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Tripathi M, Thakur Y, Syed R, Asatkar AK, Alqahtani MS, Das D, Agrawal R, Verma B, Pande R. In-vitro and in-silico analysis and antitumor studies of novel Cu(II) and V(V) complexes of N-p-Tolylbenzohydroxamic acid. Int J Biol Macromol 2024; 268:131768. [PMID: 38663706 DOI: 10.1016/j.ijbiomac.2024.131768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 03/07/2024] [Accepted: 04/20/2024] [Indexed: 05/04/2024]
Abstract
Copper(L2Cu) and vanadium(L2VOCl) complexes of N-p-tolylbenzohydroxamic acid (LH) ligand have been investigated for DNA binding efficacy by multiple analytical, spectral, and computational techniques. The results revealed that complexes as groove binders as evidenced by UV absorption. Fluorescence studies including displacement assay using classical intercalator ethidium bromide as fluorescent probe also confirmed as groove binders. The viscometric analysis too supports the inferences as strong groove binders for both the complexes. Molecular docking too exposed DNA as a target to the complexes which precisely binds L2Cu, in the minor groove region while L2VOCl in major groove region. Molecular dynamic simulation performed on L2Cu complex revealing the interaction of complex with DNA within 20 ns time. The complex stacked into the nitrogen bases of oligonucleotides and the bonding features were intrinsically preserved for longer simulation times. In-vitro cytotoxicity study was undertaken employing MTT assay against the breast cancer cell line (MCF-7). Potential cytotoxic activities were observed for L2Cu and L2VOCl complexes with IC50 values of showing 71 % and 74 % of inhibition respectively.
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Affiliation(s)
- Mamta Tripathi
- School of Studies in Chemistry, Pt. Ravishankar Shukla University, Raipur 492010, Chhattisgarh, India.
| | - Yamini Thakur
- School of Studies in Chemistry, Pt. Ravishankar Shukla University, Raipur 492010, Chhattisgarh, India; Department of Chemistry, Govt. J. Yoganandam Chhattisgarh College, Raipur C.G. - 492001
| | - Rabbani Syed
- Department of Pharmaceutics, College of Pharmacy, King Saud University, P.O. Box 2457, Riyadh 11451, Saudi Arabia
| | - Ashish Kumar Asatkar
- Department of Chemistry, Satya Narayan Agrawal Govt. Arts and Commerce College, Kohka-Neora, Dist. Raipur, CG 493114, India
| | - Mohammad S Alqahtani
- Department of Pharmaceutics, College of Pharmacy, King Saud University, P.O. Box 2457, Riyadh 11451, Saudi Arabia
| | - Devashish Das
- Department of Chemical Engineering, Konkuk University, Seoul, South Korea
| | - Rainy Agrawal
- School of Studies in Chemistry, Pt. Ravishankar Shukla University, Raipur 492010, Chhattisgarh, India
| | - Bharati Verma
- School of Studies in Chemistry, Pt. Ravishankar Shukla University, Raipur 492010, Chhattisgarh, India
| | - Rama Pande
- School of Studies in Chemistry, Pt. Ravishankar Shukla University, Raipur 492010, Chhattisgarh, India
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2
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Saha T, Sappati S, Das S. An insight into the mixed quantum mechanical-molecular dynamic simulation of a Zn II-Curcumin complex with a chosen DNA sequence that supports experimental DNA binding investigations. Int J Biol Macromol 2023:125305. [PMID: 37315676 DOI: 10.1016/j.ijbiomac.2023.125305] [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: 02/28/2023] [Revised: 05/24/2023] [Accepted: 05/30/2023] [Indexed: 06/16/2023]
Abstract
An important aspect of research pertaining to Curcumin (HCur) is the need to arrest its degradation in aqueous solution and in biological milieu. This may be achieved through complex formation with metal ions. For this reason, a complex of HCur was prepared with ZnII, that is not likely to be active in redox pathways, minimizing further complications. The complex is monomeric, tetrahedral, with one HCur, an acetate and a molecule of water bound to ZnII. It arrests degradation of HCur to a considerable extent that was realized by taking it in phosphate buffer and in biological milieu. The structure was obtained by DFT calculations. Stable adduct formation was identified between optimized structures of HCur and [Zn(Cur)] with DNA (PDB ID: 1BNA) through experiments validated with multiscale modeling approach. Molecular docking studies provide 2D and 3D representations of binding of HCur and [Zn(Cur)] through different non-covalent interactions with the nucleotides of the chosen DNA. Through molecular dynamics simulation, a detailed understanding of binding pattern and key structural characteristics of the generated DNA-complex was obtained following analysis by RMSD, RMSF, radius of gyration, SASA and aspects like formation of hydrogen bonds. Experimental studies provide binding constants for [Zn(Cur)] with calf thymus DNA at 25 °C that effectively helps one to realize its high affinity towards DNA. In the absence of an experimental binding study of HCur with DNA, owing to its tendency to degrade in solution, a theoretical analysis of the binding of HCur to DNA is extremely helpful. Besides, both experimental and simulated binding of [Zn(Cur)] to DNA may be considered as a case of pseudo-binding of HCur to DNA. In a way, such studies on interaction with DNA helps one to identify HCur's affinity for cellular target DNA, not realized through experiments. The entire investigation is an understanding of experimental and theoretical approaches that has been compared continuously, being particularly useful when a molecule's interaction with a biological target cannot realized experimentally.
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Affiliation(s)
- Tanmoy Saha
- Department of Chemistry (Inorganic Section), Jadavpur University, Kolkata 700 032, India
| | - Subrahmanyam Sappati
- Department of Physical Chemistry, Gdańsk University of Technology, Gdańsk 80-233, Poland; Department of Pharmaceutical Technology and Biochemistry, Gdańsk University of Technology, Gdańsk 80-233, Poland
| | - Saurabh Das
- Department of Chemistry (Inorganic Section), Jadavpur University, Kolkata 700 032, India.
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3
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Veclani D, Tolazzi M, Cerón-Carrasco JP, Melchior A. Intercalation Ability of Novel Monofunctional Platinum Anticancer Drugs: A Key Step in Their Biological Action. J Chem Inf Model 2021; 61:4391-4399. [PMID: 34156233 PMCID: PMC8479807 DOI: 10.1021/acs.jcim.1c00430] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
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Phenanthriplatin
(PtPPH) is a monovalent platinum(II)-based complex
with a large cytotoxicity against cancer cells. Although the aqua-activated
drug has been assumed to be the precursor for DNA damage, it is still
under debate whether the way in which that metallodrug attacks to
DNA is dominated by a direct binding to a guanine base or rather by
an intercalated intermediate product. Aiming to capture the mechanism
of action of PtPPH, the present contribution used theoretical tools
to systematically assess the sequence of all possible mechanisms on
drug activation and reactivity, for example, hydrolysis, intercalation,
and covalent damage to DNA. Ab initio quantum mechanical
(QM) methods, hybrid QM/QM′ schemes, and independent gradient
model approaches are implemented in an unbiased protocol. The performed
simulations show that the cascade of reactions is articulated in three
well-defined stages: (i) an early and fast intercalation of the complex
between the DNA bases, (ii) a subsequent hydrolysis reaction that
leads to the aqua-activated form, and (iii) a final formation of the
covalent bond between PtPPH and DNA at a guanine site. The permanent
damage to DNA is consequently driven by that latter bond to DNA but
with a simultaneous π–π intercalation of the phenanthridine
into nucleobases. The impact of the DNA sequence and the lateral backbone
was also discussed to provide a more complete picture of the forces
that anchor the drug into the double helix.
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Affiliation(s)
- Daniele Veclani
- Dipartimento Politecnico di Ingegneria e Architettura (DPIA), Laboratori di Chimica, Università di Udine, via delle Scienze 99, 33100 Udine, Italy
| | - Marilena Tolazzi
- Dipartimento Politecnico di Ingegneria e Architettura (DPIA), Laboratori di Chimica, Università di Udine, via delle Scienze 99, 33100 Udine, Italy
| | - José P Cerón-Carrasco
- Reconocimiento y Encapsulación Molecular, Universidad Católica San Antonio de Murcia (UCAM). Campus de los Jerónimos, 30107 Murcia, Spain
| | - Andrea Melchior
- Dipartimento Politecnico di Ingegneria e Architettura (DPIA), Laboratori di Chimica, Università di Udine, via delle Scienze 99, 33100 Udine, Italy
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4
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Zamora A, Wachter E, Vera M, Heidary DK, Rodríguez V, Ortega E, Fernández-Espín V, Janiak C, Glazer EC, Barone G, Ruiz J. Organoplatinum(II) Complexes Self-Assemble and Recognize AT-Rich Duplex DNA Sequences. Inorg Chem 2021; 60:2178-2187. [PMID: 33502194 PMCID: PMC8456496 DOI: 10.1021/acs.inorgchem.0c02648] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
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The
specific recognition of AT-rich DNA sequences opens up the
door to promising diagnostic and/or therapeutic strategies against
gene-related diseases. Here, we demonstrate that amphiphilic PtII complexes of the type [Pt(dmba)(N∧N)]NO3 (dmba = N,N-dimethylbenzylamine-κN, κC; N∧N = dpq (3), dppz (4), and dppn (5)) recognize AT-rich
oligonucleotides over other types of DNA, RNA, and model proteins.
The crystal structure of 4 shows the presence of significant
π-stacking interactions and a distorted coordination sphere
of the d8 PtII atom. Complex 5,
containing the largest π-conjugated ligand, forms supramolecular
assemblies at high concentrations under aqueous environment. However,
its aggregation can be promoted in the presence of DNA at concentrations
as low as 10 μM in a process that “turns on” its
excimer emission around 600 nm. Viscometry, gel electrophoresis, and
theoretical calculations demonstrate that 5 binds to
minor groove when self-assembled, while the monomers of 3 and 4 intercalate into the DNA. The complexes also
inhibit cancer cell growth with low-micromolar IC50 values
in 2D tissue culture and suppress tumor growth in 3D tumor spheroids
with a multicellular resistance (MCR) index comparable to that of
cisplatin. Cyclometalated PtII complexes
containing π-conjugated
ligands form supramolecular assemblies under aqueous environment,
and DNA-induced aggregation occurs for the one containing the highest
conjugated N,N-diimine ligand. The complexes recognize
AT-rich DNA sequences over others in DNA, RNA, and proteins. Their
DNA binding mode switches from intercalation to minor groove binding
when self-assembled. The complexes suppress tumor growth in 3D tumor
spheroids.
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Affiliation(s)
- Ana Zamora
- Departamento de Química Inorgánica, Universidad de Murcia, and Biomedical Research Institute of Murcia (IMIB-Arrixaca), E-30071 Murcia, Spain
| | - Erin Wachter
- Department of Chemistry, University of Kentucky 505 Rose Street, Lexington, Kentucky 40506, United States
| | - María Vera
- Departamento de Química Inorgánica, Universidad de Murcia, and Biomedical Research Institute of Murcia (IMIB-Arrixaca), E-30071 Murcia, Spain
| | - David K Heidary
- Department of Chemistry, University of Kentucky 505 Rose Street, Lexington, Kentucky 40506, United States
| | - Venancio Rodríguez
- Departamento de Química Inorgánica, Universidad de Murcia, and Biomedical Research Institute of Murcia (IMIB-Arrixaca), E-30071 Murcia, Spain
| | - Enrique Ortega
- Departamento de Química Inorgánica, Universidad de Murcia, and Biomedical Research Institute of Murcia (IMIB-Arrixaca), E-30071 Murcia, Spain
| | | | - Christoph Janiak
- Institut für Anorganische Chemie und Strukturchemie, Heinrich-Heine-Universität Düsseldorf, D-40204 Düsseldorf, Germany
| | - Edith C Glazer
- Department of Chemistry, University of Kentucky 505 Rose Street, Lexington, Kentucky 40506, United States
| | - Giampaolo Barone
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche (STEBICEF), Università di Palermo, 90128 Palermo, Italy
| | - José Ruiz
- Departamento de Química Inorgánica, Universidad de Murcia, and Biomedical Research Institute of Murcia (IMIB-Arrixaca), E-30071 Murcia, Spain
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5
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Shakir S, Talebi S, Abd‐ur‐Rehman HM, Moi PS, Iwamoto M, Yunus K, Periasamy V. Metallization of Silver Through Coffee‐Ring Assisted Ribonucleic Acid Scaffolding Technique. ChemistrySelect 2019. [DOI: 10.1002/slct.201902335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Sehar Shakir
- Low Dimensional Materials Research Centre (LDMRC), Department of Physics, Faculty of ScienceUniversity of Malaya 50603 Kuala Lumpur Malaysia
- US-Pakistan Center for Advanced Studies in Energy, USPCASE, NationalUniversity of Sciences and Technology, H-12 Islamabad Pakistan
| | - Sara Talebi
- Low Dimensional Materials Research Centre (LDMRC), Department of Physics, Faculty of ScienceUniversity of Malaya 50603 Kuala Lumpur Malaysia
| | - Hafiz Muhammad Abd‐ur‐Rehman
- School of Mechanical & Manufacturing Engineering (SMME), NationalUniversity of Sciences & Technology (NUST), H-12 Campus Islamabad Pakistan
| | - Phang Siew Moi
- Institute of Biological Sciences, Faculty of ScienceUniversity of Malaya 50603 Kuala Lumpur Malaysia
| | - Mitsumasa Iwamoto
- Department of Physical ElectronicsTokyo Institute of Technology, 2–12-1 O-okayama, Meguro-ku Tokyo 152-8552 Japan
| | - Kamran Yunus
- Department of Chemical Engineering and BiotechnologyUniversity of Cambridge, Philippa Fawcett Drive West Cambridge Site Cambridge, CB3 0AS United Kingdom
| | - Vengadesh Periasamy
- Low Dimensional Materials Research Centre (LDMRC), Department of Physics, Faculty of ScienceUniversity of Malaya 50603 Kuala Lumpur Malaysia
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6
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Hognon C, Gebus A, Barone G, Monari A. Human DNA Telomeres in Presence of Oxidative Lesions: The Crucial Role of Electrostatic Interactions on the Stability of Guanine Quadruplexes. Antioxidants (Basel) 2019; 8:antiox8090337. [PMID: 31443537 PMCID: PMC6770428 DOI: 10.3390/antiox8090337] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 08/14/2019] [Accepted: 08/20/2019] [Indexed: 01/23/2023] Open
Abstract
By using all atom molecular dynamics simulations, we studied the behavior of human DNA telomere sequences in guanine quadruplex (G4) conformation and in the presence of oxidative lesions, namely abasic sites. In particular, we evidenced that while removing one guanine base induces a significant alteration and destabilization of the involved leaflet, human telomere oligomers tend, in most cases, to maintain at least a partial quadruplex structure, eventually by replacing the empty site with undamaged guanines of different leaflets. This study shows that (i) the disruption of the quadruplex leaflets induces the release of at least one of the potassium cations embedded in the quadruplex channel and that (ii) the electrostatic interactions of the DNA sequence with the aforementioned cations are fundamental to the maintenance of the global quadruplex structure.
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Affiliation(s)
- Cecilia Hognon
- Université de Lorraine, CNRS, LPCT UMR 7019, F54000 Nancy, France.
| | - Adrien Gebus
- Université de Lorraine, CNRS, LPCT UMR 7019, F54000 Nancy, France
| | - Giampaolo Barone
- Department of Biological, Chenical and Pharmaceutical Sciences and Technologies, Università di Palermo, Viale delle Scienze, 90128 Palermo, Italy
| | - Antonio Monari
- Université de Lorraine, CNRS, LPCT UMR 7019, F54000 Nancy, France.
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7
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Baildya N, Dey I, Bagchi A, Chattopadhyay AP. Interaction of copper nanoparticles with DNA: structural and docking studies. J Biomol Struct Dyn 2019; 38:1256-1261. [PMID: 30898050 DOI: 10.1080/07391102.2019.1597768] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Nabajyoti Baildya
- Department of Chemistry, University of Kalyani, Kalyani, West Bengal, India
| | - Ipsita Dey
- School of Biomedical Engineering, Duquesne University, Pittsburgh, PA, USA
| | - Angshuman Bagchi
- Department of Biochemistry and Biophysics, University of Kalyani, Kalyani, West Bengal, India
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8
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Zubair S, Asghar F, Badshah A, Lal B, Hussain RA, Tabassum S, Tahir MN. New bioactive ferrocene-substituted heteroleptic copper(I) complex: Synthesis, structural elucidation, DNA interaction, and DFT study. J Organomet Chem 2019. [DOI: 10.1016/j.jorganchem.2018.10.017] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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9
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Sharma A, Delile S, Jabri M, Adamo C, Fave C, Marchal D, Perrier A. Interaction of osmium(ii) redox probes with DNA: insights from theory. Phys Chem Chem Phys 2018; 18:30029-30039. [PMID: 27774536 DOI: 10.1039/c6cp05105g] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
In the course of developing ultrasensitive and quantitative electrochemical point-of-care analytical tools for genetic detection of infectious diseases, osmium(ii) metallointercalators were revealed to be suitable and efficient redox probes to monitor the in vitro DNA amplification [Defever etal, Anal. Chem., 2011, 83, 1815-1821]. In this work, we thus propose a complete computational protocol in order to evaluate the affinity between Os(ii) complexes with double-stranded DNA. This protocol is based on molecular dynamics, with the parametrization of the GAFF force field for the Os(ii) complexes presenting an octahedral environment with polypyridine ligands, and QM/QM' calculations to evaluate the binding energy. For three Os(ii) probes and different binding sites, molecular dynamics simulations and interaction energies calculated at the QM/QM' level are successively discussed and compared to experimental data in order to identify the most stable binding sites. The computational protocol we propose should then be used to design more efficient Os(ii) metallointercalators.
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Affiliation(s)
- Ashwani Sharma
- Chimie ParisTech, PSL Research University, CNRS, Institut de Recherche de Chimie Paris (IRCP), F-75005 Paris, France and Laboratoire d'Electrochimie Moléculaire, UMR 7591 CNRS, Université Paris Diderot, Sorbonne Paris Cité, 15 rue J-A de Baif, F-75205 Paris Cedex 13, France.
| | - Sebastien Delile
- Laboratoire d'Electrochimie Moléculaire, UMR 7591 CNRS, Université Paris Diderot, Sorbonne Paris Cité, 15 rue J-A de Baif, F-75205 Paris Cedex 13, France.
| | - Mohamed Jabri
- Chimie ParisTech, PSL Research University, CNRS, Institut de Recherche de Chimie Paris (IRCP), F-75005 Paris, France and E-pôle de génoinformatique, Institut Jacques Monod, UMR7592, CNRS, Université Paris Diderot, Sorbonne Paris Cité, F-75013 Paris, France
| | - Carlo Adamo
- Chimie ParisTech, PSL Research University, CNRS, Institut de Recherche de Chimie Paris (IRCP), F-75005 Paris, France and Institut Universitaire de France, 103 Boulevard Saint Michel, F-75005 Paris, France
| | - Claire Fave
- Laboratoire d'Electrochimie Moléculaire, UMR 7591 CNRS, Université Paris Diderot, Sorbonne Paris Cité, 15 rue J-A de Baif, F-75205 Paris Cedex 13, France.
| | - Damien Marchal
- Laboratoire d'Electrochimie Moléculaire, UMR 7591 CNRS, Université Paris Diderot, Sorbonne Paris Cité, 15 rue J-A de Baif, F-75205 Paris Cedex 13, France.
| | - Aurélie Perrier
- Chimie ParisTech, PSL Research University, CNRS, Institut de Recherche de Chimie Paris (IRCP), F-75005 Paris, France and Université Paris Diderot, Sorbonne Paris Cité, 5 rue Thomas Mann, F-75205 Paris Cedex 13, France.
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10
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A new Co(III) complex of Schiff base derivative for electrochemical recognition of nitrite anion. J CHEM SCI 2017. [DOI: 10.1007/s12039-017-1363-6] [Citation(s) in RCA: 3] [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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Spinello A, Magistrato A. An omics perspective to the molecular mechanisms of anticancer metallo-drugs in the computational microscope era. Expert Opin Drug Discov 2017; 12:813-825. [DOI: 10.1080/17460441.2017.1340272] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Angelo Spinello
- CNR-IOM-DEMOCRITOS c/o International School for Advanced Studies (SISSA/ISAS), Trieste, Italy
| | - Alessandra Magistrato
- CNR-IOM-DEMOCRITOS c/o International School for Advanced Studies (SISSA/ISAS), Trieste, Italy
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12
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DNA/BSA binding ability and genotoxic effect of mono- and binuclear copper (II) complexes containing a Schiff base derived from salicylaldehyde and D, L-glutamic acid. J Organomet Chem 2017. [DOI: 10.1016/j.jorganchem.2016.11.007] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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13
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Ostojic L, Wurmbach E. Analysis of fingerprint samples, testing various conditions, for forensic DNA identification. Sci Justice 2017; 57:35-40. [DOI: 10.1016/j.scijus.2016.08.009] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Revised: 08/25/2016] [Accepted: 08/30/2016] [Indexed: 01/28/2023]
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14
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Jana S, Santra RC, Frontera A, Drew MGB, Ortega-Castro J, Fernández D, Das S, Chattopadhyay S. Copper(II) pseudohalide complexes with isomeric N2O donor Schiff base ligands: Synthesis, characterization and molecular dynamics simulations of interactions with DNA. ChemistrySelect 2016. [DOI: 10.1002/slct.201500018] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Subrata Jana
- Department of Chemistry; Inorganic Section; Jadavpur University; Kolkata - 700 032 India
| | - Ramesh Chandra Santra
- Department of Chemistry; Inorganic Section; Jadavpur University; Kolkata - 700 032 India
| | - Antonio Frontera
- Departament de Química; Universitat de les Illes Balears; Crta de Valldemossa km 7.5 07122 Palma de Mallorca (Baleares SPAIN
| | - Michael G. B. Drew
- School of Chemistry; The University of Reading; P.O. Box 224 Whiteknights Reading RG6 6AD UK
| | - Joaquín Ortega-Castro
- Departament de Química; Universitat de les Illes Balears; Crta de Valldemossa km 7.5 07122 Palma de Mallorca (Baleares SPAIN
| | - David Fernández
- Departament de Química; Universitat de les Illes Balears; Crta de Valldemossa km 7.5 07122 Palma de Mallorca (Baleares SPAIN
| | - Saurabh Das
- Department of Chemistry; Inorganic Section; Jadavpur University; Kolkata - 700 032 India
| | - Shouvik Chattopadhyay
- Department of Chemistry; Inorganic Section; Jadavpur University; Kolkata - 700 032 India
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15
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Barone G, Gennaro G, Giuliani AM, Giustini M. Interaction of Cd(ii) and Ni(ii) terpyridine complexes with model polynucleotides: a multidisciplinary approach. RSC Adv 2016. [DOI: 10.1039/c5ra24919h] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The study of the intercalation of both complexes, evidenced by CD and fluorescence spectroscopy and supported by QM/MM calculations, broadens the experimental and theoretical background on drugs/DNA interactions.
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Affiliation(s)
- G. Barone
- Dipartimento STEBICEF
- Università di Palermo
- 90128 Palermo
- Italy
| | - G. Gennaro
- Dipartimento STEBICEF
- Università di Palermo
- 90128 Palermo
- Italy
| | - A. M. Giuliani
- Dipartimento STEBICEF
- Università di Palermo
- 90128 Palermo
- Italy
| | - M. Giustini
- Dipartimento di Chimica
- Università “La Sapienza”
- 00185 Roma
- Italy
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16
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Kocak A, Yilmaz H, Faiz O, Andac O. Experimental and theoretical studies on Cu(II) complex of N,N′-disalicylidene-2,3-diaminopyridine ligand reveal indirect evidence for DNA intercalation. Polyhedron 2016. [DOI: 10.1016/j.poly.2015.11.037] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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17
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Liu C, Zhu Y, Tang M. Theoretical studies on binding modes of copper-based nucleases with DNA. J Mol Graph Model 2015; 64:11-29. [PMID: 26766349 DOI: 10.1016/j.jmgm.2015.12.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Revised: 12/15/2015] [Accepted: 12/16/2015] [Indexed: 01/06/2023]
Abstract
In the present work, molecular simulations were performed for the purpose of predicting the binding modes of four types of copper nucleases (a total 33 compounds) with DNA. Our docking results accurately predicted the groove binding and electrostatic interaction for some copper nucleases with B-DNA. The intercalation modes were also reproduced by "gap DNA". The obtained results demonstrated that the ligand size, length, functional groups and chelate ring size bound to the copper center could influence the binding affinities of copper nucleases. The binding affinities obtained from the docking calculations herein also replicated results found using MM-PBSA approach. The predicted DNA binding modes of copper nucleases with DNA will ultimately help us to better understand the interaction of copper compounds with DNA.
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Affiliation(s)
- Chunmei Liu
- College of Chemistry and Molecular Engineering, Zhengzhou University, Zhengzhou, Henan Province 450001, PR China
| | - Yanyan Zhu
- College of Chemistry and Molecular Engineering, Zhengzhou University, Zhengzhou, Henan Province 450001, PR China.
| | - Mingsheng Tang
- College of Chemistry and Molecular Engineering, Zhengzhou University, Zhengzhou, Henan Province 450001, PR China.
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18
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Zhang Q, Yu LM, Ni CH, Li X, Li X. Synthesis, Characterization, and DFT Studies of Four Dinuclear Copper(II) Complexes with Aromatic Carboxylate Ligands: Cu 2(L) 4·(CH 3OH) 2. B KOREAN CHEM SOC 2015. [DOI: 10.1002/bkcs.10418] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Qi Zhang
- Key Laboratory of Marine Chemistry Theory and Technology; Ministry of Education, Ocean University of China; Qingdao 266100 China
| | - Liang Min Yu
- Key Laboratory of Marine Chemistry Theory and Technology; Ministry of Education, Ocean University of China; Qingdao 266100 China
- Qingdao Collaborative Innovation Center of Marine Science and Technology; Ocean University of China; Qingdao 266100 China
| | - Chun Hua Ni
- Key Laboratory of Marine Chemistry Theory and Technology; Ministry of Education, Ocean University of China; Qingdao 266100 China
| | - Xin Li
- Key Laboratory of Marine Chemistry Theory and Technology; Ministry of Education, Ocean University of China; Qingdao 266100 China
| | - Xia Li
- Key Laboratory of Marine Chemistry Theory and Technology; Ministry of Education, Ocean University of China; Qingdao 266100 China
- Qingdao Collaborative Innovation Center of Marine Science and Technology; Ocean University of China; Qingdao 266100 China
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19
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Galindo-Murillo R, García-Ramos JC, Ruiz-Azuara L, Cheatham TE, Cortés-Guzmán F. Intercalation processes of copper complexes in DNA. Nucleic Acids Res 2015; 43:5364-76. [PMID: 25958394 PMCID: PMC4477671 DOI: 10.1093/nar/gkv467] [Citation(s) in RCA: 121] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Accepted: 04/28/2015] [Indexed: 11/25/2022] Open
Abstract
The family of anticancer complexes that include the transition metal copper known as Casiopeínas® shows promising results. Two of these complexes are currently in clinical trials. The interaction of these compounds with DNA has been observed experimentally and several hypotheses regarding the mechanism of action have been developed, and these include the generation of reactive oxygen species, phosphate hydrolysis and/or base-pair intercalation. To advance in the understanding on how these ligands interact with DNA, we present a molecular dynamics study of 21 Casiopeínas with a DNA dodecamer using 10 μs of simulation time for each compound. All the complexes were manually inserted into the minor groove as the starting point of the simulations. The binding energy of each complex and the observed representative type of interaction between the ligand and the DNA is reported. With this extended sampling time, we found that four of the compounds spontaneously flipped open a base pair and moved inside the resulting cavity and four compounds formed stacking interactions with the terminal base pairs. The complexes that formed the intercalation pocket led to more stable interactions.
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Affiliation(s)
- Rodrigo Galindo-Murillo
- Department of Medicinal Chemistry, College of Pharmacy, Skaggs Hall 201, University of Utah, Salt Lake City, UT 84112, USA
| | - Juan Carlos García-Ramos
- Departamento de Química Inorgánica y Nuclear, Facultad de Química, Universidad Nacional Autónoma de México. Avenida Universidad 3000, 04510 México City, Mexico
| | - Lena Ruiz-Azuara
- Departamento de Química Inorgánica y Nuclear, Facultad de Química, Universidad Nacional Autónoma de México. Avenida Universidad 3000, 04510 México City, Mexico
| | - Thomas E Cheatham
- Department of Medicinal Chemistry, College of Pharmacy, Skaggs Hall 201, University of Utah, Salt Lake City, UT 84112, USA
| | - Fernando Cortés-Guzmán
- Instituto de Química, Universidad Nacional Autónoma de México, DF 04510, Mexico Centro Conjunto de Investigación en Química Sustentable UAEMex-UNAM, carretera Toluca-Atlacomulco km 14.5, Toluca, México 50200, Mexico
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20
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Dumont É, Monari A. Interaction of Palmatine with DNA: An Environmentally Controlled Phototherapy Drug. J Phys Chem B 2014; 119:410-9. [DOI: 10.1021/jp5088515] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Élise Dumont
- Laboratoire
de Chimie, UMR 5182 CNRS, École Normale Supérieure de Lyon, 46, allée d’Italie, 69364 Lyon Cedex 07, France
| | - Antonio Monari
- Théorie-Modélisation-Simulation,
SRSMC, Université de Lorraine Nancy, Boulevard des Aiguillettes 54506, Vandoeuvre-lés-Nancy, France
- Théorie-Modélisation-Simulation,
SRSMC, CNRS, Boulevard des Aiguillettes 54506, Vandoeuvre-lés-Nancy, France
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21
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Huix-Rotllant M, Dumont E, Ferré N, Monari A. Photophysics of acetophenone interacting with DNA: why the road to photosensitization is open. Photochem Photobiol 2014; 91:323-30. [PMID: 25412588 DOI: 10.1111/php.12395] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2014] [Accepted: 11/12/2014] [Indexed: 01/12/2023]
Abstract
Deoxyribonucleic acid photosensitization, i.e. the photoinduced electron- or energy-transfer of chromophores interacting with DNA, is a crucial phenomenon that triggers important DNA lesions such as pyrimidine dimerization, even upon absorption of relatively low-energy radiation. Oxidative lesions may also be produced via the photoinduced production of reactive oxygen species. Aromatic ketones, and acetophenone in particular, are well known for their sensitization effects. In this contribution we model the structural and dynamical properties of the acetophenone/DNA aggregates as well as their spectroscopic and photophysical properties using high-level hybrid quantum mechanics/molecular mechanics methods. We show that the key steps of the photochemistry of acetophenone in gas phase are conserved in the macromolecular environment and thus an ultrafast singlet-triplet conversion of acetophenone is expected prior to the transfer to DNA.
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Affiliation(s)
- Miquel Huix-Rotllant
- Institut fur Physikalische und Theoretische Chemie, Gothe Universitat Frankfurt, Frankfurt am Main, Germany
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22
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Vargiu AV, Magistrato A. Atomistic-Level Portrayal of Drug-DNA Interplay: A History of Courtships and Meetings Revealed by Molecular Simulations. ChemMedChem 2014; 9:1966-81. [DOI: 10.1002/cmdc.201402203] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2014] [Indexed: 12/19/2022]
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23
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Biancardi A, Burgalassi A, Terenzi A, Spinello A, Barone G, Biver T, Mennucci B. A Theoretical and Experimental Investigation of the Spectroscopic Properties of a DNA-Intercalator Salphen-Type ZnIIComplex. Chemistry 2014; 20:7439-47. [DOI: 10.1002/chem.201304876] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2013] [Indexed: 01/22/2023]
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24
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He R, Yang Q, Li M. Acylation and deacylation mechanism of Helicobacter pylori AmiF formamidase: A computational DFT study. Chem Phys Lett 2014. [DOI: 10.1016/j.cplett.2014.02.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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25
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Airoldi M, Barone G, Gennaro G, Giuliani AM, Giustini M. Interaction of doxorubicin with polynucleotides. A spectroscopic study. Biochemistry 2014; 53:2197-207. [PMID: 24641674 DOI: 10.1021/bi401687v] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The interaction of doxorubicin (DX) with model polynucleotides poly(dG-dC)·poly(dG-dC) (polyGC), poly(dA-dT)·poly(dA-dT) (polyAT), and calf thymus DNA has been studied by several spectroscopic techniques in phosphate buffer aqueous solutions. UV-vis, circular dichroism, and fluorescence spectroscopic data confirm that intercalation is the prevailing mode of interaction, and also reveal that the interaction with AT-rich regions leads to the transfer of excitation energy to DX not previously documented in the literature. Moreover, the DX affinity for AT sites has been found to be on the same order of magnitude as that reported for GC sites.
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Affiliation(s)
- Marta Airoldi
- Dipartimento STEBICEF, Università di Palermo, Viale delle Scienze , Parco D'Orleans, Pad. 17, 90128 Palermo, Italy
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26
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Lentini L, Melfi R, Di Leonardo A, Spinello A, Barone G, Pace A, Palumbo Piccionello A, Pibiri I. Toward a rationale for the PTC124 (Ataluren) promoted readthrough of premature stop codons: a computational approach and GFP-reporter cell-based assay. Mol Pharm 2014; 11:653-64. [PMID: 24483936 PMCID: PMC4167060 DOI: 10.1021/mp400230s] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2013] [Revised: 12/17/2013] [Accepted: 01/31/2014] [Indexed: 01/28/2023]
Abstract
The presence in the mRNA of premature stop codons (PTCs) results in protein truncation responsible for several inherited (genetic) diseases. A well-known example of these diseases is cystic fibrosis (CF), where approximately 10% (worldwide) of patients have nonsense mutations in the CF transmembrane regulator (CFTR) gene. PTC124 (3-(5-(2-fluorophenyl)-1,2,4-oxadiazol-3-yl)-benzoic acid), also known as Ataluren, is a small molecule that has been suggested to allow PTC readthrough even though its target has yet to be identified. In the lack of a general consensus about its mechanism of action, we experimentally tested the ability of PTC124 to promote the readthrough of premature termination codons by using a new reporter. The reporter vector was based on a plasmid harboring the H2B histone coding sequence fused in frame with the green fluorescent protein (GFP) cDNA, and a TGA stop codon was introduced in the H2B-GFP gene by site-directed mutagenesis. Additionally, an unprecedented computational study on the putative supramolecular interaction between PTC124 and an 11-codon (33-nucleotides) sequence corresponding to a CFTR mRNA fragment containing a central UGA nonsense mutation showed a specific interaction between PTC124 and the UGA codon. Altogether, the H2B-GFP-opal based assay and the molecular dynamics (MD) simulation support the hypothesis that PTC124 is able to promote the specific readthrough of internal TGA premature stop codons.
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Affiliation(s)
- Laura Lentini
- Dipartimento
di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche, Università degli Studi di Palermo, Viale delle Scienze Ed. 17, 90128 Palermo, Italy
| | - Raffaella Melfi
- Dipartimento
di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche, Università degli Studi di Palermo, Viale delle Scienze Ed. 17, 90128 Palermo, Italy
| | - Aldo Di Leonardo
- Dipartimento
di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche, Università degli Studi di Palermo, Viale delle Scienze Ed. 17, 90128 Palermo, Italy
- Centro di OncoBiologia
Sperimentale (COBS), via San Lorenzo
Colli, 90145 Palermo, Italy
| | - Angelo Spinello
- Dipartimento
di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche, Università degli Studi di Palermo, Viale delle Scienze Ed. 17, 90128 Palermo, Italy
| | - Giampaolo Barone
- Dipartimento
di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche, Università degli Studi di Palermo, Viale delle Scienze Ed. 17, 90128 Palermo, Italy
- Istituto EuroMediterraneo
di Scienza e Tecnologia (IEMEST), Via
Emerico Amari 123, 90139 Palermo, Italy
| | - Andrea Pace
- Dipartimento
di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche, Università degli Studi di Palermo, Viale delle Scienze Ed. 17, 90128 Palermo, Italy
- Istituto EuroMediterraneo
di Scienza e Tecnologia (IEMEST), Via
Emerico Amari 123, 90139 Palermo, Italy
| | - Antonio Palumbo Piccionello
- Dipartimento
di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche, Università degli Studi di Palermo, Viale delle Scienze Ed. 17, 90128 Palermo, Italy
| | - Ivana Pibiri
- Dipartimento
di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche, Università degli Studi di Palermo, Viale delle Scienze Ed. 17, 90128 Palermo, Italy
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27
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Terenzi A, Bonsignore R, Spinello A, Gentile C, Martorana A, Ducani C, Högberg B, Almerico AM, Lauria A, Barone G. Selective G-quadruplex stabilizers: Schiff-base metal complexes with anticancer activity. RSC Adv 2014. [DOI: 10.1039/c4ra05355a] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Molecular dynamics simulations and quantum mechanics/molecular mechanics calculations provided a mechanism for G-quadruplex binding of three transition metal complexes.
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Affiliation(s)
- Alessio Terenzi
- Dipartimento di Scienze e Tecnologie Biologiche
- 90128 Palermo, Italy
| | | | - Angelo Spinello
- Dipartimento di Scienze e Tecnologie Biologiche
- 90128 Palermo, Italy
| | - Carla Gentile
- Dipartimento di Scienze e Tecnologie Biologiche
- 90128 Palermo, Italy
| | | | - Cosimo Ducani
- Swedish Medical Nanoscience Center
- Department of Neuroscience
- Karolinska Institutet
- Stockholm, Sweden
| | - Björn Högberg
- Swedish Medical Nanoscience Center
- Department of Neuroscience
- Karolinska Institutet
- Stockholm, Sweden
| | | | - Antonino Lauria
- Dipartimento di Scienze e Tecnologie Biologiche
- 90128 Palermo, Italy
| | - Giampaolo Barone
- Dipartimento di Scienze e Tecnologie Biologiche
- 90128 Palermo, Italy
- Istituto EuroMediterraneo di Scienza e Tecnologia
- 90139 Palermo, Italy
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28
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Lauria A, Bonsignore R, Terenzi A, Spinello A, Giannici F, Longo A, Almerico AM, Barone G. Nickel(ii), copper(ii) and zinc(ii) metallo-intercalators: structural details of the DNA-binding by a combined experimental and computational investigation. Dalton Trans 2014; 43:6108-19. [DOI: 10.1039/c3dt53066c] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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29
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Barone G, Fonseca Guerra C, Bickelhaupt FM. B-DNA Structure and Stability as Function of Nucleic Acid Composition: Dispersion-Corrected DFT Study of Dinucleoside Monophosphate Single and Double Strands. ChemistryOpen 2013; 2:186-93. [PMID: 24551565 PMCID: PMC3892189 DOI: 10.1002/open.201300019] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2013] [Indexed: 11/16/2022] Open
Abstract
We have computationally investigated the structure and stability of all 16 combinations of two out of the four natural DNA bases A, T, G and C in a di-2′-deoxyribonucleoside-monophosphate model DNA strand as well as in 10 double-strand model complexes thereof, using dispersion-corrected density functional theory (DFT-D). Optimized geometries with B-DNA conformation were obtained through the inclusion of implicit water solvent and, in the DNA models, of sodium counterions, to neutralize the negative charge of the phosphate groups. The results obtained allowed us to compare the relative stability of isomeric single and double strands. Moreover, the energy of the Watson–Crick pairing of complementary single strands to form double-helical structures was calculated. The latter furnished the following increasing stability trend of the double-helix formation energy: d(TpA)2 <d(CpA)2 <d(ApT)2 <d(ApA)2 <d(GpT)2 <d(GpA)2 <d(ApG)2 <d(CpG)2 <d(GpG)2 <d(GpC)2, where the energy differences between the last four dimers, d(ApG)2, d(CpG)2, d(GpG)2 and d(GpC)2, is within 4.0 kcal mol−1, and the energy between the most and the least stable isomers is 13.4 kcal mol−1. This trend shows that the formation energy essentially increases with the number of hydrogen bonds per base pair, that is two between A and T and three between G and C. Superimposed on this main trend are more subtle effects that depend on the order in which bases occur within a strand from the 5’- to the 3’-end.
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Affiliation(s)
- Giampaolo Barone
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche, Università di Palermo Viale delle Scienze, Edificio 17, 90128, Palermo (Italy) E-mail:
| | - Célia Fonseca Guerra
- Department of Theoretical Chemistry and Amsterdam Center for Multiscale Modeling, VU University De Boelelaan 1083, 1081 HV Amsterdam (The Netherlands) E-mail:
| | - F Matthias Bickelhaupt
- Department of Theoretical Chemistry and Amsterdam Center for Multiscale Modeling, VU University De Boelelaan 1083, 1081 HV Amsterdam (The Netherlands) E-mail: ; Institute for Molecules and Materials, Radboud University Nijmegen Heyendaalseweg 135, 6525 AJ Nijmegen (The Netherlands)
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