1
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Jesani MH, Schwarz M, Kim S, Evans FL, White A, Browning A, Abrams R, Clayden J. Selective Defluorination of Trifluoromethyl Substituents by Conformationally Induced Remote Substitution. Angew Chem Int Ed Engl 2024; 63:e202403477. [PMID: 38587304 DOI: 10.1002/anie.202403477] [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: 02/19/2024] [Revised: 03/28/2024] [Accepted: 04/02/2024] [Indexed: 04/09/2024]
Abstract
The selective reduction of an aromatic trifluoromethyl substituent to a difluoromethyl substituent may be achieved by base-promoted elimination to form a difluoro-p-quinomethide which is trapped by an intramolecular nucleophile. High yields are obtained when the nucleophilic trap entails the conformationally favoured cyclisation of an aminoisobutyric acid (Aib) derivative. The resulting cyclised difluoromethyl-substituted arylimidazolidinone products are readily converted to versatile difluoromethyl-substituted aldehydes by reduction and hydrolysis. Defluorination is successful on a range of benzenoid (both para and ortho CF3-substituted) and heterocyclic substrates. Double defluorination may likewise be achieved sequentially, or in a single step, from an Aib dipeptide derivative.
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Affiliation(s)
- Mehul H Jesani
- School of Chemistry, University of Bristol Cantock's Close, Bristol, BS8 1TS, UK
| | - Maria Schwarz
- School of Chemistry, University of Bristol Cantock's Close, Bristol, BS8 1TS, UK
| | - Shiwhu Kim
- School of Chemistry, University of Bristol Cantock's Close, Bristol, BS8 1TS, UK
| | - Finlay L Evans
- School of Chemistry, University of Bristol Cantock's Close, Bristol, BS8 1TS, UK
| | - Alexander White
- School of Chemistry, University of Bristol Cantock's Close, Bristol, BS8 1TS, UK
| | - Alex Browning
- School of Chemistry, University of Bristol Cantock's Close, Bristol, BS8 1TS, UK
| | - Roman Abrams
- School of Chemistry, University of Bristol Cantock's Close, Bristol, BS8 1TS, UK
| | - Jonathan Clayden
- School of Chemistry, University of Bristol Cantock's Close, Bristol, BS8 1TS, UK
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2
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Sigal M, Matsumoto S, Beattie A, Katoh T, Suga H. Engineering tRNAs for the Ribosomal Translation of Non-proteinogenic Monomers. Chem Rev 2024; 124:6444-6500. [PMID: 38688034 PMCID: PMC11122139 DOI: 10.1021/acs.chemrev.3c00894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 02/21/2024] [Accepted: 04/10/2024] [Indexed: 05/02/2024]
Abstract
Ribosome-dependent protein biosynthesis is an essential cellular process mediated by transfer RNAs (tRNAs). Generally, ribosomally synthesized proteins are limited to the 22 proteinogenic amino acids (pAAs: 20 l-α-amino acids present in the standard genetic code, selenocysteine, and pyrrolysine). However, engineering tRNAs for the ribosomal incorporation of non-proteinogenic monomers (npMs) as building blocks has led to the creation of unique polypeptides with broad applications in cellular biology, material science, spectroscopy, and pharmaceuticals. Ribosomal polymerization of these engineered polypeptides presents a variety of challenges for biochemists, as translation efficiency and fidelity is often insufficient when employing npMs. In this Review, we will focus on the methodologies for engineering tRNAs to overcome these issues and explore recent advances both in vitro and in vivo. These efforts include increasing orthogonality, recruiting essential translation factors, and creation of expanded genetic codes. After our review on the biochemical optimizations of tRNAs, we provide examples of their use in genetic code manipulation, with a focus on the in vitro discovery of bioactive macrocyclic peptides containing npMs. Finally, an analysis of the current state of tRNA engineering is presented, along with existing challenges and future perspectives for the field.
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Affiliation(s)
- Maxwell Sigal
- Department of Chemistry,
Graduate School of Science, The University
of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Satomi Matsumoto
- Department of Chemistry,
Graduate School of Science, The University
of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Adam Beattie
- Department of Chemistry,
Graduate School of Science, The University
of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Takayuki Katoh
- Department of Chemistry,
Graduate School of Science, The University
of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Hiroaki Suga
- Department of Chemistry,
Graduate School of Science, The University
of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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3
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Picois N, Bodero L, Milbeo P, Brigaud T, Chaume G. Bimodal Use of Chiral α-Trifluoromethylalanine in Aib Foldamers: Study of the Position Impact Towards the Helical Screw-Sense Preference. Chemistry 2024; 30:e202400540. [PMID: 38445775 DOI: 10.1002/chem.202400540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Revised: 02/28/2024] [Accepted: 03/06/2024] [Indexed: 03/07/2024]
Abstract
Oligomers of the achiral α-aminoisobutyric acid (Aib) adopt a 310 helical conformation in which the screw-sense preference can be controlled by a single chiral residue. The use of the fluorinated residue α-Trifluoromethylalanine (α-TfmAla) revealed a unique way to both induce and measure the screw-sense preference of such oligomers acting as 19F NMR probe. This work proposes a systematic study of the effect of this fluorinated chiral inducer on the helical screw-sense preference of poly-Aib oligomers. The impact of the position of the fluorinated residue into pentamers (N-terminal, central or C-terminal) as well as the nature of the C-terminal capping of the peptides was thoroughly studied in light of complete structural analysis. A deeper understanding of the fluorine effect was achieved confirming the unique ability of α-TfmAla as a helical screw-sense controller.
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Affiliation(s)
- Nathan Picois
- CY Cergy Paris Université, CNRS, BioCIS, 95000, Cergy Pontoise, France
- Université Paris-Saclay, CNRS, BioCIS, 91400, Orsay, France
| | - Lizeth Bodero
- CY Cergy Paris Université, CNRS, BioCIS, 95000, Cergy Pontoise, France
- Université Paris-Saclay, CNRS, BioCIS, 91400, Orsay, France
| | - Pierre Milbeo
- CY Cergy Paris Université, CNRS, BioCIS, 95000, Cergy Pontoise, France
- Université Paris-Saclay, CNRS, BioCIS, 91400, Orsay, France
| | - Thierry Brigaud
- CY Cergy Paris Université, CNRS, BioCIS, 95000, Cergy Pontoise, France
- Université Paris-Saclay, CNRS, BioCIS, 91400, Orsay, France
| | - Grégory Chaume
- CY Cergy Paris Université, CNRS, BioCIS, 95000, Cergy Pontoise, France
- Université Paris-Saclay, CNRS, BioCIS, 91400, Orsay, France
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4
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Renawala HK, Chandrababu KB, Smith KJ, D'Addio SM, Topp EM. A Model Study to Assess Fibrillation and Product Stability to Support Peptide Drug Design. Mol Pharm 2024; 21:2223-2237. [PMID: 38552144 DOI: 10.1021/acs.molpharmaceut.3c00996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/07/2024]
Abstract
The fibrillation of therapeutic peptides can present significant quality concerns and poses challenges for manufacturing and storage. A fundamental understanding of the mechanisms of fibrillation is critical for the rational design of fibrillation-resistant peptide drugs and can accelerate product development by guiding the selection of solution-stable candidates and formulations. The studies reported here investigated the effects of structural modifications on the fibrillation of a 29-residue peptide (PepA) and two sequence modified variants (PepB, PepC). The C-terminus of PepA was amidated, whereas both PepB and PepC retained the carboxylate, and Ser16 in PepA and PepB was substituted with a helix-stabilizing residue, α-aminoisobutyric acid (Aib), in PepC. In thermal denaturation studies by far-UV CD spectroscopy and fibrillation kinetic studies by fluorescence and turbidity measurements, PepA and PepB showed heat-induced conformational changes and were found to form fibrils, whereas PepC did not fibrillate and showed only minor changes in the CD signal. Pulsed hydrogen-deuterium exchange mass spectrometry (HDX-MS) showed a high degree of protection from HD exchange in mature PepA fibrils and its proteolytic fragments, indicating that most of the sequence had been incorporated into the fibril structure and occurred nearly simultaneously throughout the sequence. The effects of the net peptide charge and formulation pH on fibrillation kinetics were investigated. In real-time stability studies of two formulations of PepA at pH's 7.4 and 8.0, analytical methods detected significant changes in the stability of the formulations at different time points during the study, which were not observed during accelerated studies. Additionally, PepA samples were withdrawn from real-time stability and subjected to additional stress (40 °C, continuous shaking) to induce fibrillation; an approach that successfully amplified oligomers or prefibrillar species previously undetected in a thioflavin T assay. Taken together, these studies present an approach to differentiate and characterize fibrillation risk in structurally related peptides under accelerated and real-time conditions, providing a model for rapid, iterative structural design to optimize the stability of therapeutic peptides.
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Affiliation(s)
- Harshil K Renawala
- Department of Industrial and Molecular Pharmaceutics, College of Pharmacy, Purdue University, West Lafayette, Indiana 47907, United States
| | - Karthik B Chandrababu
- Department of Industrial and Molecular Pharmaceutics, College of Pharmacy, Purdue University, West Lafayette, Indiana 47907, United States
| | - Katelyn J Smith
- Pharmaceutical Sciences and Clinical Supply, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Suzanne M D'Addio
- Pharmaceutical Sciences and Clinical Supply, Merck & Co., Inc., Rahway, New Jersey 07065, United States
| | - Elizabeth M Topp
- Department of Industrial and Molecular Pharmaceutics, College of Pharmacy, Purdue University, West Lafayette, Indiana 47907, United States
- Davidson School of Chemical Engineering, College of Engineering, Purdue University, West Lafayette, Indiana 47907, United States
- National Institute for Bioprocessing Research and Training, Belfield, Blackrock, Co. Dublin A94 X099, Ireland
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5
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Shekhar S, Meena R, Lal J, Yadav M, Kant R, Reddy DN. Stabilizing Bifurcated Hydrogen Bond in 8-Aminoquinoline Appended Peptides. Chem Asian J 2024:e202400248. [PMID: 38701035 DOI: 10.1002/asia.202400248] [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: 03/06/2024] [Revised: 04/21/2024] [Accepted: 05/03/2024] [Indexed: 05/05/2024]
Abstract
The hydrogen bonding interaction between an amide N-H and the amide N of the preceding residue is prevalent in proline-containing proteins and peptides. However, the N-H⋅⋅⋅N hydrogen bonding interaction is rare in non-prolyl natural peptides due to restricted dihedral angles. Herein, we stabilize this type of interaction in 8-aminoquinoline appended non-prolyl peptides through bifurcated N⋅⋅⋅H⋅⋅⋅N hydrogen bond. The 8-aminoquinoline-incorporated model peptides 2 a-i were designed, synthesized, and the crystal structures of 2 a-c and 2 i were solved. Analysis of crystal data reveals that the amide N-H of aminoquinoline is involved in bifurcated hydrogen bonding interaction with the nitrogen of the preceding amino acid residue and the nitrogen in quinoline. Analysis of crystal packing, Hirshfeld surface and fingerprint plots confirms that the intermolecular O⋅⋅⋅H contacts significantly contribute to stabilizing bifurcated N⋅⋅⋅H⋅⋅⋅N hydrogen bonding interaction. Furthermore, NMR experiments and CD spectroscopy were conducted to examine the preferred conformation in solution, and the data corroborate with the crystal structure conformation.
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Affiliation(s)
- Shashank Shekhar
- Medicinal and Process Chemistry Division, CSIR-Central Drug Research Institute, 226031, Lucknow, India
- Academy of Scientific and Innovative Research (AcSIR), 201002, Ghaziabad, India
| | - Rachana Meena
- Medicinal and Process Chemistry Division, CSIR-Central Drug Research Institute, 226031, Lucknow, India
- Academy of Scientific and Innovative Research (AcSIR), 201002, Ghaziabad, India
| | - Jhajan Lal
- Medicinal and Process Chemistry Division, CSIR-Central Drug Research Institute, 226031, Lucknow, India
- Academy of Scientific and Innovative Research (AcSIR), 201002, Ghaziabad, India
| | - Mukul Yadav
- Medicinal and Process Chemistry Division, CSIR-Central Drug Research Institute, 226031, Lucknow, India
| | - Ruchir Kant
- Division of Biochemistry and Structural Biology, CSIR-Central Drug Research Institute, 226031, Lucknow, India
| | - Damodara N Reddy
- Medicinal and Process Chemistry Division, CSIR-Central Drug Research Institute, 226031, Lucknow, India
- Academy of Scientific and Innovative Research (AcSIR), 201002, Ghaziabad, India
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6
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Roy S, Chaturvedi A, Dey S, Puneeth Kumar DRGKR, Pahan S, Panda Mahapatra S, Mandal P, Gopi HN. Anion Tuned Structural Modulation and Nonlinear Optical Effects of Metal-Ion Directed 3 10 -Helix Networks. Chemistry 2023; 29:e202303135. [PMID: 37867145 DOI: 10.1002/chem.202303135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 10/13/2023] [Accepted: 10/19/2023] [Indexed: 10/24/2023]
Abstract
Metals play an important role in the structure and functions of various proteins. The combination of metal ions and peptides have been emerging as an attractive field to create advanced structures and biomaterials. Here, we are reporting the anion-influenced, silver ion coordinated diverse networks of designed short tripeptide 310 -helices with terminal pyridyl groups. The short peptides adopted classical right-handed, left-handed and 310 EL -helical conformations in the presence of different silver salts. The peptides have displayed conformational flexibility to accommodate different sizes and interactions of anions to yield a variety of metal-coordinated networks. The complexes of metal ions and peptides have shown different porous networks, right- and left-handed helical polymers, transformation of helix into superhelix and 2 : 2 metal-peptide macrocycles. Further, the metal-peptide crystals with inherent dipoles of helical peptides gave striking second harmonic generation response. The optical energy upconversion from NIR to red and green light is demonstrated. Overall, we have shown the utilization of short 310 -helices for the construction of diverse metal-coordinated helical networks and notable non-linear optical effects.
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Affiliation(s)
- Souvik Roy
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Dr. Homi Bhabha Road, 411008, Pune, India
| | - Aman Chaturvedi
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Dr. Homi Bhabha Road, 411008, Pune, India
| | - Sanjit Dey
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Dr. Homi Bhabha Road, 411008, Pune, India
| | - DRGKoppalu R Puneeth Kumar
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Dr. Homi Bhabha Road, 411008, Pune, India
| | - Saikat Pahan
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Dr. Homi Bhabha Road, 411008, Pune, India
| | - Souvik Panda Mahapatra
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Dr. Homi Bhabha Road, 411008, Pune, India
| | - Pankaj Mandal
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Dr. Homi Bhabha Road, 411008, Pune, India
| | - Hosahudya N Gopi
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Dr. Homi Bhabha Road, 411008, Pune, India
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7
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Oeller M, Kang RJD, Bolt HL, Gomes Dos Santos AL, Weinmann AL, Nikitidis A, Zlatoidsky P, Su W, Czechtizky W, De Maria L, Sormanni P, Vendruscolo M. Sequence-based prediction of the intrinsic solubility of peptides containing non-natural amino acids. Nat Commun 2023; 14:7475. [PMID: 37978172 PMCID: PMC10656490 DOI: 10.1038/s41467-023-42940-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 10/26/2023] [Indexed: 11/19/2023] Open
Abstract
Non-natural amino acids are increasingly used as building blocks in the development of peptide-based drugs as they expand the available chemical space to tailor function, half-life and other key properties. However, while the chemical space of modified amino acids (mAAs) such as residues containing post-translational modifications (PTMs) is potentially vast, experimental methods for measuring the developability properties of mAA-containing peptides are expensive and time consuming. To facilitate developability programs through computational methods, we present CamSol-PTM, a method that enables the fast and reliable sequence-based prediction of the intrinsic solubility of mAA-containing peptides in aqueous solution at room temperature. From a computational screening of 50,000 mAA-containing variants of three peptides, we selected five different small-size mAAs for a total number of 37 peptide variants for experimental validation. We demonstrate the accuracy of the predictions by comparing the calculated and experimental solubility values. Our results indicate that the computational screening of mAA-containing peptides can extend by over four orders of magnitude the ability to explore the solubility chemical space of peptides and confirm that our method can accurately assess the solubility of peptides containing mAAs. This method is available as a web server at https://www-cohsoftware.ch.cam.ac.uk/index.php/camsolptm .
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Affiliation(s)
- Marc Oeller
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
- Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Ryan J D Kang
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Hannah L Bolt
- Hit Discovery, Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, UK
| | - Ana L Gomes Dos Santos
- Advanced Drug Delivery, Pharmaceutical Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge, United Kingdom
| | - Annika Langborg Weinmann
- Early Chemical Development, Pharmaceutical Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Antonios Nikitidis
- Medicinal Chemistry, Research and Early Development, Respiratory and Immunology, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Pavol Zlatoidsky
- Medicinal Chemistry, Research and Early Development, Respiratory and Immunology, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Wu Su
- Medicinal Chemistry, Research and Early Development, Respiratory and Immunology, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Werngard Czechtizky
- Medicinal Chemistry, Research and Early Development, Respiratory and Immunology, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Leonardo De Maria
- Medicinal Chemistry, Research and Early Development, Respiratory and Immunology, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Pietro Sormanni
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK.
| | - Michele Vendruscolo
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK.
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8
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Takeuchi N, Taniguchi M, Kato Y, Takata R, Osaka I, Nakajima N, Hamada M, Koyama Y. Synthesis and Conformational Behaviors of Unnatural Peptides Alternating Chiral and Achiral α,α-Disubstituted α-Amino Acid Units. Macromol Rapid Commun 2023; 44:e2300323. [PMID: 37668077 DOI: 10.1002/marc.202300323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 08/27/2023] [Indexed: 09/06/2023]
Abstract
The development of peptidomimetics to modulate the conformational profile of peptides has been extensively studied in the fields of biological and medicinal chemistry. However, large-scale synthesis of peptidomimetics with both an ordered sequence and a controlled secondary structure is highly challenging. In this paper, the framework of peptidomimetics has been designed to be alternating an achiral α,α-disubstituted α-amino acid unit and a chiral α-methylphenylalanine unit. The polymers are synthesized via invented Ugi reaction-based polycondensation technique. The chiral higher-order structures of the alternating peptides are evaluated mainly through circular dichroism (CD) spectroscopy. The UV-Vis and CD spectra of the polymers in three solvents are systematically measured at various temperatures. The anisotropic factors of CD (gCD ) values are calculated to know the chiroptical response. The results indicate the characteristic conformational behaviors. In a polar solvent, the hydrogen bonds between the N-H group of MePhe unit and the C=O of α,α-diphenylglycine unit outweigh the intraresidue hydrogen bonds in α,α-diphenylglycine unit, leading to the formation of a prevailing preferred-handed 310 -helical conformation. On the other hand, in a less polar solvent, the intrachain hydrogen bonds switch to intraresidue hydrogen bonds in α,α-diphenylglycine unit, which make the polymer adopting a prevailing extended planar C5 -conformation.
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Affiliation(s)
- Nanami Takeuchi
- Department of Pharmaceutical Engineering, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama, 939-0398, Japan
| | - Masataka Taniguchi
- Department of Pharmaceutical Engineering, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama, 939-0398, Japan
| | - Yuki Kato
- Department of Pharmaceutical Engineering, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama, 939-0398, Japan
| | - Riko Takata
- Department of Pharmaceutical Engineering, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama, 939-0398, Japan
| | - Issey Osaka
- Department of Pharmaceutical Engineering, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama, 939-0398, Japan
- Biotechnology Research Center, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama, 939-0398, Japan
| | - Noriyuki Nakajima
- Department of Pharmaceutical Engineering, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama, 939-0398, Japan
- Biotechnology Research Center, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama, 939-0398, Japan
| | - Masahiro Hamada
- Department of Pharmaceutical Engineering, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama, 939-0398, Japan
- Biotechnology Research Center, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama, 939-0398, Japan
| | - Yasuhito Koyama
- Department of Pharmaceutical Engineering, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama, 939-0398, Japan
- Biotechnology Research Center, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama, 939-0398, Japan
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9
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Ousaka N, MacLachlan MJ, Akine S. Stapling strategy for slowing helicity interconversion of α-helical peptides and isolating chiral auxiliary-free one-handed forms. Nat Commun 2023; 14:6834. [PMID: 37884515 PMCID: PMC10603036 DOI: 10.1038/s41467-023-42493-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 10/12/2023] [Indexed: 10/28/2023] Open
Abstract
In nature, α-helical peptides adopt right-handed conformations that are dictated by L-amino acids. Isolating one-handed α-helical peptides composed of only achiral components remains a significant challenge. Here, this goal is achieved by optical resolution of the corresponding racemic (quasi-)static α-helical peptide with double stapling, which effectively freezes the interconversion between the right-handed (P)- and left-handed (M)-α-helices. An as-obtained doubly stapled analogue having an unprotected L-valine residue at the C-terminus transforms from a kinetically trapped (M)-α-helix to a thermodynamically stable (P)-α-helix upon heating. In contrast, the corresponding singly stapled α-helical peptide undergoes an acid/base-triggered and solvent-induced reversible inversion of its preferred helicity within minutes. The interconversion rates of the singly and doubly stapled α-helical peptide foldamers are approximately 106 and 1012 times slower, respectively, than that of a non-stapled dynamic helical peptide. Therefore, the enantiopure doubly-stapled (quasi-)static α-helical peptide would retain its optical activity for several years at 25 °C.
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Affiliation(s)
- Naoki Ousaka
- Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kakuma-machi, Kanazawa, 920-1192, Japan.
| | - Mark J MacLachlan
- Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kakuma-machi, Kanazawa, 920-1192, Japan.
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC, V6T 1Z1, Canada.
- Quantum Matter Institute, University of British Columbia, 2355 East Mall, Vancouver, BC, V6T 1Z4, Canada.
| | - Shigehisa Akine
- Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kakuma-machi, Kanazawa, 920-1192, Japan.
- Graduate School of Natural Science and Technology, Kanazawa University, Kanazawa, 920-1192, Japan.
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10
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Núñez-Villanueva D, Plata-Ruiz A, Romero-Muñiz I, Martín-Pérez I, Infantes L, González-Muñiz R, Martín-Martínez M. β-Turn Induction by a Diastereopure Azepane-Derived Quaternary Amino Acid. J Org Chem 2023; 88:14688-14696. [PMID: 37774108 PMCID: PMC10594656 DOI: 10.1021/acs.joc.3c01689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Indexed: 10/01/2023]
Abstract
β-Turns are one of the most common secondary structures found in proteins. In the interest of developing novel β-turn inducers, a diastereopure azepane-derived quaternary amino acid has been incorporated into a library of simplified tetrapeptide models in order to assess the effect of the azepane position and peptide sequence on the stabilization of β-turns. The conformational analysis of these peptides by molecular modeling, NMR spectroscopy, and X-ray crystallography showed that this azepane amino acid is an effective β-turn inducer when incorporated at the i + 1 position. Moreover, the analysis of the supramolecular self-assembly of one of the β-turn-containing peptide models in the solid state reveals that it forms a supramolecular helical arrangement while maintaining the β-turn structure. The results here presented provide the basis for the use of this azepane quaternary amino acid as a strong β-turn inducer in the search for novel peptide-based bioactive molecules, catalysts, and biomaterials.
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Affiliation(s)
| | - Adrián Plata-Ruiz
- Instituto
de Química Médica (IQM-CSIC), Juan de la Cierva 3, 28006 Madrid, Spain
| | - Ignacio Romero-Muñiz
- Instituto
de Química Médica (IQM-CSIC), Juan de la Cierva 3, 28006 Madrid, Spain
- Universidad
Autónoma de Madrid, Química Orgánica, Francisco Tomás y Valiente,
7, 28049 Madrid, Spain
| | - Ignacio Martín-Pérez
- Instituto
de Química Médica (IQM-CSIC), Juan de la Cierva 3, 28006 Madrid, Spain
| | - Lourdes Infantes
- Instituto
de Química Física Rocasolano (IQFR-CSIC), Serrano 119, 28006 Madrid, Spain
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11
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Li Y, Guo S, Li QH, Zheng K. Metal-free photoinduced C(sp 3)-H/C(sp 3)-H cross-coupling to access α‑tertiary amino acid derivatives. Nat Commun 2023; 14:6225. [PMID: 37802984 PMCID: PMC10558569 DOI: 10.1038/s41467-023-41956-6] [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: 03/31/2023] [Accepted: 09/22/2023] [Indexed: 10/08/2023] Open
Abstract
The cross-dehydrogenative coupling (CDC) reaction is the most direct and efficient method for constructing α-tertiary amino acids (ATAAs), which avoids the pre-activation of C(sp3)-H substrates. However, the use of transition metals and harsh reaction conditions are still significant challenges for these reactions that urgently require solutions. This paper presents a mild, metal-free CDC reaction for the construction of ATAAs, which is compatible with various benzyl C-H substrates, functionalized C-H substrates, and alkyl substrates, with good regioselectivity. Notably, our method exhibits excellent functional group tolerance and late-stage applicability. According to mechanistic studies, the one-step synthesized and bench-stable N-alkoxyphtalimide generates a highly electrophilic trifluoro ethoxy radical that serves as a key intermediate in the reaction process and acts as a hydrogen atom transfer reagent. Therefore, our metal-free and additive-free method offers a promising strategy for the synthesis of ATAAs under mild conditions.
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Affiliation(s)
- Yujun Li
- Key Laboratory of Green Chemistry & Technology, Ministry of Education, College of Chemistry, Sichuan University, Chengdu, PR China
| | - Shaopeng Guo
- Key Laboratory of General Chemistry of the National Ethnic Affairs Commission, College of Chemistry and Environment, Southwest Minzu University, Chengdu, PR China
| | - Qing-Han Li
- Key Laboratory of General Chemistry of the National Ethnic Affairs Commission, College of Chemistry and Environment, Southwest Minzu University, Chengdu, PR China
| | - Ke Zheng
- Key Laboratory of Green Chemistry & Technology, Ministry of Education, College of Chemistry, Sichuan University, Chengdu, PR China.
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12
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Debnath S, Rajalakshmi VS, Kumar D, Das B, Vasudev PG, Satpati P, Chatterjee S. Ambidexterity and Left-Handedness Induced by Geminally Disubstituted γ Amino Acid Residues in Chiral 3 10 Helices. ACS OMEGA 2023; 8:36370-36385. [PMID: 37810672 PMCID: PMC10552473 DOI: 10.1021/acsomega.3c05124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 08/29/2023] [Indexed: 10/10/2023]
Abstract
Chirality is an omnipresent feature in nature's architecture starting from simple molecules like amino acids to complex higher-order structures viz. proteins, DNA, and RNA. The L configuration of proteinogenic amino acids gives rise to right-handed helices. Ambidexterity is as rare in organisms as in molecules. There are only a few reports of ambidexterity in single-peptide molecules composed of either mixed L and D or achiral residues. Here, we report, for the first time, the ambidextrous and left-handed helical conformations in the chiral nonapeptides P1-P3 (Boc-LUVUγx,xULUV-OMe where U = Aib, x,x = 2,2/3,3/4,4), containing chiral L α amino acid residues, in addition to the usually observed right-handed helical conformation. The centrally located achiral γ residue, capable of adopting both left and right-handed helical conformations, induces its handedness on the neighboring chiral and achiral residues, leading to the observation of both left and right-handed helices in P2 and P3. The presence of a single water molecule proximal to the γ residue induces the reversal of helix handedness by forming distinct and stable water-mediated hydrogen bonds. This gives rise to ambidextrous helices as major conformers in P1 and P2. The absence of the observation of ambidexterity in P3 might be due to the inability of γ4,4 in the recruitment of a water molecule. Experiments (NMR, X-ray, and CD) and density functional theory (DFT) calculations suggest that the position of geminal disubstitution is crucial for determining the population of the amenable helical conformations (ambidextrous, left and right-handed) in these chiral peptides.
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Affiliation(s)
- Swapna Debnath
- Department
of Chemistry, Indian Institute of Technology,
Guwahati, Guwahati, Assam 781039, India
| | | | - Dinesh Kumar
- Plant
Biotechnology Division, CSIR-Central Institute
of Medicinal and Aromatic Plants Lucknow, Uttar Pradesh 226015, India
| | - Babulal Das
- Department
of Chemistry, Indian Institute of Technology,
Guwahati, Guwahati, Assam 781039, India
| | - Prema G. Vasudev
- Plant
Biotechnology Division, CSIR-Central Institute
of Medicinal and Aromatic Plants Lucknow, Uttar Pradesh 226015, India
| | - Priyadarshi Satpati
- Biosciences
and Bioengineering, Indian Institute of
Technology, Guwahati, Guwahati, Assam 781039, India
| | - Sunanda Chatterjee
- Department
of Chemistry, Indian Institute of Technology,
Guwahati, Guwahati, Assam 781039, India
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13
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Quintavalla A, Carboni D, Simeone M, Lombardo M. Stereoselective Synthesis of α-Disubstituted β-Homoprolines. Org Lett 2023; 25:7067-7071. [PMID: 37729003 PMCID: PMC10546376 DOI: 10.1021/acs.orglett.3c02891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2023] [Indexed: 09/22/2023]
Abstract
An efficient enantioselective synthesis of chiral α-disubstituted β-homoprolines was developed, starting with the stereodivergent allylation of chiral N-tert-butanesulfinyl imines derived from 4-bromobutanal with indium or zinc and using well-established and reliable synthetic transformations. This methodology allows the easy introduction of different substituents at the α-position of the pyrrolidine scaffold and is characterized by the possibility of switching the absolute configuration of the newly formed stereocenter either by changing the configuration of the tert-butanesufinamide chiral auxiliary or by using a different stereodivergent allylation protocol with the same auxiliary.
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Affiliation(s)
- Arianna Quintavalla
- Alma
Mater Studiorum - University of Bologna, Department of Chemistry “G. Ciamician”, via P. Gobetti 85, 40129 Bologna, Italy
- Center
for Chemical Catalysis - C3, Alma Mater
Studiorum - Università di Bologna, via P. Gobetti 85, 40129 Bologna, Italy
| | - Davide Carboni
- Alma
Mater Studiorum - University of Bologna, Department of Chemistry “G. Ciamician”, via P. Gobetti 85, 40129 Bologna, Italy
- Center
for Chemical Catalysis - C3, Alma Mater
Studiorum - Università di Bologna, via P. Gobetti 85, 40129 Bologna, Italy
| | - Maria Simeone
- Alma
Mater Studiorum - University of Bologna, Department of Chemistry “G. Ciamician”, via P. Gobetti 85, 40129 Bologna, Italy
| | - Marco Lombardo
- Alma
Mater Studiorum - University of Bologna, Department of Chemistry “G. Ciamician”, via P. Gobetti 85, 40129 Bologna, Italy
- Center
for Chemical Catalysis - C3, Alma Mater
Studiorum - Università di Bologna, via P. Gobetti 85, 40129 Bologna, Italy
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14
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Laviós A, Martínez-Pardo P, Sanz-Marco A, Vila C, Pedro JR, Blay G. Synthesis of α,α-Diaryl-α-amino Acid Precursors by Reaction of Isocyanoacetate Esters with o-Quinone Diimides. Org Lett 2023; 25:5608-5612. [PMID: 37486803 PMCID: PMC10853967 DOI: 10.1021/acs.orglett.3c01965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Indexed: 07/26/2023]
Abstract
A novel procedure for the synthesis of α,α-diaryl-α-amino acid derivatives has been developed. Silver oxide catalyzes the conjugate addition of α-aryl isocyanoacetates to o-quinone diimide, affording the corresponding α,α-diarylisocyano esters in excellent yields and regioselectivities in short reaction times. Acid hydrolysis of the isocyano group provides the corresponding amino acids bearing a diarylated tetrasubstituted carbon atom. The reaction is also amenable to the synthesis of α-alkyl-α-arylisocyano esters, while the reaction with 3-hydroxy o-quinone diimides provides 4H-benzo[e][1,3]oxazines via a conjugate addition/cyclization process.
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Affiliation(s)
- Adrián Laviós
- Departament
de Química Orgànica, Facultat de Química, Universitat de València, Burjassot E-46100, Spain
| | - Pablo Martínez-Pardo
- Departament
de Química Orgànica, Facultat de Química, Universitat de València, Burjassot E-46100, Spain
| | - Amparo Sanz-Marco
- Departament
de Química Orgànica, Facultat de Química, Universitat de València, Burjassot E-46100, Spain
| | - Carlos Vila
- Departament
de Química Orgànica, Facultat de Química, Universitat de València, Burjassot E-46100, Spain
| | - José R. Pedro
- Departament
de Química Orgànica, Facultat de Química, Universitat de València, Burjassot E-46100, Spain
| | - Gonzalo Blay
- Departament
de Química Orgànica, Facultat de Química, Universitat de València, Burjassot E-46100, Spain
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15
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Morgan DC, McDougall L, Knuhtsen A, Jamieson AG. Development of Bifunctional, Raman Active Diyne-Girder Stapled α-Helical Peptides. Chemistry 2023; 29:e202300855. [PMID: 37130830 PMCID: PMC10946806 DOI: 10.1002/chem.202300855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 05/02/2023] [Accepted: 05/02/2023] [Indexed: 05/04/2023]
Abstract
Stapled peptides are a unique class of cyclic α-helical peptides that are conformationally constrained via their amino acid side-chains. They have been transformative to the field of chemical biology and peptide drug discovery through addressing many of the physicochemical limitations of linear peptides. However, there are several issues with current chemical strategies to produce stapled peptides. For example, two distinct unnatural amino acids are required to synthesize i, i+7 alkene stapled peptides, leading to high production costs. Furthermore, low purified yields are obtained due to cis/trans isomers produced during ring-closing metathesis macrocyclisation. Here we report the development of a new i, i+7 diyne-girder stapling strategy that addresses these issues. The asymmetric synthesis of nine unnatural Fmoc-protected alkyne-amino acids facilitated a systematic study to determine the optimal (S,S)-stereochemistry and 14-carbon diyne-girder bridge length. Diyne-girder stapled T-STAR peptide 29 was demonstrated to have excellent helicity, cell permeability and stability to protease degradation. Finally, we demonstrate that the diyne-girder constraint is a Raman chromophore with potential use in Raman cell microscopy. Development of this highly effective, bifunctional diyne-girder stapling strategy leads us to believe that it can be used to produce other stapled peptide probes and therapeutics.
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Affiliation(s)
- Danielle C. Morgan
- School of ChemistryAdvanced Research CentreUniversity of Glasgow11 Chapel LaneGlasgowG11 6EWUK
| | - Laura McDougall
- School of ChemistryAdvanced Research CentreUniversity of Glasgow11 Chapel LaneGlasgowG11 6EWUK
| | - Astrid Knuhtsen
- School of ChemistryAdvanced Research CentreUniversity of Glasgow11 Chapel LaneGlasgowG11 6EWUK
| | - Andrew G. Jamieson
- School of ChemistryAdvanced Research CentreUniversity of Glasgow11 Chapel LaneGlasgowG11 6EWUK
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16
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Liu D, Bardaud JX, Imani Z, Robin S, Gloaguen E, Brenner V, Aitken DJ, Mons M. Length-Dependent Transition from Extended to Folded Shapes in Short Oligomers of an Azetidine-Based α-Amino Acid: The Critical Role of NH···N H-Bonds. Molecules 2023; 28:5048. [PMID: 37446709 DOI: 10.3390/molecules28135048] [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: 05/30/2023] [Revised: 06/15/2023] [Accepted: 06/23/2023] [Indexed: 07/15/2023] Open
Abstract
Hydrogen bonds (H-bonds) are ubiquitous in peptides and proteins and are central to the stabilization of their structures. Inter-residue H-bonds between non-adjacent backbone amide NH and C=O motifs lead to the well-known secondary structures of helices, turns and sheets, but it is recognized that other H-bonding modes may be significant, including the weak intra-residue H-bond (called a C5 H-bond) that implicates the NH and C=O motifs of the same amino acid residue. Peptide model compounds that adopt stable C5 H-bonds are not readily available and the so-called 2.05-helix, formed by successive C5 H-bonds, is an elusive secondary structure. Using a combination of theoretical chemistry and spectroscopic studies in both the gas phase and solution phase, we have demonstrated that derivatives of 3-amino-1-methylazetidine-3-carboxylic acid, Aatc(Me) can form sidechain-backbone N-H···N C6γ H-bonds that accompany-and thereby stabilize-C5 H-bonds. In the capped trimer of Aatc(Me), extended C5/C6γ motifs are sufficiently robust to challenge classical 310-helix formation in solution and the fully-extended 2.05-helix conformer has been characterized in the gas phase. Concurrent H-bonding support for successive C5 motifs is a new axiom for stabilizing the extended backbone secondary structure in short peptides.
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Affiliation(s)
- Dayi Liu
- Université Paris-Saclay, CNRS, ICMMO, 91400 Orsay, France
| | | | - Zeynab Imani
- Université Paris-Saclay, CNRS, ICMMO, 91400 Orsay, France
| | - Sylvie Robin
- Université Paris-Saclay, CNRS, ICMMO, 91400 Orsay, France
- Université Paris Cité, Faculté de Pharmacie, 75006 Paris, France
| | - Eric Gloaguen
- Université Paris-Saclay, CEA, CNRS, LIDYL, 91191 Gif-sur-Yvette, France
| | - Valérie Brenner
- Université Paris-Saclay, CEA, CNRS, LIDYL, 91191 Gif-sur-Yvette, France
| | - David J Aitken
- Université Paris-Saclay, CNRS, ICMMO, 91400 Orsay, France
| | - Michel Mons
- Université Paris-Saclay, CEA, CNRS, LIDYL, 91191 Gif-sur-Yvette, France
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17
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Dalla Torre C, Sannio F, Battistella M, Docquier JD, De Zotti M. Peptaibol Analogs Show Potent Antibacterial Activity against Multidrug Resistant Opportunistic Pathogens. Int J Mol Sci 2023; 24:ijms24097997. [PMID: 37175704 PMCID: PMC10178204 DOI: 10.3390/ijms24097997] [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: 04/05/2023] [Revised: 04/19/2023] [Accepted: 04/22/2023] [Indexed: 05/15/2023] Open
Abstract
New classes of antibacterial drugs are urgently needed to address the global issue of antibiotic resistance. In this context, peptaibols are promising membrane-active peptides since they are not involved in innate immunity and their antimicrobial activity does not involve specific cellular targets, therefore reducing the chance of bacterial resistance development. Trichogin GA IV is a nonhemolytic, natural, short-length peptaibol active against Gram-positive bacteria and resistant to proteolysis. In this work, we report on the antibacterial activity of cationic trichogin analogs. Several peptides appear non-hemolytic and strongly active against many clinically relevant bacterial species, including antibiotic-resistant clinical isolates, such as Staphylococcus aureus, Acinetobacter baumannii, and extensively drug-resistant Pseudomonas aeruginosa, against which there are only a limited number of antibiotics under development. Our results further highlight how the modification of natural peptides is a valuable strategy for obtaining improved antibacterial agents with potential therapeutic applications.
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Affiliation(s)
- Chiara Dalla Torre
- Department of Chemical Sciences, University of Padova, Via Marzolo 1, I-35131 Padova, Italy
| | - Filomena Sannio
- Dipartimento di Biotecnologie Mediche, University of Siena, Viale Bracci 16, I-53100 Siena, Italy
| | - Mattia Battistella
- Department of Chemical Sciences, University of Padova, Via Marzolo 1, I-35131 Padova, Italy
| | - Jean-Denis Docquier
- Dipartimento di Biotecnologie Mediche, University of Siena, Viale Bracci 16, I-53100 Siena, Italy
- Lead Discovery Siena s.r.l., Via Fiorentina 1, I-53100 Siena, Italy
- Laboratoire de Bactériologie Moléculaire, Centre d'Ingénierie des Protéines-UR InBioS, University of Liège, Allée du Six Août 11, B-4000 Liège, Belgium
| | - Marta De Zotti
- Department of Chemical Sciences, University of Padova, Via Marzolo 1, I-35131 Padova, Italy
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18
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Xu P, Xie J, Wang DS, Zhang XP. Metalloradical approach for concurrent control in intermolecular radical allylic C-H amination. Nat Chem 2023; 15:498-507. [PMID: 36635599 PMCID: PMC10073309 DOI: 10.1038/s41557-022-01119-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 11/28/2022] [Indexed: 01/13/2023]
Abstract
Although they offer great potentials, the high reactivity and diverse pathways of radical chemistry pose difficult problems for applications in organic synthesis. In addition to the differentiation of multiple competing pathways, the control of various selectivities in radical reactions presents both formidable challenges and great opportunities. To regulate chemoselectivity and regioselectivity, as well as diastereoselectivity and enantioselectivity, calls for the formulation of conceptually new approaches and fundamentally different governing principles. Here we show that Co(II)-based metalloradical catalysis enables the radical chemoselective intermolecular amination of allylic C-H bonds through the employment of modularly designed D2-symmetric chiral amidoporphyrins with a tunable pocket-like environment as the supporting ligand. The reaction exhibits a remarkable convergence of regioselectivity, diastereoselectivity and enantioselectivity in a single catalytic operation. In addition to demonstrating the unique opportunities of metalloradical catalysis in controlling homolytic radical reactions, the Co(II)-catalysed convergent C-H amination offers a route to synthesize valuable chiral α-tertiary amines directly from an isomeric mixture of alkenes.
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Affiliation(s)
- Pan Xu
- Department of Chemistry, Merkert Chemistry Center, Boston College, Boston, MA, USA
| | - Jingjing Xie
- Department of Chemistry, Merkert Chemistry Center, Boston College, Boston, MA, USA
| | - Duo-Sheng Wang
- Department of Chemistry, Merkert Chemistry Center, Boston College, Boston, MA, USA
| | - X Peter Zhang
- Department of Chemistry, Merkert Chemistry Center, Boston College, Boston, MA, USA.
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19
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Li Y, Yang J, Geng X, Tao P, Shen Y, Su Z, Zheng K. Modular Construction of Unnatural α‐Tertiary Amino Acid Derivatives by Multicomponent Radical Cross‐Couplings. Angew Chem Int Ed Engl 2022; 61:e202210755. [DOI: 10.1002/anie.202210755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Indexed: 11/19/2022]
Affiliation(s)
- Yujun Li
- Key Laboratory of Green Chemistry & Technology Ministry of Education College of Chemistry Sichuan University Chengdu 610064 P. R. China
| | - Jie Yang
- Key Laboratory of Green Chemistry & Technology Ministry of Education College of Chemistry Sichuan University Chengdu 610064 P. R. China
| | - Xinxin Geng
- Key Laboratory of Green Chemistry & Technology Ministry of Education College of Chemistry Sichuan University Chengdu 610064 P. R. China
| | - Pan Tao
- Key Laboratory of Green Chemistry & Technology Ministry of Education College of Chemistry Sichuan University Chengdu 610064 P. R. China
| | - Yanling Shen
- Key Laboratory of Green Chemistry & Technology Ministry of Education College of Chemistry Sichuan University Chengdu 610064 P. R. China
| | - Zhishan Su
- Key Laboratory of Green Chemistry & Technology Ministry of Education College of Chemistry Sichuan University Chengdu 610064 P. R. China
| | - Ke Zheng
- Key Laboratory of Green Chemistry & Technology Ministry of Education College of Chemistry Sichuan University Chengdu 610064 P. R. China
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20
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Rohmer M, Freudenberg J, Binder WH. Secondary Structures in Synthetic Poly(Amino Acids): Homo- and Copolymers of Poly(Aib), Poly(Glu), and Poly(Asp). Macromol Biosci 2022; 23:e2200344. [PMID: 36377468 DOI: 10.1002/mabi.202200344] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 11/02/2022] [Indexed: 11/16/2022]
Abstract
The secondary structure of poly(amino acids) is an excellent tool for controlling and understanding the functionality and properties of proteins. In this perspective article the secondary structures of the homopolymers of oligo- and poly-glutamic acid (Glu), aspartic acid (Asp), and α-aminoisobutyric acid (Aib) are discussed. Information on external and internal factors, such as the nature of side groups, interactions with solvents and interactions between chains is reviewed. A special focus is directed on the folding in hybrid-polymers consisting of oligo(amino acids) and synthetic polymers. Being part of the SFB TRR 102 "Polymers under multiple constraints: restricted and controlled molecular order and mobility" this overview is embedded into the cross section of protein fibrillation and supramolecular polymers. As polymer- and amino acid folding is an important step for the utilization and design of future biomolecules these principles guide to a deeper understanding of amyloid fibrillation.
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Affiliation(s)
- Matthias Rohmer
- Macromolecular Chemistry, Von-Danckelmann-Platz 4, 06120, Halle, Germany
| | - Jan Freudenberg
- Macromolecular Chemistry, Von-Danckelmann-Platz 4, 06120, Halle, Germany
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21
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Kulkarni P, Datta D, Ganesh KN. Gemdimethyl Peptide Nucleic Acids (α/β/γ -gdm-PNA): E/Z-Rotamers Influence the Selectivity in the Formation of Parallel/Antiparallel gdm-PNA:DNA/RNA Duplexes. ACS OMEGA 2022; 7:40558-40568. [PMID: 36385799 PMCID: PMC9647847 DOI: 10.1021/acsomega.2c05873] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 10/17/2022] [Indexed: 05/29/2023]
Abstract
Peptide nucleic acids (PNAs) consist of an aminoethylglycine (aeg) backbone to which the nucleobases are linked through a tertiary amide group and bind to complementary DNA/RNA in a sequence-specific manner. The flexible aeg backbone has been the target for several chemical modifications of the PNA to improve its properties such as specificity, solubility, etc. PNA monomers exhibit a mixture of two rotamers (Z/E) arising from the restricted rotation around the tertiary amide N-CO bond. We have recently demonstrated that achiral gemdimethyl substitution at the α, β, and γ sites on the aeg backbone induces exclusive Z (α-gdm)- or E-rotamer (β-gdm) selectivity at the monomer level. It is now shown that γ/β-gdm-PNA:DNA parallel duplexes are more stable than the analogous antiparallel duplexes, while γ/β-gdm-PNA:RNA antiparallel duplexes are more stable than parallel duplexes. Furthermore, the γ/β-gdm-PNA:RNA duplexes are more stable than the γ/β-gdm-PNA:DNA duplexes. These results with γ/β-gdm-PNA are the reverse of those previously seen with α-gdm-PNA oligomers that stabilized antiparallel α-gdm-PNA:DNA duplexes compared to α-gdm-PNA:RNA duplexes. The stability of antiparallel/parallel PNA:DNA/RNA duplexes is correlated with the preference for Z/E-rotamer selectivity in α/β-gdm-PNA monomers, with Z-rotamers (α-gdm) leading to antiparallel duplexes and E-rotamers (β/γ-gdm) leading to parallel duplexes. The results highlight the role and importance of Z- and E-rotamers in controlling the structural preferences of PNA:DNA/RNA duplexes.
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Affiliation(s)
- Pradnya Kulkarni
- Chemistry
Department, Indian Institute of Science
Education and Research (IISER) Tirupati, Karkambadi Road, Mangalam, Tirupati517507, India
| | - Dhrubajyoti Datta
- Chemistry
Department, Indian Institute of Science
Education and Research (IISER) Tirupati, Karkambadi Road, Mangalam, Tirupati517507, India
| | - Krishna N. Ganesh
- Indian
Institute of Science Education and Research (IISER) Pune, Dr Homi Bhabha Road, Pune411008, India
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22
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Ji P, Chen J, Meng X, Gao F, Dong Y, Xu H, Wang W. Design of Photoredox-Catalyzed Giese-Type Reaction for the Synthesis of Chiral Quaternary α-Aryl Amino Acid Derivatives via Clayden Rearrangement. J Org Chem 2022; 87:14706-14714. [PMID: 36264622 DOI: 10.1021/acs.joc.2c02029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Chiral quaternary α-aryl amino acids are biologically valued but synthetically challenging building blocks. Herein, we report a strategy for the synthesis of molecular architectures by unifying a photoredox catalytic asymmetric Giese-type reaction and Clayden rearrangement. A new class of chiral Karady-Beckwith dehydroalanines is designed and serves as a versatile handle for the photoredox-mediated highly stereoselective Giese-type reaction with feedstock carboxylic acids and tertiary amines. Subsequent Clayden rearrangement delivers chiral quaternary α-aryl amino acid derivatives with high stereoselectivity. The versatile approach offers a reliable source for the assembly of highly demanding chiral building blocks.
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Affiliation(s)
- Peng Ji
- Departments of Pharmacology and Toxicology and Chemistry and Biochemistry, University of Arizona, Tucson, Arizona 85721-0207, United States
| | - Jing Chen
- Departments of Pharmacology and Toxicology and Chemistry and Biochemistry, University of Arizona, Tucson, Arizona 85721-0207, United States
| | - Xiang Meng
- Departments of Pharmacology and Toxicology and Chemistry and Biochemistry, University of Arizona, Tucson, Arizona 85721-0207, United States
| | - Feng Gao
- Departments of Pharmacology and Toxicology and Chemistry and Biochemistry, University of Arizona, Tucson, Arizona 85721-0207, United States
| | - Yue Dong
- Departments of Pharmacology and Toxicology and Chemistry and Biochemistry, University of Arizona, Tucson, Arizona 85721-0207, United States
| | - Hang Xu
- Departments of Pharmacology and Toxicology and Chemistry and Biochemistry, University of Arizona, Tucson, Arizona 85721-0207, United States
| | - Wei Wang
- Departments of Pharmacology and Toxicology and Chemistry and Biochemistry, University of Arizona, Tucson, Arizona 85721-0207, United States
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23
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Torregrosa-Chinillach A, Carral-Menoyo A, Gómez-Bengoa E, Chinchilla R. Organocatalytic Enantioselective α-Nitrogenation of α,α-Disubstituted Aldehydes in the Absence of a Solvent. J Org Chem 2022; 87:14507-14513. [PMID: 36283071 PMCID: PMC9639010 DOI: 10.1021/acs.joc.2c01919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
A highly efficient enantioselective α-nitrogenation method of α,α-disubstituted aldehydes with azodicarboxylates promoted by a chiral carbamate-monoprotected cyclohexa-1,2-diamine as organocatalyst has been developed. The process was carried out without any solvent, and the corresponding α,α-disubstituted α-nitrogenated aldehydes were obtained with excellent yields and enantioselectivities up to 99% ee. The sustainability of the procedure was established through the calculation of green metrics, such as EcoScale and E-factor. In addition, theoretical calculations have been used to justify the obtained enantioselectivity sense.
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Affiliation(s)
- Alejandro Torregrosa-Chinillach
- Department
of Organic Chemistry and Institute of Organic Synthesis (ISO), University of Alicante, PO Box 99, Alicante 03080, Spain
| | - Asier Carral-Menoyo
- Department
of Organic Chemistry I, University of the
Basque Country UPV/EHU, Manuel Lardizabal 3, Donostia-San Sebastián 20018, Spain
| | - Enrique Gómez-Bengoa
- Department
of Organic Chemistry I, University of the
Basque Country UPV/EHU, Manuel Lardizabal 3, Donostia-San Sebastián 20018, Spain,
| | - Rafael Chinchilla
- Department
of Organic Chemistry and Institute of Organic Synthesis (ISO), University of Alicante, PO Box 99, Alicante 03080, Spain,
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24
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Calcatelli A, Denton RM, Ball LT. Modular Synthesis of α,α-Diaryl α-Amino Esters via Bi(V)-Mediated Arylation/S N2-Displacement of Kukhtin–Ramirez Intermediates. Org Lett 2022; 24:8002-8007. [PMID: 36278869 PMCID: PMC9641671 DOI: 10.1021/acs.orglett.2c03201] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
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We report a concise and modular approach to α,α-diaryl
α-amino esters from readily available α-keto esters. This
mild, one-pot protocol proceeds via ketone umpolung, with in situ formation of a Kukhtin–Ramirez intermediate
preceding sequential electrophilic arylation by Bi(V) and SN2 displacement by an amine. The methodology is compatible with a
wide range of anilines and primary amines - including derivatives
of drugs and proteinogenic amino acids - Bi(V) arylating agents, and
α-keto ester substrates.
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Affiliation(s)
| | - Ross M. Denton
- School of Chemistry, University of Nottingham, Nottingham NG7 2RD, U.K
- GlaxoSmithKline Carbon Neutral Laboratories for Sustainable Chemistry, University of Nottingham, 6 Triumph Road, Nottingham NG7 2GA, U.K
| | - Liam T. Ball
- School of Chemistry, University of Nottingham, Nottingham NG7 2RD, U.K
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25
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Fortier M, Côté-Cyr M, Nguyen V, Babych M, Nguyen PT, Gaudreault R, Bourgault S. Contribution of the 12–17 hydrophobic region of islet amyloid polypeptide in self-assembly and cytotoxicity. Front Mol Biosci 2022; 9:1017336. [PMID: 36262476 PMCID: PMC9573943 DOI: 10.3389/fmolb.2022.1017336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 09/15/2022] [Indexed: 11/17/2022] Open
Abstract
The islet amyloid polypeptide (IAPP) is a 37-residue aggregation-prone peptide hormone whose deposition as insoluble fibrils in the islets of Langerhans is associated with type II diabetes. Therapeutic interventions targeting IAPP amyloidogenesis, which contributes to pancreatic β-cell degeneration, remain elusive owing to the lack of understanding of the self-assembly mechanisms and of the quaternary proteospecies mediating toxicity. While countless studies have investigated the contributions of the 20–29 amyloidogenic core in self-assembly, IAPP central region, i.e. positions 11 to 19, has been less studied, notwithstanding its potential key role in oligomerization. In this context, the present study aimed at investigating the physicochemical and conformational properties driving IAPP self-assembly and associated cytotoxicity. Computational tools and all-atom molecular dynamics simulation suggested that the hydrophobic 12–17 segment promotes IAPP self-recognition and aggregation. Alanine scanning revealed that the hydrophobic side chains of Leu12, Phe15 and Val17 are critical for amyloid fibril formation. Destabilization of the α-helical folding by Pro substitution enhanced self-assembly when the pyrrolidine ring was successively introduced at positions Ala13, Asn14 and Phe15, in comparison to respective Ala-substituted counterparts. Modulating the peptide backbone flexibility at position Leu16 through successive incorporation of Pro, Gly and α-methylalanine, inhibited amyloid formation and reduced cytotoxicity, while the isobutyl side chain of Leu16 was not critical for self-assembly and IAPP-mediated toxicity. These results highlight the importance of the 12–17 hydrophobic region of IAPP for self-recognition, ultimately supporting the development of therapeutic approaches to prevent oligomerization and/or fibrillization.
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Affiliation(s)
- Mathilde Fortier
- Department of Chemistry, Succursale Centre-Ville, Université du Québec à Montréal, Montreal, QC, Canada
- Quebec Network for Research on Protein Function, Engineering and Applications, PROTEO, Montreal, QC, Canada
| | - Mélanie Côté-Cyr
- Department of Chemistry, Succursale Centre-Ville, Université du Québec à Montréal, Montreal, QC, Canada
- Quebec Network for Research on Protein Function, Engineering and Applications, PROTEO, Montreal, QC, Canada
| | - Vy Nguyen
- Department of Chemistry, Succursale Centre-Ville, Université du Québec à Montréal, Montreal, QC, Canada
- Quebec Network for Research on Protein Function, Engineering and Applications, PROTEO, Montreal, QC, Canada
| | - Margaryta Babych
- Department of Chemistry, Succursale Centre-Ville, Université du Québec à Montréal, Montreal, QC, Canada
- Quebec Network for Research on Protein Function, Engineering and Applications, PROTEO, Montreal, QC, Canada
| | - Phuong Trang Nguyen
- Department of Chemistry, Succursale Centre-Ville, Université du Québec à Montréal, Montreal, QC, Canada
- Quebec Network for Research on Protein Function, Engineering and Applications, PROTEO, Montreal, QC, Canada
| | - Roger Gaudreault
- Department of Chemistry, Succursale Centre-Ville, Université du Québec à Montréal, Montreal, QC, Canada
- Department of Physics, Université de Montréal, Succursale Centre-ville, Montreal, QC, Canada
- *Correspondence: Roger Gaudreault, ; Steve Bourgault,
| | - Steve Bourgault
- Department of Chemistry, Succursale Centre-Ville, Université du Québec à Montréal, Montreal, QC, Canada
- Quebec Network for Research on Protein Function, Engineering and Applications, PROTEO, Montreal, QC, Canada
- *Correspondence: Roger Gaudreault, ; Steve Bourgault,
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26
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Syryamina VN, Afanasyeva EF, Dzuba SA, Formaggio F, De Zotti M. Peptide-membrane binding is not enough to explain bioactivity: A case study. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2022; 1864:183978. [PMID: 35659865 DOI: 10.1016/j.bbamem.2022.183978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 05/11/2022] [Accepted: 05/26/2022] [Indexed: 06/15/2023]
Abstract
Membrane-active peptides are a promising class of antimicrobial and anticancer therapeutics. For this reason, their molecular mechanisms of action are currently actively investigated. By exploiting Electron Paramagnetic Resonance, we study the membrane interaction of two spin-labeled analogs of the antimicrobial and cytotoxic peptide trichogin GA IV (Tri), with opposite bioactivity: Tri(Api8), able to selectively kill cancer cells, and Tri(Leu4), which is completely nontoxic. In our attempt to determine the molecular basis of their different biological activity, we investigate peptide impact on the lateral organization of lipid membranes, peptide localization and oligomerization, in the zwitter-ionic 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) model membrane We show that, despite their divergent bioactivity, both peptide analogs (i) are membrane-bound, (ii) display a weak tendency to oligomerization, and (iii) do not induce significant lipid rearrangement. Conversely, literature data show that the parent peptide trichogin, which is cytotoxic without any selectivity, is strongly prone to dimerization and affects the reorganization of POPC membranes. Its dimers are involved in the rotation around the peptide helix, as observed at cryogenic temperatures in the millisecond timescale. Since this latter behavior is not observed for the inactive Tri(Leu4), we propose that for short-length peptides as trichogin oligomerization and molecular motions are crucial for bioactivity, and membrane binding alone is not enough to predict or explain it. We envisage that small changes in the peptide sequence that affect only their ability to oligomerize, or their molecular motions inside the membrane, can tune the peptide activity on membranes of different compositions.
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Affiliation(s)
- Victoria N Syryamina
- Voevodsky Institute of Chemical Kinetics and Combustion, RAS, Novosibirsk 630090, Russian Federation.
| | - Ekaterina F Afanasyeva
- Voevodsky Institute of Chemical Kinetics and Combustion, RAS, Novosibirsk 630090, Russian Federation
| | - Sergei A Dzuba
- Voevodsky Institute of Chemical Kinetics and Combustion, RAS, Novosibirsk 630090, Russian Federation; Department of Physics, Novosibirsk State University,630090 Novosibirsk, Russian Federation
| | - Fernando Formaggio
- ICB-CNR, Padova Unit, Department of Chemistry, University of Padova, 35131 Padova, Italy
| | - Marta De Zotti
- ICB-CNR, Padova Unit, Department of Chemistry, University of Padova, 35131 Padova, Italy.
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27
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Helbing T, Kirchner M, Becker J, Göttlich R. Separation of the Thorpe‐Ingold and Reactive Rotamer Effect by Using the Formation of Bicyclic Aziridinium Ions. European J Org Chem 2022. [DOI: 10.1002/ejoc.202200597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Tim Helbing
- Justus Liebig Universitat Giessen Biology and Chemistry Heinrich-Buff-Ring 17 35392 Giessen GERMANY
| | | | - Jonathan Becker
- Justus Liebig Universitat Giessen Biology and Chemistry GERMANY
| | - Richard Göttlich
- University of Giessen: Justus Liebig Universitat Giessen Biology and Chemistry Heinrich-Buff-Ring 17 35392 Gießen GERMANY
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28
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Ayre J, Redmond JM, Vitulli G, Tomlinson L, Weaver R, Comeo E, Bosquillon C, Stocks MJ. Design, Synthesis, and Evaluation of Lung-Retentive Prodrugs for Extending the Lung Tissue Retention of Inhaled Drugs. J Med Chem 2022; 65:9802-9818. [PMID: 35798565 PMCID: PMC9340777 DOI: 10.1021/acs.jmedchem.2c00416] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
A major limitation
of pulmonary delivery is that drugs can exhibit
suboptimal pharmacokinetic profiles resulting from rapid elimination
from the pulmonary tissue. This can lead to systemic side effects
and a short duration of action. A series of dibasic dipeptides attached
to the poorly lung-retentive muscarinic M3 receptor antagonist piperidin-4-yl
2-hydroxy-2,2-diphenylacetate (1) through a pH-sensitive-linking
group have been evaluated. Extensive optimization resulted in 1-(((R)-2-((S)-2,6-diaminohexanamido)-3,3-dimethylbutanoyl)oxy)ethyl
4-(2-hydroxy-2,2-diphenylacetoxy)piperidine-1-carboxylate (23), which combined very good in vitro stability and
very high rat lung binding. Compound 23 progressed to
pharmacokinetic studies in rats, where, at 24 h post dosing in the
rat lung, the total lung concentration of 23 was 31.2
μM. In addition, high levels of liberated drug 1 were still detected locally, demonstrating the benefit of this novel
prodrug approach for increasing the apparent pharmacokinetic half-life
of drugs in the lungs following pulmonary dosing.
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Affiliation(s)
- Jack Ayre
- School of Pharmacy, Biodiscovery Institute, University Park Nottingham, Nottingham NG7 2RD, U.K
| | - Joanna M Redmond
- GSK Medicines Research Centre, Gunnels Wood Road, Stevenage SG1 2NY, U.K
| | - Giovanni Vitulli
- GSK Medicines Research Centre, Gunnels Wood Road, Stevenage SG1 2NY, U.K
| | - Laura Tomlinson
- GSK Medicines Research Centre, Gunnels Wood Road, Stevenage SG1 2NY, U.K
| | - Richard Weaver
- XenoGesis Ltd, Discovery Building, BioCity, Pennyfoot Street, Nottingham NG1 1GR, U.K
| | - Eleonora Comeo
- School of Pharmacy, Biodiscovery Institute, University Park Nottingham, Nottingham NG7 2RD, U.K
| | - Cynthia Bosquillon
- School of Pharmacy, Boots Science Building, University Park Nottingham, Nottingham NG7 2RD, U.K
| | - Michael J Stocks
- School of Pharmacy, Biodiscovery Institute, University Park Nottingham, Nottingham NG7 2RD, U.K
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29
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Babawale F, Murugesan K, Narobe R, König B. Synthesis of Unnatural α-Amino Acid Derivatives via Photoredox Activation of Inert C(sp 3)-H Bonds. Org Lett 2022; 24:4793-4797. [PMID: 35749614 DOI: 10.1021/acs.orglett.2c01822] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The synthesis of unnatural, tertiary amino acids is a challenging task. While decarboxylation-radical addition has been an important strategy for their formation, the use of alkyl radicals from C(sp3)-H bonds has not been fully explored. Herein, we report a photocatalytic protocol for the synthesis of unnatural α-amino esters employing abundant alkanes and imines retaining full atom economy. When this method is applied, several amino acid derivatives are synthesized in moderate to good yields.
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Affiliation(s)
- Florence Babawale
- Institute of Organic Chemistry, Faculty of Chemistry and Pharmacy, University of Regensburg, 93053 Regensburg, Germany
| | - Kathiravan Murugesan
- Institute of Organic Chemistry, Faculty of Chemistry and Pharmacy, University of Regensburg, 93053 Regensburg, Germany
| | - Rok Narobe
- Institute of Organic Chemistry, Faculty of Chemistry and Pharmacy, University of Regensburg, 93053 Regensburg, Germany
| | - Burkhard König
- Institute of Organic Chemistry, Faculty of Chemistry and Pharmacy, University of Regensburg, 93053 Regensburg, Germany
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30
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Wang X, Li J, Hayashi Y. Highly Sterically Hindered Peptide Bond Formation between α,α-Disubstituted α-Amino Acids and N-Alkyl Cysteines Using α,α-Disubstituted α-Amidonitrile. J Am Chem Soc 2022; 144:10145-10150. [PMID: 35658430 DOI: 10.1021/jacs.2c02993] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Peptides and proteins attract enormous attention in many fields of academia and industry. The introduction of unusual amino acids such as α,α-disubstituted α-amino acids or N-alkyl α-amino acids into normal peptide backbones is a well-utilized and useful tool for the modification of properties such as conformation, biological activity, and pharmacological profile. Despite the significant interest in sterically hindered peptides, research on peptides bearing an amide bond between an α,α-disubstituted α-amino acid and an N-alkyl α-amino acid remains underexplored because of the lack of an efficient synthetic approach. Herein, we describe a high-yielding synthetic method to access such extremely sterically hindered peptide bonds between amino acids. The reaction takes place between a peptide with an α,α-disubstituted α-amidonitrile and a second peptide bearing an N-alkyl cysteine, without a coupling reagent.
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Affiliation(s)
- Xiaoling Wang
- Department of Chemistry, Graduate School of Science, Tohoku University, 6-3 Aramaki Aza-Aoba, Aoba-ku, Sendai, Miyagi 980-8578, Japan
| | - Jing Li
- Department of Chemistry, Graduate School of Science, Tohoku University, 6-3 Aramaki Aza-Aoba, Aoba-ku, Sendai, Miyagi 980-8578, Japan
| | - Yujiro Hayashi
- Department of Chemistry, Graduate School of Science, Tohoku University, 6-3 Aramaki Aza-Aoba, Aoba-ku, Sendai, Miyagi 980-8578, Japan
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31
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Misra R, Vijayakanth T, Shimon LJW, Adler-Abramovich L. Atomic insight into short helical peptide comprised of consecutive multiple aromatic residues. Chem Commun (Camb) 2022; 58:6445-6448. [PMID: 35548938 DOI: 10.1039/d2cc01038k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The occurrence of sequential multiple aromatic residues in a helical sequence is rare compared to the β-sheet rich structure. Here, using helix promoting α-aminoisobutyric acid (Aib) residues, we unravel atomistic details of the helical secondary structure formation and the super helical assembly of two heptapeptides composed of sequential five and six phenylalanine (Phe) residues.
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Affiliation(s)
- Rajkumar Misra
- Department of Oral Biology, The Goldschleger School of Dental Medicine, Sackler Faculty of Medicine, The Center for Physics & Chemistry of Living Systems, and the Center for Nanoscience and Nanotechnology, Tel-Aviv University, 69978, Israel. .,Dept. of Med. Chem, NIPER Mohali, S.A.S. Nagar, Mohali, 160062, India
| | - Thangavel Vijayakanth
- The Shmunis School of Biomedicine and Cancer Research George S. Wise, Faculty of Life Sciences, Tel Aviv University, Tel Aviv, 6997801, Israel
| | - Linda J W Shimon
- Department of Chemical Research Support, The Weizmann Institute of Science, 761000, Rehovot, Israel
| | - Lihi Adler-Abramovich
- Department of Oral Biology, The Goldschleger School of Dental Medicine, Sackler Faculty of Medicine, The Center for Physics & Chemistry of Living Systems, and the Center for Nanoscience and Nanotechnology, Tel-Aviv University, 69978, Israel.
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32
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Baccelli I, Luti S, Bernardi R, Favaron F, De Zotti M, Sella L. Water-Soluble Trichogin GA IV-Derived Peptaibols Protect Tomato Plants From Botrytis cinerea Infection With Limited Impact on Plant Defenses. FRONTIERS IN PLANT SCIENCE 2022; 13:881961. [PMID: 35665189 PMCID: PMC9161086 DOI: 10.3389/fpls.2022.881961] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 04/27/2022] [Indexed: 06/02/2023]
Abstract
Peptaibols are non-ribosomal linear peptides naturally produced by a wide variety of fungi and represent the largest group of peptaibiotic molecules produced by Trichoderma species. Trichogin GA IV is an 11-residue lipopeptaibol naturally produced by Trichoderma longibrachiatum. Peptaibols possess the ability to form pores in lipid membranes or perturb their surface, and have been studied as antibiotics or anticancer drugs in human medicine, or as antimicrobial molecules against plant pathogens. When applied to plants, peptaibols may also elicit defense responses. A major drawback to the exploitation and application of peptaibols in agriculture is their poor water solubility. In a previous study, we designed water-soluble Lys-containing Trichogin GA IV analogs, which were able to inhibit the growth of several fungal plant pathogens in vitro. In the present study, we shed light on the mechanism underpinning their efficacy on plants, focusing on six Trichogin GA IV analogs. Our results highlighted peptide hydrophilicity, rather than helix stability, as the major determinant of their activity against B. cinerea infection in tomato leaves. The peptides showed preventive but not curative efficacy against infection, and lack of translaminar activity, with results reproducible on two tomato cultivars, Marmande and Micro-Tom. Reactive oxygen species (ROS) detection analysis in tomato and Arabidopsis, and expression of defense genes in tomato, highlighted a transient and limited impact of the peptides on the plant defense system. The treatment did not result in significant modulation of defense genes or defense priming. The antimicrobial effect thus emerges as the only mechanism behind the plant protection ability exerted by water-soluble Trichogin GA IV analogs, and limited effects on the plant metabolism are expected to occur.
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Affiliation(s)
- Ivan Baccelli
- Institute for Sustainable Plant Protection, National Research Council of Italy, Sesto Fiorentino, Italy
| | - Simone Luti
- Institute for Sustainable Plant Protection, National Research Council of Italy, Sesto Fiorentino, Italy
| | - Rodolfo Bernardi
- Department of Agriculture, Food and Environment, University of Pisa, Pisa, Italy
| | - Francesco Favaron
- Department of Land, Environment, Agriculture, and Forestry (TESAF), University of Padova, Legnaro, Italy
| | - Marta De Zotti
- Department of Chemistry, University of Padova, Padova, Italy
| | - Luca Sella
- Department of Land, Environment, Agriculture, and Forestry (TESAF), University of Padova, Legnaro, Italy
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33
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Catalyst-free nitration of the aliphatic C-H bonds of tertiary β-keto esters with tert-butyl nitrite: access to α-quaternary α-amino acid precursors. Tetrahedron Lett 2022. [DOI: 10.1016/j.tetlet.2022.153844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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34
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Biondi B, Syryamina VN, Rocchio G, Barbon A, Formaggio F, Toniolo C, Raap J, Dzuba SA. Is Cys(MTSL) the Best α-Amino Acid Residue to Electron Spin Labeling of Synthetically Accessible Peptide Molecules with Nitroxides? ACS OMEGA 2022; 7:5154-5165. [PMID: 35187331 PMCID: PMC8851612 DOI: 10.1021/acsomega.1c06227] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 12/27/2021] [Indexed: 06/14/2023]
Abstract
Electron paramagnetic resonance spectroscopy, particularly its pulse technique double electron-electron resonance (DEER) (also termed PELDOR), is rapidly becoming an extremely useful tool for the experimental determination of side chain-to-side chain distances between free radicals in molecules fundamental for life, such as polypeptides. Among appropriate probes, the most popular are undoubtedly nitroxide electron spin labels. In this context, suitable biosynthetically derived, helical regions of proteins, along with synthetic peptides with amphiphilic properties and antibacterial activities, are the most extensively investigated compounds. A strict requirement for a precise distance measurement has been identified in a minimal dynamic flexibility of the two nitroxide-bearing α-amino acid side chains. To this end, in this study, we have experimentally compared in detail the side-chain mobility properties of the two currently most widely utilized residues, namely, Cys(MTSL) and 2,2,6,6-tetramethylpiperidine-1-oxyl-4-amino-4-carboxylic acid (TOAC). In particular, two double-labeled, chemically synthesized 20-mer peptide molecules have been adopted as appropriate templates for our investigation on the determination of the model intramolecular separations. These double-Cys(MTSL) and double-TOAC compounds are both analogues of the almost completely rigid backbone peptide ruler which we have envisaged and 3D structurally analyzed as our original, unlabeled compound. Here, we have clearly found that the TOAC side-chain labels are largely more 3D structurally restricted than the MTSL labels. From this result, we conclude that the TOAC residue offers more precise information than the Cys(MTSL) residue on the side chain-to-side chain distance distribution in synthetically accessible peptide molecules.
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Affiliation(s)
- Barbara Biondi
- Institute
of Biomolecular Chemistry, Padova Unit, CNR, 35131 Padova, Italy
| | - Victoria N. Syryamina
- Institute
of Chemical Kinetics and Combustion, 630090 Novosibirsk, Russian Federation
| | - Gabriele Rocchio
- Department
of Chemical Sciences, University of Padova, 35131 Padova, Italy
| | - Antonio Barbon
- Department
of Chemical Sciences, University of Padova, 35131 Padova, Italy
| | - Fernando Formaggio
- Institute
of Biomolecular Chemistry, Padova Unit, CNR, 35131 Padova, Italy
- Department
of Chemical Sciences, University of Padova, 35131 Padova, Italy
| | - Claudio Toniolo
- Institute
of Biomolecular Chemistry, Padova Unit, CNR, 35131 Padova, Italy
- Department
of Chemical Sciences, University of Padova, 35131 Padova, Italy
| | - Jan Raap
- Leiden
Institute of Chemistry, Gorlaeus Laboratories,
Leiden University, 2300 RA Leiden, The Netherlands
| | - Sergei A. Dzuba
- Institute
of Chemical Kinetics and Combustion, 630090 Novosibirsk, Russian Federation
- Department
of Physics, Novosibirsk State University, 630090 Novosibirsk, Russian Federation
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35
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Gatto E, Toniolo C, Venanzi M. Peptide Self-Assembled Nanostructures: From Models to Therapeutic Peptides. NANOMATERIALS 2022; 12:nano12030466. [PMID: 35159810 PMCID: PMC8838750 DOI: 10.3390/nano12030466] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 01/24/2022] [Accepted: 01/26/2022] [Indexed: 11/25/2022]
Abstract
Self-assembly is the most suitable approach to obtaining peptide-based materials on the nano- and mesoscopic scales. Applications span from peptide drugs for personalized therapy to light harvesting and electron conductive media for solar energy production and bioelectronics, respectively. In this study, we will discuss the self-assembly of selected model and bioactive peptides, in particular reviewing our recent work on the formation of peptide architectures of nano- and mesoscopic size in solution and on solid substrates. The hierarchical and cooperative characters of peptide self-assembly will be highlighted, focusing on the structural and dynamical properties of the peptide building blocks and on the nature of the intermolecular interactions driving the aggregation phenomena in a given environment. These results will pave the way for the understanding of the still-debated mechanism of action of an antimicrobial peptide (trichogin GA IV) and the pharmacokinetic properties of a peptide drug (semaglutide) currently in use for the therapy of type-II diabetes.
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Affiliation(s)
- Emanuela Gatto
- PEPSA-LAB, Department of Chemical Science and Technologies, University of Rome, Tor Vergata, 00133 Rome, Italy;
| | - Claudio Toniolo
- Department of Chemical Sciences, University of Padua, 35131 Padua, Italy;
| | - Mariano Venanzi
- PEPSA-LAB, Department of Chemical Science and Technologies, University of Rome, Tor Vergata, 00133 Rome, Italy;
- Correspondence: ; Tel.: +39-06-7259-4468
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36
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Ueda A, Makura Y, Kakazu S, Kato T, Umeno T, Hirayama K, Doi M, Oba M, Tanaka M. E-Selective Ring-Closing Metathesis in α-Helical Stapled Peptides Using Carbocyclic α,α-Disubstituted α-Amino Acids. Org Lett 2022; 24:1049-1054. [PMID: 35073100 DOI: 10.1021/acs.orglett.1c04256] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We present an E-selective ring-closing metathesis reaction in α-helical stapled peptides at positions i and i + 4. The use of two chiral carbocyclic α,α-disubstituted α-amino acids, (1S,3S)-Ac5c3OAll and (1R,3S)-Ac5c3OAll, provides a high E-selectivity of a ≤59:1 E:Z ratio, while mixtures with E:Z ratios of 2.1-0.5:1 were produced with standard acyclic (S)-(4-pentenyl)alanine amino acids. A stapled octapeptide composed of (1S,3S)- and (1R,3S)-Ac5c3OAll amino acids showed a right-handed α-helical crystal structure.
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Affiliation(s)
- Atsushi Ueda
- Graduate School of Biomedical Sciences, Nagasaki University, 1-14 Bunkyo-machi, Nagasaki 852-8521, Japan
| | - Yui Makura
- Graduate School of Biomedical Sciences, Nagasaki University, 1-14 Bunkyo-machi, Nagasaki 852-8521, Japan
| | - Sana Kakazu
- Graduate School of Biomedical Sciences, Nagasaki University, 1-14 Bunkyo-machi, Nagasaki 852-8521, Japan
| | - Takuma Kato
- Faculty of Pharmacy, Osaka Medical and Pharmaceutical University, Osaka 569-1094, Japan
| | - Tomohiro Umeno
- Graduate School of Biomedical Sciences, Nagasaki University, 1-14 Bunkyo-machi, Nagasaki 852-8521, Japan
| | - Kazuhiro Hirayama
- Graduate School of Biomedical Sciences, Nagasaki University, 1-14 Bunkyo-machi, Nagasaki 852-8521, Japan
| | - Mitsunobu Doi
- Faculty of Pharmacy, Osaka Medical and Pharmaceutical University, Osaka 569-1094, Japan
| | - Makoto Oba
- Graduate School of Biomedical Sciences, Nagasaki University, 1-14 Bunkyo-machi, Nagasaki 852-8521, Japan.,Graduate School of Medicine, Kyoto Prefectural University of Medicine, Kyoto 606-0823, Japan
| | - Masakazu Tanaka
- Graduate School of Biomedical Sciences, Nagasaki University, 1-14 Bunkyo-machi, Nagasaki 852-8521, Japan
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37
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Zhang D, Wen J, Zhang X. Construction of a quaternary stereogenic center by asymmetric hydroformylation: a straightforward method to prepare chiral α-quaternary amino acids. Chem Sci 2022; 13:7215-7223. [PMID: 35799829 PMCID: PMC9214857 DOI: 10.1039/d2sc02139k] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 05/26/2022] [Indexed: 01/01/2023] Open
Abstract
The construction of chiral quaternary carbon stereocenters has been a long-standing challenge in organic chemistry. Particularly, α-quaternary amino acids that are of high importance in biochemistry still lack a straightforward synthetic method. We here reported a hydroformylation approach to access chiral quaternary stereogenic centers, which has been a long-standing challenge in transition metal catalysis. α,β-Unsaturated carboxylic acid derivatives undergo hydroformylation with a rhodium catalyst to generate an α-quaternary stereocenter under mild conditions. By using this method, a variety of chiral α-quaternary amino acids could be synthesized with satisfactory enantioselectivity. In-depth investigation revealed that the regioselectivity is dramatically influenced by the electronic properties of the substituents attached to the target C
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C bond. By applying NMR and DFT analyses, the chiral environment of a rhodium/Yanphos complex was depicted, based on which a substrate-catalyst interaction model was proposed. A rhodium-catalyzed asymmetric hydroformylation reaction was reported to construct chiral α-quaternary amino acid derivatives. High chemo-, regio- and enantioselectivity were realized in one step.![]()
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Affiliation(s)
- Dequan Zhang
- Department of Chemistry, Guangdong Provincial Key Laboratory of Catalysis, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Jialin Wen
- Department of Chemistry, Guangdong Provincial Key Laboratory of Catalysis, Southern University of Science and Technology, Shenzhen, 518055, China
- Academy for Advanced Interdisciplinary Studies, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Xumu Zhang
- Department of Chemistry, Guangdong Provincial Key Laboratory of Catalysis, Southern University of Science and Technology, Shenzhen, 518055, China
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38
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Abstract
In this highlight, we describe the construction of supramolecular single/double/triple-helical assemblies from small di/tri/tetrapeptides and their applications.
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Affiliation(s)
- Rajat Subhra Giri
- Department of Chemistry, Laboratory of Peptide and Amyloid Research, Indian Institute of Technology Guwahati, Assam-781039, India
| | - Bhubaneswar Mandal
- Department of Chemistry, Laboratory of Peptide and Amyloid Research, Indian Institute of Technology Guwahati, Assam-781039, India
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39
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Xiao Y, Huang Y, Zeng Z, Luo X, Qian X, Yang Y. Harnessing Thorpe-Ingold Dialkylation to Access High-Hill-Percentage pH Probes. J Org Chem 2021; 87:85-93. [PMID: 34958219 DOI: 10.1021/acs.joc.1c01887] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Sensitivity is an important parameter for a molecular probe. Hill-type pH probes exhibit improved detection sensitivity compared to the traditional pH probes following the Henderson-Hasselbalch equation. Exploiting positive cooperativity, we recently devised a novel molecular scaffold (PHX) to offer such an unconventional Hill-type pH titration profile. We previously confirmed that PHX is not a pure Hill-type probe yet. Only 64% of its absorbance/fluorescence turn-on is the result of a Hill-type pathway. The remaining 36% is from an undesired Henderson-Hasselbalch-type pathway (HH pathway). In this work, the Thorpe-Ingold dialkylation was harnessed to further suppress the percent contribution of the HH pathway down to 16%. We also propose that PHX is a viable molecular model for assessing the efficacy of the steric compressing effect induced by different Thorpe-Ingold dialkylations.
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Affiliation(s)
- Yansheng Xiao
- State Key Laboratory of Bioreactor Engineering. Shanghai Key Laboratory of Chemical Biology, School of Pharmacy. East China University of Science and Technology, Meilong Road 130, Shanghai 200237, China
| | - Yunxia Huang
- State Key Laboratory of Bioreactor Engineering. Shanghai Key Laboratory of Chemical Biology, School of Pharmacy. East China University of Science and Technology, Meilong Road 130, Shanghai 200237, China
| | - Zhenhua Zeng
- State Key Laboratory of Bioreactor Engineering. Shanghai Key Laboratory of Chemical Biology, School of Pharmacy. East China University of Science and Technology, Meilong Road 130, Shanghai 200237, China
| | - Xiao Luo
- School of Chemistry and Molecular Engineering, East China Normal University, Dongchuan Road 500, Shanghai 200241, China
| | - Xuhong Qian
- State Key Laboratory of Bioreactor Engineering. Shanghai Key Laboratory of Chemical Biology, School of Pharmacy. East China University of Science and Technology, Meilong Road 130, Shanghai 200237, China
| | - Youjun Yang
- State Key Laboratory of Bioreactor Engineering. Shanghai Key Laboratory of Chemical Biology, School of Pharmacy. East China University of Science and Technology, Meilong Road 130, Shanghai 200237, China
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40
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Bodero L, Guitot K, Lensen N, Lequin O, Brigaud T, Ongeri S, Chaume G. Introducing the Chiral Constrained α-Trifluoromethylalanine in Aib foldamers to Control, Quantify and Assign the Helical Screw-Sense. Chemistry 2021; 28:e202103887. [PMID: 34890083 DOI: 10.1002/chem.202103887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Indexed: 11/11/2022]
Abstract
Oligomers of α-aminoisobutyric acid (Aib) are achiral peptides that adopt 3 10 helical structures with equal population of left- and right-handed conformers. Yet, the screw-sense preference of the helical chain may be controlled by a single chiral residue located at one terminus. 1 H and 19 F NMR, X-ray crystallography and circular dichroism studies on new Aib oligomers show that the incorporation of a chiral quaternary α-trifluoromethylalanine at their N -terminus induces a reversal of the screw-sense preference of the 3 10 -helix compared to that of a non-fluorinated analogue having an l-α-methyl valine residue. This work demonstrates that, among the many particular properties of introducing a trifluoromethyl group into foldamers, its stereo-electronic properties are of major interest to control the helical screw sense. Its use as an easy-to-handle 19 F NMR probe to reliably determine both the magnitude of the screw-sense preference and its sign assignment is also of remarkable interest.
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Affiliation(s)
| | | | | | - Olivier Lequin
- Sorbonne Université Campus Pierre et Marie Curie: Sorbonne Universite Campus Pierre et Marie Curie, chemistry, FRANCE
| | | | | | - Grégory Chaume
- CY Cergy Paris Universite, Chemistry, 5 mail Gay Lussac, 95000, Cergy-Pontoise, FRANCE
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41
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Locarno S, Bucci R, Impresari E, Gelmi ML, Pellegrino S, Clerici F. Ultrashort Peptides and Gold Nanoparticles: Influence of Constrained Amino Acids on Colloidal Stability. Front Chem 2021; 9:736519. [PMID: 34660531 PMCID: PMC8517408 DOI: 10.3389/fchem.2021.736519] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 09/16/2021] [Indexed: 11/13/2022] Open
Abstract
Poor colloidal stability of gold nanoparticles (AuNPs) in physiological environments remains one of the major limitations that contribute to their difficult translation from bench to clinic. For this reason, an active research field is the development of molecules able to hamper AuNPs aggregation tendency in physiological environments. In this context, synthetic peptides are gaining an increased interest as an alternative to the use of biomacromolecules and polymers, due to their easiness of synthesis and their profitable pharmacokinetic profile. In this work, we reported on the use of ultrashort peptides containing conformationally constrained amino acids (AAs) for the stabilization of AuNPs. A small library of non-natural self-assembled oligopeptides were synthesized and used to functionalize spherical AuNPs of 20 nm diameter, via the ligand exchange method. The aim was to investigate the role of the constrained AA, the anchor point (at C- or N-terminus) and the peptide length on their potential use as gold binding motif. Ultrashort Aib containing peptides were identified as effective tools for AuNPs colloidal stabilization. Furthermore, peptide coated AuNPs were found to be storable as powders without losing the stabilization properties once re-dispersed in water. Finally, the possibility to exploit the developed systems for binding proteins via molecular recognition was also evaluated using biotin as model.
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Affiliation(s)
- Silvia Locarno
- Dipartimento di Fisica “Aldo Pontremoli”, Università degli Studi di Milano, Milano, Italy
| | - Raffaella Bucci
- DISFARM-Dipartimento di Scienze Farmaceutiche, Sezione Chimica Generale e Organica ‘‘A. Marchesini”, Università degli Studi di Milano, Milano, Italy
| | - Elisa Impresari
- DISFARM-Dipartimento di Scienze Farmaceutiche, Sezione Chimica Generale e Organica ‘‘A. Marchesini”, Università degli Studi di Milano, Milano, Italy
| | - Maria Luisa Gelmi
- DISFARM-Dipartimento di Scienze Farmaceutiche, Sezione Chimica Generale e Organica ‘‘A. Marchesini”, Università degli Studi di Milano, Milano, Italy
| | - Sara Pellegrino
- DISFARM-Dipartimento di Scienze Farmaceutiche, Sezione Chimica Generale e Organica ‘‘A. Marchesini”, Università degli Studi di Milano, Milano, Italy
| | - Francesca Clerici
- DISFARM-Dipartimento di Scienze Farmaceutiche, Sezione Chimica Generale e Organica ‘‘A. Marchesini”, Università degli Studi di Milano, Milano, Italy
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42
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Asano A, Nakagawa M, Miyajima C, Yasui M, Minoura K, Yamada T, Doi M. Effect of the powerful plasticity of the tert-butyl side chain on the conformational equilibrium of ascidiacyclamides. J Pept Sci 2021; 27:e3363. [PMID: 34462993 DOI: 10.1002/psc.3363] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 07/28/2021] [Accepted: 07/31/2021] [Indexed: 11/06/2022]
Abstract
Ascidiacyclamide [cyclo(-Ile1,5 -oxazoline2,6 -d-Val3,7 -thiazole4,8 -)2 ] is a cytotoxic cyclic peptide from ascidian. Through structural analyses using monosubstituted analogues (Xaa1 : Ala, 2-aminobutyric acid, Val, cyclohexylglycine, and phenylglycine), we previously demonstrated the conformational equilibrium between its square and folded forms. As the bulkiness of the Xaa1 residue side chain was reduced, spontaneous folding was promoted, and the cytotoxicity decreased accordingly. In the present study, five disubstituted analogues in which a tert-leucine residue (Tle) was incorporated at the 5-position of the abovementioned monosubstituted analogues were synthesized, after which their structures were analyzed using X-ray diffraction, circular dichroism (CD) spectral measurements, and 1 H NMR-based quantitative analysis. The side chains of the Tle and Ile residues are structural isomers of one another, and the Tle residue bearing the tert-butyl group can be expected to play a role as a building block. In fact, peptides incorporating Tle5 exhibited much less spontaneous folding than their Ile5 counterparts in both crystal and solution. Increases in enthalpy and entropy due to the tert-butyl group during the folding process resulted in increased conformational free energy (ΔG°). The powerful plasticity of the tert-butyl group would stabilize the square form relating with cytotoxicity.
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Affiliation(s)
- Akiko Asano
- Faculty of Pharmacy, Osaka Medical and Pharmaceutical University, Osaka, Japan
| | - Maki Nakagawa
- Faculty of Pharmacy, Osaka Medical and Pharmaceutical University, Osaka, Japan
| | - Chihiro Miyajima
- Faculty of Pharmacy, Osaka Medical and Pharmaceutical University, Osaka, Japan
| | - Mami Yasui
- Faculty of Pharmacy, Osaka Medical and Pharmaceutical University, Osaka, Japan
| | - Katsuhiko Minoura
- Faculty of Pharmacy, Osaka Medical and Pharmaceutical University, Osaka, Japan
| | - Takeshi Yamada
- Faculty of Pharmacy, Osaka Medical and Pharmaceutical University, Osaka, Japan
| | - Mitsunobu Doi
- Faculty of Pharmacy, Osaka Medical and Pharmaceutical University, Osaka, Japan
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43
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Sato K, Umeno T, Ueda A, Kato T, Doi M, Tanaka M. Asymmetric 1,4-Addition Reactions Catalyzed by N-Terminal Thiourea-Modified Helical l-Leu Peptide with Cyclic Amino Acids. Chemistry 2021; 27:11216-11220. [PMID: 34028101 DOI: 10.1002/chem.202101252] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Indexed: 11/12/2022]
Abstract
N-terminal thiourea-modified l-Leu-based peptide {(3,5-diCF3 Ph)NHC(=S)-(l-Leu-l-Leu-Ac5 c)2 -OMe} with five-membered ring α,α-disubstituted α-amino acids (Ac5 c) catalyzed a highly enantioselective 1,4-addition reaction between β-nitrostyrene and dimethyl malonate. The enantioselective reaction required only 0.5 mol % chiral peptide-catalyst in the presence of i Pr2 EtN (2.5 equiv.), and gave a 1,4-adduct with 93 % ee of an 85 % yield. As Michael acceptors, various β-nitrostyrene derivatives such as methyl, p-fluoro, p-bromo, and p-methoxy substituents on the phenyl group, 2-furyl, 2-thiophenyl, and naphthyl β-nitroethylenes could be applied. Furthermore, various alkyl malonates and cyclic β-keto-esters could be used as Michael donors. It became clear that the length of the peptide chain, a right-handed helical structure, amide N-Hs, and the N-terminal thiourea moiety play crucial roles in asymmetric induction.
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Affiliation(s)
- Kazuki Sato
- Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, 8528521, Japan
| | - Tomohiro Umeno
- Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, 8528521, Japan
| | - Atsushi Ueda
- Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, 8528521, Japan
| | - Takuma Kato
- Osaka Medical and Pharmaceutical University, Osaka, 5698686, Japan
| | - Mitsunobu Doi
- Osaka Medical and Pharmaceutical University, Osaka, 5698686, Japan
| | - Masakazu Tanaka
- Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, 8528521, Japan
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44
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Guryanov I, Korzhikov-Vlakh V, Bhattacharya M, Biondi B, Masiero G, Formaggio F, Tennikova T, Urtti A. Conformationally Constrained Peptides with High Affinity to the Vascular Endothelial Growth Factor. J Med Chem 2021; 64:10900-10907. [PMID: 34269584 DOI: 10.1021/acs.jmedchem.1c00219] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The design of efficient vascular endothelial growth factor (VEGF) inhibitors is a high-priority research area aimed at the treatment of pathological angiogenesis. Among other compounds, v114* has been identified as a potent VEGF-binding peptide. In order to improve the affinity to VEGF, we built a conformational constrain in its structure. To this aim, Cα-tetrasubstituted amino acid Aib was introduced into the N-terminal tail, peptide loop, or C-terminal helix. NMR studies confirmed the stabilization of the helical conformation in proximity to the Aib residue. We found that the induction of the N-terminal helical structure or stabilization of the C-terminal helix can noticeably increase the peptide affinity to the VEGF. These peptides efficiently inhibited VEGF-stimulated cell proliferation as well. The insertion of the non-proteinogenic Aib residue significantly enhanced the stability of the peptides in the vitreous environment. Thus, these Aib-containing peptides are promising candidates for the design of VEGF inhibitors with improved properties.
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Affiliation(s)
- Ivan Guryanov
- Institute of Chemistry, St. Petersburg State University, Universitetsky pr. 26, Peterhof, St. Petersburg 198504, Russia
| | - Viktor Korzhikov-Vlakh
- Institute of Chemistry, St. Petersburg State University, Universitetsky pr. 26, Peterhof, St. Petersburg 198504, Russia
| | - Madhushree Bhattacharya
- Division of Pharmaceutical Biosciences, University of Helsinki, Viikinkaari 5 E, Helsinki 00014, Finland
| | - Barbara Biondi
- ICB, Padova Unit, CNR, Department of Chemistry, University of Padova, via Marzolo 1, Padova 35131, Italy
| | - Giulia Masiero
- ICB, Padova Unit, CNR, Department of Chemistry, University of Padova, via Marzolo 1, Padova 35131, Italy
| | - Fernando Formaggio
- ICB, Padova Unit, CNR, Department of Chemistry, University of Padova, via Marzolo 1, Padova 35131, Italy
| | - Tatiana Tennikova
- Institute of Chemistry, St. Petersburg State University, Universitetsky pr. 26, Peterhof, St. Petersburg 198504, Russia
| | - Arto Urtti
- Division of Pharmaceutical Biosciences, University of Helsinki, Viikinkaari 5 E, Helsinki 00014, Finland.,School of Pharmacy, University of Eastern Finland, Yliopistonranta 1 C, Kuopio 70211, Finland
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45
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Leonard DJ, Zieleniewski F, Wellhöfer I, Baker EG, Ward JW, Woolfson DN, Clayden J. Scalable synthesis and coupling of quaternary α-arylated amino acids: α-aryl substituents are tolerated in α-helical peptides. Chem Sci 2021; 12:9386-9390. [PMID: 34349911 PMCID: PMC8278958 DOI: 10.1039/d1sc01378e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 06/08/2021] [Indexed: 11/21/2022] Open
Abstract
Quaternary amino acids are important tools for the modification and stabilisation of peptide secondary structures. Here we describe a practical and scalable synthesis applicable to quaternary alpha-arylated amino acids (Q4As), and the development of solid-phase synthesis conditions for their incorporation into peptides. Monomeric and dimeric α-helical peptides are synthesised with varying degrees of Q4A substitution and their structures examined using biophysical methods. Both enantiomers of the Q4As are tolerated in folded monomeric and oligomeric α-helical peptides, with the (R)-enantiomer slightly more so than the (S).
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Affiliation(s)
- Daniel J Leonard
- School of Chemistry, University of Bristol Cantock's Close Bristol BS8 1TS UK
| | | | - Isabelle Wellhöfer
- School of Chemistry, University of Bristol Cantock's Close Bristol BS8 1TS UK
| | - Emily G Baker
- School of Chemistry, University of Bristol Cantock's Close Bristol BS8 1TS UK
- School of Biochemistry, University of Bristol, Medical Sciences Building, University Walk Bristol BS8 1TS UK
- Bristol BioDesign Institute, University of Bristol, Life Sciences Building Tyndall Avenue Bristol BS8 1TQ UK
| | - John W Ward
- School of Chemistry, University of Bristol Cantock's Close Bristol BS8 1TS UK
| | - Derek N Woolfson
- School of Chemistry, University of Bristol Cantock's Close Bristol BS8 1TS UK
- School of Biochemistry, University of Bristol, Medical Sciences Building, University Walk Bristol BS8 1TS UK
- Bristol BioDesign Institute, University of Bristol, Life Sciences Building Tyndall Avenue Bristol BS8 1TQ UK
| | - Jonathan Clayden
- School of Chemistry, University of Bristol Cantock's Close Bristol BS8 1TS UK
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46
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Misra R, Rudnick-Glick S, Adler-Abramovich L. From Folding to Assembly: Functional Supramolecular Architectures of Peptides Comprised of Non-Canonical Amino Acids. Macromol Biosci 2021; 21:e2100090. [PMID: 34142442 DOI: 10.1002/mabi.202100090] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 05/06/2021] [Indexed: 12/27/2022]
Abstract
The engineering of biological molecules is the fundamental concept behind the design of complex materials with desirable functions. Over the last few decades, peptides and proteins have emerged as useful building blocks for well-defined nanostructures with controlled size and dimensions. Short peptides in particular have received much attention due to their inherent biocompatibility, lower synthetic cost, and ease of tunability. In addition to the diverse self-assembling properties of short peptides comprising coded amino acids and their emerging applications in nanotechnology, there is now growing interest in the properties of peptides composed of non-canonical amino acids. Such non-natural oligomers have been shown in recent years to form well-defined secondary structures similar to natural proteins, with the ability to self-assemble to generate a wide variety of nanostructures with excellent biostability. This review describes recent events in the development of supramolecular assemblies of peptides composed completely of non-coded amino acids and their hybrid analogues. Special attention is paid to understanding the supramolecular assemblies at the atomic level and to considering their potential applications in nanotechnology.
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Affiliation(s)
- Rajkumar Misra
- Department of Oral Biology, The Goldschleger School of Dental Medicine, Sackler Faculty of Medicine and the Center for Nanoscience and Nanotechnology, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Safra Rudnick-Glick
- Department of Oral Biology, The Goldschleger School of Dental Medicine, Sackler Faculty of Medicine and the Center for Nanoscience and Nanotechnology, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Lihi Adler-Abramovich
- Department of Oral Biology, The Goldschleger School of Dental Medicine, Sackler Faculty of Medicine and the Center for Nanoscience and Nanotechnology, Tel Aviv University, Tel Aviv, 69978, Israel
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47
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Santi S, Bisello A, Cardena R, Tomelleri S, Schiesari R, Biondi B, Crisma M, Formaggio F. Flat, C α,β -Didehydroalanine Foldamers with Ferrocene Pendants: Assessing the Role of α-Peptide Dipolar Moments. Chempluschem 2021; 86:723-730. [PMID: 33825347 DOI: 10.1002/cplu.202100072] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Revised: 03/22/2021] [Indexed: 12/28/2022]
Abstract
The foldamer field is continuously expanding as it allows to produce molecules endowed with 3D-structures and functions never observed in nature. We synthesized flat foldamers based on the natural, but non-coded, Cα,β -didehydroalanine α-amino acid, and covalently linked to them two ferrocene (Fc) moieties, as redox probes. These conjugates retain the flat and extended conformation of the 2.05 -helix, both in solution and in the crystal state (X-ray diffraction). Cyclic voltammetry measurements agree with the adoption of the 2.05 -helix, characterized by a negligible dipole moment. Thus, elongated α-peptide stretches of this type are insulators rather than charge conductors, the latter being constituted by peptide α-helices. Also, our homo-tetrapeptide has a N-to-C length of about 18.2 Å, almost double than that (9.7 Å) of an α-helical α-tetrapeptide.
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Affiliation(s)
- Saverio Santi
- Department of Chemical Sciences, University of Padova, via Marzolo 1, 35131, Padova, Italy
| | - Annalisa Bisello
- Department of Chemical Sciences, University of Padova, via Marzolo 1, 35131, Padova, Italy
| | - Roberta Cardena
- Department of Chemical Sciences, University of Padova, via Marzolo 1, 35131, Padova, Italy
| | - Silvia Tomelleri
- Department of Chemical Sciences, University of Padova, via Marzolo 1, 35131, Padova, Italy
| | - Renato Schiesari
- Department of Chemical Sciences, University of Padova, via Marzolo 1, 35131, Padova, Italy
| | - Barbara Biondi
- Institute of Biomolecular Chemistry, Padova Unit, CNR, via Marzolo 1, 35131, Padova, Italy
| | - Marco Crisma
- Institute of Biomolecular Chemistry, Padova Unit, CNR, via Marzolo 1, 35131, Padova, Italy
| | - Fernando Formaggio
- Department of Chemical Sciences, University of Padova, via Marzolo 1, 35131, Padova, Italy
- Institute of Biomolecular Chemistry, Padova Unit, CNR, via Marzolo 1, 35131, Padova, Italy
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48
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Pollastrini M, Marafon G, Clayden J, Moretto A. Light-mediated control of activity in a photosensitive foldamer that mimics an esterase. Chem Commun (Camb) 2021; 57:2269-2272. [PMID: 33533349 DOI: 10.1039/d0cc08309g] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report a catalytic foldamer in which a fumaramide chromophore links a Ser residue to a helical domain that contains within its sequence the residues His and Asp. Photoisomerization of the fumaramide chromophore (with E geometry) to the corresponding maleamide (with Z geometry) brings together a 'catalytic triad' of Ser, His, and Asp, triggering esterase activity that is absent in the fumaramide isomer. The fumaramide/maleamide linker thus acts as a light-sensitive switchable cofactor for activation of catalytic activity in short foldamers.
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Affiliation(s)
- Matteo Pollastrini
- Department of Chemical Sciences, University of Padova, Padova 35131, Italy.
| | - Giulia Marafon
- Department of Chemical Sciences, University of Padova, Padova 35131, Italy.
| | - Jonathan Clayden
- School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, UK
| | - Alessandro Moretto
- Department of Chemical Sciences, University of Padova, Padova 35131, Italy.
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49
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Vicens L, Bietti M, Costas M. General Access to Modified α-Amino Acids by Bioinspired Stereoselective γ-C-H Bond Lactonization. Angew Chem Int Ed Engl 2021; 60:4740-4746. [PMID: 33210804 DOI: 10.1002/anie.202007899] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 11/02/2020] [Indexed: 01/06/2023]
Abstract
α-Amino acids represent a valuable class of natural products employed as building blocks in biological and chemical synthesis. Because of the limited number of natural amino acids available, and of their widespread application in proteomics, diagnosis, drug delivery and catalysis, there is an increasing demand for the development of procedures for the preparation of modified analogues. Herein, we show that the use of bioinspired manganese catalysts and H2 O2 under mild conditions, provides access to modified α-amino acids via γ-C-H bond lactonization. The system can efficiently target 1°, 2° and 3° γ-C-H bonds of α-substituted and achiral α,α-disubstituted α-amino acids with outstanding site-selectivity, good to excellent diastereoselectivity and (where applicable) enantioselectivity. This methodology may be considered alternative to well-established organometallic procedures.
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Affiliation(s)
- Laia Vicens
- Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química, Universitat de Girona, Campus Montilivi, 17071, Girona, Catalonia, Spain
| | - Massimo Bietti
- Dipartimento di Scienze e Tecnologie Chimiche, Università "Tor Vergata", Via della Ricerca Scientifica, 1, 00133, Rome, Italy
| | - Miquel Costas
- Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química, Universitat de Girona, Campus Montilivi, 17071, Girona, Catalonia, Spain
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Gessmann R, Brückner H, Petratos K. The first non-helical Aib-containing hexapeptide: The crystal structure of Z-Gly-Aib-Gly-Aib-Gly-Aib-OtBu. J Pept Sci 2021; 27:e3307. [PMID: 33599060 DOI: 10.1002/psc.3307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 02/05/2021] [Accepted: 02/05/2021] [Indexed: 11/11/2022]
Abstract
The synthetic peptide Z-Gly-Aib-Gly-Aib-Gly-Aib-OtBu was crystallized from a mixture of ethyl acetate and n-hexane. The crystals belong to the centrosymmetric space group Pbca. There are three molecules in the asymmetric unit. The three molecules differ mainly in the Z-group conformation. The first Gly residue adopts a fully extended conformation, residues 2 and 3 lie in the left-handed helical region, residues 4 and 5 in the right-handed helical region, and residue 6 again in the left-handed helical region of the Ramachandran plot. There are only two of four possible intramolecular hydrogen bonds formed, namely, between Aib4 and Gly1 forming a β-turn of type III' and between Aib6 and Gly3 forming a β-turn of type I. The inverted molecules (by space group symmetry) lie in the regions with opposite handedness and form β-turns of type III and I'. In contrast to all known long synthetic and naturally occurring Aib-containing peptides that fold as 310 - or α-helix, Z-(Gly-Aib)3 -OtBu folds in a quite flat structure from which only the protecting groups bulge out.
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Affiliation(s)
| | - Hans Brückner
- Department of Food Sciences, Interdisciplinary Research Center, Justus-Liebig-University of Giessen, Giessen, Germany
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