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Tang W, Ma J, Chen K, Wang K, Chen Z, Chen C, Li X, Wang Y, Shu Y, Zhang W, Yuan X, Shi G, Chen T, Wang P, Chen Y. Berbamine ameliorates DSS-induced colitis by inhibiting peptidyl-arginine deiminase 4-dependent neutrophil extracellular traps formation. Eur J Pharmacol 2024; 975:176634. [PMID: 38710356 DOI: 10.1016/j.ejphar.2024.176634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Revised: 03/29/2024] [Accepted: 05/03/2024] [Indexed: 05/08/2024]
Abstract
Ulcerative colitis (UC) is a chronic inflammatory bowel disease with immune dysregulation affecting colon inflammatory response. Recent studies have highlighted that neutrophil extracellular traps (NETs) play an important role in the pathogenesis of UC. Berbamine (BBM), one of the bioactive ingredients extracted from Chinese herbal medicine Berberis vulgaris L, has attracted intensive attentions due to its significant anti-inflammatory activity and a marketing drug for treating leukemia in China. However, the exact role and potential molecular mechanism of BBM against UC remains elusive. In the present study, our results showed that BBM could markedly improve the pathological phenotype and the colon inflammation in mice with dextran sulfate sodium (DSS)-induced colitis. Then, comprehensive approaches combining network pharmacology and molecular docking analyses were employed to predict the therapeutic potential of BBM in treating UC by peptidyl-arginine deiminase 4 (PAD4), a crucial molecule involved in NETs formation. The molecular docking results showed BBM had a high affinity for PAD4 with a binding energy of -9.3 kcal/mol Moreover, PAD4 expression and NETs productions, including citrullination of histone H3 (Cit-H3), neutrophil elastase (NE), myeloperoxidase (MPO) in both neutrophils and colonic tissue were reduced after BBM administration. However, in the mice with DSS-induced colitis pretreated with GSK484, a PAD4-specific inhibitor, BBM could not further reduce disease related indexes, expression of PAD4 and NETs productions. Above all, the identification of PAD4 as a potential target for BBM to inhibit NETs formation in colitis provides novel insights into the development of BBM-derived drugs for the clinical management of UC.
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Affiliation(s)
- Wenwen Tang
- Department of Colorectal Surgery, Jiangsu Province Hospital of Chinese Medicine, The Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, 210029, PR China; Jiangsu Province Key Laboratory of Tumor Systems Biology and Chinese Medicine, The Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, 210029, PR China
| | - Jiaze Ma
- Department of Colorectal Surgery, Jiangsu Province Hospital of Chinese Medicine, The Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, 210029, PR China; Jiangsu Province Key Laboratory of Tumor Systems Biology and Chinese Medicine, The Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, 210029, PR China
| | - Kaidi Chen
- Department of Colorectal Surgery, Jiangsu Province Hospital of Chinese Medicine, The Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, 210029, PR China; Jiangsu Province Key Laboratory of Tumor Systems Biology and Chinese Medicine, The Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, 210029, PR China
| | - Kuiling Wang
- Department of Colorectal Surgery, Jiangsu Province Hospital of Chinese Medicine, The Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, 210029, PR China; Jiangsu Province Key Laboratory of Tumor Systems Biology and Chinese Medicine, The Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, 210029, PR China
| | - Zepeng Chen
- Department of Colorectal Surgery, Jiangsu Province Hospital of Chinese Medicine, The Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, 210029, PR China; Jiangsu Province Key Laboratory of Tumor Systems Biology and Chinese Medicine, The Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, 210029, PR China
| | - Chen Chen
- Department of Colorectal Surgery, Jiangsu Province Hospital of Chinese Medicine, The Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, 210029, PR China; Jiangsu Province Key Laboratory of Tumor Systems Biology and Chinese Medicine, The Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, 210029, PR China
| | - Xun Li
- Institute for Molecular Bioscience, the University of Queensland, Brisbane, 4702, Australia
| | - Yuji Wang
- Department of Colorectal Surgery, Jiangsu Province Hospital of Chinese Medicine, The Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, 210029, PR China; Jiangsu Province Key Laboratory of Tumor Systems Biology and Chinese Medicine, The Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, 210029, PR China
| | - Yi Shu
- Department of Colorectal Surgery, Jiangsu Province Hospital of Chinese Medicine, The Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, 210029, PR China; Jiangsu Province Key Laboratory of Tumor Systems Biology and Chinese Medicine, The Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, 210029, PR China
| | - Wei Zhang
- Department of Colorectal Surgery, Jiangsu Province Hospital of Chinese Medicine, The Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, 210029, PR China; Jiangsu Province Key Laboratory of Tumor Systems Biology and Chinese Medicine, The Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, 210029, PR China
| | - Xiaomin Yuan
- Department of Colorectal Surgery, Jiangsu Province Hospital of Chinese Medicine, The Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, 210029, PR China; Jiangsu Province Key Laboratory of Tumor Systems Biology and Chinese Medicine, The Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, 210029, PR China
| | - Guoping Shi
- Department of Colorectal Surgery, Jiangsu Province Hospital of Chinese Medicine, The Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, 210029, PR China; Jiangsu Province Key Laboratory of Tumor Systems Biology and Chinese Medicine, The Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, 210029, PR China
| | - Tuo Chen
- Jiangsu Province Key Laboratory of Tumor Systems Biology and Chinese Medicine, The Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, 210029, PR China; Department of Orthopedics, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, 210029, PR China; Department of Orthopedics, Jiangsu Province Hospital of Chinese Medicine, Nanjing 210029, PR China; Institute for Molecular Bioscience, the University of Queensland, Brisbane, 4702, Australia.
| | - Peimin Wang
- Department of Orthopedics, Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, 210029, PR China; Department of Orthopedics, Jiangsu Province Hospital of Chinese Medicine, Nanjing 210029, PR China.
| | - Yugen Chen
- Department of Colorectal Surgery, Jiangsu Province Hospital of Chinese Medicine, The Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, 210029, PR China; Jiangsu Province Key Laboratory of Tumor Systems Biology and Chinese Medicine, The Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, 210029, PR China; Jiangsu Collaborative Innovation Center of Chinese Medicine in Prevention and Treatment of Tumor, The Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing 210029, PR China.
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2
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Targeting RNA G-quadruplex with repurposed drugs blocks SARS-CoV-2 entry. PLoS Pathog 2023; 19:e1011131. [PMID: 36701392 PMCID: PMC9904497 DOI: 10.1371/journal.ppat.1011131] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 02/07/2023] [Accepted: 01/18/2023] [Indexed: 01/27/2023] Open
Abstract
The rapid emergence of SARS-CoV-2 variants of concern, the complexity of infection, and the functional redundancy of host factors, underscore an urgent need for broad-spectrum antivirals against the continuous COVID-19 pandemic, with drug repurposing as a viable therapeutic strategy. Here we report the potential of RNA G-quadruplex (RG4)-targeting therapeutic strategy for SARS-CoV-2 entry. Combining bioinformatics, biochemical and biophysical approaches, we characterize the existence of RG4s in several SARS-CoV-2 host factors. In silico screening followed by experimental validation identify Topotecan (TPT) and Berbamine (BBM), two clinical approved drugs, as RG4-stabilizing agents with repurposing potential for COVID-19. Both TPT and BBM can reduce the protein level of RG4-containing host factors, including ACE2, AXL, FURIN, and TMPRSS2. Intriguingly, TPT and BBM block SARS-CoV-2 pseudovirus entry into target cells in vitro and murine tissues in vivo. These findings emphasize the significance of RG4 in SARS-CoV-2 pathogenesis and provide a potential broad-spectrum antiviral strategy for COVID-19 prevention and treatment.
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Ribaudo G, Ongaro A, Oselladore E, Memo M, Gianoncelli A. Combining Electrospray Mass Spectrometry (ESI-MS) and Computational Techniques in the Assessment of G-Quadruplex Ligands: A Hybrid Approach to Optimize Hit Discovery. J Med Chem 2021; 64:13174-13190. [PMID: 34510895 PMCID: PMC8474113 DOI: 10.1021/acs.jmedchem.1c00962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
![]()
Guanine-rich sequences
forming G-quadruplexes (GQs) are present
in several genomes, ranging from viral to human. Given their peculiar
localization, the induction of GQ formation or GQ stabilization with
small molecules represents a strategy for interfering with crucial
biological functions. Investigating the recognition event at the molecular
level, with the aim of fully understanding the triggered pharmacological
effects, is challenging. Native electrospray ionization mass spectrometry
(ESI-MS) is being optimized to study these noncovalent assemblies.
Quantitative parameters retrieved from ESI-MS studies, such as binding
affinity, the equilibrium binding constant, and sequence selectivity,
will be overviewed. Computational experiments supporting the ESI-MS
investigation and boosting its efficiency in the search for GQ ligands
will also be discussed with practical examples. The combination of
ESI-MS and in silico techniques in a hybrid high-throughput-screening
workflow represents a valuable tool for the medicinal chemist, providing
data on the quantitative and structural aspects of ligand–GQ
interactions.
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Affiliation(s)
- Giovanni Ribaudo
- Department of Molecular and Translational Medicine, University of Brescia, Viale Europa 11, 25123 Brescia, Italy
| | - Alberto Ongaro
- Department of Molecular and Translational Medicine, University of Brescia, Viale Europa 11, 25123 Brescia, Italy
| | - Erika Oselladore
- Department of Molecular and Translational Medicine, University of Brescia, Viale Europa 11, 25123 Brescia, Italy
| | - Maurizio Memo
- Department of Molecular and Translational Medicine, University of Brescia, Viale Europa 11, 25123 Brescia, Italy
| | - Alessandra Gianoncelli
- Department of Molecular and Translational Medicine, University of Brescia, Viale Europa 11, 25123 Brescia, Italy
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Berbamine Suppresses the Progression of Bladder Cancer by Modulating the ROS/NF- κB Axis. OXIDATIVE MEDICINE AND CELLULAR LONGEVITY 2021; 2021:8851763. [PMID: 33520087 PMCID: PMC7817266 DOI: 10.1155/2021/8851763] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 11/27/2020] [Accepted: 12/22/2020] [Indexed: 01/23/2023]
Abstract
Berbamine (BBM), one of the bioactive ingredients extracted from Berberis plants, has attracted intensive attention because of its significant antitumor activity against various malignancies. However, the exact role and potential molecular mechanism of berbamine in bladder cancer (BCa) remain unclear. In the present study, our results showed that berbamine inhibited cell viability, colony formation, and proliferation. Additionally, berbamine induced cell cycle arrest at S phase by a synergistic mechanism involving stimulation of P21 and P27 protein expression as well as downregulation of CyclinD, CyclinA2, and CDK2 protein expression. In addition to suppressing epithelial-mesenchymal transition (EMT), berbamine rearranged the cytoskeleton to inhibit cell metastasis. Mechanistically, the expression of P65, P-P65, and P-IκBα was decreased upon berbamine treatment, yet P65 overexpression abrogated the effects of berbamine on the proliferative and metastatic potential of BCa cells, which indicated that berbamine attenuated the malignant biological activities of BCa cells by inhibiting the NF-κB pathway. More importantly, berbamine increased the intracellular reactive oxygen species (ROS) level through the downregulation of antioxidative genes such as Nrf2, HO-1, SOD2, and GPX-1. Following ROS accumulation, the intrinsic apoptotic pathway was triggered by an increase in the ratio of Bax/Bcl-2. Furthermore, berbamine-mediated ROS accumulation negatively regulated the NF-κB pathway to a certain degree. Consistent with our in vitro results, berbamine successfully inhibited tumor growth and blocked the NF-κB pathway in our xenograft model. To summarize, our data demonstrated that berbamine exerts antitumor effects via the ROS/NF-κB signaling axis in bladder cancer, which provides a basis for further comprehensive study and presents a potential candidate for clinical treatment strategies against bladder cancer.
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Bartas M, Brázda V, Bohálová N, Cantara A, Volná A, Stachurová T, Malachová K, Jagelská EB, Porubiaková O, Červeň J, Pečinka P. In-Depth Bioinformatic Analyses of Nidovirales Including Human SARS-CoV-2, SARS-CoV, MERS-CoV Viruses Suggest Important Roles of Non-canonical Nucleic Acid Structures in Their Lifecycles. Front Microbiol 2020; 11:1583. [PMID: 32719673 PMCID: PMC7347907 DOI: 10.3389/fmicb.2020.01583] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Accepted: 06/17/2020] [Indexed: 12/15/2022] Open
Abstract
Non-canonical nucleic acid structures play important roles in the regulation of molecular processes. Considering the importance of the ongoing coronavirus crisis, we decided to evaluate genomes of all coronaviruses sequenced to date (stated more broadly, the order Nidovirales) to determine if they contain non-canonical nucleic acid structures. We discovered much evidence of putative G-quadruplex sites and even much more of inverted repeats (IRs) loci, which in fact are ubiquitous along the whole genomic sequence and indicate a possible mechanism for genomic RNA packaging. The most notable enrichment of IRs was found inside 5'UTR for IRs of size 12+ nucleotides, and the most notable enrichment of putative quadruplex sites (PQSs) was located before 3'UTR, inside 5'UTR, and before mRNA. This indicates crucial regulatory roles for both IRs and PQSs. Moreover, we found multiple G-quadruplex binding motifs in human proteins having potential for binding of SARS-CoV-2 RNA. Non-canonical nucleic acids structures in Nidovirales and in novel SARS-CoV-2 are therefore promising druggable structures that can be targeted and utilized in the future.
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Affiliation(s)
- Martin Bartas
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czechia
| | - Václav Brázda
- Department of Biophysical Chemistry and Molecular Oncology, Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czechia
- Faculty of Chemistry, Brno University of Technology, Brno, Czechia
| | - Natália Bohálová
- Department of Biophysical Chemistry and Molecular Oncology, Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czechia
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czechia
| | - Alessio Cantara
- Department of Biophysical Chemistry and Molecular Oncology, Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czechia
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czechia
| | - Adriana Volná
- Department of Physics, Faculty of Science, University of Ostrava, Ostrava, Czechia
| | - Tereza Stachurová
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czechia
| | - Kateřina Malachová
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czechia
| | - Eva B. Jagelská
- Department of Biophysical Chemistry and Molecular Oncology, Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czechia
| | - Otília Porubiaková
- Department of Biophysical Chemistry and Molecular Oncology, Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czechia
- Faculty of Chemistry, Brno University of Technology, Brno, Czechia
| | - Jiří Červeň
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czechia
| | - Petr Pečinka
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czechia
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6
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Ongaro A, Ribaudo G, Braud E, Ethève-Quelquejeu M, De Franco M, Garbay C, Demange L, Gresh N, Zagotto G. Design and synthesis of a peptide derivative of ametantrone targeting the major groove of the d(GGCGCC) 2palindromic sequence. NEW J CHEM 2020. [DOI: 10.1039/c9nj03817e] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report the synthesis of a peptide derivative of antitumor anthraquinones, designed to target GC-rich palindromic sequences. It has micromolar activities on three cancer cell lines and is fifty times less toxic than mitoxantrone on a healthy line.
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Affiliation(s)
- Alberto Ongaro
- Department of Molecular and Translational Medicine
- Division of Pharmacology
- University of Brescia
- 25123 Brescia
- Italy
| | - Giovanni Ribaudo
- Department of Molecular and Translational Medicine
- Division of Pharmacology
- University of Brescia
- 25123 Brescia
- Italy
| | - Emmanuelle Braud
- Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques
- Team “Chemistry of RNAs, nucleosides
- peptides and heterocycles” Université de Paris
- CNRS UMR 8601
- Paris
| | - Mélanie Ethève-Quelquejeu
- Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques
- Team “Chemistry of RNAs, nucleosides
- peptides and heterocycles” Université de Paris
- CNRS UMR 8601
- Paris
| | - Michele De Franco
- Department of Pharmaceutical and Pharmacological Sciences
- University of Padova
- 35131 Padova
- Italy
| | - Christiane Garbay
- Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques
- Team “Chemistry of RNAs, nucleosides
- peptides and heterocycles” Université de Paris
- CNRS UMR 8601
- Paris
| | - Luc Demange
- Université de Paris
- CiTCoM
- UMR 8038 CNRS
- Faculté de Pharmacie
- F-75006 Paris
| | - Nohad Gresh
- Laboratoire de Chimie Théorique
- UMR 7616 CNRS
- Sorbonne Université
- Paris
- France
| | - Giuseppe Zagotto
- Department of Pharmaceutical and Pharmacological Sciences
- University of Padova
- 35131 Padova
- Italy
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7
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Jackson SN, Barbacci DC, Bonci A, Woods AS. An In Vitro Study of Aromatic Stacking of Drug Molecules. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2019; 30:1199-1203. [PMID: 30949967 PMCID: PMC7520095 DOI: 10.1007/s13361-019-02166-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 02/13/2019] [Accepted: 02/17/2019] [Indexed: 06/09/2023]
Abstract
In this paper, drug-drug chemical interactions between two different aromatic compounds were studied by mass spectrometry. Specifically, we examined non-covalent complexes (NCX) between paclitaxel, a chemotherapeutic compound, and medications widely used in palliative care for depression, psychosis, and anxiety. It is unknown whether psychotropic medications directly interact with paclitaxel. Here, we use a simple and rapid electrospray ionization mass spectrometry in vitro assay, which has been predictive in the case of neuropeptides, to measure the relative strength of non-covalent interactions. This chemical interaction is most likely due to the overlap of aromatic rings of π-orbitals between paclitaxel and five commonly used medications: diazepam, clonozepam, sertraline, fluoxetine, and haloperidol. Molecular modeling illustrates that differences in the stability of the NCXs are likely due to the distance between the aromatic rings present in both the paclitaxel and antidepressant medications. Graphical Abstract.
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Affiliation(s)
- Shelley N Jackson
- Structural Biology Unit, Integrative Neuroscience Branch, NIDA IRP, NIH, Baltimore, MD, USA
| | | | | | - Amina S Woods
- Structural Biology Unit, Integrative Neuroscience Branch, NIDA IRP, NIH, Baltimore, MD, USA.
- Structural Biology Unit, Cellular Neurobiology Branch, NIDA IRP, NIH, 333 Cassell Drive, Baltimore, MD, 21224, USA.
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8
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Li F, Guo D, Kang L. Study on the recognition of G-quadruplexes by two stereoisomers of alkaloids. Anal Bioanal Chem 2019; 411:5555-5561. [PMID: 31197422 DOI: 10.1007/s00216-019-01937-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 05/06/2019] [Accepted: 05/21/2019] [Indexed: 11/26/2022]
Abstract
G-quadruplexes have been widely researched as new targets for cancer treatment owing to their non-canonical structure and crucial role in biological processes. Although attention has been paid to the development of selective G-quadruplex ligands, few studies have focused on the binding affinity of stereoisomers towards G-quadruplex, which will be conducive to support the optimal design of G-quadruplex ligands in future studies. Here, tetrandrine and isotetrandrine were used to study the binding affinity and difference of stereoisomers towards G-quadruplex structures. The results showed that tetrandrine had a high possibility of binding to the N-myc and Bcl-2 G-quadruplexes through hydrogen bonding, whereas the possibility of binding of isotetrandrine was low and it seemed to have no possibility of forming hydrogen bonds. Our study shows that optical isomerism of ligand molecules has an important effect on G-quadruplex recognition, which is helpful for the design of G-quadruplex ligands in future studies. Graphical abstract.
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Affiliation(s)
- Fangyuan Li
- Central Research Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China.
| | - Dan Guo
- Central Research Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
| | - Lin Kang
- Central Research Laboratory, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China
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9
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Ribaudo G, Ongaro A, Zorzan M, Pezzani R, Redaelli M, Zagotto G, Memo M, Gianoncelli A. Investigation of the molecular reactivity of bioactive oxiranylmethyloxy anthraquinones. Arch Pharm (Weinheim) 2019; 352:e1900030. [DOI: 10.1002/ardp.201900030] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Revised: 03/22/2019] [Accepted: 03/25/2019] [Indexed: 01/09/2023]
Affiliation(s)
- Giovanni Ribaudo
- Department of Pharmaceutical and Pharmacological SciencesUniversity of PadovaPadova Italy
| | - Alberto Ongaro
- Department of Molecular and Translational MedicineUniversity of BresciaBrescia Italy
| | - Maira Zorzan
- Department of Molecular Medicine (DMM)University of PadovaPadova Italy
| | | | - Marco Redaelli
- Department of Pharmaceutical and Pharmacological SciencesUniversity of PadovaPadova Italy
| | - Giuseppe Zagotto
- Department of Pharmaceutical and Pharmacological SciencesUniversity of PadovaPadova Italy
| | - Maurizio Memo
- Department of Molecular and Translational MedicineUniversity of BresciaBrescia Italy
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10
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Fu H, Yang P, Hai J, Li H. Utilization of circular dichroism and electrospray ionization mass spectrometry to understand the formation and conversion of G-quadruplex DNA at the human c-myb proto-oncogene. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2018; 203:70-76. [PMID: 29860170 DOI: 10.1016/j.saa.2018.05.079] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2017] [Revised: 05/25/2018] [Accepted: 05/26/2018] [Indexed: 06/08/2023]
Abstract
G-quadruplex DNAs are involved in a number of key biological processes, including gene expression, transcription, and apoptosis. The c-myb oncogene contains a number of GGA repeats in its promoter which forms G-quadruplex, thus it could be used as a target in cancer therapeutics. Several in-vitro studies have used Circular Dichroism (CD) spectroscopy or electrospray ionization mass spectrometry (ESI-MS) to demonstrate formation and stability of G-quadruplex DNA structure in the promoter region of human c-myb oncogene. The factors affecting the c-myb G-quadruplex structures were investigated, such as cations (i.e. K+, NH4+ and Na+) and co-solutes (methanol and polyethylene glycol). The results indicated that the presence of cations and co-solutes could change the G-quadruplex structural population and promote its thermodynamic stabilization as indicated by CD melting curves. It indicated that the co-solutes preferentially stabilize the c-myb G-quadruplex structure containing both homo- and hetero-stacking. In addition, protopine was demonstrated as a binder of c-myb G-quadruplex as screened from a library of natural alkaloids using ESI-MS method. CD spectra showed that it could selectively stabilize the c-myb G-quadruplex structure compared to other six G-quadruplexes from tumor-related G-rich sequences and the duplex DNAs (both long and short-chain ones). The binding of protopine could induce the change in the G-quadruplex structural populations. Therefore, protopine with its high binding specificity could be considered as a precursor for the design of drugs to target and regulate c-myb oncogene transcription.
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Affiliation(s)
- Hengqing Fu
- National and Local Joint Engineering Research Center of Biomedical Functional Materials, Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, School of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210023, PR China
| | - Pengfei Yang
- National and Local Joint Engineering Research Center of Biomedical Functional Materials, Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, School of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210023, PR China
| | - Jinhui Hai
- National and Local Joint Engineering Research Center of Biomedical Functional Materials, Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, School of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210023, PR China
| | - Huihui Li
- National and Local Joint Engineering Research Center of Biomedical Functional Materials, Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, School of Chemistry and Materials Science, Nanjing Normal University, Nanjing 210023, PR China.
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Cao Y, Cao J, Yu B, Wang S, Liu L, Tao L, Sun W. Berbamine induces SMMC-7721 cell apoptosis via upregulating p53, downregulating survivin expression and activating mitochondria signaling pathway. Exp Ther Med 2017; 15:1894-1901. [PMID: 29434780 PMCID: PMC5776608 DOI: 10.3892/etm.2017.5637] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Accepted: 11/22/2017] [Indexed: 12/20/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is a primary malignancy in the liver, which is a global health problem. The present study aimed to observe the apoptotic effects of berbamine on SMMC-7721 cell lines and to investigate the effects of berbamine on induction of the intrinsic apoptotic pathway. The human HCC SMMC-7721 cells were cultured and cell morphology observed using a phase contrast microscope. SMMC-7721 cell apoptosis was examined by employing a flow cytometry assay. The nuclei of SMMC-7721 cells were stained with DAPI and observed by utilizing a laser fluorescence microscope. Cytochrome c (Cyto c) levels were evaluated by using immunofluorescence staining. The reverse transcription-semi-quantitative polymerase chain reaction (RT-sqPCR) and western blot analysis were used to examine the mRNA and protein levels of B-cell lymphoma 2, (Bcl-2), Bax, Bcl-2-associated X, apoptosis regulator, p53 and survivin, respectively. Berbamine inhibited SMMC-7721 cell growth at 20 and 0 µmol/l, compared with control group (0 µmol/l berbamine). DAPI results demonstrated that berbamine affected the nucleus morphology of SMMC-7721 cells. Berbamine at a concentration of 20 µmol/l (P<0.05) and 40 µmol/l (P<0.01) significantly enhanced apoptosis rate compared with control group. Berbamine triggered Cyto c release from SMMC-7721 cell nuclei to the cytoplasm. Berbamine (10, 20, 40 µmol/l) significantly enhanced Bax and p53 levels and decreased Bcl-2 and survivin levels compared with control group, according to RT-sqPCR and western blot assay findings. In conclusion, berbamine induced SMMC-7721 cell apoptosis, through upregulating p53 expression and downregulating survivin expression, which further triggered mitochondria signaling pathway-mediated apoptosis.
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Affiliation(s)
- Ying Cao
- Department of Pharmacy, Zhangjiagang Hospital Affiliated to Soochow University, Zhangjiagang, Jiangsu 215600, P.R. China
| | - Jianbo Cao
- Department of Pharmacy, Zhangjiagang Hospital Affiliated to Soochow University, Zhangjiagang, Jiangsu 215600, P.R. China
| | - Binbin Yu
- Department of Pharmacy, Zhangjiagang Hospital Affiliated to Soochow University, Zhangjiagang, Jiangsu 215600, P.R. China
| | - Shusheng Wang
- Department of Surgery, Zhangjiagang Hospital Affiliated to Soochow University, Zhangjiagang, Jiangsu 215600, P.R. China
| | - Lili Liu
- Department of Pharmacy, Zhangjiagang Hospital Affiliated to Soochow University, Zhangjiagang, Jiangsu 215600, P.R. China
| | - Li Tao
- Department of Pharmacy, Zhangjiagang Hospital Affiliated to Soochow University, Zhangjiagang, Jiangsu 215600, P.R. China
| | - Wanping Sun
- Laboratory of Molecular Diagnostics, College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu 215123, P.R. China
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12
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Zhang L, Tan W, Zhou J, Xu M, Yuan G. Investigation of G-quadruplex formation in the FGFR2 promoter region and its transcriptional regulation by liensinine. Biochim Biophys Acta Gen Subj 2017; 1861:884-891. [PMID: 28132898 DOI: 10.1016/j.bbagen.2017.01.028] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Revised: 01/21/2017] [Accepted: 01/25/2017] [Indexed: 01/09/2023]
Abstract
BACKGROUND Fibroblast growth factor receptor 2 (FGFR2) is overexpressed in breast cancer tissues and cells, and has been shown to be a susceptibility factor for breast cancer. In this study, we found that the G-rich sequences in the FGFR2 promoter region can form G-quadruplexes, which could be the target and inhibitor of the FGFR2 gene. METHODS Initially, the formation of G-quadruplexes was confirmed by ESI-MS and CD, and DMS footprinting experiments gave the folding pattern of the G-quadruplexes. After luciferase reporter assays revealed that the G-quadruplex could inhibit the activity of the FGFR2 promoter, MS and SPR showed binding affinity and selectivity of the ligand. Then cell culture experiments and ChIP assay showed the bioactivity of the ligand. RESULTS We found that three G-rich sequences (S1-S3) in the FGFR2 promoter region can form G-quadruplex structures. And a natural alkaloid, liensinine, was found to bind to the S1 G-quadruplex with relative high affinity and selectivity. Cell culture experiments showed that liensinine inhibits FGFR2 activity at both the transcriptional and translational levels. Moreover, chromatin immunoprecipitation assay (ChIP) results showed that liensinine blocks the binding of E2F1 at the transcription factor binding site (TFBS) in the S1 sequence, which is the mechanism through which liensinine inhibits the FGFR2 gene. CONCLUSIONS A natural alkaloid was discovered to selectively bind to the S1 G-quadruplex with relative high affinity, and therefore inhibited FGFR2 transcription and translation. GENERAL SIGNIFICANCE Our discovery offers a useful strategy to inhibit FGFR2 transcription, i.e., targeting the G-quadruplex with a natural alkaloid.
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Affiliation(s)
- Lulu Zhang
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Department of Chemical Biology, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Wei Tan
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Department of Chemical Biology, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Jiang Zhou
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Department of Chemical Biology, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China; Analytical Instrumentation Center, Peking University, Beijing 100871, China.
| | - Ming Xu
- Institute of Vascular Medicine, Department of Cardiology, Peking University Third Hospital, Key Laboratory of Molecular Cardiovascular Sciences of Ministry of Education, Beijing 100191, China.
| | - Gu Yuan
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Department of Chemical Biology, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China.
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13
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Targeting human telomeric and c-myc G-quadruplexes with alkynylplatinum(II) terpyridine complexes under molecular crowding conditions. J Inorg Biochem 2016; 166:126-134. [PMID: 27852004 DOI: 10.1016/j.jinorgbio.2016.11.012] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2016] [Revised: 11/05/2016] [Accepted: 11/08/2016] [Indexed: 12/27/2022]
Abstract
The interactions between alkynylplatinum(II) terpyridine complexes 1-3 and the G-quadruplex DNA, including c-myc and telomeric quadruplex DNA, are investigated both in dilute solution and under molecular crowding conditions. The UV-vis absorption spectroscopy, circular dichroism and molecular docking studies suggest that 1-3 associate with telomeric and c-myc G-quadruplexes via groove binding, and electrostatic interactions. Experimental studies indicate that under molecular crowding conditions (in the presence of 40wt% PEG 200), 1-2 show weak affinity for c-myc, while 3 still displays high affinity and selectivity for c-myc. On the other hand, 1-3 act as efficient and selective ligand for telomeric quadruplex DNA under molecular crowding conditions. The complex 3 exhibits excellent cytotoxicity against A549, K562 and SGC-7901, with IC50 values that are 35.0-fold, 10.0-fold, and 12.1-fold lower than the values of cisplatin under the same conditions, respectively.
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14
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Berbamine inhibited the growth of prostate cancer cells in vivo and in vitro via triggering intrinsic pathway of apoptosis. Prostate Cancer Prostatic Dis 2016; 19:358-366. [DOI: 10.1038/pcan.2016.29] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Revised: 05/28/2016] [Accepted: 06/07/2016] [Indexed: 12/14/2022]
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15
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Li H, Hai J, Zhou J, Yuan G. Exploration of binding affinity and selectivity of brucine with G-quadruplex in the c-myb proto-oncogene by electrospray ionization mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2016; 30:407-414. [PMID: 26754134 DOI: 10.1002/rcm.7454] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2015] [Revised: 11/07/2015] [Accepted: 11/09/2015] [Indexed: 06/05/2023]
Abstract
RATIONALE The c-myb gene is a potential therapeutic target for human tumors and leukemias. Active ingredients from natural products may be used as drugs in chemotherapy for human cancers. Here, electrospray ionization mass spectrometry (ESI-MS) was used to probe the formation and recognition of the G-quadruplex structure from the G-rich sequence that is found in the c-myb gene promoter, 5'-GGGCTGGGCTGGGCGGGG-3'. The aim of our study is to evaluate a potential binder for the c-myb gene from natural products, and thereby to modulate c-myb gene expression. METHODS ESI-MS, as an effective method, was utilized not only to characterize the formation of the G-quadruplex in the c-myb oncogene, but also as a tool to probe the binding characteristics of alkaloid molecules with the target G-quadruplex DNA. RESULTS ESI-MS results with the support of circular dichroism (CD) spectra demonstrated the formation of an intramolecular parallel-stranded G-quadruplex in the c-myb oncogene promoter. A screening of six alkaloid molecules showed that brucine (P1) had a strong binding affinity to the c-myb G-quadruplex DNA. It is notable that P1 can bind selectively to the c-myb G-quadruplex with respect to duplex DNAs, as well as to G-quadruplexes in other types of gene sequences. According to ESI-MS results, in which the stability was tested by capillary heating and collision-induced dissociation, the binding of P1 could thermally stabilize the c-myb G-quadruplex DNA. CONCLUSIONS In this work, brucine (P1), an alkaloid molecule, has been found to bind to the intramolecular parallel G-quadruplex in the c-myb oncogene promoter with high affinity and selectivity, and could thermally stabilize the c-myb G-quadruplex DNA, indicating that the binding of P1 has the potential to modulate c-myb gene expression. Copyright © 2015 John Wiley & Sons, Ltd.
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Affiliation(s)
- Huihui Li
- National and Local Joint Engineering Research Center of Biomedical Functional Materials, Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, College of Chemistry and Materials Science, Nanjing Normal University, Nanjing, 210023, China
| | - Jinhui Hai
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Department of Chemical Biology, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
- National and Local Joint Engineering Research Center of Biomedical Functional Materials, Jiangsu Collaborative Innovation Center of Biomedical Functional Materials, College of Chemistry and Materials Science, Nanjing Normal University, Nanjing, 210023, China
| | - Jiang Zhou
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Department of Chemical Biology, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
| | - Gu Yuan
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Department of Chemical Biology, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
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16
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Ou Z, Qian Y, Gao Y, Wang Y, Yang G, Li Y, Jiang K, Wang X. Photophysical, G-quadruplex DNA binding and cytotoxic properties of terpyridine complexes with a naphthalimide ligand. RSC Adv 2016. [DOI: 10.1039/c6ra01441k] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The complex3inhibits A549 cells selectively over non-cancerous NIH3T3 cells, which may correlate with its selective G-quadruplex binding and nuclear location.
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Affiliation(s)
- Zhize Ou
- The Key Laboratory of Space Applied Physics and Chemistry
- Ministry of Education
- Department of Applied Chemistry
- School of Science
- Northwestern Polytechnical University
| | - Yimeng Qian
- The Key Laboratory of Space Applied Physics and Chemistry
- Ministry of Education
- Department of Applied Chemistry
- School of Science
- Northwestern Polytechnical University
| | - Yunyan Gao
- The Key Laboratory of Space Applied Physics and Chemistry
- Ministry of Education
- Department of Applied Chemistry
- School of Science
- Northwestern Polytechnical University
| | - Yunqing Wang
- The Key Laboratory of Space Applied Physics and Chemistry
- Ministry of Education
- Department of Applied Chemistry
- School of Science
- Northwestern Polytechnical University
| | - Guoqiang Yang
- CAS Key Laboratory of Photochemistry
- Institute of Chemistry
- Chinese Academy of Sciences
- Beijing 100190
- People's Republic of China
| | - Yi Li
- Key Laboratory of Photochemical Convesion and Optoelectronic Material
- Technical Institute of Physics and Chemistry
- Chinese Academy of Sciences
- Beijing
- People's Republic of China
| | - Kaiyue Jiang
- The Key Laboratory of Space Applied Physics and Chemistry
- Ministry of Education
- Department of Applied Chemistry
- School of Science
- Northwestern Polytechnical University
| | - Xin Wang
- The Key Laboratory of Space Applied Physics and Chemistry
- Ministry of Education
- Department of Applied Chemistry
- School of Science
- Northwestern Polytechnical University
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Perrone R, Doria F, Butovskaya E, Frasson I, Botti S, Scalabrin M, Lago S, Grande V, Nadai M, Freccero M, Richter SN. Synthesis, Binding and Antiviral Properties of Potent Core-Extended Naphthalene Diimides Targeting the HIV-1 Long Terminal Repeat Promoter G-Quadruplexes. J Med Chem 2015; 58:9639-52. [PMID: 26599611 PMCID: PMC4690987 DOI: 10.1021/acs.jmedchem.5b01283] [Citation(s) in RCA: 81] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
![]()
We have previously reported that
stabilization of the G-quadruplex
structures in the HIV-1 long terminal repeat (LTR) promoter suppresses
viral transcription. Here we sought to develop new G-quadruplex ligands
to be exploited as antiviral compounds by enhancing binding toward
the viral G-quadruplex structures. We synthesized naphthalene diimide
derivatives with a lateral expansion of the aromatic core. The new
compounds were able to bind/stabilize the G-quadruplex to a high extent,
and some of them displayed clear-cut selectivity toward the viral
G-quadruplexes with respect to the human telomeric G-quadruplexes.
This feature translated into low nanomolar anti-HIV-1 activity toward
two viral strains and encouraging selectivity indexes. The selectivity
depended on specific recognition of LTR loop residues; the mechanism
of action was ascribed to inhibition of LTR promoter activity in cells.
This is the first example of G-quadruplex ligands that show increased
selectivity toward the viral G-quadruplexes and display remarkable
antiviral activity.
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Affiliation(s)
- Rosalba Perrone
- Department of Molecular Medicine, University of Padua , via Gabelli 63, 35121 Padua, Italy
| | - Filippo Doria
- Department of Chemistry, University of Pavia , V.le Taramelli 10, 27100 Pavia, Italy
| | - Elena Butovskaya
- Department of Molecular Medicine, University of Padua , via Gabelli 63, 35121 Padua, Italy
| | - Ilaria Frasson
- Department of Molecular Medicine, University of Padua , via Gabelli 63, 35121 Padua, Italy
| | - Silvia Botti
- Department of Chemistry, University of Pavia , V.le Taramelli 10, 27100 Pavia, Italy
| | - Matteo Scalabrin
- Department of Molecular Medicine, University of Padua , via Gabelli 63, 35121 Padua, Italy
| | - Sara Lago
- Department of Molecular Medicine, University of Padua , via Gabelli 63, 35121 Padua, Italy
| | - Vincenzo Grande
- Department of Chemistry, University of Pavia , V.le Taramelli 10, 27100 Pavia, Italy
| | - Matteo Nadai
- Department of Molecular Medicine, University of Padua , via Gabelli 63, 35121 Padua, Italy
| | - Mauro Freccero
- Department of Chemistry, University of Pavia , V.le Taramelli 10, 27100 Pavia, Italy
| | - Sara N Richter
- Department of Molecular Medicine, University of Padua , via Gabelli 63, 35121 Padua, Italy
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18
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Li F, Chen H, Zhou J, Yuan G. Exploration of the selective recognition of the G-quadruplex in the N-myc oncogene by electrospray ionization mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2015; 29:247-252. [PMID: 26411622 DOI: 10.1002/rcm.7101] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Revised: 10/29/2014] [Accepted: 11/17/2014] [Indexed: 06/05/2023]
Abstract
RATIONALE The N-myc gene is a member of the MYC family and its amplification is highly correlated with the pathophysiology of cancers. The G-rich sequence, d(AG3CG3AG3AG3A), in the first intron of N-myc can form a G-quadruplex structure. Small molecules binding to it with high affinity and selectivity may provide a potential approach to modulate the expression of the N-myc gene. METHODS Electrospray ionization (ESI) mass spectrometry was used to analyze the G-quadruplex formation of the d(AG3CG3AG3AG3A) sequence, and to evaluate the binding affinities and selectivities of natural small molecules with the N-myc G-quadruplex. RESULTS Enniatin B was found to have the highest binding affinity with this G-quadruplex within the 12 small molecules. Moreover, it also showed a biased selectivity toward the N-myc G-quadruplex compared with the other five G-quadruplexes derived from C-myc, Bcl2, Chl1, c-kit promoters and telomere G-rich sequences. CONCLUSIONS In this study, we found a natural small molecule, enniatin B, which could bind to the G-quadruplex of the d(AG3CG3AG3AG3A) sequence from the first intron of the N-myc gene with high affinity and selectivity, which may lead to a potential modulation of the N-myc gene.
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Affiliation(s)
- Fangyuan Li
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Department of Chemical Biology, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
| | - Han Chen
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Department of Chemical Biology, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
| | - Jiang Zhou
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Department of Chemical Biology, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
| | - Gu Yuan
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Department of Chemical Biology, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
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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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