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Woźniczka M, Sutradhar M, Chmiela M, Gonciarz W, Pająk M. Equilibria in the aqueous system of cobalt(II) based on 2-picolinehydroxamic acid and N-(2-hydroxybenzyl)phenylalanine and its ability to inhibit the propagation of cancer cells. J Inorg Biochem 2023; 249:112389. [PMID: 37806005 DOI: 10.1016/j.jinorgbio.2023.112389] [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: 08/03/2023] [Revised: 09/15/2023] [Accepted: 09/25/2023] [Indexed: 10/10/2023]
Abstract
Mixed-ligand complexes of cobalt(II) with two bioligands, viz. 2-picolinehydroxamic acid and the reduced Schiff base N-(2-hydroxybenzyl)phenylalanine, were studied in aqueous solution by potentiometry and UV-Vis spectroscopic analysis. The coordination mode of the complexes and their stability were determined and compared to their parent species. Stacking interactions between the rings present in the ligands influence the stability of the complexes. Also, UV-Vis spectroscopy revealed that the stacking interactions affected the intercalation of DNA and mixed-ligand complexes. The in vitro anticancer activity of the free ligand 2-picolinehydroxamic acid and the complexes was tested against cervical and gastric human adenocarcinoma epithelial cell lines. At concentrations of 0.06 and 0.11 mM, the mixed-ligand structures showed the ability to reduce gastric cancer cells with no inhibitory effect on mouse fibroblasts. The cytotoxic effect was accompanied by damage to the cell nuclei, which may confirm that the complexes demonstrate effective binding to DNA. No determination of minimal inhibitory and bactericidal/fungicidal concentrations against the test organisms was possible at higher complex concentrations due to precipitation.
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Affiliation(s)
- Magdalena Woźniczka
- Department of Physical and Biocoordination Chemistry, Faculty of Pharmacy, Medical University of Lodz, Muszyńskiego 1, 90-151 Lodz, Poland.
| | - Manas Sutradhar
- Faculdade de Engenharia, Universidade Lusófona - Centro Universitário de Lisboa, Campo Grande 376, Lisboa 1749-024, Portugal; Centro de Química Estrutural, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal
| | - Magdalena Chmiela
- Department of Immunology and Infectious Biology, Institute of Microbiology, Biotechnology and Immunology, Faculty of Biology and Environmental Protection, University of Lodz, Banacha 12/16, 90-237 Lodz, Poland
| | - Weronika Gonciarz
- Department of Immunology and Infectious Biology, Institute of Microbiology, Biotechnology and Immunology, Faculty of Biology and Environmental Protection, University of Lodz, Banacha 12/16, 90-237 Lodz, Poland
| | - Marek Pająk
- Department of Physical and Biocoordination Chemistry, Faculty of Pharmacy, Medical University of Lodz, Muszyńskiego 1, 90-151 Lodz, Poland
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2
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Deepa P, Thirumeignanam D. Understanding the impact of halogen functional group (Br, Cl, F, OH) in amprenavir ligand of the HIV protease. J Biomol Struct Dyn 2023; 41:12157-12170. [PMID: 36645135 DOI: 10.1080/07391102.2023.2166121] [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: 03/22/2022] [Accepted: 01/01/2023] [Indexed: 01/17/2023]
Abstract
We focused our attention towards the most dreadful disease that threatens the mankind of 20th century - Acquired immunodeficiency syndrome (AIDS), caused through the human immunodeficiency virus (HIV) and a sexually transmitted infection (STI). In this study, our foremost interest was to identify the potency and stability of HIV ligand- Amprenavir (APV) and its modelled functional group (Br, Cl, F, CF3, CH3, NH2) ligands through halogen and hydrogen bond contact, which will have a clear portrait on the structure activity of protein ligand interactions. This will assist chemist in synthesizing novel APV ligands, which are expected to inhibit the activity of HIV-1 protease enzyme. The binding strength of Amprenavir ligand with interacting hinge region amino acid side chains: Isoleucine (ILE 147, 150, 184), Valine (VAL 82), Alanine (ALA 28), Aspartic acid (25, 30, 125, 130) and Glycine (GLY 127, 149) were understood through interaction energy calculations at HF, B3LYP, M052X, MP2 level of theories for different basis set (6-311 G**, LANL2DZ). The present work will reveal an understandable picture about the halogen and hydrogen bond interaction that grip the contact of ligand and amino acids in the hinge region. Overall the Halogen atom (Br, Cl, F) functional groups improved the binding strength of APV in HIV protease; which provide a new novel path for the functional group preference on the ligand that enclose perfectly with the amino acid in the hinge region.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Palanisamy Deepa
- Department of Physics, Manonmaniam Sundaranar University, Tirunelveli, India
| | - Duraisamy Thirumeignanam
- Department of Animal Nutrition, Veterinary College and Research Institute, Tamil Nadu Veterinary and Animal Sciences University, Tirunelveli, India
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3
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Alirezapour F, Bamdad K, Khanmohammadi A, Ebrahimi N. A computational study on acetaminophen drug complexed with Mn +, Fe 2+, Co +, Ni 2+, and Cu + ions: structural analysis, electronic properties, and solvent effects. J Mol Model 2022; 28:302. [PMID: 36066774 DOI: 10.1007/s00894-022-05305-6] [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: 07/03/2022] [Accepted: 08/30/2022] [Indexed: 11/24/2022]
Abstract
In the present research, the cation-π interactions in acetaminophen-M complexes (M = Mn+, Fe2+, Co+, Ni2+, and Cu+) are investigated using density functional theory (DFT/ωB97XD) in the gas phase and solution. The results show that the absolute values of energy are reduced in going from the gas phase to the solution. Based on the obtained data, the complexes in water are the most stable. The natural bond orbital (NBO) and the atoms in molecules (AIM) analyses are also applied to achieve more details about the nature of interactions. These results are useful for understanding the role of the drug-receptor interactions in the complexes. According to AIM outcomes, the cation-π interactions are the closed-shell and may indicate the partially covalent nature in the complexes. A comprehensive analysis is also performed on the conceptual DFT parameters of the complexes to evaluate their electronic properties. Our findings show increasing the stability and decreasing the reactivity of the complexes in the solution phase with respect to the gas phase. These interactions are ubiquitous in biological systems, and their importance in theoretical models led us to study such important interactions. The results of this study may be useful for the design and synthesis of a variety of supramolecular complexes with the desired properties.
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Affiliation(s)
- Fahimeh Alirezapour
- Department of Chemistry, Payame Noor University (PNU), P.O. Box 19395-4697, Tehran, Iran.
| | - Kourosh Bamdad
- Department of Chemistry, Payame Noor University (PNU), P.O. Box 19395-4697, Tehran, Iran
| | - Azadeh Khanmohammadi
- Department of Chemistry, Payame Noor University (PNU), P.O. Box 19395-4697, Tehran, Iran
| | - Narjes Ebrahimi
- Department of Chemistry, Payame Noor University (PNU), P.O. Box 19395-4697, Tehran, Iran
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4
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Sánchez-González Á, Grenut P, Gil A. Influence of conventional hydrogen bonds in the intercalation of phenanthroline derivatives with DNA: The important role of the sugar and phosphate backbone. J Comput Chem 2022; 43:804-821. [PMID: 35297513 PMCID: PMC9313584 DOI: 10.1002/jcc.26836] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 02/28/2022] [Indexed: 12/14/2022]
Abstract
The influence of hydrogen bonds in model intercalated systems between guanine‐cytosine and adenine‐thymine DNA base pairs (bps) was analyzed with the popular intercalator 1,10‐phenanthroline (phen) and derivatives obtained by substitution with —OH and —NH2 groups in positions 4 and 7. Semiempirical and Density Functional Theory (DFT) methods were used both including dispersion effects: PM6‐DH2, M06‐2X and B3LYP‐D3 along with the recently developed near linear‐scaling coupled cluster method DLPNO‐CCSD(T) for benchmark calculations. Our results given by QTAIM and non‐covalent interaction analysis confirmed the existence of hydrogen bonds created by —OH and —NH2. The trends in the energy decomposition analysis for the interaction energy, ΔEint, showed that the ΔEelstat contributions are equal or even a little bit higher than the values for ΔEdisp. Such important ΔEelstat attractive contribution comes mainly from the conventional hydrogen bonds formed by —OH and —NH2 functional groups with DNA not only with bps but specially with the sugar and phosphate backbone. This behavior is very different from that of phen and other classical intercalators that cannot form conventional hydrogen bonds, where the ΔEdisp is the most important attractive contribution to the ΔEint. The inclusion of explicit water molecules in molecular dynamics simulations showed, as a general trend, that the hydrogen bonds with the bps disappear during the simulations but those with the sugar and phosphate backbone remain in time, which highlights the important role of the sugar and phosphate backbone in the stabilization of these systems.
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Affiliation(s)
- Ángel Sánchez-González
- BioISI-Biosystems and Integrative Sciences Institute, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, Lisbon, Portugal
| | - Pierre Grenut
- BioISI-Biosystems and Integrative Sciences Institute, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, Lisbon, Portugal
| | - Adrià Gil
- BioISI-Biosystems and Integrative Sciences Institute, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, Lisbon, Portugal.,ARAID Foundation, Zaragoza, Spain.,Departamento de Química Inorgánica, Instituto de Síntesis Química y Catálisis Homogénea (ISQCH) CSIC-Universidad de Zaragoza, c/ Pedro Cerbuna 12, Zaragoza, Spain
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5
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Sánchez-González Á, Bandeira NAG, Ortiz de Luzuriaga I, Martins FF, Elleuchi S, Jarraya K, Lanuza J, Lopez X, Calhorda MJ, Gil A. New Insights on the Interaction of Phenanthroline Based Ligands and Metal Complexes and Polyoxometalates with Duplex DNA and G-Quadruplexes. Molecules 2021; 26:4737. [PMID: 34443326 PMCID: PMC8397986 DOI: 10.3390/molecules26164737] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 07/28/2021] [Accepted: 07/29/2021] [Indexed: 12/24/2022] Open
Abstract
This work provides new insights from our team regarding advances in targeting canonical and non-canonical nucleic acid structures. This modality of medical treatment is used as a form of molecular medicine specifically against the growth of cancer cells. Nevertheless, because of increasing concerns about bacterial antibiotic resistance, this medical strategy is also being explored in this field. Up to three strategies for the use of DNA as target have been studied in our research lines during the last few years: (1) the intercalation of phenanthroline derivatives with duplex DNA; (2) the interaction of metal complexes containing phenanthroline with G-quadruplexes; and (3) the activity of Mo polyoxometalates and other Mo-oxo species as artificial phosphoesterases to catalyze the hydrolysis of phosphoester bonds in DNA. We demonstrate some promising computational results concerning the favorable interaction of these small molecules with DNA that could correspond to cytotoxic effects against tumoral cells and microorganisms. Therefore, our results open the door for the pharmaceutical and medical applications of the compounds we propose.
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Affiliation(s)
- Ángel Sánchez-González
- Faculdade de Ciências, BioISI-Biosystems and Integrative Sciences Institute, Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal; (Á.S.-G.); (N.A.G.B.); (F.F.M.); (M.J.C.)
| | - Nuno A. G. Bandeira
- Faculdade de Ciências, BioISI-Biosystems and Integrative Sciences Institute, Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal; (Á.S.-G.); (N.A.G.B.); (F.F.M.); (M.J.C.)
| | - Iker Ortiz de Luzuriaga
- CIC nanoGUNE BRTA, Tolosa Hiribidea 76, Euskadi, 20018 Donostia-San Sebastián, Spain;
- Polimero eta Material Aurreratuak, Fisika, Kimika eta Teknologia Saila, Kimika Fakultatea, Euskal Herriko Unibertsitatea (UPV/EHU), Paseo Manuel de Lardizabal 3, 20018 Donostia-San Sebastián, Spain; (J.L.); (X.L.)
| | - Frederico F. Martins
- Faculdade de Ciências, BioISI-Biosystems and Integrative Sciences Institute, Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal; (Á.S.-G.); (N.A.G.B.); (F.F.M.); (M.J.C.)
| | - Sawssen Elleuchi
- Laboratoire de Chimie Inorganique, LR17ES07, Faculté de Sciences de Sfax, Université de Sfax, Sfax 3000, Tunisia; (S.E.); (K.J.)
| | - Khaled Jarraya
- Laboratoire de Chimie Inorganique, LR17ES07, Faculté de Sciences de Sfax, Université de Sfax, Sfax 3000, Tunisia; (S.E.); (K.J.)
| | - Jose Lanuza
- Polimero eta Material Aurreratuak, Fisika, Kimika eta Teknologia Saila, Kimika Fakultatea, Euskal Herriko Unibertsitatea (UPV/EHU), Paseo Manuel de Lardizabal 3, 20018 Donostia-San Sebastián, Spain; (J.L.); (X.L.)
- Donostia International Physics Center (DIPC), Paseo Manuel de Lardizabal 4, 20018 Donostia-San Sebastián, Spain
| | - Xabier Lopez
- Polimero eta Material Aurreratuak, Fisika, Kimika eta Teknologia Saila, Kimika Fakultatea, Euskal Herriko Unibertsitatea (UPV/EHU), Paseo Manuel de Lardizabal 3, 20018 Donostia-San Sebastián, Spain; (J.L.); (X.L.)
- Donostia International Physics Center (DIPC), Paseo Manuel de Lardizabal 4, 20018 Donostia-San Sebastián, Spain
| | - Maria José Calhorda
- Faculdade de Ciências, BioISI-Biosystems and Integrative Sciences Institute, Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal; (Á.S.-G.); (N.A.G.B.); (F.F.M.); (M.J.C.)
| | - Adrià Gil
- Faculdade de Ciências, BioISI-Biosystems and Integrative Sciences Institute, Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal; (Á.S.-G.); (N.A.G.B.); (F.F.M.); (M.J.C.)
- CIC nanoGUNE BRTA, Tolosa Hiribidea 76, Euskadi, 20018 Donostia-San Sebastián, Spain;
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6
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Alirezapour F, Khanmohammadi A. Theoretical study on the interaction of phenylalaninal with group
IA
(Li
+
, Na
+
, K
+
) and
IIA
(Be
2+
, Mg
2+
, Ca
2+
) metal cations. J CHIN CHEM SOC-TAIP 2021. [DOI: 10.1002/jccs.202000383] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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7
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Alirezapour F, Khanmohammadi A. The effect of cation-π interactions on the stability and electronic properties of anticancer drug Altretamine: a theoretical study. Acta Crystallogr C Struct Chem 2020; 76:982-991. [PMID: 33016269 DOI: 10.1107/s2053229620012589] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Accepted: 09/15/2020] [Indexed: 11/10/2022] Open
Abstract
The present work utilizes density functional theory (DFT) calculations to study the influence of cation-π interactions on the electronic properties of the complexes formed by Altretamine [2,4,6-tris(dimethylamino)-1,3,5-triazine], an anticancer drug, with mono- and divalent (Li+, Na+, K+, Be2+, Mg2+ and Ca2+) metal cations. The structures were optimized with the M06-2X method and the 6-311++G(d,p) basis set in the gas phase and in solution. The theory of `Atoms in Molecules' (AIM) was applied to study the nature of the interactions by calculating the electron density ρ(r) and its Laplacian at the bond critical points. The charge-transfer process during complexation was evaluated using natural bond orbital (NBO) analysis. The results of DFT calculations demonstrate that the strongest/weakest interactions belong to Be2+/K+ complexes. There are good correlations between the achieved densities and the amounts of charge transfer with the interaction energies. Finally, the stability and reactivity of the cation-π interactions can be determined by quantum chemical computation based on the molecular orbital (MO) theory.
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Affiliation(s)
- Fahimeh Alirezapour
- Department of Chemistry, Payame Noor University, PO Box 19395-3697 Tehran, Iran
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8
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Thomaz DV, de Oliveira MG, Rodrigues ESB, da Silva VB, dos Santos PA. Physicochemical Investigation of Psoralen Binding to Double Stranded DNA through Electroanalytical and Cheminformatic Approaches. Pharmaceuticals (Basel) 2020; 13:ph13060108. [PMID: 32481669 PMCID: PMC7344847 DOI: 10.3390/ph13060108] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 05/13/2020] [Accepted: 05/24/2020] [Indexed: 02/05/2023] Open
Abstract
This work showcased the first physicochemical investigation of psoralen (PSO) binding to double stranded DNA (dsDNA) through electroanalytical methods. Results evidenced that PSO presents one non-reversible anodic peak at electric potential (Epa) ≈ 1.42 V, which is associated with its oxidation and the formation of an epoxide derivative. Moreover, PSO analytical signal (i.e., faradaic current) decreases linearly with the addition of dsDNA, while the electric potential associated to PSO oxidation shifts towards more positive values, indicating thence that dsDNA addition hinders PSO oxidation. These findings were corroborated by the chemoinformatic study, which evidenced that PSO intercalated noncovalently at first between base-pairs of the DNA duplex, and then irreversibly formed adducts with both DNA strands, leading up to the formation of a cross-link which bridges the DNA helix, which explains the linear dependence between the faradaic current generated by PSO oxidation and the concentration of DNA in the test-solution, as well as the dependence between Ep and the addition of dsDNA solution. Therefore, the findings herein reported evidence of the applicability of electroanalytical approaches, such as voltammetry in the study of DNA intercalating agents.
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Affiliation(s)
- Douglas Vieira Thomaz
- Faculty of Pharmacy, Federal University of Goias, Goiania-GO 74605-170, Brazil; (M.G.d.O.); (E.S.B.R.)
- Correspondence: (D.V.T.); (P.A.d.S.)
| | | | | | | | - Pierre Alexandre dos Santos
- Faculty of Pharmacy, Federal University of Goias, Goiania-GO 74605-170, Brazil; (M.G.d.O.); (E.S.B.R.)
- Correspondence: (D.V.T.); (P.A.d.S.)
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9
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Understanding the potency of malarial ligand (D44) in plasmodium FKBP35 and modelled halogen atom (Br, Cl, F) functional groups. J Mol Graph Model 2020; 97:107553. [PMID: 32035313 DOI: 10.1016/j.jmgm.2020.107553] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 01/10/2020] [Accepted: 01/27/2020] [Indexed: 11/21/2022]
Abstract
The present study clearly depicts the understanding of the D44 in Plasmodium FKBP35 around the hinge region. To analyse the binding stability of D44 ligand and to understand the role of halogen bond, hydrogen bond interaction formed between the hinge region amino acids: Isoleucine (Ile74), Phenylalanine (Phe54), Aspartic acid (Asp55) Phenylalanine (Phe64),Tyrosine (Tyr100), Tryptophan (TRP 77) and ligand D44 was portrayed specifically through interaction energy calculations at HF, M062X, MP2 level of theories for different basis set (6-311G**, 6-31+G*, LANL2DZ). The investigation will provide an apparent picture regarding the non-covalent interaction that hold the contact of ligand and amino acids in the hinge region and the implication of modelled functional groups (Br, Cl, F, OSO and NH2) on ligand, which will help chemist in synthesizing new novel ligands. HOMO, LUMO chart calculated for D44 ligands reveals graphic illustration of orbital's that stimulate for contact. The aim and natural bond orbital analysis identified key contribution of individual hydrogen/halogen bonds that contribute for the binding strength through stabilization energy, ρ and ∇2ρ values. Overall this study finds out that the Stability of D44 in Plasmodium FKBP35 was enhanced by the Halogen atom (Br, Cl, F) functional groups; which provide an innovative pathway for the selection of functional groups that opt for the hinge region side chains on the ligand.
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10
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Hrivnák T, Budzák Š, Reis H, Zaleśny R, Carbonnière P, Medveď M. Electric properties of hydrated uracil: From micro- to macrohydration. J Mol Liq 2019. [DOI: 10.1016/j.molliq.2018.11.044] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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11
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Deepa P, Thirumeignanam D, Kolandaivel P. An overview about the impact of hinge region towards the anticancer binding affinity of the Ck2 ligands: a quantum chemical analysis. J Biomol Struct Dyn 2018; 37:3859-3876. [DOI: 10.1080/07391102.2018.1533498] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- P. Deepa
- Department of Physics, Manonmaniam Sundaranar University, Tirunelveli, Tamil Nadu, India
| | - D. Thirumeignanam
- Department of Animal Nutrition, Veterinary College and Research Institute, Tirunelveli, Tamil Nadu, India
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12
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Palanisamy D, Pandiyan BV, Duraisamy T, Kolandaivel P. Understanding the potency of fatty acids with the amino acid side chains of bovine β lactoglobulin—A quantum chemical approach. J Mol Graph Model 2017; 74:105-116. [DOI: 10.1016/j.jmgm.2017.03.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2016] [Revised: 03/11/2017] [Accepted: 03/15/2017] [Indexed: 10/19/2022]
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13
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Galliot A, Gil A, Calhorda MJ. Effects of oxygenation on the intercalation of 1,10-phenanthroline-5,6/4,7-dione between DNA base pairs: a computational study. Phys Chem Chem Phys 2017. [PMID: 28621352 DOI: 10.1039/c7cp00532f] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The effects of oxygen in positions 4,7 and 5,6 of phenanthroline have been studied computationally when this ligand intercalates between DNA base pairs. Our results indicate that solvation energy could be the driving force of the process and thus, it can be also related with the cytotoxicity of the drug.
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Affiliation(s)
- Aurellia Galliot
- Centro de Química e Bioquímica
- DQB
- Faculdade de Ciências
- Universidade de Lisboa
- Campo Grande 1749-016 Lisboa
| | - Adrià Gil
- Centro de Química e Bioquímica
- DQB
- Faculdade de Ciências
- Universidade de Lisboa
- Campo Grande 1749-016 Lisboa
| | - Maria José Calhorda
- Centro de Química e Bioquímica
- DQB
- Faculdade de Ciências
- Universidade de Lisboa
- Campo Grande 1749-016 Lisboa
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14
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Salehzadeh S, Maleki F. New equation for calculating total interaction energy in one noncyclic ABC triad and new insights into cooperativity of noncovalent bonds. J Comput Chem 2016; 37:2799-2807. [PMID: 27753119 DOI: 10.1002/jcc.24505] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Revised: 09/02/2016] [Accepted: 09/07/2016] [Indexed: 11/10/2022]
Abstract
In this work, a new equation consist of A⋅⋅⋅B, B⋅⋅⋅C, A⋅⋅⋅BC, and AB⋅⋅⋅C interactions is proposed for calculating the total interaction energy of noncyclic ABC triads. New equations are also proposed for calculating the changes in values of A⋅⋅⋅B and B⋅⋅⋅C interactions on the formation of triad from the corresponding dyads. The advantages of equations proposed here in comparison with many-body interaction energy approach are discussed. All proposed equations were tested in F3 MLi⋅⋅⋅NCH⋅⋅⋅HLH and F3 MLi⋅⋅⋅HLH⋅⋅⋅HCN (M = C, Si; L = Be, Mg) as well as H3 N⋅⋅⋅XY⋅⋅⋅HF (X, Y = F, Cl, Br) noncyclic A⋅⋅⋅B⋅⋅⋅C triads. The data show that the total cooperativity of triad correlates well with the sum of the changes in values of A⋅⋅⋅B and B⋅⋅⋅C interactions calculated through new equations proposed here. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
| | - Farahnaz Maleki
- Department of Chemistry, Bu-Ali Sina University, Hamedan, Iran
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15
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Gil A, Branchadell V, Calhorda MJ. A theoretical study of methylation and CH/π interactions in DNA intercalation: methylated 1,10-phenanthroline in adenine–thymine base pairs. RSC Adv 2016. [DOI: 10.1039/c6ra15495f] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
This work shows that quality is better that quantity to estabilize the intercalation of methylated phen.
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Affiliation(s)
- A. Gil
- Centro de Química e Bioquímica
- Faculdade de Ciências
- Universidade de Lisboa
- 1749-016 Lisboa
- Portugal
| | - V. Branchadell
- Departament de Química
- Universitat Autònoma de Barcelona
- Barcelona
- Spain
| | - M. J. Calhorda
- Centro de Química e Bioquímica
- Faculdade de Ciências
- Universidade de Lisboa
- 1749-016 Lisboa
- Portugal
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16
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Gil A, Melle-Franco M, Branchadell V, Calhorda MJ. How the Intercalation of Phenanthroline Affects the Structure, Energetics, and Bond Properties of DNA Base Pairs: Theoretical Study Applied to Adenine–Thymine and Guanine–Cytosine Tetramers. J Chem Theory Comput 2015; 11:2714-28. [DOI: 10.1021/ct5006104] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Adrià Gil
- Centro
de Química e Bioquímica, DQB, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal
| | | | - Vicenç Branchadell
- Departament
de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
| | - Maria José Calhorda
- Centro
de Química e Bioquímica, DQB, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal
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17
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Hokmabady L, Raissi H, Khanmohammadi A. Interactions of the 5-fluorouracil anticancer drug with DNA pyrimidine bases: a detailed computational approach. Struct Chem 2015. [DOI: 10.1007/s11224-015-0578-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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18
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Wang L, Tao M, Zhang G, Li S, Gong D. Partial intercalative binding of the food colorant erythrosine to herring sperm DNA. RSC Adv 2015. [DOI: 10.1039/c5ra19626d] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Erythrosine partially inserts into the G–C rich region of hsDNA and induces moderate conformational perturbation of the DNA.
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Affiliation(s)
- Langhong Wang
- State Key Laboratory of Food Science and Technology
- Nanchang University
- Nanchang 330047
- China
| | - Mo Tao
- State Key Laboratory of Food Science and Technology
- Nanchang University
- Nanchang 330047
- China
| | - Guowen Zhang
- State Key Laboratory of Food Science and Technology
- Nanchang University
- Nanchang 330047
- China
| | - Song Li
- State Key Laboratory of Food Science and Technology
- Nanchang University
- Nanchang 330047
- China
| | - Deming Gong
- School of Biological Sciences
- The University of Auckland
- Auckland 1142
- New Zealand
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19
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Azadbakht A, Gholivand MB. polyethyleneimine wrapped carbon nanotubes in situ formed gold nanoparticles decorated with DNA and NAD+ as a novel bioeletrochemical sensing platform. Electrochim Acta 2014. [DOI: 10.1016/j.electacta.2014.04.046] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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20
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Zhou X, Zhang G, Wang L. Probing the binding mode of psoralen to calf thymus DNA. Int J Biol Macromol 2014; 67:228-37. [DOI: 10.1016/j.ijbiomac.2014.03.038] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2014] [Revised: 03/13/2014] [Accepted: 03/14/2014] [Indexed: 01/31/2023]
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21
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Mirmoghtadaie L, Ensafi AA, Kadivar M, Norouzi P. Highly selective electrochemical biosensor for the determination of folic acid based on DNA modified-pencil graphite electrode using response surface methodology. MATERIALS SCIENCE & ENGINEERING. C, MATERIALS FOR BIOLOGICAL APPLICATIONS 2013; 33:1753-8. [PMID: 23827633 DOI: 10.1016/j.msec.2012.12.090] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2012] [Revised: 11/21/2012] [Accepted: 12/28/2012] [Indexed: 11/30/2022]
Abstract
An electrochemical DNA biosensor was proposed as a screening device for the rapid analysis of folic acid using a pencil graphite electrode modified with salmon sperm ds-DNA. At first, immobilization of the ds-DNA on pencil graphite electrode was optimized using response surface methodology. Solution pH, DNA concentration, time of DNA deposition and potential of deposition was optimized each at three levels. The optimum combinations for the reaction were pH 4.8, DNA concentration of 24 μg mL(-1), deposition time of 304 s, and deposition potential of 0.60 V, by which the adenine signal was recorded as 3.04 μA. Secondly the binding of folic acid to DNA immobilized on a pencil graphite electrode was measured through the variation of the electrochemical signal of adenine. Folic acid could be measure in the range of 0.1-10.0 μmol L(-1) with a detection limit of 1.06×10(-8) μmol L(-1). The relative standard deviations for ten replicate differential pulse voltammetric measurements of 2.0 and 5.0 μmol L(-1) folic acid were 4.6% and 4.3%, respectively. The biosensor was successfully used to measure folic acid in different real samples.
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Affiliation(s)
- Leila Mirmoghtadaie
- Department of Food Science and Technology, College of agriculture, Isfahan University of Technology, Isfahan 84156-83111, Iran
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22
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