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Joshi J, McCauley MJ, Morse M, Muccio MR, Kanlong JG, Rocha MS, Rouzina I, Musier-Forsyth K, Williams MC. Mechanism of DNA Intercalation by Chloroquine Provides Insights into Toxicity. Int J Mol Sci 2024; 25:1410. [PMID: 38338688 PMCID: PMC10855526 DOI: 10.3390/ijms25031410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2024] [Revised: 01/18/2024] [Accepted: 01/20/2024] [Indexed: 02/12/2024] Open
Abstract
Chloroquine has been used as a potent antimalarial, anticancer drug, and prophylactic. While chloroquine is known to interact with DNA, the details of DNA-ligand interactions have remained unclear. Here we characterize chloroquine-double-stranded DNA binding with four complementary approaches, including optical tweezers, atomic force microscopy, duplex DNA melting measurements, and isothermal titration calorimetry. We show that chloroquine intercalates into double stranded DNA (dsDNA) with a KD ~ 200 µM, and this binding is entropically driven. We propose that chloroquine-induced dsDNA intercalation, which happens in the same concentration range as its observed toxic effects on cells, is responsible for the drug's cytotoxicity.
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Affiliation(s)
- Joha Joshi
- Department of Physics, Northeastern University, Boston, MA 02115, USA; (J.J.); (M.J.M.); (M.M.)
| | - Micah J. McCauley
- Department of Physics, Northeastern University, Boston, MA 02115, USA; (J.J.); (M.J.M.); (M.M.)
| | - Michael Morse
- Department of Physics, Northeastern University, Boston, MA 02115, USA; (J.J.); (M.J.M.); (M.M.)
| | - Michael R. Muccio
- Department of Chemistry and Biochemistry, Center for RNA Biology, Ohio State University, Columbus, OH 43210, USA; (M.R.M.); (J.G.K.); (I.R.); (K.M.-F.)
| | - Joseph G. Kanlong
- Department of Chemistry and Biochemistry, Center for RNA Biology, Ohio State University, Columbus, OH 43210, USA; (M.R.M.); (J.G.K.); (I.R.); (K.M.-F.)
| | - Márcio S. Rocha
- Department of Physics, Universidade Federal de Viçosa, Viçosa CEP 36570-900, MG, Brazil;
| | - Ioulia Rouzina
- Department of Chemistry and Biochemistry, Center for RNA Biology, Ohio State University, Columbus, OH 43210, USA; (M.R.M.); (J.G.K.); (I.R.); (K.M.-F.)
| | - Karin Musier-Forsyth
- Department of Chemistry and Biochemistry, Center for RNA Biology, Ohio State University, Columbus, OH 43210, USA; (M.R.M.); (J.G.K.); (I.R.); (K.M.-F.)
| | - Mark C. Williams
- Department of Physics, Northeastern University, Boston, MA 02115, USA; (J.J.); (M.J.M.); (M.M.)
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Dhal A, Nayim S, Pattanayek S, Khatun M, Barman S, Paria S, Shit B, Kundu S, Jha PK, Hossain M. Evaluation of calf thymus DNA binding of newly synthesize five 9 O Imidazolyl alkyl berberine derivative: A comparative multi-spectroscopic and calorimetric study. Int J Biol Macromol 2023; 253:126958. [PMID: 37739293 DOI: 10.1016/j.ijbiomac.2023.126958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 09/07/2023] [Accepted: 09/13/2023] [Indexed: 09/24/2023]
Abstract
DNA binding with small molecule plays an important role in the designing of various anticancer drugs with greater efficacy. The five 9-O-imidazolyl alkyl berberine derivatives (BI) of different chain length has been synthesized and fully characterized. The binding study of calf thymus DNA with these newly synthesized berberine derivative was performed using various biophysical techniques. The binding affinity of BI to calf thymus DNA increased with increasing the chain length. The binding constant value obtained from UV-Vis spectral analysis was 1.84x105for BI1, 2.01x105for BI2, 1.51 × 106 for BI3, 3.66 × 106 for BI4, 6.68 × 106. Partial intercalative binding with strong stabilization of the DNA helix was revealed from circular dichroism spectral study and viscosity measurement. From the ITC experiment it was revealed that the bindings of BI1, BI2, BI3, BI4 and BI5 to calf thymus DNA were favoured by a large positive favourable entropy and negative enthalpy change and the highest spontaneity found for BI5. With the increase in chain length the binding was driven by a stronger entropy term with a higher binding constant indicates involvement of hydrophobic force for all these interaction. High binding affinities of calf thymus DNA with berberine-imidazole derivatives might be helpful for new drug design.
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Affiliation(s)
- Asima Dhal
- Department of Chemistry, Vidyasagar University, Midnapore - 721102, West Bengal, India
| | - Sk Nayim
- Department of Chemistry, Vidyasagar University, Midnapore - 721102, West Bengal, India
| | - Swadesh Pattanayek
- Department of Chemistry, Vidyasagar University, Midnapore - 721102, West Bengal, India
| | - Munira Khatun
- Department of Chemistry, Vidyasagar University, Midnapore - 721102, West Bengal, India
| | - Subhajit Barman
- Department of Chemistry, Vidyasagar University, Midnapore - 721102, West Bengal, India
| | - Samaresh Paria
- Department of Chemistry, Vidyasagar University, Midnapore - 721102, West Bengal, India
| | - Basudev Shit
- Department of Chemistry, Vidyasagar University, Midnapore - 721102, West Bengal, India
| | - Somenath Kundu
- Department of Chemistry, Vidyasagar University, Midnapore - 721102, West Bengal, India
| | - Pradeep K Jha
- Research and Development, Ghaziabad, ACE Green Recycling Inc, Singapore
| | - Maidul Hossain
- Department of Chemistry, Vidyasagar University, Midnapore - 721102, West Bengal, India.
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Beg M, Maji A, Aktara MN, Kundu S, Paria S, Shit B, Dhal A, Islam MM, Hossain M. Multi-spectroscopic and thermodynamic profiles on HSA binding of Cassia fistula leaf based potential antibacterial and anticancer silver nanoparticles. J Biomol Struct Dyn 2023:1-13. [PMID: 37990582 DOI: 10.1080/07391102.2023.2283148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Accepted: 11/06/2023] [Indexed: 11/23/2023]
Abstract
Here, a simple, one step, lucrative and green synthesis of Cassia fistula leaf extract inspired antibacterial silver nanoparticles (CF-SNPs) was provided. Characterization of these CF-SNPs were achieved by using various spectroscopic techniques for instance Ultraviolet Visible (UV-Vis) Spectroscopy, Fourier-Transform Infrared (FTIR) Spectroscopy, Dynamic Light Scattering (DLS), Transmission Electron Microscopy (TEM) and Energy Dispersive X-ray (EDX). The effective antibacterial action of the CF-SNPs was checked against Escherichia coli (E. Coli) DH5-Alpha where MIC was 1.6 nM. Anticancer dynamism of the CF-SNPs was also tested in opposition to skin melanoma, A375 cell lines in which 4.4 nM was IC50. The binding proneness of HSA towards CF-SNPs was investigated by means of UV-Vis Spectroscopy, Fluorescence Spectroscopy, Time Resolved Fluorescence Spectroscopy, Circular Dichroism (CD) Spectroscopy, Dynamic Light Scattering, and Isothermal Titration Colorimetry (ITC). CD spectroscopy established minor secondary structural exchange of HSA in HSA-CF-SNPs complex. ITC and Time Resolved Fluorescence Spectroscopy verified the static type quenching mechanism involved in HSA-CF-SNPs complex. The binding constant was 3.45 × 108 M-1 at 298.15K from ITC study. The thermodynamic parameters showed that the interaction was occurred spontaneously by the hydrophilic forces and hydrogen bonding.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Maidul Beg
- Department of Chemistry, Vidyasagar University, Midnapore, India
| | - Anukul Maji
- Department of Chemistry, Vidyasagar University, Midnapore, India
| | - Mt Nasima Aktara
- Department of Chemistry, Vidyasagar University, Midnapore, India
| | - Somenath Kundu
- Department of Chemistry, Vidyasagar University, Midnapore, India
| | - Samaresh Paria
- Department of Chemistry, Vidyasagar University, Midnapore, India
| | - Basudev Shit
- Department of Chemistry, Vidyasagar University, Midnapore, India
| | - Asima Dhal
- Department of Chemistry, Vidyasagar University, Midnapore, India
| | | | - Maidul Hossain
- Department of Chemistry, Vidyasagar University, Midnapore, India
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Karan P, Shit B, Panja P, Khatun A, Pal J, Chakarabarti S, Pal S, Ghosh A, Hossain M. Synthesis of water-soluble novel bioactive pyridine-based azo coumarin derivative and competitive cytotoxicity, DNA binding, BSA binding study, and in silico analysis with coumarin. Bioorg Chem 2023; 138:106532. [PMID: 37172438 DOI: 10.1016/j.bioorg.2023.106532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 04/02/2023] [Accepted: 04/05/2023] [Indexed: 05/15/2023]
Abstract
The diazo coupliling reaction of 3- amino pyridine with coumarin in water medium produces water soluble 6-[3-pyridyl]azocoumarin. The synthesised compound has been fully charecterised by IR, NMR, and Mass spectroscopy. The frontier molecular orbital calculations reveal that 6-[3-pyridyl]azocoumarin is more biologically and chemically active in comparison to coumarin. The cytotoxicity evaluation confirms that 6-[3-pyridyl]azocoumarin is more active than coumarin against human brain glioblastoma cell lines, LN-229 with IC50 value 9.09 μM (IC50 value for coumarin is 9.9 μM). The compound (I) has been synthesized by coupling of diazotized solution of 3-aminopyridine with coumarin in an aqueous medium at ∼ pH 10. The structure of the compound (I) has been characterized using UV-vis, IR, NMR, and Mass spectral studies. Frontier molecular orbital calculations reveal that 6-[3-pyridyl]azocoumarin (I) is more active chemically and biologically in comparison to coumarin. IC50 value 9.09 and 9.9 μM of 6-[3-pyridyl]azocoumarin and coumarin respectively obtained in cytotoxicity evaluation confirms the enhanced activity of the synthesized compound against human brain glioblastoma cell lines, LN-229. The synthesized compound also shows strong binding interactions with DNA and BSA in comparison with coumarin. The DNA binding study shows groove binding interaction of the synthesized compound with CT-DNA. The nature of interaction, binding parameters and structural variations of BSA in the presence of the synthesized compound and coumarin have been evaluated using several usefull spectroscopy approaches such as UV -Vis, time resolved and stady state flurescence. The molecular docking interaction has been carried out to justify the experimental binding interaction with DNA and BSA.
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Affiliation(s)
- Putul Karan
- Department of Chemistry, Midnapore City College, Kuturia, Bhadutala, PaschimMedinipur, West Bengal 721129, India; Midnapore City College, Kuturia, Bhadutala, PaschimMedinipur, West Bengal 721129, India
| | - Basudev Shit
- Department of Chemistry and Chemical Technology, Vidyasagar University, Midnapore 721102, West Bengal, India
| | - Poulami Panja
- Department of Chemistry, Indian Institute Of Technology, Kharagpur, West Bengal 721302, India
| | - Amina Khatun
- Department of Biological Science, Midnapore City College, Kuturia, Bhadutala, PaschimMedinipur, West Bengal 721129, India; Midnapore City College, Kuturia, Bhadutala, PaschimMedinipur, West Bengal 721129, India
| | - Jagannath Pal
- Department of Chemistry, Midnapore City College, Kuturia, Bhadutala, PaschimMedinipur, West Bengal 721129, India; Midnapore City College, Kuturia, Bhadutala, PaschimMedinipur, West Bengal 721129, India
| | - Sudipta Chakarabarti
- Department of Biological Science, Midnapore City College, Kuturia, Bhadutala, PaschimMedinipur, West Bengal 721129, India; Midnapore City College, Kuturia, Bhadutala, PaschimMedinipur, West Bengal 721129, India
| | - Sutanuka Pal
- SutanukaPal, TCG Life Sciences, Salt Lake Sector V, Kolkata 700091, India
| | - Avishek Ghosh
- Department of Chemistry, Midnapore City College, Kuturia, Bhadutala, PaschimMedinipur, West Bengal 721129, India; Midnapore City College, Kuturia, Bhadutala, PaschimMedinipur, West Bengal 721129, India.
| | - Maidul Hossain
- Department of Chemistry and Chemical Technology, Vidyasagar University, Midnapore 721102, West Bengal, India.
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Zhang Q, Yu W, Liu Z, Li H, Liu Y, Liu X, Han Z, He J, Zeng Y, Guo Y, Liu Y. Design, synthesis, antitumor activity and ct-DNA binding study of photosensitive drugs based on porphyrin framework. Int J Biol Macromol 2023; 230:123147. [PMID: 36621729 DOI: 10.1016/j.ijbiomac.2023.123147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 11/29/2022] [Accepted: 01/01/2023] [Indexed: 01/07/2023]
Abstract
Photodynamic therapy is a promising novel tumor treatment method. In this study, novel porphyrin-chrysin photosensitizer derivatives were synthesized. Most of the compounds showed antitumor activity against human cervical cancer HeLa cells and human lung cancer A549 cells, among which compound 4c had the best photodynamic therapy effect on HeLa cells and A549 cells, with IC50 values of 6.26 μM and 23.37 μM, respectively. Free-base porphyrin-chrysin derivatives bind to DNA through surface self-stacking, and zinc metalloporphyrin-chrysin derivatives bind to ct-DNA through intercalation. Notably, the tightness of compound binding to ct-DNA was positively correlated with its antitumor activity. What's more, three-dimensional quantitative conformation studies have shown that increasing the positive charge of the porphyrin ring and introducing a strong electron-withdrawing group at the meso position of the porphyrin ring at the para-position of the benzene ring or reducing the space volume of the compound can enhance the antitumor activity.
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Affiliation(s)
- Qizhi Zhang
- Institute of Pharmacy & Pharmacology, Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, University of South China, Hengyang City, Hunan Province 421001, PR China; Hunan Provincial Key Laboratory of Tumor Microenvironment Responsive Drug Research, 28 Western Changshen Road, Hengyang City, Hunan Province 421001, PR China
| | - Wenmei Yu
- Institute of Pharmacy & Pharmacology, Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, University of South China, Hengyang City, Hunan Province 421001, PR China; Hunan Provincial Key Laboratory of Tumor Microenvironment Responsive Drug Research, 28 Western Changshen Road, Hengyang City, Hunan Province 421001, PR China
| | - Zhenhua Liu
- Institute of Pharmacy & Pharmacology, Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, University of South China, Hengyang City, Hunan Province 421001, PR China; Hunan Provincial Key Laboratory of Tumor Microenvironment Responsive Drug Research, 28 Western Changshen Road, Hengyang City, Hunan Province 421001, PR China
| | - Hui Li
- Institute of Pharmacy & Pharmacology, Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, University of South China, Hengyang City, Hunan Province 421001, PR China; Hunan Provincial Key Laboratory of Tumor Microenvironment Responsive Drug Research, 28 Western Changshen Road, Hengyang City, Hunan Province 421001, PR China
| | - Yihui Liu
- The second Hospital, University of South China, PR China
| | - Xin Liu
- Institute of Pharmacy & Pharmacology, Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, University of South China, Hengyang City, Hunan Province 421001, PR China; Hunan Provincial Key Laboratory of Tumor Microenvironment Responsive Drug Research, 28 Western Changshen Road, Hengyang City, Hunan Province 421001, PR China
| | - Zhaoshun Han
- Institute of Chemistry & Chemical Engineering, University of South China, Hengyang City, Hunan Province 421001, PR China
| | - Jun He
- Institute of Chemistry & Chemical Engineering, University of South China, Hengyang City, Hunan Province 421001, PR China
| | - Yaofu Zeng
- Institute of Pharmacy & Pharmacology, Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, University of South China, Hengyang City, Hunan Province 421001, PR China; Hunan Provincial Key Laboratory of Tumor Microenvironment Responsive Drug Research, 28 Western Changshen Road, Hengyang City, Hunan Province 421001, PR China
| | - Yu Guo
- Institute of Pharmacy & Pharmacology, Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, University of South China, Hengyang City, Hunan Province 421001, PR China; Hunan Provincial Key Laboratory of Tumor Microenvironment Responsive Drug Research, 28 Western Changshen Road, Hengyang City, Hunan Province 421001, PR China
| | - Yunmei Liu
- Institute of Pharmacy & Pharmacology, Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, University of South China, Hengyang City, Hunan Province 421001, PR China; Hunan Provincial Key Laboratory of Tumor Microenvironment Responsive Drug Research, 28 Western Changshen Road, Hengyang City, Hunan Province 421001, PR China.
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Khatun M, Jana GC, Nayim S, Dhal A, Patra A, Hossain M. Evaluation of the size effect of hydrophobic ring substitution on 9-O position of berberine on DNA binding. J Biomol Struct Dyn 2023; 41:14299-14307. [PMID: 38073529 DOI: 10.1080/07391102.2023.2180436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 02/08/2023] [Indexed: 02/25/2023]
Abstract
The interaction of deoxyribonucleic acid (DNA) with medicinally significant small molecules has long piqued the interest of researchers because its applications are directly related to the discovery of new classes of drugs. Keeping this in mind, here we report berberine derivatives and their interaction with calf thymus DNA (CT-DNA). In this report we discussed on the structural perspectives and thermodynamic characteristics of the interaction of four 9-O-substituted berberines (BRDR1 to BRDR4) with CT-DNA. The binding affinity of BRDR-DNA complexes increased with increasing the cycloalkane ring size of the substitution except BRDR2. The binding constant value obtained from UV-Visible spectral analysis was 1.12 × 106 for BRDR1, 0.37 × 106 for BRDR2, 1.72 × 106 for BRDR3 and 3.20 × 106 for BRDR4. Ferrocyanide quenching experiments revealed unequivocally that the analogues except BRDR2 had a partly intercalative binding to DNA. From the ITC experiment it was found that the bindings of BRDR1, BRDR3 and BRDR4 to DNA was favoured by negative enthalpy and positive entropy while BRDR2 was driven by positive enthalpy and positive entropy. In all cases the hydrophobic interaction plays a crucial role. Thus, the complete multispectroscopic and thermodynamic binding studies may be useful for new drug design and development.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Munira Khatun
- Department of Chemistry, Vidyasagar University, Midnapore, West Bengal, India
| | - Gopal Chandra Jana
- Department of Chemistry, Vidyasagar University, Midnapore, West Bengal, India
| | - Sk Nayim
- Department of Chemistry, Vidyasagar University, Midnapore, West Bengal, India
| | - Asima Dhal
- Department of Chemistry, Vidyasagar University, Midnapore, West Bengal, India
| | - Anirudha Patra
- Department of Chemistry, Vidyasagar University, Midnapore, West Bengal, India
| | - Maidul Hossain
- Department of Chemistry, Vidyasagar University, Midnapore, West Bengal, India
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Prostate Apoptosis Response-4 (Par-4): A Novel Target in Pyronaridine-Induced Apoptosis in Glioblastoma (GBM) Cells. Cancers (Basel) 2022; 14:cancers14133198. [PMID: 35804970 PMCID: PMC9264948 DOI: 10.3390/cancers14133198] [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: 06/03/2022] [Accepted: 06/27/2022] [Indexed: 12/10/2022] Open
Abstract
Simple Summary GBM treatment is an area of high unmet need due to the heterogeneous and anaplastic character of this cancer in turn leading to an extremely poor prognosis. Finding new molecular entities by traditional or de novo approaches to drug discovery is lengthy and expensive. Repurposing existing drugs can be attractive as the process is often less risky, more cost, and time-effective. Amongst potential drug-repurposing candidates, Pyronaridine (PYR), an antimalarial drug has shown anti-cancer effects against several cancers, however, its potential for the treatment of GBM has not been explored. In this study, we have identified a unique mechanism of action of PYR against GBM by upregulating a tumor suppressor protein, Par-4 along with the elucidation of the complex network of pathways mediated through Par-4 leading to GBM cell death. Abstract Glioblastoma (GBM) is an aggressive form of brain tumor with a median survival of approximately 12 months. With no new drugs in the last few decades and limited success in clinics for known therapies, drug repurposing is an attractive choice for its treatment. Here, we examined the efficacy of pyronaridine (PYR), an anti-malarial drug in GBM cells. PYR induced anti-proliferative activity in GBM cells with IC50 ranging from 1.16 to 6.82 µM. Synergistic activity was observed when PYR was combined with Doxorubicin and Ritonavir. Mechanistically, PYR triggered mitochondrial membrane depolarization and enhanced the ROS levels causing caspase-3 mediated apoptosis. PYR significantly decreased markers associated with proliferation, EMT, hypoxia, and stemness and upregulated the expression of E-cadherin. Interestingly, PYR induced the expression of intracellular as well as secretory Par-4, a tumor suppressor in GBM cells, which was confirmed using siRNA. Notably, Par-4 levels in plasma samples of GBM patients were significantly lower than normal healthy volunteers. Thus, our study demonstrates for the first time that PYR can be repurposed against GBM with a novel mechanism of action involving Par-4. Herewith, we discuss the role of upregulated Par-4 in a highly interconnected signaling network thereby advocating its importance as a therapeutic target.
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Small Molecule Screening Discovers Compounds that Reduce FMRpolyG Protein Aggregates and Splicing Defect Toxicity in Fragile X-Associated Tremor/Ataxia Syndrome. Mol Neurobiol 2022; 59:1992-2007. [PMID: 35040038 DOI: 10.1007/s12035-021-02697-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 12/10/2021] [Indexed: 12/20/2022]
Abstract
Expansion of CGG trinucleotide repeats in 5' untranslated region of the FMR1 gene is the causative mutation of neurological diseases such as fragile X syndrome (FXS), fragile X-associated tremor/ataxia syndrome (FXTAS), and ovarian disorder such as fragile X-associated primary ovarian insufficiency (FXPOI). CGG repeats containing FMR1 transcripts form the toxic ribonuclear aggregates, abrupt pre-mRNA splicing, and cause repeat-associated non-AUG translation, leading to the disease symptoms. Here, we utilized a small molecule library of ~ 250,000 members obtained from the National Cancer Institute (NCI) and implemented a shape-based screening approach to identify the candidate small molecules that mitigate toxic CGG RNA-mediated pathogenesis. The compounds obtained from screening were further assessed for their affinity and selectivity towards toxic CGG repeat RNA by employing fluorescence-binding experiment and isothermal calorimetry titration assay. Three candidate molecules B1, B4, and B11 showed high affinity and selectivity for expanded CGG repeats RNA. Further, NMR spectroscopy, gel mobility shift assay, CD spectroscopy, UV-thermal denaturation assay, and molecular docking affirmed their high affinity and selectivity for toxic CGG RNAs. Next, these lead compounds selectively improved the pre-mRNA alternative splicing defects with no perturbation in global splicing efficacy and simultaneously reduced the FMR1polyG protein aggregate formation without affecting the downstream expression of the gene. Taken together these findings, we addressed compound B1, B4, and B11 as potential lead molecules for developing promising therapeutics against FXTAS. Herein, this study, we have utilized shape similarity approach to screen the NCI library and found out the potential candidate which improves the pre-mRNA splicing defects and reduces FMR1polyG aggregations.
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9
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Zhang W, Du B, Gao M, Tung CH. A Hybrid Nanogel to Preserve Lysosome Integrity for Fluorescence Imaging. ACS NANO 2021; 15:16442-16451. [PMID: 34612039 DOI: 10.1021/acsnano.1c05864] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Fluorescence imaging of lysosomes provides a powerful tool to probe the lysosome physiology in living cells, yet the continuous light exposure inevitably causes lysosome damage and phototoxicity, which remains a formidable challenge. Here the long-term lysosome tracking with minimized photodamage was realized using a multifunctional nanoprobe, a platinum nanoparticle, and a quinacrine co-loaded nanogel. To construct the hybrid nanogel, cisplatin first functioned as cross-linker to withhold all components and then was reduced to a platinum nanoparticle in situ by ethanol. The platinum nanoparticle enabled a long-term quinacrine fluorescence imaging of lysosome by scavenging the light induced reactive oxygen species which could damage lysosomal membranes.
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Affiliation(s)
- Weiqi Zhang
- State Key Laboratory of Medical Molecular Biology & Department of Biomedical Engineering, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing 100005, People's Republic of China
- Molecular Imaging Innovations Institute, Department of Radiology, Weill Cornell Medicine, New York, New York 10065, United States
| | - Baoji Du
- Molecular Imaging Innovations Institute, Department of Radiology, Weill Cornell Medicine, New York, New York 10065, United States
| | - Menghan Gao
- State Key Laboratory of Medical Molecular Biology & Department of Biomedical Engineering, Institute of Basic Medical Sciences Chinese Academy of Medical Sciences, School of Basic Medicine Peking Union Medical College, Beijing 100005, People's Republic of China
| | - Ching-Hsuan Tung
- Molecular Imaging Innovations Institute, Department of Radiology, Weill Cornell Medicine, New York, New York 10065, United States
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A mononuclear PdII complex with Naphcon; crystal structure, experimental and computational studies of the interaction with DNA/BSA and evaluation of anticancer activity. Polyhedron 2021. [DOI: 10.1016/j.poly.2021.115333] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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11
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Vardevanyan PO, Antonyan AP, Parsadanyan MA, Shahinyan MA, Petrosyan NH. Study of interaction of methylene blue with DNA and albumin. J Biomol Struct Dyn 2021; 40:7779-7785. [PMID: 33729082 DOI: 10.1080/07391102.2021.1902397] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
The interaction of thiazine dye methylene blue (MB) with Calf thymus DNA and human blood serum albumin (HSA) has been studied. MB was revealed to stabilize the native structure of DNA and HSA, since the melting temperature of the complexes is shifted to higher values in relation to that of both macromolecules in pure state. It was also revealed that the absorption and fluorescence spectra of the MB-DNA complexes change significantly, while those of MB-albumin complexes do not change noticeably. Analysis of the obtained data allows to conclude that MB binds to DNA by two modes, including intercalation and electrostatic mechanisms. In the case of HSA, the main binding mode of MB, conditioning the stabilization of the protein native structure, is the electrostatic mechanism.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Poghos O Vardevanyan
- Faculty of Biology, Department of Biophysics, Yerevan State University, Yerevan, Armenia
| | - Ara P Antonyan
- Faculty of Biology, Department of Biophysics, Yerevan State University, Yerevan, Armenia
| | - Marine A Parsadanyan
- Faculty of Biology, Department of Biophysics, Yerevan State University, Yerevan, Armenia
| | - Mariam A Shahinyan
- Faculty of Biology, Department of Biophysics, Yerevan State University, Yerevan, Armenia
| | - Nara H Petrosyan
- Faculty of Biology, Department of Biophysics, Yerevan State University, Yerevan, Armenia
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12
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Current and Future Challenges in Modern Drug Discovery. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2021; 2114:1-17. [PMID: 32016883 DOI: 10.1007/978-1-0716-0282-9_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Drug discovery is an expensive, time-consuming, and risky business. To avoid late-stage failure, learnings from past projects and the development of new approaches are crucial. New modalities and emerging new target spaces allow the exploration of unprecedented indications or to address so far undrugable targets. Late-stage attrition is usually attributed to the lack of efficacy or to compound-related safety issues. Efficacy has been shown to be related to a strong genetic link to human disease, a better understanding of the target biology, and the availability of biomarkers to bridge from animals to humans. Compound safety can be improved by ligand optimization, which is becoming increasingly demanding for difficult targets. Therefore, new strategies include the design of allosteric ligands, covalent binders, and other modalities. Design methods currently heavily rely on artificial intelligence and advanced computational methods such as free energy calculations and quantum chemistry. Especially for quantum chemical methods, a more detailed overview is given in this chapter.
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Bailly C. Pyronaridine: An update of its pharmacological activities and mechanisms of action. Biopolymers 2020; 112:e23398. [PMID: 33280083 DOI: 10.1002/bip.23398] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 08/14/2020] [Accepted: 08/17/2020] [Indexed: 02/06/2023]
Abstract
Pyronaridine (PYR) is an erythrocytic schizonticide with a potent antimalarial activity against multidrug-resistant Plasmodium. The drug is used in combination with artesunate for the treatment of uncomplicated P. falciparum malaria, in adults and children. The present review briefly retraces the discovery of PYR and recent antimalarial studies which has led to the approval of PYR/artesunate combination (Pyramax) by the European Medicines Agency to treat uncomplicated malaria worldwide. PYR also presents a marked antitumor activity and has revealed efficacy for the treatment of other parasitic diseases (notably Babesia and Trypanosoma infections) and to mitigate the Ebola virus propagation. On the one hand, PYR functions has an inhibitor of hemozoin (biomineral malaria pigment, by-product of hemoglobin digestion) formation, blocking the biopolymerization of β-hematin and thus facilitating the accumulation of toxic hematin into the digestive vacuole of the parasite. On the other hand, PYR is a bona fide DNA-intercalating agent and an inhibitor of DNA topoisomerase 2, leading to DNA damages and cell death. Inhibition of hematin polymerization represents the prime mechanism at the origin of the antimalarial activity, whereas anticancer effects relies essentially on the interference with DNA metabolism, as with structurally related anticancer drugs like amsacrine and quinacrine. In addition, recent studies point to an immune modulatory activity of PYR and the implication of a mitochondrial oxidative pathway. An analogy with the mechanism of action of artemisinin drugs is underlined. In brief, the biological actions of pyronaridine are recapitulated to shed light on the diverse health benefits of this unsung drug.
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Lu F, Yang L, Hou T, Li F. Label-free and "signal-on" homogeneous photoelectrochemical cytosensing strategy for ultrasensitive cancer cell detection. Chem Commun (Camb) 2020; 56:11126-11129. [PMID: 32959814 DOI: 10.1039/d0cc04516k] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
We report a label-free and "signal-on" homogeneous photoelectrochemical cytosensing system for ultrasensitive detection of cancer cells, which is a truly homogeneous PEC cytosensing system without the photoactive material immobilization and target recognition probe modification, providing a new avenue in early and accurate cancer diagnosis and clinical analysis.
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Affiliation(s)
- Fangfang Lu
- College of Chemistry and Pharmaceutical Sciences, Qingdao Agricultural University, Qingdao, 266109, People's Republic of China.
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15
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Yang L, Yin X, Gai P, Li F. A label-free homogeneous electrochemical cytosensor for the ultrasensitive detection of cancer cells based on multiaptamer-functionalized DNA tetrahedral nanostructures. Chem Commun (Camb) 2020; 56:3883-3886. [PMID: 32134083 DOI: 10.1039/d0cc00788a] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
We developed a label-free homogeneous electrochemical cytosensor for ultrasensitive detection of cancer cells based on multiaptamer-functionalized DNA tetrahedral nanostructures, which avoided expensive labeling and sophisticated immobilization procedures, providing opportunities for precisely detecting cancer cells in clinical applications.
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Affiliation(s)
- Limin Yang
- College of Chemistry and Pharmaceutical Sciences, Qingdao Agricultural University, Qingdao, 266109, People's Republic of China.
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16
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The 3D Genome as a Target for Anticancer Therapy. Trends Mol Med 2020; 26:141-149. [PMID: 31679987 PMCID: PMC9929230 DOI: 10.1016/j.molmed.2019.09.011] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 09/23/2019] [Accepted: 09/23/2019] [Indexed: 01/08/2023]
Abstract
The role of 3D genome organization in the precise regulation of gene expression is well established. Accordingly, the mechanistic connections between 3D genome alterations and disease development are becoming increasingly apparent. This opinion article provides a snapshot of our current understanding of the 3D genome alterations associated with cancers. We discuss potential connections of the 3D genome and cancer transcriptional addiction phenomenon as well as molecular mechanisms of action of 3D genome-disrupting drugs. Finally, we highlight issues and perspectives raised by the discovery of the first pharmaceutical strongly affecting 3D genome organization.
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Development of inhalable quinacrine loaded bovine serum albumin modified cationic nanoparticles: Repurposing quinacrine for lung cancer therapeutics. Int J Pharm 2020; 577:118995. [PMID: 31935471 DOI: 10.1016/j.ijpharm.2019.118995] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 12/18/2019] [Accepted: 12/22/2019] [Indexed: 01/05/2023]
Abstract
Drug repurposing is on the rise as an atypical strategy for discovery of new molecules, involving use of pre-existing molecules for a different therapeutic application than the approved indication. Using this strategy, the current study aims to leverage effects of quinacrine (QA), a well-known anti-malarial drug, for treatment of non-small cell lung cancer (NSCLC). For respiratory diseases, designing a QA loaded inhalable delivery system has multiple advantages over invasive delivery. QA-loaded nanoparticles (NPs) were thus prepared using polyethyleneimine (PEI) as a cationic stabilizer. While the use of PEI provided cationic charge on the particles, it also mediated a burst release of QA and demonstrated potential particle toxicity. These concerns were circumvented by coating nanoparticles with bovine serum albumin (BSA), which retained the cationic charge, reduced NP toxicity and modulated QA release. Prepared nanoparticles were characterized for physicochemical properties along with their aerosolization potential. Therapeutic efficacy of the formulations was tested in different NSCLC cells. Mechanism of higher anti-proliferation was evaluated by studying cell cycle profile, apoptosis and molecular markers involved in the progression of lung cancer. BSA coated QA nanoparticles demonstrated good aerosolization potential with a mass median aerodynamic diameter of significantly less than 5 µm. Nanoparticles also demonstrated improved therapeutic efficacy against NSCLC cells in terms of low IC50 values, cell cycle arrest at G2/M phase and autophagy inhibition leading to increased apoptosis. BSA coated QA NPs also demonstrated enhanced therapeutic efficacy in a 3D cell culture model. The present study thus lays solid groundwork for pre-clinical and eventual clinical studies as a standalone therapy and in combination with existing chemotherapeutics.
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18
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Purwanto MGM, Weisz K. NMR studies on oligonucleotide - Methylene blue conjugates targeting double-helical nucleic acids. Biophys Chem 2019; 257:106314. [PMID: 31862498 DOI: 10.1016/j.bpc.2019.106314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2019] [Revised: 11/30/2019] [Accepted: 12/03/2019] [Indexed: 10/25/2022]
Abstract
Methylene blue (MB) - nucleic acid interactions are of considerable interest due to the photosensitizing activity of the dye with potential applications in medicine and biotechnology. Covalent attachment of the MB to an oligonucleotide through a flexible heptamethylene linker enabled a positioning of the dye moiety to specific sites through triplex formation with a target duplex. NMR studies demonstrated interactions of MB with the nucleic acids. In sequences with the MB moiety facing the triplex-duplex junction with an alternating CG duplex overhang next to a T·A·T triple-helical tract, proton resonances experienced severe linebroadening upon MB binding and point to kinetically labile complexes with exchange among different binding modes. For sequences with the MB moiety facing a terminal T·A·T base triad of the triplex tract, structural heterogeneity decreased when compared to a triplex without MB attached to the third strand. Also, the thermal stability of the latter construct increased significantly in the presence of MB, indicating external end stacking as predominant binding mode. Without any obvious disruptions of sequential imino-imino NOE contacts within the triplex and duplex tracts, a most favorable intercalation between T·A·T base triples or CG base pairs is not supported by the present data under our experimental conditions.
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Affiliation(s)
| | - Klaus Weisz
- University of Surabaya, Faculty of Biotechnology, Surabaya, Indonesia; University of Greifswald, Institute of Biochemistry, 17489 Greifswald, Germany.
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Oien DB, Pathoulas CL, Ray U, Thirusangu P, Kalogera E, Shridhar V. Repurposing quinacrine for treatment-refractory cancer. Semin Cancer Biol 2019; 68:21-30. [PMID: 31562955 DOI: 10.1016/j.semcancer.2019.09.021] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Revised: 09/19/2019] [Accepted: 09/24/2019] [Indexed: 02/07/2023]
Abstract
Quinacrine, also known as mepacrine, has originally been used as an antimalarial drug for close to a century, but was recently rediscovered as an anticancer agent. The mechanisms of anticancer effects of quinacrine are not well understood. The anticancer potential of quinacrine was discovered in a screen for small molecule activators of p53, and was specifically shown to inhibit NFκB suppression of p53. However, quinacrine can cause cell death in cells that lack p53 or have p53 mutations, which is a common occurrence in many malignant tumors including high grade serous ovarian cancer. Recent reports suggest quinacrine may inhibit cancer cell growth through multiple mechanisms including regulating autophagy, FACT (facilitates chromatin transcription) chromatin trapping, and the DNA repair process. Additional reports also suggest quinacrine is effective against chemoresistant gynecologic cancer. In this review, we discuss anticancer effects of quinacrine and potential mechanisms of action with a specific focus on gynecologic and breast cancer where treatment-refractory tumors are associated with increased mortality rates. Repurposing quinacrine as an anticancer agent appears to be a promising strategy based on its ability to target multiple pathways, its selectivity against cancer cells, and the synergistic cytotoxicity when combined with other anticancer agents with limited side effects and good tolerability profile.
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Affiliation(s)
- Derek B Oien
- Division of Experimental Pathology and Laboratory Medicine, Mayo Clinic, Rochester, MN, United States
| | - Christopher L Pathoulas
- Division of Experimental Pathology and Laboratory Medicine, Mayo Clinic, Rochester, MN, United States
| | - Upasana Ray
- Division of Experimental Pathology and Laboratory Medicine, Mayo Clinic, Rochester, MN, United States
| | - Prabhu Thirusangu
- Division of Experimental Pathology and Laboratory Medicine, Mayo Clinic, Rochester, MN, United States
| | | | - Viji Shridhar
- Division of Experimental Pathology and Laboratory Medicine, Mayo Clinic, Rochester, MN, United States.
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Veselinovic J, Almashtoub S, Seker E. Anomalous Trends in Nucleic Acid-Based Electrochemical Biosensors with Nanoporous Gold Electrodes. Anal Chem 2019; 91:11923-11931. [PMID: 31429540 DOI: 10.1021/acs.analchem.9b02686] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Molecular diagnostics have significantly advanced the early detection of diseases, where electrochemical sensing of biomarkers has shown considerable promise. For a nucleic acid-based electrochemical sensor with signal-off behavior, the performance is evaluated by percent signal suppression (% ss), which indicates the change in current after hybridization. The % ss is generally due to more redox molecules (e.g., methylene blue) associating with the probe DNA bases in the single-strand form than the double-strand form upon hybridization with the target nucleic acid. Nanostructured electrodes generally enhance electrochemical sensor performance via several mechanisms, including increased number of capture probes per electrode volume and unique nanoscale transport phenomena. Here, we employ nanoporous gold (np-Au) as a model electrode material to study the influence of probe immobilization solution concentration on sensor performance and the underlying mechanisms. Unlike planar gold (pl-Au) electrodes, where % ss reaches a steady state with increasing concentration of the grafting solution, the % ss displays peak performance at certain grafting solution concentrations followed by rapid deterioration and reversal of the % ss polarity, suggesting an unexpected case of increased charge transfer upon hybridization. Fluorometric assessments of electrochemically desorbed nucleic acids for different electrode morphologies reveal that a significant amount of DNA molecules (unhybridized and hybridized) remain within the nanopores posthybridization. Analysis of electrochemical signals (e.g., square wave voltammogram shape) suggests that the large unbound nucleic acid concentration may be altering the modes of methylene blue interaction with the nucleic acids and charge transfer to the electrode surfaces.
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Affiliation(s)
- Jovana Veselinovic
- Department of Chemical Engineering , University of California, Davis , Davis , California 95616 , United States
| | - Suzan Almashtoub
- Department of Chemical Engineering , University of California, Davis , Davis , California 95616 , United States
| | - Erkin Seker
- Department of Electrical and Computer Engineering , University of California, Davis , Davis , California 95616 , United States
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Jiang Q, Lou Z, Wang H, Chen C. Antimicrobial effect and proposed action mechanism of cordycepin against Escherichia coli and Bacillus subtilis. J Microbiol 2019; 57:288-297. [PMID: 30929229 DOI: 10.1007/s12275-019-8113-z] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Revised: 08/07/2018] [Accepted: 08/13/2018] [Indexed: 12/01/2022]
Abstract
The detailed antibacterial mechanism of cordycepin efficacy against food-borne germs remains ambiguous. In this study, the antibacterial activity and action mechanism of cordycepin were assessed. The results showed that cordycepin effectively inhibited the growth of seven bacterial pathogens including both Gram-positive and Gram-negative bacterial pathogens; the minimum inhibitory concentrations (MIC) were 2.5 and 1.25 mg/ml against Escherichia coli and Bacillus subtilis, respectively. Scanning electron microscope and transmission electron microscope examination confirmed that cordycepin caused obvious damages in the cytoplasmatic membranes of both E. coli and B. subtilis. Outer membrane permeability assessment indicated the loss of barrier function and the leakage of cytoplasmic contents. Propidium iodide and carboxyfluorescein diacetate double staining approach coupled with flow cytometry analysis indicated that the integrity of cell membrane was severely damaged during a short time, while the intracellular enzyme system still remained active. This clearly suggested that membrane damage was one of the reasons for cordycepin efficacy against bacteria. Additionally, results from circular dichroism and fluorescence analysis indicated cordycepin could insert to genome DNA base and double strand, which disordered the structure of genomic DNA. Basis on these results, the mode of bactericidal action of cordycepin against E. coli and B. subtilis was found to be a dual mechanism, disrupting bacterial cell membranes and binding to bacterial genomic DNA to interfere in cellular functions, ultimately leading to cell death.
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Affiliation(s)
- Qi Jiang
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, 214122, P. R. China.,National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, 214122, P. R. China
| | - Zaixiang Lou
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, 214122, P. R. China. .,National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, 214122, P. R. China.
| | - Hongxin Wang
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, 214122, P. R. China. .,National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, 214122, P. R. China.
| | - Chen Chen
- National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, 214122, P. R. China
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Vardevanyan PO, Antonyan AP, Parsadanyan MA, Shahinyan MA, Mikaelyan MS. Study of Methylene Blue Interaction with Human Serum Albumin. ACTA ACUST UNITED AC 2019. [DOI: 10.1142/s1793048019500012] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The thiosine dye methylene blue (MB) interaction with human serum albumin (HSA) has been studied. MB was revealed to stabilize the native structure of HSA, since the denaturation temperature of the complexes is shifted to higher values in relation to that of the pure protein. It was also revealed that the absorption spectra of the complexes do not change noticeably, while in the fluorescence spectra the maximal intensity of MB decreases with the albumin concentration enhancement. Analysis of the obtained data allows to conclude that the main binding mode of MB to HSA, providing the stabilization of the protein native structure, is the electrostatic mechanism.
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Affiliation(s)
- Poghos O. Vardevanyan
- Department of Biophysics, Faculty of Biology, Yerevan State University, Alex Manoogian 1, Yerevan, 0025, Armenia
| | - Ara P. Antonyan
- Department of Biophysics, Faculty of Biology, Yerevan State University, Alex Manoogian 1, Yerevan, 0025, Armenia
| | - Marine A. Parsadanyan
- Department of Biophysics, Faculty of Biology, Yerevan State University, Alex Manoogian 1, Yerevan, 0025, Armenia
| | - Mariam A. Shahinyan
- Department of Biophysics, Faculty of Biology, Yerevan State University, Alex Manoogian 1, Yerevan, 0025, Armenia
| | - Marieta S. Mikaelyan
- Department of Biophysics, Faculty of Biology, Yerevan State University, Alex Manoogian 1, Yerevan, 0025, Armenia
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Ding XF, Wu Y, Qu WR, Fan M, Zhao YQ. Quinacrine pretreatment reduces microwave-induced neuronal damage by stabilizing the cell membrane. Neural Regen Res 2018; 13:449-455. [PMID: 29623929 PMCID: PMC5900507 DOI: 10.4103/1673-5374.228727] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Quinacrine, widely used to treat parasitic diseases, binds to cell membranes. We previously found that quinacrine pretreatment reduced microwave radiation damage in rat hippocampal neurons, but the molecular mechanism remains poorly understood. Considering the thermal effects of microwave radiation and the protective effects of quinacrine on heat damage in cells, we hypothesized that quinacrine would prevent microwave radiation damage to cells in a mechanism associated with cell membrane stability. To test this, we used retinoic acid to induce PC12 cells to differentiate into neuron-like cells. We then pretreated the neurons with quinacrine (20 and 40 mM) and irradiated them with 50 mW/cm2 microwaves for 3 or 6 hours. Flow cytometry, atomic force microscopy and western blot assays revealed that irradiated cells pretreated with quinacrine showed markedly less apoptosis, necrosis, and membrane damage, and greater expression of heat shock protein 70, than cells exposed to microwave irradiation alone. These results suggest that quinacrine stabilizes the neuronal membrane structure by upregulating the expression of heat shock protein 70, thus reducing neuronal injury caused by microwave radiation.
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Affiliation(s)
- Xue-Feng Ding
- Department of Cognitive Sciences, Beijing Institute of Basic Medical Sciences, Beijing, China
| | - Yan Wu
- Department of Cognitive Sciences, Beijing Institute of Basic Medical Sciences, Beijing, China
| | - Wen-Rui Qu
- Hand & Foot Surgery and Reparative & Reconstructive Surgery Center, Orthopedic Hospital of the Second Hospital of Jilin University, Changchun, Jilin Province, China
| | - Ming Fan
- Department of Cognitive Sciences, Beijing Institute of Basic Medical Sciences, Beijing, China
| | - Yong-Qi Zhao
- Department of Cognitive Sciences, Beijing Institute of Basic Medical Sciences, Beijing, China
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24
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Synthesis and characterization of two new trans palladium (II) complexes containing benzylamine ligand: DNA/BSA interactions, molecular docking and in vitro cytotoxic activity. Inorganica Chim Acta 2018. [DOI: 10.1016/j.ica.2017.02.027] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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25
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Abstract
A number of electrochemical DNA sensors based on the target-induced change in the conformation and/or flexibility of surface-bound oligonucleotides have been developed in recent years. These sensors, which are often termed E-DNA sensors, are comprised of an oligonucleotide probe modified with a redox label (e.g., methylene blue) at one terminus and attached to a gold electrode via a thiol-gold bond at the other. Binding of the target to the DNA probe changes its structure and dynamics, which, in turn, influences the efficiency of electron transfer to the interrogating electrode. Since electrochemically active contaminants are less common, these sensors are resistant to false-positive signals arising from the nonspecific adsorption of contaminants and perform well even when employed directly in serum, whole blood, and other realistically complex sample matrices. Moreover, because all of the sensor components are chemisorbed to the electrode, the E-DNA sensors are essentially label-free and readily reusable. To date, these sensors have achieved state-of-the-art sensitivity, while offering the unprecedented selectivity, reusability, and the operational convenience of direct electrochemical detection. This chapter reviews the recent advances in the development of both "signal-off" and "signal-on" E-DNA sensors. Critical aspects that dictate the stability and performance of these sensors are also addressed so as to provide a realistic overview of this oligonucleotide detection platform.
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Affiliation(s)
- Rebecca Y Lai
- University of Nebraska-Lincoln, Lincoln, NE, United States.
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Das S, Islam MM, Jana GC, Patra A, Jha PK, Hossain M. Molecular binding of toxic phenothiazinium derivatives, azures to bovine serum albumin: A comparative spectroscopic, calorimetric, and in silico study. J Mol Recognit 2017; 30. [PMID: 28101950 DOI: 10.1002/jmr.2609] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Revised: 12/21/2016] [Accepted: 12/22/2016] [Indexed: 11/09/2022]
Affiliation(s)
- Somnath Das
- Department of Chemistry and Chemical Technology; Vidyasagar University; Midnapore West Bengal India
| | - Md. Maidul Islam
- Department of Chemistry; Aliah University; Kolkata West Bengal India
| | - Gopal Chandra Jana
- Department of Chemistry and Chemical Technology; Vidyasagar University; Midnapore West Bengal India
| | - Anirudha Patra
- Department of Chemistry and Chemical Technology; Vidyasagar University; Midnapore West Bengal India
| | - Pradeep K. Jha
- SMST; Indian Institute of Technology Kharagpur; Kharagpur West Bengal India
| | - Maidul Hossain
- Department of Chemistry and Chemical Technology; Vidyasagar University; Midnapore West Bengal India
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Moreau M, Delile S, Sharma A, Fave C, Perrier A, Limoges B, Marchal D. Detection of a few DNA copies by real-time electrochemical polymerase chain reaction. Analyst 2017; 142:3432-3440. [DOI: 10.1039/c7an00978j] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In the current work, accurate quantification over 10 to 108 DNA copies has been successfully achieved for the first time by real-time electrochemical PCR.
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Affiliation(s)
- M. Moreau
- Laboratoire d'Electrochimie Moléculaire
- UMR 7591 CNRS
- Université Paris Diderot
- Sorbonne Paris Cité
- F-75205 Paris Cedex 13
| | - S. Delile
- Laboratoire d'Electrochimie Moléculaire
- UMR 7591 CNRS
- Université Paris Diderot
- Sorbonne Paris Cité
- F-75205 Paris Cedex 13
| | - A. Sharma
- Laboratoire d'Electrochimie Moléculaire
- UMR 7591 CNRS
- Université Paris Diderot
- Sorbonne Paris Cité
- F-75205 Paris Cedex 13
| | - C. Fave
- Laboratoire d'Electrochimie Moléculaire
- UMR 7591 CNRS
- Université Paris Diderot
- Sorbonne Paris Cité
- F-75205 Paris Cedex 13
| | - A. Perrier
- Equipe de Chimie Théorique et Modélisation (CTM)
- Chimie ParisTech
- PSL Research University
- CNRS
- Institut de Recherche de Chimie Paris (IRCP)
| | - B. Limoges
- Laboratoire d'Electrochimie Moléculaire
- UMR 7591 CNRS
- Université Paris Diderot
- Sorbonne Paris Cité
- F-75205 Paris Cedex 13
| | - D. Marchal
- Laboratoire d'Electrochimie Moléculaire
- UMR 7591 CNRS
- Université Paris Diderot
- Sorbonne Paris Cité
- F-75205 Paris Cedex 13
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Paul P, Mati SS, Bhattacharya SC, Kumar GS. Exploring the interaction of phenothiazinium dyes methylene blue, new methylene blue, azure A and azure B with tRNAPhe: spectroscopic, thermodynamic, voltammetric and molecular modeling approach. Phys Chem Chem Phys 2017; 19:6636-6653. [DOI: 10.1039/c6cp07888e] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
RNA targeting by small molecules.
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Affiliation(s)
- Puja Paul
- Biophysical Chemistry Laboratory
- Organic and Medicinal Chemistry Division
- CSIR-Indian Institute of Chemical Biology
- Kolkata 700 032
- India
| | | | | | - Gopinatha Suresh Kumar
- Biophysical Chemistry Laboratory
- Organic and Medicinal Chemistry Division
- CSIR-Indian Institute of Chemical Biology
- Kolkata 700 032
- India
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29
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Binding interaction of phenothiazinium dyes with double stranded RNAs: Spectroscopic and calorimetric investigation. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2016; 167:99-110. [PMID: 28056395 DOI: 10.1016/j.jphotobiol.2016.12.022] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Revised: 11/23/2016] [Accepted: 12/05/2016] [Indexed: 01/19/2023]
Abstract
RNA targeting through small molecules is an emerging and promising therapeutic route that necessitates identification of small molecules that can selectively target specific RNA structures. In this context a comparative study of the interaction of two phenothiazinium dyes thionine (THN) and toluidine blue O (TBO) with three double stranded RNA polynucleotides (ds RNAs) viz. poly(I).poly(C), poly(A).poly(U) and poly(C).poly(G) was conducted by various biophysical techniques. A higher binding of THN with poly(I).poly(C) over poly(A).poly(U) and poly(C).poly(G) was observed. The intercalative binding and RNA induced fluorescence quenching of the dyes through a static mechanism was confirmed by viscosity studies and steady state polarization anisotropy experiments. Binding induced structural perturbation in the RNA polynucleotides was confirmed from circular dichroism spectroscopy. DSC and thermal melting experiments confirmed that the binding resulted in strong thermal stabilization. The binding affinity of THN with poly(I).poly(C) was the highest followed by that to poly(A).poly(U) and poly(C).poly(G). The trend was the same for TBO also, but THN bound stronger than TBO. The binding of the dyes was characterized by strong negative enthalpy changes with minimum positive entropy changes indicating typical intercalative interaction. The results presented here may be useful to design new types of RNA binding antitumor, antibacterial and anticancer agents.
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Gomes A, Fernandes I, Teixeira C, Mateus N, Sottomayor MJ, Gomes P. A Quinacrine Analogue Selective Against Gastric Cancer Cells: Insight from Biochemical and Biophysical Studies. ChemMedChem 2016; 11:2703-2712. [PMID: 27863116 DOI: 10.1002/cmdc.201600477] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Revised: 11/11/2016] [Indexed: 12/29/2022]
Abstract
One of the earliest synthetic antimalarial drugs, quinacrine, was recently reported as interesting for the treatment of acute myeloid leukemia. Inspired by this and similar findings, we evaluated a set of quinacrine analogues against gastric (MKN-28), colon (Caco-2), and breast (MFC-7) cancer cell lines and one normal human fibroblast cell line (HFF-1). All the compounds, previously developed by us as dual-stage antimalarial leads, displayed antiproliferative activity, and one of the set stood out as selective toward the gastric cancer cell line, MKN-28. Interestingly, this compound was transported across an in vitro MKN-28 model cell line in low amounts, and approximately 80 % was trapped inside those cells. Nuclear targeting of the same compound and its interactions with calf thymus DNA were assessed through combined fluorescence microscopy, spectroscopy, and calorimetry studies, which provided evidence for the compound's ability to reach the nucleus and to interact with DNA.
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Affiliation(s)
- Ana Gomes
- UCIBIO-REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre 687, 4169-007, Porto, Portugal
| | - Iva Fernandes
- LAQV-REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre 687, 4169-007, Porto, Portugal
| | - Cátia Teixeira
- UCIBIO-REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre 687, 4169-007, Porto, Portugal
| | - Nuno Mateus
- LAQV-REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre 687, 4169-007, Porto, Portugal
| | - M J Sottomayor
- CIQ-UP, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre 687, 4169-007, Porto, Portugal
| | - Paula Gomes
- UCIBIO-REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre 687, 4169-007, Porto, Portugal
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Bose D, Su Y, Marcus A, Raulet DH, Hammond MC. An RNA-Based Fluorescent Biosensor for High-Throughput Analysis of the cGAS-cGAMP-STING Pathway. Cell Chem Biol 2016; 23:1539-1549. [PMID: 27889408 DOI: 10.1016/j.chembiol.2016.10.014] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Revised: 09/02/2016] [Accepted: 10/25/2016] [Indexed: 12/15/2022]
Abstract
In mammalian cells, the second messenger (2'-5',3'-5') cyclic guanosine monophosphate-adenosine monophosphate (2',3'-cGAMP), is produced by the cytosolic DNA sensor cGAMP synthase (cGAS), and subsequently bound by the stimulator of interferon genes (STING) to trigger interferon response. Thus, the cGAS-cGAMP-STING pathway plays a critical role in pathogen detection, as well as pathophysiological conditions including cancer and autoimmune disorders. However, studying and targeting this immune signaling pathway has been challenging due to the absence of tools for high-throughput analysis. We have engineered an RNA-based fluorescent biosensor that responds to 2',3'-cGAMP. The resulting "mix-and-go" cGAS activity assay shows excellent statistical reliability as a high-throughput screening (HTS) assay and distinguishes between direct and indirect cGAS inhibitors. Furthermore, the biosensor enables quantitation of 2',3'-cGAMP in mammalian cell lysates. We envision this biosensor-based assay as a resource to study the cGAS-cGAMP-STING pathway in the context of infectious diseases, cancer immunotherapy, and autoimmune diseases.
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Affiliation(s)
- Debojit Bose
- Department of Chemistry, University of California, Berkeley, CA 94720, USA
| | - Yichi Su
- Department of Chemistry, University of California, Berkeley, CA 94720, USA
| | - Assaf Marcus
- Department of Molecular & Cell Biology, University of California, Berkeley, CA 94720, USA
| | - David H Raulet
- Department of Molecular & Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Ming C Hammond
- Department of Chemistry, University of California, Berkeley, CA 94720, USA; Department of Molecular & Cell Biology, University of California, Berkeley, CA 94720, USA.
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Spectroscopic and calorimetric investigations on the binding of phenazinium dyes safranine-O and phenosafranine to double stranded RNA polynucleotides. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2016; 161:129-40. [PMID: 27236048 DOI: 10.1016/j.jphotobiol.2016.03.062] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Revised: 03/21/2016] [Accepted: 03/23/2016] [Indexed: 12/13/2022]
Abstract
RNA targeting through small molecules that can selectively bind specific RNA structures is an important current strategy in therapeutic drug development. Towards this strategy a comparative study on the interaction of two phenazinium dyes, safranine-O and phenosafranine to double stranded RNAs, poly(I).poly(C), poly(A).poly(U) and poly(C).poly(G) was performed. Spectrophotometric and spectrofluorimetric studies revealed non-cooperative binding of the dyes to the duplex RNA with binding constants of the order 10(5)M(-1) with a higher affinity of safranine-O to poly(I).poly(C) followed by poly(A).poly(U) and poly(C).poly(G). Anisotropy and fluorescence quenching results confirmed an intercalation mode of binding for the dyes on these RNAs. Binding induced conformational changes in the RNA polynucleotides were revealed from circular dichroism data. Thermal melting study and DSC experiments demonstrated stabilization of dye-RNA complexes. Calorimetric studies revealed that the binding was accompanied by a large positive entropy term with a small negative enthalpy contributions. Significant hydrophobic forces in the complexation of the double stranded RNAs with the dyes were confirmed from the negative heat capacity changes. Enthalpy-entropy compensation was also observed in the binding. Parsing of the Gibbs energy suggested a larger non-electrostatic contribution in all the cases. The results presented here may be helpful to design new types of RNA-based therapeutic agents.
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Vardevanyan PO, Antonyan AP, Parsadanyan MA, Torosyan MA, Karapetian AT. Joint interaction of ethidium bromide and methylene blue with DNA. The effect of ionic strength on binding thermodynamic parameters. J Biomol Struct Dyn 2016; 34:1377-82. [PMID: 26239502 DOI: 10.1080/07391102.2015.1079557] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Large amount of data of experimental and theoretical studies have shown that ethidium bromide (EtBr) and methylene blue (MB) may bind to nucleic acids via three modes: intercalation between two adjacent base pairs, insertion into the plane between neighboring bases in the same strand (semi-intercalation), and outside binding with negatively charged backbone phosphate groups. The aim of the given research is to examine the behavior of these two ligands at both separate and joint DNA binding. The obtained experimental data show that the effect of simultaneous binding of EtBr and MB on double-stranded DNA has a non-additive effect of separate binding. The analyses of the melting thermodynamic parameters of DNA complexes with two bound ligands suggest competitive mechanism of interaction.
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Affiliation(s)
- Poghos O Vardevanyan
- a Department of Biophysics , Yerevan State University , Alex Manoogian 1, 0025 Yerevan , Armenia
| | - Ara P Antonyan
- a Department of Biophysics , Yerevan State University , Alex Manoogian 1, 0025 Yerevan , Armenia
| | - Marine A Parsadanyan
- a Department of Biophysics , Yerevan State University , Alex Manoogian 1, 0025 Yerevan , Armenia
| | - Margarita A Torosyan
- b Department of Physics and Electric Engineering , National University of Architecture and Construction , Yerevan 0009 , Armenia
| | - Armen T Karapetian
- b Department of Physics and Electric Engineering , National University of Architecture and Construction , Yerevan 0009 , Armenia
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Kocak A, Yilmaz H, Faiz O, Andac O. Experimental and theoretical studies on Cu(II) complex of N,N′-disalicylidene-2,3-diaminopyridine ligand reveal indirect evidence for DNA intercalation. Polyhedron 2016. [DOI: 10.1016/j.poly.2015.11.037] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Leung KKK, Shilton BH. Binding of DNA-Intercalating Agents to Oxidized and Reduced Quinone Reductase 2. Biochemistry 2015; 54:7438-48. [DOI: 10.1021/acs.biochem.5b00884] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Kevin K. K. Leung
- Department of Biochemistry, University of Western Ontario, 1151 Richmond Street, London, Ontario, Canada N6A 5C1
| | - Brian H. Shilton
- Department of Biochemistry, University of Western Ontario, 1151 Richmond Street, London, Ontario, Canada N6A 5C1
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Das D, Dutta A, Mondal P. Interaction of aquated form of ruthenium(III) anticancer complexes with normal and mismatch base pairs: A density functional theoretical study. COMPUT THEOR CHEM 2015. [DOI: 10.1016/j.comptc.2015.08.020] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Paul P, Kumar GS. Photophysical and calorimetric investigation on the structural reorganization of poly(A) by phenothiazinium dyes azure A and azure B. Photochem Photobiol Sci 2015; 13:1192-202. [PMID: 24953877 DOI: 10.1039/c4pp00085d] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Poly(A) has significant relevance to mRNA stability, protein synthesis and cancer biology. The ability of two phenothiazinium dyes azure A (AA) and azure B (AB) to bind single-stranded poly(A) was studied by spectroscopic and calorimetric techniques. Strong binding of the dyes and the higher affinity of AA over AB were ascertained from absorbance and fluorescence experiments. Significant perturbation of the circular dichroism spectrum of poly(A) in the presence of these molecules with formation of induced CD bands in the 300-700 nm region was observed. Strong emission polarization of the bound dyes and strong energy transfer from the adenine base pairs of poly(A) suggested intercalative binding to poly(A). Intercalative binding was confirmed from fluorescence quenching experiments and was predominantly entropy driven as evidenced from isothermal titration calorimetry data. The negative values of heat capacity indicated involvement of hydrophobic forces and enthalpy-entropy compensation suggested noncovalent interactions in the complexation for both the dyes. Poly(A) formed a self-assembled structure on the binding of both the dyes that was more favored under higher salt conditions. New insights in terms of spectroscopic and thermodynamic aspects into the self-structure formation of poly(A) by two new phenothiazinium dyes that may lead to structural and functional damage of mRNA are revealed from these studies.
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Affiliation(s)
- Puja Paul
- Biophysical Chemistry Laboratory, Chemisry Division, CSIR-Indian Institute of Chemical Biology, Kolkata 700 032, India.
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Sarkar S, Pandya P, Bhadra K. Sequence specific binding of beta carboline alkaloid harmalol with deoxyribonucleotides: binding heterogeneity, conformational, thermodynamic and cytotoxic aspects. PLoS One 2014; 9:e108022. [PMID: 25247695 PMCID: PMC4172587 DOI: 10.1371/journal.pone.0108022] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Accepted: 08/25/2014] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Base dependent binding of the cytotoxic alkaloid harmalol to four synthetic polynucleotides, poly(dA).poly(dT), poly(dA-dT).poly(dA-dT), poly(dG).poly(dC) and poly(dG-dC).poly(dG-dC) was examined by various photophysical and calorimetric studies, and molecular docking. METHODOLOGY/PRINCIPAL FINDINGS Binding data obtained from absorbance according to neighbor exclusion model indicated that the binding constant decreased in the order poly(dG-dC).poly(dG-dC)>poly(dA-dT).poly(dA-dT)>poly(dA).poly(dT)>poly(dG).poly(dC). The same trend was shown by the competition dialysis, change in fluorescence steady state intensity, stabilization against thermal denaturation, increase in the specific viscosity and perturbations in circular dichroism spectra. Among the polynucleotides, poly(dA).poly(dT) and poly(dG).poly(dC) showed positive cooperativity where as poly(dG-dC).poly(dG-dC) and poly(dA-dT).poly(dA-dT) showed non cooperative binding. Isothermal calorimetric data on the other hand showed enthalpy driven exothermic binding with a hydrophobic contribution to the binding Gibbs energy with poly(dG-dC).poly(dG-dC), and poly(dA-dT).poly(dA-dT) where as harmalol with poly(dA).poly(dT) showed entropy driven endothermic binding and with poly(dG).poly(dC) it was reported to be entropy driven exothermic binding. The study also tested the in vitro chemotherapeutic potential of harmalol in HeLa, MDA-MB-231, A549, and HepG2 cell line by MTT assay. CONCLUSIONS/SIGNIFICANCE Studies unequivocally established that harmalol binds strongly with hetero GC polymer by mechanism of intercalation where the alkaloid resists complete overlap to the DNA base pairs inside the intercalation cavity and showed maximum cytotoxicity on HepG2 with IC50 value of 14 µM. The results contribute to the understanding of binding, specificity, energetic, cytotoxicity and docking of harmalol-DNA complexation that will guide synthetic efforts of medicinal chemists for developing better therapeutic agents.
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Affiliation(s)
- Sarita Sarkar
- Department of Zoology, University of Kalyani, Nadia, West Bengal, India
| | - Prateek Pandya
- Department of Zoology, University of Kalyani, Nadia, West Bengal, India
| | - Kakali Bhadra
- Department of Zoology, University of Kalyani, Nadia, West Bengal, India
- * E-mail:
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Afzal S, Bukhari MH. Endometrial abnormalities on transvaginal ultrasonography and histopathology in women after quinacrine sterilization. Pak J Med Sci 2014; 30:778-83. [PMID: 25097516 PMCID: PMC4121697 DOI: 10.12669/pjms.304.5091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2014] [Revised: 04/03/2013] [Accepted: 04/08/2013] [Indexed: 11/15/2022] Open
Abstract
OBJECTIVE To describe endometrial abnormalities on transvaginal ultrasonography and histopathology in women after quinacrine sterilization. METHODS It was an analytical cross sectional study conducted during February 2012 to April 2013. The sample size calculated at 95% confidence level was 540. Sampling technique used was simple random sampling. The medical history, examination, transvaginal ultrasonography and biopsy of suspected lesion was performed in quinacrine sterilized women. RESULTS The calculation of statistics showed the mean age at quinacrine sterilization was 38.5 years, standard deviation 6.517, and standard error 0.461. The endometrium was regular and smooth with homogenous images in 86% (n= 466), irregular endometrium with heterogeneous images on transvaginal ultrasound in 9.4% (n =51) and endometrial growth with high level echoes in 4.2% women (n= 23). The histological findings included hyperplasia and well differentiated adenocarcinoma in two patients respectively. CONCLUSION The irregular endometrium, adhesions, and growths were found after quinacrine sterilization. The risk of endometrial growth was more after 10 years duration of quinacrine sterilization.
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Affiliation(s)
- Saira Afzal
- Dr Saira Afzal, MBBS, MCPS, M.Phil, FCPS, Chairperson and Head, Department of Community Medicine, King Edward Medical University, Lahore, Pakistan
| | - Mulazim Hussain Bukhari
- Prof. Mulazim Hussain Bukhari, MBBS, MCPS, M.Phil, FCPS, PhD, Deputy Dean, Pathology Department, Medical School.American University of Barbados, School of Medicine 18 Wildey Estate, Main Wildey Road, St Michael, Barbados, USA
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Zhang H, Wei K, Zhang M, Liu R, Chen Y. Assessing the mechanism of DNA damage induced by lead through direct and indirect interactions. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2014; 136:46-53. [DOI: 10.1016/j.jphotobiol.2014.04.020] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2014] [Revised: 04/22/2014] [Accepted: 04/24/2014] [Indexed: 01/19/2023]
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Shankar R, Radhika R, Thangamani D, Senthil Kumar L, Kolandaivel P. Theoretical studies on interaction of anticancer drugs (dacarbazine, procarbazine and triethylenemelamine) with normal (AT and GC) and mismatch (GG, CC, AA and TT) base pairs. MOLECULAR SIMULATION 2014. [DOI: 10.1080/08927022.2014.913098] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Yu ZG, Zaitouna AJ, Lai RY. Effect of redox label tether length and flexibility on sensor performance of displacement-based electrochemical DNA sensors. Anal Chim Acta 2014; 812:176-83. [DOI: 10.1016/j.aca.2013.12.040] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2013] [Revised: 12/19/2013] [Accepted: 12/28/2013] [Indexed: 10/25/2022]
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Paul P, Kumar GS. Targeting ribonucleic acids by toxic small molecules: structural perturbation and energetics of interaction of phenothiazinium dyes thionine and toluidine blue O to tRNA phe. JOURNAL OF HAZARDOUS MATERIALS 2013; 263 Pt 2:735-745. [PMID: 24231328 DOI: 10.1016/j.jhazmat.2013.10.040] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2013] [Revised: 09/17/2013] [Accepted: 10/19/2013] [Indexed: 06/02/2023]
Abstract
This study was designed to examine the toxic interaction of two phenothiazinium dyes thionine (TO) and toluidine blue O (TBO) with tRNA(phe) by spectroscopic and calorimetric techniques. While phenothiazinium dye complexation with DNA is known, their bindings to RNA are not fully investigated. The non cooperative binding of both the dyes to tRNA was revealed from absorbance and fluorescence studies. From absorption, steady-state emission, the effect of ferrocyanide ion-induced steady-state fluorescence quenching, circular dichroism, the mode of binding of these dyes into the tRNA helix has been substantiated to be principally by intercalative in nature. Both dyes enhanced the thermal stability of tRNA. Circular dichroism studies provided evidence for the structural perturbations associated with the tRNA structure with induction of optical activity in the CD inactive dye molecules. Results from isothermal titration calorimetry experiments suggested that the binding of both dyes was predominantly entropy driven with a smaller but favorable enthalpy term that increased with temperature. The binding was dependent on the Na(+) concentration, but had a larger non-electrostatic contribution to the Gibbs energy. A small heat capacity value and the enthalpy-entropy compensation in the energetics of the interaction characterized the binding of the dyes to tRNA. This study confirms that the tRNA(phe) binding affinity is greater for TO compared to TBO. The utility of the present work lies in understanding the potential binding and consequent damage to tRNA by these toxic dyes in their development as therapeutic agents.
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Affiliation(s)
- Puja Paul
- Biophysical Chemistry Laboratory, Chemistry Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Kolkata 700032, India
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Zięba A, Latocha M, Sochanik A. Synthesis and in vitro antiproliferative activity of novel 12( H)-quino[3,4- b][1,4]benzothiazine derivatives. Med Chem Res 2013; 22:4158-4163. [PMID: 23914127 PMCID: PMC3720991 DOI: 10.1007/s00044-012-0384-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2012] [Accepted: 11/15/2012] [Indexed: 11/26/2022]
Abstract
Novel method of N-dealkylating quinobenzothiazinium salts 2, promoted by reaction with benzimidazole, led to a series of new azaphenothiazine derivatives having 12(H)-quino[3,4-b][1,4] benzothiazine 4 structure. Reaction of compounds 4 in an alkaline milieu with alkylating agents occur as N-alkylation of the thiazine nitrogen and yields quinobenzothiazine derivatives 7. In vitro antiproliferative activity of compounds 4 and 7 was tested using two cancer cell lines (SNB-19 and C-32) and cisplatin as a reference. Most of the studied azaphenothiazine derivatives showed activity against both cell lines investigated (5.6-12.4 μg/ml concentration range tested). Compounds 4(b-e) containing a halogen atom or methyl group at the 9-position of the quinobenzothiazine ring show activity in the tested concentration range only against C-32 cell line. Compound 4f with methyl group in 11-position of quinobenzothiazine ring lacked activity against either cell line. The presence of additional aminoalkyl substituents at the thiazine nitrogen atom in compounds 7 increases their activity against both examined cell lines, when compared to compounds 4.
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Affiliation(s)
- Andrzej Zięba
- Department of Organic Chemistry, Medical University of Silesia, 41-200 Sosnowiec, Poland
| | - Małgorzata Latocha
- Department of Cell Biology, Medical University of Silesia, 41-200 Sosnowiec, Poland
| | - Aleksander Sochanik
- Center for Translational Research and Molecular Biology of Cancer, Maria Skłodowska-Curie Memorial Cancer Center and Institute of Oncology, 44-100 Gliwice, Poland
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Sateriale A, Bessoff K, Sarkar IN, Huston CD. Drug repurposing: mining protozoan proteomes for targets of known bioactive compounds. J Am Med Inform Assoc 2013; 21:238-44. [PMID: 23757409 DOI: 10.1136/amiajnl-2013-001700] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
OBJECTIVE To identify potential opportunities for drug repurposing by developing an automated approach to pre-screen the predicted proteomes of any organism against databases of known drug targets using only freely available resources. MATERIALS AND METHODS We employed a combination of Ruby scripts that leverage data from the DrugBank and ChEMBL databases, MySQL, and BLAST to predict potential drugs and their targets from 13 published genomes. Results from a previous cell-based screen to identify inhibitors of Cryptosporidium parvum growth were used to validate our in-silico prediction method. RESULTS In-vitro validation of these results, using a cell-based C parvum growth assay, showed that the predicted inhibitors were significantly more likely than expected by chance to have confirmed activity, with 8.9-15.6% of predicted inhibitors confirmed depending on the drug target database used. This method was then used to predict inhibitors for the following 13 disease-causing protozoan parasites, including: C parvum, Entamoeba histolytica, Giardia intestinalis, Leishmania braziliensis, Leishmania donovani, Leishmania major, Naegleria gruberi (in proxy of Naegleria fowleri), Plasmodium falciparum, Plasmodium vivax, Toxoplasma gondii, Trichomonas vaginalis, Trypanosoma brucei and Trypanosoma cruzi. CONCLUSIONS Although proteome-wide screens for drug targets have disadvantages, in-silico methods can be developed that are fast, broad, inexpensive, and effective. In-vitro validation of our results for C parvum indicate that the method presented here can be used to construct a library for more directed small molecule screening, or pipelined into structural modeling and docking programs to facilitate target-based drug development.
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Affiliation(s)
- Adam Sateriale
- Cell, Molecular, and Biomedical Sciences Graduate Program, University of Vermont College of Medicine, Burlington, Vermont, USA
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Hossain M, Kabir A, Suresh Kumar G. Binding of the anticancer alkaloid sanguinarine with tRNA(phe): spectroscopic and calorimetric studies. J Biomol Struct Dyn 2012; 30:223-34. [PMID: 22702734 DOI: 10.1080/07391102.2012.677774] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The interaction of the natural plant alkaloid and anticancer agent sanguinarine with tRNA(phe) has been investigated by spectroscopic and calorimetric techniques. Sanguinarine iminium binds to tRNA(phe) cooperatively; alkanolamine does not bind but in presence of large tRNA(phe) concentration, a conversion from alkanolamine to iminium occurs resulting in concomitant binding of the latter. The binding affinity of the iminium to tRNA(phe) obtained from isothermal titration calorimetry was of the order of 10(5) M(-1), which is close to that evaluated from spectroscopy. The binding was driven largely by negative enthalpy and a smaller but favourable positive entropy change. The binding was dependent on the [Na(+)] concentration, but had a larger non-electrostatic contribution to the Gibbs energy. A small heat capacity value and the enthalpy-entropy compensation in the energetics of the interaction characterized the binding of the iminium form to tRNA(phe). This study confirms that the tRNA(phe) binding moiety is the iminium form of sanguinarine.
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Affiliation(s)
- Maidul Hossain
- Biophysical Chemistry Laboratory, CSIR-Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Kolkata, 700032, India
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Sun H, Xiang J, Li Q, Liu Y, Li L, Shang Q, Xu G, Tang Y. Recognize three different human telomeric G-quadruplex conformations by quinacrine. Analyst 2012; 137:862-7. [PMID: 22223064 DOI: 10.1039/c2an15870a] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Recognition of different human telomeric G-quadruplex structures has been a very important task for developing anti-cancer drug design. However, it also is a very challenging question since multiple conformational isomers of telomeric G-quadruplexes coexist under some conditions. Here, three different conformations including parallel, antiparallel, and mixed-type telomeric G-quadruplex structures have been well recognized by quinacrine (QNA) through monitoring its absorption, fluorescence, and fluorescence lifetime spectra. The multiple structures of H22 G-quadruplexes under physiological K(+) conditions could also be easily determined to coexist as mixed-type and antiparallel G-quadruplexes. The recognition mechanism based on the different binding affinity and binding sites has been further elucidated by association with the nuclear magnetic resonance (NMR) results.
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Affiliation(s)
- Hongxia Sun
- National Laboratory for Molecular Sciences, Center for Molecular Sciences, Institute of Chemistry Chinese Academy of Sciences, Beijing, 100190, PR China
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Sinha R, Saha I, Kumar GS. Protoberberine Alkaloids Berberine, Palmatine, and Coralyne Binding to Poly(dT)⋅(Poly(dA)⋅Poly(dT)) Triplex: Comparative Structural Aspects and Energetics Profiles of the Interaction. Chem Biodivers 2011. [DOI: 10.1002/cbdv.201000182] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Das A, Bhadra K, Suresh Kumar G. Targeting RNA by small molecules: comparative structural and thermodynamic aspects of aristololactam-β-D-glucoside and daunomycin binding to tRNA(phe). PLoS One 2011; 6:e23186. [PMID: 21858023 PMCID: PMC3156712 DOI: 10.1371/journal.pone.0023186] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2011] [Accepted: 07/11/2011] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Interaction of aristololactam-β-D-glucoside and daunomycin with tRNA(phe) was investigated using various biophysical techniques. METHODOLOGY/PRINCIPAL FINDINGS Absorption and fluorescence studies revealed that both the compounds bind tRNA(phe) non-cooperatively. The binding of daunomycin was about one order of magnitude higher than that of aristololactam-β-D-glucoside. Stronger binding of the former was also inferred from fluorescence quenching data, quantum efficiency values and circular dichroic results. Results from isothermal titration calorimetry experiments suggested that the binding of both compounds was predominantly entropy driven with a smaller but favorable enthalpy term that increased with temperature. A large favorable electrostatic contribution to the binding of daunomycin to tRNA(phe) was revealed from salt dependence data and the dissection of the free energy values. The electrostatic component to the free energy change for aristololactam-β-D-glucoside-tRNA(phe) interaction was smaller than that of daunomycin. This was also inferred from the slope of log K versus [Na(+)] plots. Both compounds enhanced the thermal stability of tRNA(phe). The small heat capacity changes of -47 and -99 cal/mol K, respectively, observed for aristololactam-β-D-glucoside and daunomycin, and the observed enthalpy-entropy compensation phenomenon confirmed the involvement of multiple weak noncovalent interactions. Molecular aspects of the interaction have been revealed. CONCLUSIONS/SIGNIFICANCE This study presents the structural and energetic aspects of the binding of aristololactam-β-D-glucoside and daunomycin to tRNA(phe).
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MESH Headings
- Algorithms
- Antibiotics, Antineoplastic/chemistry
- Antibiotics, Antineoplastic/metabolism
- Antibiotics, Antineoplastic/pharmacology
- Aristolochic Acids/chemistry
- Aristolochic Acids/metabolism
- Aristolochic Acids/pharmacology
- Binding Sites
- Binding, Competitive
- Calorimetry
- Circular Dichroism
- Daunorubicin/chemistry
- Daunorubicin/metabolism
- Daunorubicin/pharmacology
- Entropy
- Glucosides/chemistry
- Glucosides/metabolism
- Glucosides/pharmacology
- Kinetics
- Molecular Structure
- Nucleic Acid Conformation/drug effects
- RNA/chemistry
- RNA/genetics
- RNA/metabolism
- RNA, Transfer, Phe/chemistry
- RNA, Transfer, Phe/genetics
- RNA, Transfer, Phe/metabolism
- Spectrometry, Fluorescence
- Thermodynamics
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Affiliation(s)
- Abhi Das
- Biophysical Chemistry Laboratory, Indian Institute of Chemical Biology, Council of Scientific and Industrial Research, Kolkata, West Bengal, India
| | - Kakali Bhadra
- Biophysical Chemistry Laboratory, Indian Institute of Chemical Biology, Council of Scientific and Industrial Research, Kolkata, West Bengal, India
| | - Gopinatha Suresh Kumar
- Biophysical Chemistry Laboratory, Indian Institute of Chemical Biology, Council of Scientific and Industrial Research, Kolkata, West Bengal, India
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Das S, Kundu S, Suresh Kumar G. Quinacrine and 9-Amino Acridine Inhibit B-Z and B-HL Form DNA Conformational Transitions. DNA Cell Biol 2011; 30:525-35. [PMID: 21395448 DOI: 10.1089/dna.2010.1206] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Suman Das
- Department of Chemistry, Jadavpur University, Kolkata, India
| | - Suprabhat Kundu
- Department of Chemistry, Jadavpur University, Kolkata, India
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