1
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Le Roy MM, Claes S, Saffon-Merceron N, Schols D, Troadec T, Tripier R. Selective synthesis of an elusive C-functional bis-cyclam and study of its inhibition of the CXCR4 chemokine receptor. Org Biomol Chem 2024; 22:3059-3067. [PMID: 38545887 DOI: 10.1039/d3ob02050a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/18/2024]
Abstract
This article presents the controlled synthesis of a rare example of C,C'-linked bis-cyclam architecture in mild conditions through the "bis-aminal" route previously used for the advantageous synthesis of cyclam, N- and C-functional cyclams and N,N'-bis-cyclams. Two synthetic pathways were explored with the smart design of α,β-unsaturated ketones or alkyl halides bis-cyclizing agents. The first led to the isolation of a key intermediate for the future design of N-functionalized bis-cyclams, whereas the second allowed the preparation of the targeted C,C'-xylylene-bis-cyclam under mild conditions with decent yield. This compound was then studied as a CXCR4 receptor inhibitor, one of the main applications known for bis-macrocyclic compounds, in particular in the context of HIV (human immunodeficiency virus) infection. Although results demonstrated that its potency is lower (i.e. 137-fold higher IC50) than the gold standard AMD3100 against HIV infection, clear evidence of CXCR4 inhibition is presented, confirming the potential of this novel architecture and related compounds in this research field.
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Affiliation(s)
- Marie M Le Roy
- Univ Brest, UMR CNRS 6521 CEMCA, 6 Avenue Victor le Gorgeu, 29200 Brest, France.
| | - Sandra Claes
- Rega Institute for Medical Research, KU Leuven, Herestraat 49, 3000 Leuven, Belgium
| | | | - Dominique Schols
- Rega Institute for Medical Research, KU Leuven, Herestraat 49, 3000 Leuven, Belgium
| | - Thibault Troadec
- Univ Brest, UMR CNRS 6521 CEMCA, 6 Avenue Victor le Gorgeu, 29200 Brest, France.
| | - Raphaël Tripier
- Univ Brest, UMR CNRS 6521 CEMCA, 6 Avenue Victor le Gorgeu, 29200 Brest, France.
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2
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Nizou G, Garda Z, Molnár E, Esteban-Gómez D, Le Fur M, Fougère O, Rousseaux O, Platas-Iglesias C, Tripier R, Tircsó G, Beyler M. Exploring the Limits of Ligand Rigidification in Transition Metal Complexes with Mono- N-Functionalized Pyclen Derivatives. Inorg Chem 2024; 63:3931-3947. [PMID: 38348851 DOI: 10.1021/acs.inorgchem.3c04451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
We report the synthesis of a new family of side-bridged pyclen ligands. The incorporation of an ethylene bridge between two adjacent nitrogen atoms was reached from the pyclen-oxalate precursor described previously. Three new side-bridged pyclen macrocycles, Hsb-3-pc1a, sb-3-pc1py, and Hsb-3-pc1pa, were obtained with the aim to assess their coordination properties toward Cu2+ and Zn2+ ions. We also prepared their nonreinforced analogues H3-pc1a, 3-pc1py, and H3-pc1pa as comparative benchmarks. The two series of ligands were characterized and their coordination properties were investigated in detail. The Zn2+ and Cu2+ complexes with the nonside-bridged series H3-pc1a, 3-pc1py, and H3-pc1pa were successfully isolated and their structures were assessed by X-ray diffraction studies. In the case of the side-bridged family, the synthesis of the complexes was far more difficult and, in some cases, unsuccessful. The results of our studies demonstrate that this difficulty is related to the extreme stiffening and basicity of such side-bridged pyclens.
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Affiliation(s)
- Gwladys Nizou
- Univ Brest, UMR CNRS 6521 CEMCA, 6 Avenue Victor Le Gorgeu, Brest 29200, France
| | - Zoltán Garda
- Department of Physical Chemistry, Faculty of Science and Technology, University of Debrecen, Egyetem tér 1, H-4032 Debrecen, Hungary
| | - Enikő Molnár
- Department of Physical Chemistry, Faculty of Science and Technology, University of Debrecen, Egyetem tér 1, H-4032 Debrecen, Hungary
| | - David Esteban-Gómez
- Centro Interdisciplinar de Química e Bioloxía (CICA) and Departamento de Química, Universidade da Coruña, Campus da Zapateira-Rúa da Fraga 10, 15008 A Coruña, Spain
| | - Mariane Le Fur
- Univ Brest, UMR CNRS 6521 CEMCA, 6 Avenue Victor Le Gorgeu, Brest 29200, France
| | - Olivier Fougère
- Groupe Guerbet, Centre de Recherche d'Aulnay-sous-Bois, BP 57400, 95943 Roissy CdG Cedex, France
| | - Olivier Rousseaux
- Groupe Guerbet, Centre de Recherche d'Aulnay-sous-Bois, BP 57400, 95943 Roissy CdG Cedex, France
| | - Carlos Platas-Iglesias
- Centro Interdisciplinar de Química e Bioloxía (CICA) and Departamento de Química, Universidade da Coruña, Campus da Zapateira-Rúa da Fraga 10, 15008 A Coruña, Spain
| | - Raphaël Tripier
- Univ Brest, UMR CNRS 6521 CEMCA, 6 Avenue Victor Le Gorgeu, Brest 29200, France
| | - Gyula Tircsó
- Department of Physical Chemistry, Faculty of Science and Technology, University of Debrecen, Egyetem tér 1, H-4032 Debrecen, Hungary
| | - Maryline Beyler
- Univ Brest, UMR CNRS 6521 CEMCA, 6 Avenue Victor Le Gorgeu, Brest 29200, France
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3
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Silva F, Veiga F, Paulo Jorge Rodrigues S, Cardoso C, Cláudia Paiva-Santos A. COSMO Models for the Pharmaceutical Development of Parenteral Drug Formulations. Eur J Pharm Biopharm 2023; 187:156-165. [PMID: 37120066 DOI: 10.1016/j.ejpb.2023.04.019] [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: 01/12/2023] [Revised: 03/31/2023] [Accepted: 04/21/2023] [Indexed: 05/01/2023]
Abstract
The aqueous solubility of active pharmaceutical ingredients is one of the most important features to be considered during the development of parenteral formulations in the pharmaceutical industry. Computational modelling has become in the last years an integral part of pharmaceutical development. In this context, ab initio computational models, such as COnductor-like Screening MOdel (COSMO), have been proposed as promising tools for the prediction of results without the effective use of resources. Nevertheless, despite the clear evaluation of computational resources, some authors had not achieved satisfying results and new calculations and algorithms have been proposed over the years to improve the outcomes. In the development and production of aqueous parenteral formulations, the solubility of Active Pharmaceutical Ingredients (APIs) in an aqueous and biocompatible vehicle is a decisive step. This work aims to study the hypothesis that COSMO models could be useful in the development of new parenteral formulations, mainly aqueous ones.
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Affiliation(s)
- Fernando Silva
- Department of Pharmaceutical Technology, Faculty of Pharmacy of the University of Coimbra, University of Coimbra, Coimbra, Portugal; REQUIMTE/LAQV, Group of Pharmaceutical Technology, Faculty of Pharmacy of the University of Coimbra, University of Coimbra, Coimbra, Portugal.
| | - Francisco Veiga
- Department of Pharmaceutical Technology, Faculty of Pharmacy of the University of Coimbra, University of Coimbra, Coimbra, Portugal; REQUIMTE/LAQV, Group of Pharmaceutical Technology, Faculty of Pharmacy of the University of Coimbra, University of Coimbra, Coimbra, Portugal
| | - Sérgio Paulo Jorge Rodrigues
- Coimbra Chemistry Centre, Chemistry Department, Faculty of Sciences and Technology of the University of Coimbra of the University of Coimbra, Coimbra, Portugal
| | - Catarina Cardoso
- Laboratórios Basi, Parque Industrial Manuel Lourenço Ferreira, lote 15, 3450-232 Mortágua, Portugal
| | - Ana Cláudia Paiva-Santos
- Department of Pharmaceutical Technology, Faculty of Pharmacy of the University of Coimbra, University of Coimbra, Coimbra, Portugal; REQUIMTE/LAQV, Group of Pharmaceutical Technology, Faculty of Pharmacy of the University of Coimbra, University of Coimbra, Coimbra, Portugal
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4
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Lisi D, Vezzoni CA, Casnati A, Sansone F, Salvio R. Intra- and Intermolecular Cooperativity in the Catalytic Activity of Phosphodiester Cleavage by Self-Assembled Systems Based on Guanidinylated Calix[4]arenes. Chemistry 2023; 29:e202203213. [PMID: 36382737 DOI: 10.1002/chem.202203213] [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: 10/13/2022] [Revised: 11/15/2022] [Accepted: 11/15/2022] [Indexed: 11/17/2022]
Abstract
The calix[4]arene scaffold, blocked in the cone conformation through alkylation with long alkyl chains, and decorated at the upper rim with four guanidine or arginine units, effectively catalyzes the cleavage of the phosphodiester bond of DNA and RNA model compounds in water. An exhaustive kinetic investigation unequivocally points to the existence of spontaneous aggregation phenomena, driven by hydrophobic effect, occurring at different critical concentrations that depend on the identity of the compound. A pronounced superiority of the assembled structures compared with the monomers in solution was observed. Moreover, the catalytically active units, clustered on the macrocyclic tetrafunctional scaffold, were proved to efficiently cooperate in the catalytic mechanism and result in improved reaction rates compared to those of the monofunctional model compounds. The kinetic analysis is also integrated and corroborated with further experiments based on fluorescence spectroscopy and light scattering. The advantage of the supramolecular assemblies based on tetrafunctional calixarenes leads to believe that the active units can cooperate not only intramolecularly but also intermolecularly. The molecules in the aggregates can probably mold, flex and rearrange but, at the same time, keep an ordered structure that favors phosphodiester bond cleavage. This dynamic preorganization can allow the catalytic units to reach a better fitting with the substrates and perform a superior catalytic activity.
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Affiliation(s)
- Daniele Lisi
- Dipartimento di Scienze e Tecnologie Chimiche, Università "Tor Vergata", Via della Ricerca Scientifica, 1, 00133, Roma, Italy
| | - Carlo Alberto Vezzoni
- Dipartimento di Scienze Chimiche, della Vita e della Sostenibilità Ambientale, Università degli Studi di Parma, Parco Area delle Scienze, 17/A, 43124, Parma, Italy
| | - Alessandro Casnati
- Dipartimento di Scienze Chimiche, della Vita e della Sostenibilità Ambientale, Università degli Studi di Parma, Parco Area delle Scienze, 17/A, 43124, Parma, Italy
| | - Francesco Sansone
- Dipartimento di Scienze Chimiche, della Vita e della Sostenibilità Ambientale, Università degli Studi di Parma, Parco Area delle Scienze, 17/A, 43124, Parma, Italy
| | - Riccardo Salvio
- Dipartimento di Scienze e Tecnologie Chimiche, Università "Tor Vergata", Via della Ricerca Scientifica, 1, 00133, Roma, Italy.,ISB - CNR Sezione Meccanismi di Reazione, Università La Sapienza, 00185, Roma, Italy
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5
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Anjomshoa M, Amirheidari B. Nuclease-like metalloscissors: Biomimetic candidates for cancer and bacterial and viral infections therapy. Coord Chem Rev 2022; 458:214417. [PMID: 35153301 PMCID: PMC8816526 DOI: 10.1016/j.ccr.2022.214417] [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: 09/01/2021] [Accepted: 01/09/2022] [Indexed: 12/25/2022]
Abstract
Despite the extensive and rapid discovery of modern drugs for treatment of cancer, microbial infections, and viral illnesses; these diseases are still among major global health concerns. To take inspiration from natural nucleases and also the therapeutic potential of metallopeptide antibiotics such as the bleomycin family, artificial metallonucleases with the ability of promoting DNA/RNA cleavage and eventually affecting cellular biological processes can be introduced as a new class of therapeutic candidates. Metal complexes can be considered as one of the main categories of artificial metalloscissors, which can prompt nucleic acid strand scission. Accordingly, biologists, inorganic chemists, and medicinal inorganic chemists worldwide have been designing, synthesizing and evaluating the biological properties of metal complexes as artificial metalloscissors. In this review, we try to highlight the recent studies conducted on the nuclease-like metalloscissors and their potential therapeutic applications. Under the light of the concurrent Covid-19 pandemic, the human need for new therapeutics was highlighted much more than ever before. The nuclease-like metalloscissors with the potential of RNA cleavage of invading viral pathogens hence deserve prime attention.
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6
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Pecina A, Rosa-Gastaldo D, Riccardi L, Franco-Ulloa S, Milan E, Scrimin P, Mancin F, De Vivo M. On the Metal-Aided Catalytic Mechanism for Phosphodiester Bond Cleavage Performed by Nanozymes. ACS Catal 2021; 11:8736-8748. [PMID: 34476110 PMCID: PMC8397296 DOI: 10.1021/acscatal.1c01215] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 06/03/2021] [Indexed: 12/20/2022]
Abstract
![]()
Recent studies have
shown that gold nanoparticles (AuNPs) functionalized
with Zn(II) complexes can cleave phosphate esters and nucleic acids.
Remarkably, such synthetic nanonucleases appear to catalyze metal
(Zn)-aided hydrolytic reactions of nucleic acids similar to metallonuclease
enzymes. To clarify the reaction mechanism of these nanocatalysts,
here we have comparatively analyzed two nanonucleases with a >10-fold
difference in the catalytic efficiency for the hydrolysis of the 2-hydroxypropyl-4-nitrophenylphosphate
(HPNP, a typical RNA model substrate). We have used microsecond-long
atomistic simulations, integrated with NMR experiments, to investigate
the structure and dynamics of the outer coating monolayer of these
nanoparticles, either alone or in complex with HPNP, in solution.
We show that the most efficient one is characterized by coating ligands
that promote a well-organized monolayer structure, with the formation
of solvated bimetallic catalytic sites. Importantly, we have found
that these nanoparticles can mimic two-metal-ion enzymes for nucleic
acid processing, with Zn ions that promote HPNP binding at the reaction
center. Thus, the two-metal-ion-aided hydrolytic strategy of such
nanonucleases helps in explaining their catalytic efficiency for substrate
hydrolysis, in accordance with the experimental evidence. These mechanistic
insights reinforce the parallelism between such functionalized AuNPs
and proteins toward the rational design of more efficient catalysts.
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Affiliation(s)
- Adam Pecina
- Laboratory of Molecular Modeling and Drug Discovery, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genoa, Italy
| | - Daniele Rosa-Gastaldo
- Dipartimento di Scienze Chimiche, Università di Padova, Via Marzolo 1, 35131 Padova, Italy
| | - Laura Riccardi
- Laboratory of Molecular Modeling and Drug Discovery, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genoa, Italy
| | - Sebastian Franco-Ulloa
- Laboratory of Molecular Modeling and Drug Discovery, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genoa, Italy
| | - Emil Milan
- Dipartimento di Scienze Chimiche, Università di Padova, Via Marzolo 1, 35131 Padova, Italy
| | - Paolo Scrimin
- Dipartimento di Scienze Chimiche, Università di Padova, Via Marzolo 1, 35131 Padova, Italy
| | - Fabrizio Mancin
- Dipartimento di Scienze Chimiche, Università di Padova, Via Marzolo 1, 35131 Padova, Italy
| | - Marco De Vivo
- Laboratory of Molecular Modeling and Drug Discovery, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genoa, Italy
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7
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8
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Bhattacharjee A, Das S, Das B, Roy P. Intercalative DNA binding, protein binding, antibacterial activities and cytotoxicity studies of a mononuclear copper(II) complex. Inorganica Chim Acta 2021. [DOI: 10.1016/j.ica.2020.119961] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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9
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Salvio R, D'Abramo M. Conformational Mobility and Efficiency in Supramolecular Catalysis. A Computational Approach to Evaluate the Performances of Enzyme Mimics. European J Org Chem 2020. [DOI: 10.1002/ejoc.202001022] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Riccardo Salvio
- Dipartimento di Scienze e Tecnologie Chimiche Università degli Studi di Roma “Tor Vergata” Via della Ricerca Scientifica 1 00133 Roma Italy
- ISB CNR Sezione Meccanismi di Reazione Università degli Studi di Roma La Sapienza 00185 Roma Italy
| | - Marco D'Abramo
- Dipartimento di Chimica Università degli Studi di Roma La Sapienza P. le Aldo Moro 5 00185 Roma Italy
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10
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Affiliation(s)
- Luca Gabrielli
- Department of Chemical Sciences University of Padova, via Marzolo, 1 35131 Padova Italy
| | - Leonard J. Prins
- Department of Chemical Sciences University of Padova, via Marzolo, 1 35131 Padova Italy
| | - Federico Rastrelli
- Department of Chemical Sciences University of Padova, via Marzolo, 1 35131 Padova Italy
| | - Fabrizio Mancin
- Department of Chemical Sciences University of Padova, via Marzolo, 1 35131 Padova Italy
| | - Paolo Scrimin
- Department of Chemical Sciences University of Padova, via Marzolo, 1 35131 Padova Italy
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11
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Hu L, Arifuzzaman MD, Zhao Y. Controlling Product Inhibition through Substrate-Specific Active Sites in Nanoparticle-Based Phosphodiesterase and Esterase. ACS Catal 2019. [DOI: 10.1021/acscatal.9b00630] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Lan Hu
- Department of Chemistry, Iowa State University, Ames, Iowa 50011-3111, United States
| | - MD Arifuzzaman
- Department of Chemistry, Iowa State University, Ames, Iowa 50011-3111, United States
| | - Yan Zhao
- Department of Chemistry, Iowa State University, Ames, Iowa 50011-3111, United States
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12
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Liu Z, Wang F, Ren J, Qu X. A series of MOF/Ce-based nanozymes with dual enzyme-like activity disrupting biofilms and hindering recolonization of bacteria. Biomaterials 2019; 208:21-31. [PMID: 30986610 DOI: 10.1016/j.biomaterials.2019.04.007] [Citation(s) in RCA: 136] [Impact Index Per Article: 27.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Revised: 03/08/2019] [Accepted: 04/05/2019] [Indexed: 12/13/2022]
Abstract
Notorious bacterial biofilms are becoming severe threats to public health worldwide. As the important component in biofilm extracellular polymeric substances (EPS), extracellular DNA (eDNA) has been manifested to connect different EPS components and bacteria together, leading biofilms hard to eliminate. Herein a series of MOF/Ce-based nanozymes with deoxyribonuclease (DNase) and peroxidase mimetic activities have been designed and synthesized for combating biofilms. The cerium (IV) complexes (DNase mimics) are capable of hydrolyzing eDNA and disrupting established biofilms, while the MOF with peroxidase-like activity can kill bacteria exposed in dispersed biofilms in the presence of H2O2. This can avoid the recolonization of bacteria and recurrence of biofilms. Given the fact that single-modal antibacterial agent is difficult to drastically eradicate biofilms, the marriage of two kinds of nanozymes is a rational strategy to acquire enhanced performance in combating biofilms. Besides, the utilization of nanozymes circumvents drawbacks of natural enzymes which are costly and vulnerable. Further studies have demonstrated that this kind of artificial enzyme with dual enzyme-mimetic activities can penetrate the biofilms, and inhibit bacterial biofilm formation intensively. Consistently, in vivo anti-biofilm application in treating subcutaneous abscess exhibits commendable wound healing and admirable bactericidal effect. To the best of our knowledge, it is the first time to devise an integrated nanozyme based on the peroxidase-like activity of MOF to eliminate biofilms and kill bacteria on site. This work may promote the application of MOF in the antibacterial field.
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Affiliation(s)
- Zhengwei Liu
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, PR China; University of Chinese Academy of Sciences, Beijing, 100039, PR China
| | - Faming Wang
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, PR China; University of Chinese Academy of Sciences, Beijing, 100039, PR China
| | - Jinsong Ren
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, PR China
| | - Xiaogang Qu
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, PR China.
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13
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Erxleben A. Mechanistic Studies of Homo- and Heterodinuclear Zinc Phosphoesterase Mimics: What Has Been Learned? Front Chem 2019; 7:82. [PMID: 30847339 PMCID: PMC6393734 DOI: 10.3389/fchem.2019.00082] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Accepted: 01/30/2019] [Indexed: 11/13/2022] Open
Abstract
Phosphoesterases hydrolyze the phosphorus oxygen bond of phosphomono-, di- or triesters and are involved in various important biological processes. Carboxylate and/or hydroxido-bridged dizinc(II) sites are a widespread structural motif in this enzyme class. Much effort has been invested to unravel the mechanistic features that provide the enormous rate accelerations observed for enzymatic phosphate ester hydrolysis and much has been learned by using simple low-molecular-weight model systems for the biological dizinc(II) sites. This review summarizes the knowledge and mechanistic understanding of phosphoesterases that has been gained from biomimetic dizinc(II) complexes, showing the power as well as the limitations of model studies.
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Affiliation(s)
- Andrea Erxleben
- School of Chemistry, National University of Ireland Galway, Galway, Ireland
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14
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Salvio R, Volpi S, Folcarelli T, Casnati A, Cacciapaglia R. A calix[4]arene with acylguanidine units as an efficient catalyst for phosphodiester bond cleavage in RNA and DNA model compounds. Org Biomol Chem 2019; 17:7482-7492. [DOI: 10.1039/c9ob01141b] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Conjugated carbonyl units in a calixarene scaffold provide the right amount of flexibility for catalysis with a minimum entropic cost.
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Affiliation(s)
- Riccardo Salvio
- Dipartimento di Scienze e Tecnologie Chimiche
- Università “Tor Vergata”
- I-00133 Roma
- Italy
- ISB - CNR Sezione Meccanismi di Reazione
| | - Stefano Volpi
- Dipartimento di Scienze Chimiche
- della Vita e della Sostenibilità Ambientale
- Università degli Studi di Parma
- 43124 Parma
- Italy
| | | | - Alessandro Casnati
- Dipartimento di Scienze Chimiche
- della Vita e della Sostenibilità Ambientale
- Università degli Studi di Parma
- 43124 Parma
- Italy
| | - Roberta Cacciapaglia
- ISB - CNR Sezione Meccanismi di Reazione
- Università La Sapienza
- 00185 Roma
- Italy
- Dipartimento di Chimica
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15
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Bencze ES, Zonta C, Mancin F, Prins LJ, Scrimin P. Distance between Metal Centres Affects Catalytic Efficiency of Dinuclear CoIII
Complexes in the Hydrolysis of a Phosphate Diester. European J Org Chem 2018. [DOI: 10.1002/ejoc.201800300] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Eva Szusanna Bencze
- Department of Chemical Sciences; University of Padova; Via Marzolo 1-35131 Padova Italy
| | - Cristiano Zonta
- Department of Chemical Sciences; University of Padova; Via Marzolo 1-35131 Padova Italy
| | - Fabrizio Mancin
- Department of Chemical Sciences; University of Padova; Via Marzolo 1-35131 Padova Italy
| | - Leonard J. Prins
- Department of Chemical Sciences; University of Padova; Via Marzolo 1-35131 Padova Italy
| | - Paolo Scrimin
- Department of Chemical Sciences; University of Padova; Via Marzolo 1-35131 Padova Italy
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16
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Mikkola S, Lönnberg T, Lönnberg H. Phosphodiester models for cleavage of nucleic acids. Beilstein J Org Chem 2018; 14:803-837. [PMID: 29719577 PMCID: PMC5905247 DOI: 10.3762/bjoc.14.68] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Accepted: 03/12/2018] [Indexed: 12/12/2022] Open
Abstract
Nucleic acids that store and transfer biological information are polymeric diesters of phosphoric acid. Cleavage of the phosphodiester linkages by protein enzymes, nucleases, is one of the underlying biological processes. The remarkable catalytic efficiency of nucleases, together with the ability of ribonucleic acids to serve sometimes as nucleases, has made the cleavage of phosphodiesters a subject of intensive mechanistic studies. In addition to studies of nucleases by pH-rate dependency, X-ray crystallography, amino acid/nucleotide substitution and computational approaches, experimental and theoretical studies with small molecular model compounds still play a role. With small molecules, the importance of various elementary processes, such as proton transfer and metal ion binding, for stabilization of transition states may be elucidated and systematic variation of the basicity of the entering or departing nucleophile enables determination of the position of the transition state on the reaction coordinate. Such data is important on analyzing enzyme mechanisms based on synergistic participation of several catalytic entities. Many nucleases are metalloenzymes and small molecular models offer an excellent tool to construct models for their catalytic centers. The present review tends to be an up to date summary of what has been achieved by mechanistic studies with small molecular phosphodiesters.
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Affiliation(s)
- Satu Mikkola
- Department of Chemistry, University of Turku, FIN-20014 Turku, Finland
| | - Tuomas Lönnberg
- Department of Chemistry, University of Turku, FIN-20014 Turku, Finland
| | - Harri Lönnberg
- Department of Chemistry, University of Turku, FIN-20014 Turku, Finland
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17
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Gutten O, Bím D, Řezáč J, Rulíšek L. Macrocycle Conformational Sampling by DFT-D3/COSMO-RS Methodology. J Chem Inf Model 2017; 58:48-60. [PMID: 29182321 DOI: 10.1021/acs.jcim.7b00453] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
To find and calibrate a robust and reliable computational protocol for mapping conformational space of medium-sized molecules, exhaustive conformational sampling has been carried out for a series of seven macrocyclic compounds of varying ring size and one acyclic analogue. While five of them were taken from the MD/LLMOD/force field study by Shelley and co-workers ( Watts , K. S. ; Dalal , P. ; Tebben , A. J. ; Cheney , D. L. ; Shelley , J. C. Macrocycle Conformational Sampling with MacroModel . J. Chem. Inf. MODEL 2014 , 54 , 2680 - 2696 ), three represent potential macrocyclic inhibitors of human cyclophilin A. The free energy values (GDFT/COSMO-RS) for all of the conformers of each compound were obtained by a composite protocol based on in vacuo quantum mechanics (DFT-D3 method in a large basis set), standard gas-phase thermodynamics, and the COSMO-RS solvation model. The GDFT/COSMO-RS values were used as the reference for evaluating the performance of conformational sampling algorithms: standard and extended MD/LLMOD search (simulated-annealing molecular dynamics with low-lying eigenvector following algorithms, employing the OPLS2005 force field plus GBSA solvation) available in MacroModel and plain molecular dynamics (MD) sampling at high temperature (1000 K) using the semiempirical quantum mechanics (SQM) potential SQM(PM6-D3H4/COSMO) followed by energy minimization of the snapshots. It has been shown that the former protocol (MD/LLMOD) may provide a more complete set of initial structures that ultimately leads to the identification of a greater number of low-energy conformers (as assessed by GDFT/COSMO-RS) than the latter (i.e., plain SQM MD). The CPU time needed to fully evaluate one medium-sized compound (∼100 atoms, typically resulting in several hundred or a few thousand conformers generated and treated quantum-mechanically) is approximately 1,000-100,000 CPU hours on today's computers, which transforms to 1-7 days on a small-sized computer cluster with a few hundred CPUs. Finally, our data sets based on the rigorous quantum-chemical approach allow us to formulate a composite conformational sampling protocol with multiple checkpoints and truncation of redundant structural data that offers superior insights at affordable computational cost.
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Affiliation(s)
- Ondrej Gutten
- The Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences , Gilead Sciences Research Center & IOCB, Flemingovo náměstí 2, 166 10 Praha 6, Czech Republic
| | - Daniel Bím
- The Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences , Gilead Sciences Research Center & IOCB, Flemingovo náměstí 2, 166 10 Praha 6, Czech Republic
| | - Jan Řezáč
- The Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences , Gilead Sciences Research Center & IOCB, Flemingovo náměstí 2, 166 10 Praha 6, Czech Republic
| | - Lubomír Rulíšek
- The Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences , Gilead Sciences Research Center & IOCB, Flemingovo náměstí 2, 166 10 Praha 6, Czech Republic
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Tseberlidis G, Intrieri D, Caselli A. Catalytic Applications of Pyridine-Containing Macrocyclic Complexes. Eur J Inorg Chem 2017. [DOI: 10.1002/ejic.201700633] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Giorgio Tseberlidis
- Department of Chemistry; Università degli Studi di Milano and ISTM-CNR-Milano; Via Golgi 19 20133 Milan Italy
| | - Daniela Intrieri
- Department of Chemistry; Università degli Studi di Milano and ISTM-CNR-Milano; Via Golgi 19 20133 Milan Italy
| | - Alessandro Caselli
- Department of Chemistry; Università degli Studi di Milano and ISTM-CNR-Milano; Via Golgi 19 20133 Milan Italy
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Barman SK, Mondal T, Koley D, Lloret F, Mukherjee R. A phenoxo-bridged dicopper(ii) complex as a model for phosphatase activity: mechanistic insights from a combined experimental and computational study. Dalton Trans 2017; 46:4038-4054. [PMID: 28271106 DOI: 10.1039/c6dt03514k] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
A μ-phenoxo-bis(μ2-1,3-acetato)-bridged dicopper(ii) complex [Cu(L1)(μ-O2CMe)2][NO3] (1) has been synthesized from the perspective of modeling phosphodiesterase activity. Structural characterization was done initially with 1·3Et2O (vapour diffusion of Et2O into MeOH solution of 1; poor crystal quality) and finally with its perchlorate salt [Cu(L1)(μ-O2CMe)2][ClO4]·1.375MeCN·0.25H2O, crystallized from vapour diffusion of n-pentane into a MeCN-MeOH mixture (comparatively better crystal quality). An asymmetric unit of such a crystal contains two independent molecules of compositions [Cu(L1)(μ-O2CMe)2][ClO4] and [Cu(L1)(μ-O2CMe)2(MeCN)][ClO4] (coordinated MeCN with 0.75 occupancy), and two molecules of MeCN and H2O (each H2O molecule with 0.25 occupancy) as the solvent of crystallization. These two cations, each having five-coordinate (μ-phenoxo)bis(μ-acetato)-bridged CuII ions, differ by only the coordination environment of only one CuII ion, which has a weakly coordinated acetonitrile molecule in its sixth position. Temperature-dependent magnetic studies on 1 reveal that the copper(ii) centres are antiferromagnetically coupled with the exchange-coupling constant J = -124(1) cm-1. Theoretically calculated J = -126.51 cm-1, employing a broken-symmetry DFT approach, is in excellent agreement with the experimental value. The dicopper(ii) complex has been found to be catalytically efficient in the hydrolysis of 2-hydroxypropyl-p-nitrophenylphosphate (HPNP). Detailed kinetic experiments and solution studies (potentiometry, species distribution and ESI-MS) were performed to elucidate the reaction mechanism. DFT calculations were performed to discriminate between different possible mechanistic pathways. The free-energy barrier for HPNP hydrolysis catalyzed by 1 is comparable to that obtained from the experimentally-determined value. The involvement of non-covalent (hydrogen-bonding) interaction has also been probed by DFT calculations. The activity of 1 is found to be the highest, compared to the structurally-characterized Mn, Co, Ni and Zn complexes of L1(-) reported earlier, under identical experimental conditions, in which each metal centre is six-coordinate.
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Affiliation(s)
- Suman K Barman
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208 016, India. and Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur 741 246, India
| | - Totan Mondal
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur 741 246, India
| | - Debasis Koley
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur 741 246, India
| | - Francesc Lloret
- Departament de Química Inorgànica/Fundació General de la Universitat de València (FGUV)/Instituto de Ciencia, Molecular (ICMOL), Universitat de València, Polígono de la Coma, s/n, 46980-Paterna, València, Spain
| | - Rabindranath Mukherjee
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208 016, India. and Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur 741 246, India
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