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Roy S, Chakraborty N, Maiti B, Muniyappa K, Bhattacharya S. Design and Synthesis of Xanthone Analogues Conjugated with Aza-aromatic Substituents as Promising G-Quadruplex Stabilizing Ligands and their Selective Cancer Cell Cytotoxic Action. Chembiochem 2023; 24:e202200609. [PMID: 36455103 DOI: 10.1002/cbic.202200609] [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: 10/24/2022] [Revised: 11/24/2022] [Accepted: 11/25/2022] [Indexed: 12/03/2022]
Abstract
We have examined the stabilization of higher-order noncanonical G-quadruplex (G4) DNA structures formed by the G-rich sequences in the promoter region of oncogenes such as c-MYC, c-KIT, VEGF and BCl2 by newly synthesized, novel nitrogen-containing aromatics conjugated to xanthone moiety. Compounds with N-heterocyclic substituents such as pyridine (XNiso), benzimidazole (XBIm), quinoxaline (XQX) and fluorophore dansyl (XDan) showed greater effectiveness in stabilizing the G4 DNA as well as selective cytotoxicity for cancer cells (mainly A549) over normal cells both in terms of UV-Vis spectral titrations and cytotoxicity assay. Both fluorescence spectral titrimetric measurements and circular dichroism (CD) melting experiments further substantiated the G4 stabilization phenomenon by these small-molecular ligands. In addition, these compounds could induce the formation of parallel G4 structures in the absence of any added salt condition in Tris⋅HCl buffer at 25 °C. In a polymerase stop assay, the formation of stable G4 structures in the promoter of oncogenes and halting of DNA synthesis in the presence of the above-mentioned compounds was demonstrated by using oncogene promoter as the DNA synthesis template. Apoptosis-mediated cell death of the cancer cells was proved by Annexin V-PI dual staining assay and cell-cycle arrest occurred in the S phase of the cell cycles. The plausible mode of binding involves the stacking of the xanthone core on the G4 DNA plane with the possibility of interaction with the 5'-overhang as indicated by molecular dynamics simulation studies.
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Affiliation(s)
- Soma Roy
- Department of Organic Chemistry, Indian Institute of Science, Bangalore, 560012, India.,School of Applied & Interdisciplinary Sciences Indian Association for the Cultivation of Science, Kolkata, 700032, India
| | - Nirmal Chakraborty
- School of Applied & Interdisciplinary Sciences Indian Association for the Cultivation of Science, Kolkata, 700032, India
| | - Bappa Maiti
- School of Applied & Interdisciplinary Sciences Indian Association for the Cultivation of Science, Kolkata, 700032, India
| | - Kalappa Muniyappa
- Department of Biochemistry, Indian Institute of Science, Bangalore, 560012, India
| | - Santanu Bhattacharya
- Department of Organic Chemistry, Indian Institute of Science, Bangalore, 560012, India.,School of Applied & Interdisciplinary Sciences Indian Association for the Cultivation of Science, Kolkata, 700032, India
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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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4
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Filli MS, Ibrahim AA, Kesse S, Aquib M, Boakye-Yiadom KO, Farooq MA, Raza F, Zhang Y, Wang B. Synthetic berberine derivatives as potential new drugs. BRAZ J PHARM SCI 2022. [DOI: 10.1590/s2175-97902020000318835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Affiliation(s)
| | | | | | - Md Aquib
- China Pharmaceutical University, China
| | | | | | | | | | - Bo Wang
- China Pharmaceutical University, China
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5
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Khvostov MV, Gladkova ED, Borisov SA, Zhukova NA, Marenina MK, Meshkova YV, Luzina OA, Tolstikova TG, Salakhutdinov NF. Discovery of the First in Class 9-N-Berberine Derivative as Hypoglycemic Agent with Extra-Strong Action. Pharmaceutics 2021; 13:pharmaceutics13122138. [PMID: 34959419 PMCID: PMC8708145 DOI: 10.3390/pharmaceutics13122138] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 12/06/2021] [Accepted: 12/10/2021] [Indexed: 12/13/2022] Open
Abstract
Berberine is well known for its ability to reduce the blood glucose level, but its high effective dose and poor bioavailability limits its use. In this work we synthesized a new derivative of berberine, 9-(hexylamino)-2,3-methylenedioxy-10-methoxyprotoberberine chloride (SHE-196), and analyzed the profile of its hypoglycemic effects. Biological tests have shown that the substance has a very pronounced hypoglycemic activity due to increased insulin sensitivity after single and multiple dosing. In obese type 2 diabetes mellitus (T2DM) mice, it was characterized by improved glucose tolerance, decreased fasting insulin levels and sensitivity, decreased total body weight and interscapular fat mass, and increased interscapular brown fat activity. All these effects were also confirmed histologically, where a decrease in fatty degeneration of the liver, an improvement in the condition of the islets of Langerhans and a decrease in the size of fat droplets in brown adipose tissue were found. Our results indicate that 9-(hexylamino)-2,3-methylenedioxy-10-methoxyprotoberberine chloride could be the first in a new series of therapeutic agents for the treatment of diabetes mellitus.
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Ruan S, Wu S, Yang L, Li M, Zhang Y, Wang Z, Wang S. A novel turn-on fluorescent probe based on berberine for detecting Hg2+ and ClO− with the different fluorescence signals. Microchem J 2021. [DOI: 10.1016/j.microc.2021.106199] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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7
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Therapeutic Effects of Berberine in Metabolic Diseases and Diabetes Mellitus. REVISTA BRASILEIRA DE FARMACOGNOSIA 2021. [DOI: 10.1007/s43450-021-00159-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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The Anticancer Effect of Natural Plant Alkaloid Isoquinolines. Int J Mol Sci 2021; 22:ijms22041653. [PMID: 33562110 PMCID: PMC7915290 DOI: 10.3390/ijms22041653] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 02/02/2021] [Accepted: 02/03/2021] [Indexed: 12/24/2022] Open
Abstract
Isoquinoline alkaloids-enriched herbal plants have been used as traditional folk medicine for their anti-inflammatory, antimicrobial, and analgesic effects. They induce cell cycle arrest, apoptosis, and autophagy, leading to cell death. While the molecular mechanisms of these effects are not fully understood, it has been suggested that binding to nucleic acids or proteins, enzyme inhibition, and epigenetic modulation by isoquinoline alkaloids may play a role in the effects. This review discusses recent evidence on the molecular mechanisms by which the isoquinoline alkaloids can be a therapeutic target of cancer treatment.
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Becher J, Berdnikova DV, Ihmels H, Stremmel C. Synthesis and investigation of quadruplex-DNA-binding, 9- O-substituted berberine derivatives. Beilstein J Org Chem 2020; 16:2795-2806. [PMID: 33281983 PMCID: PMC7684686 DOI: 10.3762/bjoc.16.230] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Accepted: 11/02/2020] [Indexed: 12/20/2022] Open
Abstract
A small series of five novel berberine derivatives was synthesized by the Cu-catalyzed click reaction of 9-propargyladenine with 9-O-(azidoalkyl)berberine derivatives. The association of the resulting berberine-adenine conjugates with representative quadruplex-forming oligonucleotides 22AG dA(G3TTA)3G3 and a2 d(ACAG4TGTG4)2 was examined with photometric and fluorimetric titrations, thermal DNA denaturation analysis, and CD spectroscopy. The results from the spectrometric titrations indicated the formation of 2:1 or 1:1 complexes (ligand:G4-DNA) with log K b values of 10-11 (2:1) and 5-6 (1:1), which are typical for berberine derivatives. Notably, a clear relationship between the binding affinity of the ligands with the length of the alkyl linker chain, n, was not observed. However, depending on the structure, the ligands exhibited different effects when bound to the G4-DNA, such as fluorescent light-up effects and formation of ICD bands, which are mostly pronounced with a linker length of n = 4 (with a2) and n = 5 (with 22AG), thus indicating that each ligand-G4-DNA complex has a specific structure with respect to relative alignment and conformational flexibility of the ligand in the binding site. It was shown exemplarily with one representative ligand from the series that such berberine-adenine conjugates exhibit a selective binding, specifically a selectivity to quadruplex DNA in competition with duplex DNA, and a preferential thermal stabilization of the G4-DNA forms 22AG and KRAS. Notably, the experimental data do not provide evidence for a significant effect of the adenine unit on the binding affinity of the ligands, for example, by additional association with the loops, presumably because the adenine residue is sterically shielded by the neighboring triazole unit.
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Affiliation(s)
- Jonas Becher
- Department of Chemistry and Biology, University of Siegen and Center of Micro- and Nanochemistry and Engineering (Cμ); Adolf-Reichwein-Str. 2, 57068 Siegen, Germany
| | - Daria V Berdnikova
- Department of Chemistry and Biology, University of Siegen and Center of Micro- and Nanochemistry and Engineering (Cμ); Adolf-Reichwein-Str. 2, 57068 Siegen, Germany
| | - Heiko Ihmels
- Department of Chemistry and Biology, University of Siegen and Center of Micro- and Nanochemistry and Engineering (Cμ); Adolf-Reichwein-Str. 2, 57068 Siegen, Germany
| | - Christopher Stremmel
- Department of Chemistry and Biology, University of Siegen and Center of Micro- and Nanochemistry and Engineering (Cμ); Adolf-Reichwein-Str. 2, 57068 Siegen, Germany
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10
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Mari G, De Crescentini L, Benedetti S, Palma F, Santeusanio S, Mantellini F. Synthesis of new dihydroberberine and tetrahydroberberine analogues and evaluation of their antiproliferative activity on NCI-H1975 cells. Beilstein J Org Chem 2020; 16:1606-1616. [PMID: 32704327 PMCID: PMC7356317 DOI: 10.3762/bjoc.16.133] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 06/24/2020] [Indexed: 01/02/2023] Open
Abstract
Dihydroberberine (DHBER), the partially reduced form of the alkaloid berberine (BER), is known to exhibit important biological activities. Despite this fact, there have been only few studies that concern the biological properties of functionalized DHBER. Attracted by the potentiality of this latter compound, we have realized the preparation of new arylhydrazono-functionalized DHBERs, starting from BER and some α-bromohydrazones. On the other hand, also the fully reduced form of BER, namely tetrahydroberberine (THBER), and its derivatives have proven to present different biological activities. Therefore, the obtained arylhydrazono-functionalized DHBERs were reduced to the corresponding arylhydrazono-THBERs. The antiproliferative activity of both arylhydrazono-DHBERs and -THBERs has been evaluated on NCI-H1975 lung cancer cells.
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Affiliation(s)
- Giacomo Mari
- Section of Chemistry and Pharmaceutical Technologies, Department of Biomolecular Sciences, University of Urbino “Carlo Bo”, Via I Maggetti 24, 61029 Urbino, Italy
| | - Lucia De Crescentini
- Section of Chemistry and Pharmaceutical Technologies, Department of Biomolecular Sciences, University of Urbino “Carlo Bo”, Via I Maggetti 24, 61029 Urbino, Italy
| | - Serena Benedetti
- Section of Biochemistry and Molecular Biology, Department of Biomolecular Sciences, University of Urbino “Carlo Bo”, Via Saffi 2, 61029 Urbino, Italy
| | - Francesco Palma
- Section of Biochemistry and Molecular Biology, Department of Biomolecular Sciences, University of Urbino “Carlo Bo”, Via Saffi 2, 61029 Urbino, Italy
| | - Stefania Santeusanio
- Section of Chemistry and Pharmaceutical Technologies, Department of Biomolecular Sciences, University of Urbino “Carlo Bo”, Via I Maggetti 24, 61029 Urbino, Italy
| | - Fabio Mantellini
- Section of Chemistry and Pharmaceutical Technologies, Department of Biomolecular Sciences, University of Urbino “Carlo Bo”, Via I Maggetti 24, 61029 Urbino, Italy
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11
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Papi F, Bazzicalupi C, Ferraroni M, Ciolli G, Lombardi P, Khan AY, Kumar GS, Gratteri P. Pyridine Derivative of the Natural Alkaloid Berberine as Human Telomeric G 4-DNA Binder: A Solution and Solid-State Study. ACS Med Chem Lett 2020; 11:645-650. [PMID: 32435365 DOI: 10.1021/acsmedchemlett.9b00516] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Accepted: 02/07/2020] [Indexed: 12/18/2022] Open
Abstract
Telomerase is an enzyme deputed to the maintenance of eukaryotic chromosomes; however, its overexpression is a recognized hallmark of many cancer forms. A viable route for the inhibition of telomerase in malignant cells is the stabilization of G-quadruplex structures (G4) at the 3' overhang of telomeres. Berberine has shown in this regard valuable G4 binding properties together with a significant anticancer activity and telomerase inhibition effects. Here, we focused on a berberine derivative featuring a pyridine containing side group at the 13th position. Such modification actually improves the binding toward telomeric G-quadruplexes and establishes a degree of selectivity in the interaction with different sequences. Moreover, the X-ray crystal structure obtained for the complex formed by the ligand and a bimolecular human telomeric quadruplex affords a better understanding of the 13-berberine derivatives behavior with telomeric G4 and allows to draw useful insights for the future design of derivatives with remarkable anticancer properties.
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Affiliation(s)
- Francesco Papi
- Department of Chemistry ’Ugo Schiff’, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino (FI), Italy
| | - Carla Bazzicalupi
- Department of Chemistry ’Ugo Schiff’, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino (FI), Italy
| | - Marta Ferraroni
- Department of Chemistry ’Ugo Schiff’, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino (FI), Italy
| | - Giulia Ciolli
- Department of Chemistry ’Ugo Schiff’, University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino (FI), Italy
| | - Paolo Lombardi
- Naxospharma srl, Via G. Di Vittorio 70, 20026 Novate Milanese (MI), Italy
| | - Asma Yasmeen Khan
- Biophysical Chemistry Laboratory, CSIR-Indian Institute of Chemical Biology, Kolkata 700 032, India
| | - Gopinatha Suresh Kumar
- Biophysical Chemistry Laboratory, CSIR-Indian Institute of Chemical Biology, Kolkata 700 032, India
| | - Paola Gratteri
- Department NEUROFARBA − Pharmaceutical and Nutraceutical Section and Laboratory of Molecular Modeling Cheminformatics & QSAR, University of Florence, Via U. Schiff 6, 50019 Sesto Fiorentino, Florence, Italy
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New Modified Deoxythymine with Dibranched Tetraethylene Glycol Stabilizes G-Quadruplex Structures. Molecules 2020; 25:molecules25030705. [PMID: 32041318 PMCID: PMC7036917 DOI: 10.3390/molecules25030705] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 01/28/2020] [Accepted: 02/02/2020] [Indexed: 11/24/2022] Open
Abstract
Methods for stabilizing G-quadruplex formation is a promising therapeutic approach for cancer treatment and other biomedical applications because stable G-quadruplexes efficiently inhibit biological reactions. Oligo and polyethylene glycols are promising biocompatible compounds, and we have shown that linear oligoethylene glycols can stabilize G-quadruplexes. Here, we developed a new modified deoxythymine with dibranched or tribranched tetraethylene glycol (TEG) and incorporated these TEG-modified deoxythymines into a loop region that forms an antiparallel G-quadruplex. We analyzed the stability of the modified G-quadruplexes, and the results showed that the tribranched TEG destabilized G-quadruplexes through entropic contributions, likely through steric hindrance. Interestingly, the dibranched TEG modification increased G-quadruplex stability relative to the unmodified DNA structures due to favorable enthalpic contributions. Molecular dynamics calculations suggested that dibranched TEG interacts with the G-quadruplex through hydrogen bonding and CH-π interactions. Moreover, these branched TEG-modified deoxythymine protected the DNA oligonucleotides from degradation by various nucleases in human serum. By taking advantage of the unique interactions between DNA and branched TEG, advanced DNA materials can be developed that affect the regulation of DNA structure.
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Anti-Inflammation Associated Protective Mechanism of Berberine and its Derivatives on Attenuating Pentylenetetrazole-Induced Seizures in Zebrafish. J Neuroimmune Pharmacol 2020; 15:309-325. [DOI: 10.1007/s11481-019-09902-w] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2019] [Accepted: 12/10/2019] [Indexed: 12/13/2022]
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Ruan S, Gao Y, Wang Y, Li M, Yang H, Song J, Wang Z, Wang S. A novel berberine-based colorimetric and fluorimetric probe for hydrazine detection. NEW J CHEM 2020. [DOI: 10.1039/d0nj03599h] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Hydrazine in water and soil has caused serious diseases for human health. In this work, a simple fluorescent probe (BP) for hydrazine detection was synthesized from berberine. The probe has excellent fluorescence properties and naked-eye detection.
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Affiliation(s)
- Shutang Ruan
- Co-Innovation Centre of Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, College of Light Industry and Food, Nanjing Forestry University
- Nanjing
- China
| | - Yu Gao
- Co-Innovation Centre of Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, College of Light Industry and Food, Nanjing Forestry University
- Nanjing
- China
| | - Yunyun Wang
- Co-Innovation Centre of Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, College of Light Industry and Food, Nanjing Forestry University
- Nanjing
- China
| | - Mingxin Li
- Co-Innovation Centre of Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, College of Light Industry and Food, Nanjing Forestry University
- Nanjing
- China
| | - Haiyan Yang
- Co-Innovation Centre of Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, College of Light Industry and Food, Nanjing Forestry University
- Nanjing
- China
| | - Jie Song
- Department of Chemistry and Biochemistry, University of Michigan-Flint
- Flint
- USA
| | - Zhonglong Wang
- Co-Innovation Centre of Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, College of Light Industry and Food, Nanjing Forestry University
- Nanjing
- China
| | - Shifa Wang
- Co-Innovation Centre of Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, College of Light Industry and Food, Nanjing Forestry University
- Nanjing
- China
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Hu XM, Li RT, Zhang MM, Wu KY, Li HH, Huang NH, Sun B, Chen JX. Phenanthroline-linked berberine dimer and fluorophore-tagged DNA conjugate for the selective detection of microRNA-185: Experimental and molecular docking studies. Anal Chim Acta 2019; 1051:153-159. [DOI: 10.1016/j.aca.2018.11.022] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Revised: 09/06/2018] [Accepted: 11/12/2018] [Indexed: 10/27/2022]
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Duan Y, Liu T, Zhou Y, Dou T, Yang Q. Glycoside hydrolase family 18 and 20 enzymes are novel targets of the traditional medicine berberine. J Biol Chem 2018; 293:15429-15438. [PMID: 30135205 DOI: 10.1074/jbc.ra118.004351] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Revised: 08/03/2018] [Indexed: 02/01/2023] Open
Abstract
Berberine is a traditional medicine that has multiple medicinal and agricultural applications. However, little is known about whether berberine can be a bioactive molecule toward carbohydrate-active enzymes, which play numerous vital roles in the life process. In this study, berberine and its analogs were discovered to be competitive inhibitors of glycoside hydrolase family 20 β-N-acetyl-d-hexosaminidase (GH20 Hex) and GH18 chitinase from both humans and the insect pest Ostrinia furnacalis Berberine and its analog SYSU-1 inhibit insect GH20 Hex from O. furnacalis (OfHex1), with Ki values of 12 and 8.5 μm, respectively. Co-crystallization of berberine and its analog SYSU-1 in complex with OfHex1 revealed that the positively charged conjugate plane of berberine forms π-π stacking interactions with Trp490, which are vital to its inhibitory activity. Moreover, the 1,3-dioxole group of berberine binds an unexplored pocket formed by Trp322, Trp483, and Val484, which also contributes to its inhibitory activity. Berberine was also found to be an inhibitor of human GH20 Hex (HsHexB), human GH18 chitinase (HsCht and acidic mammalian chitinase), and insect GH18 chitinase (OfChtI). Besides GH18 and GH20 enzymes, berberine was shown to weakly inhibit human GH84 O-GlcNAcase (HsOGA) and Saccharomyces cerevisiae GH63 α-glucosidase I (ScGluI). By analyzing the published crystal structures, berberine was revealed to bind with its targets in an identical mechanism, namely via π-π stacking and electrostatic interactions with the aromatic and acidic residues in the binding pockets. This paper reports new molecular targets of berberine and may provide a berberine-based scaffold for developing multitarget drugs.
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Affiliation(s)
- Yanwei Duan
- From the State Key Laboratory of Fine Chemical Engineering, School of Life Science and Biotechnology and School of Software, Dalian University of Technology, Dalian 116024
| | - Tian Liu
- From the State Key Laboratory of Fine Chemical Engineering, School of Life Science and Biotechnology and School of Software, Dalian University of Technology, Dalian 116024,
| | - Yong Zhou
- From the State Key Laboratory of Fine Chemical Engineering, School of Life Science and Biotechnology and School of Software, Dalian University of Technology, Dalian 116024
| | - Tongyi Dou
- the School of Life Science and Medicine, Dalian University of Technology, Panjin 124221, and
| | - Qing Yang
- From the State Key Laboratory of Fine Chemical Engineering, School of Life Science and Biotechnology and School of Software, Dalian University of Technology, Dalian 116024, .,the Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
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Che T, Wang YQ, Huang ZL, Tan JH, Huang ZS, Chen SB. Natural Alkaloids and Heterocycles as G-Quadruplex Ligands and Potential Anticancer Agents. Molecules 2018; 23:molecules23020493. [PMID: 29473874 PMCID: PMC6017894 DOI: 10.3390/molecules23020493] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2017] [Revised: 02/04/2018] [Accepted: 02/20/2018] [Indexed: 12/23/2022] Open
Abstract
G-quadruplexes are four-stranded nucleic acid secondary structures that are formed in guanine-rich sequences. G-quadruplexes are widely distributed in functional regions of the human genome and transcriptome, such as human telomeres, oncogene promoter regions, replication initiation sites, and untranslated regions. Many G-quadruplex-forming sequences are found to be associated with cancer, and thus, these non-canonical nucleic acid structures are considered to be attractive molecular targets for cancer therapeutics with novel mechanisms of action. In this mini review, we summarize recent advances made by our lab in the study of G-quadruplex-targeted natural alkaloids and their derivatives toward the development of potential anticancer agents.
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Affiliation(s)
- Tong Che
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China.
| | - Yu-Qing Wang
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China.
| | - Zhou-Li Huang
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China.
| | - Jia-Heng Tan
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China.
| | - Zhi-Shu Huang
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China.
| | - Shuo-Bin Chen
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China.
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18
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Ganesan K, Xu B. Telomerase Inhibitors from Natural Products and Their Anticancer Potential. Int J Mol Sci 2017; 19:ijms19010013. [PMID: 29267203 PMCID: PMC5795965 DOI: 10.3390/ijms19010013] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Revised: 12/10/2017] [Accepted: 12/19/2017] [Indexed: 12/25/2022] Open
Abstract
Telomeres and telomerase are nowadays exploring traits on targets for anticancer therapy. Telomerase is a unique reverse transcriptase enzyme, considered as a primary factor in almost all cancer cells, which is mainly responsible to regulate the telomere length. Hence, telomerase ensures the indefinite cell proliferation during malignancy—a hallmark of cancer—and this distinctive feature has provided telomerase as the preferred target for drug development in cancer therapy. Deactivation of telomerase and telomere destabilization by natural products provides an opening to succeed new targets for cancer therapy. This review aims to provide a fundamental knowledge for research on telomere, working regulation of telomerase and its various binding proteins to inhibit the telomere/telomerase complex. In addition, the review summarizes the inhibitors of the enzyme catalytic subunit and RNA component, natural products that target telomeres, and suppression of transcriptional and post-transcriptional levels. This extensive understanding of telomerase biology will provide indispensable information for enhancing the efficiency of rational anti-cancer drug design.
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Affiliation(s)
- Kumar Ganesan
- Food Science and Technology Program, Beijing Normal University-Hong Kong Baptist University United International College, Zhuhai 519087, China.
| | - Baojun Xu
- Food Science and Technology Program, Beijing Normal University-Hong Kong Baptist University United International College, Zhuhai 519087, China.
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Ligand binding to telomeric G-quadruplex DNA investigated by funnel-metadynamics simulations. Proc Natl Acad Sci U S A 2017; 114:E2136-E2145. [PMID: 28232513 PMCID: PMC5358390 DOI: 10.1073/pnas.1612627114] [Citation(s) in RCA: 81] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
A thorough characterization of the binding interaction between a drug and its molecular target is fundamental to successfully lead drug design. We demonstrate that this characterization is also possible using the recently developed method of funnel-metadynamics (FM), here applied to investigate the binding of berberine to DNA G-quadruplex. We computed a quantitatively well-characterized free-energy landscape that allows identifying two low-energy ligand binding modes and the presence of higher energy prebinding states. We validated the accuracy of our calculations by steady-state fluorescence experiments. The good agreement between the theoretical and experimental binding free-energy value demonstrates that FM is a most reliable method to study ligand/DNA interaction. G-quadruplexes (G4s) are higher-order DNA structures typically present at promoter regions of genes and telomeres. Here, the G4 formation decreases the replicative DNA at each cell cycle, finally leading to apoptosis. The ability to control this mitotic clock, particularly in cancer cells, is fascinating and passes through a rational understanding of the ligand/G4 interaction. We demonstrate that an accurate description of the ligand/G4 binding mechanism is possible using an innovative free-energy method called funnel-metadynamics (FM), which we have recently developed to investigate ligand/protein interaction. Using FM simulations, we have elucidated the binding mechanism of the anticancer alkaloid berberine to the human telomeric G4 (d[AG3(T2AG3)3]), computing also the binding free-energy landscape. Two ligand binding modes have been identified as the lowest energy states. Furthermore, we have found prebinding sites, which are preparatory to reach the final binding mode. In our simulations, the ions and the water molecules have been explicitly represented and the energetic contribution of the solvent during ligand binding evaluated. Our theoretical results provide an accurate estimate of the absolute ligand/DNA binding free energy (ΔGb0 = −10.3 ± 0.5 kcal/mol) that we validated through steady-state fluorescence binding assays. The good agreement between the theoretical and experimental value demonstrates that FM is a most powerful method to investigate ligand/DNA interaction and can be a useful tool for the rational design also of G4 ligands.
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Padmapriya K, Barthwal R. NMR based structural studies decipher stacking of the alkaloid coralyne to terminal guanines at two different sites in parallel G-quadruplex DNA, [d(TTGGGGT)]4 and [d(TTAGGGT)]4. Biochim Biophys Acta Gen Subj 2017; 1861:37-48. [DOI: 10.1016/j.bbagen.2016.11.011] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Revised: 10/13/2016] [Accepted: 11/08/2016] [Indexed: 01/15/2023]
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21
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Xiong YX, Su HF, Lv P, Ma Y, Wang SK, Miao H, Liu HY, Tan JH, Ou TM, Gu LQ, Huang ZS. A newly identified berberine derivative induces cancer cell senescence by stabilizing endogenous G-quadruplexes and sparking a DNA damage response at the telomere region. Oncotarget 2016; 6:35625-35. [PMID: 26462146 PMCID: PMC4742130 DOI: 10.18632/oncotarget.5521] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Accepted: 09/28/2015] [Indexed: 12/16/2022] Open
Abstract
The guanine-rich sequences are able to fold into G-quadruplexes in living cells, making these structures promising anti-cancer drug targets. In the current study, we identified a small molecule, Ber8, from a series of 9-substituted berberine derivatives and found that it could induce acute cell growth arrest and senescence in cancer cells, but not in normal fibroblasts. Further analysis revealed that the cell growth arrest was directly associated with apparent cell cycle arrest, cell senescence, and profound DNA damage at the telomere region. Significantly, our studies also provided evidence that Ber8 could stabilize endogenous telomeric G-quadruplexes structures in cells. Ber8 could then induce the delocalization of TRF1 and POT1 from the telomere accompanied by a rapid telomere uncapping. These results provide compelling insights into direct binding of telomeric G-quadruplexes and might contribute to the development of more selective, effective anticancer drugs.
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Affiliation(s)
- Yun-Xia Xiong
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, P.R.China
| | - Hua-Fei Su
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, P.R.China
| | - Peng Lv
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, P.R.China
| | - Yan Ma
- Department of Medical Science, Shunde Polytechnic, Foshan 528333, P.R.China
| | - Shi-Ke Wang
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, P.R.China
| | - Hui Miao
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, P.R.China
| | - Hui-Yun Liu
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, P.R.China
| | - Jia-Heng Tan
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, P.R.China
| | - Tian-Miao Ou
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, P.R.China
| | - Lian-Quan Gu
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, P.R.China
| | - Zhi-Shu Huang
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, P.R.China
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Recent advances in targeting the telomeric G-quadruplex DNA sequence with small molecules as a strategy for anticancer therapies. Future Med Chem 2016; 8:1259-90. [PMID: 27442231 DOI: 10.4155/fmc-2015-0017] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Human telomeric DNA (hTelo), present at the ends of chromosomes to protect their integrity during cell division, comprises tandem repeats of the sequence d(TTAGGG) which is known to form a G-quadruplex secondary structure. This unique structural formation of DNA is distinct from the well-known helical structure that most genomic DNA is thought to adopt, and has recently gained prominence as a molecular target for new types of anticancer agents. In particular, compounds that can stabilize the intramolecular G-quadruplex formed within the human telomeric DNA sequence can inhibit the activity of the enzyme telomerase which is known to be upregulated in tumor cells and is a major contributor to their immortality. This provides the basis for the discovery and development of small molecules with the potential for selective toxicity toward tumor cells. This review summarizes the various families of small molecules reported in the literature that have telomeric quadruplex stabilizing properties, and assesses the potential for compounds of this type to be developed as novel anticancer therapies. A future perspective is also presented, emphasizing the need for researchers to adopt approaches that will allow the discovery of molecules with more drug-like properties in order to improve the chances of lead molecules reaching the clinic in the next decade.
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23
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Chen Y, Zhang Y. Functional and mechanistic analysis of telomerase: An antitumor drug target. Pharmacol Ther 2016; 163:24-47. [DOI: 10.1016/j.pharmthera.2016.03.017] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Accepted: 03/29/2016] [Indexed: 01/26/2023]
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24
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Lao YX, Zhang SS, Liu XG, Jiang CY, Wu JQ, Li Q, Huang ZS, Wang H. High-Valent Pentamethylcyclopentadienylcobalt(III) or -iridium(III)-Catalyzed CH Annulation with Alkynes: Synthesis of Heterocyclic Quaternary Ammonium Salts. Adv Synth Catal 2016. [DOI: 10.1002/adsc.201600194] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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25
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Ferraroni M, Bazzicalupi C, Papi F, Fiorillo G, Guamán-Ortiz LM, Nocentini A, Scovassi AI, Lombardi P, Gratteri P. Solution and Solid-State Analysis of Binding of 13-Substituted Berberine Analogues to Human Telomeric G-quadruplexes. Chem Asian J 2016; 11:1107-15. [DOI: 10.1002/asia.201600116] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Indexed: 12/29/2022]
Affiliation(s)
- Marta Ferraroni
- Department of Chemistry; University of Florence; Via della Lastruccia 3 50019 Sesto Fiorentino FI Italy
| | - Carla Bazzicalupi
- Department of Chemistry; University of Florence; Via della Lastruccia 3 50019 Sesto Fiorentino FI Italy
| | - Francesco Papi
- Department of Chemistry; University of Florence; Via della Lastruccia 3 50019 Sesto Fiorentino FI Italy
- Department NEUROFARBA-Pharmaceutical and nutraceutical section; Laboratory of Molecular Modeling Cheminformatics&QSAR; University of Firenze; via Ugo Schiff 6 50019 Sesto Fiorentino, Firenze Italy
| | - Gaetano Fiorillo
- Naxospharma srl; via G. Di Vittorio, 70 20026 Novate Milanese Italy
| | - Luis Miguel Guamán-Ortiz
- Universidad Técnica Particular de Loja; Departamento de Ciencias de la Salud; San Cayetano Alto Calle Paris 1101608 Loja Ecuador
- Istituto di Genetica Molecolare del CNR, Via Abbiategrasso 207; 27100 Pavia Italy
| | - Alessio Nocentini
- Department NEUROFARBA-Pharmaceutical and nutraceutical section; Laboratory of Molecular Modeling Cheminformatics&QSAR; University of Firenze; via Ugo Schiff 6 50019 Sesto Fiorentino, Firenze Italy
| | - Anna Ivana Scovassi
- Istituto di Genetica Molecolare del CNR, Via Abbiategrasso 207; 27100 Pavia Italy
| | - Paolo Lombardi
- Naxospharma srl; via G. Di Vittorio, 70 20026 Novate Milanese Italy
| | - Paola Gratteri
- Department NEUROFARBA-Pharmaceutical and nutraceutical section; Laboratory of Molecular Modeling Cheminformatics&QSAR; University of Firenze; via Ugo Schiff 6 50019 Sesto Fiorentino, Firenze Italy
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26
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Experimental and quantum-chemical study of nucleophilic substitution mechanism in berberine. Chem Heterocycl Compd (N Y) 2016. [DOI: 10.1007/s10593-016-1810-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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27
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Zhou CQ, Yang JW, Dong C, Wang YM, Sun B, Chen JX, Xu YS, Chen WH. Highly selective, sensitive and fluorescent sensing of dimeric G-quadruplexes by a dimeric berberine. Org Biomol Chem 2016; 14:191-7. [DOI: 10.1039/c5ob01723h] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
This paper describes the highly selective, sensitive and topology-specific fluorescent sensing of dimeric G-quadruplexes by a polyether-tethered dimeric berberine.
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Affiliation(s)
- Chun-Qiong Zhou
- Guangdong Provincial Key Laboratory of New Drug Screening
- School of Pharmaceutical Sciences
- Southern Medical University
- Guangzhou 510515
- P. R. China
| | - Jian-Wei Yang
- Guangdong Provincial Key Laboratory of New Drug Screening
- School of Pharmaceutical Sciences
- Southern Medical University
- Guangzhou 510515
- P. R. China
| | - Cheng Dong
- Guangdong Provincial Key Laboratory of New Drug Screening
- School of Pharmaceutical Sciences
- Southern Medical University
- Guangzhou 510515
- P. R. China
| | - Yong-Min Wang
- Guangdong Provincial Key Laboratory of New Drug Screening
- School of Pharmaceutical Sciences
- Southern Medical University
- Guangzhou 510515
- P. R. China
| | - Bin Sun
- Guangdong Provincial Key Laboratory of New Drug Screening
- School of Pharmaceutical Sciences
- Southern Medical University
- Guangzhou 510515
- P. R. China
| | - Jin-Xiang Chen
- Guangdong Provincial Key Laboratory of New Drug Screening
- School of Pharmaceutical Sciences
- Southern Medical University
- Guangzhou 510515
- P. R. China
| | - Ya-Shi Xu
- Guangdong Provincial Key Laboratory of New Drug Screening
- School of Pharmaceutical Sciences
- Southern Medical University
- Guangzhou 510515
- P. R. China
| | - Wen-Hua Chen
- Guangdong Provincial Key Laboratory of New Drug Screening
- School of Pharmaceutical Sciences
- Southern Medical University
- Guangzhou 510515
- P. R. China
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28
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Tera M, Hirokawa T, Okabe S, Sugahara K, Seimiya H, Shimamoto K. Design and synthesis of a berberine dimer: a fluorescent ligand with high affinity towards G-quadruplexes. Chemistry 2015; 21:14519-28. [PMID: 26272465 DOI: 10.1002/chem.201501693] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Indexed: 12/20/2022]
Abstract
G-quadruplexes (G4) are thought to be important factors for telomerase inhibition and transcriptional/translational modulations. Bioinformatic analyses imply that the human genome and mRNA contain a multitude of G4-forming sequences; however, their analysis requires selective and detectable ligands. Given that two molecules of fluorescent berberine (BBR) coordinate to telomeric G4 in their co-crystals, we designed hydrocarbon-linked BBR-analogue dimers because we expected the alignment of two BBR chromophores would avoid Watson-Crick base pair intercalation, which should result in high selectivity towards G4. An alkene-cis-C2 BBR dimer showed the highest affinity (Kd ≤2.6 nM) and selectivity (ca. 900-fold vs. duplex) towards G4. The intrinsic "light-up" fluorescence properties of this BBR dimer, derived from its conformational switching by G4, allowed a selective visualization of various G4 in the gel without using additional bulky fluorescence dyes, which, combined with the observed lack of conformational change of the ligand, suggested future applications in in vitro detection systems.
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Affiliation(s)
- Masayuki Tera
- Bioorganic Research Institute, Suntory Foundation for Life Sciences, 8-1-1 Seikadai, Seikacho, Soraku, Kyoto 619-0284 (Japan).
| | - Takatsugu Hirokawa
- Molecular Profiling Research Center for Drug Discovery, National Institute of Advanced Industrial Science and Technology, 2-4-7 Aomi, Koto-ward, Tokyo, 135-0064 (Japan)
| | - Sachiko Okabe
- Division of Molecular Biotherapy, Cancer Chemotherapy Center, Japanese Foundation for Cancer Research, 3-8-31 Ariake, Koto-ward, Tokyo, 135-8550 (Japan)
| | - Kohtaro Sugahara
- Bioorganic Research Institute, Suntory Foundation for Life Sciences, 8-1-1 Seikadai, Seikacho, Soraku, Kyoto 619-0284 (Japan)
| | - Hiroyuki Seimiya
- Division of Molecular Biotherapy, Cancer Chemotherapy Center, Japanese Foundation for Cancer Research, 3-8-31 Ariake, Koto-ward, Tokyo, 135-8550 (Japan)
| | - Keiko Shimamoto
- Bioorganic Research Institute, Suntory Foundation for Life Sciences, 8-1-1 Seikadai, Seikacho, Soraku, Kyoto 619-0284 (Japan)
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29
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Pereira DM, Valentão P, Correia-da-Silva G, Teixeira N, Andrade PB. Translating endoplasmic reticulum biology into the clinic: a role for ER-targeted natural products? Nat Prod Rep 2015; 32:705-22. [PMID: 25703279 DOI: 10.1039/c4np00102h] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
ER stress has been identified as a hallmark, and sometimes trigger, of several pathologies, notably cancer, inflammation and neurodegenerative diseases like Alzheimer's and Parkinson's. Among the molecules described in literature known to affect ER function, the majority are natural products, suggesting that natural molecules may constitute a significant arsenal of chemical entities for modulating this cellular target. In this review, we will start by presenting the current knowledge of ER biology and the hallmarks of ER stress, thus paving the way for presenting the natural products that have been described as being ER modulators, either stress inducers or ER protectors. The chemistry, distribution and mechanism of action of these compounds will be presented and discussed.
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Affiliation(s)
- David M Pereira
- REQUIMTE/LAQV, Laboratório de Farmacognosia, Departamento de Química, Faculdade de Farmácia, Universidade do Porto, Rua de Jorge Viterbo Ferreira, no. 228, 4050-313 Porto, Portugal.
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30
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Bhowmik D, Fiorillo G, Lombardi P, Suresh Kumar G. Recognition of human telomeric G-quadruplex DNA by berberine analogs: effect of substitution at the 9 and 13 positions of the isoquinoline moiety. J Mol Recognit 2015; 28:722-30. [DOI: 10.1002/jmr.2486] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Revised: 05/11/2015] [Accepted: 05/23/2015] [Indexed: 11/11/2022]
Affiliation(s)
- Debipreeta Bhowmik
- Biophysical Chemistry Laboratory; CSIR-Indian Institute of Chemical Biology; Kolkata 700 032 India
| | - Gaetano Fiorillo
- Naxospharma srl; Via G. Di Vittorio 70 20026 Novate Milanese MI Italy
| | - Paolo Lombardi
- Naxospharma srl; Via G. Di Vittorio 70 20026 Novate Milanese MI Italy
| | - G. Suresh Kumar
- Biophysical Chemistry Laboratory; CSIR-Indian Institute of Chemical Biology; Kolkata 700 032 India
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31
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Shan C, Lin J, Hou JQ, Liu HY, Chen SB, Chen AC, Ou TM, Tan JH, Li D, Gu LQ, Huang ZS. Chemical intervention of the NM23-H2 transcriptional programme on c-MYC via a novel small molecule. Nucleic Acids Res 2015; 43:6677-91. [PMID: 26117539 PMCID: PMC4538829 DOI: 10.1093/nar/gkv641] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Accepted: 06/10/2015] [Indexed: 11/15/2022] Open
Abstract
c-MYC is an important oncogene that is considered as an effective target for anticancer therapy. Regulation of this gene's transcription is one avenue for c-MYC-targeting drug design. Direct binding to a transcription factor and generating the intervention of a transcriptional programme appears to be an effective way to modulate gene transcription. NM23-H2 is a transcription factor for c-MYC and is proven to be related to the secondary structures in the promoter. Here, we first screened our small-molecule library for NM23-H2 binders and then sifted through the inhibitors that could target and interfere with the interaction process between NM23-H2 and the guanine-rich promoter sequence of c-MYC. As a result, a quinazolone derivative, SYSU-ID-01, showed a significant interference effect towards NM23-H2 binding to the guanine-rich promoter DNA sequence. Further analyses of the compound–protein interaction and the protein–DNA interaction provided insight into the mode of action for SYSU-ID-01. Cellular evaluation results showed that SYSU-ID-01 could abrogate NM23-H2 binding to the c-MYC promoter, resulting in downregulation of c-MYC transcription and dramatically suppressed HeLa cell growth. These findings provide a new way of c-MYC transcriptional control through interfering with NM23-H2 binding to guanine-rich promoter sequences by small molecules.
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Affiliation(s)
- Chan Shan
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Jing Lin
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China Guangdong Province Key Laboratory of Pharmacodynamic Constituents of TCM and New Drugs Research, College of Pharmacy, Jinan University, Guangzhou, China
| | - Jin-Qiang Hou
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Hui-Yun Liu
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Shuo-Bin Chen
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Ai-Chun Chen
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Tian-Miao Ou
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Jia-Heng Tan
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Ding Li
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Lian-Quan Gu
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Zhi-Shu Huang
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
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32
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Ebrahimi M, Khayamian T, Hadadzadeh H, Sayed Tabatabaei BE, Jannesari Z, Khaksar G. Spectroscopic, biological, and molecular modeling studies on the interactions of [Fe(III)-meloxicam] with G-quadruplex DNA and investigation of its release from bovine serum albumin (BSA) nanoparticles. J Biomol Struct Dyn 2015; 33:2316-29. [PMID: 25563680 DOI: 10.1080/07391102.2014.1003195] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The guanine-rich sequence, specifically in DNA, telomeric DNA, is a potential target of anticancer drugs. In this work, a mononuclear Fe(III) complex containing two meloxicam ligands was synthesized as a G-quadruplex stabilizer. The interaction between the Fe(III) complex and G-quadruplex with sequence of 5'-G3(T2AG3)3-3' (HTG21) was investigated using spectroscopic methods, molecular modeling, and polymerase chain reaction (PCR) assays. The spectroscopic methods of UV-vis, fluorescence, and circular dichroism showed that the metal complex can effectively induce and stabilize G-quadruplex structure in the G-rich 21-mer sequence. Also, the binding constant between the Fe(III) complex and G-quadruplex was measured by these methods and it was found to be 4.53(±0.30) × 10(5) M(-1)). The PCR stop assay indicated that the Fe(III) complex inhibits DNA amplification. The cell viability assay showed that the complex has significant antitumor activities against Hela cells. According to the UV-vis results, the interaction of the Fe(III) complex with duplex DNA is an order of magnitude lower than G-quadruplex. Furthermore, the release of the complex incorporated in bovine serum albumin nanoparticles was also investigated in physiological conditions. The release of the complex followed a bi-phasic release pattern with high and low releasing rates at the first and second phases, respectively. Also, in order to obtain the binding mode of the Fe(III) complex with G-quadruplex, molecular modeling was performed. The molecular docking results showed that the Fe(III) complex was docked to the end-stacked of the G-quadruplex with a π-π interaction, created between the meloxicam ligand and the guanine bases of the G-quadruplex.
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Affiliation(s)
- Malihe Ebrahimi
- a Department of Chemistry , Isfahan University of Technology , Isfahan 84156-83111 , Iran
| | - Taghi Khayamian
- a Department of Chemistry , Isfahan University of Technology , Isfahan 84156-83111 , Iran
| | - Hassan Hadadzadeh
- a Department of Chemistry , Isfahan University of Technology , Isfahan 84156-83111 , Iran
| | | | - Zahra Jannesari
- a Department of Chemistry , Isfahan University of Technology , Isfahan 84156-83111 , Iran
| | - Ghazale Khaksar
- b Department of Agricultural Biotechnology, College of Agriculture , Isfahan University of Technology , Isfahan 84156-83111 , Iran
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33
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Yang F, Wang J, Tang J, Yu LF, Li J, Li JY. Berberine Analogues: Progress towards Versatile Applications. HETEROCYCLES 2015. [DOI: 10.3987/rev-15-825] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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34
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Structure-based virtual screening of novel natural alkaloid derivatives as potential binders of h-telo and c-myc DNA G-quadruplex conformations. Molecules 2014; 20:206-23. [PMID: 25547724 PMCID: PMC6272608 DOI: 10.3390/molecules20010206] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2014] [Accepted: 12/15/2014] [Indexed: 01/08/2023] Open
Abstract
Several ligands can bind to the non-canonical G-quadruplex DNA structures thereby stabilizing them. These molecules can act as effective anticancer agents by stabilizing the telomeric regions of DNA or by regulating oncogene expression. In order to better interact with the quartets of G-quadruplex structures, G-binders are generally characterized by a large aromatic core involved in π-π stacking. Some natural flexible cyclic molecules from Traditional Chinese Medicine have shown high binding affinity with G-quadruplex, such as berbamine and many other alkaloids. Using the structural information available on G-quadruplex structures, we performed a high throughput in silico screening of commercially available alkaloid derivative databases by means of a structure-based approach based on docking and molecular dynamics simulations against the human telomeric sequence d[AG3(T2AG3)3] and the c-myc promoter structure. We identified 69 best hits reporting an improved theoretical binding affinity with respect to the active set. Among them, a berberine derivative, already known to remarkably inhibit telomerase activity, was related to a better theoretical affinity versusc-myc.
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35
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Targeting G-quadruplex nucleic acids with heterocyclic alkaloids and their derivatives. Eur J Med Chem 2014; 97:538-51. [PMID: 25466923 DOI: 10.1016/j.ejmech.2014.11.021] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2014] [Revised: 11/05/2014] [Accepted: 11/11/2014] [Indexed: 01/25/2023]
Abstract
G-Quadruplex nucleic acids or G-quadruplexes (G4s) are four-stranded DNA or RNA secondary structures that are formed in guanine-rich sequences. They are widely distributed in functional regions of the human genome, such as telomeres, ribosomal DNA (rDNA), transcription start sites, promoter regions and untranslated regions of mRNA, suggesting that G-quadruplex structures may play a pivotal role in the control of a variety of cellular processes. G-Quadruplexes are viewed as valid therapeutic targets in human cancer diseases. Small molecules, from naturally occurring to synthetic, are exploited to specifically target G-quadruplexes and have proven to be a new class of anticancer agents. Notably, alkaloids are an important source of G-quadruplex ligands and have significant bioactivities in anticancer therapy. In this review, the authors provide a brief, up-to-date summary of heterocyclic alkaloids and their derivatives targeting G-quadruplexes.
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36
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Salem AA, El Haty IA, Abdou IM, Mu Y. Interaction of human telomeric G-quadruplex DNA with thymoquinone: a possible mechanism for thymoquinone anticancer effect. Biochim Biophys Acta Gen Subj 2014; 1850:329-42. [PMID: 25450185 DOI: 10.1016/j.bbagen.2014.10.018] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2014] [Revised: 10/16/2014] [Accepted: 10/20/2014] [Indexed: 01/10/2023]
Abstract
BACKGROUND Thymoquinone (TQ) has been documented to possess chemo-preventive and chemotherapeutic antitumor effects. Studies reported that TQ inhibits the growth of cancer cells in animal models, culture and xenografted tumors. Molecular mechanisms underlying these anticancer effects were attributed to inductions of cell cycle arrest, apoptosis, oxidative damage of cellular macromolecules, blockade of tumor angiogenesis and inhibitions in migration, invasion and metastasis of cancer cells. On the other hand, human telomere DNA plays a role in regulating genes' transcriptions. It folds up into G-quadruplex structures that inhibit telomerase enzyme over-expressed in cancerous cells. Molecules that selectively stabilize G-quadruplex are potential anticancer agents. Therefore, this work aimed to explore the interaction of TQ with G-quadruplex DNA as a possible underlying mechanism for the anticancer effect of TQ. METHODS Interactions of TQ with telomeric G-quadruplex (5'-AGGG(TTAGGG)3-3') and duplex DNAs were studied using UV-vis, fluorescence, circular dichroism, liquid and solid NMR (1H and 13C), melting temperature and docking simulation. RESULTS Changes in UV-vis, CD, fluorescence, 1H NMR and 13C NMR, spectra as well as melting temperatures and docking simulations provided evidences for TQ's interactions with G-quadruplex. TQ was found to interact with G-quadruplex on two binding sites adjacent to the TTA loop with binding constants 1.80×10(5) and 1.12×10(7) M(-1). Melting temperatures indicated that TQ stabilized G-quadruplex by 5.6 °C and destabilized ct-DNA by 5.1 °C. Selectivity experiment indicated that TQ is preferentially binding to G-quadruplex over duplex with selectivity coefficients of 2.80-3.33×10(-3). Results suggested an intercalation binding mode based on π-π stacking. CONCLUSION Our results propose that TQ can possibly act as a G-quadruplex DNA stabilizer and subsequently contribute to the inhibition of telomerase enzyme and cancer's proliferation. GENERAL SIGNIFICANCE Our results represent a change in the paradigms reported for structural features of G-quadruplex's stabilizers and anticancer mechanisms of TQ.
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Affiliation(s)
- Alaa A Salem
- Department of Chemistry, College of Science, United Arab Emirates University, P.O. Box 15551, Al Ain, United Arab Emirates.
| | - Ismail A El Haty
- Department of Chemistry, College of Science, United Arab Emirates University, P.O. Box 15551, Al Ain, United Arab Emirates
| | - Ibrahim M Abdou
- Department of Chemistry, College of Science, United Arab Emirates University, P.O. Box 15551, Al Ain, United Arab Emirates
| | - Yuguang Mu
- School of Biological Sciences, College of Science, Nanyang Technological University, Singapore 637551, Singapore
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37
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A benzimidazopyridoquinoxaline as promising scaffold for G-quadruplex DNA targeting. Med Chem Res 2014. [DOI: 10.1007/s00044-014-0985-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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38
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DNA binders in clinical trials and chemotherapy. Bioorg Med Chem 2014; 22:4506-21. [DOI: 10.1016/j.bmc.2014.05.030] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2014] [Revised: 05/09/2014] [Accepted: 05/14/2014] [Indexed: 01/09/2023]
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39
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Small-molecule quadruplex-targeted drug discovery. Bioorg Med Chem Lett 2014; 24:2602-12. [DOI: 10.1016/j.bmcl.2014.04.029] [Citation(s) in RCA: 149] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Revised: 04/06/2014] [Accepted: 04/08/2014] [Indexed: 01/24/2023]
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40
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Tateishi-Karimata H, Isono N, Sugimoto N. New insights into transcription fidelity: thermal stability of non-canonical structures in template DNA regulates transcriptional arrest, pause, and slippage. PLoS One 2014; 9:e90580. [PMID: 24594642 PMCID: PMC3940900 DOI: 10.1371/journal.pone.0090580] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2013] [Accepted: 02/04/2014] [Indexed: 11/25/2022] Open
Abstract
The thermal stability and topology of non-canonical structures of G-quadruplexes and hairpins in template DNA were investigated, and the effect of non-canonical structures on transcription fidelity was evaluated quantitatively. We designed ten template DNAs: A linear sequence that does not have significant higher-order structure, three sequences that form hairpin structures, and six sequences that form G-quadruplex structures with different stabilities. Templates with non-canonical structures induced the production of an arrested, a slipped, and a full-length transcript, whereas the linear sequence produced only a full-length transcript. The efficiency of production for run-off transcripts (full-length and slipped transcripts) from templates that formed the non-canonical structures was lower than that from the linear. G-quadruplex structures were more effective inhibitors of full-length product formation than were hairpin structure even when the stability of the G-quadruplex in an aqueous solution was the same as that of the hairpin. We considered that intra-polymerase conditions may differentially affect the stability of non-canonical structures. The values of transcription efficiencies of run-off or arrest transcripts were correlated with stabilities of non-canonical structures in the intra-polymerase condition mimicked by 20 wt% polyethylene glycol (PEG). Transcriptional arrest was induced when the stability of the G-quadruplex structure (−ΔGo37) in the presence of 20 wt% PEG was more than 8.2 kcal mol−1. Thus, values of stability in the presence of 20 wt% PEG are an important indicator of transcription perturbation. Our results further our understanding of the impact of template structure on the transcription process and may guide logical design of transcription-regulating drugs.
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Affiliation(s)
- Hisae Tateishi-Karimata
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, Kobe, Japan
| | - Noburu Isono
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, Kobe, Japan
| | - Naoki Sugimoto
- Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University, Kobe, Japan
- Faculty of Frontiers of Innovative Research in Science and Technology (FIRST), Konan University, Kobe, Japan
- * E-mail:
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41
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Maji B, Bhattacharya S. Advances in the molecular design of potential anticancer agents via targeting of human telomeric DNA. Chem Commun (Camb) 2014; 50:6422-38. [DOI: 10.1039/c4cc00611a] [Citation(s) in RCA: 105] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Telomerase is an attractive drug target to develop new generation drugs against cancer.
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Affiliation(s)
- Basudeb Maji
- Department of Organic Chemistry
- Indian Institute of Science
- Bangalore-560012, India
| | - Santanu Bhattacharya
- Department of Organic Chemistry
- Indian Institute of Science
- Bangalore-560012, India
- Chemical Biology Unit
- Jawaharlal Nehru Centre for Advanced Scientific Research
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42
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Interactions of G-quadruplex DNA binding site with berberine derivatives and construct a structure-based QSAR using docking descriptors. Med Chem Res 2013. [DOI: 10.1007/s00044-013-0733-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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43
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Shan C, Tan JH, Ou TM, Huang ZS. Natural products and their derivatives as G-quadruplex binding ligands. Sci China Chem 2013. [DOI: 10.1007/s11426-013-4920-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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44
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Molecular basis of recognition of quadruplexes human telomere and c-myc promoter by the putative anticancer agent sanguinarine. Biochim Biophys Acta Gen Subj 2013; 1830:4189-201. [DOI: 10.1016/j.bbagen.2013.03.027] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2013] [Revised: 03/19/2013] [Accepted: 03/26/2013] [Indexed: 01/24/2023]
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45
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Yue Q, Shen T, Wang C, Wang L, Li H, Xu S, Wang H, Liu J. Construction of a controllable Förster resonance energy transfer system based on G-quadruplex for DNA sensing. Biosens Bioelectron 2013; 40:75-81. [DOI: 10.1016/j.bios.2012.06.026] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2012] [Revised: 05/16/2012] [Accepted: 06/14/2012] [Indexed: 02/03/2023]
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46
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Zhang SL, Chang JJ, Damu GL, Fang B, Zhou XD, Geng RX, Zhou CH. Novel berberine triazoles: Synthesis, antimicrobial evaluation and competitive interactions with metal ions to Human Serum Albumin. Bioorg Med Chem Lett 2013; 23:1008-12. [DOI: 10.1016/j.bmcl.2012.12.036] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2012] [Revised: 11/26/2012] [Accepted: 12/12/2012] [Indexed: 01/09/2023]
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47
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Bazzicalupi C, Ferraroni M, Bilia AR, Scheggi F, Gratteri P. The crystal structure of human telomeric DNA complexed with berberine: an interesting case of stacked ligand to G-tetrad ratio higher than 1:1. Nucleic Acids Res 2012; 41:632-8. [PMID: 23104378 PMCID: PMC3592469 DOI: 10.1093/nar/gks1001] [Citation(s) in RCA: 114] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
The first crystal structure of human telomeric DNA in complex with the natural alkaloid berberine, produced by different plant families and used in folk medicine for millennia, was solved by X-ray diffraction method. The G-quadruplex unit features all-parallel strands. The overall folding assumed by DNA is the same found in previously reported crystal structures. Similarly to previously reported structures the ligand molecules were found to be stacked onto the external 5′ and 3′-end G-tetrads. However, the present crystal structure highlighted for the first time, the presence of two berberine molecules in the two binding sites, directly interacting with each tetrad. As a consequence, our structural data point out a 2:1 ligand to G-tetrad molar ratio, which has never been reported before in a telomeric intramolecular quadruplex structure.
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Affiliation(s)
- Carla Bazzicalupi
- Department of Chemistry Ugo Schiff, University of Firenze, Via della Lastruccia 3-13, I-50019 Sesto Fiorentino, Firenze, Italy
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48
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Tillhon M, Guamán Ortiz LM, Lombardi P, Scovassi AI. Berberine: new perspectives for old remedies. Biochem Pharmacol 2012; 84:1260-7. [PMID: 22842630 DOI: 10.1016/j.bcp.2012.07.018] [Citation(s) in RCA: 306] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2012] [Revised: 07/13/2012] [Accepted: 07/16/2012] [Indexed: 02/06/2023]
Abstract
Chemical compounds derived from plants have been used since the origin of human beings to counteract a number of diseases. Among them, the natural isoquinoline alkaloid berberine has been employed in Ayurvedic and Chinese Medicine for hundreds of years with a wide range of pharmacological and biochemical effects. More recently, a growing body of reports supports the evidence that berberine has anticancer effects, being able to block the proliferation of and to kill cancer cells. This review addresses the properties and therapeutic use of berberine and focuses on the recent advances as promising anticancer drug lead.
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49
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Xu N, Yang H, Cui M, Song F, Liu Z, Liu S. Evaluation of alkaloids binding to the parallel quadruplex structure [d(TGGGGT)]4 by electrospray ionization mass spectrometry. JOURNAL OF MASS SPECTROMETRY : JMS 2012; 47:694-700. [PMID: 22707161 DOI: 10.1002/jms.2997] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
In this study, electrospray ionization mass spectrometry (ESI-MS) was used to investigate the binding interaction of six alkaloids with parallel intermolecular G-quadruplex [d(TGGGGT)](4), and five alkaloids including berberine, jatrorrhizine, palmatine, tetrandrine, and fangchinoline showed complexation with the target DNA. Relative binding affinities were estimated on the basis of mass spectrometric data. The slight differences in chemical structures of berberine, jatrorrhizine, and palmatine had little influence on their binding affinities to [d(TGGGGT)](4). Tetrandrine and fangchinoline selectively bound to [d(TGGGGT)](4) versus duplex DNA. Collision-induced dissociation (CID) experiments showed that the complexes with berberine, jatrorrhizine, and palmatine dissociated via strand separation and ligand retaining in the strand while the complexes with tetrandrine and fangchinoline were dissociated via ligand elimination. A comparison of dissociation patterns in CID experiments of complexes with the alkaloids to those with the traditional G-quadruplex DNA binders suggested an end-stacking binding mode for tetrandrine and fangchinoline and an intercalation binding mode for berberine, jatrorrhizine, and palmatine to the target DNA. The current work not only provides deep insight into alkaloid/[d(TGGGGT)](4) complexes and useful guidelines for design of efficient anticancer agents but also demonstrates the utility of ESI-MS as a powerful tool for evaluating interaction between ligand and quadruplex DNA.
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Affiliation(s)
- Niusheng Xu
- Changchun Center of Mass Spectrometry, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, China
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50
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Bhowmik D, Das S, Hossain M, Haq L, Suresh Kumar G. Biophysical characterization of the strong stabilization of the RNA triplex poly(U)•poly(A)*poly(U) by 9-O-(ω-amino) alkyl ether berberine analogs. PLoS One 2012; 7:e37939. [PMID: 22666416 PMCID: PMC3362543 DOI: 10.1371/journal.pone.0037939] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2012] [Accepted: 04/26/2012] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Binding of two 9-O-(ω-amino) alkyl ether berberine analogs BC1 and BC2 to the RNA triplex poly(U)(•)poly(A)(*)poly(U) was studied by various biophysical techniques. METHODOLOGY/PRINCIPAL FINDINGS Berberine analogs bind to the RNA triplex non-cooperatively. The affinity of binding was remarkably high by about 5 and 15 times, respectively, for BC1 and BC2 compared to berberine. The site size for the binding was around 4.3 for all. Based on ferrocyanide quenching, fluorescence polarization, quantum yield values and viscosity results a strong intercalative binding of BC1 and BC2 to the RNA triplex has been demonstrated. BC1 and BC2 stabilized the Hoogsteen base paired third strand by about 18.1 and 20.5 °C compared to a 17.5 °C stabilization by berberine. The binding was entropy driven compared to the enthalpy driven binding of berbeine, most likely due to additional contacts within the grooves of the triplex and disruption of the water structure by the alkyl side chain. CONCLUSIONS/SIGNIFICANCE Remarkably higher binding affinity and stabilization effect of the RNA triplex by the amino alkyl berberine analogs was achieved compared to berberine. The length of the alkyl side chain influence in the triplex stabilization phenomena.
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Affiliation(s)
- Debipreeta Bhowmik
- Biophysical Chemistry Laboratory, Chemistry Division, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Suman Das
- Department of Chemistry, Jadavpur University, Kolkata, India
| | - Maidul Hossain
- Biophysical Chemistry Laboratory, Chemistry Division, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Lucy Haq
- Department of Chemistry, Jadavpur University, Kolkata, India
| | - Gopinatha Suresh Kumar
- Biophysical Chemistry Laboratory, Chemistry Division, CSIR-Indian Institute of Chemical Biology, Kolkata, India
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