1
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Lin Q, Lan H, Ma C, Stendall RT, Shankland K, Musgrave RA, Horton PN, Baldauf C, Hofmann H, Butts CP, Müller MM, Cobb AJA. Crystal Structure and NMR of an α,δ-Peptide Foldamer Helix Shows Side-Chains are Well Placed for Bifunctional Catalysis: Application as a Minimalist Aldolase Mimic. ANGEWANDTE CHEMIE (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 135:e202305326. [PMID: 38516402 PMCID: PMC10952562 DOI: 10.1002/ange.202305326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Indexed: 03/23/2024]
Abstract
We report the first NMR and X-ray diffraction (XRD) structures of an unusual 13/11-helix (alternating i, i+1 {NH-O=C} and i, i+3 {C=O-H-N} H-bonds) formed by a heteromeric 1 : 1 sequence of α- and δ-amino acids, and demonstrate the application of this framework towards catalysis. Whilst intramolecular hydrogen bonds (IMHBs) are the clear driver of helix formation in this system, we also observe an apolar interaction between the ethyl residue of one δ-amino acid and the cyclohexyl group of the next δ-residue in the sequence that seems to stabilize one type of helix over another. To the best of our knowledge this type of additional stabilization leading to a specific helical preference has not been observed before. Critically, the helix type realized places the α-residue functionalities in positions proximal enough to engage in bifunctional catalysis as demonstrated in the application of our system as a minimalist aldolase mimic.
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Affiliation(s)
- Qi Lin
- Department of ChemistryKing's College London7 Trinity StreetLondonSE1 1DBUK
| | - Hao Lan
- School of ChemistryUniversity of BristolCantocks CloseBristolBS8 1TSUK
| | - Chunmiao Ma
- School of Chemistry and Chemical EngineeringHuazhong University of Science and TechnologyWuhan430074P. R. China
| | - Ryan T. Stendall
- Department of ChemistryKing's College London7 Trinity StreetLondonSE1 1DBUK
| | - Kenneth Shankland
- School of ChemistryFood and Pharmacy (SCFP)University of ReadingWhiteknights BerksReadingRG6 6ADUK
| | | | - Peter N. Horton
- EPSRC National Crystallography ServiceSchool of ChemistryUniversity of Southampton HighfieldSouthamptonSO17 1BJUK
| | - Carsten Baldauf
- Fritz-Haber-Institut der Max-Planck-GesellschaftFaradayweg 4–614195BerlinGermany
| | - Hans‐Jörg Hofmann
- Institut für BiochemieUniversität LeipzigBrüderstrasse 3404103LeipzigGermany
| | - Craig P. Butts
- School of ChemistryUniversity of BristolCantocks CloseBristolBS8 1TSUK
| | - Manuel M. Müller
- Department of ChemistryKing's College London7 Trinity StreetLondonSE1 1DBUK
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2
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Lin Q, Lan H, Ma C, Stendall RT, Shankland K, Musgrave RA, Horton PN, Baldauf C, Hofmann H, Butts CP, Müller MM, Cobb AJA. Crystal Structure and NMR of an α,δ-Peptide Foldamer Helix Shows Side-Chains are Well Placed for Bifunctional Catalysis: Application as a Minimalist Aldolase Mimic. Angew Chem Int Ed Engl 2023; 62:e202305326. [PMID: 37218617 PMCID: PMC10952276 DOI: 10.1002/anie.202305326] [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: 04/15/2023] [Revised: 05/17/2023] [Accepted: 05/22/2023] [Indexed: 05/24/2023]
Abstract
We report the first NMR and X-ray diffraction (XRD) structures of an unusual 13/11-helix (alternating i, i+1 {NH-O=C} and i, i+3 {C=O-H-N} H-bonds) formed by a heteromeric 1 : 1 sequence of α- and δ-amino acids, and demonstrate the application of this framework towards catalysis. Whilst intramolecular hydrogen bonds (IMHBs) are the clear driver of helix formation in this system, we also observe an apolar interaction between the ethyl residue of one δ-amino acid and the cyclohexyl group of the next δ-residue in the sequence that seems to stabilize one type of helix over another. To the best of our knowledge this type of additional stabilization leading to a specific helical preference has not been observed before. Critically, the helix type realized places the α-residue functionalities in positions proximal enough to engage in bifunctional catalysis as demonstrated in the application of our system as a minimalist aldolase mimic.
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Affiliation(s)
- Qi Lin
- Department of ChemistryKing's College London7 Trinity StreetLondonSE1 1DBUK
| | - Hao Lan
- School of ChemistryUniversity of BristolCantocks CloseBristolBS8 1TSUK
| | - Chunmiao Ma
- School of Chemistry and Chemical EngineeringHuazhong University of Science and TechnologyWuhan430074P. R. China
| | - Ryan T. Stendall
- Department of ChemistryKing's College London7 Trinity StreetLondonSE1 1DBUK
| | - Kenneth Shankland
- School of ChemistryFood and Pharmacy (SCFP)University of ReadingWhiteknights BerksReadingRG6 6ADUK
| | | | - Peter N. Horton
- EPSRC National Crystallography ServiceSchool of ChemistryUniversity of Southampton HighfieldSouthamptonSO17 1BJUK
| | - Carsten Baldauf
- Fritz-Haber-Institut der Max-Planck-GesellschaftFaradayweg 4–614195BerlinGermany
| | - Hans‐Jörg Hofmann
- Institut für BiochemieUniversität LeipzigBrüderstrasse 3404103LeipzigGermany
| | - Craig P. Butts
- School of ChemistryUniversity of BristolCantocks CloseBristolBS8 1TSUK
| | - Manuel M. Müller
- Department of ChemistryKing's College London7 Trinity StreetLondonSE1 1DBUK
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3
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Roe WE, Warnock TMC, Knipe PC. A spirocyclic backbone accesses new conformational space in an extended, dipole-stabilized foldamer. Commun Chem 2023; 6:71. [PMID: 37069245 PMCID: PMC10110530 DOI: 10.1038/s42004-023-00868-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 03/24/2023] [Indexed: 04/19/2023] Open
Abstract
Most aromatic foldamers adopt uniform secondary structures, offering limited potential for the exploration of conformational space and the formation of tertiary structures. Here we report the incorporation of spiro bis-lactams to allow controlled rotation of the backbone of an iteratively synthesised foldamer. This enables precise control of foldamer shape along two orthogonal directions, likened to the aeronautical yaw and roll axes. XRD, NMR and computational data suggest that homo-oligomers adopt an extended right-handed helix with a pitch of over 30 Å, approximately that of B-DNA. Compatibility with extant foldamers to form hetero-oligomers is demonstrated, allowing greater structural complexity and function in future hybrid foldamer designs.
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Affiliation(s)
- William Edward Roe
- School of Chemistry and Chemical Engineering, Queen's University Belfast, David Keir Building, Belfast, BT9 5AG, UK
| | - Toyah Mary Catherine Warnock
- School of Chemistry and Chemical Engineering, Queen's University Belfast, David Keir Building, Belfast, BT9 5AG, UK
| | - Peter Clarke Knipe
- School of Chemistry and Chemical Engineering, Queen's University Belfast, David Keir Building, Belfast, BT9 5AG, UK.
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4
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Nagata M, Watanabe M, Doi R, Uemura M, Ochiai N, Ichinose W, Fujiwara K, Sato Y, Kameda T, Takeuchi K, Shuto S. Helix-forming aliphatic homo-δ-peptide foldamers based on the conformational restriction effects of cyclopropane. Org Biomol Chem 2023; 21:970-980. [PMID: 36426637 DOI: 10.1039/d2ob01715f] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Considerable effort has been directed toward developing artificial peptide-based foldamers. However, detailed structural analysis of δ-peptide foldamers consisting of only aliphatic δ-amino acids has not been reported. Herein, we rationally designed and stereoselectively synthesized aliphatic homo-δ-peptides forming a stable helical structure by using a chiral cyclopropane δ-amino acid as a monomer unit. Structural analysis of the homo-δ-peptides using circular dichroism, infrared, and NMR spectroscopy indicated that they form a stable 14-helical structure in solution. Furthermore, we successfully conducted X-ray crystallographic analysis of the homo-δ-peptides, demonstrating a right-handed 14-helical structure. This helical structure of the crystal was consistent with those predicted by theoretical calculations and those obtained based on NMR spectroscopy in solution. This stable helical structure is due to the effective restriction of the backbone conformation by the structural characteristics of cyclopropane. This work reports the first example of aliphatic homo-δ-peptide foldamers having a stable helical structure both in the solution and crystal states.
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Affiliation(s)
- Makoto Nagata
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan.
| | - Mizuki Watanabe
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan.
| | - Ryohei Doi
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan.
| | - Mai Uemura
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan.
| | - Nanase Ochiai
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan.
| | - Wataru Ichinose
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan.
| | - Koichi Fujiwara
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan.
| | - Yoshihiro Sato
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan.
| | - Tomoshi Kameda
- Artificial Intelligence Research Center, National Institute of Advanced Industrial Science and Technology (AIST), 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan
| | - Koh Takeuchi
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Satoshi Shuto
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo 060-0812, Japan.
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5
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Helical Foldamers and Stapled Peptides as New Modalities in Drug Discovery: Modulators of Protein-Protein Interactions. Processes (Basel) 2022. [DOI: 10.3390/pr10050924] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
A “foldamer” is an artificial oligomeric molecule with a regular secondary or tertiary structure consisting of various building blocks. A “stapled peptide” is a peptide with stabilized secondary structures, in particular, helical structures by intramolecular covalent side-chain cross-linking. Helical foldamers and stapled peptides are potential drug candidates that can target protein-protein interactions because they enable multipoint molecular recognition, which is difficult to achieve with low-molecular-weight compounds. This mini-review describes a variety of peptide-based foldamers and stapled peptides with a view to their applications in drug discovery, including our recent progress.
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6
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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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7
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Said Stålsmeden A, Paterson AJ, Szigyártó IC, Thunberg L, Johansson JR, Beke-Somfai T, Kann N. Chiral 1,5-disubstituted 1,2,3-triazoles - versatile tools for foldamers and peptidomimetic applications. Org Biomol Chem 2020; 18:1957-1967. [PMID: 32101244 DOI: 10.1039/d0ob00168f] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
1,4- and 1,5-Disubstituted triazole amino acid monomers have gained increasing interest among peptidic foldamers, as they are easily prepared via Cu- and Ru-catalyzed click reactions, with the potential for side chain variation. While the latter is key to their applicability, the synthesis and structural properties of the chiral mono- or disubstituted triazole amino acids have only been partially addressed. We here present the synthesis of all eight possible chiral derivatives of a triazole monomer prepared via a ruthenium-catalyzed azide alkyne cycloaddition (RuAAC). To evaluate the conformational properties of the individual building units, a systematic quantum chemical study was performed on all monomers, indicating their capacity to form several low energy conformers. This feature may be used to effect structural diversity when the monomers are inserted into various peptide sequences. We envisage that these results will facilitate new applications for these artificial oligomeric compounds in diverse areas, ranging from pharmaceutics to biotechnology.
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Affiliation(s)
- Anna Said Stålsmeden
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, SE-41296 Göteborg, Sweden.
| | - Andrew J Paterson
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, SE-41296 Göteborg, Sweden.
| | - Imola Cs Szigyártó
- Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudósok krt. 2, H-1117 Budapest, Hungary.
| | - Linda Thunberg
- Early Chemical Development, Pharmaceutical Sciences, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
| | - Johan R Johansson
- Medicinal Chemistry, Research and Early Development Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden.
| | - Tamás Beke-Somfai
- Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudósok krt. 2, H-1117 Budapest, Hungary.
| | - Nina Kann
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, SE-41296 Göteborg, Sweden.
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8
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Reja RM, Patel R, Kumar V, Jha A, Gopi HN. Divergent Supramolecular Gelation of Backbone Modified Short Hybrid δ-Peptides. Biomacromolecules 2019; 20:1254-1262. [DOI: 10.1021/acs.biomac.8b01684] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Rahi M. Reja
- Department of Chemistry, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pune-411008, India
| | - Rajat Patel
- 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
| | - Anjali Jha
- Nanobioscience Group, Agharkar Research Institute, G. G. Agarkar Road, Pune-411004, 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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9
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Reddy RG, Dachavaram SS, Reddy BR, Kalyankar KB, Rajan WD, Kootar S, Kumar A, Das S, Chakravarty S. Fellutamide B Synthetic Path Intermediates with in Vitro Neuroactive Function Shows Mood-Elevating Effect in Stress-Induced Zebrafish Model. ACS OMEGA 2018; 3:10534-10544. [PMID: 30320245 PMCID: PMC6173481 DOI: 10.1021/acsomega.8b00456] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Accepted: 08/17/2018] [Indexed: 06/08/2023]
Abstract
Fellutamide B is reported to have cytotoxic and proteasome inhibitory activity. Interestingly, fellutamide B and its simplified analogues have also been observed for the neurotrophic activity by stimulating the synthesis and secretion of neurotrophins. Owing to the interesting structural and potent neurotrophic role of fellutamide B (a lipopeptide aldehyde), we have assessed the synthetic path intermediates (compounds A-D) of fellutamide B for their neuroactive potential (in vitro and in vivo). We have observed few compounds (comp #A-D) to have potential neurite outgrowth activity in Neuro2a cells with no observable negative effect on the cell viability. In addition, most compounds (comp #A, C, and D) have shown neurogenic activity ex vivo in hippocampal neurosphere culture, with increased acetyl H3 and acetyl H4 induction ability (comp #C). Furthermore, the intermediate product comp #C has shown anxiolytic and antidepressant-like activity in novel tank test and social interaction test, in the chronic unpredictable stress model of zebrafish mood disorder, inducing BDNF gene expression in the telencephalon region of the fish brain. Our results thus demonstrate that the fellutamide B synthetic path intermediates have potential neurotrophic, neurogenic, and mood-elevating effects and thus good prospect to be developed as potential therapeutics to treat psychiatric disorders.
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Affiliation(s)
- R. Gajendra Reddy
- Chemical
Biology and Natural Products Chemistry, CSIR-Indian
Institute of Chemical Technology, Tarnaka, Uppal Road, Hyderabad 500007, India
- Academy
of Scientific and Innovative Research (AcSIR), Chennai 600113, India
| | - Soma Shekar Dachavaram
- Chemical
Biology and Natural Products Chemistry, CSIR-Indian
Institute of Chemical Technology, Tarnaka, Uppal Road, Hyderabad 500007, India
| | - B. Raghunath Reddy
- Chemical
Biology and Natural Products Chemistry, CSIR-Indian
Institute of Chemical Technology, Tarnaka, Uppal Road, Hyderabad 500007, India
- Academy
of Scientific and Innovative Research (AcSIR), Chennai 600113, India
| | - Kondbarao Balasaheb Kalyankar
- Chemical
Biology and Natural Products Chemistry, CSIR-Indian
Institute of Chemical Technology, Tarnaka, Uppal Road, Hyderabad 500007, India
- Academy
of Scientific and Innovative Research (AcSIR), Chennai 600113, India
| | - Wenson D. Rajan
- CSIR-Centre
for Cellular and Molecular Biology, Habsiguda, Uppal Road, Hyderabad 500007, India
| | - Scherazad Kootar
- CSIR-Centre
for Cellular and Molecular Biology, Habsiguda, Uppal Road, Hyderabad 500007, India
| | - Arvind Kumar
- CSIR-Centre
for Cellular and Molecular Biology, Habsiguda, Uppal Road, Hyderabad 500007, India
- Academy
of Scientific and Innovative Research (AcSIR), Chennai 600113, India
| | - Saibal Das
- Chemical
Biology and Natural Products Chemistry, CSIR-Indian
Institute of Chemical Technology, Tarnaka, Uppal Road, Hyderabad 500007, India
- Academy
of Scientific and Innovative Research (AcSIR), Chennai 600113, India
| | - Sumana Chakravarty
- Chemical
Biology and Natural Products Chemistry, CSIR-Indian
Institute of Chemical Technology, Tarnaka, Uppal Road, Hyderabad 500007, India
- Academy
of Scientific and Innovative Research (AcSIR), Chennai 600113, India
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10
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Stendall RT, Cobb AJ. Syntheses and applications of enantiopure δ-amino acids and their precursors. Tetrahedron 2018. [DOI: 10.1016/j.tet.2018.05.034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
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11
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Misra R, Raja KMP, Hofmann HJ, Gopi HN. Modulating the Structural Properties of α,γ-Hybrid Peptides by α-Amino Acid Residues: Uniform 12-Helix Versus "Mixed" 12/10-Helix. Chemistry 2017; 23:16644-16652. [PMID: 28922503 DOI: 10.1002/chem.201703871] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Indexed: 01/06/2023]
Abstract
The most important natural α- and 310 -helices are stabilized by unidirectional intramolecular hydrogen bonds along the helical cylinder. In contrast, we report here on 12/10-helical conformations with alternately changing hydrogen-bond directionality in sequences of α,γ-hybrid peptides P1-P5 [P1: Boc-Ala-Aic-Ala-Aic-COOH; P2: Boc-Leu-Aic-Leu-Aic-OEt; P3: Boc-Leu-Aic-Leu-Aic-Leu-Aic-Aib-OMe; P4: Boc-Ala-Aic-Ala-Aic-Ala-Aic-Ala-OMe; P5: Boc-Leu-Aic-Leu-Aic-Leu-Aic-Leu-Aic-Aib-OMe; Aic=4-aminoisocaproic acid, Aib=2-aminoisobutyric acid] composed of natural α-amino acids and the achiral γ4,4 -dimethyl substituted γ-amino acid Aic in solution and in single crystals. The helical conformations are stabilized by alternating i→i+3 and i→i-1 intramolecular hydrogen bonds. The experimental data are supported by ab initio MO calculations. Surprisingly, replacing the natural α-amino acids of the sequence by the achiral dialkyl amino acid Ac6 c [P6: Boc-Ac6 c-Aic-Ac6 c-Aic-Ac6 c-Aic-Ac6 c-Aic-Ac6 c-CONHMe; Ac6 c = 1-aminocyclohexane-1-carboxylic acid] led to a 12-helix with unidirectional hydrogen bonds showing an entirely different backbone conformation. The results presented here emphasize the influence of the structure of the α-amino acid residues in dictating the helix types in α,γ-hybrid peptide foldamers and demonstrate the consequences for folding of small structural variations in the monomers.
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Affiliation(s)
- Rajkumar Misra
- Department of Chemistry, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pashan, Pune, 411 008, India
| | - K Muruga Poopathi Raja
- Department of Physical Chemistry, School of Chemistry, Madurai Kamaraj University, Madurai, 625 021, India
| | - Hans-Jörg Hofmann
- Institute of Biochemistry, Faculty of Biosciences, Pharmacy and Psychology, Brüderstrasse 34, 04103, Leipzig, Germany
| | - Hosahudya N Gopi
- Department of Chemistry, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pashan, Pune, 411 008, India
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12
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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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13
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Thodupunuri P, Hanumaiah M, Bommagani S, Sharma GVM. Stereoselective synthesis of the C-11 to C-19 segment of macrolactin 3 via a center inversion followed by Oxa-Michael addition approach. J Carbohydr Chem 2017. [DOI: 10.1080/07328303.2017.1354012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Prashanth Thodupunuri
- Organic and Bimolecular Chemistry Division, CSIR-Indian Institute of Chemical Technology, Hyderabad, India
| | - Marumamula Hanumaiah
- Organic and Bimolecular Chemistry Division, CSIR-Indian Institute of Chemical Technology, Hyderabad, India
| | - Shobanbabu Bommagani
- Organic and Bimolecular Chemistry Division, CSIR-Indian Institute of Chemical Technology, Hyderabad, India
| | - Gangavaram V. M. Sharma
- Organic and Bimolecular Chemistry Division, CSIR-Indian Institute of Chemical Technology, Hyderabad, India
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14
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Misra R, Saseendran A, George G, Veeresh K, Raja KMP, Raghothama S, Hofmann HJ, Gopi HN. Structural Dimorphism of Achiral α,γ-Hybrid Peptide Foldamers: Coexistence of 12- and 15/17-Helices. Chemistry 2017; 23:3764-3772. [DOI: 10.1002/chem.201605753] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Indexed: 01/17/2023]
Affiliation(s)
- Rajkumar Misra
- Department of Chemistry; Indian Institution of Science Education and Research; Dr. Homi Bhabha Road Pune 411021 India
| | - Abhijith Saseendran
- Department of Chemistry; Indian Institution of Science Education and Research; Dr. Homi Bhabha Road Pune 411021 India
| | - Gijo George
- NMR Research Center; Indian Institute of Science; Bangalore 560012 India
| | - Kuruva Veeresh
- Department of Chemistry; Indian Institution of Science Education and Research; Dr. Homi Bhabha Road Pune 411021 India
| | - K. Muruga Poopathi Raja
- Department of Physical Chemistry; School of Chemistry; Madurai Kamaraj University; Madurai 625 021 India
| | | | - Hans-Jörg Hofmann
- Institute of Biochemistry; Faculty of Biosciences, Pharmacy and Psychology; Talstraße 33 04103 Leipzig Germany
| | - Hosahudya N. Gopi
- Department of Chemistry; Indian Institution of Science Education and Research; Dr. Homi Bhabha Road Pune 411021 India
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15
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Romero E, Moussodia RO, Kriznik A, Wenger E, Acherar S, Jamart-Grégoire B. Spontaneous Self-Assembly of Fully Protected Ester 1:1 [α/α-N α-Bn-hydrazino] Pseudodipeptides into a Twisted Parallel β-Sheet in the Crystal State. J Org Chem 2016; 81:9037-9045. [PMID: 27627436 DOI: 10.1021/acs.joc.6b01680] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Previous studies have demonstrated that amidic α/β-pseudodipeptides, 1:1 [α/α-Nα-Bn-hydrazino], have the ability to fold via a succession of γ-turn (C7 pseudocycle) and hydrazinoturn in CDCl3 solution, their amide terminals enabling the formation of an intramolecular H-bond network. Despite their lack of a primary amide terminals allowing the formation of the hydrazinoturn, their ester counterparts 1-4 were proven to self-assemble into C6 and C7 pseudocycles by intramolecular H-bonds in solution state and into an uncommon twisted parallel β-sheet through intermolecular H-bonding in the crystal state to form a supramolecular helix, with eight molecules needed to complete a full 360° rotation. Such self-organization (with eight molecules) has only been observed in a specific α/α-pseudodipeptide, depsipeptide (Boc-Leu-Lac-OEt). Relying on IR absorption, NMR, X-ray diffraction, and CD analyses, the aim of this study was to demonstrate that stereoisomers of ester 1:1 [α/α-Nα-Bn-hydrazino] pseudodipeptides 1-4 are able to self-assemble into this β-helical structure. The absolute configuration of the asymmetric Cα-atom of the α-amino acid residue influences the left- or right-handed twist without changing the pitch of the formed helix.
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Affiliation(s)
- Eugénie Romero
- Laboratoire de Chimie Physique Macromoléculaire (LCPM), Université de Lorraine-CNRS, UMR 7375 , 1 rue Grandville, BP 20451, 54001 Nancy cedex, France
| | - Ralph-Olivier Moussodia
- Laboratoire de Chimie Physique Macromoléculaire (LCPM), Université de Lorraine-CNRS, UMR 7375 , 1 rue Grandville, BP 20451, 54001 Nancy cedex, France
| | - Alexandre Kriznik
- Ingénierie Moléculaire et Physiopathologie Articulaire (IMoPA), Université de Lorraine-CNRS, UMR 7365 and Service Commun de Biophysique Interactions Moléculaires (SCBIM), Université de Lorraine, FR3209, Biopôle de l'Université de Lorraine, Campus Biologie Santé - Faculté de Médecine , 9 Avenue de la Forêt de Haye, CS 50184, 54505 Vandœuvre-lès-Nancy, France
| | - Emmanuel Wenger
- Laboratoire de Crystallographie, Résonance Magnétique et Modélisations (CRM2), Université de Lorraine-CNRS, UMR 7036, Faculté des Sciences et Technologies , BP 70239, Boulevard des Aiguillettes, 54506 Vandœuvre-lès-Nancy cedex, France
| | - Samir Acherar
- Laboratoire de Chimie Physique Macromoléculaire (LCPM), Université de Lorraine-CNRS, UMR 7375 , 1 rue Grandville, BP 20451, 54001 Nancy cedex, France
| | - Brigitte Jamart-Grégoire
- Laboratoire de Chimie Physique Macromoléculaire (LCPM), Université de Lorraine-CNRS, UMR 7375 , 1 rue Grandville, BP 20451, 54001 Nancy cedex, France
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16
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Rjabovs V, Ostrovskis P, Posevins D, Kiseļovs G, Kumpiņš V, Mishnev A, Turks M. Synthesis of Building Blocks for Carbopeptoids and Their Triazole Isoster Assembly. European J Org Chem 2015. [DOI: 10.1002/ejoc.201500695] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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17
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Nicholas S. The tripeptide N-Cbz-βGly-Gly-Gly-Obz. Acta Crystallogr E Crystallogr Commun 2015; 71:o240-1. [PMID: 26029434 PMCID: PMC4438843 DOI: 10.1107/s2056989015004272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2015] [Accepted: 03/02/2015] [Indexed: 11/10/2022]
Abstract
The title peptide, N-benzyloxycarbonyl-β-glycylglycylglycine benzyl ester, C22H25N3O6, contains a non-proteinogenic amino acid residue, β-glycine, which is a homologated analogue of glycine. In the molecular structure, β-glycine adopts an extended conformation with a trans conformation about its Cβ—Cα bond. The second glycine residue adopts an extended conformation while the third glycine residue adopts a helical conformation. In the crystal, three N—H⋯O hydrogen bonds, two involving the same carbonyl O atom as acceptor, results in an infinite two-dimensional network parallel to the bc plane.
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18
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Kann N, Johansson JR, Beke-Somfai T. Conformational properties of 1,4- and 1,5-substituted 1,2,3-triazole amino acids – building units for peptidic foldamers. Org Biomol Chem 2015; 13:2776-85. [PMID: 25605623 PMCID: PMC4718141 DOI: 10.1039/c4ob02359e] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2014] [Accepted: 01/02/2015] [Indexed: 01/22/2023]
Abstract
Peptidic foldamers have recently emerged as a novel class of artificial oligomers with properties and structural diversity similar to that of natural peptides, but possessing additional interesting features granting them great potential for applications in fields from nanotechnology to pharmaceuticals. Among these, foldamers containing 1,4- and 1,5-substitued triazole amino acids are easily prepared via the Cu- and Ru-catalyzed click reactions and may offer increased side chain variation, but their structural capabilities have not yet been widely explored. We here describe a systematic analysis of the conformational space of the two most important basic units, the 1,4-substitued (4Tzl) and the 1,5-substitued (5Tzl) 1,2,3-triazole amino acids, using quantum chemical calculations and NMR spectroscopy. Possible conformations of the two triazoles were scanned and their potential minima were located using several theoretical approaches (B3LYP/6-311++G(2d,2p), ωB97X-D/6-311++G(2d,2p), M06-2X/6-311++G(2d,2p) and MP2/6-311++G(2d,2p)) in different solvents. BOC-protected versions of 4Tzl and 5Tzl were also prepared via one step transformations and analyzed by 2D NOESY NMR. Theoretical results show 9 conformers for 5Tzl derivatives with relative energies lying close to each other, which may lead to a great structural diversity. NMR analysis also indicates that conformers preferring turn, helix and zig-zag secondary structures may coexist in solution. In contrast, 4Tzl has a much lower number of conformers, only 4, and these lack strong intraresidual interactions. This is again supported by NMR suggesting the presence of both extended and bent conformers. The structural information provided on these building units could be employed in future design of triazole foldamers.
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Affiliation(s)
- Nina Kann
- Department of Chemical and Biological Engineering , Chalmers University of Technology , SE-41296 Göteborg , Sweden . ; ; http://www.chalmers.se/chem/ ; Fax: +46-31-7723858 ; Tel: +46 (0)31 772 3029, +46 (0)31 772 3070
| | - Johan R. Johansson
- AstraZeneca R&D Mölndal , RIA IMED , Medicinal Chemistry , SE-43183 Mölndal , Sweden .
| | - Tamás Beke-Somfai
- Department of Chemical and Biological Engineering , Chalmers University of Technology , SE-41296 Göteborg , Sweden . ; ; http://www.chalmers.se/chem/ ; Fax: +46-31-7723858 ; Tel: +46 (0)31 772 3029, +46 (0)31 772 3070
- Research Centre for Natural Sciences , Hungarian Academy of Sciences , Pázmány Péter sétány 1 , H-1125 Budapest , Hungary
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19
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Sharma GVM, Thodupunuri P, Sirisha K, Basha SJ, Gurava Reddy P, Sarma AVS. Design and synthesis of peptides with hybrid helix-turn-helix (HTH) motif and their conformational study. J Org Chem 2014; 79:8614-28. [PMID: 25180942 DOI: 10.1021/jo501267k] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The present study is aimed at the design and synthesis of peptides with hybrid helix-turn-helix (HTH) motif and their conformational analysis (NMR, MD, and CD studies). The requisite peptides with heterogeneous backbones were prepared from β-, γ-, and δ-amino acids with carbohydrate side chains and α-amino acid, L-Ala. The α/β-peptides were prepared from (S)-β-Caa(l) (C-linked carbo-β-amino acid with D-lyxo furanoside side chain) and L-Ala with a 1:1 alternation. The α/β-peptides with "helix-turn" motif displayed a 11/9-helix nucleating a 13-atom H-bonding turn. The α/β-octapeptides showed the presence of HTH structures with bifurcated 11/15-H-bonded turn. Further, the α/β-hexapeptide with HT motif, independently on coupling with γ/α/γ/α- and δ/α/δ/α-tetrapeptides at the C-terminus provided access to the decapeptides with "hybrid HTH" motifs. The decapeptide ("α-β-α-β-α-β-γ-α-γ-α") showed a hybrid HTH with "11/9/11/9/11/16/9/12/10" H-bonding, while the decapeptide ("α-β-α-β-α-β-δ-α-δ-α") revealed the presence of a "11/9/11/9/11/17/9/13/11" helical pattern. The above peptides thus have shown compatibility between different types of helices and serendipitous bifurcated 11/16- and 11/17-turns. The present study thus provided the first opportunity for the design and study of "hybrid HTH" motifs with more than one kind of helical structures in them.
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Affiliation(s)
- Gangavaram V M Sharma
- Organic and Bimolecular Chemistry Division, CSIR-Indian Institute of Chemical Technology , Hyderabad 500 007, India
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20
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Milli L, Larocca M, Tedesco M, Castellucci N, Ghibaudi E, Cornia A, Calvaresi M, Zerbetto F, Tomasini C. α,ε-Hybrid Foldamers with 1,2,3-Triazole Rings: Order versus Disorder. J Org Chem 2014; 79:5958-69. [DOI: 10.1021/jo500963n] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Lorenzo Milli
- Dipartimento
di Chimica “G. Ciamician”, Alma Mater Studiorum Università di Bologna, Via F. Selmi 2, 40126 Bologna, Italy
| | - Michele Larocca
- Dipartimento
di Chimica “G. Ciamician”, Alma Mater Studiorum Università di Bologna, Via F. Selmi 2, 40126 Bologna, Italy
| | - Mattia Tedesco
- Dipartimento
di Chimica, Università di Torino, Via P. Giuria 7, 10125 Torino, Italy
| | - Nicola Castellucci
- Dipartimento
di Chimica “G. Ciamician”, Alma Mater Studiorum Università di Bologna, Via F. Selmi 2, 40126 Bologna, Italy
| | - Elena Ghibaudi
- Dipartimento
di Chimica, Università di Torino, Via P. Giuria 7, 10125 Torino, Italy
| | - Andrea Cornia
- Department of Chemical and Geological Sciences, University of Modena and Reggio Emilia & INSTM Research Unit, Via G. Campi 183, 41125 Modena, Italy
| | - Matteo Calvaresi
- Dipartimento
di Chimica “G. Ciamician”, Alma Mater Studiorum Università di Bologna, Via F. Selmi 2, 40126 Bologna, Italy
| | - Francesco Zerbetto
- Dipartimento
di Chimica “G. Ciamician”, Alma Mater Studiorum Università di Bologna, Via F. Selmi 2, 40126 Bologna, Italy
| | - Claudia Tomasini
- Dipartimento
di Chimica “G. Ciamician”, Alma Mater Studiorum Università di Bologna, Via F. Selmi 2, 40126 Bologna, Italy
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21
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Johansson JR, Hermansson E, Nordén B, Kann N, Beke-Somfai T. δ-Peptides from RuAAC-Derived 1,5-Disubstituted Triazole Units. European J Org Chem 2014. [DOI: 10.1002/ejoc.201400018] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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22
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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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23
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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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24
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Sharma GVM, Yadav TA, Choudhary M, Kunwar AC. Design of β-Amino Acid with Backbone–Side Chain Interactions: Stabilization of 14/15-Helix in α/β-Peptides. J Org Chem 2012; 77:6834-48. [DOI: 10.1021/jo300865d] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Gangavaram V. M. Sharma
- Organic and
Biomolecuar Chemistry
Division, CSIR-Indian Institute of Chemical Technology, Hyderabad 500 007, India
| | - Thota Anupama Yadav
- Organic and
Biomolecuar Chemistry
Division, CSIR-Indian Institute of Chemical Technology, Hyderabad 500 007, India
| | - Madavi Choudhary
- Centre for Nuclear Magnetic Resonance, CSIR-Indian Institute of Chemical Technology, Hyderabad
500 007, India
| | - Ajit C. Kunwar
- Centre for Nuclear Magnetic Resonance, CSIR-Indian Institute of Chemical Technology, Hyderabad
500 007, India
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25
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Andreini M, Felten AS, Thien HTT, Taillefumier C, Pellegrini-Moïse N, Chapleur Y. Synthesis of new C-glycosyl aza-β3-amino acids building blocks. Tetrahedron Lett 2012. [DOI: 10.1016/j.tetlet.2012.03.072] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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26
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27
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Mali SM, Bandyopadhyay A, Jadhav SV, Kumar MG, Gopi HN. Synthesis of α, β-unsaturated γ-amino esters with unprecedented high (E)-stereoselectivity and their conformational analysis in peptides. Org Biomol Chem 2011; 9:6566-74. [PMID: 21826295 DOI: 10.1039/c1ob05732d] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Mild, efficient and racemization-free synthesis of N-protected α, β-unsaturated γ-amino esters with unprecedented high E- stereoselectivity is described. This method is found to be compatible with Boc-, Fmoc- and other side chain protecting groups. The crystal conformations of the vinylogous γ-amino esters in monomers and in homo- and mixed dipeptides are studied. Further, the vinylogous homo-dipeptide showed a β-sheet conformation, while mixed α- and α,β-unsaturated γ-hybrid dipeptide adapted an irregular structure in single crystals.
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Affiliation(s)
- Sachitanand M Mali
- Department of Chemistry Indian Institute of Science Education and Research, Garware Circle Pashan, Pune, Maharashtra 411021, India
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28
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Affiliation(s)
- Claudia Tomasini
- Dipartimento di Chimica “G. Ciamician” Alma Mater Studiorum Università di Bologna via Selmi 2, 40126 Bologna, Italy, Fax: +39‐051‐2099456
| | - Gaetano Angelici
- Department of Chemistry, University of Basel, St. Johanns‐Ring 19, 4056 Basel, Switzerland
| | - Nicola Castellucci
- Dipartimento di Chimica “G. Ciamician” Alma Mater Studiorum Università di Bologna via Selmi 2, 40126 Bologna, Italy, Fax: +39‐051‐2099456
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29
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Jiao ZG, Chang XW, Ding W, Liu GJ, Song KS, Zhu NY, Zhang DW, Yang D. β NO Turns and Helices Induced by β2-Aminoxy Peptides: Synthesis and Conformational Studies. Chem Asian J 2011; 6:1791-9. [DOI: 10.1002/asia.201000933] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2010] [Indexed: 11/07/2022]
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30
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Sharma GVM, Sai Reddy P, Chatterjee D, Kunwar AC. Synthesis and Structural Studies of Homooligomers of Geminally Disubstituted β2,2-Amino Acids with Carbohydrate Side Chain. J Org Chem 2011; 76:1562-71. [DOI: 10.1021/jo101763t] [Citation(s) in RCA: 20] [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
| | - Post Sai Reddy
- 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
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31
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Sharma GVM, Reddy KS, Basha SJ, Reddy KR, Sarma AVS. Design and synthesis of trans-3-aminopyran-2-carboxylic acid (APyC) and α/β-peptides with 9/11-helix. Org Biomol Chem 2011; 9:8102-11. [DOI: 10.1039/c1ob06279d] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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32
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Roy A, Prabhakaran P, Baruah PK, Sanjayan GJ. Diversifying the structural architecture of synthetic oligomers: the hetero foldamer approach. Chem Commun (Camb) 2011; 47:11593-611. [DOI: 10.1039/c1cc13313f] [Citation(s) in RCA: 106] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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33
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Chakraborty TK, Kumar NVS, Roy S, Dutta SK, Kunwar AC, Sridhar B, Singh H. Stereochemical control in the structures of linear δ
,α
-hybrid tripeptides containing tetrahydrofuran amino acids. J PHYS ORG CHEM 2010. [DOI: 10.1002/poc.1818] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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34
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Sharma GVM, Chandramouli N, Basha SJ, Nagendar P, Ramakrishna KVS, Sarma AVS. The Design of α/β-Peptides: Study on Three-Residue Turn Motifs and the Influence of Achiral Glycine on Helix and Turn. Chem Asian J 2010; 6:84-97. [DOI: 10.1002/asia.201000438] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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35
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Guo L, Almeida AM, Zhang W, Reidenbach AG, Choi SH, Guzei IA, Gellman SH. Helix formation in preorganized beta/gamma-peptide foldamers: hydrogen-bond analogy to the alpha-helix without alpha-amino acid residues. J Am Chem Soc 2010; 132:7868-9. [PMID: 20491510 DOI: 10.1021/ja103233a] [Citation(s) in RCA: 84] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We report the first high-resolution structural data for the beta/gamma-peptide 13-helix (i,i+3 C=O...H-N H-bonds), a secondary structure that is formed by oligomers with a 1:1 alternation of beta- and gamma-amino acid residues. Our characterization includes both crystallographic and 2D NMR data. Previous studies suggested that beta/gamma-peptides constructed from conformationally flexible residues adopt a different helical secondary structure in solution. Our design features preorganized beta- and gamma-residues, which strongly promote 13-helical folding by the 1:1 beta/gamma backbone.
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Affiliation(s)
- Li Guo
- Department of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, USA
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36
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Raju G, Ramesh V, Srinivas R, Sharma GVM, Shoban Babu B. Differentiation of Boc-protected alpha,delta-/delta,alpha- and beta,delta-/delta,beta-hybrid peptide positional isomers by electrospray ionization tandem mass spectrometry. JOURNAL OF MASS SPECTROMETRY : JMS 2010; 45:651-663. [PMID: 20527034 DOI: 10.1002/jms.1756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Two new series of Boc-N-alpha,delta-/delta,alpha- and beta,delta-/delta,beta-hybrid peptides containing repeats of L-Ala-delta(5)-Caa/delta(5)-Caa-L-Ala and beta(3)-Caa-delta(5)-Caa/delta(5)-Caa-beta(3)-Caa (L-Ala = L-alanine, Caa = C-linked carbo amino acid derived from D-xylose) have been differentiated by both positive and negative ion electrospray ionization (ESI) ion trap tandem mass spectrometry (MS/MS). MS(n) spectra of protonated isomeric peptides produce characteristic fragmentation involving the peptide backbone, the Boc-group, and the side chain. The dipeptide positional isomers are differentiated by the collision-induced dissociation (CID) of the protonated peptides. The loss of 2-methylprop-1-ene is more pronounced for Boc-NH-L-Ala-delta-Caa-OCH(3) (1), whereas it is totally absent for its positional isomer Boc-NH-delta-Caa-L-Ala-OCH(3) (7), instead it shows significant loss of t-butanol. On the other hand, second isomeric pair shows significant loss of t-butanol and loss of acetone for Boc-NH-delta-Caa-beta-Caa-OCH(3) (18), whereas these are insignificant for its positional isomer Boc-NH-beta-Caa-delta-Caa-OCH(3) (13). The tetra- and hexapeptide positional isomers also show significant differences in MS(2) and MS(3) CID spectra. It is observed that 'b' ions are abundant when oxazolone structures are formed through five-membered cyclic transition state and cyclization process for larger 'b' ions led to its insignificant abundance. However, b(1)(+) ion is formed in case of delta,alpha-dipeptide that may have a six-membered substituted piperidone ion structure. Furthermore, ESI negative ion MS/MS has also been found to be useful for differentiating these isomeric peptide acids. Thus, the results of MS/MS of pairs of di-, tetra-, and hexapeptide positional isomers provide peptide sequencing information and distinguish the positional isomers.
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Affiliation(s)
- G Raju
- National Centre for Mass Spectrometry, Indian Institute of Chemical Technology, Hyderabad 500 007, India
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37
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Sharma GVM, Manohar V, Dutta SK, Sridhar B, Ramesh V, Srinivas R, Kunwar AC. Self-Assembling Cyclic Tetrapeptide from Alternating C-Linked Carbo-β-amino Acid [(S)-β-Caa] and α-Aminoxy Acid [(R)-Ama]: A Selective Chloride Ion Receptor. J Org Chem 2010; 75:1087-94. [DOI: 10.1021/jo901923q] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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38
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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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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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