1
|
Yoo SH, Buratto J, Roy A, Pasco M, Pulka-Ziach K, Collie GW, Guichard G. Oligourea helix bundle binds detergents with diverse polar head groups. Org Biomol Chem 2024; 22:731-734. [PMID: 38169016 DOI: 10.1039/d3ob01873c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Here we report a series of crystal structures (and accompanying biophysical data) of an array of diverse detergent guests bound to an oligourea foldamer helix bundle. These results significantly increase our structural and chemical understanding of aqueous guest recognition by oligourea foldamers and will aid the design of further functionalised oligourea-based self-assemblies.
Collapse
Affiliation(s)
- Sung Hyun Yoo
- Univ. Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, IECB, 2 rue Robert Escarpit, 33607, Pessac, France.
- Department of Chemistry, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Jérémie Buratto
- Univ. Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, IECB, 2 rue Robert Escarpit, 33607, Pessac, France.
| | - Arup Roy
- Univ. Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, IECB, 2 rue Robert Escarpit, 33607, Pessac, France.
| | - Morgane Pasco
- Univ. Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, IECB, 2 rue Robert Escarpit, 33607, Pessac, France.
| | | | - Gavin W Collie
- Discovery Sciences, R&D, AstraZeneca, Cambridge CB4 0WG, UK.
| | - Gilles Guichard
- Univ. Bordeaux, CNRS, Bordeaux INP, CBMN, UMR 5248, IECB, 2 rue Robert Escarpit, 33607, Pessac, France.
| |
Collapse
|
2
|
Pike SJ, Telford R, Male L. Reversible conformational switching of a photo-responsive ortho-azobenzene/2,6-pyridyldicarboxamide heterofoldamer. Org Biomol Chem 2023; 21:7717-7723. [PMID: 37565617 DOI: 10.1039/d3ob01137b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/12/2023]
Abstract
We report on a convenient synthetic route to rapidly access a new photo-responsive ortho-azobenzene/2,6-pyridyldicarboxamide heterofoldamer. The adoption of a stable helical conformation has been established for this scaffold in both the solid state and in solution using single crystal X-ray diffraction and circular dichroism (CD) spectroscopy respectively. Reversible control over the stimuli-driven structural re-ordering of the supramolecular scaffold, from a stable helical conformation under non-irradiative conditions, to a less well-ordered state under irradiative conditions, has been identified. The robust nature of the responsive, conformational, molecular switching behaviour has been determined using UV/Vis, 1H NMR and CD spectroscopy. Minimal loss in the efficiency of the stimuli-driven, structural re-ordering processes of the foldamer scaffold is observed, even upon multiple cyclic treatments with irradiative/non-irradiative conditions.
Collapse
Affiliation(s)
- Sarah J Pike
- School of Chemistry, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK.
- School of Chemistry and Biosciences, Faculty of Life Sciences, University of Bradford, Bradford, West Yorkshire, BD7 1DP, UK
| | - Richard Telford
- School of Chemistry and Biosciences, Faculty of Life Sciences, University of Bradford, Bradford, West Yorkshire, BD7 1DP, UK
| | - Louise Male
- School of Chemistry, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK.
| |
Collapse
|
3
|
Sang P, Cai J. Unnatural helical peptidic foldamers as protein segment mimics. Chem Soc Rev 2023; 52:4843-4877. [PMID: 37401344 PMCID: PMC10389297 DOI: 10.1039/d2cs00395c] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Indexed: 07/05/2023]
Abstract
Unnatural helical peptidic foldamers have attracted considerable attention owing to their unique folding behaviours, diverse artificial protein binding mechanisms, and promising applications in chemical, biological, medical, and material fields. Unlike the conventional α-helix consisting of molecular entities of native α-amino acids, unnatural helical peptidic foldamers are generally comprised of well-defined backbone conformers with unique and unnatural structural parameters. Their folded structures usually arise from unnatural amino acids such as N-substituted glycine, N-substituted-β-alanine, β-amino acid, urea, thiourea, α-aminoxy acid, α-aminoisobutyric acid, aza-amino acid, aromatic amide, γ-amino acid, as well as sulfono-γ-AA amino acid. They can exhibit intriguing and predictable three-dimensional helical structures, generally featuring superior resistance to proteolytic degradation, enhanced bioavailability, and improved chemodiversity, and are promising in mimicking helical segments of various proteins. Although it is impossible to include every piece of research work, we attempt to highlight the research progress in the past 10 years in exploring unnatural peptidic foldamers as protein helical segment mimics, by giving some representative examples and discussing the current challenges and future perspectives. We expect that this review will help elucidate the principles of structural design and applications of existing unnatural helical peptidic foldamers in protein segment mimicry, thereby attracting more researchers to explore and generate novel unnatural peptidic foldamers with unique structural and functional properties, leading to more unprecedented and practical applications.
Collapse
Affiliation(s)
- Peng Sang
- Tianjian Laboratory of Advanced Biomedical Sciences, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, China.
| | - Jianfeng Cai
- Department of Chemistry, University of South Florida, Tampa, FL 33620, USA.
| |
Collapse
|
4
|
Rao SR, Harmon TW, Heath SL, Wolfe JA, Santhouse JR, O'Brien GL, Distefano AN, Reinert ZE, Horne WS. Chemical Shifts of Artificial Monomers Used to Construct Heterogeneous-Backbone Protein Mimetics in Random Coil and Folded States. Pept Sci (Hoboken) 2023; 115:e24297. [PMID: 37397503 PMCID: PMC10312354 DOI: 10.1002/pep2.24297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 10/27/2022] [Indexed: 03/03/2024]
Abstract
The construction of protein-sized synthetic chains that blend natural amino acids with artificial monomers to create so-called heterogeneous-backbones is a powerful approach to generate complex folds and functions from bio-inspired agents. A variety of techniques from structural biology commonly used to study natural proteins have been adapted to investigate folding in these entities. In NMR characterization of proteins, proton chemical shift is a straightforward to acquire, information-rich metric that bears directly on a variety of properties related to folding. Leveraging chemical shift to gain insight into folding requires a set of reference chemical shift values corresponding to each building block type (i.e., the 20 canonical amino acids in the case of natural proteins) in a random coil state and knowledge of systematic changes in chemical shift associated with particular folded conformations. Although well documented for natural proteins, these issues remain unexplored in the context of protein mimetics. Here, we report random coil chemical shift values for a library of artificial amino acid monomers frequently used to construct heterogeneous-backbone protein analogues as well as a spectroscopic signature associated with one monomer class, β3-residues bearing proteinogenic side chains, adopting a helical folded conformation. Collectively, these results will facilitate the continued utilization of NMR for the study of structure and dynamics in protein-like artificial backbones.
Collapse
Affiliation(s)
- Shilpa R Rao
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Thomas W Harmon
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Shelby L Heath
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Jacob A Wolfe
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | | | - Gregory L O'Brien
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Alexis N Distefano
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Zachary E Reinert
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - W Seth Horne
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| |
Collapse
|
5
|
Liu B, Xing P. Hydrogen Bonded Foldamers with Axial Chirality: Chiroptical Properties and Applications. Chemistry 2023; 29:e202202665. [PMID: 36281580 DOI: 10.1002/chem.202202665] [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: 08/26/2022] [Revised: 10/24/2022] [Accepted: 10/25/2022] [Indexed: 11/07/2022]
Abstract
Folding phenomenon refers to the formation of a specific conformation widely featured by the intramolecular interactions, which broadly exist in biomacromolecules, and are closely related to their structures and functions. A variety of oligomeric folded molecules have been designed and synthesized, namely "foldamer", exhibiting potentials in pharmaceutical and catalysis. Molecular folding is a promising strategy to transfer chirality from substituents to the whole skeleton, when chirality transfer, amplification, evolution, and other behaviors could be achieved. Investigating chirality using foldamer model deepens the understanding of the structure-function correlation in biomacromolecules and expands the molecular toolbox towards chiroptical and asymmetrical chemistry. Substitutes with abundant hydrogen bonding sites conjugated to a rotatable aryl group afford a parallel β-sheet-like conformation, which enables the emergence and manipulation of axial chirality. This concept aims to give a brief introduction and summary of the hydrogen bonded foldamers with anchored axial chirality, by taking some recent cases as examples. Design principles, control over axial chirality and applications are also reviewed.
Collapse
Affiliation(s)
- Bingyu Liu
- Key Laboratory of Colloid and Interface Chemistry of Ministry of Education and School of Chemistry and Chemical Engineering, Shandong University, Jinan, 250100, P. R. China
| | - Pengyao Xing
- Key Laboratory of Colloid and Interface Chemistry of Ministry of Education and School of Chemistry and Chemical Engineering, Shandong University, Jinan, 250100, P. R. China
| |
Collapse
|
6
|
Schnitzer T, Rackl JW, Wennemers H. Stereoselective Peptide Catalysis in Complex Environments – From River Water to Cell Lysates. Chem Sci 2022; 13:8963-8967. [PMID: 36091207 PMCID: PMC9365096 DOI: 10.1039/d2sc02044k] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Accepted: 05/27/2022] [Indexed: 11/21/2022] Open
Abstract
Many stereoselective peptide catalysts have been established. They consist, like nature's catalysts, of amino acids but have significantly lower molecular weights than enzymes. Whereas enzymes operate with exquisite chemoselectivity in complex biological environments, peptide catalysts are used in pure organic solvents and at higher concentrations. Can a peptide catalyst exhibit chemoselectivity reminiscent of enzymes? Here, we investigated the properties of tripeptide catalysts in complex mixtures in hydrophobic and aqueous solvents. We challenged the catalysts with biomolecules bearing functional groups that could interfere by coordination or reaction with the peptide, the substrates, or intermediates. H-dPro-αMePro-Glu-NHC12H15 emerged through tailoring of the trans/cis ratio of the tertiary amide as a conformationally well-defined tripeptide that catalyzes C–C bond formations with high reactivity and stereoselectivity – regardless of the solvent and compound composition. The chemoselectivity of the tripeptide is so high that it even catalyzes reactions in cell lysates. The findings provoke the question of the potential role of peptide catalysis in nature and during the evolution of enzymes. The reactivity, stereo-, and chemoselectivity of a tripeptide are so high that it catalyzes conjugate addition reactions with high stereoselectivity in complex compound mixtures—even in cell lysates.![]()
Collapse
Affiliation(s)
- Tobias Schnitzer
- Laboratory of Organic Chemistry, ETH Zürich Vladimir-Prelog-Weg 3 8093 Zürich Switzerland
| | - Jonas W Rackl
- 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
| |
Collapse
|
7
|
Tilly DP, Cullen W, Zhong H, Jamagne R, Vitórica-Yrezábal I, Webb SJ. α-Amino-iso-butyric acid foldamers terminated with rhodium(I) N-heterocyclic carbene catalysts. Chemistry 2021; 28:e202104293. [PMID: 34932229 PMCID: PMC9305545 DOI: 10.1002/chem.202104293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Indexed: 12/01/2022]
Abstract
To investigate how remotely induced changes in ligand folding might affect catalysis by organometallic complexes, dynamic α‐amino‐iso‐butyric acid (Aib) peptide foldamers bearing rhodium(I) N‐heterocyclic carbene (NHC) complexes have been synthesized and studied. X‐ray crystallography of a foldamer with an N‐terminal azide and a C‐terminal Rh(NHC)(Cl)(diene) complex showed a racemate with a chiral axis in the Rh(NHC) complex and a distorted 310 helical body. Replacing the azide with either one or two chiral L‐α‐methylvaline (L‐αMeVal) residues gave diastereoisomeric foldamers that each possessed point, helical and axial chirality. NMR spectroscopy revealed an unequal ratio of diastereoisomers for some foldamers, indicating that the chiral conformational preference of the N‐terminal residue(s) was relayed down the 1 nm helical body to the axially chiral Rh(NHC) complex. Although the remote chiral residue(s) did not affect the stereoselectivity of hydrosilylation reactions catalysed by these foldamers, these studies suggest a potential pathway towards remote conformational control of organometallic catalysts.
Collapse
Affiliation(s)
- David P Tilly
- The University of Manchester, Department of Chemistry, UNITED KINGDOM
| | - William Cullen
- The University of Manchester, Department of Chemistry, UNITED KINGDOM
| | - Heng Zhong
- The University of Manchester, Department of Chemistry, UNITED KINGDOM
| | - Romain Jamagne
- The University of Manchester, Department of Chemistry, UNITED KINGDOM
| | | | - Simon John Webb
- University of Manchester, School of Chemistry and MIB, 131 Princess St, M1 7DN, Manchester, UNITED KINGDOM
| |
Collapse
|
8
|
Khatri B, Raghunathan S, Chakraborti S, Rahisuddin R, Kumaran S, Tadala R, Wagh P, Priyakumar UD, Chatterjee J. Desolvation of Peptide Bond by O to S Substitution Impacts Protein Stability. Angew Chem Int Ed Engl 2021; 60:24870-24874. [PMID: 34519402 DOI: 10.1002/anie.202110978] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Revised: 09/10/2021] [Indexed: 12/31/2022]
Abstract
Amino acid side chains are key to fine-tuning the microenvironment polarity in proteins composed of polar amide bonds. Here, we report that substituting an oxygen atom of the backbone amide bond with sulfur atom desolvates the thioamide bond, thereby increasing its lipophilicity. The impact of such local desolvation by O to S substitution in proteins was tested by synthesizing thioamidated variants of Pin1 WW domain. We observe that a thioamide acts in synergy with nonpolar amino acid side chains to reduce the microenvironment polarity and increase protein stability by more than 14 °C. Through favorable van der Waals and hydrogen bonding interactions, this single atom substitution significantly stabilizes proteins without altering the amino acid sequence and structure of the native protein.
Collapse
Affiliation(s)
- Bhavesh Khatri
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, 560012, India
| | - Shampa Raghunathan
- Center for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology, Hyderabad, 500032, India.,Present Address: École Centrale School of Engineering, Mahindra University, Hyderabad, 500043, India
| | - Sohini Chakraborti
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, 560012, India
| | - R Rahisuddin
- CSIR- Institute of Microbial Technology, Chandigarh 1, 60036, India
| | - S Kumaran
- CSIR- Institute of Microbial Technology, Chandigarh 1, 60036, India
| | | | | | - U Deva Priyakumar
- Center for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology, Hyderabad, 500032, India
| | - Jayanta Chatterjee
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, 560012, India
| |
Collapse
|
9
|
Khatri B, Raghunathan S, Chakraborti S, Rahisuddin R, Kumaran S, Tadala R, Wagh P, Priyakumar UD, Chatterjee J. Desolvation of Peptide Bond by O to S Substitution Impacts Protein Stability. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202110978] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Bhavesh Khatri
- Molecular Biophysics Unit Indian Institute of Science Bangalore 560012 India
| | - Shampa Raghunathan
- Center for Computational Natural Sciences and Bioinformatics International Institute of Information Technology Hyderabad 500032 India
- Present Address: École Centrale School of Engineering Mahindra University Hyderabad 500043 India
| | - Sohini Chakraborti
- Molecular Biophysics Unit Indian Institute of Science Bangalore 560012 India
| | - R. Rahisuddin
- CSIR- Institute of Microbial Technology Chandigarh 1 60036 India
| | - S. Kumaran
- CSIR- Institute of Microbial Technology Chandigarh 1 60036 India
| | | | | | - U. Deva Priyakumar
- Center for Computational Natural Sciences and Bioinformatics International Institute of Information Technology Hyderabad 500032 India
| | - Jayanta Chatterjee
- Molecular Biophysics Unit Indian Institute of Science Bangalore 560012 India
| |
Collapse
|
10
|
Zhang T, Hansen K, Politis A, Müller MM. An Unusually Rapid Protein Backbone Modification Stabilizes the Essential Bacterial Enzyme MurA. Biochemistry 2020; 59:3683-3695. [PMID: 32930597 DOI: 10.1021/acs.biochem.0c00502] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Proteins are subject to spontaneous rearrangements of their backbones. Most prominently, asparagine and aspartate residues isomerize to their β-linked isomer, isoaspartate (isoAsp), on time scales ranging from days to centuries. Such modifications are typically considered "molecular wear-and-tear", destroying protein function. However, the observation that some proteins, including the essential bacterial enzyme MurA, harbor stoichiometric amounts of isoAsp suggests that this modification can confer advantageous properties. Here, we demonstrate that nature exploits an isoAsp residue within a hairpin to stabilize MurA. We found that isoAsp formation in MurA is unusually rapid and critically dependent on folding status. Moreover, perturbation of the isoAsp-containing hairpin via site-directed mutagenesis causes aggregation of MurA variants. Structural mass spectrometry revealed that this effect is caused by local protein unfolding in MurA mutants. Our findings demonstrate that MurA evolved to "mature" via a spontaneous post-translational incorporation of a β-amino acid, which raises the possibility that isoAsp-containing hairpins may serve as a structural motif of biological importance.
Collapse
Affiliation(s)
- Tianze Zhang
- Department of Chemistry, King's College London, 7 Trinity Street, London SE1 1DB, United Kingdom
| | - Kjetil Hansen
- Department of Chemistry, King's College London, 7 Trinity Street, London SE1 1DB, United Kingdom
| | - Argyris Politis
- Department of Chemistry, King's College London, 7 Trinity Street, London SE1 1DB, United Kingdom
| | - Manuel M Müller
- Department of Chemistry, King's College London, 7 Trinity Street, London SE1 1DB, United Kingdom
| |
Collapse
|
11
|
Szigyártó IC, Mihály J, Wacha A, Bogdán D, Juhász T, Kohut G, Schlosser G, Zsila F, Urlacher V, Varga Z, Fülöp F, Bóta A, Mándity I, Beke-Somfai T. Membrane active Janus-oligomers of β 3-peptides. Chem Sci 2020; 11:6868-6881. [PMID: 33042513 PMCID: PMC7504880 DOI: 10.1039/d0sc01344g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 06/12/2020] [Indexed: 11/21/2022] Open
Abstract
Self-assembly of an acyclic β3-hexapeptide with alternating side chain chirality, into nanometer size oligomeric bundles showing membrane activity and hosting capacity for hydrophobic small molecules.
Self-assembling peptides offer a versatile set of tools for bottom-up construction of supramolecular biomaterials. Among these compounds, non-natural peptidic foldamers experience increased focus due to their structural variability and lower sensitivity to enzymatic degradation. However, very little is known about their membrane properties and complex oligomeric assemblies – key areas for biomedical and technological applications. Here we designed short, acyclic β3-peptide sequences with alternating amino acid stereoisomers to obtain non-helical molecules having hydrophilic charged residues on one side, and hydrophobic residues on the other side, with the N-terminus preventing formation of infinite fibrils. Our results indicate that these β-peptides form small oligomers both in water and in lipid bilayers and are stabilized by intermolecular hydrogen bonds. In the presence of model membranes, they either prefer the headgroup regions or they insert between the lipid chains. Molecular dynamics (MD) simulations suggest the formation of two-layered bundles with their side chains facing opposite directions when compared in water and in model membranes. Analysis of the MD calculations showed hydrogen bonds inside each layer, however, not between the layers, indicating a dynamic assembly. Moreover, the aqueous form of these oligomers can host fluorescent probes as well as a hydrophobic molecule similarly to e.g. lipid transfer proteins. For the tested, peptides the mixed chirality pattern resulted in similar assemblies despite sequential differences. Based on this, it is hoped that the presented molecular framework will inspire similar oligomers with diverse functionality.
Collapse
Affiliation(s)
- Imola Cs Szigyártó
- Institute of Materials and Environmental Chemistry , Research Centre for Natural Sciences , H-1117 Budapest , Hungary . ;
| | - Judith Mihály
- Institute of Materials and Environmental Chemistry , Research Centre for Natural Sciences , H-1117 Budapest , Hungary . ;
| | - András Wacha
- Institute of Materials and Environmental Chemistry , Research Centre for Natural Sciences , H-1117 Budapest , Hungary . ;
| | - Dóra Bogdán
- Institute of Materials and Environmental Chemistry , Research Centre for Natural Sciences , H-1117 Budapest , Hungary . ; .,Department of Organic Chemistry , Faculty of Pharmacy , Semmelweis University , H-1092 Budapest , Hungary
| | - Tünde Juhász
- Institute of Materials and Environmental Chemistry , Research Centre for Natural Sciences , H-1117 Budapest , Hungary . ;
| | - Gergely Kohut
- Institute of Materials and Environmental Chemistry , Research Centre for Natural Sciences , H-1117 Budapest , Hungary . ; .,Institute of Chemistry , Eötvös Loránd University , H-1117 Budapest , Hungary
| | - Gitta Schlosser
- Institute of Chemistry , Eötvös Loránd University , H-1117 Budapest , Hungary
| | - Ferenc Zsila
- Institute of Materials and Environmental Chemistry , Research Centre for Natural Sciences , H-1117 Budapest , Hungary . ;
| | - Vlada Urlacher
- Institute of Biochemistry , Heinrich-Heine University , 40225 Düsseldorf , Germany
| | - Zoltán Varga
- Institute of Materials and Environmental Chemistry , Research Centre for Natural Sciences , H-1117 Budapest , Hungary . ;
| | - Ferenc Fülöp
- MTA-SZTE Stereochemistry Research Group , Institute of Pharmaceutical Chemistry , University of Szeged , H-6720 Szeged , Hungary
| | - Attila Bóta
- Institute of Materials and Environmental Chemistry , Research Centre for Natural Sciences , H-1117 Budapest , Hungary . ;
| | - István Mándity
- Institute of Materials and Environmental Chemistry , Research Centre for Natural Sciences , H-1117 Budapest , Hungary . ; .,Department of Organic Chemistry , Faculty of Pharmacy , Semmelweis University , H-1092 Budapest , Hungary
| | - Tamás Beke-Somfai
- Institute of Materials and Environmental Chemistry , Research Centre for Natural Sciences , H-1117 Budapest , Hungary . ; .,Department of Chemistry and Chemical Engineering , Physical Chemistry , Chalmers University of Technology , SE-41296 Göteborg , Sweden
| |
Collapse
|
12
|
Abstract
Enzymes are predominantly proteins able to effectively and selectively catalyze highly complex biochemical reactions in mild reaction conditions. Nevertheless, they are limited to the arsenal of reactions that have emerged during natural evolution in compliance with their intrinsic nature, three-dimensional structures and dynamics. They optimally work in physiological conditions for a limited range of reactions, and thus exhibit a low tolerance for solvent and temperature conditions. The de novo design of synthetic highly stable enzymes able to catalyze a broad range of chemical reactions in variable conditions is a great challenge, which requires the development of programmable and finely tunable artificial tools. Interestingly, over the last two decades, chemists developed protein secondary structure mimics to achieve some desirable features of proteins, which are able to interfere with the biological processes. Such non-natural oligomers, so called foldamers, can adopt highly stable and predictable architectures and have extensively demonstrated their attractiveness for widespread applications in fields from biomedical to material science. Foldamer science was more recently considered to provide original solutions to the de novo design of artificial enzymes. This review covers recent developments related to peptidomimetic foldamers with catalytic properties and the principles that have guided their design.
Collapse
|
13
|
Abstract
Protein semisynthesis-defined herein as the assembly of a protein from a combination of synthetic and recombinant fragments-is a burgeoning field of chemical biology that has impacted many areas in the life sciences. In this review, we provide a comprehensive survey of this area. We begin by discussing the various chemical and enzymatic methods now available for the manufacture of custom proteins containing noncoded elements. This section begins with a discussion of methods that are more chemical in origin and ends with those that employ biocatalysts. We also illustrate the commonalities that exist between these seemingly disparate methods and show how this is allowing for the development of integrated chemoenzymatic methods. This methodology discussion provides the technical foundation for the second part of the review where we cover the great many biological problems that have now been addressed using these tools. Finally, we end the piece with a short discussion on the frontiers of the field and the opportunities available for the future.
Collapse
Affiliation(s)
| | - Tom W. Muir
- Department of Chemistry, Princeton University, Frick Laboratory, Princeton, New Jersey 08544, United States
| |
Collapse
|
14
|
Horne WS, Grossmann TN. Proteomimetics as protein-inspired scaffolds with defined tertiary folding patterns. Nat Chem 2020; 12:331-337. [PMID: 32029906 DOI: 10.1038/s41557-020-0420-9] [Citation(s) in RCA: 75] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Accepted: 01/09/2020] [Indexed: 12/29/2022]
Abstract
Proteins have evolved as a variable platform that provides access to molecules with diverse shapes, sizes and functions. These features have inspired chemists for decades to seek artificial mimetics of proteins with improved or novel properties. Such work has focused primarily on small protein fragments, often isolated secondary structures; however, there has lately been a growing interest in the design of artificial molecules that mimic larger, more complex tertiary folds. In this Perspective, we define these agents as 'proteomimetics' and discuss the recent advances in the field. Proteomimetics can be divided into three categories: protein domains with side-chain functionality that alters the native linear-chain topology; protein domains in which the chemical composition of the polypeptide backbone has been partially altered; and protein-like folded architectures that are composed entirely of non-natural monomer units. We give an overview of these proteomimetic approaches and outline remaining challenges facing the field.
Collapse
Affiliation(s)
- W Seth Horne
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, USA.
| | - Tom N Grossmann
- Department of Chemistry and Pharmaceutical Sciences, VU University Amsterdam, Amsterdam, the Netherlands.
| |
Collapse
|
15
|
Sang P, Shi Y, Lu J, Chen L, Yang L, Borcherds W, Abdulkadir S, Li Q, Daughdrill G, Chen J, Cai J. α-Helix-Mimicking Sulfono-γ-AApeptide Inhibitors for p53-MDM2/MDMX Protein-Protein Interactions. J Med Chem 2020; 63:975-986. [PMID: 31971801 PMCID: PMC7025332 DOI: 10.1021/acs.jmedchem.9b00993] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The use of peptidomimetic scaffolds is a promising strategy for the inhibition of protein-protein interactions (PPIs). Herein, we demonstrate that sulfono-γ-AApeptides can be rationally designed to mimic the p53 α-helix and inhibit p53-MDM2 PPIs. The best inhibitor, with Kd and IC50 values of 26 nM and 0.891 μM toward MDM2, respectively, is among the most potent unnatural peptidomimetic inhibitors disrupting the p53-MDM2/MDMX interaction. Using fluorescence polarization assays, circular dichroism, nuclear magnetic resonance spectroscopy, and computational simulations, we demonstrate that sulfono-γ-AApeptides adopt helical structures resembling p53 and competitively inhibit the p53-MDM2 interaction by binding to the hydrophobic cleft of MDM2. Intriguingly, the stapled sulfono-γ-AApeptides showed promising cellular activity by enhancing p53 transcriptional activity and inducing expression of MDM2 and p21. Moreover, sulfono-γ-AApeptides exhibited remarkable resistance to proteolysis, augmenting their biological potential. Our results suggest that sulfono-γ-AApeptides are a new class of unnatural helical foldamers that disrupt PPIs.
Collapse
Affiliation(s)
- Peng Sang
- Department of Chemistry , University of South Florida , 4202 E. Fowler Avenue , Tampa , Florida 33620 , United States
| | - Yan Shi
- Department of Chemistry , University of South Florida , 4202 E. Fowler Avenue , Tampa , Florida 33620 , United States
| | - Junhao Lu
- Department of Molecular Oncology , H. Lee Moffitt Cancer Center and Research Institute , 12902 Magnolia Drive , Tampa , Florida 33612 , United States
| | - Lihong Chen
- Department of Molecular Oncology , H. Lee Moffitt Cancer Center and Research Institute , 12902 Magnolia Drive , Tampa , Florida 33612 , United States
| | - Leixiang Yang
- Department of Molecular Oncology , H. Lee Moffitt Cancer Center and Research Institute , 12902 Magnolia Drive , Tampa , Florida 33612 , United States
| | - Wade Borcherds
- Department of Cell Biology, Microbiology and Molecular Biology , University of South Florida , Tampa , Florida 33620 , United States
| | - Sami Abdulkadir
- Department of Chemistry , University of South Florida , 4202 E. Fowler Avenue , Tampa , Florida 33620 , United States
| | - Qi Li
- Department of Medical Oncology , Shuguang Hospital, Shanghai University of Traditional Chinese Medicine , Shanghai 201203 , China
| | - Gary Daughdrill
- Department of Cell Biology, Microbiology and Molecular Biology , University of South Florida , Tampa , Florida 33620 , United States
| | - Jiandong Chen
- Department of Molecular Oncology , H. Lee Moffitt Cancer Center and Research Institute , 12902 Magnolia Drive , Tampa , Florida 33612 , United States
| | - Jianfeng Cai
- Department of Chemistry , University of South Florida , 4202 E. Fowler Avenue , Tampa , Florida 33620 , United States
| |
Collapse
|
16
|
Mazzier D, De S, Wicher B, Maurizot V, Huc I. Interplay of secondary and tertiary folding in abiotic foldamers. Chem Sci 2019; 10:6984-6991. [PMID: 31588265 PMCID: PMC6676331 DOI: 10.1039/c9sc01322a] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Accepted: 06/08/2019] [Indexed: 12/30/2022] Open
Abstract
The first true abiotic tertiary folded structures, i.e. at the exclusion of any aliphatic amino acid, have recently been introduced under the form of aromatic oligoamide helix-turn-helix foldamers stabilized by hydrogen bonds in organic solvents. We present an investigation of the interplay of secondary and tertiary folding and of some cooperative effects in these systems. A solid phase synthesis approach to the preparation of these sequences was developed to facilitate systematic variation. Flexible pyridine-based units were introduced in various proportions in replacement of more rigid quinoline-based units. Conformational behaviour was assessed in solution by NMR, in the solid state by X-ray crystallography, and computationally through molecular dynamics simulations. Altogether, our results demonstrate that tertiary folding stabilizes otherwise flexible secondary structures, and that the disruption of tertiary folds upon adding polar solvents follows different mechanisms depending on whether secondary structures are inherently stable or not. These findings constitute a solid basis on which to further increase the size and complexity of abiotic folded structures and to eventually orchestrate folding dynamics and responsiveness.
Collapse
Affiliation(s)
- Daniela Mazzier
- Department of Pharmacy , Centre for Integrated Protein Science , Ludwig-Maximilians-Universität , Butenandtstraße 5-13 , D-81377 Munich , Germany .
- CBMN Laboratory , Université de Bordeaux , CNRS , IPB , Institut Européen de Chimie et Biologie , 2 rue Escarpit , 33600 Pessac , France
| | - Soumen De
- CBMN Laboratory , Université de Bordeaux , CNRS , IPB , Institut Européen de Chimie et Biologie , 2 rue Escarpit , 33600 Pessac , France
| | - Barbara Wicher
- Department of Chemical Technology of Drugs , Poznan University of Medical Sciences , Grunwaldzka 6 , 60-780 Poznan , Poland
| | - Victor Maurizot
- CBMN Laboratory , Université de Bordeaux , CNRS , IPB , Institut Européen de Chimie et Biologie , 2 rue Escarpit , 33600 Pessac , France
| | - Ivan Huc
- Department of Pharmacy , Centre for Integrated Protein Science , Ludwig-Maximilians-Universität , Butenandtstraße 5-13 , D-81377 Munich , Germany .
- CBMN Laboratory , Université de Bordeaux , CNRS , IPB , Institut Européen de Chimie et Biologie , 2 rue Escarpit , 33600 Pessac , France
| |
Collapse
|
17
|
Tarasenko EA, Shestakov IV, Rybakov VB, Beletskaya IP. Enantioselective Copper(II)/Box‐Catalyzed Synthesis of Chiral
β
3
‐Tryptophan Derivatives. ChemCatChem 2019. [DOI: 10.1002/cctc.201900575] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Elena A. Tarasenko
- Department of ChemistryM. V. Lomonosov Moscow State University Leninskie Gory, GSP-1 Moscow 119991 Russian Federation
| | - Ivan V. Shestakov
- Department of ChemistryM. V. Lomonosov Moscow State University Leninskie Gory, GSP-1 Moscow 119991 Russian Federation
| | - Victor B. Rybakov
- Department of ChemistryM. V. Lomonosov Moscow State University Leninskie Gory, GSP-1 Moscow 119991 Russian Federation
| | - Irina P. Beletskaya
- Department of ChemistryM. V. Lomonosov Moscow State University Leninskie Gory, GSP-1 Moscow 119991 Russian Federation
| |
Collapse
|
18
|
Inhibition of β-catenin/B cell lymphoma 9 protein-protein interaction using α-helix-mimicking sulfono-γ-AApeptide inhibitors. Proc Natl Acad Sci U S A 2019; 116:10757-10762. [PMID: 31088961 DOI: 10.1073/pnas.1819663116] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The rational design of α-helix-mimicking peptidomimetics provides a streamlined approach to discover potent inhibitors for protein-protein interactions (PPIs). However, designing cell-penetrating long peptidomimetic scaffolds equipped with various functional groups necessary for interacting with large protein-binding interfaces remains challenging. This is particularly true for targeting β-catenin/BCL9 PPIs. Here we designed a series of unprecedented helical sulfono-γ-AApeptides that mimic the binding mode of the α-helical HD2 domain of B Cell Lymphoma 9 (BCL9). Our studies show that sulfono-γ-AApeptides can structurally and functionally mimic the α-helical domain of BCL9 and selectively disrupt β-catenin/BCL9 PPIs with even higher potency. More intriguingly, these sulfono-γ-AApeptides can enter cancer cells, bind with β-catenin and disrupt β-catenin/BCL9 PPIs, and exhibit excellent cellular activity, which is much more potent than the BCL9 peptide. Furthermore, our enzymatic stability studies demonstrate the remarkable stability of the helical sulfono-γ-AApeptides, with no degradation in the presence of pronase for 24 h, augmenting their biological potential. This work represents not only an example of helical sulfono-γ-AApeptides that mimic α-helix and disrupt protein-protein interactions, but also an excellent example of potent, selective, and cell-permeable unnatural foldameric peptidomimetics that disrupt the β-catenin/BCL9 PPI. The design of helical sulfono-γ-AApeptides may lead to a new strategy to modulate a myriad of protein-protein interactions.
Collapse
|
19
|
Hegedus Z, Grison CM, Miles JA, Rodriguez-Marin S, Warriner SL, Webb ME, Wilson AJ. A catalytic protein-proteomimetic complex: using aromatic oligoamide foldamers as activators of RNase S. Chem Sci 2019; 10:3956-3962. [PMID: 31015935 PMCID: PMC6461108 DOI: 10.1039/c9sc00374f] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Accepted: 02/21/2019] [Indexed: 12/27/2022] Open
Abstract
Foldamers are abiotic molecules that mimic the ability of bio-macromolecules to adopt well-defined and organised secondary, tertiary or quaternary structure. Such templates have enabled the generation of defined architectures which present structurally defined surfaces that can achieve molecular recognition of diverse and complex targets. Far less explored is whether this mimicry of nature can extend to more advanced functions of biological macromolecules such as the generation and activation of catalytic function. In this work, we adopt a novel replacement strategy whereby a segment of protein structure (the S-peptide from RNase S) is replaced by a foldamer that mimics an α-helix. The resultant prosthetic replacement forms a non-covalent complex with the S-protein leading to restoration of catalytic function, despite the absence of a key catalytic residue. Thus this functional protein-proteomimetic complex provides proof that significant segments of protein can be replaced with non-natural building blocks that may, in turn, confer advantageous properties.
Collapse
Affiliation(s)
- Zsofia Hegedus
- School of Chemistry , University of Leeds , Woodhouse Lane , Leeds LS2 9JT , UK . .,Astbury Centre For Structural Molecular Biology , University of Leeds , Woodhouse Lane , Leeds LS2 9JT , UK
| | - Claire M Grison
- School of Chemistry , University of Leeds , Woodhouse Lane , Leeds LS2 9JT , UK . .,Astbury Centre For Structural Molecular Biology , University of Leeds , Woodhouse Lane , Leeds LS2 9JT , UK
| | - Jennifer A Miles
- School of Chemistry , University of Leeds , Woodhouse Lane , Leeds LS2 9JT , UK . .,Astbury Centre For Structural Molecular Biology , University of Leeds , Woodhouse Lane , Leeds LS2 9JT , UK
| | - Silvia Rodriguez-Marin
- School of Chemistry , University of Leeds , Woodhouse Lane , Leeds LS2 9JT , UK . .,Astbury Centre For Structural Molecular Biology , University of Leeds , Woodhouse Lane , Leeds LS2 9JT , UK
| | - Stuart L Warriner
- School of Chemistry , University of Leeds , Woodhouse Lane , Leeds LS2 9JT , UK . .,Astbury Centre For Structural Molecular Biology , University of Leeds , Woodhouse Lane , Leeds LS2 9JT , UK
| | - Michael E Webb
- School of Chemistry , University of Leeds , Woodhouse Lane , Leeds LS2 9JT , UK . .,Astbury Centre For Structural Molecular Biology , University of Leeds , Woodhouse Lane , Leeds LS2 9JT , UK
| | - Andrew J Wilson
- School of Chemistry , University of Leeds , Woodhouse Lane , Leeds LS2 9JT , UK . .,Astbury Centre For Structural Molecular Biology , University of Leeds , Woodhouse Lane , Leeds LS2 9JT , UK
| |
Collapse
|
20
|
Drewniak M, Węglarz-Tomczak E, Ożga K, Rudzińska-Szostak E, Macegoniuk K, Tomczak JM, Bejger M, Rypniewski W, Berlicki Ł. Helix-loop-helix peptide foldamers and their use in the construction of hydrolase mimetics. Bioorg Chem 2018; 81:356-361. [PMID: 30195249 DOI: 10.1016/j.bioorg.2018.07.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Revised: 07/02/2018] [Accepted: 07/12/2018] [Indexed: 01/18/2023]
Abstract
De novo designed helix-loop-helix peptide foldamers containing cis-2-aminocyclopentanecarboxylic acid residues were evaluated for their conformational stability and possible use in enzyme mimetic development. The correlation between hydrogen bond network size and conformational stability was demonstrated through CD and NMR spectroscopies. Molecules incorporating a Cys/His/Glu triad exhibited enzyme-like hydrolytic activity.
Collapse
Affiliation(s)
- Magda Drewniak
- Department of Bioorganic Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland
| | - Ewelina Węglarz-Tomczak
- Department of Bioorganic Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland
| | - Katarzyna Ożga
- Department of Bioorganic Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland
| | - Ewa Rudzińska-Szostak
- Department of Bioorganic Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland
| | - Katarzyna Macegoniuk
- Department of Bioorganic Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland
| | - Jakub M Tomczak
- Amsterdam Machine Learning Lab, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Magdalena Bejger
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznań, Poland
| | - Wojciech Rypniewski
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznań, Poland
| | - Łukasz Berlicki
- Department of Bioorganic Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland.
| |
Collapse
|
21
|
Lockhart Z, Knipe PC. Conformationally Programmable Chiral Foldamers with Compact and Extended Domains Controlled by Monomer Structure. Angew Chem Int Ed Engl 2018; 57:8478-8482. [PMID: 29737622 PMCID: PMC6055681 DOI: 10.1002/anie.201802822] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Revised: 04/24/2018] [Indexed: 11/17/2022]
Abstract
Foldamers are an important class of abiotic macromolecules, with potential therapeutic applications in the disruption of protein–protein interactions. The majority adopt a single conformational motif such as a helix. A class of foldamer is now introduced where the choice of heterocycle within each monomer, coupled with a strong conformation‐determining dipole repulsion effect, allows both helical and extended conformations to be selected. Combining these monomers into hetero‐oligomers enables highly controlled exploration of conformational space and projection of side‐chains along multiple vectors. The foldamers were rapidly constructed via an iterative deprotection‐cross‐coupling sequence, and their solid‐ and solution‐phase conformations were analysed by X‐ray crystallography and NMR and CD spectroscopy. These molecules may find applications in protein surface recognition where the interface does not involve canonical peptide secondary structures.
Collapse
Affiliation(s)
- Zachariah Lockhart
- School of Chemistry and Chemical Engineering, Queen's University Belfast, David Keir Building, Belfast, BT9 5AG, UK
| | - Peter C Knipe
- School of Chemistry and Chemical Engineering, Queen's University Belfast, David Keir Building, Belfast, BT9 5AG, UK
| |
Collapse
|
22
|
Lockhart Z, Knipe PC. Conformationally Programmable Chiral Foldamers with Compact and Extended Domains Controlled by Monomer Structure. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201802822] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Zachariah Lockhart
- School of Chemistry and Chemical Engineering Queen's University Belfast David Keir Building Belfast BT9 5AG UK
| | - Peter C. Knipe
- School of Chemistry and Chemical Engineering Queen's University Belfast David Keir Building Belfast BT9 5AG UK
| |
Collapse
|
23
|
Abstract
The prospect of recreating the complex structural hierarchy of protein folding in synthetic oligomers with backbones that are artificial in covalent structure ("foldamers") has long fascinated chemists. Foldamers offer complex functions from biostable scaffolds and have found widespread applications in fields from biomedical to materials science. Most precedent has focused on isolated secondary structures or their assemblies. In considering the goal of complex protein-like tertiary folding patterns, a key barrier became apparent. How does one design a backbone with covalent connectivity and a sequence of side-chain functional groups that will support defined intramolecular packing of multiple artificial secondary structures? Two developments were key to overcoming this challenge. First was the recognition of the power of blending α-amino acid residues with monomers differing in backbone connectivity to create "heterogeneous-backbone" foldamers. Second was the finding that replacing some of the natural α-residues in a biological sequence with artificial-backbone variants can result in a mimic that retains both the fold and function of the native sequence and, in some cases, gains advantageous characteristics. Taken together, these precedents lead to a view of a protein as chemical entity having two orthogonal sequences: a sequence of side-chain functional groups and a separate sequence of backbone units displaying those functional groups. In this Account, we describe our lab's work over the last ∼10 years to leverage the above concept of protein sequence duality in order to develop design principles for constructing heterogeneous-backbone foldamers that adopt complex protein-like tertiary folds. Fundamental to the approach is the utilization of a variety of artificial building blocks (e.g., d-α-residues, Cα-Me-α-residues, N-Me-α-residues, β-residues, γ-residues, δ-residues, polymer segments) in concert, replacing a fraction of α-residues in a given prototype sequence. We provide an overview of the state-of-the-art in terms of design principles for choosing substitutions based on consideration of local secondary structure and retention of key side-chain functional groups. We survey high-resolution structures of backbone-modified proteins to illustrate how diverse artificial moieties are accommodated in tertiary fold contexts. We detail efforts to elucidate how backbone alteration impacts folding thermodynamics and describe how such data informs the development of improved design rules. Collectively, a growing body of results by our lab and others spanning multiple protein systems suggests there is a great deal of plasticity with respect to the backbone chemical structures upon which sequence-encoded tertiary folds can manifest. Moreover, these efforts suggest sequence-guided backbone alteration as a broadly applicable strategy for generating foldamers with complex tertiary folding patterns. We conclude by offering some perspective regarding the near future of this field, in terms of unanswered questions, technological needs, and opportunities for new areas of inquiry.
Collapse
Affiliation(s)
- Kelly L. George
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - W. Seth Horne
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| |
Collapse
|
24
|
Gratzer K, Diemer V, Clayden J. Signal transduction in oligoamide foldamers by selective non-covalent binding of chiral phosphates at a urea binding site. Org Biomol Chem 2018; 15:3585-3589. [PMID: 28397923 DOI: 10.1039/c7ob00660h] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
The transduction of biological signals depends on the spatial communication of conformational change. We report a synthetic mimic of this signal transduction process in which non-covalent binding induces a change in the position of equilibrium between two rapidly interconverting screw-sense conformers of a synthetic helical polyamide. Selectivity was achieved by incorporating at the N-terminus of the polyamide a urea-based anion recognition site capable of binding chiral phosphate anions. As a result of solvent-dependent binding, an induced conformational change propagates from the binding site through the amide chain, leading to a screw-sense preference detectable in the form of a chemical shift separation between two NMR active 13C labels. The remote induction of screw sense preference indicates successful communication of a signal originating solely from non-covalent binding.
Collapse
Affiliation(s)
- Katharina Gratzer
- School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, UK.
| | | | | |
Collapse
|
25
|
Lahiri P, Verma H, Ravikumar A, Chatterjee J. Protein stabilization by tuning the steric restraint at the reverse turn. Chem Sci 2018; 9:4600-4609. [PMID: 29899953 PMCID: PMC5969505 DOI: 10.1039/c7sc05163h] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Accepted: 04/24/2018] [Indexed: 11/23/2022] Open
Abstract
The incorporation of pseudoallylic strain by N-methylation at the solvent exposed loop in proteins leads to a stark increase in their thermodynamic stability that can be tuned by altering the amino acid composition.
Reverse turns are solvent-exposed motifs in proteins that are crucial in nucleating β-sheets and drive the protein folding. The solvent-exposed nature makes reverse turns more amenable to chemical modifications than α-helices or β-sheets towards modulating the stability of re-engineered proteins. Here, we utilize van der Waals repulsive forces in tuning the steric restraint at the reverse turn. The steric restraint induced upon N-methylation of the i+1–i+2 amide bond at the reverse turn results in well-folded and stable β-sheets in aqueous solution at room temperature. The developed superactive turn inducing motif is tolerant to a wide variety of functional groups present on coded amino acids making the designed turn fully compatible with bioactive loops in proteins. We demonstrate that the steric restraint and the functional groups at the reverse turn act in synergy to modulate the folding of re-engineered β-sheets. Introduction of the turn motifs onto a three-stranded β-sheet protein, Pin 1 WW domain, resulted in various analogs showing a cooperative two-state transition with thermal stability (TM) ranging from 62 °C to 82 °C. Despite modulating the stability of Pin 1 variants by ∼2.8 kcal mol–1 (ΔΔGf), the native fold in all the protein variants was found to be unperturbed. This structural stability is brought about by conformational preorganization at the engineered reverse turn that results in strong intramolecular hydrogen bonds along the three dimensional structure of the protein. Thus, this simple loop engineering strategy via two amino acid substitution provides us a “toolkit” to modulate the stability of β-sheet containing peptides and proteins in aqueous solution that will greatly expand the scope of de novo protein and foldamer design.
Collapse
Affiliation(s)
- Priyanka Lahiri
- Molecular Biophysics Unit , Indian Institute of Science , Bangalore 560012 , India .
| | - Hitesh Verma
- Molecular Biophysics Unit , Indian Institute of Science , Bangalore 560012 , India .
| | - Ashraya Ravikumar
- Molecular Biophysics Unit , Indian Institute of Science , Bangalore 560012 , India .
| | - Jayanta Chatterjee
- Molecular Biophysics Unit , Indian Institute of Science , Bangalore 560012 , India .
| |
Collapse
|
26
|
Yu J, Noda H, Shibasaki M. Quaternary β
2,2
‐Amino Acids: Catalytic Asymmetric Synthesis and Incorporation into Peptides by Fmoc‐Based Solid‐Phase Peptide Synthesis. Angew Chem Int Ed Engl 2017; 57:818-822. [DOI: 10.1002/anie.201711143] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Indexed: 11/09/2022]
Affiliation(s)
- Jin‐Sheng Yu
- Institute of Microbial Chemistry (BIKAKEN), Tokyo 3-14-23 Kamiosaki, Shinagawa-ku Tokyo 141-0021 Japan
| | - Hidetoshi Noda
- Institute of Microbial Chemistry (BIKAKEN), Tokyo 3-14-23 Kamiosaki, Shinagawa-ku Tokyo 141-0021 Japan
| | - Masakatsu Shibasaki
- Institute of Microbial Chemistry (BIKAKEN), Tokyo 3-14-23 Kamiosaki, Shinagawa-ku Tokyo 141-0021 Japan
| |
Collapse
|
27
|
Yu J, Noda H, Shibasaki M. Quaternary β
2,2
‐Amino Acids: Catalytic Asymmetric Synthesis and Incorporation into Peptides by Fmoc‐Based Solid‐Phase Peptide Synthesis. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201711143] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Jin‐Sheng Yu
- Institute of Microbial Chemistry (BIKAKEN), Tokyo 3-14-23 Kamiosaki, Shinagawa-ku Tokyo 141-0021 Japan
| | - Hidetoshi Noda
- Institute of Microbial Chemistry (BIKAKEN), Tokyo 3-14-23 Kamiosaki, Shinagawa-ku Tokyo 141-0021 Japan
| | - Masakatsu Shibasaki
- Institute of Microbial Chemistry (BIKAKEN), Tokyo 3-14-23 Kamiosaki, Shinagawa-ku Tokyo 141-0021 Japan
| |
Collapse
|
28
|
Kinghorn MJ, Valdivia-Berroeta GA, Chantry DR, Smith MS, Ence CC, Draper SRE, Duval JS, Masino BM, Cahoon SB, Flansburg RR, Conder CJ, Price JL, Michaelis DJ. Proximity-Induced Reactivity and Product Selectivity with a Rationally Designed Bifunctional Peptide Catalyst. ACS Catal 2017. [DOI: 10.1021/acscatal.7b02699] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Michael J. Kinghorn
- Department of Chemistry and
Biochemistry, Brigham Young University, Provo, Utah 84602, United States
| | | | - Donalee R. Chantry
- Department of Chemistry and
Biochemistry, Brigham Young University, Provo, Utah 84602, United States
| | - Mason S. Smith
- Department of Chemistry and
Biochemistry, Brigham Young University, Provo, Utah 84602, United States
| | - Chloe C. Ence
- Department of Chemistry and
Biochemistry, Brigham Young University, Provo, Utah 84602, United States
| | - Steven R. E. Draper
- Department of Chemistry and
Biochemistry, Brigham Young University, Provo, Utah 84602, United States
| | - Jared S. Duval
- Department of Chemistry and
Biochemistry, Brigham Young University, Provo, Utah 84602, United States
| | - Bryan M. Masino
- Department of Chemistry and
Biochemistry, Brigham Young University, Provo, Utah 84602, United States
| | - Samuel B. Cahoon
- Department of Chemistry and
Biochemistry, Brigham Young University, Provo, Utah 84602, United States
| | - Rachael R. Flansburg
- Department of Chemistry and
Biochemistry, Brigham Young University, Provo, Utah 84602, United States
| | - Cory J. Conder
- Department of Chemistry and
Biochemistry, Brigham Young University, Provo, Utah 84602, United States
| | - Joshua L. Price
- Department of Chemistry and
Biochemistry, Brigham Young University, Provo, Utah 84602, United States
| | - David J. Michaelis
- Department of Chemistry and
Biochemistry, Brigham Young University, Provo, Utah 84602, United States
| |
Collapse
|
29
|
Tian Y, Jiang Y, Li J, Wang D, Zhao H, Li Z. Effect of Stapling Architecture on Physiochemical Properties and Cell Permeability of Stapled α-Helical Peptides: A Comparative Study. Chembiochem 2017; 18:2087-2093. [DOI: 10.1002/cbic.201700352] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2017] [Indexed: 11/05/2022]
Affiliation(s)
- Yuan Tian
- Laboratory of Cytophysiology; Key Laboratory of Chemical Genomics; Peking University Shenzhen Graduate School; Shenzhen 518055 China
- School of Life Science and Engineering; Southwest Jiaotong University; Chengdu 611756 China
| | - Yanhong Jiang
- Laboratory of Cytophysiology; Key Laboratory of Chemical Genomics; Peking University Shenzhen Graduate School; Shenzhen 518055 China
| | - Jingxu Li
- Laboratory of Cytophysiology; Key Laboratory of Chemical Genomics; Peking University Shenzhen Graduate School; Shenzhen 518055 China
| | - Dongyuan Wang
- Laboratory of Cytophysiology; Key Laboratory of Chemical Genomics; Peking University Shenzhen Graduate School; Shenzhen 518055 China
| | - Hui Zhao
- Laboratory of Cytophysiology; Key Laboratory of Chemical Genomics; Peking University Shenzhen Graduate School; Shenzhen 518055 China
| | - Zigang Li
- Laboratory of Cytophysiology; Key Laboratory of Chemical Genomics; Peking University Shenzhen Graduate School; Shenzhen 518055 China
| |
Collapse
|
30
|
De S, Chi B, Granier T, Qi T, Maurizot V, Huc I. Designing cooperatively folded abiotic uni- and multimolecular helix bundles. Nat Chem 2017; 10:51-57. [PMID: 29256508 DOI: 10.1038/nchem.2854] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Accepted: 07/27/2017] [Indexed: 01/09/2023]
Abstract
Abiotic foldamers, that is foldamers that have backbones chemically remote from peptidic and nucleotidic skeletons, may give access to shapes and functions different to those of peptides and nucleotides. However, design methodologies towards abiotic tertiary and quaternary structures are yet to be developed. Here we report rationally designed interactional patterns to guide the folding and assembly of abiotic helix bundles. Computational design facilitated the introduction of hydrogen-bonding functionalities at defined locations on the aromatic amide backbones that promote cooperative folding into helix-turn-helix motifs in organic solvents. The hydrogen-bond-directed aggregation of helices not linked by a turn unit produced several thermodynamically and kinetically stable homochiral dimeric and trimeric bundles with structures that are distinct from the designed helix-turn-helix. Relative helix orientation within the bundles may be changed from parallel to tilted on subtle solvent variations. Altogether, these results prefigure the richness and uniqueness of abiotic tertiary structure behaviour.
Collapse
Affiliation(s)
- Soumen De
- CBMN Laboratory, Université de Bordeaux, CNRS, IPB, Institut Européen de Chimie et Biologie, 2 rue Escarpit, 33600 Pessac, France
| | - Bo Chi
- CBMN Laboratory, Université de Bordeaux, CNRS, IPB, Institut Européen de Chimie et Biologie, 2 rue Escarpit, 33600 Pessac, France
| | - Thierry Granier
- CBMN Laboratory, Université de Bordeaux, CNRS, IPB, Institut Européen de Chimie et Biologie, 2 rue Escarpit, 33600 Pessac, France
| | - Ting Qi
- CBMN Laboratory, Université de Bordeaux, CNRS, IPB, Institut Européen de Chimie et Biologie, 2 rue Escarpit, 33600 Pessac, France
| | - Victor Maurizot
- CBMN Laboratory, Université de Bordeaux, CNRS, IPB, Institut Européen de Chimie et Biologie, 2 rue Escarpit, 33600 Pessac, France
| | - Ivan Huc
- CBMN Laboratory, Université de Bordeaux, CNRS, IPB, Institut Européen de Chimie et Biologie, 2 rue Escarpit, 33600 Pessac, France
| |
Collapse
|
31
|
Hu L, Zhao Y. Cross‐Linked Micelles with Enzyme‐Like Active Sites for Biomimetic Hydrolysis of Activated Esters. Helv Chim Acta 2017. [DOI: 10.1002/hlca.201700147] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Lan Hu
- Department of Chemistry Iowa State University Ames Iowa 50011‐3111 USA
| | - Yan Zhao
- Department of Chemistry Iowa State University Ames Iowa 50011‐3111 USA
| |
Collapse
|
32
|
Rennie ML, Doolan AM, Raston CL, Crowley PB. Protein Dimerization on a Phosphonated Calix[6]arene Disc. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201701500] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Martin L. Rennie
- School of Chemistry; National University of Ireland Galway; University Road Galway Ireland
| | - Aishling M. Doolan
- School of Chemistry; National University of Ireland Galway; University Road Galway Ireland
| | - Colin L. Raston
- Centre for Nanoscale Science and Technology; School of Chemical and Physical Sciences; Flinders University; GPO Box 2100 Adelaide Australia
| | - Peter B. Crowley
- School of Chemistry; National University of Ireland Galway; University Road Galway Ireland
| |
Collapse
|
33
|
Rennie ML, Doolan AM, Raston CL, Crowley PB. Protein Dimerization on a Phosphonated Calix[6]arene Disc. Angew Chem Int Ed Engl 2017; 56:5517-5521. [DOI: 10.1002/anie.201701500] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Indexed: 01/14/2023]
Affiliation(s)
- Martin L. Rennie
- School of Chemistry; National University of Ireland Galway; University Road Galway Ireland
| | - Aishling M. Doolan
- School of Chemistry; National University of Ireland Galway; University Road Galway Ireland
| | - Colin L. Raston
- Centre for Nanoscale Science and Technology; School of Chemical and Physical Sciences; Flinders University; GPO Box 2100 Adelaide Australia
| | - Peter B. Crowley
- School of Chemistry; National University of Ireland Galway; University Road Galway Ireland
| |
Collapse
|
34
|
Szefczyk M, Węglarz-Tomczak E, Fortuna P, Krzysztoń A, Rudzińska-Szostak E, Berlicki Ł. Controlling the Helix Handedness of ααβ-Peptide Foldamers through Sequence Shifting. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201610154] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Monika Szefczyk
- Department of Bioorganic Chemistry; Wrocław University of Science and Technology; Wybrzeże Wyspiańskiego 27 50-370 Wrocław Poland
| | - Ewelina Węglarz-Tomczak
- Department of Bioorganic Chemistry; Wrocław University of Science and Technology; Wybrzeże Wyspiańskiego 27 50-370 Wrocław Poland
| | - Paulina Fortuna
- Department of Bioorganic Chemistry; Wrocław University of Science and Technology; Wybrzeże Wyspiańskiego 27 50-370 Wrocław Poland
| | - Agnieszka Krzysztoń
- Department of Bioorganic Chemistry; Wrocław University of Science and Technology; Wybrzeże Wyspiańskiego 27 50-370 Wrocław Poland
| | - Ewa Rudzińska-Szostak
- Department of Bioorganic Chemistry; Wrocław University of Science and Technology; Wybrzeże Wyspiańskiego 27 50-370 Wrocław Poland
| | - Łukasz Berlicki
- Department of Bioorganic Chemistry; Wrocław University of Science and Technology; Wybrzeże Wyspiańskiego 27 50-370 Wrocław Poland
| |
Collapse
|
35
|
Szefczyk M, Węglarz-Tomczak E, Fortuna P, Krzysztoń A, Rudzińska-Szostak E, Berlicki Ł. Controlling the Helix Handedness of ααβ-Peptide Foldamers through Sequence Shifting. Angew Chem Int Ed Engl 2017; 56:2087-2091. [DOI: 10.1002/anie.201610154] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Revised: 12/02/2016] [Indexed: 02/05/2023]
Affiliation(s)
- Monika Szefczyk
- Department of Bioorganic Chemistry; Wrocław University of Science and Technology; Wybrzeże Wyspiańskiego 27 50-370 Wrocław Poland
| | - Ewelina Węglarz-Tomczak
- Department of Bioorganic Chemistry; Wrocław University of Science and Technology; Wybrzeże Wyspiańskiego 27 50-370 Wrocław Poland
| | - Paulina Fortuna
- Department of Bioorganic Chemistry; Wrocław University of Science and Technology; Wybrzeże Wyspiańskiego 27 50-370 Wrocław Poland
| | - Agnieszka Krzysztoń
- Department of Bioorganic Chemistry; Wrocław University of Science and Technology; Wybrzeże Wyspiańskiego 27 50-370 Wrocław Poland
| | - Ewa Rudzińska-Szostak
- Department of Bioorganic Chemistry; Wrocław University of Science and Technology; Wybrzeże Wyspiańskiego 27 50-370 Wrocław Poland
| | - Łukasz Berlicki
- Department of Bioorganic Chemistry; Wrocław University of Science and Technology; Wybrzeże Wyspiańskiego 27 50-370 Wrocław Poland
| |
Collapse
|
36
|
Grison CM, Miles JA, Robin S, Wilson AJ, Aitken DJ. An α-Helix-Mimicking 12,13-Helix: Designed α/β/γ-Foldamers as Selective Inhibitors of Protein-Protein Interactions. Angew Chem Int Ed Engl 2016; 55:11096-100. [PMID: 27467859 PMCID: PMC5014220 DOI: 10.1002/anie.201604517] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Revised: 06/28/2016] [Indexed: 12/31/2022]
Abstract
A major current challenge in bioorganic chemistry is the identification of effective mimics of protein secondary structures that act as inhibitors of protein-protein interactions (PPIs). In this work, trans-2-aminocyclobutanecarboxylic acid (tACBC) was used as the key β-amino acid component in the design of α/β/γ-peptides to structurally mimic a native α-helix. Suitably functionalized α/β/γ-peptides assume an α-helix-mimicking 12,13-helix conformation in solution, exhibit enhanced proteolytic stability in comparison to the wild-type α-peptide parent sequence from which they are derived, and act as selective inhibitors of the p53/hDM2 interaction.
Collapse
Affiliation(s)
- Claire M Grison
- CP3A Organic Synthesis Group, ICMMO, CNRS, Université Paris Sud, Université Paris Saclay, 15 Rue George Clemenceau, 91405, Orsay Cedex, France
| | - Jennifer A Miles
- School of Chemistry, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK
- Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK
| | - Sylvie Robin
- CP3A Organic Synthesis Group, ICMMO, CNRS, Université Paris Sud, Université Paris Saclay, 15 Rue George Clemenceau, 91405, Orsay Cedex, France
- UFR Sciences Pharmaceutiques et Biologiques, Université Paris Descartes, 4 Avenue de l'Observatoire, 75270, Paris cedex 06, France
| | - Andrew J Wilson
- School of Chemistry, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK.
- Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK.
| | - David J Aitken
- CP3A Organic Synthesis Group, ICMMO, CNRS, Université Paris Sud, Université Paris Saclay, 15 Rue George Clemenceau, 91405, Orsay Cedex, France.
| |
Collapse
|
37
|
Grison CM, Miles JA, Robin S, Wilson AJ, Aitken DJ. An α-Helix-Mimicking 12,13-Helix: Designed α/β/γ-Foldamers as Selective Inhibitors of Protein-Protein Interactions. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201604517] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Claire M. Grison
- CP3A Organic Synthesis Group, ICMMO, CNRS; Université Paris Sud, Université Paris Saclay; 15 Rue George Clemenceau 91405 Orsay Cedex France
| | - Jennifer A. Miles
- School of Chemistry; University of Leeds; Woodhouse Lane Leeds LS2 9JT UK
- Astbury Centre for Structural Molecular Biology; University of Leeds; Woodhouse Lane Leeds LS2 9JT UK
| | - Sylvie Robin
- CP3A Organic Synthesis Group, ICMMO, CNRS; Université Paris Sud, Université Paris Saclay; 15 Rue George Clemenceau 91405 Orsay Cedex France
- UFR Sciences Pharmaceutiques et Biologiques; Université Paris Descartes; 4 Avenue de l'Observatoire 75270 Paris cedex 06 France
| | - Andrew J. Wilson
- School of Chemistry; University of Leeds; Woodhouse Lane Leeds LS2 9JT UK
- Astbury Centre for Structural Molecular Biology; University of Leeds; Woodhouse Lane Leeds LS2 9JT UK
| | - David J. Aitken
- CP3A Organic Synthesis Group, ICMMO, CNRS; Université Paris Sud, Université Paris Saclay; 15 Rue George Clemenceau 91405 Orsay Cedex France
| |
Collapse
|
38
|
Kreitler DF, Mortenson DE, Forest KT, Gellman SH. Effects of Single α-to-β Residue Replacements on Structure and Stability in a Small Protein: Insights from Quasiracemic Crystallization. J Am Chem Soc 2016; 138:6498-505. [PMID: 27171550 DOI: 10.1021/jacs.6b01454] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Synthetic peptides that contain backbone modifications but nevertheless adopt folded structures similar to those of natural polypeptides are of fundamental interest and may provide a basis for biomedical applications. Such molecules can, for example, mimic the ability of natural prototypes to bind to specific target macromolecules but resist degradation by proteases. We have previously shown that oligomers containing mixtures of α- and β-amino acid residues ("α/β-peptides") can mimic the α-helix secondary structure, and that properly designed α/β-peptides can bind to proteins that evolved to bind to α-helical partners. Here we report fundamental studies that support the long-range goal of extending the α/β approach to tertiary structures. We have evaluated the impact of single α → β modifications on the structure and stability of the small and well-studied villin headpiece subdomain (VHP). The native state of this 35-residue polypeptide contains several α-helical segments packed around a small hydrophobic core. We examined α → β substitution at four solvent-exposed positions, Asn19, Trp23, Gln26 and Lys30. In each case, both the β(3) homologue of the natural α residue and a cyclic β residue were evaluated. All α → β(3) substitutions caused significant destabilization of the tertiary structure as measured by variable-temperature circular dichroism, although at some of these positions, replacing the β(3) residue with a cyclic β residue led to improved stability. Atomic-resolution structures of four VHP analogues were obtained via quasiracemic crystallization. These findings contribute to a fundamental α/β-peptide knowledge-base by confirming that β(3)-amino acid residues can serve as effective structural mimics of homologous α-amino acid residues within a natural tertiary fold, which should support rational design of functional α/β analogues of natural poly-α-peptides.
Collapse
Affiliation(s)
- Dale F Kreitler
- Department of Chemistry and ‡Department of Bacteriology, University of Wisconsin-Madison , Madison, Wisconsin 53706, United States
| | - David E Mortenson
- Department of Chemistry and ‡Department of Bacteriology, University of Wisconsin-Madison , Madison, Wisconsin 53706, United States
| | - Katrina T Forest
- Department of Chemistry and ‡Department of Bacteriology, University of Wisconsin-Madison , Madison, Wisconsin 53706, United States
| | - Samuel H Gellman
- Department of Chemistry and ‡Department of Bacteriology, University of Wisconsin-Madison , Madison, Wisconsin 53706, United States
| |
Collapse
|
39
|
Burslem GM, Kyle HF, Breeze AL, Edwards TA, Nelson A, Warriner SL, Wilson AJ. Towards "bionic" proteins: replacement of continuous sequences from HIF-1α with proteomimetics to create functional p300 binding HIF-1α mimics. Chem Commun (Camb) 2016; 52:5421-4. [PMID: 27009828 PMCID: PMC4843846 DOI: 10.1039/c6cc01812b] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Accepted: 03/11/2016] [Indexed: 12/15/2022]
Abstract
Using the HIF-1α transcription factor as a model, this manuscript illustrates how an extended sequence of α-amino acids in a polypeptide can be replaced with a non-natural topographical mimic of an α-helix comprised from an aromatic oligoamide. The resultant hybrid is capable of reproducing the molecular recognition profile of the p300 binding sequence of HIF-1α from which it is derived.
Collapse
Affiliation(s)
- George M Burslem
- School of Chemistry, University of Leeds, Woodhouse Lane, Leeds, LS29JT, UK and Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds, LS29JT, UK.
| | - Hannah F Kyle
- Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds, LS29JT, UK. and School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, UK
| | - Alexander L Breeze
- Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds, LS29JT, UK. and School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, UK and Discovery Sciences, AstraZeneca R&D, Alderley Park, Cheshire, SK10 4TG, UK
| | - Thomas A Edwards
- Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds, LS29JT, UK. and School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Woodhouse Lane, Leeds LS2 9JT, UK
| | - Adam Nelson
- School of Chemistry, University of Leeds, Woodhouse Lane, Leeds, LS29JT, UK and Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds, LS29JT, UK.
| | - Stuart L Warriner
- School of Chemistry, University of Leeds, Woodhouse Lane, Leeds, LS29JT, UK and Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds, LS29JT, UK.
| | - Andrew J Wilson
- School of Chemistry, University of Leeds, Woodhouse Lane, Leeds, LS29JT, UK and Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds, LS29JT, UK.
| |
Collapse
|
40
|
Collie GW, Pulka-Ziach K, Guichard G. Surfactant-facilitated crystallisation of water-soluble foldamers. Chem Sci 2016; 7:3377-3383. [PMID: 29997832 PMCID: PMC6006954 DOI: 10.1039/c6sc00090h] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Accepted: 02/10/2016] [Indexed: 12/16/2022] Open
Abstract
Common surfactants promote the crystallisation of a series of water-soluble oligourea foldamers which had previously proven resistant to crystallisation efforts.
X-ray crystallography has played a major role in the advancement of foldamer research, however, obtaining well-formed single crystals of suitable quality for structure determination by X-ray diffraction methods is often rather challenging. Towards this end, we report here the ability of common surfactants to promote the crystallisation of a series of water-soluble oligourea foldamers which had previously proven highly resistant to crystallisation. Four high-resolution crystal structures are reported, suggesting certain surfactants could be potentially useful tools for the crystallisation of intractable water-soluble foldamers (or peptides).
Collapse
Affiliation(s)
- G W Collie
- Univ. Bordeaux , CBMN , UMR 5248 , Institut Européen de Chimie et Biologie , 2 rue Robert Escarpit , 33607 Pessac , France . .,CNRS , CBMN , UMR 5248 , F-33600 , Pessac , France
| | - K Pulka-Ziach
- Univ. Bordeaux , CBMN , UMR 5248 , Institut Européen de Chimie et Biologie , 2 rue Robert Escarpit , 33607 Pessac , France . .,CNRS , CBMN , UMR 5248 , F-33600 , Pessac , France
| | - G Guichard
- Univ. Bordeaux , CBMN , UMR 5248 , Institut Européen de Chimie et Biologie , 2 rue Robert Escarpit , 33607 Pessac , France . .,CNRS , CBMN , UMR 5248 , F-33600 , Pessac , France
| |
Collapse
|
41
|
|
42
|
Collie GW, Pulka-Ziach K, Guichard G. In situ iodination and X-ray crystal structure of a foldamer helix bundle. Chem Commun (Camb) 2016; 52:1202-5. [DOI: 10.1039/c5cc07916k] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
We report here the efficient in situ iodination of tyrosine-type side-chains located within a foldamer helix bundle, permitting structure determination using single-wavelength anomalous diffraction (SAD) methods.
Collapse
Affiliation(s)
| | | | - Gilles Guichard
- Université de Bordeaux
- CNRS
- UMR 5248
- CBMN
- Institut Européen de Chimie et Biologie
| |
Collapse
|
43
|
Kwon S, Kim BJ, Lim HK, Kang K, Yoo SH, Gong J, Yoon E, Lee J, Choi IS, Kim H, Lee HS. Magnetotactic molecular architectures from self-assembly of β-peptide foldamers. Nat Commun 2015; 6:8747. [PMID: 26510658 PMCID: PMC4640081 DOI: 10.1038/ncomms9747] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Accepted: 09/25/2015] [Indexed: 01/10/2023] Open
Abstract
The design of stimuli-responsive self-assembled molecular systems capable of undergoing mechanical work is one of the most important challenges in synthetic chemistry and materials science. Here we report that foldectures, that is, self-assembled molecular architectures of β-peptide foldamers, uniformly align with respect to an applied static magnetic field, and also show instantaneous orientational motion in a dynamic magnetic field. This response is explained by the amplified anisotropy of the diamagnetic susceptibilities as a result of the well-ordered molecular packing of the foldectures. In addition, the motions of foldectures at the microscale can be translated into magnetotactic behaviour at the macroscopic scale in a way reminiscent to that of magnetosomes in magnetotactic bacteria. This study will provide significant inspiration for designing the next generation of biocompatible peptide-based molecular machines with applications in biological systems.
Collapse
Affiliation(s)
- Sunbum Kwon
- Molecular-Level Interface Research Center, Department of Chemistry, KAIST, Daejeon 305-701, Korea
| | - Beom Jin Kim
- Molecular-Level Interface Research Center, Department of Chemistry, KAIST, Daejeon 305-701, Korea
- Center for Cell-Encapsulation Research, Department of Chemistry, KAIST, Daejeon 305-701, Korea
| | - Hyung-Kyu Lim
- Graduate School of Energy Environment Water Sustainability (EEWS), KAIST, Daejeon 305-701, Korea
| | - Kyungtae Kang
- Molecular-Level Interface Research Center, Department of Chemistry, KAIST, Daejeon 305-701, Korea
- Center for Cell-Encapsulation Research, Department of Chemistry, KAIST, Daejeon 305-701, Korea
| | - Sung Hyun Yoo
- Molecular-Level Interface Research Center, Department of Chemistry, KAIST, Daejeon 305-701, Korea
| | - Jintaek Gong
- Molecular-Level Interface Research Center, Department of Chemistry, KAIST, Daejeon 305-701, Korea
| | - Eunyoung Yoon
- Molecular-Level Interface Research Center, Department of Chemistry, KAIST, Daejeon 305-701, Korea
| | - Juno Lee
- Molecular-Level Interface Research Center, Department of Chemistry, KAIST, Daejeon 305-701, Korea
- Center for Cell-Encapsulation Research, Department of Chemistry, KAIST, Daejeon 305-701, Korea
| | - Insung S. Choi
- Molecular-Level Interface Research Center, Department of Chemistry, KAIST, Daejeon 305-701, Korea
- Center for Cell-Encapsulation Research, Department of Chemistry, KAIST, Daejeon 305-701, Korea
| | - Hyungjun Kim
- Graduate School of Energy Environment Water Sustainability (EEWS), KAIST, Daejeon 305-701, Korea
| | - Hee-Seung Lee
- Molecular-Level Interface Research Center, Department of Chemistry, KAIST, Daejeon 305-701, Korea
| |
Collapse
|
44
|
Fremaux J, Mauran L, Pulka-Ziach K, Kauffmann B, Odaert B, Guichard G. α-Peptide-Oligourea Chimeras: Stabilization of Short α-Helices by Non-Peptide Helical Foldamers. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201500901] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
|
45
|
Fremaux J, Mauran L, Pulka‐Ziach K, Kauffmann B, Odaert B, Guichard G. α‐Peptide–Oligourea Chimeras: Stabilization of Short α‐Helices by Non‐Peptide Helical Foldamers. Angew Chem Int Ed Engl 2015; 54:9816-20. [DOI: 10.1002/anie.201500901] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Revised: 04/23/2015] [Indexed: 01/27/2023]
Affiliation(s)
- Juliette Fremaux
- Univ. Bordeaux, CBMN, UMR 5248, Institut Européen de Chimie et Biologie (IECB), 2 rue Robert Escarpit, 33607 Pessac (France)
- CNRS, CBMN, UMR 5248, 33600 Pessac (France)
- UREkA, Sarl, 2 rue Robert Escarpit, 33607 Pessac (France)
| | - Laura Mauran
- Univ. Bordeaux, CBMN, UMR 5248, Institut Européen de Chimie et Biologie (IECB), 2 rue Robert Escarpit, 33607 Pessac (France)
- CNRS, CBMN, UMR 5248, 33600 Pessac (France)
- UREkA, Sarl, 2 rue Robert Escarpit, 33607 Pessac (France)
| | - Karolina Pulka‐Ziach
- Univ. Bordeaux, CBMN, UMR 5248, Institut Européen de Chimie et Biologie (IECB), 2 rue Robert Escarpit, 33607 Pessac (France)
- CNRS, CBMN, UMR 5248, 33600 Pessac (France)
- Present address: Faculty of Chemistry, University of Warsaw, Pasteura 1, 02‐093 Warsaw (Poland)
| | - Brice Kauffmann
- Univ. Bordeaux, IECB, UMS 3033/US 001, 2 rue Escarpit, 33607 Pessac (France)
- CNRS, IECB, UMS 3033, 33600 Pessac (France)
- INSERM, IECB, US 001, 33600 Pessac (France)
| | - Benoit Odaert
- CNRS, CBMN, UMR 5248, 33600 Pessac (France)
- Univ. Bordeaux, CBMN, UMR 5248, All. Geoffroy Saint‐Hilaire, 33600 Pessac (France)
| | - Gilles Guichard
- Univ. Bordeaux, CBMN, UMR 5248, Institut Européen de Chimie et Biologie (IECB), 2 rue Robert Escarpit, 33607 Pessac (France)
- CNRS, CBMN, UMR 5248, 33600 Pessac (France)
| |
Collapse
|
46
|
Tian Y, Wang L, Shi J, Yu HZ. Desulfurization Mechanism of Cysteine in Synthesis of Polypeptides. CHINESE J CHEM PHYS 2015. [DOI: 10.1063/1674-0068/28/cjcp1501009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
|
47
|
Azzarito V, Miles JA, Fisher J, Edwards TA, Warriner SL, Wilson AJ. Stereocontrolled protein surface recognition using chiral oligoamide proteomimetic foldamers. Chem Sci 2015; 6:2434-2443. [PMID: 29308155 PMCID: PMC5646261 DOI: 10.1039/c4sc03559c] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Accepted: 01/29/2015] [Indexed: 12/26/2022] Open
Abstract
An oligoamide helix mimicking foldamer with well-defined conformation is shown to recognize its target protein hDM2 in a manner that depends upon the composition, spatial projection and stereochemistry of functional groups appended to the scaffold.
The development of foldamers capable of selective molecular recognition of solvent exposed protein surfaces represents an outstanding challenge in supramolecular chemical biology. Here we introduce an oligoamide foldamer with well-defined conformation that bears all the hallmarks of an information rich oligomer. Specifically, the foldamer recognizes its target protein hDM2 leading to inhibition of its protein–protein interaction with p53 in a manner that depends upon the composition, spatial projection and stereochemistry of functional groups appended to the scaffold. Most significantly, selective inhibition of p53/hDM2 can be achieved against four other targets and the selectivity for p53/hDM2 inhibition versus Mcl-1/NOXA-B inhibition is critically dependent upon the stereochemistry of the helix mimetic.
Collapse
Affiliation(s)
- Valeria Azzarito
- School of Chemistry , University of Leeds , Woodhouse Lane , Leeds , LS2 9JT , UK . .,Astbury Centre for Structural and Molecular Biology , University of Leeds , Woodhouse Lane , Leeds , LS2 9JT , UK
| | - Jennifer A Miles
- School of Chemistry , University of Leeds , Woodhouse Lane , Leeds , LS2 9JT , UK . .,Astbury Centre for Structural and Molecular Biology , University of Leeds , Woodhouse Lane , Leeds , LS2 9JT , UK
| | - Julie Fisher
- School of Chemistry , University of Leeds , Woodhouse Lane , Leeds , LS2 9JT , UK .
| | - Thomas A Edwards
- Astbury Centre for Structural and Molecular Biology , University of Leeds , Woodhouse Lane , Leeds , LS2 9JT , UK.,School of Molecular and Cellular Biology , University of Leeds , Woodhouse Lane , Leeds , LS2 9JT , UK
| | - Stuart L Warriner
- School of Chemistry , University of Leeds , Woodhouse Lane , Leeds , LS2 9JT , UK . .,Astbury Centre for Structural and Molecular Biology , University of Leeds , Woodhouse Lane , Leeds , LS2 9JT , UK
| | - Andrew J Wilson
- School of Chemistry , University of Leeds , Woodhouse Lane , Leeds , LS2 9JT , UK . .,Astbury Centre for Structural and Molecular Biology , University of Leeds , Woodhouse Lane , Leeds , LS2 9JT , UK
| |
Collapse
|
48
|
Reinert ZE, Horne WS. Protein backbone engineering as a strategy to advance foldamers toward the frontier of protein-like tertiary structure. Org Biomol Chem 2014; 12:8796-802. [PMID: 25285575 PMCID: PMC4211622 DOI: 10.1039/c4ob01769b] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
A variety of non-biological structural motifs have been incorporated into the backbone of natural protein sequences. In parallel work, diverse unnatural oligomers of de novo design (termed "foldamers") have been developed that fold in defined ways. In this Perspective article, we survey foundational studies on protein backbone engineering, with a focus on alterations made in the context of complex tertiary folds. We go on to summarize recent work illustrating the potential promise of these methods to provide a general framework for the construction of foldamer mimics of protein tertiary structures.
Collapse
Affiliation(s)
- Zachary E Reinert
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, USA.
| | | |
Collapse
|
49
|
Miller J, Melicher MS, Schepartz A. Positive allostery in metal ion binding by a cooperatively folded β-peptide bundle. J Am Chem Soc 2014; 136:14726-9. [PMID: 25290247 PMCID: PMC4210112 DOI: 10.1021/ja508872q] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2014] [Indexed: 01/19/2023]
Abstract
Metal ion binding is exploited by proteins in nature to catalyze reactions, bind molecules, and favor discrete structures, but it has not been demonstrated in β-peptides or their assemblies. Here we report the design, synthesis, and characterization of a β-peptide bundle that uniquely binds two Cd(II) ions in a distinct bicoordinate array. The two Cd(II) ions bind with positive allosteric cooperativity and increase the thermodynamic stability of the bundle by more than 50 °C. This system provides a unique, synthetic context to explore allosteric regulation and should pave the way to sophisticated molecular assemblies with catalytic and substrate-sensing functions that have historically not been available to de novo designed synthetic proteomimetics in water.
Collapse
Affiliation(s)
- Jonathan
P. Miller
- Department
of Chemistry and Department of Molecular, Cellular and Developmental
Biology, Yale University, New Haven, Connecticut 06520-8107, United States
| | - Michael S. Melicher
- Department
of Chemistry and Department of Molecular, Cellular and Developmental
Biology, Yale University, New Haven, Connecticut 06520-8107, United States
| | - Alanna Schepartz
- Department
of Chemistry and Department of Molecular, Cellular and Developmental
Biology, Yale University, New Haven, Connecticut 06520-8107, United States
| |
Collapse
|