1
|
Kuila S, Singh AK, Shrivastava A, Dey S, Singha T, Roy L, Satpati B, Nanda J. Probing Molecular Chirality on the Self-Assembly and Gelation of Naphthalimide-Conjugated Dipeptides. J Phys Chem B 2023. [PMID: 37196104 DOI: 10.1021/acs.jpcb.3c01273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
In this work, 1,8-naphthalimide (NMI)-conjugated three hybrid dipeptides constituted of a β-amino acid and an α-amino acid have been designed, synthesized, and purified. Here, in the design, the chirality of the α-amino acid was varied to study the effect of molecular chirality on the supramolecular assembly. Self-assembly and gelation of three NMI conjugates were studied in mixed solvent systems [water and dimethyl sulphoxide (DMSO)]. Interestingly, chiral NMI derivatives [NMI-βAla-lVal-OMe (NLV) and NMI-βAla-dVal-OMe (NDV)] formed self-supported gels, while the achiral NMI derivative [NMI-βAla-Aib-OMe, (NAA)] failed to form any kind of gel at 1 mM concentration and in a mixed solvent (70% water in DMSO medium). Self-assembly processes were thoroughly investigated using UV-vis spectroscopy, nuclear magnetic resonance (NMR), fluorescence, and circular dichroism (CD) spectroscopy. A J-type molecular assembly was observed in the mixed solvent system. The CD study indicated the formation of chiral assembled structures for NLV and NDV, which were mirror images of one another, and the self-assembled state by NAA was CD-silent. The nanoscale morphology of the three derivatives was studied using scanning electron microscopy (SEM). In the case of NLV and NDV, left- and right-handed fibrilar morphologies were observed, respectively. In contrast, a flake-like morphology was noticed for NAA. The DFT study indicated that the chirality of the α-amino acid influenced the orientation of π-π stacking interactions of naphthalimide units in the self-assembled structure that in turn regulated the helicity. This is a unique work where molecular chirality controls the nanoscale assembly as well as the macroscopic self-assembled state.
Collapse
Affiliation(s)
- Soumen Kuila
- Department of Chemistry, University of North Bengal, Raja Rammohanpur, Siliguri 734013, West Bengal, India
| | - Ajeet Kumar Singh
- Institute of Chemical Technology Mumbai-IOC Odisha Campus Bhubaneswar, IIT Kharagpur Extension Centre, Bhubaneswar 751013, India
| | - Akash Shrivastava
- Department of Chemistry, University of North Bengal, Raja Rammohanpur, Siliguri 734013, West Bengal, India
| | - Sukantha Dey
- Department of Chemistry, University of North Bengal, Raja Rammohanpur, Siliguri 734013, West Bengal, India
| | - Tukai Singha
- Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata 700064, West Bengal, India
| | - Lisa Roy
- Institute of Chemical Technology Mumbai-IOC Odisha Campus Bhubaneswar, IIT Kharagpur Extension Centre, Bhubaneswar 751013, India
| | - Biswarup Satpati
- Saha Institute of Nuclear Physics, 1/AF Bidhannagar, Kolkata 700064, West Bengal, India
| | - Jayanta Nanda
- Department of Chemistry, University of North Bengal, Raja Rammohanpur, Siliguri 734013, West Bengal, India
| |
Collapse
|
2
|
Morris DTJ, Clayden J. Screw sense and screw sensibility: communicating information by conformational switching in helical oligomers. Chem Soc Rev 2023; 52:2480-2496. [PMID: 36928473 PMCID: PMC10068589 DOI: 10.1039/d2cs00982j] [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: 01/23/2023] [Indexed: 03/18/2023]
Abstract
Biological systems have evolved a number of different strategies to communicate information on the molecular scale. Among these, the propagation of conformational change is among the most important, being the means by which G-protein coupled receptors (GPCRs) use extracellular signals to modulate intracellular processes, and the way that opsin proteins translate light signals into nerve impulses. The developing field of foldamer chemistry has allowed chemists to employ conformationally well-defined synthetic structures likewise to mediate information transfer, making use of mechanisms that are not found in biological contexts. In this review, we discuss the use of switchable screw-sense preference as a communication mechanism. We discuss the requirements for functional communication devices, and show how dynamic helical foldamers derived from the achiral monomers such as α-aminoisobutyric acid (Aib) and meso-cyclohexane-1,2-diamine fulfil them by communicating information in the form of switchable screw-sense preference. We describe the various stimuli that can be used to switch screw sense, and explore the way that propagation of the resulting conformational preference in a well-defined helical molecule allows screw sense to control chemical events remote from a source of information. We describe the operation of these conformational switches in the membrane phase, and outline the progress that has been made towards using conformational switching to communicate between the exterior and interior of a phospholipid vesicle.
Collapse
Affiliation(s)
- David T J Morris
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK.
| | - Jonathan Clayden
- School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, UK.
| |
Collapse
|
3
|
Menke FS, Wicher B, Maurizot V, Huc I. Homochiral versus Heterochiral Dimeric Helical Foldamer Bundles: Chlorinated-Solvent-Dependent Self-Sorting. Angew Chem Int Ed Engl 2023; 62:e202217325. [PMID: 36625790 DOI: 10.1002/anie.202217325] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 01/09/2023] [Accepted: 01/10/2023] [Indexed: 01/11/2023]
Abstract
Aromatic oligoamide sequences programmed to fold into stable helical conformations were designed to display a linear array of hydrogen-bond donors and acceptors at their surface. Sequences were prepared by solid-phase synthesis. Solution 1 H NMR spectroscopic studies and solid-state crystallographic structures demonstrated the formation of stable hydrogen-bond-mediated dimeric helix bundles that could be either heterochiral (with a P and an M helix) or homochiral (with two P or two M helices). Formation of the hetero- or homochiral dimers could be driven quantitatively using different chlorinated solvents-exemplifying a remarkable case of either social or narcissistic chiral self-sorting or upon imposing absolute handedness to the helices to forbid PM species.
Collapse
Affiliation(s)
- Friedericke S Menke
- Department of Pharmacy, Ludwig-Maximilians-University of Munich, Butenandtstr. 5-13, 81377, München, Germany
| | - Barbara Wicher
- Department of Chemical Technology of Drugs, Poznan University of Medical Sciences, 6 Grunwaldzka St., 60-780, Poznan, Poland
| | - Victor Maurizot
- CBMN (UMR 5248), Univ. Bordeaux, CNRS, Bordeaux INP, 2, Rue Robert Escarpit, 33600, Pessac, France
| | - Ivan Huc
- Department of Pharmacy, Ludwig-Maximilians-University of Munich, Butenandtstr. 5-13, 81377, München, Germany
| |
Collapse
|
4
|
Menke FS, Mazzier D, Wicher B, Allmendinger L, Kauffmann B, Maurizot V, Huc I. Molecular torsion springs: alteration of helix curvature in frustrated tertiary folds. Org Biomol Chem 2023; 21:1275-1283. [PMID: 36645374 DOI: 10.1039/d2ob02109a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The first abiotic foldamer tertiary structures have been recently reported in the form of aromatic helix-turn-helix motifs based on oligo-quinolinecarboxamides held together by intramolecular hydrogen bonds. Tertiary folds were predicted by computational modelling of the hydrogen-bonding interfaces between helices and later verified by X-ray crystallography. However, the prognosis of how the conformational preference inherent to each helix influences the tertiary structure warranted further investigation. Several new helix-turn-helix sequences were synthesised in which some hydrogen bonds have been removed. Contrary to expectations, this change did not strongly destabilise the tertiary folds. On closer inspection, a new crystal structure revealed that helices adopt their natural curvature when some hydrogen bonds are missing and undergo some spring torsion upon forming the said hydrogen bonds, thus potentially giving rise to a conformational frustration. This phenomenon sheds light on the aggregation behaviour of the helices when they are not linked by a turn unit.
Collapse
Affiliation(s)
- Friedericke S Menke
- Department of Pharmacy, Ludwig-Maximilians-University, Butenandstraße 5-13, 81377 Munich, Germany.
| | - Daniela Mazzier
- Department of Pharmacy, Ludwig-Maximilians-University, Butenandstraße 5-13, 81377 Munich, Germany.
| | - Barbara Wicher
- Department of Chemical Technology of Drugs, Poznan University of Medical Sciences, Grunwaldzka 6, 60-780 Poznan, Poland
| | - Lars Allmendinger
- Department of Pharmacy, Ludwig-Maximilians-University, Butenandstraße 5-13, 81377 Munich, Germany.
| | - Brice Kauffmann
- Institut Européen de Chimie et Biologie (UMS3011/US001), CNRS, Inserm, Université de Bordeaux, 2 rue Robert Escarpit, F-33600 Pessac, France
| | - Victor Maurizot
- CBMN (UMR 5248), Univ. Bordeaux, CNRS, Bordeaux INP, 2 rue Robert Escarpit, 33600 Pessac, France
| | - Ivan Huc
- Department of Pharmacy, Ludwig-Maximilians-University, Butenandstraße 5-13, 81377 Munich, Germany.
| |
Collapse
|
5
|
Wang J, Wicher B, Maurizot V, Huc I. Directing the Self-Assembly of Aromatic Foldamer Helices using Acridine Appendages and Metal Coordination. Chemistry 2022; 28:e202201345. [PMID: 35965255 PMCID: PMC9826129 DOI: 10.1002/chem.202201345] [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: 05/01/2022] [Indexed: 01/11/2023]
Abstract
Folded molecules provide complex interaction interfaces amenable to sophisticated self-assembly motifs. Because of their high conformational stability, aromatic foldamers constitute suitable candidates for the rational elaboration of self-assembled architectures. Several multiturn helical aromatic oligoamides have been synthesized that possess arrays of acridine appendages pointing in one or two directions. The acridine units were shown to direct self-assembly in the solid state via aromatic stacking leading to recurrent helix-helix association patterns under the form of discrete dimers or extended arrays. In the presence of Pd(II), metal coordination of the acridine units overwhelms other forces and generates new metal-mediated multihelical self-assemblies, including macrocycles. These observations demonstrate simple access to different types of foldamer-containing architectures, ranging from discrete objects to 1D and, by extension, 2D and 3D arrays.
Collapse
Affiliation(s)
- Jinhua Wang
- CBMN (UMR5248)Univ. Bordeaux – CNRS – IPBInstitut Européen de Chimie et Biologie2 rue Escarpit33600PessacFrance
| | - Barbara Wicher
- Department of Chemical Technology of DrugsPoznan University of Medical SciencesGrunwaldzka 660-780PoznanPoland
| | - Victor Maurizot
- CBMN (UMR5248)Univ. Bordeaux – CNRS – IPBInstitut Européen de Chimie et Biologie2 rue Escarpit33600PessacFrance
| | - Ivan Huc
- CBMN (UMR5248)Univ. Bordeaux – CNRS – IPBInstitut Européen de Chimie et Biologie2 rue Escarpit33600PessacFrance,Department of PharmacyLudwig-Maximilians-UniversitätButenandtstrasse 5–1381377MünchenGermany,Cluster of Excellence e-conversion85748GarchingGermany
| |
Collapse
|
6
|
Fobe TL, Walker CC, Meek GA, Shirts MR. Folding Coarse-Grained Oligomer Models with PyRosetta. J Chem Theory Comput 2022; 18:6354-6369. [PMID: 36179376 DOI: 10.1021/acs.jctc.2c00519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Non-biological foldamers are a promising class of macromolecules that share similarities to classical biopolymers such as proteins and nucleic acids. Currently, designing novel foldamers is a non-trivial process, often involving many iterations of trial synthesis and characterization until folded structures are observed. In this work, we aim to tackle these foldamer design challenges using computational modeling techniques. We developed CG PyRosetta, an extension to the popular protein folding python package, PyRosetta, which introduces coarse-grained (CG) residues into PyRosetta, enabling the folding of toy CG foldamer models. Although these models are simplified, they can help explore overarching physical hypotheses about how oligomers can form. Through systematic variation of CG parameters in these models, we can investigate various folding hypotheses at the CG scale to inform the design process of new foldamer chemistries. In this study, we demonstrate CG PyRosetta's ability to identify minimum energy structures with a diverse structural search over a range of simple models, as well as two hypothesis-driven parameter scans investigating the effects of side-chain size and internal backbone angle on secondary structures. We are able to identify several types of secondary structures from single- and double-helices to sheet-like and knot-like structures. We show how side-chain size and backbone bond angle both play an important role in the structure and energetics of these toy models. Optimal side-chain sizes promote favorable packing of side chains, while specific backbone bond angles influence the specific helix type found in folded structures.
Collapse
Affiliation(s)
- Theodore L Fobe
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, Colorado80309, United States
| | - Christopher C Walker
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, Colorado80309, United States
| | - Garrett A Meek
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, Colorado80309, United States
| | - Michael R Shirts
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, Colorado80309, United States
| |
Collapse
|
7
|
Jang HJ, Lee S, An BJ, Song G, Jeon HG, Jeong KS. Tweezer-type binding cavity formed by the helical folding of a carbazole-pyridine oligomer. Chem Commun (Camb) 2022; 58:1410-1413. [PMID: 34994755 DOI: 10.1039/d1cc06569f] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
We have synthesised a new aromatic foldamer based on the carbazole-pyridine oligomers that adopt helical conformations via dipole-dipole interactions and π-stacking between two ethynyl bond-linked monomers. This foldamer scaffold has been further modified into a synthetic receptor with a tweezer-type binding cavity outside the helical backbone upon folding, in contrast to most aromatic foldamers with internal binding cavities. The tweezer-type cavity is composed of two parallel pyrenyl planes, allowing for the intercalation of a naphthalenediimide guest via π-stacking and CH⋯O interactions, as demonstrated using its 1H NMR spectra and X-ray crystal structure.
Collapse
Affiliation(s)
- Hye Jin Jang
- Department of Chemistry, Yonsei University, Seoul 03722, Republic of Korea.
| | - Seungwon Lee
- Department of Chemistry, Yonsei University, Seoul 03722, Republic of Korea.
| | - Byung Jun An
- Department of Chemistry, Yonsei University, Seoul 03722, Republic of Korea.
| | - Geunmoo Song
- Department of Chemistry, Yonsei University, Seoul 03722, Republic of Korea.
| | - Hae-Geun Jeon
- Department of Chemistry, Yonsei University, Seoul 03722, Republic of Korea.
| | - Kyu-Sung Jeong
- Department of Chemistry, Yonsei University, Seoul 03722, Republic of Korea.
| |
Collapse
|
8
|
Bindl D, Mandal PK, Allmendinger L, Huc I. Discrete Stacked Dimers of Aromatic Oligoamide Helices. Angew Chem Int Ed Engl 2021; 61:e202116509. [PMID: 34962351 PMCID: PMC9305948 DOI: 10.1002/anie.202116509] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Indexed: 12/03/2022]
Abstract
Tight binding was observed between the C‐terminal cross section of aromatic oligoamide helices in aqueous solution, leading to the formation of discrete head‐to‐head dimers in slow exchange on the NMR timescale with the corresponding monomers. The nature and structure of the dimers was evidenced by 2D NOESY and DOSY spectroscopy, mass spectrometry and X‐ray crystallography. The binding interface involves a large hydrophobic aromatic surface and hydrogen bonding. Dimerization requires that helices have the same handedness and the presence of a C‐terminal carboxy function. The protonation state of the carboxy group plays a crucial role, resulting in pH dependence of the association. Dimerization is also influenced by neighboring side chains and can be programmed to selectively produce heteromeric aggregates.
Collapse
Affiliation(s)
- Daniel Bindl
- LMU München: Ludwig-Maximilians-Universitat Munchen, Pharmacy, GERMANY
| | - Pradeep K Mandal
- LMU München: Ludwig-Maximilians-Universitat Munchen, Pharmacy, GERMANY
| | - Lars Allmendinger
- LMU München: Ludwig-Maximilians-Universitat Munchen, Pharmacy, GERMANY
| | - Ivan Huc
- Ludwig-Maximilians-Universitat Munchen, Pharmacy, Butenandtstraße 5 - 13, 81377, Munich, GERMANY
| |
Collapse
|
9
|
Bindl D, Mandal PK, Allmendinger L, Huc I. Discrete Stacked Dimers of Aromatic Oligoamide Helices. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202116509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Daniel Bindl
- LMU München: Ludwig-Maximilians-Universitat Munchen Pharmacy GERMANY
| | - Pradeep K. Mandal
- LMU München: Ludwig-Maximilians-Universitat Munchen Pharmacy GERMANY
| | - Lars Allmendinger
- LMU München: Ludwig-Maximilians-Universitat Munchen Pharmacy GERMANY
| | - Ivan Huc
- Ludwig-Maximilians-Universitat Munchen Pharmacy Butenandtstraße 5 - 13 81377 Munich GERMANY
| |
Collapse
|
10
|
Rhys GG, Dawson WM, Beesley JL, Martin FJO, Brady RL, Thomson AR, Woolfson DN. How Coiled-Coil Assemblies Accommodate Multiple Aromatic Residues. Biomacromolecules 2021; 22:2010-2019. [PMID: 33881308 DOI: 10.1021/acs.biomac.1c00131] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Rational protein design requires understanding the contribution of each amino acid to a targeted protein fold. For a subset of protein structures, namely, α-helical coiled coils (CCs), knowledge is sufficiently advanced to allow the rational de novo design of many structures, including entirely new protein folds. Current CC design rules center on using aliphatic hydrophobic residues predominantly to drive the folding and assembly of amphipathic α helices. The consequences of using aromatic residues-which would be useful for introducing structural probes, and binding and catalytic functionalities-into these interfaces are not understood. There are specific examples of designed CCs containing such aromatic residues, e.g., phenylalanine-rich sequences, and the use of polar aromatic residues to make buried hydrogen-bond networks. However, it is not known generally if sequences rich in tyrosine can form CCs, or what CC assemblies these would lead to. Here, we explore tyrosine-rich sequences in a general CC-forming background and resolve new CC structures. In one of these, an antiparallel tetramer, the tyrosine residues are solvent accessible and pack at the interface between the core and the surface. In another more complex structure, the residues are buried and form an extended hydrogen-bond network.
Collapse
Affiliation(s)
- Guto G Rhys
- School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, United Kingdom.,Department of Biochemistry, University of Bayreuth, Universitätsstraße 30, 95447 Bayreuth, Germany
| | - William M Dawson
- School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, United Kingdom
| | - Joseph L Beesley
- School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, United Kingdom
| | - Freddie J O Martin
- School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, United Kingdom
| | - R Leo Brady
- School of Biochemistry, University of Bristol, Medical Sciences Building, University Walk, Bristol BS8 1TD, United Kingdom
| | - Andrew R Thomson
- School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, United Kingdom.,School of Chemistry, University of Glasgow, Glasgow G12 8QQ, United Kingdom
| | - Derek N Woolfson
- School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, United Kingdom.,School of Biochemistry, University of Bristol, Medical Sciences Building, University Walk, Bristol BS8 1TD, United Kingdom.,Bristol BioDesign Institute, University of Bristol, Life Sciences Building, Tyndall Avenue, Bristol BS8 1TQ, United Kingdom
| |
Collapse
|
11
|
Zheng L, Guo S, Wang C, Wang Y, Fan Y, Chen X, Zhang K, Jiang H. Distance-Dependent Chiral Communication between Two Quinoline Oligoamide Foldamers Connected by Alkyl Chains. Chempluschem 2021; 86:340-346. [PMID: 33624952 DOI: 10.1002/cplu.202000824] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 02/13/2021] [Indexed: 11/09/2022]
Abstract
A series of macrocycles that contain two quinoline oligoamide foldamers (QOFs) using various length of alkyl chains as linkers (2, 3, 6, 8 or 12 hydrocarbons) were synthesized. The two QOFs interact with each other through the linkers and the intramolecular helix chiral communications between the two QOFs were studied by 1 H NMR spectroscopy and crystal structures. Investigations show that the intensity of the intramolecular helix chiral communications between the two QOFs is dependent on the length of the linkers, and the interaction between the two QOFs increases with decreasing length of the linkers. When the length of the linkers decreased to C2 linkers, only one conformer is present in solution. Moreover, increasing the length of the foldamers would enhance the intramolecular helix chiral communication if the linkers are short, indicating that the length of the foldamers also has significant impact on intramolecular helix chiral communication.
Collapse
Affiliation(s)
- Lu Zheng
- School of Biotechnology and Health Sciences, Wuyi University, Jiangmen, 529020, P. R. China.,International Healthcare Innovation Institute (Jiangmen), Jiangmen, 529040, P. R. China.,School of Pharmacy, Jiangsu Ocean University, Lianyungang, 222005, P. R. China
| | - Shengzhu Guo
- School of Biotechnology and Health Sciences, Wuyi University, Jiangmen, 529020, P. R. China.,International Healthcare Innovation Institute (Jiangmen), Jiangmen, 529040, P. R. China
| | - Chu Wang
- College of Chemistry, Beijing Normal University, Beijing, 100875, P. R. China
| | - Yanru Wang
- College of Chemistry, Beijing Normal University, Beijing, 100875, P. R. China
| | - Yanqing Fan
- College of Chemistry, Beijing Normal University, Beijing, 100875, P. R. China
| | - Xuebo Chen
- College of Chemistry, Beijing Normal University, Beijing, 100875, P. R. China
| | - Kun Zhang
- School of Biotechnology and Health Sciences, Wuyi University, Jiangmen, 529020, P. R. China.,International Healthcare Innovation Institute (Jiangmen), Jiangmen, 529040, P. R. China
| | - Hua Jiang
- School of Biotechnology and Health Sciences, Wuyi University, Jiangmen, 529020, P. R. China.,International Healthcare Innovation Institute (Jiangmen), Jiangmen, 529040, P. R. China.,College of Chemistry, Beijing Normal University, Beijing, 100875, P. R. China
| |
Collapse
|
12
|
Song Y, Schaufelberger F, Ashbridge Z, Pirvu L, Vitorica-Yrezabal IJ, Leigh DA. Effects of turn-structure on folding and entanglement in artificial molecular overhand knots. Chem Sci 2020; 12:1826-1833. [PMID: 34163946 PMCID: PMC8179330 DOI: 10.1039/d0sc05897a] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
The length and constitution of spacers linking three 2,6-pyridinedicarboxamide units in a molecular strand influence the tightness of the resulting overhand (open-trefoil) knot that the strand folds into in the presence of lanthanide(iii) ions. The use of β-hairpin forming motifs as linkers enables a metal-coordinated pseudopeptide with a knotted tertiary structure to be generated. The resulting pseudopeptide knot has one of the highest backbone-to-crossing ratios (BCR)—a measure of knot tightness (a high value corresponding to looseness)—for a synthetic molecular knot to date. Preorganization in the crossing-free turn section of the knot affects aromatic stacking interactions close to the crossing region. The metal-coordinated pseudopeptide knot is compared to overhand knots with other linkers of varying tightness and turn preorganization, and the entangled architectures characterized by NMR spectroscopy, ESI-MS, CD spectroscopy and, in one case, X-ray crystallography. The results show how it is possible to program specific conformational properties into different key regions of synthetic molecular knots, opening the way to systems where knotting can be systematically incorporated into peptide-like chains through design. Spacers linking 2,6-pyridinedicarboxamide units influence the tightness of the corresponding lanthanide-coordinated overhand knot. β-Hairpin forming motifs generate a metal-coordinated pseudopeptide with a knotted tertiary structure.![]()
Collapse
Affiliation(s)
- Yiwei Song
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University Shanghai 200062 PR China
| | | | - Zoe Ashbridge
- Department of Chemistry, University of Manchester Oxford Road Manchester M13 9PL UK
| | - Lucian Pirvu
- Department of Chemistry, University of Manchester Oxford Road Manchester M13 9PL UK
| | | | - David A Leigh
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University Shanghai 200062 PR China .,Department of Chemistry, University of Manchester Oxford Road Manchester M13 9PL UK
| |
Collapse
|
13
|
Kirinda VC, Schrage BR, Ziegler CJ, Hartley CS. ortho
‐Phenylene‐Based Macrocyclic Hydrocarbons Assembled Using Olefin Metathesis. European J Org Chem 2020. [DOI: 10.1002/ejoc.202000950] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Viraj C. Kirinda
- Department of Chemistry & Biochemistry Miami University 45056 Oxford OH USA
| | | | | | - C. Scott Hartley
- Department of Chemistry & Biochemistry Miami University 45056 Oxford OH USA
| |
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
|
Mazzier D, De S, Wicher B, Maurizot V, Huc I. Parallele homochirale und antiparallele heterochirale Wasserstoffbrücken‐Interaktionsflächen in multihelikalen abiotischen Foldameren. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201912805] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Daniela Mazzier
- Department of Pharmacy and Centre for Integrated Protein Science Ludwig-Maximilians-Universität Butenandtstraße 5–13 81377 Munich Deutschland
- CBMN Laboratory Université de Bordeaux CNRS, IPB Institut Européen de Chimie et Biologie 2 rue Escarpit 33600 Pessac Frankreich
| | - Soumen De
- CBMN Laboratory Université de Bordeaux CNRS, IPB Institut Européen de Chimie et Biologie 2 rue Escarpit 33600 Pessac Frankreich
| | - Barbara Wicher
- Department of Chemical Technology of Drugs Poznan University of Medical Sciences Grunwaldzka 6 60–780 Poznan Polen
| | - Victor Maurizot
- CBMN Laboratory Université de Bordeaux CNRS, IPB Institut Européen de Chimie et Biologie 2 rue Escarpit 33600 Pessac Frankreich
| | - Ivan Huc
- Department of Pharmacy and Centre for Integrated Protein Science Ludwig-Maximilians-Universität Butenandtstraße 5–13 81377 Munich Deutschland
- CBMN Laboratory Université de Bordeaux CNRS, IPB Institut Européen de Chimie et Biologie 2 rue Escarpit 33600 Pessac Frankreich
| |
Collapse
|
16
|
Mazzier D, De S, Wicher B, Maurizot V, Huc I. Parallel Homochiral and Anti-Parallel Heterochiral Hydrogen-Bonding Interfaces in Multi-Helical Abiotic Foldamers. Angew Chem Int Ed Engl 2020; 59:1606-1610. [PMID: 31671236 PMCID: PMC7004161 DOI: 10.1002/anie.201912805] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Indexed: 11/25/2022]
Abstract
A hydrogen-bonding interface between helical aromatic oligoamide foldamers has been designed to promote the folding of a helix-turn-helix motif with a head-to-tail arrangement of two helices of opposite handedness. This design complements an earlier helix-turn-helix motif with a head-to-head arrangement of two helices of identical handedness interface. The two motifs were shown to have comparable stability and were combined in a unimolecular tetra-helix fold constituting the largest abiotic tertiary structure to date.
Collapse
Affiliation(s)
- Daniela Mazzier
- Department of Pharmacy and Centre for Integrated Protein ScienceLudwig-Maximilians-UniversitätButenandtstrasse 5–1381377MunichGermany
- CBMN LaboratoryUniversité de BordeauxCNRS, IPBInstitut Européen de Chimie et Biologie2 rue Escarpit33600PessacFrance
| | - Soumen De
- CBMN LaboratoryUniversité de BordeauxCNRS, IPBInstitut Européen de Chimie et Biologie2 rue Escarpit33600PessacFrance
| | - Barbara Wicher
- Department of Chemical Technology of DrugsPoznan University of Medical SciencesGrunwaldzka 660–780PoznanPoland
| | - Victor Maurizot
- CBMN LaboratoryUniversité de BordeauxCNRS, IPBInstitut Européen de Chimie et Biologie2 rue Escarpit33600PessacFrance
| | - Ivan Huc
- Department of Pharmacy and Centre for Integrated Protein ScienceLudwig-Maximilians-UniversitätButenandtstrasse 5–1381377MunichGermany
- CBMN LaboratoryUniversité de BordeauxCNRS, IPBInstitut Européen de Chimie et Biologie2 rue Escarpit33600PessacFrance
| |
Collapse
|
17
|
Pavlović RZ, Border SE, Finnegan TJ, Zhiquan L, Gunther MJ, Mu̅noz E, Moore CE, Hadad CM, Badjić JD. Twist–Turn–Twist Motif Chaperoned Inside Molecular Baskets. J Am Chem Soc 2019; 141:16600-16604. [PMID: 31592662 DOI: 10.1021/jacs.9b09003] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Radoslav Z. Pavlović
- Department of Chemistry & Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Sarah E. Border
- Department of Chemistry & Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Tyler J. Finnegan
- Department of Chemistry & Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Lei Zhiquan
- Department of Chemistry & Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Michael J. Gunther
- Department of Chemistry & Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Eva Mu̅noz
- Affinimeter, Edificio Emprendia, Campus Vida, Santiago de Compostela, Spain
| | - Curtis E. Moore
- Department of Chemistry & Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Christopher M. Hadad
- Department of Chemistry & Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| | - Jovica D. Badjić
- Department of Chemistry & Biochemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, United States
| |
Collapse
|