1
|
Correa WA, das Neves SC, Oliveira RJ, Kassuya CA, Navarro SD, Faustino Martins AC, Saroja B, Mitsuyasu B, Ostaciana Maia Freitas da Silveira I, Vitor N, Coelho HRS, Vilela MLB, do Nascimento VA, de Lima DP, Beatriz A, da Silva Gomes R. Chemotherapeutic Mechanism of Action of the Synthetic Resorcinolic Methyl 3,5-dimethoxy-2-octanoylbenzoate. Chem Res Toxicol 2024; 37:259-273. [PMID: 38183658 DOI: 10.1021/acs.chemrestox.3c00269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2024]
Abstract
Resorcinolic lipids are described as potential examples of selective chemotherapeutic adjuvants that can enhance the effects of cyclophosphamide (CYC) while promoting cell death without causing DNA damage. Therefore, the current study attempted to describe how the resorcinolic lipid methyl 3,5-dimethoxy-2-octanoylbenzoate (AMS35BB) interacted with DNA (DNA docking) and how this compound affected genetic toxicology models and other biological characteristics when combined with CYC. We observed that AMS35BB, used alone (7.5 and 10 mg/kg), increases the frequency of genomic damage (comet assay) but not chromosomal damage (micronuclei assay), lowers phagocytosis, and promotes cell death in Swiss male mice. When used in association with CYC, AMS35BB can reduce the risk of genomic damage by up to 33.8% as well as chromosomal damage, splenic phagocytosis, cell death, and lymphocyte frequency. Molecular docking showed that AMS35BB had a higher affinity than the active metabolite of CYC for binding to the DNA double helix major groove. As a result, AMS35BB has the potential to be both an adjuvant when used in association with CYC and a therapeutic candidate for the development of a selective chemotherapeutic drug.
Collapse
Affiliation(s)
- Willian Ayala Correa
- Institute of Chemistry, Federal University of Mato Grosso do Sul, Campo Grande, Mato Grosso do Sul 79070-900, Brazil
| | - Silvia Cordeiro das Neves
- Stem Cell, Cell Therapy and Toxicological Genetics Research Centre (CeTroGen), Medical School, Federal University of Mato Grosso do Sul, Campo Grande, Mato Grosso do Sul 79080-190, Brazil
- Graduate Program in Health and Development in the Midwest Region, Medical School, Federal University of Mato Grosso do Sul, Campo Grande, Mato Grosso do Sul 79070-900, Brazil
| | - Rodrigo Juliano Oliveira
- Stem Cell, Cell Therapy and Toxicological Genetics Research Centre (CeTroGen), Medical School, Federal University of Mato Grosso do Sul, Campo Grande, Mato Grosso do Sul 79080-190, Brazil
- Graduate Program in Health and Development in the Midwest Region, Medical School, Federal University of Mato Grosso do Sul, Campo Grande, Mato Grosso do Sul 79070-900, Brazil
| | - Cândida A Kassuya
- School of Health Sciences, Federal University of Grande Dourados, Dourados, Mato Grosso do Sul 79804-970, Brazil
| | - Stephanie D Navarro
- Institute of Chemistry, Federal University of Mato Grosso do Sul, Campo Grande, Mato Grosso do Sul 79070-900, Brazil
- Stem Cell, Cell Therapy and Toxicological Genetics Research Centre (CeTroGen), Medical School, Federal University of Mato Grosso do Sul, Campo Grande, Mato Grosso do Sul 79080-190, Brazil
| | | | - Baby Saroja
- Department of Pharmaceutical Sciences, North Dakota State University, Fargo, North Dakota 58102, United States
| | - Barbara Mitsuyasu
- Department of Pharmaceutical Sciences, North Dakota State University, Fargo, North Dakota 58102, United States
- Department of Chemical and Biological Sciences, Institute of Biosciences, São Paulo State University (UNESP), Botucatu, São Paulo 18618-689, Brazil
| | | | - Neimar Vitor
- Institute of Chemistry, Federal University of Mato Grosso do Sul, Campo Grande, Mato Grosso do Sul 79070-900, Brazil
| | - Henrique Rodrigues Scherer Coelho
- Stem Cell, Cell Therapy and Toxicological Genetics Research Centre (CeTroGen), Medical School, Federal University of Mato Grosso do Sul, Campo Grande, Mato Grosso do Sul 79080-190, Brazil
| | - Marcelo L B Vilela
- Institute of Chemistry, Federal University of Mato Grosso do Sul, Campo Grande, Mato Grosso do Sul 79070-900, Brazil
| | - Valter A do Nascimento
- Graduate Program in Health and Development in the Midwest Region, Medical School, Federal University of Mato Grosso do Sul, Campo Grande, Mato Grosso do Sul 79070-900, Brazil
| | - Dênis P de Lima
- Institute of Chemistry, Federal University of Mato Grosso do Sul, Campo Grande, Mato Grosso do Sul 79070-900, Brazil
| | - Adilson Beatriz
- Institute of Chemistry, Federal University of Mato Grosso do Sul, Campo Grande, Mato Grosso do Sul 79070-900, Brazil
| | - Roberto da Silva Gomes
- Department of Pharmaceutical Sciences, North Dakota State University, Fargo, North Dakota 58102, United States
| |
Collapse
|
2
|
das Neves SC, de Araújo FH, Correa WA, Martins ACF, Coelho HRS, Vilela MLB, do Nascimento VA, Kassuya CAL, de Lima DP, Beatriz A, Oliveira RJ, Gomes RDS. 3-Heptylidene-4,6-Dimethoxy-3 H-Isobenzofuran-1-One Is Genotoxic, Increases the Frequency of Cell Death, and Potentiates the Effects of Cyclophosphamide and Cisplatin. Molecules 2023; 28:1044. [PMID: 36770711 PMCID: PMC9922015 DOI: 10.3390/molecules28031044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 01/17/2023] [Accepted: 01/18/2023] [Indexed: 01/22/2023] Open
Abstract
3-heptylidene-4,6-dimethoxy-3H-isobenzofuran-1-one (Phthalide 1) is the precursor of three resorcinol lipids that have been described as potential chemotherapeutic agents and capable of potentiating the effects of cyclophosphamide. In this study, we evaluated the genotoxic potential, cell-killing potential, and interactions with cyclophosphamide and cisplatin of phthalide 1. Twelve groups were created from 120 mice: Negative Control, cyclophosphamide (100 mg/kg), cisplatin (6 mg/kg), Phthalide 1 (5, 10 and 20 mg/kg), and associations of 1 with cyclophosphamide and 1 with cisplatin. The results demonstrate that 1 increases (p < 0.05) the frequency of chromosomal damage, liver and kidney cell death, and splenic phagocytosis. The association of 1 with cyclophosphamide and cisplatin demonstrated a chemopreventive effect and, therefore, a reduction (p < 0.05) in the frequency of chromosomal damage. However, cell death and splenic phagocytosis did not suffer significant variations. As a result of the above, 1 has potential chemotherapeutic application and may be a candidate for developing a new generation of chemotherapeutics. In addition, it has characteristics to be used as a chemotherapy adjuvant in association with cyclophosphamide and cisplatin since it increases the frequency of cell death induced by chemotherapy. We also reported that the chemopreventive effect of 1, in association with cyclophosphamide and cisplatin, can prevent adverse effects (induction of DNA damage in non-tumor cells) without interfering with the mode of action of chemotherapy drugs and, therefore, without reducing the induction of cell death.
Collapse
Affiliation(s)
- Silvia Cordeiro das Neves
- Stem Cell, Cell Therapy and Toxicological Genetics Research Centre (CeTroGen), Medical School, Federal University of Mato Grosso do Sul, Campo Grande 79080-190, MS, Brazil
- Graduate Programme in Health and Development in the Midwest Region, Medical School, Federal University of Mato Grosso do Sul, Campo Grande 79070-900, MS, Brazil
| | - Flavio Henrique de Araújo
- Stem Cell, Cell Therapy and Toxicological Genetics Research Centre (CeTroGen), Medical School, Federal University of Mato Grosso do Sul, Campo Grande 79080-190, MS, Brazil
| | - Willian Ayala Correa
- Institute of Chemistry, Federal University of Mato Grosso do Sul, Campo Grande 79070-900, MS, Brazil
| | | | - Henrique Rodrigues Scherer Coelho
- Stem Cell, Cell Therapy and Toxicological Genetics Research Centre (CeTroGen), Medical School, Federal University of Mato Grosso do Sul, Campo Grande 79080-190, MS, Brazil
| | | | - Valter Aragão do Nascimento
- Graduate Programme in Health and Development in the Midwest Region, Medical School, Federal University of Mato Grosso do Sul, Campo Grande 79070-900, MS, Brazil
| | | | - Dênis Pires de Lima
- Institute of Chemistry, Federal University of Mato Grosso do Sul, Campo Grande 79070-900, MS, Brazil
| | - Adilson Beatriz
- Institute of Chemistry, Federal University of Mato Grosso do Sul, Campo Grande 79070-900, MS, Brazil
| | - Rodrigo Juliano Oliveira
- Stem Cell, Cell Therapy and Toxicological Genetics Research Centre (CeTroGen), Medical School, Federal University of Mato Grosso do Sul, Campo Grande 79080-190, MS, Brazil
- Graduate Programme in Health and Development in the Midwest Region, Medical School, Federal University of Mato Grosso do Sul, Campo Grande 79070-900, MS, Brazil
| | - Roberto da Silva Gomes
- Department of Pharmaceutical Sciences, North Dakota State University, Fargo, ND 58102, USA
| |
Collapse
|
3
|
Oliveira RJ, da Silveira IOMF, das Neves SC, Mitsuyasu B, Martins AC, Berno C, Mohammad J, Raj H, de Araujo FHS, Hortelan CR, Machado L, da Silva Júnior EN, Vilela MLB, Nascimento VA, Beatriz A, da Silva Gomes R. ZIM, a Norbornene Derived from 4-Aminoantipyrine, Induces DNA Damage and Cell Death but in Association Reduces the Effect of Commercial Chemotherapeutics. Chem Res Toxicol 2023; 36:66-82. [PMID: 36548215 DOI: 10.1021/acs.chemrestox.2c00275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Cancer incidence is increasing, and the drugs are not very selective. These drugs cause adverse effects, and the cells become resistant. Therefore, new drugs are needed. Here, we evaluated the effects of ZIM, a candidate for chemotherapy, and 4-AA alone and in association with commercial chemotherapeutic agents. Subsequently, the results of ZIM and 4-AA were compared. Male Swiss mice were treated with doses of 12, 24, or 48 mg/kg ZIM or 4-AA alone or in association with cisplatin (6 mg/kg), doxorubicin (16 mg/kg), and cyclophosphamide (100 mg/kg). Biometric parameters, DNA damage (comet and micronuclei), cell death, and splenic phagocytosis were evaluated. DNA docking was also performed to confirm the possible interactions of ZIM and 4-AA with DNA. 4-AA has been shown to have low genotoxic potential, increase the frequency of cell death, and activate phagocytosis. ZIM causes genomic and chromosomal damage in addition to causing cell death and activating phagocytosis. In association with chemotherapeutical agents, both 4-AA and ZIM have a chemopreventive effect and, therefore, reduce the frequency of DNA damage, cell death, and splenic phagocytosis. The association of 4-AA and ZIM with commercial chemotherapeutic agents increased the frequency of lymphocytes compared to chemotherapeutic agents alone. Molecular docking demonstrated that ZIM has more affinity for DNA than 4-AA and its precursors (1 and 2). This was confirmed by the lower interaction energy of the complex (-119.83 kcal/mol). ZIM can break the DNA molecule and, therefore, its chemotherapeutic effect can be related to DNA damage. It is considered that ZIM has chemotherapeutic potential. However, it should not be used in combination with cisplatin, doxorubicin, and cyclophosphamide as it reduces the effects of these drugs.
Collapse
Affiliation(s)
- Rodrigo Juliano Oliveira
- Stem Cell, Cell Therapy and Toxicological Genetics Research Centre (CeTroGen), Medical School, Federal University of Mato Grosso do Sul, Campo Grande, Mato Grosso do Sul79080-190, Brazil.,Graduate Program in Health and Development in the Midwest Region, Medical School, Federal University of Mato Grosso do Sul, Campo Grande, Mato Grosso do Sul79070-900, Brazil
| | - Ingridhy Ostaciana Maia Freitas da Silveira
- Institute of Chemistry, Federal University of Mato Grosso do Sul, Campo Grande, Mato Grosso do Sul79070-900, Brazil.,Department of Pharmaceutical Sciences, North Dakota State University, Fargo, North Dakota58102, United States
| | - Silvia C das Neves
- Stem Cell, Cell Therapy and Toxicological Genetics Research Centre (CeTroGen), Medical School, Federal University of Mato Grosso do Sul, Campo Grande, Mato Grosso do Sul79080-190, Brazil.,Graduate Program in Health and Development in the Midwest Region, Medical School, Federal University of Mato Grosso do Sul, Campo Grande, Mato Grosso do Sul79070-900, Brazil
| | - Barbara Mitsuyasu
- Department of Pharmaceutical Sciences, North Dakota State University, Fargo, North Dakota58102, United States.,Department of Chemical and Biological Sciences, Institute of Biosciences, São Paulo State University (UNESP), Botucatu, SP18618-689, Brazil
| | - Allana C Martins
- Department of Pharmaceutical Sciences, North Dakota State University, Fargo, North Dakota58102, United States
| | - Claudia Berno
- Stem Cell, Cell Therapy and Toxicological Genetics Research Centre (CeTroGen), Medical School, Federal University of Mato Grosso do Sul, Campo Grande, Mato Grosso do Sul79080-190, Brazil
| | - Jiyan Mohammad
- Department of Pharmaceutical Sciences, North Dakota State University, Fargo, North Dakota58102, United States
| | - Halie Raj
- Department of Pharmaceutical Sciences, North Dakota State University, Fargo, North Dakota58102, United States
| | - Flavio H S de Araujo
- Stem Cell, Cell Therapy and Toxicological Genetics Research Centre (CeTroGen), Medical School, Federal University of Mato Grosso do Sul, Campo Grande, Mato Grosso do Sul79080-190, Brazil
| | | | - Luana Machado
- Institute of Exact Sciences, Department of Chemistry, Federal University of Minas Gerais, Belo Horizonte, MGCEP 31270-901, Brazil.,Department of Chemistry, Fluminense Federal University, Niteroi, RJ24020-141, Brazil
| | - Eufrânio N da Silva Júnior
- Institute of Exact Sciences, Department of Chemistry, Federal University of Minas Gerais, Belo Horizonte, MGCEP 31270-901, Brazil
| | - Marcelo L B Vilela
- Medical School, Federal University of Mato Grosso do Sul, Campo Grande, Mato Grosso do Sul79070-900, Brazil
| | - Valter Aragão Nascimento
- Graduate Program in Health and Development in the Midwest Region, Medical School, Federal University of Mato Grosso do Sul, Campo Grande, Mato Grosso do Sul79070-900, Brazil
| | - Adilson Beatriz
- Institute of Chemistry, Federal University of Mato Grosso do Sul, Campo Grande, Mato Grosso do Sul79070-900, Brazil
| | - Roberto da Silva Gomes
- Department of Pharmaceutical Sciences, North Dakota State University, Fargo, North Dakota58102, United States
| |
Collapse
|
4
|
The Mammalian High Mobility Group Protein AT-Hook 2 (HMGA2): Biochemical and Biophysical Properties, and Its Association with Adipogenesis. Int J Mol Sci 2020; 21:ijms21103710. [PMID: 32466162 PMCID: PMC7279267 DOI: 10.3390/ijms21103710] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 04/30/2020] [Accepted: 05/12/2020] [Indexed: 12/11/2022] Open
Abstract
The mammalian high-mobility-group protein AT-hook 2 (HMGA2) is a small DNA-binding protein and consists of three “AT-hook” DNA-binding motifs and a negatively charged C-terminal motif. It is a multifunctional nuclear protein directly linked to obesity, human height, stem cell youth, human intelligence, and tumorigenesis. Biochemical and biophysical studies showed that HMGA2 is an intrinsically disordered protein (IDP) and could form homodimers in aqueous buffer solution. The “AT-hook” DNA-binding motifs specifically bind to the minor groove of AT-rich DNA sequences and induce DNA-bending. HMGA2 plays an important role in adipogenesis most likely through stimulating the proliferative expansion of preadipocytes and also through regulating the expression of transcriptional factor Peroxisome proliferator-activated receptor γ (PPARγ) at the clonal expansion step from preadipocytes to adipocytes. Current evidence suggests that a main function of HMGA2 is to maintain stemness and renewal capacity of stem cells by which HMGA2 binds to chromosome and lock chromosome into a specific state, to allow the human embryonic stem cells to maintain their stem cell potency. Due to the importance of HMGA2 in adipogenesis and tumorigenesis, HMGA2 is considered a potential therapeutic target for anticancer and anti-obesity drugs. Efforts are taken to identify inhibitors targeting HMGA2.
Collapse
|
5
|
Filipović NR, Ristić P, Janjić G, Klisurić O, Puerta A, Padrón JM, Donnard M, Gulea M, Todorović TR. Silver-based monomer and coordination polymer with organic thiocyanate ligand: Structural, computational and antiproliferative activity study. Polyhedron 2019. [DOI: 10.1016/j.poly.2019.114132] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
|
6
|
Padroni G, Parkinson JA, Fox KR, Burley GA. Structural basis of DNA duplex distortion induced by thiazole-containing hairpin polyamides. Nucleic Acids Res 2019; 46:42-53. [PMID: 29194552 PMCID: PMC5758887 DOI: 10.1093/nar/gkx1211] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Accepted: 11/28/2017] [Indexed: 01/05/2023] Open
Abstract
This manuscript reports the molecular basis for double-stranded DNA (dsDNA) binding of hairpin polyamides incorporating a 5-alkyl thiazole (Nt) unit. Hairpin polyamides containing an N-terminal Nt unit induce higher melting stabilisation of target dsDNA sequences relative to an archetypical hairpin polyamide incorporating an N-terminal imidazole (Im) unit. However, modification of the N-terminus from Im to Nt-building blocks results in an increase in dsDNA binding affinity but lower G-selectivity. A general G-selectivity trend is observed for Nt-containing polyamide analogues. G-selectivity increases as the steric bulk in the Nt 5-position increases. Solution-based NMR structural studies reveal differences in the modulation of the target DNA duplex of Nt-containing hairpin polyamides relative to the Im-containing archetype. A structural hallmark of an Nt polyamide•dsDNA complex is a more significant degree of major groove compression of the target dsDNA sequence relative to the Im-containing hairpin polyamide.
Collapse
Affiliation(s)
- Giacomo Padroni
- Department of Pure and Applied Chemistry, University of Strathclyde, Thomas Graham Building, 295 Cathedral Street, Glasgow G1 1XL, UK
| | - John A Parkinson
- Department of Pure and Applied Chemistry, University of Strathclyde, Thomas Graham Building, 295 Cathedral Street, Glasgow G1 1XL, UK
| | - Keith R Fox
- Centre for Biological Sciences, University of Southampton, Life Sciences Building 85, Southampton SO17 1BJ, UK
| | - Glenn A Burley
- Department of Pure and Applied Chemistry, University of Strathclyde, Thomas Graham Building, 295 Cathedral Street, Glasgow G1 1XL, UK
| |
Collapse
|
7
|
Konovalov B, Živković MD, Milovanović JZ, Djordjević DB, Arsenijević AN, Vasić IR, Janjić GV, Franich A, Manojlović D, Skrivanj S, Milovanović MZ, Djuran MI, Rajković S. Synthesis, cytotoxic activity and DNA interaction studies of new dinuclear platinum(ii) complexes with an aromatic 1,5-naphthyridine bridging ligand: DNA binding mode of polynuclear platinum(ii) complexes in relation to the complex structure. Dalton Trans 2019; 47:15091-15102. [PMID: 30303498 DOI: 10.1039/c8dt01946k] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The synthesis, spectroscopic characterization, cytotoxic activity and DNA binding evaluation of seven new dinuclear platinum(ii) complexes Pt1-Pt7, with the general formula [{Pt(L)Cl}2(μ-1,5-nphe)](ClO4)2 (1,5-nphe is 1,5-naphthyridine; while L is two ammines (Pt1) or one bidentate coordinated diamine: ethylenediamine (Pt2), (±)-1,2-propylenediamine (Pt3), trans-(±)-1,2-diaminocyclohexane (Pt4), 1,3-propylenediamine (Pt5), 2,2-dimethyl-1,3-propylenediamine (Pt6), and 1,3-pentanediamine (Pt7)), were reported. In vitro cytotoxic activity of these complexes was evaluated against three tumor cell lines, murine colon carcinoma (CT26), murine mammary carcinoma (4T1) and murine lung cancer (LLC1) and two normal cell lines, murine mesenchymal stem cells (MSC) and human fibroblast (MRC-5) cells. The results of the MTT assay indicate that all investigated complexes have almost no cytotoxic effects on 4T1 and very low cytotoxicity toward LLC1 cell lines. In contrast to the effects on LLC1 and 4T1 cells, complexes Pt1 and Pt2 had significant cytotoxic activity toward CT26 cells. Complex Pt1 had a much lower IC50 value for activity on CT26 cells compared with cisplatin. In comparison with cisplatin, all dinuclear Pt1-Pt7 complexes showed lower cytotoxicity toward normal MSC and MRC-5 cells. In order to measure the amount of platinum(ii) complexes taken up by the cells, we quantified the cellular platinum content using inductively coupled plasma mass spectrometry (ICP-QMS). Molecular docking studies performed to evaluate the potential binding mode of dinuclear platinum(ii) complexes Pt1-Pt7 and their aqua derivatives W1-W7, respectively, at the double stranded DNA showed that groove spanning and backbone tracking are the most stable binding modes.
Collapse
Affiliation(s)
- Bata Konovalov
- University of Kragujevac, Faculty of Science, Department of Chemistry, R. Domanovića 12, 34000 Kragujevac, Serbia.
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
8
|
Prusov AN, Smirnova TA, Kolomijtseva GY. Thermodynamic Study of Interactions of Distamycin A with Chromatin in Rat Liver Nuclei in the Presence of Polyamines. BIOCHEMISTRY (MOSCOW) 2018; 83:1231-1244. [PMID: 30472960 DOI: 10.1134/s0006297918100085] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
We studied the thermodynamics of melting of isolated rat liver nuclei with different degrees of chromatin condensation determined by the concentration of polyamines (PA) and the solution ionic strength, as well as the effect of the antibiotic distamycin A (DM) on melting. Differential scanning calorimetry (DSC) profiles of nuclear preparations contained three peaks that reflected melting of three main chromatin domains. The number of peaks did not depend on the degree of condensation; however, nuclei with more condensed chromatin had a higher total enthalpy. DM stabilized peaks II and III corresponding to the melting of relaxed and topologically strained DNA, respectively, but destabilized peak I corresponding to the melting of nucleosome core histones. At the saturating concentration (DM/DNA molar ratio = 0.1), DM increased Tm of peaks II and III by ~5°C and decreased Tm of peak I by ~2.5°C. Based on the dependence of ΔH on DM concentration, we established that at low DM/DNA ratio (≤0.03), when DM interacted predominantly with AT-rich DNA regions, the enthalpy of peak II decreased in parallel with the increase in the enthalpy of peak III, which indicated that DM induces structural transitions in the nuclear chromatin associated with the increase in torsional stress in DNA. An increase in free energy under saturation conditions was equal to the change in the free energy of DM interaction with DNA. However, the increase in the enthalpy of melting of the nuclei in the presence of DM was much greater than the enthalpy of titration of nuclei with DM. This indicates a significant increase in the strength of interaction between the two DNA strands apparently due, among other things, to changes in the torsional stress of DNA in the nuclei. Titration of the nuclei with increasing PA concentrations resulted in the decrease in the number of DM-binding sites and the non-monotonous dependence of the enthalpy and entropy contribution to the binding free energy on the PA content. We suggested that the observed differences in the thermodynamic parameters were due to the different width of the minor groove in the nuclear chromatin DNA, which depends on PA concentration.
Collapse
Affiliation(s)
- A N Prusov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia.
| | - T A Smirnova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia.,Institute of Agricultural Biotechnology, Moscow, 127550, Russia
| | - G Ya Kolomijtseva
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119991, Russia
| |
Collapse
|
9
|
Liu B, Wang S, Aston K, Koeller KJ, Kermani SFH, Castañeda CH, Scuderi MJ, Luo R, Bashkin JK, Wilson WD. β-Alanine and N-terminal cationic substituents affect polyamide-DNA binding. Org Biomol Chem 2018; 15:9880-9888. [PMID: 29143012 DOI: 10.1039/c7ob02513k] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Minor-groove binding hairpin polyamides (PAs) bind specific DNA sequences. Synthetic modifications can improve PA-DNA binding affinity and include flexible modules, such as β-alanine (β) motifs to replace pyrroles (Py), and increasing compound charge using N-terminal cationic substituents. To better understand the variations in kinetics and affinities caused by these modifications on PA-DNA interactions, a comprehensive set of PAs with different numbers and positions of β and different types of N-cationic groups was systematically designed and synthesized to bind their cognate sequence, the λB motif. The λB motif is also a strong binding promoter site of the major groove targeting transcription factor PU.1. The PA binding affinities and kinetics were evaluated using a spectrum of powerful biophysical methods: thermal melting, biosensor surface plasmon resonance and circular dichroism. The results show that β inserts affect PA-DNA interactions in a number and position dependent manner. Specifically, a β replacement between two imidazole heterocycles (ImβIm) generally strengthens binding. In addition, N-terminal cationic groups can accelerate the association between PA and DNA, but the bulky size of TMG can cause steric hindrance and unfavourable repulsive electrostatic interactions in some PAs. The future design of stronger binding PA requires careful combination of βs and cationic substituents.
Collapse
Affiliation(s)
- Beibei Liu
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA.
| | | | | | | | | | | | | | | | | | | |
Collapse
|
10
|
Harika NK, Germann MW, Wilson WD. First Structure of a Designed Minor Groove Binding Heterocyclic Cation that Specifically Recognizes Mixed DNA Base Pair Sequences. Chemistry 2017; 23:17612-17620. [PMID: 29044822 PMCID: PMC6360951 DOI: 10.1002/chem.201704563] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Indexed: 12/24/2022]
Abstract
The high-resolution NMR structure of the first heterocyclic, non-amide, organic cation that strongly and selectively recognizes mixed AT/GC bp (bp=base pair) sequences of DNA in a 1:1 complex is described. Compound designs of this type provide essential methods for control of functional, non-genomic DNA sequences and have broad cell uptake capability, based on studies from animals to humans. The high-resolution structural studies described in this report are essential for understanding the molecular basis for the sequence-specific binding as well as for new ideas for additional compound designs for sequence-specific recognition. The molecular features, in this report, explain the mechanism of recognition of both A⋅T and G⋅C bps and are an interesting molecular recognition story. Examination of the experimental structure and the NMR restrained molecular dynamics model suggests that recognition of the G⋅C base pair involves two specific H-bonds. The structure illustrates a wealth of information on different DNA interactions and illustrates an interfacial water molecule that is a key component of the complex.
Collapse
Affiliation(s)
- Narinder K. Harika
- Department of Chemistry, Georgia State University, Atlanta, GA 30303-3083, USA
| | - Markus W. Germann
- Department of Chemistry, Georgia State University, Atlanta, GA 30303-3083, USA
| | - W. David Wilson
- Department of Chemistry, Georgia State University, Atlanta, GA 30303-3083, USA
| |
Collapse
|
11
|
Shahabadi N, Asadian AA, Mahdavi M. Intercalation of a Zn(II) complex containing ciprofloxacin drug between DNA base pairs. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2017; 36:676-689. [PMID: 29185900 DOI: 10.1080/15257770.2017.1388394] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
In this study, an attempt has been made to study the interaction of a Zn(II) complex containing an antibiotic drug, ciprofloxacin, with calf thymus DNA using spectroscopic methods. It was found that Zn(II) complex could bind with DNA via intercalation mode as evidenced by: hyperchromism in UV-Vis spectrum; these spectral characteristics suggest that the Zn(II) complex interacts with DNA most likely through a mode that involves a stacking interaction between the aromatic chromophore and the base pairs of DNA. DNA binding constant (Kb = 1.4 × 104 M-1) from spectrophotometric studies of the interaction of Zn(II) complex with DNA is comparable to those of some DNA intercalative polypyridyl Ru(II) complexes 1.0 -4.8 × 104 M-1. CD study showed stabilization of the right-handed B form of DNA in the presence of Zn(II) complex as observed for the classical intercalator methylene blue. Thermodynamic parameters (ΔH < 0 and ΔS < 0) indicated that hydrogen bond and Van der Waals play main roles in this binding prose. Competitive fluorimetric studies with methylene blue (MB) dye have shown that Zn(II) complex exhibits the ability of this complex to displace with DNA-MB, indicating that it binds to DNA in strong competition with MB for the intercalation.
Collapse
Affiliation(s)
- Nahid Shahabadi
- a Inorganic Chemistry Department, Faculty of Chemistry , Razi University , Kermanshah , Iran.,b Medical Biology Research Center (MBRC) Kermanshah University of Medical Sciences , Kermanshah , Iran
| | - Ali Ashraf Asadian
- a Inorganic Chemistry Department, Faculty of Chemistry , Razi University , Kermanshah , Iran
| | - Mryam Mahdavi
- a Inorganic Chemistry Department, Faculty of Chemistry , Razi University , Kermanshah , Iran.,b Medical Biology Research Center (MBRC) Kermanshah University of Medical Sciences , Kermanshah , Iran
| |
Collapse
|
12
|
Ivanov AA, Salyanov VI, Zhuze AL. DNA sequence-specific ligands: XV. Synthesis and spectral characteristics of a new series of dimeric bisbenzimidazoles DB(1, 2, 6, 8, 9, 10, 12). RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2016. [DOI: 10.1134/s1068162016020059] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
13
|
Wang S, Aston K, Koeller KJ, Harris GD, Rath NP, Bashkin JK, Wilson WD. Modulation of DNA-polyamide interaction by β-alanine substitutions: a study of positional effects on binding affinity, kinetics and thermodynamics. Org Biomol Chem 2015; 12:7523-36. [PMID: 25141096 DOI: 10.1039/c4ob01456a] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Hairpin polyamides (PAs) are an important class of sequence-specific DNA minor groove binders, and frequently employ a flexible motif, β-alanine (β), to reduce the molecular rigidity to maintain the DNA recognition register. To better understand the diverse effects that β can have on DNA-PA binding affinity, selectivity, and especially kinetics, which have rarely been reported, we have initiated a detailed study for an eight-heterocyclic hairpin PA and its β derivatives with their cognate and mutant sequences. With these derivatives, all internal pyrroles of the parent PA are systematically substituted with single or double βs. A set of complementary experiments have been conducted to evaluate the molecular interactions in detail: UV-melting, biosensor-surface plasmon resonance, circular dichroism and isothermal titration calorimetry. The β substitutions generally weaken the binding affinities of these PAs with cognate DNA, and have large and diverse influences on PA binding kinetics in a position- and number-dependent manner. The DNA base mutations have also shown positional effects on the binding of a single PA. Besides the β substitutions, the monocationic Dp group [3-(dimethylamino)propylamine] in parent PA has been modified into a dicationic Ta group (3,3'-diamino-N-methyldipropylamine) to minimize the frequently observed PA aggregation with ITC experiments. The results clearly show that the Ta modification not only maintains the DNA binding mode and affinity of PA, but also significantly reduces PA aggregation and allows the complete thermodynamic signature of eight-ring hairpin PA to be determined for the first time. This combined set of results significantly extends our understanding of the energetic basis of specific DNA recognition by PAs.
Collapse
Affiliation(s)
- Shuo Wang
- Department of Chemistry, Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303, USA.
| | | | | | | | | | | | | |
Collapse
|
14
|
Bruce CD, Ferrara MM, Manka JL, Davis ZS, Register J. Dynamic hydrogen bonding and DNA flexibility in minor groove binders: molecular dynamics simulation of the polyamide f-ImPyIm bound to the Mlu1 (MCB) sequence 5'-ACGCGT-3' in 2:1 motif. J Mol Recognit 2015; 28:325-37. [PMID: 25711379 DOI: 10.1002/jmr.2448] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Revised: 10/10/2014] [Accepted: 11/09/2014] [Indexed: 12/28/2022]
Abstract
Molecular dynamics simulations of the DNA 10-mer 5'-CCACGCGTGG-3' alone and complexed with the formamido-imidazole-pyrrole-imidazole (f-ImPyIm) polyamide minor groove binder in a 2:1 fashion were conducted for 50 ns using the pbsc0 parameters within the AMBER 12 software package. The change in DNA structure upon binding of f-ImPyIm was evaluated via minor groove width and depth, base pair parameters of Slide, Twist, Roll, Stretch, Stagger, Opening, Propeller, and x-displacement, dihedral angle distributions of ζ, ε, α, and γ determined using the Curves+ software program, and hydrogen bond formation. The dynamic hydrogen bonding between the f-ImPyIm and its cognate DNA sequence was compared to the static image used to predict sequence recognition by polyamide minor groove binders. Many of the predicted hydrogen bonds were present in less than 50% of the simulation; however, persistent hydrogen bonds between G5/15 and the formamido group of f-ImPyIm were observed. It was determined that the DNA is wider in the Complex than without the polyamide binder; however, there is flexibility in this particular sequence, even in the presence of the f-ImPyIm as evidenced by the range of minor groove widths the DNA exhibits and the dynamics of the hydrogen bonding that binds the two f-ImPyIm ions to the minor groove. The Complex consisting of the DNA and the 2 f-ImPyIm binders shows slight fraying of the 5' end of the 10-mer at the end of the simulation, but the portion of the oligomer responsible for recognition and binding is stable throughout the simulation. Several structural changes in the Complex indicate that minor groove binders may have a more active role in inhibiting transcription than just preventing binding of important transcription factors.
Collapse
Affiliation(s)
- Chrystal D Bruce
- Department of Chemistry, John Carroll University, 1 John Carroll Boulevard, University Heights, OH, 44118, USA
| | | | | | | | | |
Collapse
|
15
|
Contribution of phenylalanine side chain intercalation to the TATA-box binding protein–DNA interaction: molecular dynamics and dispersion-corrected density functional theory studies. J Mol Model 2014; 20:2499. [DOI: 10.1007/s00894-014-2499-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Accepted: 10/13/2014] [Indexed: 10/24/2022]
|
16
|
Navarro E, Serrano-Heras G, Castaño MJ, Solera J. Real-time PCR detection chemistry. Clin Chim Acta 2014; 439:231-50. [PMID: 25451956 DOI: 10.1016/j.cca.2014.10.017] [Citation(s) in RCA: 234] [Impact Index Per Article: 23.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Revised: 10/09/2014] [Accepted: 10/11/2014] [Indexed: 12/28/2022]
Abstract
Real-time PCR is the method of choice in many laboratories for diagnostic and food applications. This technology merges the polymerase chain reaction chemistry with the use of fluorescent reporter molecules in order to monitor the production of amplification products during each cycle of the PCR reaction. Thus, the combination of excellent sensitivity and specificity, reproducible data, low contamination risk and reduced hand-on time, which make it a post-PCR analysis unnecessary, has made real-time PCR technology an appealing alternative to conventional PCR. The present paper attempts to provide a rigorous overview of fluorescent-based methods for nucleic acid analysis in real-time PCR described in the literature so far. Herein, different real-time PCR chemistries have been classified into two main groups; the first group comprises double-stranded DNA intercalating molecules, such as SYBR Green I and EvaGreen, whereas the second includes fluorophore-labeled oligonucleotides. The latter, in turn, has been divided into three subgroups according to the type of fluorescent molecules used in the PCR reaction: (i) primer-probes (Scorpions, Amplifluor, LUX, Cyclicons, Angler); (ii) probes; hydrolysis (TaqMan, MGB-TaqMan, Snake assay) and hybridization (Hybprobe or FRET, Molecular Beacons, HyBeacon, MGB-Pleiades, MGB-Eclipse, ResonSense, Yin-Yang or displacing); and (iii) analogues of nucleic acids (PNA, LNA, ZNA, non-natural bases: Plexor primer, Tiny-Molecular Beacon). In addition, structures, mechanisms of action, advantages and applications of such real-time PCR probes and analogues are depicted in this review.
Collapse
Affiliation(s)
- E Navarro
- Research Unit, General University Hospital, Laurel s/n, 02006 Albacete, Spain.
| | - G Serrano-Heras
- Research Unit, General University Hospital, Laurel s/n, 02006 Albacete, Spain.
| | - M J Castaño
- Research Unit, General University Hospital, Laurel s/n, 02006 Albacete, Spain.
| | - J Solera
- Internal Medicine Department, General University Hospital, Hermanos Falcó 37, 02006 Albacete, Spain.
| |
Collapse
|
17
|
Wang S, Chai Y, Babu B, Satam V, Lee M, David Wilson W. Conformational modulation of DNA by polyamide binding: structural effects of f-Im-Py-Im based derivatives on 5'-ACGCGT-3'. J Mol Recognit 2014; 26:331-40. [PMID: 23784989 DOI: 10.1002/jmr.2273] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2013] [Revised: 02/14/2013] [Accepted: 02/15/2013] [Indexed: 12/13/2022]
Abstract
The DNA sequence 5'-ACGCGT-3' is in the core site of the Mlu 1 cell-cycle box, a transcriptional element in the promoter region of human Dbf4 gene that is highly correlated with a large number of aggressive solid cancers. The polyamide formamido-imidazole-pyrrole-imidazole-amine(+) (f-Im-Py-Im-Am(+) ) can target the minor groove of 5'-ACGCGT-3' as an antiparallel stacked dimer and has shown good activity in inhibiting transcription factor binding. Recently, f-Im-Py-Im-Am(+) derivatives that involve different orthogonally positioned substituents were synthesized to target the same binding site, and some of them have displayed improved binding and pharmacological properties. In this study, the gel electrophoresis-ligation ladders assay was used to evaluate the conformational effects of f-Im-Py-Im-Am(+) and derivatives on the target DNA, an essential factor for establishing the molecular basis of polyamide-DNA complexes and their transcription factor inhibition. The results show that the ACGCGT site in DNA has a relatively wide minor groove and a B-form like overall structure. After binding with f-Im-Py-Im-Am(+) derivatives, the DNA conformation is changed as indicated by the different mobilities in the gel. These conformational effects on DNA will at least help to point to the mechanism for the observed Mlu 1 inhibition activity of these polyamides. Therefore, modulating DNA transcription by locking the DNA shape or altering the minor groove geometry to affect the binding affinity of certain transcription factors is an attractive possible therapeutic mechanism for polyamides. Some of the substituents are charged with electrostatic interactions with DNA phosphate groups, and their charge effects on DNA gel mobility have been observed.
Collapse
Affiliation(s)
- Shuo Wang
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA
| | | | | | | | | | | |
Collapse
|
18
|
Madureira J, Ramos CIV, Marques M, Maia C, de Sousa B, Campino L, Santana-Marques MG, Farrell N. Nonclassic Metallointercalators with Dipyridophenazine: DNA Interaction Studies and Leishmanicidal Activity. Inorg Chem 2013; 52:8881-94. [DOI: 10.1021/ic401067d] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- João Madureira
- Department of Chemistry, Virginia Commonwealth University, 1001 West Main Street, Richmond,
Virginia 23284, United States
- Departamento de Química e Bioquímica, Universidade de Lisboa, Campo Grande, 1749-016 Lisboa,
Portugal
| | - Catarina I. V. Ramos
- Departamento de
Química, Universidade de Aveiro,
Campus de Santiago, 3810-193 Aveiro, Portugal
| | | | | | | | - Lenea Campino
- Departamento Ciências Biomédicas e Medicina, Universidade do Algarve, Campus de Gambelas, 8000-117
Faro, Portugal
| | | | - Nicholas Farrell
- Department of Chemistry, Virginia Commonwealth University, 1001 West Main Street, Richmond,
Virginia 23284, United States
| |
Collapse
|
19
|
Jędrzejewska B, Bajorek A, Moraczewska J. Interaction of carbocyanine dyes with DNA: synthesis and spectroscopic studies. APPLIED SPECTROSCOPY 2013; 67:672-680. [PMID: 23735253 DOI: 10.1366/12-06887] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Six carbocyanine dyes have been synthesized and their interactions with DNA have been investigated for their prospective use as fluorescent markers in molecular biology. The noncovalent binding of the compounds with DNA was explored by fluorescence spectroscopy, ultraviolet/visible spectrophotometry, and photobleaching. The electron-withdrawing ability of the substituents in N-position of free thio- and selenocarbocyanines strongly affected their photostabilities. Changes in the experimental conditions, such as the presence or absence of oxygen, had an impact on the rate of photobleaching. In the presence of DNA, absorbance photofading and fluorescence photobleaching occurred. It appears that the reduction of fluorescence intensity was due to quenching of the dye fluorescence by interaction with DNA.
Collapse
Affiliation(s)
- Beata Jędrzejewska
- Faculty of Chemical Technology and Engineering, University of Technology and Life Sciences, Seminaryjna 3, 85-326 Bydgoszcz, Poland.
| | | | | |
Collapse
|
20
|
Kashanian S, Javanmardi S, Chitsazan A, Paknejad M, Omidfar K. Fluorometric study of fluoxetine DNA binding. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2012; 113:1-6. [DOI: 10.1016/j.jphotobiol.2012.04.002] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2012] [Revised: 04/03/2012] [Accepted: 04/04/2012] [Indexed: 11/27/2022]
|
21
|
Beckford SJ, Dixon DW. Molecular Dynamics of Anthraquinone DNA Intercalators with Polyethylene Glycol Side Chains. J Biomol Struct Dyn 2012; 29:1065-80. [DOI: 10.1080/073911012010525031] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
|
22
|
Brucoli F, Natoli A, Marimuthu P, Borrello MT, Stapleton P, Gibbons S, Schätzlein A. Efficient synthesis and biological evaluation of proximicins A, B and C. Bioorg Med Chem 2012; 20:2019-24. [PMID: 22364744 DOI: 10.1016/j.bmc.2012.01.043] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2011] [Accepted: 01/26/2012] [Indexed: 10/14/2022]
Abstract
A quick and efficient synthesis and the biological evaluation of promising antitumor-antibiotics proximicins A, B and C are reported. The characteristic repetitive unit of these molecules, the methyl 4-Boc-aminofuran-2-carboxylate 15, was prepared in three synthetic steps in good yield using an optimised copper-catalysed amidation method. The proximicins were evaluated for their antitumor activity using cellular methods. Proximicin B induced apoptosis in both Hodgkin's lymphoma and T-cell leukemia cell lines and proximicin C exhibited significantly high cytotoxicity against glioblastoma and breast carcinoma cells. The proximicins were also screened against Escherichia coli, Enterococcus faecalis and several strains of methicillin-and multidrug-resistant Staphylococcus aureus. Proximicin B showed noteworthy activity against antibiotic-resistant Gram-positive cocci.
Collapse
Affiliation(s)
- Federico Brucoli
- UCL School of Pharmacy, 29-39 Brunswick Square, London, WC1N 1AX, UK.
| | | | | | | | | | | | | |
Collapse
|
23
|
Wang S, Munde M, Wang S, Wilson WD. Minor groove to major groove, an unusual DNA sequence-dependent change in bend directionality by a distamycin dimer. Biochemistry 2011; 50:7674-83. [PMID: 21800847 DOI: 10.1021/bi201010g] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
DNA sequence-dependent conformational changes induced by the minor groove binder, distamycin, have been evaluated by polyacrylamide gel electrophoresis. The distamycin binding affinity, cooperativity, and stoichiometry with three target DNA sequences that have different sizes of alternating AT sites, ATAT, ATATA, and ATATAT, have been determined by mass spectrometry and surface plasmon resonance to help explain the conformational changes. The results show that distamycin binds strongly to and bends five or six AT base pair minor groove sites as a dimer with positive cooperativity, while it binds to ATAT as a weak, slightly anticooperative dimer. The bending direction was evaluated with an in phase A-tract reference sequence. Unlike other similar monomer minor groove binding compounds, such as netropsin, the distamycin dimer changes the directionality of the overall curvature away from the minor groove to the major groove. This distinct structural effect may allow designed distamycin derivatives to have selective therapeutic effects.
Collapse
Affiliation(s)
- Shuo Wang
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30303, United States
| | | | | | | |
Collapse
|
24
|
Pazos E, Mosquera J, Vázquez ME, Mascareñas JL. DNA Recognition by Synthetic Constructs. Chembiochem 2011; 12:1958-73. [DOI: 10.1002/cbic.201100247] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2011] [Indexed: 12/29/2022]
|
25
|
Lo ATS, Salam NK, Hibbs DE, Rutledge PJ, Todd MH. Polyamide-scorpion cyclam lexitropsins selectively bind AT-rich DNA independently of the nature of the coordinated metal. PLoS One 2011; 6:e17446. [PMID: 21573061 PMCID: PMC3090394 DOI: 10.1371/journal.pone.0017446] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2010] [Accepted: 02/03/2011] [Indexed: 01/17/2023] Open
Abstract
Cyclam was attached to 1-, 2- and 3-pyrrole lexitropsins for the first time through a synthetically facile copper-catalyzed "click" reaction. The corresponding copper and zinc complexes were synthesized and characterized. The ligand and its complexes bound AT-rich DNA selectively over GC-rich DNA, and the thermodynamic profile of the binding was evaluated by isothermal titration calorimetry. The metal, encapsulated in a scorpion azamacrocyclic complex, did not affect the binding, which was dominated by the organic tail.
Collapse
Affiliation(s)
- Anthony T. S. Lo
- School of Chemistry, University of Sydney, Sydney, New South Wales,
Australia
| | - Noeris K. Salam
- Schrödinger, Inc., New York, New York, United States of
America
| | - David E. Hibbs
- Faculty of Pharmacy, University of Sydney, Sydney, New South Wales,
Australia
| | - Peter J. Rutledge
- School of Chemistry, University of Sydney, Sydney, New South Wales,
Australia
| | - Matthew H. Todd
- School of Chemistry, University of Sydney, Sydney, New South Wales,
Australia
| |
Collapse
|
26
|
Srivastava HK, Chourasia M, Kumar D, Sastry GN. Comparison of Computational Methods to Model DNA Minor Groove Binders. J Chem Inf Model 2011; 51:558-71. [DOI: 10.1021/ci100474n] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Hemant Kumar Srivastava
- Molecular Modelling Group, Indian Institute of Chemical Technology, Taranaka, Hyderabad 500 607, India
| | - Mukesh Chourasia
- Molecular Modelling Group, Indian Institute of Chemical Technology, Taranaka, Hyderabad 500 607, India
| | - Devesh Kumar
- Molecular Modelling Group, Indian Institute of Chemical Technology, Taranaka, Hyderabad 500 607, India
| | - G. Narahari Sastry
- Molecular Modelling Group, Indian Institute of Chemical Technology, Taranaka, Hyderabad 500 607, India
| |
Collapse
|
27
|
Sánchez MI, Vázquez O, Vázquez ME, Mascareñas JL. Light-controlled DNA binding of bisbenzamidines. Chem Commun (Camb) 2011; 47:11107-9. [DOI: 10.1039/c1cc13355a] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
|
28
|
Yue H, Zhu Y, Wang Y, Chen G. Investigation and improvement of DNA cleavage models of polyamide + Cu(II) nuclease + OOH- ligands bound to DNA. BMC STRUCTURAL BIOLOGY 2010; 10:35. [PMID: 20950488 PMCID: PMC2984560 DOI: 10.1186/1472-6807-10-35] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2010] [Accepted: 10/17/2010] [Indexed: 11/10/2022]
Abstract
Background Copper nucleases as a famous class of artificial metallonucleases have attracted considerable interest in relation to their diverse potentials not only as therapeutic agents but also in genomic researches. Copper nucleases present high efficient oxidative cleavage of DNA, in which DNA strand scission occurs generally after hydrogen atom abstracted from a sugar moiety. In order to achieve the selective cleavage of DNA sequences by copper nucleases, the DNA specific recognition agents of the Dervan-type hairpin and cyclic polyamides can be considered as proper carriers of copper nucleases. Investigation of the DNA cleavage selectivity of copper nucleases assisted by the hairpin and cyclic polyamides at the molecular level has not yet been elucidated. Results We carried out a series of molecular dynamics simulations for the nuclease [Cu(BPA)]2+ or [Cu(IDB)]2+ bound to the hairpin/cyclic polyamide and associated with DNA to investigate the selective DNA cleavage properties of Cu(II)-based artificial nucleases. The simulated results demonstrate that the DNA cleavage selectivity of the two nucleases assisted by the hairpin polyamide is improved efficiently. The [Cu(BPA)]2+ or [Cu(IDB)]2+ nuclease with a substrate OOH- bound to the hairpin polyamide can be stably located at the minor groove of DNA, and possibly abstracts H atom from the sugar of DNA. However, the DNA cleavage properties of the two nucleases assisted by the cyclic polyamide are significantly poor due to the rigidity of linking region between the cyclic polyamide and nuclease. With introduction of the flexible linker -CH2CH2CH2NH2, the modified cyclic polyamide can assist the two copper nucleases to improve the selective DNA cleavage properties efficiently. Conclusion A flexible linker and a proper binding site of the polyamide-type recognition agents play an important role in improving the DNA cleavage selectivity of copper nucleases. Current investigations provide an insight into the DNA cleavage specificities of chemical nucleases assisted by an appropriate nucleic acid recognition agent.
Collapse
Affiliation(s)
- Hongwei Yue
- College of Chemistry, Beijing Normal University, Beijing100875, China
| | | | | | | |
Collapse
|
29
|
Wang M, Holmes-Davis R, Rafinski Z, Jedrzejewska B, Choi KY, Zwick M, Bupp C, Izmailov A, Paczkowski J, Warner B, Koshinsky H. Accelerated photobleaching of a cyanine dye in the presence of a ternary target DNA, PNA probe, dye catalytic complex: a molecular diagnostic. Anal Chem 2010; 81:2043-52. [PMID: 19231844 DOI: 10.1021/ac702519k] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
In many settings, molecular testing is needed but unavailable due to complexity and cost. Simple, rapid, and specific DNA detection technologies would provide important alternatives to existing detection methods. Here we report a novel, rapid nucleic acid detection method based on the accelerated photobleaching of the light-sensitive cyanine dye, 3,3'-diethylthiacarbocyanine iodide (DiSC(2)(3) I(-)), in the presence of a target genomic DNA and a complementary peptide nucleic acid (PNA) probe. On the basis of the UV-vis, circular dichroism, and fluorescence spectra of DiSC(2)(3) with PNA-DNA oligomer duplexes and on characterization of a product of photolysis of DiSC(2)(3) I(-), a possible reaction mechanism is proposed. We propose that (1) a novel complex forms between dye, PNA, and DNA, (2) this complex functions as a photosensitizer producing (1)O(2), and (3) the (1)O(2) produced promotes photobleaching of dye molecules in the mixture. Similar cyanine dyes (DiSC(3)(3), DiSC(4)(3), DiSC(5)(3), and DiSC(py)(3)) interact with preformed PNA-DNA oligomer duplexes but do not demonstrate an equivalent accelerated photobleaching effect in the presence of PNA and target genomic DNA. The feasibility of developing molecular diagnostic assays based on the accelerated photobleaching (the smartDNA assay) that results from the novel complex formed between DiSC(2)(3) and PNA-DNA is under way.
Collapse
Affiliation(s)
- M Wang
- Investigen Inc., Hercules, California, USA
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
30
|
Selective binding of small molecules to DNA: Application and perspectives. Colloids Surf B Biointerfaces 2010; 79:1-4. [DOI: 10.1016/j.colsurfb.2010.03.048] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2010] [Accepted: 03/31/2010] [Indexed: 11/22/2022]
|
31
|
Jain AK, Bhattacharya S. Groove Binding Ligands for the Interaction with Parallel-Stranded ps-Duplex DNA and Triplex DNA. Bioconjug Chem 2010; 21:1389-403. [DOI: 10.1021/bc900247s] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Akash K. Jain
- Department of Organic Chemistry, Indian Institute of Science, Bangalore 560012, India, Chemical Biology Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore 560012, India
| | - Santanu Bhattacharya
- Department of Organic Chemistry, Indian Institute of Science, Bangalore 560012, India, Chemical Biology Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore 560012, India
| |
Collapse
|
32
|
Specificity landscapes of DNA binding molecules elucidate biological function. Proc Natl Acad Sci U S A 2010; 107:4544-9. [PMID: 20176964 DOI: 10.1073/pnas.0914023107] [Citation(s) in RCA: 87] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Evaluating the specificity spectra of DNA binding molecules is a nontrivial challenge that hinders the ability to decipher gene regulatory networks or engineer molecules that act on genomes. Here we compare the DNA sequence specificities for different classes of proteins and engineered DNA binding molecules across the entire sequence space. These high-content data are visualized and interpreted using an interactive "specificity landscape" which simultaneously displays the affinity and specificity of a million-plus DNA sequences. Contrary to expectation, specificity landscapes reveal that synthetic DNA ligands match, and often surpass, the specificities of eukaryotic DNA binding proteins. The landscapes also identify differential specificity constraints imposed by diverse structural folds of natural and synthetic DNA binders. Importantly, the sequence context of a binding site significantly influences binding energetics, and utilizing the full contextual information permits greater accuracy in annotating regulatory elements within a given genome. Assigning such context-dependent binding values to every DNA sequence across the genome yields predictive genome-wide binding landscapes (genomescapes). A genomescape of a synthetic DNA binding molecule provided insight into its differential regulatory activity in cultured cells. The approach we describe will accelerate the creation of precision-tailored DNA therapeutics and uncover principles that govern sequence-specificity of DNA binding molecules.
Collapse
|
33
|
Lahiri D, Roy S, Saha S, Majumdar R, Dighe RR, Chakravarty AR. Anaerobic DNA cleavage activity in red light and photocytotoxicity of (pyridine-2-thiol)cobalt(iii) complexes of phenanthroline bases. Dalton Trans 2010; 39:1807-16. [DOI: 10.1039/b917860k] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
|
34
|
Synthesis and evaluation of a netropsin–proximicin-hybrid library for DNA binding and cytotoxicity. Bioorg Med Chem Lett 2009; 19:3811-5. [DOI: 10.1016/j.bmcl.2009.04.042] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2009] [Revised: 04/07/2009] [Accepted: 04/08/2009] [Indexed: 11/21/2022]
|
35
|
Wolter FE, Schneider K, Davies BP, Socher ER, Nicholson G, Seitz O, Süssmuth RD. Total Synthesis of Proximicin A−C and Synthesis of New Furan-Based DNA Binding Agents. Org Lett 2009; 11:2804-7. [DOI: 10.1021/ol901003p] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Falko E. Wolter
- Institut für Chemie, TU Berlin, Strasse des 17. Juni 124, 10623 Berlin, Germany, Institut für Chemie, HU Berlin, Brook-Taylor-Strasse 2, 12489 Berlin, Germany, and Institut für Chemie, Eberhard-Karls-Universität Tübingen, Auf der Morgenstelle 18, 72076 Tübingen, Germany
| | - Kathrin Schneider
- Institut für Chemie, TU Berlin, Strasse des 17. Juni 124, 10623 Berlin, Germany, Institut für Chemie, HU Berlin, Brook-Taylor-Strasse 2, 12489 Berlin, Germany, and Institut für Chemie, Eberhard-Karls-Universität Tübingen, Auf der Morgenstelle 18, 72076 Tübingen, Germany
| | - Brian P. Davies
- Institut für Chemie, TU Berlin, Strasse des 17. Juni 124, 10623 Berlin, Germany, Institut für Chemie, HU Berlin, Brook-Taylor-Strasse 2, 12489 Berlin, Germany, and Institut für Chemie, Eberhard-Karls-Universität Tübingen, Auf der Morgenstelle 18, 72076 Tübingen, Germany
| | - Elke R. Socher
- Institut für Chemie, TU Berlin, Strasse des 17. Juni 124, 10623 Berlin, Germany, Institut für Chemie, HU Berlin, Brook-Taylor-Strasse 2, 12489 Berlin, Germany, and Institut für Chemie, Eberhard-Karls-Universität Tübingen, Auf der Morgenstelle 18, 72076 Tübingen, Germany
| | - Graeme Nicholson
- Institut für Chemie, TU Berlin, Strasse des 17. Juni 124, 10623 Berlin, Germany, Institut für Chemie, HU Berlin, Brook-Taylor-Strasse 2, 12489 Berlin, Germany, and Institut für Chemie, Eberhard-Karls-Universität Tübingen, Auf der Morgenstelle 18, 72076 Tübingen, Germany
| | - Oliver Seitz
- Institut für Chemie, TU Berlin, Strasse des 17. Juni 124, 10623 Berlin, Germany, Institut für Chemie, HU Berlin, Brook-Taylor-Strasse 2, 12489 Berlin, Germany, and Institut für Chemie, Eberhard-Karls-Universität Tübingen, Auf der Morgenstelle 18, 72076 Tübingen, Germany
| | - Roderich D. Süssmuth
- Institut für Chemie, TU Berlin, Strasse des 17. Juni 124, 10623 Berlin, Germany, Institut für Chemie, HU Berlin, Brook-Taylor-Strasse 2, 12489 Berlin, Germany, and Institut für Chemie, Eberhard-Karls-Universität Tübingen, Auf der Morgenstelle 18, 72076 Tübingen, Germany
| |
Collapse
|
36
|
Nguyen B, Neidle S, Wilson WD. A role for water molecules in DNA-ligand minor groove recognition. Acc Chem Res 2009; 42:11-21. [PMID: 18798655 DOI: 10.1021/ar800016q] [Citation(s) in RCA: 100] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Targeting the minor groove of DNA through binding to a small molecule has long been considered an important molecular-recognition strategy in biology. A wide range of synthetic heterocyclic molecules bind noncovalently in the minor groove of the double helix and are also effective against a number of human and animal diseases. A classic structural concept, the isohelicity principle, has guided much of this work: such heterocyclic molecules require a shape that complements the convex surface of the minor groove. Researchers have used this principle to design molecules that can read DNA sequences. This principle also predicts that molecules that lack the complementary shape requirement would only bind weakly to DNA. Recently, however, researchers have unexpectedly found that some essentially linear compounds, which do not have this feature, can have high DNA affinity. In this Account, we discuss an alternative recognition concept based on these new findings. We demonstrate that highly structured water molecules can play a key role in mediating between the ligand and DNA minor groove without loss of binding affinity. Combined structural and thermodynamic approaches to understanding the behavior of these molecules have shown that there are different categories of bound water in their DNA complexes. For example, application of this water-bridging concept to the phenylamidine platform has resulted in the discovery of molecules with high levels of biological activity and low nonspecific toxicity. Some of these molecules are now in advanced clinical trials.
Collapse
Affiliation(s)
- Binh Nguyen
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30302
| | - Stephen Neidle
- CRUK Biomolecular Structure Group, The School of Pharmacy, University of London, London WC1N 1AX, U.K
| | - W. David Wilson
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30302
| |
Collapse
|
37
|
Vázquez O, Blanco-Canosa JB, Vázquez ME, Martínez-Costas J, Castedo L, Mascareñas JL. Efficient DNA binding and nuclear uptake by distamycin derivatives conjugated to octa-arginine sequences. Chembiochem 2009; 9:2822-9. [PMID: 18942688 DOI: 10.1002/cbic.200800345] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Efficient targeting of DNA by designed molecules requires not only careful fine-tuning of their DNA-recognition properties, but also appropriate cell internalization of the compounds so that they can reach the cell nucleus in a short period of time. Previous observations in our group on the relatively high affinity displayed by conjugates between distamycin derivatives and bZIP basic regions for A-rich DNA sites, led us to investigate whether the covalent attachment of a positively charged cell-penetrating peptide to a distamycin-like tripyrrole might yield high affinity DNA binders with improved cell internalization properties. Our work has led to the discovery of synthetic tripyrrole-octa-arginine conjugates that are capable of targeting specific DNA sites that contain A-rich tracts with low nanomolar affinity; they simultaneously exhibit excellent membrane and nuclear translocation properties in living HeLa cells.
Collapse
Affiliation(s)
- Olalla Vázquez
- Departamento de Química Orgánica, Universidad de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | | | | | | | | | | |
Collapse
|
38
|
Mura C, McCammon JA. Molecular dynamics of a kappaB DNA element: base flipping via cross-strand intercalative stacking in a microsecond-scale simulation. Nucleic Acids Res 2008; 36:4941-55. [PMID: 18653524 PMCID: PMC2528173 DOI: 10.1093/nar/gkn473] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
The sequence-dependent structural variability and conformational dynamics of DNA play pivotal roles in many biological milieus, such as in the site-specific binding of transcription factors to target regulatory elements. To better understand DNA structure, function, and dynamics in general, and protein···DNA recognition in the ‘κB’ family of genetic regulatory elements in particular, we performed molecular dynamics simulations of a 20-bp DNA encompassing a cognate κB site recognized by the proto-oncogenic ‘c-Rel’ subfamily of NF-κB transcription factors. Simulations of the κB DNA in explicit water were extended to microsecond duration, providing a broad, atomically detailed glimpse into the structural and dynamical behavior of double helical DNA over many timescales. Of particular note, novel (and structurally plausible) conformations of DNA developed only at the long times sampled in this simulation—including a peculiar state arising at ≈0.7 μs and characterized by cross-strand intercalative stacking of nucleotides within a longitudinally sheared base pair, followed (at ≈1 μs) by spontaneous base flipping of a neighboring thymine within the A-rich duplex. Results and predictions from the microsecond-scale simulation include implications for a dynamical NF-κB recognition motif, and are amenable to testing and further exploration via specific experimental approaches that are suggested herein.
Collapse
Affiliation(s)
- Cameron Mura
- Department of Chemistry and Biochemistry and Center for Theoretical Biological Physics, University of California, San Diego, La Jolla, CA 92093-0365, USA.
| | | |
Collapse
|
39
|
Holt PA, Chaires JB, Trent JO. Molecular docking of intercalators and groove-binders to nucleic acids using Autodock and Surflex. J Chem Inf Model 2008; 48:1602-15. [PMID: 18642866 DOI: 10.1021/ci800063v] [Citation(s) in RCA: 144] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The molecular docking tools Autodock and Surflex accurately reproduce the crystallographic structures of a collection of small molecule ligands that have been shown to bind nucleic acids. Docking studies were performed with the intercalators daunorubicin and ellipticine and the minor groove binders distamycin and pentamidine. Autodock and Surflex dock daunorubicin and distamycin to their nucleic acid targets within a resolution of approximately 2 A, which is similar to the limit of the crystal structure resolution. However, for the top ranked poses, Autodock and Surflex both dock ellipticine into the correct site but in a different orientation compared to the crystal structure. This appears not only to be partly related to the symmetry of the target nucleic acid, as ellipticine is able to dock from either side of the intercalation site, but also due to the shape of the ligand and docking accuracy. Surflex docks pentamidine in a symmetrically equivalent orientation relative to the crystal structure, while Autodock was able to dock this molecule in the original orientation. In the case of the Surflex docking of pentamidine, the initial rmsd is misleading, given the symmetrical structure of pentamidine. Importantly, the ranking functions of both of these programs are able to return a top pose within approximately 2 A rmsd for daunorubicin, distamycin, and pentamidine and approximately 3 A rmsd for ellipticine compared to their respective crystal structures. Some docking challenges and potential pitfalls are explored, such as the importance of hydrogen treatment on ligands as well as the scoring functions of Autodock and Surflex. Overall for this set of complexes, Surflex is preferred over Autodock for virtual screening, as although the results are comparable, Surflex has significantly faster performance and ease of use under the optimal software conditions tested. These experiments show that molecular docking techniques can be successfully extended to include nucleic acid targets, a finding which has important implications for virtual screening applications and in the design of new small molecules to target therapeutically relevant morphologies of nucleic acids.
Collapse
Affiliation(s)
- Patrick A Holt
- James Graham Brown Cancer Center and the Department of Medicine, University of Louisville, 5239 S. Jackson Street, Louisville, KY 40202, USA
| | | | | |
Collapse
|
40
|
Bouchemal K. New challenges for pharmaceutical formulations and drug delivery systems characterization using isothermal titration calorimetry. Drug Discov Today 2008; 13:960-72. [PMID: 18617012 DOI: 10.1016/j.drudis.2008.06.004] [Citation(s) in RCA: 110] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2008] [Revised: 02/29/2008] [Accepted: 06/04/2008] [Indexed: 11/25/2022]
Abstract
Long viewed as the 'method of choice' for characterizing thermodynamics and stoichiometry of molecular interactions, with high sensitivity, isothermal titration calorimetry (ITC) has been applied to many areas of pharmaceutical analysis. This review highlights ITC employment to measure binding thermodynamics and their use for pharmaceutical formulations and drug delivery system characterization particularly cyclodextrin-guest interactions, investigation of micellar-based systems, polyelectrolytes, nucleic acid interactions with multivalent cations and the optimization of DNA targeting and delivery. Furthermore, the potential of ITC for the characterization of different functionalities carried by nanoparticles as well as their interaction with living systems was outlined.
Collapse
Affiliation(s)
- Kawthar Bouchemal
- Université Paris-Sud 11, School of Pharmacy, UMR CNRS 8612, 5 Rue J.B. Clément, 92296 Châtenay Malabry, France.
| |
Collapse
|
41
|
Hampshire AJ, Fox KR. The effects of local DNA sequence on the interaction of ligands with their preferred binding sites. Biochimie 2008; 90:988-98. [DOI: 10.1016/j.biochi.2008.01.001] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2007] [Accepted: 01/04/2008] [Indexed: 10/22/2022]
|
42
|
Affiliation(s)
- Jonathan B. Chaires
- James Graham Brown Cancer Center, University of Louisville, Louisville, Kentucky 40202;
| |
Collapse
|
43
|
Mai A, Khan GS, Clark GR, Barker D. N-{3-[Bis(2-hydroxy-ethyl)amino-meth-yl]-5-nitro-phen-yl}benzamide. Acta Crystallogr Sect E Struct Rep Online 2008; 64:o978-9. [PMID: 21202707 PMCID: PMC2961623 DOI: 10.1107/s1600536808009410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2008] [Accepted: 04/06/2008] [Indexed: 12/03/2022]
Abstract
The title compound, C18H21N3O5, was prepared by the reaction of 3-benzamido-5-nitrobenzyl methanesulfonate with diethanolamine and is an intermediate in the synthesis of DNA minor-groove-binding polybenzamide agents capable of being conjugated to additional biologically active species. The asymmetric unit contains two independent molecules, which differ only in the orientations of the hydroxyethyl groups. In the crystal structure, intermolecular N—H⋯O and O—H⋯O hydrogen bonds link molecules into one-dimensional chains.
Collapse
Affiliation(s)
- Anna Mai
- Department of Chemistry, The University of Auckland, Private Bag 92019, Auckland, New Zealand
| | | | | | | |
Collapse
|
44
|
Pierce SE, Sherman CL, Jayawickramarajah J, Lawrence CM, Sessler JL, Brodbelt JS. ESI-MS characterization of a novel pyrrole-inosine nucleoside that interacts with guanine bases. Anal Chim Acta 2008; 627:129-35. [PMID: 18790136 DOI: 10.1016/j.aca.2008.04.018] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2008] [Revised: 04/03/2008] [Accepted: 04/08/2008] [Indexed: 11/27/2022]
Abstract
Based on binding studies undertaken by electrospray ionization-mass spectrometry, a synthetic pyrrole-inosine nucleoside, 1, capable of forming an extended three-point Hoogsteen-type hydrogen-bonding interaction with guanine, is shown to form specific complexes with two different quadruplex DNA structures [dTG(4)T](4) and d(T(2)G(4))(4) as well as guanine-rich duplex DNA. The binding interactions of two other analogs were evaluated in order to unravel the structural features that contribute to specific DNA recognition. The importance of the Hoogsteen interactions was confirmed through the absence of specific binding when the pyrrole NH hydrogen-bonding site was blocked or removed. While 2, with a large blocking group, was not found to interact with virtually any form of DNA, 3, with the pyrrole functionality missing, was found to interact non-specifically with several types of DNA. The specific binding of 1 to guanine-rich DNA emphasizes the necessity of careful ligand design for specific sequence recognition.
Collapse
Affiliation(s)
- Sarah E Pierce
- Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, TX 78712-1167, United States
| | | | | | | | | | | |
Collapse
|
45
|
Bielawski K, Bielawska A. Small-Molecule based Delivery Systems for Alkylating Antineoplastic Compounds. ChemMedChem 2008; 3:536-42. [DOI: 10.1002/cmdc.200700229] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
|
46
|
Moretti R, Ansari AZ. Expanding the specificity of DNA targeting by harnessing cooperative assembly. Biochimie 2008; 90:1015-25. [PMID: 18343232 DOI: 10.1016/j.biochi.2008.02.014] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2008] [Accepted: 02/18/2008] [Indexed: 12/24/2022]
Abstract
The precise control of developmental and regulatory processes in the cell requires accurate recognition of specific DNA sites. For genomes as large as that of humans, single-molecule-DNA binders have difficulties accurately and specifically recognizing the intended targets. Natural transcription factors overcome these difficulties by forming non-covalent complexes on the DNA with other transcription factors. These cooperative complexes overcome the difficulties of single-molecule transcription factors, allowing specific, combinatorial control of a range of transcriptional targets. Artificial transcription factors have been designed to take advantage of this technique of cooperative assembly, facilitating future studies in whole genome targeting. In contrast to a simple model of component independence, cooperative complexes as a whole often display slightly altered DNA specificity from what would be expected from the analysis of their separate components. The true sequence specificity of cooperative complexes, and thus their presumed in vivo targets, have to be experimentally probed. A number of techniques, such as the cognate site identity array, now allow for rapid, high-throughput determination of the specificity of cooperative complexes.
Collapse
Affiliation(s)
- Rocco Moretti
- Department of Biochemistry, The Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, WI 53706, USA
| | | |
Collapse
|
47
|
Ishizuka T, Yoshida J, Yamamoto Y, Sumaoka J, Tedeschi T, Corradini R, Sforza S, Komiyama M. Chiral introduction of positive charges to PNA for double-duplex invasion to versatile sequences. Nucleic Acids Res 2008; 36:1464-71. [PMID: 18203747 PMCID: PMC2275137 DOI: 10.1093/nar/gkm1154] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2007] [Revised: 12/12/2007] [Accepted: 12/12/2007] [Indexed: 11/12/2022] Open
Abstract
Invasion of two PNA strands to double-stranded DNA is one of the most promising methods to recognize a predetermined site in double-stranded DNA (PNA = peptide nucleic acid). In order to facilitate this 'double-duplex invasion', a new type of PNA was prepared by using chiral PNA monomers in which a nucleobase was bound to the alpha-nitrogen of N-(2-aminoethyl)-d-lysine. These positively charged monomer units, introduced to defined positions in Nielsen's PNAs (poly[N-(2-aminoethyl)glycine] derivatives), promoted the invasion without impairing mismatch-recognizing activity. When pseudo-complementary nucleobases 2,6-diaminopurine and 2-thiouracil were bound to N-(2-aminoethyl)-d-lysine, the invasion successfully occurred even at highly G-C-rich regions [e.g. (G/C)7(A/T)3 and (G/C)8(A/T)2] which were otherwise hardly targeted. Thus, the scope of sequences available as the target site has been greatly expanded. In contrast with the promotion by the chiral PNA monomers derived from N-(2-aminoethyl)-d-lysine, their l-isomers hardly invaded, showing crucial importance of the d-chirality. The promotion of double-duplex invasion by the chiral (d) PNA monomer units was ascribed to both destabilization of PNA/PNA duplex and stabilization of PNA/DNA duplexes.
Collapse
Affiliation(s)
- Takumi Ishizuka
- Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo, 153-8904 Japan and Department of Organic and Industrial Chemistry, University of Parma, Viale G.P. Usberti 17/a, University Campus, Parma, I-43100 Italy
| | - Junya Yoshida
- Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo, 153-8904 Japan and Department of Organic and Industrial Chemistry, University of Parma, Viale G.P. Usberti 17/a, University Campus, Parma, I-43100 Italy
| | - Yoji Yamamoto
- Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo, 153-8904 Japan and Department of Organic and Industrial Chemistry, University of Parma, Viale G.P. Usberti 17/a, University Campus, Parma, I-43100 Italy
| | - Jun Sumaoka
- Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo, 153-8904 Japan and Department of Organic and Industrial Chemistry, University of Parma, Viale G.P. Usberti 17/a, University Campus, Parma, I-43100 Italy
| | - Tullia Tedeschi
- Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo, 153-8904 Japan and Department of Organic and Industrial Chemistry, University of Parma, Viale G.P. Usberti 17/a, University Campus, Parma, I-43100 Italy
| | - Roberto Corradini
- Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo, 153-8904 Japan and Department of Organic and Industrial Chemistry, University of Parma, Viale G.P. Usberti 17/a, University Campus, Parma, I-43100 Italy
| | - Stefano Sforza
- Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo, 153-8904 Japan and Department of Organic and Industrial Chemistry, University of Parma, Viale G.P. Usberti 17/a, University Campus, Parma, I-43100 Italy
| | - Makoto Komiyama
- Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo, 153-8904 Japan and Department of Organic and Industrial Chemistry, University of Parma, Viale G.P. Usberti 17/a, University Campus, Parma, I-43100 Italy
| |
Collapse
|
48
|
2-Aminopurine/cytosine base pair containing oligonucleotides: fluorescence spectroscopy studies on DNA-polyamide binding. Biochem Biophys Res Commun 2008; 369:630-4. [PMID: 18294452 DOI: 10.1016/j.bbrc.2008.02.049] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2008] [Accepted: 02/14/2008] [Indexed: 11/22/2022]
Abstract
Studies on the binding of a triamide f-IPI (1) to its cognate sequence labeled with a 2-aminopurine (2AP or G( *)) group are described. ITC studies showed that f-IPI (1) bound to the cognate site (ACG( *)CGT) with only 3.5-fold lower affinity than binding to the unlabeled DNA (ACGCGT) (K(eq)=2 x 10(7) and 7 x 10(7)M(-1), respectively). Titration of f-IPI (1) to both sequences gave strong induced bands at 330 nm via circular dichroism studies. The compound also gave comparable DeltaT(m) values of 5.0 and 7.8 degrees C, respectively. These techniques also proved that the sequence selectivity of f-IPI (1) was uncompromised, as only limited binding to the non-cognate sequence ACCG( *)GT was observed. Fluorescence studies demonstrated a 2:1 ligand:DNA binding motif as anticipated, and indicated that the limit of detection for this technique was 20muM DNA concentration. The results demonstrate that 2-aminopurine is a sufficient substitute for guanine in a G.C base pair useful in DNA binding studies.
Collapse
|
49
|
Mulder K, Sexton J, Taherbhai Z, Jones J, Uthe P, Brown T, Lee M. N‐Formamido‐Containing Mono‐ and Diheterocyclic Pyrrole‐and Imidazole‐2‐carboxylic Acids as Building Blocks for Polyamide Synthesis. SYNTHETIC COMMUN 2008. [DOI: 10.1080/00397910701648785] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Keith Mulder
- a Division of Natural and Applied Sciences and Department of Chemistry , Hope College , Holland, Michigan, USA
| | - Jim Sexton
- b Department of Chemistry , Furman University , Greenville, South Carolina, USA
| | - Zarmeen Taherbhai
- b Department of Chemistry , Furman University , Greenville, South Carolina, USA
| | - Justin Jones
- b Department of Chemistry , Furman University , Greenville, South Carolina, USA
| | - Peter Uthe
- b Department of Chemistry , Furman University , Greenville, South Carolina, USA
| | - Toni Brown
- a Division of Natural and Applied Sciences and Department of Chemistry , Hope College , Holland, Michigan, USA
- b Department of Chemistry , Furman University , Greenville, South Carolina, USA
| | - Moses Lee
- a Division of Natural and Applied Sciences and Department of Chemistry , Hope College , Holland, Michigan, USA
- b Department of Chemistry , Furman University , Greenville, South Carolina, USA
| |
Collapse
|
50
|
Lah J, Drobnak I, Dolinar M, Vesnaver G. What drives the binding of minor groove-directed ligands to DNA hairpins? Nucleic Acids Res 2007; 36:897-904. [PMID: 18086706 PMCID: PMC2241884 DOI: 10.1093/nar/gkm1110] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Understanding the molecular basis of ligand-DNA-binding events, and its application to the rational design of novel drugs, requires knowledge of the structural features and forces that drive the corresponding recognition processes. Existing structural evidence on DNA complexation with classical minor groove-directed ligands and the corresponding studies of binding energetics have suggested that this type of binding can be described as a rigid-body association. In contrast, we show here that the binding-coupled conformational changes may be crucial for the interpretation of DNA (hairpin) association with a classical minor groove binder (netropsin). We found that, although the hairpin form is the only accessible state of ligand-free DNA, its association with the ligand may lead to its transition into a duplex conformation. It appears that formation of the fully ligated duplex from the ligand-free hairpin, occurring via two pathways, is enthalpically driven and accompanied by a significant contribution of the hydrophobic effect. Our thermodynamic and structure-based analysis, together with corresponding theoretical studies, shows that none of the predicted binding steps can be considered as a rigid-body association. In this light we anticipate our thermodynamic approach to be the basis of more sophisticated nucleic acid recognition mechanisms, which take into account the dynamic nature of both the nucleic acid and the ligand molecule.
Collapse
Affiliation(s)
- Jurij Lah
- University of Ljubljana, Faculty of Chemistry and Chemical Technology, Askerceva 5, 1000 Ljubljana, Slovenia.
| | | | | | | |
Collapse
|