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Joaquin D, Lee MA, Kastner DW, Singh J, Morrill ST, Damstedt G, Castle SL. Impact of Dehydroamino Acids on the Structure and Stability of Incipient 3 10-Helical Peptides. J Org Chem 2019; 85:1601-1613. [PMID: 31730750 DOI: 10.1021/acs.joc.9b02747] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
A comparative study of the impact of small, medium-sized, and bulky α,β-dehydroamino acids (ΔAAs) on the structure and stability of Balaram's incipient 310-helical peptide (1) is reported. Replacement of the N-terminal Aib residue of 1 with a ΔAA afforded peptides 2a-c that maintained the 310-helical shape of 1. In contrast, installation of a ΔAA in place of Aib-3 yielded peptides 3a-c that preferred a β-sheet-like conformation. The impact of the ΔAA on peptide structure was independent of size, with small (ΔAla), medium-sized (Z-ΔAbu), and bulky (ΔVal) ΔAAs exerting similar effects. The proteolytic stabilities of 1 and its analogs were determined by incubation with Pronase. Z-ΔAbu and ΔVal increased the resistance of peptides to proteolysis when incorporated at the 3-position and had negligible impact on stability when placed at the 1-position, whereas ΔAla-containing peptides degraded rapidly regardless of position. Exposure of peptides 2a-c and 3a-c to the reactive thiol cysteamine revealed that ΔAla-containing peptides underwent conjugate addition at room temperature, while Z-ΔAbu- and ΔVal-containing peptides were inert even at elevated temperatures. These results suggest that both bulky and more accessible medium-sized ΔAAs should be valuable tools for bestowing rigidity and proteolytic stability on bioactive peptides.
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Affiliation(s)
- Daniel Joaquin
- Department of Chemistry and Biochemistry , Brigham Young University , Provo , Utah 84602 , United States
| | - Michael A Lee
- Department of Chemistry and Biochemistry , Brigham Young University , Provo , Utah 84602 , United States
| | - David W Kastner
- Department of Chemistry and Biochemistry , Brigham Young University , Provo , Utah 84602 , United States
| | - Jatinder Singh
- Department of Chemistry and Biochemistry , Brigham Young University , Provo , Utah 84602 , United States
| | - Shardon T Morrill
- Department of Chemistry and Biochemistry , Brigham Young University , Provo , Utah 84602 , United States
| | - Gracie Damstedt
- Department of Chemistry and Biochemistry , Brigham Young University , Provo , Utah 84602 , United States
| | - Steven L Castle
- Department of Chemistry and Biochemistry , Brigham Young University , Provo , Utah 84602 , United States
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2
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Jalan A, Kastner DW, Webber KGI, Smith MS, Price JL, Castle SL. Bulky Dehydroamino Acids Enhance Proteolytic Stability and Folding in β-Hairpin Peptides. Org Lett 2017; 19:5190-5193. [PMID: 28910115 PMCID: PMC6085080 DOI: 10.1021/acs.orglett.7b02455] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The bulky dehydroamino acids dehydrovaline (ΔVal) and dehydroethylnorvaline (ΔEnv) can be inserted into the turn regions of β-hairpin peptides without altering their secondary structures. These residues increase proteolytic stability, with ΔVal at the (i + 1) position having the most substantial impact. Additionally, a bulky dehydroamino acid can be paired with a d-amino acid (i.e., d-Pro) to synergistically enhance resistance to proteolysis. A link between proteolytic stability and peptide structure is established by the finding that a stabilized ΔVal-containing β-hairpin is more highly folded than its Asn-containing congener.
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Affiliation(s)
- Ankur Jalan
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, 84602, United States
| | - David W. Kastner
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, 84602, United States
| | - Kei G. I. Webber
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, 84602, United States
| | - Mason S. Smith
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, 84602, United States
| | - Joshua L. Price
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, 84602, United States
| | - Steven L. Castle
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, 84602, United States
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3
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Jiang J, Ma Z, Castle SL. Bulky α,β-dehydroamino acids: their occurrence in nature, synthesis, and applications. Tetrahedron 2015. [DOI: 10.1016/j.tet.2015.06.001] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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Jiang J, Luo S, Castle SL. Solid-phase synthesis of peptides containing bulky dehydroamino acids. Tetrahedron Lett 2015. [DOI: 10.1016/j.tetlet.2014.12.097] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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5
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Siodłak D, Bujak M, Staś M. Intra- and intermolecular forces dependent main chain conformations of esters of α,β-dehydroamino acids. J Mol Struct 2013. [DOI: 10.1016/j.molstruc.2013.04.078] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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6
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Siodłak D, Grondys J, Lis T, Bujak M, Broda MA, Rzeszotarska B. The conformational properties of dehydrobutyrine and dehydrovaline: theoretical and solid-state conformational studies. J Pept Sci 2010; 16:496-505. [PMID: 20645424 DOI: 10.1002/psc.1267] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Dehydrobutyrine is the most naturally occurring dehydroamino acid. It is also the simplest dehydroamino acid having the geometrical isomers E/Z. To investigate its conformational properties, a theoretical analysis was performed on N-acetyl-alpha,beta-dehydrobutyrine N'-methylamides, Ac-(E)-DeltaAbu-NHMe and Ac-(Z)-DeltaAbu-NHMe, as well as the dehydrovaline derivative Ac-DeltaVal-NHMe. The phi, psi potential energy surfaces and the localised conformers were calculated at the B3LYP/6-311 + + G(d,p) level of theory both in vacuo and with inclusion of the solvent (chloroform, water) effect (SCRF method). The X-ray crystal structures of Ac-(Z)-DeltaAbu-NHMe and Ac-DeltaVal-NHMe were determined at 85 and 100 K, respectively. The solid-state conformational preferences for the studied residues have been analysed and compared with the other related structures. Despite the limitations imposed by the C(alpha) = C(beta) double bond on the topography of the side chains, the main chains of the studied dehydroamino acids are more flexible than in standard alanine. The studied dehydroamino acids differ in their conformational preferences, which depend on the polarity of the environment. This might be a reason why the nature quite precisely differentiates between DeltaVal and each of the DeltaAbu isomers, and why, particularly so with the latter, they are used as a conformational tool to influence the biological action of usually small, cyclic dehydropeptides.
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Affiliation(s)
- Dawid Siodłak
- Faculty of Chemistry, University of Opole, Oleska 48, 45-052 Opole, Poland.
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Lisowski M, Jaremko Ł, Jaremko M, Mazur A, Latajka R, Makowski M. Effect of the ΔPhe residue configuration on a didehydropeptides conformation: A combined CD and NMR study. Biopolymers 2010; 93:1055-64. [DOI: 10.1002/bip.21522] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Lisowski M, Latajka R, Picur B, Lis T, Bryndal I, Rospenk M, Makowski M, Kafarski P. Combined effect of the ΔPhe or ΔAla residue and thep-nitroanilide group on a didehydropeptides conformation. Biopolymers 2008; 89:220-34. [DOI: 10.1002/bip.20897] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Broda MA, Ciszak EM, Koziol AE, Pietrzynski G, Rzeszotarska B. Conformational investigation of α,β-dehydropeptides. XVI. β-turn tendency in Ac-Pro-ΔXaa-NHMe: crystallographic and theoretical studies. J Pept Sci 2006; 12:538-49. [PMID: 16733828 DOI: 10.1002/psc.763] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
The crystal structures of two diastereomeric alpha,beta-dehydrobutyrine peptides Ac-Pro-(Z)-DeltaAbu-NHMe (I) and Ac-Pro-(E)-DeltaAbu-NHMe (II) have been determined. Both dehydropeptides adopt betaI-turn conformation characterized by the pairs of (phi(i+1), psi(i+1)) and (phi(i+2), psi(i+2)) angles as -66, -19, -97, 11 degrees for I and -59, -27, -119, 29 degrees for II. In each peptide, the betaI turn is stabilized by (i + 3) --> i intramolecular hydrogen bonds with N...O distance of 3.12 A for I and 2.93 A for II. These structures have been compared to the crystal structures of homologous peptides Ac-Pro-DeltaVal-NHMe and Ac-Pro-DeltaAla-NHMe. Theoretical analyses by DFT/B3LYP/6-31 + G** method of conformers formed by these four peptides and by the saturated peptide Ac-Pro-Ala-NHMe revealed that peptides with a (Z) substituent at the C(beta) (i+2) atom of dehydroamino acid, i.e. Ac-Pro-DeltaVal-NHMe and Ac-Pro-(Z)-DeltaAbu-NHMe, predominantly form beta turns, both in vacuo and in polar environment. The tendency to adopt beta-turn conformation is much weaker for the peptides lacking the (Z) substituent, Ac-Pro-(E)-DeltaAbu-NHMe and Ac-Pro-DeltaAla-NHMe. The latter adopts a semi-extended or an extended conformation in every polar environment, including a weakly polar solvent. The saturated peptide Ac-Pro-Ala-NHMe in vacuo prefers a beta-turn conformation, but in polar environment the differences between various conformers are small. The role of pi-electron correlation and intramolecular hydrogen bonds interaction in stabilizing the hairpin structures are discussed.
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Affiliation(s)
- Malgorzata A Broda
- Institute of Chemistry, University of Opole, Olesja Street 48, 45-052 Opole, Poland.
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Goel VK, Somvanshi RK, Dey S, Singh TP. Effects of branched beta-carbon dehydro-residues on peptide conformations: syntheses, crystal structures and molecular conformations of two tetrapeptides: (a) N-(benzyloxycarbonyl)-DeltaVal-Leu-DeltaPhe-Leu-OCH3 and (b) N-(benzyloxycarbonyl)-DeltaIle-Ala-DeltaPhe-Ala-OCH3. ACTA ACUST UNITED AC 2005; 66:68-74. [PMID: 16000120 DOI: 10.1111/j.1399-3011.2005.00274.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The roles of branched beta-carbon dehydro-residues in the design of peptide conformations have not been systematically explored so far. In order to determine the effects of branched beta-carbon dehydro-residues on the peptide conformations, two N-protected tetrapeptides containing new combinations of DeltaVal and DeltaPhe in (a) N-(benzyloxycarbonyl)-DeltaVal-Leu-DeltaPhe-Leu-OCH(3) and DeltaIle and DeltaPhe in (b) N-(benzyloxycarbonyl)-DeltaIle-Ala-DeltaPhe-Ala-OCH(3) were synthesized by solution procedure. The crystal structures of these peptides were determined by X-ray diffraction methods. Single crystals of both peptides were grown by slow evaporation method from their solutions in acetone-water mixtures (80 : 20) at 25 degrees C. The crystals of these peptides belong to the orthorhombic space group P2(1)2(1)2(1) with cell dimensions of a = 12.342(1) A, b = 15.659(1) A, c = 18.970(1) A for peptide (a) and a = 8.093(1) A, b = 15.791(1) A, c = 23.816(1) A for peptide (b) having Z = 4 in the unit cells of both peptides. The structures were refined by full-matrix least-squares procedure to R-factors of 0.076 and 0.052 respectively. Both peptides adopt the right-handed 3(10)-helical conformations stabilized by two intramolecular (i + 3-->i) hydrogen bonds between the CO of N-terminal benzyloxycarbonyl (Cbz) group and the NH of residue at position 3, and between the CO of residue at position 1 and NH of the residue at position 4. The two consecutive 10-membered rings formed by the hydrogen bonds have dihedral angles corresponding to the standard values for type III beta-turns. DeltaVal and DeltaIle in peptides (a) and (b) respectively are located at the (i + 1) position of the first beta-turn while DeltaPhe is located at the (i + 2) position of the second beta-turn. In the crystals, the molecules are linked head to tail by intermolecular hydrogen bonds to form long helical chains. The axes of helices are parallel to the b-axes while the neighbouring helices run in the opposite directions. The crystal packings are further stabilized by van der Waals forces between the columns of molecular packings.
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Affiliation(s)
- V K Goel
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi 110029, India
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Dey S, Vijayaraghavan R, Goel V, Kumar S, Kumar P, Singh T. Design rules for peptides with α, β-dehydro-residues: synthesis of a model peptide Boc-Ile-ΔAla-OCH3 and its crystal structures obtained from two different solvents. J Mol Struct 2005. [DOI: 10.1016/j.molstruc.2004.10.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Goel V, Guha M, Baxla A, Dey S, Singh T. Design of peptides with α,β-dehydro-residues: synthesis, crystal structure and molecular conformation of a peptide N-tertiary-butyloxycarbonyl-l-Leu-ΔPhe-L-Ile-OCH3. J Mol Struct 2003. [DOI: 10.1016/s0022-2860(03)00464-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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