similar to those for ordered polypeptides. These results indicate that physical modeling can successfully perform de novo structure prediction for small peptoid molecules.
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