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Bak-Sypien I, Pawlak T, Paluch P, Wroblewska A, Dolot R, Pawlowicz A, Szczesio M, Wielgus E, Kaźmierski S, Górecki M, Pawlowska R, Chworos A, Potrzebowski MJ. Influence of heterochirality on the structure, dynamics, biological properties of cyclic(PFPF) tetrapeptides obtained by solvent-free ball mill mechanosynthesis. Sci Rep 2024; 14:12825. [PMID: 38834643 DOI: 10.1038/s41598-024-63552-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Accepted: 05/30/2024] [Indexed: 06/06/2024] Open
Abstract
Cyclic tetrapeptides c(Pro-Phe-Pro-Phe) obtained by the mechanosynthetic method using a ball mill were isolated in a pure stereochemical form as a homochiral system (all L-amino acids, sample A) and as a heterochiral system with D configuration at one of the stereogenic centers of Phe (sample B). The structure and stereochemistry of both samples were determined by X-ray diffraction studies of single crystals. In DMSO and acetonitrile, sample A exists as an equimolar mixture of two conformers, while only one is monitored for sample B. The conformational space and energetic preferences for possible conformers were calculated using DFT methods. The distinctly different conformational flexibility of the two samples was experimentally proven by Variable Temperature (VT) and 2D EXSY NMR measurements. Both samples were docked to histone deacetylase HDAC8. Cytotoxic studies proved that none of the tested cyclic peptide is toxic.
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Affiliation(s)
- Irena Bak-Sypien
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112 St., 90-363, Lodz, Poland
| | - Tomasz Pawlak
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112 St., 90-363, Lodz, Poland
| | - Piotr Paluch
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112 St., 90-363, Lodz, Poland
| | - Aneta Wroblewska
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112 St., 90-363, Lodz, Poland
| | - Rafał Dolot
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112 St., 90-363, Lodz, Poland
| | - Aleksandra Pawlowicz
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14 St., 61-704, Poznan, Poland
| | - Małgorzata Szczesio
- Institute of General and Ecological Chemistry, Faculty of Chemistry, Lodz University of Technology, Żeromskiego 116 St., 90-924, Lodz, Poland
| | - Ewelina Wielgus
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112 St., 90-363, Lodz, Poland
| | - Sławomir Kaźmierski
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112 St., 90-363, Lodz, Poland
| | - Marcin Górecki
- Institute of Organic Chemistry, Polish Academy of Sciences, Kasprzaka 44/52 St., 01-224, Warsaw, Poland
| | - Roza Pawlowska
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112 St., 90-363, Lodz, Poland
| | - Arkadiusz Chworos
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112 St., 90-363, Lodz, Poland
| | - Marek J Potrzebowski
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112 St., 90-363, Lodz, Poland.
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Keiderling TA. Structure of Condensed Phase Peptides: Insights from Vibrational Circular Dichroism and Raman Optical Activity Techniques. Chem Rev 2020; 120:3381-3419. [DOI: 10.1021/acs.chemrev.9b00636] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Timothy A. Keiderling
- Department of Chemistry, University of Illinois at Chicago 845 West Taylor Street m/c 111, Chicago, Illinois 60607-7061, United States
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3
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Rode JE, Lyczko K, Jawiczuk M, Kawęcki R, Stańczyk W, Jaglińska A, Dobrowolski JC. The Vibrational Circular Dichroism Pattern of the ν(C=O) Bands in Isoindolinones. Chemphyschem 2018; 19:2411-2422. [DOI: 10.1002/cphc.201800244] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Indexed: 12/15/2022]
Affiliation(s)
- Joanna E. Rode
- Institute of Nuclear Chemistry and Technology 16 Dorodna Street 03-195 Warsaw Poland
| | - Krzysztof Lyczko
- Institute of Nuclear Chemistry and Technology 16 Dorodna Street 03-195 Warsaw Poland
| | - Magdalena Jawiczuk
- Institute of Organic ChemistryPolish Academy of Sciences Kasprzaka 44/52 01-224 Warsaw Poland
- Current address: Centre of New TechnologiesUniversity of Warsaw Banacha 2C 02-097 Warszawa Poland
| | - Robert Kawęcki
- Siedlce University, Faculty of Science 3 Maja Street No 54 08-110 Siedlce Poland
| | - Wojciech Stańczyk
- Siedlce University, Faculty of Science 3 Maja Street No 54 08-110 Siedlce Poland
| | - Agnieszka Jaglińska
- Siedlce University, Faculty of Science 3 Maja Street No 54 08-110 Siedlce Poland
| | - Jan Cz. Dobrowolski
- Institute of Nuclear Chemistry and Technology 16 Dorodna Street 03-195 Warsaw Poland
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Angelici G, Górecki M, Pescitelli G, Zanna N, Monari M, Tomasini C. Synthesis and structure analysis of ferrocene-containing pseudopeptides. Biopolymers 2017; 110. [PMID: 29058321 DOI: 10.1002/bip.23072] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Revised: 09/11/2017] [Accepted: 09/20/2017] [Indexed: 11/06/2022]
Abstract
Ferrocene with its aromaticity and facile redox properties is an attractive moiety to be incorporated into functional moieties. Medicinal applications of ferrocene are well known and ferrocene itself shows cytotoxic and antianemic properties. In this article, we will describe the synthesis and the structure analysis of two pseudopeptides containing a ferrocene moiety as N-terminal group. After purification, Fc-l-Phe-d-Oxd-OBn [l-Phel-phenylalanine; d-Oxd(4R,5S)-4-Methyl-5-carboxy-oxazolidin-2-one] appears as bright brown solid that spontaneously forms brown needles. The X-ray diffraction of the crystals shows the presence of strong π interactions between the ferrocenyl moiety and the phenyl rings, while no NH•••OC hydrogen bonds are formed. This result is confirmed by FT-IR and 1 H NMR analysis. In contrast, both FT-IR and 1 H NMR analysis suggest that Fc-(l-Phe-d-Oxd)2 -OBn forms a turn conformation stabilized by intramolecular NH•••OC hydrogen bonds in solution. Chiroptical spectroscopies (ECD and VCD) substantially confirmed the absence of a well-defined folded structure. The presence of the Fc moiety is responsible for specific ECD signals, one of which displayed pronounced temperature dependence and is directly related with the helicity assumed by the Fc core. Solid-state ECD spectra were recorded and rationalized on the basis of the X-ray geometry and quantum-mechanical calculations.
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Affiliation(s)
- Gaetano Angelici
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa - Via Moruzzi 13, Pisa, 56124, Italy
| | - Marcin Górecki
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa - Via Moruzzi 13, Pisa, 56124, Italy
- Institute of Organic Chemistry - Polish Academy of Sciences - ul. Kasprzaka 44/52, Warsaw, 01-224, Poland
| | - Gennaro Pescitelli
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa - Via Moruzzi 13, Pisa, 56124, Italy
| | - Nicola Zanna
- Dipartimento di Chimica "Giacomo Ciamician", Università di Bologna - Via Selmi, 2, Bologna, 40126, Italy
| | - Magda Monari
- Dipartimento di Chimica "Giacomo Ciamician", Università di Bologna - Via Selmi, 2, Bologna, 40126, Italy
| | - Claudia Tomasini
- Dipartimento di Chimica "Giacomo Ciamician", Università di Bologna - Via Selmi, 2, Bologna, 40126, Italy
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Rode JE, Dobrowolski JC, Lyczko K, Wasiewicz A, Kaczorek D, Kawęcki R, Zając G, Baranska M. Chiral Thiophene Sulfonamide—A Challenge for VOA Calculations. J Phys Chem A 2017; 121:6713-6726. [DOI: 10.1021/acs.jpca.6b11015] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Joanna E. Rode
- Institute of Nuclear Chemistry and Technology, 16 Dorodna Street, 03-195 Warsaw, Poland
| | - Jan Cz. Dobrowolski
- Institute of Nuclear Chemistry and Technology, 16 Dorodna Street, 03-195 Warsaw, Poland
| | - Krzysztof Lyczko
- Institute of Nuclear Chemistry and Technology, 16 Dorodna Street, 03-195 Warsaw, Poland
| | - Aleksandra Wasiewicz
- Siedlce University, Faculty of Science, 3 Maja Street No 54, 80-110 Siedlce, Poland
| | - Dorota Kaczorek
- Siedlce University, Faculty of Science, 3 Maja Street No 54, 80-110 Siedlce, Poland
| | - Robert Kawęcki
- Siedlce University, Faculty of Science, 3 Maja Street No 54, 80-110 Siedlce, Poland
| | - Grzegorz Zając
- Faculty of Chemistry, Jagiellonian University, 3 Ingardena
Street, 30-060 Krakow, Poland
- Jagiellonian Centre for Experimental Therapeutics, Jagiellonian University, 14 Bobrzynskiego Street, 30-348 Krakow, Poland
| | - Malgorzata Baranska
- Faculty of Chemistry, Jagiellonian University, 3 Ingardena
Street, 30-060 Krakow, Poland
- Jagiellonian Centre for Experimental Therapeutics, Jagiellonian University, 14 Bobrzynskiego Street, 30-348 Krakow, Poland
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Górecki M, Groszek G, Frelek J. Chirality sensing of bioactive compounds with amino alcohol unit via circular dichroism. Chirality 2017; 29:589-598. [PMID: 28771833 DOI: 10.1002/chir.22736] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2017] [Revised: 06/24/2017] [Accepted: 06/26/2017] [Indexed: 12/31/2022]
Abstract
The aim of the present work was to test various chiroptical techniques, including in particular the in situ dirhodium methodology, to assign the absolute configuration of 1,2- and 1,3-amino alcohols. As models, we selected mainly compounds that have both an additional strongly absorbing and interfering chromophoric system and application in medicinal chemistry. Determination of the absolute configuration (AC) of the tested molecules such as cinchona alkaloids, Tamiflu, and others was carried out using a combination of electronic and vibrational circular dichroism (ECD, VCD) spectroscopy. It has been demonstrated that both 1,2- and 1,3-aminol moieties are subject to the same sector rule correlating stereostructure of formed Rh2 -complex with chiroptical properties, and that the changes in the position of the stereogenic center do not affect its proper use.
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Affiliation(s)
- Marcin Górecki
- Institute of Organic Chemistry, Polish Academy of Sciences, Warsaw, Poland
| | - Grażyna Groszek
- Faculty of Chemistry, Rzeszów University of Technology, Rzeszów, Poland
| | - Jadwiga Frelek
- Institute of Organic Chemistry, Polish Academy of Sciences, Warsaw, Poland
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C-3 epimers of sugar amino acids as foldameric building blocks: improved synthesis, useful derivatives, coupling strategies. Amino Acids 2016; 49:223-240. [PMID: 27803987 DOI: 10.1007/s00726-016-2346-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Accepted: 10/04/2016] [Indexed: 10/20/2022]
Abstract
To obtain key sugar derivatives for making homooligomeric foldamers or α/β-chimera peptides, economic and multigram scale synthetic methods were to be developed. Though described in the literature, the cost-effective making of both 3-amino-3-deoxy-ribofuranuronic acid (H-t X-OH) and its C-3 epimeric stereoisomer, the 3-amino-3-deoxy-xylofuranuronic acid (H-c X-OH) from D-glucose is described here. The present synthetic route elaborated is (1) appropriate for large-scale synthesis; (2) reagent costs reduced (e.g. by a factor of 400); (3) yields optimized are ~80% or higher for all six consecutive steps concluding -t X- or -c X- and (4) reaction times shortened. Thus, a new synthetic route step-by-step optimized for yield, cost, time and purification is given both for D-xylo and D-ribo-amino-furanuronic acids using sustainable chemistry (e.g. less chromatography with organic solvents; using continuous-flow reactor). Our study encompasses necessary building blocks (e.g. -X-OMe, -X-OiPr, -X-NHMe, Fmoc-X-OH) and key coupling reactions making -Aaa-t X-Aaa- or -Aaa-t X-t X-Aaa- type "inserts". Completed for both stereoisomers of X, including the newly synthesized Fmoc-c X-OH, producing longer oligomers for drug design and discovery is more of a reality than a wish.
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Górecki M. A configurational and conformational study of (−)-Oseltamivir using a multi-chiroptical approach. Org Biomol Chem 2015; 13:2999-3010. [DOI: 10.1039/c4ob02369b] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Four chiroptical methods, i.e. electronic circular dichroism (ECD), optical rotatory dispersion (ORD), vibrational circular dichroism (VCD), and Raman optical activity (ROA) were employed to discover a set of the most probable conformations of (−)-Oseltamivir in solution.
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Affiliation(s)
- Marcin Górecki
- Institute of Organic Chemistry
- Polish Academy of Sciences
- 01-224 Warsaw
- Poland
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9
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Parchaňský V, Kapitán J, Bouř P. Inspecting chiral molecules by Raman optical activity spectroscopy. RSC Adv 2014. [DOI: 10.1039/c4ra10416a] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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