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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
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da Silva JBP, Hallwass F, da Silva AG, Moreira DR, Ramos MN, Espíndola JWP, de Oliveira ADT, Brondani DJ, Leite ACL, Merz KM. Intermolecular interaction of thiosemicarbazone derivatives to solvents and a potential Aedes aegypti target. J Mol Struct 2015. [DOI: 10.1016/j.molstruc.2015.03.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Nelli YR, Antunes S, Salaün A, Thinon E, Massip S, Kauffmann B, Douat C, Guichard G. Isosteric Substitutions of Urea to Thiourea and Selenourea in Aliphatic Oligourea Foldamers: Site-Specific Perturbation of the Helix Geometry. Chemistry 2014; 21:2870-80. [DOI: 10.1002/chem.201405792] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2014] [Indexed: 01/05/2023]
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De Zotti M, Biondi B, Peggion C, De Poli M, Fathi H, Oancea S, Toniolo C, Formaggio F. Partial thioamide scan on the lipopeptaibiotic trichogin GA IV. Effects on folding and bioactivity. Beilstein J Org Chem 2012; 8:1161-71. [PMID: 23019444 PMCID: PMC3458734 DOI: 10.3762/bjoc.8.129] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2012] [Accepted: 06/21/2012] [Indexed: 02/04/2023] Open
Abstract
Backbone modification is a common chemical tool to control the conformation of linear peptides and to explore potentially useful effects on their biochemical and biophysical properties. The thioamide, ψ[CS-NH], group is a nearly isosteric structural mimic of the amide (peptide) functionality. In this paper, we describe the solution synthesis, chemical characterization, preferred conformation, and membrane and biological activities of three, carefully selected, peptide analogues of the lipopeptaibiotic [Leu11-OMe] trichogin GA IV. In each analogue, a single thioamide replacement was incorporated. Sequence positions near the N-terminus, at the center, and near the C-terminus were investigated. Our results indicate that (i) a thioamide linkage is well tolerated in the overall helical conformation of the [Leu11-OMe] lipopeptide analogue and (ii) this backbone modification is compatible with the preservation of its typical membrane leakage and antibiotic properties, although somewhat attenuated.
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Affiliation(s)
- Marta De Zotti
- ICB, Padova Unit, CNR, Department of Chemistry, University of Padova, 35131 Padova, Italy
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7
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Huang W, Eichenberger AP, van Gunsteren WF. Molecular dynamics simulation of thionated hen egg white lysozyme. Protein Sci 2012; 21:1153-61. [PMID: 22653637 DOI: 10.1002/pro.2102] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2012] [Revised: 05/02/2012] [Accepted: 05/23/2012] [Indexed: 11/11/2022]
Abstract
Understanding of the driving forces of protein folding is a complex challenge because different types of interactions play a varying role. To investigate the role of hydrogen bonding involving the backbone, the effect of thio substitutions in a protein, hen egg white lysozyme (HEWL), was investigated through molecular dynamics simulations of native as well as partly (only residues in loops) and fully thionated HEWL using the GROMOS 54A7 force field. The results of the three simulations show that the structural properties of fully thionated HEWL clearly differ from those of the native protein, while for partly thionated HEWL they only changed slightly compared with native HEWL. The analysis of the torsional-angle distributions and hydrogen bonds in the backbone suggests that the α-helical segments of native HEWL tend to show a propensity to convert to 3(10)-helical geometry in fully thionated HEWL. A comparison of the simulated quantities with experimental NMR data such as nuclear overhauser effect (NOE) atom-atom distance bounds and (3)J((H)(N)(H)(α))-couplings measured for native HEWL illustrates that the information content of these quantities with respect to the structural changes induced by thionation of the protein backbone is rather limited.
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Affiliation(s)
- Wei Huang
- Department of Chemistry, Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, Zürich, Switzerland
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Defining scaffold geometries for interacting with proteins: geometrical classification of secondary structure linking regions. J Comput Aided Mol Des 2010; 24:917-34. [PMID: 20862601 DOI: 10.1007/s10822-010-9384-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2009] [Accepted: 08/31/2010] [Indexed: 12/22/2022]
Abstract
Medicinal chemists synthesize arrays of molecules by attaching functional groups to scaffolds. There is evidence suggesting that some scaffolds yield biologically active molecules more than others, these are termed privileged substructures. One role of the scaffold is to present its side-chains for molecular recognition, and biologically relevant scaffolds may present side-chains in biologically relevant geometries or shapes. Since drug discovery is primarily focused on the discovery of compounds that bind to proteinaceous targets, we have been deciphering the scaffold shapes that are used for binding proteins as they reflect biologically relevant shapes. To decipher the scaffold architecture that is important for binding protein surfaces, we have analyzed the scaffold architecture of protein loops, which are defined in this context as continuous four residue segments of a protein chain that are not part of an α-helix or β-strand secondary structure. Loops are an important molecular recognition motif of proteins. We have found that 39 clusters reflect the scaffold architecture of 89% of the 23,331 loops in the dataset, with average intra-cluster and inter-cluster RMSD of 0.47 and 1.91, respectively. These protein loop scaffolds all have distinct shapes. We have used these 39 clusters that reflect the scaffold architecture of protein loops as biological descriptors. This involved generation of a small dataset of scaffold-based peptidomimetics. We found that peptidomimetic scaffolds with reported biological activities matched loop scaffold geometries and those peptidomimetic scaffolds with no reported biologically activities did not. This preliminary evidence suggests that organic scaffolds with tight matches to the preferred loop scaffolds of proteins, implies the likelihood of the scaffold to be biologically relevant.
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Lee HJ, Kim JH, Jung HJ, Kim KY, Kim EJ, Choi YS, Yoon CJ. Computational study of conformational preferences of thioamide-containing azaglycine peptides. J Comput Chem 2003; 25:169-78. [PMID: 14648616 DOI: 10.1002/jcc.10364] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The effect of thioamide substitution on the conformational stability of an azaglycine-containing peptide, For-AzaGly-NH2 (1), was investigated for the sake of finding possible applications by using ab initio and DFT methods. As model compounds, For-[psiCSNH]-AzaGly-NH2 (2), For-AzaGly-[psiCSNH]-NH2 (3), and For-[psiCSNH]-AzaGly-[psiCSNH]-NH2 (4) were used. Two-dimensional phi-psi potential energy surfaces (PESs) for 2-4 were calculated at the B3LYP/6-31G*//HF/6-31G* level in gas (epsilon = 1.0) and in water (epsilon = 78.4) by applying the isodensity polarizable continuum model (IPCM) method. On the basis of these PESs, the minimum energy conformations for 2-4 were characterized at the B3LYP level with 6-31G*, 6-311G**, and 6-31+G** basis sets. The remarkable structural effect of thioamide substitution for 2-4 is that beta-strand structure is observed as a global or local minimum. The minima of 2-4 are also compared with those for glycine and thioamide-containing glycine peptides. Our theoretical results demonstrate that compounds 2-4 would be used to design controllable secondary structures.
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Affiliation(s)
- Ho-Jin Lee
- Department of Chemistry, Korea University, 1 Anam dong, Seoul, 136-701, Korea
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Affiliation(s)
- Ho-Jin Lee
- Department of Chemistry, Korea University, 1 Anam-dong, Seoul, 136-701, Republic of Korea, Advanced Analysis Center, Korea Institute of Science and Technology, Seoul 136-791, Republic of Korea, Department of Chemistry, Korea University, 208 Seochang-dong, Jochiwon 339-700, Republic of Korea, Department of Chemistry, The Catholic University of Korea, Pucheon, 420-743, Republic of Korea
| | - Young-Sang Choi
- Department of Chemistry, Korea University, 1 Anam-dong, Seoul, 136-701, Republic of Korea, Advanced Analysis Center, Korea Institute of Science and Technology, Seoul 136-791, Republic of Korea, Department of Chemistry, Korea University, 208 Seochang-dong, Jochiwon 339-700, Republic of Korea, Department of Chemistry, The Catholic University of Korea, Pucheon, 420-743, Republic of Korea
| | - Kang-Bong Lee
- Department of Chemistry, Korea University, 1 Anam-dong, Seoul, 136-701, Republic of Korea, Advanced Analysis Center, Korea Institute of Science and Technology, Seoul 136-791, Republic of Korea, Department of Chemistry, Korea University, 208 Seochang-dong, Jochiwon 339-700, Republic of Korea, Department of Chemistry, The Catholic University of Korea, Pucheon, 420-743, Republic of Korea
| | - Jeunghee Park
- Department of Chemistry, Korea University, 1 Anam-dong, Seoul, 136-701, Republic of Korea, Advanced Analysis Center, Korea Institute of Science and Technology, Seoul 136-791, Republic of Korea, Department of Chemistry, Korea University, 208 Seochang-dong, Jochiwon 339-700, Republic of Korea, Department of Chemistry, The Catholic University of Korea, Pucheon, 420-743, Republic of Korea
| | - Chang-Ju Yoon
- Department of Chemistry, Korea University, 1 Anam-dong, Seoul, 136-701, Republic of Korea, Advanced Analysis Center, Korea Institute of Science and Technology, Seoul 136-791, Republic of Korea, Department of Chemistry, Korea University, 208 Seochang-dong, Jochiwon 339-700, Republic of Korea, Department of Chemistry, The Catholic University of Korea, Pucheon, 420-743, Republic of Korea
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Tran TT, Burgess AW, Treutlein H, Zeng J. Conformational analysis of thiopeptides: free energy calculations on the effects of thio-substitutions on the conformational distributions of alanine dipeptides. J Mol Graph Model 2002; 20:245-56. [PMID: 11766049 DOI: 10.1016/s1093-3263(01)00118-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
When the oxygen atom in a peptide bond is replaced by a sulfur atom, the restriction in the available conformational space and the ability of thioamides to confer resistance to enzymatic degradation renders thioamides as potentially useful building blocks for drug design and protein engineering. The solvation free energy differences between conformers of the same dipeptide can be high. Yet, previous conformational studies, basing on the (phi, psi) conformational energy maps of thio-substituted dipeptides, neglected both explicit water interactions and free energy considerations. In this paper, the (phi, psi) conformational free energy maps are obtained by single umbrella sampling in an explicit water environment for both alanine dipeptide and the corresponding thioamide derivatives. The phi and psi angles for the minima in the relative energy maps calculated with dielectric of 80 are similar to the corresponding phi and psi angles in the relative free energy maps for both Ac-Ala-NHMe (Ac: acetyl; Ala: alanine) and Act-Alat-NHMe (Act: thio-acetyl; Alat: thio-alanine). However, some large differences between the relative energy and relative free energy of major minima indicate that the consideration of free energy is important in determination of the relative occupancy of particular minima. Free energy maps for both Ac-Ala-NHMe and Act-Alat-NHMe show that thio-substitution favors conformations where phi < 0 because of the deeper beta and alphaR minima. The changes in the position and relative stability of minima were explained in terms of the destabilization of the regions near phi = -120, 0 and 120, psi = 60, -60, 180, which correspond to the increased steric hindrance due to the bulkier sulfur atom.
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Affiliation(s)
- T T Tran
- Ludwig Institute for Cancer Research, Cooperative Research Center for Cellular and Growth Factors, Royal Melbourne Hospital, Parkville, Vic., Australia.
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