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Ramesh S, Cherkupally P, Govender T, Kruger HG, Albericio F, de la Torre BG. Highly chemoselective ligation of thiol- and amino-peptides on a bromomaleimide core. Chem Commun (Camb) 2016; 52:2334-7. [PMID: 26728847 DOI: 10.1039/c5cc09457g] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Application of a bromomaleimide core allows for the incorporation of three different peptides. The key reactions of the process are the selective stapling of both thiol- and amino-peptides on two different sites of the core. The thiol-peptide attacks and replaces the bromide whereas the amino-peptide attaches to the ene-position of the core revealing differential and selective reactivity. This platform will have further application in protein chemistry, multidrug presentation and vaccine preparation.
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Affiliation(s)
- Suhas Ramesh
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban 4001, South Africa.
| | - Prabhakar Cherkupally
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban 4001, South Africa.
| | - Thavendran Govender
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban 4001, South Africa.
| | - Hendrik G Kruger
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban 4001, South Africa.
| | - Fernando Albericio
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban 4001, South Africa. and School of Chemistry and Physics, University of KwaZulu-Natal, Durban 4001, South Africa.
| | - Beatriz G de la Torre
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban 4001, South Africa.
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2
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Delsuc N, Massip S, Léger JM, Kauffmann B, Huc I. Relative helix-helix conformations in branched aromatic oligoamide foldamers. J Am Chem Soc 2011; 133:3165-72. [PMID: 21306159 DOI: 10.1021/ja110677a] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The de novo design and synthesis of large and well-organized, tertiary-like, α-peptidic folded architectures is difficult because it relies on multiple cooperative interactions within and between secondary folded motifs of relatively weak intrinsic stability. The very stable helical structures of oligoamides of 8-amino-2-quinoline carboxylic acid offer a way to circumvent this difficulty thanks to their ability to fold into predictable and stable secondary motifs. Branched architectures comprised of two pairs of tetrameric (1), pentameric (2), or octameric (3) oligomers connected via an ethylene glycol spacer were designed and synthesized. The short spacer holds two helices in close proximity, thus enabling interactions between them. Degrees of freedom allowed in the system are well-defined: the relative P or M handedness of the two helices; the relative orientation of the helix axes; and the gauche or anti conformation of the ethylene spacer. Investigating the structures of 1-3 in the solid state and in solution allowed a detailed picture to be drawn of their conformational preferences and dynamics. The high variability of the solid state structures provides many snapshots of possible solution conformations. Helix-helix handedness communication was evidenced and shown to depend both on solvent and on a defined set of side chains at the helix-helix interface. Interdigitation of the side chains was found to restrict free rotation about the ethylene spacer. One solid state structure shows a high level of symmetry and provides a firm basis to further design specific side chain/side chain directional interactions.
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Affiliation(s)
- Nicolas Delsuc
- Institut Européen de Chimie et Biologie, Université de Bordeaux-CNRS UMR5248 and UMS3033, 2 rue Robert Escarpit, 33607 Pessac, France
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3
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Freeman JO, Lee WC, Murphy MEP, Sherman JC. X-ray crystal analysis of a TASP: structural insights of a cavitein dimer. J Am Chem Soc 2009; 131:7421-9. [PMID: 19422242 DOI: 10.1021/ja901404w] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Cavitein Q4 is a template assembled synthetic protein designed for X-ray crystallographic analysis. It is based on a previous monomeric helical bundle cavitein (N1GG) that consists of four identical parallel helical peptides. Crystals that were grown in the presence of bromide ions were used to solve the initial phases via single-wavelength anomalous dispersion (SAD). A 1.4 A resolution data set was then refined starting with the SAD phases to provide the crystal structure of cavitein Q4. The crystal structure revealed cavitein Q4 as an asymmetric dimer, although the cavitein appears to be largely monomeric in solution. A comparative analysis is carried out to discern any intrinsic differences between Q4 and its parent cavitein N1GG. We present herein the first X-ray crystal structure of a TASP system and relate this structure to the solution data for both Q4 and its parent N1GG.
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Affiliation(s)
- Jon O Freeman
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC, Canada V6T 1Z1
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4
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Chopra N, Gan W, Schreiber H, Kurutz JW, Meredith SC. Versatile cyclic templates for assembly of axially oriented ligands. Bioconjug Chem 2009; 20:231-40. [PMID: 19159293 DOI: 10.1021/bc800312x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In this paper, we describe two novel types of planar cyclic peptide templates for the facile addition of ligands that extend axially from the plane of the template ring. The first uses beta-amino acids of alternating D- and L-chirality, since the insertion of the additional methylene group in the peptide backbone was predicted and subsequently shown by NMR and molecular modeling, to reorient ligands attached to amino acid side chain axially with respect to the template ring. A second contains alternating D- and L-amino acids with an achiral Gly residue interposed between each chiral amino acid. The inserted Gly residues also tend to reorient side chains axially rather than radially, as was demonstrated by NMR and molecular modeling. The axial orientation of attached ligands is intended to foster or allow interactions among attached ligands in situations in which this is desired. Two such situations that we consider are (1) development of immunological reagents with avidity effects and (2) modeling of oligomers in fibril-forming peptides. Toward the first of these goals, we demonstrated that these templates are suitable for attaching macromolecules, by incorporating two types of protein, neutravidin and trypsinogen. Toward the second goal, we demonstrate the attachment of two different fibril-forming peptides to the template. The templates described herein thus have many of the desirable traits of such molecules, i.e., (1) multivalency for the attachment of multiple ligands, (2) suitable chemical functions for facile attachment of ligands, (3) versatility as to the number and spacing of ligand attachment sites, (4) sufficient rigidity so that the attached ligands can be similarly oriented with respect to the template, and (5) sufficient flexibility to allow even large ligands, such as proteins, to attach and interact.
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Affiliation(s)
- Neeraj Chopra
- Department of Pathology, The University of Chicago, Chicago, Illinois 60637, USA
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5
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Avrutina O, Empting M, Fabritz S, Daneschdar M, Frauendorf H, Diederichsen U, Kolmar H. Application of copper(i) catalyzed azide–alkyne [3+2] cycloaddition to the synthesis of template-assembled multivalent peptide conjugates. Org Biomol Chem 2009; 7:4177-85. [DOI: 10.1039/b908261a] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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6
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Rational design of antithrombotic peptides to target the von Willebrand Factor (vWf) - GPIb integrin interaction. J Mol Model 2008; 14:1191-202. [DOI: 10.1007/s00894-008-0375-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2008] [Accepted: 09/22/2008] [Indexed: 10/21/2022]
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7
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Boturyn D, Defrancq E, Dolphin GT, Garcia J, Labbe P, Renaudet O, Dumy P. RAFT Nano-constructs: surfing to biological applications. J Pept Sci 2008; 14:224-40. [DOI: 10.1002/psc.964] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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8
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Seo ES, Scott WRP, Straus SK, Sherman JC. Optimal Attachment Position and Linker Length Promote Native-like Character of Cavitand-Based Template-Assembled Synthetic Proteins (TASPs). Chemistry 2007; 13:3596-605. [PMID: 17295367 DOI: 10.1002/chem.200601784] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
We have designed, synthesised and characterised a series of template-assembled de novo four-helix bundles, each differing in the linker length between the template and the peptides. The helix is based on an earlier peptide sequence: EELLKKLEELLKKLG (first-generation sequence), which was designed to link the hydrophilic/hydrophobic interface of the helices. Increasing or decreasing the linker length by one glycine residue had a significant effect on the structure and properties of the template-assembled synthetic proteins (TASPs). Here, the effect of the linker length is further probed by linking the peptides closer to the hydrophobic face by using the second-generation sequence, AEELLKKLEELLKKG, in an effort to improve the packing between the helices and to better understand the helical bundles. The peptides were synthesised with 0-4 Gly linker residues and linked onto a cavitand template. The proteins were found to be alpha-helical, stable to guanidine hydrochloride (GuHCl) and to unfold cooperatively. However, their stabilities toward GuHCl, propensity to self-aggregate and structural specificity differed. The two-glycine variant of the second-generation series demonstrated the highest stability and most native-like character of all the mononeric TASPs in both the first- and second-generation series. The structural specificity of this two glycine variant is comparable to that of other known native-like de novo proteins. Molecular dynamics simulations showed that the two-glycine variant contains helices that are tilted with respect to the cavitand template and may account for its unique properties.
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Affiliation(s)
- Emily S Seo
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC, V6T 1Z1, Canada
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9
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Freeman JO, Wallhorn D, Sherman JC. Four-helix bundle cavitein reveals middle leucine as linchpin. Biopolymers 2007; 88:725-32. [PMID: 17351918 DOI: 10.1002/bip.20718] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
A template-assembled de novo four-helix bundle is used to examine the hydrophobic effect within the bundle interior. Leu to Ala variants of the basis sequence GG-EELLKKLEELLKKG were characterized by GuHCl denaturation, NMR dispersion, and N-H/D exchange experiments. The results show that the middle leucine (L7) is imperative in maintaining bundle stability. The average leucine was found to contribute 1.8 kcal mol(-1) toward stability, whereas the middle leucines contribute 2.7 kcal mol(-1) each. Substituting alanine into the middle position (7) constitutes a striking 95% reduction of the overall cavitein stability.
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Affiliation(s)
- Jon O Freeman
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC, Canada V6T 1Z1
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10
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Hocquelet C, Blu J, Jankowski C, Arseneau S, Buisson D, Mauclaire L. Synthesis of calixarene–cyclodextrin coupling products. Tetrahedron 2006. [DOI: 10.1016/j.tet.2006.09.089] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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11
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Tsukamoto K, Ohishi H, Maezaki N, Tanaka T, Ishida T. Calix[6]arene-Based Template for X-ray Crystallographic Analysis of Template-Assembled Synthetic Proteins. Chembiochem 2006; 7:1559-62. [PMID: 16960819 DOI: 10.1002/cbic.200600132] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Koji Tsukamoto
- Graduate School of Pharmaceutical Sciences, Osaka University 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
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12
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Bao X, Isaacsohn I, Drew AF, Smithrud DB. Determining the Intracellular Transport Mechanism of a Cleft−[2]Rotaxane. J Am Chem Soc 2006; 128:12229-38. [PMID: 16967974 DOI: 10.1021/ja063667f] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Rotaxanes are a class of interlocked compounds that have been extensively investigated for their potential utility as switches or sensors. We recently demonstrated that rotaxanes have further application as agents that transport material into cells. This novel finding prompted our investigation into the mechanism by which rotaxanes are involved in transmembrane transport. Two-dimensional NMR analysis showed that a cleft-containing rotaxane exists in two dominant conformations ("closed" and "open"). To determine the importance of conformational flexibility on the ability of the rotaxanes to bind guests and transport material into cells, the rotaxane was chemically modified to lock it in the closed conformation. Charged guests interact less favorably with the locked rotaxane, as compared to the unmodified rotaxane, both in an aqueous solution and in DMSO. In a chloroform solution, both rotaxanes bind the guests with similar affinities. The locked rotaxane exhibited a reduced capacity to transport a fluoresceinated peptide into cells, whereas the unmodified rotaxane efficiently delivers the peptide. Flow cytometry experiments demonstrated that a high percentage of the cells contained the delivered peptide (89-98%), the level of delivery is concentration dependent, and the rotaxanes and peptide have low toxicity. Cellular uptake of the peptide was largely temperature and ATP independent, suggesting that the rotaxane-peptide complex passes through the cellular membrane without requiring active cell-mediated processes. The results show that the sliding motion of the wheel is necessary for the delivery of materials into cells and can enhance the association of guests. These studies demonstrate the potential for rotaxanes as a new class of mechanical devices that deliver a variety of therapeutic agents into targeted cell populations.
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Affiliation(s)
- Xiaofeng Bao
- Department of Chemistry, University of Cincinnati, Cincinnati, Ohio 45221, USA
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Singh Y, Dolphin GT, Razkin J, Dumy P. Synthetic Peptide Templates for Molecular Recognition: Recent Advances and Applications. Chembiochem 2006; 7:1298-314. [PMID: 16892470 DOI: 10.1002/cbic.200600078] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The creation of molecular systems that can mimic some of the properties of natural macromolecules is one of the major endeavors in contemporary protein chemistry. However, the construction of artificial proteins with predetermined structure and function is difficult on account of complex folding pathways. The use of topological peptide templates has been suggested to induce and stabilize defined secondary and tertiary structures. This is because the recent advances in the chemistry of coupling reagents, protecting groups, and solid-phase synthesis have made the chemical synthesis of peptides with conformationally controlled and complex structures feasible. Besides their use as structure-inducing devices, these peptide templates can also be utilized to construct novel structures with tailor-made functions. Herein, we present recent advances in the field of peptide-template-based approaches with particular emphasis on the demonstrated utility of this approach in molecular recognition, along with related applications.
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Affiliation(s)
- Yashveer Singh
- LEDSS, UMR CNRS 5616, ICMG FR 2607, Universite Joseph Fourier, Grenoble Cedex 9, France
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14
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Affiliation(s)
- Gabriele Tuchscherer
- Ecole Polytechnique Fédérale de Lausanne, Institute of Molecular Sciences and Engineering, CH-1015 Lausanne, Switzerland
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15
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Abstract
Novel chemical variants of proteins have been found in nature, including potent 'microprotein' natural products and folded protein molecules that contain a cyclic polypeptide chain. Researchers have used chemical synthesis and genetic methods to make these proteins and more: protein catenanes, neoglycoproteins, and artificial protein molecules with novel architectures or made from novel building blocks. De novo design has taken a big step forward with the accurate design and construction of proteins with complex molecular structure. A variety of non-coded amino acids and other building blocks has been used to make increasingly sophisticated protein molecular devices for use as biosensors and for the study of signal transduction inside living cells.
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Affiliation(s)
- Stephen Kent
- Cummings Life Sciences Center #325, The University of Chicago, 920 East 58th Street, Chicago, Illinois 60637, USA.
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