Journal articles: 'Ligand-DNA adducts'

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Astarina, Astrid, Mun Juinn Chow, and Wee Han Ang. "Transcription Inhibition by Organometallic Ruthenium - Arene Anticancer Complexes in Live Mammalian Cells." Australian Journal of Chemistry 65, no. 9 (2012): 1271. http://dx.doi.org/10.1071/ch12059.

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Organometallic ruthenium–arene RAPTA complexes, currently being actively pursued as potential anticancer agents, interact with intracellular biological targets to form covalent adducts. Because their mode of action is still unclear, we investigated their binding with DNA and the ability of ruthenated-DNA adducts to elicit cellular responses such as transcription inhibition and repair. To investigate the influence of the spectator arene ligands on RAPTA activity, a novel RAPTA complex containing the bulky 1,3,5-triisopropylbenzene ligand was synthesized and characterized. Transcription experiments carried out in live mammalian cells using ruthenated plasmid probes revealed that increasing steric bulk of the arene ligand did not improve its ability to arrest transcription.

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Gómez-Bosquet, M., V. Moreno, M. Font-Bardía, and X. Solans. "Pd(II) and Pt(II) Complexes of Schiff Thiobases Derived From 2-Carbonylpyridine." Metal-Based Drugs 5, no. 3 (January 1, 1998): 161–70. http://dx.doi.org/10.1155/mbd.1998.161.

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Pd(ll) and Pt(ll) complexes of three series of Schiff thiobases derived from 2- carbonylpyridine have been synthesized and characterized. The crystal structure of the Pt(ll) derivative of methyl-3-(2-pyridylmethylene)hydrazinecarbodithioate (HFp) was resolved. The ligand coordinates the platinum ion in tridentate fashion by heterocycle and imine nitrogen and thiocarbonyl sulfur. The fourth ligand is a chloride ion. The structure of the complexes is suitable for the formation of monofunctional adducts with DNA. Studies on the interaction of the complexes with Calf thymus DNA by CD reveal modifications in the B form of lineal DNA. Interaction with plasmid DNA was also confirmed in the images obtained by atomic force microscopy.

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Babu, Surendra, Pitchika Krishna, Hussain Reddy, and G. H. Philip. "Synthesis, characterization and DNA cleavage activity of nickel(II) adducts with aromatic heterocyclic bases." Journal of the Serbian Chemical Society 75, no. 1 (2010): 61–74. http://dx.doi.org/10.2298/jsc1001061b.

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Mixed ligand complexes of nickel(II) with 2,4-dihydroxyacetophenone oxime (DAPO) and 2,4-dihydroxybenzophenone oxime (DBPO) as primary ligands, and pyridine (Py) and imidazole (Im) as secondary ligands were synthesized and characterized by molar conductivity, magnetic moments measurements, as well as by electronic, IR, and 1H-NMR spectroscopy. Electrochemical studies were performed by cyclic voltammetry. The active signals are assignable to the NiIII/II and NiII/I redox couples. The binding interactions between the metal complexes and calf thymus DNA were investigated by absorption and thermal denaturation. The cleavage activity of the complexes was determined using double-stranded pBR322 circular plasmid DNA by gel electrophoresis. All complexes showed increased nuclease activity in the presence of the oxidant H2O2. The nuclease activities of mixed ligand complexes were compared with those of the parent copper(II) complexes.

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Caron, Coralie, Xuan N. T. Duong, Régis Guillot, Sophie Bombard, and Anton Granzhan. "Interaction of Functionalized Naphthalenophanes with Abasic Sites in DNA: DNA Cleavage, DNA Cleavage Inhibition, and Formation of Ligand–DNA Adducts." Chemistry – A European Journal 25, no. 8 (January 16, 2019): 1949–62. http://dx.doi.org/10.1002/chem.201805555.

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Suzuki, Yasuhito, Hulin Tai, Kaori Saito, Tomokazu Shibata, Masashi Kinoshita, Akihiro Suzuki, and Yasuhiko Yamamoto. "Structural characterization of imidazole adducts of heme-DNA complexes." Journal of Porphyrins and Phthalocyanines 18, no. 08n09 (August 2014): 741–51. http://dx.doi.org/10.1142/s1088424614500515.

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Ternary complexes composed of protoheme (heme( Fe 3+)) or 13,17-bis(2-carboxylatoethyl)-3,7-diethyl-12,18-trimethyl-2,8-ditrifluoromethylporphyrinatoiron(III) (2,8-DPF( Fe 3+)), a parallel G-quadruplex DNA formed from a single repeat sequence of the human telomere, d(TTAGGG), and imidazole (Im), in a ratio of 1:1:1, were prepared and their structures were characterized using optical, circular dichroism, and NMR spectroscopies. The study revealed that heme( Fe 3+) and 2,8-DPF( Fe 3+) stack onto the 3′-terminal G-quartet of the G-quadruplex DNA, ~0.4 nm apart, and that Im is coordinated to the Fe atom on the side of the heme opposite to the G-quartet in the complex. The stacking of the pseudo-C2 symmetric heme( Fe 3+) onto the C4 symmetric G-quartet in the complex resulted in the formation of two isomers with heme orientations differing by 180° about the pseudo-C2 axis, with respect to the DNA. The Im affinity of the 2,8-DPF( Fe 3+)-DNA complex was higher by a factor of ~2 than that of the heme( Fe 3+)-DNA one, which is possibly due to the stronger ligand-to-metal π donation in the 2,8-DPF( Fe 3+) as a result of a decrease in the electron density of the heme Fe atom caused by substitution of the two strongly electron-withdrawing trifluoromethyl groups.

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Nishino, Satoshi, Teruyuki Kobayashi, Mami Kunita, Sayo Ito, and Yuzo Nishida. "Structural Variety of Copper(II)-Peroxide Adducts and Its Relevance to DNA Cleavage." Zeitschrift für Naturforschung C 54, no. 1-2 (February 1, 1999): 94–99. http://dx.doi.org/10.1515/znc-1999-1-216.

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The reactivity of copper(II) compounds with several tetradentate ligands towards some spin-trapping reagents was studied in the presence of hydrogen peroxide. The compounds used in this study are roughly divided into two groups based on the reactivity towards 2 ,2 ,6 ,6 -tetramethyl-4-piperidinol(and also 2,2,6,6-tetramethyl-4-piperidone), which are trapping agents for singlet oxygen, 1O2 (1Δg); The A-group compounds exhibited a high activity to form the corresponding nitrone radical, which was detected by ESR spectroscopy, but corresponding activity of the B-group compounds was very low. The A-group compounds defined as above exhibited high activity for cleavage of DNA(supercoiled Form I) in the presence of hydrogen peroxide, yielding DNA Form II (relaxed circular) or Form III (linear duplex) under our experimental conditions ([Cu(II)]=0.1~0.5 mᴍ). On the other hand, the B-group compounds effected complete degradation of the DNA (double-strand scission) under the same experimental conditions, formation of Form II or Form III DNA was negligible. Two different DNA cleavage patterns observed for A-and B-group compounds were elucidated by the different structural property of the copper(II)-peroxide adducts, which is controlled by the interaction through both DNA and the peripheral group of the ligand system

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Vikulova, Evgeniia S., Taisiya S. Sukhikh, Sergey A. Gulyaev, Igor Yu Ilyin, and Natalia B. Morozova. "Structural Diversity of Silver Fluorinated β-Diketonates: Effect of the Terminal Substituent and Solvent." Molecules 27, no. 3 (January 20, 2022): 677. http://dx.doi.org/10.3390/molecules27030677.

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In order to demonstrate the role of the fluorination and some solvents in the structural organization of the Ag(I) coordination polymers with β-diketonate ligands (R1C(O)CαHC(O)R2)− we synthesized a series of the compounds containing tfac- (R1 = CH3, R2 = CF3) and pfpac- (R1 = CH3, R2 = C2F5) anions. Solvent-free [Ag(L)]∞ (L = tfac 1, pfpac 2) compounds and the corresponding acetonitrile and toluene adducts have been characterized by elemental analysis and/or NMR, IR and single-crystal XRD. This series includes five new coordination polymers. Compound 1 is a 3D coordination framework based on Ag–Ochelate/bridge, Ag–Cα bonds, and argentophilic interactions. An increase in the fluorinated group leads to a chain coordination polymer 2 of an unusual structural organization. These chains can be represented as a “DNA-type”, where two intertwined helices based on Ag–Ochelate and Ag–Cα bonds are connected through Ag–Obridge ones. Two structural types of chain coordination polymers, [Ag(tfac)(CH3CN)] and [Ag2(L)2(solvent)], have been revealed for the adducts. The latter structural type differs significantly from the previously studied toluene and acetonitrile adducts of fluorinated Ag(I) β-diketonates of the same stoichiometry. Thermal analysis in helium showed that both 1 and 2 decompose to metallic silver with the compound of pfpac-ligand being slightly more stable.

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Caron, Coralie, Xuan N. T. Duong, Régis Guillot, Sophie Bombard, and Anton Granzhan. "Cover Feature: Interaction of Functionalized Naphthalenophanes with Abasic Sites in DNA: DNA Cleavage, DNA Cleavage Inhibition, and Formation of Ligand–DNA Adducts (Chem. Eur. J. 8/2019)." Chemistry – A European Journal 25, no. 8 (January 17, 2019): 1837. http://dx.doi.org/10.1002/chem.201806037.

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Alsaedi, Sammar, Bandar A. Babgi, Magda H. Abdellattif, Muhammad N. Arshad, Abdul-Hamid M. Emwas, Mariusz Jaremko, Mark G. Humphrey, Abdullah M. Asiri, and Mostafa A. Hussien. "DNA-Binding and Cytotoxicity of Copper(I) Complexes Containing Functionalized Dipyridylphenazine Ligands." Pharmaceutics 13, no. 5 (May 20, 2021): 764. http://dx.doi.org/10.3390/pharmaceutics13050764.

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A set of copper(I) coordination compounds with general formula [CuBr(PPh3)(dppz-R)] (dppz-R = dipyrido[3,2-a:2’,3’-c]phenazine (Cu-1), 11-nitrodipyrido[3,2-a:2’,3’-c]phenazine (Cu-2), 11-cyanodipyrido[3,2-a:2’,3’-c]phenazine (Cu-3), dipyrido[3,2-a:2’,3’-c]phenazine-11-phenone (Cu-4), 11,12-dimethyldipyrido[3,2-a:2’,3’-c]phenazine (Cu-5)) have been prepared and characterized by elemental analysis, 1H-NMR and 31P-NMR spectroscopies as well as mass spectrometry. The structure of Cu-1 was confirmed by X-ray crystallography. The effect of incorporating different functional groups on the dppz ligand on the binding into CT-DNA was evaluated by absorption spectroscopy, fluorescence quenching of EtBr-DNA adducts, and viscosity measurements. The functional groups affected the binding modes and hence the strength of binding affinities, as suggested by the changes in the relative viscosity. The differences in the quenching constants (Ksv) obtained from the fluorescence quenching assay highlight the importance of the functional groups in altering the binding sites on the DNA. The molecular docking data support the DNA-binding studies, with the sites and mode of interactions against B-DNA changing with the different functional groups. Evaluation of the anticancer activities of the five copper compounds against two different cancer cell lines (M-14 and MCF-7) indicated the importance of the functional groups on the dppz ligand on the anticancer activities. Among the five copper complexes, the cyano-containing complex (Cu-3) has the best anticancer activities.

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Colgrave, Michelle L., Paula Iannitti-Tito, Geoffrey Wickham, and Margaret M. Sheil. "Rapid Determination of Sequence Selectivity and Stability of Alkylated Oligonucleotide Adducts by Electrospray Tandem Mass Spectrometry." Australian Journal of Chemistry 56, no. 5 (2003): 401. http://dx.doi.org/10.1071/ch02205.

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The binding of the antitumor antibiotics, duocarmycin C2 (pyrindamycin A), duocarmycin C1 (pyrindamycin B), hedamycin, and DC92-B to self complementary oligonucleotides (ranging from 6 to 14-mers) has been studied using electrospray ionization mass spectrometry (ESI-MS) and tandem mass spectrometry (MS/MS). The duocarmycins bind via non-covalent interactions in the minor groove of DNA with subsequent alkylation of the N3 atom of adenine. Hedamycin and DC92-B are intercalating, alkylating agents that target the N7 of guanines within 5′-CGT, and to a lesser extent, 5′-CGG sequences. We show here that the site(s) of alkylation by these ligands are strongly influenced by the location of high affinity binding sites within these short oligonucleotides. These data clearly demonstrate value of using ESI-MS/MS to pre-screen ligand–oligonucleotide complexes prior to performing more detailed structural studies, since subtle selectivity differences have been detected by this technique that were not evident from conventional sequencing studies on larger segments of DNA.

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Vaisman, Alexandra, Susan E. Lim, Steve M. Patrick, William C. Copeland, David C. Hinkle, John J. Turchi, and Stephen G. Chaney. "Effect of DNA Polymerases and High Mobility Group Protein 1 on the Carrier Ligand Specificity for Translesion Synthesis past Platinum−DNA Adducts†." Biochemistry 38, no. 34 (August 1999): 11026–39. http://dx.doi.org/10.1021/bi9909187.

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Malina, Jaroslav, Marie Vojtiskova, Viktor Brabec, Connie I. Diakos, and Trevor W. Hambley. "DNA adducts of the enantiomers of the Pt(II) complexes of the ahaz ligand (ahaz=3-aminohexahydroazepine) and recognition of these adducts by HMG domain proteins." Biochemical and Biophysical Research Communications 332, no. 4 (July 2005): 1034–41. http://dx.doi.org/10.1016/j.bbrc.2005.05.047.

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Slocik, Joseph M., Richard A. Kortes, and Rex E. Shepherd. "Developing Carrier Complexes for “Caged NO”: RuCl3(NO)(H2O)2 Complexes of Dipyridylamine, (dpaH), N,N,N'N'-Tetrakis (2-Pyridyl) Adipamide, (tpada), and (2-Pyridylmethyl) Iminodiacetate, (pida2-)." Metal-Based Drugs 7, no. 2 (January 1, 2000): 67–75. http://dx.doi.org/10.1155/mbd.2000.67.

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Delivery agents which can carry the {Ru(NO)}6 chromophore (“caged NO”) are desired for vasodilation and for photodynamic therapy of tumors. Toward these goals, complexes derived from [RuCl3(NO)(H2O)2]= (1) have been prepared using dipyridylamine (dpaH) as mono and bis adducts, [Ru(NO)Cl3(dpaH)] = (2) and [Ru(NO)Cl(dpaH)2]Cl2 = (3). The dpaH ligands coordinate cis to the Ru(NO) axis.The mono derivative is a model for a potential DNA groove-spanning binuclear complex {[Ru(NO)Cl3]2(tpada)} = (4) which has two DNA-coordinating RuII centers, photo-labile {Ru(NO)}6 sites, and a groove-spanning tether moiety.The binuclear assembly is prepared from the tethered dipyridylamine ligand N,N,N',N'-tetrakis(2-pyridylmethyl)adipamide (tpada) which has recently been shown to provide a binuclear carrier complex suited to transporting RuII and PdII agents. A related complex, [Ru(NO)Cl(pida)] = (5) with the {Ru(NO)}6 moiety bound to (2-pyridylmethyl) iminodiacetate (pida2-) is also characterized as a potential “caged NO” carrier. Structural information concerning the placement of the pyridyl donor groups relative to the {Ru(NO)}6 unit has been obtained from H1 and C13 NMR and infrared methods, noting that a pyridyl donor trans to NO+ causes “trans strengthening” of this ligand for [Ru(NO)Cl(pida)], whereas placement of pyridyl groups cis to NO+ causes a weakening of the N-O bond and a lower NO stretching frequency in the dpa-based complexes.

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Inagaki, Kenji, Chikako Ninomiya, and Yoshinori Kidani. "INTERACTION OF DNA WITH ANTITUMOR ACTIVE PLATINUM COMPLEXES. PLATINUM COMPLEXES INVOLVING MESO DIAMINE LIGAND GAVE TWO Pt-d(GpG) ADDUCTS." Chemistry Letters 15, no. 2 (February 5, 1986): 233–36. http://dx.doi.org/10.1246/cl.1986.233.

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Galanski, Markus, Susanna Slaby, Michael A. Jakupec, and Bernhard K. Keppler. "Synthesis andin vitroAntitumor Potency of (Cyclohexane-1,2-Diamine)Platinum(II) Complexes with Aminotris(Methylenephosphonic Acid) as Bone-Seeking Ligand." Bioinorganic Chemistry and Applications 3, no. 3-4 (2005): 179–90. http://dx.doi.org/10.1155/bca.2005.179.

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In order to develop platinum complexes with selective activity in primary and secondary bone malignancies and with the aim to optimize antitumor activity, platinum(II) complexes with aminotris(methylenephosphonic acid) as bone-seeking (osteotropic) ligand have been synthesized, characterized and tested in the cisplatin-sensitive ovarian carcinoma cell line CH1. As non-leaving diamine ligands, which are decisive for the cellular processing of DNA adducts,cis-R,S-cyclohexane-1,2-diamine,trans-S,S-cyclohexane-1,2-diamine andtrans-R,R-cyclohexane-1,2-diamine have been used, resulting in complexes 1, 2, and 3, respectively. The cytotoxicity of the complexes under investigation decreases in the order 3>2>1 which is in accord with structure-activity relationships with other (cyclohexane-1,2- diamine)platinum(II) and platinum(IV) complexes: Bothtranscomplexes (2 and 3) display a higherin vitropotency than the correspondingcisisomer (I), with thetrans-R,Risomer (3) being the most active in this series. In comparison to the analogous (cyclohexane-1,2-diamine)platinum(II) complexes with bis(phosphonomethyl)aminoacetic acid as osteotropic carrier ligand, the cytotoxicity of 1-3 was found to be 1.5 – 2 fold higher, which is explainable by a different coordination mode of the phosphonic acid ligands (acetato versus phosphonato).

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Šmidlehner, Tamara, Ivo Piantanida, and Gennaro Pescitelli. "Polarization spectroscopy methods in the determination of interactions of small molecules with nucleic acids – tutorial." Beilstein Journal of Organic Chemistry 14 (January 8, 2018): 84–105. http://dx.doi.org/10.3762/bjoc.14.5.

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The structural characterization of non-covalent complexes between nucleic acids and small molecules (ligands) is of a paramount significance to bioorganic research. Highly informative methods about nucleic acid/ligand complexes such as single crystal X-ray diffraction or NMR spectroscopy cannot be performed under biologically compatible conditions and are extensively time consuming. Therefore, in search for faster methods which can be applied to conditions that are at least similar to the naturally occurring ones, a set of polarization spectroscopy methods has shown highly promising results. Electronic circular dichroism (ECD) is the most commonly used method for the characterization of the helical structure of DNA and RNA and their complexes with ligands. Less common but complementary to ECD, is flow-oriented linear dichroism (LD). Other methods such as vibrational CD (VCD) and emission-based methods (FDCD, CPL), can also be used for suitable samples. Despite the popularity of polarization spectroscopy in biophysics, aside several highly focused reviews on the application of these methods to DNA/RNA research, there is no systematic tutorial covering all mentioned methods as a tool for the characterization of adducts between nucleic acids and small ligands. This tutorial aims to help researchers entering the research field to organize experiments accurately and to interpret the obtained data reliably.

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Beljanski, Vladimir, Julie M. Villanueva, Paul W. Doetsch, Giovanni Natile, and Luigi G. Marzilli. "Marked Dependence on Carrier-Ligand Bulk but Not on Carrier-Ligand Chirality of the Duplex versus Single-Strand Forms of a DNA Oligonucleotide with a Series of G−Pt(II)−G Intrastrand Cross-Links Modeling Cisplatin−DNA Adducts." Journal of the American Chemical Society 127, no. 45 (November 2005): 15833–42. http://dx.doi.org/10.1021/ja053089n.

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Ano, Susan O., Francesco P. Intini, Giovanni Natile, and Luigi G. Marzilli. "Retro Models of Pt Anticancer Drug DNA Adducts: Chirality-Controlling Chelate Ligand Restriction of Guanine Dynamic Motion in (2,2‘-Bipiperidine)PtG2Complexes (G = Guanine Derivative)." Inorganic Chemistry 38, no. 12 (June 1999): 2989–99. http://dx.doi.org/10.1021/ic981409g.

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Winardi, Daniel, Pei-Yi Chu, Guan-Yu Chen, Ke Wang, Wei-Yu Hsu, Ching-Liang Hsieh, Yung-Hsiang Chen, Yang-Chang Wu, and Juan-Cheng Yang. "Novel Aurora A Kinase Inhibitor Fangchinoline Enhances Cisplatin–DNA Adducts and Cisplatin Therapeutic Efficacy in OVCAR-3 Ovarian Cancer Cells-Derived Xenograft Model." International Journal of Molecular Sciences 23, no. 3 (February 7, 2022): 1868. http://dx.doi.org/10.3390/ijms23031868.

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Aurora A kinase (Aurora A) is a serine/threonine kinase regulating control of multiple events during cell-cycle progression. Playing roles in promoting proliferation and inhibiting cell death in cancer cells leads Aurora A to become a target for cancer therapy. It is overexpressed and associated with a poor prognosis in ovarian cancer. Improving cisplatin therapy outcomes remains an important issue for advanced-stage ovarian cancer treatment, and Aurora A inhibitors may improve it. In the present study, we identified natural compounds with higher docking scores than the known Aurora A ligand through structure-based virtual screening, including the natural compound fangchinoline, which has been associated with anticancer activities but not yet investigated in ovarian cancer. The binding and inhibition of Aurora A by fangchinoline were verified using cellular thermal shift and enzyme activity assays. Fangchinoline reduced viability and proliferation in ovarian cancer cell lines. Combination fangchinoline and cisplatin treatment enhanced cisplatin–DNA adduct levels, and the combination index revealed synergistic effects on cell viability. An in vivo study showed that fangchinoline significantly enhanced cisplatin therapeutic effects in OVCAR-3 ovarian cancer-bearing mice. Fangchinoline may inhibit tumor growth and enhance cisplatin therapy in ovarian cancer. This study reveals a novel Aurora A inhibitor, fangchinoline, as a potentially viable adjuvant for ovarian cancer therapy.

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Salishcheva, Olesya, and Alexander Prosekov. "Antimicrobial activity of mono- and polynuclear platinum and palladium complexes." Foods and Raw Materials 8, no. 2 (September 30, 2020): 298–311. http://dx.doi.org/10.21603/2308-4057-2020-2-298-311.

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Introduction. Infectious diseases remain a serious threat to humanity worldwide as bacterial pathogens grow more diverse. Bacteria, fungi, and parasites develop resistance to clinically approved antimicrobials, which reduces the efficacy of available drugs and treatment measures. As a result, there is an ever growing demand for new highly effective pharmaceuticals. This review describes mono- and polynuclear platinum and palladium complexes with antimicrobial properties. We compared several groups of antibacterial agents: antibiotics, antioxidant biologically active substances, antimicrobial nanoparticles, nanocomposite materials, biopolymers, micellar systems, and plant extracts. Study objects and methods. The review covered relevant articles published in Web of Science, Scopus, and Russian Science Citation Index for the last decade. The list of descriptors included such terms as mononuclear and binuclear complexes of platinum, palladium, and antimicrobial activity. Results and discussion. Chelates of platinum, palladium, silver, iridium, rhodium, ruthenium, cobalt, and nickel are popular therapeutic agents. Their antimicrobial activity against pathogenic microorganisms can be enhanced by increasing their bioavailability. Metalbased drugs facilitate the transport of organic ligands towards the bacterial cell. The nature of the ligand and its coordination change the thermodynamic stability, kinetic lability, and lipophilic properties of the complex, as well as the reactivity of the central atom. Polynuclear platinum and palladium complexes contain two or more bound metal (coordinate) centers. Covalent bonding with bacterial DNA enables them to form a type of DNA adducts, which is completely different from that of mononuclear complexes. Conclusion. Metal-based drugs with functional monodentate ligands exhibit a greater antimicrobial effect compared to free ligands. Poly- and heteronuclear complexes can increase the number of active centers that block the action of bacterial cells. When combined with other antibacterial agents, they provide a synergistic effect, which makes them a promising subject of further research.

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Ávila-Rosales, Oscar Samuel, Mauricio Díaz-Muñoz, Rafael Camacho-Carranza, Elvia Coballase-Urrutia, José Pedraza-Chaverri, Jorge Omar García-Rebollar, and Jesús Javier Espinosa-Aguirre. "Daytime Restricted Feeding Modifies the Temporal Expression of CYP1A1 and Attenuated Damage Induced by Benzo[a]pyrene in Rat Liver When Administered before CYP1A1 Acrophase." Toxics 9, no. 6 (June 4, 2021): 130. http://dx.doi.org/10.3390/toxics9060130.

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The aryl hydrocarbon receptor (AhR) is a ligand-activated transcription factor that heterodimerizes with the AhR nuclear translocator (ARNT) to modulate CYP1A1 expression, a gene involved in the biotransformation of benzo[a]pyrene (BaP). The AhR pathway shows daily variations under the control of the circadian timing system. Daytime restricted feeding (DRF) entrains the expression of genes involved in the processing of nutrients and xenobiotics to food availability. Therefore, we evaluate if temporal AhR, ARNT, and CYP1A1 hepatic expression in rats are due to light/dark cycles or fasting/feeding cycles promoted by DRF. Our results show that AhR oscillates throughout the 24 h period in DRF and ad libitum feeding rats (ALF), showing maximum expression at the same time points. DRF modified the peak of ARNT expression at ZT5; meanwhile, ALF animals showed a peak of maximum expression at ZT17. An increased expression of CYP1A1 was linked to the meal time in both groups of animals. Although a high CYP1A1 expression has been previously associated with BaP genotoxicity, our results show that, compared with the ALF group, DRF attenuated the BaP-CYP1A1 induction potency, the liver DNA-BaP adducts, the liver concentration of unmetabolized BaP, and the blood aspartate aminotransferase and alanine aminotransferase activities when BaP is administered prior to the acrophase of CYP1A1 expression. These results demonstrate that DRF modifies the ARNT and CYP1A1 expression and protects from BaP toxicity.

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Arakawa, Hirohumi, and Moon-shong Tang. "Recognition and Incision of Cr(III) Ligand-Conjugated DNA Adducts by the Nucleotide Excision Repair Proteins UvrABC: Importance of the Cr(III)−Purine Moiety in the Enzymatic Reaction." Chemical Research in Toxicology 21, no. 6 (June 2008): 1284–89. http://dx.doi.org/10.1021/tx800046y.

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Salishcheva, Olesya, Alyeksandr Prosyekov, and V. Dolganuk. "Antimicrobial Activity of Mononuclear and Bionuclear Nitrite Complexes of Platinum (II) and Platinum (IV)." Food Processing: Techniques and Technology 50, no. 2 (June 27, 2020): 329–42. http://dx.doi.org/10.21603/2074-9414-2020-2-329-342.

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Introduction. Pathogens keep evolving and develop resistance to antimicrobial drugs. As a result, science is constantly searching for new antimicrobial agents. Their complex forms based on organic and inorganic ligands exhibit a stronger synergistic antimicrobial effect, if compared to free ligands. The Scopus database contains 73 thousand scientific articles about antimicrobial activity descriptors published during the last five years. This selection includes ten thousand reviews and three thousand publications that feature the antimicrobial activity of platinum complexes. The research objective was to screen the antimicrobial properties of platinum nitrite complexes. The present paper highlights some of the current domestic and foreign trends in this field of research: the biochemical synthesis of peptides as metabolites of bacteria; the development of anti-biofilm agents that act on the protective systems of pathogens; the creation of antimicrobial nanosystems; the synthesis of antimicrobial surfactants; the synthesis and study of the antimicrobial activity of platinum complexes, etc. The authors also give a brief description of the mechanisms of antibacterial action. Study objects and methods. Five previously synthesized complexes of platinum (II) and platinum (IV), both mononuclear and bionuclear, were tested for antimicrobial activity. The platinum complexes contained terminal and bridged nitrite ligands. The test cultures included Bacillus subtilis and Aspergillus niger. The experiment involved the disk-diffusion method and the macro method of serial dilutions. Results and discussion. All the complexes inhibited the metabolic growth of microorganisms to various degrees. The results depended on the composition and structure of the complex, the number and charge of the coordination centers, the degree of platinum oxidation, and the thermodynamic stability and lability of ligand bonds with the complexing agent. The response to Aspergillus niger proved more pronounced. The Pt+2 nonelectrolyte complex containing both terminal and bridged nitrite ligands was less active than the Pt+2 cationic complex, which contained only bridged NO2– ligands. The highest antibacterial activity belonged to the bionuclear complex of PtIV-PtII [(NH3)2 (NO2)2PtIV(µ-NO2)2PtII(NH3)2](NO3)2 in relation to Bacillus subtilis B4647 and Aspergillus niger. The minimum inhibitory concentration (MIC) was > 125 μmol. Conclusion. The complexing resulted in a synergistic effect between the ligand and the complexing substance. The poly-core complexes contain two or more linked platinum centers that can covalently bind to DNA. They form a completely different type of DNA adducts compared to mononuclear complexes, as well as cross-links between DNA chains with fixation on different parts. The octahedral platinum complexes are kinetic and thermodynamically inert. Unlike similar squamous complexes, they proved to be able to act as prodrugs, recovering inside or outside the bacterial cell. The antimicrobial activity of the mixed-valence PtIV-PtII bionuclear complex [(NH3)2 (NO2)2PtIV(µ-NO2)2PtII(NH3)2](NO3)2 produced inhibitory effect comparable to the existing antimicrobial drugs. A further research will focus on composite mixtures of platinum complexes with other existing antimicrobial agents, as well as on other bacterial strains.

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Sullivan, Sharon T., Antonella Ciccarese, Francesco P. Fanizzi, and Luigi G. Marzilli. "A Rare Example of Three Abundant Conformers in One Retro Model of the Cisplatin−DNA d(GpG) Intrastrand Cross Link. Unambiguous Evidence That Guanine O6 to Carrier Amine Ligand Hydrogen Bonding Is Not Important. Possible Effect of the Lippard Base Pair Step Adjacent to the Lesion on Carrier Ligand Hydrogen Bonding in DNA Adducts." Journal of the American Chemical Society 123, no. 38 (September 2001): 9345–55. http://dx.doi.org/10.1021/ja010483m.

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El-Saidi, Manal Mohamed Talaat, Ahmed Ali El-Sayed, Erik Bjerregaard Pedersen, Mohamed Abdelhamid Tantawy, Nadia Ragab Mohamed, and Wafaa Ahmed Gad. "Synthesis, Characterization and Docking Study of Novel Pyrimidine Derivatives as Anticancer Agents." Indonesian Journal of Chemistry 20, no. 5 (July 18, 2020): 1163. http://dx.doi.org/10.22146/ijc.50582.

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New compounds 5 and 9 using DNA bases e.g. Adenine 1 and Guanine 6 derivatives have been synthesized. The use of simple methods to synthesize compounds 5 and 9 were done using pyrimidine as an alternative DNA base ring. Another design to synthesize new simple pyrimidine rings utilizing thiourea and ethylcyano acetate to afford 6-amino-2-thiouracil was adopted. The reaction of thiouracil 10 with chloro cyano or chloro ester and ketone, resulted in the formation of adduct compounds 18-21, rather than the formation of compound 17. All the synthesized compounds were subjected to docking study, in order to gain insights into their binding modes against cyclin-dependent protein kinase 2 (CDK-2) that is involved heavily in cell cycle regulation and receptor protein B-cell lymphoma 2 (BCL-2) which is involved in cell apoptosis. These targets were selected based on their key roles in cancer progression via the regulation of the cell cycle and DNA replication. Molecular-docking analyses showed that compound 14e was the best docked ligand against both targets, as it displayed the lowest binding energy, critical hydrogen bonds and hydrophobic interactions with the targets.

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Lambert, B., B. K. Jones, B. P. Roques, J. B. Le Pecq, and A. T. Yeung. "The noncovalent complex between DNA and the bifunctional intercalator ditercalinium is a substrate for the UvrABC endonuclease of Escherichia coli." Proceedings of the National Academy of Sciences 86, no. 17 (September 1989): 6557–61. http://dx.doi.org/10.1073/pnas.86.17.6557.

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We have demonstrated that the noncovalent complex formed between DNA and an antitumor bifunctional intercalator, ditercalinium, is recognized in vitro as bulky covalent DNA lesions by the purified Escherichia coli UvrABC endonuclease. It was established that no covalent drug-DNA adduct was formed during the incubation of the drug with DNA or during subsequent incubation with the UvrAB proteins. The nucleoprotein-ditercalinium complexes appear different from those generated by repair of pyrimidine dimers. The UvrA protein is able to form a stable complex with ditercalinium-intercalated DNA in the presence of ATP, whereas both UvrA and UvrB proteins are required to form a stable complex with pyrimidine dimer-containing DNA. The apparent half-life of the UvrA- and UvrAB-ditercalinium-DNA complexes following removal of free ditercalinium is 5 min. However, if the free ditercalinium concentration is maintained to allow the intercalation of one molecule of ditercalinium per 3000 base pairs, the half-life of the UvrA- or UvrAB-ditercalinium-DNA complex is 50 min, comparable to that of the complex of UvrAB proteins formed with pyrimidine dimer-containing DNA. UvrABC endonuclease incises ditercalinium-intercalated DNA as efficiently as pyrimidine dimer-containing DNA. However, unlike repair of pyrimidine dimers, the incision reaction is strongly favored by the supercoiling of the DNA substrate. Because UvrA- or UvrAB-ditercalinium-DNA complexes can be formed with relaxed DNA without leading to a subsequent incision reaction, these apparently dead-end nucleoprotein complexes may become lesions in themselves resulting in the cytotoxicity of ditercalinium. Our results show that binding of excision repair proteins to a noncovalent DNA-ligand complex may lead to cell toxicity.

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Silverman, Adam P., Weiming Bu, Seth M. Cohen, and Stephen J. Lippard. "2.4-Å Crystal Structure of the Asymmetric Platinum Complex {Pt(ammine)(cyclohexylamine)}2+Bound to a Dodecamer DNA Duplex." Journal of Biological Chemistry 277, no. 51 (October 10, 2002): 49743–49. http://dx.doi.org/10.1074/jbc.m206979200.

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cis-trans-cis-Ammine(cyclohexylamine)diacetatodichloroplatinum(IV) is an oral analog of the platinum anti-cancer drug cisplatin that is currently in phase III clinical trials. Its active form, {Pt(ammine)(cyclohexylamine)}2+, binds to DNA similarly to cisplatin, forming intra- and interstrand cross-links between adjacent purine bases. Since {Pt(ammine)(cyclohexylamine)}2+contains two different ligands, it can form two isomeric 1,2-d(GpG) intrastrand cross-links. Here we report the 2.4-Å resolution x-ray crystal structure of the major adduct between {Pt(ammine)(cyclohexylamine)}2+and a DNA dodecamer, using the same sequence as previously reported for crystal structures of cisplatin-DNA (Takahara, P. M., Rosenzweig, A. C., Frederick, C. A., and Lippard, S. J. (1995)Nature377, 649–652) and oxaliplatin-DNA (Spingler, B., Whittington, D. A., and Lippard, S. J. (2001)Inorg. Chem.40, 5596–5602). Both duplexes in the asymmetric unit contain 1,2-intrastrand cross-links in which the cyclohexylamine ligand is directed toward the 3′-end of the platinated strand. The chair conformation of the cyclohexyl group is clearly resolved. Platination distorts the duplex, resulting in a global bend angle of about 38oand a dihedral angle between platinated guanine bases of ∼31o. Both end-to-end and end-to-groove packing interactions occur in the crystal lattice, the latter positioned in the minor groove across from the site of the platinum cross-link. A high degree of homology observed between this structure and the previously reported platinum-DNA structures suggests that these platinum complexes distort the DNA duplex in a very similar manner. These results suggest that differences in activity between these drugs are unlikely to result from gross conformational distortions in DNA structure following platinum intrastrand cross-link formation.

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Scalese, Gonzalo, Ignacio Machado, Gustavo Salinas, Leticia Pérez-Díaz, and Dinorah Gambino. "Heteroleptic Oxidovanadium(V) Complexes with Activity against Infective and Non-Infective Stages of Trypanosoma cruzi." Molecules 26, no. 17 (September 3, 2021): 5375. http://dx.doi.org/10.3390/molecules26175375.

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Five heteroleptic compounds, [VVO(IN-2H)(L-H)], where L are 8-hydroxyquinoline derivatives and IN is a Schiff base ligand, were synthesized and characterized in both the solid and solution state. The compounds were evaluated on epimastigotes and trypomastigotes of Trypanosoma cruzi as well as on VERO cells, as a mammalian cell model. Compounds showed activity against trypomastigotes with IC50 values of 0.29–3.02 μM. IN ligand and the new [VVO2(IN-H)] complex showed negligible activity. The most active compound [VVO(IN-2H)(L2-H)], with L2 = 5-chloro-7-iodo-8-hydroxyquinoline, showed good selectivity towards the parasite and was selected to carry out further biological studies. Stability studies suggested a partial decomposition in solution. [VVO(IN-2H)(L2-H)] affects the infection potential of cell-derived trypomastigotes. Low total vanadium uptake by parasites and preferential accumulation in the soluble proteins fraction were determined. A trypanocide effect was observed when incubating epimastigotes with 10 × IC50 values of [VVO(IN-2H)(L2-H)] and the generation of ROS after treatments was suggested. Fluorescence competition measurements with DNA:ethidium bromide adduct showed a moderate DNA interaction of the complexes. In vivo toxicity study on C. elegans model showed no toxicity up to a 100 μM concentration of [VVO(IN-2H)(L2-H)]. This compound could be considered a prospective anti-T. cruzi agent that deserves further research.

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Dayanidhi, P. David, and V. G. Vaidyanathan. "Understanding the ancillary ligand effect on luminescent cyclometalated Ir(III) complex as a reporter for 2-acetylaminofluorene DNA(AAF-dG) adduct." JBIC Journal of Biological Inorganic Chemistry 27, no. 1 (November 29, 2021): 189–99. http://dx.doi.org/10.1007/s00775-021-01920-5.

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Ramos, Catarina I. V., Ana R. Monteiro, Nuno M. M. Moura, Maria Amparo F. Faustino, Tito Trindade, and Maria Graça P. M. S. Neves. "The Interactions of H2TMPyP, Analogues and Its Metal Complexes with DNA G-Quadruplexes—An Overview." Biomolecules 11, no. 10 (September 25, 2021): 1404. http://dx.doi.org/10.3390/biom11101404.

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The evidence that telomerase is overexpressed in almost 90% of human cancers justifies the proposal of this enzyme as a potential target for anticancer drug design. The inhibition of telomerase by quadruplex stabilizing ligands is being considered a useful approach in anticancer drug design proposals. Several aromatic ligands, including porphyrins, were exploited for telomerase inhibition by adduct formation with G-Quadruplex (GQ). 5,10,15,20-Tetrakis(N-methyl-4-pyridinium)porphyrin (H2TMPyP) is one of the most studied porphyrins in this field, and although reported as presenting high affinity to GQ, its poor selectivity for GQ over duplex structures is recognized. To increase the desired selectivity, porphyrin modifications either at the peripheral positions or at the inner core through the coordination with different metals have been handled. Herein, studies involving the interactions of TMPyP and analogs with different DNA sequences able to form GQ and duplex structures using different experimental conditions and approaches are reviewed. Some considerations concerning the structural diversity and recognition modes of G-quadruplexes will be presented first to facilitate the comprehension of the studies reviewed. Additionally, considering the diversity of experimental conditions reported, we decided to complement this review with a screening where the behavior of H2TMPyP and of some of the reviewed metal complexes were evaluated under the same experimental conditions and using the same DNA sequences. In this comparison under unified conditions, we also evaluated, for the first time, the behavior of the AgII complex of H2TMPyP. In general, all derivatives showed good affinity for GQ DNA structures with binding constants in the range of 106–107 M−1 and ligand-GQ stoichiometric ratios of 3:1 and 4:1. A promising pattern of selectivity was also identified for the new AgII derivative.

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Bazzicalupi, Carla, Alessandro Bonardi, Tarita Biver, Marta Ferraroni, Francesco Papi, Matteo Savastano, Paolo Lombardi, and Paola Gratteri. "Probing the Efficiency of 13-Pyridylalkyl Berberine Derivatives to Human Telomeric G-Quadruplexes Binding: Spectroscopic, Solid State and In Silico Analysis." International Journal of Molecular Sciences 23, no. 22 (November 14, 2022): 14061. http://dx.doi.org/10.3390/ijms232214061.

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The interaction between the series of berberine derivatives 1–5 (NAX071, NAX120, NAX075, NAX077 and NAX079) and human telomeric G-quadruplexes (G4), which are able to inhibit the Telomerase enzyme’s activity in malignant cells, was investigated. The derivatives bear a pyridine moiety connected by a hydrocarbon linker of varying length (n = 1–5, with n number of aliphatic carbon atoms) to the C13 position of the parent berberine. As for the G4s, both bimolecular 5′-TAGGGTTAGGGT-3′ (Tel12) and monomolecular 5′-TAGGGTTAGGGTTAGGGTTAGGG-3′ (Tel23) DNA oligonucleotides were considered. Spectrophotometric titrations, melting tests, X-ray diffraction solid state analysis and in silico molecular dynamics (MD) simulations were used to describe the different systems. The results were compared in search of structure–activity relationships. The analysis pointed out the formation of 1:1 complexes between Tel12 and all ligands, whereas both 1:1 and 2:1 ligand/G4 stoichiometries were found for the adduct formed by NAX071 (n = 1). Tel12, with tetrads free from the hindrance by the loop, showed a higher affinity. The details of the different binding geometries were discussed, highlighting the importance of H-bonds given by the berberine benzodioxole group and a correlation between the strength of binding and the hydrocarbon linker length. Theoretical (MD) and experimental (X-ray) structural studies evidence the possibility for the berberine core to interact with one or both G4 strands, depending on the constraints given by the linker length, thus affecting the G4 stabilization effect.

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Jarrett, Stuart G., Katharine M. Carter, Brent J. Shelton, and John A. D’Orazio. "RETRACTED ARTICLE: The melanocortin signaling cAMP axis accelerates repair and reduces mutagenesis of platinum-induced DNA damage." Scientific Reports 7, no. 1 (September 15, 2017). http://dx.doi.org/10.1038/s41598-017-12056-5.

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AbstractUsing primary melanocytes and HEK293 cells, we found that cAMP signaling accelerates repair of bi- and mono-functional platinum-induced DNA damage. Elevating cAMP signaling either by the agonistic MC1R ligand melanocyte stimulating hormone (MSH) or by pharmacologic cAMP induction by forskolin enhanced clearance of intrastrand cisplatin-adducts in melanocytes or MC1R-transfected HEK293 cells. MC1R antagonists human beta-defensin 3 and agouti signaling protein blocked MSH- but not forskolin-mediated enhancement of platinum-induced DNA damage. cAMP-enhanced repair of cisplatin-induced DNA damage was dependent on PKA-mediated phosphorylation of ATR on S435 which promoted ATR’s interaction with the key NER factor xeroderma pigmentosum A (XPA) and facilitated recruitment of an XPA-ATR-pS435 complex to sites of cisplatin DNA damage. Moreover, we developed an oligonucleotide retrieval immunoprecipitation (ORiP) assay using a novel platinated-DNA substrate to establish kinetics of ATR-pS435 and XPA’s associations with cisplatin-damaged DNA. Expression of a non-phosphorylatable ATR-S435A construct or deletion of A kinase-anchoring protein 12 (AKAP12) impeded platinum adduct clearance and prevented cAMP-mediated enhancement of ATR and XPA’s associations with cisplatin-damaged DNA, indicating that ATR phosphorylation at S435 is necessary for cAMP-enhanced repair of platinum-induced damage and protection against cisplatin-induced mutagenesis. These data implicate cAMP signaling as a critical regulator of genomic stability against platinum-induced mutagenesis.

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Bai, Hehe, Jia Shi, Qingyu Guo, Wenming Wang, Zhigang Zhang, Yafeng Li, Manohar Vennampalli, Xuan Zhao, and Hongfei Wang. "Spectroscopy, Structure, Biomacromolecular Interactions, and Antiproliferation Activity of a Fe(II) Complex With DPA-Bpy as Pentadentate Ligand." Frontiers in Chemistry 10 (April 25, 2022). http://dx.doi.org/10.3389/fchem.2022.888693.

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An Fe(II) complex with DPA-Bpy (DPA-Bpy = N,N-bis(2-pyridinylmethyl)-2,20-bipyridine-6 -methanamine) as the ligand was synthesized and characterized to mimic bleomycin. The binding constants (Kb) of the complex with calf thymus DNA and human serum albumin (HSA) were quantitatively evaluated using fluorescence spectroscopy, with Kb as 5.53×105 and 2.40×104 M−1, respectively; the number of the average binding site (n) is close to 1. The thermodynamic analyses suggested that the electrostatic interactions exist between the complex and DNA, and the hydrogen bonding and Van der Waals force exist for the complex and HSA. The Fe complex exhibits cleavage ability toward pBR322 DNA, and the crystal structure of the HSA Fe complex adduct at 2.4 Å resolution clearly shows that His288 serves as the axial ligand of the Fe center complexed with a pentadentate DPA-Bpy ligand. Furthermore, the cytotoxicity of the complex was evaluated against HeLa cells. Both the Fe complex and HSA Fe complex adduct show obvious effect on cell proliferation with an IC50 of 1.18 and 0.82 μM, respectively; they induced cell apoptosis and arrested cell cycles at S phase. This study provides insight into the plausible mechanism underlying their metabolism and pharmacological activity.

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García-Ramos, Juan Carlos, Rodrigo Galindo-Murillo, Fernando Cortés-Guzmán, and Lena Ruiz-Azuara. "Metal-Based Drug-DNA Interactions." Journal of the Mexican Chemical Society 57, no. 3 (October 12, 2017). http://dx.doi.org/10.29356/jmcs.v57i3.213.

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Coordination compounds that bind to DNA have been an active area of research since the discovery of cisplatin and the platinum based drugs. In this review we offer a general overview about transition-metal compounds that binds DNA through several ways and some examples are given to understand the role played by the different factors that promotes it, such as the intercalant ligand and the nature and position of the substituent over it. Several techniques to follow metal-based drugs interactions with DNA are mentioned as well as a brief description of computational techniques that can be used as a powerful tool in order to reach a deep knowledge of the parameters involved in the stabilization of coordination compound-DNA adduct.

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Journal articles on the topic 'Ligand-DNA adducts'

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