1
|
Just D, Palivec V, Bártová K, Bednárová L, Pazderková M, Císařová I, Martinez-Seara H, Jahn U. Foldamers controlled by functional triamino acids: structural investigation of α/γ-hybrid oligopeptides. Commun Chem 2024; 7:114. [PMID: 38796536 PMCID: PMC11128005 DOI: 10.1038/s42004-024-01201-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 05/14/2024] [Indexed: 05/28/2024] Open
Abstract
Peptide-like foldamers controlled by normal amide backbone hydrogen bonding have been extensively studied, and their folding patterns largely rely on configurational and conformational constraints induced by the steric properties of backbone substituents at appropriate positions. In contrast, opportunities to influence peptide secondary structure by functional groups forming individual hydrogen bond networks have not received much attention. Here, peptide-like foldamers consisting of alternating α,β,γ-triamino acids 3-amino-4-(aminomethyl)-2-methylpyrrolidine-3-carboxylate (AAMP) and natural amino acids glycine and alanine are reported, which were obtained by solution phase peptide synthesis. They form ordered secondary structures, which are dominated by a three-dimensional bridged triazaspiranoid-like hydrogen bond network involving the non-backbone amino groups, the backbone amide hydrogen bonds, and the relative configuration of the α,β,γ-triamino and α-amino acid building blocks. This additional stabilization leads to folding in both nonpolar organic as well as in aqueous environments. The three-dimensional arrangement of the individual foldamers is supported by X-ray crystallography, NMR spectroscopy, chiroptical methods, and molecular dynamics simulations.
Collapse
Affiliation(s)
- David Just
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo náměstí 2, 16610, Prague 6, Czech Republic
| | - Vladimír Palivec
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo náměstí 2, 16610, Prague 6, Czech Republic
| | - Kateřina Bártová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo náměstí 2, 16610, Prague 6, Czech Republic
| | - Lucie Bednárová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo náměstí 2, 16610, Prague 6, Czech Republic
| | - Markéta Pazderková
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo náměstí 2, 16610, Prague 6, Czech Republic
| | - Ivana Císařová
- Department of Inorganic Chemistry, Faculty of Science, Charles University in Prague, Hlavova 2030/8, 12843, Prague 2, Czech Republic
| | - Hector Martinez-Seara
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo náměstí 2, 16610, Prague 6, Czech Republic.
| | - Ullrich Jahn
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo náměstí 2, 16610, Prague 6, Czech Republic.
| |
Collapse
|
2
|
Park HS, Lee JY, Kang YK. Exploring helix structures of γ-peptides based on 2-(aminomethyl)cyclopentanecarboxylic acid. Biopolymers 2024; 115:e23575. [PMID: 38465777 DOI: 10.1002/bip.23575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 02/27/2024] [Accepted: 02/28/2024] [Indexed: 03/12/2024]
Abstract
Conformational search and density functional theory calculations were performed to explore the preferences of helical structures for chiro-specific oligo-γ-peptides of 2-(aminomethyl)cyclopentanecarboxylic acid (γAmc5) with a cyclopentyl constraint on the Cα-Cβ bond in solution. The dimer and tetramer of γAmc5 (1) with homochiral (1S, 2S) configurations exhibited a strong preference for the 9-membered helix foldamer in solution, except for the tetramer in water. However, the oligomers of γAmc5 (1) longer than tetramer preferentially adopted a right-handed (P)-2.614-helix (H1-14) as the peptide sequence becomes longer and as solvent polarity increases. The high stabilities for H1-14 foldamers of γAmc5 (1) in solution were ascribed to the favored solvation free energies. The calculated mean backbone torsion angles for H1-14 helix foldamers of γAmc5 (1) were similar to those calculated for oligomers of other γ-residues with cyclopentane or cyclohexane rings. However, the substitution of cyclopentane constraints on the Cα-Cβ bond of the γAmc5 (1) residue resulted in different conformational preferences and/or handedness of helix foldamers. In particular, the pyrrolidine-substituted analogs of the H1-14 foldamers of γAmc5 (1) with adjacent amine diads substituted at a proximal distance are expected to be potential catalysts for the crossed aldol condensation in nonpolar and polar solvents.
Collapse
Affiliation(s)
- Hae Sook Park
- Department of Nursing, Cheju Halla University, Cheju, Republic of Korea
| | - Joo Yun Lee
- AI Team, Yunovia Co., Ltd., Hwaseong-si, Gyeonggi, Republic of Korea
| | - Young Kee Kang
- Department of Chemistry, Chungbuk National University, Cheongju, Chungbuk, Republic of Korea
| |
Collapse
|
3
|
De Franceschi I, Badi N, Du Prez FE. Telechelic sequence-defined oligoamides: their step-economical synthesis, depolymerization and use in polymer networks. Chem Sci 2024; 15:2805-2816. [PMID: 38404375 PMCID: PMC10882489 DOI: 10.1039/d3sc04820a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 01/13/2024] [Indexed: 02/27/2024] Open
Abstract
The application of sequence-defined macromolecules in material science remains largely unexplored due to their challenging, low yielding and time-consuming synthesis. This work first describes a step-economical method for synthesizing unnatural sequence-defined oligoamides through fluorenylmethyloxycarbonyl chemistry. The use of a monodisperse soluble support enables homogeneous reactions at elevated temperature (up to 65 °C), leading to rapid coupling times (<10 min) and improved synthesis protocols. Moreover, a one-pot procedure for the two involved iterative steps is demonstrated via an intermediate quenching step, eliminating the need for in-between purification. The protocol is optimized using γ-aminobutyric acid (GABA) as initial amino acid, and the unique ability of the resulting oligomers to depolymerize, with the formation of cyclic γ-butyrolactame, is evidenced. Furthermore, in order to demonstrate the versatility of the present protocol, a library of 17 unnatural amino acid monomers is synthesized, starting from the readily available GABA-derivative 4-amino-2-hydroxybutanoic acid, and then used to create multifunctional tetramers. Notably, the obtained tetramers show higher thermal stability than a similar thiolactone-based sequence-defined macromolecule, which enables its exploration within a material context. To that end, a bidirectional growth approach is proposed as a greener alternative that reduces the number of synthetic steps to obtain telechelic sequence-defined oligoamides. The latter are finally used as macromers for the preparation of polymer networks. We expect this strategy to pave the way for the further exploration of sequence-defined macromolecules in material science.
Collapse
Affiliation(s)
- Irene De Franceschi
- Polymer Chemistry Research Group, Centre of Macromolecular Chemistry (CMaC), Department of Organic and Macromolecular Chemistry, Faculty of Sciences, Ghent University 9000 Ghent Belgium
| | - Nezha Badi
- Polymer Chemistry Research Group, Centre of Macromolecular Chemistry (CMaC), Department of Organic and Macromolecular Chemistry, Faculty of Sciences, Ghent University 9000 Ghent Belgium
| | - Filip E Du Prez
- Polymer Chemistry Research Group, Centre of Macromolecular Chemistry (CMaC), Department of Organic and Macromolecular Chemistry, Faculty of Sciences, Ghent University 9000 Ghent Belgium
| |
Collapse
|
4
|
Patel AR, Lawer A, Bhadbhade M, Hunter L. The influence of backbone fluorination on the helicity of α/γ-hybrid peptides. Org Biomol Chem 2024; 22:1608-1612. [PMID: 38305470 DOI: 10.1039/d3ob02016a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2024]
Abstract
Peptides that are composed of an alternating pattern of α- and γ-amino acids are potentially valuable as metabolism-resistant bioactive agents. For optimal function, some kind of conformational restriction is usually required to either stabilize the dominant 12-helix, or else to divert the peptide away from this conformation in a controlled way. Herein, we explore stereoselective fluorination as a method for controlling the conformations of α/γ-hybrid peptides. We show through a combination of X-ray, NMR and CD analyses that fluorination can either stabilize or disrupt the 12-helix, depending on the fluorine stereochemistry. These findings could inform the ongoing development of diverse functional hybrid peptides.
Collapse
Affiliation(s)
| | - Aggie Lawer
- School of Chemistry, University of New South Wales (UNSW), Sydney, Australia.
| | - Mohan Bhadbhade
- Mark Wainwright Analytical Centre, University of New South Wales (UNSW), Sydney, Australia
| | - Luke Hunter
- School of Chemistry, University of New South Wales (UNSW), Sydney, Australia.
| |
Collapse
|
5
|
Debnath S, Rajalakshmi VS, Kumar D, Das B, Vasudev PG, Satpati P, Chatterjee S. Ambidexterity and Left-Handedness Induced by Geminally Disubstituted γ Amino Acid Residues in Chiral 3 10 Helices. ACS OMEGA 2023; 8:36370-36385. [PMID: 37810672 PMCID: PMC10552473 DOI: 10.1021/acsomega.3c05124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 08/29/2023] [Indexed: 10/10/2023]
Abstract
Chirality is an omnipresent feature in nature's architecture starting from simple molecules like amino acids to complex higher-order structures viz. proteins, DNA, and RNA. The L configuration of proteinogenic amino acids gives rise to right-handed helices. Ambidexterity is as rare in organisms as in molecules. There are only a few reports of ambidexterity in single-peptide molecules composed of either mixed L and D or achiral residues. Here, we report, for the first time, the ambidextrous and left-handed helical conformations in the chiral nonapeptides P1-P3 (Boc-LUVUγx,xULUV-OMe where U = Aib, x,x = 2,2/3,3/4,4), containing chiral L α amino acid residues, in addition to the usually observed right-handed helical conformation. The centrally located achiral γ residue, capable of adopting both left and right-handed helical conformations, induces its handedness on the neighboring chiral and achiral residues, leading to the observation of both left and right-handed helices in P2 and P3. The presence of a single water molecule proximal to the γ residue induces the reversal of helix handedness by forming distinct and stable water-mediated hydrogen bonds. This gives rise to ambidextrous helices as major conformers in P1 and P2. The absence of the observation of ambidexterity in P3 might be due to the inability of γ4,4 in the recruitment of a water molecule. Experiments (NMR, X-ray, and CD) and density functional theory (DFT) calculations suggest that the position of geminal disubstitution is crucial for determining the population of the amenable helical conformations (ambidextrous, left and right-handed) in these chiral peptides.
Collapse
Affiliation(s)
- Swapna Debnath
- Department
of Chemistry, Indian Institute of Technology,
Guwahati, Guwahati, Assam 781039, India
| | | | - Dinesh Kumar
- Plant
Biotechnology Division, CSIR-Central Institute
of Medicinal and Aromatic Plants Lucknow, Uttar Pradesh 226015, India
| | - Babulal Das
- Department
of Chemistry, Indian Institute of Technology,
Guwahati, Guwahati, Assam 781039, India
| | - Prema G. Vasudev
- Plant
Biotechnology Division, CSIR-Central Institute
of Medicinal and Aromatic Plants Lucknow, Uttar Pradesh 226015, India
| | - Priyadarshi Satpati
- Biosciences
and Bioengineering, Indian Institute of
Technology, Guwahati, Guwahati, Assam 781039, India
| | - Sunanda Chatterjee
- Department
of Chemistry, Indian Institute of Technology,
Guwahati, Guwahati, Assam 781039, India
| |
Collapse
|
6
|
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.
Collapse
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.
| |
Collapse
|
7
|
Zhou M, Feng Z, Zhang X. Recent advances in the synthesis of fluorinated amino acids and peptides. Chem Commun (Camb) 2023; 59:1434-1448. [PMID: 36651307 DOI: 10.1039/d2cc06787k] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
The site-selective modification of amino acids, peptides, and proteins has always been an intensive topic in organic synthesis, medicinal chemistry, and chemical biology due to the vital role of amino acids in life. Among the developed methods, the site-selective introduction of fluorine functionalities into amino acids and peptides has emerged as a useful approach to change their physicochemical and biological properties. With the increasing demand for life science, the direct fluorination/fluoroalkylation of proteins has also received increasing attention because of the unique properties of fluorine atom(s) that can change the protein structure, increase their lipophilicity, and enable fluorine functionality as a biological tracer or probe for chemical biology studies. In this feature article, we summarized the recent advances in the synthesis of fluorinated amino acids and peptides, wherein two strategies have been discussed. One is based on the fluorinated building blocks to prepare fluorinated amino acids and peptides with diversified structures, including the transformations of fluorinated imines and nickel-catalyzed dicarbofunctionalization of alkenes with bromodifluoroacetate and its derivatives; the other is direct fluorination/fluoroakylation of amino acids, peptides, and proteins, in which the selective transformations of the functional groups on serine, threonine, tyrosine, tryptophan, and cysteine lead to a wide range of fluorinated α-amino acids, peptides, and proteins, featuring synthetic convenience and late-stage modification of biomacromolecules. These two strategies complement each other, wherein transition-metal catalysis and new fluoroalkylating reagents provide powerful tools to selectively access fluorinated amino acids, peptides, and proteins, showing the prospect of medicinal chemistry and chemical biology.
Collapse
Affiliation(s)
- Minqi Zhou
- College of Chemistry, Institute of Green Catalysis, Zhengzhou University, Zhengzhou 450001, P. R. China
| | - Zhang Feng
- Key Laboratory of Organofluorine Chemistry, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China.
| | - Xingang Zhang
- College of Chemistry, Institute of Green Catalysis, Zhengzhou University, Zhengzhou 450001, P. R. China.,Key Laboratory of Organofluorine Chemistry, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China.
| |
Collapse
|
8
|
Boruah A, Roy A. Advances in hybrid peptide-based self-assembly systems and their applications. Biomater Sci 2022; 10:4694-4723. [PMID: 35899853 DOI: 10.1039/d2bm00775d] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Self-assembly of peptides demonstrates a great potential for designing highly ordered, finely tailored supramolecular arrangements enriched with high specificity, improved efficacy and biological activity. Along with natural peptides, hybrid peptide systems composed of natural and chemically diverse unnatural amino acids have been used in various fields, including drug delivery, wound healing, potent inhibition of diseases, and prevention of biomaterial related diseases to name a few. In this review, we provide a brief outline of various methods that have been utilized for obtaining fascinating structures that create an avenue to reproduce a range of functions resulting from these folds. An overview of different self-assembled structures as well as their applications will also be provided. We believe that this review is very relevant to the current scenario and will cover conformations of hybrid peptides and resulting self-assemblies from the late 20th century through 2022. This review aims to be a comprehensive and reliable account of the hybrid peptide-based self-assembly owing to its enormous influence in understanding and mimicking biological processes.
Collapse
Affiliation(s)
- Alpana Boruah
- Applied Organic Chemistry Group, Chemical Sciences and Technology Division, Council of Scientific and Industrial Research-North East Institute of Science and Technology (CSIR-NEIST), Pulibor, Jorhat-785006, Assam, India. .,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad-201002, India
| | - Arup Roy
- Applied Organic Chemistry Group, Chemical Sciences and Technology Division, Council of Scientific and Industrial Research-North East Institute of Science and Technology (CSIR-NEIST), Pulibor, Jorhat-785006, Assam, India. .,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad-201002, India
| |
Collapse
|
9
|
Takada H, Tsuchiya K, Demizu Y. Helix-Stabilized Cell-Penetrating Peptides for Delivery of Antisense Morpholino Oligomers: Relationships among Helicity, Cellular Uptake, and Antisense Activity. Bioconjug Chem 2022; 33:1311-1318. [PMID: 35737901 DOI: 10.1021/acs.bioconjchem.2c00199] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The secondary structures of cell-penetrating peptides (CPPs) influence their properties including their cell-membrane permeability, tolerability to proteases, and intracellular distribution. Herein, we developed helix-stabilized arginine-rich peptides containing α,α-disubstituted α-amino acids and their conjugates with antisense phosphorodiamidate morpholino oligomers (PMOs), to investigate the relationships among the helicity of the peptides, cellular uptake, and antisense activity of the peptide-conjugated PMOs. We demonstrated that helical CPPs can efficiently deliver the conjugated PMO into cells compared with nonhelical CPPs and that their antisense activities are synergistically enhanced in the presence of an endosomolytic reagent or an endosomal escape domain peptide.
Collapse
Affiliation(s)
- Hiroyuki Takada
- Division of Organic Chemistry, National Institute of Health Sciences, Kanagawa 210-9501, Japan.,Graduate School of Medical Life Science, Yokohama City University, Kanagawa 236-0027, Japan
| | - Keisuke Tsuchiya
- Division of Organic Chemistry, National Institute of Health Sciences, Kanagawa 210-9501, Japan.,Graduate School of Pharmacy, Showa University, Tokyo 142-8555, Japan
| | - Yosuke Demizu
- Division of Organic Chemistry, National Institute of Health Sciences, Kanagawa 210-9501, Japan.,Graduate School of Medical Life Science, Yokohama City University, Kanagawa 236-0027, Japan.,Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama 700-8530, Japan
| |
Collapse
|
10
|
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.
Collapse
|
11
|
Fischer JL, Blodgett KN, Harrilal CP, Walsh PS, Davis ZS, Choi S, Choi SH, Zwier TS. Conformer-Specific Spectroscopy and IR-Induced Isomerization of a Model γ-Peptide: Ac-γ 4-Phe-NHMe. J Phys Chem A 2022; 126:1837-1847. [PMID: 35275624 DOI: 10.1021/acs.jpca.2c00112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Single-conformation IR and UV spectroscopy of the prototypical capped γ-peptide Ac-γ4-Phe-NHMe (γ4F) was carried out under jet-cooled conditions in the gas phase in order to understand its innate conformational preferences in the absence of a solvent. We obtained conformer-specific IR and UV spectra and compared the results with calculations to make assignments and explore the differences between the γ2- and γ4-substituted molecules. We found four conformers of γ4F in our experiment. Three conformers form nine-membered hydrogen-bonded rings (C9) enclosed by an NH···O═C H-bond but differing in their phenyl ring positions (a, g+, and g-). The fourth conformer forms a strained seven-membered hydrogen-bonded ring in which the amide groups lie in a nominally anti-parallel arrangement stacked on top of one another (labeled S7). This conformer is a close analogue of the amide-stacked conformer (S) found previously in γ2F, in which the Phe side chain is substituted at the γ2 position, Ac-γ2-Phe-NHMe (J. Am. Chem. Soc. 2009, 131, 14243-14245). IR population transfer spectroscopy was used to determine the fractional abundances of the γ4F conformers in the expansion. A combination of force field and density functional theory calculations is used to map out the conformational potential energy surfaces for γ4F and compare it with its γ2F counterpart. Based on this analysis, the phenyl ring prefers to take up structures that facilitate NH···π interactions in γ4F or avoid phenyl interactions with the C═O group in γ2F. The disconnectivity graph for γ4F reveals separate basins associated with the C9 and amide-stacked conformational families, which are separated by a barrier of about 42 kJ/mol. The overall shape of the potential energy surface bears a resemblance to peptides and proteins that have a misfolding pathway that competes with the formation of the native structure.
Collapse
Affiliation(s)
- Joshua L Fischer
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, United States
| | - Karl N Blodgett
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, United States
| | - Christopher P Harrilal
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, United States
| | - Patrick S Walsh
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, United States
| | - Zachary S Davis
- Department of Chemistry, Wofford College, Spartanburg, South Carolina 29303, United States
| | - Sunglim Choi
- Department of Chemistry, Yonsei University, Seoul 03722, South Korea
| | - Soo Hyuk Choi
- Department of Chemistry, Yonsei University, Seoul 03722, South Korea
| | - Timothy S Zwier
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, United States.,Gas Phase Chemical Physics, Sandia National Laboratories, Livermore, California 94550, United States
| |
Collapse
|
12
|
Fang YQ, Chen T, Huang G, Ni S, Dang L. Reaction mechanism for copper catalyzed functionalization of unsaturated side chains of amides via domino rearrangement. J Organomet Chem 2022. [DOI: 10.1016/j.jorganchem.2021.122233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
|
13
|
Singh MK, Lakshman MK. Recent developments in the utility of saturated azaheterocycles in peptidomimetics. Org Biomol Chem 2022; 20:963-979. [PMID: 35018952 DOI: 10.1039/d1ob01329g] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
To a large extent, the physical and chemical properties of peptidomimetic molecules are dictated by the integrated heterocyclic scaffolds they contain. Heterocyclic moieties are introduced into a majority of peptide-mimicking molecules to modulate conformational flexibility, improve bioavailability, and fine-tune electronics, and in order to achieve potency similar to or better than that of the natural peptide ligand. This mini-review delineates recent developments, limited to the past five years, in the utility of selected saturated 3- to 6-membered heterocyclic moieties in peptidomimetic design. Also discussed is the chemistry involved in the synthesis of the azaheterocyclic scaffolds and the structural implications of the introduction of these azaheterocycles in peptide backbones as well as side chains of the peptide mimics.
Collapse
Affiliation(s)
- Manish K Singh
- Department of Science, Technology, and Mathematics, Lincoln University, 820 Chestnut Street, Jefferson City, Missouri 65101, USA.
| | - Mahesh K Lakshman
- Department of Chemistry and Biochemistry, The City College of New York, 160 Convent Avenue, New York, New York 10031, USA.,The Ph.D. Program in Chemistry, The Graduate Center of the City University of New York, New York, NY 10016, USA
| |
Collapse
|
14
|
Oh BC, Yoon E, Gong J, Kim J, Driver RW, Kim Y, Kim WY, Lee HS. Morphology Transformation of Foldamer Assemblies Triggered by Single Oxygen Atom on Critical Residue Switch. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2021; 17:e2102525. [PMID: 34310034 DOI: 10.1002/smll.202102525] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 07/06/2021] [Indexed: 06/13/2023]
Abstract
The synthesis of morphologically well-defined peptidic materials via self-assembly is challenging but demanding for biocompatible functional materials. Moreover, switching morphology from a given shape to other predictable forms by molecular modification of the identical building block is an even more complicated subject because the self-assembly of flexible peptides is prone to diverge upon subtle structural change. To accomplish controllable morphology transformation, systematic self-assembly studies are performed using congener short β-peptide foldamers to find a minimal structural change that alters the self-assembled morphology. Introduction of oxygen-containing β-amino acid (ATFC) for subtle electronic perturbation on hydrophobic foldamer induces a previously inaccessible solid-state conformational split to generate the most susceptible modification site for morphology transformation of the foldamer assemblies. The site-dependent morphological switching power of ATFC is further demonstrated by dual substitution experiments and proven by crystallographic analyses. Stepwise morphology transformation is shown by modifying an identical foldamer scaffold. This study will guide in designing peptidic molecules from scratch to create complex and biofunctional assemblies with nonspherical shapes.
Collapse
Affiliation(s)
- Byung-Chang Oh
- Center for Multiscale Chiral Architectures, Department of Chemistry, Korea Advanced Institute of Science and Technology, Yuseong-gu, Daejeon, 34141, Korea
| | - Eunyoung Yoon
- Korea Research Institute of Chemical Technology, Yuseong-gu, Daejeon, 34114, Korea
| | - Jintaek Gong
- Center for Multiscale Chiral Architectures, Department of Chemistry, Korea Advanced Institute of Science and Technology, Yuseong-gu, Daejeon, 34141, Korea
| | - Jaewook Kim
- Center for Multiscale Chiral Architectures, Department of Chemistry, Korea Advanced Institute of Science and Technology, Yuseong-gu, Daejeon, 34141, Korea
| | - Russell W Driver
- Department of Chemistry and Physics, Halmos College of Arts and Sciences, Nova Southeastern University, Fort Lauderdale, FL, 33314, USA
| | - Yongjun Kim
- Center for Multiscale Chiral Architectures, Department of Chemistry, Korea Advanced Institute of Science and Technology, Yuseong-gu, Daejeon, 34141, Korea
| | - Woo Youn Kim
- Center for Multiscale Chiral Architectures, Department of Chemistry, Korea Advanced Institute of Science and Technology, Yuseong-gu, Daejeon, 34141, Korea
| | - Hee-Seung Lee
- Center for Multiscale Chiral Architectures, Department of Chemistry, Korea Advanced Institute of Science and Technology, Yuseong-gu, Daejeon, 34141, Korea
| |
Collapse
|
15
|
Hirano M, Saito C, Goto C, Yokoo H, Kawano R, Misawa T, Demizu Y. Rational Design of Helix-Stabilized Antimicrobial Peptide Foldamers Containing α,α-Disubstituted Amino Acids or Side-Chain Stapling. Chempluschem 2021; 85:2731-2736. [PMID: 33369262 DOI: 10.1002/cplu.202000749] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 12/15/2020] [Indexed: 12/19/2022]
Abstract
Antimicrobial peptides (AMPs) are expected to be good candidate molecules for novel antimicrobial therapies. Most AMPs exert their antimicrobial activity through disruption of microbial membranes due to their amphipathic properties. Recently, the helical peptide 'Stripe' was reported by our group, a rationally designed amphipathic AMP focused on distribution of natural cationic and hydrophobic amino acid residues. In this study, a set of Stripe-based AMP foldamers was designed, synthesized and investigated that contain α,α-disubstituted amino acids or side-chain stapling to stabilize their helical structures. Our results showed that a peptide containing 2-aminoisobutyric acid (Aib) residues exhibited potent antimicrobial activity against both Gram-positive S.aureus (MIC value: 3.125 μM) and Gram-negative bacteria (including a multidrug-resistant strain, MDRP, MIC value: 1.56 μM), without significant hemolytic activity (>100 μM). Electrophysiological measurements revealed that this peptide formed stable pores in a 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine (DOPE)/1,2-dioleoyl-sn-glycero-3-phosphoglycerol (DOPG) bilayer but not in a dioleoylphosphocholine (DOPC) bilayer. The introduction of Aib residues into Stripe could be a promising way to increase the antimicrobial activity of AMP foldamers, and the peptide could represent a promising novel therapeutic candidate to treat multidrug-resistant bacterial infection.
Collapse
Affiliation(s)
- Motoharu Hirano
- Division of Organic Chemistry, National Institute of Health Sciences, 3-25-26, Tonomachi, Kawasaki, Kanagawa, 210-9501, Japan.,Graduate School of Medical Life Science, Yokohama City University, 1-7-29, Yokohama, Kanagawa, 230-0045, Japan
| | - Chihiro Saito
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-6 Naka-cho, Koganei, Tokyo, 184-8588, Japan
| | - Chihiro Goto
- Division of Organic Chemistry, National Institute of Health Sciences, 3-25-26, Tonomachi, Kawasaki, Kanagawa, 210-9501, Japan.,Graduate School of Medical Life Science, Yokohama City University, 1-7-29, Yokohama, Kanagawa, 230-0045, Japan
| | - Hidetomo Yokoo
- Division of Organic Chemistry, National Institute of Health Sciences, 3-25-26, Tonomachi, Kawasaki, Kanagawa, 210-9501, Japan
| | - Ryuji Kawano
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-6 Naka-cho, Koganei, Tokyo, 184-8588, Japan
| | - Takashi Misawa
- Division of Organic Chemistry, National Institute of Health Sciences, 3-25-26, Tonomachi, Kawasaki, Kanagawa, 210-9501, Japan
| | - Yosuke Demizu
- Division of Organic Chemistry, National Institute of Health Sciences, 3-25-26, Tonomachi, Kawasaki, Kanagawa, 210-9501, Japan.,Graduate School of Medical Life Science, Yokohama City University, 1-7-29, Yokohama, Kanagawa, 230-0045, Japan
| |
Collapse
|
16
|
Legrand B, Maillard LT. α,β-Unsaturated γ-Peptide Foldamers. Chempluschem 2021; 86:629-645. [PMID: 33856125 DOI: 10.1002/cplu.202100045] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 03/31/2021] [Indexed: 01/01/2023]
Abstract
Despite their concomitant emergence in the 1990s, γ-peptide foldamers have not developed as fast as β-peptide foldamers and to date, only a few γ-oligomer structures have been reported, and with sparse applications. Among these examples, sequences containing α,β-unsaturated γ-amino acids have recently drawn attention since the Z/E configurations of the double bond provide opposite planar restrictions leading to divergent conformational behaviors, from helix to extended structures. In this Review, we give a comprehensive overview of the developments of γ-peptide foldamers containing α,β-unsaturated γ-amino acids with examples of applications for health and catalysis, as well as materials science.
Collapse
Affiliation(s)
- Baptiste Legrand
- Institut des Biomolécules Max Mousseron, IBMM, University of Montpellier, ENSCM, CNRS, Montpellier, France., 15 Av. Charles Flahault BP 14 491, 34093, Montpellier Cedex 5, France
| | - Ludovic T Maillard
- Institut des Biomolécules Max Mousseron, IBMM, University of Montpellier, ENSCM, CNRS, Montpellier, France., 15 Av. Charles Flahault BP 14 491, 34093, Montpellier Cedex 5, France
| |
Collapse
|
17
|
Lawer A, Hunter L. Controlling γ‐Peptide Helicity with Stereoselective Fluorination. European J Org Chem 2021. [DOI: 10.1002/ejoc.202001619] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Aggie Lawer
- School of Chemistry The University of New South Wales (UNSW) Sydney 2052 Australia
| | - Luke Hunter
- School of Chemistry The University of New South Wales (UNSW) Sydney 2052 Australia
| |
Collapse
|
18
|
Wątły J, Miller A, Kozłowski H, Rowińska-Żyrek M. Peptidomimetics - An infinite reservoir of metal binding motifs in metabolically stable and biologically active molecules. J Inorg Biochem 2021; 217:111386. [PMID: 33610030 DOI: 10.1016/j.jinorgbio.2021.111386] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Revised: 01/14/2021] [Accepted: 01/27/2021] [Indexed: 12/12/2022]
Abstract
The involvement of metal ions in interactions with therapeutic peptides is inevitable. They are one of the factors able to fine-tune the biological properties of antimicrobial peptides, a promising group of drugs with one large drawback - a problematic metabolic stability. Appropriately chosen, proteolytically stable peptidomimetics seem to be a reasonable solution of the problem, and the use of D-, β-, γ-amino acids, unnatural amino acids, azapeptides, peptoids, cyclopeptides and dehydropeptides is an infinite reservoir of metal binding motifs in metabolically stable, well-designed, biologically active molecules. Below, their specific structural features, metal-chelating abilities and antimicrobial potential are discussed.
Collapse
Affiliation(s)
- Joanna Wątły
- Faculty of Chemistry, University of Wroclaw, Joliot - Curie 14, Wroclaw 50-383, Poland.
| | - Adriana Miller
- Faculty of Chemistry, University of Wroclaw, Joliot - Curie 14, Wroclaw 50-383, Poland
| | - Henryk Kozłowski
- Faculty of Chemistry, University of Wroclaw, Joliot - Curie 14, Wroclaw 50-383, Poland; Department of Health Sciences, University of Opole, Katowicka 68, Opole 45-060, Poland
| | | |
Collapse
|
19
|
Reese HR, Shanahan CC, Proulx C, Menegatti S. Peptide science: A "rule model" for new generations of peptidomimetics. Acta Biomater 2020; 102:35-74. [PMID: 31698048 DOI: 10.1016/j.actbio.2019.10.045] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2019] [Revised: 10/17/2019] [Accepted: 10/30/2019] [Indexed: 02/07/2023]
Abstract
Peptides have been heavily investigated for their biocompatible and bioactive properties. Though a wide array of functionalities can be introduced by varying the amino acid sequence or by structural constraints, properties such as proteolytic stability, catalytic activity, and phase behavior in solution are difficult or impossible to impart upon naturally occurring α-L-peptides. To this end, sequence-controlled peptidomimetics exhibit new folds, morphologies, and chemical modifications that create new structures and functions. The study of these new classes of polymers, especially α-peptoids, has been highly influenced by the analysis, computational, and design techniques developed for peptides. This review examines techniques to determine primary, secondary, and tertiary structure of peptides, and how they have been adapted to investigate peptoid structure. Computational models developed for peptides have been modified to predict the morphologies of peptoids and have increased in accuracy in recent years. The combination of in vitro and in silico techniques have led to secondary and tertiary structure design principles that mirror those for peptides. We then examine several important developments in peptoid applications inspired by peptides such as pharmaceuticals, catalysis, and protein-binding. A brief survey of alternative backbone structures and research investigating these peptidomimetics shows how the advancement of peptide and peptoid science has influenced the growth of numerous fields of study. As peptide, peptoid, and other peptidomimetic studies continue to advance, we will expect to see higher throughput structural analyses, greater computational accuracy and functionality, and wider application space that can improve human health, solve environmental challenges, and meet industrial needs. STATEMENT OF SIGNIFICANCE: Many historical, chemical, and functional relations draw a thread connecting peptides to their recent cognates, the "peptidomimetics". This review presents a comprehensive survey of this field by highlighting the width and relevance of these familial connections. In the first section, we examine the experimental and computational techniques originally developed for peptides and their morphing into a broader analytical and predictive toolbox. The second section presents an excursus of the structures and properties of prominent peptidomimetics, and how the expansion of the chemical and structural diversity has returned new exciting properties. The third section presents an overview of technological applications and new families of peptidomimetics. As the field grows, new compounds emerge with clear potential in medicine and advanced manufacturing.
Collapse
|
20
|
Misra R, George G, Saseendran A, Raghothama S, Gopi HN. Ambidextrous α,γ-Hybrid Peptide Foldamers. Chem Asian J 2019; 14:4408-4414. [PMID: 31670907 DOI: 10.1002/asia.201901411] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 10/21/2019] [Indexed: 12/12/2022]
Abstract
Molecular chirality is ubiquitous in nature. The natural biopolymers, proteins and DNA, preferred a right-handed helical bias due to the inherent stereochemistry of the monomer building blocks. Here, we are reporting a rare co-existence of left- and right-handed helical conformations and helix-terminating property at the C-terminus within a single molecule of α,γ-hybrid peptide foldamers composed of achiral Aib (α-aminoisobutyric acid) and 3,3-dimethyl-substituted γ-amino acid (Adb; 4-amino-3,3-dimethylbutanoic acid). At the molecular level, the left- and right-handed helical screw sense of α,γ-hybrid peptides are representing a macroscopic tendril perversion. The pronounced helix-terminating behaviour of C-terminal Adb residues was further explored to design helix-Schellman loop mimetics and to study their conformations in solution and single crystals. The stereochemical constraints of dialkyl substitutions on γ-amino acids showed a marked impact on the folding behaviour of α,γ-hybrid peptides.
Collapse
Affiliation(s)
- Rajkumar Misra
- Department of Chemistry, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pashan, Pune, 411008, India
| | - Gijo George
- NMR Research Center, Indian Institute of Science, Bangalore, 560012, India
| | - Abhijith Saseendran
- Department of Chemistry, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pashan, Pune, 411008, India
| | | | - Hosahudya N Gopi
- Department of Chemistry, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pashan, Pune, 411008, India
| |
Collapse
|
21
|
Oliva F, Bucci R, Tamborini L, Pieraccini S, Pinto A, Pellegrino S. Bicyclic Pyrrolidine-Isoxazoline γ Amino Acid: A Constrained Scaffold for Stabilizing α-Turn Conformation in Isolated Peptides. Front Chem 2019; 7:133. [PMID: 30937302 PMCID: PMC6431668 DOI: 10.3389/fchem.2019.00133] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 02/20/2019] [Indexed: 12/22/2022] Open
Abstract
Unnatural amino acids have tremendously expanded the folding possibilities of peptides and peptide mimics. While α,α-disubstituted and β-amino acids are widely studied, γ-derivatives have been less exploited. Here we report the conformational study on the bicyclic unnatural γ amino acid, 4,5,6,6a-tetrahydro-3aH-pyrrolo[3,4-d]isoxazole-3-carboxylic acid 1. In model peptides, the (+)-(3aR6aS)-enantiomer is able to stabilize α-turn conformation when associated to glycine, as showed by 1H-NMR, FT-IR, and circular dichroism experiments, and molecular modeling studies. α-turn is a structural motif occurring in many biologically active protein sites, although its stabilization on isolated peptides is quite uncommon. Our results make the unnatural γ-amino acid 1 of particular interest for the development of bioactive peptidomimetics.
Collapse
Affiliation(s)
| | - Raffaella Bucci
- Department of Pharmaceutical Sciences, University of Milan, Milan, Italy
| | - Lucia Tamborini
- Department of Pharmaceutical Sciences, University of Milan, Milan, Italy
| | | | - Andrea Pinto
- Department of Food, Environmental and Nutritional Sciences, University of Milan, Milan, Italy
| | - Sara Pellegrino
- Department of Pharmaceutical Sciences, University of Milan, Milan, Italy
| |
Collapse
|
22
|
Kerres S, Plut E, Malcherek S, Rehbein J, Reiser O. Visible Light‐Mediated Synthesis of Enantiopure γ‐Cyclobutane Amino and 3‐(Aminomethyl)‐5‐phenylpentanoic Acids. Adv Synth Catal 2019. [DOI: 10.1002/adsc.201801413] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Sabine Kerres
- Institut für Organische ChemieUniversität Regensburg Universitätstrasse 31 93053 Regensburg Germany
| | - Eva Plut
- Institut für Organische ChemieUniversität Regensburg Universitätstrasse 31 93053 Regensburg Germany
| | - Simon Malcherek
- Institut für Organische ChemieUniversität Regensburg Universitätstrasse 31 93053 Regensburg Germany
| | - Julia Rehbein
- Institut für Organische ChemieUniversität Regensburg Universitätstrasse 31 93053 Regensburg Germany
| | - Oliver Reiser
- Institut für Organische ChemieUniversität Regensburg Universitätstrasse 31 93053 Regensburg Germany
| |
Collapse
|
23
|
Wan Y, Baltaze JP, Kouklovsky C, Miclet E, Alezra V. Unexpected dimerization of a tripeptide comprising a β,γ-diamino acid. J Pept Sci 2018; 25:e3143. [DOI: 10.1002/psc.3143] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Revised: 11/22/2018] [Accepted: 11/30/2018] [Indexed: 11/10/2022]
Affiliation(s)
- Yang Wan
- National Pharmaceutical Engineering Center for Solid Preparation in Chinese Herbal Medicine; Jiangxi University of Traditional Chinese Medicine; Nanchang China
- Faculté des Sciences d'Orsay, Laboratoire de Méthodologie, Synthèse et Molécules Thérapeutiques, ICMMO, UMR 8182, CNRS; Université Paris-Saclay; Orsay France
| | - Jean-Pierre Baltaze
- Faculté des Sciences d'Orsay, Laboratoire de Méthodologie, Synthèse et Molécules Thérapeutiques, ICMMO, UMR 8182, CNRS; Université Paris-Saclay; Orsay France
| | - Cyrille Kouklovsky
- Faculté des Sciences d'Orsay, Laboratoire de Méthodologie, Synthèse et Molécules Thérapeutiques, ICMMO, UMR 8182, CNRS; Université Paris-Saclay; Orsay France
| | - Emeric Miclet
- Laboratoire des biomolécules; Sorbonne Université, École normale supérieure, PSL University, CNRS; Paris France
| | - Valérie Alezra
- Faculté des Sciences d'Orsay, Laboratoire de Méthodologie, Synthèse et Molécules Thérapeutiques, ICMMO, UMR 8182, CNRS; Université Paris-Saclay; Orsay France
| |
Collapse
|
24
|
Just D, Hernandez-Guerra D, Kritsch S, Pohl R, Císařová I, Jones PG, Mackman R, Bahador G, Jahn U. Lithium Chloride Catalyzed Asymmetric Domino Aza-Michael Addition/[3 + 2] Cycloaddition Reactions for the Synthesis of Spiro- and Bicyclic α,β,γ-Triamino Acid Derivatives. European J Org Chem 2018. [DOI: 10.1002/ejoc.201800585] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- David Just
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences; Flemingovo nám. 2 166 10 Prague 6 Czech Republic
| | - Daniel Hernandez-Guerra
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences; Flemingovo nám. 2 166 10 Prague 6 Czech Republic
| | - Susanne Kritsch
- Fachbereich Chemie; Technische Universität Braunschweig; Hagenring 30 38106 Braunschweig Germany
| | - Radek Pohl
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences; Flemingovo nám. 2 166 10 Prague 6 Czech Republic
| | - Ivana Císařová
- Department of Inorganic Chemistry; Faculty of Science; Charles University; Hlavova 2030/8 128 43 Prague 2 Czech Republic
| | - Peter G. Jones
- Fachbereich Chemie; Technische Universität Braunschweig; Hagenring 30 38106 Braunschweig Germany
| | - Richard Mackman
- Gilead Sciences, Inc.; 333 Lakeside Drive 94404 Foster City CA USA
| | - Gina Bahador
- Gilead Sciences, Inc.; 333 Lakeside Drive 94404 Foster City CA USA
| | - Ullrich Jahn
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences; Flemingovo nám. 2 166 10 Prague 6 Czech Republic
| |
Collapse
|
25
|
Shin YH, Gellman SH. Impact of Backbone Pattern and Residue Substitution on Helicity in α/β/γ-Peptides. J Am Chem Soc 2018; 140:1394-1400. [PMID: 29350033 DOI: 10.1021/jacs.7b10868] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
We have evaluated the impact of changes in the chemical structure of peptidic oligomers containing α-, β-, and γ-amino acid residues (α/β/γ-peptides) on the propensities of these oligomers to adopt helical conformations in aqueous and alcoholic solutions. These studies were inspired by our previous discovery that α/β/γ-peptides containing a regular αγααβα hexad repeat adopt an α-helix-like conformation in which the β and γ residues are aligned in a stripe along one side, and the remainder of the helix surface is defined by the α residues. This helix was found to be most stable when the β and γ residues were rigidified with specific cyclic constraints. Relaxation of the β residue constraints caused profound conformational destabilization, but relaxation of the γ residue constraints led to only a moderate drop in helicity. The new work more broadly characterizes the effect of γ residue substitution on helix stability, based on circular dichroism and two-dimensional NMR measurements. We find that even a fully unsubstituted γ residue (derived from γ-aminobutyric acid) supports a moderate helical propensity, which is surprising in light of the strong destabilizing effect of glycine residues on α-helix stability. Additional studies examine the effects of altering sequence in terms of amino acid type, by comparing a prototype with the αγααβα hexad pattern to isomers with irregular arrangements of the α, β, and γ residues along the backbone. The data indicate that the strong helix-forming propensity previously discovered for α/β/γ-peptide 12-mers is retained when sequence is varied, with small variations detected across diverse α-β-γ placements. These structural findings suggest that α/β/γ-peptide scaffolds represent versatile scaffolds for the design of peptidic foldamers that display specific functions.
Collapse
Affiliation(s)
- Young-Hee Shin
- Department of Chemistry, University of Wisconsin-Madison , Madison, Wisconsin 53706, United States
| | - Samuel H Gellman
- Department of Chemistry, University of Wisconsin-Madison , Madison, Wisconsin 53706, United States
| |
Collapse
|
26
|
Wan Y, Auberger N, Thétiot-Laurent S, Bouillère F, Zulauf A, He J, Courtiol-Legourd S, Guillot R, Kouklovsky C, Cote des Combes S, Pacaud C, Devillers I, Alezra V. Constrained Cyclic β,γ-Diamino Acids from Glutamic Acid: Synthesis of Both Diastereomers and Unexpected Kinetic Resolution. European J Org Chem 2018. [DOI: 10.1002/ejoc.201701477] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Yang Wan
- Laboratoire de Méthodologie, Synthèse et Molécules Thérapeutiques; ICMMO; UMR 8182, CNRS, Univ. Paris-Sud; Université Paris-Saclay; Faculté des Sciences d'Orsay; Bât 410 91405 Orsay France
| | - Nicolas Auberger
- Laboratoire de Méthodologie, Synthèse et Molécules Thérapeutiques; ICMMO; UMR 8182, CNRS, Univ. Paris-Sud; Université Paris-Saclay; Faculté des Sciences d'Orsay; Bât 410 91405 Orsay France
| | - Sophie Thétiot-Laurent
- Laboratoire de Méthodologie, Synthèse et Molécules Thérapeutiques; ICMMO; UMR 8182, CNRS, Univ. Paris-Sud; Université Paris-Saclay; Faculté des Sciences d'Orsay; Bât 410 91405 Orsay France
| | - Francelin Bouillère
- Laboratoire de Méthodologie, Synthèse et Molécules Thérapeutiques; ICMMO; UMR 8182, CNRS, Univ. Paris-Sud; Université Paris-Saclay; Faculté des Sciences d'Orsay; Bât 410 91405 Orsay France
| | - Anaïs Zulauf
- Laboratoire de Méthodologie, Synthèse et Molécules Thérapeutiques; ICMMO; UMR 8182, CNRS, Univ. Paris-Sud; Université Paris-Saclay; Faculté des Sciences d'Orsay; Bât 410 91405 Orsay France
| | - Jiefang He
- Laboratoire de Méthodologie, Synthèse et Molécules Thérapeutiques; ICMMO; UMR 8182, CNRS, Univ. Paris-Sud; Université Paris-Saclay; Faculté des Sciences d'Orsay; Bât 410 91405 Orsay France
| | - Stéphanie Courtiol-Legourd
- Laboratoire de Méthodologie, Synthèse et Molécules Thérapeutiques; ICMMO; UMR 8182, CNRS, Univ. Paris-Sud; Université Paris-Saclay; Faculté des Sciences d'Orsay; Bât 410 91405 Orsay France
| | - Régis Guillot
- Laboratoire de Méthodologie, Synthèse et Molécules Thérapeutiques; ICMMO; UMR 8182, CNRS, Univ. Paris-Sud; Université Paris-Saclay; Faculté des Sciences d'Orsay; Bât 410 91405 Orsay France
| | - Cyrille Kouklovsky
- Laboratoire de Méthodologie, Synthèse et Molécules Thérapeutiques; ICMMO; UMR 8182, CNRS, Univ. Paris-Sud; Université Paris-Saclay; Faculté des Sciences d'Orsay; Bât 410 91405 Orsay France
| | - Sylvain Cote des Combes
- Sanofi Recherche et Développement; 1 avenue Pierre Brossolette 91385 Chilly Mazarin CEDEX France
| | - Christophe Pacaud
- Sanofi Recherche et Développement; 1 avenue Pierre Brossolette 91385 Chilly Mazarin CEDEX France
| | - Ingrid Devillers
- Sanofi Recherche et Développement; 1 avenue Pierre Brossolette 91385 Chilly Mazarin CEDEX France
| | - Valérie Alezra
- Laboratoire de Méthodologie, Synthèse et Molécules Thérapeutiques; ICMMO; UMR 8182, CNRS, Univ. Paris-Sud; Université Paris-Saclay; Faculté des Sciences d'Orsay; Bât 410 91405 Orsay France
| |
Collapse
|
27
|
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.
Collapse
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
| |
Collapse
|
28
|
Bonnel C, Legrand B, Simon M, Martinez J, Bantignies JL, Kang YK, Wenger E, Hoh F, Masurier N, Maillard LT. C9/12
Ribbon-Like Structures in Hybrid Peptides Alternating α- and Thiazole-Based γ-Amino Acids. Chemistry 2017; 23:17584-17591. [DOI: 10.1002/chem.201704001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Indexed: 11/08/2022]
Affiliation(s)
- Clément Bonnel
- Institut des Biomolécules Max Mousseron; UMR CNRS-UM-ENSCM 5247, UFR des Sciences Pharmaceutiques et Biologiques; 15 Avenue Charles Flahault 34093 Montpellier Cedex 5 France
| | - Baptiste Legrand
- Institut des Biomolécules Max Mousseron; UMR CNRS-UM-ENSCM 5247, UFR des Sciences Pharmaceutiques et Biologiques; 15 Avenue Charles Flahault 34093 Montpellier Cedex 5 France
| | - Matthieu Simon
- Institut des Biomolécules Max Mousseron; UMR CNRS-UM-ENSCM 5247, UFR des Sciences Pharmaceutiques et Biologiques; 15 Avenue Charles Flahault 34093 Montpellier Cedex 5 France
| | - Jean Martinez
- Institut des Biomolécules Max Mousseron; UMR CNRS-UM-ENSCM 5247, UFR des Sciences Pharmaceutiques et Biologiques; 15 Avenue Charles Flahault 34093 Montpellier Cedex 5 France
| | | | - Young Kee Kang
- Department of Chemistry; Chungbuk National University, Cheongju; Chungbuk 28644 Republic of Korea
| | - Emmanuel Wenger
- Laboratoire de Cristallographie, Résonance Magnétique et Modélisation; Université de Lorraine, CNRS, UMR 7036; Nancy France
| | - Francois Hoh
- Centre de Biochimie Structurale, CNRS UMR 5048-INSERM 1054; University of Montpellier; Montpellier France
| | - Nicolas Masurier
- Institut des Biomolécules Max Mousseron; UMR CNRS-UM-ENSCM 5247, UFR des Sciences Pharmaceutiques et Biologiques; 15 Avenue Charles Flahault 34093 Montpellier Cedex 5 France
| | - Ludovic T. Maillard
- Institut des Biomolécules Max Mousseron; UMR CNRS-UM-ENSCM 5247, UFR des Sciences Pharmaceutiques et Biologiques; 15 Avenue Charles Flahault 34093 Montpellier Cedex 5 France
| |
Collapse
|
29
|
Illa O, Olivares JA, Nolis P, Ortuño RM. The relevance of the relative configuration in the folding of hybrid peptides containing β-cyclobutane amino acids and γ-amino- l -proline residues. Tetrahedron 2017. [DOI: 10.1016/j.tet.2017.09.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
|
30
|
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]
|
31
|
Benke SN, Thulasiram HV, Gopi HN. Potent Antimicrobial Activity of Lipidated Short α,γ-Hybrid Peptides. ChemMedChem 2017; 12:1610-1615. [DOI: 10.1002/cmdc.201700370] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Indexed: 11/07/2022]
Affiliation(s)
- Sushil N. Benke
- Department of Chemistry; Indian Institute of Science Education and Research; Dr. Homi Bhabha Road Pune 41108 India
| | | | - Hosahudya N. Gopi
- Department of Chemistry; Indian Institute of Science Education and Research; Dr. Homi Bhabha Road Pune 41108 India
| |
Collapse
|
32
|
Awada H, Grison CM, Charnay-Pouget F, Baltaze JP, Brisset F, Guillot R, Robin S, Hachem A, Jaber N, Naoufal D, Yazbeck O, Aitken DJ. Conformational Effects through Hydrogen Bonding in a Constrained γ-Peptide Template: From Intraresidue Seven-Membered Rings to a Gel-Forming Sheet Structure. J Org Chem 2017; 82:4819-4828. [PMID: 28398045 DOI: 10.1021/acs.joc.7b00494] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
A series of three short oligomers (di-, tri-, and tetramers) of cis-2-(aminomethyl)cyclobutane carboxylic acid, a γ-amino acid featuring a cyclobutane ring constraint, were prepared, and their conformational behavior was examined spectroscopically and by molecular modeling. In dilute solutions, these peptides showed a number of low-energy conformers, including ribbonlike structures pleated around a rarely observed series of intramolecular seven-membered hydrogen bonds. In more concentrated solutions, these interactions defer to an organized supramolecular assembly, leading to thermoreversible organogel formation notably for the tripeptide, which produced fibrillar xerogels. In the solid state, the dipeptide adopted a fully extended conformation featuring a one-dimensional network of intermolecularly H-bonded molecules stacked in an antiparallel sheet alignment. This work provides unique insight into the interplay between inter- and intramolecular H-bonded conformer topologies for the same peptide template.
Collapse
Affiliation(s)
- Hawraà Awada
- CP3A Organic Synthesis Group and Services Communs, ICMMO, UMR 8182, CNRS, Université Paris Sud, Université Paris Saclay , Bât. 420, 15 rue Georges Clemenceau, 91405 Orsay cedex, France.,Inorganic and Organometallic Coordination Chemistry Laboratory and Laboratory for Medicinal Chemistry and Natural Products, Faculty of Sciences (I) & PRASE-EDST, Lebanese University , Hadath, Lebanon
| | - Claire M Grison
- CP3A Organic Synthesis Group and Services Communs, ICMMO, UMR 8182, CNRS, Université Paris Sud, Université Paris Saclay , Bât. 420, 15 rue Georges Clemenceau, 91405 Orsay cedex, France
| | - Florence Charnay-Pouget
- CP3A Organic Synthesis Group and Services Communs, ICMMO, UMR 8182, CNRS, Université Paris Sud, Université Paris Saclay , Bât. 420, 15 rue Georges Clemenceau, 91405 Orsay cedex, France
| | - Jean-Pierre Baltaze
- CP3A Organic Synthesis Group and Services Communs, ICMMO, UMR 8182, CNRS, Université Paris Sud, Université Paris Saclay , Bât. 420, 15 rue Georges Clemenceau, 91405 Orsay cedex, France
| | - François Brisset
- CP3A Organic Synthesis Group and Services Communs, ICMMO, UMR 8182, CNRS, Université Paris Sud, Université Paris Saclay , Bât. 420, 15 rue Georges Clemenceau, 91405 Orsay cedex, France
| | - Régis Guillot
- CP3A Organic Synthesis Group and Services Communs, ICMMO, UMR 8182, CNRS, Université Paris Sud, Université Paris Saclay , Bât. 420, 15 rue Georges Clemenceau, 91405 Orsay cedex, France
| | - Sylvie Robin
- CP3A Organic Synthesis Group and Services Communs, ICMMO, UMR 8182, CNRS, Université Paris Sud, Université Paris Saclay , Bât. 420, 15 rue Georges Clemenceau, 91405 Orsay cedex, France.,UFR Sciences Pharmaceutiques et Biologiques, Université Paris Descartes , 4 avenue de l'Observatoire, 75270 Paris cedex 06, France
| | - Ali Hachem
- Inorganic and Organometallic Coordination Chemistry Laboratory and Laboratory for Medicinal Chemistry and Natural Products, Faculty of Sciences (I) & PRASE-EDST, Lebanese University , Hadath, Lebanon
| | - Nada Jaber
- Inorganic and Organometallic Coordination Chemistry Laboratory and Laboratory for Medicinal Chemistry and Natural Products, Faculty of Sciences (I) & PRASE-EDST, Lebanese University , Hadath, Lebanon
| | - Daoud Naoufal
- Inorganic and Organometallic Coordination Chemistry Laboratory and Laboratory for Medicinal Chemistry and Natural Products, Faculty of Sciences (I) & PRASE-EDST, Lebanese University , Hadath, Lebanon
| | - Ogaritte Yazbeck
- Inorganic and Organometallic Coordination Chemistry Laboratory and Laboratory for Medicinal Chemistry and Natural Products, Faculty of Sciences (I) & PRASE-EDST, Lebanese University , Hadath, Lebanon
| | - David J Aitken
- CP3A Organic Synthesis Group and Services Communs, ICMMO, UMR 8182, CNRS, Université Paris Sud, Université Paris Saclay , Bât. 420, 15 rue Georges Clemenceau, 91405 Orsay cedex, France
| |
Collapse
|
33
|
Vasantha B, George G, Raghothama S, Balaram P. Homooligomeric β 3 (R)-valine peptides: Transformation between C 14 and C 12 helical structures induced by a guest Aib residue. Biopolymers 2017; 108. [PMID: 27539268 DOI: 10.1002/bip.22935] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2016] [Revised: 08/08/2016] [Accepted: 08/17/2016] [Indexed: 11/10/2022]
Abstract
Novel helical, structures unprecedented in the chemistry of α-polypeptides, may be found in polypeptides containing β and γ amino acids. The structural characterization of C12 and C14 -helices in oligo β-peptides was originally achieved using conformationally constrained cyclic β-residues. This study explores the conformational characteristics of proteinogenic β3 residues in homooligomeric sequences and addresses the issue of inducing a transition between C14 and C12 helices by the introduction of a guest α-residue. Folded C14 -helical structures are demonstrated for the nonapeptide Boc-[β3 (R)Val]9 -OMe by NMR methods in CDCl3 -DMSO mixtures, while the peptide was found to be aggregated in CDCl3 . The insertion of a guest Aib residue into an oligo-β-valine sequence in the octapeptide model Boc-[(β3 (R)Val)3 -Aib-(β3 (R)Val]4 -OMe results in well dispersed NH region in the NMR spectrum indicating folded structures in CDCl3 . Structure calculations for both the peptides using NOE distance constraints support a C14 helical structure in the homooligomer which transform into a C12 helix on introduction of the guest Aib residue.
Collapse
Affiliation(s)
| | - Gijo George
- Department of Physics, NMR Research Center, Indian Institute of Science, Bangalore, 560012, India
| | | | - Padmanabhan Balaram
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, 560 012, India
| |
Collapse
|
34
|
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
| |
Collapse
|
35
|
Thodupunuri P, Katukuri S, Ramakrishna KVS, Sharma GVM, Kunwar AC, Sarma AVS, Hofmann HJ. Solvent-Directed Switch of a Left-Handed 10/12-Helix into a Right-Handed 12/10-Helix in Mixed β-Peptides. J Org Chem 2017; 82:2018-2031. [DOI: 10.1021/acs.joc.6b02856] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Prashanth Thodupunuri
- Organic
and Biomolecular Chemistry Division, CSIR-Indian Institute of Chemical Technology, Hyderabad 500 007, India
| | - Sirisha Katukuri
- Nuclear Magnetic Resonance & Structural Chemistry Division, CSIR-Indian Institute of Chemical Technology, Hyderabad 500 007, India
| | - Kallaganti V. S. Ramakrishna
- Nuclear Magnetic Resonance & Structural Chemistry Division, CSIR-Indian Institute of Chemical Technology, Hyderabad 500 007, India
| | - Gangavaram V. M. Sharma
- Organic
and Biomolecular Chemistry Division, CSIR-Indian Institute of Chemical Technology, Hyderabad 500 007, India
| | - Ajit C. Kunwar
- Nuclear Magnetic Resonance & Structural Chemistry Division, CSIR-Indian Institute of Chemical Technology, Hyderabad 500 007, India
| | - Akella V. S. Sarma
- Nuclear Magnetic Resonance & Structural Chemistry Division, CSIR-Indian Institute of Chemical Technology, Hyderabad 500 007, India
| | - Hans-Jörg Hofmann
- Institute
of Biochemistry, Faculty of Biosciences, University of Leipzig, Brüderstrasse 34, D-04103 Leipzig, Germany
| |
Collapse
|
36
|
Malik A, Kumar MG, Bandyopadhyay A, Gopi HN. Helices with additional H-bonds: crystallographic conformations of α,γ-hybrid peptides helices composed of β-hydroxy γ-amino acids (statines). Biopolymers 2017; 108. [DOI: 10.1002/bip.22978] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Revised: 08/05/2016] [Accepted: 08/25/2016] [Indexed: 12/31/2022]
Affiliation(s)
- Ankita Malik
- Department of Chemistry; Indian Institute of Science Education and Research-Pune; Dr. Homi Bhabha Road Pune 411008 India
| | - Mothukuri Ganesh Kumar
- Department of Chemistry; Indian Institute of Science Education and Research-Pune; Dr. Homi Bhabha Road Pune 411008 India
| | - Anupam Bandyopadhyay
- Department of Chemistry; Indian Institute of Science Education and Research-Pune; Dr. Homi Bhabha Road Pune 411008 India
| | - Hosahudya N. Gopi
- Department of Chemistry; Indian Institute of Science Education and Research-Pune; Dr. Homi Bhabha Road Pune 411008 India
| |
Collapse
|
37
|
Vasantha B, Yamanappa H, Raghothama S, Balaram P. Conformational properties and aggregation of homo-oligomeric β 3 (R)-valine peptides in organic solvents. Biopolymers 2016; 108. [PMID: 28026005 DOI: 10.1002/bip.23011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Revised: 12/12/2016] [Accepted: 12/16/2016] [Indexed: 11/07/2022]
Abstract
The conformational characteristics of protected homo-oligomeric Boc-[β3 (R)Val]n -OMe, n = 1, 2, 3, 4, 6, 9, and 12 have been investigated in organic solvents using nuclear magnetic resonance (NMR), Fourier transform infrared (FTIR) absorption spectroscopy and circular dichroism (CD) methods. The detailed 1 H NMR analysis of Boc-[β3 (R)Val]12 -OMe reveals that the peptide aggregates extensively in CDCl3 , but is disaggregated in 20%, (v/v) dimethyl sulfoxide (DMSO) in CDCl3 and in CD3 OH. Limited assignment of the N-terminus NH groups, together with solvent dependence of NH chemical shifts and temperature coefficients provides evidence for 14-helix conformation in the 12-residue peptide. FTIR analysis in CHCl3 establishes that the onset of folding and aggregation, as evidenced by NH stretching bands at 3375 cm-1 (intramolecular) and 3285 cm-1 (intermolecular), begins at the level of the tetrapeptide. The observed CD bands, 214 nm (negative) and 198 nm (positive), support 14-helix formation in the 9 and 12 residue sequences. The folding and aggregation tendencies of homo-oligomeric α-, β-, and γ- residues is compared in the model peptides Boc-[ωVal]n -NHMe, ω = α, β, and γ and n = 1, 2, and 3. Analysis of the FTIR spectra in CHCl3 , establish that the tendency to aggregate at the di and tripeptide level follows the order β > α∼γ, while the tendency to fold follows the order γ > β > α.
Collapse
Affiliation(s)
| | - Hunashal Yamanappa
- NMR Research Center, Indian Institute of Science, Bangalore, 560 012, India
| | | | - Padmanabhan Balaram
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, 560 012, India
| |
Collapse
|
38
|
Clerici F, Erba E, Gelmi ML, Pellegrino S. Non-standard amino acids and peptides: From self-assembly to nanomaterials. Tetrahedron Lett 2016. [DOI: 10.1016/j.tetlet.2016.11.022] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
|
39
|
Ordóñez M, Cativiela C, Romero-Estudillo I. An update on the stereoselective synthesis of γ-amino acids. ACTA ACUST UNITED AC 2016. [DOI: 10.1016/j.tetasy.2016.08.011] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
40
|
Scope, limitations and classification of lactamases. J Biotechnol 2016; 235:11-23. [DOI: 10.1016/j.jbiotec.2016.03.050] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Revised: 03/29/2016] [Accepted: 03/31/2016] [Indexed: 01/06/2023]
|
41
|
Fisher BF, Gellman SH. Impact of γ-Amino Acid Residue Preorganization on α/γ-Peptide Foldamer Helicity in Aqueous Solution. J Am Chem Soc 2016; 138:10766-9. [PMID: 27529788 DOI: 10.1021/jacs.6b06177] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
α/γ-Peptide foldamers containing either γ(4)-amino acid residues or ring-constrained γ-amino acid residues have been reported to adopt 12-helical secondary structure in nonpolar solvents and in the solid state. These observations have engendered speculation that the seemingly flexible γ(4) residues have a high intrinsic helical propensity and that residue-based preorganization may not significantly stabilize the 12-helical conformation. However, the prior studies were conducted in environments that favor intramolecular H-bond formation. Here, we use 2D-NMR to compare the ability of γ(4) residues and cyclic γ residues to support 12-helix formation in more challenging environments, methanol and water. Both γ residue types support 12-helical folding in methanol, but only the cyclically constrained γ residues promote helicity in water. These results demonstrate the importance of residue-based preorganization strategies for achieving stable folding among short foldamers in aqueous solution.
Collapse
Affiliation(s)
- Brian F Fisher
- Department of Chemistry, University of Wisconsin-Madison , Madison, Wisconsin 53706, United States
| | - Samuel H Gellman
- Department of Chemistry, University of Wisconsin-Madison , Madison, Wisconsin 53706, United States
| |
Collapse
|
42
|
Crystallographic characterization of the α
,γ C 12
helix in hybrid peptide sequences. J Pept Sci 2016; 22:504-10. [DOI: 10.1002/psc.2896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Revised: 04/23/2016] [Accepted: 04/26/2016] [Indexed: 11/07/2022]
|
43
|
Ganesh Kumar M, Thombare VJ, Katariya MM, Veeresh K, Raja KMP, Gopi HN. Non-classical Helices withcisCarbon-Carbon Double Bonds in the Backbone: Structural Features of α,γ-Hybrid Peptide Foldamers. Angew Chem Int Ed Engl 2016; 55:7847-51. [DOI: 10.1002/anie.201602861] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Indexed: 11/06/2022]
Affiliation(s)
- Mothukuri Ganesh Kumar
- Department of Chemistry; Indian Institute of Science Education and Research; Dr. Homi Bhabha Road, Pashan Pune- 411008 India
| | - Varsha J. Thombare
- Department of Chemistry; Indian Institute of Science Education and Research; Dr. Homi Bhabha Road, Pashan Pune- 411008 India
| | - Mona M. Katariya
- Department of Chemistry; Indian Institute of Science Education and Research; Dr. Homi Bhabha Road, Pashan Pune- 411008 India
| | - Kuruva Veeresh
- Department of Chemistry; Indian Institute of Science Education and Research; Dr. Homi Bhabha Road, Pashan Pune- 411008 India
| | - K. Muruga Poopathi Raja
- Department of Physical Chemistry; School of Chemistry; Madurai Kamaraj University; Madurai- 625 021 India
| | - Hosahudya N. Gopi
- Department of Chemistry; Indian Institute of Science Education and Research; Dr. Homi Bhabha Road, Pashan Pune- 411008 India
| |
Collapse
|
44
|
Ganesh Kumar M, Thombare VJ, Katariya MM, Veeresh K, Raja KMP, Gopi HN. Non-classical Helices withcisCarbon-Carbon Double Bonds in the Backbone: Structural Features of α,γ-Hybrid Peptide Foldamers. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201602861] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Mothukuri Ganesh Kumar
- Department of Chemistry; Indian Institute of Science Education and Research; Dr. Homi Bhabha Road, Pashan Pune- 411008 India
| | - Varsha J. Thombare
- Department of Chemistry; Indian Institute of Science Education and Research; Dr. Homi Bhabha Road, Pashan Pune- 411008 India
| | - Mona M. Katariya
- Department of Chemistry; Indian Institute of Science Education and Research; Dr. Homi Bhabha Road, Pashan Pune- 411008 India
| | - Kuruva Veeresh
- Department of Chemistry; Indian Institute of Science Education and Research; Dr. Homi Bhabha Road, Pashan Pune- 411008 India
| | - K. Muruga Poopathi Raja
- Department of Physical Chemistry; School of Chemistry; Madurai Kamaraj University; Madurai- 625 021 India
| | - Hosahudya N. Gopi
- Department of Chemistry; Indian Institute of Science Education and Research; Dr. Homi Bhabha Road, Pashan Pune- 411008 India
| |
Collapse
|
45
|
Auberger N, Stanovych A, Thétiot-Laurent S, Guillot R, Kouklovsky C, Cote des Combes S, Pacaud C, Devillers I, Alezra V. Efficient synthesis of both diastereomers of β,γ-diamino acids from phenylalanine and tryptophan. Amino Acids 2016; 48:2237-42. [DOI: 10.1007/s00726-016-2262-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Accepted: 05/12/2016] [Indexed: 01/06/2023]
|
46
|
Friestad GK, Banerjee K, Marié JC, Mali U, Yao L. Stereoselective access to tubuphenylalanine and tubuvaline: improved Mn-mediated radical additions and assembly of a tubulysin tetrapeptide analog. J Antibiot (Tokyo) 2016; 69:294-8. [PMID: 26883395 PMCID: PMC4924578 DOI: 10.1038/ja.2016.7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Revised: 01/12/2016] [Accepted: 01/18/2016] [Indexed: 01/05/2023]
Abstract
Synthesis of tubuphenylalanine and tubuvaline (Tuv), α-substituted γ-amino acid building blocks for tubulysin family of antimitotic compounds, has been improved using a radical addition reaction in the presence of unprotected hydroxyl functionality. The key carbon-carbon bond construction entails stereoselective Mn-mediated photolytic additions of alkyl iodides to the C=N bond of chiral N-acylhydrazones, and generates the chiral amines in high yield with complete stereocontrol. Reductive N-N bond cleavage and alcohol oxidation converted these amino alcohols into the corresponding γ-amino acids. The route to Tuv proceeded via peptide coupling with serine methyl ester, followed by a high-yielding sequence to convert the serine amide to a thiazole. Finally, peptide bond construction established the tubulysin framework in the form of a C-terminal alcohol analog. Attempted oxidation to the C-terminal carboxylate was unsuccessful; control experiments with dipeptide 18 showed a cyclization interfered with the desired oxidation process.
Collapse
Affiliation(s)
| | - Koushik Banerjee
- Department of Chemistry, University of Iowa, Iowa City, Iowa 52242 USA
| | | | - Umesh Mali
- Department of Chemistry, University of Iowa, Iowa City, Iowa 52242 USA
| | - Lei Yao
- Department of Chemistry, University of Iowa, Iowa City, Iowa 52242 USA
| |
Collapse
|
47
|
Sharma GVM, Anjaiah G, Kanakaraju M, Sudhakar B, Chatterjee D, Kunwar AC. Synthesis of a new β-amino acid with a 3-deoxy-L-ara furnaoside side chain: the influence of the side chain on the conformation of α/β-peptides. Org Biomol Chem 2016; 14:503-515. [PMID: 26489370 DOI: 10.1039/c5ob01753j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The important role of side chains in the stabilization of helical folds in peptidic foldamers containing C-linked carbo-β-amino acids (β-Caa), an interesting class of β-amino acids, with carbohydrate side chains has been extensively elaborated. As a pragmatic approach to alleviate the interference of substituents in the side chains on the folding propensities of the peptides, they are often modified or removed. The present study reports the synthesis of a new β-Caa with a 3-deoxy-L-ara furanoside side chain, [(R)-β-Caa(da)], from D-glucose, and its use in the synthesis of α/β-peptides in 1 : 1 alternation with D-Ala. The synthesis of peptides using (R)-β-Caa(da), was facile unlike those from (R)-β-Caa(a) having the L-ara furanoside side chain. The detailed NMR, molecular dynamics (MD) and CD studies on the new α/β-peptides showed the presence of robust left-handed 11/9-mixed helices. The study demonstrates that the new (R)-β-Caa(da), behaves differently compared to the other two related monomers, (R)-β-Caa(x) with the D-xylo furanoside side chain and (R)-β-Caa(a).
Collapse
Affiliation(s)
- Gangavaram V M Sharma
- Organic and Biomolecular Chemistry Division, CSIR-Indian Institute of Chemical Technology, Hyderabad 500 007, India.
| | | | | | | | | | | |
Collapse
|
48
|
Ingole TS, Kotmale AS, Gawade RL, Gonnade RG, Rajamohanan PR, Sanjayan GJ. 3-Aminothiophenecarboxylic acid (3-Atc)-induced folding in peptides. NEW J CHEM 2016. [DOI: 10.1039/c6nj01667g] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
This article demonstrates the consequences of incorporating a constrained β-amino acid into a peptide chain and its effect on conformation of oligomers.
Collapse
Affiliation(s)
- Tukaram S. Ingole
- Division of Organic Chemistry
- National Chemical Laboratory
- Pune 411 008
- India
| | - Amol S. Kotmale
- Central NMR Facility
- National Chemical Laboratory
- Pune 411 008
- India
| | - Rupesh L. Gawade
- Center for Materials Characterization
- National Chemical Laboratory
- Pune
- India
| | - Rajesh G. Gonnade
- Center for Materials Characterization
- National Chemical Laboratory
- Pune
- India
| | | | | |
Collapse
|
49
|
Ganesh Kumar M, Gopi HN. γ- and β-Peptide Foldamers from Common Multifaceted Building Blocks: Synthesis and Structural Characterization. Org Lett 2015; 17:4738-41. [DOI: 10.1021/acs.orglett.5b02263] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Mothukuri Ganesh Kumar
- Department of Chemistry, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pune 411008, India
| | - Hosahudya N. Gopi
- Department of Chemistry, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pune 411008, India
| |
Collapse
|
50
|
Szakonyi Z, Csőr Á, Haukka M, Fülöp F. Stereoselective synthesis of carane-based chiral β- and γ-amino acid derivatives via conjugate addition. Tetrahedron 2015. [DOI: 10.1016/j.tet.2015.05.019] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
|