1
|
El Khabchi M, Mcharfi M, Benzakour M, Fitri A, Benjelloun AT, Song JW, Lee KB, Lee HJ. Computational Investigation of Conformational Properties of Short Azapeptides: Insights from DFT Study and NBO Analysis. Molecules 2023; 28:5454. [PMID: 37513326 PMCID: PMC10386235 DOI: 10.3390/molecules28145454] [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: 06/09/2023] [Revised: 07/05/2023] [Accepted: 07/12/2023] [Indexed: 07/30/2023] Open
Abstract
Azapeptides have gained much attention due to their ability to enhance the stability and bioavailability of peptide drugs. Their structural preferences, essential to understanding their function and potential application in the peptide drug design, remain largely unknown. In this work, we systematically investigated the conformational preferences of three azaamino acid residues in tripeptide models, Ac-azaXaa-Pro-NHMe [Xaa = Asn (4), Asp (5), Ala (6)], using the popular DFT functionals, B3LYP and B3LYP-D3. A solvation model density (SMD) was used to mimic the solvation effect on the conformational behaviors of azapeptides in water. During the calculation, we considered the impact of the amide bond in the azapeptide models on the conformational preferences of models 4-6. We analyzed the effect of the HB between the side-chain main chain and main-chain main-chain on the conformational behaviors of azapeptides 4-6. We found that the predicted lowest energy conformation for the three models differs depending on the calculation methods. In the gas phase, B3LYP functional indicates that the conformers tttANP-1 and tttADP-1 of azapeptides 4 and 5 correspond to the type I of β-turn, the lowest energy conformation with all-trans amide bonds. Considering the dispersion correction, B3LYP-D3 functional predicts the conformers tctANP-2 and tctADP-3 of azapeptide 4 and 5, which contain the cis amide bond preceding the Pro residue, as the lowest energy conformation in the gas phase. The results imply that azaAsx and Pro residues may involve cis-trans isomerization in the gas phase. In water, the predicted lowest energy conformer of azapeptides 4 and 5 differs from the gas phase results and depends on the calculational method. For azapeptide 6, regardless of calculation methods and phases, tttAAP-1 (β-I turn) is predicted as the lowest energy conformer. The results imply that the effect of the side chain that can form HBs on the conformational preferences of azapeptides 4 and 5 may not be negligible. We compared the theoretical results of azaXaa-Pro models with those of Pro-azaXaa models, showing that incorporating azaamino acid residue in peptides at different positions can significantly impact the folding patterns and stability of azapeptides.
Collapse
Affiliation(s)
- Mouna El Khabchi
- LIMAS, Department of Chemistry, Faculty of Sciences Dhar El Mahraz, Sidi Mohamed Ben Abdallah University, Fez 30000, Morocco
| | - Mohammed Mcharfi
- LIMAS, Department of Chemistry, Faculty of Sciences Dhar El Mahraz, Sidi Mohamed Ben Abdallah University, Fez 30000, Morocco
| | - Mohammed Benzakour
- LIMAS, Department of Chemistry, Faculty of Sciences Dhar El Mahraz, Sidi Mohamed Ben Abdallah University, Fez 30000, Morocco
| | - Asmae Fitri
- LIMAS, Department of Chemistry, Faculty of Sciences Dhar El Mahraz, Sidi Mohamed Ben Abdallah University, Fez 30000, Morocco
| | - Adil Touimi Benjelloun
- LIMAS, Department of Chemistry, Faculty of Sciences Dhar El Mahraz, Sidi Mohamed Ben Abdallah University, Fez 30000, Morocco
| | - Jong-Won Song
- Department of Chemistry Education, Daegu University, Daegudae-ro 201, Gyeongsan-si 38453, Republic of Korea
| | - Kang-Bong Lee
- Climate and Environmental Research Institute, Korea Institute of Science & Technology, Hwarang-ro 14-gil 5, Seoul 02792, Republic of Korea
| | - Ho-Jin Lee
- Department of Natural Sciences, Southwest Tennessee Community College, Memphis, TN 38134, USA
| |
Collapse
|
2
|
Harris T, Chenoweth DM. Sterics and Stereoelectronics in Aza-Glycine: Impact of Aza-Glycine Preorganization in Triple Helical Collagen. J Am Chem Soc 2019; 141:18021-18029. [DOI: 10.1021/jacs.9b05524] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Trevor Harris
- Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, Pennsylvania 19104-6323, United States
| | - David M. Chenoweth
- Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, Pennsylvania 19104-6323, United States
| |
Collapse
|
3
|
Zimnicka MM. Conformational Features of Thioamide-Containing Dipeptoids and Peptoid–Peptide Hybrids—Computational and Experimental Approaches. J Phys Chem A 2018; 122:7819-7831. [DOI: 10.1021/acs.jpca.8b05456] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Magdalena M. Zimnicka
- Institute of Organic Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
| |
Collapse
|
4
|
De Zotti M, Peggion C, Biondi B, Crisma M, Formaggio F, Toniolo C. Endothioxopeptides: A conformational overview. Biopolymers 2016; 106:697-713. [DOI: 10.1002/bip.22899] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Revised: 06/08/2016] [Accepted: 06/25/2016] [Indexed: 12/16/2022]
Affiliation(s)
- Marta De Zotti
- Department of Chemical Sciences; University of Padova; Padova 35131 Italy
| | - Cristina Peggion
- Department of Chemical Sciences; University of Padova; Padova 35131 Italy
| | - Barbara Biondi
- Institute of Biomolecular Chemistry, Padova Unit, CNR; Padova 35131 Italy
| | - Marco Crisma
- Institute of Biomolecular Chemistry, Padova Unit, CNR; Padova 35131 Italy
| | - Fernando Formaggio
- Department of Chemical Sciences; University of Padova; Padova 35131 Italy
- Institute of Biomolecular Chemistry, Padova Unit, CNR; Padova 35131 Italy
| | - Claudio Toniolo
- Department of Chemical Sciences; University of Padova; Padova 35131 Italy
- Institute of Biomolecular Chemistry, Padova Unit, CNR; Padova 35131 Italy
| |
Collapse
|
5
|
|
6
|
Ottersbach PA, Schnakenburg G, Gütschow M. Induction of chirality: experimental evidence of atropisomerism in azapeptides. Chem Commun (Camb) 2012; 48:5772-4. [PMID: 22552375 DOI: 10.1039/c2cc31161e] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Methylation of the peptide bond in model azadipeptides leads to the E configuration and hence to atropisomerism due to a restricted rotation around the N-N axis.
Collapse
Affiliation(s)
- Philipp A Ottersbach
- Pharmaceutical Institute, Pharmaceutical Chemistry I, University of Bonn, An der Immenburg 4, 53121 Bonn, Germany
| | | | | |
Collapse
|
7
|
Zimnicka M, Gregersen JA, Tureček F. A Stable Aminothioketyl Radical in the Gas Phase. J Am Chem Soc 2011; 133:10290-301. [DOI: 10.1021/ja203611x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Magdalena Zimnicka
- Department of Chemistry, University of Washington, Bagley Hall, Box 351700, Seattle, Washington 981195-1700, United States
| | - Joshua A. Gregersen
- Department of Chemistry, University of Washington, Bagley Hall, Box 351700, Seattle, Washington 981195-1700, United States
| | - František Tureček
- Department of Chemistry, University of Washington, Bagley Hall, Box 351700, Seattle, Washington 981195-1700, United States
| |
Collapse
|
8
|
Lee HJ, Park HM, Lee KB. The β-turn scaffold of tripeptide containing an azaphenylalanine residue. Biophys Chem 2007; 125:117-26. [PMID: 16890344 DOI: 10.1016/j.bpc.2006.05.028] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2005] [Revised: 05/10/2006] [Accepted: 05/10/2006] [Indexed: 11/27/2022]
Abstract
The conformational preferences of azaphenylalanine-containing peptide were investigated using a model compound, Ac-azaPhe-NHMe with ab initio method at the HF/3-21G and HF/6-31G(*) levels, and the seven minimum energy conformations with trans orientation of acetyl group and the 4 minimum energy conformations with cis orientation of acetyl group were found at the HF/6-31G(*) level if their mirror images were not considered. An average backbone dihedral angle of the 11 minimum energy conformations is phi=+/-91 degrees +/-24 degrees , psi =+/-18 degrees +/-10 degrees (or +/-169 degrees +/-8 degrees ), corresponding to the i+2 position of beta-turn (delta(R)) or polyproline II (beta(P)) structure, respectively. The chi(1) angle in the aromatic side chain of azaPhe residue adopts preferentially between +/-60 degrees and +/-130 degrees, which reflect a steric hindrance between the N-terminal carbonyl group or the C-terminal amide group and the aromatic side chain with respect to the configuration of the acetyl group. These conformational preferences of Ac-azaPhe-NHMe predicted theoretically were compared with those of For-Phe-NHMe to characterize the structural role of azaPhe residue. Four tripeptides containing azaPhe residue, Boc-Xaa-azaPhe-Ala-OMe [Xaa=Gly(1), Ala(2), Phe(3), Asn(4)] were designed and synthesized to verify whether the backbone torsion angles of azaPhe reside are still the same as compared with theoretical conformations and how the preceding amino acids of azaPhe residue perturb the beta-turn skeleton in solution. The solution conformations of these tripeptide models containing azaPhe residue were determined in CDCl(3) and DMSO solvents using NMR and molecular modeling techniques. The characteristic NOE patterns, the temperature coefficients of amide protons and small solvent accessibility for the azapeptides 1-4 reveal to adopt the beta-turn structure. The structures of azapeptides containing azaPhe residue from a restrained molecular dynamics simulation indicated that average dihedral angles [(phi(1), psi(1)), (phi(2), psi(2))] of Xaa-azaPhe fragment in azapeptide, Boc-Xaa-azaPhe-Ala-OMe were [(-68 degrees, 135 degrees ), (116 degrees, -1 degrees )], and this implies that the intercalation of an azaPhe residue in tripeptide induces the betaII-turn conformation, and the volume change of a preceding amino acid of azaPhe residue in tripeptides would not perturb seriously the backbone dihedral angle of beta-turn conformation. We believe such information could be critical in designing useful molecules containing azaPhe residue for drug discovery and peptide engineering.
Collapse
Affiliation(s)
- Ho-Jin Lee
- Advanced Analysis Center, Korea Institute of Science and Technology, P.O. Box 131 Cheongryangri, Seoul 130-650, Korea
| | | | | |
Collapse
|
9
|
Song JW, Lee HJ, Choi YS, Yoon CJ. Origin of Rotational Barriers of the N−N Bond in Hydrazine: NBO Analysis. J Phys Chem A 2006; 110:2065-71. [PMID: 16451044 DOI: 10.1021/jp055755c] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Hydrazine passes through two transition states, TS1 (phi = 0 degrees ) and TS2 (phi = 180 degrees ), in the course of internal rotation around its N-N bond. The origin of the corresponding rotational barriers in hydrazine has been extensively studied by experimental and theoretical methods. Here, we used natural bond orbital (NBO) analysis and energy decomposition of rotational barrier energy (DeltaE(barrier)) to understand the origin of the torsional potential energy profile of this molecule. DeltaE(barrier) was dissected into structural (DeltaE(struc)), steric exchange (DeltaE(steric)), and hyperconjugative (DeltaE(deloc)) energy contributions. In both transition states, the major barrier-forming contribution is DeltaE(deloc). The TS2 barrier is lowered by pyramidalization of nitrogen atoms through lowering DeltaE(struc), not by N-N bond lengthening through lowering DeltaE(steric). Higher pyramidality of nitrogen atoms of TS2 than that of TS1 explains well why the N-N bond of TS2 is longer than that of TS1. Finally, the steric repulsion between nitrogen lone pairs does not determine the rotational barrier; nuclear-nuclear Coulombic repulsion between outer H/H atoms in TS1 plays an important role in increasing DeltaE(struc). Taken together, we explain the reason for the different TS1 and TS2 barriers. We show that NBO analysis is a useful tool for understanding structures and potential energy surfaces of compounds containing the N-N bond.
Collapse
Affiliation(s)
- Jong-Won Song
- Department of Chemistry, Korea University, 1 Anam-dong, Seoul 136-701, Korea
| | | | | | | |
Collapse
|
10
|
Wang CS, Zhang Y, Gao K, Yang ZZ. A new scheme for determining the intramolecular seven-membered ring N–H⋯OC hydrogen-bonding energies of glycine and alanine peptides. J Chem Phys 2005; 123:24307. [PMID: 16050745 DOI: 10.1063/1.1979471] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
In this paper a new scheme was proposed to calculate the intramolecular hydrogen-bonding energies in peptides and was applied to calculate the intramolecular seven-membered ring N-H...O=C hydrogen-bonding energies of the glycine and alanine peptides. The density-functional theory B3LYP6-31G(d) and B3LYP6-311G(d,p) methods and the second-order Moller-Plesset perturbation theory MP26-31G(d) method were used to calculate the optimal geometries and frequencies of glycine and alanine peptides and related structures. MP26-311++G(d,p), MP26-311++G(3df,2p), and MP2/aug-cc-pVTZ methods were then used to evaluate the single-point energies. It was found that the B3LYP6-31G(d), MP26-31G(d), and B3LYP6-311G(d,p) methods yield almost similar structural parameters for the conformers of the glycine and alanine dipeptides. MP2/aug-cc-pVTZ predicts that the intramolecular seven-membered ring N-H...O=C hydrogen-bonding strength has a value of 5.54 kcal/mol in glycine dipeptide and 5.73 and 5.19 kcal/mol in alanine dipeptides, while the steric repulsive interactions of the seven-membered ring conformers are 4.13 kcal/mol in glycine dipeptide and 6.62 and 3.71 kcal/mol in alanine dipeptides. It was also found that MP26-311++G(3df,2p) gives as accurate intramolecular N-H...O=C hydrogen-bonding energies and steric repulsive interactions as the much more costly MP2/aug-cc-pVTZ does.
Collapse
Affiliation(s)
- Chang-Sheng Wang
- Department of Chemistry, Liaoning Normal University, Dalian 116029, People's Republic of China.
| | | | | | | |
Collapse
|