1
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Kubyshkin V, Rubini M. Proline Analogues. Chem Rev 2024; 124:8130-8232. [PMID: 38941181 DOI: 10.1021/acs.chemrev.4c00007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/30/2024]
Abstract
Within the canonical repertoire of the amino acid involved in protein biogenesis, proline plays a unique role as an amino acid presenting a modified backbone rather than a side-chain. Chemical structures that mimic proline but introduce changes into its specific molecular features are defined as proline analogues. This review article summarizes the existing chemical, physicochemical, and biochemical knowledge about this peculiar family of structures. We group proline analogues from the following compounds: substituted prolines, unsaturated and fused structures, ring size homologues, heterocyclic, e.g., pseudoproline, and bridged proline-resembling structures. We overview (1) the occurrence of proline analogues in nature and their chemical synthesis, (2) physicochemical properties including ring conformation and cis/trans amide isomerization, (3) use in commercial drugs such as nirmatrelvir recently approved against COVID-19, (4) peptide and protein synthesis involving proline analogues, (5) specific opportunities created in peptide engineering, and (6) cases of protein engineering with the analogues. The review aims to provide a summary to anyone interested in using proline analogues in systems ranging from specific biochemical setups to complex biological systems.
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Affiliation(s)
| | - Marina Rubini
- School of Chemistry, University College Dublin, Belfield, Dublin 4, Ireland
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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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Schnitzer T, Trapp N, Fischer LM, Wennemers H. Crystal structure analysis of N-acetylated proline and ring size analogs. J Pept Sci 2022; 29:e3473. [PMID: 36579722 DOI: 10.1002/psc.3473] [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: 10/23/2022] [Revised: 12/16/2022] [Accepted: 12/19/2022] [Indexed: 12/30/2022]
Abstract
Crystal structures of N-acetylated proline and homologs with four- and six-membered rings (azetidine carboxylic acid and piperidine carboxylic acid) were obtained and compared. The distinctly different conformations of the four-, five-, and six-membered rings reflect Bayer strain, n → π* interaction, and allylic strain, and result in crystal lattices with a zigzag structure.
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Affiliation(s)
- Tobias Schnitzer
- Laboratory of Organic Chemistry, ETH Zürich, D-CHAB, Zurich, Switzerland
| | - Nils Trapp
- Laboratory of Organic Chemistry, ETH Zürich, D-CHAB, Zurich, Switzerland
| | - Lisa-Marie Fischer
- Laboratory of Organic Chemistry, ETH Zürich, D-CHAB, Zurich, Switzerland
| | - Helma Wennemers
- Laboratory of Organic Chemistry, ETH Zürich, D-CHAB, Zurich, 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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Fiala T, Barros EP, Ebert MO, Ruijsenaars E, Riniker S, Wennemers H. Frame Shifts Affect the Stability of Collagen Triple Helices. J Am Chem Soc 2022; 144:18642-18649. [PMID: 36179150 DOI: 10.1021/jacs.2c08727] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Collagen model peptides (CMPs), composed of proline-(2S,4R)-hydroxyproline-glycine (POG) repeat units, have been extensively used to study the structure and stability of triple-helical collagen─the dominant structural protein in mammals─at the molecular level. Despite the more than 50-year history of CMPs and numerous studies on the relationship between the composition of single-stranded CMPs and the thermal stability of the assembled triple helices, little attention has been paid to the effects arising from their terminal residues. Here, we show that frame-shifted CMPs, which share POG repeat units but terminate with P, O, or G, form triple helices with vastly different thermal stabilities. A melting temperature difference as high as 16 °C was found for triple helices from 20-mers Ac-OG[POG]6-NH2 and Ac-[POG]6PO-NH2, and triple helices of the constitutional isomers Ac-[POG]7-NH2 and Ac-[GPO]7-NH2 melt 10 °C apart. A combination of thermal denaturation, circular dichroism and NMR spectroscopic studies, and molecular dynamics simulations revealed that the stability differences originate from the propensity of the peptide termini to preorganize into a polyproline-II helical structure. Our results advise that care must be taken when designing peptide mimics of structural proteins, as subtle changes in the terminal residues can significantly affect their properties. Our findings also provide a general and straightforward tool for tuning the stability of CMPs for applications as synthetic materials and biological probes.
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Affiliation(s)
- Tomas Fiala
- Laboratory of Organic Chemistry, ETH Zurich, D-CHAB, Vladimir-Prelog-Weg 3, Zurich 8093, Switzerland
| | - Emilia P Barros
- Laboratory of Physical Chemistry, ETH Zurich, D-CHAB, Vladimir-Prelog-Weg 2, Zurich 8093, Switzerland
| | - Marc-Olivier Ebert
- Laboratory of Organic Chemistry, ETH Zurich, D-CHAB, Vladimir-Prelog-Weg 3, Zurich 8093, Switzerland
| | - Enrico Ruijsenaars
- Laboratory of Physical Chemistry, ETH Zurich, D-CHAB, Vladimir-Prelog-Weg 2, Zurich 8093, Switzerland
| | - Sereina Riniker
- Laboratory of Physical Chemistry, ETH Zurich, D-CHAB, Vladimir-Prelog-Weg 2, Zurich 8093, Switzerland
| | - Helma Wennemers
- Laboratory of Organic Chemistry, ETH Zurich, D-CHAB, Vladimir-Prelog-Weg 3, Zurich 8093, Switzerland
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6
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Matinkhoo K, Wong AAWL, Hambira CM, Kato B, Wei C, Müller C, Hechler T, Braun A, Gallo F, Pahl A, Perrin DM. Design, Synthesis, and Biochemical Evaluation of Alpha-Amanitin Derivatives Containing Analogs of the trans-Hydroxyproline Residue for Potential Use in Antibody-Drug Conjugates. Chemistry 2021; 27:10282-10292. [PMID: 34058032 DOI: 10.1002/chem.202101373] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Indexed: 01/08/2023]
Abstract
Alpha-amanitin, an extremely toxic bicyclic octapeptide extracted from the death-cap mushroom, Amanita phalloides, is a highly selective allosteric inhibitor of RNA polymerase II. Following on growing interest in using this toxin as a payload in antibody-drug conjugates, herein we report the synthesis and biochemical evaluation of several new derivatives of this toxin to probe the role of the trans-hydroxyproline (Hyp), which is known to be critical for toxicity. This structure activity relationship (SAR) study represents the first of its kind to use various Hyp-analogs to alter the conformational and H-bonding properties of Hyp in amanitin.
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Affiliation(s)
- Kaveh Matinkhoo
- Chemistry Department, University of British Columbia, 2036 Main Mall, Vancouver, British Columbia, V6T-1Z1, Canada
| | - Antonio A W L Wong
- Chemistry Department, University of British Columbia, 2036 Main Mall, Vancouver, British Columbia, V6T-1Z1, Canada
| | - Chido M Hambira
- Chemistry Department, University of British Columbia, 2036 Main Mall, Vancouver, British Columbia, V6T-1Z1, Canada
| | - Brandon Kato
- Chemistry Department, University of British Columbia, 2036 Main Mall, Vancouver, British Columbia, V6T-1Z1, Canada
| | - Charlie Wei
- Chemistry Department, University of British Columbia, 2036 Main Mall, Vancouver, British Columbia, V6T-1Z1, Canada
| | - Christoph Müller
- Heidelberg Pharma, Gregor-Mendel-Straße 22, 68526, Ladenburg, Germany
| | - Torsten Hechler
- Heidelberg Pharma, Gregor-Mendel-Straße 22, 68526, Ladenburg, Germany
| | - Alexandra Braun
- Heidelberg Pharma, Gregor-Mendel-Straße 22, 68526, Ladenburg, Germany
| | - Francesca Gallo
- Heidelberg Pharma, Gregor-Mendel-Straße 22, 68526, Ladenburg, Germany
| | - Andreas Pahl
- Heidelberg Pharma, Gregor-Mendel-Straße 22, 68526, Ladenburg, Germany
| | - David M Perrin
- Chemistry Department, University of British Columbia, 2036 Main Mall, Vancouver, British Columbia, V6T-1Z1, Canada
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7
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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: 19] [Impact Index Per Article: 6.3] [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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8
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Morimoto J, Sando S. Peptoids with Substituents on the Backbone Carbons as Conformationally Constrained Synthetic Oligoamides. J SYN ORG CHEM JPN 2020. [DOI: 10.5059/yukigoseikyokaishi.78.1076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
| | - Shinsuke Sando
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo
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9
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Conjugates of Chitosan and Calcium Alginate with Oligoproline and Oligohydroxyproline Derivatives for Potential Use in Regenerative Medicine. MATERIALS 2020; 13:ma13143079. [PMID: 32664253 PMCID: PMC7412561 DOI: 10.3390/ma13143079] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 06/27/2020] [Accepted: 07/06/2020] [Indexed: 11/16/2022]
Abstract
New materials that are as similar as possible in terms of structure and biology to the extracellular matrix (external environment) of cells are of great interest for regenerative medicine. Oligoproline and oligohydroxyproline derivatives (peptides 2-5) are potential mimetics of collagen fragments. Peptides 2-5 have been shown to be similar to the model collagen fragment (H-Gly-Hyp-Pro-Ala-Hyp-Pro-OH, 1) in terms of both their spatial structure and biological activity. In this study, peptides 2-5 were covalently bound to nonwovens based on chitosan and calcium alginate. Incorporation of the peptides was confirmed by Fourier transform -infrared (FT-IR) and zeta potential measurements. Biological studies (cell metabolic activity by using 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) test and Live/Dead assay) proved that the obtained peptide-polysaccharide conjugates were not toxic to the endothelial cell line EA.hy 926. In many cases, the conjugates had a highly affirmative influence on cell proliferation. The results of this study show that conjugates of chitosan and calcium alginate with oligoproline and oligohydroxyproline derivatives have potential for use in regenerative medicine.
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10
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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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11
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Li M, Ning Y, Chen J, Duan X, Song N, Ding D, Su X, Yu Z. Proline Isomerization-Regulated Tumor Microenvironment-Adaptable Self-Assembly of Peptides for Enhanced Therapeutic Efficacy. NANO LETTERS 2019; 19:7965-7976. [PMID: 31596096 DOI: 10.1021/acs.nanolett.9b03136] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Nanomedicines have been demonstrated as promising strategies for cancer therapy due to the advantages in pharmacokinetics and drug targeting delivery to tumor tissues. However, creation of delivery platforms able to intrinsically and spatially optimize drug cellular uptake during the entire delivering process remain challenging. To address this challenge, here we report on tumor microenvironment-adaptable self-assembly (TMAS) of pentapeptides regulated by the pH-sensitive cis/trans isomerization of 4-amino-proline (Amp) amide bonds for enhanced drug delivery and photodynamic therapeutic (PDT) efficacy. We found that decreasing solution pH led to the cis → trans isomerization of Amp amide bonds, thus promoting reversible self-assembly of pentapeptide FF-Amp-FF (AmpF) into superhelices and nanoparticles upon alternating exposure to neutral and mild acidic conditions. Co-assembly of peptide AmpF with its derivative containing a photosensitizer Chlorin e6 (AmpF-C) allows for creation of TMAS systems undergoing a morphological transition adaptable to the pH gradient present in cellular uptake pathway. Ex vivo studies revealed that TMAS nanomedicines prolonged circulation in the animal body and improved accumulation at tumor sites compared to morphology-persistent nanomedicines. In addition to the optimized cellular uptake, the morphological transition of TMAS into nanofibers in cytoplasm caused an enhanced intracellular ROS level compared to nanoparticle counterparts, thus leading to a lowered half lethal dose value for cancer cells. The combined advantages of TMAS eventually allowed in vivo PDT therapy for significant inhibition of tumor growth, thus demonstrating the improved drug delivery efficiency and therapeutic efficacy of TMAS systems toward new-generation nanomedicines.
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Affiliation(s)
- Mingming Li
- Key Laboratory of Functional Polymer Materials, Ministry of Education, State Key Laboratory of Medicinal Chemical Biology, Institute of Polymer Chemistry, College of Chemistry , Nankai University , Weijin Road 94 , Tianjin 300071 , China
| | - Yashan Ning
- Key Laboratory of Functional Polymer Materials, Ministry of Education, State Key Laboratory of Medicinal Chemical Biology, Institute of Polymer Chemistry, College of Chemistry , Nankai University , Weijin Road 94 , Tianjin 300071 , China
| | - Jialiang Chen
- State Key Laboratory of Elemento-organic Chemistry, College of Chemistry , Nankai University , Tianjin 300071 , China
| | - Xingchen Duan
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Bioactive Materials, Ministry of Education, and College of Life Sciences , Nankai University , Tianjin 300071 , China
| | - Na Song
- Key Laboratory of Functional Polymer Materials, Ministry of Education, State Key Laboratory of Medicinal Chemical Biology, Institute of Polymer Chemistry, College of Chemistry , Nankai University , Weijin Road 94 , Tianjin 300071 , China
| | - Dan Ding
- State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Bioactive Materials, Ministry of Education, and College of Life Sciences , Nankai University , Tianjin 300071 , China
| | - Xuncheng Su
- State Key Laboratory of Elemento-organic Chemistry, College of Chemistry , Nankai University , Tianjin 300071 , China
| | - Zhilin Yu
- Key Laboratory of Functional Polymer Materials, Ministry of Education, State Key Laboratory of Medicinal Chemical Biology, Institute of Polymer Chemistry, College of Chemistry , Nankai University , Weijin Road 94 , Tianjin 300071 , China
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12
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Kubyshkin V. Stabilization of the triple helix in collagen mimicking peptides. Org Biomol Chem 2019; 17:8031-8047. [PMID: 31464337 DOI: 10.1039/c9ob01646e] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Collagen mimics are peptides designed to reproduce structural features of natural collagen. A triple helix is the first element in the hierarchy of collagen folding. It is an assembly of three parallel peptide chains stabilized by packing and interchain hydrogen bonds. In this review we summarize the existing chemical approaches towards stabilization of this structure including the most recent developments. Currently proposed methods include manipulation of the amino acid composition, application of unnatural amino acid analogues, stimuli-responsive modifications, chain tethering approaches, peptide amphiphiles, modifications that target interchain interactions and more. This ability to manipulate the triple helix as a supramolecular self-assembly contributes to our understanding of the collagen folding. It also provides essential information needed to design collagen-based biomaterials of the future.
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Affiliation(s)
- Vladimir Kubyshkin
- Institute of Chemistry, University of Manitoba, Dysart Rd. 144, R3T 2N2, Winnipeg, Manitoba, Canada.
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13
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Abstract
A complete inventory of the forces governing protein folding is critical for productive protein modeling, including structure prediction and de novo design, as well as understanding protein misfolding diseases of clinical significance. The dominant contributors to protein folding include the hydrophobic effect and conventional hydrogen bonding, along with Coulombic and van der Waals interactions. Over the past few decades, important additional contributors have been identified, including C-H···O hydrogen bonding, n→π* interactions, C5 hydrogen bonding, chalcogen bonding, and interactions involving aromatic rings (cation-π, X-H···π, π-π, anion-π, and sulfur-arene). These secondary contributions fall into two general classes: (1) weak but abundant interactions of the protein main chain and (2) strong but less frequent interactions involving protein side chains. Though interactions with high individual energies play important roles in specifying nonlocal molecular contacts and ligand binding, we estimate that weak but abundant interactions are likely to make greater overall contributions to protein folding, particularly at the level of secondary structure. Further research is likely to illuminate additional roles of these noncanonical interactions and could also reveal contributions yet unknown.
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Affiliation(s)
| | - Ronald T. Raines
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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14
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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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15
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Tiwari VS, Singh G, Gurudayal, Ampapathi RS, Haq W. Pyrrolidine ring puckering and prolyl amide bond configurations of 2-methyl-allo-hydroxyproline-based dipeptides. Org Biomol Chem 2019; 17:4460-4464. [PMID: 30994683 DOI: 10.1039/c9ob00150f] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
An expeditious method for the synthesis of homo and heterochiral dipeptides containing l-alanine and d/l 2-methyl allo-hydroxyl prolines was developed using direct aminolysis of bicyclic lactones derived from d/l alanine. The impact of C-2 methylation and its spatial orientation on the pyrrolidine ring puckering and prolyl amide bond configuration was ascertained by solution NMR studies. The present studies reveal that C-2 methylation causes the prolyl amide bond to exist exclusively in the trans geometry in both homo- and heterochiral dipeptides. However, the spatial orientation of the C-2 methyl group and its i + 2 position in appropriately capped model dipeptides may nucleate into a turn like structure.
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Affiliation(s)
- Vinay Shankar Tiwari
- Medicinal and Process Chemistry Division, CSIR-Central Drug Research Institute, Lucknow 226031, India.
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16
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Park HS, Kang YK. Which DFT levels of theory are appropriate in predicting the prolyl cis–trans isomerization in solution? NEW J CHEM 2019. [DOI: 10.1039/c9nj02946j] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
DFTs were assessed for the conformational preferences of the peptides containing Pro and its derivatives in chloroform and water.
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Affiliation(s)
- Hae Sook Park
- Department of Nursing
- Cheju Halla University
- Cheju 63092
- Republic of Korea
| | - Young Kee Kang
- Department of Chemistry
- Chungbuk National University
- Cheongju
- Republic of Korea
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17
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Kilgore HR, Raines RT. n→π* Interactions Modulate the Properties of Cysteine Residues and Disulfide Bonds in Proteins. J Am Chem Soc 2018; 140:17606-17611. [PMID: 30403347 DOI: 10.1021/jacs.8b09701] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Noncovalent interactions are ubiquitous in biology, taking on roles that include stabilizing the conformation of and assembling biomolecules, and providing an optimal environment for enzymatic catalysis. Here, we describe a noncovalent interaction that engages the sulfur atoms of cysteine residues and disulfide bonds in proteins-their donation of electron density into an antibonding orbital of proximal amide carbonyl groups. This n→ π* interaction tunes the reactivity of the CXXC motif, which is the critical feature of thioredoxin and other enzymes involved in redox homeostasis. In particular, an n→ π* interaction lowers the p Ka value of the N-terminal cysteine residue of the motif, which is the nucleophile that initiates catalysis. In addition, the interplay between disulfide n→ π* interactions and C5 hydrogen bonds leads to hyperstable β-strands. Finally, n→ π* interactions stabilize vicinal disulfide bonds, which are naturally diverse in function. These previously unappreciated n→ π* interactions are strong and underlie the ability of cysteine residues and disulfide bonds to engage in the structure and function of proteins.
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Affiliation(s)
- Henry R Kilgore
- Department of Chemistry , Massachusetts Institute of Technology , Cambridge , Massachusetts 02139 , United States
| | - Ronald T Raines
- Department of Chemistry , Massachusetts Institute of Technology , Cambridge , Massachusetts 02139 , United States
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18
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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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19
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Melton SD, Chenoweth DM. Variation in the Yaa position of collagen peptides containing azaGlycine. Chem Commun (Camb) 2018; 54:11937-11940. [PMID: 30288510 DOI: 10.1039/c8cc06372a] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Herein, we report the systematic investigation of amino acid variation in the Yaa position of collagen peptides containing an adjacent azaGlycine residue. We demonstrate the reliability of azaGlycine as a glycine replacement and provide a sequence independent strategy for stabilizing the triple helical assembly of collagen peptides.
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Affiliation(s)
- Samuel D Melton
- Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, Pennsylvania 19104, USA.
| | - David M Chenoweth
- Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, Pennsylvania 19104, USA.
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20
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Dobitz S, Aronoff MR, Wennemers H. Oligoprolines as Molecular Entities for Controlling Distance in Biological and Material Sciences. Acc Chem Res 2017; 50:2420-2428. [PMID: 28885830 DOI: 10.1021/acs.accounts.7b00340] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Nature utilizes large biomolecules to fulfill tasks that require spatially well-defined arrangements at the molecular level such as electron transfer, ligand-receptor interactions, or catalysis. The creation of synthetic molecules that enable precise control over spacing and functionalization provides opportunities across diverse disciplines. Key requirements of functionalizable oligomeric scaffolds include the specific control of their molecular properties where the correct balance of flexibility and rigidity must be maintained in addition to the prerequisite of defined length. These molecules must ideally be equally applicable in aqueous and organic environments, they must be easy to synthesize in a controlled stepwise fashion, and they must be easily modified with a palette of chemical appendages having diverse functionalities. Oligoproline, a peptidic polymer comprised of repeating units of the amino acid proline, is an ideal platform to meet such challenges. Oligoproline derives its characteristic rigidity and well-defined secondary structure from the innate features of proline. It is the only naturally occurring amino acid that has its side-chain cyclized to its α-amino group, generating often-populated trans and cis conformers around the tertiary amide bonds formed in proline oligomers. Oligoprolines are widely applied to define distance on the molecular level as they are capable of serving as both a "molecular ruler" with a defined length and as a "molecular scaffold" with precisely located and predictably oriented substitutions along the polymeric backbone. Our investigations focus on the use of oligoproline as a molecular scaffold. Toward this end, we have investigated the role of solvent upon helical structure of oligoproline, and the effect that substituents on the pyrrolidine ring and the oligomer termini have on the stability of the helix. We have also further explored the molecular characteristics of oligoproline through spectroscopic and crystallographic methods. All of these structural insights laid the basis for implementation of oligoproline in materials science and chemical biology. Within this Account, we highlight the value of oligoprolines for applications in distinctly different research areas. Toward materials chemistry, we have utilized oligoprolines for the size-controlled generation of noble metal nanoparticles, and to probe the role of spatial preorganization of π-systems for molecular self-assembly. Within the biological realm, we have applied oligoprolines to probe the role of distance on G-protein coupled receptor-mediated ligand uptake by cancerous cells and to investigate the effects of charge preorganization on the efficacy of cationic cell-penetrating peptides.
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Affiliation(s)
- Stefanie Dobitz
- ETH Zürich, Laboratory of Organic Chemistry, D-CHAB, Vladimir-Prelog-Weg 3, CH-8093 Zürich, Switzerland
| | - Matthew R. Aronoff
- ETH Zürich, Laboratory of Organic Chemistry, D-CHAB, Vladimir-Prelog-Weg 3, CH-8093 Zürich, Switzerland
| | - Helma Wennemers
- ETH Zürich, Laboratory of Organic Chemistry, D-CHAB, Vladimir-Prelog-Weg 3, CH-8093 Zürich, Switzerland
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21
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Abstract
The carbonyl group holds a prominent position in chemistry and biology not only because it allows diverse transformations but also because it supports key intermolecular interactions, including hydrogen bonding. More recently, carbonyl groups have been found to interact with a variety of nucleophiles, including other carbonyl groups, in what we have termed an n→π* interaction. In an n→π* interaction, a nucleophile donates lone-pair (n) electron density into the empty π* orbital of a nearby carbonyl group. Mixing of these orbitals releases energy, resulting in an attractive interaction. Hints of such interactions were evident in small-molecule crystal structures as early as the 1970s, but not until 2001 was the role of such interactions articulated clearly. These non-covalent interactions were first discovered during investigations into the thermostability of the proline-rich protein collagen, which achieves a robust structure despite a relatively low potential for hydrogen bonding. It was found that by modulating the distance between two carbonyl groups in the peptide backbone, one could alter the conformational preferences of a peptide bond to proline. Specifically, only the trans conformation of a peptide bond to proline allows for an attractive interaction with an adjacent carbonyl group, so when one increases the proximity of the two carbonyl groups, one enhances their interaction and promotes the trans conformation of the peptide bond, which increases the thermostability of collagen. More recently, attention has been paid to the nature of these interactions. Some have argued that rather than resulting from electron donation, carbonyl interactions are a particular example of dipolar interactions that are well-approximated by classical mechanics. However, experimental evidence has demonstrated otherwise. Numerous examples now exist where an increase in the dipole moment of a carbonyl group decreases the strength of its interactions with other carbonyl groups, demonstrating unequivocally that a dipolar mechanism is insufficient to describe these interactions. Rather, these interactions have important quantum-mechanical character that can be evaluated through careful experimental analysis and judicious use of computation. Although individual n→π* interactions are relatively weak (∼0.3-0.7 kcal/mol), the ubiquity of carbonyl groups across chemistry and biology gives the n→π* interaction broad impact. In particular, the n→π* interaction is likely to play an important role in dictating protein structure. Indeed, bioinformatics analysis suggests that approximately one-third of residues in folded proteins satisfy the geometric requirements to engage in an n→π* interaction, which is likely to be of particular importance for the α-helix. Other carbonyl-dense polymeric materials like polyesters and peptoids are also influenced by n→π* interactions, as are a variety of small molecules, some with particular medicinal importance. Research will continue to identify molecules whose conformation and activity are affected by the n→π* interaction and will clarify their specific contributions to the structures of biomacromolecules.
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Affiliation(s)
- Robert W. Newberry
- 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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22
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Lieblich SA, Fang KY, Cahn JKB, Rawson J, LeBon J, Ku HT, Tirrell DA. 4S-Hydroxylation of Insulin at ProB28 Accelerates Hexamer Dissociation and Delays Fibrillation. J Am Chem Soc 2017; 139:8384-8387. [PMID: 28598606 PMCID: PMC5812673 DOI: 10.1021/jacs.7b00794] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Daily injections of insulin provide lifesaving benefits to millions of diabetics. But currently available prandial insulins are suboptimal: The onset of action is delayed by slow dissociation of the insulin hexamer in the subcutaneous space, and insulin forms amyloid fibrils upon storage in solution. Here we show, through the use of noncanonical amino acid mutagenesis, that replacement of the proline residue at position 28 of the insulin B-chain (ProB28) by (4S)-hydroxyproline (Hzp) yields an active form of insulin that dissociates more rapidly, and fibrillates more slowly, than the wild-type protein. Crystal structures of dimeric and hexameric insulin preparations suggest that a hydrogen bond between the hydroxyl group of Hzp and a backbone amide carbonyl positioned across the dimer interface may be responsible for the altered behavior. The effects of hydroxylation are stereospecific; replacement of ProB28 by (4R)-hydroxyproline (Hyp) causes little change in the rates of fibrillation and hexamer disassociation. These results demonstrate a new approach that fuses the concepts of medicinal chemistry and protein design, and paves the way to further engineering of insulin and other therapeutic proteins.
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Affiliation(s)
- Seth A. Lieblich
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Katharine Y. Fang
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Jackson K. B. Cahn
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Jeffrey Rawson
- Department of Translational Research and Cellular Therapeutics, Diabetes and Metabolism Research Institute, City of Hope, Duarte, CA 91010, USA
- Beckman Research Institute of City of Hope, Duarte, CA 91010, USA
| | - Jeanne LeBon
- Department of Translational Research and Cellular Therapeutics, Diabetes and Metabolism Research Institute, City of Hope, Duarte, CA 91010, USA
| | - H. Teresa Ku
- Department of Translational Research and Cellular Therapeutics, Diabetes and Metabolism Research Institute, City of Hope, Duarte, CA 91010, USA
- Beckman Research Institute of City of Hope, Duarte, CA 91010, USA
- Irell & Manella Graduate School of Biological Sciences, City of Hope, Duarte, CA 91010, USA
| | - David A. Tirrell
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
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23
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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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24
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Bansode ND, Madhanagopal B, Sonar MV, Ganesh KN. Stereodependent and solvent-specific formation of unusual β-structure through side chain-backbone H-bonding in C4(S)-(NH2/OH/NHCHO)-L-prolyl polypeptides. Biopolymers 2017; 108. [DOI: 10.1002/bip.22981] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2016] [Revised: 08/08/2016] [Accepted: 08/25/2016] [Indexed: 01/10/2023]
Affiliation(s)
- Nitin D. Bansode
- Chemical Biology Unit, Chemistry Discipline, Indian Institute of Science Education and Research; Dr. Homi Bhabha Road Pashan, Pune 411008
| | - B. Madhanagopal
- Chemical Biology Unit, Chemistry Discipline, Indian Institute of Science Education and Research; Dr. Homi Bhabha Road Pashan, Pune 411008
| | - Mahesh V. Sonar
- Chemical Biology Unit, Chemistry Discipline, Indian Institute of Science Education and Research; Dr. Homi Bhabha Road Pashan, Pune 411008
| | - Krishna N. Ganesh
- Chemical Biology Unit, Chemistry Discipline, Indian Institute of Science Education and Research; Dr. Homi Bhabha Road Pashan, Pune 411008
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25
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Zhao X, Sun H, Zhang X, Ren J, Shao F, Liu K, Li W, Zhang A. OEGylated collagen mimetic polypeptides with enhanced supramolecular assembly. POLYMER 2016. [DOI: 10.1016/j.polymer.2016.07.027] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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26
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Collagen structure: new tricks from a very old dog. Biochem J 2016; 473:1001-25. [PMID: 27060106 DOI: 10.1042/bj20151169] [Citation(s) in RCA: 159] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Accepted: 02/01/2016] [Indexed: 12/22/2022]
Abstract
The main features of the triple helical structure of collagen were deduced in the mid-1950s from fibre X-ray diffraction of tendons. Yet, the resulting models only could offer an average description of the molecular conformation. A critical advance came about 20 years later with the chemical synthesis of sufficiently long and homogeneous peptides with collagen-like sequences. The availability of these collagen model peptides resulted in a large number of biochemical, crystallographic and NMR studies that have revolutionized our understanding of collagen structure. High-resolution crystal structures from collagen model peptides have provided a wealth of data on collagen conformational variability, interaction with water, collagen stability or the effects of interruptions. Furthermore, a large increase in the number of structures of collagen model peptides in complex with domains from receptors or collagen-binding proteins has shed light on the mechanisms of collagen recognition. In recent years, collagen biochemistry has escaped the boundaries of natural collagen sequences. Detailed knowledge of collagen structure has opened the field for protein engineers who have used chemical biology approaches to produce hyperstable collagens with unnatural residues, rationally designed collagen heterotrimers, self-assembling collagen peptides, etc. This review summarizes our current understanding of the structure of the collagen triple helical domain (COL×3) and gives an overview of some of the new developments in collagen molecular engineering aiming to produce novel collagen-based materials with superior properties.
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27
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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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28
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Brahmi J, Aouadi K, Msaddek M, Praly JP, Vidal S. A stereoselective method for the synthesis of enantiopure 3-substituted 4-hydroxyproline derivatives via 1,3-dipolar cycloadditions. CR CHIM 2016. [DOI: 10.1016/j.crci.2016.03.003] [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]
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29
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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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30
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López-Martínez C, Flores-Morales P, Cruz M, González T, Feliz M, Diez A, Campanera JM. Proline cis-trans isomerization and its implications for the dimerization of analogues of cyclopeptide stylostatin 1: a combined computational and experimental study. Phys Chem Chem Phys 2016; 18:12755-67. [PMID: 27097793 DOI: 10.1039/c5cp05937b] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Cis and trans proline conformers are often associated with dramatic changes in the biological function of peptides. A slow equilibrium between cis and trans Ile-Pro amide bond conformers occurs in constrained derivatives of the native marine cyclic heptapeptide stylostatin 1 (cyclo-(NSLAIPF)), a potential anticancer agent. In this work, four cyclopeptides, cyclo-(NSTAIPF), cyclo-(KSTAIPF), cyclo-(RSTAIPF) and cyclo-(DSTAIPF), which are structurally related to stylostatin 1, are experimentally and computationally examined in order to assess the effect of residue mutations on the cis-trans conformational ratio and the apparent capacity to form dimeric aggregates. Primarily, cyclo-(KSTAIPF) and cyclo-(RSTAIPF) showed specific trends in circular dichroism, MALDI-TOF and HPLC purification experiments, which suggests the occurrence of peptide dimerization. Meanwhile, the NMR spectrum of cyclo-(KSTAIPF) indicates that this cyclopeptide exists in the two slow-exchange families of conformations mentioned above. Molecular dynamics simulations combined with quantum mechanical calculations have shed light on the factors governing the cis/trans conformational ratio. In particular, we have found that residue mutations affect the internal hydrogen bond pattern which ultimately tunes the cis/trans conformational ratio and that only trans conformers are capable of aggregating due to the shape complementarity of the two subunits.
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Affiliation(s)
- C López-Martínez
- Laboratori de Química Orgànica and Institut de Biomedicina (IBUB), Facultat de Farmàcia, Universitat de Barcelona, 08028 Barcelona, Spain
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31
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Guo P, Lei X, Gao Y. Conformational flexibility of PPII-helix: A density functional theory study. Chem Phys Lett 2016. [DOI: 10.1016/j.cplett.2016.03.032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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32
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Sahu S, Das M, Krishnamoorthy G. Switching between cis and trans anions of 2-(2'-hydroxyphenyl)benzimidazole: a molecular rotation perturbed by chemical stabilization. Phys Chem Chem Phys 2016; 18:11081-90. [PMID: 27051888 DOI: 10.1039/c5cp07949g] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Despite the fact that 2-(2'-hydroxyphenyl)benzimidazole (HPBI) exists as the cis and trans enol in neutral form, it was reported to exist only in the trans form upon deprotonation in an aqueous medium. It was also shown that the dianion formed in the ground state can be re-protonated to form the trans-anion in the excited state. In the present study, the cis-anion and dianion could be obtained upon proper stabilization in suitable environments. Switching between the cis and trans-anion was demonstrated to be possible by changing the environment. Theoretical calculations were performed to substantiate the existence of the cis-anion and dianion. In contrast to a literature report, it was shown that the 'OH' group deprotonates before the 'NH' group to form a monoanion not only in protic solvents but also in aprotic solvents.
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Affiliation(s)
- Saugata Sahu
- Department of chemistry, Indian Institute of Technology Guwahati, Guwahati, Assam, India - 781039.
| | - Minati Das
- Department of chemistry, Indian Institute of Technology Guwahati, Guwahati, Assam, India - 781039.
| | - G Krishnamoorthy
- Department of chemistry, Indian Institute of Technology Guwahati, Guwahati, Assam, India - 781039.
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33
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Forbes CR, Pandey AK, Ganguly HK, Yap GPA, Zondlo NJ. 4R- and 4S-iodophenyl hydroxyproline, 4R-pentynoyl hydroxyproline, and S-propargyl-4-thiolphenylalanine: conformationally biased and tunable amino acids for bioorthogonal reactions. Org Biomol Chem 2016; 14:2327-46. [PMID: 26806113 PMCID: PMC5824642 DOI: 10.1039/c5ob02473k] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Bioorthogonal reactions allow the introduction of new functionalities into peptides, proteins, and other biological molecules. The most readily accessible amino acids for bioorthogonal reactions have modest conformational preferences or bases for molecular interactions. Herein we describe the synthesis of 4 novel amino acids containing functional groups for bioorthogonal reactions. (2S,4R)- and (2S,4S)-iodophenyl ethers of hydroxyproline are capable of modification via rapid, specific Suzuki and Sonogashira reactions in water. The synthesis of these amino acids, as Boc-, Fmoc- and free amino acids, was achieved through succinct sequences. These amino acids exhibit well-defined conformational preferences, with the 4S-iodophenyl hydroxyproline crystallographically exhibiting β-turn (ϕ, ψ∼-80°, 0°) or relatively extended (ϕ, ψ∼-80°, +170°) conformations, while the 4R-diastereomer prefers a more compact conformation (ϕ∼-60°). The aryloxyproline diastereomers present the aryl groups in a highly divergent manner, suggesting their stereospecific use in molecular design, medicinal chemistry, and catalysis. Thus, the 4R- and 4S-iodophenyl hydroxyprolines can be differentially applied in distinct structural contexts. The pentynoate ester of 4R-hydroxyproline introduces an alkyne functional group within an amino acid that prefers compact conformations. The propargyl thioether of 4-thiolphenylalanine was synthesized via copper-mediated cross-coupling reaction of thioacetic acid with protected 4-iodophenylalanine, followed by thiolysis and alkylation. This amino acid combines an alkyne functional group with an aromatic amino acid and the ability to tune aromatic and side chain properties via sulfur oxidation. These amino acids provide novel loci for peptide functionalization, with greater control of conformation possible than with other amino acids containing these functional groups.
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Affiliation(s)
- Christina R. Forbes
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Anil K. Pandey
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Himal K. Ganguly
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Glenn P. A. Yap
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Neal J. Zondlo
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, United States
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34
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Singh SK, Mishra KK, Sharma N, Das A. Direct Spectroscopic Evidence for an n→π* Interaction. Angew Chem Int Ed Engl 2016; 55:7801-5. [PMID: 26879929 DOI: 10.1002/anie.201511925] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2015] [Indexed: 11/12/2022]
Abstract
The n→π* interaction is an extremely weak but very important noncovalent interaction. Although this interaction is widely present in biomolecules and materials, its existence is counterintuitive and so has been debated extensively. Herein, we have reported direct spectroscopic evidence for an n→π* interaction for the first time by probing the carbonyl stretching frequency in phenyl formate using isolated gas-phase IR spectroscopy. This result also demonstrates that the conformational preference for the cis conformer of phenyl formate compared to the trans conformer arises due to the presence of the n→π* interaction in the former. The direct proof reported herein for this controversial but important noncovalent interaction should stimulate further experimental and theoretical investigation on this intriguing research topic.
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Affiliation(s)
- Santosh K Singh
- Department of Chemistry, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pune-, 411008, Maharashtra, India
| | - Kamal K Mishra
- Department of Chemistry, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pune-, 411008, Maharashtra, India
| | - Neha Sharma
- Department of Chemistry, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pune-, 411008, Maharashtra, India
| | - Aloke Das
- Department of Chemistry, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pune-, 411008, Maharashtra, India.
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35
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Singh SK, Mishra KK, Sharma N, Das A. Direct Spectroscopic Evidence for an n→π* Interaction. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201511925] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Santosh K. Singh
- Department of Chemistry; Indian Institute of Science Education and Research; Dr. Homi Bhabha Road Pune- 411008 Maharashtra India
| | - Kamal K. Mishra
- Department of Chemistry; Indian Institute of Science Education and Research; Dr. Homi Bhabha Road Pune- 411008 Maharashtra India
| | - Neha Sharma
- Department of Chemistry; Indian Institute of Science Education and Research; Dr. Homi Bhabha Road Pune- 411008 Maharashtra India
| | - Aloke Das
- Department of Chemistry; Indian Institute of Science Education and Research; Dr. Homi Bhabha Road Pune- 411008 Maharashtra India
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36
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Siebler C, Maryasin B, Kuemin M, Erdmann RS, Rigling C, Grünenfelder C, Ochsenfeld C, Wennemers H. Importance of dipole moments and ambient polarity for the conformation of Xaa-Pro moieties - a combined experimental and theoretical study. Chem Sci 2015; 6:6725-6730. [PMID: 30154996 PMCID: PMC6090429 DOI: 10.1039/c5sc02211h] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Accepted: 07/27/2015] [Indexed: 12/04/2022] Open
Abstract
NMR spectroscopic studies with a series of proline derivatives revealed that the polarity of the environment has a significant effect on the trans : cis isomer ratio of Xaa-Pro bonds. Computational studies showed that this effect is due to differences in the overall dipole moments of trans and cis conformers. Comparisons between the conformational properties of amide and ester derivatives revealed an intricate balance between polarity effects and n → π* interactions of adjacent carbonyl groups. The findings have important implications for protein folding and signaling as well as the performance of proline-based stereoselective catalysts.
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Affiliation(s)
- Christiane Siebler
- Laboratory of Organic Chemistry , D-CHAB , ETH Zürich , Vladimir Prelog Weg 3 , CH-8093 Zürich , Switzerland .
| | - Boris Maryasin
- Chair of Theoretical Chemistry , Department of Chemistry , University of Munich (LMU) , Butenandtstr. 7 , D-81377 Munich , Germany
- Center of Integrated Protein Science (CIPSM) at the Department of Chemistry , University of Munich (LMU) , Butenandtstr. 5-13 , D-81377 Munich , Germany
| | - Michael Kuemin
- Laboratory of Organic Chemistry , D-CHAB , ETH Zürich , Vladimir Prelog Weg 3 , CH-8093 Zürich , Switzerland .
| | - Roman S Erdmann
- Laboratory of Organic Chemistry , D-CHAB , ETH Zürich , Vladimir Prelog Weg 3 , CH-8093 Zürich , Switzerland .
| | - Carla Rigling
- Laboratory of Organic Chemistry , D-CHAB , ETH Zürich , Vladimir Prelog Weg 3 , CH-8093 Zürich , Switzerland .
| | - Claudio Grünenfelder
- Laboratory of Organic Chemistry , D-CHAB , ETH Zürich , Vladimir Prelog Weg 3 , CH-8093 Zürich , Switzerland .
| | - Christian Ochsenfeld
- Chair of Theoretical Chemistry , Department of Chemistry , University of Munich (LMU) , Butenandtstr. 7 , D-81377 Munich , Germany
- Center of Integrated Protein Science (CIPSM) at the Department of Chemistry , University of Munich (LMU) , Butenandtstr. 5-13 , D-81377 Munich , Germany
| | - Helma Wennemers
- Laboratory of Organic Chemistry , D-CHAB , ETH Zürich , Vladimir Prelog Weg 3 , CH-8093 Zürich , Switzerland .
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37
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Berger G, Vilchis‐Reyes M, Hanessian S. Structural Properties and Stereochemically Distinct Folding Preferences of 4,5‐
cis
and
trans
‐Methano‐
L
‐Proline Oligomers: The Shortest Crystalline PPII‐Type Helical Proline‐Derived Tetramer. Angew Chem Int Ed Engl 2015; 54:13268-72. [DOI: 10.1002/anie.201506208] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Indexed: 12/12/2022]
Affiliation(s)
- Gilles Berger
- Department of Chemistry, Université de Montréal, Station Centre‐Ville, C.P. 6128, Montreal, QC, H3C 3J7 (Canada)
- Faculty of Pharmacy, Laboratory of Pharmaceutical Chemistry, Université Libre de Bruxelles, Campus Plaine CP205/5, Université Libre de Bruxelles, Bd du Triomphe, 1050 Brussels (Belgium)
| | - Miguel Vilchis‐Reyes
- Department of Chemistry, Université de Montréal, Station Centre‐Ville, C.P. 6128, Montreal, QC, H3C 3J7 (Canada)
| | - Stephen Hanessian
- Department of Chemistry, Université de Montréal, Station Centre‐Ville, C.P. 6128, Montreal, QC, H3C 3J7 (Canada)
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38
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Berger G, Vilchis‐Reyes M, Hanessian S. Structural Properties and Stereochemically Distinct Folding Preferences of 4,5‐
cis
and
trans
‐Methano‐
L
‐Proline Oligomers: The Shortest Crystalline PPII‐Type Helical Proline‐Derived Tetramer. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201506208] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Gilles Berger
- Department of Chemistry, Université de Montréal, Station Centre‐Ville, C.P. 6128, Montreal, QC, H3C 3J7 (Canada)
- Faculty of Pharmacy, Laboratory of Pharmaceutical Chemistry, Université Libre de Bruxelles, Campus Plaine CP205/5, Université Libre de Bruxelles, Bd du Triomphe, 1050 Brussels (Belgium)
| | - Miguel Vilchis‐Reyes
- Department of Chemistry, Université de Montréal, Station Centre‐Ville, C.P. 6128, Montreal, QC, H3C 3J7 (Canada)
| | - Stephen Hanessian
- Department of Chemistry, Université de Montréal, Station Centre‐Ville, C.P. 6128, Montreal, QC, H3C 3J7 (Canada)
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39
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Umashankara M, Sonar MV, Bansode ND, Ganesh KN. Orchestration of Structural, Stereoelectronic, and Hydrogen-Bonding Effects in Stabilizing Triplexes from Engineered Chimeric Collagen Peptides (ProX-ProY-Gly)6 Incorporating 4(R/S)-Aminoproline. J Org Chem 2015; 80:8552-60. [DOI: 10.1021/acs.joc.5b01032] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Muddegowda Umashankara
- Department
of Studies in Chemistry, Karnataka State Open University, Muktagangotri, Mysore 570006, India
| | - Mahesh V. Sonar
- Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pune 411008, India
| | - Nitin D. Bansode
- Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pune 411008, India
| | - Krishna N. Ganesh
- Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pune 411008, India
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40
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Bartuschat AL, Wicht K, Heinrich MR. Switching and Conformational Fixation of Amides Through Proximate Positive Charges. Angew Chem Int Ed Engl 2015; 54:10294-8. [DOI: 10.1002/anie.201502474] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Indexed: 01/03/2023]
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41
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Bartuschat AL, Wicht K, Heinrich MR. Schaltung und Fixierung der Konformation von Amiden durch nahegelegene positive Ladungen. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201502474] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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42
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Garbuio L, Lewandowski B, Wilhelm P, Ziegler L, Yulikov M, Wennemers H, Jeschke G. Shape Persistence of Polyproline II Helical Oligoprolines. Chemistry 2015; 21:10747-53. [PMID: 26089127 DOI: 10.1002/chem.201501190] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Indexed: 11/06/2022]
Abstract
Oligoprolines are commonly used as molecular scaffolds. Past studies on the persistence length of their secondary structure, the polyproline II (PPII) helix, and on the fraction of backbone cis amide bonds have provided conflicting results. We resolved this debate by studying a series of spin-labeled proline octadecamers with EPR spectroscopy. Distance distributions between an N-terminal Gd(III) -DOTA (DOTA=1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetic acid) label and a nitroxide label at one of five evenly spaced backbone sites allowed us to discriminate between the flexibility of the PPII helix and the cis amide contributions. An upper limit of 2 % cis amide bonds per residue was found in a 7:3 (v/v) water/glycerol mixture, whereas cis amides were not observed in trifluoroethanol. Extrapolation of Monte Carlo models from the glass transition to ambient temperature predicts a persistence length of ≈3-3.5 nm in both solvents. The method is generally applicable to any type of oligomer for which the persistence length is of interest.
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Affiliation(s)
- Luca Garbuio
- ETH Zurich, Department of Chemistry and Applied Bioscience, Laboratory of Physical Chemistry, Vladimir Prelog Weg 2, 8093, Zurich (Switzerland)
| | - Bartosz Lewandowski
- ETH Zurich, Department of Chemistry and Applied Bioscience, Laboratory of Organic Chemistry, Vladimir Prelog Weg 3, 8093, Zurich (Switzerland)
| | - Patrick Wilhelm
- ETH Zurich, Department of Chemistry and Applied Bioscience, Laboratory of Organic Chemistry, Vladimir Prelog Weg 3, 8093, Zurich (Switzerland)
| | - Ludmila Ziegler
- ETH Zurich, Department of Chemistry and Applied Bioscience, Laboratory of Organic Chemistry, Vladimir Prelog Weg 3, 8093, Zurich (Switzerland)
| | - Maxim Yulikov
- ETH Zurich, Department of Chemistry and Applied Bioscience, Laboratory of Physical Chemistry, Vladimir Prelog Weg 2, 8093, Zurich (Switzerland).
| | - Helma Wennemers
- ETH Zurich, Department of Chemistry and Applied Bioscience, Laboratory of Organic Chemistry, Vladimir Prelog Weg 3, 8093, Zurich (Switzerland).
| | - Gunnar Jeschke
- ETH Zurich, Department of Chemistry and Applied Bioscience, Laboratory of Physical Chemistry, Vladimir Prelog Weg 2, 8093, Zurich (Switzerland).
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43
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Jiang T, Vail OA, Jiang Z, Zuo X, Conticello VP. Rational Design of Multilayer Collagen Nanosheets with Compositional and Structural Control. J Am Chem Soc 2015; 137:7793-802. [DOI: 10.1021/jacs.5b03326] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Tao Jiang
- Department
of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Owen A. Vail
- School
of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Zhigang Jiang
- School
of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Xiaobing Zuo
- X-ray
Science Division, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, Illinois 60439, United States
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44
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Kaplaneris N, Koutoulogenis G, Raftopoulou M, Kokotos CG. 4-Fluoro and 4-Hydroxy Pyrrolidine-thioxotetrahydropyrimidinones: Organocatalysts for Green Asymmetric Transformations in Brine. J Org Chem 2015; 80:5464-73. [PMID: 25942500 DOI: 10.1021/acs.joc.5b00283] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The synthesis of both trans- and cis-diastereomers of pyrrolidinine-thioxotetrahydropyrimidinone bearing either a fluorine or a hydroxyl group was accomplished. The new compounds were tested for their catalytic properties in a variety of asymmetric organic transformations and compared with the first generation catalyst. It was found that the new catalysts could efficiently catalyze the reactions in brine, without the use of organic solvent, and by employing an almost stoichiometric amount of reagents. Thus, the products were isolated by simple extractions, avoiding the use of chromatography in excellent yields, diastereoselectivities, and enantioselectivities.
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Affiliation(s)
- Nikolaos Kaplaneris
- Laboratory of Organic Chemistry, Department of Chemistry, University of Athens, Panepistimiopolis, Athens 15771, Greece
| | - Giorgos Koutoulogenis
- Laboratory of Organic Chemistry, Department of Chemistry, University of Athens, Panepistimiopolis, Athens 15771, Greece
| | - Marianna Raftopoulou
- Laboratory of Organic Chemistry, Department of Chemistry, University of Athens, Panepistimiopolis, Athens 15771, Greece
| | - Christoforos G Kokotos
- Laboratory of Organic Chemistry, Department of Chemistry, University of Athens, Panepistimiopolis, Athens 15771, Greece
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45
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Nsengiyumva O, Hamedzadeh S, McDaniel J, Macho J, Simpson G, Panda SS, Ha K, Lebedyeva I, Faidallah HM, Al-Mohammadi MM, Hall CD, Katritzky AR. A benzotriazole-mediated route to protected marine-derived hetero-2,5-diketopiperazines containing proline. Org Biomol Chem 2015; 13:4399-403. [PMID: 25762208 DOI: 10.1039/c5ob00023h] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A procedure for the cyclization of dipeptidoyl benzotriazolides containing proline derivatives promoted by triethylamine under MW activation is introduced. The reaction is general for a variety of dipeptidoyl benzotriazolides and represents a very practical and convenient method for the preparation of Pro- or Hyp-derived 2,5-diketopiperazines (2,5-DKPs) and bis-DKPs with a disulfide linker. This method can be used for the construction of 2,5-DKP compound libraries and for the synthesis of natural products with diketopiperazine cores.
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Affiliation(s)
- Olivier Nsengiyumva
- Center for Heterocyclic Compounds, Department of Chemistry, University of Florida, Gainesville, FL 32611-7200, USA.
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46
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Siebler C, Trapp N, Wennemers H. Crystal structure of (4S
)-aminoproline: conformational insight into a pH-responsive proline derivative. J Pept Sci 2015; 21:208-11. [DOI: 10.1002/psc.2734] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Accepted: 12/03/2014] [Indexed: 12/23/2022]
Affiliation(s)
- Christiane Siebler
- Laboratorium für Organische Chemie; ETH Zürich; Vladimir-Prelog-Weg 3 CH-8093 Zürich Switzerland
| | - Nils Trapp
- Laboratorium für Organische Chemie; ETH Zürich; Vladimir-Prelog-Weg 3 CH-8093 Zürich Switzerland
| | - Helma Wennemers
- Laboratorium für Organische Chemie; ETH Zürich; Vladimir-Prelog-Weg 3 CH-8093 Zürich Switzerland
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47
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Park EB, Jeong KS. Chloride transport activities of trans- and cis-amide-linked bisureas. Chem Commun (Camb) 2015; 51:9197-200. [DOI: 10.1039/c5cc02757h] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
A stimuli-responsive synthetic chloride transporter has been devised based on the different transport abilities of bisurea compounds linked by cis- and trans-amides.
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Affiliation(s)
- Eun Bit Park
- Department of Chemistry
- Yonsei University
- Seoul
- Korea
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48
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Wilhelm P, Lewandowski B, Trapp N, Wennemers H. A crystal structure of an oligoproline PPII-helix, at last. J Am Chem Soc 2014; 136:15829-32. [PMID: 25368901 DOI: 10.1021/ja507405j] [Citation(s) in RCA: 136] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The first crystal structure of an oligoproline adopting an all-trans polyproline II (PPII) helix is presented. The high-resolution structure provides detailed insight into the dimensions and conformational properties of oligoprolines that are important for, e.g., their use as "molecular rulers" and "molecular scaffolds". The structure also showed that the amides interact with each other within a PPII helix and that water is not necessary for PPII helicity.
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Affiliation(s)
- Patrick Wilhelm
- Laboratory of Organic Chemistry, ETH Zurich , Vladimir-Prelog-Weg 3, CH-8093 Zurich, Switzerland
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49
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Lin YJ, Chang CH, Horng JC. The Impact of 4-Thiaproline on Polyproline Conformation. J Phys Chem B 2014; 118:10813-20. [DOI: 10.1021/jp503915p] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yu-Ju Lin
- Department of Chemistry and Frontier Research Center on Fundamental and Applied
Sciences of Matters, National Tsing Hua University, Hsinchu, Taiwan 30013, R.O.C
| | - Chiao-Hsin Chang
- Department of Chemistry and 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 and Frontier Research Center on Fundamental and Applied
Sciences of Matters, National Tsing Hua University, Hsinchu, Taiwan 30013, R.O.C
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50
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Pandey AK, Thomas KM, Forbes C, Zondlo NJ. Tunable control of polyproline helix (PPII) structure via aromatic electronic effects: an electronic switch of polyproline helix. Biochemistry 2014; 53:5307-14. [PMID: 25075447 PMCID: PMC4139158 DOI: 10.1021/bi500696k] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2014] [Revised: 07/28/2014] [Indexed: 01/10/2023]
Abstract
Aromatic rings exhibit defined interactions via the unique aromatic π face. Aromatic amino acids interact favorably with proline residues via both the hydrophobic effect and aromatic-proline interactions, C-H/π interactions between the aromatic π face and proline ring C-H bonds. The canonical aromatic amino acids Trp, Tyr, and Phe strongly disfavor a polyproline helix (PPII) when they are present in proline-rich sequences because of the large populations of cis amide bonds induced by favorable aromatic-proline interactions (aromatic-cis-proline and proline-cis-proline-aromatic interactions). We demonstrate the ability to tune polyproline helix conformation and cis-trans isomerism in proline-rich sequences using aromatic electronic effects. Electron-rich aromatic residues strongly disfavor polyproline helix and exhibit large populations of cis amide bonds, while electron-poor aromatic residues exhibit small populations of cis amide bonds and favor polyproline helix. 4-Aminophenylalanine is a pH-dependent electronic switch of polyproline helix, with cis amide bonds favored as the electron-donating amine, but trans amide bonds and polyproline helix preferred as the electron-withdrawing ammonium. Peptides with block proline-aromatic PPXPPXPPXPP sequences exhibited electronically switchable pH-dependent structures. Electron-poor aromatic amino acids provide special capabilities to integrate aromatic residues into polyproline helices and to serve as the basis of aromatic electronic switches to change structure.
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Affiliation(s)
- Anil K. Pandey
- Department
of Chemistry and
Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Krista M. Thomas
- Department
of Chemistry and
Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Christina
R. Forbes
- Department
of Chemistry and
Biochemistry, University of Delaware, Newark, Delaware 19716, United States
| | - Neal J. Zondlo
- Department
of Chemistry and
Biochemistry, University of Delaware, Newark, Delaware 19716, United States
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