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Rai Deka JK, Sahariah B, Sarma BK. Understanding the Cis-Trans Amide Bond Isomerization of N, N'-Diacylhydrazines to Develop Guidelines for A Priori Prediction of Their Most Stable Solution Conformers. J Org Chem 2024; 89:10419-10433. [PMID: 36700530 DOI: 10.1021/acs.joc.2c01891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
N,N'-diacylhydrazines (R1CO-NR3-NR4-COR2) are a class of small molecules with a wide range of applications in chemistry and biology. They are structurally unique in the sense that their two amide groups are connected via a N-N single bond, and as a result, these molecules can exist in eight different isomeric forms. Four of these are amide isomers [trans-trans (t-t), trans-cis (t-c), cis-trans (c-t), and cis-cis (c-c)] arising from C-N bond restricted rotation. In addition, each of these amide isomers can exist in two different isomeric forms due to N-N bond restricted rotation, especially when R3 and R4 groups are relatively bigger. Herein, we have systematically investigated the conformations of 55 N,N'-diacylhydrazines using a combination of solution NMR spectroscopy, X-ray crystallography, and density functional theory calculations. Our data suggest that when the substituents R3 and R4 on the nitrogen atoms are both hydrogens. These molecules prefer twisted trans-trans (t-t) (>90%) geometries (H-N-C═O ∼ 180°), whereas the N-alkylated and N,N'-dialkylated molecules prefer twisted trans-cis (t-c) geometries. Herein, we have analyzed the stabilization of the various isomers of these molecules in light of steric and stereoelectronic effects. We provide a guideline to a priori predict the most stable conformers of the N,N'-diacylhydrazines just by examining their substituents (R1-R4).
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Affiliation(s)
- Jugal Kishore Rai Deka
- New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Bangalore 560064, India
| | - Biswajit Sahariah
- New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Bangalore 560064, India
| | - Bani Kanta Sarma
- New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Bangalore 560064, India
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2
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Lee HJ, Liu SW, Sulyok-Eiler M, Harmat V, Farkas V, Bánóczi Z, El Khabchi M, Shawn Fan HJ, Hirao K, Song JW. Neighbor effect on conformational spaces of alanine residue in azapeptides. Heliyon 2024; 10:e33159. [PMID: 39021983 PMCID: PMC11253059 DOI: 10.1016/j.heliyon.2024.e33159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Revised: 06/10/2024] [Accepted: 06/14/2024] [Indexed: 07/20/2024] Open
Abstract
The conformational properties of Alanine (Ala) residue have been investigated to understand protein folding and develop force fields. In this work, we examined the neighbor effect on the conformational spaces of Ala residue using model azapeptides, Ac-Ala-azaGly-NHMe (3, AaG), and Ac-azaGly-Ala-NHMe (4, aGA1). Ramachandran energy maps were generated by scanning (φ, ψ) dihedral angles of the Ala residues in models with the fixed dihedral angles (φ = ±90°, ψ = ±0° or ±180°) of azaGly residue using LCgau-BOP and LCgau-BOP + LRD functionals in the gas and water phases. The integral-equation-formalism polarizable continuum model (IEF-PCM) and a solvation model density (SMD) were employed to mimic the solvation effect. The most favorable conformation of Ala residue in azapeptide models is found as the polyproline II (βP), inverse γ-turn (γ'), β-sheet (βS), right-handed helix (αR), or left-handed helix (αL) depending on the conformation of neighbor azaGly residue in isolated form. Solvation methods exhibit that the Ala residue favors the βP, δR, and αR conformations regardless of its position in azapeptides 3 and 4 in water. Azapeptide 5, Ac-azaGly-Ala-NH2 (aGA2), was synthesized to evaluate the theoretical results. The X-ray structure showed that azaGly residue adopts the polyproline II (βP) and Ala residue adopts the right-handed helical (αR) structure in aGA2. The conformational preferences of aGA2 and the dimer structure of aGA2 based on the X-ray structure were examined to assess the performance of DFT functionals. In addition, the local minima of azapeptide 6, Ac-Phe-azaGly-NH2 (FaG), were compared with the previous experimental results. SMD/LCgau-BOP + LRD methods agreed well with the reported experimental results. The results suggest the importance of weak dispersion interactions, neighbor effect, and solvent influence in the conformational preferences of Ala residue in model azapeptides.
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Affiliation(s)
- Ho-Jin Lee
- Division of Natural and Mathematics Sciences, LeMoyne-Own College, Memphis, TN, 38126, USA
- Department of Natural Sciences, Southwest Tennessee Community College, Memphis, TN, 38015, USA
| | - Shi-Wei Liu
- College of Chemical Engineering, Sichuan University of Science and Engineering, Zigong City, Sichuan Province, 64300, PR China
| | - Máté Sulyok-Eiler
- Laboratory of Structural Biology and Chemistry, Institute of Chemistry, Eötvös Loránd University, Budapest, Hungary
- Hevesy György PhD School of Chemistry, Eötvös Loránd University, Budapest, Hungary
| | - Veronika Harmat
- Laboratory of Structural Biology and Chemistry, Institute of Chemistry, Eötvös Loránd University, Budapest, Hungary
- HUN-REN - ELTE Protein Modeling Research Group, Budapest, Hungary
| | - Viktor Farkas
- Laboratory of Structural Biology and Chemistry, Institute of Chemistry, Eötvös Loránd University, Budapest, Hungary
- HUN-REN - ELTE Protein Modeling Research Group, Budapest, Hungary
| | - Zoltán Bánóczi
- Department of Organic Chemistry, Institute of Chemistry, ELTE Eötvös Loránd University, 1117, Budapest, Hungary
- HUN-REN-ELTE Research Group of Peptide Chemistry, 1117, Budapest, Hungary
| | - Mouna El Khabchi
- LIMAS, Faculty of Sciences Dhar El Mahraz, University Sidi Mohamed Ben Abdallah, Fez, Morocco
| | - Hua-Jun Shawn Fan
- College of Chemical Engineering, Sichuan University of Science and Engineering, Zigong City, Sichuan Province, 64300, PR China
| | - Kimihiko Hirao
- Fukui Institute for Fundamental Chemistry, Kyoto University, Takano, Nishihiraki-cho 34-4, Sakyo-ku, Kyoto, 606-8103, Japan
| | - Jong-Won Song
- Department of Chemistry Education, Daegu University, Daegudae-ro 201, Gyeongsan-si, Gyeongsangbuk-do, 38453, Republic of Korea
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Wang XD, Zhu J, Wang DX. Intermolecular n→π* Interactions in Supramolecular Chemistry and Catalysis. Chempluschem 2023; 88:e202300288. [PMID: 37609956 DOI: 10.1002/cplu.202300288] [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: 06/14/2023] [Revised: 08/19/2023] [Accepted: 08/21/2023] [Indexed: 08/24/2023]
Abstract
The n→π* interactions describing attractive force between lone pairs (lps) of nucleophile and carbonyl or polarized unsaturated bonds have recently attracted growing attentions in various disciplines. So far, such non-covalent driving force are mainly concentrated to intramolecular systems. Intermolecular n→π* interactions in principle could produce fascinated supramolecular systems or facilitate organic reactions, however, they remain largely underexplored due to the very weak energy of individual interaction. This review attempts to give an overview of the challenging intermolecular n→π* interactions, much efforts emphasize the supramolecular systems, catalytic processes and spectroscopic measurements.
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Affiliation(s)
- Xu-Dong Wang
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Molecular Recognition and Function, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China
| | - Jun Zhu
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Molecular Recognition and Function, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - De-Xian Wang
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Molecular Recognition and Function, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
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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.
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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
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5
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Zhu J, Wang XD, Ao YF, Wang QQ, Wang DX. Intermolecular n→π* Interactions Based on a Tailored Multicarbonyl-Containing Macrocycle. Chemistry 2023; 29:e202203485. [PMID: 36445795 DOI: 10.1002/chem.202203485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 11/24/2022] [Accepted: 11/24/2022] [Indexed: 11/30/2022]
Abstract
Towards unexplored intermolecular n→π* interactions, presented herein are the synthesis, structure, self-assembly and function of a multicarbonyl-containing macrocycle calix[2]arene[2]barbiturate 1. X-ray single crystal diffraction reveals the presence of Cl⋅⋅⋅C=O interactions in CH2 Cl2 ⊂1 host-guest complex and multiple intermolecular C=O⋅⋅⋅C=O interactions between molecules 1 in crystalline state. The intermolecular C=O⋅⋅⋅C=O interactions as attractive driving force led to unprecedented self-assembly of nanotube with diameter around 1.4 nm and inner surface engineered by aromatic rings. SEM and TEM images of the self-assembly of 1 demonstrated temperature-dependent morphologies which allows the observation of spheres at 25 °C and rods at 0 °C, respectively. XRD analysis indicated consistent hexagonal patterns in the self-assembly and single crystal lattice, indicating the nanotubes driven by C=O⋅⋅⋅C=O interactions constitute the basic structural architectures of both aggregates. The nanoscopic tubes (pores) formed in the rodlike single crystal engendering the separation of moving dyes were preliminarily investigated by a single-crystal chromatography and crystal-packed column chromatography.
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Affiliation(s)
- Jun Zhu
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Molecular Recognition and Function, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China.,University of Chinese Academy of Sciences, Beijing, 100049, P. R. China)
| | - Xu-Dong Wang
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Molecular Recognition and Function, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China
| | - Yu-Fei Ao
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Molecular Recognition and Function, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China.,University of Chinese Academy of Sciences, Beijing, 100049, P. R. China)
| | - Qi-Qiang Wang
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Molecular Recognition and Function, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China.,University of Chinese Academy of Sciences, Beijing, 100049, P. R. China)
| | - De-Xian Wang
- Beijing National Laboratory for Molecular Sciences, CAS Key Laboratory of Molecular Recognition and Function, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China.,University of Chinese Academy of Sciences, Beijing, 100049, P. R. China)
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6
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Hulgan SAH, Hartgerink JD. Recent Advances in Collagen Mimetic Peptide Structure and Design. Biomacromolecules 2022; 23:1475-1489. [PMID: 35258280 DOI: 10.1021/acs.biomac.2c00028] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Collagen mimetic peptides (CMPs) fold into a polyproline type II triple helix, allowing the study of the structure and function (or misfunction) of the collagen family of proteins. This Perspective will focus on recent developments in the use of CMPs toward understanding the structure and controlling the stability of the triple helix. Triple helix assembly is influenced by various factors, including the single amino acid propensity for the triple helix fold, pairwise interactions between these amino acids, and long-range effects observed across the helix, such as bend, twist, and fraying. Important progress in creating a comprehensive and predictive understanding of these factors for peptides with exclusively natural amino acids has been made. In contrast, several groups have successfully developed unnatural amino acids that are engineered to stabilize the triple helical structure. A third approach to controlling the triple helical structure includes covalent cross-linking of the triple helix to stabilize the assembly, which eliminates the problematic equilibrium of unfolding into monomers and enforces compositional control. Advances in all these areas have resulted in significant improvements to our understanding and control of this important class of protein, allowing for the design and application of more chemically complex and well-controlled collagen mimetic biomaterials.
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Affiliation(s)
- Sarah A H Hulgan
- Rice University, Department of Chemistry, 6100 Main Street, Houston, Texas 77005, United States
| | - Jeffrey D Hartgerink
- Rice University, Department of Chemistry, 6100 Main Street, Houston, Texas 77005, United States
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7
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Athiyarath V, Madhusudhanan MC, Kunnikuruvan S, Sureshan KM. Secondary Structure Tuning of a Pseudoprotein Between β‐Meander and α‐Helical Forms in the Solid‐State. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202113129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Vignesh Athiyarath
- School of Chemistry Indian Institute of Science Education and Research Thiruvananthapuram Kerala 695551 India
| | - Mithun C. Madhusudhanan
- School of Chemistry Indian Institute of Science Education and Research Thiruvananthapuram Kerala 695551 India
| | - Sooraj Kunnikuruvan
- School of Chemistry Indian Institute of Science Education and Research Thiruvananthapuram Kerala 695551 India
| | - Kana M. Sureshan
- School of Chemistry Indian Institute of Science Education and Research Thiruvananthapuram Kerala 695551 India
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8
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Arcoria PJ, Ware RI, Makwana SV, Troya D, Etzkorn FA. Conformational Analysis of Fluoro-, Chloro-, and Proteo-Alkene Gly-Pro and Pro-Pro Isosteres to Mimic Collagen. J Phys Chem B 2021; 126:217-228. [PMID: 34968406 DOI: 10.1021/acs.jpcb.1c09180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Collagen is the most abundant human protein, with the canonical sequence (Gly-Pro-Hyp)n in its triple helix region. Cis-trans isomerization of the Xaa-Pro amide has made two of these amide bonds the target of alkene replacement: the Gly-Pro and the Pro-Hyp positions. The conformations of Gly-Pro and Pro-Pro (as a Pro-Hyp model) fluoro-, chloro-, and proteo-alkene mimic models were investigated computationally to determine whether these alkenes can stabilize the polyproline type II (PPII) conformation of collagen. Second-order Møller-Plesset (MP2) calculations with various basis sets were used to perform the conformational analyses and locate stationary points. The calculation results predict that fluoro- and chloro-alkene mimics of Gly-Pro and Pro-Pro can participate in n→π* donation to stabilize PPII conformations, yet they are poor n→π* acceptors, shifting the global minima away from PPII conformations. For the proteo-alkene mimics, the lack of significant n→π* interactions and unstable PPII-like geometries explains their known destabilization of the triple helix in collagen-like peptides.
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Affiliation(s)
- Paul J Arcoria
- Department of Chemistry, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Rachel I Ware
- Department of Chemistry, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Sunny V Makwana
- Department of Chemistry, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Diego Troya
- Department of Chemistry, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Felicia A Etzkorn
- Department of Chemistry, Virginia Tech, Blacksburg, Virginia 24061, United States
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Godbe JM, Freeman R, Lewis JA, Sasselli IR, Sangji MH, Stupp SI. Hydrogen Bonding Stiffens Peptide Amphiphile Supramolecular Filaments by Aza-Glycine Residues. Acta Biomater 2021; 135:87-99. [PMID: 34481055 DOI: 10.1016/j.actbio.2021.08.044] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Revised: 08/25/2021] [Accepted: 08/26/2021] [Indexed: 12/30/2022]
Abstract
Peptide amphiphiles (PAs) are a class of molecules comprised of short amino acid sequences conjugated to hydrophobic moieties that may exhibit self-assembly in water into supramolecular structures. We investigate here how mechanical properties of hydrogels formed by PA supramolecular nanofibers are affected by hydrogen bond densities within their internal structure by substituting glycine for aza-glycine (azaG) residues. We found that increasing the number of PA molecules that contain azaG up to 5 mol% in PA supramolecular nanofibers increases their persistence length fivefold and decreases their diffusion coefficients as measured by fluorescence recovery after photobleaching. When these PAs are used to create hydrogels, their bulk storage modulus (G') was found to increase as azaG PA content in the supramolecular assemblies increases up to a value of 10 mol% and beyond this value a decrease was observed, likely due to diminished levels of nanofiber entanglement in the hydrogels as a direct result of increased supramolecular rigidity. Interestingly, we found that the bioactivity of the scaffolds toward dopaminergic neurons derived from induced pluripotent stem cells can be enhanced directly by persistence length independently of storage modulus. We hypothesize that this is due to interactions between the cells and the extracellular environment across different size scales: from filopodia adhering to individual nanofiber bundles to cell adhesion sites that interact with the hydrogel as a bulk substrate. Fine tuning of hydrogen bond density in self-assembling peptide biomaterials such as PAs provides an approach to control nanoscale stiffness as part of an overall strategy to optimize bioactivity in these supramolecular systems. supramolecular biomaterials. STATEMENT OF SIGNIFICANCE: Hydrogen bonding is an important driving force for the self-assembly of peptides in both biological and artificial systems. Here, we increase the amount of hydrogen bonding within self-assembled peptide amphiphile (PA) nanofibers by substituting glycine for an aza-glycine (azaG). We show that increasing the molar concentration of azaG increases the internal order of individual nanofibers and increases their persistence length. We also show that these changes are sufficient to increase survival and tyrosine hydroxylase expression in induced pluripotent stem cell-derived dopaminergic neurons cultured in 3D gels made of these materials. Our strategy of tuning the number of hydrogen bonds in a supramolecular assembly provides mechanical customization for 3D cell culture and tissue engineering.
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Affiliation(s)
- Jacqueline M Godbe
- Simpson Querrey Institute for BioNanotechnology, Northwestern University, 303 E. Superior St, Chicago, Illinois 60611, United States; Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Ronit Freeman
- Simpson Querrey Institute for BioNanotechnology, Northwestern University, 303 E. Superior St, Chicago, Illinois 60611, United States
| | - Jacob A Lewis
- Simpson Querrey Institute for BioNanotechnology, Northwestern University, 303 E. Superior St, Chicago, Illinois 60611, United States; Department of Biomedical Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Ivan R Sasselli
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - M Hussain Sangji
- Department of Biomedical Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Samuel I Stupp
- Simpson Querrey Institute for BioNanotechnology, Northwestern University, 303 E. Superior St, Chicago, Illinois 60611, United States; Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States; Department of Biomedical Engineering, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States; Department of Medicine, Northwestern University, 676 N St Clair St Suite 1600, Chicago, IL 60611, United States; Department of Materials Science and Engineering, Northwestern University, 2220 Campus Drive, Evanston, Illinois 60208, United States.
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Deka JKR, Kalita D, Sahariah B, Sarma BK. n N → π* Ar interactions stabilize the E-ac isomers of arylhydrazides and facilitate their S NAr autocyclizations. Chem Commun (Camb) 2021; 57:11236-11239. [PMID: 34632997 DOI: 10.1039/d1cc04533d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We describe a novel mechanism of stabilization of the E-ac isomer of an arylhydrazide via nN → π*Ar interactions. We further show that when a leaving group (F) is present at the ortho-position of the carbonyl group of such an arylhydrazide, the nN → π*Ar interaction facilitates an SNAr autocyclization reaction to produce indazolone, an important heterocycle with biological activity. Faster autocyclization of arylhydrazide is observed when an electron withdrawing group is present in the aryl ring, which is a characteristic of SNAr reactions.
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Affiliation(s)
- Jugal Kishore Rai Deka
- Department of Chemistry, School of Natural Sciences, Shiv Nadar University, Dadri, Uttar Pradesh 201314, India
| | - Debajit Kalita
- New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Bangalore 560064, India.
| | - Biswajit Sahariah
- New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Bangalore 560064, India.
| | - Bani Kanta Sarma
- New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Bangalore 560064, India.
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11
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Athiyarath V, Madhusudhanan MC, Kunnikuruvan S, Sureshan KM. Secondary Structure Tuning of a Pseudoprotein Between β-Meander and α-Helical Forms in the Solid-State. Angew Chem Int Ed Engl 2021; 61:e202113129. [PMID: 34699112 DOI: 10.1002/anie.202113129] [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: 09/27/2021] [Indexed: 12/23/2022]
Abstract
Tuning the secondary structure of a protein or polymer in the solid-state is challenging. Here we report the topochemical synthesis of a pseudoprotein and its secondary structure tuning in the solid-state. We designed the dipeptide monomer N3 -Leu-Ala-NH-CH2 -C≡CH (1) for topochemical azide-alkyne cycloaddition (TAAC) polymerization. Dipeptide 1 adopts an anti-parallel β-sheet-like stacked arrangement in its crystals. Upon heating, the dipeptide undergoes quantitative TAAC polymerization in a crystal-to-crystal fashion yielding large polymers. The reaction occurs between the adjacent monomers in the H-bonded anti-parallel stack, yielding pseudoprotein having a β-meander structure. When dissolved in methanol, this pseudoprotein changes its secondary structure from β-meander to α-helical form and it retains the new secondary structure upon desolvation. This work demonstrates a novel paradigm for tuning the secondary structure of a polymer in the solid-state.
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Affiliation(s)
- Vignesh Athiyarath
- School of Chemistry, Indian Institute of Science Education and Research, Thiruvananthapuram, Kerala, 695551, India
| | - Mithun C Madhusudhanan
- School of Chemistry, Indian Institute of Science Education and Research, Thiruvananthapuram, Kerala, 695551, India
| | - Sooraj Kunnikuruvan
- School of Chemistry, Indian Institute of Science Education and Research, Thiruvananthapuram, Kerala, 695551, India
| | - Kana M Sureshan
- School of Chemistry, Indian Institute of Science Education and Research, Thiruvananthapuram, Kerala, 695551, India
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12
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Cutini M, Ugliengo P. Infrared harmonic features of collagen models at B3LYP-D3: From amide bands to the THz region. J Chem Phys 2021; 155:075102. [PMID: 34418922 DOI: 10.1063/5.0056422] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
In this paper, we have studied the vibrational spectral features for the collagen triple helix using a dispersion corrected hybrid density functional theory (DFT-D) approach. The protein is simulated by an infinite extended polymer both in the gas phase and in a water micro-solvated environment. We have adopted proline-rich collagen models in line with the high content of proline in natural collagens. Our scaled harmonic vibrational spectra are in very good agreement with the experiments and allow for the peak assignment of the collagen amide I and III bands, supporting or questioning the experimental interpretation by means of vibrational normal modes analysis. Furthermore, we demonstrated that IR spectroscopy in the THz region can detect the small variations inherent to the triple helix helicity (10/3 over 7/2), thus elucidating the packing state of the collagen. So far, identifying the collagen helicity is only possible by means of crystal x-ray diffraction.
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Affiliation(s)
- Michele Cutini
- Department of Chemistry and NIS (Nanostructured Interfaces and Surfaces) Center, University of Torino, Via P. Giuria 7, 10125 Turin, Italy
| | - Piero Ugliengo
- Department of Chemistry and NIS (Nanostructured Interfaces and Surfaces) Center, University of Torino, Via P. Giuria 7, 10125 Turin, Italy
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13
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Baruah K, Sahariah B, Sakpal SS, Deka JKR, Bar AK, Bagchi S, Sarma BK. Stabilization of Azapeptides by N amide···H-N amide Hydrogen Bonds. Org Lett 2021; 23:4949-4954. [PMID: 34060858 DOI: 10.1021/acs.orglett.1c01111] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
An unusual Namide···H-Namide hydrogen bond (HB) was previously proposed to stabilize the azapeptide β-turns. Herein we provide experimental evidence for the Namide···H-Namide HB and show that this HB endows a stabilization of 1-3 kcal·mol-1 and enforces the trans-cis-trans (t-c-t) and cis-cis-trans (c-c-t) amide bond conformations in azapeptides and N-methyl-azapeptides, respectively. Our results indicate that these Namide···H-Namide HBs can have stabilizing contributions even in short azapeptides that cannot fold to form β-turns.
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Affiliation(s)
- Kalpita Baruah
- Department of Chemistry, School of Natural Sciences, Shiv Nadar University, Dadri, Uttar Pradesh 201314, India
| | - Biswajit Sahariah
- New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Jakkur, Bangalore, Karnataka 560064, India
| | - Sushil S Sakpal
- Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory, Pune, Maharashtra 411008, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India
| | - Jugal Kishore Rai Deka
- Department of Chemistry, School of Natural Sciences, Shiv Nadar University, Dadri, Uttar Pradesh 201314, India
| | - Arun Kumar Bar
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Tirupati, Tirupati, Andhra Pradesh 501507, India
| | - Sayan Bagchi
- Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory, Pune, Maharashtra 411008, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India
| | - Bani Kanta Sarma
- New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Jakkur, Bangalore, Karnataka 560064, India
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14
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Kalhor S, Zarei M, Sepehrmansourie H, Zolfigol MA, Shi H, Wang J, Arjomandi J, Hasani M, Schirhagl R. Novel uric acid-based nano organocatalyst with phosphorous acid tags: Application for synthesis of new biologically-interest pyridines with indole moieties via a cooperative vinylogous anomeric based oxidation. MOLECULAR CATALYSIS 2021. [DOI: 10.1016/j.mcat.2021.111549] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
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15
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Melton SD, Brackhahn EAE, Orlin SJ, Jin P, Chenoweth DM. Rules for the design of aza-glycine stabilized triple-helical collagen peptides. Chem Sci 2020; 11:10638-10646. [PMID: 34094319 PMCID: PMC8162259 DOI: 10.1039/d0sc03003a] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The stability of the triple-helical structure of collagen is modulated by a delicate balance of effects including polypeptide backbone geometry, a buried hydrogen bond network, dispersive interfacial interactions, and subtle stereoelectronic effects. Although the different amino acid propensities for the Xaa and Yaa positions of collagen's repeating (Glycine-Xaa-Yaa) primary structure have been described, our understanding of the impact of incorporating aza-glycine (azGly) residues adjacent to varied Xaa and Yaa position residues has been limited to specific sequences. Here, we detail the impact of variation in the Xaa position adjacent to an azGly residue and compare these results to our study on the impact of the Yaa position. For the first time, we present a set of design rules for azGly-stabilized triple-helical collagen peptides, accounting for all canonical amino acids in the Xaa and Yaa positions adjacent to an azGly residue, and extend these rules using multiple azGly residues. To gain atomic level insight into these new rules we present two high-resolution crystal structures of collagen triple helices, with the first peptoid-containing collagen peptide structure. In conjunction with biophysical and computational data, we highlight the critical importance of preserving the triple helix geometry and protecting the hydrogen bonding network proximal to the azGly residue from solvent. Our results provide a set of design guidelines for azGly-stabilized triple-helical collagen peptides and fundamental insight into collagen structure and stability.
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Affiliation(s)
- Samuel D Melton
- Department of Chemistry, University of Pennsylvania 231 South 34th Street Philadelphia Pennsylvania 19104 USA
| | - Emily A E Brackhahn
- Department of Chemistry, University of Pennsylvania 231 South 34th Street Philadelphia Pennsylvania 19104 USA
| | - Samuel J Orlin
- Department of Chemistry, University of Pennsylvania 231 South 34th Street Philadelphia Pennsylvania 19104 USA
| | - Pengfei Jin
- Department of Chemistry, University of Pennsylvania 231 South 34th Street Philadelphia Pennsylvania 19104 USA
| | - David M Chenoweth
- Department of Chemistry, University of Pennsylvania 231 South 34th Street Philadelphia Pennsylvania 19104 USA
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