1
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Bhatt MR, Zondlo NJ. Electronic Control of Polyproline II Helix Stability via the Identity of Acyl Capping Groups: the Pivaloyl Group Particularly Promotes PPII. Chemistry 2024; 30:e202401454. [PMID: 38661017 DOI: 10.1002/chem.202401454] [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: 04/14/2024] [Revised: 04/24/2024] [Accepted: 04/25/2024] [Indexed: 04/26/2024]
Abstract
The type II polyproline helix (PPII) is a fundamental secondary structure of proteins, important in globular proteins, in intrinsically disordered proteins, and at protein-protein interfaces. PPII is stabilized in part by n→π* interactions between consecutive carbonyls, via electron delocalization between an electron-donor carbonyl lone pair (n) and an electron-acceptor carbonyl (π*) on the subsequent residue. We previously demonstrated that changes to the electronic properties of the acyl donor can predictably modulate the strength of n→π* interactions, with data from model compounds, in solution in chloroform, in the solid state, and computationally. Herein, we examined whether the electronic properties of acyl capping groups could modulate the stability of PPII in peptides in water. In X-PPGY-NH2 peptides (X=10 acyl capping groups), the effect of acyl group identity on PPII was quantified by circular dichroism and NMR spectroscopy. Electron-rich acyl groups promoted PPII relative to the standard acetyl (Ac-) group, with the pivaloyl and iso-butyryl groups most significantly increasing PPII. In contrast, acyl derivatives with electron-withdrawing substituents and the formyl group relatively disfavored PPII. Similar results, though lesser in magnitude, were also observed in X-APPGY-NH2 peptides, indicating that the capping group can impact PPII conformation at both proline and non-proline residues. The pivaloyl group was particularly favorable in promoting PPII. The effects of acyl capping groups were further analyzed in X-DfpPGY-NH2 and X-ADfpPGY-NH2 peptides, Dfp=4,4-difluoroproline. Data on these peptides indicated that acyl groups induced order Piv- > Ac- > For-. These results suggest that greater consideration should be given to the identity of acyl capping groups in inducing structure in peptides.
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Affiliation(s)
- Megh R Bhatt
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, 19716, United States
| | - Neal J Zondlo
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, 19716, United States
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2
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Antoniazzi G, Schäfer RJB, Biedermann M, Rüttimann E, Wennemers H. Isonitrile-Proline - A Versatile Handle for the Chemoselective Derivatization of Collagen Peptides. Chemistry 2023; 29:e202302389. [PMID: 37498143 DOI: 10.1002/chem.202302389] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 07/26/2023] [Accepted: 07/27/2023] [Indexed: 07/28/2023]
Abstract
Functional groups that allow for chemoselective and bioorthogonal derivatization are valuable tools for the labelling of peptides and proteins. The isonitrile is such a group but synthetic methods for its incorporation into peptides by solid-phase peptide synthesis are not known. Here, we introduce (4S)- and (4R)-isonitrileproline (Inp) as building blocks for solid-phase peptide synthesis. Conformational studies of (4S)- and (4R)-Inp and thermal stability analysis of Inp-containing collagen triple helices revealed that the isonitrile group exerts a stereoelectronic gauche effect. We showcase the value of Inp for bioorthogonal labelling by derivatization of Inp-containing collagen model peptides (CMPs). Dual labelling with a pair of bioorthogonal reactions of a CMP containing Inp and azidoproline residues further highlights the versatility of the new isonitrile-containing amino acids.
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Affiliation(s)
- Giuseppe Antoniazzi
- Laboratory of Organic Chemistry, ETH Zürich, Vladimir-Prelog-Weg 3, 8093, Zürich, Switzerland
| | - Rebecca J B Schäfer
- Laboratory of Organic Chemistry, ETH Zürich, Vladimir-Prelog-Weg 3, 8093, Zürich, Switzerland
| | - Maurice Biedermann
- Laboratory of Organic Chemistry, ETH Zürich, Vladimir-Prelog-Weg 3, 8093, Zürich, Switzerland
| | - Eric Rüttimann
- Laboratory of Organic Chemistry, ETH Zürich, Vladimir-Prelog-Weg 3, 8093, Zürich, Switzerland
| | - Helma Wennemers
- Laboratory of Organic Chemistry, ETH Zürich, Vladimir-Prelog-Weg 3, 8093, Zürich, Switzerland
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3
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Fiala T, Heeb R, Vigliotti L, Wennemers H. The Yin and Yang of How N-Terminal Acyl Caps Affect Collagen Triple Helices. Biomacromolecules 2023; 24:3954-3960. [PMID: 37227696 DOI: 10.1021/acs.biomac.3c00241] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
N-terminal acylation is a common tool for the installation of functional moieties (e.g., sensors or bioactive molecules) on collagen model peptides (CMPs). The N-acyl group and its length are generally assumed to have little or no influence on the properties of the collagen triple helix formed by the CMP. Here, we show that the length of short (C1-C4) acyl capping groups has different effects on the thermal stability of collagen triple helices in POG, OGP, and GPO frames. While the effect of different capping groups on the stability of triple helices in the GPO frame is negligible, longer acyl chains stabilize OGP triple helices but destabilize POG analogues. The observed trends arise from a combination of steric repulsion, the hydrophobic effect, and n → π* interactions. Our study provides a basis for the design of N-terminally functionalized CMPs with predictable effects on triple helix stability.
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Affiliation(s)
- Tomas Fiala
- Laboratory of Organic Chemistry, ETH Zurich, D-CHAB, Vladimir-Prelog-Weg 3, 8093 Zürich, Switzerland
| | - Rahel Heeb
- Laboratory of Organic Chemistry, ETH Zurich, D-CHAB, Vladimir-Prelog-Weg 3, 8093 Zürich, Switzerland
| | - Luca Vigliotti
- Laboratory of Organic Chemistry, ETH Zurich, D-CHAB, Vladimir-Prelog-Weg 3, 8093 Zürich, Switzerland
| | - Helma Wennemers
- Laboratory of Organic Chemistry, ETH Zurich, D-CHAB, Vladimir-Prelog-Weg 3, 8093 Zürich, Switzerland
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4
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Pollastrini M, Pasquinelli L, Górecki M, Balzano F, Cupellini L, Lipparini F, Uccello Barretta G, Marchetti F, Pescitelli G, Angelici G. A Unique and Stable Polyproline I Helix Sorted out from Conformational Equilibrium by Solvent Polarity. J Org Chem 2022; 87:13715-13725. [PMID: 36242553 PMCID: PMC9639007 DOI: 10.1021/acs.joc.2c01377] [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
Polyproline I helical structures are often considered as the hidden face of their most famous geminal sibling, Polyproline II, as PPI is generally spotted only within a conformational equilibrium. We designed and synthesized a stable Polyproline I structure exploiting the striking tendency of (S)-indoline-2-carboxylic acid to drive the peptide bond conformation toward the cis amide isomer, when dissolved in polar solvents. The cooperative effect of only four amino acidic units is sufficient to form a preferential structure in solution. We shed light on this rare secondary structure with a thorough analysis of the spectroscopic and chiroptical properties of the tetramer, supported by X-ray crystallography and computational studies.
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Affiliation(s)
- Matteo Pollastrini
- Dipartimento
di Chimica e Chimica Industriale, Università
di Pisa, Via G. Moruzzi 13, Pisa 56124, Italy
| | - Luca Pasquinelli
- Dipartimento
di Chimica e Chimica Industriale, Università
di Pisa, Via G. Moruzzi 13, Pisa 56124, Italy
| | - Marcin Górecki
- Dipartimento
di Chimica e Chimica Industriale, Università
di Pisa, Via G. Moruzzi 13, Pisa 56124, Italy,Institute
of Organic Chemistry, Polish Academy of
Sciences, ul. Kasprzaka
44/52, Warsaw 01-224, Poland
| | - Federica Balzano
- Dipartimento
di Chimica e Chimica Industriale, Università
di Pisa, Via G. Moruzzi 13, Pisa 56124, Italy
| | - Lorenzo Cupellini
- Dipartimento
di Chimica e Chimica Industriale, Università
di Pisa, Via G. Moruzzi 13, Pisa 56124, Italy
| | - Filippo Lipparini
- Dipartimento
di Chimica e Chimica Industriale, Università
di Pisa, Via G. Moruzzi 13, Pisa 56124, Italy
| | - Gloria Uccello Barretta
- Dipartimento
di Chimica e Chimica Industriale, Università
di Pisa, Via G. Moruzzi 13, Pisa 56124, Italy
| | - Fabio Marchetti
- Dipartimento
di Chimica e Chimica Industriale, Università
di Pisa, Via G. Moruzzi 13, Pisa 56124, Italy
| | - Gennaro Pescitelli
- Dipartimento
di Chimica e Chimica Industriale, Università
di Pisa, Via G. Moruzzi 13, Pisa 56124, Italy,
| | - Gaetano Angelici
- Dipartimento
di Chimica e Chimica Industriale, Università
di Pisa, Via G. Moruzzi 13, Pisa 56124, Italy,
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5
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Zondlo NJ. Solvation stabilizes intercarbonyl n→π* interactions and polyproline II helix. Phys Chem Chem Phys 2022; 24:13571-13586. [PMID: 35635541 DOI: 10.1039/d2cp00857b] [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
n→π* interactions between consecutive carbonyls stabilize the α-helix and polyproline II helix (PPII) conformations in proteins. n→π* interactions have been suggested to provide significant conformational biases to the disordered states of proteins. To understand the roles of solvation on the strength of n→π* interactions, computational investigations were conducted on a model n→π* interaction, the twisted-parallel-offset formaldehyde dimer, as a function of explicit solvation of the donor and acceptor carbonyls, using water and HF. In addition, the effects of urea, thiourea, guanidinium, and monovalent cations on n→π* interaction strength were examined. Solvation of the acceptor carbonyl significantly strengthens the n→π* interaction, while solvation of the donor carbonyl only modestly weakens the n→π* interaction. The n→π* interaction strength was maximized with two solvent molecules on the acceptor carbonyl. Urea stabilized the n→π* interaction via simultaneous engagement of both oxygen lone pairs on the acceptor carbonyl. Solvent effects were further investigated in the model peptides Ac-Pro-NMe2, Ac-Ala-NMe2, and Ac-Pro2-NMe2. Solvent effects in peptides were similar to those in the formaldehyde dimer, with solvation of the acceptor carbonyl increasing n→π* interaction strength and resulting in more compact conformations, in both the proline endo and exo ring puckers, as well as a reduction in the energy difference between these ring puckers. Carbonyl solvation leads to an energetic preference for PPII over both the α-helix and β/extended conformations, consistent with experimental data that protic solvents and protein denaturants both promote PPII. Solvation of the acceptor carbonyl weakens the intraresidue C5 hydrogen bond that stabilizes the β conformation.
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Affiliation(s)
- Neal J Zondlo
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE 19716, USA.
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6
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Müller WA, Sarkis JR, Marczak LDF, Muniz AR. Molecular dynamics study of the effects of static and oscillating electric fields in ovalbumin. INNOV FOOD SCI EMERG 2022. [DOI: 10.1016/j.ifset.2021.102911] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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7
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Linclau B, Wang Z, Jeffries B, Graton J, Carbajo RJ, Sinnaeve D, Le Questel J, Scott JS, Chiarparin E. Relating Conformational Equilibria to Conformer‐Specific Lipophilicities: New Opportunities in Drug Discovery. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202114862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Bruno Linclau
- School of Chemistry University of Southampton Highfield, Southampton SO17 1BJ UK
- Department of Organic and Macromolecular Chemistry, Ghent University Campus Sterre, S4 Krijgslaan 281 9000 Ghent Belgium
| | - Zhong Wang
- School of Chemistry University of Southampton Highfield, Southampton SO17 1BJ UK
| | - Benjamin Jeffries
- School of Chemistry University of Southampton Highfield, Southampton SO17 1BJ UK
| | - Jérôme Graton
- CEISAM UMR CNRS 6230 Université de Nantes CNRS CEISAM UMR 6230 44000 Nantes France
| | | | - Davy Sinnaeve
- Univ. Lille Inserm Institut Pasteur de Lille CHU Lille U1167—RID-AGE—Risk Factors and Molecular Determinants of Aging-Related Diseases 59000 Lille France
- CNRS ERL9002—Integrative Structural Biology 59000 Lille France
| | - Jean‐Yves Le Questel
- CEISAM UMR CNRS 6230 Université de Nantes CNRS CEISAM UMR 6230 44000 Nantes France
| | - James S. Scott
- Medicinal Chemistry, Oncology R&D AstraZeneca Cambridge CB4 0WG UK
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8
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Kovačević M, Čakić Semenčić M, Radošević K, Molčanov K, Roca S, Šimunović L, Kodrin I, Barišić L. Conformational Preferences and Antiproliferative Activity of Peptidomimetics Containing Methyl 1'-Aminoferrocene-1-carboxylate and Turn-Forming Homo- and Heterochiral Pro-Ala Motifs. Int J Mol Sci 2021; 22:ijms222413532. [PMID: 34948332 PMCID: PMC8705031 DOI: 10.3390/ijms222413532] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 12/09/2021] [Accepted: 12/14/2021] [Indexed: 11/16/2022] Open
Abstract
The concept of peptidomimetics is based on structural modifications of natural peptides that aim not only to mimic their 3D shape and biological function, but also to reduce their limitations. The peptidomimetic approach is used in medicinal chemistry to develop drug-like compounds that are more active and selective than natural peptides and have fewer side effects. One of the synthetic strategies for obtaining peptidomimetics involves mimicking peptide α-helices, β-sheets or turns. Turns are usually located on the protein surface where they interact with various receptors and are therefore involved in numerous biological events. Among the various synthetic tools for turn mimetic design reported so far, our group uses an approach based on the insertion of different ferrocene templates into the peptide backbone that both induce turn formation and reduce conformational flexibility. Here, we conjugated methyl 1'-aminoferrocene-carboxylate with homo- and heterochiral Pro-Ala dipeptides to investigate the turn formation potential and antiproliferative properties of the resulting peptidomimetics 2-5. Detailed spectroscopic (IR, NMR, CD), X-ray and DFT studies showed that the heterochiral conjugates 2 and 3 were more suitable for the formation of β-turns. Cell viability study, clonogenic assay and cell death analysis showed the highest biological potential of homochiral peptide 4.
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Affiliation(s)
- Monika Kovačević
- Department of Chemistry and Biochemistry, Faculty of Food Technology and Biotechnology, University of Zagreb, 10000 Zagreb, Croatia; (M.K.); (M.Č.S.); (L.Š.)
| | - Mojca Čakić Semenčić
- Department of Chemistry and Biochemistry, Faculty of Food Technology and Biotechnology, University of Zagreb, 10000 Zagreb, Croatia; (M.K.); (M.Č.S.); (L.Š.)
| | - Kristina Radošević
- Department of Biochemical Engineering, Faculty of Food Technology and Biotechnology, University of Zagreb, 10000 Zagreb, Croatia;
| | - Krešimir Molčanov
- Division of Physical Chemistry, Ruđer Bošković Institute, 10000 Zagreb, Croatia;
| | - Sunčica Roca
- NMR Centre, Ruđer Bošković Institute, 10000 Zagreb, Croatia;
| | - Lucija Šimunović
- Department of Chemistry and Biochemistry, Faculty of Food Technology and Biotechnology, University of Zagreb, 10000 Zagreb, Croatia; (M.K.); (M.Č.S.); (L.Š.)
| | - Ivan Kodrin
- Department of Organic Chemistry, Faculty of Science, University of Zagreb, 10000 Zagreb, Croatia
- Correspondence: (I.K.); (L.B.); Tel.: +385-1-4606-403 (I.K.); +385-1-4605-069 (L.B.)
| | - Lidija Barišić
- Department of Chemistry and Biochemistry, Faculty of Food Technology and Biotechnology, University of Zagreb, 10000 Zagreb, Croatia; (M.K.); (M.Č.S.); (L.Š.)
- Correspondence: (I.K.); (L.B.); Tel.: +385-1-4606-403 (I.K.); +385-1-4605-069 (L.B.)
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9
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Linclau B, Wang Z, Jeffries B, Graton J, Carbajo RJ, Sinnaeve D, Le Questel JY, Scott JS, Chiarparin E. Relating Conformational Equilibria to Conformer-Specific Lipophilicities: New Opportunities in Drug Discovery. Angew Chem Int Ed Engl 2021; 61:e202114862. [PMID: 34913249 PMCID: PMC9304282 DOI: 10.1002/anie.202114862] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Indexed: 11/10/2022]
Abstract
Efficient drug discovery is based on a concerted effort in optimizing bioactivity and compound properties such as lipophilicity, and is guided by efficiency metrics that reflect both aspects. While conformation–activity relationships and ligand conformational control are known strategies to improve bioactivity, the use of conformer‐specific lipophilicities (logp) is much less explored. Here we show how conformer‐specific logp values can be obtained from knowledge of the macroscopic logP value, and of the equilibrium constants between the individual species in water and in octanol. This is illustrated with fluorinated amide rotamers, with integration of rotamer 19F NMR signals as a facile, direct method to obtain logp values. The difference between logp and logP optimization is highlighted, giving rise to a novel avenue for lipophilicity control in drug discovery.
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Affiliation(s)
- Bruno Linclau
- School of Chemistry, University of Southampton, Highfield, Southampton, SO17 1BJ, UK.,Department of Organic and Macromolecular Chemistry, Ghent University, Campus Sterre, S4, Krijgslaan 281, 9000, Ghent, Belgium
| | - Zhong Wang
- School of Chemistry, University of Southampton, Highfield, Southampton, SO17 1BJ, UK
| | - Benjamin Jeffries
- School of Chemistry, University of Southampton, Highfield, Southampton, SO17 1BJ, UK
| | - Jérôme Graton
- CEISAM UMR CNRS 6230, Université de Nantes, CNRS, CEISAM UMR 6230, 44000, Nantes, France
| | - Rodrigo J Carbajo
- Medicinal Chemistry, Oncology R&D, AstraZeneca, Cambridge, CB4 0WG, UK
| | - Davy Sinnaeve
- Univ. Lille, Inserm, Institut Pasteur de Lille, CHU Lille, U1167-RID-AGE-Risk Factors and Molecular, Determinants of Aging-Related Diseases, 59000, Lille, France.,CNRS, ERL9002-Integrative Structural Biology, 59000, Lille, France
| | - Jean-Yves Le Questel
- CEISAM UMR CNRS 6230, Université de Nantes, CNRS, CEISAM UMR 6230, 44000, Nantes, France
| | - James S Scott
- Medicinal Chemistry, Oncology R&D, AstraZeneca, Cambridge, CB4 0WG, UK
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10
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Dones JM, Abularrage NS, Khanal N, Gold B, Raines RT. Acceleration of 1,3-Dipolar Cycloadditions by Integration of Strain and Electronic Tuning. J Am Chem Soc 2021; 143:9489-9497. [PMID: 34151576 DOI: 10.1021/jacs.1c03133] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
The 1,3-dipolar cycloaddition between azides and alkynes provides new means to probe and control biological processes. A major challenge is to achieve high reaction rates with stable reagents. The optimization of alkynyl reagents has relied on two strategies: increasing strain and tuning electronics. We report on the integration of these strategies. A computational analysis suggested that a CH → N aryl substitution in dibenzocyclooctyne (DIBO) could be beneficial. In transition states, the nitrogen of 2-azabenzo-benzocyclooctyne (ABC) engages in an n→π* interaction with the C=O of α-azidoacetamides and forms a hydrogen bond with the N-H of α-diazoacetamides. These dipole-specific interactions act cooperatively with electronic activation of the strained π-bond to increase reactivity. We found that ABC does indeed react more quickly with α-azidoacetamides and α-diazoacetamides than its constitutional isomer, dibenzoazacyclooctyne (DIBAC). ABC and DIBAC have comparable chemical stability in a biomimetic solution. Both ABC and DIBO are accessible in three steps by the alkylidene carbene-mediated ring expansion of commercial cycloheptanones. Our findings enhance the accessibility and utility of 1,3-dipolar cycloadditions and encourage further innovation.
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Affiliation(s)
- Jesús M Dones
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Nile S Abularrage
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Namrata Khanal
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico 87131, United States
| | - Brian Gold
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States.,Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico 87131, United States
| | - Ronald T Raines
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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11
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Pollastrini M, Lipparini F, Pasquinelli L, Balzano F, Barretta GU, Pescitelli G, Angelici G. A Proline Mimetic for the Design of New Stable Secondary Structures: Solvent-Dependent Amide Bond Isomerization of ( S)-Indoline-2-carboxylic Acid Derivatives. J Org Chem 2021; 86:7946-7954. [PMID: 34080867 PMCID: PMC8456495 DOI: 10.1021/acs.joc.1c00184] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
![]()
A thorough experimental and computational study on the conformational properties of
(S)-indoline-2-carboxylic acid derivatives has been conducted. Methyl
(S)-1-acetylindoline-2-carboxylate, both a mimetic of proline and
phenylalanine, shows a remarkable tendency toward the cis amide isomer
when dissolved in polar solvents. This behavior is opposite to the general preference of
proline for the trans isomer, making indoline-2-carboxylic acid a good
candidate for the design of different secondary structures and new materials.
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Affiliation(s)
- Matteo Pollastrini
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via G. Moruzzi 13, 56124 Pisa, Italy
| | - Filippo Lipparini
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via G. Moruzzi 13, 56124 Pisa, Italy
| | - Luca Pasquinelli
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via G. Moruzzi 13, 56124 Pisa, Italy
| | - Federica Balzano
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via G. Moruzzi 13, 56124 Pisa, Italy
| | - Gloria Uccello Barretta
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via G. Moruzzi 13, 56124 Pisa, Italy
| | - Gennaro Pescitelli
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via G. Moruzzi 13, 56124 Pisa, Italy
| | - Gaetano Angelici
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Via G. Moruzzi 13, 56124 Pisa, Italy
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12
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Mondal R, Agbaria M, Nairoukh Z. Fluorinated Rings: Conformation and Application. Chemistry 2021; 27:7193-7213. [PMID: 33512034 DOI: 10.1002/chem.202005425] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Indexed: 12/16/2022]
Abstract
The introduction of fluorine atoms into molecules and materials across many fields of academic and industrial research is now commonplace, owing to their unique properties. A particularly interesting feature is the impact of fluorine substitution on the relative orientation of a C-F bond when incorporated into organic molecules. In this Review, we will be discussing the conformational behavior of fluorinated aliphatic carbo- and heterocyclic systems. The conformational preference of each system is associated with various interactions introduced by fluorine substitution such as charge-dipole, dipole-dipole, and hyperconjugative interactions. The contribution of each interaction on the stabilization of the fluorinated alicyclic system, which manifests itself in low conformations, will be discussed in detail. The novelty of this feature will be demonstrated by presenting the most recent applications.
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Affiliation(s)
- Rajarshi Mondal
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Jerusalem, 9190401, Israel
| | - Mohamed Agbaria
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Jerusalem, 9190401, Israel
| | - Zackaria Nairoukh
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Jerusalem, 9190401, Israel
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13
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Egli J, Esposito C, Müri M, Riniker S, Wennemers H. Influence of Lipidation on the Folding and Stability of Collagen Triple Helices-An Experimental and Theoretical Study. J Am Chem Soc 2021; 143:5937-5942. [PMID: 33830753 DOI: 10.1021/jacs.1c01512] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The folding of triple-helical collagen, the most abundant protein in nature, relies on the nucleation and propagation along the strands. Hydrophobic moieties are crucial for the folding and stability of numerous proteins. Instead, nature uses for collagen a trimerization domain and cis-trans prolyl isomerases to facilitate and accelerate triple helix formation. Yet, pendant hydrophobic moieties endow triple-helical collagen with hyperstability and accelerate the cis-trans isomerization to an extent that thermally induced unfolding and folding of collagen triple helices take place at the same speed. Here, we systematically explored the effect of pendant fatty acids on the folding and stability of collagen triple helices. Thermal denaturation and kinetic studies with a series of collagen mimetic peptides (CMPs) bearing saturated and unsaturated fatty acids with different lengths revealed that longer and more flexible fatty acid appendages increase the stability and the folding rate of collagen triple helices. Molecular dynamics simulations combined with experimental data indicate that the hydrophobic appendages stabilize the triple helix by interaction with the grooves of the collagen triple helix and accelerate the folding and unfolding process by creating a molten globule-like intermediate.
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Affiliation(s)
- Jasmine Egli
- Laboratory of Organic Chemistry, ETH Zurich, D-CHAB, Vladimir-Prelog-Weg 3, 8093 Zurich, Switzerland
| | - Carmen Esposito
- Laboratory of Physical Chemistry, ETH Zurich, D-CHAB, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland
| | - Mike Müri
- Laboratory of Organic Chemistry, ETH Zurich, D-CHAB, Vladimir-Prelog-Weg 3, 8093 Zurich, Switzerland
| | - Sereina Riniker
- Laboratory of Physical Chemistry, ETH Zurich, D-CHAB, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland
| | - Helma Wennemers
- Laboratory of Organic Chemistry, ETH Zurich, D-CHAB, Vladimir-Prelog-Weg 3, 8093 Zurich, Switzerland
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14
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Lamers B, Herdlitschka A, Schnitzer T, Mabesoone MF, Schoenmakers SM, de Waal BF, Palmans AR, Wennemers H, Meijer E. Oligodimethylsiloxane-Oligoproline Block Co-Oligomers: the Interplay between Aggregation and Phase Segregation in Bulk and Solution. J Am Chem Soc 2021; 143:4032-4042. [PMID: 33660998 PMCID: PMC8041288 DOI: 10.1021/jacs.1c01076] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Indexed: 12/14/2022]
Abstract
Discrete block co-oligomers (BCOs) assemble into highly ordered nanostructures, which adopt a variety of morphologies depending on their environment. Here, we present a series of discrete oligodimethylsiloxane-oligoproline (oDMS-oPro) BCOs with varying oligomer lengths and proline end-groups, and study the nanostructures formed in both bulk and solution. The conjugation of oligoprolines to apolar siloxanes permits a study of the aggregation behavior of oligoproline moieties in a variety of solvents, including a highly apolar solvent like methylcyclohexane. The apolar solvent is more reminiscent of the polarity of the siloxane bulk, which gives insights into the supramolecular interactions that govern both bulk and solution assembly processes of the oligoproline. This extensive structural characterization allows the bridging of the gap between solution and bulk assembly. The interplay between the aggregation of the oligoproline block and the phase segregation induced by the siloxane drives the assembly. This gives rise to disordered, micellar microstructures in apolar solution and crystallization-driven lamellar nanostructures in the bulk. While most di- and triblock co-oligomers adopt predictable morphological features, one of them, oDMS15-oPro6-NH2, exhibits pathway complexity leading to gel formation. The pathway selection in the complex interplay between aggregation and phase segregation gives rise to interesting material properties.
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Affiliation(s)
- Brigitte
A.G. Lamers
- Institute
for Complex Molecular Systems and Laboratory of Macromolecular and
Organic Chemistry, Eindhoven University
of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Andreas Herdlitschka
- Laboratory
of Organic Chemistry, ETH Zurich, D-CHAB, Vladimir-Prelog-Weg 3, 8093 Zurich, Switzerland
| | - Tobias Schnitzer
- Institute
for Complex Molecular Systems and Laboratory of Macromolecular and
Organic Chemistry, Eindhoven University
of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Mathijs F.J. Mabesoone
- Institute
for Complex Molecular Systems and Laboratory of Macromolecular and
Organic Chemistry, Eindhoven University
of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Sandra M.C. Schoenmakers
- Institute
for Complex Molecular Systems and Laboratory of Macromolecular and
Organic Chemistry, Eindhoven University
of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Bas F.M. de Waal
- Institute
for Complex Molecular Systems and Laboratory of Macromolecular and
Organic Chemistry, Eindhoven University
of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Anja R.A. Palmans
- Institute
for Complex Molecular Systems and Laboratory of Macromolecular and
Organic Chemistry, Eindhoven University
of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
| | - Helma Wennemers
- Laboratory
of Organic Chemistry, ETH Zurich, D-CHAB, Vladimir-Prelog-Weg 3, 8093 Zurich, Switzerland
| | - E.W. Meijer
- Institute
for Complex Molecular Systems and Laboratory of Macromolecular and
Organic Chemistry, Eindhoven University
of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
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15
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Sanchez CA, Gadais C, Chaume G, Girard S, Chelain E, Brigaud T. Enantiopure 5-CF 3-Proline: Synthesis, Incorporation in Peptides, and Tuning of the Peptide Bond Geometry. Org Lett 2021; 23:382-387. [PMID: 33369434 DOI: 10.1021/acs.orglett.0c03880] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The straightforward synthesis of enantiopure 5-(R)-and 5-(S)-trifluoromethylproline is reported. The key steps are a Ruppert-Prakash reagent addition on l-pyroglutamic esters followed by an elimination reaction and a selective reduction. The solution-phase and solid-phase incorporation of this unprotected enantiopure fluorinated amino acid in a short peptide chain was demonstrated. Compared to proline, the CF3 group provides a decrease of the trans to cis amide bond isomerization energy and an increase of the cis conformer population.
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Affiliation(s)
- Clément A Sanchez
- CNRS, BioCIS, CY Cergy Paris Université, 95000 Cergy Pontoise, France.,CNRS, BioCIS, Université Paris-Saclay, 92290 Châtenay-Malabry, France
| | - Charlène Gadais
- CNRS, BioCIS, CY Cergy Paris Université, 95000 Cergy Pontoise, France.,CNRS, BioCIS, Université Paris-Saclay, 92290 Châtenay-Malabry, France
| | - Grégory Chaume
- CNRS, BioCIS, CY Cergy Paris Université, 95000 Cergy Pontoise, France.,CNRS, BioCIS, Université Paris-Saclay, 92290 Châtenay-Malabry, France
| | - Sylvaine Girard
- CNRS, BioCIS, CY Cergy Paris Université, 95000 Cergy Pontoise, France.,CNRS, BioCIS, Université Paris-Saclay, 92290 Châtenay-Malabry, France
| | - Evelyne Chelain
- CNRS, BioCIS, CY Cergy Paris Université, 95000 Cergy Pontoise, France.,CNRS, BioCIS, Université Paris-Saclay, 92290 Châtenay-Malabry, France
| | - Thierry Brigaud
- CNRS, BioCIS, CY Cergy Paris Université, 95000 Cergy Pontoise, France.,CNRS, BioCIS, Université Paris-Saclay, 92290 Châtenay-Malabry, France
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16
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Metrano AJ, Chinn AJ, Shugrue CR, Stone EA, Kim B, Miller SJ. Asymmetric Catalysis Mediated by Synthetic Peptides, Version 2.0: Expansion of Scope and Mechanisms. Chem Rev 2020; 120:11479-11615. [PMID: 32969640 PMCID: PMC8006536 DOI: 10.1021/acs.chemrev.0c00523] [Citation(s) in RCA: 98] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Low molecular weight synthetic peptides have been demonstrated to be effective catalysts for an increasingly wide array of asymmetric transformations. In many cases, these peptide-based catalysts have enabled novel multifunctional substrate activation modes and unprecedented selectivity manifolds. These features, along with their ease of preparation, modular and tunable structures, and often biomimetic attributes make peptides well-suited as chiral catalysts and of broad interest. Many examples of peptide-catalyzed asymmetric reactions have appeared in the literature since the last survey of this broad field in Chemical Reviews (Chem. Rev. 2007, 107, 5759-5812). The overarching goal of this new Review is to provide a comprehensive account of the numerous advances in the field. As a corollary to this goal, we survey the many different types of catalytic reactions, ranging from acylation to C-C bond formation, in which peptides have been successfully employed. In so doing, we devote significant discussion to the structural and mechanistic aspects of these reactions that are perhaps specific to peptide-based catalysts and their interactions with substrates and/or reagents.
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Affiliation(s)
- Anthony J. Metrano
- AstraZeneca Oncology R&D, 35 Gatehouse Dr., Waltham, MA 02451, United States
| | - Alex J. Chinn
- Department of Chemistry, Princeton University, Princeton, NJ 08544, United States
| | - Christopher R. Shugrue
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, United States
| | - Elizabeth A. Stone
- Department of Chemistry, Yale University, P.O. Box 208107, New Haven, CT 06520, United States
| | - Byoungmoo Kim
- Department of Chemistry, Clemson University, Clemson, SC 29634, United States
| | - Scott J. Miller
- Department of Chemistry, Yale University, P.O. Box 208107, New Haven, CT 06520, United States
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17
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Sphaerostilbellins, New Antimicrobial Aminolipopeptide Peptaibiotics from Sphaerostilbella toxica. Biomolecules 2020; 10:biom10101371. [PMID: 32993102 PMCID: PMC7600149 DOI: 10.3390/biom10101371] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 09/18/2020] [Accepted: 09/25/2020] [Indexed: 02/07/2023] Open
Abstract
Sphaerostilbella toxica is a mycoparasitic fungus that can be found parasitizing wood-decay basidiomycetes in the southern USA. Organic solvent extracts of fermented strains of S. toxica exhibited potent antimicrobial activity, including potent growth inhibition of human pathogenic yeasts Candida albicans and Cryptococcus neoformans, the respiratory pathogenic fungus Aspergillus fumigatus, and the Gram-positive bacterium Staphylococcus aureus. Bioassay-guided separations led to the purification and structure elucidation of new peptaibiotics designated as sphaerostilbellins A and B. Their structures were established mainly by analysis of NMR and HRMS data, verification of amino acid composition by Marfey's method, and by comparison with published data of known compounds. They incorporate intriguing structural features, including an N-terminal 2-methyl-3-oxo-tetradecanoyl (MOTDA) residue and a C-terminal putrescine residue. The minimal inhibitory concentrations for sphaerostilbellins A and B were measured as 2 μM each for C. neoformans, 1 μM each for A. fumigatus, and 4 and 2 μM, respectively, for C. albicans. Murine macrophage cells were unaffected at these concentrations.
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18
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Kubyshkin V. Polarity effects in 4-fluoro- and 4-(trifluoromethyl)prolines. Beilstein J Org Chem 2020; 16:1837-1852. [PMID: 32765799 PMCID: PMC7385359 DOI: 10.3762/bjoc.16.151] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 07/06/2020] [Indexed: 12/14/2022] Open
Abstract
Fluorine-containing analogues of proline are valuable tools in engineering and NMR spectroscopic studies of peptides and proteins. Their use relies on the fundamental understanding of the interplay between the substituents and the main chain groups of the amino acid residue. This study aims to showcase the polarity-related effects that arise from the interaction between the functional groups in molecular models. Properties such as conformation, acid-base transition, and amide-bond isomerism were examined for diastereomeric 4-fluoroprolines, 4-(trifluoromethyl)prolines, and 1,1-difluoro-5-azaspiro[2.4]heptane-6-carboxylates. The preferred conformation on the proline ring originated from a preferential axial positioning for a single fluorine atom, and an equatorial positioning for a trifluoromethyl- or a difluoromethylene group. This orientation of the substituents explains the observed trends in the pK a values, lipophilicity, and the kinetics of the amide bond rotation. The study also provides a set of evidences that the transition state of the amide-bond rotation in peptidyl-prolyl favors C4-exo conformation of the pyrrolidine ring.
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19
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Guo LE, Tang YX, Zhang SY, Hong Y, Yan XS, Li Z, Jiang YB. Balancing interactions in proline-based receptors for chiral recognition of l-/d-DOPA. Org Biomol Chem 2020; 18:4590-4598. [PMID: 32497164 DOI: 10.1039/d0ob00493f] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Proline based receptors (1-14) attached with phenylboronic acid and benzaldehyde binding groups at the N-/C- or C-/N-termini of the proline residue were created for chiral recognition of l-/d-DOPA, in an attempt to examine if balancing the two binding events would influence the recognition. By changing the positions of boronic acid and aldehyde groups substituted on the phenyl rings (1-4, 5-8) and the site at which phenylboronic acid and benzaldehyde moieties attached respectively to the N- and C-termini or C- and N-termini of the proline residue (1-4vs.5-8), and by introducing an electron-withdrawing fluorine atom in the phenyl ring of the weaker binder the benzaldehyde moiety (11vs.1, 14vs.5), we were able to show that a better balance of the two binding events does improve the chiral recognition. This finding can only be made with the current version of receptors that were equipped with two different binding groups. Together with the finding that the chiral recognition performance in mixed organic-aqueous solutions is tunable by varying the solvent composition, we have now arrived at a protocol for designing proline based receptors for extended applications in chiral recognition.
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Affiliation(s)
- Lin-E Guo
- Department of Chemistry, College of Chemistry and Chemical Engineering, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, and iChEM, Xiamen University, Xiamen 361005, China.
| | - Yu-Xin Tang
- Department of Chemistry, College of Chemistry and Chemical Engineering, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, and iChEM, Xiamen University, Xiamen 361005, China.
| | - Shu-Ying Zhang
- Department of Chemistry, College of Chemistry and Chemical Engineering, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, and iChEM, Xiamen University, Xiamen 361005, China.
| | - Yuan Hong
- Department of Chemistry, College of Chemistry and Chemical Engineering, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, and iChEM, Xiamen University, Xiamen 361005, China.
| | - Xiao-Sheng Yan
- Department of Chemistry, College of Chemistry and Chemical Engineering, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, and iChEM, Xiamen University, Xiamen 361005, China.
| | - Zhao Li
- Department of Chemistry, College of Chemistry and Chemical Engineering, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, and iChEM, Xiamen University, Xiamen 361005, China.
| | - Yun-Bao Jiang
- Department of Chemistry, College of Chemistry and Chemical Engineering, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, and iChEM, Xiamen University, Xiamen 361005, China.
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20
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Egli J, Schnitzer T, Dietschreit JCB, Ochsenfeld C, Wennemers H. Why Proline? Influence of Ring-Size on the Collagen Triple Helix. Org Lett 2019; 22:348-351. [DOI: 10.1021/acs.orglett.9b03528] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Jasmine Egli
- Laboratory of Organic Chemistry, ETH Zürich, Vladimir-Prelog-Weg 3, 8093 Zürich, Switzerland
| | - Tobias Schnitzer
- Laboratory of Organic Chemistry, ETH Zürich, Vladimir-Prelog-Weg 3, 8093 Zürich, Switzerland
| | - Johannes C. B. Dietschreit
- Chair of Theoretical Chemistry, Department of Chemistry, University of Munich, Butenandtstr. 7, 81377 Munich, Germany
| | - Christian Ochsenfeld
- Chair of Theoretical Chemistry, Department of Chemistry, University of Munich, Butenandtstr. 7, 81377 Munich, Germany
| | - Helma Wennemers
- Laboratory of Organic Chemistry, ETH Zürich, Vladimir-Prelog-Weg 3, 8093 Zürich, Switzerland
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21
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Dai W, Zhang Z, Du Y. Modulation of Conformational Preferences of Heteroaromatic Ethers and Amides through Protonation and Ionization: Charge Effect. Chemistry 2019; 8:840-851. [PMID: 31304077 PMCID: PMC6604235 DOI: 10.1002/open.201900103] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Revised: 05/06/2019] [Indexed: 12/16/2022]
Abstract
Multiple approaches reveal the strong effects of a positive charge introduced by protonation or ionization on the conformation of o‐heteroaromatic ethers and amides. The ethers and amides containing an ortho‐N heteroatom are syn‐preferring while those containing an ortho‐O or ortho‐S heteroatom are mostly anti‐preferring. However, for all the monocyclic o‐heteroaromatic ethers and amides, the protonated ones are all anti‐preferring while the ionized ones are all syn‐preferring. Interestingly, although both the protonation and ionization introduce a positive charge, they have such different effects on molecular conformation, very informative for understanding the origin of conformational preferences. Detailed analysis shows that the population of the introduced positive charge dictates the conformational preferences via electrostatic and orbital interactions. Compared to ortho‐heteroatoms, meta‐heteroatoms have weaker effect on conformational preference. Achieved by complete inductive method, the regularity of conformational preferences and switching provides easy ways to modulate conformers (by pH or redox), and makes this kind of ether or amide bond a conformational hinge applicable to design of functional molecules (drugs and materials) and modulation of molecular biological processes.
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Affiliation(s)
- Wenshuai Dai
- Beijing National Laboratory of Molecular Science, State Key laboratory of Molecular Reaction Dynamics Institute of Chemistry, Chinese Academy of Sciences Beijing 100190 Beijing PR China.,School of Chemical Engineering University of Chinese Academy of Sciences Beijing 100049 P. R. China
| | - Zhe Zhang
- Beijing National Laboratory of Molecular Science, State Key laboratory of Molecular Reaction Dynamics Institute of Chemistry, Chinese Academy of Sciences Beijing 100190 Beijing PR China.,School of Chemical Engineering University of Chinese Academy of Sciences Beijing 100049 P. R. China
| | - Yikui Du
- Beijing National Laboratory of Molecular Science, State Key laboratory of Molecular Reaction Dynamics Institute of Chemistry, Chinese Academy of Sciences Beijing 100190 Beijing PR China
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22
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Zheng H, Ye H, Yu X, You L. Interplay between n→π* Interactions and Dynamic Covalent Bonds: Quantification and Modulation by Solvent Effects. J Am Chem Soc 2019; 141:8825-8833. [PMID: 31075197 DOI: 10.1021/jacs.9b01006] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Orbital donor-acceptor interactions play critical roles throughout chemistry, and hence, their regulation and functionalization are of great significance. Herein we demonstrate for the first time the investigation of n→π* interactions through the strategy of dynamic covalent chemistry (DCC), and we further showcase its use in the stabilization of imine. The n→π* interaction between donor X and acceptor aldehyde/imine within 2-X-2'-formylbiphenyl derivatives was found to significantly influence the thermodynamics of imine exchange. The orbital interaction was then quantified through imine exchange, the equilibrium of which was successfully correlated with the difference in natural bond orbital stabilization energy of n→π* interactions of aldehyde and its imine. Moreover, the examination of solvent effects provided insights into the distinct feature of the modulation of n→π* interaction with aprotic and protic solvents. The n→π* interaction involving imine was enhanced in protic solvents due to hydrogen bonding with the solvent. This finding further enabled the stabilization of imine in purely aqueous solution. The strategies and results reported should find application in many fields, including molecular recognition, biological labeling, and asymmetric catalysis.
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Affiliation(s)
- Hao Zheng
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter , Chinese Academy of Sciences , Fuzhou 350002 , China.,College of Chemistry and Material Science , Fujian Normal University , Fuzhou 350007 China
| | - Hebo Ye
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter , Chinese Academy of Sciences , Fuzhou 350002 , China.,University of Chinese of Academy of Sciences , Beijing 100049 , China
| | - Xiaoxia Yu
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter , Chinese Academy of Sciences , Fuzhou 350002 , China.,College of Chemistry and Material Science , Fujian Normal University , Fuzhou 350007 China
| | - Lei You
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter , Chinese Academy of Sciences , Fuzhou 350002 , China.,University of Chinese of Academy of Sciences , Beijing 100049 , China
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23
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Kalinin DV, Agoglitta O, Van de Vyver H, Melesina J, Wagner S, Riemann B, Schäfers M, Sippl W, Löffler B, Holl R. Proline-based hydroxamates targeting the zinc-dependent deacetylase LpxC: Synthesis, antibacterial properties, and docking studies. Bioorg Med Chem 2019; 27:1997-2018. [DOI: 10.1016/j.bmc.2019.03.056] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2019] [Revised: 03/28/2019] [Accepted: 03/29/2019] [Indexed: 01/05/2023]
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24
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Egli J, Siebler C, Köhler M, Zenobi R, Wennemers H. Hydrophobic Moieties Bestow Fast-Folding and Hyperstability on Collagen Triple Helices. J Am Chem Soc 2019; 141:5607-5611. [DOI: 10.1021/jacs.8b13871] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Jasmine Egli
- Laboratory of Organic Chemistry, ETH Zurich, D-CHAB, Vladimir-Prelog-Weg 3, Zurich 8093, Switzerland
| | - Christiane Siebler
- Laboratory of Organic Chemistry, ETH Zurich, D-CHAB, Vladimir-Prelog-Weg 3, Zurich 8093, Switzerland
| | - Martin Köhler
- Laboratory of Organic Chemistry, ETH Zurich, D-CHAB, Vladimir-Prelog-Weg 3, Zurich 8093, Switzerland
| | - Renato Zenobi
- Laboratory of Organic Chemistry, ETH Zurich, D-CHAB, Vladimir-Prelog-Weg 3, Zurich 8093, Switzerland
| | - Helma Wennemers
- Laboratory of Organic Chemistry, ETH Zurich, D-CHAB, Vladimir-Prelog-Weg 3, Zurich 8093, Switzerland
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25
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Hofman GJ, Ottoy E, Light ME, Kieffer B, Martins JC, Kuprov I, Sinnaeve D, Linclau B. Synthesis and Conformational Properties of 3,4-Difluoro-l-prolines. J Org Chem 2019; 84:3100-3120. [PMID: 30777755 DOI: 10.1021/acs.joc.8b02920] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Fluorinated proline derivatives have found diverse applications in areas ranging from medicinal chemistry over structural biochemistry to organocatalysis. Depending on the stereochemistry of monofluorination at the proline 3- or 4-position, different effects on the conformational properties of proline (ring pucker, cis/ trans isomerization) are introduced. With fluorination at both 3- and 4-positions, matching or mismatching effects can occur depending on the relative stereochemistry. Here we report, in full, the syntheses and conformational properties of three out of the four possible 3,4-difluoro-l-proline diastereoisomers. The yet unreported conformational properties are described for (3 S,4 S)- and (3 R,4 R)-difluoro-l-proline, which are shown to bias ring pucker and cis/ trans ratios on the same order of magnitude as their respective monofluorinated progenitors, although with significantly faster amide cis/ trans isomerization rates. The reported analogues thus expand the scope of available fluorinated proline analogues as tools to tailor proline's distinct conformational and dynamical properties, allowing for the interrogation of its role in, for instance, protein stability or folding.
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Affiliation(s)
- Gert-Jan Hofman
- School of Chemistry , University of Southampton , Highfield, Southampton SO17 1BJ , United Kingdom.,Department of Organic and Macromolecular Chemistry , Ghent University , Campus Sterre, S4, Krijgslaan 281 , Ghent B-9000 , Belgium
| | - Emile Ottoy
- Department of Organic and Macromolecular Chemistry , Ghent University , Campus Sterre, S4, Krijgslaan 281 , Ghent B-9000 , Belgium
| | - Mark E Light
- School of Chemistry , University of Southampton , Highfield, Southampton SO17 1BJ , United Kingdom
| | - Bruno Kieffer
- Biomolecular NMR , University of Strasbourg , IGBMC, CNRS UMR 7104, INSERM U1258, 1 rue Laurent Fries/BP 10142 , Illkirch Cedex 67404 , France
| | - Jose C Martins
- Department of Organic and Macromolecular Chemistry , Ghent University , Campus Sterre, S4, Krijgslaan 281 , Ghent B-9000 , Belgium
| | - Ilya Kuprov
- School of Chemistry , University of Southampton , Highfield, Southampton SO17 1BJ , United Kingdom
| | - Davy Sinnaeve
- Department of Organic and Macromolecular Chemistry , Ghent University , Campus Sterre, S4, Krijgslaan 281 , Ghent B-9000 , Belgium
| | - Bruno Linclau
- School of Chemistry , University of Southampton , Highfield, Southampton SO17 1BJ , United Kingdom
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26
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Guo LE, Hong Y, Zhang SY, Zhang M, Yan XS, Cao JL, Li Z, James TD, Jiang YB. Proline-Based Boronic Acid Receptors for Chiral Recognition of Glucose. J Org Chem 2018; 83:15128-15135. [DOI: 10.1021/acs.joc.8b02425] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Lin-E Guo
- Department of Chemistry, College of Chemistry and Chemical Engineering, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, and iChEM, Xiamen University, Xiamen 361005, China
| | - Yuan Hong
- Department of Chemistry, College of Chemistry and Chemical Engineering, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, and iChEM, Xiamen University, Xiamen 361005, China
| | - Shu-Ying Zhang
- Department of Chemistry, College of Chemistry and Chemical Engineering, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, and iChEM, Xiamen University, Xiamen 361005, China
| | - Miao Zhang
- Department of Chemistry, College of Chemistry and Chemical Engineering, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, and iChEM, Xiamen University, Xiamen 361005, China
| | - Xiao-Sheng Yan
- Department of Chemistry, College of Chemistry and Chemical Engineering, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, and iChEM, Xiamen University, Xiamen 361005, China
| | - Jin-Lian Cao
- Department of Chemistry, College of Chemistry and Chemical Engineering, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, and iChEM, Xiamen University, Xiamen 361005, China
| | - Zhao Li
- Department of Chemistry, College of Chemistry and Chemical Engineering, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, and iChEM, Xiamen University, Xiamen 361005, China
| | - Tony D. James
- Department of Chemistry, University of Bath, Bath BA2 7AY, United Kingdom
| | - Yun-Bao Jiang
- Department of Chemistry, College of Chemistry and Chemical Engineering, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, and iChEM, Xiamen University, Xiamen 361005, China
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27
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Hofman GJ, Ottoy E, Light ME, Kieffer B, Kuprov I, Martins JC, Sinnaeve D, Linclau B. Minimising conformational bias in fluoroprolines through vicinal difluorination. Chem Commun (Camb) 2018; 54:5118-5121. [PMID: 29717724 DOI: 10.1039/c8cc01493k] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Monofluorination at the proline 4-position results in conformational effects, which is exploited for a range of applications. However, this conformational distortion is a hindrance when the natural proline conformation is important. Here we introduce (3S,4R)-3,4-difluoroproline, in which the individual fluorine atoms instil opposite conformational effects, as a suitable probe for fluorine NMR studies.
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Affiliation(s)
- Gert-Jan Hofman
- Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, UK.
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28
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Kubyshkin V, Budisa N. Exploring hydrophobicity limits of polyproline helix with oligomeric octahydroindole-2-carboxylic acid. J Pept Sci 2018; 24:e3076. [PMID: 29582506 DOI: 10.1002/psc.3076] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Revised: 02/24/2018] [Accepted: 02/26/2018] [Indexed: 12/12/2022]
Abstract
The polyproline-II helix is the most extended naturally occurring helical structure and is widely present in polar, exposed stretches and "unstructured" denatured regions of polypeptides. Can it be hydrophobic? In this study, we address this question using oligomeric peptides formed by a hydrophobic proline analogue, (2S,3aS,7aS)-octahydroindole-2-carboxylic acid (Oic). Previously, we found the molecular principles underlying the structural stability of the polyproline-II conformation in these oligomers, whereas the hydrophobicity of the peptide constructs remains to be examined. Therefore, we investigated the octan-1-ol/water partitioning and inclusion in detergent micelles of the oligo-Oic peptides. The results showed that the hydrophobicity is remarkably enhanced in longer oligomeric sequences, and the oligo-Oic peptides with 3 to 4 residues and higher are specific towards hydrophobic environments. This contrasts significantly to the parent oligoproline peptides, which were moderately hydrophilic. With these findings, we have demonstrated that the polyproline-II structure is compatible with nonpolar media, whereas additional manipulations of the terminal functionalities feature solubility in extremely nonpolar solvents such as hexane.
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Affiliation(s)
- Vladimir Kubyshkin
- Institute of Chemistry, Technical University of Berlin, Müller-Breslau-Str. 10, Berlin, 10623, Germany
| | - Nediljko Budisa
- Institute of Chemistry, Technical University of Berlin, Müller-Breslau-Str. 10, Berlin, 10623, Germany
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29
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Abstract
Amide rotation of peptidyl-prolyl fragments is an important factor in backbone structure organization of proteins. Computational studies have indicated that this rotation preferentially proceeds through a defined transition-state structure (syn/exo). Here, we complement the computational findings by determining the amide bond rotation barriers for derivatives of the two symmetric proline analogues, meso and racemic pyrrolidine-2,5-dicarboxylic acids. The rotations around these residues represent syn/exo-syn/exo and anti/endo-syn/exo hybrid transition states for the meso and racemic diastereomer, respectively. The rotation barriers are lower for the former rotation by about 9 kJ mol-1 (aqueous medium), suggesting a strong preference for the syn/exo (clockwise) rotation over the anti/endo (anticlockwise) rotation. The results show that both hybrid rotation processes are enthalpically driven but respond differently to solvent polarity changes due to the different transition state dipole-dipole interactions.
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Affiliation(s)
- Vladimir Kubyshkin
- Biocatalysis Group, Institute of Chemistry, Technical University of Berlin, Müller-Breslau-Str. 10, Berlin 10623, Germany.
| | - Nediljko Budisa
- Biocatalysis Group, Institute of Chemistry, Technical University of Berlin, Müller-Breslau-Str. 10, Berlin 10623, Germany.
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30
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Kubyshkin V, Budisa N. Hydrolysis, polarity, and conformational impact of C-terminal partially fluorinated ethyl esters in peptide models. Beilstein J Org Chem 2017; 13:2442-2457. [PMID: 29234471 PMCID: PMC5704756 DOI: 10.3762/bjoc.13.241] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Accepted: 10/19/2017] [Indexed: 12/17/2022] Open
Abstract
Fluorinated moieties are highly valuable to chemists due to the sensitive NMR detectability of the 19F nucleus. Fluorination of molecular scaffolds can also selectively influence a molecule's polarity, conformational preferences and chemical reactivity, properties that can be exploited for various chemical applications. A powerful route for incorporating fluorine atoms in biomolecules is last-stage fluorination of peptide scaffolds. One of these methods involves esterification of the C-terminus of peptides using a diazomethane species. Here, we provide an investigation of the physicochemical consequences of peptide esterification with partially fluorinated ethyl groups. Derivatives of N-acetylproline are used to model the effects of fluorination on the lipophilicity, hydrolytic stability and on conformational properties. The conformational impact of the 2,2-difluoromethyl ester on several neutral and charged oligopeptides was also investigated. Our results demonstrate that partially fluorinated esters undergo variable hydrolysis in biologically relevant buffers. The hydrolytic stability can be tailored over a broad pH range by varying the number of fluorine atoms in the ester moiety or by introducing adjacent charges in the peptide sequence.
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Affiliation(s)
- Vladimir Kubyshkin
- Biocatalysis group, Institute of Chemistry, Technical University of Berlin, Müller-Breslau-Strasse 10, Berlin 10623, Germany
| | - Nediljko Budisa
- Biocatalysis group, Institute of Chemistry, Technical University of Berlin, Müller-Breslau-Strasse 10, Berlin 10623, Germany
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31
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Schnitzer T, Wennemers H. Influence of the Trans/Cis Conformer Ratio on the Stereoselectivity of Peptidic Catalysts. J Am Chem Soc 2017; 139:15356-15362. [DOI: 10.1021/jacs.7b06194] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Tobias Schnitzer
- Eidgenossische Technische Hochschule Zurich, Laboratory of Organic Chemistry, Vladimir-Prelog-Weg 3, Zurich 8093, Switzerland
| | - Helma Wennemers
- Eidgenossische Technische Hochschule Zurich, Laboratory of Organic Chemistry, Vladimir-Prelog-Weg 3, Zurich 8093, Switzerland
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32
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Kusakiewicz-Dawid A, Porada M, Ochędzan-Siodłak W, Broda MA, Bujak M, Siodłak D. Pyrazole amino acids: hydrogen bonding directed conformations of 3-amino-1H-pyrazole-5-carboxylic acid residue. J Pept Sci 2017; 23:716-726. [PMID: 28608410 DOI: 10.1002/psc.3018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2017] [Revised: 05/24/2017] [Accepted: 05/25/2017] [Indexed: 11/06/2022]
Abstract
A series of model compounds containing 3-amino-1H-pyrazole-5-carboxylic acid residue with N-terminal amide/urethane and C-terminal amide/hydrazide/ester groups were investigated by using NMR, Fourier transform infrared, and single-crystal X-ray diffraction methods, additionally supported by theoretical calculations. The studies demonstrate that the most preferred is the extended conformation with torsion angles ϕ and ψ close to ±180°. The studied 1H-pyrazole with N-terminal amide/urethane and C-terminal amide/hydrazide groups solely adopts this energetically favored conformation confirming rigidity of that structural motif. However, when the C-terminal ester group is present, the second conformation with torsion angles ϕ and ψ close to ±180° and 0°, respectively, is accessible. The conformational equilibrium is observed in NMR and Fourier transform infrared studies in solution in polar environment as well as in the crystal structures of other related compounds. The observed conformational preferences are clearly related to the presence of intramolecular interactions formed within the studied residue. Copyright © 2017 European Peptide Society and John Wiley & Sons, Ltd.
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Affiliation(s)
| | - Monika Porada
- Faculty of Chemistry, University of Opole, Oleska 48, 45-052, Opole, Poland
| | | | - Małgorzata A Broda
- Faculty of Chemistry, University of Opole, Oleska 48, 45-052, Opole, Poland
| | - Maciej Bujak
- Faculty of Chemistry, University of Opole, Oleska 48, 45-052, Opole, Poland
| | - Dawid Siodłak
- Faculty of Chemistry, University of Opole, Oleska 48, 45-052, Opole, Poland
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33
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Egli J, Siebler C, Maryasin B, Erdmann RS, Bergande C, Ochsenfeld C, Wennemers H. pH-Responsive Aminoproline-Containing Collagen Triple Helices. Chemistry 2017; 23:7938-7944. [DOI: 10.1002/chem.201701134] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Indexed: 11/10/2022]
Affiliation(s)
- Jasmine Egli
- Laboratory of Organic Chemistry; ETH Zürich; Vladimir-Prelog-Weg 3 8093 Zürich Switzerland
| | - Christiane Siebler
- Laboratory of Organic Chemistry; ETH Zürich; Vladimir-Prelog-Weg 3 8093 Zürich Switzerland
| | - Boris Maryasin
- Chair of Theoretical Chemistry; Department of Chemistry; University of Munich (LMU); Butenandtstr. 7 81377 Munich Germany
- Center of Integrated Protein Science (CIPSM) at the Department of Chemistry; University of Munich (LMU); Butenandtstr. 5-13 81377 Munich Germany
| | - Roman S. Erdmann
- Laboratory of Organic Chemistry; ETH Zürich; Vladimir-Prelog-Weg 3 8093 Zürich Switzerland
| | - Cedric Bergande
- Laboratory of Organic Chemistry; ETH Zürich; Vladimir-Prelog-Weg 3 8093 Zürich Switzerland
| | - Christian Ochsenfeld
- Chair of Theoretical Chemistry; Department of Chemistry; University of Munich (LMU); Butenandtstr. 7 81377 Munich Germany
- Center of Integrated Protein Science (CIPSM) at the Department of Chemistry; University of Munich (LMU); Butenandtstr. 5-13 81377 Munich Germany
| | - Helma Wennemers
- Laboratory of Organic Chemistry; ETH Zürich; Vladimir-Prelog-Weg 3 8093 Zürich Switzerland
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34
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Bröhl A, Albrecht B, Zhang Y, Maginn E, Giernoth R. Influence of Hofmeister Ions on the Structure of Proline-Based Peptide Models: A Combined Experimental and Molecular Modeling Study. J Phys Chem B 2017; 121:2062-2072. [PMID: 28191953 DOI: 10.1021/acs.jpcb.6b12465] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The influence of three sodium salts, covering a wide range of the Hofmeister series, on the conformation of three proline-based peptide models in aqueous solution is examined using a combination of nuclear magnetic resonance spectroscopy and molecular dynamics simulations. The anions preferentially interact with the cis conformers of the peptide models, which is rationalized by the respective electrostatic potential surfaces. These preferred interactions have a strong impact on the thermodynamics of the cis/trans equilibria, leading to a higher population of the cis conformers. In distinct cases, these equilibria are nearly independent of temperature, showing that the salts are also able to stabilize the conformers over wide temperature ranges.
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Affiliation(s)
- Andreas Bröhl
- Department of Chemistry, Organic Chemistry, University of Cologne , Greinstrasse 4, 50939 Cologne, Germany
| | - Benjamin Albrecht
- Department of Chemistry, Organic Chemistry, University of Cologne , Greinstrasse 4, 50939 Cologne, Germany
| | - Yong Zhang
- Department of Chemical and Biomolecular Engineering, University of Notre Dame , Notre Dame, Indiana 46556, United States
| | - Edward Maginn
- Department of Chemical and Biomolecular Engineering, University of Notre Dame , Notre Dame, Indiana 46556, United States
| | - Ralf Giernoth
- Department of Chemistry, Organic Chemistry, University of Cologne , Greinstrasse 4, 50939 Cologne, Germany
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35
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Metrano A, Abascal NC, Mercado BQ, Paulson EK, Hurtley AE, Miller SJ. Diversity of Secondary Structure in Catalytic Peptides with β-Turn-Biased Sequences. J Am Chem Soc 2017; 139:492-516. [PMID: 28029251 PMCID: PMC5312972 DOI: 10.1021/jacs.6b11348] [Citation(s) in RCA: 84] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Indexed: 11/30/2022]
Abstract
X-ray crystallography has been applied to the structural analysis of a series of tetrapeptides that were previously assessed for catalytic activity in an atroposelective bromination reaction. Common to the series is a central Pro-Xaa sequence, where Pro is either l- or d-proline, which was chosen to favor nucleation of canonical β-turn secondary structures. Crystallographic analysis of 35 different peptide sequences revealed a range of conformational states. The observed differences appear not only in cases where the Pro-Xaa loop-region is altered, but also when seemingly subtle alterations to the flanking residues are introduced. In many instances, distinct conformers of the same sequence were observed, either as symmetry-independent molecules within the same unit cell or as polymorphs. Computational studies using DFT provided additional insight into the analysis of solid-state structural features. Select X-ray crystal structures were compared to the corresponding solution structures derived from measured proton chemical shifts, 3J-values, and 1H-1H-NOESY contacts. These findings imply that the conformational space available to simple peptide-based catalysts is more diverse than precedent might suggest. The direct observation of multiple ground state conformations for peptides of this family, as well as the dynamic processes associated with conformational equilibria, underscore not only the challenge of designing peptide-based catalysts, but also the difficulty in predicting their accessible transition states. These findings implicate the advantages of low-barrier interconversions between conformations of peptide-based catalysts for multistep, enantioselective reactions.
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Affiliation(s)
- Anthony
J. Metrano
- Department of Chemistry, Yale University, P.O.
Box 208107, New Haven, Connecticut 06520-8107, United States
| | - Nadia C. Abascal
- Department of Chemistry, Yale University, P.O.
Box 208107, New Haven, Connecticut 06520-8107, United States
| | - Brandon Q. Mercado
- Department of Chemistry, Yale University, P.O.
Box 208107, New Haven, Connecticut 06520-8107, United States
| | - Eric K. Paulson
- Department of Chemistry, Yale University, P.O.
Box 208107, New Haven, Connecticut 06520-8107, United States
| | - Anna E. Hurtley
- Department of Chemistry, Yale University, P.O.
Box 208107, New Haven, Connecticut 06520-8107, United States
| | - Scott J. Miller
- Department of Chemistry, Yale University, P.O.
Box 208107, New Haven, Connecticut 06520-8107, United States
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36
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Properties of the Amide Bond Involving Proline 4,5-methanologues: an Experimental and Theoretical Study. Isr J Chem 2016. [DOI: 10.1002/ijch.201600106] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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37
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Abstract
Because carbonyl groups can participate in both hydrogen bonds and n→π* interactions, these two interactions likely affect one another. Herein, enhancement of an amidic n→π* interaction is shown to reduce the ability of β-keto amides to tautomerize to the enol, indicating decreased hydrogen-bonding capacity of the amide carbonyl group. Thus, an n→π* interaction can have a significant effect on the strength of a hydrogen bond to the same carbonyl group.
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Affiliation(s)
- Robert W. Newberry
- Department of Chemistry, University of Wisconsin–Madison, Madison, Wisconsin 53706, United States
| | - Samuel J. Orke
- Department of Chemistry, University of Wisconsin–Madison, Madison, Wisconsin 53706, United States
| | - Ronald T. Raines
- Department of Chemistry, University of Wisconsin–Madison, Madison, Wisconsin 53706, United States
- Department of Biochemistry, University of Wisconsin–Madison, Madison, Wisconsin 53706, United States
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38
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Yamamoto T, Dai J, Jacobsen NE, Ammam M, Hall GB, Mozziconacci O, Schöneich C, Wilson GS, Glass RS. Neighboring π-Amide Participation in Thioether Oxidation: Conformational Control. Org Lett 2016; 18:3522-5. [DOI: 10.1021/acs.orglett.6b01309] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Takuhei Yamamoto
- Department
of Chemistry and Biochemistry, The University of Arizona, Tucson, Arizona 85721, United States
| | - Jixun Dai
- Department
of Chemistry and Biochemistry, The University of Arizona, Tucson, Arizona 85721, United States
| | - Neil E. Jacobsen
- Department
of Chemistry and Biochemistry, The University of Arizona, Tucson, Arizona 85721, United States
| | - Malika Ammam
- Department
of Chemistry, The University of Kansas, Lawrence, Kansas 66045, United States
| | - Gabriel B. Hall
- Department
of Chemistry and Biochemistry, The University of Arizona, Tucson, Arizona 85721, United States
| | - Olivier Mozziconacci
- Department
of Pharmaceutical Chemistry, The University of Kansas, Lawrence, Kansas 66047, United States
| | - Christian Schöneich
- Department
of Pharmaceutical Chemistry, The University of Kansas, Lawrence, Kansas 66047, United States
| | - George S. Wilson
- Department
of Chemistry, The University of Kansas, Lawrence, Kansas 66045, United States
| | - Richard S. Glass
- Department
of Chemistry and Biochemistry, The University of Arizona, Tucson, Arizona 85721, United States
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39
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Newberry RW, Raines RT. 4-Fluoroprolines: Conformational Analysis and Effects on the Stability and Folding of Peptides and Proteins. TOPICS IN HETEROCYCLIC CHEMISTRY 2016; 48:1-25. [PMID: 28690684 PMCID: PMC5501414 DOI: 10.1007/7081_2015_196] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Proline is unique among proteinogenic amino acids because a pyrrolidine ring links its amino group to its side chain. This heterocycle constrains the conformations of the main chain and thus templates particular secondary structures. Proline residues undergo post-translational modification at the 4-position to yield 4-hydroxyproline, which is especially prevalent in collagen. Interest in characterizing the effects of this modification led to the use of 4-fluoroprolines to enhance inductive properties relative to the hydroxyl group of 4-hydroxyproline and to eliminate contributions from hydrogen bonding. The strong inductive effect of the fluoro group has three main consequences: enforcing a particular pucker upon the pyrrolidine ring, biasing the conformation of the preceding peptide bond, and accelerating cis/trans prolyl peptide bond isomerization. These subtle, yet reliable modulations make 4-fluoroproline-incorporation a complement to traditional genetic approaches for exploring structure-function relationships in peptides and proteins, as well as for endowing peptides and proteins with conformational stability.
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Affiliation(s)
- Robert W Newberry
- Departments of Chemistry and Biochemistry, University of Wisconsin-Madison, Madison, WI 53706 USA
| | - Ronald T Raines
- Departments of Chemistry and Biochemistry, University of Wisconsin-Madison, Madison, WI 53706 USA
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40
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Lin YJ, Chu LK, Horng JC. Effects of the Terminal Aromatic Residues on Polyproline Conformation: Thermodynamic and Kinetic Studies. J Phys Chem B 2015; 119:15796-806. [PMID: 26641495 DOI: 10.1021/acs.jpcb.5b08717] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
In a peptide or protein, the sequence of aromatic residue-proline or proline-aromatic residue shows a high propensity in forming cis prolyl bonds due to aromatic-proline interactions. In this work, we designed and prepared the polyproline peptides with aromatic amino acids (F, Y, W) incorporated into their N-terminal or C-terminal end to investigate the effects of a terminal aromatic residue on polyproline conformation and the transition kinetics of polyproline I (PPI) to polyproline II (PPII) helices. Circular dichroism measurements reveal that the N-terminal aromatic-proline interaction imposes a more pronounced consequence on the forming propensity of PPI conformation than does the C-terminal aromatic-proline interaction in n-propanol. The propensity of forming PPI is correlated with the strength of aromatic-proline interactions in the order of Tyr-Pro > Trp-Pro > Phe-Pro. In aqueous solution, kinetic studies indicate that aromatic-substitution effects are nondirectional and indistinct on the PPI → PPII conversion rates, suggesting that aromatic-proline interactions may not be an important factor in this process. In addition, the temperature-dependent kinetics shows that the hydrophobicity of aromatic side chain may play a critical role affecting the activation enthalpy and entropy of the conversion of PPI to PPII, providing new insights into the folding of polyproline helices.
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Affiliation(s)
- Yu-Ju Lin
- Department of Chemistry, National Tsing Hua University , Hsinchu, Taiwan 30013, R.O.C
| | - Li-Kang Chu
- Department of Chemistry, National Tsing Hua University , Hsinchu, Taiwan 30013, R.O.C.,Frontier Research Center on Fundamental and Applied Sciences of Matters, National Tsing Hua University , Hsinchu, Taiwan 30013, R.O.C
| | - Jia-Cherng Horng
- Department of Chemistry, National Tsing Hua University , Hsinchu, Taiwan 30013, R.O.C.,Frontier Research Center on Fundamental and Applied Sciences of Matters, National Tsing Hua University , Hsinchu, Taiwan 30013, R.O.C
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