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Khilari R, Chauhan S, Tripathi M, Pande R, Alqahtani MS, Syed R, Shahid M, Das D, Sarkar A. Nucleic acid binding affinity and antioxidant activity of N-m-Tolyl-4-Chlorophenoxyacetohydroxamicacid. Sci Rep 2024; 14:22465. [PMID: 39341868 PMCID: PMC11439026 DOI: 10.1038/s41598-024-72477-x] [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: 03/30/2024] [Accepted: 09/09/2024] [Indexed: 10/01/2024] Open
Abstract
Hydroxamic acids represent a group of weak organic acids, both naturally occurring and synthetically derived, characterized by the general formula RC(= O)N(R'OH). In this study, we investigated the binding behavior of N-m-tolyl-4-chlorophenoxyaceto hydroxamic acid with calf thymus DNA (ct-DNA) and torula yeast RNA (t-RNA) through a combination of techniques including UV-visible spectroscopy, fluorescence emission analysis, viscometry, and computational simulations using AutoDock4 software. Our findings reveal that the mode of binding between the compound and the nucleic acids is consistent with intercalation. Competitive binding experiments demonstrated that the complex competes effectively with ethidium bromide (EB) for binding to ct-DNA/t-RNA, displacing EB from its binding sites. Additionally, the introduction of the compound into the DNA-EB system resulted in a quenching of fluorescence emission peaks. Analysis of absorption spectra indicated a red shift and hypochromic shift when the compound interacted with DNA, further supporting the intercalative binding mode. The calculated binding constant (Kb) value for the compound is 6.62 × 104 M-1 and 5.40 × 103 M-1 indicating a strong interaction with ct-DNA and t-RNA respectively. We determined the Stern-Volmer constants for ct-DNA and t-RNA as 9.96 × 104 M-1 and 8.13 × 105 M-1, respectively. The binding free energy values for ct-DNA/t-RNA were calculated to be - 3.741 × 107 and - 5.425 × 108 kcal/mol, respectively. Viscometric studies corroborated the UV results, showing a continuous increase in relative viscosity of ct-DNA/t-RNA solutions with the addition of the optimal hydroxamic acid concentration. Furthermore, we assessed the antioxidant activity of the compound using DPPH-radical scavenging and β-carotene linoleic acid assays. Gel electrophoresis results demonstrated the compound's remarkable efficacy in preventing DNA damage. Collectively, all experimental evidence supports the conclusion that N-m-tolyl-4-chlorophenoxyaceto hydroxamic acid binds to ct-DNA/t-RNA through an intercalative mechanism, which is consistent with our molecular docking simulations.
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Affiliation(s)
- Rubi Khilari
- School of Studies in Chemistry, Pt. Ravishankar Shukla University, Raipur-492010, Chhattisgarh, Raipur, India
| | - Sohilkhan Chauhan
- Department of Chemistry, Smt. S. S. Patel Nootan Science and Commerce College, Sankalchand Patel University Visnagar Gujarat, Visnagar, 384315, India
| | - Mamta Tripathi
- School of Studies in Chemistry, Pt. Ravishankar Shukla University, Raipur-492010, Chhattisgarh, Raipur, India.
| | - Rama Pande
- School of Studies in Chemistry, Pt. Ravishankar Shukla University, Raipur-492010, Chhattisgarh, Raipur, India
| | - Mohammed S Alqahtani
- Department of Pharmaceutics, College of Pharmacy, King Saud University, 11451, Riyadh, Saudi Arabia
| | - Rabbani Syed
- Department of Pharmaceutics, College of Pharmacy, King Saud University, 11451, Riyadh, Saudi Arabia
| | - Mudassar Shahid
- Department of Pharmaceutics, College of Pharmacy, King Saud University, 11451, Riyadh, Saudi Arabia
| | - Devashish Das
- Department of Chemical Engineering, Konkuk University, Seoul, South Korea
| | - Avijit Sarkar
- Department of Chemistry, Bhairab Ganguly College, Kolkata, West Bengal, India
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Sarkar P, Gopi P, Pandya P, Paria S, Hossain M, Siddiqui MH, Alamri S, Bhadra K. Insights on the comparative affinity of ribonucleic acids with plant-based beta carboline alkaloid, harmine: Spectroscopic, calorimetric and computational evaluation. Heliyon 2024; 10:e34183. [PMID: 39100473 PMCID: PMC11295990 DOI: 10.1016/j.heliyon.2024.e34183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Revised: 07/04/2024] [Accepted: 07/04/2024] [Indexed: 08/06/2024] Open
Abstract
Small molecules as ligands target multifunctional ribonucleic acids (RNA) for therapeutic engagement. This study explores how the anticancer DNA intercalator harmine interacts various motifs of RNAs, including the single-stranded A-form poly (rA), the clover leaf tRNAphe, and the double-stranded A-form poly (rC)-poly (rG). Harmine showed the affinity to the polynucleotides in the order, poly (rA) > tRNAphe > poly (rC)·poly (rG). While no induced circular dichroism change was detected with poly (rC)poly (rG), significant structural alterations of poly (rA) followed by tRNAphe and occurrence of concurrent initiation of optical activity in the attached achiral molecule of alkaloid was reported. At 25 °C, the affinity further showed exothermic and entropy-driven binding. The interaction also highlighted heat capacity (ΔC o p ) and Gibbs energy contribution from the hydrophobic transfer (ΔG hyd) of binding with harmine. Molecular docking calculations indicated that harmine exhibits higher affinity for poly (rA) compared to tRNAphe and poly (rC)·poly (rG). Subsequent molecular dynamics simulations were conducted to investigate the binding mode and stability of harmine with poly(A), tRNAphe, and poly (rC)·poly (rG). The results revealed that harmine adopts a partial intercalative binding with poly (rA) and tRNAphe, characterized by pronounced stacking forces and stronger binding free energy observed with poly (rA), while a comparatively weaker binding free energy was observed with tRNAphe. In contrast, the stacking forces with poly (rC)·poly (rG) were comparatively less pronounced and adopts a groove binding mode. It was also supported by ferrocyanide quenching analysis. All these findings univocally provide detailed insight into the binding specificity of harmine, to single stranded poly (rA) over other RNA motifs, probably suggesting a self-structure formation in poly (rA) with harmine and its potential as a lead compound for RNA based drug targeting.
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Affiliation(s)
- Paromita Sarkar
- University of Kalyani, Department of Zoology, Nadia, W. Bengal, 741235, India
| | - Priyanka Gopi
- Amity Institute of Forensic Sciences, Amity University, Noida, Uttar Pradesh, India
| | - Prateek Pandya
- Amity Institute of Forensic Sciences, Amity University, Noida, Uttar Pradesh, India
| | - Samaresh Paria
- Vidyasagar University, Department of Chemistry, Midnapore 721 102, West Bengal, India
| | - Maidul Hossain
- Vidyasagar University, Department of Chemistry, Midnapore 721 102, West Bengal, India
| | - Manzer H. Siddiqui
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Saud Alamri
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Kakali Bhadra
- University of Kalyani, Department of Zoology, Nadia, W. Bengal, 741235, India
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Das M, Mukherjee S, Islam MM, Choudhuri I, Bhattacharyya N, Samanta BC, Dutta B, Maity T. Response of Ancillary Azide Ligand in Designing a 1D Copper(II) Polymeric Complex along with the Introduction of High DNA- and HAS-Binding Efficacy, Leading to Impressive Anticancer Activity: A Compact Experimental and Theoretical Approach. ACS OMEGA 2022; 7:23276-23288. [PMID: 35847281 PMCID: PMC9281303 DOI: 10.1021/acsomega.2c01403] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
A new versatile azide-bridged polymeric Cu(II) complex, namely, [Cu(L)(μ1,3-N3)]∞ (1), was synthesized utilizing an N,N,O-donor piperidine-based Schiff base ligand (E)-4-bromo-2-((2-(-1-yl)imino)methyl)phenol (HL), obtained via the condensation reaction of 1-(2-aminoethyl) piperidine and 5-bromo salicylaldehyde. The single-crystal X-ray diffraction analysis reveals that complex 1 consists of an end-to-end azido-bridged polymeric network, which is further rationalized with the help of a density functional theory (DFT) study. After routine characterization with a range of physicochemical studies, complex 1 is exploited to evaluate its biomedical potential. Initially, theoretical inspection with the help of a molecular docking study indicated the ability of complex 1 to effectively bind with macromolecules such as DNA and the human serum albumin (HSA) protein. The theoretical aspect was further verified by adopting several spectroscopic techniques. The electronic absorption spectroscopic analysis indicates a remarkable binding efficiency of Complex 1 with both DNA and HSA. The notable fluorescence intensity reduction of the ethidium bromide (EtBr)-DNA adduct, 4',6-diamidino-2-phenylindole (DAPI)-DNA adduct, and HSA after the gradual addition of complex 1 authenticates its promising binding potential with the macromolecules. The retention of the canonical B form of DNA and α form of HSA during the association of complex 1 was confirmed by implementing a circular dichroism spectral study. The association ability of complex 1 with macromolecules further inspired us to inspect its impact on different cell lines such as HeLa (cervical cancer cell), PA1 (ovarian cancer cell), and HEK (normal cell). The dose-dependent and time-dependent in vitro 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay suggests an effective antiproliferative property of complex 1 with low toxicity toward the normal cell line. Finally, the anticancer activity of complex 1 toward carcinoma cell lines was analyzed by nuclear and cellular staining techniques, unveiling the cell death mechanism.
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Affiliation(s)
- Manik Das
- Department
of Chemistry, Prabhat Kumar College, Contai, Purba Medinipur, Contai 721404, India
| | - Somali Mukherjee
- School
of Chemical Sciences, Indian Association
for the Cultivation of Science, Jadavpur, Kolkata 700032, West Bengal, India
| | - Md. Maidul Islam
- Department
of Chemistry, Aliah University, Kolkata 700064, India
| | - Indranil Choudhuri
- Department
of Chemistry, Panskura Banamali College, Panskura 721152, India
| | | | - Bidhan Chandra Samanta
- Department
of Chemistry, Mugberia Gangadhar Mahavidyalaya, Purba Medinipur 721425, India
| | - Basudeb Dutta
- Department
of Chemical Science, IISER Kolkata, Mohanpur, Kolkata 741246, India
| | - Tithi Maity
- Department
of Chemistry, Prabhat Kumar College, Contai, Purba Medinipur, Contai 721404, India
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Farias RL, Polez AMR, Silva DES, Zanetti RD, Moreira MB, Batista VS, Reis BL, Nascimento-Júnior NM, Rocha FV, Lima MA, Oliveira AB, Ellena J, Scarim CB, Zambom CR, Brito LD, Garrido SS, Melo APL, Bresolin L, Tirloni B, Pereira JCM, Netto AVG. In vitro and in silico assessment of antitumor properties and biomolecular binding studies for two new complexes based on Ni II bearing k 2N,S-donor ligands. MATERIALS SCIENCE & ENGINEERING. C, MATERIALS FOR BIOLOGICAL APPLICATIONS 2020; 121:111815. [PMID: 33579459 DOI: 10.1016/j.msec.2020.111815] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 11/20/2020] [Accepted: 12/13/2020] [Indexed: 12/30/2022]
Abstract
This work deals with two new molecule-based materials, namely NiII-complexes of general formulae [Ni(L1)2] (Ni1) and [Ni(L2)2] (Ni2), where L1 = trans-cinnamaldehyde-N(4)-methyl thiosemicarbazone and L2 = trans-cinnamaldehyde-N(4)-ethyl thiosemicarbazone, as potential antitumor agents. Both compounds were characterized by elemental analysis, molar conductivity and spectroscopic techniques (FTIR and NMR). Their molecular structures were obtained by single-crystal X-ray diffraction analysis. Each one crystallizes in a monoclinic space group P 21/c, also the asymmetric unit comprises of one NiII ion located on an inversion centre and one anionic ligand, which acts as a κ2N,S-donor affording a five-membered metallaring. The compounds were screened against two selected tumour cell lines (MCF-7 and A549) and non-tumour fibroblasts cell line (MRC-5) via MTT assays. In both tumour cells, all compounds exhibited higher cytotoxicity than the control drug (cisplatin). The IC50 values ranges of 3.70 - 41.37 μM and 1.06 - 14.91 μM were found for MCF-7 and A549, respectively. Importantly, all of them were less toxicity than cisplatin in MRC-5 with SI values ranged at 11.80 - 86.60. The red blood cell (RBC) assay revealed Ni2 as non-toxic due to its reduced haemolytic effect (0--9% at 1--10 μM). The DNA binding was investigated through a combination of spectrophotometric absorption and emission titrations, electrophoresis, and circular dichroism experiments. As a result, these metal complexes were not able to strongly binding to DNA (Kb values ~104 mol L--1) but suggesting groove-binding interactions. The scavenging ability of them towards 2,2-diphenyl-1-picrylhydrazyl (DPPH) free-radical was also evaluated in this work, but no important antioxidant behaviour was detected. Further, the interaction of Ni1 and Ni2 to human serum albumin (HSA) was explored by quenching of tryptophan emission, warfarin competitive assay, and molecular docking protocols. The HSA binding analyses indicated good affinity of both complexes to Sudlow site I (Kb values ⁓103 mol L-1).
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Affiliation(s)
- R L Farias
- Univ. Estadual Paulista (Unesp), Instituto de Química, Departamento de Química Analítica, Físico-Química e Inorgânica, Araraquara, Brazil.
| | - A M R Polez
- Univ. Estadual Paulista (Unesp), Instituto de Química, Departamento de Química Analítica, Físico-Química e Inorgânica, Araraquara, Brazil
| | - D E S Silva
- Univ. Estadual Paulista (Unesp), Instituto de Química, Departamento de Química Analítica, Físico-Química e Inorgânica, Araraquara, Brazil
| | - R D Zanetti
- Univ. Estadual Paulista (Unesp), Instituto de Química, Departamento de Química Analítica, Físico-Química e Inorgânica, Araraquara, Brazil
| | - M B Moreira
- Univ. Estadual Paulista (Unesp), Instituto de Química, Departamento de Química Analítica, Físico-Química e Inorgânica, Araraquara, Brazil; Univ. Estadual de Londrina (UEL), Departamento de Química, Londrina, Brazil
| | - V S Batista
- Univ. Estadual Paulista (Unesp), Instituto de Química, Laboratório de Química Medicinal, Síntese Orgânica e Modelagem Molecular (LaQMedSOMM), Araraquara, Brazil
| | - B L Reis
- Univ. Estadual Paulista (Unesp), Instituto de Química, Laboratório de Química Medicinal, Síntese Orgânica e Modelagem Molecular (LaQMedSOMM), Araraquara, Brazil; Technische Universität Dresden (TUD), Department of Chemistry and Food Chemistry, Dresden, Germany
| | - N M Nascimento-Júnior
- Univ. Estadual Paulista (Unesp), Instituto de Química, Laboratório de Química Medicinal, Síntese Orgânica e Modelagem Molecular (LaQMedSOMM), Araraquara, Brazil
| | - F V Rocha
- Univ. Federal de São Carlos (UFSCar), Departamento de Química, São Carlos, Brazil
| | - M A Lima
- Univ. Federal de São Carlos (UFSCar), Departamento de Química, São Carlos, Brazil
| | - A B Oliveira
- Univ. Federal de Sergipe (UFS), Departamento de Química, São Cristóvão, Brazil
| | - J Ellena
- Univ. de São Paulo (USP), Instituto de Física de São Carlos, São Carlos, Brazil
| | - C B Scarim
- Univ. Estadual Paulista (Unesp), Faculdade de Ciências Farmacêuticas, Araraquara, Brazil
| | - C R Zambom
- Univ. Estadual Paulista (Unesp), Instituto de Química, Departamento de Bioquímica e Química Orgânica, Araraquara, Brazil
| | - L D Brito
- Univ. Estadual Paulista (Unesp), Instituto de Química, Departamento de Bioquímica e Química Orgânica, Araraquara, Brazil
| | - S S Garrido
- Univ. Estadual Paulista (Unesp), Instituto de Química, Departamento de Bioquímica e Química Orgânica, Araraquara, Brazil
| | - A P L Melo
- Univ. Federal do Rio Grande (FURG), Escola de Química e Alimentos, Rio Grande, Brazil
| | - L Bresolin
- Univ. Federal do Rio Grande (FURG), Escola de Química e Alimentos, Rio Grande, Brazil
| | - B Tirloni
- Univ. Federal de Santa Maria (UFSM), Departamento de Química, Santa Maria, Brazil
| | - J C M Pereira
- Univ. Estadual Paulista (Unesp), Instituto de Química, Departamento de Química Analítica, Físico-Química e Inorgânica, Araraquara, Brazil
| | - A V G Netto
- Univ. Estadual Paulista (Unesp), Instituto de Química, Departamento de Química Analítica, Físico-Química e Inorgânica, Araraquara, Brazil
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Shaban NZ, Aboelsaad AM, Shoueir KR, Abdulmalek SA, Awad D, Shaban SY, Mansour H. Chitosan-based dithiophenolato nanoparticles: Preparation, mechanistic information of DNA binding, antibacterial and cytotoxic activities. J Mol Liq 2020. [DOI: 10.1016/j.molliq.2020.114252] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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Đukić MB, Jeremić MS, Filipović IP, Klisurić OR, Kojić VV, Jakimov DS, Jelić RM, Onnis V, Matović ZD. Synthesis, characterization, HSA/DNA interactions and antitumor activity of new [Ru(η 6-p-cymene)Cl 2(L)] complexes. J Inorg Biochem 2020; 213:111256. [PMID: 32980642 DOI: 10.1016/j.jinorgbio.2020.111256] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 09/08/2020] [Accepted: 09/10/2020] [Indexed: 12/18/2022]
Abstract
Three new ruthenium(II) complexes were synthesized from different substituted isothiazole ligands 5-(methylamino)-3-pyrrolidine-1-ylisothiazole-4-carbonitrile (1), 5-(methylamino)-3-(4-methylpiperazine-1-yl)isothiazole-4-carbonitrile (2) and 5-(methylamino)-3-morpholine-4-ylisothiazole-4-carbonitrile (3): [Ru(η6-p-cymene)Cl2(L1)]·H2O (4), [Ru(η6-p-cymene)Cl2(L2)] (5) and [Ru(η6-p-cymene)Cl2(L3)] (6). All complexes were characterized by IR, UV-Vis, NMR spectroscopy, and elemental analysis. The molecular structures of all ligands and complexes 4 and 6 were determined by an X-ray. The results of the interactions of CT-DNA (calf thymus deoxyribonucleic acid) and HSA (human serum albumin) with ruthenium (II) complexes reveal that complex 4 binds well to CT-DNA and HSA. Kinetic and thermodynamic parameters for the reaction between complex and HSA confirmed the associative mode of interaction. The results of Quantum mechanics (QM) modelling and docking experiments toward DNA dodecamer and HSA support the strongest binding of the complex 4 to DNA major groove, as well as its binding to IIa domain of HSA with the lowest ΔG energy, which agrees with the solution studies. The modified GOLD docking results are indicative for Ru(p-cymene)LCl··(HSA··GLU292) binding and GOLD/MOPAC(QM) docking/modelling of DNA/Ligand (Ru(II)-N(7)dG7) covalent binding. The cytotoxic activity of compounds was evaluated by MTT (3-(4,5-dimethyl-2-thiazolyl)-2,5-diphenyl-2H-tetrazolium bromide) assay. Neither of the tested compounds shows activity against a healthy MRC-5 cell line while the MCF-7 cell line is the most sensitive to all. Compounds 3, 4 and 5 were about two times more active than cisplatin, while the antiproliferative activity of 6 was almost the same as with cisplatin. Flow cytometry analysis showed the apoptotic death of the cells with a cell cycle arrest in the subG1 phase.
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Affiliation(s)
- Maja B Đukić
- University of Kragujevac, Faculty of Science, Department of Chemistry, Radoja Domanovića 12, 34000 Kragujevac, Serbia
| | - Marija S Jeremić
- University of Kragujevac, Faculty of Science, Department of Chemistry, Radoja Domanovića 12, 34000 Kragujevac, Serbia
| | - Ignjat P Filipović
- University of Kragujevac, Faculty of Science, Department of Chemistry, Radoja Domanovića 12, 34000 Kragujevac, Serbia
| | - Olivera R Klisurić
- University of Novi Sad, Faculty of Sciences, Department of Physics, Trg Dositeja Obradovića 4, 21000 Novi Sad, Serbia
| | - Vesna V Kojić
- Oncology Institute of Vojvodina, Faculty of Medicine, University of Novi Sad, Put Doktora Goldmana 4, 21204 Sremska Kamenica, Serbia
| | - Dimitar S Jakimov
- Oncology Institute of Vojvodina, Faculty of Medicine, University of Novi Sad, Put Doktora Goldmana 4, 21204 Sremska Kamenica, Serbia
| | - Ratomir M Jelić
- University of Kragujevac, Faculty of Medical Sciences, Department of Pharmacy, Svetozara Markovića 69, 34000 Kragujevac, Serbia
| | - Valentina Onnis
- Department of Life and Environmental Sciences, Unit of Pharmaceutical, Pharmacological and Nutraceutical Sciences, University of Cagliari, University Campus, S.P. n° 8, Km 0.700, I-09042 Monserrato (CA), Italy
| | - Zoran D Matović
- University of Kragujevac, Faculty of Science, Department of Chemistry, Radoja Domanovića 12, 34000 Kragujevac, Serbia.
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Botti V, Urbanelli L, Sagini K, Tarpani L, Cesaretti A, Fortuna CG, Elisei F. Quaternized styryl-azinium fluorophores as cellular RNA-binders. Photochem Photobiol Sci 2020; 19:362-370. [PMID: 32147676 DOI: 10.1039/c9pp00465c] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The capability of three quaternized styryl-azinium iodides to bind cellular RNA has been tested by means of Fluorescence Confocal Microscopy imaging of stained MCF-7 cells treated with RNase. Their association constants have been estimated through spectrophotometric and fluorimetric titrations with tRNA and compared to their affinity toward DNA. Transient absorption spectroscopy with femtosecond resolution confirmed the binding of the investigated compounds with tRNA and shed new light on the excited state dynamics of their complexes, by revealing a significant lengthening of the lifetime of S1 upon complexation, which parallels the fluorescence quantum yield enhancement.
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Affiliation(s)
- Valentina Botti
- Department of Chemistry, Biology and Biotechnology and Center of Excellence on Innovative Nanostructured Materials (CEMIN), University of Perugia, via Elce di Sotto 8, 06123, Perugia, Italy.
| | - Lorena Urbanelli
- Department of Chemistry, Biology and Biotechnology, University of Perugia, via del Giochetto, 06126, Perugia, Italy
| | - Krizia Sagini
- Department of Chemistry, Biology and Biotechnology, University of Perugia, via del Giochetto, 06126, Perugia, Italy
| | - Luigi Tarpani
- Department of Chemistry, Biology and Biotechnology and Center of Excellence on Innovative Nanostructured Materials (CEMIN), University of Perugia, via Elce di Sotto 8, 06123, Perugia, Italy
| | - Alessio Cesaretti
- Department of Chemistry, Biology and Biotechnology and Center of Excellence on Innovative Nanostructured Materials (CEMIN), University of Perugia, via Elce di Sotto 8, 06123, Perugia, Italy
| | - Cosimo G Fortuna
- Department of Chemical Sciences, University of Catania, viale Andrea Doria 6, 95125, Catania, Italy
| | - Fausto Elisei
- Department of Chemistry, Biology and Biotechnology and Center of Excellence on Innovative Nanostructured Materials (CEMIN), University of Perugia, via Elce di Sotto 8, 06123, Perugia, Italy
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Paul P, Mati SS, Kumar GS. Insights on the interaction of phenothiazinium dyes methylene blue and new methylene blue with synthetic duplex RNAs through spectroscopy and modeling. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2020; 204:111804. [PMID: 32007677 DOI: 10.1016/j.jphotobiol.2020.111804] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 01/18/2020] [Accepted: 01/21/2020] [Indexed: 12/31/2022]
Abstract
The ubiquitous influence of double stranded RNAs in biological events makes them imperative to gather data based on specific binding procedure of small molecules to various RNA conformations. Particular interest may be attributed to situations wherein small molecules target RNAs altering their structures and causing functional modifications. The main focus of this study is to delve into the interactive pattern of two small molecule phenothiazinium dyes, methylene blue and new methylene blue, with three duplex RNA polynucleotides-poly(A).poly(U), poly(C).poly(G) and poly(I).poly(C) by spectroscopic and molecular modeling techniques. Analysis of data as per Scatchard and Benesi-Hildebrand methodologies revealed highest affinity of these dyes to poly(A).poly(U) and least to poly(I).poly(C). In addition to fluorescence quenching, viscometric studies also substantiated that the dyes follow different modes of binding to different RNA polynucleotides. Distortion in the RNA structures with induced optical activity in the otherwise optically inactive dye molecules was evidenced from circular dichroism results. Dye-induced RNA structural modification occurred from extended conformation to compact particles visualized by atomic force microscopy. Molecular docking results revealed different binding patterns of the dye molecules within the RNA duplexes. The novelty of the present work lies towards a new contribution of the phenothiazinium dyes in dysfunctioning double stranded RNAs, advancing our knowledge to their potential use as RNA targeted small molecules.
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Affiliation(s)
- Puja Paul
- Department of Chemistry, Dinabandhu Mahavidyalaya, Bongaon, West Bengal 743235, India; CSIR-Indian Institute of Chemical Biology, Kolkata 700 032, India
| | - Soumya Sundar Mati
- Government GD College, Keshiary, Paschim Medinipur, West Bengal 721135, India
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9
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Erenpreisa J, Krigerts J, Salmina K, Selga T, Sorokins H, Freivalds T. Differential staining of peripheral nuclear chromatin with Acridine orange implies an A-form epichromatin conformation of the DNA. Nucleus 2019; 9:171-181. [PMID: 29363398 PMCID: PMC5973139 DOI: 10.1080/19491034.2018.1431081] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The chromatin observed by conventional electron microscopy under the nuclear envelope constitutes a single layer of dense 30–35 nm granules, while ∼30 nm fibrils laterally attached to them, form large patches of lamin-associated domains (LADs). This particular surface “epichromatin” can be discerned by specific (H2A+H2B+DNA) conformational antibody at the inner nuclear envelope and around mitotic chromosomes. In order to differentiate the DNA conformation of the peripheral chromatin we applied an Acridine orange (AO) DNA structural test involving RNAse treatment and the addition of AO after acid pre-treatment. MCF-7 cells treated in this way revealed yellow/red patches of LADs attached to a thin green nuclear rim and with mitotic chromosomes outlined in green, topologically corresponding to epichromatin epitope staining by immunofluorescence. Differentially from LADs, the epichromatin was unable to provide metachromatic staining by AO, unless thermally denatured at 94oC. DNA enrichment in GC stretches has been recently reported for immunoprecipitated ∼ 1Kb epichromatin domains. Together these data suggest that certain epichromatin segments assume the relatively hydrophobic DNA A-conformation at the nuclear envelope and surface of mitotic chromosomes, preventing AO side dimerisation. We hypothesize that epichromatin domains form nucleosome superbeads. Hydrophobic interactions stack these superbeads and align them at the nuclear envelope, while repulsing the hydrophilic LADs. The hydrophobicity of epichromatin explains its location at the surface of mitotic chromosomes and its function in mediating chromosome attachment to the restituting nuclear envelope during telophase.
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Affiliation(s)
| | - Jekabs Krigerts
- a Latvian Biomedical Research & Study Centre , Ratsupites 1, Riga , Latvia.,b Institute of Biomedical Engineering and Nanotechnologies, Riga Technical University , Kalku iela 1, Riga , Latvia
| | - Kristine Salmina
- a Latvian Biomedical Research & Study Centre , Ratsupites 1, Riga , Latvia
| | - Turs Selga
- c Faculty of Biology, University of Latvia , Raina bulvaris 19, Riga , Latvia
| | - Hermanis Sorokins
- b Institute of Biomedical Engineering and Nanotechnologies, Riga Technical University , Kalku iela 1, Riga , Latvia
| | - Talivaldis Freivalds
- d Institute of Kardiology and Regenerative Medicine, University of Latvia , Raina bulvaris 19, Riga , Latvia
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Shahabadi N, Abbasi AR, Moshtkob A, Hadidi S. Design, synthesis and DNA interaction studies of new fluorescent platinum complex containing anti-HIV drug didanosine. J Biomol Struct Dyn 2019; 38:2837-2848. [DOI: 10.1080/07391102.2019.1658643] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Nahid Shahabadi
- Department of Inorganic Chemistry, Faculty of Chemistry, Razi University, Kermanshah, Iran
- Medical Biology Research Center (MBRC), Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Amir Reza Abbasi
- Department of Inorganic Chemistry, Faculty of Chemistry, Razi University, Kermanshah, Iran
- Institute of Nano Science and Nano Technology, Razi University, Kermanshah, Iran
| | - Ayda Moshtkob
- Department of Inorganic Chemistry, Faculty of Chemistry, Razi University, Kermanshah, Iran
| | - Saba Hadidi
- Department of Inorganic Chemistry, Faculty of Chemistry, Razi University, Kermanshah, Iran
- Medical Biology Research Center (MBRC), Kermanshah University of Medical Sciences, Kermanshah, Iran
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11
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Design, DNA binding and kinetic studies, antibacterial and cytotoxic activities of stable dithiophenolato titanium(IV)-chitosan Nanocomposite. J Mol Liq 2019. [DOI: 10.1016/j.molliq.2019.111002] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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12
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Das A, Suresh Kumar G, Dutta S. Interaction of aloe active compounds with calf thymus DNA. J Mol Recognit 2019; 32:e2786. [PMID: 31062439 DOI: 10.1002/jmr.2786] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Revised: 04/02/2019] [Accepted: 04/03/2019] [Indexed: 01/09/2023]
Abstract
Natural anthraquinone compounds have emerged as potent anticancer chemotherapeutic agents because of their promising DNA-binding properties. Aloe vera is among one of the very well-known medicinal plants, and the anthraquinone derivatives like aloe emodin (ALM), aloins (ALN), and aloe emodin-8-glucoside (ALMG) are known to have immense biological activities. Here, we have used biophysical methods to elucidate the comparative DNA-binding abilities of these three molecules. Steady-state fluorescence study indicated complexation between calf thymus DNA (ctDNA) and both the molecules ALM and ALMG whereas ALN showed very weak interaction with DNA. Displacement assays with ctDNA-bound intercalator (ethidium bromide) and a groove binder (Hoechst 33258) indicated preferential binding of both ALM and ALMG to minor groove of DNA. Isothermal titration calorimetric (ITC) data suggested spontaneous exothermic single binding mode of both the molecules: ALM and ALMG. Entropy is the most important factor which contributed to the standard molar Gibbs energy associated with relatively small favorable enthalpic contribution. The equilibrium constants of binding to ctDNA were (6.02 ± 0.10) × 104 M-1 and (4.90 ± 0.11) × 104 M-1 at 298.15 K, for ALM and ALMG, respectively. The enthalpy vs temperature plot yielded negative standard molar heat capacity value, and a strong negative correlation between enthalpy and entropy terms was observed which indicates the enthalpy entropy compensation behavior in both systems. All these thermodynamic phenomena indicate that hydrophobic force is the key factor which is involved in the binding process. Moreover, the enhancement of thermal stability of DNA helix by ALM and ALMG fully agreed to the complexation of these molecules with DNA.
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Affiliation(s)
- Abhi Das
- Organic and Medicinal Chemistry Division, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Gopinatha Suresh Kumar
- Organic and Medicinal Chemistry Division, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Sanjay Dutta
- Organic and Medicinal Chemistry Division, CSIR-Indian Institute of Chemical Biology, Kolkata, India
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Sarkar S, Shmatova OI, Nenajdenko VG, Bhadra K. Trifluoromethylated carboline compounds targeting DNA: Synthesis, binding and anti-proliferative effects on human cancer cell lines. Bioorg Chem 2019; 86:61-79. [DOI: 10.1016/j.bioorg.2019.01.028] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Revised: 12/14/2018] [Accepted: 01/17/2019] [Indexed: 01/26/2023]
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14
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Spiropyran as a potential molecular diagnostic tool for double-stranded RNA detection. BMC Biomed Eng 2019; 1:6. [PMID: 32903305 PMCID: PMC7421392 DOI: 10.1186/s42490-019-0008-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Accepted: 02/25/2019] [Indexed: 11/10/2022] Open
Abstract
Background Long double-stranded RNAs (dsRNAs) are duplex RNAs that can induce immune response when present in mammalian cells. These RNAs are historically associated with viral replication, but recent evidence suggests that human cells naturally encode endogenous dsRNAs that can regulate antiviral machineries in cellular contexts beyond immune response. Results In this study, we use photochromic organic compound spiropyran to profile and quantitate dsRNA expression. We show that the open form of spiropyran, merocyanine, can intercalate between RNA base pairs, which leads to protonation and alteration in the spectral property of the compound. By quantifying the spectral change, we can detect and quantify dsRNA expression level, both synthetic and cellular. We further demonstrate that spiropyrans can be used as a molecular diagnostic tool to profile endogenously expressed dsRNAs. Particularly, we show that spiropyrans can robustly detect elevated dsRNA levels when colorectal cancer cells are treated with 5-aza-2'-deoxycytidine, an FDA-approved DNA-demethylating agent used for chemotherapy, thus demonstrating the use of spiropyran for predicting responsiveness to the drug treatment. Conclusion As dsRNAs are signature of virus and accumulation of dsRNAs is implicated in various degenerative disease, our work establishes potential application of spiropyrans as a simple spectral tool to diagnose human disease based on dsRNA expression.
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Tripathi M, Giri CG, Das D, Pande R, Sarkar S, Giri S, Roymahapatra G, Sarkar A. Synthesis, characterization and nucleic acid binding studies of mononuclear copper(II) complexes derived from azo containing O, O donor ligands. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2018; 37:563-584. [PMID: 30422758 DOI: 10.1080/15257770.2018.1508694] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Azo linked salicyldehyde and a new 2-hydroxy acetophenone based ligands (HL1 and HL2) with their copper(II) complexes [Cu(L1)2] (1) and [Cu(L2)2] (2) were synthesized and characterized by spectroscopic methods such as 1H, 13C NMR, UV-Vis spectroscopy and elemental analyses. Calculation based on Density Functional Theory (DFT), have been performed to obtain optimized structures. Binding studies of these copper (II) complexes with calf thymus DNA (ct-DNA) and torula yeast RNA (t-RNA) were analyzed by absorption spectra, emission spectra and Viscosity studies and Molecular Docking techniques. The absorption spectral study indicated that the copper(II) complexes of 1 and 2 had intrinsic binding constants with DNA or RNA in the range of 7.6 ± 0.2 × 103 M-1 or 6.5 ± 0.3 × 103M-1 and 5.7 ± 0.4 × 104 M-1 or 1.8 ± 0.5 × 103 M-1 respectively. The synthesized compounds and nucleic acids were simulated by molecular docking to explore more details mode of interaction of the complexes and their orientations in the active site of the receptor.
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Affiliation(s)
- Mamta Tripathi
- a School of Studies in Chemistry , Pt. Ravishankar Shukla University , Raipur , Chhattisgarh , India
| | | | - Devashish Das
- c DNA Skew Analytics Pvt. Ltd , Bengaluru , Karnataka , India
| | - Rama Pande
- a School of Studies in Chemistry , Pt. Ravishankar Shukla University , Raipur , Chhattisgarh , India
| | - Sougata Sarkar
- d Department of Chemistry , Ramakrishna Mission Vivekananda Centenary College , Kolkata , India
| | - Santanab Giri
- e Department of Chemistry , National Institute of Technology Rourkela , Rourkela , India
| | | | - Avijit Sarkar
- b Department of Chemistry , Bhairab Ganguly College , Kolkata , India
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16
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Karmakar P, Manna S, Maiti K, Ali SS, Guria UN, Sarkar R, Datta P, Mandal D, Mahapatra AK. A Perylene diimide based fluorescent probe for caffeine in aqueous medium. Supramol Chem 2018. [DOI: 10.1080/10610278.2018.1530352] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Parthasarathi Karmakar
- Department of Chemistry, Indian Institute of Engineering Science and Technology, Shibpur,Howrah, India
| | - Srimanta Manna
- Department of Chemistry, Indian Institute of Engineering Science and Technology, Shibpur,Howrah, India
| | - Kalipada Maiti
- Department of Chemistry, Indian Institute of Engineering Science and Technology, Shibpur,Howrah, India
| | - Syed Samim Ali
- Department of Chemistry, Indian Institute of Engineering Science and Technology, Shibpur,Howrah, India
| | - Uday Narayan Guria
- Department of Chemistry, Indian Institute of Engineering Science and Technology, Shibpur,Howrah, India
| | - Ripon Sarkar
- Centre for Healthcare Science and Technology, Indian Institute of Engineering Science and Technology, Shibpur, India
| | - Pallab Datta
- Centre for Healthcare Science and Technology, Indian Institute of Engineering Science and Technology, Shibpur, India
| | - Debasish Mandal
- School of Chemistry and Biochemistry, Thapar Institute of Engineering and Technology, Patiala, India
| | - Ajit Kumar Mahapatra
- Department of Chemistry, Indian Institute of Engineering Science and Technology, Shibpur,Howrah, India
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17
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Dolai M, Saha U, Kumar GS, Ali M. Amidooxime-Based Mononuclear Mn(II) Complexes: Synthesis, Characterization, and Studies on DNA Binding and Nuclease Activity. ChemistrySelect 2018. [DOI: 10.1002/slct.201801298] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Malay Dolai
- Department of Chemistry; Jadavpur University; Raja S.C. Mullick Road Kolkata 700 032
- Department of Chemistry; Prabhat Kumar College, Purba Medinipur; 721404 India
| | - Urmila Saha
- Biophysical Chemistry Laboratory; Organic and Medicinal Chemistry Division; CSIR-Indian Institute of Chemical Biology; 4, Raja S.C. Mullick Road Kolkata 700 032 India
| | - Gopinatha S. Kumar
- Biophysical Chemistry Laboratory; Organic and Medicinal Chemistry Division; CSIR-Indian Institute of Chemical Biology; 4, Raja S.C. Mullick Road Kolkata 700 032 India
| | - Mahammad Ali
- Department of Chemistry; Jadavpur University; Raja S.C. Mullick Road Kolkata 700 032
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18
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Stojković DL, Jevtić VV, Radić GP, Đukić MB, Jelić RM, Zarić MM, Anđelković MV, Mišić MS, Baskić DD, Trifunović SR. Stereospecific ligands and their complexes. XXIV. Synthesis, characterization and some biological properties of Pd(ii) and Pt(ii) complexes with R2-S,S-eddtyr. NEW J CHEM 2018. [DOI: 10.1039/c7nj04437b] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In vitro activity of ligands and corresponding platinum(ii) and palladium(ii) complexes.
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Affiliation(s)
| | - Verica V. Jevtić
- University of Kragujevac
- Faculty of Science
- Department of Chemistry
- 34000 Kragujevac
| | - Gordana P. Radić
- University of Kragujevac
- Faculty of Medical Sciences
- Department of Pharmacy
- 34000 Kragujevac
| | - Maja B. Đukić
- University of Kragujevac
- Faculty of Science
- Department of Chemistry
- 34000 Kragujevac
| | - Ratomir M. Jelić
- University of Kragujevac
- Faculty of Medical Sciences
- Department of Pharmacy
- 34000 Kragujevac
| | - Milan M. Zarić
- University of Kragujevac
- Faculty of Medical Sciences
- Department of Biochemistry
- 34000 Kragujevac
| | - Marija V. Anđelković
- University of Kragujevac
- Faculty of Medical Sciences
- Department of Biochemistry
- 34000 Kragujevac
| | | | - Dejan D. Baskić
- Public Health Institute Kragujevac
- University of Kragujevac
- Faculty of Medical Sciences
- Centre for Molecular Medicine and Stem Cell Research
- 34000 Kragujevac
| | - Srećko R. Trifunović
- University of Kragujevac
- Faculty of Science
- Department of Chemistry
- 34000 Kragujevac
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Bhattacharjee P, Ghosh T, Sarkar S, Pandya P, Bhadra K. Binding affinity and in vitro
cytotoxicity of harmaline targeting different motifs of nucleic acids: An ultimate drug designing approach. J Mol Recognit 2017; 31. [PMID: 29243872 DOI: 10.1002/jmr.2687] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2017] [Revised: 10/22/2017] [Accepted: 10/22/2017] [Indexed: 01/18/2023]
Affiliation(s)
| | - Tapas Ghosh
- Department of Zoology; University of Kalyani; Kalyani Nadia, West Bengal India
| | - Sarita Sarkar
- Department of Zoology; University of Kalyani; Kalyani Nadia, West Bengal India
| | - Prateek Pandya
- Amity Institute of Forensic Sciences; Amity University; Noida Uttar Pradesh India
| | - Kakali Bhadra
- Department of Zoology; University of Kalyani; Kalyani Nadia, West Bengal India
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20
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Zhu P, Ding Y, Guo R. Coil-globule structure transition and binding characteristics of DNA molecules induced by isoquinoline-based photoactive ionic liquid surfactant. Colloids Surf A Physicochem Eng Asp 2017. [DOI: 10.1016/j.colsurfa.2017.07.082] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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21
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Khan AY, Suresh Kumar G. Exploring the binding interaction of potent anticancer drug topotecan with human serum albumin: spectroscopic, calorimetric and fibrillation study. J Biomol Struct Dyn 2017; 36:2463-2473. [DOI: 10.1080/07391102.2017.1359671] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Asma Yasmeen Khan
- 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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22
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Basu P, Suresh Kumar G. Small molecule-RNA recognition: Binding of the benzophenanthridine alkaloids sanguinarine and chelerythrine to single stranded polyribonucleotides. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2017; 174:173-181. [PMID: 28779690 DOI: 10.1016/j.jphotobiol.2017.07.022] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Revised: 07/18/2017] [Accepted: 07/21/2017] [Indexed: 01/18/2023]
Abstract
Single stranded RNAs are biologically potent as they participate in various key cellular processes. The binding efficacy of two potent anticancer alkaloids, sanguinarine (here after SANG) and chelerythrine (here after CHEL), with single-stranded ribonucleic acids poly(rI), poly(rG), and poly(rC) were studied using spectroscopic and thermodynamic tools. Results reveal that both SANG and CHEL binds well with single stranded RNAs with affinity in the order poly(rI)>poly(rG)>poly(rC). CHEL showed slightly higher affinity compared to SANG with all the single stranded RNAs. Both SANG and CHEL showed association affinity of the lower 106 order with poly(rI), higher 105 order binding with poly(rG) and lower 105 order with poly(rC). The binding mode was partial intercalation due to the staking interaction between the bases and the alkaloids. The complexation of both the SANG and CHEL to the RNAs were mainly enthalpy driven and also favoured by entropy changes. Perturbation was observed in the RNA conformation due to binding of the alkaloids. In this present study we have deciphered the fundamental structural and calorimetric aspects of the interaction of the natural benzophenanthridine alkaloids with single stranded RNAs and these results may help to develop new generation alkaloid based therapeutics targeting single stranded RNAs.
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Affiliation(s)
- Pritha Basu
- Organic and Medicinal Chemistry Division, CSIR-Indian Institute of Chemical Biology, Kolkata 700 032, India
| | - Gopinatha Suresh Kumar
- Organic and Medicinal Chemistry Division, CSIR-Indian Institute of Chemical Biology, Kolkata 700 032, India.
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23
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Das A, Chatterjee S, Suresh Kumar G. Targeting human telomeric G-quadruplex DNA with antitumour natural alkaloid aristololactam-β-D-glucoside and its comparison with daunomycin. J Mol Recognit 2017; 30. [DOI: 10.1002/jmr.2639] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Revised: 04/05/2017] [Accepted: 04/11/2017] [Indexed: 11/05/2022]
Affiliation(s)
| | - Sabyasachi Chatterjee
- Biophysical Chemistry Laboratory, Organic and Medicinal Chemistry Division; CSIR-Indian Institute of Chemical Biology; Kolkata India
| | - Gopinatha Suresh Kumar
- Biophysical Chemistry Laboratory, Organic and Medicinal Chemistry Division; CSIR-Indian Institute of Chemical Biology; Kolkata India
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24
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Synthesis, characterization, structure, DNA binding aspects and molecular docking study of a novel Schiff base ligand and its bis(μ-chloro) bridged Cu(II) dimer. Polyhedron 2017. [DOI: 10.1016/j.poly.2017.01.033] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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25
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Tripathi M, Khilari R, Thakur Y, Verma B, Pardhi M, Pande R. Oxovanadium complex as potential nucleic acid binder. JOURNAL OF MACROMOLECULAR SCIENCE PART A-PURE AND APPLIED CHEMISTRY 2017. [DOI: 10.1080/10601325.2017.1261620] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Mamta Tripathi
- School of Studies in Chemistry, Pt. Ravishankar Shukla University, Raipur, Chhattisgarh, India
| | - Rubi Khilari
- School of Studies in Chemistry, Pt. Ravishankar Shukla University, Raipur, Chhattisgarh, India
| | - Yamini Thakur
- School of Studies in Chemistry, Pt. Ravishankar Shukla University, Raipur, Chhattisgarh, India
| | - Bharati Verma
- School of Studies in Chemistry, Pt. Ravishankar Shukla University, Raipur, Chhattisgarh, India
| | - Manish Pardhi
- School of Studies in Chemistry, Pt. Ravishankar Shukla University, Raipur, Chhattisgarh, India
| | - Rama Pande
- School of Studies in Chemistry, Pt. Ravishankar Shukla University, Raipur, Chhattisgarh, India
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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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Bhattacharjee P, Sarkar S, Pandya P, Bhadra K. Targeting different RNA motifs by beta carboline alkaloid, harmalol: a comparative photophysical, calorimetric, and molecular docking approach. J Biomol Struct Dyn 2016; 34:2722-2740. [DOI: 10.1080/07391102.2015.1126694] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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28
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Guhathakurta B, Basu P, Kumar GS, Lu L, Zhu M, Bandyopadhyay N, Naskar JP. Synthetic, structural, electrochemical and DNA-binding aspects of a novel oximato bridged copper(II) dimer. Polyhedron 2016. [DOI: 10.1016/j.poly.2016.03.011] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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29
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Basu A, Kumar GS. Spectroscopic and microcalorimetric studies on the molecular binding of food colorant acid red 27 with deoxyribonucleic acid. J Mol Recognit 2016; 29:363-9. [DOI: 10.1002/jmr.2536] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Revised: 12/26/2015] [Accepted: 12/26/2015] [Indexed: 12/22/2022]
Affiliation(s)
- Anirban Basu
- 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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30
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Khan AY, Suresh Kumar G. Spectroscopic studies on the binding interaction of phenothiazinium dyes, azure A and azure B to double stranded RNA polynucleotides. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2016; 152:417-425. [PMID: 26241827 DOI: 10.1016/j.saa.2015.07.091] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2015] [Revised: 07/08/2015] [Accepted: 07/23/2015] [Indexed: 06/04/2023]
Abstract
This manuscript presents spectroscopic characterization of the interaction of two phenothiazinium dyes, azure A and azure B with double stranded (ds) ribonucleic acids, poly(A).poly(U), poly(C).poly(G) and poly(I).poly(C). Absorbance and fluorescence studies revealed that these dyes bind to the RNAs with binding affinities of the order 10(6)M(-1) to poly(A).poly(U), and 10(5)M(-1) to poly(C).poly(G) and poly(I).poly(C), respectively. Fluorescence quenching and viscosity data gave conclusive evidence for the intercalation of the dyes to these RNA duplexes. Circular dichroism results suggested that the conformation of the RNAs was perturbed on interaction and the dyes acquired strong induced optical activity on binding. Azure B bound to all the three RNAs stronger than azure A and the binding affinity varied as poly(A).poly(U)>poly(C).poly(G)>poly(I).poly(C) for both dyes.
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Affiliation(s)
- Asma Yasmeen Khan
- 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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Zhao Y, Zhou H, Shen J, Wang M, Wu X. Study on the interaction of berberine with nucleic acids in the presence of silver nanoparticles, and the fluorometric determination of nucleic acids. RSC Adv 2016. [DOI: 10.1039/c6ra02346k] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The partial intercalation binding between BER and ctDNA, and the anti-photobleaching ability of BER were both strengthened by AgNPs. A metal enhanced fluorescence-based sensitive method for the determination of nucleic acids was obtained.
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Affiliation(s)
- Yanyan Zhao
- Key Laboratory of Colloid and Interface Chemistry (Shandong University)
- Ministry of Education
- School of Chemistry and Chemical Engineering
- Shandong University
- Jinan 250100
| | - Haiping Zhou
- Key Laboratory of Colloid and Interface Chemistry (Shandong University)
- Ministry of Education
- School of Chemistry and Chemical Engineering
- Shandong University
- Jinan 250100
| | - Jin Shen
- Key Laboratory of Colloid and Interface Chemistry (Shandong University)
- Ministry of Education
- School of Chemistry and Chemical Engineering
- Shandong University
- Jinan 250100
| | - Minqin Wang
- College of Life Science Shandong University
- Jinan 250100
- P. R. China
| | - Xia Wu
- Key Laboratory of Colloid and Interface Chemistry (Shandong University)
- Ministry of Education
- School of Chemistry and Chemical Engineering
- Shandong University
- Jinan 250100
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KUMAR SARATCHANDRA, PAL ABHIJIT, MITRA MERRY, MANIKANDAMATHAVAN VM, LIN CHIAHER, NAIR BALACHANDRANUNNI, GHOSH RAJARSHI. DNA binding and cleavage activity of a structurally characterized Ni(II) Schiff base complex. J CHEM SCI 2015. [DOI: 10.1007/s12039-015-0900-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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33
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Synthesis, Fluorescence Spectra, Redox Property and the DNA Binding Studies of 7-phenylacenaphtho[1,2-b]quinoxalin-7-ium chloride: Evidences of the Formation of Neutral Radical Analogue. J Fluoresc 2015; 25:1645-54. [DOI: 10.1007/s10895-015-1651-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Accepted: 09/09/2015] [Indexed: 10/23/2022]
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Khilari R, Thakur Y, Pardhi M, Pande R. RNA-Binding Efficacy of N-Phenylbenzohydroxamic Acid: An Invitro and Insilico Approach. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2015; 34:332-47. [PMID: 25874942 DOI: 10.1080/15257770.2014.1001073] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
RNA has attracted recent attention for its key role in gene expression and hence targeting by small molecules for therapeutic intervention. This study is aimed to elucidate the specificity of RNA binding affinity of parent compound of N-arylhydroxamic acids series, N-phenylbenzohydroxamic acid trivially named as PBHA,C6H5NOH.C6H5C˭O. The binding behavior was examined by various biophysical methods such as absorption, fluorescence, and viscosity measurements. Molecular docking was also done. The value of affinity constant and overall binding constant was calculated 5.79±0.03×10(4) M(-1) and K'=1.09±0.03×10(5) M(-1), respectively. The Stern-Volmer constant Ksv obtained was 2.28±0.04×10(4) M(-1). The compound (PBHA) shows a concentration-based enhancement of fluorescence intensity with increasing RNA concentration. Fluorescence quenching of PBHA-RNA complex in presence of K4 [Fe(CN)6] was also observed. Viscometric studies complimented the UV results where a continuous increase in relative viscosity of the RNA solution was observed with added optimal PBHA concentration. All the experimental evidences indicate that PBHA can strongly bind to RNA through an intercalative mode.
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Affiliation(s)
- Rubi Khilari
- a School of Studies in Chemistry, Pt. Ravishankar Shukla University , Raipur , Chhattisgarh , India
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35
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Basu A, Suresh Kumar G. Studies on the interaction of the food colorant tartrazine with double stranded deoxyribonucleic acid. J Biomol Struct Dyn 2015; 34:935-42. [DOI: 10.1080/07391102.2015.1057766] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Anirban Basu
- Biophysical Chemistry Laboratory, Chemistry Division, CSIR-Indian Institute of Chemical Biology, Kolkata 700 032, India
| | - Gopinatha Suresh Kumar
- Biophysical Chemistry Laboratory, Chemistry Division, CSIR-Indian Institute of Chemical Biology, Kolkata 700 032, India
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36
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Bhowmik D, Fiorillo G, Lombardi P, Suresh Kumar G. Recognition of human telomeric G-quadruplex DNA by berberine analogs: effect of substitution at the 9 and 13 positions of the isoquinoline moiety. J Mol Recognit 2015; 28:722-30. [DOI: 10.1002/jmr.2486] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Revised: 05/11/2015] [Accepted: 05/23/2015] [Indexed: 11/11/2022]
Affiliation(s)
- Debipreeta Bhowmik
- Biophysical Chemistry Laboratory; CSIR-Indian Institute of Chemical Biology; Kolkata 700 032 India
| | - Gaetano Fiorillo
- Naxospharma srl; Via G. Di Vittorio 70 20026 Novate Milanese MI Italy
| | - Paolo Lombardi
- Naxospharma srl; Via G. Di Vittorio 70 20026 Novate Milanese MI Italy
| | - G. Suresh Kumar
- Biophysical Chemistry Laboratory; CSIR-Indian Institute of Chemical Biology; Kolkata 700 032 India
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37
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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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38
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Basu P, Kumar GS. A comparative study on the interaction of the putative anticancer alkaloids, sanguinarine and chelerythrine, with single- and double-stranded, and heat-denatured DNAs. J Biomol Struct Dyn 2015; 33:2594-605. [PMID: 25562701 DOI: 10.1080/07391102.2014.1002425] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
A detailed investigation on the interaction of two benzophenanthridine alkaloids, sanguinarine (SGR) and chelerythrine (CHL), with the double-stranded (ds), heat-denatured (hd), and single-stranded (ss) DNA was performed by spectroscopy and calorimetry techniques. Binding to the three DNA conformations leads to quenching of fluorescence of SGR and enhancement in the fluorescence of CHL. The binding was cooperative for both of the alkaloids with all the three DNA conformations. The binding constant values of both alkaloids with the ds DNA were in the order of 10(6) M(-1); binding was weak with hd and much weaker to the ss DNA. The fluorescence emission of the alkaloid molecules bound to the ds and hd DNAs was quenched much less compared to those bound to the ss DNA based on competition with the anionic quencher KI. For both double stranded and heat denatured structures the emission of the bound alkaloid molecules was polarized significantly and strong energy transfer from the DNA bases to the alkaloid molecules occurred. Intercalation of SGR and CHL to ds, hd, and ss DNA was proved from these fluorescence results. Calorimetric studies suggested that the binding to all DNA conformations was both enthalpy and entropy favored. Both the alkaloids preferred double-helical regions for binding, but SGR was a stronger binder than CHL to all the three DNA structures.
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Affiliation(s)
- Pritha Basu
- a Biophysical Chemistry Laboratory , CSIR-Indian Institute of Chemical Biology , 4, Raja S. C. Mullick Road, Kolkata 700 032 , India
| | - Gopinatha Suresh Kumar
- a Biophysical Chemistry Laboratory , CSIR-Indian Institute of Chemical Biology , 4, Raja S. C. Mullick Road, Kolkata 700 032 , India
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Chatterjee S, Mallick S, Buzzetti F, Fiorillo G, Syeda TM, Lombardi P, Saha KD, Kumar GS. New 13-pyridinealkyl berberine analogues intercalate to DNA and induce apoptosis in HepG2 and MCF-7 cells through ROS mediated p53 dependent pathway: biophysical, biochemical and molecular modeling studies. RSC Adv 2015. [DOI: 10.1039/c5ra17214d] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
A new series of 13-pyridinealkyl berberine analogues was synthesized and their DNA binding efficacy studied by employing spectroscopic, calorimetric and molecular modeling techniques.
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Affiliation(s)
- Sabyasachi Chatterjee
- Biophysical Chemistry Laboratory
- Organic and Medicinal Chemistry Division
- CSIR-Indian Institute of Chemical Biology
- Kolkata 700 032
- India
| | - Sumana Mallick
- Cancer Biology and Inflammatory Disorder Division
- CSIR-Indian Institute of Chemical Biology
- Kolkata 700 032
- India
| | | | | | | | | | - Krishna Das Saha
- Cancer Biology and Inflammatory Disorder 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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40
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Basu P, Kumar GS. Structural and thermodynamic basis of interaction of the putative anticancer agent chelerythrine with single, double and triple-stranded RNAs. RSC Adv 2015. [DOI: 10.1039/c5ra00660k] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Interaction of chl with poly(uau), poly(au) and poly(u).
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Affiliation(s)
- Pritha Basu
- Biophysical Chemistry Laboratory
- Chemistry Division
- CSIR-Indian Institute of Chemical Biology
- Kolkata 700 032
- India
| | - Gopinatha Suresh Kumar
- Biophysical Chemistry Laboratory
- Chemistry Division
- CSIR-Indian Institute of Chemical Biology
- Kolkata 700 032
- India
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41
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Jash C, Payghan PV, Ghoshal N, Suresh Kumar G. Binding of the Iminium and Alkanolamine Forms of Sanguinarine to Lysozyme: Spectroscopic Analysis, Thermodynamics, and Molecular Modeling Studies. J Phys Chem B 2014; 118:13077-91. [DOI: 10.1021/jp5068704] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Chandrima Jash
- Biophysical Chemistry Laboratory, Chemistry Division and ‡Structural Biology
and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, Kolkata 700 032, India
| | - Pavan V. Payghan
- Biophysical Chemistry Laboratory, Chemistry Division and ‡Structural Biology
and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, Kolkata 700 032, India
| | - Nanda Ghoshal
- Biophysical Chemistry Laboratory, Chemistry Division and ‡Structural Biology
and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, Kolkata 700 032, India
| | - Gopinatha Suresh Kumar
- Biophysical Chemistry Laboratory, Chemistry Division and ‡Structural Biology
and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, Kolkata 700 032, India
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42
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Hazra M, Dolai T, Pandey A, Dey SK, Patra A. Synthesis and Characterisation of Copper(II) Complexes with Tridentate NNO Functionalized Ligand: Density Function Theory Study, DNA Binding Mechanism, Optical Properties, and Biological Application. Bioinorg Chem Appl 2014; 2014:104046. [PMID: 25386109 PMCID: PMC4214117 DOI: 10.1155/2014/104046] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2014] [Revised: 08/02/2014] [Accepted: 08/14/2014] [Indexed: 11/17/2022] Open
Abstract
The photo physical properties of two mononuclear pentacoordinated copper(II) complexes formulated as [Cu(L)(Cl)(H2O)] (1) and [Cu(L)(Br)(H2O)] (2) HL = (1-[(3-methyl-pyridine-2-ylimino)-methyl]-naphthalen-2-ol) were synthesized and characterized by elemental, physicochemical, and spectroscopic methods. The density function theory calculations are used to investigate the electronic structures and the electronic properties of ligand and complex. The interactions of copper(II) complexes towards calf thymus DNA were examined with the help of absorption, viscosity, and fluorescence spectroscopic techniques at pH 7.40. All spectroscopy's result indicates that complexes show good binding activity to calf thymus DNA through groove binding. The optical absorption and fluorescence emission properties of microwires were characterized by fluorescence microscope. From a spectroscopic viewpoint, all compounds strongly emit green light in the solid state. The microscopy investigation suggested that microwires exhibited optical waveguide behaviour which are applicable as fluorescent nanomaterials and can be used as building blocks for miniaturized photonic devices. Antibacterial study reveals that complexes are better antimicrobial agents than free Schiff base due to bacterial cell penetration by chelation. Moreover, the antioxidant study of the ligand and complexes is evaluated by using 1,1-diphenyl-2-picrylhydrazyl (DPPH) free-radical assays, which demonstrate that the complexes are of higher antioxidant activity than free ligand.
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Affiliation(s)
- Madhumita Hazra
- Postgraduate Department of Chemistry, Midnapore College, Midnapore 721101, India
- Department of Chemistry, Sidho-Kanho-Birsha University, Purulia, West Bengal 723101, India
| | - Tanushree Dolai
- Postgraduate Department of Chemistry, Midnapore College, Midnapore 721101, India
| | - Akhil Pandey
- Department of Microbiology, Midnapore College, Midnapore 721101, India
| | - Subrata Kumar Dey
- Department of Chemistry, Sidho-Kanho-Birsha University, Purulia, West Bengal 723101, India
| | - Animesh Patra
- Postgraduate Department of Chemistry, Midnapore College, Midnapore 721101, India
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43
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Khan AY, Saha B, Kumar GS. Interaction of phenazinium dyes with double-stranded poly(A): spectroscopy and isothermal titration calorimetry studies. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2014; 131:615-624. [PMID: 24861262 DOI: 10.1016/j.saa.2014.04.087] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2014] [Revised: 03/19/2014] [Accepted: 04/14/2014] [Indexed: 06/03/2023]
Abstract
A comprehensive study on the binding of phenazinium dyes viz. janus green B, indoine blue, safranine O and phenosafranine with double stranded poly(A) using various spectroscopic and calorimetric techniques is presented. A higher binding of janus green B and indoine blue over safranine O and phenosafranine to poly(A) was observed from all experiments. Intercalative mode of binding of the dyes was inferred from fluorescence polarization anisotropy, iodide quenching and viscosity experiments. Circular dichroism study revealed significant perturbation of the secondary structure of poly(A) on binding of these dyes. Results from isothermal titration calorimetry experiments suggested that the binding was predominantly entropy driven with a minor contribution of enthalpy to the standard molar Gibbs energy. The results presented here may open new opportunities in the application of these dyes as RNA targeted therapeutic agents.
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Affiliation(s)
- Asma Yasmeen Khan
- Biophysical Chemistry Laboratory, Chemistry Division, CSIR-Indian Institute of Chemical Biology, Kolkata 700 032, India
| | - Baishakhi Saha
- Biophysical Chemistry Laboratory, Chemistry Division, CSIR-Indian Institute of Chemical Biology, Kolkata 700 032, India
| | - Gopinatha Suresh Kumar
- Biophysical Chemistry Laboratory, Chemistry Division, CSIR-Indian Institute of Chemical Biology, Kolkata 700 032, India.
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44
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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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45
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Basu P, Suresh Kumar G. Elucidation of the DNA binding specificity of the natural plant alkaloid chelerythrine: A biophysical approach. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2014; 138:282-94. [DOI: 10.1016/j.jphotobiol.2014.06.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Revised: 05/20/2014] [Accepted: 06/09/2014] [Indexed: 12/20/2022]
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Interaction of 9-O-N-aryl/arylalkyl amino carbonyl methyl berberine analogs with single stranded ribonucleotides. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2014; 134:64-74. [PMID: 24792476 DOI: 10.1016/j.jphotobiol.2014.03.024] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 09/18/2013] [Revised: 01/27/2014] [Accepted: 03/31/2014] [Indexed: 12/20/2022]
Abstract
Studies on the molecular aspects of alkaloid-RNA complexation are of prime importance for the development of rational RNA targeted drug design strategies. Towards this goal, the binding aspects of three novel 9-O-N-aryl/arylalkyl amino carbonyl methyl substituted berberine analogs to four single stranded ribonucleotides, poly(G), poly(I), poly(C) and poly(U), were studied for the first time employing multifaceted biophysical tools. Absorbance and fluorescence studies revealed that these analogs bound non-cooperatively to poly(G) and poly(I) with binding affinities remarkably higher than berberine. The binding of these analogs to poly(U) and poly(C) was weaker in comparison to poly(G) and poly(I) but were one order higher in comparison to berberine. Quantum efficiency values revealed that energy transfer occurred from the RNA bases to the analogs upon complexation. The binding was dominated by large positive entropic contributions and small but favorable enthalpic contributions. Salt dependent studies established that the binding was dominated by hydrophobic forces that contributed around 90% of the total standard molar Gibbs energy. The chain length of the substitution at the 9-position was found to be critical in modulating the binding affinities. These results provide new insights into the binding efficacy of these novel berberine analogs to single stranded RNA sequences.
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47
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Ghosh S, Chakrabarty S, Bhowmik D, Kumar GS, Chattopadhyay N. Stepwise Unfolding of Bovine and Human Serum Albumin by an Anionic Surfactant: An Investigation Using the Proton Transfer Probe Norharmane. J Phys Chem B 2014; 119:2090-102. [DOI: 10.1021/jp501150p] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Saptarshi Ghosh
- Department
of Chemistry, Jadavpur University, Kolkata 700 032, India
| | | | - Debipreeta Bhowmik
- Biophysical
Chemistry Laboratory, Chemistry Division, CSIR-Indian Institute of Chemical Biology, Kolkata 700 032, India
| | - Gopinatha Suresh Kumar
- Biophysical
Chemistry Laboratory, Chemistry Division, CSIR-Indian Institute of Chemical Biology, Kolkata 700 032, India
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Khan AY, Saha B, Suresh Kumar G. Phenazinium dyes safranine O and phenosafranine induce self-structure in single stranded polyadenylic acid: structural and thermodynamic studies. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2014; 132:17-26. [PMID: 24565690 DOI: 10.1016/j.jphotobiol.2014.01.014] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 11/05/2013] [Revised: 12/30/2013] [Accepted: 01/19/2014] [Indexed: 11/29/2022]
Abstract
The interaction of phenazinium dyes, safranine O and phenosafranine with single stranded polyadenylic acid was studied using spectroscopic viscometric and calorimetric techniques. Both dyes bind to polyadenylic acid strongly with association constant of the order of 10(5)M(-1). Safranine O showed higher affinity over phenosafranine. The binding induced conformational changes in polyadenylic acid, but the extent of change was much higher with safranine O. The bound safranine O molecules acquired strong induced circular dichroism spectra compared to the weak induced circular dichroism of phenosafranine. Fluorescence polarization, iodide quenching, viscosity results and energy transfer from bases to bound dyes suggested intercalation of the dye molecules to polyadenylic acid structure. The binding was entropy driven in both the cases. Circular dichroism and optical melting studies revealed cooperative melting profiles for dye-polyadenylic acid complexes that provided evidence for the formation of self-structured polyadenylic acid on dye binding. This structural reorganization was further confirmed by differential scanning calorimetry results.
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Affiliation(s)
- Asma Yasmeen Khan
- Biophysical Chemistry Laboratory, Chemistry Division, CSIR-Indian Institute of Chemical Biology, Kolkata 700 032, India
| | - Baishakhi Saha
- Biophysical Chemistry Laboratory, Chemistry Division, CSIR-Indian Institute of Chemical Biology, Kolkata 700 032, India
| | - Gopinatha Suresh Kumar
- Biophysical Chemistry Laboratory, Chemistry Division, CSIR-Indian Institute of Chemical Biology, Kolkata 700 032, India.
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Basu A, Kumar GS. Minor groove binding of the food colorant carmoisine to DNA: spectroscopic and calorimetric characterization studies. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2014; 62:317-326. [PMID: 24328331 DOI: 10.1021/jf404960n] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
The interaction of the food additive carmoisine with herring testes DNA was studied by multifaceted biophysical techniques. Carmoisine exhibited hypochromic effects in absorbance, whereas in fluorescence the intensity enhanced upon complexation with DNA. Energy transfer from the DNA base pairs to carmoisine molecules occurred upon complexation. A groove binding model of interaction was envisaged for carmoisine-DNA complexation from 4',6-diamidino-2-phenylindole (DAPI) and Hoechst displacement studies. The binding of carmoisine stabilized the DNA structure against thermal denaturation. The binding induced moderate conformational perturbations in the B-form structure of DNA. The binding affinity (10(4) M(-1)) values, calculated from absorbance and fluorescence data, and calorimetry titrations were in close agreement with each other. The binding was characterized to be exothermic and favored by small negative enthalpic and large positive entropic contributions. Salt-dependent calorimetric studies revealed that the binding reaction was dominated by nonpolyelectrolytic forces. The negative heat capacity value suggested the role of hydrophobic effect in the interaction.
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Affiliation(s)
- Anirban Basu
- Biophysical Chemistry Laboratory, Chemistry Division, CSIR-Indian Institute of Chemical Biology , Kolkata 700 032, India
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50
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Synthesis, structural characterization and biological activity of a trinuclear zinc(II) complex: DNA interaction study and antimicrobial activity. J CHEM SCI 2014. [DOI: 10.1007/s12039-013-0528-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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