1
|
Yin J, Wu S, Yang Y, Wang D, Ma Y, Zhao Y, Sheth S, Huang H, Song B, Chen Z. In Addition to Damaging the Plasma Membrane, Phenolic Monoterpenoid Carvacrol Can Bind to the Minor Groove of DNA of Phytopathogenic Fungi to Potentially Control Tea Leaf Spot Caused by Lasiodiplodia theobromae. PHYTOPATHOLOGY 2024; 114:700-716. [PMID: 37856707 DOI: 10.1094/phyto-07-23-0263-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2023]
Abstract
Carvacrol expresses a wide range of biological activities, but the studies of its mechanisms focused on bacteria, mainly involving the destruction of the plasma membrane. In this study, carvacrol exhibited strong activities against several phytopathogenic fungi and demonstrated a novel antifungal mechanism against Lasiodiplodia theobromae. RNA sequencing indicated that many genes of L. theobromae hyphae were predominately induced by carvacrol, particularly those involved in replication and transcription. Hyperchromic, hypsochromic, and bathochromic effects in the UV-visible absorption spectrum were observed following titration of calf thymus DNA (ctDNA) and carvacrol, which indicated the formation of a DNA-carvacrol complex. Circular dichroism (CD) spectroscopy indicated that the response of DNA to carvacrol was similar to that of 4',6-diamidino-2-phenylindole (DAPI) but different from that of ethidium bromide (EB), implying the ionic bonds between carvacrol and ctDNA. Fluorescence spectrum (FS) analysis indicated that carvacrol quenched the fluorescence of double-stranded DNA (dsDNA) more than single-stranded DNA, indicating that carvacrol mainly bound to dsDNA. A displacement assay showed that carvacrol reduced the fluorescence intensity of the DNA-DAPI complex through competition with DAPI, but this did not occur for DNA-EB. The FS assay revealed that carvacrol bound to the AAA sequence on the minor groove of ds-oligonucleotides. The hydroxyl of carvacrol was verified to bind to ctDNA through a comparative test in which structural analogs of carvacrol, including thymol and 4-ethyl-1,2-dimethyl, were analyzed. The current study indicated carvacrol can destruct plasma membranes and bind to the minor groove of DNA, inhibiting fungal proliferation by disturbing the stability of dsDNA.
Collapse
Affiliation(s)
- Jiayu Yin
- National Key Laboratory of Green Pesticide, Guiyang, Guizhou 550025, China
- Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang, Guizhou 550025, China
| | - Shuang Wu
- National Key Laboratory of Green Pesticide, Guiyang, Guizhou 550025, China
- Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang, Guizhou 550025, China
| | - Yongli Yang
- National Key Laboratory of Green Pesticide, Guiyang, Guizhou 550025, China
- Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang, Guizhou 550025, China
| | - Delu Wang
- College of Forestry, Guizhou University, Guiyang, Guizhou 550025, China
| | - Yue Ma
- National Key Laboratory of Green Pesticide, Guiyang, Guizhou 550025, China
- Institute of Crop Protection, Guizhou University, Guiyang 550025, China
| | - Yongtian Zhao
- National Key Laboratory of Green Pesticide, Guiyang, Guizhou 550025, China
- School of Life Science and Agriculture, Qiannan Normal University for Nationalities, Duyun 558000, Guizhou, China
| | - Sujitraj Sheth
- National Key Laboratory of Green Pesticide, Guiyang, Guizhou 550025, China
| | - Honglin Huang
- National Key Laboratory of Green Pesticide, Guiyang, Guizhou 550025, China
- Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang, Guizhou 550025, China
| | - Baoan Song
- National Key Laboratory of Green Pesticide, Guiyang, Guizhou 550025, China
- Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang, Guizhou 550025, China
| | - Zhuo Chen
- National Key Laboratory of Green Pesticide, Guiyang, Guizhou 550025, China
- Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Guizhou University, Guiyang, Guizhou 550025, China
| |
Collapse
|
2
|
Viushkov VS, Lomov NA, Rubtsov MA, Vassetzky YS. Visualizing the Genome: Experimental Approaches for Live-Cell Chromatin Imaging. Cells 2022; 11:cells11244086. [PMID: 36552850 PMCID: PMC9776900 DOI: 10.3390/cells11244086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 12/07/2022] [Accepted: 12/13/2022] [Indexed: 12/24/2022] Open
Abstract
Over the years, our vision of the genome has changed from a linear molecule to that of a complex 3D structure that follows specific patterns and possesses a hierarchical organization. Currently, genomics is becoming "four-dimensional": our attention is increasingly focused on the study of chromatin dynamics over time, in the fourth dimension. Recent methods for visualizing the movements of chromatin loci in living cells by targeting fluorescent proteins can be divided into two groups. The first group requires the insertion of a special sequence into the locus of interest, to which proteins that recognize the sequence are recruited (e.g., FROS and ParB-INT methods). In the methods of the second approach, "programmed" proteins are targeted to the locus of interest (i.e., systems based on CRISPR/Cas, TALE, and zinc finger proteins). In the present review, we discuss these approaches, examine their strengths and weaknesses, and identify the key scientific problems that can be studied using these methods.
Collapse
Affiliation(s)
- Vladimir S. Viushkov
- Department of Molecular Biology, Faculty of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Nikolai A. Lomov
- Department of Molecular Biology, Faculty of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Mikhail A. Rubtsov
- Department of Molecular Biology, Faculty of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
- Department of Biochemistry, Center for Industrial Technologies and Entrepreneurship, I.M. Sechenov First Moscow State Medical University (Sechenov University), 119435 Moscow, Russia
| | - Yegor S. Vassetzky
- CNRS UMR9018, Université Paris-Saclay, Gustave Roussy, 94805 Villejuif, France
- Koltzov Institute of Developmental Biology, Russian Academy of Sciences, 119334 Moscow, Russia
- Correspondence:
| |
Collapse
|
3
|
RNA-targeted drug discovery: moving beyond promiscuous small-molecule scaffolds. Future Med Chem 2020; 11:2487-2490. [PMID: 31633403 DOI: 10.4155/fmc-2019-0200] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
|
4
|
Grosch M, Ittermann S, Rusha E, Greisle T, Ori C, Truong DJJ, O'Neill AC, Pertek A, Westmeyer GG, Drukker M. Nucleus size and DNA accessibility are linked to the regulation of paraspeckle formation in cellular differentiation. BMC Biol 2020; 18:42. [PMID: 32321486 PMCID: PMC7178590 DOI: 10.1186/s12915-020-00770-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 03/16/2020] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Many long noncoding RNAs (lncRNAs) have been implicated in general and cell type-specific molecular regulation. Here, we asked what underlies the fundamental basis for the seemingly random appearance of nuclear lncRNA condensates in cells, and we sought compounds that can promote the disintegration of lncRNA condensates in vivo. RESULTS As a basis for comparing lncRNAs and cellular properties among different cell types, we screened lncRNAs in human pluripotent stem cells (hPSCs) that were differentiated to an atlas of cell lineages. We found that paraspeckles, which form by aggregation of the lncRNA NEAT1, are scaled by the size of the nucleus, and that small DNA-binding molecules promote the disintegration of paraspeckles and other lncRNA condensates. Furthermore, we found that paraspeckles regulate the differentiation of hPSCs. CONCLUSIONS Positive correlation between the size of the nucleus and the number of paraspeckles exist in numerous types of human cells. The tethering and structure of paraspeckles, as well as other lncRNAs, to the genome can be disrupted by small molecules that intercalate in DNA. The structure-function relationship of lncRNAs that regulates stem cell differentiation is likely to be determined by the dynamics of nucleus size and binding site accessibility.
Collapse
Affiliation(s)
- Markus Grosch
- Institute of Stem Cell Research (ISF), Helmholtz Zentrum München, Neuherberg, Germany
| | - Sebastian Ittermann
- Institute of Stem Cell Research (ISF), Helmholtz Zentrum München, Neuherberg, Germany
| | - Ejona Rusha
- Institute of Stem Cell Research (ISF), iPSC Core Facility, Helmholtz Zentrum München, Neuherberg, Germany
| | - Tobias Greisle
- Institute of Stem Cell Research (ISF), Helmholtz Zentrum München, Neuherberg, Germany
| | - Chaido Ori
- Institute of Stem Cell Research (ISF), Helmholtz Zentrum München, Neuherberg, Germany.,Comprehensive Pneumology Center (CPC), Helmholtz Zentrum München, Member of the German Center for Lung Research (DZL), Munich, Germany
| | | | - Adam C O'Neill
- Institute of Stem Cell Research (ISF), Helmholtz Zentrum München, Neuherberg, Germany
| | - Anna Pertek
- Institute of Stem Cell Research (ISF), iPSC Core Facility, Helmholtz Zentrum München, Neuherberg, Germany
| | - Gil Gregor Westmeyer
- Institute of Biological and Medical Imaging (IBMI), Helmholtz Zentrum München, Neuherberg, Germany
| | - Micha Drukker
- Institute of Stem Cell Research (ISF), Helmholtz Zentrum München, Neuherberg, Germany. .,Institute of Stem Cell Research (ISF), iPSC Core Facility, Helmholtz Zentrum München, Neuherberg, Germany.
| |
Collapse
|
5
|
Hassan AA, Aly AA, Mohamed NK, El Shaieb KM, Makhlouf MM, Abdelhafez ESMN, Bräse S, Nieger M, Dalby KN, Kaoud TS. Design, synthesis, and DNA interaction studies of furo-imidazo[3.3.3]propellane derivatives: Potential anticancer agents. Bioorg Chem 2019; 85:585-599. [PMID: 30878891 PMCID: PMC6543821 DOI: 10.1016/j.bioorg.2019.02.027] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Revised: 02/10/2019] [Accepted: 02/11/2019] [Indexed: 11/26/2022]
Abstract
A large number of natural products containing the propellane scaffold have been reported to exhibit cytotoxicity against several cancers; however, their mechanism of action is still unknown. Anticancer drugs targeting DNA are mainly composed of small planar molecule/s that can interact with the DNA helix, causing DNA malfunction and cell death. The aim of this study was to design and synthesize propellane derivatives that can act as DNA intercalators and/or groove binders. The unique structure of the propellane derivatives and their ability to display planar ligands with numerous possible geometries, renders them potential starting points to design new drugs targeting DNA in cancer cells. New substituted furo-imidazo[3.3.3]propellanes were synthesized via the reaction of substituted alkenylidene-hydrazinecarbothioamides with 2-(1,3-dioxo-2,3-dihydro-1H-2-ylidene)propanedinitrile in tetrahydrofuran at room temperature. The structures of the products were confirmed by a combination of elemental analysis, NMR, ESI-MS, IR and single crystal X-ray analysis. Interestingly, 5c, 5d and 5f showed an ability to interact with Calf Thymus DNA (CT-DNA). Their DNA-binding mode was investigated using a combination of absorption spectroscopy, DNA melting, viscosity, CD spectroscopy measurements, as well as competitive binding studies with several dyes. Their cytotoxicity was evaluated against the NCI-60 panel of cancer cell lines. 5c, 5d and 5f exhibited similar anti-proliferative activity against the A549 non-small cell lung cancer (NSCLC) cell line. Further mechanistic studies revealed their ability to induce DNA damage in the A549 cell line, as well as apoptosis, evidenced by elevated Annexin V expression, enhanced caspase 3/7 activation and PARP cleavage. In this study, we present the potential for designing novel propellanes to provoke cytotoxic activity, likely through DNA binding-induced DNA damage and apoptosis.
Collapse
Affiliation(s)
- Alaa A Hassan
- Chemistry Department, Faculty of Science, Minia University, El-Minia 61519, Egypt.
| | - Ashraf A Aly
- Chemistry Department, Faculty of Science, Minia University, El-Minia 61519, Egypt
| | - Nasr K Mohamed
- Chemistry Department, Faculty of Science, Minia University, El-Minia 61519, Egypt
| | - Kamal M El Shaieb
- Chemistry Department, Faculty of Science, Minia University, El-Minia 61519, Egypt
| | - Maysa M Makhlouf
- Chemistry Department, Faculty of Science, Minia University, El-Minia 61519, Egypt
| | | | - Stefan Bräse
- Institute of Organic Chemistry, Karlsruhe Institute of Technology, Fritz-Haber-Weg 6, Karlsruhe 76131, Germany; Institute of Toxicology and Genetics, Hermann-von-Helmholtz-Platz 1, D-76344 Eggenstein-Leopoldshafen, Germany
| | - Martin Nieger
- Department of Chemistry, University of Helsinki, P.O. Box 55, A.I. Virtasen aukio I, Helsinki 00014, Finland
| | - Kevin N Dalby
- Division of Chemical Biology and Medicinal Chemistry, The University of Texas at Austin, Austin, TX 78712, USA
| | - Tamer S Kaoud
- Department of Medicinal Chemistry, Faculty of Pharmacy, Minia University, El-Minia 61519, Egypt; Division of Chemical Biology and Medicinal Chemistry, The University of Texas at Austin, Austin, TX 78712, USA.
| |
Collapse
|
6
|
Klimova RR, Momotyuk ED, Demidova NA, Chernoryzh YY, Koval VS, Ivanov AA, Zhuze AL, Kushch AA. [Dimeric bisbenzimidazoles suppress the herpes simplex virus and human cytomegalovirus infections in cell сultures]. Vopr Virusol 2018; 62:162-168. [PMID: 29733165 DOI: 10.18821/0507-4088-2017-62-4-162-168] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Accepted: 02/28/2017] [Indexed: 11/17/2022]
Abstract
Antiviral activity of new AТ-specific fluorescent symmetric dimeric bisbenzimidazoles of DBА(n) series was assessed in the cell models of infections caused by type 1 herpes simplex virus (HSV1) and human cytomegalovirus (CMV). In DBA(n) molecules bisbenzimidazole fragments are bound to an oligomethylene liner with varied number of methylene groups in the linker (n = 1, 3, 5, 7, 9, 11). In contrast to DB(n) dimeric bisbenzimidazoles, in DBA(n) series terminal fragments of macromolecules contain N-dimethylaminopropylcarboxamide groups instead of N-methylpiperazine groups. DBА(n) compounds better dissolve in water, pass across plasma and nuclear membrane, and stain DNA in living cells. DBA(1) and DBA(7) produced therapeutic effects in HSV1 infection; DBA(7) completely suppressed the infection. DBA(11) displayed in vitro therapeutic activity in HSV1 and CMV infections. In addition, DBA(7) and DBA(1) showed microbicidal activity. Thus, DBA(11), which is active against two viruses causing severe diseases with serious health consequences for immunodeficient individuals, should be further investigated. High antiviral activity of DBA(7) in all test models indicates that this compound is a promising active agent for innovative antiviral drugs.
Collapse
Affiliation(s)
- R R Klimova
- D.I. Ivanovsky Institute of Virology «Federal Research Center of Epidemiology and Microbiology named after the honorary academician N.F. Gamaleya», Moscow, 123098, Russian Federation
| | - E D Momotyuk
- D.I. Ivanovsky Institute of Virology «Federal Research Center of Epidemiology and Microbiology named after the honorary academician N.F. Gamaleya», Moscow, 123098, Russian Federation.,Skryabin Moscow State Academy of Veterinary Medicine and Biotechnology, Moscow, 109473, Russian Federation
| | - N A Demidova
- Skryabin Moscow State Academy of Veterinary Medicine and Biotechnology, Moscow, 109473, Russian Federation
| | - Ya Yu Chernoryzh
- D.I. Ivanovsky Institute of Virology «Federal Research Center of Epidemiology and Microbiology named after the honorary academician N.F. Gamaleya», Moscow, 123098, Russian Federation
| | - V S Koval
- Engelhardt Institute of Molecular Biology, Moscow, 119991, Russian Federation.,Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Moscow, 117997, Russian Federation
| | - A A Ivanov
- Blokhin Russian Cancer Research Center, Research Institute of Carcinogenesis, Moscow, 115478, Russian Federation
| | - A L Zhuze
- Engelhardt Institute of Molecular Biology, Moscow, 119991, Russian Federation
| | - A A Kushch
- D.I. Ivanovsky Institute of Virology «Federal Research Center of Epidemiology and Microbiology named after the honorary academician N.F. Gamaleya», Moscow, 123098, Russian Federation
| |
Collapse
|
7
|
Ji L, Yang S, Li S, Liu S, Tang S, Liu Z, Meng X, Yu S. A novel triazolonaphthalimide induces apoptosis and inhibits tumor growth by targeting DNA and DNA-associated processes. Oncotarget 2018; 8:37394-37408. [PMID: 28445124 PMCID: PMC5514917 DOI: 10.18632/oncotarget.16962] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Accepted: 03/27/2017] [Indexed: 12/28/2022] Open
Abstract
DNA and DNA-associated processes have been classes of the most important targets of chemotherapeutic drugs. As classic DNA intercalators and topoisomerase inhibitors, naphthalimides have been extensively investigated as potential anti-cancer drugs. We recently synthesized a novel series of triazolonaphthalimides with excellent anti-cancer activities. In the present study, one of the most potent triazolonaphthalimides, LSS-11, was investigated. LSS-11 bound to DNA in vitro and in cell mainly by minor groove binding and significantly increased the stability of DNA, which could be fundamental for the biological activities of LSS-11. In addition to inhibiting DNA topoisomerase II-catalyzed decatenation of knotted circulated DNA, LSS-11 dramatically inhibited DNA replication mediated by polymerase chain reaction and isothermal helicase-dependent amplification, as well as the expression of luciferase driven by a minimal TA promoter in cell. Furthermore, LSS-11 exhibited strong cytotoxicity in selected human colon cancer cell lines by inducing cell cycle arrest and apoptosis, which was accompanied by DNA damage response. Finally, LSS-11 potently inhibited the growth of S180 murine sarcoma and SW480 human colorectal cancer xenografts in vivo without significant major toxicities. These results suggest that LSS-11 deserves further research and development as a novel anti-cancer agent, and provided new understandings of mechanisms by which LSS-11 inhibited multiple DNA-associated processes and tumor growth.
Collapse
Affiliation(s)
- Liyan Ji
- Department of Chemical Biology, Peking University School of Pharmaceutical Sciences, Beijing 100191, China.,International Institute for Translational Chinese Medicine, Guangzhou Traditional Chinese Medicine University, Guangzhou 510006, China
| | - Simin Yang
- Department of Chemical Biology, Peking University School of Pharmaceutical Sciences, Beijing 100191, China
| | - Shasha Li
- Department of Chemical Biology, Peking University School of Pharmaceutical Sciences, Beijing 100191, China
| | - Shan Liu
- Department of Chemical Biology, Peking University School of Pharmaceutical Sciences, Beijing 100191, China
| | - Shunan Tang
- Department of Chemical Biology, Peking University School of Pharmaceutical Sciences, Beijing 100191, China
| | - Zhongqiu Liu
- International Institute for Translational Chinese Medicine, Guangzhou Traditional Chinese Medicine University, Guangzhou 510006, China
| | - Xiangbao Meng
- Department of Chemical Biology, Peking University School of Pharmaceutical Sciences, Beijing 100191, China
| | - Siwang Yu
- Department of Chemical Biology, Peking University School of Pharmaceutical Sciences, Beijing 100191, China
| |
Collapse
|
8
|
Isouronium and N -hydroxyguanidinium derivatives as Cell growth inhibitors: A comparative study. Eur J Med Chem 2016; 117:269-82. [DOI: 10.1016/j.ejmech.2016.03.047] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Revised: 03/16/2016] [Accepted: 03/17/2016] [Indexed: 12/21/2022]
|
9
|
Harika NK, Paul A, Stroeva E, Chai Y, Boykin DW, Germann MW, Wilson WD. Imino proton NMR guides the reprogramming of A•T specific minor groove binders for mixed base pair recognition. Nucleic Acids Res 2016; 44:4519-27. [PMID: 27131382 PMCID: PMC4889958 DOI: 10.1093/nar/gkw353] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Accepted: 04/17/2016] [Indexed: 12/19/2022] Open
Abstract
Sequence-specific binding to DNA is crucial for targeting transcription factor-DNA complexes to modulate gene expression. The heterocyclic diamidine, DB2277, specifically recognizes a single G•C base pair in the minor groove of mixed base pair sequences of the type AAAGTTT. NMR spectroscopy reveals the presence of major and minor species of the bound compound. To understand the principles that determine the binding affinity and orientation in mixed sequences of DNA, over thirty DNA hairpin substrates were examined by NMR and thermal melting. The NMR exchange dynamics between major and minor species shows that the exchange is much faster than compound dissociation determined from biosensor–surface plasmon resonance. Extensive modifications of DNA sequences resulted in a unique DNA sequence with binding site AAGATA that binds DB2277 in a single orientation. A molecular docking result agrees with the model representing rapid flipping of DB2277 between major and minor species. Imino spectral analysis of a 15N-labeled central G clearly shows the crucial role of the exocyclic amino group of G in sequence-specific recognition. Our results suggest that this approach can be expanded to additional modules for recognition of more sequence-specific DNA complexes. This approach provides substantial information about the sequence-specific, highly efficient, dynamic nature of minor groove binding agents.
Collapse
Affiliation(s)
- Narinder K Harika
- Department of Chemistry, Georgia State University, Atlanta, GA 30303-3083, USA
| | - Ananya Paul
- Department of Chemistry, Georgia State University, Atlanta, GA 30303-3083, USA
| | - Ekaterina Stroeva
- Department of Chemistry, Georgia State University, Atlanta, GA 30303-3083, USA
| | - Yun Chai
- Department of Chemistry, Georgia State University, Atlanta, GA 30303-3083, USA
| | - David W Boykin
- Department of Chemistry, Georgia State University, Atlanta, GA 30303-3083, USA
| | - Markus W Germann
- Department of Chemistry, Georgia State University, Atlanta, GA 30303-3083, USA
| | - W David Wilson
- Department of Chemistry, Georgia State University, Atlanta, GA 30303-3083, USA
| |
Collapse
|
10
|
Abstract
PARP-1 is a nuclear enzyme regulating transcription, chromatin restructuring, and DNA repair. PARP-1 is activated by interaction with NAD+, DNA, and core histones. Each route of PARP-1 activation leads to somewhat different outcomes. PARP-1 interactions with core histones control PARP-1 functions during transcriptional activation in euchromatin. DNA-dependent regulation of PARP-1 determines its localization in heterochromatin and PARP-1-dependent silencing. Here we address the biological significance of DNA-dependent PARP-1 regulation in vitro and in vivo. We report that minor grove binding ligands (MGBLs) specifically target PARP-1 interaction with DNA, and, hence, the DNA-dependent pathway of PARP-1 activation. By obstructing its interaction with DNA molecules, MGBLs block PARP-1 activity in vitro and in vivo, as we demonstrate using Drosophila, as well as human cancer-derived cells. We also demonstrate synergistic inhibition of PARP-1, combining MGBLs with conventional NAD+-dependent inhibitors in human cancer cells. These results suggest that combining different classes of PARP-1 inhibitors can precisely modulate PARP-1 activity in living cells, thus holding promise for new avenues of cancer treatment.
Collapse
|
11
|
O'Sullivan P, Rozas I. Understanding the guanidine-like cationic moiety for optimal binding into the DNA minor groove. ChemMedChem 2014; 9:2065-73. [PMID: 25087855 DOI: 10.1002/cmdc.201402264] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Indexed: 01/01/2023]
Abstract
Based on our previous positive results with bis-guanidine-like diaromatic compounds as DNA minor groove binders, we propose a new family: bis-2-amino-1,4,5,6-tetrahydropyrimidines. According to calculated parameters, these dicationic systems would have a more suitable size and lipophilicity for binding into the minor groove than previous series. Moreover, their DFT-optimised structures and docking into an AT oligomer model show that they would bind in the minor groove with good strength and without energy penalty. Hence, we prepared compounds 4 a-c and evaluated their binding to ssDNA and poly(dA-dT)2 by thermal denaturation experiments. The results showed that 4 a (CO) and 4 d (NH) were the best DNA binders. Compared to the previous series, 4 a-d are better binders than bis-guanidiniums but poorer than bis-2-aminoimidazolinium derivatives. Moreover, circular dichroism experiments using ssDNA and poly(dA-dT)2 confirmed binding into the minor groove. Based on our computational design as well as biophysical studies, we have been able to determine that the optimal interaction of guanidine-like dications in the minor grove occurs with bis-2-aminoimidazolinium systems.
Collapse
Affiliation(s)
- Patrick O'Sullivan
- School of Chemistry, Trinity Biomedical Sciences Institute, Trinity College, University of Dublin, 152-160 Pearse St., Dublin 2 (Ireland)
| | | |
Collapse
|
12
|
Cao H, Qiao Y, Meng F, Liu X. Spacing-Dependent Antimicrobial Efficacy of Immobilized Silver Nanoparticles. J Phys Chem Lett 2014; 5:743-748. [PMID: 26270846 DOI: 10.1021/jz5000269] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Silver nanoparticles (Ag NPs) with a similar mean particle diameter (∼5.0 nm) but distinguished dispersion densities were in situ fabricated and immobilized on plasma-sprayed titanium oxide coatings by a silver plasma immersion ion implantation process (Ag PIII). Experiments and theoretical predictions demonstrated that the efficacy of these Ag NPs against bacteria relies on their electron storage capability, which is the interparticle distance associated in the dark, and it is inversely dose-dependent. A particle population with a relatively large spacing distance is superior in concentrating the electrons extruded by bacterial cells, activating oxidative reactions, and disrupting the bacterial cells. The finding opens up a new window leading to active design and control of the interactions between materials and biological systems.
Collapse
Affiliation(s)
- Huiliang Cao
- State Key Laboratory of High Performance Ceramics and Superfine Microstructure, Shanghai Institute of Ceramics, Chinese Academy of Sciences, Shanghai 200050, China
| | - Yuqin Qiao
- State Key Laboratory of High Performance Ceramics and Superfine Microstructure, Shanghai Institute of Ceramics, Chinese Academy of Sciences, Shanghai 200050, China
| | - Fanhao Meng
- State Key Laboratory of High Performance Ceramics and Superfine Microstructure, Shanghai Institute of Ceramics, Chinese Academy of Sciences, Shanghai 200050, China
| | - Xuanyong Liu
- State Key Laboratory of High Performance Ceramics and Superfine Microstructure, Shanghai Institute of Ceramics, Chinese Academy of Sciences, Shanghai 200050, China
| |
Collapse
|
13
|
Stockert JC. Predictive binding geometry of ligands to DNA minor groove: isohelicity and hydrogen-bonding pattern. Methods Mol Biol 2014; 1094:1-12. [PMID: 24162975 DOI: 10.1007/978-1-62703-706-8_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
The interaction of drugs and dyes with nucleic acids, particularly when binding to DNA minor groove occurs, has increasing importance in biomedical sciences. This is due to the resulting biological activity and to the possibility of recognizing AT and GC base pairs. In such cases, DNA binding can be predicted if appropriate helical and hydrogen-bonding parameters are deduced from DNA models, and a simplified geometrical rule in the form of a stencil is then applied on computer-drawn molecules of interest. Relevant structure parameter values for minor groove binders are the length (4.6 < L < 5.4 Å) and angle (152 < σ < 156.5°) between three consecutive units, measured at the level of hydrogen donor or acceptor groups. Application of the stencil shows that predictive methods can aid in the design of new compounds, by checking the possible binding of isohelical sequence-specific ligands along the DNA minor groove.
Collapse
Affiliation(s)
- Juan C Stockert
- Department of Biology, Faculty of Sciences, Autonomous University of Madrid, Cantoblanco, Madrid, Spain
| |
Collapse
|
14
|
Electron storage mediated dark antibacterial action of bound silver nanoparticles: smaller is not always better. Acta Biomater 2013; 9:5100-10. [PMID: 23085265 DOI: 10.1016/j.actbio.2012.10.017] [Citation(s) in RCA: 104] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2012] [Revised: 09/26/2012] [Accepted: 10/11/2012] [Indexed: 11/23/2022]
Abstract
Size tunable silver nanoparticles (Ag NPs) are synthesized and incorporated into titanium oxide coatings (TOCs) by manipulating the atomic-scale heating effect of silver plasma immersion ion implantation (Ag PIII). The resulting Ag NPs/TOC composite coatings possess electron storage capability that gives rise to both controlled antibacterial activity and excellent compatibility with mammalian cells. The precipitation behavior of these Ag NPs is qualitatively constrained by the classical nucleation theory. Both photoluminescence (PL) spectra and fluorescence microscopy results demonstrate that larger Ag NPs (5-25 nm) are better at reserving electrons than smaller ones (∼4 nm). The antibacterial activities of the as-sprayed and Ag PIII treated TOCs show that Ag NPs with a different size act distinctively to bacteria: large particles induce serious cytosolic content leakage and lysis of both Staphylococcus aureus and Escherichia coli cells while small ones do not. The excellent activity of larger Ag NPs against bacteria is highly related to their stronger electron storage capability, which can induce accumulation of adequate valence-band holes (h⁺) at the titanium oxide side, arousing oxidation reactions to bacterial cells in the dark. Moreover, the in vitro cell culture assay (using both MG63 and MC3T3 cells) reveals no significant cytotoxicity and even good cytocompatibility on the Ag PIII treated samples. Our results show that, by taking advantage of the boundary property between Ag NP and titanium oxide, the antibacterial activity of Ag NPs can be accurately controlled. This study provides a distinct criterion for the design of nanostructured surfaces such that their osteoblast functions and antibacterial activity are perfectly balanced.
Collapse
|