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Velmurugan G, Baur P, Comba P. A Dicopper(II)-Based Carbonic Anhydrase Model-Quantum-Chemical Evaluation of the Mechanistic Pathway. Angew Chem Int Ed Engl 2024; 63:e202319530. [PMID: 38628137 DOI: 10.1002/anie.202319530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Indexed: 06/11/2024]
Abstract
The cyanobacterium Prochloron didemni, an obligate symbiont of different species of colonial ascidians, occurring in the Pacific and Indian Oceans, produces a variety of cyclic peptides. These patellamide-type macrocycles lead to relatively stable dicopper(II) complexes that are extremely efficient carbonic anhydrase mimics, the most active model systems known so far. Importantly, it recently was shown that copper(II) is coordinated to patellamide derivatives in Prochloron cells. An interesting question therefore is, whether the biological function of patellamide-type macrocycles is related to the catalytic activity in CO2 hydration or its reverse. Here, we present a computational study to evaluate the energetics of the catalytic cycle in search of a possible answer to these questions and compare the computed energy barriers with the experimental kinetic data. It emerges that release of the bridging carbonate is a critical step and that the catalysis product inhibits catalysis at pH values above approx. 7. Therefore, carbonate transport rather than CO2 hydrolysis is proposed as the biological function of copper(II)-patellamide complexes in the Prochloron-Ascidian symbiosis.
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Affiliation(s)
- Gunasekaran Velmurugan
- Universität Heidelberg, Anorganisch-Chemisches Institut and Interdisziplinäres Zentrum für Wissenschaftliches Rechnen (IWR), INF 270, D-69120, Heidelberg, Germany
| | - Philipp Baur
- Universität Heidelberg, Anorganisch-Chemisches Institut and Interdisziplinäres Zentrum für Wissenschaftliches Rechnen (IWR), INF 270, D-69120, Heidelberg, Germany
| | - Peter Comba
- Universität Heidelberg, Anorganisch-Chemisches Institut and Interdisziplinäres Zentrum für Wissenschaftliches Rechnen (IWR), INF 270, D-69120, Heidelberg, Germany
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2
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Marinova P, Tamahkyarova K. Synthesis and Biological Activities of Some Metal Complexes of Peptides: A Review. BIOTECH 2024; 13:9. [PMID: 38651489 PMCID: PMC11036290 DOI: 10.3390/biotech13020009] [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: 02/29/2024] [Revised: 03/28/2024] [Accepted: 04/03/2024] [Indexed: 04/25/2024] Open
Abstract
Peptides, both natural and synthetic, are well suited for a wide range of purposes and offer versatile applications in different fields such as biocatalysts, injectable hydrogels, tumor treatment, and drug delivery. The research of the better part of the cited papers was conducted using various database platforms such as MetalPDB. The rising prominence of therapeutic peptides encompasses anticancer, antiviral, antimicrobial, and anti-neurodegenerative properties. The metals Na, K, Mg, Ca, Fe, Mn, Co, Cu, Zn, and Mo are ten of the twenty elements that are considered essential for life. Crucial for understanding the biological role of metals is the exploration of metal-bound proteins and peptides. Aside from essential metals, there are other non-essential metals that also interact biologically, exhibiting either therapeutic or toxic effects. Irregularities in metal binding contribute to diseases like Alzheimer's, neurodegenerative disorders, Wilson's, and Menkes disease. Certain metal complexes have potential applications as radiopharmaceuticals. The examination of these complexes was achieved by preforming UV-Vis, IR, EPR, NMR spectroscopy, and X-ray analysis. This summary, although unable to cover all of the studies in the field, offers a review of the ongoing experimentation and is a basis for new ideas, as well as strategies to explore and gain knowledge from the extensive realm of peptide-chelated metals and biotechnologies.
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Affiliation(s)
- Petja Marinova
- Department of General and Inorganic Chemistry with Methodology of Chemistry Education, Faculty of Chemistry, University of Plovdiv, “Tzar Assen” Str. 24, 4000 Plovdiv, Bulgaria;
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Witkowski M, Trzybiński D, Pawlędzio S, Woźniak K, Dzwolak W, Królikowska A. The Structural Characterisation and DFT-Aided Interpretation of Vibrational Spectra for Cyclo(l-Cys-d-Cys) Cyclic Dipeptide in a Solid State. Molecules 2023; 28:5902. [PMID: 37570871 PMCID: PMC10421304 DOI: 10.3390/molecules28155902] [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: 06/30/2023] [Revised: 07/25/2023] [Accepted: 08/01/2023] [Indexed: 08/13/2023] Open
Abstract
Cyclic dipeptides with two intramolecular peptide bonds forming a six-membered 2,5-diketopiperazine ring are gaining significant attention due to their biological and chemical properties. Small changes in the local geometry of such molecules (from cis to trans) can lead to significant structural differences. This work presents the results of a study of cyclo(l-Cys-d-Cys), a dipeptide comprising two cysteine molecules in opposite chiral configurations, with the functional groups situated at both sides of the diketopiperazine ring. X-ray diffraction (XRD) experiment revealed that the molecule crystallises in the P-1 space group, which includes the centre of inversion. The IR and Raman vibrational spectra of the molecule were acquired and interpreted in terms of the potential energy distribution (PED) according to the results of density functional theory (DFT) calculations. The DFT-assisted analysis of energy frameworks for the hydrogen bond network within molecular crystals was performed to support the interpretation of X-ray structural data. The optimisation of the computational model based on three-molecule geometry sections from the crystallographic structure, selected to appropriately reflect the intermolecular interactions responsible for the formation of 1D molecular tapes in cyclo(l-Cys-d-Cys) crystal, allowed for better correspondence between theoretical and experimental vibrational spectra. This work can be considered the first complete structural characterisation of cyclo(l-Cys-d-Cys), complemented via vibrational spectroscopy results with full band assignment aided with the use of the DFT method.
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Affiliation(s)
- Marcin Witkowski
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warszawa, Poland
| | - Damian Trzybiński
- Biological and Chemical Research Centre, Chemistry Department, University of Warsaw, Żwirki i Wigury 101, 02-089 Warszawa, Poland
| | - Sylwia Pawlędzio
- Biological and Chemical Research Centre, Chemistry Department, University of Warsaw, Żwirki i Wigury 101, 02-089 Warszawa, Poland
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Krzysztof Woźniak
- Biological and Chemical Research Centre, Chemistry Department, University of Warsaw, Żwirki i Wigury 101, 02-089 Warszawa, Poland
| | - Wojciech Dzwolak
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warszawa, Poland
- Biological and Chemical Research Centre, Chemistry Department, University of Warsaw, Żwirki i Wigury 101, 02-089 Warszawa, Poland
| | - Agata Królikowska
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warszawa, Poland
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Donalle GC, Martorell MM, Siless GE, Ruberto L, Cabrera GM. Cyclic heptapeptides with metal binding properties isolated from the fungus Cadophora malorum from Antarctic soil. NATURAL PRODUCTS AND BIOPROSPECTING 2022; 12:26. [PMID: 35831516 PMCID: PMC9279517 DOI: 10.1007/s13659-022-00348-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 05/09/2022] [Indexed: 06/15/2023]
Abstract
The Antarctic fungus Cadophora malorum produces previously undescribed cyclic heptapeptides (cadophorin A and B) containing an anthranilic acid residue. The planar structure of these peptides was determined by high-resolution mass spectrometry combined with extensive 1D and 2D NMR spectroscopy. The absolute configuration of the amino acids was determined by Marfey's method, with HPLC analysis of FDVA (Nα-(2,4-dinitro-5-fluorphenyl)-L-valinamide) derivatives making use of a PFP column. Remarkably, cadophorin 2 possesses both the uncommon D-Ile and D-allo-Ile in its structure. The peptides have metal binding properties as shown by LCMS with post column addition of metal salt solutions. These results were supported by DFT calculations.
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Affiliation(s)
- Guidmar C Donalle
- Facultad de Ciencias Exactas y Naturales, Departamento de Química Orgánica, Universidad de Buenos Aires, Buenos Aires, Argentina
- Unidad de Microanálisis y Métodos Físicos Aplicados a la Química Orgánica (UMYMFOR), CONICET-Universidad de Buenos Aires, Buenos Aires, Argentina
| | - María Martha Martorell
- Instituto Antártico Argentino, Instituto Nanobiotec, CONICET-Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Gastón E Siless
- Facultad de Ciencias Exactas y Naturales, Departamento de Química Orgánica, Universidad de Buenos Aires, Buenos Aires, Argentina
- Unidad de Microanálisis y Métodos Físicos Aplicados a la Química Orgánica (UMYMFOR), CONICET-Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Lucas Ruberto
- Instituto Antártico Argentino, Instituto Nanobiotec, CONICET-Universidad de Buenos Aires, Buenos Aires, Argentina.
| | - Gabriela M Cabrera
- Facultad de Ciencias Exactas y Naturales, Departamento de Química Orgánica, Universidad de Buenos Aires, Buenos Aires, Argentina.
- Unidad de Microanálisis y Métodos Físicos Aplicados a la Química Orgánica (UMYMFOR), CONICET-Universidad de Buenos Aires, Buenos Aires, Argentina.
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Baur P, Comba P, Velmurugan G. Efficient Synthesis for a Wide Variety of Patellamide Derivatives and Phosphatase Activity of Copper‐Patellamide Complexes. Chemistry 2022; 28:e202200249. [PMID: 35179261 PMCID: PMC9311697 DOI: 10.1002/chem.202200249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Indexed: 11/08/2022]
Affiliation(s)
- Philipp Baur
- Universität Heidelberg Anorganisch-Chemisches Institut und Interdisziplinäres Zentrum für Wissenschaftliches Rechnen Im Neuenheimer Feld 270 69120 Heidelberg Germany
| | - Peter Comba
- Universität Heidelberg Anorganisch-Chemisches Institut und Interdisziplinäres Zentrum für Wissenschaftliches Rechnen Im Neuenheimer Feld 270 69120 Heidelberg Germany
| | - Gunasekaran Velmurugan
- Universität Heidelberg Anorganisch-Chemisches Institut und Interdisziplinäres Zentrum für Wissenschaftliches Rechnen Im Neuenheimer Feld 270 69120 Heidelberg Germany
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Possible Functional Roles of Patellamides in the Ascidian-Prochloron Symbiosis. Mar Drugs 2022; 20:md20020119. [PMID: 35200648 PMCID: PMC8875616 DOI: 10.3390/md20020119] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 01/27/2022] [Accepted: 01/27/2022] [Indexed: 02/04/2023] Open
Abstract
Patellamides are highly bioactive compounds found along with other cyanobactins in the symbiosis between didemnid ascidians and the enigmatic cyanobacterium Prochloron. The biosynthetic pathway of patellamide synthesis is well understood, the relevant operons have been identified in the Prochloron genome and genes involved in patellamide synthesis are among the most highly transcribed cyanobacterial genes in hospite. However, a more detailed study of the in vivo dynamics of patellamides and their function in the ascidian-Prochloron symbiosis is complicated by the fact that Prochloron remains uncultivated despite numerous attempts since its discovery in 1975. A major challenge is to account for the highly dynamic microenvironmental conditions experienced by Prochloron in hospite, where light-dark cycles drive rapid shifts between hyperoxia and anoxia as well as pH variations from pH ~6 to ~10. Recently, work on patellamide analogues has pointed out a range of different catalytic functions of patellamide that could prove essential for the ascidian-Prochloron symbiosis and could be modulated by the strong microenvironmental dynamics. Here, we review fundamental properties of patellamides and their occurrence and dynamics in vitro and in vivo. We discuss possible functions of patellamides in the ascidian-Prochloron symbiosis and identify important knowledge gaps and needs for further experimental studies.
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Improved Recovery and Selectivity of Lanthanide-Ion-Binding Cyclic Peptide Hosts by Changing the Position of Acidic Amino Acids. MINERALS 2022. [DOI: 10.3390/min12020148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The development of an effective host molecule to separate lanthanide (Ln) ions and a method for predicting its guest recognition/self-assembly behavior based on primary chemical structures are highly sought after in both academia and industry. Herein, we report the improvement of one-pot Ln ion recovery and a performance prediction method for four new cyclic peptide hosts that differ in the position of acidic amino acids. These cyclic peptide hosts could recognize Ln3+ directly through a 1:1 complexation–precipitation process and exhibited high Lu3+ selectivity in spite of similar ion size and electronegativity when the positions of the acidic amino acids were changed. This unpredictable selectivity was explained by considering the dipole moment, lowest unoccupied molecular orbital, and cohesion energy. In addition, a semi-empirical function using these parameters was proposed for screening the sequence and estimating the isolated yields without long-time molecular dynamics calculations. The insights obtained from this study can be employed for the development of high-performance peptides for the selective recovery of Ln and other metal ions, as well as for the construction of diverse supramolecular recognition systems.
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Cho Y, Mirzapour-Kouhdasht A, Yun H, Park JH, Min HJ, Lee CW. Development of Cobalt-Binding Peptide Chelate from Human Serum Albumin: Cobalt-Binding Properties and Stability. Int J Mol Sci 2022; 23:719. [PMID: 35054904 PMCID: PMC8775498 DOI: 10.3390/ijms23020719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 01/04/2022] [Accepted: 01/07/2022] [Indexed: 11/16/2022] Open
Abstract
Radioactive isotopes are used as drugs or contrast agents in the medical field after being conjugated with chelates such as DOTA, NOTA, DTPA, TETA, CyDTA, TRITA, and DPDP. The N-terminal sequence of human serum albumin (HSA) is known as a metal binding site, such as for Co2+, Cu2+, and Ni2+. For this study, we designed and synthesized wAlb12 peptide from the N-terminal region of HSA, which can bind to cobalt, to develop a peptide-based chelate. The wAlb12 with a random coil structure tightly binds to the Co(II) ion. Moreover, the binding property of wAlb12 toward Co(II) was confirmed using various spectroscopic experiments. To identify the binding site of wAlb12, the analogs were synthesized by alanine scanning mutagenesis. Among them, H3A and Ac-wAlb12 did not bind to Co(II). The analysis of the binding regions confirmed that the His3 and α-amino group of the N-terminal region are important for Co(II) binding. The wAlb12 bound to Co(II) with Kd of 75 μM determined by isothermal titration calorimetry when analyzed by a single-site binding model. For the use of wAlb12 as a chelate in humans, its cytotoxicity and stability were investigated. Trypsin stability showed that the wAlb12 - Co(II) complex was more stable than wAlb12 alone. Furthermore, the cell viability analysis showed wAlb12 and wAlb12 + Co(II) to be non-toxic to the Raw 264.7 and HEK 293T cell lines. Therefore, a hot radioactive isotope such as cobalt-57 will have the same effect as a stable isotope cobalt. Accordingly, we expect wAlb12 to be used as a peptide chelate that binds with radioactive isotopes.
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Affiliation(s)
- Yeonje Cho
- Department of Chemistry, Chonnam National University, Gwangju 61186, Korea; (Y.C.); (A.M.-K.); (H.Y.)
| | - Armin Mirzapour-Kouhdasht
- Department of Chemistry, Chonnam National University, Gwangju 61186, Korea; (Y.C.); (A.M.-K.); (H.Y.)
- School of Agriculture and Food Science, University College Dublin, Belfield, D04 V1W8 Dublin, Ireland
| | - Hyosuk Yun
- Department of Chemistry, Chonnam National University, Gwangju 61186, Korea; (Y.C.); (A.M.-K.); (H.Y.)
| | - Jeong Hoon Park
- Accelerator Radioisotope Development Laboratory, Korea Atomic Energy Research Institute, Jeongeup-si 56212, Jeollabuk-do, Korea;
| | - Hye Jung Min
- Department of Cosmetic Science, Kwangju Women’s University, Gwangju 62396, Korea;
| | - Chul Won Lee
- Department of Chemistry, Chonnam National University, Gwangju 61186, Korea; (Y.C.); (A.M.-K.); (H.Y.)
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Ji F, Shao S, Li Z, Wang S, Chaudhuri R, Guo Z, Perkins NG, Sarkar P, Xue M. A cyclic peptide antenna ligand for enhancing terbium luminescence. Analyst 2021; 146:3474-3481. [PMID: 33913937 PMCID: PMC8169603 DOI: 10.1039/d1an00530h] [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] [Indexed: 11/21/2022]
Abstract
We present here a cyclic peptide ligand, cy(WQETR), that binds to the terbium ion (Tb3+) and enhances Tb3+ luminescence intensity through the antenna effect. This peptide was identified through screening a cyclic peptide library against Tb3+ with an apparent EC50 of 540 μM. The tryptophan residue from the peptide directly interacts with the Tb3+ ion, which provides access to a low-lying triplet excited state of the tryptophan. Direct excitation of this triplet state enables energy transfer to the Tb3+ ion and enhances Tb3+ luminescence intensity by 150 fold. We further showcase the application of this cy(WQETR)-Tb3+ system by demonstrating the detection of tromethamine with a detection limit of 0.5 mM.
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Affiliation(s)
- Fei Ji
- Department of Chemistry, University of California, Riverside, Riverside, California 92521, USA.
| | - Shiqun Shao
- Department of Chemistry, University of California, Riverside, Riverside, California 92521, USA.
| | - Zhonghan Li
- Department of Chemistry, University of California, Riverside, Riverside, California 92521, USA.
| | - Siwen Wang
- Department of Chemistry, University of California, Riverside, Riverside, California 92521, USA.
| | - Rohit Chaudhuri
- Department of Chemistry, University of California, Riverside, Riverside, California 92521, USA.
| | - Zhili Guo
- Department of Chemistry, University of California, Riverside, Riverside, California 92521, USA.
| | - Nicole G Perkins
- Department of Chemistry, University of California, Riverside, Riverside, California 92521, USA.
| | - Priyanka Sarkar
- Department of Chemistry, University of California, Riverside, Riverside, California 92521, USA.
| | - Min Xue
- Department of Chemistry, University of California, Riverside, Riverside, California 92521, USA.
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Staś M, Broda MA, Siodłak D. Thiazole-amino acids: influence of thiazole ring on conformational properties of amino acid residues. Amino Acids 2021; 53:673-686. [PMID: 33837859 PMCID: PMC8128816 DOI: 10.1007/s00726-021-02974-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Accepted: 03/29/2021] [Indexed: 12/29/2022]
Abstract
Post-translational modified thiazole-amino acid (Xaa-Tzl) residues have been found in macrocyclic peptides (e.g., thiopeptides and cyanobactins), which mostly inhibit protein synthesis in Gram + bacteria. Conformational study of the series of model compounds containing this structural motif with alanine, dehydroalanine, dehydrobutyrine and dehydrophenylalanine were performed using DFT method in various environments. The solid-state crystal structure conformations of thiazole-amino acid residues retrieved from the Cambridge Structural Database were also analysed. The studied structural units tend to adopt the unique semi-extended β2 conformation; which is stabilised mainly by N-H⋯NTzl hydrogen bond, and for dehydroamino acids also by π-electron conjugation. The conformational preferences of amino acids with a thiazole ring were compared with oxazole analogues and the role of the sulfur atom in stabilising the conformations of studied peptides was discussed.
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Affiliation(s)
- Monika Staś
- Faculty of Chemistry, University of Opole, 45-052, Opole, Poland.
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Science, Flemingovo Náměstí 2, 166 10, Praha 6, Czech Republic.
| | | | - Dawid Siodłak
- Faculty of Chemistry, University of Opole, 45-052, Opole, Poland.
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