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Fu L, Mou J, Deng Y, Ren X. Structural modifications of berberine and their binding effects towards polymorphic deoxyribonucleic acid structures: A review. Front Pharmacol 2022; 13:940282. [PMID: 36016553 PMCID: PMC9395745 DOI: 10.3389/fphar.2022.940282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 07/14/2022] [Indexed: 11/19/2022] Open
Abstract
Berberine (BBR) is a plant derived quaternary benzylisoquinoline alkaloid, which has been widely used in traditional medicines for a long term. It possesses broad pharmacological effects and is widely applied in clinical. In recent years, the anti-tumor effects of BBR have attracted more and more attention of the researchers. The canonical right-handed double-stranded helical deoxyribonucleic acid (B-DNA) and its polymorphs occur under various environmental conditions and are involved in a plethora of genetic instability-related diseases especially tumor. BBR showed differential binding effects towards various polymorphic DNA structures. But its poor lipophilicity and fast metabolism limited its clinical utility. Structural modification of BBR is an effective approach to improve its DNA binding activity and bioavailability in vivo. A large number of studies dedicated to improving the binding affinities of BBR towards different DNA structures have been carried out and achieved tremendous advancements. In this article, the main achievements of BBR derivatives in polymorphic DNA structures binding researches in recent 20 years were reviewed. The structural modification strategy of BBR, the DNA binding effects of its derivatives, and the structure activity relationship (SAR) analysis have also been discussed.
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Affiliation(s)
| | - Jiajia Mou
- *Correspondence: Jiajia Mou, ; Xiaoliang Ren,
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2
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Ling P, Cheng S, Wang L, Sun X, Gao X, Gao F. Electrochemically classifying DNA structure based on the small molecule-DNA recognition. Bioelectrochemistry 2022; 147:108193. [PMID: 35753199 DOI: 10.1016/j.bioelechem.2022.108193] [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: 04/05/2022] [Revised: 06/12/2022] [Accepted: 06/15/2022] [Indexed: 11/02/2022]
Abstract
Herein, we reported the differential binding ability of aminoglycosides to DNA structures using electrochemical method through principal component analysis (PCA) to classify different DNA secondary structures and understand the link between secondary structure and DNA conformation. In these analyses, the DNA with different secondary structure motifs: bulge, internal loop, hairpin loop and stem loop were designed. The aminoglycosides as receptors were modified on the surface of electrode. In the presence of DNA, the DNA will be absorbed on the surface of electrode via the recognition of DNA and aminoglycosides, resulting in the electrochemical signal observed in [Fe(CN)6]3-/4-. Furthermore, the DNA structures labeled with 2-aminopurine (2-AP) at the structural motif of interest were also employed to study the binding affinity between aminoglycosides and different DNA motifs. The PCA suggested that this method may achieve nucleotide-specific classification of two independent secondary structure motifs, and the structure and sequence of DNA and the size and structure of small molecule could affect the binding ability of the aminoglycosides and DNA. This approach presents a new approach to classify DNA structure and offers ideas for designing targeted drugs small molecule compounds for wound dressing and drug delivery.
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Affiliation(s)
- Pinghua Ling
- Laboratory of Functionalized Molecular Solids, Ministry of Education, Anhui Key Laboratory of Chemo/Biosensing, College of Chemistry and Materials Science, Anhui Normal University, Wuhu 241002, PR China.
| | - Shan Cheng
- Laboratory of Functionalized Molecular Solids, Ministry of Education, Anhui Key Laboratory of Chemo/Biosensing, College of Chemistry and Materials Science, Anhui Normal University, Wuhu 241002, PR China
| | - Linyu Wang
- Laboratory of Functionalized Molecular Solids, Ministry of Education, Anhui Key Laboratory of Chemo/Biosensing, College of Chemistry and Materials Science, Anhui Normal University, Wuhu 241002, PR China
| | - Xinyu Sun
- Laboratory of Functionalized Molecular Solids, Ministry of Education, Anhui Key Laboratory of Chemo/Biosensing, College of Chemistry and Materials Science, Anhui Normal University, Wuhu 241002, PR China
| | - Xianping Gao
- Laboratory of Functionalized Molecular Solids, Ministry of Education, Anhui Key Laboratory of Chemo/Biosensing, College of Chemistry and Materials Science, Anhui Normal University, Wuhu 241002, PR China
| | - Feng Gao
- Laboratory of Functionalized Molecular Solids, Ministry of Education, Anhui Key Laboratory of Chemo/Biosensing, College of Chemistry and Materials Science, Anhui Normal University, Wuhu 241002, PR China.
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3
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Luikham S, Bhattacharyya J. Targeting Natural Polymeric DNAs with Harmane: An Insight into Binding and Thermodynamic Interaction Through Biophysical Approach. DNA Cell Biol 2022; 41:91-102. [PMID: 35049377 DOI: 10.1089/dna.2021.0132] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
DNA is one of the major molecular targets for a broad range of anticancer drugs. Hence, interaction studies involving cellular DNA and small molecules can be highly beneficial as they often lead to rational and efficient drug design. In this study, the binding interaction of Harmane (a naturally occurring, bioactive indole alkaloid) with two natural polymeric DNAs, that is, Calf thymus (CT) DNA and Herring testis (HT) DNA has been elucidated using biophysical techniques. A ground state, 1:1 complexation, was revealed by steady-state fluorescence spectroscopy. The thermodynamic profile and energetics of the associated reaction were evaluated by temperature-dependent fluorescence spectroscopy. The spontaneity of the binding was confirmed by the negative ΔG° values in both cases. Negative enthalpy change, along with stronger positive entropic contribution, indicated the dominant electrostatic nature of the interaction and finally the entropy-driven exothermic binding process throughout. Salt-dependent studies further demonstrated the significant contribution of electrostatic interactions in ligand binding toward DNA. Infrared data substantiated the structural information of the said interactions, leading to the exploration of the structure-function relationship.
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Affiliation(s)
- Soching Luikham
- Department of Chemistry, National Institute of Technology Nagaland, Chumukedima, Dimapur, India
| | - Jhimli Bhattacharyya
- Department of Chemistry, National Institute of Technology Nagaland, Chumukedima, Dimapur, India
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4
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Ekeuku SO, Pang KL, Chin KY. Palmatine as an Agent Against Metabolic Syndrome and Its Related Complications: A Review. Drug Des Devel Ther 2020; 14:4963-4974. [PMID: 33235437 PMCID: PMC7680161 DOI: 10.2147/dddt.s280520] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 10/29/2020] [Indexed: 12/20/2022] Open
Abstract
Palmatine is a naturally occurring isoquinoline alkaloid with various pharmacological properties. Given its antioxidant and anti-inflammatory properties, palmatine may be able to impede the effects of metabolic syndrome (MetS) and its related diseases triggered by inflammation and oxidative stress. This review summarises the existing literature about the effects of palmatine supplementation on MetS and its complications. The evidence shows that palmatine could protect against MetS, and cardiovascular diseases, osteoporosis and osteoarthritis, which might be associated with MetS. These protective effects are mediated by the antioxidant and anti-inflammatory properties of palmatine. Although preclinical experiments have demonstrated the efficacy of palmatine against MetS and its related diseases, no human clinical trials have been performed to validate these effects. This research gap should be bridged to validate the efficacy and safety of palmatine supplementation in protecting humans against MetS and its related diseases.
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Affiliation(s)
- Sophia Ogechi Ekeuku
- Department of Pharmacology, Faculty of Medicine, Universiti Kebangsaan Malaysia, Cheras, Kuala Lumpur, Malaysia
| | - Kok-Lun Pang
- Department of Pharmacology, Faculty of Medicine, Universiti Kebangsaan Malaysia, Cheras, Kuala Lumpur, Malaysia
| | - Kok-Yong Chin
- Department of Pharmacology, Faculty of Medicine, Universiti Kebangsaan Malaysia, Cheras, Kuala Lumpur, Malaysia
- State Key Laboratory of Oncogenes and Related Genes, Renji-Med X Clinical Stem Cell Research Center, Department of Urology, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, People’s Republic of China
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5
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Saha U, Dolai M, Kumar GS. Targeting nucleic acid with a bioactive fluorophore: Insights from spectroscopic and calorimetric studies. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2020.128690] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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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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7
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Saha U, Dolai M, Konar S, Das A, Butcher RJ, Kumar GS, Mukhopadhyay S. Design and synthesis of a sulphur containing Schiff base drug: DNA binding studies and theoretical calculations. J Biomol Struct Dyn 2019; 39:263-271. [PMID: 31870222 DOI: 10.1080/07391102.2019.1708799] [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] [Indexed: 02/08/2023]
Abstract
The Schiff base compound MTA ((E)-5-methyl-N'-((5-methylthiophen-2-yl)methylene)-1H-pyrazole-3-carbohydrazide) derived from 2-thiophenecarboxaldehyde and 5-methylpyrazole-3-carbohydrazide has been designed to develop new sulphur containing DNA targeted molecule. The MTA has been characterized by elemental analyses, 1H-NMR, single crystal X-ray diffraction studies as well as by geometry optimization of using DFT/B3LYP. The interaction of MTA with Calf thymus DNA (CT-DNA) was studied by spectroscopic and calorimetric techniques. The synthesized compound was found to bind with CT-DNA through groove binding mode, and the binding constant was estimated to be (4.15 ± 0.08) × 104 M-1. The negative ΔG0 and positive ΔS0 values obtained from the calorimetric technique confirmed the spontaneity of the binding of MTA with DNA.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Urmila Saha
- Biophysical Chemistry Laboratory, Organic and Medicinal Chemistry Division, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Malay Dolai
- Department of Chemistry, Prabhat Kumar College, Contai, India
| | - Saugata Konar
- Department of Chemistry, The Bhawanipur Education Society College, Kolkata, India
| | - Amit Das
- Department of Chemistry, Ramsaday College, Howrah, India
| | - Ray J Butcher
- Department of Chemistry, Howard University, Washington, DC, USA
| | - Gopinatha Suresh Kumar
- Biophysical Chemistry Laboratory, Organic and Medicinal Chemistry Division, CSIR-Indian Institute of Chemical Biology, Kolkata, India
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8
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Mandal NK, Guhathakurta B, Basu P, Pradhan AB, Purohit CS, Chowdhury S, Naskar JP. DNA and RNA binding studies on a novel bromo-bridged dimeric copper(II) complex stabilized from a Schiff base ligand. J COORD CHEM 2019. [DOI: 10.1080/00958972.2019.1704276] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- Naba Kr Mandal
- Department of Chemistry, Jadavpur University, Kolkata, India
| | | | - Pritha Basu
- Department of Chemistry, Sunderwati Mahila College, Bhagalpur, Bihar, India
| | | | - Chandra Shekhar Purohit
- School of Chemical Sciences, National Institute of Science Education and Research, Bhubaneswar, India
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9
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Tarabasz D, Kukula-Koch W. Palmatine: A review of pharmacological properties and pharmacokinetics. Phytother Res 2019; 34:33-50. [PMID: 31496018 DOI: 10.1002/ptr.6504] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Revised: 06/18/2019] [Accepted: 08/19/2019] [Indexed: 12/11/2022]
Abstract
The aim of this review is to collect together the results of the numerous studies over the last two decades on the pharmacological properties of palmatine published in scientific databases like Scopus and PubMed, which are scattered across different publications. Palmatine, an isoquinoline alkaloid from the class of protoberberines, is a yellow compound present in the extracts from different representatives of Berberidaceae, Papaveraceae, Ranunculaceae, and Menispermaceae. It has been extensively used in traditional medicine of Asia in the treatment of jaundice, liver-related diseases, hypertension, inflammation, and dysentery. New findings describe its possible applications in the treatment of civilization diseases like central nervous system-related problems. This review intends to let this alkaloid come out from the shade of a more frequently described alkaloid: berberine. The toxicity, pharmacokinetics, and biological activities of this protoberberine alkaloid will be developed in this work.
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Affiliation(s)
| | - Wirginia Kukula-Koch
- Chair and Department of Pharmacognosy with Medicinal Plants Unit, Medical University of Lublin, Lublin, Poland
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10
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Saha U, Dolai M, Suresh Kumar G. Adaptable sensor for employing fluorometric detection of methanol molecules: theoretical aspects and DNA binding studies. NEW J CHEM 2019. [DOI: 10.1039/c9nj01018a] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The multifunctional ligand NO2-H2SALNN has been synthesized and employed for the selective fluorometric detection of methanol and its interaction with DNA.
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Affiliation(s)
- Urmila Saha
- Biophysical Chemistry Laboratory
- Organic and Medicinal Chemistry Division
- CSIR-Indian Institute of Chemical Biology
- Kolkata 700 032
- India
| | - Malay Dolai
- Department of Chemistry
- Prabhat Kumar College
- Purba Medinipur 721404
- 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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11
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Dolai M, Saha U, Suresh Kumar G, Zangrando E, Ali M. Synthesis, structure and DNA binding studies of oxime based [Mn3(µ3-O)]7+ complex. Inorganica Chim Acta 2018. [DOI: 10.1016/j.ica.2018.07.050] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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12
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Basu A, Kumar GS. Nucleic acids binding strategies of small molecules: Lessons from alkaloids. Biochim Biophys Acta Gen Subj 2018; 1862:1995-2016. [DOI: 10.1016/j.bbagen.2018.06.010] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Revised: 06/11/2018] [Accepted: 06/11/2018] [Indexed: 01/14/2023]
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13
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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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14
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Padmapriya Kumar, Barthwal R. Structural and biophysical insight into dual site binding of the protoberberine alkaloid palmatine to parallel G-quadruplex DNA using NMR, fluorescence and Circular Dichroism spectroscopy. Biochimie 2018; 147:153-169. [DOI: 10.1016/j.biochi.2018.02.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Accepted: 02/05/2018] [Indexed: 01/12/2023]
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Padmapriya K, Barthwal R. WITHDRAWN: Structural and biophysical insight into dual site binding of the protoberberine alkaloid palmatine to parallel G-quadruplex DNA using NMR, fluorescence and circular dichroism spectroscopy. Biochimie 2018:S0300-9084(18)30042-7. [PMID: 29474974 DOI: 10.1016/j.biochi.2018.01.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Revised: 01/05/2018] [Accepted: 01/07/2018] [Indexed: 11/17/2022]
Abstract
The Publisher regrets that this article is an accidental duplication of an article that has already been published, http://dx.doi.org/10.1016/j.biochi.2018.02.002. The duplicate article has therefore been withdrawn. The full Elsevier Policy on Article Withdrawal can be found at https://www.elsevier.com/about/our-business/policies/article-withdrawal.
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Affiliation(s)
- Kumar Padmapriya
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, 247667, India
| | - Ritu Barthwal
- Department of Biotechnology, Indian Institute of Technology Roorkee, Roorkee, 247667, India
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Haque L, Bhuiya S, Das S. Self-structure assembly in single stranded polyriboadenylic acid by benzophenanthridine alkaloid: Spectroscopic and calorimetric exploration. Int J Biol Macromol 2018; 106:1130-1138. [DOI: 10.1016/j.ijbiomac.2017.08.119] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Revised: 08/19/2017] [Accepted: 08/21/2017] [Indexed: 02/07/2023]
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17
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Varrica MG, Zagni C, Mineo PG, Floresta G, Monciino G, Pistarà V, Abbadessa A, Nicosia A, Castilho RM, Amata E, Rescifina A. DNA intercalators based on (1,10-phenanthrolin-2-yl)isoxazolidin-5-yl core with better growth inhibition and selectivity than cisplatin upon head and neck squamous cells carcinoma. Eur J Med Chem 2018; 143:583-590. [DOI: 10.1016/j.ejmech.2017.11.067] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2017] [Revised: 11/22/2017] [Accepted: 11/24/2017] [Indexed: 02/04/2023]
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Bhowmick R, Islam ASM, Saha U, Suresh Kumar G, Ali M. Rhodamine based turn-on chemosensor for Fe3+ in aqueous medium and interactions of its Fe3+ complex with DNA. NEW J CHEM 2018. [DOI: 10.1039/c7nj04505k] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
A novel di-coordinating rhodamine-based chemosensor, HL with NO donor atoms, selectively and rapidly recognizes Fe3+ in the presence of all biologically relevant as well as toxic metal ions and numerous anions and also with other reactive oxygen and nitrogen species.
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Affiliation(s)
- Rahul Bhowmick
- Department of Chemistry, Jadavpur University
- Kolkata
- India
| | | | - Urmila Saha
- Organic & Medicinal Chemistry Division, CSIR-Indian Institute of Chemical Biology
- Kolkata-700032
- India
| | - Gopinatha Suresh Kumar
- Organic & Medicinal Chemistry Division, CSIR-Indian Institute of Chemical Biology
- Kolkata-700032
- India
| | - Mahammad Ali
- Department of Chemistry, Jadavpur University
- Kolkata
- India
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Binding of Harmine Derivatives to DNA: A Spectroscopic Investigation. Molecules 2017; 22:molecules22111831. [PMID: 29077046 PMCID: PMC6150274 DOI: 10.3390/molecules22111831] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Revised: 10/20/2017] [Accepted: 10/24/2017] [Indexed: 12/20/2022] Open
Abstract
Harmine belongs to a group of β-carboline alkaloids endowed with antitumor properties. Harmine and its derivatives are thought to bind to DNA and interfere with topoisomerase activities. We investigated the base-dependent binding of harmine, and three of its synthetic anticancer-active derivatives to the genomic DNA from calf thymus and two synthetic 20-mer double helices, the poly(dG-dC)·poly(dG-dC) and the poly(dA-dT)·poly(dA-dT), by means of UV-Vis and circular dichroism (CD) spectroscopies. The data show that the DNA binding and stabilising properties of the investigated derivatives are base pair-dependent. These results could be used as a guide to design and develop further bioactive analogues.
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20
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Bandyopadhyay N, Basu P, Kumar GS, Guhathakurta B, Singh P, Naskar JP. Biophysical studies on the interaction of a novel oxime based palladium(II) complex with DNA and RNA. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2017; 173:560-570. [DOI: 10.1016/j.jphotobiol.2017.06.044] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Revised: 06/28/2017] [Accepted: 06/29/2017] [Indexed: 12/13/2022]
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21
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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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22
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Synthesis, characterization, structure and DNA binding aspects of a trinuclear copper(II) complex having a Cu3O core. Inorganica Chim Acta 2017. [DOI: 10.1016/j.ica.2017.03.025] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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23
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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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Niu Y, Li S, Lin Z, Liu M, Wang D, Wang H, Chen S. Development of propidium iodide as a fluorescence probe for the on-line screening of non-specific DNA-intercalators in Fufang Banbianlian Injection. J Chromatogr A 2016; 1463:102-9. [DOI: 10.1016/j.chroma.2016.08.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Revised: 08/02/2016] [Accepted: 08/06/2016] [Indexed: 11/27/2022]
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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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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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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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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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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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Callies O, Hernández Daranas A. Application of isothermal titration calorimetry as a tool to study natural product interactions. Nat Prod Rep 2016; 33:881-904. [DOI: 10.1039/c5np00094g] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The study of molecular interactions of natural products by isothermal titration calorimetry (ITC) is a potent tool to get new insights of the underpinning driving forces.
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Affiliation(s)
- O. Callies
- Institute of Bioorganic Chemistry “Antonio González”
- Center for Biomedical Research of the Canary Islands
- University of La Laguna
- 38206 La Laguna
- Spain
| | - A. Hernández Daranas
- Institute of Bioorganic Chemistry “Antonio González”
- Center for Biomedical Research of the Canary Islands
- University of La Laguna
- 38206 La Laguna
- Spain
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Manna SK, Mandal A, Mondal SK, Adak AK, Jana A, Das S, Chattopadhyay S, Roy S, Ghorai SK, Samanta S, Hossain M, Baidya M. Pyrido[1,2-a]pyrimidinium ions--a novel bridgehead nitrogen heterocycles: synthesis, characterisation, and elucidation of DNA binding and cell imaging properties. Org Biomol Chem 2015; 13:8037-47. [PMID: 26130466 DOI: 10.1039/c5ob01082a] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A novel class of bridgehead nitrogen heterocycles, pyrido[1,2-a]pyrimidinium ions, has been readily synthesized by a two-step one-pot reaction in high yields (up to 93%). These ionic compounds are bench stable and moisture tolerant and have highly fluorescent properties (quantum yield up to 0.65). A characteristic bright bluish fluorescence was observed in polar solvents such as acetonitrile and fluorescent intensity gradually diminishes with decreasing the polarity of the medium, which becomes almost negligible in toluene. These compounds also show interesting bioactivity. DNA interaction, imaging, and viability experiments with human leukemic Jurkat and KG-1A cells revealed that they are potential candidates for cancer diagnosis.
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Rájecký M, Šebrlová K, Mravec F, Táborský P. Influence of Solvent Polarity and DNA-Binding on Spectral Properties of Quaternary Benzo[c]phenanthridine Alkaloids. PLoS One 2015; 10:e0129925. [PMID: 26091027 PMCID: PMC4474729 DOI: 10.1371/journal.pone.0129925] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Accepted: 05/14/2015] [Indexed: 11/19/2022] Open
Abstract
Quaternary benzo[c]phenanthridine alkaloids are secondary metabolites of the plant families Papaveraceae, Rutaceae, and Ranunculaceae with anti-inflammatory, antifungal, antimicrobial and anticancer activities. Their spectral changes induced by the environment could be used to understand their interaction with biomolecules as well as for analytical purposes. Spectral shifts, quantum yield and changes in lifetime are presented for the free form of alkaloids in solvents of different polarity and for alkaloids bound to DNA. Quantum yields range from 0.098 to 0.345 for the alkanolamine form and are below 0.033 for the iminium form. Rise of fluorescence lifetimes (from 2-5 ns to 3-10 ns) and fluorescence intensity are observed after binding of the iminium form to the DNA for most studied alkaloids. The alkanolamine form does not bind to DNA. Acid-base equilibrium constant of macarpine is determined to be 8.2-8.3. Macarpine is found to have the highest increase of fluorescence upon DNA binding, even under unfavourable pH conditions. This is probably a result of its unique methoxy substitution at C12 a characteristic not shared with other studied alkaloids. Association constant for macarpine-DNA interaction is 700000 M(-1).
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Affiliation(s)
- Michal Rájecký
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic
| | - Kristýna Šebrlová
- Department of Biochemistry, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Filip Mravec
- Materials Research Centre, Faculty of Chemistry, Brno University of Technology, Brno, Czech Republic
| | - Petr Táborský
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic
- Department of Chemistry, Faculty of Science, Masaryk University, Brno, Czech Republic
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Mi R, Tu B, Bai XT, Chen J, Ouyang Y, Hu YJ. Binding properties of palmatine to DNA: spectroscopic and molecular modeling investigations. LUMINESCENCE 2015; 30:1344-51. [PMID: 25829078 DOI: 10.1002/bio.2904] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Revised: 02/21/2015] [Accepted: 02/22/2015] [Indexed: 12/20/2022]
Abstract
Palmatine, an isoquinoline alkaloid, is an important medicinal herbal extract with diverse pharmacological and biological properties. In this work, spectroscopic and molecular modeling approaches were employed to reveal the interaction between palmatine and DNA isolated from herring sperm. The absorption spectra and iodide quenching results indicated that groove binding was the main binding mode of palmatine to DNA. Fluorescence studies indicated that the binding constant (K) of palmatine and DNA was ~ 10(4)L·mol(-1). The associated thermodynamic parameters, ΔG, ΔH, and ΔS, indicated that hydrogen bonds and van der Waals forces played major roles in the interaction. The effects of chemical denaturant, thermal denaturation and pH on the interaction were investigated and provided further support for the groove binding mode. In addition to experimental approaches, molecular modeling was conducted to verify binding pattern of palmatine-DNA.
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Affiliation(s)
- Ran Mi
- Hubei Collaborative Innovation Center for Rare Metal Chemistry, Hubei Key Laboratory of Pollutant Analysis & Reuse Technology, Department of Chemistry, Hubei Normal University, Huangshi, 435002, People's Republic of China
| | - Bao Tu
- Hubei Collaborative Innovation Center for Rare Metal Chemistry, Hubei Key Laboratory of Pollutant Analysis & Reuse Technology, Department of Chemistry, Hubei Normal University, Huangshi, 435002, People's Republic of China
| | - Xiao-Ting Bai
- Hubei Collaborative Innovation Center for Rare Metal Chemistry, Hubei Key Laboratory of Pollutant Analysis & Reuse Technology, Department of Chemistry, Hubei Normal University, Huangshi, 435002, People's Republic of China
| | - Jun Chen
- Hubei Collaborative Innovation Center for Rare Metal Chemistry, Hubei Key Laboratory of Pollutant Analysis & Reuse Technology, Department of Chemistry, Hubei Normal University, Huangshi, 435002, People's Republic of China
| | - Yu Ouyang
- Hubei Collaborative Innovation Center for Rare Metal Chemistry, Hubei Key Laboratory of Pollutant Analysis & Reuse Technology, Department of Chemistry, Hubei Normal University, Huangshi, 435002, People's Republic of China
| | - Yan-Jun Hu
- Hubei Collaborative Innovation Center for Rare Metal Chemistry, Hubei Key Laboratory of Pollutant Analysis & Reuse Technology, Department of Chemistry, Hubei Normal University, Huangshi, 435002, People's Republic of China
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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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Tao M, Zhang G, Xiong C, Pan J. Characterization of the interaction between resmethrin and calf thymus DNA in vitro. NEW J CHEM 2015. [DOI: 10.1039/c4nj02321h] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Resmethrin preferentially binds to the G–C rich region of the ctDNA groove, and the UV-vis spectral matrix is decomposed by MCR-ALS.
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Affiliation(s)
- Mo Tao
- State Key Laboratory of Food Science and Technology
- Nanchang University
- Nanchang 330047
- China
| | - Guowen Zhang
- State Key Laboratory of Food Science and Technology
- Nanchang University
- Nanchang 330047
- China
| | - Chunhong Xiong
- State Key Laboratory of Food Science and Technology
- Nanchang University
- Nanchang 330047
- China
| | - Junhui Pan
- State Key Laboratory of Food Science and Technology
- Nanchang University
- Nanchang 330047
- China
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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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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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Kabir A, Kumar GS. Probing the interaction of spermine and 1-naphthyl acetyl spermine with DNA polynucleotides: a comparative biophysical and thermodynamic investigation. MOLECULAR BIOSYSTEMS 2014; 10:1172-83. [PMID: 24643290 DOI: 10.1039/c3mb70616h] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The interaction of spermine and its analogue, 1-naphthyl acetyl spermine with four double stranded DNA polynucleotides has been studied to understand the structural and thermodynamic basis of the binding. The efficacy and specificity of DNA binding of this analogue has not yet been revealed. The energetics of the interaction was studied by isothermal titration calorimetry and differential scanning calorimetry. Circular dichroism spectroscopy, UV-thermal melting and ethidium bromide displacement assay have been employed to characterize the association. Circular dichroism studies showed that 1-naphthyl acetyl spermine caused a stronger structural perturbation in the polynucleotides. Among the adenine-thymine polynucleotides the alternating polynucleotide was more preferred by naphthyl acetyl spermine compared to the preference of spermine for the homo sequence. The higher melting stabilization revealed by the optical melting and differential scanning calorimetry results suggested that the binding of 1-naphthyl acetyl spermine increased the melting temperature and the total standard molar enthalpy of the transition of adenine-thymine polynucleotides. Microcalorimetry results revealed that unlike spermine the binding of 1-naphthyl acetyl spermine was endothermic. The interaction was characterized by total enthalpy-entropy compensation and high standard molar heat capacity values. There are differences in the mode of association of 1-naphthyl acetyl spermine and spermine. 1-naphthyl acetyl spermine binds with an enhanced affinity with the adenine-thymine hetero polynucleotide. Thus, the result suggests the importance of polyamine analogues and their ability to interfere with normal polyamine interactions.
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Affiliation(s)
- Ayesha Kabir
- Biophysical Chemistry Laboratory, Chemistry Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Kolkata 700 032, India.
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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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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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Kabir A, Suresh Kumar G. Targeting double-stranded RNA with spermine, 1-naphthylacetyl spermine and spermidine: a comparative biophysical investigation. J Phys Chem B 2014; 118:11050-64. [PMID: 25184857 DOI: 10.1021/jp5035294] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
RNA targeting is an evolving new approach to anticancer therapeutics that requires identification of small molecules to selectively target specific RNA structures. In this report, the interaction of biogenic polyamines spermine, spermidine and the synthetic analogue 1-naphthylacetyl spermine with three double-stranded RNA polynucleotides--poly(I)·poly(C), poly(C)·poly(G), and poly(A)·poly(U)--has been described to understand the structural and thermodynamic basis of the binding and the comparative efficacy of the analogue over the natural polyamines. Circular dichroism spectroscopy, thermal melting experiments, and ethidium bromide displacement assay were used to characterize the interaction. Microcalorimetry studies were performed to deduce the energetics of the interaction and atomic force microscopy experiments done to gain insight into the interaction at the molecular level. The experiments demonstrated structural perturbations in the polynucleotides on binding of the polyamines. Thermal melting studies showed enhanced stabilization of RNA-polyamine complexes with increase in the total standard molar enthalpy of transition. The binding affinity was strongest for poly(I)·poly(C) as revealed by microcalorimetry results and varied as poly(I)·poly(C) > poly(C)·poly(G) > poly(A)·poly(U). The order of affinity for the polyamines was spermine >1-naphthylacetyl spermine > spermidine. Total enthalpy-entropy compensation and high standard molar heat capacity values characterized the interactions. The results of the study on the binding of polyamines to dsRNAs presented here have been compared to those reported earlier with dsDNAs. The present findings advance our knowledge on the mechanism of interaction of polyamines with RNA and may help in the search for analogues that can interfere with biogenic polyamine metabolism and function.
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Affiliation(s)
- Ayesha Kabir
- Biophysical Chemistry Laboratory, Chemistry Division, CSIR - Indian Institute of Chemical Biology , Kolkata 700 032, India
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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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Czerwinska I, Sato S, Juskowiak B, Takenaka S. Interactions of cyclic and non-cyclic naphthalene diimide derivatives with different nucleic acids. Bioorg Med Chem 2014; 22:2593-601. [PMID: 24726302 DOI: 10.1016/j.bmc.2014.03.034] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2014] [Revised: 03/05/2014] [Accepted: 03/21/2014] [Indexed: 12/11/2022]
Abstract
Recently, strategy based on stabilization of G-quadruplex telomeric DNA by small organic molecule has been realized by naphthalene diimide derivatives (NDIs). At the same time NDIs bind to DNA duplex as threading intercalators. Here we present cyclic derivative of naphthalene diimide (ligand 1) as DNA-binding ligand with ability to recognition of different structures of telomeric G-quadruplexes and ability to bis-intercalate to double-stranded helixes. The results have been compared to non-cyclic derivative (ligand 2) and revealed that preferential binding of ligands to nucleic acids strongly depends on their topology and structural features of ligands.
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Affiliation(s)
- Izabella Czerwinska
- Research Center for Bio-microsensing Technology, 1-1 Sensui-cho, Tobata-ku, Kitakyushu-shi, Fukuoka 804-8550, Japan.
| | - Shinobu Sato
- Research Center for Bio-microsensing Technology, 1-1 Sensui-cho, Tobata-ku, Kitakyushu-shi, Fukuoka 804-8550, Japan; Department of Applied Chemistry, Kyushu Institute of Technology, 1-1 Sensui-cho, Tobata-ku, Kitakyushu-shi, Fukuoka 804-8550, Japan
| | - Bernard Juskowiak
- Laboratory of Bioanalytical Chemistry, Faculty of Chemistry, A. Mickiewicz University, Umultowska 89b, 61-614 Poznań, Poland
| | - Shigeori Takenaka
- Research Center for Bio-microsensing Technology, 1-1 Sensui-cho, Tobata-ku, Kitakyushu-shi, Fukuoka 804-8550, Japan; Department of Applied Chemistry, Kyushu Institute of Technology, 1-1 Sensui-cho, Tobata-ku, Kitakyushu-shi, Fukuoka 804-8550, Japan
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Tan K, Li J, Li H, Wang Y, Yuan R. A highly sensitive dual-readout assay based on poly(A) and gold nanoparticles for palmatine hydrochloride. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2014; 122:198-203. [PMID: 24316533 DOI: 10.1016/j.saa.2013.11.075] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2013] [Revised: 11/08/2013] [Accepted: 11/12/2013] [Indexed: 06/02/2023]
Abstract
This report presents a highly sensitive, poly(A)-stabilized gold nanoparticle-based assay with dual readouts (resonance light scattering and colorimetric) for detecting palmatine hydrochloride (PaH) in real samples. The detection mechanism is based on the fact that palmatine hydrochloride has strong affinity to poly(A), which can stabilize gold nanoparticles at high ionic strength, and cause the aggregation of poly(A)-stabilized AuNPs, resulting in the enhanced resonance light scattering (RLS). At the same time, the color change of poly(A)-stabilized AuNPs solution is from red to blue via purple. Thus a highly sensitive RLS assay for PaH has been developed with a linear range of 0.023-2.5 μg/mL. The limit of detection (LOD, 3σ) is 2.3 ng/mL. In this work, the reaction mechanism of this system was investigated by scanning electron microscope (SEM), dark-field light scattering images (DLSI), dynamiclight scattering (DLS) and circular dichroism (CD). This proposed method was also applied successfully for the determination of PaH in pharmaceutical preparations and urine samples with RSD⩽4.0%. The results are in good agreement with those from the official method.
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Affiliation(s)
- Kejun Tan
- Key Laboratory on Luminescence and Real-Time Analysis, Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China.
| | - Jiayu Li
- Key Laboratory on Luminescence and Real-Time Analysis, Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Huachun Li
- Key Laboratory on Luminescence and Real-Time Analysis, Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Yingying Wang
- Key Laboratory on Luminescence and Real-Time Analysis, Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
| | - Rui Yuan
- Key Laboratory on Luminescence and Real-Time Analysis, Ministry of Education, School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, PR China
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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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Das A, Kumar GS. Binding studies of aristololactam-β-d-glucoside and daunomycin to human serum albumin. RSC Adv 2014. [DOI: 10.1039/c4ra04327h] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The binding of two carbohydrate containing molecules aristololactam-β-d-glucoside and daunomycin with human serum albumin was evaluated by biophysical techniques.
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Affiliation(s)
- Abhi Das
- 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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Bhowmik D, Buzzetti F, Fiorillo G, Orzi F, Syeda TM, Lombardi P, Suresh Kumar G. Synthesis of new 13-diphenylalkyl analogues of berberine and elucidation of their base pair specificity and energetics of DNA binding. MEDCHEMCOMM 2014. [DOI: 10.1039/c3md00254c] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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Sarkar S, Bhadra K. Binding of alkaloid harmalol to DNA: Photophysical and calorimetric approach. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2014; 130:272-80. [DOI: 10.1016/j.jphotobiol.2013.11.021] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2013] [Revised: 11/18/2013] [Accepted: 11/19/2013] [Indexed: 11/16/2022]
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