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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] [What about the content of this article? (0)] [Affiliation(s)] [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.
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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
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Park HS, Kang YK. Exploring Helical Folding in Oligomers of Cyclopentane-Based ϵ-Amino Acids: A Computational Study. Chemistry 2022; 11:e202100253. [PMID: 35083888 PMCID: PMC8886640 DOI: 10.1002/open.202100253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 12/21/2021] [Indexed: 11/28/2022]
Abstract
The conformational preferences of oligopeptides of an ϵ‐amino acid (2‐((1R,3S)‐3‐(aminomethyl)cyclopentyl)acetic acid, Amc5a) with a cyclopentane substituent in the Cβ−Cγ−Cδ sequence of the backbone were investigated using DFT methods in chloroform and water. The most preferred conformation of Amc5a oligomers (dimer to hexamer) was the H16 helical structure both in chloroform and water. Four residues were found to be sufficient to induce a substantial H16 helix population in solution. The Amc5a hexamer adopted a stable left‐handed (M)‐2.316 helical conformation with a rise of 4.8 Å per turn. The hexamer of Ampa (an analogue of Amc5a with replacing cyclopentane by pyrrolidine) adopted the right‐handed mixed (P)‐2.918/16 helical conformation in chloroform and the (M)‐2.416 helical conformation in water. Therefore, hexamers of ϵ‐amino acid residues exhibited different preferences of helical structures depending on the substituents in peptide backbone and the solvent polarity as well as the chain length.
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Affiliation(s)
- Hae Sook Park
- Department of Nursing, Cheju Halla University, Cheju, 63092, Republic of Korea
| | - Young Kee Kang
- Department of Chemistry, Chungbuk National University, Cheongju, Chungbuk, 28644, Republic of Korea
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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] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
A series of three short oligomers (di-, tri-, and tetramers) of cis-2-(aminomethyl)cyclobutane carboxylic acid, a γ-amino acid featuring a cyclobutane ring constraint, were prepared, and their conformational behavior was examined spectroscopically and by molecular modeling. In dilute solutions, these peptides showed a number of low-energy conformers, including ribbonlike structures pleated around a rarely observed series of intramolecular seven-membered hydrogen bonds. In more concentrated solutions, these interactions defer to an organized supramolecular assembly, leading to thermoreversible organogel formation notably for the tripeptide, which produced fibrillar xerogels. In the solid state, the dipeptide adopted a fully extended conformation featuring a one-dimensional network of intermolecularly H-bonded molecules stacked in an antiparallel sheet alignment. This work provides unique insight into the interplay between inter- and intramolecular H-bonded conformer topologies for the same peptide template.
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Affiliation(s)
- Hawraà Awada
- CP3A Organic Synthesis Group and Services Communs, ICMMO, UMR 8182, CNRS, Université Paris Sud, Université Paris Saclay , Bât. 420, 15 rue Georges Clemenceau, 91405 Orsay cedex, France.,Inorganic and Organometallic Coordination Chemistry Laboratory and Laboratory for Medicinal Chemistry and Natural Products, Faculty of Sciences (I) & PRASE-EDST, Lebanese University , Hadath, Lebanon
| | - Claire M Grison
- CP3A Organic Synthesis Group and Services Communs, ICMMO, UMR 8182, CNRS, Université Paris Sud, Université Paris Saclay , Bât. 420, 15 rue Georges Clemenceau, 91405 Orsay cedex, France
| | - Florence Charnay-Pouget
- CP3A Organic Synthesis Group and Services Communs, ICMMO, UMR 8182, CNRS, Université Paris Sud, Université Paris Saclay , Bât. 420, 15 rue Georges Clemenceau, 91405 Orsay cedex, France
| | - Jean-Pierre Baltaze
- CP3A Organic Synthesis Group and Services Communs, ICMMO, UMR 8182, CNRS, Université Paris Sud, Université Paris Saclay , Bât. 420, 15 rue Georges Clemenceau, 91405 Orsay cedex, France
| | - François Brisset
- CP3A Organic Synthesis Group and Services Communs, ICMMO, UMR 8182, CNRS, Université Paris Sud, Université Paris Saclay , Bât. 420, 15 rue Georges Clemenceau, 91405 Orsay cedex, France
| | - Régis Guillot
- CP3A Organic Synthesis Group and Services Communs, ICMMO, UMR 8182, CNRS, Université Paris Sud, Université Paris Saclay , Bât. 420, 15 rue Georges Clemenceau, 91405 Orsay cedex, France
| | - Sylvie Robin
- CP3A Organic Synthesis Group and Services Communs, ICMMO, UMR 8182, CNRS, Université Paris Sud, Université Paris Saclay , Bât. 420, 15 rue Georges Clemenceau, 91405 Orsay cedex, France.,UFR Sciences Pharmaceutiques et Biologiques, Université Paris Descartes , 4 avenue de l'Observatoire, 75270 Paris cedex 06, France
| | - Ali Hachem
- Inorganic and Organometallic Coordination Chemistry Laboratory and Laboratory for Medicinal Chemistry and Natural Products, Faculty of Sciences (I) & PRASE-EDST, Lebanese University , Hadath, Lebanon
| | - Nada Jaber
- Inorganic and Organometallic Coordination Chemistry Laboratory and Laboratory for Medicinal Chemistry and Natural Products, Faculty of Sciences (I) & PRASE-EDST, Lebanese University , Hadath, Lebanon
| | - Daoud Naoufal
- Inorganic and Organometallic Coordination Chemistry Laboratory and Laboratory for Medicinal Chemistry and Natural Products, Faculty of Sciences (I) & PRASE-EDST, Lebanese University , Hadath, Lebanon
| | - Ogaritte Yazbeck
- Inorganic and Organometallic Coordination Chemistry Laboratory and Laboratory for Medicinal Chemistry and Natural Products, Faculty of Sciences (I) & PRASE-EDST, Lebanese University , Hadath, Lebanon
| | - David J Aitken
- CP3A Organic Synthesis Group and Services Communs, ICMMO, UMR 8182, CNRS, Université Paris Sud, Université Paris Saclay , Bât. 420, 15 rue Georges Clemenceau, 91405 Orsay cedex, France
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