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Ezzatzadeh E, Hargalani FZ, Shafaei F. Bio-Fe 3O 4-MNPs Promoted Green Synthesis of Pyrido[2,1- a]isoquinolines and Pyrido[1,2- a]quinolines: Study of Antioxidant and Antimicrobial Activity. Polycycl Aromat Compd 2022. [DOI: 10.1080/10406638.2021.1879882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Affiliation(s)
- Elham Ezzatzadeh
- Department of Chemistry, Ardabil Branch, Islamic Azad University, Ardabil, Iran
| | - Fariba Zamani Hargalani
- Department of Natural Resources and Environment, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Faezeh Shafaei
- Department of Chemistry, East Tehran Branch, Islamic Azad University, Tehran, Iran
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2
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Faal Hamedani N, Ghazvini M, Azad L, Noushin A. Green synthesis of pyrido[2,1‐
a
]isoquinolines and pyrido[1,2‐
a
]quinolins using Fe
3
O
4
‐MNPs as efficient nanocatalyst: Study of antioxidant activity. J Heterocycl Chem 2020. [DOI: 10.1002/jhet.3782] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Naghmeh Faal Hamedani
- Department of Chemistry, Faculty of ValiasrTechnical and Vocational University (TVU) Tehran Iran
| | | | - Leila Azad
- Department of ChemistryIslamic Azad University Khodabandeh Iran
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3
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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: 9.2] [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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4
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Wang Y, Patil P, Kurpiewska K, Kalinowska-Tluscik J, Dömling A. Diverse Isoquinoline Scaffolds by Ugi/Pomeranz-Fritsch and Ugi/Schlittler-Müller Reactions. Org Lett 2019; 21:3533-3537. [PMID: 31033297 PMCID: PMC6528277 DOI: 10.1021/acs.orglett.9b00778] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
![]()
The Pomeranz–Fritsch reaction
and its Schlittler–Müller modification were successfully
applied in the Ugi postcyclization strategy by using orthogonally
protected aminoacetaldehyde diethyl acetal and complementary electron
rich building blocks. Several scaffolds, including isoquinolines,
carboline, alkaloid-like tetrazole-fused tetracyclic compounds, and
benzo[d]azepinone scaffolds, were synthesized in
generally moderate to good yield. All our syntheses provide a short
MCR-based sequence to novel or otherwise difficult to access scaffolds.
Hence, we foresee multiple applications of these synthesis technologies.
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Affiliation(s)
- Yuanze Wang
- Drug Design , University of Groningen , Deusinglaan 1 , 7313 AV Groningen , The Netherlands
| | - Pravin Patil
- Drug Design , University of Groningen , Deusinglaan 1 , 7313 AV Groningen , The Netherlands
| | - Katarzyna Kurpiewska
- Faculty of Chemistry , Jagiellonian University , 3 Ingardena Street , 30-060 Krakow , Poland
| | | | - Alexander Dömling
- Drug Design , University of Groningen , Deusinglaan 1 , 7313 AV Groningen , The Netherlands
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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: 1.9] [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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6
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Chatterjee S, Suresh Kumar G. Small molecule induced poly(A) single strand to self-structure conformational switching: evidence for the prominent role of H-bonding interactions. MOLECULAR BIOSYSTEMS 2018; 13:1000-1009. [PMID: 28405661 DOI: 10.1039/c7mb00031f] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
All messenger RNAs (mRNAs) have a polyadenylic acid tail that is added during post transcriptional RNA processing. Investigation of the structure-function and interactions of polyadenylic acid is an important area to target for cancer and related diseases. Jatrorrhizine and coptisine are two important isoquinoline alkaloids that are structurally very similar, differing only in the substituents on the isoquinoline chromophore. Here we demonstrate that these alkaloids differentially induce a self-structure in single stranded poly(A) using absorbance, thermal melting and differential scanning calorimetry experiments. Jatrorrhizine was found to be more effective than coptisine in binding to poly(A) from spectroscopy and calorimetry data. Molecular modeling results suggested the involvement of more H-bonds in the complexation of the former with poly(A). It appears that the presence of substituents on the alkaloid that can form H-bonding interactions with the adenine nucleotides may play a critical role in the binding and structural rearrangement of poly(A) into the self-structure. The atomic force microscopy data directly visualized the poly(A) self-structured network. We propose a plausible mechanism of the small molecule induced self-structure formation in poly(A). The results presented here may help in the design of effective poly(A) targeted molecules for therapeutic use.
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Affiliation(s)
- Sabyasachi Chatterjee
- Biophysical Chemistry Laboratory, Organic and Medicinal Chemistry Division, CSIR-Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Kolkata 700 032, 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: 0.6] [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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Nucleobase-Guanidiniocarbonyl-Pyrrole Conjugates as Novel Fluorimetric Sensors for Single Stranded RNA. Molecules 2017; 22:molecules22122213. [PMID: 29236076 PMCID: PMC6149679 DOI: 10.3390/molecules22122213] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Revised: 12/04/2017] [Accepted: 12/09/2017] [Indexed: 01/13/2023] Open
Abstract
We demonstrate here for the first time that a guanidiniocarbonyl-pyrrole (GCP) unit can be applied for the fine recognition of single stranded RNA sequences—an intuitively unexpected result since so far binding of the GCP unit to ds-DNA or ds-RNA relied strongly on minor or major groove interactions, as shown in previous work. Two novel nucleobase–GCP isosteric conjugates differing in the flexibility of GCP unit revealed a fluorimetric recognition of various single stranded RNA, which could be additionally regulated by pH. The more rigid conjugate showed a specific fluorescence increase for poly A only at pH 7, whereby this response could be reversibly switched-off at pH 5. The more flexible derivative revealed selective fluorescence quenching by poly G at pH 7 but no change for poly A, whereas its recognition of poly AH+ can be switched-on at pH 5. The computational analysis confirmed the important role of the GCP fragment and its protonation states in the sensing of polynucleotides and revealed that it is affected by the intrinsic dynamical features of conjugates themselves. Both conjugates showed a negligible response to uracil and cytosine ss-RNA as well as ds-RNA at pH 7, and only weak interactions with ds-DNA. Thus, nucleobase–GCP conjugates can be considered as novel lead compounds for the design of ss-RNA or ss-DNA selective fluorimetric probes.
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Kumar GS, Basu A. The use of calorimetry in the biophysical characterization of small molecule alkaloids binding to RNA structures. Biochim Biophys Acta Gen Subj 2015; 1860:930-944. [PMID: 26522497 DOI: 10.1016/j.bbagen.2015.10.026] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Revised: 10/06/2015] [Accepted: 10/27/2015] [Indexed: 11/16/2022]
Abstract
BACKGROUND RNA has now emerged as a potential target for therapeutic intervention. RNA targeted drug design requires detailed thermodynamic characterization that provides new insights into the interactions and this together with structural data, may be used in rational drug design. The use of calorimetry to characterize small molecule-RNA interactions has emerged as a reliable and sensitive tool after the recent advancements in biocalorimetry. SCOPE OF THE REVIEW This review summarizes the recent advancements in thermodynamic characterization of small molecules, particularly some natural alkaloids binding to various RNA structures. Thermodynamic characterization provides information that can supplement structural data leading to more effective drug development protocols. MAJOR CONCLUSIONS This review provides a concise report on the use of isothermal titration calorimetry (ITC) and differential scanning calorimetry (DSC) techniques in characterizing small molecules, mostly alkaloids-RNA interactions with particular reference to binding of tRNA, single stranded RNA, double stranded RNA, poly(A), triplex RNA. GENERAL SIGNIFICANCE It is now apparent that a combination of structural and thermodynamic data is essential for rational design of specific RNA targeted drugs. Recent advancements in biocalorimetry instrumentation have led to detailed understanding of the thermodynamics of small molecules binding to various RNA structures paving the path for the development of many new natural and synthetic molecules as specific binders to various RNA structures. RNA targeted drug design, that remained unexplored, will immensely benefit from the calorimetric studies leading to the development of effective drugs for many diseases.
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Affiliation(s)
- Gopinatha Suresh Kumar
- Biophysical Chemistry Laboratory, Organic and Medicinal Chemistry Division, CSIR-Indian Institute of Chemical Biology, Kolkata 700 032, India.
| | - Anirban Basu
- Biophysical Chemistry Laboratory, Organic and Medicinal Chemistry Division, CSIR-Indian Institute of Chemical Biology, Kolkata 700 032, India
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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: 0.5] [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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11
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Roviello GN, Musumeci D, Roviello V, Pirtskhalava M, Egoyan A, Mirtskhulava M. Natural and artificial binders of polyriboadenylic acid and their effect on RNA structure. BEILSTEIN JOURNAL OF NANOTECHNOLOGY 2015; 6:1338-1347. [PMID: 26199837 PMCID: PMC4505092 DOI: 10.3762/bjnano.6.138] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Accepted: 05/22/2015] [Indexed: 06/10/2023]
Abstract
The employment of molecular tools with nucleic acid binding ability to specifically control crucial cellular functions represents an important scientific area at the border between biochemistry and pharmaceutical chemistry. In this review we describe several molecular systems of natural or artificial origin, which are able to bind polyriboadenylic acid (poly(rA)) both in its single-stranded or structured forms. Due to the fundamental role played by the poly(rA) tail in the maturation and stability of mRNA, as well as in the initiation of the translation process, compounds able to bind this RNA tract, influencing the mRNA fate, are of special interest for developing innovative biomedical strategies mainly in the field of anticancer therapy.
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Affiliation(s)
- Giovanni N Roviello
- Istituto di Biostrutture e Bioimmagini - CNR, via Mezzocannone 16, 80134 Napoli, Italy
| | - Domenica Musumeci
- Istituto di Biostrutture e Bioimmagini - CNR, via Mezzocannone 16, 80134 Napoli, Italy
- Dipartimento di Scienze Chimiche, Università di Napoli “Federico II”, 80126 Napoli, Italy
| | - Valentina Roviello
- Dipartimento di Ingegneria Chimica, dei Materiali e della Produzione Industriale (DICMaPI), Università di Napoli “Federico II”, 80125 Napoli, Italy
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12
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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: 1.4] [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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Ouyang K, Li J, Huang H, Que Q, Li P, Chen X. A simple method for RNA isolation from various tissues of the tree Neolamarckia cadamba. BIOTECHNOL BIOTEC EQ 2014; 28:1008-1013. [PMID: 26019587 PMCID: PMC4434054 DOI: 10.1080/13102818.2014.981086] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Accepted: 07/28/2014] [Indexed: 10/31/2022] Open
Abstract
Plant tissues contain abundant polysaccharides, phenolic compounds and other metabolites, which makes it difficult to isolate high-quality RNA from them. In addition, Neolamarckia cadamba contains large quantities of other components, particularly RNA-binding alkaloids, which makes the isolation even more challenging. Here, we describe a concise and efficient RNA isolation method that combines the cetyltrimethyl ammonium bromide (CTAB) and Plant RNA Kit (Omega) protocols. Gel electrophoresis showed that RNA extracted from all tissues, using this protocol, was of good integrity and without DNA contamination. Furthermore, the isolated RNA was of high purity, with an A260/A280 ratio of 2.1 and an A260/A230 ratio of >2.0. The isolated RNA was also suitable for downstream applications, such as reverse transcription-polymerase chain reaction (RT-PCR) and quantitative RT-PCR (RT-qPCR). The RNA isolation method was also efficient for recalcitrant plant tissues.
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Affiliation(s)
- Kunxi Ouyang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, South China Agricultural University , Guangzhou , Guangdong , P.R. China
| | - Juncheng Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, South China Agricultural University , Guangzhou , Guangdong , P.R. China
| | - Hao Huang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, South China Agricultural University , Guangzhou , Guangdong , P.R. China ; Guangxi Botanical Garden of Medicinal Plants , Nanning , Guangxi , P.R. China
| | - Qingmin Que
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, South China Agricultural University , Guangzhou , Guangdong , P.R. China
| | - Pei Li
- Key Laboratory for Genetics and Breeding of Forest Trees and Ornamental Plants, Ministry of Education, National Engineering Laboratory for Forest Tree Breeding, Beijing Forestry University , Beijing , P.R. China
| | - Xiaoyang Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, South China Agricultural University , Guangzhou , Guangdong , P.R. China
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Interactions with polynucleotides and antitumor activity of amidino and imidazolinyl substituted 2-phenylbenzothiazole mesylates. Eur J Med Chem 2014; 86:406-19. [PMID: 25194933 DOI: 10.1016/j.ejmech.2014.08.072] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2014] [Revised: 06/12/2014] [Accepted: 08/30/2014] [Indexed: 11/23/2022]
Abstract
Based on previously reported antiproliferative activity screening, four most promising disubstituted 2-phenylbenzothiazole hydrochlorides were chosen for detailed study. Water solubility, as well as liphophilicity/hydrophilicity balance of organic core were modified by conversion to mesylate salts. For purpose of structure/activity studies their structures were determined by X-ray structure analysis. Detailed analysis of interactions of new compounds with double stranded (ds-) DNA/RNA by UV/Vis and CD titrations, thermal melting and viscometry experiments revealed that most of studied compounds intercalate into ds-RNA but bind into minor groove of AT-DNA, and agglomerate along GC-DNA. Furthermore, compounds also interact with ss-RNA, but only amino-imidazolinyl 2-phenylbenzothiazole, 4b displayed well defined orientation and dominant binding mode (by induced CD signals) with poly A and poly G. Besides, in vitro investigations revealed moderate to high antiproliferative activity of benzothiazoles against seven human cancer cell lines, while in some cases (HTC 116, SW620, MIA PaCa-2) high correlation between the type of the amidino group and cytotoxic activity was observed.
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Paul P, Suresh Kumar G. Self-structure formation in polyadenylic acid by small molecules: new insights from the binding of planar dyes thionine and toluidine blue O. RSC Adv 2014. [DOI: 10.1039/c4ra02671c] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Thionine and toluidine blue targeting poly(A).
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Affiliation(s)
- Puja Paul
- 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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Ali H, Dixit S. Extraction optimization of Tinospora cordifolia and assessment of the anticancer activity of its alkaloid palmatine. ScientificWorldJournal 2013; 2013:376216. [PMID: 24379740 PMCID: PMC3863568 DOI: 10.1155/2013/376216] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2013] [Accepted: 09/23/2013] [Indexed: 12/02/2022] Open
Abstract
OBJECTIVE To optimize the conditions for the extraction of alkaloid palmatine from Tinospora cordifolia by using response surface methodology (RSM) and study its anticancerous property against 7,12-dimethylbenz(a)anthracene (DMBA) induced skin carcinogenesis in Swiss albino mice. METHODS The effect of three independent variables, namely, extraction temperature, time, and cycles was investigated by using central composite design. A single topical application of DMBA (100 μg/100 μL of acetone), followed 2 weeks later by repeated application of croton oil (1% in acetone three times a week) for 16 weeks, exhibited 100 percent tumor incidence (Group 2). RESULTS The highest yield of alkaloid from Tinospora cordifolia could be achieved at 16 hours of extraction time under 40°C with 4 extraction cycles. Alkaloid administration significantly decreases tumor size, number, and the activity of serum enzyme when compared with the control (Group 2). In addition, depleted levels of reduced glutathione (GSH), superoxide dismutase (SOD), and catalase and increased DNA damage were restored in palmatine treated groups. CONCLUSION The data of the present study clearly indicate the anticancer potential of palmatine alkaloid in DMBA induced skin cancer model in mice.
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Affiliation(s)
- Huma Ali
- Department of Chemistry, MANIT, Bhopal, Madhya Pardesh, India
| | - Savita Dixit
- Department of Chemistry, MANIT, Bhopal, Madhya Pardesh, India
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Basu A, Jaisankar P, Suresh Kumar G. Binding of the 9-O-N-aryl/arylalkyl amino carbonyl methyl substituted berberine analogs to tRNA(phe.). PLoS One 2013; 8:e58279. [PMID: 23526972 PMCID: PMC3602459 DOI: 10.1371/journal.pone.0058279] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2012] [Accepted: 02/01/2013] [Indexed: 12/19/2022] Open
Abstract
Background Three new analogs of berberine with aryl/arylalkyl amino carbonyl methyl substituent at the 9-position of the isoquinoline chromophore along with berberrubine were studied for their binding to tRNAphe by wide variety of biophysical techniques like spectrophotometry, spectrofluorimetry, circular dichroism, thermal melting, viscosity and isothermal titration calorimetry. Methodology/Principal Findings Scatchard binding isotherms revealed that the cooperative binding mode of berberine was propagated in the analogs also. Thermal melting studies showed that all the 9-O-N-aryl/arylalkyl amino carbonyl methyl substituted berberine analogs stabilized the tRNAphe more in comparison to berberine. Circular dichroism studies showed that these analogs perturbed the structure of tRNAphe more in comparison to berberine. Ferrocyanide quenching studies and viscosity results proved the intercalative binding mode of these analogs into the helical organization of tRNAphe. The binding was entropy driven for the analogs in sharp contrast to the enthalpy driven binding of berberine. The introduction of the aryl/arylalkyl amino carbonyl methyl substituent at the 9-position thus switched the enthalpy driven binding of berberine to entropy dominated binding. Salt and temperature dependent calorimetric studies established the involvement of multiple weak noncovalent interactions in the binding process. Conclusions/Significance The results showed that 9-O-N-aryl/arylalkyl amino carbonyl methyl substituted berberine analogs exhibited almost ten folds higher binding affinity to tRNAphe compared to berberine whereas the binding of berberrubine was dramatically reduced by about twenty fold in comparison to berberine. The spacer length of the substitution at the 9-position of the isoquinoline chromophore appears to be critical in modulating the binding affinities towards tRNAphe.
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Affiliation(s)
- Anirban Basu
- Chemistry Division, CSIR-Indian Institute of Chemical Biology, Kolkata, India
- Biophysical Chemistry Laboratory, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | | | - Gopinatha Suresh Kumar
- Chemistry Division, CSIR-Indian Institute of Chemical Biology, Kolkata, India
- Biophysical Chemistry Laboratory, CSIR-Indian Institute of Chemical Biology, Kolkata, India
- * E-mail:
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18
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Kumar GS. RNA targeting by small molecules: Binding of protoberberine, benzophenanthridine and aristolochia alkaloids to various RNA structures. J Biosci 2012; 37:539-52. [DOI: 10.1007/s12038-012-9217-3] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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19
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Das A, Bhadra K, Suresh Kumar G. Targeting RNA by small molecules: comparative structural and thermodynamic aspects of aristololactam-β-D-glucoside and daunomycin binding to tRNA(phe). PLoS One 2011; 6:e23186. [PMID: 21858023 PMCID: PMC3156712 DOI: 10.1371/journal.pone.0023186] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2011] [Accepted: 07/11/2011] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Interaction of aristololactam-β-D-glucoside and daunomycin with tRNA(phe) was investigated using various biophysical techniques. METHODOLOGY/PRINCIPAL FINDINGS Absorption and fluorescence studies revealed that both the compounds bind tRNA(phe) non-cooperatively. The binding of daunomycin was about one order of magnitude higher than that of aristololactam-β-D-glucoside. Stronger binding of the former was also inferred from fluorescence quenching data, quantum efficiency values and circular dichroic results. Results from isothermal titration calorimetry experiments suggested that the binding of both compounds was predominantly entropy driven with a smaller but favorable enthalpy term that increased with temperature. A large favorable electrostatic contribution to the binding of daunomycin to tRNA(phe) was revealed from salt dependence data and the dissection of the free energy values. The electrostatic component to the free energy change for aristololactam-β-D-glucoside-tRNA(phe) interaction was smaller than that of daunomycin. This was also inferred from the slope of log K versus [Na(+)] plots. Both compounds enhanced the thermal stability of tRNA(phe). The small heat capacity changes of -47 and -99 cal/mol K, respectively, observed for aristololactam-β-D-glucoside and daunomycin, and the observed enthalpy-entropy compensation phenomenon confirmed the involvement of multiple weak noncovalent interactions. Molecular aspects of the interaction have been revealed. CONCLUSIONS/SIGNIFICANCE This study presents the structural and energetic aspects of the binding of aristololactam-β-D-glucoside and daunomycin to tRNA(phe).
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MESH Headings
- Algorithms
- Antibiotics, Antineoplastic/chemistry
- Antibiotics, Antineoplastic/metabolism
- Antibiotics, Antineoplastic/pharmacology
- Aristolochic Acids/chemistry
- Aristolochic Acids/metabolism
- Aristolochic Acids/pharmacology
- Binding Sites
- Binding, Competitive
- Calorimetry
- Circular Dichroism
- Daunorubicin/chemistry
- Daunorubicin/metabolism
- Daunorubicin/pharmacology
- Entropy
- Glucosides/chemistry
- Glucosides/metabolism
- Glucosides/pharmacology
- Kinetics
- Molecular Structure
- Nucleic Acid Conformation/drug effects
- RNA/chemistry
- RNA/genetics
- RNA/metabolism
- RNA, Transfer, Phe/chemistry
- RNA, Transfer, Phe/genetics
- RNA, Transfer, Phe/metabolism
- Spectrometry, Fluorescence
- Thermodynamics
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Affiliation(s)
- Abhi Das
- Biophysical Chemistry Laboratory, Indian Institute of Chemical Biology, Council of Scientific and Industrial Research, Kolkata, West Bengal, India
| | - Kakali Bhadra
- Biophysical Chemistry Laboratory, Indian Institute of Chemical Biology, Council of Scientific and Industrial Research, Kolkata, West Bengal, India
| | - Gopinatha Suresh Kumar
- Biophysical Chemistry Laboratory, Indian Institute of Chemical Biology, Council of Scientific and Industrial Research, Kolkata, West Bengal, India
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Das A, Bhadra K, Achari B, Chakraborty P, Kumar GS. Interaction of aristololactam-β-D-glucoside and daunomycin with poly(A): spectroscopic and calorimetric studies. Biophys Chem 2011; 155:10-9. [PMID: 21392880 DOI: 10.1016/j.bpc.2011.01.011] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2010] [Revised: 01/11/2011] [Accepted: 01/30/2011] [Indexed: 11/19/2022]
Abstract
The binding of two sugar containing antibiotics viz. aristololactam-β-D-glucoside and daunomycin with single and double stranded poly(A) was investigated by spectroscopic and calorimetric studies. The binding affinity of daunomycin to ss poly(A) was of the order of 10⁶ M⁻¹ and that to ds poly(A) was of the order of 10⁵ M⁻¹. Aristololactam-β-D-glucoside showed a relatively weaker binding with an affinity of the order of 10⁴ M⁻¹ with both the conformations of poly(A). Fluorescence studies showed maximum quenching for daunomycin-ss poly(A) complexes. The binding constants calculated from fluorescence spectroscopy were in good agreement with that obtained from UV spectroscopy. Moderate perturbation of circular dichroic spectra of both the conformations of poly(A) in presence of these molecules with concomitant formation of prominent extrinsic CD bands in the 300-450 nm region further revealed the association. Isothermal titration calorimetry results showed an overall entropy driven binding in all the four systems though the entropy change was maximum in daunomycin-ss poly(A) binding. The binding affinity was also maximum for daunomycin-ss poly(A) and varied as daunomycin-ds poly(A) > aristololactam-β-D-glucoside-ds poly(A) > aristololactam-β-D-glucoside-ss poly(A). A 1:1 binding stoichiometry was observed in all the cases, as confirmed by Job plot analysis, indicating the interaction to consist of a single binding mode. Ferrocyanide quenching studies showed good stacking interaction in all cases but was best for daunomycin-ss poly(A) interaction. No self-structure formation was observed in poly(A) with both daunomycin and aristololactam-β-D-glucoside suggesting the hindrance of the sugar moiety for such structural organization.
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Affiliation(s)
- Abhi Das
- Biophysical Chemistry Laboratory, Indian Institute of Chemical Biology, CSIR, Kolkata 700032, India
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21
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Islam MM, Basu A, Suresh Kumar G. Binding of 9-O-(ω-amino) alkyl ether analogues of the plant alkaloid berberine to poly(A): insights into self-structure induction. MEDCHEMCOMM 2011. [DOI: 10.1039/c0md00209g] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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22
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Suzuki H, Tanabe H, Mizukami H, Inoue M. Selective regulation of multidrug resistance protein in vascular smooth muscle cells by the isoquinoline alkaloid coptisine. Biol Pharm Bull 2010; 33:677-82. [PMID: 20410605 DOI: 10.1248/bpb.33.677] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
When the biological activites of hydrophobic drugs or xenobiotics are studied, it is important to clarify their effects on expression and function of multidrug resistance (MDR) protein. We therefore evaluated the effects of coptisine on MDR in comparison with the structurally related isoquinoline alkaloids berberine and palmatine. To achieve this, we investigated the effects of the three alkaloids on the expression and function of P-glycoprotein/MDR1, MDR1 gene products, in vascular smooth muscle cells (VSMCs). In A10 cells (a rat VSMC line), coptisine upregulated the mRNAs of Mdr1a and Mdr1b, rodent homologues of human MDR1, and these effects were completely abrogated by actinomycin D. Coptisine also induced Mdr1a/1b protein expression and enhanced the efflux of rhodamine 123 from A10 cells. In contrast, berberine and palmatine slightly upregulated the mRNAs of Mdr1a and Mdr1b, but failed to induce Mdr1a/1b protein expression or stimulate rhodamine 123 efflux. To clarify whether these effects occurred in other cells, the effects of the three alkaloids on Mdr1a/1b function were examined in 3Y1, dRLh-84 and B16 cells. Coptisine and berberine enhanced rhodamine 123 efflux in all three cell types, while palmatine inhibited it, based on the finding that palmatine efficiently activated the Mdr1a ATPase activity as a good substrate for Mdr1a. Therefore, the three isoquinoline alkaloids regulated MDR differently in cell type-specific manners. In particular, only coptisine induced Mdr1a/1b in A10 cells and stimulated rhodamine 123 efflux. Taken together, coptisine appears to exert VSMC-selective effects on Mdr1a/1b induction in contrast to berberine and palmatine.
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Affiliation(s)
- Hiroka Suzuki
- Laboratory of Medicinal Resources, School of Pharmacy, Aichi Gakuin University, Japan
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23
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Bhadra K, Kumar GS. Therapeutic potential of nucleic acid-binding isoquinoline alkaloids: Binding aspects and implications for drug design. Med Res Rev 2010; 31:821-62. [DOI: 10.1002/med.20202] [Citation(s) in RCA: 219] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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24
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Maiti M, Kumar GS. Polymorphic nucleic Acid binding of bioactive isoquinoline alkaloids and their role in cancer. J Nucleic Acids 2009; 2010. [PMID: 20814427 PMCID: PMC2915887 DOI: 10.4061/2010/593408] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2009] [Revised: 09/11/2009] [Accepted: 09/14/2009] [Indexed: 12/20/2022] Open
Abstract
Bioactive alkaloids occupy an important position in applied chemistry and play an indispensable role in medicinal chemistry. Amongst them, isoquinoline alkaloids like berberine, palmatine and coralyne of protoberberine group, sanguinarine of the benzophenanthridine group, and their derivatives represent an important class of molecules for their broad range of clinical and pharmacological utility. In view of their extensive occurrence in various plant species and significantly low toxicities, prospective development and use of these alkaloids as effective anticancer agents are matters of great current interest. This review has focused on the interaction of these alkaloids with polymorphic nucleic acid structures (B-form, A-form, Z-form, HL-form, triple helical form, quadruplex form) and their topoisomerase inhibitory activity reported by several research groups using various biophysical techniques like spectrophotometry, spectrofluorimetry, thermal melting, circular dichroism, NMR spectroscopy, electrospray ionization mass spectroscopy, viscosity, isothermal titration calorimetry, differential scanning calorimetry, molecular modeling studies, and so forth, to elucidate their mode and mechanism of action for structure-activity relationships. The DNA binding of the planar sanguinarine and coralyne are found to be stronger and thermodynamically more favoured compared to the buckled structure of berberine and palmatine and correlate well with the intercalative mechanism of sanguinarine and coralyne and the partial intercalation by berberine and palmatine. Nucleic acid binding properties are also interpreted in relation to their anticancer activity.
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Affiliation(s)
- Motilal Maiti
- Biophysical Chemistry Laboratory, Indian Institute of Chemical Biology (CSIR), Kolkata 700032, India
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25
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Sosniak AM, Gasser G, Metzler-Nolte N. Thermal melting studies of alkyne- and ferrocene-containing PNA bioconjugates. Org Biomol Chem 2009; 7:4992-5000. [PMID: 19907791 DOI: 10.1039/b913964h] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The preparation of new metal-containing Peptide Nucleic Acids (PNAs) is currently a field of research intensively studied for various purposes, e.g. DNA biosensors. The role played by the metal centre, notably on the stability of the PNA.DNA hybrid, is obviously crucial, but has not yet been fully investigated. In this work, UV-Vis spectroscopic measurements of solutions of DNA.PNA hybrids, whose 11/12-mer PNA oligomers contained either one or two alkyne- (1) or ferrocene-containing (2) PNA monomers, were carried out to determine the effect of these monomers on the thermal stability of the hybrids (PNA: H-Gly-X-gggtc-Y-agctt-X-Lys-NH2 with X = 1 or and Y = 1 or 2 or blank position). Supplementary CD spectroscopic measurements were performed to gain insight into the structures of the PNA.DNA duplexes formed. The effect of both modified monomers was found to depend on their actual positions within the PNA sequences. Insertions at the N- or C-termini of a PNA oligomer did not change the melting temperatures (T(m) values of about 72 degrees C) of the DNA.PNA hybrids significantly. Insertion of monomers 1 or 2 in the middle of a PNA sequence induced a substantial decrease in the T(m) of the hybrids (by about 23 degrees C) when bound to the same DNA oligomer. Interestingly, it was found that the type of modification, namely alkyne or ferrocene, did not significantly influence the T(m) values in these cases. However, the thermal stability of hybrids with the DNA oligomers containing one to four additional thymines and the PNA oligomers containing the ferrocene moiety in its middle, varied significantly with the number of thymines added compared to its alkyne analogues (DeltaT(m) up to -13 degrees C). The presence of the ferrocene moiety induced a significant decrease in thermal stability of the hybrids, probably due to its bulkiness. In order to assess the effect of PNA backbone rigidity on the stability of DNA.PNA hybrids, PNA oligomers with an internal amino acid, propargylglycine (Pgl) or the dipeptide glycine-propargylglycine (Gly-Pgl), were synthesised. It was assumed that the orientation of the alkyne moiety in the Pgl-containing PNA sequence is not identical to an alkyne-containing PNA sequence, as a significantly higher T(m) value (DeltaT(m) = +10 degrees C) was measured. It is anticipated that the alkyne moiety in Pgl is not facing the DNA base and therefore does not disturb as much the neighbouring nucleobases and base-stacking of the complementary DNA, in contrast to the alkyne moiety of 1. Interestingly, no significant differences in the thermal stability of the hybrids was observed between Pgl-containing and dipeptide-containing PNA oligomers, although the former contracts the PNA backbone by three atoms.
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Affiliation(s)
- Anna M Sosniak
- Ruhr-University Bochum, Faculty of Chemistry and Biochemistry, Inorganic Chemistry I-Bioinorganic Chemistry, Universitätsstrasse 150, D-44801, Bochum, Germany
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26
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Giri P, Suresh Kumar G. Molecular recognition of poly(A) targeting by protoberberine alkaloids: in vitro biophysical studies and biological perspectives. MOLECULAR BIOSYSTEMS 2009; 6:81-8. [PMID: 20024069 DOI: 10.1039/b910706a] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The use of small molecules to specifically control important cellular functions through binding to nucleic acids is an area of major current interest at the interface of chemical biology and medicinal chemistry. The polyadenylic acid [poly(A)] tail of mRNA has been recently established as a potential drug target due to its significant role in the initiation of translation, maturation and stability of mRNA as well as in the production of alternate proteins in eukaryotic cells. Very recently some small molecule alkaloids of the isoquinoline group have been found to bind poly(A) with remarkably high affinity leading to self-structure formation. Plant alkaloids are small molecules known to have important traditional roles in medicinal chemistry due to their extensive biological activity. Especially, noteworthy are the protoberberine alkaloids that are widely distributed in several botanical families exhibiting myriad therapeutic applications. This review focuses on the structural and biological significance of poly(A) and interaction of protoberberine alkaloids with this RNA structure for the development of new small molecule alkaloids targeted to poly(A) structures as futuristic therapeutic agents.
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Affiliation(s)
- Prabal Giri
- Biophysical Chemistry Laboratory, Indian Institute of Chemical Biology (CSIR), 4, Raja S.C. Mullick Road, Kolkata 700032, West Bengal, India.
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27
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Xi H, Gray D, Kumar S, Arya DP. Molecular recognition of single-stranded RNA: neomycin binding to poly(A). FEBS Lett 2009; 583:2269-75. [PMID: 19520078 DOI: 10.1016/j.febslet.2009.06.007] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2009] [Revised: 06/01/2009] [Accepted: 06/03/2009] [Indexed: 02/04/2023]
Abstract
Poly(A) is a relevant sequence in cell biology due to its importance in mRNA stability and translation initiation. Neomycin is an aminoglycoside antibiotic that is well known for its ability to target various nucleic acid structures. Here it is reported that neomycin is capable of binding tightly to a single-stranded oligonucleotide (A(30)) with a K(d) in the micromolar range. CD melting experiments support complex formation and indicate a melting temperature of 47 degrees C. The poly(A) duplex, which melts at 44 degrees C (pH 5.5), was observed to melt at 61 degrees C in the presence of neomycin, suggesting a strong stabilization of the duplex by the neomycin.
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Affiliation(s)
- Hongjuan Xi
- Department of Chemistry, Clemson University, Clemson, SC 29634, USA
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28
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Islam MM, Chowdhury SR, Kumar GS. Spectroscopic and calorimetric studies on the binding of alkaloids berberine, palmatine and coralyne to double stranded RNA polynucleotides. J Phys Chem B 2009; 113:1210-24. [PMID: 19132839 DOI: 10.1021/jp806597w] [Citation(s) in RCA: 131] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The interaction of two natural protoberberine plant alkaloids berberine and palmatine and a synthetic derivative coralyne to three double stranded ribonucleic acids, poly(A). poly(U), poly(I).poly(C) and poly(C).poly(G) was studied using various biophysical techniques. Absorbance and fluorescence studies showed that the alkaloids bound cooperatively to these RNAs with the binding affinities of the order 10(4) M(-1). Circular dichroic results suggested that the conformation of poly(A). poly(U) was perturbed by all the three alkaloids, that of poly(I).poly(C) by coralyne only and that of poly(C).poly(G) by none. Fluorescence quenching studies gave evidence for partial intercalation of berberine and palmatine and complete intercalation of coralyne to these RNA duplexes. Isothermal titration calorimetric studies revealed that the binding was characterized by negative enthalpy and positive entropy changes and the affinity constants derived were in agreement with the overall binding affinity from spectral data. The binding of all the three alkaloids considerably stabilized the melting of poly(A). poly(U) and poly(I).poly(C) and the binding data evaluated from the melting data were in agreement with that obtained from other techniques. The overall binding affinity of the alkaloids to these double stranded RNAs varied in the order, berberine = palmatine < coralyne. The temperature dependence of the enthalpy changes afforded large negative values of heat capacity changes for the binding of palmatine and coralyne to poly(A).poly(U) and of coralyne to poly(I).poly(C), suggesting substantial hydrophobic contribution in the binding process. Further, enthalpy-entropy compensation was also seen in almost all the systems that showed binding. These results further advance our understanding on the binding of small molecules that are specific binders to double stranded RNA sequences.
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Affiliation(s)
- Md Maidul Islam
- Biophysical Chemistry Laboratory, Indian Institute of Chemical Biology, Council of Scientific and Industrial Research, Kolkata 700 032, India
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29
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Binding of DNA-binding alkaloids berberine and palmatine to tRNA and comparison to ethidium: Spectroscopic and molecular modeling studies. J Mol Struct 2008. [DOI: 10.1016/j.molstruc.2008.04.043] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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30
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Villari V, Micali N. Light Scattering as Spectroscopic Tool for the Study of Disperse Systems Useful in Pharmaceutical Sciences. J Pharm Sci 2008; 97:1703-30. [PMID: 17803199 DOI: 10.1002/jps.21067] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The use of colloidal systems in pharmaceutical formulations, for addressing the issue of selective and controlled drug delivery or for improving drug availability, requires an accurate previous characterization of their chemical and physical properties. Light scattering is a useful and non-invasive method to study the structure and conformation of colloids in a wide space-scale, encompassing nanometric- to micrometric-sized particles, as well as their size distribution, surface electrostatic potential and aggregation phenomena occurring under proper conditions. In this review the physical bases of the light scattering approach are described and many examples are reported to discuss the examination of various multiphase systems useful in pharmaceutical fields.
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Affiliation(s)
- Valentina Villari
- CNR-Istituto per i Processi Chimico-Fisici, Via La Farina 237, 98123 Messina, Italy.
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Giri P, Kumar GS. Self-structure induction in single stranded poly(A) by small molecules: Studies on DNA intercalators, partial intercalators and groove binding molecules. Arch Biochem Biophys 2008; 474:183-92. [PMID: 18387354 DOI: 10.1016/j.abb.2008.03.013] [Citation(s) in RCA: 87] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2008] [Revised: 03/13/2008] [Accepted: 03/15/2008] [Indexed: 11/17/2022]
Abstract
Self-structure induction in single stranded poly(A) has been one typical example of the various ways that could be used to modulate nucleic acid structural aspects through binding of small molecules. For the first time, the interaction between a series of small molecules and poly(A) has been investigated to understand the nature of the structural features in DNA binding small molecules that could be responsible for the formation of self-structure in single stranded poly(A) molecules. Classical intercalators like ethidium, coralyne, quinacrine and proflavine, partial intercalators like berberine and palmatine and classical minor groove binders like hoechst 33258 and DAPI have been chosen for this study. The binding of each of these molecules to poly(A) has been characterized by absorption spectral titration, job plot and isothermal titration calorimetry. Self-structure formation was monitored from circular dichroic melting, optical melting and differential scanning calorimetry. The results revealed that while all the intercalators studied induced self-structure formation, partial intercalators did not induce the same in poly(A). Of the two classical DNA minor groove binding molecules investigated, hoechst was effective in inducing self-structure while DAPI was ineffective. Self-structure induction in poly(A) was observed to be directly linked to the cooperative binding of the molecules to poly(A) in that all the molecules that bound cooperatively induced self-structure in poly(A). Structural and thermodynamic aspects of the interaction leading to self-structure formation are described.
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Affiliation(s)
- Prabal Giri
- Biophysical Chemistry Laboratory, Indian Institute of Chemical Biology, 4, Raja S.C. Mullick Road, Jadavpur, Kolkata, West Bengal 700032, India
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32
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Islam MM, Suresh Kumar G. RNA targeting by small molecule alkaloids: Studies on the binding of berberine and palmatine to polyribonucleotides and comparison to ethidium. J Mol Struct 2008. [DOI: 10.1016/j.molstruc.2007.05.004] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Giri P, Kumar GS. Spectroscopic and calorimetric studies on the binding of the phototoxic and cytotoxic plant alkaloid sanguinarine with double helical poly(A). J Photochem Photobiol A Chem 2008. [DOI: 10.1016/j.jphotochem.2007.07.022] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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34
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Okhrimenko O, Jelesarov I. A survey of the year 2006 literature on applications of isothermal titration calorimetry. J Mol Recognit 2008; 21:1-19. [DOI: 10.1002/jmr.859] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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35
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Giri P, Kumar GS. Binding of protoberberine alkaloid coralyne with double stranded poly(A): a biophysical study. MOLECULAR BIOSYSTEMS 2008; 4:341-8. [DOI: 10.1039/b716356h] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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36
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Molecular aspects on the interaction of phenosafranine to deoxyribonucleic acid: Model for intercalative drug–DNA binding. J Mol Struct 2008. [DOI: 10.1016/j.molstruc.2007.02.016] [Citation(s) in RCA: 111] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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37
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Bhadra K, Maiti M, Kumar GS. Molecular recognition of DNA by small molecules: AT base pair specific intercalative binding of cytotoxic plant alkaloid palmatine. Biochim Biophys Acta Gen Subj 2007; 1770:1071-80. [PMID: 17434677 DOI: 10.1016/j.bbagen.2007.03.001] [Citation(s) in RCA: 119] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2006] [Revised: 02/27/2007] [Accepted: 03/03/2007] [Indexed: 11/28/2022]
Abstract
The base dependent binding of the cytotoxic alkaloid palmatine 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 competition dialysis, spectrophotometric, spectrofluorimetric, thermal melting, circular dichroic, viscometric and isothermal titration calorimetric (ITC) studies. Binding of the alkaloid to various polynucleotides was dependent upon sequences of base pairs. Binding data obtained from absorbance measurements according to neighbour exclusion model indicated that the intrinsic binding constants decreased in the order poly(dA).poly(dT)>poly(dA-dT).poly(dA-dT)>poly(dG-dC).poly(dG-dC)>poly(dG).poly(dC). This affinity was also revealed by the competition dialysis, increase of steady state fluorescence intensity, increase in fluorescence quantum yield, stabilization against thermal denaturation and perturbations in circular dichroic spectrum. Among the polynucleotides, poly(dA).poly(dT) showed positive cooperativity at binding values lower than r=0.05. Viscosity studies revealed that in the strong binding region, the increase of contour length of DNA depended strongly on the sequence of base pairs being higher for AT polymers and induction of unwinding-rewinding process of covalently closed superhelical DNA. Isothermal titration calorimetric data showed a single entropy driven binding event in the AT homo polymer while that with the hetero polymer involved two binding modes, an entropy driven strong binding followed by an enthalpy driven weak binding. These results unequivocally established that the alkaloid palmatine binds strongly to AT homo and hetero polymers by mechanism of intercalation.
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Affiliation(s)
- Kakali Bhadra
- Biophysical Chemistry Laboratory, Indian Institute of Chemical Biology, Kolkata 700 032, India
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38
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Giri P, Kumar GS. Specific binding and self-structure induction to poly(A) by the cytotoxic plant alkaloid sanguinarine. Biochim Biophys Acta Gen Subj 2007; 1770:1419-26. [PMID: 17600625 DOI: 10.1016/j.bbagen.2007.05.005] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2007] [Revised: 05/17/2007] [Accepted: 05/21/2007] [Indexed: 11/24/2022]
Abstract
The cytotoxic plant alkaloid sanguinarine was found to bind preferentially and strongly to single stranded poly(A) with an association constant (K(a)) in the range 3.6-4.6 x 10(6) M(-1) in comparison to several nucleic acids. The binding induced unique self-structure formation in poly(A) that showed cooperative melting transition in circular dichroism, absorbance, and differential scanning calorimetry studies. The alkaloid binding was characterized to be intercalation as revealed from fluorescence quenching experiments and was predominantly enthalpy driven as revealed from isothermal titration calorimetry. Sanguinarine is the first and only natural product so far known to induce a self-structure formation in poly(A).
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Affiliation(s)
- Prabal Giri
- Biophysical Chemistry Laboratory, Indian Institute of Chemical Biology, Kolkata 700032, India
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Micali N, Villari V, Cusumano M, Pietro MLD, Giannetto A. Role of the coulombic interaction in ligand-induced biopolymer aggregation. J Phys Chem B 2007; 111:1231-7. [PMID: 17266279 DOI: 10.1021/jp065795w] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The interaction mechanisms responsible for the binding between metal complexes and biopolymers in aqueous solution, as well as the consequent aggregation process of biopolymers themselves, involve many factors, from geometrical aspects and hydrophobic contributions, as examples, to the electrostatic potential. In this paper aqueous solutions of a polynucleotide, polyadenylic acid (PolyA), which mimics the helix arrangement of RNA or single-stranded DNA but has a simpler structure, are used as a model system. The role of the electrostatic interactions in the binding process between some platinum(II) complexes and PolyA and in the aggregation among PolyA molecules is investigated, by means of elastic and quasielastic light scattering and electrophoretic mobility. The results show that the presence of large, planar aromatic moiety in the dicationic platinum(II) complexes is essential for the binding with PolyA and suggest that the consequent lowering of the local electrostatic barrier between PolyA molecules can be involved in triggering the aggregation process.
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Affiliation(s)
- Norberto Micali
- CNR-Istituto per i Processi Chimico-Fisici, Via La Farina 237, I-98123, Messina, Italy.
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Islam MM, Sinha R, Kumar GS. RNA binding small molecules: Studies on t-RNA binding by cytotoxic plant alkaloids berberine, palmatine and the comparison to ethidium. Biophys Chem 2007; 125:508-20. [PMID: 17156912 DOI: 10.1016/j.bpc.2006.11.001] [Citation(s) in RCA: 120] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2006] [Revised: 11/03/2006] [Accepted: 11/03/2006] [Indexed: 11/30/2022]
Abstract
The interaction of two natural protoberberine plant alkaloids berberine and palmatine with t-RNA(phe) was studied using various biophysical techniques and the data was compared with the binding of the classical DNA intercalator, ethidium. The results of optical thermal melting, differential scanning calorimetry and circular dichroism characterized the native cloverleaf structure of t-RNA under the conditions of the study. The strong binding of the alkaloids and ethidium to t-RNA was revealed from the absorption and fluorescence studies. The salt dependence of the binding constants enabled the dissection of the binding free energy to electrostatic and non-electrostatic contributions. This analysis revealed a surprisingly large favourable component of the non-electrostatic contribution to the binding of these charged alkaloids and ethidium to t-RNA. Isothermal titration calorimetric studies revealed that the binding of both the alkaloids is driven by a moderately favourable enthalpy decrease and a moderately favourable entropy increase while that of ethidium is driven by a large favourable enthalpy decrease. Taken together, the results suggest that the binding of these alkaloid molecules on the t-RNA structure appears to be mostly by partial intercalation while ethidium intercalates to the t-RNA. These results reveal the molecular aspects on the interaction of these alkaloids to t-RNA.
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Affiliation(s)
- Md Maidul Islam
- Biophysical Chemistry Laboratory, Indian Institute of Chemical Biology, 4, Raja S. C. Mullick Road, Kolkata 700032, India
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Protoberberine Alkaloids: Physicochemical and Nucleic Acid Binding Properties. TOPICS IN HETEROCYCLIC CHEMISTRY 2007. [DOI: 10.1007/7081_2007_071] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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Giri P, Hossain M, Kumar GS. Molecular aspects on the specific interaction of cytotoxic plant alkaloid palmatine to poly(A). Int J Biol Macromol 2006; 39:210-21. [PMID: 16678250 DOI: 10.1016/j.ijbiomac.2006.03.026] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2006] [Revised: 03/27/2006] [Accepted: 03/27/2006] [Indexed: 11/26/2022]
Abstract
The interaction of the protoberberine alkaloid palmatine with single and double stranded structures of poly(A) was studied by various biophysical techniques. Comparative binding studies were also performed with double stranded DNA, t-RNA, poly(C).poly(G), poly(U) and poly(C). The results of competition dialysis, fluorescence, and absorption spectral studies converge to reveal the molecular aspects of the strong and specific binding of palmatine to single stranded poly(A). The binding affinity of palmatine to natural DNA, t-RNA and double stranded poly(A) was weaker while no binding was apparent with single stranded poly(U), poly(C) and double stranded poly(C).poly(G). The strong affinity of the alkaloid to single stranded poly(A) in comparison to the double stranded structure was also revealed from circular dichroic and viscometric studies. The effect of [Na+] ion concentration on the binding process revealed the significant role of electrostatic forces in the complexation. The presence of bound alkaloid also remarkably affected denaturation-renaturation of stacked helical poly(A). The energetics of the strong binding to poly(A) was studied from thermodynamic estimation from van Hoff' analysis of the temperature dependent binding constants and ultra sensitive isothermal titration calorimertry, both suggesting the binding to be exothermic and enthalpy driven. This study provides detailed insight into the binding specificity of the natural alkaloid to single stranded poly(A) over several other single and double stranded nucleic acid structures suggesting its potential as a lead compound for RNA based drug targeting.
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Affiliation(s)
- Prabal Giri
- Biophysical Chemistry Laboratory, Indian Institute of Chemical Biology, Kolkata, India
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