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Koshti B, Kshtriya V, Naskar S, Narode H, Gour N. Controlled aggregation properties of single amino acids modified with protecting groups. NEW J CHEM 2022. [DOI: 10.1039/d1nj05172e] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The self-assembling properties of single amino acids modified with protecting groups under controlled conditions of temperature and concentration are illustrated.
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Affiliation(s)
- Bharti Koshti
- Department of Chemistry, Indrashil University, Kadi, Mehsana, Gujarat, India
| | - Vivekshinh Kshtriya
- Department of Chemistry, Indrashil University, Kadi, Mehsana, Gujarat, India
| | - Soumick Naskar
- Department of Chemistry, Indrashil University, Kadi, Mehsana, Gujarat, India
| | - Hanuman Narode
- Department of Chemistry, Indrashil University, Kadi, Mehsana, Gujarat, India
| | - Nidhi Gour
- Department of Chemistry, Indrashil University, Kadi, Mehsana, Gujarat, India
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Koshti B, Kshtriya V, Nardin C, Gour N. Chemical Perspective of the Mechanism of Action of Antiamyloidogenic Compounds Using a Minimalistic Peptide as a Reductionist Model. ACS Chem Neurosci 2021; 12:2851-2864. [PMID: 34264635 DOI: 10.1021/acschemneuro.1c00221] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The diphenylalanine (FF) residue which is present at the 19 and 20 positions of the amyloid beta (1-42) (Aβ42) peptide sequence is considered as a reductionist model for studying Aβ42 aggregation. FF self-assembles into well-ordered tubular structures via aromatic π-π stacking. Herein the manuscript, we have presented a chemical perspective on the mechanism of action of antiamyloid compounds by assessing their interaction with FF. Therefore, we first coincubated FF fibers with single amino acids, since they are constituted of different R side chains yet have a common structural unit. This study revealed a crucial role of aromatic rings and functional groups like thiol (-SH) in causing destabilization of FF assembly via their interaction with π-electrons participating in π-π stacking present in FF. We further studied the interaction of different nonsteroidal anti-inflammatory drugs (NSAIDs), other known antiamyloidogenic compounds, and host-guest inclusion compounds like cyclodextrin (CD) to assess their mechanism of action and to decipher the functional moiety present in these compounds which could cause destabilization of π-π stacking. From the coincubation experiments, we could surmise a crucial role of aromatic rings present in these compounds for causing interference in aromatic stacking. We further consolidated our observations through microscopy analysis by various spectroscopic methods such as aggregation-induced emission enhancement (AIEE), fluorescence spectroscopy, solution-state 1H NMR, FTIR, and circular dichroism. The studies presented in the manuscript thus provide significant insights into the role of functional groups in imparting antiamyloid action and open new avenues for an efficient design of antiamyloid drugs in the future.
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Affiliation(s)
- Bharti Koshti
- Department of Chemistry, School of Science, Indrashil University, Kadi, Mehsana, Gujarat 382740, India
| | - Vivekshinh Kshtriya
- Department of Chemistry, School of Science, Indrashil University, Kadi, Mehsana, Gujarat 382740, India
| | - Corinne Nardin
- Universite de Pau et des Pays de l’Adour, E2S UPPA, CNRS, IPREM, Pau 64053, France
| | - Nidhi Gour
- Department of Chemistry, School of Science, Indrashil University, Kadi, Mehsana, Gujarat 382740, India
- Department of Medicinal Chemistry, Indian Institute of Advanced Research, Gandhinagar, Gujarat 382426, India
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Kshtriya V, Koshti B, Pandey DK, Kharbanda S, Kanth P C, Singh DK, Bhatia D, Gour N. Sequential and cellular detection of copper and lactic acid by disaggregation and reaggregation of the fluorescent panchromatic fibres of an acylthiourea based sensor. SOFT MATTER 2021; 17:4304-4316. [PMID: 33908562 DOI: 10.1039/d1sm00038a] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
We report, for the first time, the self-assembly of an acyl-thiourea based sensor, N-{(6-methoxy-pyridine-2-yl) carbamothioyl}benzamide (NG1), with panchromatic fluorescent fibres and its dual-sensing properties for the sequential detection of Cu2+ ions and lactic acid. The panchromatic fibres formed by NG1 were disrupted in the presence of Cu2+ ions and this was accompanied by a visible colour change in the solution from colourless to yellow. The addition of lactic acid to the NG1 + Cu2+ solution, on the other hand, induced re-aggregation to fibrillar structures and the colour of the solution again changed to colourless. Hence, it may be surmised that the disaggregation and re-aggregation impart unique dual-sensing properties to NG1 for the sequential detection of Cu2+ ions and lactic acid. The application of NG1 as a selective sensor for Cu2+ ions and lactic acid has been assessed in detail by UV-visible and fluorescence spectroscopy. Furthermore, two structural variants of NG1, namely, NG2 and NG3, were synthesized, which suggest the crucial role of pyridine in imparting panchromatic emission properties and of both pyridine and acyl-thiourea side chain in the binding of Cu2+ ions. The O-methoxy group plays an important part in making NG1 the most sensitive probe of its structural analogs. Finally, the utility of NG1 for the sequential and cellular detection of Cu2+ ions and lactic acid was studied in human RPE cells. The experimental results of the interaction of NG1 with Cu2+ ions and lactic acid have also been validated theoretically by using quantum chemical calculations based on density functional theory (DFT). To the best of our knowledge, this is the first report wherein a dual sensor for Cu2+ ions and lactate ions is synthesized. More importantly, the aggregation properties of the sensor have been studied extensively and an interesting correlation of the photophysical properties of the probe with its self-assembling behavior has been elucidated.
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Affiliation(s)
- Vivekshinh Kshtriya
- Department of Chemistry, Indrashil University, Kadi, Mehsana, Gujarat 382740, India.
| | - Bharti Koshti
- Department of Chemistry, Indrashil University, Kadi, Mehsana, Gujarat 382740, India.
| | - Deepak K Pandey
- Department of Basic Sciences, Institute of Infrastructure Technology Research and Management, Ahmedabad, 380026, India
| | - Sumit Kharbanda
- Biological Engineering Discipline and Center for Biomedical Research, Indian Institute of Technology Gandhinagar, Palaj 382355, Gandhinagar, India
| | - Chandra Kanth P
- Department of Science, School of Technology, Pandit Deendayal Petroleum University, Gandhinagar, Gujarat, India
| | - Dheeraj K Singh
- Department of Basic Sciences, Institute of Infrastructure Technology Research and Management, Ahmedabad, 380026, India
| | - Dhiraj Bhatia
- Biological Engineering Discipline and Center for Biomedical Research, Indian Institute of Technology Gandhinagar, Palaj 382355, Gandhinagar, India
| | - Nidhi Gour
- Department of Chemistry, Indrashil University, Kadi, Mehsana, Gujarat 382740, India.
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Vangala M, Yousf S, Chugh J, Hotha S. Solid‐Phase Synthesis of Clickable Psicofuranose Glycocarbamates and Application of Their Self‐Assembled Nanovesicles for Curcumin Encapsulation. ChemistrySelect 2020. [DOI: 10.1002/slct.201904430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Madhuri Vangala
- Department of ChemistryIndian Institute of Science Education and Research Pune 411008 India
| | - Saleem Yousf
- Department of ChemistryIndian Institute of Science Education and Research Pune 411008 India
| | - Jeetender Chugh
- Department of ChemistryIndian Institute of Science Education and Research Pune 411008 India
| | - Srinivas Hotha
- Department of ChemistryIndian Institute of Science Education and Research Pune 411008 India
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Delbianco M, Bharate P, Varela-Aramburu S, Seeberger PH. Carbohydrates in Supramolecular Chemistry. Chem Rev 2015; 116:1693-752. [PMID: 26702928 DOI: 10.1021/acs.chemrev.5b00516] [Citation(s) in RCA: 191] [Impact Index Per Article: 21.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Carbohydrates are involved in a variety of biological processes. The ability of sugars to form a large number of hydrogen bonds has made them important components for supramolecular chemistry. We discuss recent advances in the use of carbohydrates in supramolecular chemistry and reveal that carbohydrates are useful building blocks for the stabilization of complex architectures. Systems are presented according to the scaffold that supports the glyco-conjugate: organic macrocycles, dendrimers, nanomaterials, and polymers are considered. Glyco-conjugates can form host-guest complexes, and can self-assemble by using carbohydrate-carbohydrate interactions and other weak interactions such as π-π interactions. Finally, complex supramolecular architectures based on carbohydrate-protein interactions are discussed.
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Affiliation(s)
- Martina Delbianco
- Department of Biomolecular Systems, Max-Planck-Institute of Colloids and Interfaces , Am Mühlenberg 1, 14476 Potsdam, Germany
| | - Priya Bharate
- Department of Biomolecular Systems, Max-Planck-Institute of Colloids and Interfaces , Am Mühlenberg 1, 14476 Potsdam, Germany.,Institute of Chemistry and Biochemistry, Freie Universität Berlin , Arnimallee 22, 14195 Berlin, Germany
| | - Silvia Varela-Aramburu
- Department of Biomolecular Systems, Max-Planck-Institute of Colloids and Interfaces , Am Mühlenberg 1, 14476 Potsdam, Germany.,Institute of Chemistry and Biochemistry, Freie Universität Berlin , Arnimallee 22, 14195 Berlin, Germany
| | - Peter H Seeberger
- Department of Biomolecular Systems, Max-Planck-Institute of Colloids and Interfaces , Am Mühlenberg 1, 14476 Potsdam, Germany.,Institute of Chemistry and Biochemistry, Freie Universität Berlin , Arnimallee 22, 14195 Berlin, Germany
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Kočar V, Božič Abram S, Doles T, Bašić N, Gradišar H, Pisanski T, Jerala R. TOPOFOLD, the designed modular biomolecular folds: polypeptide-based molecular origami nanostructures following the footsteps of DNA. WILEY INTERDISCIPLINARY REVIEWS-NANOMEDICINE AND NANOBIOTECHNOLOGY 2014; 7:218-37. [PMID: 25196147 DOI: 10.1002/wnan.1289] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2014] [Revised: 07/08/2014] [Accepted: 07/20/2014] [Indexed: 12/14/2022]
Abstract
Biopolymers, the essential components of life, are able to form many complex nanostructures, and proteins in particular are the material of choice for most cellular processes. Owing to numerous cooperative interactions, rational design of new protein folds remains extremely challenging. An alternative strategy is to design topofolds-nanostructures built from polypeptide arrays of interacting modules that define their topology. Over the course of the last several decades DNA has successfully been repurposed from its native role of information storage to a smart nanomaterial used for nanostructure self-assembly of almost any shape, which is largely because of its programmable nature. Unfortunately, polypeptides do not possess the straightforward complementarity as do nucleic acids. However, a modular approach can nevertheless be used to assemble polypeptide nanostructures, as was recently demonstrated on a single-chain polypeptide tetrahedron. This review focuses on the current state-of-the-art in the field of topological polypeptide folds. It starts with a brief overview of the field of structural DNA and RNA nanotechnology, from which it draws parallels and possible directions of development for the emerging field of polypeptide-based nanotechnology. The principles of topofold strategy and unique properties of such polypeptide nanostructures in comparison to native protein folds are discussed. Reasons for the apparent absence of such folds in nature are also examined. Physicochemical versatility of amino acid residues and cost-effective production makes polypeptides an attractive platform for designed functional bionanomaterials.
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Affiliation(s)
- Vid Kočar
- Department of Biotechnology, National Institute of Chemistry, Ljubljana, Slovenia
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Gradišar H, Jerala R. Self-assembled bionanostructures: proteins following the lead of DNA nanostructures. J Nanobiotechnology 2014; 12:4. [PMID: 24491139 PMCID: PMC3938474 DOI: 10.1186/1477-3155-12-4] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2013] [Accepted: 01/29/2014] [Indexed: 01/02/2023] Open
Abstract
Natural polymers are able to self-assemble into versatile nanostructures based on the information encoded into their primary structure. The structural richness of biopolymer-based nanostructures depends on the information content of building blocks and the available biological machinery to assemble and decode polymers with a defined sequence. Natural polypeptides comprise 20 amino acids with very different properties in comparison to only 4 structurally similar nucleotides, building elements of nucleic acids. Nevertheless the ease of synthesizing polynucleotides with selected sequence and the ability to encode the nanostructural assembly based on the two specific nucleotide pairs underlay the development of techniques to self-assemble almost any selected three-dimensional nanostructure from polynucleotides. Despite more complex design rules, peptides were successfully used to assemble symmetric nanostructures, such as fibrils and spheres. While earlier designed protein-based nanostructures used linked natural oligomerizing domains, recent design of new oligomerizing interaction surfaces and introduction of the platform for topologically designed protein fold may enable polypeptide-based design to follow the track of DNA nanostructures. The advantages of protein-based nanostructures, such as the functional versatility and cost effective and sustainable production methods provide strong incentive for further development in this direction.
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Affiliation(s)
- Helena Gradišar
- Department of Biotechnology, National Institute of Chemistry, Ljubljana, Slovenia
- Excellent NMR – Future Innovation for Sustainable Technologies, Centre of Excellence, Ljubljana, Slovenia
| | - Roman Jerala
- Department of Biotechnology, National Institute of Chemistry, Ljubljana, Slovenia
- Excellent NMR – Future Innovation for Sustainable Technologies, Centre of Excellence, Ljubljana, Slovenia
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Barman AK, Verma S. Solid state structures and solution phase self-assembly of clicked mannosylated diketopiperazines. RSC Adv 2013. [DOI: 10.1039/c3ra42310g] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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Gour N, Kedracki D, Safir I, Ngo KX, Vebert-Nardin C. Self-assembling DNA-peptide hybrids: morphological consequences of oligonucleotide grafting to a pathogenic amyloid fibrils forming dipeptide. Chem Commun (Camb) 2012; 48:5440-2. [PMID: 22534735 DOI: 10.1039/c2cc31458d] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
For the very first time, highly efficient synthesis of DNA-peptide hybrids to scaffold self-assembled nanostructures is described. Oligonucleotide conjugation to the diphenylalanine dipeptide triggers a morphological transition from fibrillar to vesicular structures which may potentially be used as delivery vehicles, since they exhibit pH triggered release.
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Affiliation(s)
- Nidhi Gour
- Department of Inorganic and Analytical Chemistry, University of Geneva, Sciences II, 30, quai Ernest-Ansermet, CH-1211 Geneva 4, Switzerland
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