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Le Bris N, Pineau J, Lima LM, Tripier R. Palladium(II) coordination with polyazacycloalkanes. Coord Chem Rev 2022. [DOI: 10.1016/j.ccr.2021.214343] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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2
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Jiao Y, Hong J, Chen Y, Zhang Y, Guo Z, Han Z, He W. A novel binuclear Pd(ii) complex displaying synergic peptide cleavage behaviour. Dalton Trans 2020; 49:3164-3173. [PMID: 32095803 DOI: 10.1039/d0dt00130a] [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
Mononuclear Pd(ii) complexes with two leaving groups are able to promote His-, Cys- and Met-orientated peptide hydrolysis, and exploring the peptide cleavage behavior of a novel Pd(ii) complex may provide "Omics" studies a promising artificial protease. In this study, a novel binuclear Pd(ii) complex [Pd2(μ-O-L-H)(μ-Cl)](ClO4)2 (L = 2,6-bis(N-2'-aminoethylaminomethyl)-p-cresol) was constructed to promote peptide hydrolysis. Although each Pd(ii) center has only one leaving group (Cl) in this complex, electrophoresis and LC-MS-MS determination discloses that this complex enables myoglobin cleavage on the second upstream peptide bond from His and Met. A study on peptide cleavage also confirms the His- and Met-orientated peptide hydrolysis, yet no Cys-orientated hydrolysis was observed, although the cysteine-induced peptide/complex binding is distinct. Cysteine in the peptide even prevents the complex from promoting His-orientated hydrolysis, whereas the oxidized cysteine residue recovers the His-orientated hydrolysis. This peptide cleavage behavior is quite different from the simultaneous His-, Cys-, and Met-orientated hydrolysis promoted by the mononuclear Pd(ii) complexes. A theoretical study suggests that the two Pd(ii) centers of this complex might promote His- and Met-orientated hydrolysis in a synergic manner: one Pd(ii) center binds selectively on peptides or proteins and the other coordinates with the amide bond and water favoring nucleophilic attack on the peptide bond. The thiol group of cysteine is inclined to bridge the two Pd(ii) centers to form a "closed" sulphur-bridged structure, disfavoring the Cys-orientated hydrolysis. This study not only demonstrates the peptide cleavage behavior of this binuclear Pd(ii) complex, but also provides a polynuclear strategy to regulate the peptide cleavage behavior of Pd(ii) complexes.
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Affiliation(s)
- Yang Jiao
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China.
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Estevan F, Hirva P, Ofori A, Sanaú M, Špec T, Úbeda MA. Pyrazole and Pyrazolate as Ligands in the Synthesis and Stabilization of New Palladium(II) and (III) Compounds. Inorg Chem 2016; 55:2101-13. [DOI: 10.1021/acs.inorgchem.5b02506] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Francisco Estevan
- Departament de Química Inorgànica, Universitat de València, Dr. Moliner 50, 46100-Burjassot, València, Spain
| | - Pipsa Hirva
- Department of Chemistry, University of Eastern Finland, Joensuu
Campus, P.O. Box 111, FI-80101 Joensuu, Finland
| | - Albert Ofori
- Department of Chemistry, University of Eastern Finland, Joensuu
Campus, P.O. Box 111, FI-80101 Joensuu, Finland
| | - Mercedes Sanaú
- Departament de Química Inorgànica, Universitat de València, Dr. Moliner 50, 46100-Burjassot, València, Spain
| | - Tanja Špec
- Departament de Química Inorgànica, Universitat de València, Dr. Moliner 50, 46100-Burjassot, València, Spain
| | - MAngeles Úbeda
- Departament de Química Inorgànica, Universitat de València, Dr. Moliner 50, 46100-Burjassot, València, Spain
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López-Banet L, Santana MD, Piernas MJ, García G, Cerezo J, Requena A, Zúñiga J, Pérez J, García L. Structure and Spectroscopic Properties of Nickel Benzazolate Complexes with Hydrotris(pyrazolyl)borate Ligand. Inorg Chem 2014; 53:5502-14. [DOI: 10.1021/ic5001655] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Luisa López-Banet
- Departamento
de Química Inorgánica, Universidad de Murcia, E-30071 Murcia, Spain
| | - M. Dolores Santana
- Departamento
de Química Inorgánica, Universidad de Murcia, E-30071 Murcia, Spain
| | - María José Piernas
- Departamento
de Química Inorgánica, Universidad de Murcia, E-30071 Murcia, Spain
| | - Gabriel García
- Departamento
de Química Inorgánica, Universidad de Murcia, E-30071 Murcia, Spain
| | - Javier Cerezo
- Departamento de
Química Física, Universidad de Murcia, E-30071 Murcia, Spain
| | - Alberto Requena
- Departamento de
Química Física, Universidad de Murcia, E-30071 Murcia, Spain
| | - José Zúñiga
- Departamento de
Química Física, Universidad de Murcia, E-30071 Murcia, Spain
| | - José Pérez
- Departamento de Ingeniería
Minera, Geológica y Cartográfica, Área de Química
Inorgánica, Universidad Politécnica de Cartagena, E-30203 Cartagena, Spain
| | - Luís García
- Departamento de Ingeniería
Minera, Geológica y Cartográfica, Área de Química
Inorgánica, Universidad Politécnica de Cartagena, E-30203 Cartagena, Spain
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5
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Suh J. Progress in Designing Artificial Proteases: A New Therapeutic Option for Amyloid Diseases. ASIAN J ORG CHEM 2013. [DOI: 10.1002/ajoc.201300135] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Khusnutdinova JR, Rath NP, Mirica LM. The Aerobic Oxidation of a Pd(II) Dimethyl Complex Leads to Selective Ethane Elimination from a Pd(III) Intermediate. J Am Chem Soc 2012; 134:2414-22. [DOI: 10.1021/ja210841f] [Citation(s) in RCA: 92] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Julia R. Khusnutdinova
- Department of Chemistry, Washington University, One Brookings Drive, St. Louis,
Missouri 63130-4899, United States
| | - Nigam P. Rath
- Department of Chemistry and
Biochemistry, One University Boulevard, University of Missouri—St. Louis, Missouri 63121-4400, United
States
| | - Liviu M. Mirica
- Department of Chemistry, Washington University, One Brookings Drive, St. Louis,
Missouri 63130-4899, United States
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8
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Zhu X, Barman A, Ozbil M, Zhang T, Li S, Prabhakar R. Mechanism of peptide hydrolysis by co-catalytic metal centers containing leucine aminopeptidase enzyme: a DFT approach. J Biol Inorg Chem 2011; 17:209-22. [PMID: 21918843 DOI: 10.1007/s00775-011-0843-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2011] [Accepted: 08/30/2011] [Indexed: 11/28/2022]
Abstract
In this density functional theory study, reaction mechanisms of a co-catalytic binuclear metal center (Zn1-Zn2) containing enzyme leucine aminopeptidase for two different metal bridging nucleophiles (H(2)O and -OH) have been investigated. In addition, the effects of the substrate (L-leucine-p-nitroanilide → L-leucyl-p-anisidine) and metal (Zn1 → Mg and Zn2 → Co, i.e., Mg1-Zn2 and Mg1-Co2 variants) substitutions on the energetics of the mechanism have been investigated. The general acid/base mechanism utilizing a bicarbonate ion followed by this enzyme is divided into two steps: (1) the formation of the gem-diolate intermediate, and (2) the cleavage of the peptide bond. With the computed barrier of 17.8 kcal/mol, the mechanism utilizing a hydroxyl nucleophile was found to be in excellent agreement with the experimentally measured barrier of 18.7 kcal/mol. The rate-limiting step for reaction with L-leucine-p-nitroanilide is the cleavage of the peptide bond with a barrier of 17.8 kcal/mol. However, for L-leucyl-p-anisidine all steps of the mechanism were found to occur with similar barriers (18.0-19.0 kcal/mol). For the metallovariants, cleavage of the peptide bond occurs in the rate-limiting step with barriers of 17.8, 18.0, and 24.2 kcal/mol for the Zn1-Zn2, Mg1-Zn2, and Mg1-Co2 enzymes, respectively. The nature of the metal ion was found to affect only the creation of the gem-diolate intermediate, and after that all three enzymes follow essentially the same energetics. The results reported in this study have elucidated specific roles of both metal centers, the nucleophile, indirect ligands, and substrates in the catalytic functioning of this important class of binuclear metallopeptidases.
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Affiliation(s)
- Xiaoxia Zhu
- Department of Chemistry, University of Miami, 1301 Memorial Drive, Coral Gables, FL 33146, USA
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Serrano JL, García L, Pérez J, Pérez E, Galiana JM, García J, Martínez M, Sánchez G, da Silva I. New cyclometallated precursors of unsubstituted N-phenylpyrazole [{Pd(phpz)(μ-X)}2] (X = AcO or OH) and study of their reactivity towards selected ligands. Dalton Trans 2011; 40:156-68. [DOI: 10.1039/c0dt00814a] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Affiliation(s)
- José Luis Serrano
- Departamento de Ingeniería Minera, Geológica y Cartográfica. Área de Química Inorgánica, 30203, Cartagena, Spain
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10
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Quantum chemical calculations of stability constants: study of ligand effects on the relative stability of Pd(II)–peptide complexes. Theor Chem Acc 2010. [DOI: 10.1007/s00214-010-0862-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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11
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Bora RP, Barman A, Zhu X, Ozbil M, Prabhakar R. Which One Among Aspartyl Protease, Metallopeptidase, and Artificial Metallopeptidase is the Most Efficient Catalyst in Peptide Hydrolysis? J Phys Chem B 2010; 114:10860-75. [DOI: 10.1021/jp104294x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Ram Prasad Bora
- Department of Chemistry, University of Miami, 1301 Memorial Drive, Coral Gables, Florida 33146
| | - Arghya Barman
- Department of Chemistry, University of Miami, 1301 Memorial Drive, Coral Gables, Florida 33146
| | - Xiaoxia Zhu
- Department of Chemistry, University of Miami, 1301 Memorial Drive, Coral Gables, Florida 33146
| | - Mehmet Ozbil
- Department of Chemistry, University of Miami, 1301 Memorial Drive, Coral Gables, Florida 33146
| | - Rajeev Prabhakar
- Department of Chemistry, University of Miami, 1301 Memorial Drive, Coral Gables, Florida 33146
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Tamilselvi A, Mugesh G. Hydrolysis of Organophosphate Esters: Phosphotriesterase Activity of Metallo-β-lactamase and Its Functional Mimics. Chemistry 2010; 16:8878-86. [DOI: 10.1002/chem.201000282] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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13
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Yeguas V, Campomanes P, López R, Díaz N, Suárez D. Understanding Regioselective Cleavage in Peptide Hydrolysis by a Palladium(II) Aqua Complex: A Theoretical Point of View. J Phys Chem B 2010; 114:8525-35. [DOI: 10.1021/jp101870j] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Violeta Yeguas
- Departamento de Química Física y Analítica, Universidad de Oviedo, C/Julián Clavería, 8, 33006 Oviedo, Spain, and Laboratory of Computational Chemistry and Biochemistry, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Pablo Campomanes
- Departamento de Química Física y Analítica, Universidad de Oviedo, C/Julián Clavería, 8, 33006 Oviedo, Spain, and Laboratory of Computational Chemistry and Biochemistry, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Ramón López
- Departamento de Química Física y Analítica, Universidad de Oviedo, C/Julián Clavería, 8, 33006 Oviedo, Spain, and Laboratory of Computational Chemistry and Biochemistry, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Natalia Díaz
- Departamento de Química Física y Analítica, Universidad de Oviedo, C/Julián Clavería, 8, 33006 Oviedo, Spain, and Laboratory of Computational Chemistry and Biochemistry, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Dimas Suárez
- Departamento de Química Física y Analítica, Universidad de Oviedo, C/Julián Clavería, 8, 33006 Oviedo, Spain, and Laboratory of Computational Chemistry and Biochemistry, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
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14
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Soluble artificial metalloproteases with broad substrate selectivity, high reactivity, and high thermal and chemical stabilities. J Biol Inorg Chem 2010; 15:1023-31. [DOI: 10.1007/s00775-010-0662-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2010] [Accepted: 04/12/2010] [Indexed: 10/19/2022]
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15
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Kumar A, Zhu X, Walsh K, Prabhakar R. Theoretical Insights into the Mechanism of Selective Peptide Bond Hydrolysis Catalyzed by [Pd(H2O)4]2+. Inorg Chem 2009; 49:38-46. [DOI: 10.1021/ic901071v] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Amit Kumar
- Department of Chemistry, University of Miami, 1301 Memorial Drive, Coral Gables, Florida 33146
| | - Xiaoxia Zhu
- Department of Chemistry, University of Miami, 1301 Memorial Drive, Coral Gables, Florida 33146
| | - Kathryn Walsh
- Department of Chemistry, University of Miami, 1301 Memorial Drive, Coral Gables, Florida 33146
| | - Rajeev Prabhakar
- Department of Chemistry, University of Miami, 1301 Memorial Drive, Coral Gables, Florida 33146
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16
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Jiang J, Wu QJ, Cai XY, Zhu LG, Wang WJ. Mass spectrometry assisted assignments of binding and cleavage sites of Zn(II) complex towards oxidized insulin B chain. CHINESE CHEM LETT 2009. [DOI: 10.1016/j.cclet.2008.09.043] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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17
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Cao L, Jennings MC, Puddephatt RJ. A dipalladium complex with a single hydroxo bridge and its methylpalladium precursor. Dalton Trans 2009:5171-6. [DOI: 10.1039/b906038c] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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18
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Serrano JL, García L, Pérez J, Pérez E, García J, Sánchez G, López G, Liu M. Reactivity Towards Acidic Protic Ligands of Cyclopalladated Di‐μ‐hydroxo Complexes. Eur J Inorg Chem 2008. [DOI: 10.1002/ejic.200800445] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- José Luis Serrano
- Departamento de Ingeniería Minera, Geológica y Cartográfica.Universidad Politécnica de Cartagena Área de Química Inorgánica, 30203 Cartagena, Spain
| | - Luis García
- Departamento de Ingeniería Minera, Geológica y Cartográfica.Universidad Politécnica de Cartagena Área de Química Inorgánica, 30203 Cartagena, Spain
| | - José Pérez
- Departamento de Ingeniería Minera, Geológica y Cartográfica.Universidad Politécnica de Cartagena Área de Química Inorgánica, 30203 Cartagena, Spain
| | - Eduardo Pérez
- Departamento de Ingeniería Minera, Geológica y Cartográfica.Universidad Politécnica de Cartagena Área de Química Inorgánica, 30203 Cartagena, Spain
| | - Joaquín García
- Departamento de Química Inorgánica, Universidad de Murcia, 30071 Murcia, Spain
| | - Gregorio Sánchez
- Departamento de Química Inorgánica, Universidad de Murcia, 30071 Murcia, Spain
| | - Gregorio López
- Departamento de Química Inorgánica, Universidad de Murcia, 30071 Murcia, Spain
| | - Malva Liu
- Departamento de Termodinámica, Universidad de Valencia, 46100 Burjassot (Valencia), Spain
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Fonari MS, Ganin EV, Gelmboldt VO, Basok SS, Luisi BS, Moulton B. Binding of fluoro-containing anions to hexaazamacrocyclic ligand: Competitive interactions of fluoride and tetrafluoroborate anions with hexaprotonated [18]aneN6. INORG CHEM COMMUN 2008. [DOI: 10.1016/j.inoche.2008.01.028] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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20
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Kwak OK, Kim JJ, Min KS, Kim J, Kim BG. Twisted dinuclear Pd(II) complex with an exo-hexadentate ligand bearing bipyridine and carbamoly groups: Synthesis and structure. INORG CHEM COMMUN 2007. [DOI: 10.1016/j.inoche.2007.04.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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21
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Site-specifically cleavage of oxidized insulin B chain with Zn(II) ion studied by electrospray ionization mass spectrometry. CHINESE CHEM LETT 2007. [DOI: 10.1016/j.cclet.2007.03.016] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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