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Takeuchi N, Taniguchi M, Kato Y, Takata R, Osaka I, Nakajima N, Hamada M, Koyama Y. Synthesis and Conformational Behaviors of Unnatural Peptides Alternating Chiral and Achiral α,α-Disubstituted α-Amino Acid Units. Macromol Rapid Commun 2023; 44:e2300323. [PMID: 37668077 DOI: 10.1002/marc.202300323] [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: 06/02/2023] [Revised: 08/27/2023] [Indexed: 09/06/2023]
Abstract
The development of peptidomimetics to modulate the conformational profile of peptides has been extensively studied in the fields of biological and medicinal chemistry. However, large-scale synthesis of peptidomimetics with both an ordered sequence and a controlled secondary structure is highly challenging. In this paper, the framework of peptidomimetics has been designed to be alternating an achiral α,α-disubstituted α-amino acid unit and a chiral α-methylphenylalanine unit. The polymers are synthesized via invented Ugi reaction-based polycondensation technique. The chiral higher-order structures of the alternating peptides are evaluated mainly through circular dichroism (CD) spectroscopy. The UV-Vis and CD spectra of the polymers in three solvents are systematically measured at various temperatures. The anisotropic factors of CD (gCD ) values are calculated to know the chiroptical response. The results indicate the characteristic conformational behaviors. In a polar solvent, the hydrogen bonds between the N-H group of MePhe unit and the C=O of α,α-diphenylglycine unit outweigh the intraresidue hydrogen bonds in α,α-diphenylglycine unit, leading to the formation of a prevailing preferred-handed 310 -helical conformation. On the other hand, in a less polar solvent, the intrachain hydrogen bonds switch to intraresidue hydrogen bonds in α,α-diphenylglycine unit, which make the polymer adopting a prevailing extended planar C5 -conformation.
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Affiliation(s)
- Nanami Takeuchi
- Department of Pharmaceutical Engineering, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama, 939-0398, Japan
| | - Masataka Taniguchi
- Department of Pharmaceutical Engineering, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama, 939-0398, Japan
| | - Yuki Kato
- Department of Pharmaceutical Engineering, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama, 939-0398, Japan
| | - Riko Takata
- Department of Pharmaceutical Engineering, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama, 939-0398, Japan
| | - Issey Osaka
- Department of Pharmaceutical Engineering, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama, 939-0398, Japan
- Biotechnology Research Center, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama, 939-0398, Japan
| | - Noriyuki Nakajima
- Department of Pharmaceutical Engineering, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama, 939-0398, Japan
- Biotechnology Research Center, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama, 939-0398, Japan
| | - Masahiro Hamada
- Department of Pharmaceutical Engineering, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama, 939-0398, Japan
- Biotechnology Research Center, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama, 939-0398, Japan
| | - Yasuhito Koyama
- Department of Pharmaceutical Engineering, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama, 939-0398, Japan
- Biotechnology Research Center, Toyama Prefectural University, 5180 Kurokawa, Imizu, Toyama, 939-0398, Japan
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Calcatelli A, Denton RM, Ball LT. Modular Synthesis of α,α-Diaryl α-Amino Esters via Bi(V)-Mediated Arylation/S N2-Displacement of Kukhtin–Ramirez Intermediates. Org Lett 2022; 24:8002-8007. [PMID: 36278869 PMCID: PMC9641671 DOI: 10.1021/acs.orglett.2c03201] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
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We report a concise and modular approach to α,α-diaryl
α-amino esters from readily available α-keto esters. This
mild, one-pot protocol proceeds via ketone umpolung, with in situ formation of a Kukhtin–Ramirez intermediate
preceding sequential electrophilic arylation by Bi(V) and SN2 displacement by an amine. The methodology is compatible with a
wide range of anilines and primary amines - including derivatives
of drugs and proteinogenic amino acids - Bi(V) arylating agents, and
α-keto ester substrates.
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Affiliation(s)
| | - Ross M. Denton
- School of Chemistry, University of Nottingham, Nottingham NG7 2RD, U.K
- GlaxoSmithKline Carbon Neutral Laboratories for Sustainable Chemistry, University of Nottingham, 6 Triumph Road, Nottingham NG7 2GA, U.K
| | - Liam T. Ball
- School of Chemistry, University of Nottingham, Nottingham NG7 2RD, U.K
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Crisma M, Peggion C, Moretto A, Banerjee R, Supakar S, Formaggio F, Toniolo C. The 2.0₅-helix in hetero-oligopeptides entirely composed of C(α,α)-disubstituted glycines with both side chains longer than methyls. Biopolymers 2016; 102:145-58. [PMID: 24307568 DOI: 10.1002/bip.22450] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2013] [Revised: 11/15/2013] [Accepted: 12/02/2013] [Indexed: 02/02/2023]
Abstract
The existence of the very uncommon, but potentially quite interesting, multiple, consecutive fully-extended conformation (2.0₅-helix) has been already clearly demonstrated in homo-oligopeptides based on quaternary α-amino acids with both side chains longer than methyls, but not cyclized on the α-carbon atom. To extend the scope of this research, in this work we investigated the occurrence of this flat 3D-structure in hetero-oligopeptides, each composed of two or three different residues of that class. The synthesis of a terminally protected peptide series to the tetrapeptide level was carried out by solution methods. The resulting oligomers were chemically and conformationally characterized. The data obtained point to an overwhelming population of the fully-extended conformation in CDCl3. However, a solvent-driven switch to a predominant 3₁₀-helical structure was seen in CD3CN. A delicate, local balance between these two conformations is confirmed to occur in the crystalline state. Molecular dynamics simulations in CHCl3 on a hetero-tetrapeptide converged to the fully-extended conformation even starting from the 3₁₀-helical structure.
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Affiliation(s)
- Marco Crisma
- Department of Chemistry, ICB, Padova Unit, CNR, University of Padova, 35131, Padova, Italy
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4
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Peggion C, Moretto A, Formaggio F, Crisma M, Toniolo C. Multiple, consecutive, fully-extended 2.0₅-helix peptide conformation. Biopolymers 2016; 100:621-36. [PMID: 23893391 DOI: 10.1002/bip.22267] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2013] [Revised: 04/16/2013] [Accepted: 04/19/2013] [Indexed: 02/01/2023]
Abstract
The peptide 2.0(5)-helix does exist. It has been experimentally authenticated both in the crystalline state (by X-ray diffraction) and in solution (by several spectroscopic techniques). It is the most common conformation for C(α)-tetrasubstituted α-amino acids with at least two atoms in each side chain, provided that cyclization on the C(α)-atom is absent. X-Ray diffraction has allowed a detailed description of its geometrical and three-dimensional (3D)-structural features. The infrared absorption and the nuclear magnetic resonance parameters characteristics of this multiple, consecutive, fully-extended structure have been described. Conformational energy calculations are in agreement with the experimental findings. As the contribution per amino acid residue to the length of this helix is the longest possible, its exploitation as a molecular spacer is quite promising. However, it is a rather fragile 3D-structure and particularly sensitive to solvent polarity. Interestingly, in such a case, it may reversibly convert to the much shorter 3(10)-helix, thus generating an attractive molecular spring.
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Affiliation(s)
- Cristina Peggion
- Institute of Biomolecular Chemistry, CNR, Padova Unit, Department of Chemistry, University of Padova, 35131, Padova, Italy
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Tumminakatti S, Reddy DN, Prabhakaran EN. Exploring the consequences of a representative "disallowed" conformation of Aib on a 3₁₀-helical fold. Biopolymers 2014; 104:21-36. [PMID: 25488434 DOI: 10.1002/bip.22599] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2013] [Revised: 11/28/2014] [Accepted: 12/01/2014] [Indexed: 01/24/2023]
Abstract
The structural effects of a representative "disallowed" conformation of Aib on the 3(10)-helical fold of an octapeptidomimetic are explored. The 1D ((1)H, (13)C) & 2D NMR, FT-IR and CD data reveal that the octapeptide 1, adopts a 3(10)-helical conformation in solution, as it does in its crystal structure. The C-terminal methyl carboxylate (CO2Me) of 1 was modified into an 1,3-oxazine (Oxa) functional group in the peptidomimetic 2. This modification results in the stabilization of the backbone of the C-terminal Aib (Aib*-Oxa) of 2, in a conformation (ϕ, ψ = 180, 0) that is natively disallowed to Aib. Consequent to the presence of this natively disallowed conformation, the 3(10)-helical fold is not disrupted in the body of the peptidomimetic 2. But the structural distortions that do occur in 2 are primarily in residues in the immediate vicinity of the natively disallowed conformation, rather than in the whole peptide body. Non-native electronic effects resulting from modifications in backbone functional groups can be at the origin of stabilizing residues in natively disallowed conformations.
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Affiliation(s)
- Shama Tumminakatti
- Department of Organic Chemistry, Indian Institute of Science, Bangalore, 560012, Karnataka, India
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Castro TG, Micaêlo NM. Conformational and thermodynamic properties of non-canonical α,α-dialkyl glycines in the peptaibol Alamethicin: molecular dynamics studies. J Phys Chem B 2014; 118:9861-70. [PMID: 25091499 DOI: 10.1021/jp505400q] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In this work, we investigate the structure, dynamic and thermodynamic properties of noncanonical disubstituted amino acids (α,α-dialkyl glycines), also known as non-natural amino acids, in the peptaibol Alamethicin. The amino acids under study are Aib (α-amino isobutyric acid or α-methyl alanine), Deg (α,α-diethyl glycine), Dpg (α,α-dipropyl glycine), Dibg (α,α-di-isobutyl glycine), Dhg (α,α-dihexyl glycine), DΦg (α,α-diphenyl glycine), Dbzg (α,α-dibenzyl glycine), Ac6c (α,α-cyclohexyl glycine), and Dmg (α,α-dihydroxymethyl glycine). It is hypothesized that these amino acids are able to induce well-defined secondary structure in peptidomimetics. To test this hypothesis, new peptidomimetics of Alamethicin were constructed by replacing the native Aib positions of Alamethicin by one or more new α,α-dialkyl glycines. Dhg and Ac6c demonstrated the capacity to induce well-defined α-helical structures. Dhg and Ac6c also promote the thermodynamic stabilization of these peptides in a POPC model membrane and are better alternatives to the Aib in Alamethicin. These noncanonical amino acids also improved secondary structure properties, revealing preorganization in water and maintenance of α helical structure in POPC. We show that it is possible to optimize the helicity and thermodynamic properties of native Alamethicin, and we suggest that these amino acids could be incorporated in other peptides with similar structural effect.
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Affiliation(s)
- Tarsila G Castro
- Departamento de Química, Escola de Ciências, Universidade do Minho , Largo do Paço, Braga 4704-553, Portugal
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Castro TG, Micaêlo NM. Modeling of Peptaibol Analogues Incorporating Nonpolar α,α-Dialkyl Glycines Shows Improved α-Helical Preorganization and Spontaneous Membrane Permeation. J Phys Chem B 2014; 118:649-58. [DOI: 10.1021/jp4074587] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Tarsila G. Castro
- Departamento de Química, Escola de Ciências, Universidade do Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - Nuno M. Micaêlo
- Departamento de Química, Escola de Ciências, Universidade do Minho, Campus de Gualtar, 4710-057 Braga, Portugal
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Bett CK, Ngunjiri JN, Serem WK, Fontenot KR, Hammer RP, McCarley RL, Garno JC. Structure-activity relationships in peptide modulators of β-amyloid protein aggregation: variation in α,α-disubstitution results in altered aggregate size and morphology. ACS Chem Neurosci 2010; 1:608-26. [PMID: 22778850 DOI: 10.1021/cn100045q] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2010] [Accepted: 06/25/2010] [Indexed: 12/20/2022] Open
Abstract
Neuronal cytotoxicity observed in Alzheimer's disease (AD) is linked to the aggregation of β-amyloid peptide (Aβ) into toxic forms. Increasing evidence points to oligomeric materials as the neurotoxic species, not Aβ fibrils; disruption or inhibition of Aβ self-assembly into oligomeric or fibrillar forms remains a viable therapeutic strategy to reduce Aβ neurotoxicity. We describe the synthesis and characterization of amyloid aggregation mitigating peptides (AAMPs) whose structure is based on the Aβ "hydrophobic core" Aβ(17-20), with α,α-disubstituted amino acids (ααAAs) added into this core as potential disrupting agents of fibril self-assembly. The number, positional distribution, and side-chain functionality of ααAAs incorporated into the AAMP sequence were found to influence the resultant aggregate morphology as indicated by ex situ experiments using atomic force microscopy (AFM) and transmission electron microscopy (TEM). For instance, AAMP-5, incorporating a sterically hindered ααAA with a diisobutyl side chain in the core sequence, disrupted Aβ(1-40) fibril formation. However, AAMP-6, with a less sterically hindered ααAA with a dipropyl side chain, altered fibril morphology, producing shorter and larger sized fibrils (compared with those of Aβ(1-40)). Remarkably, ααAA-AAMPs caused disassembly of existing Aβ fibrils to produce either spherical aggregates or protofibrillar structures, suggesting the existence of equilibrium between fibrils and prefibrillar structures.
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Affiliation(s)
- Cyrus K. Bett
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803
| | - Johnpeter N. Ngunjiri
- NanoInk, Inc., Illinois Science & Technology Park, 8025 Lamon Ave, Skokie, Illinois 60077
| | - Wilson K. Serem
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803
| | - Krystal R. Fontenot
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803
| | - Robert P. Hammer
- New England Peptide LLC, 65 Zub Lane, Gardner, Massachusetts 01440
| | - Robin L. McCarley
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803
| | - Jayne C. Garno
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803
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Hanyu M, Murashima T, Miyazawa T, Yamada T. Synthesis of tripeptides containing a very crowded α,α-disubstituted glycine with pyridine rings by solid-phase Ugi reaction. Tetrahedron Lett 2004. [DOI: 10.1016/j.tetlet.2004.09.171] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Yamada T, Ichino T, Hanyu M, Ninomiya D, Yanagihara R, Miyazawa T, Murashima T. A novel intramolecular hydrogen bonding between a side-chain pyridine ring and an amide hydrogen of the peptide backbone in tripeptides containing the new amino acid, α,α-di(2-pyridyl)glycine. Org Biomol Chem 2004; 2:2335-9. [PMID: 15305215 DOI: 10.1039/b406545j] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Four tripeptides (Z-AA1-2Dpy-AA3-OMe; AA1, AA3 = Gly, Aib) containing a novel amino acid, alpha, alpha-di(2-pyridyl)glycine (2Dpy), were synthesized by the modified Ugi reaction. NMR analysis clearly indicated that the 2Dpy-containing tripeptides except the peptide in which AA1, AA3 = Aib, adopt a unique conformation with two intramolecular hydrogen bonds between 2Dpy-NH and a pyridine nitrogen and between AA3-NH and another pyridine nitrogen. This conformation has so far not been reported. On the other hand, the peptide Z-Aib-2Dpy-Aib-OMe probably adopts a beta-turn structure which is stabilized by two intramolecular hydrogen bonds between 2Dpy-NH and a pyridine nitrogen and between AA3-NH and the C=O of the Z group.
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Affiliation(s)
- Takashi Yamada
- Department of Chemistry, Faculty of Science and Engineering, Konan University, Kobe, Japan.
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Toniolo C, Crisma M, Formaggio F, Peggion C. Control of peptide conformation by the Thorpe-Ingold effect (C alpha-tetrasubstitution). Biopolymers 2002; 60:396-419. [PMID: 12209474 DOI: 10.1002/1097-0282(2001)60:6<396::aid-bip10184>3.0.co;2-7] [Citation(s) in RCA: 580] [Impact Index Per Article: 26.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
The preferred conformations of peptides heavily based on the currently extensively exploited achiral and chiral alpha-amino acids with a quaternary alpha-carbon atom, as determined by conformational energy computations, crystal-state (x-ray diffraction) analyses, and solution ((1)H-NMR and spectroscopic) investigations, are reviewed. It is concluded that 3(10)/alpha-helical structures and the fully extended (C(5)) conformation are preferentially adopted by peptide sequences characterized by this family of amino acids, depending upon overall bulkiness and nature (e.g., whether acyclic or C(alpha) (i) <--> C(alpha) (i) cyclized) of their side chains. The intriguing relationship between alpha-carbon chirality and bend/helix handedness is also illustrated. gamma-Bends and semiextended conformations are rarely observed. Formation of beta-sheet structures is prevented.
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Affiliation(s)
- C Toniolo
- Department of Organic Chemistry, University of Padova, Institute of Biomolecular Chemistry, CNR, 35131 Padova, Italy.
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