1
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Aguilar MI, Yarovsky I. Quest for New Generation Biocompatible Materials: Tailoring β-Peptide Structure and Interactions via Synergy of Experiments and Modelling. J Mol Biol 2024:168646. [PMID: 38848868 DOI: 10.1016/j.jmb.2024.168646] [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: 04/10/2024] [Revised: 06/03/2024] [Accepted: 06/03/2024] [Indexed: 06/09/2024]
Abstract
Peptide-based self-assembly has been used to produce a wide range of nanostructures. While most of these systems involve self-assembly of α-peptides, more recently β-peptides have also been shown to undergo supramolecular self-assembly, and have been used to produce materials for applications in tissue engineering, cell culture and drug delivery. In order to engineer new materials with specific structure and function, theoretical molecular modelling can provide significant insights into the collective balance of non-covalent interactions that drive the self-assembly and determine the structure of the resultant supramolecular materials under different conditions. However, this approach has only recently become feasible for peptide-based self-assembled nanomaterials, particularly those that incorporate non α-amino acids. This perspective provides an overview of the challenges associated with computational modelling of the self-assembly of β-peptides and the recent success using a combination of experimental and computational techniques to provide insights into the self-assembly mechanisms and fully atomistic models of these new biocompatible materials.
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Affiliation(s)
- Marie-Isabel Aguilar
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia.
| | - Irene Yarovsky
- School of Engineering, RMIT University, Melbourne, Victoria 3001, Australia.
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2
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Mondal A, Ahmad M, Mondal D, Talukdar P. Progress and prospects toward supramolecular bioactive ion transporters. Chem Commun (Camb) 2023; 59:1917-1938. [PMID: 36691926 DOI: 10.1039/d2cc06761g] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The majority of cellular physiological processes depend on natural ion channels, which are pore-forming membrane-embedded proteins that let ions flow across the cell membranes selectively. This selective movement of ions across the membranes balances the osmolality within and outside the cell. However, mutations in the genes that encode essential membrane transport proteins or structural reorganisation of these proteins can cause life-threatening diseases like cystic fibrosis. Artificial ion transport systems have opened up a way to replace dysfunctional natural ion channels to cure such diseases through channel replacement therapy. Moreover, recent research has also demonstrated the ability of these systems to kill cancer cells, reigniting interest in the field among scientists. Our contributions to the recent progress in the design and development of artificial chloride ion transporters and their effect on biological systems have been discussed in this review. This review would provide current vistas and future directions toward the development of novel ion transporters with improved biocompatibility and desired anti-cancer properties. Additionally, it strongly emphasises stimuli-responsive ion transport systems, which are crucial for obtaining target-specificity and may speed up the application of these systems in clinical therapeutics.
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Affiliation(s)
- Abhishek Mondal
- Chemistry Department, Indian Institute of Science Education and Research Pune, Dr. Homi Bhabha Road, Pashan, Pune 411008, Maharashtra, India.
| | - Manzoor Ahmad
- Chemistry Department, Indian Institute of Science Education and Research Pune, Dr. Homi Bhabha Road, Pashan, Pune 411008, Maharashtra, India. .,Chemistry Research Laboratory, Mansfield Road, Oxford, OX1 3TA, UK
| | - Debashis Mondal
- Chemistry Department, Indian Institute of Science Education and Research Pune, Dr. Homi Bhabha Road, Pashan, Pune 411008, Maharashtra, India. .,Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Zwirkii Wigury 101, Warsaw 02-089, Poland
| | - Pinaki Talukdar
- Chemistry Department, Indian Institute of Science Education and Research Pune, Dr. Homi Bhabha Road, Pashan, Pune 411008, Maharashtra, India.
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3
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Kubik S. Synthetic Receptors Based on Abiotic Cyclo(pseudo)peptides. Molecules 2022; 27:2821. [PMID: 35566168 PMCID: PMC9103335 DOI: 10.3390/molecules27092821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 04/26/2022] [Accepted: 04/27/2022] [Indexed: 11/17/2022] Open
Abstract
Work on the use of cyclic peptides or pseudopeptides as synthetic receptors started even before the field of supramolecular chemistry was firmly established. Research initially focused on the development of synthetic ionophores and involved the use of macrocycles with a repeating sequence of subunits along the ring to facilitate the correlation between structure, conformation, and binding properties. Later, nonnatural amino acids as building blocks were also considered. With growing research in this area, cyclopeptides and related macrocycles developed into an important and structurally diverse receptor family. This review provides an overview of these developments, starting from the early years. The presented systems are classified according to characteristic structural elements present along the ring. Wherever possible, structural aspects are correlated with binding properties to illustrate how natural or nonnatural amino acids affect binding properties.
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Affiliation(s)
- Stefan Kubik
- Fachbereich Chemie-Organische Chemie, Technische Universität Kaiserslautern, Erwin-Schrödinger-Str. 54, 67663 Kaiserslautern, Germany
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4
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Wu F, Li X, Jia H, Han X, Shen X. Iodine(III)-Promoted Oxidative Cross-Coupling Reactions of C—H Bonds via a Free Radical Process. CHINESE J ORG CHEM 2022. [DOI: 10.6023/cjoc202109012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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5
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Iodine(III) promotes cross-dehydrogenative coupling of N-hydroxyphthalimide and unactivated C(sp 3)-H bonds. Commun Chem 2021; 4:46. [PMID: 36697770 PMCID: PMC9814821 DOI: 10.1038/s42004-021-00480-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 02/26/2021] [Indexed: 01/28/2023] Open
Abstract
Cross-dehydrogenative coupling reactions provide a method to construct new chemical bonds by direct C-H activation without any pre-functionalization. Compared to functionalization of a C-H bond α- to ether oxygen, α- to carbonyl, or at a benzylic position, functionalization of unactivated hydrocarbons is difficult and often requires high temperatures, a transition-metal catalyst, or a superstoichiometric quantity of volatile, toxic, and explosive tert-butylhydroperoxide. Here, a cross-dehydrogenative C-O coupling reaction of N-hydroxyphthalimide with unactivated alkanes, nitriles, ethers, and thioethers has been realized by using iodobenzene diacetate as the radical initiator. The current protocol enables efficient functionalization of unactivated hydrocarbons and nitriles through inert C(sp3)-H bond activation under mild reaction conditions. O-substituted NHPI derivatives are generated in good yields under metal-free conditions.
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6
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Kulsi G, Sannigrahi A, Mishra S, Das Saha K, Datta S, Chattopadhyay P, Chattopadhyay K. A Novel Cyclic Mobile Transporter Can Induce Apoptosis by Facilitating Chloride Anion Transport into Cells. ACS OMEGA 2020; 5:16395-16405. [PMID: 32685802 PMCID: PMC7364434 DOI: 10.1021/acsomega.0c00438] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 06/03/2020] [Indexed: 06/11/2023]
Abstract
We report here the preparation of an aminoxy amide-based pseudopeptide-derived building block using furanoid sugar molecules. Through the cyclo-oligomerization reaction, we generate a hybrid triazole/aminoxy amide macrocycle using the as-prepared building block. The novel conformation of the macrocycle has been characterized using NMR and molecular modeling studies, which show a strong resemblance of our synthesized compound to d-,l-α-aminoxy acid-based cyclic peptides that contain uniform backbone chirality. We observe that the macrocycle can efficiently and selectively bind Cl- ion and transport Cl- ion across a lipid bilayer. 1H NMR anion binding studies suggest a coherent relationship between the acidity of aminoxy amide N-H and triazole C-H proton binding strength. Using time-based fluorescence assay, we show that the macrocycle acts as a mobile transporter and follows an antiport mechanism. Our synthesized macrocycle imposes cancer cell death by disrupting ionic homeostasis through Cl- ion transport. The macrocycle induced cytochrome c leakage and changes in mitochondrial membrane potential along with activation of family of caspases, suggesting that the cellular apoptosis occurs through a caspase-dependent intrinsic pathway. The present results suggest the possibility of using the macrocycle as a biological tool of high therapeutic value.
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Affiliation(s)
- Goutam Kulsi
- Structural
Biology and Bioinformatics Division, CSIR-
Indian Institute of Chemical Biology (IICB), Kolkata 700032, India
- Organic
and Medicinal Chemistry Division, CSIR-
Indian Institute of Chemical Biology (IICB), Kolkata 700032, India
| | - Achinta Sannigrahi
- Structural
Biology and Bioinformatics Division, CSIR-
Indian Institute of Chemical Biology (IICB), Kolkata 700032, India
| | - Snehasis Mishra
- Cancer
Biology and Inflammatory Disorder Division, CSIR- Indian Institute of Chemical Biology (IICB), Kolkata 700032, India
- Department
of Chemical Technology, University of Calcutta, Kolkata 700009, India
| | - Krishna Das Saha
- Cancer
Biology and Inflammatory Disorder Division, CSIR- Indian Institute of Chemical Biology (IICB), Kolkata 700032, India
| | - Sriparna Datta
- Department
of Chemical Technology, University of Calcutta, Kolkata 700009, India
| | - Partha Chattopadhyay
- Organic
and Medicinal Chemistry Division, CSIR-
Indian Institute of Chemical Biology (IICB), Kolkata 700032, India
| | - Krishnananda Chattopadhyay
- Structural
Biology and Bioinformatics Division, CSIR-
Indian Institute of Chemical Biology (IICB), Kolkata 700032, India
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7
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Vidović N, Horvat G, Riva D, Rinkovec T, Cindro N, Tomišić V, Speranza G. Chloride-Assisted Peptide Macrocyclization. Org Lett 2020; 22:2129-2134. [PMID: 32154727 DOI: 10.1021/acs.orglett.0c00036] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The role of the Cl- anion as a templating agent for the synthesis of cyclopeptides was assessed through the preparation of three new homocyclolysines and other six cyclic peptides by head-to-tail lactamization. Isolated yields of products obtained by chloride-templating approach were considerably higher than those gained by a cation-promoted procedure, whereby, in some cases, only the anion-assisted synthesis yielded the desired cyclopeptides.
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Affiliation(s)
- Nikolina Vidović
- Dipartimento di Chimica, Università degli Studi di Milano, via C. Golgi, 19, 20133 Milano, Italy
| | - Gordan Horvat
- Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, 10000 Zagreb, Croatia
| | - Davide Riva
- Dipartimento di Chimica, Università degli Studi di Milano, via C. Golgi, 19, 20133 Milano, Italy
| | - Tamara Rinkovec
- Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, 10000 Zagreb, Croatia
| | - Nikola Cindro
- Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, 10000 Zagreb, Croatia
| | - Vladislav Tomišić
- Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, 10000 Zagreb, Croatia
| | - Giovanna Speranza
- Dipartimento di Chimica, Università degli Studi di Milano, via C. Golgi, 19, 20133 Milano, Italy
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8
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Krylov IB, Lopat'eva ER, Budnikov AS, Nikishin GI, Terent'ev AO. Metal-Free Cross-Dehydrogenative C-O Coupling of Carbonyl Compounds with N-Hydroxyimides: Unexpected Selective Behavior of Highly Reactive Free Radicals at an Elevated Temperature. J Org Chem 2020; 85:1935-1947. [PMID: 31886660 DOI: 10.1021/acs.joc.9b02656] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Cross-dehydrogenative C-O coupling of N-hydroxyimides with ketones, esters, and carboxylic acids was achieved employing the di-tert-butyl peroxide as a source of free radicals and a dehydrogenating agent. The proposed method is experimentally simple and demonstrates the outstanding efficiency for the challenging CH substrates, such as unactivated esters and carboxylic acids. It was shown that N-hydroxyphthalimide drastically affects the oxidative properties of t-BuOOt-Bu by intercepting the t-BuO• radicals with the formation of phthalimide-N-oxyl radicals, a species responsible for both hydrogen atom abstraction from the CH reagent and the selective formation of the C-O coupling product by selective radical cross-recombination. The practical applicability of the developed method was exemplified by the single-stage synthesis of commercial reagent (known as Baran aminating reagent precursor) from isobutyric acid and N-hydroxysuccinimide, whereas in the standard synthetic approach, four stages are necessary.
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Affiliation(s)
- Igor B Krylov
- N. D. Zelinsky Institute of Organic Chemistry of the Russian Academy of Sciences , 47 Leninsky prosp ., 119991 Moscow , Russian Federation
| | - Elena R Lopat'eva
- N. D. Zelinsky Institute of Organic Chemistry of the Russian Academy of Sciences , 47 Leninsky prosp ., 119991 Moscow , Russian Federation.,Mendeleev University of Chemical Technology of Russia , 9 Miusskaya sq. , Moscow 125047 , Russian Federation
| | - Alexander S Budnikov
- N. D. Zelinsky Institute of Organic Chemistry of the Russian Academy of Sciences , 47 Leninsky prosp ., 119991 Moscow , Russian Federation.,Mendeleev University of Chemical Technology of Russia , 9 Miusskaya sq. , Moscow 125047 , Russian Federation
| | - Gennady I Nikishin
- N. D. Zelinsky Institute of Organic Chemistry of the Russian Academy of Sciences , 47 Leninsky prosp ., 119991 Moscow , Russian Federation
| | - Alexander O Terent'ev
- N. D. Zelinsky Institute of Organic Chemistry of the Russian Academy of Sciences , 47 Leninsky prosp ., 119991 Moscow , Russian Federation
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9
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John-White M, Gardiner J, Johanesen P, Lyras D, Dumsday G. β-Aminopeptidases: Insight into Enzymes without a Known Natural Substrate. Appl Environ Microbiol 2019; 85:e00318-19. [PMID: 31126950 PMCID: PMC6643246 DOI: 10.1128/aem.00318-19] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Accepted: 05/08/2019] [Indexed: 02/05/2023] Open
Abstract
β-Aminopeptidases have the unique capability to hydrolyze N-terminal β-amino acids, with varied preferences for the nature of β-amino acid side chains. This unique capability makes them useful as biocatalysts for synthesis of β-peptides and to kinetically resolve β-peptides and amides for the production of enantiopure β-amino acids. To date, six β-aminopeptidases have been discovered and functionally characterized, five from Gram-negative bacteria and one from a fungus, Aspergillus Here we report on the purification and characterization of an additional four β-aminopeptidases, one from a Gram-positive bacterium, Mycolicibacterium smegmatis (BapAMs), one from a yeast, Yarrowia lipolytica (BapAYlip), and two from Gram-negative bacteria isolated from activated sludge identified as Burkholderia spp. (BapABcA5 and BapABcC1). The genes encoding β-aminopeptidases were cloned, expressed in Escherichia coli, and purified. The β-aminopeptidases were produced as inactive preproteins that underwent self-cleavage to form active enzymes comprised of two different subunits. The subunits, designated α and β, appeared to be tightly associated, as the active enzyme was recovered after immobilized-metal affinity chromatography (IMAC) purification, even though only the α-subunit was 6-histidine tagged. The enzymes were shown to hydrolyze chromogenic substrates with the N-terminal l-configurations β-homo-Gly (βhGly) and β3-homo-Leu (β3hLeu) with high activities. These enzymes displayed higher activity with H-βhGly-p-nitroanilide (H-βhGly-pNA) than previously characterized enzymes from other microorganisms. These data indicate that the new β-aminopeptidases are fully functional, adding to the toolbox of enzymes that could be used to produce β-peptides. Overexpression studies in Pseudomonas aeruginosa also showed that the β-aminopeptidases may play a role in some cellular functions.IMPORTANCE β-Aminopeptidases are unique enzymes found in a diverse range of microorganisms that can utilize synthetic β-peptides as a sole carbon source. Six β-aminopeptidases have been previously characterized with preferences for different β-amino acid substrates and have demonstrated the capability to catalyze not only the degradation of synthetic β-peptides but also the synthesis of short β-peptides. Identification of other β-aminopeptidases adds to this toolbox of enzymes with differing β-amino acid substrate preferences and kinetics. These enzymes have the potential to be utilized in the sustainable manufacture of β-amino acid derivatives and β-peptides for use in biomedical and biomaterial applications. This is important, because β-amino acids and β-peptides confer increased proteolytic resistance to bioactive compounds and form novel structures as well as structures similar to α-peptides. The discovery of new enzymes will also provide insight into the biological importance of these enzymes in nature.
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Affiliation(s)
- Marietta John-White
- CSIRO Manufacturing, Clayton, Victoria, Australia
- Infection and Immunity Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
- Department of Microbiology, Monash University, Clayton, Victoria, Australia
| | | | - Priscilla Johanesen
- Infection and Immunity Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
- Department of Microbiology, Monash University, Clayton, Victoria, Australia
| | - Dena Lyras
- Infection and Immunity Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
- Department of Microbiology, Monash University, Clayton, Victoria, Australia
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10
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Xie S, Savchenko AI, Kerscher M, Grange RL, Krenske EH, Harmer JR, Bauer MJ, Broit N, Watters DJ, Boyle GM, Bernhardt PV, Parsons PG, Comba P, Gahan LR, Williams CM. Heteroatom-Interchanged Isomers of Lissoclinamide 5: Copper(II) Complexation, Halide Binding, and Biological Activity. European J Org Chem 2018. [DOI: 10.1002/ejoc.201701659] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Sida Xie
- School of Chemistry and Molecular Biosciences; The University of Queensland; 4072 Brisbane Queensland Australia
- Southwest Forestry University; 650224 Kunming P. R. China
| | - Andrei I. Savchenko
- School of Chemistry and Molecular Biosciences; The University of Queensland; 4072 Brisbane Queensland Australia
| | - Marion Kerscher
- Anorganisch-Chemisches Institut and Interdisciplinary Centre for Scientific Computing; Universität Heidelberg; INF 270; 69120 Heidelberg Germany
| | - Rebecca L. Grange
- School of Chemistry and Molecular Biosciences; The University of Queensland; 4072 Brisbane Queensland Australia
| | - Elizabeth H. Krenske
- School of Chemistry and Molecular Biosciences; The University of Queensland; 4072 Brisbane Queensland Australia
| | - Jeffrey R. Harmer
- Center for Advanced Imaging; The University of Queensland; 4072 Brisbane Queensland Australia
| | - Michelle J. Bauer
- QIMR Berghofer Medical Research Institute; PO Royal Brisbane Hospital; 4029 Brisbane Queensland Australia
| | - Natasa Broit
- QIMR Berghofer Medical Research Institute; PO Royal Brisbane Hospital; 4029 Brisbane Queensland Australia
| | - Dianne J. Watters
- School of Environment and Science; Griffith University; 4111 Brisbane QLD Australia
| | - Glen M. Boyle
- QIMR Berghofer Medical Research Institute; PO Royal Brisbane Hospital; 4029 Brisbane Queensland Australia
| | - Paul V. Bernhardt
- School of Chemistry and Molecular Biosciences; The University of Queensland; 4072 Brisbane Queensland Australia
| | - Peter G. Parsons
- QIMR Berghofer Medical Research Institute; PO Royal Brisbane Hospital; 4029 Brisbane Queensland Australia
| | - Peter Comba
- Anorganisch-Chemisches Institut and Interdisciplinary Centre for Scientific Computing; Universität Heidelberg; INF 270; 69120 Heidelberg Germany
| | - Lawrence R. Gahan
- School of Chemistry and Molecular Biosciences; The University of Queensland; 4072 Brisbane Queensland Australia
| | - Craig M. Williams
- School of Chemistry and Molecular Biosciences; The University of Queensland; 4072 Brisbane Queensland Australia
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11
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Abstract
Nucleic acids and carbohydrates are essential biomolecules involved in numerous biological and pathological processes. Development of multifunctional building blocks based on nucleosides and sugars is in high demand for the generation of novel oligonucleotide mimics and glycoconjugates for biomedical applications. Recently, aminooxyl-functionalized compounds have attracted increasing research interest because of their easy derivatization through oxime ligation or N-oxyamide formation reactions. Various biological applications have been reported for O-amino carbohydrate- and nucleoside-derived compounds. Here, we report our efforts in the design and synthesis of glyco-, glycosyl, nucleoside- and nucleo-aminooxy acid derivatives from readily available sugars and amino acids, and their use for the generation of N-oxyamide-linked oligosaccharides, glycopeptides, glycolipids, oligonucleosides and nucleopeptides as novel glycoconjugates or oligonucleotide mimics. Delicate and key points in the synthesis will be emphasized.
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12
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Burade SS, Saha T, Bhuma N, Kumbhar N, Kotmale A, Rajamohanan PR, Gonnade RG, Talukdar P, Dhavale DD. Self-Assembly of Fluorinated Sugar Amino Acid Derived α,γ-Cyclic Peptides into Transmembrane Anion Transport. Org Lett 2017; 19:5948-5951. [DOI: 10.1021/acs.orglett.7b02942] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Sachin S. Burade
- Garware
Research Center, Department of Chemistry, Savitribai Phule Pune University (formerly Pune University), Pune 411007, India
| | - Tanmoy Saha
- Indian Institute of Science Education and Research (IISER), Pune 411008, India
| | - Naresh Bhuma
- Garware
Research Center, Department of Chemistry, Savitribai Phule Pune University (formerly Pune University), Pune 411007, India
| | - Navanath Kumbhar
- Garware
Research Center, Department of Chemistry, Savitribai Phule Pune University (formerly Pune University), Pune 411007, India
| | | | | | | | - Pinaki Talukdar
- Indian Institute of Science Education and Research (IISER), Pune 411008, India
| | - Dilip D. Dhavale
- Garware
Research Center, Department of Chemistry, Savitribai Phule Pune University (formerly Pune University), Pune 411007, India
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13
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Clerici F, Erba E, Gelmi ML, Pellegrino S. Non-standard amino acids and peptides: From self-assembly to nanomaterials. Tetrahedron Lett 2016. [DOI: 10.1016/j.tetlet.2016.11.022] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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14
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Sharma GVM, Anjaiah G, Kanakaraju M, Sudhakar B, Chatterjee D, Kunwar AC. Synthesis of a new β-amino acid with a 3-deoxy-L-ara furnaoside side chain: the influence of the side chain on the conformation of α/β-peptides. Org Biomol Chem 2016; 14:503-515. [PMID: 26489370 DOI: 10.1039/c5ob01753j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The important role of side chains in the stabilization of helical folds in peptidic foldamers containing C-linked carbo-β-amino acids (β-Caa), an interesting class of β-amino acids, with carbohydrate side chains has been extensively elaborated. As a pragmatic approach to alleviate the interference of substituents in the side chains on the folding propensities of the peptides, they are often modified or removed. The present study reports the synthesis of a new β-Caa with a 3-deoxy-L-ara furanoside side chain, [(R)-β-Caa(da)], from D-glucose, and its use in the synthesis of α/β-peptides in 1 : 1 alternation with D-Ala. The synthesis of peptides using (R)-β-Caa(da), was facile unlike those from (R)-β-Caa(a) having the L-ara furanoside side chain. The detailed NMR, molecular dynamics (MD) and CD studies on the new α/β-peptides showed the presence of robust left-handed 11/9-mixed helices. The study demonstrates that the new (R)-β-Caa(da), behaves differently compared to the other two related monomers, (R)-β-Caa(x) with the D-xylo furanoside side chain and (R)-β-Caa(a).
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Affiliation(s)
- Gangavaram V M Sharma
- Organic and Biomolecular Chemistry Division, CSIR-Indian Institute of Chemical Technology, Hyderabad 500 007, India.
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15
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Abstract
The synthesis and chemical and physicochemical properties as well as biological and medical applications of various hydroxylamine-functionalized carbohydrate derivatives are summarized.
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Affiliation(s)
- N. Chen
- PPSM
- ENS Cachan
- CNRS
- Alembert Institute
- Université Paris-Saclay
| | - J. Xie
- PPSM
- ENS Cachan
- CNRS
- Alembert Institute
- Université Paris-Saclay
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16
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Abstract
Cyclic peptides provide excellent scaffolds for anion recognition and improved binding affinity and selectivity has been achieved through peptide backbone rigidification and the introduction of side chains bearing anion recognition groups.
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17
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Zhang HL, Zang Y, Xie J, Li J, Chen GR, He XP, Tian H. A 'clicked' tetrameric hydroxamic acid glycopeptidomimetic antagonizes sugar-lectin interactions on the cellular level. Sci Rep 2014; 4:5513. [PMID: 24981800 PMCID: PMC4076733 DOI: 10.1038/srep05513] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2014] [Accepted: 06/11/2014] [Indexed: 01/10/2023] Open
Abstract
A tetrameric N-acetyl galactosaminyl (GalNAc) peptidomimetic was constructed by N-acetylation of repeating proline-based hydroxamic acid units, followed by a convergent ‘click chemistry' coupling. This novel glycopeptidomimetic was determined to effectively antagonize the interaction between a transmembrane hepatic lectin and GalNAc on the cellular level.
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Affiliation(s)
- Hai-Lin Zhang
- Key Laboratory for Advanced Materials & Institute of Fine Chemicals, East China University of Science and Technology, 130 Meilong Rd., Shanghai 200237, PR China
| | - Yi Zang
- National Center for Drug Screening, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 189 Guo Shoujing Rd., Shanghai 201203, PR China
| | - Juan Xie
- PPSM, Institut d'Alembert, ENS de Cachan, CNRS UMR 8531, 61 Avenue du Pt Wilson, F-94235 Cachan, France
| | - Jia Li
- National Center for Drug Screening, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 189 Guo Shoujing Rd., Shanghai 201203, PR China
| | - Guo-Rong Chen
- Key Laboratory for Advanced Materials & Institute of Fine Chemicals, East China University of Science and Technology, 130 Meilong Rd., Shanghai 200237, PR China
| | - Xiao-Peng He
- Key Laboratory for Advanced Materials & Institute of Fine Chemicals, East China University of Science and Technology, 130 Meilong Rd., Shanghai 200237, PR China
| | - He Tian
- Key Laboratory for Advanced Materials & Institute of Fine Chemicals, East China University of Science and Technology, 130 Meilong Rd., Shanghai 200237, PR China
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18
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Avan I, Hall CD, Katritzky AR. Peptidomimetics via modifications of amino acids and peptide bonds. Chem Soc Rev 2014; 43:3575-94. [DOI: 10.1039/c3cs60384a] [Citation(s) in RCA: 183] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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Preferential heterochiral cyclic trimerization of 5-(aminoethyl)-2-furancarboxylic acid (AEFC) driven by non-covalent interactions. J Mol Graph Model 2012; 38:13-25. [PMID: 23079639 DOI: 10.1016/j.jmgm.2012.05.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2012] [Revised: 05/03/2012] [Accepted: 05/05/2012] [Indexed: 11/20/2022]
Abstract
Theoretical justification for preferential heterochiral cyclic trimerization of 5-(aminoethyl)-2-furancarboxylic acid (AEFC) is attempted using density functional theory (DFT) calculations. Results from explicit solvent assisted reaction pathways indicate greater stability of heterochiral cyclic tripeptides over their homochiral counterparts, contrary to findings from gas phase and implicit solvent phase results. Pathways explored at M06/6-31G(d,p) and MP2/6-31G(d,p) levels of theory show kinetic preference for heterochiral cyclization. Analysis of optimized geometries reveals existence of strong hydrogen bonding interactions in the solvated heterochiral tripeptides. Thus, the ability of the cyclic tripeptides to form strong noncovalent interactions increases with conversion of stereochemistry at one of its chiral centers from homo to heterochiral conformation. The resulting change in molecular symmetry facilitates the interacting sites to reorient such that the peptide can interact with a nucleophile from both the faces. This is further substantiated by computed IR spectra, NBO and AIM data. Additionally, justification for the stability of heterochiral cyclic tripeptides comes from molecular electrostatic potential and electron density surfaces. These studies show clearly that for the kind of systems presented here, gas phase or implicit solvent phase studies are inadequate in explaining realistic situations. Calculations with solvent molecules, even if a few only, are necessary to substantiate experimental observations.
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Sharma GV, Reddy PS, Chatterjee D, Kunwar AC. Investigation of folding patterns in homo-oligomers of (R)-β2,2-amino acids with carbohydrate side chain. Tetrahedron 2012. [DOI: 10.1016/j.tet.2012.02.032] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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Molina L, Moreno-Clavijo E, Moreno-Vargas AJ, Carmona AT, Robina I. Synthesis of a C3-Symmetric Furyl-Cyclopeptide Platform with Anion Recognition Properties. European J Org Chem 2010. [DOI: 10.1002/ejoc.201000219] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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