1
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Dasgupta S, Sen S, Sathe RY, Pophali S, Kadu A, Jain R, Bera S, Roy S, Misra R. Conformation Controlled Hydrogelation of Minimalistic α, γ Hybrid Peptide. Biomacromolecules 2024; 25:3715-3723. [PMID: 38723225 DOI: 10.1021/acs.biomac.4c00270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
A majority of short peptide (≤7 amino acids) hydrogels are primarily assembled via cross β-structure formation. In contrast to the natural trend, herein, we report the formation of supramolecular hydrogel from the ultrashort hybrid folded peptide composed of canonical α-amino acid and noncanonical γ-amino acid, Fmoc-γPhe-Phe-OH. The designed hybrid peptide hydrogel is composed of entangled fibers, has viscoelastic properties, exhibits proteolytic stability, and exhibits cytocompatibility with L929 fibroblast cells. Mutating the peptide sequence by altering the position of γPhe from the N-termini to C-termini transforms the self-assembly into crystalline aggregates. Combining FTIR, 2D NMR, and DFT calculations revealed that the hydrogel-forming peptide adopts a C9 H-bonded conformation, resembling the well-known γ-turn. However, the isomeric hybrid peptide adopts an extended structure. The present study highlights the importance of secondary structure in the higher order assembly of minimalist hybrid peptides and broadens the range of secondary structures to design short peptide-based hydrogels.
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Affiliation(s)
- Sneha Dasgupta
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER) Mohali, S.A.S. Nagar (Mohali) 160062, India
| | - Sourav Sen
- Institute of Nano Science and Technology (INST), Sector 81, Knowledge City, Mohali 140306, Punjab, India
| | - Rohit Y Sathe
- Department of Biological Sciences and Biotechnology, Institute of Chemical Technology, Mumbai, Maharashtra 400019, India
| | - Salil Pophali
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER) Mohali, S.A.S. Nagar (Mohali) 160062, India
| | - Archit Kadu
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER) Mohali, S.A.S. Nagar (Mohali) 160062, India
| | - Rahul Jain
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER) Mohali, S.A.S. Nagar (Mohali) 160062, India
| | - Santu Bera
- Department of Chemistry, Ashoka University, Sonipat, Haryana 131029, India
| | - Sangita Roy
- Institute of Nano Science and Technology (INST), Sector 81, Knowledge City, Mohali 140306, Punjab, India
| | - Rajkumar Misra
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER) Mohali, S.A.S. Nagar (Mohali) 160062, India
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2
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Sukumar G, Rahul, Nayani K, Mainkar PS, Prashanth J, Sridhar B, Sarma AVS, Bharatam J, Chandrasekhar S. 6-Strand to Stable 10/12 Helix Conformational Switch by Incorporating Flexible β-hGly in the Homooligomers of Camphor Derived β-Amino Acid: NMR and X-Ray Crystallographic Evidence. Angew Chem Int Ed Engl 2024; 63:e202403321. [PMID: 38482551 DOI: 10.1002/anie.202403321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Indexed: 04/07/2024]
Abstract
Rational design of unnatural amino acid building blocks capable of stabilizing predictable secondary structures similar to protein fragments is pivotal for foldamer chemistry/catalysis. Here, we introduce novel β-amino acid building blocks: [1S,2R,4R]exoCDA and [1S,2S,4R]endoCDA, derived from the abundantly available R(+)-camphor, which is traditionally known for its medicinal value. Further, we demonstrate that the homooligomers of exoCDA adopt 6-strand conformation, which switches to a robust 10/12-helix simply by inserting flexible β-hGly spacer at alternate positions (1 : 1 β-hGly/exoCDA heterooligomers), as evident by DFT-calculations, solution-state NMR spectroscopy and X-ray crystallography. To the best of our knowledge, this is the first example of crystalline-state structure of left-handed 10/12-mixed helix, that is free from the conventional approach of employing β-amino acids of either alternate chirality or alternate β2/β3 substitutions, to access the 10/12-helix. The results also show that the homooligomers of heterochiral exoCDA don't adopt helical fold, instead exhibit banana-shaped strands, whereas the homodimers of the other diastereomer endoCDA, nucleate 8-membered turns. Furthermore, the homo-exoCDA and hetero-[β-hGly-exoCDA] oligomers are found to exhibit self-association properties with distinct morphological features. Overall, the results offer new possibilties of constructing discrete stable secondary and tertiary structures based on CDAs, which can accommodate flexible residues with desired side-chain substitutions.
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Affiliation(s)
- Genji Sukumar
- Department of Organic Synthesis and Process Chemistry, CSIR-Indian Institute of Chemical Technology, Hyderabad, 500007, India
- Department of Chemistry, Adikavi Nannaya University, Rajamahendravaram, Andhra Pradesh, 533296, India
| | - Rahul
- Centre for NMR, Department of Analytical & Structural Chemistry, CSIR-Indian Institute of Chemical Technology, Hyderabad, 500007, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Kiranmai Nayani
- Department of Organic Synthesis and Process Chemistry, CSIR-Indian Institute of Chemical Technology, Hyderabad, 500007, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Prathama S Mainkar
- Department of Organic Synthesis and Process Chemistry, CSIR-Indian Institute of Chemical Technology, Hyderabad, 500007, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Jupally Prashanth
- Centre for X-ray Crystallography, Department of Analytical & Structural Chemistry, CSIR-Indian Institute of Chemical Technology, Hyderabad, 500007, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Balasubramanian Sridhar
- Centre for X-ray Crystallography, Department of Analytical & Structural Chemistry, CSIR-Indian Institute of Chemical Technology, Hyderabad, 500007, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Akella V S Sarma
- Centre for NMR, Department of Analytical & Structural Chemistry, CSIR-Indian Institute of Chemical Technology, Hyderabad, 500007, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Jagadeesh Bharatam
- Centre for NMR, Department of Analytical & Structural Chemistry, CSIR-Indian Institute of Chemical Technology, Hyderabad, 500007, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Srivari Chandrasekhar
- Department of Organic Synthesis and Process Chemistry, CSIR-Indian Institute of Chemical Technology, Hyderabad, 500007, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
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3
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Debnath S, Rajalakshmi VS, Kumar D, Das B, Vasudev PG, Satpati P, Chatterjee S. Ambidexterity and Left-Handedness Induced by Geminally Disubstituted γ Amino Acid Residues in Chiral 3 10 Helices. ACS OMEGA 2023; 8:36370-36385. [PMID: 37810672 PMCID: PMC10552473 DOI: 10.1021/acsomega.3c05124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 08/29/2023] [Indexed: 10/10/2023]
Abstract
Chirality is an omnipresent feature in nature's architecture starting from simple molecules like amino acids to complex higher-order structures viz. proteins, DNA, and RNA. The L configuration of proteinogenic amino acids gives rise to right-handed helices. Ambidexterity is as rare in organisms as in molecules. There are only a few reports of ambidexterity in single-peptide molecules composed of either mixed L and D or achiral residues. Here, we report, for the first time, the ambidextrous and left-handed helical conformations in the chiral nonapeptides P1-P3 (Boc-LUVUγx,xULUV-OMe where U = Aib, x,x = 2,2/3,3/4,4), containing chiral L α amino acid residues, in addition to the usually observed right-handed helical conformation. The centrally located achiral γ residue, capable of adopting both left and right-handed helical conformations, induces its handedness on the neighboring chiral and achiral residues, leading to the observation of both left and right-handed helices in P2 and P3. The presence of a single water molecule proximal to the γ residue induces the reversal of helix handedness by forming distinct and stable water-mediated hydrogen bonds. This gives rise to ambidextrous helices as major conformers in P1 and P2. The absence of the observation of ambidexterity in P3 might be due to the inability of γ4,4 in the recruitment of a water molecule. Experiments (NMR, X-ray, and CD) and density functional theory (DFT) calculations suggest that the position of geminal disubstitution is crucial for determining the population of the amenable helical conformations (ambidextrous, left and right-handed) in these chiral peptides.
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Affiliation(s)
- Swapna Debnath
- Department
of Chemistry, Indian Institute of Technology,
Guwahati, Guwahati, Assam 781039, India
| | | | - Dinesh Kumar
- Plant
Biotechnology Division, CSIR-Central Institute
of Medicinal and Aromatic Plants Lucknow, Uttar Pradesh 226015, India
| | - Babulal Das
- Department
of Chemistry, Indian Institute of Technology,
Guwahati, Guwahati, Assam 781039, India
| | - Prema G. Vasudev
- Plant
Biotechnology Division, CSIR-Central Institute
of Medicinal and Aromatic Plants Lucknow, Uttar Pradesh 226015, India
| | - Priyadarshi Satpati
- Biosciences
and Bioengineering, Indian Institute of
Technology, Guwahati, Guwahati, Assam 781039, India
| | - Sunanda Chatterjee
- Department
of Chemistry, Indian Institute of Technology,
Guwahati, Guwahati, Assam 781039, India
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4
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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.
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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.
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5
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Misra R, Rudnick-Glick S, Adler-Abramovich L. From Folding to Assembly: Functional Supramolecular Architectures of Peptides Comprised of Non-Canonical Amino Acids. Macromol Biosci 2021; 21:e2100090. [PMID: 34142442 DOI: 10.1002/mabi.202100090] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 05/06/2021] [Indexed: 12/27/2022]
Abstract
The engineering of biological molecules is the fundamental concept behind the design of complex materials with desirable functions. Over the last few decades, peptides and proteins have emerged as useful building blocks for well-defined nanostructures with controlled size and dimensions. Short peptides in particular have received much attention due to their inherent biocompatibility, lower synthetic cost, and ease of tunability. In addition to the diverse self-assembling properties of short peptides comprising coded amino acids and their emerging applications in nanotechnology, there is now growing interest in the properties of peptides composed of non-canonical amino acids. Such non-natural oligomers have been shown in recent years to form well-defined secondary structures similar to natural proteins, with the ability to self-assemble to generate a wide variety of nanostructures with excellent biostability. This review describes recent events in the development of supramolecular assemblies of peptides composed completely of non-coded amino acids and their hybrid analogues. Special attention is paid to understanding the supramolecular assemblies at the atomic level and to considering their potential applications in nanotechnology.
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Affiliation(s)
- Rajkumar Misra
- Department of Oral Biology, The Goldschleger School of Dental Medicine, Sackler Faculty of Medicine and the Center for Nanoscience and Nanotechnology, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Safra Rudnick-Glick
- Department of Oral Biology, The Goldschleger School of Dental Medicine, Sackler Faculty of Medicine and the Center for Nanoscience and Nanotechnology, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Lihi Adler-Abramovich
- Department of Oral Biology, The Goldschleger School of Dental Medicine, Sackler Faculty of Medicine and the Center for Nanoscience and Nanotechnology, Tel Aviv University, Tel Aviv, 69978, Israel
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6
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Legrand B, Maillard LT. α,β-Unsaturated γ-Peptide Foldamers. Chempluschem 2021; 86:629-645. [PMID: 33856125 DOI: 10.1002/cplu.202100045] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 03/31/2021] [Indexed: 01/01/2023]
Abstract
Despite their concomitant emergence in the 1990s, γ-peptide foldamers have not developed as fast as β-peptide foldamers and to date, only a few γ-oligomer structures have been reported, and with sparse applications. Among these examples, sequences containing α,β-unsaturated γ-amino acids have recently drawn attention since the Z/E configurations of the double bond provide opposite planar restrictions leading to divergent conformational behaviors, from helix to extended structures. In this Review, we give a comprehensive overview of the developments of γ-peptide foldamers containing α,β-unsaturated γ-amino acids with examples of applications for health and catalysis, as well as materials science.
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Affiliation(s)
- Baptiste Legrand
- Institut des Biomolécules Max Mousseron, IBMM, University of Montpellier, ENSCM, CNRS, Montpellier, France., 15 Av. Charles Flahault BP 14 491, 34093, Montpellier Cedex 5, France
| | - Ludovic T Maillard
- Institut des Biomolécules Max Mousseron, IBMM, University of Montpellier, ENSCM, CNRS, Montpellier, France., 15 Av. Charles Flahault BP 14 491, 34093, Montpellier Cedex 5, France
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7
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Lawer A, Hunter L. Controlling γ‐Peptide Helicity with Stereoselective Fluorination. European J Org Chem 2021. [DOI: 10.1002/ejoc.202001619] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Aggie Lawer
- School of Chemistry The University of New South Wales (UNSW) Sydney 2052 Australia
| | - Luke Hunter
- School of Chemistry The University of New South Wales (UNSW) Sydney 2052 Australia
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8
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Park HS, Kang YK. Conformational Preferences of Cyclopentane-Based Oligo-δ-peptides in the Gas Phase and in Solution. Chempluschem 2021; 86:533-539. [PMID: 33540490 DOI: 10.1002/cplu.202000807] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Revised: 01/27/2021] [Indexed: 11/06/2022]
Abstract
The conformational preferences of oligomers of δ-amino acid (δAc5 a) with a cyclopentyl constraint in the Cβ -Cγ bond of the backbone were investigated by using DFT methods in the gas phase and in solution. The folded structures with C10 H-bonded pseudocycles were most preferred for dimer and tetramer of δAc5 a residues both in chloroform and water. However, for the hexameric Ac-(δAc5 a)6 -NHMe, the mixed H16/14 helical structure was found to be most preferred in chloroform (populated at 68 %), whereas the H14 helical structure was the most dominant conformation in water (populated at 60 %). The stability of the former was ascribed to the intrinsic conformational energy, whereas the solvation free energy was crucial to stabilize the latter. Pyrrolidine-substituted analogues of the hexameric Ac-(δAc5 a)6 -NHMe, with adjacent amine diads that are almost exactly one turn apart with two nitrogen atoms separated by ca. 5.5 Å, adopted helical structures. They are potential catalysts in nonpolar and polar solvents as they have similar structures to a helical 1 : 2 α:β-heptapeptide that exhibited good catalytic performance in the crossed aldol condensation.
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Affiliation(s)
- Hae Sook Park
- Department of Nursing, Cheju Halla University, Cheju, 63092, Republic of Korea
| | - Young Kee Kang
- Department of Chemistry, Chungbuk National University, Cheongju, Chungbuk, 28644, Republic of Korea
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9
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Reja RM, Kumar V, George G, Patel R, Puneeth Kumar DRGKR, Raghothama S, Gopi HN. Structural Investigation of Hybrid Peptide Foldamers Composed of α-Dipeptide Equivalent β-Oxy-δ 5 -amino Acids. Chemistry 2020; 26:4304-4309. [PMID: 31960517 DOI: 10.1002/chem.201904780] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 01/15/2020] [Indexed: 01/05/2023]
Abstract
Due to their equivalent lengths, δ-amino acids can serve as surrogates of α-dipeptides. However, δ-amino acids with proteinogenic side chains have not been well studied because of synthetic difficulties and because of their insolubility in organic solvents. Recently we reported the spontaneous supramolecular gelation of δ-peptides composed of β(O)-δ5 -amino acids. Here, we report the incorporation of β(O)-δ5 -amino acids as guests into the host α-helix, α,γ-hybrid peptide 12-helix and their single-crystal conformations. In addition, we studied the solution conformations of hybrid peptides composed of 1:1 alternating α and β(O)-δ5 -amino acids. In contrast to the control α-helix structures, the crystal structure of peptides with β(O)-δ5 -amino acids exhibit α-helical conformations consisting of both 13- and 10-membered H-bonds. The α,δ-hybrid peptide adopted mixed 13/11-helix conformation in solution with alternating H-bond directionality. Crystal-structure analysis revealed that the α,γ4 -hybrid peptide accommodated the guest β(O)-δ5 -amino acid without significant deviation to the overall helix folding. The results reported here emphasize that β(O)-δ5 -amino acids with proteinogenic side chains can be accommodated into regular α-helix or 12-helix as guests without much deviation of the overall helix folding of the peptides.
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Affiliation(s)
- Rahi M Reja
- Department of Chemistry, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pune, 411008, India
| | - Vivek Kumar
- Department of Chemistry, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pune, 411008, India
| | - Gijo George
- NMR Research Centre, Indian Institute of Science, Bangalore, 560012, India
| | - Rajat Patel
- Department of Chemistry, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pune, 411008, India
| | - DRGKoppalu R Puneeth Kumar
- Department of Chemistry, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pune, 411008, India
| | | | - Hosahudya N Gopi
- Department of Chemistry, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pune, 411008, India
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10
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Misra R, George G, Saseendran A, Raghothama S, Gopi HN. Ambidextrous α,γ-Hybrid Peptide Foldamers. Chem Asian J 2019; 14:4408-4414. [PMID: 31670907 DOI: 10.1002/asia.201901411] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 10/21/2019] [Indexed: 12/12/2022]
Abstract
Molecular chirality is ubiquitous in nature. The natural biopolymers, proteins and DNA, preferred a right-handed helical bias due to the inherent stereochemistry of the monomer building blocks. Here, we are reporting a rare co-existence of left- and right-handed helical conformations and helix-terminating property at the C-terminus within a single molecule of α,γ-hybrid peptide foldamers composed of achiral Aib (α-aminoisobutyric acid) and 3,3-dimethyl-substituted γ-amino acid (Adb; 4-amino-3,3-dimethylbutanoic acid). At the molecular level, the left- and right-handed helical screw sense of α,γ-hybrid peptides are representing a macroscopic tendril perversion. The pronounced helix-terminating behaviour of C-terminal Adb residues was further explored to design helix-Schellman loop mimetics and to study their conformations in solution and single crystals. The stereochemical constraints of dialkyl substitutions on γ-amino acids showed a marked impact on the folding behaviour of α,γ-hybrid peptides.
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Affiliation(s)
- Rajkumar Misra
- Department of Chemistry, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pashan, Pune, 411008, India
| | - Gijo George
- NMR Research Center, Indian Institute of Science, Bangalore, 560012, India
| | - Abhijith Saseendran
- Department of Chemistry, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pashan, Pune, 411008, India
| | | | - Hosahudya N Gopi
- Department of Chemistry, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pashan, Pune, 411008, India
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11
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Richard M, Felten AS, Chrétien F, Averlant-Petit MC, Pellegrini-Moïse N. Synthesis and conformational studies of short mixed γ/α-glycopeptides based on sugar γ 3,3 -amino acids. Tetrahedron 2017. [DOI: 10.1016/j.tet.2017.10.038] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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12
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Jadhav SV, Amabili P, Stammler H, Sewald N. Remarkable Modulation of Self‐Assembly in Short γ‐Peptides by Neighboring Ions and Orthogonal H‐Bonding. Chemistry 2017; 23:10352-10357. [DOI: 10.1002/chem.201701450] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Indexed: 12/20/2022]
Affiliation(s)
- Sandip V. Jadhav
- Department of Chemistry, Organic and Bioorganic ChemistryBielefeld University Universitätsstrasse 25 33615 Bielefeld Germany
| | - Paolo Amabili
- Department of Chemistry, Organic and Bioorganic ChemistryBielefeld University Universitätsstrasse 25 33615 Bielefeld Germany
- Department of Life and Environmental SciencesUniversità Politecnica delle Marche Ancona Italy
| | - Hans‐Georg Stammler
- Department of Chemistry, Inorganic ChemistryBielefeld University Universitätsstrasse 25 33615 Bielefeld Germany
| | - Norbert Sewald
- Department of Chemistry, Organic and Bioorganic ChemistryBielefeld University Universitätsstrasse 25 33615 Bielefeld Germany
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13
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Awada H, Grison CM, Charnay-Pouget F, Baltaze JP, Brisset F, Guillot R, Robin S, Hachem A, Jaber N, Naoufal D, Yazbeck O, Aitken DJ. Conformational Effects through Hydrogen Bonding in a Constrained γ-Peptide Template: From Intraresidue Seven-Membered Rings to a Gel-Forming Sheet Structure. J Org Chem 2017; 82:4819-4828. [PMID: 28398045 DOI: 10.1021/acs.joc.7b00494] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
A series of three short oligomers (di-, tri-, and tetramers) of cis-2-(aminomethyl)cyclobutane carboxylic acid, a γ-amino acid featuring a cyclobutane ring constraint, were prepared, and their conformational behavior was examined spectroscopically and by molecular modeling. In dilute solutions, these peptides showed a number of low-energy conformers, including ribbonlike structures pleated around a rarely observed series of intramolecular seven-membered hydrogen bonds. In more concentrated solutions, these interactions defer to an organized supramolecular assembly, leading to thermoreversible organogel formation notably for the tripeptide, which produced fibrillar xerogels. In the solid state, the dipeptide adopted a fully extended conformation featuring a one-dimensional network of intermolecularly H-bonded molecules stacked in an antiparallel sheet alignment. This work provides unique insight into the interplay between inter- and intramolecular H-bonded conformer topologies for the same peptide template.
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Affiliation(s)
- Hawraà Awada
- CP3A Organic Synthesis Group and Services Communs, ICMMO, UMR 8182, CNRS, Université Paris Sud, Université Paris Saclay , Bât. 420, 15 rue Georges Clemenceau, 91405 Orsay cedex, France.,Inorganic and Organometallic Coordination Chemistry Laboratory and Laboratory for Medicinal Chemistry and Natural Products, Faculty of Sciences (I) & PRASE-EDST, Lebanese University , Hadath, Lebanon
| | - Claire M Grison
- CP3A Organic Synthesis Group and Services Communs, ICMMO, UMR 8182, CNRS, Université Paris Sud, Université Paris Saclay , Bât. 420, 15 rue Georges Clemenceau, 91405 Orsay cedex, France
| | - Florence Charnay-Pouget
- CP3A Organic Synthesis Group and Services Communs, ICMMO, UMR 8182, CNRS, Université Paris Sud, Université Paris Saclay , Bât. 420, 15 rue Georges Clemenceau, 91405 Orsay cedex, France
| | - Jean-Pierre Baltaze
- CP3A Organic Synthesis Group and Services Communs, ICMMO, UMR 8182, CNRS, Université Paris Sud, Université Paris Saclay , Bât. 420, 15 rue Georges Clemenceau, 91405 Orsay cedex, France
| | - François Brisset
- CP3A Organic Synthesis Group and Services Communs, ICMMO, UMR 8182, CNRS, Université Paris Sud, Université Paris Saclay , Bât. 420, 15 rue Georges Clemenceau, 91405 Orsay cedex, France
| | - Régis Guillot
- CP3A Organic Synthesis Group and Services Communs, ICMMO, UMR 8182, CNRS, Université Paris Sud, Université Paris Saclay , Bât. 420, 15 rue Georges Clemenceau, 91405 Orsay cedex, France
| | - Sylvie Robin
- CP3A Organic Synthesis Group and Services Communs, ICMMO, UMR 8182, CNRS, Université Paris Sud, Université Paris Saclay , Bât. 420, 15 rue Georges Clemenceau, 91405 Orsay cedex, France.,UFR Sciences Pharmaceutiques et Biologiques, Université Paris Descartes , 4 avenue de l'Observatoire, 75270 Paris cedex 06, France
| | - Ali Hachem
- Inorganic and Organometallic Coordination Chemistry Laboratory and Laboratory for Medicinal Chemistry and Natural Products, Faculty of Sciences (I) & PRASE-EDST, Lebanese University , Hadath, Lebanon
| | - Nada Jaber
- Inorganic and Organometallic Coordination Chemistry Laboratory and Laboratory for Medicinal Chemistry and Natural Products, Faculty of Sciences (I) & PRASE-EDST, Lebanese University , Hadath, Lebanon
| | - Daoud Naoufal
- Inorganic and Organometallic Coordination Chemistry Laboratory and Laboratory for Medicinal Chemistry and Natural Products, Faculty of Sciences (I) & PRASE-EDST, Lebanese University , Hadath, Lebanon
| | - Ogaritte Yazbeck
- Inorganic and Organometallic Coordination Chemistry Laboratory and Laboratory for Medicinal Chemistry and Natural Products, Faculty of Sciences (I) & PRASE-EDST, Lebanese University , Hadath, Lebanon
| | - David J Aitken
- CP3A Organic Synthesis Group and Services Communs, ICMMO, UMR 8182, CNRS, Université Paris Sud, Université Paris Saclay , Bât. 420, 15 rue Georges Clemenceau, 91405 Orsay cedex, France
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14
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Shankar S, Wani NA, Singh UP, Rai R. Incipient Twisted Ribbon Structure Stabilized by C12Helical Turns in γ4/α Hybrid Peptide. ChemistrySelect 2016. [DOI: 10.1002/slct.201600793] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Sudha Shankar
- Medicinal Chemistry Division; CSIR-Indian Institute of Integrative Medicine; Canal Road Jammu Tawi- 180001 India
- Academy of Scientific and Innovative Research; New Delhi India
| | - Naiem Ahmad Wani
- Medicinal Chemistry Division; CSIR-Indian Institute of Integrative Medicine; Canal Road Jammu Tawi- 180001 India
| | - Umesh Prasad Singh
- CSIR-Indian Institute of Chemical Biology; 4, Raja, S.C. Mullick Road Kolkata- 700032 India
| | - Rajkishor Rai
- Medicinal Chemistry Division; CSIR-Indian Institute of Integrative Medicine; Canal Road Jammu Tawi- 180001 India
- Academy of Scientific and Innovative Research; New Delhi India
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15
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Wani NA, Kant R, Gupta VK, Aravinda S, Rai R. Ribbon structure stabilized by C10
and C12
turns in αγ
hybrid peptide. J Pept Sci 2016; 22:208-13. [DOI: 10.1002/psc.2864] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Revised: 01/23/2016] [Accepted: 01/25/2016] [Indexed: 01/03/2023]
Affiliation(s)
- Naiem Ahmad Wani
- Medicinal Chemistry Division; Indian Institute of Integrative Medicine; Canal Road Jammu Tawi 180001 India
| | - Rajni Kant
- X-ray Crystallography Laboratory, Post-Graduate Department of Physics and Electronics; University of Jammu; Jammu Tawi 180 006 India
| | - Vivek Kumar Gupta
- X-ray Crystallography Laboratory, Post-Graduate Department of Physics and Electronics; University of Jammu; Jammu Tawi 180 006 India
| | - Subrayashastry Aravinda
- Medicinal Chemistry Division; Indian Institute of Integrative Medicine; Canal Road Jammu Tawi 180001 India
| | - Rajkishor Rai
- Medicinal Chemistry Division; Indian Institute of Integrative Medicine; Canal Road Jammu Tawi 180001 India
- Academy of Scientific and Innovative Research; New Delhi India
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16
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Konda M, Kauffmann B, Rasale DB, Das AK. Structural and morphological diversity of self-assembled synthetic γ-amino acid containing peptides. Org Biomol Chem 2016; 14:4089-102. [DOI: 10.1039/c6ob00380j] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
We report the synthesis of constrained amino acid building block gabapentin (Gpn) based hybrid peptides and their structural and morphological diversity in different conditions.
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Affiliation(s)
- Maruthi Konda
- Department of Chemistry
- Indian Institute of Technology Indore
- Indore 452020
- India
| | - Brice Kauffmann
- Université de Bordeaux
- UMS3033
- Institut Européen de Chimie et Biologie (IECB)
- 33600 Pessac
- France
| | | | - Apurba K. Das
- Department of Chemistry
- Indian Institute of Technology Indore
- Indore 452020
- India
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17
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Ganesh Kumar M, Gopi HN. γ- and β-Peptide Foldamers from Common Multifaceted Building Blocks: Synthesis and Structural Characterization. Org Lett 2015; 17:4738-41. [DOI: 10.1021/acs.orglett.5b02263] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Mothukuri Ganesh Kumar
- Department of Chemistry, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pune 411008, India
| | - Hosahudya N. Gopi
- Department of Chemistry, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pune 411008, India
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18
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Priya G, Kotmale AS, Chakravarty D, Puranik VG, Rajamohanan PR, Sanjayan GJ. Conformational modulation of peptides using β-amino benzenesulfonic acid (SAnt). Org Biomol Chem 2015; 13:2087-91. [DOI: 10.1039/c4ob02421d] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
This communication describes the utility of the conformationally restricted aromatic β-amino acid (2-aminobenzenesulfonic acid, SAnt) for inducing various folding interactions in short peptides.
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Affiliation(s)
- Gowri Priya
- Division of Organic Chemistry
- National Chemical Laboratory
- Pune 411 008
- India
| | - Amol S. Kotmale
- Centre for Materials Characterisation
- National Chemical Laboratory
- Pune 411 008
- India
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19
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Abstract
Oligo-γ-peptides based on 2-aminocyclopentylacetic acid (γAc5a) with a cyclopentyl constraint on the Cβ–Cγ bond and homochiral (1S,2S) configurations preferentially adopt the right-handed 14-helix foldamers in the gas phase and in solution.
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Affiliation(s)
- Young Kee Kang
- Department of Chemistry and BK21 PLUS Research Team
- Chungbuk National University
- Cheongju
- Republic of Korea
| | - Joo Yun Lee
- Department of Chemistry and BK21 PLUS Research Team
- Chungbuk National University
- Cheongju
- Republic of Korea
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20
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Grison CM, Robin S, Aitken DJ. The discovery of 9/8-ribbons, β/γ-peptides with curved shapes governed by a combined configuration-conformation code. Chem Commun (Camb) 2015; 51:16233-6. [DOI: 10.1039/c5cc07136d] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The design of a β/γ-peptide reveals an unprecedented 9/8-ribbon whose curvature depends on the β-residue configuration and the γ-residue conformation.
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Affiliation(s)
- Claire M. Grison
- CP3A Organic Synthesis Group
- ICMMO-UMR 8182
- Université Paris-Sud
- Université Paris-Saclay
- 91405 Orsay cedex
| | - Sylvie Robin
- CP3A Organic Synthesis Group
- ICMMO-UMR 8182
- Université Paris-Sud
- Université Paris-Saclay
- 91405 Orsay cedex
| | - David J. Aitken
- CP3A Organic Synthesis Group
- ICMMO-UMR 8182
- Université Paris-Sud
- Université Paris-Saclay
- 91405 Orsay cedex
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21
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Richard M, Felten AS, Didierjean C, Ruiz-Lopez M, Chapleur Y, Pellegrini-Moïse N. Toward BisC,C-Glycosyl Compounds and Anomeric γ-Glycoamino Acids through Michael Addition Reaction of Nitromethane onZ/EPush-Pull Sugar Olefins. European J Org Chem 2014. [DOI: 10.1002/ejoc.201402958] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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22
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Kee Kang Y, Yoo IK. Influence of substituents on conformational preferences of helix foldamers of γ-dipeptides. Biopolymers 2014; 101:1077-87. [DOI: 10.1002/bip.22507] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Revised: 05/02/2014] [Accepted: 05/14/2014] [Indexed: 12/13/2022]
Affiliation(s)
- Young Kee Kang
- Department of Chemistry and BK21 PLUS Research Team; Chungbuk National University, Cheongju; Chungbuk 361-763 Republic of Korea
| | - In Kee Yoo
- Department of Chemistry and BK21 PLUS Research Team; Chungbuk National University, Cheongju; Chungbuk 361-763 Republic of Korea
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23
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Lee JY, Chae CH, Kang YK. Helix foldamers of γ-peptides based on 2-aminocyclohexylacetic acid: a computational study. NEW J CHEM 2014. [DOI: 10.1039/c3nj01217d] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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24
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Nelli YR, Fischer L, Collie GW, Kauffmann B, Guichard G. Structural characterization of short hybrid urea/carbamate (U/C) foldamers: A case of partial helix unwinding. Biopolymers 2013; 100:687-97. [DOI: 10.1002/bip.22302] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2013] [Revised: 05/21/2013] [Accepted: 05/28/2013] [Indexed: 12/31/2022]
Affiliation(s)
- Yella Reddy Nelli
- Université de Bordeaux, CNRS UMR 5248; CBMN, Institut Européen de Chimie et Biologie; 2 rue Robert Escarpit 33607 Pessac France
| | - Lucile Fischer
- Université de Bordeaux, CNRS UMR 5248; CBMN, Institut Européen de Chimie et Biologie; 2 rue Robert Escarpit 33607 Pessac France
| | - Gavin W. Collie
- Université de Bordeaux, CNRS UMR 5248; CBMN, Institut Européen de Chimie et Biologie; 2 rue Robert Escarpit 33607 Pessac France
| | - Brice Kauffmann
- Université de Bordeaux, CNRS UMS 3033; INSERM US001, Institut Européen de Chimie et Biologie; 2 rue Robert Escarpit 33607 Pessac France
| | - Gilles Guichard
- Université de Bordeaux, CNRS UMR 5248; CBMN, Institut Européen de Chimie et Biologie; 2 rue Robert Escarpit 33607 Pessac France
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25
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Byun BJ, Kang YK. Conformational preferences of helix foldamers of γ-peptides based on 2-(aminomethyl)cyclohexanecarboxylic acid. Biopolymers 2013; 101:87-95. [DOI: 10.1002/bip.22287] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2013] [Revised: 03/17/2013] [Accepted: 05/09/2013] [Indexed: 12/11/2022]
Affiliation(s)
- Byung Jin Byun
- Department of Chemistry; Chungbuk National University; Cheongju Chungbuk 361-763 Republic of Korea
| | - Young Kee Kang
- Department of Chemistry; Chungbuk National University; Cheongju Chungbuk 361-763 Republic of Korea
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26
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Basuroy K, Dinesh B, Reddy MBM, Chandrappa S, Raghothama S, Shamala N, Balaram P. Unconstrained Homooligomeric γ-Peptides Show High Propensity for C14 Helix Formation. Org Lett 2013; 15:4866-9. [DOI: 10.1021/ol402248s] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Krishnayan Basuroy
- Molecular Biophysics Unit, Department of Physics, Sophisticated Instrumentation Facility, Indian Institute of Science, Bangalore 560 012, India
| | - Bhimareddy Dinesh
- Molecular Biophysics Unit, Department of Physics, Sophisticated Instrumentation Facility, Indian Institute of Science, Bangalore 560 012, India
| | - M. B. Madhusudana Reddy
- Molecular Biophysics Unit, Department of Physics, Sophisticated Instrumentation Facility, Indian Institute of Science, Bangalore 560 012, India
| | - Siddapa Chandrappa
- Molecular Biophysics Unit, Department of Physics, Sophisticated Instrumentation Facility, Indian Institute of Science, Bangalore 560 012, India
| | - Srinivasarao Raghothama
- Molecular Biophysics Unit, Department of Physics, Sophisticated Instrumentation Facility, Indian Institute of Science, Bangalore 560 012, India
| | - Narayanaswamy Shamala
- Molecular Biophysics Unit, Department of Physics, Sophisticated Instrumentation Facility, Indian Institute of Science, Bangalore 560 012, India
| | - Padmanabhan Balaram
- Molecular Biophysics Unit, Department of Physics, Sophisticated Instrumentation Facility, Indian Institute of Science, Bangalore 560 012, India
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27
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A compendium of cyclic sugar amino acids and their carbocyclic and heterocyclic nitrogen analogues. Amino Acids 2013; 45:613-89. [DOI: 10.1007/s00726-013-1521-1] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2013] [Accepted: 05/21/2013] [Indexed: 12/19/2022]
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28
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Mathieu L, Legrand B, Deng C, Vezenkov L, Wenger E, Didierjean C, Amblard M, Averlant-Petit MC, Masurier N, Lisowski V, Martinez J, Maillard LT. Helical oligomers of thiazole-based γ-amino acids: synthesis and structural studies. Angew Chem Int Ed Engl 2013; 52:6006-10. [PMID: 23619818 DOI: 10.1002/anie.201302106] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2013] [Indexed: 12/12/2022]
Abstract
9-Helix: 4-Amino(methyl)-1,3-thiazole-5-carboxylic acids (ATCs) were synthesized as new γ-amino acid building blocks. The structures of various ATC oligomers were analyzed in solution by CD and NMR spectroscopy and in the solid state by X-ray crystallography. The ATC sequences adopted a well-defined 9-helix structure in the solid state and in aprotic and protic organic solvents as well as in aqueous solution.
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Affiliation(s)
- Loïc Mathieu
- Institut des Biomolécules Max Mousseron, UMR 5247, CNRS, Universités Montpellier I et II, UFR des Sciences Pharmaceutiques et Biologiques, 15 Avenue Charles Flahault, 34093 Montpellier Cedex 5, France
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29
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Mathieu L, Legrand B, Deng C, Vezenkov L, Wenger E, Didierjean C, Amblard M, Averlant-Petit MC, Masurier N, Lisowski V, Martinez J, Maillard LT. Helical Oligomers of Thiazole-Based γ-Amino Acids: Synthesis and Structural Studies. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201302106] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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30
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Ganesh Kumar M, Mali SM, Gopi HN. Synthesis and stereochemical analysis of β-nitromethane substituted γ-amino acids and peptides. Org Biomol Chem 2013; 11:803-13. [DOI: 10.1039/c2ob27070f] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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31
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Baldauf C, Hofmann HJ. Ab initioMO Theory - An Important Tool in Foldamer Research: Prediction of Helices in Oligomers ofω-Amino Acids. Helv Chim Acta 2012. [DOI: 10.1002/hlca.201200436] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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32
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Sharma GVM, Kodeti SR, Dutta SK, Velaparthi S, Narsimulu K, Anjaiah G, Basha SJ, Kunwar AC. Chirality and Template-Mediated Induction of Helical Preferences in Achiral β-Peptides. Chemistry 2012; 18:16046-60. [DOI: 10.1002/chem.201201892] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2012] [Revised: 08/20/2012] [Indexed: 11/06/2022]
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33
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Basuroy K, Rajagopal A, Raghothama S, Shamala N, Balaram P. β-Turn analogues in model αβ-hybrid peptides: structural characterization of peptides containing β(2,2)Ac6c and β(3,3)Ac6c residues. Chem Asian J 2012; 7:1671-8. [PMID: 22555984 DOI: 10.1002/asia.201200052] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2012] [Indexed: 01/04/2023]
Abstract
The effect of gem-dialkyl substituents on the backbone conformations of β-amino acid residues in peptides has been investigated by using four model peptides: Boc-Xxx-β(2,2)Ac(6)c(1-aminomethylcyclohexanecarboxylic acid)-NHMe (Xxx = Leu (1), Phe (2); Boc = tert-butyloxycarbonyl) and Boc-Xxx-β(3,3)Ac(6)c(1-aminocyclohexaneacetic acid)-NHMe (Xxx = Leu (3), Phe (4)). Tetrasubstituted carbon atoms restrict the ranges of stereochemically allowed conformations about flanking single bonds. The crystal structure of Boc-Leu-β(2,2)Ac(6)c-NHMe (1) established a C(11) hydrogen-bonded turn in the αβ-hybrid sequence. The observed torsion angles (α(ϕ≈-60°, ψ≈-30°), β(ϕ≈-90°, θ≈60°, ψ≈-90°)) corresponded to a C(11) helical turn, which was a backbone-expanded analogue of the type III β turn in αα sequences. The crystal structure of the peptide Boc-Phe-β(3,3)Ac(6)c-NHMe (4) established a C(11) hydrogen-bonded turn with distinctly different backbone torsion angles (α(ϕ≈-60°, ψ≈120°), β(ϕ≈60°, θ≈60°, ψ≈-60°)), which corresponded to a backbone-expanded analogue of the type II β turn observed in αα sequences. In peptide 4, the two molecules in the asymmetric unit adopted backbone torsion angles of opposite signs. In one of the molecules, the Phe residue adopted an unfavorable backbone conformation, with the energetic penalty being offset by a favorable aromatic interaction between proximal molecules in the crystal. NMR spectroscopy studies provided evidence for the maintenance of folded structures in solution in these αβ-hybrid sequences.
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Affiliation(s)
- Krishnayan Basuroy
- Department of Physics, Indian Institute of Science, Bangalore-560 012, India
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34
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Thétiot-Laurent S, Bouillère F, Baltaze JP, Brisset F, Feytens D, Kouklovsky C, Miclet E, Alezra V. Original β,γ-diamino acid as an inducer of a γ-turn mimic in short peptides. Org Biomol Chem 2012; 10:9660-3. [DOI: 10.1039/c2ob26828k] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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35
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36
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James WH, Buchanan EG, Guo L, Gellman SH, Zwier TS. Competition between Amide Stacking and Intramolecular H Bonds in γ-Peptide Derivatives: Controlling Nearest-Neighbor Preferences. J Phys Chem A 2011; 115:11960-70. [PMID: 21928850 DOI: 10.1021/jp2081319] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- William H. James
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, United States
| | - Evan G. Buchanan
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, United States
| | - Li Guo
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, United States
| | - Samuel H. Gellman
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, United States
| | - Timothy S. Zwier
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, United States
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37
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Guo L, Zhang W, Reidenbach AG, Giuliano MW, Guzei IA, Spencer LC, Gellman SH. Characteristic Structural Parameters for the γ-Peptide 14-Helix: Importance of Subunit Preorganization. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201101301] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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38
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Guo L, Zhang W, Reidenbach AG, Giuliano MW, Guzei IA, Spencer LC, Gellman SH. Characteristic structural parameters for the γ-peptide 14-helix: importance of subunit preorganization. Angew Chem Int Ed Engl 2011; 50:5843-6. [PMID: 21567680 DOI: 10.1002/anie.201101301] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2011] [Indexed: 11/09/2022]
Affiliation(s)
- Li Guo
- Department of Chemistry, University of Wisconsin, Madison, Madison, WI 53706, USA
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39
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Foldamers containing γ-amino acid residues or their analogues: structural features and applications. Amino Acids 2011; 41:687-707. [DOI: 10.1007/s00726-011-0893-3] [Citation(s) in RCA: 101] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2011] [Accepted: 03/18/2011] [Indexed: 12/21/2022]
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40
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Solid Phase and Solution Phase Synthesis of Gamma Amino Acid Homo-Oligomers and Mixed Oligomers. Int J Pept Res Ther 2011. [DOI: 10.1007/s10989-011-9248-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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41
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Aitken DJ, Drouin L, Goretta S, Guillot R, Ollivier J, Spiga M. Stereoselective preparation of β,γ-methano-GABA derivatives. Org Biomol Chem 2011; 9:7517-24. [DOI: 10.1039/c1ob06095c] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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42
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Balaram P. Hybrid polypeptides: Gabapentin as a stereochemically constrained γ-amino acid residue. Biopolymers 2010; 94:733-41. [DOI: 10.1002/bip.21468] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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43
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Vasudev PG, Chatterjee S, Shamala N, Balaram P. Structural Chemistry of Peptides Containing Backbone Expanded Amino Acid Residues: Conformational Features of β, γ, and Hybrid Peptides. Chem Rev 2010; 111:657-87. [DOI: 10.1021/cr100100x] [Citation(s) in RCA: 273] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Prema. G. Vasudev
- Department of Physics and Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
| | - Sunanda Chatterjee
- Department of Physics and Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
| | - Narayanaswamy Shamala
- Department of Physics and Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
| | - Padmanabhan Balaram
- Department of Physics and Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India
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44
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Gajcy K, Pękala J, Frąckowiak-Wojtasek B, Librowski T, Lochyński S. Stereochemistry of terpene derivatives. Part 7: Novel rigidified amino acids from (+)-3-carene designed as chiral GABA analogues. ACTA ACUST UNITED AC 2010. [DOI: 10.1016/j.tetasy.2010.06.026] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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45
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Sharma GVM, Chandramouli N, Choudhary M, Nagendar P, Ramakrishna KVS, Kunwar AC, Schramm P, Hofmann HJ. Hybrid Helices: Motifs for Secondary Structure Scaffolds in Foldamers. J Am Chem Soc 2009; 131:17335-44. [DOI: 10.1021/ja907074u] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Gangavaram V. M. Sharma
- Organic Chemistry Division III, Indian Institute of Chemical Technology (CSIR), Hyderabad 500 607, India, Centre for Nuclear Magnetic Resonance, Indian Institute of Chemical Technology (CSIR), Hyderabad 500 607, India, and Institute of Biochemistry, Faculty of Biosciences, University of Leipzig, Brüderstrasse 34, D-04103 Leipzig, Germany
| | - Nagula Chandramouli
- Organic Chemistry Division III, Indian Institute of Chemical Technology (CSIR), Hyderabad 500 607, India, Centre for Nuclear Magnetic Resonance, Indian Institute of Chemical Technology (CSIR), Hyderabad 500 607, India, and Institute of Biochemistry, Faculty of Biosciences, University of Leipzig, Brüderstrasse 34, D-04103 Leipzig, Germany
| | - Madavi Choudhary
- Organic Chemistry Division III, Indian Institute of Chemical Technology (CSIR), Hyderabad 500 607, India, Centre for Nuclear Magnetic Resonance, Indian Institute of Chemical Technology (CSIR), Hyderabad 500 607, India, and Institute of Biochemistry, Faculty of Biosciences, University of Leipzig, Brüderstrasse 34, D-04103 Leipzig, Germany
| | - Pendem Nagendar
- Organic Chemistry Division III, Indian Institute of Chemical Technology (CSIR), Hyderabad 500 607, India, Centre for Nuclear Magnetic Resonance, Indian Institute of Chemical Technology (CSIR), Hyderabad 500 607, India, and Institute of Biochemistry, Faculty of Biosciences, University of Leipzig, Brüderstrasse 34, D-04103 Leipzig, Germany
| | - Kallaganti V. S. Ramakrishna
- Organic Chemistry Division III, Indian Institute of Chemical Technology (CSIR), Hyderabad 500 607, India, Centre for Nuclear Magnetic Resonance, Indian Institute of Chemical Technology (CSIR), Hyderabad 500 607, India, and Institute of Biochemistry, Faculty of Biosciences, University of Leipzig, Brüderstrasse 34, D-04103 Leipzig, Germany
| | - Ajit C. Kunwar
- Organic Chemistry Division III, Indian Institute of Chemical Technology (CSIR), Hyderabad 500 607, India, Centre for Nuclear Magnetic Resonance, Indian Institute of Chemical Technology (CSIR), Hyderabad 500 607, India, and Institute of Biochemistry, Faculty of Biosciences, University of Leipzig, Brüderstrasse 34, D-04103 Leipzig, Germany
| | - Peter Schramm
- Organic Chemistry Division III, Indian Institute of Chemical Technology (CSIR), Hyderabad 500 607, India, Centre for Nuclear Magnetic Resonance, Indian Institute of Chemical Technology (CSIR), Hyderabad 500 607, India, and Institute of Biochemistry, Faculty of Biosciences, University of Leipzig, Brüderstrasse 34, D-04103 Leipzig, Germany
| | - Hans-Jörg Hofmann
- Organic Chemistry Division III, Indian Institute of Chemical Technology (CSIR), Hyderabad 500 607, India, Centre for Nuclear Magnetic Resonance, Indian Institute of Chemical Technology (CSIR), Hyderabad 500 607, India, and Institute of Biochemistry, Faculty of Biosciences, University of Leipzig, Brüderstrasse 34, D-04103 Leipzig, Germany
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Vasudev PG, Chatterjee S, Shamala N, Balaram P. Gabapentin: a stereochemically constrained gamma amino acid residue in hybrid peptide design. Acc Chem Res 2009; 42:1628-39. [PMID: 19572698 DOI: 10.1021/ar9001153] [Citation(s) in RCA: 87] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Nature has used the all-alpha-polypeptide backbone of proteins to create a remarkable diversity of folded structures. Sequential patterns of 20 distinct amino acids, which differ only in their side chains, determine the shape and form of proteins. Our understanding of these specific secondary structures is over half a century old and is based primarily on the fundamental elements: the Pauling alpha-helix and beta-sheet. Researchers can also generate structural diversity through the synthesis of polypeptide chains containing homologated (omega) amino acid residues, which contain a variable number of backbone atoms. However, incorporating amino acids with more atoms within the backbone introduces additional torsional freedom into the structure, which can complicate the structural analysis. Fortunately, gabapentin (Gpn), a readily available bulk drug, is an achiral beta,beta-disubstituted gamma amino acid residue that contains a cyclohexyl ring at the C(beta) carbon atom, which dramatically limits the range of torsion angles that can be obtained about the flanking C-C bonds. Limiting conformational flexibility also has the desirable effect of increasing peptide crystallinity, which permits unambiguous structural characterization by X-ray diffraction methods. This Account describes studies carried out in our laboratory that establish Gpn as a valuable residue in the design of specifically folded hybrid peptide structures. The insertion of additional atoms into polypeptide backbones facilitates the formation of intramolecular hydrogen bonds whose directionality is opposite to that observed in canonical alpha-peptide helices. If hybrid structures mimic proteins and biologically active peptides, the proteolytic stability conferred by unusual backbones can be a major advantage in the area of medicinal chemistry. We have demonstrated a variety of internally hydrogen-bonded structures in the solid state for Gpn-containing peptides, including the characterization of the C(7) and C(9) hydrogen bonds, which can lead to ribbons in homo-oligomeric sequences. In hybrid alphagamma sequences, distinct C(12) hydrogen-bonded turn structures support formation of peptide helices and hairpins in longer sequences. Some peptides that include the Gpn residue have hydrogen-bond directionality that matches alpha-peptide helices, while others have the opposite directionality. We expect that expansion of the polypeptide backbone will lead to new classes of foldamer structures, which are thus far unknown to the world of alpha-polypeptides. The diversity of internally hydrogen-bonded structures observed in hybrid sequences containing Gpn shows promise for the rational design of novel peptide structures incorporating hybrid backbones.
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Affiliation(s)
- Prema G. Vasudev
- Department of Physics
- Molecular Biophysics Unit
- Indian institute of Science, Bangalore 560012, India
| | - Sunanda Chatterjee
- Department of Physics
- Molecular Biophysics Unit
- Indian institute of Science, Bangalore 560012, India
| | - Narayanaswamy Shamala
- Department of Physics
- Molecular Biophysics Unit
- Indian institute of Science, Bangalore 560012, India
| | - Padmanabhan Balaram
- Department of Physics
- Molecular Biophysics Unit
- Indian institute of Science, Bangalore 560012, India
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Schramm P, Sharma GVM, Hofmann HJ. Helix formation in β/δ-hybrid peptides: Correspondence between helices of different peptide foldamer classes. Biopolymers 2009; 94:279-91. [DOI: 10.1002/bip.21325] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Sharma GVM, Babu BS, Chatterjee D, Ramakrishna KVS, Kunwar AC, Schramm P, Hofmann HJ. Theoretical and Experimental Studies on α/ε-Hybrid Peptides: Design of a 14/12-Helix from Peptides with Alternating (S)-C-Linked Carbo-ε-amino Acid [(S)-ε-Caa(x)] and l-Ala. J Org Chem 2009; 74:6703-13. [DOI: 10.1021/jo901277a] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Gangavaram V. M. Sharma
- Organic Chemistry Division III, Indian Institute of Chemical Technology (CSIR), Hyderabad 500 607, India
| | - Bommagani Shoban Babu
- Organic Chemistry Division III, Indian Institute of Chemical Technology (CSIR), Hyderabad 500 607, India
| | - Deepak Chatterjee
- Centre for Nuclear Magnetic Resonance, Indian Institute of Chemical Technology (CSIR), Hyderabad 500 607, India
| | | | - Ajit C. Kunwar
- Centre for Nuclear Magnetic Resonance, Indian Institute of Chemical Technology (CSIR), Hyderabad 500 607, India
| | - Peter Schramm
- Institute of Biochemistry, Faculty of Biosciences, University of Leipzig, Brüderstrasse 34, D-04103 Leipzig, Germany
| | - Hans-Jörg Hofmann
- Institute of Biochemistry, Faculty of Biosciences, University of Leipzig, Brüderstrasse 34, D-04103 Leipzig, Germany
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Sharma GV, Babu BS, Ramakrishna KV, Nagendar P, Kunwar AC, Schramm P, Baldauf C, Hofmann HJ. Synthesis and Structure of α/δ-Hybrid Peptides-Access to Novel Helix Patterns in Foldamers. Chemistry 2009; 15:5552-66. [DOI: 10.1002/chem.200802078] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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