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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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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5
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Park HS, Kang YK. Exploring Helical Folding in Oligomers of Cyclopentane-Based ϵ-Amino Acids: A Computational Study. Chemistry 2022; 11:e202100253. [PMID: 35083888 PMCID: PMC8886640 DOI: 10.1002/open.202100253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 12/21/2021] [Indexed: 11/28/2022]
Abstract
The conformational preferences of oligopeptides of an ϵ‐amino acid (2‐((1R,3S)‐3‐(aminomethyl)cyclopentyl)acetic acid, Amc5a) with a cyclopentane substituent in the Cβ−Cγ−Cδ sequence of the backbone were investigated using DFT methods in chloroform and water. The most preferred conformation of Amc5a oligomers (dimer to hexamer) was the H16 helical structure both in chloroform and water. Four residues were found to be sufficient to induce a substantial H16 helix population in solution. The Amc5a hexamer adopted a stable left‐handed (M)‐2.316 helical conformation with a rise of 4.8 Å per turn. The hexamer of Ampa (an analogue of Amc5a with replacing cyclopentane by pyrrolidine) adopted the right‐handed mixed (P)‐2.918/16 helical conformation in chloroform and the (M)‐2.416 helical conformation in water. Therefore, hexamers of ϵ‐amino acid residues exhibited different preferences of helical structures depending on the substituents in peptide backbone and the solvent polarity as well as the chain length.
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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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6
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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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7
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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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8
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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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9
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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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10
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Ramesh Babu A, Raju G, Purna Chander C, Shoban Babu B, Srinivas R, Sharma GVM. Electrospray ionization tandem mass spectrometric study of protonated and alkali- cationized α/ε-hybrid peptides: differentiation of a pair of dipeptide positional isomers. EUROPEAN JOURNAL OF MASS SPECTROMETRY (CHICHESTER, ENGLAND) 2016; 22:181-191. [PMID: 27882883 DOI: 10.1255/ejms.1431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
A new class of Boc-N-protected hybrid peptides derived from L- Ala and ε6-Caa (L-Ala = L-Alanine, Caa = C-linked carboamino acid derived from D-xylose) have been studied by positive ion electrospray ionization (ESI) ion-trap tandem mass spectrometry (MS/MS). MSn spectra of protonated and alkali-cationized hybrid peptides produce characteristic fragmentation involving the peptide backbone, the tert-butyloxycarbonyl (Boc) group, and the side chain. The dipeptide positional isomers are differentiated by the collision-induced dissociation (CID) of the protonated and alkali-cationized peptides. The CID of [M + H]+ ion of Boc-NH-L-Ala-ε-Caa- OCH3 (1) shows a prominent [M + H - C4H8]+ ion, which is totally absent for its positional isomer Boc-NH-ε-Caa-L-Ala-OCH3 (6), which instead shows significant loss of t-butanol. The formation of the [M + Cat - C4H8]+ ion is totally absent and [M + Cat - Boc + H]+ is prominent in the CID of the [M + Cat]+ ion of Boc-NH-L-Ala-ε-Caa- OCH3 (1), whereas the former is highly abundant and the latter is of low abundance for its positional isomer Boc-NH-ε-Caa-L-Ala-OCH3 (6). It is observed that 'b' ions are abundant when oxazolone structures are formed through a five-membered cyclic transition state in tetra-, penta-, and hexapeptides and the cyclization process for larger 'b' ions led to an insignificant abundance. However, the significant 'b' ion is formed in ε,α-dipeptide, which may have a seven-membered substituted 2-oxoazepanium ion structure. The MSn spectra of [M + Cat - Boc + H]+ ions of these peptides are found to be significantly different to those of [M + H - Boc + H]+ ions. The CID spectra of [M + Cat - Boc + H]+ ions of peptide acids containing L-Ala at the C-terminus show an abundant N-terminal rearrangement ion, [bn + 17 + Cat]+, which is absent for the peptide acids containing ε-Caa at the C-terminus. Thus, the results of these hybrid peptides provide sequencing information, the structure of the cyclic intermediate involved in the formation of the rearrangement ion, and distinguish a pair of dipeptide positional isomers.
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Affiliation(s)
- A Ramesh Babu
- National Centre for Mass Spectrometry, CSIR-Indian Institute of Chemical Technology, Hyderabad 500007, India
| | - G Raju
- National Centre for Mass Spectrometry, CSIR-Indian Institute of Chemical Technology, Hyderabad 500007, India
| | - C Purna Chander
- National Centre for Mass Spectrometry, CSIR-Indian Institute of Chemical Technology, Hyderabad 500007, India
| | - B Shoban Babu
- Organic and Biomolecular Chemistry Division, CSIR-Indian Institute of Chemical Technology, Hyderabad 500 007, India
| | - R Srinivas
- National Centre for Mass Spectrometry, CSIR-Indian Institute of Chemical Technology, Hyderabad 500007, India.
| | - G V M Sharma
- Organic and Biomolecular Chemistry Division, CSIR-Indian Institute of Chemical Technology, Hyderabad 500 007, India.
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11
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Sharma GVM, Venkateshwarlu G, Reddy PP, Kunwar AC. New Helical Folds in α-Peptides with Alternating Chirality. Chemistry 2014; 20:11428-38. [DOI: 10.1002/chem.201403164] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2014] [Indexed: 11/08/2022]
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12
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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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13
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Lee M, Shim J, Kang P, Guzei IA, Choi SH. Structural Characterization of α/β-Peptides having Alternating Residues: X-ray Structures of the 11/9-Helix from Crystals of Racemic Mixtures. Angew Chem Int Ed Engl 2013; 52:12564-7. [DOI: 10.1002/anie.201306404] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2013] [Revised: 09/05/2013] [Indexed: 11/06/2022]
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14
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Lee M, Shim J, Kang P, Guzei IA, Choi SH. Structural Characterization of α/β-Peptides having Alternating Residues: X-ray Structures of the 11/9-Helix from Crystals of Racemic Mixtures. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201306404] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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15
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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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16
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Sundararaju B, Sridhar T, Achard M, Sharma GVM, Bruneau C. Ring Closing and Macrocyclization of β-Dipeptides by Olefin Metathesis. European J Org Chem 2013. [DOI: 10.1002/ejoc.201300608] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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17
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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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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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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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20
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Seebach D, Lukaszuk A, Patora-Komisarska K, Podwysocka D, Gardiner J, Ebert MO, Reubi JC, Cescato R, Waser B, Gmeiner P, Hübner H, Rougeot C. On the Terminal Homologation of Physiologically Active Peptides as a Means of Increasing Stability in Human Serum - Neurotensin, Opiorphin, B27-KK10 Epitope, NPY. Chem Biodivers 2011; 8:711-39. [DOI: 10.1002/cbdv.201100093] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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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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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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23
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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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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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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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