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Li J, Chen M, Jiang J, Huang J, Chen H, Pan L, Nesterov DS, Ma Z, Pombeiro AJL. A New Concept of Enhancing the Anticancer Activity of Manganese Terpyridine Complex by Oxygen-Containing Substituent Modification. Int J Mol Sci 2023; 24:ijms24043903. [PMID: 36835315 PMCID: PMC9963696 DOI: 10.3390/ijms24043903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Revised: 01/31/2023] [Accepted: 02/02/2023] [Indexed: 02/17/2023] Open
Abstract
Eleven manganese 4'-substituted-2,2':6',2″-terpyridine complexes (1a-1c and 2a-2h) with three non-oxygen-containing substituents (L1a-L1c: phenyl, naphthalen-2-yl and naphthalen-1-yl, L1a-L1c) and eight oxygen-containing substituents (L2a-L2h: 4-hydroxyl-phenyl, 3-hydroxyl-phenyl, 2-hydroxyl-phenyl, 4-methoxyl-phenyl, 4-carboxyl-phenyl, 4-(methylsulfonyl)phenyl, 4-nitrophenyl and furan-2-yl) were prepared and characterized by IR, elemental analysis or single crystal X-ray diffraction. In vitro data demonstrate that all of these show higher antiproliferative activities than cisplatin against five human carcinoma cell lines: A549, Bel-7402, Eca-109, HeLa and MCF-7. Compound 2d presents the strongest antiproliferative effect against A549 and HeLa cells, with IC50 values being 0.281 μM and 0.356 μM, respectively. The lowest IC50 values against Bel-7402 (0.523 μM) Eca-109 (0.514 μM) and MCF-7 (0.356 μM) were obtained for compounds 2h, 2g and 2c, respectively. Compound 2g with a nitro group showed the best results on the whole, with relevantly low IC50 values against all the tested tumor cells. The DNA interactions with these compounds were studied by circular dichroism spectroscopic and molecular modeling methods. Spectrophotometric results revealed that the compounds have strong affinities in binding with DNA as intercalators, and the binding induces DNA conformational transition. Molecular docking studies indicate that the binding is contributed by the π-π stacking and hydrogen bonds. The anticancer activities of the compounds are correlated with their DNA binding ability, and the modification of oxygen-containing substituents significantly enhanced the anticancer activity, which could provide a new rationale for the future design of terpyridine-based metal complexes with antitumor potential.
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Affiliation(s)
- Jiahe Li
- School of Chemistry and Chemical Engineering, Guangxi University, Nanning 530004, China
- National Engineering Research Center for Non-Food Biorefinery, State Key Laboratory of Non-Food Biomass and Enzyme Technology, Guangxi Academy of Sciences, Nanning 530007, China
- Centro de Química Estrutural, Institute of Molecular Sciences, Instituto Superior Técnico, Universidade de Lisboa, 1049-001 Lisbon, Portugal
| | - Min Chen
- School of Chemistry and Chemical Engineering, Guangxi University, Nanning 530004, China
| | - Jinzhang Jiang
- School of Chemistry and Chemical Engineering, Guangxi University, Nanning 530004, China
| | - Jieyou Huang
- School of Chemistry and Chemical Engineering, Guangxi University, Nanning 530004, China
| | - Hailan Chen
- School of Animal Science and Technology, Guangxi University, Nanning 530004, China
| | - Lixia Pan
- National Engineering Research Center for Non-Food Biorefinery, State Key Laboratory of Non-Food Biomass and Enzyme Technology, Guangxi Academy of Sciences, Nanning 530007, China
- Correspondence: (L.P.); or (Z.M.)
| | - Dmytro S. Nesterov
- Centro de Química Estrutural, Institute of Molecular Sciences, Instituto Superior Técnico, Universidade de Lisboa, 1049-001 Lisbon, Portugal
| | - Zhen Ma
- School of Chemistry and Chemical Engineering, Guangxi University, Nanning 530004, China
- Centro de Química Estrutural, Institute of Molecular Sciences, Instituto Superior Técnico, Universidade de Lisboa, 1049-001 Lisbon, Portugal
- Correspondence: (L.P.); or (Z.M.)
| | - Armando J. L. Pombeiro
- Centro de Química Estrutural, Institute of Molecular Sciences, Instituto Superior Técnico, Universidade de Lisboa, 1049-001 Lisbon, Portugal
- Research Institute of Chemistry, Peoples’ Friendship University of Russia (RUDN University), Moscow 117198, Russia
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Nevinsky GA. How Enzymes, Proteins, and Antibodies Recognize Extended DNAs; General Regularities. Int J Mol Sci 2021; 22:1369. [PMID: 33573045 PMCID: PMC7866405 DOI: 10.3390/ijms22031369] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 01/25/2021] [Accepted: 01/26/2021] [Indexed: 11/17/2022] Open
Abstract
X-ray analysis cannot provide quantitative estimates of the relative contribution of non-specific, specific, strong, and weak contacts of extended DNA molecules to their total affinity for enzymes and proteins. The interaction of different enzymes and proteins with long DNA and RNA at the quantitative molecular level can be successfully analyzed using the method of the stepwise increase in ligand complexity (SILC). The present review summarizes the data on stepwise increase in ligand complexity (SILC) analysis of nucleic acid recognition by various enzymes-replication, restriction, integration, topoisomerization, six different repair enzymes (uracil DNA glycosylase, Fpg protein from Escherichia coli, human 8-oxoguanine-DNA glycosylase, human apurinic/apyrimidinic endonuclease, RecA protein, and DNA-ligase), and five DNA-recognizing proteins (RNA helicase, human lactoferrin, alfa-lactalbumin, human blood albumin, and IgGs against DNA). The relative contributions of structural elements of DNA fragments "covered" by globules of enzymes and proteins to the total affinity of DNA have been evaluated. Thermodynamic and catalytic factors providing discrimination of unspecific and specific DNAs by these enzymes on the stages of primary complex formation following changes in enzymes and DNAs or RNAs conformations and direct processing of the catalysis of the reactions were found. General regularities of recognition of nucleic acid by DNA-dependent enzymes, proteins, and antibodies were established.
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Affiliation(s)
- Georgy A Nevinsky
- Institute of Chemical Biology and Fundamental Medicine, Siberian Division of Russian Academy of Sciences, 63009 Novosibirsk, Russia
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Luzhetskaya OP, Sedykh SE, Nevinsky GA. How Human H1 Histone Recognizes DNA. Molecules 2020; 25:E4556. [PMID: 33028027 PMCID: PMC7582325 DOI: 10.3390/molecules25194556] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 09/25/2020] [Accepted: 10/01/2020] [Indexed: 11/24/2022] Open
Abstract
Linker H1 histone is one of the five main histone proteins (H1, H2A, H2B, H3, and H4), which are components of chromatin in eukaryotic cells. Here we have analyzed the patterns of DNA recognition by free H1 histone using a stepwise increase of the ligand complexity method; the affinity of H1 histone for various single- and double-stranded oligonucleotides (d(pN)n; n = 1-20) was evaluated using their competition with 12-mer [32P]labeled oligonucleotide and protein-oligonucleotide complex delaying on nitrocellulose membrane filters. It was shown that minimal ligands of H1 histone (like other DNA-dependent proteins and enzymes) are different mononucleotides (dNMPs; Kd = (1.30 ± 0.2) × 10-2 M). An increase in the length of single-stranded (ss) homo- and hetero-oligonucleotides (d(pA)n, d(pT)n, d(pC)n, and d(pN)n with different bases) by one nucleotide link regardless of their bases, leads to a monotonic increase in their affinity by a factor of f = 3.0 ± 0.2. This factor f corresponds to the Kd value = 1/f characterizing the affinity of one nucleotide of different ss d(pN)n for H1 at n = 2-6 (which are covered by this protein globule) is approximately 0.33 ± 0.02 M. The affinity of five out of six DNA nucleotide units is approximately 25 times lower than for one of the links. The affinity of duplexes of complementary homo- and hetero-d(pN)20 is only 1.3-3.3-fold higher in comparison with corresponding ss oligonucleotides. H1 histone forms mainly weak additive contacts with internucleoside phosphate groups of ssDNAs and one chain of double-stranded DNAs, but not with the bases.
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Affiliation(s)
| | | | - Georgy A. Nevinsky
- Institute of Chemical Biology and Fundamental Medicine, SD of Russian Academy of Sciences, 8 Lavrentiev Ave., 630090 Novosibirsk, Russia; (O.P.L.); (S.E.S.)
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Alinovskaya LI, Sedykh SE, Ivanisenko NV, Soboleva SE, Nevinsky GA. How human serum albumin recognizes DNA and RNA. Biol Chem 2018; 399:347-360. [PMID: 29252186 DOI: 10.1515/hsz-2017-0243] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Accepted: 11/28/2017] [Indexed: 11/15/2022]
Abstract
We show here for the first time that HSA possesses two nucleic acid-(NA) binding sites and we estimated the relative contributions of the nucleotide links of (pN)n to their total affinity for these binding sites with higher and lower affinity for NAs. The minimal ligands of these binding sites are orthophosphate (Kd=3.0 and 20.0 mm), various dNMPs (5.6-400 μm and 0.063-18 mm) and different rNMPs (4.9-30 μm and 14-250 μm). Maximal contribution to the total affinity of all NAs to the first and second sites was observed for one nucleotide and was remarkably lower for three additional nucleotide units of (pN)n (n=1-4) with a significant decrease in the contribution at n=5-6, and at n≥7-8 all dependencies reached plateaus. For d(pA)n and r(pA)n a relatively gradual decrease in the contribution to the affinity at n=1-6 was observed, while several d(pN)n, demonstrated a sharp increase in the contribution at n=2-4. Finally, all (pN)n>10 demonstrated high affinity for the first (1.4-150 nm) and the second (80-2400 nm) sites of HSA. Double-stranded NAs showed significantly lower affinity comparing with single-stranded ligands. The thermodynamic parameters characterizing the specific contribution of every nucleotide link of all (pN)1-9 (ΔG°) to their total affinity for HSA were estimated.
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Affiliation(s)
- Ludmila I Alinovskaya
- Institute of Chemical Biology and Fundamental Medicine of SB RAS, 8 Lavrentiev Ave., Novosibirsk 630090, Russia
| | - Sergey E Sedykh
- Institute of Chemical Biology and Fundamental Medicine of SB RAS, 8 Lavrentiev Ave., Novosibirsk 630090, Russia
| | - Nikita V Ivanisenko
- Institute of Cytology and Genetics, Siberian Division of Russian Academy of Sciences, 10 Lavrentiev Ave., 630090 Novosibirsk, Russia
| | - Svetlana E Soboleva
- Institute of Chemical Biology and Fundamental Medicine of SB RAS, 8 Lavrentiev Ave., Novosibirsk 630090, Russia
| | - Georgy A Nevinsky
- Institute of Chemical Biology and Fundamental Medicine of SB RAS, 8 Lavrentiev Ave., Novosibirsk 630090, Russia
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Yang Z, Jiang T, Zhong H, Kang Y. Bulge oligonucleotide as an inhibitory agent of bacterial topoisomerase I. J Enzyme Inhib Med Chem 2018; 33:319-323. [PMID: 29281935 PMCID: PMC6009931 DOI: 10.1080/14756366.2017.1419218] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Bacterial topoisomerase I (Btopo I) was defined as potential target for discovery of new antibacterial compounds. Various oligonucleotides containing bulge structure were designed and synthesised as inhibitors to Btopo I in this investigation. The results of this study demonstrated that the designed oligonucleotides display high inhibitory efficiency on the activity of Btopo I and the inhibitory effect could be modulated by the amount of bulge DNA bases. The most efficient one among them showed an IC50 value of 63.1 nM in its inhibition on the activity of Btopo I. In addition, our studies confirmed that the designed oligonucleotide would induce irreversible damages to Btopo I and without any effects occur to eukaryotic topoisomerase I. It is our hope that the results provided in these studies could provide a novel way to inhibit Btopo I.
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Affiliation(s)
- Zhaoqi Yang
- a School of Pharmaceutical Sciences , Jiangnan University , Jiangsu , People's Republic of China.,b Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, School of Food Science and Technology, Jiangnan University , Jiangsu , People's Republic of China
| | - Tuoyu Jiang
- b Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, School of Food Science and Technology, Jiangnan University , Jiangsu , People's Republic of China
| | - Hanshi Zhong
- b Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, School of Food Science and Technology, Jiangnan University , Jiangsu , People's Republic of China
| | - Yu Kang
- b Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province, School of Food Science and Technology, Jiangnan University , Jiangsu , People's Republic of China
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Yang Z, Jiang T, Zhong H, Liu Y. Portion mismatch in duplex oligonucleotides as inhibitors of bacterial topoisomerase I. RSC Adv 2016. [DOI: 10.1039/c6ra23304j] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The activities of bacterial topoisomerase I can be modulated by non-perfect match duplex oligonucleotides.
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Affiliation(s)
- Zhaoqi Yang
- Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province
- School of Food Science and Technology
- Jiangnan University
- China
- School of Pharmaceutical Sciences
| | - Tuoyu Jiang
- Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province
- School of Food Science and Technology
- Jiangnan University
- China
| | - Hanshi Zhong
- Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province
- School of Food Science and Technology
- Jiangnan University
- China
| | - Yuanfa Liu
- Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province
- School of Food Science and Technology
- Jiangnan University
- China
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Kirpota OO, Endutkin AV, Ponomarenko MP, Ponomarenko PM, Zharkov DO, Nevinsky GA. Thermodynamic and kinetic basis for recognition and repair of 8-oxoguanine in DNA by human 8-oxoguanine-DNA glycosylase. Nucleic Acids Res 2011; 39:4836-50. [PMID: 21343179 PMCID: PMC3113562 DOI: 10.1093/nar/gkq1333] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
We have used a stepwise increase in ligand complexity approach to estimate the relative contributions of the nucleotide units of DNA containing 7,8-dihydro-8-oxoguanine (oxoG) to its total affinity for human 8-oxoguanine DNA glycosylase (OGG1) and construct thermodynamic models of the enzyme interaction with cognate and non-cognate DNA. Non-specific OGG1 interactions with 10–13 nt pairs within its DNA-binding cleft provides approximately 5 orders of magnitude of its affinity for DNA (ΔG° approximately −6.7 kcal/mol). The relative contribution of the oxoG unit of DNA (ΔG° approximately −3.3 kcal/mol) together with other specific interactions (ΔG° approximately −0.7 kcal/mol) provide approximately 3 orders of magnitude of the affinity. Formation of the Michaelis complex of OGG1 with the cognate DNA cannot account for the major part of the enzyme specificity, which lies in the kcat term instead; the rate increases by 6–7 orders of magnitude for cognate DNA as compared with non-cognate one. The kcat values for substrates of different sequences correlate with the DNA twist, while the KM values correlate with ΔG° of the DNA fragments surrounding the lesion (position from −6 to +6). The functions for predicting the KM and kcat values for different sequences containing oxoG were found.
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Affiliation(s)
- Oleg O Kirpota
- SB RAS Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Avenue, Department of Molecular Biology, Novosibirsk State University, 2 Pirogova Street and SB RAS Institute of Cytology and Genetics, 10 Lavrentieva Avenue, Novosibirsk 630090, Russia
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Li X, Tao Ng MT, Wang Y, Liu X, Li T. Dumbbell-shaped circular oligonucleotides as inhibitors of human topoisomerase I. Bioorg Med Chem Lett 2007; 17:4967-71. [PMID: 17591440 DOI: 10.1016/j.bmcl.2007.06.035] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2007] [Revised: 06/04/2007] [Accepted: 06/07/2007] [Indexed: 10/23/2022]
Abstract
A dumbbell-shaped circular oligonucleotide containing topoisomerase I-binding sites and two mismatched base pairs in its sequence has been designed and synthesized. Our further studies demonstrate that this particularly designed oligonucleotide displays an IC(50) value of 9 nM in its inhibition on the activity of human topoisomerase I, a magnitude smaller than that of camptothecin, an anticancer drug currently in clinical use.
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Affiliation(s)
- Xinming Li
- Department of Chemistry, 3 Science Drive 3, National University of Singapore, Singapore, Singapore
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Beloglazova NG, Kirpota OO, Starostin KV, Ishchenko AA, Yamkovoy VI, Zharkov DO, Douglas KT, Nevinsky GA. Thermodynamic, kinetic and structural basis for recognition and repair of abasic sites in DNA by apurinic/apyrimidinic endonuclease from human placenta. Nucleic Acids Res 2004; 32:5134-46. [PMID: 15459284 PMCID: PMC521659 DOI: 10.1093/nar/gkh846] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2004] [Revised: 08/25/2004] [Accepted: 09/07/2004] [Indexed: 11/14/2022] Open
Abstract
X-ray analysis of enzyme-DNA interactions is very informative in revealing molecular contacts, but provides neither quantitative estimates of the relative importance of these contacts nor information on the relative contributions of specific and nonspecific interactions to the total affinity of enzymes for specific DNA. A stepwise increase in the ligand complexity approach is used to estimate the relative contributions of virtually every nucleotide unit of synthetic DNA containing abasic sites to its affinity for apurinic/apyrimidinic endonuclease (APE1) from human placenta. It was found that APE1 interacts with 9-10 nt units or base pairs of single-stranded and double-stranded ribooligonucleotides and deoxyribooligonucleotides of different lengths and sequences, mainly through weak additive contacts with internucleotide phosphate groups. Such nonspecific interactions of APE1 with nearly every nucleotide within its DNA-binding cleft provides up to seven orders of magnitude (DeltaG degrees approximately -8.7 to -9.0 kcal/mol) of the enzyme affinity for any DNA substrate. In contrast, interactions with the abasic site together with other specific APE1-DNA interactions provide only one order of magnitude (DeltaG degrees approximately -1.1 to -1.5 kcal/mol) of the total affinity of APE1 for specific DNA. We conclude that the enzyme's specificity for abasic sites in DNA is mostly due to a great increase (six to seven orders of magnitude) in the reaction rate with specific DNA, with formation of the Michaelis complex contributing to the substrate preference only marginally.
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Affiliation(s)
- Natalia G Beloglazova
- Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Avenue, Novosibirsk 630090, Russia
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