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Lázaro A, Bosque R, Marín S, Pérez-León R, Badia J, Baldomà L, Rodríguez L, Crespo M, Cascante M. Exploring the effect of the axial ligands on the anticancer activity of [C,N,N'] Pt(IV) cyclometallated compounds. Dalton Trans 2024; 53:13030-13043. [PMID: 39028273 DOI: 10.1039/d4dt01225a] [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: 07/20/2024]
Abstract
The synthesis of three novel [C,N,N'] Pt(IV) cyclometallated compounds containing hydroxo, dichloroacetato or trifluoroacetato axial ligands is reported. Compound [PtCl(OH)2{(CH3)2N(CH2)2NCH(4-FC6H3)}] (3) was prepared by the oxidative addition of hydrogen peroxide to [C,N,N'] Pt(II) cyclometallated compound [PtCl{(CH3)2N(CH2)2NCH(4-FC6H3)}] (1) and further the reaction of compound 3 with dichloroacetate or trifluoroacetate anhydrides led to the formation of the corresponding compounds [PtCl(CHCl2COO)2{(CH3)2N(CH2)2NCH(4-FC6H3)}] (4) and [PtCl(CF3COO)2{(CH3)2N(CH2)2NCH(4-FC6H3)}] (5). The properties of the new compounds along with those of the compound [PtCl3{(CH3)2N(CH2)2NCH(4-FC6H3)}] (2), including stability in aqueous media, reduction potential using cyclic voltammetry, cytotoxic activity against the HCT116 CRC cell line, DNA interaction, topoisomerase I and cathepsin inhibition, and computational studies involving reduction of the Pt(IV) compounds and molecular docking studies, are presented. Interestingly, the antiproliferative activity of these compounds against the HCT116 CRC cell line, which is in all cases higher than that of cisplatin, follows the same trend as the reduction potentials so that the most easily reduced compound 2 is the most potent. In contrast, according to the electrophoretic mobility and molecular docking studies, the efficacy of these compounds in binding to DNA is not related to their cytotoxicity. The most active compound 2 does not modify the DNA electrophoretic mobility while the less potent compound 3 is the most efficient in binding to DNA. Although compounds 2 and 3 have only a slight effect on cell cycle distribution and apoptosis induction, generation of ROS to a higher extent for the most easily reduced compound 2 was observed.
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Affiliation(s)
- Ariadna Lázaro
- Departament de Química Inorgànica i Orgànica, Secció de Química Inorgànica, Facultat de Química, Universitat de Barcelona, E-08028-Barcelona, Spain.
- Institut de Nanociència i Nanotecnologia (IN2UB), Universitat de Barcelona, E-08028 Barcelona, Spain
| | - Ramón Bosque
- Departament de Química Inorgànica i Orgànica, Secció de Química Inorgànica, Facultat de Química, Universitat de Barcelona, E-08028-Barcelona, Spain.
| | - Silvia Marín
- Institut de Biomedicina de la Universitat de Barcelona (IBUB), Universitat de Barcelona, E-08028 Barcelona, Spain.
- Departament de Bioquímica i Biomedicina molecular, Facultat de Biologia, Universitat de Barcelona, E-08028-Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y digestivas (CIBEREHD), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Raúl Pérez-León
- Departament de Bioquímica i Biomedicina molecular, Facultat de Biologia, Universitat de Barcelona, E-08028-Barcelona, Spain
| | - Josefa Badia
- Institut de Biomedicina de la Universitat de Barcelona (IBUB), Universitat de Barcelona, E-08028 Barcelona, Spain.
- Departament de Bioquímica i Fisiologia, Secció de Bioquímica i Biologia Molecular, Facultat de Farmàcia, E-08028-Barcelona, Spain
| | - Laura Baldomà
- Institut de Biomedicina de la Universitat de Barcelona (IBUB), Universitat de Barcelona, E-08028 Barcelona, Spain.
- Departament de Bioquímica i Fisiologia, Secció de Bioquímica i Biologia Molecular, Facultat de Farmàcia, E-08028-Barcelona, Spain
| | - Laura Rodríguez
- Departament de Química Inorgànica i Orgànica, Secció de Química Inorgànica, Facultat de Química, Universitat de Barcelona, E-08028-Barcelona, Spain.
- Institut de Nanociència i Nanotecnologia (IN2UB), Universitat de Barcelona, E-08028 Barcelona, Spain
| | - Margarita Crespo
- Departament de Química Inorgànica i Orgànica, Secció de Química Inorgànica, Facultat de Química, Universitat de Barcelona, E-08028-Barcelona, Spain.
- Institut de Biomedicina de la Universitat de Barcelona (IBUB), Universitat de Barcelona, E-08028 Barcelona, Spain.
| | - Marta Cascante
- Institut de Biomedicina de la Universitat de Barcelona (IBUB), Universitat de Barcelona, E-08028 Barcelona, Spain.
- Departament de Bioquímica i Biomedicina molecular, Facultat de Biologia, Universitat de Barcelona, E-08028-Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y digestivas (CIBEREHD), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
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2
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Alniss HY, Saber-Ayad MM, Ramadan WS, Manasa Bhamidimarri P, Msallam YA, Al-Jubeh HM, Ravi A, Menon V, Hamoudi R, El-Awady R. Transcriptomic analysis of MCF7 breast cancer cells treated with MGBs reveals a profound inhibition of estrogen receptor genes. Bioorg Chem 2024; 151:107680. [PMID: 39084151 DOI: 10.1016/j.bioorg.2024.107680] [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: 05/16/2024] [Revised: 07/21/2024] [Accepted: 07/26/2024] [Indexed: 08/02/2024]
Abstract
Breast cancer poses a significant health risk worldwide. However, the effectiveness of current chemotherapy is limited due to increasing drug resistance and side effects, making it crucial to develop new compounds with novel mechanism of action that can surpass these limitations. As a consequence of their reversible and targeted mechanism, DNA minor groove binders (MGBs) are considered as a relatively safer and more effective alternative. In this study, transcriptomic analysis was conducted to reveal the dysregulated genes and signaling pathways in MCF7 cancer cells following treatment with novel MGB ligands to gain insights into the mechanism of action of MGBs at the molecular level. The transcriptomic results were validated using real-time PCR. The findings of this study indicate that the investigated MGBs primarily inhibit the genes associated with the estrogen receptor. Remarkably, ligand 5 showed downregulation of 34 out of the 35 genes regulated by estrogen receptor, highlighting its potential as a promising candidate for breast cancer therapy.
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Affiliation(s)
- Hasan Y Alniss
- College of Pharmacy, Department of Medicinal Chemistry, University of Sharjah, Sharjah 27272, United Arab Emirates; Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates.
| | - Maha M Saber-Ayad
- Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates; College of Medicine, University of Sharjah, Sharjah 27272, United Arab Emirates
| | - Wafaa S Ramadan
- Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates
| | - Poorna Manasa Bhamidimarri
- Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates
| | - Yousef A Msallam
- College of Pharmacy, Department of Medicinal Chemistry, University of Sharjah, Sharjah 27272, United Arab Emirates; Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates
| | - Hadeel M Al-Jubeh
- Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates
| | - Anil Ravi
- Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates
| | - Varsha Menon
- Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates
| | - Rifat Hamoudi
- Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates; College of Medicine, University of Sharjah, Sharjah 27272, United Arab Emirates; Center of Excellence for Precision Medicine, University of Sharjah, Sharjah 27272, United Arab Emirates; BIMAI-Lab, Biomedically Informed Artificial Intelligence Laboratory, University of Sharjah, Sharjah 27272, United Arab Emirates; Division of Surgery and Interventional Science, Faculty of Medicine, University College London, London, United Kingdom
| | - Raafat El-Awady
- College of Pharmacy, Department of Medicinal Chemistry, University of Sharjah, Sharjah 27272, United Arab Emirates; Research Institute for Medical and Health Sciences, University of Sharjah, Sharjah 27272, United Arab Emirates
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3
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Ruddell SA, Mostert D, Sieber SA. Target identification of usnic acid in bacterial and human cells. RSC Chem Biol 2024; 5:617-621. [PMID: 38966671 PMCID: PMC11221533 DOI: 10.1039/d4cb00040d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Accepted: 05/07/2024] [Indexed: 07/06/2024] Open
Abstract
Usnic acid is a natural product with versatile biological activities against various organisms. Here, we utilise a chemical proteomic strategy to gain insights into its target scope in bacterial and human cells. First, we excluded DNA binding as a major reason for its antibacterial activity, and second, we commenced with target profiling, which unravelled several metal cofactor-dependent enzymes in both species indicating a polypharmacological mode of action. Interestingly, our synthetic studies revealed a selectivity switch at usnic acid, which maintains antibacterial activity but lacks strong cytotoxic effects.
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Affiliation(s)
- Stuart A Ruddell
- Center for Functional Protein Assemblies, Department of Bioscience, TUM School of Natural Sciences, Technical University of Munich Ernst-Otto-Fischer-Straße 8 85748 Garching Germany
| | - Dietrich Mostert
- Center for Functional Protein Assemblies, Department of Bioscience, TUM School of Natural Sciences, Technical University of Munich Ernst-Otto-Fischer-Straße 8 85748 Garching Germany
| | - Stephan A Sieber
- Center for Functional Protein Assemblies, Department of Bioscience, TUM School of Natural Sciences, Technical University of Munich Ernst-Otto-Fischer-Straße 8 85748 Garching Germany
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4
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Alniss HY, Al-Jubeh HM, Msallam YA, Siddiqui R, Makhlouf Z, Ravi A, Hamdy R, Soliman SSM, Khan NA. Structure-based drug design of DNA minor groove binders and evaluation of their antibacterial and anticancer properties. Eur J Med Chem 2024; 271:116440. [PMID: 38678825 DOI: 10.1016/j.ejmech.2024.116440] [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: 12/07/2023] [Revised: 04/09/2024] [Accepted: 04/18/2024] [Indexed: 05/01/2024]
Abstract
Antimicrobial and chemotherapy resistance are escalating medical problem of paramount importance. Yet, research for novel antimicrobial and anticancer agents remains lagging behind. With their reported medical applications, DNA minor groove binders (MGBs) are worthy of exploration. In this study, the approach of structure-based drug design was implemented to generate 11 MGB compounds including a novel class of bioactive alkyne-linked MGBs. The NCI screening protocol was utilized to evaluate the antitumor activity of the target MGBs. Furthermore, a variety of bactericidal, cytopathogenicity, MIC90, and cytotoxicity assays were carried out using these MGBs against 6 medically relevant bacteria: Salmonella enterica, Escherichia coli, Serratia marcescens, Bacillus cereus, Streptococcus pneumoniae and Streptococcus pyogenes. Moreover, molecular docking, molecular dynamic simulations, DNA melting, and isothermal titration calorimetry (ITC) analyses were utilized to explore the binding mode and interactions between the most potent MGBs and the DNA duplex d(CGACTAGTCG)2. NCI results showed that alkyne-linked MGBs (26 & 28) displayed the most significant growth inhibition among the NCI-60 panel. In addition, compounds MGB3, MGB4, MGB28, and MGB32 showed significant bactericidal effects, inhibited B. cereus and S. enterica-mediated cytopathogenicity, and exhibited low cytotoxicity. MGB28 and MGB32 demonstrated significant inhibition of S. pyogenes, whereas MGB28 notably inhibited S. marcescens and all four minor groove binders significantly inhibited B. cereus. The ability of these compounds to bind with DNA and distort its groove dimensions provides the molecular basis for the allosteric perturbation of proteins-DNA interactions by MGBs. This study shed light on the mechanism of action of MGBs and revealed the important structural features for their antitumor and antibacterial activities, which are important to guide future development of MGB derivatives as novel antibacterial and anticancer agents.
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Affiliation(s)
- Hasan Y Alniss
- College of Pharmacy, Department of Medicinal Chemistry, University of Sharjah, 27272, Sharjah, United Arab Emirates; Research Institute for Medical and Health Sciences, University of Sharjah, 27272, Sharjah, United Arab Emirates.
| | - Hadeel M Al-Jubeh
- Research Institute for Medical and Health Sciences, University of Sharjah, 27272, Sharjah, United Arab Emirates
| | - Yousef A Msallam
- College of Pharmacy, Department of Medicinal Chemistry, University of Sharjah, 27272, Sharjah, United Arab Emirates; Research Institute for Medical and Health Sciences, University of Sharjah, 27272, Sharjah, United Arab Emirates
| | - Ruqaiyyah Siddiqui
- Institute of Biological Chemistry, Biophysics and Bioengineering, Heriot-Watt University Edinburgh, EH14 4AS, United Kingdom; Department of Medical Biology, Faculty of Medicine, Istinye University, Istanbul, 34010, Turkey
| | - Zinb Makhlouf
- College of Medicine, Department of Clinical Sciences, University of Sharjah, 27272, Sharjah, United Arab Emirates
| | - Anil Ravi
- Research Institute for Medical and Health Sciences, University of Sharjah, 27272, Sharjah, United Arab Emirates
| | - Rania Hamdy
- Research Institute for Medical and Health Sciences, University of Sharjah, 27272, Sharjah, United Arab Emirates
| | - Sameh S M Soliman
- College of Pharmacy, Department of Medicinal Chemistry, University of Sharjah, 27272, Sharjah, United Arab Emirates; Research Institute for Medical and Health Sciences, University of Sharjah, 27272, Sharjah, United Arab Emirates
| | - Naveed A Khan
- Department of Medical Biology, Faculty of Medicine, Istinye University, Istanbul, 34010, Turkey.
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5
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Kalyani Bhardwaj B, James A, Tomy J, K B S, Suresh PS. Multi-spectroscopic and in silico investigation of gambogic acid-calf thymus DNA interactions. J Biomol Struct Dyn 2024:1-12. [PMID: 38433426 DOI: 10.1080/07391102.2024.2323694] [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: 11/03/2023] [Accepted: 02/20/2024] [Indexed: 03/05/2024]
Abstract
Gambogic acid (GA), a xanthanoid compound, is derived from Garcinia Hanbury gamboge resin. Studying GA's DNA binding and targeting processes is crucial to understanding its tumor-targeting potentiality. This study used spectroscopic and in silico methods to investigate the GA-calf thymus DNA-binding interaction. The results of the UV-visible absorbance spectroscopy revealed that GA binds to DNA and forms a complex. Investigation of fluorescence quenching using ethidium bromide-DNA revealed that GA displaced ethidium bromide, and the type of quenching was static in nature, as determined by Stern-Volmer plot data. Thermodynamic analysis of the DNA-GA complex revealed a spontaneous, favorable interaction involving hydrogen bonding and hydrophobic interactions. Quenching experiments with potassium iodide, Acridine orange, and NaCl verified GA's groove-binding nature and the presence of weak electrostatic interactions. The thermal melting temperature of DNA in its native and bound states with GA did not differ significantly (69.27° C to 71.25° C), validating the binding of GA to the groove region. Furthermore, the groove-binding nature of GA was confirmed by studying its interaction with ssDNA and DNA viscosity. The methods of DSC, FT-IR, and CD spectroscopy have not revealed any structural aberrations in DNA bound with GA. Molecular docking and modeling studies revealed that GA has a groove-binding nature with DNA, which is consistent with prior experimental results. Finally, the findings shed information by which GA attaches to DNA and provide insights into its recognized anticancer effects via topoisomerase inhibition causing DNA cleavage, inhibition of cell proliferation and apoptosis.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
| | - Arsha James
- Department of Bioscience and Engineering, National Institute of Technology, Calicut, Kerala, India
| | - Jiya Tomy
- Department of Bioscience and Engineering, National Institute of Technology, Calicut, Kerala, India
| | - Shalini K B
- Department of Bioscience and Engineering, National Institute of Technology, Calicut, Kerala, India
| | - Padmanaban S Suresh
- Department of Bioscience and Engineering, National Institute of Technology, Calicut, Kerala, India
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6
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Nasiri M, Bahadorani M, Dellinger K, Aravamudhan S, Vivero-Escoto JL, Zadegan R. Improving DNA nanostructure stability: A review of the biomedical applications and approaches. Int J Biol Macromol 2024; 260:129495. [PMID: 38228209 PMCID: PMC11060068 DOI: 10.1016/j.ijbiomac.2024.129495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 01/10/2024] [Accepted: 01/12/2024] [Indexed: 01/18/2024]
Abstract
DNA's programmable, predictable, and precise self-assembly properties enable structural DNA nanotechnology. DNA nanostructures have a wide range of applications in drug delivery, bioimaging, biosensing, and theranostics. However, physiological conditions, including low cationic ions and the presence of nucleases in biological systems, can limit the efficacy of DNA nanostructures. Several strategies for stabilizing DNA nanostructures have been developed, including i) coating them with biomolecules or polymers, ii) chemical cross-linking of the DNA strands, and iii) modifications of the nucleotides and nucleic acids backbone. These methods significantly enhance the structural stability of DNA nanostructures and thus enable in vivo and in vitro applications. This study reviews the present perspective on the distinctive properties of the DNA molecule and explains various DNA nanostructures, their advantages, and their disadvantages. We provide a brief overview of the biomedical applications of DNA nanostructures and comprehensively discuss possible approaches to improve their biostability. Finally, the shortcomings and challenges of the current biostability approaches are examined.
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Affiliation(s)
- Mahboobeh Nasiri
- Department of Nanoengineering, Joint School of Nanoscience & Nanoengineering, North Carolina Agriculture and Technical State University, USA
| | - Mehrnoosh Bahadorani
- Department of Nanoengineering, Joint School of Nanoscience & Nanoengineering, North Carolina Agriculture and Technical State University, USA
| | - Kristen Dellinger
- Department of Nanoengineering, Joint School of Nanoscience & Nanoengineering, North Carolina Agriculture and Technical State University, USA
| | - Shyam Aravamudhan
- Department of Nanoengineering, Joint School of Nanoscience & Nanoengineering, North Carolina Agriculture and Technical State University, USA
| | - Juan L Vivero-Escoto
- Department of Chemistry, The University of North Carolina at Charlotte, Charlotte, NC, USA
| | - Reza Zadegan
- Department of Nanoengineering, Joint School of Nanoscience & Nanoengineering, North Carolina Agriculture and Technical State University, USA.
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7
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Gupta MK, Senthilkumar S, Rangan L. 3, 5-Dihydroxy 4', 7-dimethoxyflavone-DNA interaction study for nucleic acid detection and differential cell staining. Int J Biol Macromol 2024; 261:129713. [PMID: 38281518 DOI: 10.1016/j.ijbiomac.2024.129713] [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: 11/08/2023] [Revised: 01/11/2024] [Accepted: 01/19/2024] [Indexed: 01/30/2024]
Abstract
The present study is focused on application of a natural compound, 3, 5-dihydroxy 4', 7-dimethoxyflavone (DHDM) from a medicinal plant Alpinia nigra for nucleic acid detection and differential cell staining. DHDM was found to interact with nucleic acid and forms complex, which was investigated for various applications. It was successfully utilized to visualize plasmid, genomic, and ds-linear DNA in agarose gel electrophoresis without affecting the DNA mobility in the gel. Fluorescence of DHDM increased several fold upon binding to dsDNA. Photostability of the compound was assessed and showed photobleaching effect that decreased gradually over time. Application of the compound was further extended to differential cell staining. When observed in fluorescence microscope, DHDM stained the dead cells and differentiated them from live cells in the case of bacterial, yeast, and mammalian cells. Higher concentration of the compound was found to be less cytotoxic to cancerous cells. Nucleic acid staining dyes like Ethidium bromide (EtBr), Propidium iodide (PI), etc. are carcinogens and environmental pollutants and therefore DHDM a natural compound, is a major benefit and thus can serve as an alternative to the current dyes.
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Affiliation(s)
- Manish Kumar Gupta
- Applied Biodiversity Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Assam 781039, India
| | - Sanjana Senthilkumar
- Applied Biodiversity Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Assam 781039, India
| | - Latha Rangan
- Applied Biodiversity Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Assam 781039, India.
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8
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Okus F, Yuzbasioglu D, Unal F. Molecular docking study of frequently used food additives for selected targets depending on the chromosomal abnormalities they cause. Toxicology 2024; 502:153716. [PMID: 38159899 DOI: 10.1016/j.tox.2023.153716] [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: 10/26/2023] [Revised: 12/26/2023] [Accepted: 12/27/2023] [Indexed: 01/03/2024]
Abstract
Food additives (FAs) (flavor enhancers, sweeteners, etc.) protect foods during storage and transportation, making them attractive to consumers. Today, while the desire to access natural foods is increasing, the chemicals added to foods have started to be questioned. In this respect, genotoxicity tests have gained importance. Studies show that some food additives may have genotoxic risks. Previous studies carried out in our laboratory also revealed genotoxic effects of Monopotassium glutamate (MPG), Monosodium glutamate (MSG), Magnesium diglutamate (MDG) as flavor enhancers; Potassium benzoate (PB), Potassium sorbate (PS), Sodium benzoate (SB), Sodium sorbate (SS) as preservatives; Acesulfame potassium (ACE-K), Xylitol (XYL) as sweeteners. In this study, we determined the interactions of these food additives with ATM and p53 proteins, which are activated in the cell due to genotoxic effects, and with DNA by employing the molecular docking method for the first time. Among the food additives, SB (-4.307) for ATM, XYL (-4.629) for p53, and XYL (-4.927) for DNA showed the highest affinity. Therefore, flexible docking (IFD) scores were determined for SB, XYL, and MDG from flavor enhancers. The potential binding modes of the food additives to target molecules' possible inhibition mechanisms were determined by molecular docking. Thus, new information was obtained to show how these additives cause chromosomal abnormalities.
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Affiliation(s)
- Fatma Okus
- Graduate School of Natural and Applied Sciences, Gazi University, Teknikokullar, Ankara, Türkiye
| | - Deniz Yuzbasioglu
- Genetic Toxicology Laboratory, Department of Biology, Science Faculty, Gazi University, Teknikokullar, Ankara, Türkiye.
| | - Fatma Unal
- Genetic Toxicology Laboratory, Department of Biology, Science Faculty, Gazi University, Teknikokullar, Ankara, Türkiye
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9
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Nué-Martinez JJ, Cisneros D, Moreno-Blázquez MD, Fonseca-Berzal C, Manzano JI, Kraeutler D, Ungogo MA, Aloraini MA, Elati HAA, Ibáñez-Escribano A, Lagartera L, Herraiz T, Gamarro F, de Koning HP, Gómez-Barrio A, Dardonville C. Synthesis and Biophysical and Biological Studies of N-Phenylbenzamide Derivatives Targeting Kinetoplastid Parasites. J Med Chem 2023; 66:13452-13480. [PMID: 37729094 PMCID: PMC10578353 DOI: 10.1021/acs.jmedchem.3c00697] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Indexed: 09/22/2023]
Abstract
The AT-rich mitochondrial DNA (kDNA) of trypanosomatid parasites is a target of DNA minor groove binders. We report the synthesis, antiprotozoal screening, and SAR studies of three series of analogues of the known antiprotozoal kDNA binder 2-((4-(4-((4,5-dihydro-1H-imidazol-3-ium-2-yl)amino)benzamido)phenyl)amino)-4,5-dihydro-1H-imidazol-3-ium (1a). Bis(2-aminoimidazolines) (1) and bis(2-aminobenzimidazoles) (2) showed micromolar range activity against Trypanosoma brucei, whereas bisarylimidamides (3) were submicromolar inhibitors of T. brucei, Trypanosoma cruzi, and Leishmania donovani. None of the compounds showed relevant activity against the urogenital, nonkinetoplastid parasite Trichomonas vaginalis. We show that series 1 and 3 bind strongly and selectively to the minor groove of AT DNA, whereas series 2 also binds by intercalation. The measured pKa indicated different ionization states at pH 7.4, which correlated with the DNA binding affinities (ΔTm) for series 2 and 3. Compound 3a, which was active and selective against the three parasites and displayed adequate metabolic stability, is a fine candidate for in vivo studies.
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Affiliation(s)
- J. Jonathan Nué-Martinez
- Instituto
de Química Médica, IQM−CSIC, Juan de la Cierva 3, E-28006 Madrid, Spain
- PhD
Programme in Medicinal Chemistry, Doctoral School, Universidad Complutense de Madrid (UCM), 28040 Madrid, Spain
| | - David Cisneros
- Instituto
de Química Médica, IQM−CSIC, Juan de la Cierva 3, E-28006 Madrid, Spain
- PhD
Programme in Medicinal Chemistry, Doctoral School, Universidad Complutense de Madrid (UCM), 28040 Madrid, Spain
| | | | - Cristina Fonseca-Berzal
- Departamento
de Microbiología y Parasitología, Facultad de Farmacia, Universidad Complutense de Madrid (UCM), Plaza de Ramón y Cajal s/n, 28040 Madrid, Spain
| | - José Ignacio Manzano
- Instituto
de Parasitología y Biomedicina “Löpez Neyra”,
IPBLN-CSIC, Parque Tecnolögico
de Ciencias de la Salud, 18016 Granada, Spain
| | - Damien Kraeutler
- Instituto
de Química Médica, IQM−CSIC, Juan de la Cierva 3, E-28006 Madrid, Spain
| | - Marzuq A. Ungogo
- Institute
of Infection, Immunity and Inflammation, College of Medical, Veterinary
and Life Sciences, University of Glasgow, G12 8TA Glasgow, U.K.
| | - Maha A. Aloraini
- Institute
of Infection, Immunity and Inflammation, College of Medical, Veterinary
and Life Sciences, University of Glasgow, G12 8TA Glasgow, U.K.
| | - Hamza A. A. Elati
- Institute
of Infection, Immunity and Inflammation, College of Medical, Veterinary
and Life Sciences, University of Glasgow, G12 8TA Glasgow, U.K.
| | - Alexandra Ibáñez-Escribano
- Departamento
de Microbiología y Parasitología, Facultad de Farmacia, Universidad Complutense de Madrid (UCM), Plaza de Ramón y Cajal s/n, 28040 Madrid, Spain
| | - Laura Lagartera
- Instituto
de Química Médica, IQM−CSIC, Juan de la Cierva 3, E-28006 Madrid, Spain
| | - Tomás Herraiz
- Instituto
de Ciencia y Tecnología de Alimentos y Nutrición, ICTAN−CSIC, José Antonio Novais 10, Ciudad
Universitaria, 28040 Madrid, Spain
| | - Francisco Gamarro
- Instituto
de Parasitología y Biomedicina “Löpez Neyra”,
IPBLN-CSIC, Parque Tecnolögico
de Ciencias de la Salud, 18016 Granada, Spain
| | - Harry P. de Koning
- Institute
of Infection, Immunity and Inflammation, College of Medical, Veterinary
and Life Sciences, University of Glasgow, G12 8TA Glasgow, U.K.
| | - Alicia Gómez-Barrio
- Departamento
de Microbiología y Parasitología, Facultad de Farmacia, Universidad Complutense de Madrid (UCM), Plaza de Ramón y Cajal s/n, 28040 Madrid, Spain
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10
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Gomes AR, Varela CL, Pires AS, Tavares-da-Silva EJ, Roleira FMF. Synthetic and natural guanidine derivatives as antitumor and antimicrobial agents: A review. Bioorg Chem 2023; 138:106600. [PMID: 37209561 DOI: 10.1016/j.bioorg.2023.106600] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 04/15/2023] [Accepted: 05/05/2023] [Indexed: 05/22/2023]
Abstract
Guanidines are fascinating small nitrogen-rich organic compounds, which have been frequently associated with a wide range of biological activities. This is mainly due to their interesting chemical features. For these reasons, for the past decades, researchers have been synthesizing and evaluating guanidine derivatives. In fact, there are currently on the market several guanidine-bearing drugs. Given the broad panoply of pharmacological activities displayed by guanidine compounds, in this review, we chose to focus on antitumor, antibacterial, antiviral, antifungal, and antiprotozoal activities presented by several natural and synthetic guanidine derivatives, which are undergoing preclinical and clinical studies from January 2010 to January 2023. Moreover, we also present guanidine-containing drugs currently in the market for the treatment of cancer and several infectious diseases. In the preclinical and clinical setting, most of the synthesized and natural guanidine derivatives are being evaluated as antitumor and antibacterial agents. Even though DNA is the most known target of this type of compounds, their cytotoxicity also involves several other different mechanisms, such as interference with bacterial cell membranes, reactive oxygen species (ROS) formation, mitochondrial-mediated apoptosis, mediated-Rac1 inhibition, among others. As for the compounds already used as pharmacological drugs, their main application is in the treatment of different types of cancer, such as breast, lung, prostate, and leukemia. Guanidine-containing drugs are also being used for the treatment of bacterial, antiprotozoal, antiviral infections and, recently, have been proposed for the treatment of COVID-19. To conclude, the guanidine group is a privileged scaffold in drug design. Its remarkable cytotoxic activities, especially in the field of oncology, still make it suitable for a deeper investigation to afford more efficient and target-specific drugs.
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Affiliation(s)
- Ana R Gomes
- Univ Coimbra, CIEPQPF, Faculty of Pharmacy, Laboratory of Pharmaceutical Chemistry, Azinhaga de Santa Comba, Pólo III - Pólo das Ciências da Saúde, 3000-548 Coimbra, Portugal; Univ Coimbra, Coimbra Institute for Clinical and Biomedical Research (iCBR) area of Environment Genetics and Oncobiology (CIMAGO), Institute of Biophysics, Faculty of Medicine, Azinhaga de Santa Comba, Pólo III - Pólo das Ciências da Saúde, 3000-548 Coimbra, Portugal
| | - Carla L Varela
- Clinical Academic Center of Coimbra (CACC), Praceta Professor Mota Pinto, 3004-561 Coimbra, Portugal; Univ Coimbra, Center for Innovative Biomedicine and Biotechnology (CIBB), Rua Larga, 3004-504 Coimbra, Portugal; Univ Coimbra, CIEPQPF, Faculty of Medicine, Azinhaga de Santa Comba, Pólo III - Pólo das Ciências da Saúde, 3000-548 Coimbra, Portugal
| | - Ana S Pires
- Univ Coimbra, Coimbra Institute for Clinical and Biomedical Research (iCBR) area of Environment Genetics and Oncobiology (CIMAGO), Institute of Biophysics, Faculty of Medicine, Azinhaga de Santa Comba, Pólo III - Pólo das Ciências da Saúde, 3000-548 Coimbra, Portugal; Clinical Academic Center of Coimbra (CACC), Praceta Professor Mota Pinto, 3004-561 Coimbra, Portugal; Univ Coimbra, Center for Innovative Biomedicine and Biotechnology (CIBB), Rua Larga, 3004-504 Coimbra, Portugal
| | - Elisiário J Tavares-da-Silva
- Univ Coimbra, CIEPQPF, Faculty of Pharmacy, Laboratory of Pharmaceutical Chemistry, Azinhaga de Santa Comba, Pólo III - Pólo das Ciências da Saúde, 3000-548 Coimbra, Portugal.
| | - Fernanda M F Roleira
- Univ Coimbra, CIEPQPF, Faculty of Pharmacy, Laboratory of Pharmaceutical Chemistry, Azinhaga de Santa Comba, Pólo III - Pólo das Ciências da Saúde, 3000-548 Coimbra, Portugal.
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11
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Janse van Rensburg HD, Suganuma K, N'Da DD. In vitro trypanocidal activities and structure-activity relationships of ciprofloxacin analogs. Mol Divers 2023:10.1007/s11030-023-10704-9. [PMID: 37481633 DOI: 10.1007/s11030-023-10704-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 07/16/2023] [Indexed: 07/24/2023]
Abstract
Tropical diseases, such as African trypanosomiasis, by their nature and prevalence lack the necessary urgency regarding drug development, despite the increasing need for novel, structurally diverse antitrypanosomal drugs, using different mechanisms of action that would improve drug efficacy and safety. Traditionally antibacterial agents, the fluoroquinolones, reportedly possess in vitro trypanocidal activities against Trypanosoma brucei organisms. During our research, the fluroquinolone, ciprofloxacin (1), and its analogs (2-24) were tested against bloodstream forms of T. brucei brucei, T. b. gambiense, T. b. rhodesiense, T. evansi, T. equiperdum, and T. congolense and Madin-Darby bovine kidney cells (cytotoxicity). Ciprofloxacin [CPX (1)] demonstrated selective trypanocidal activity against T. congolense (IC50 7.79 µM; SI 39.6), whereas the CPX derivatives (2-10) showed weak selective activity (25 < IC50 < 65 µM; 2 < SI < 4). Selectivity and activity of the CPX and 1,2,3-triazole (TZ) hybrids (11-24) were governed by their chemical functionality at C-3 (carboxylic acid, or 4-methylpiperazinyl amide) and their electronic effect (electron-donating or electron-withdrawing para-benzyl substituent), respectively. Trypanocidal hits in the micromolar range were identified against bloodstream forms of T. congolense [CPX (1); CPX amide derivatives 18: IC50 8.95 µM; SI 16.84; 22: IC50 5.42 µM; SI 25.2] and against T. brucei rhodesiense (CPX acid derivative 13: IC50 4.51 µM; SI 10.2), demonstrating more selectivity toward trypanosomes than mammalian cells. Hence, the trypanocidal hit compound 22 may be optimized by retaining the 4-methylpiperazine amide functional group (C-3) and the TZ moiety at position N-15 and introducing other electron-withdrawing ortho-, meta-, and/or para-substituents on the aryl ring in an effort to improve the pharmacokinetic properties and increase the trypanocidal activity. Structure-activity relationships of ciprofloxacin-1,2,3-triazole hybrids were governed by the chemical functionality at C-3 and electronic effect.
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Affiliation(s)
| | - Keisuke Suganuma
- National Research Center for Protozoan Diseases, Obihiro University of Agriculture and Veterinary Medicine, Inada, Obihiro, Hokkaido, 080-8555, Japan.
| | - David D N'Da
- Centre of Excellence for Pharmaceutical Sciences, North-West University, Potchefstroom, 2520, South Africa
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12
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El-Sayed SM, Ahmed SA, Gulia K, Lenhard JR, Hassan AHE, Farahat AA. Small Molecules Incorporating Privileged Amidine Moiety as Potential Hits Combating Antibiotic-Resistant Bacteria. Pharmaceuticals (Basel) 2023; 16:1040. [PMID: 37513951 PMCID: PMC10384254 DOI: 10.3390/ph16071040] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 07/07/2023] [Accepted: 07/19/2023] [Indexed: 07/30/2023] Open
Abstract
The continuing need for the discovery of potent antibacterial agents against antibiotic-resistant pathogens is the driving force for many researchers to design and develop such agents. Herein, we report the design, synthesis, and biological evaluation of amidine derivatives as new antibacterial agents. Compound 13d was the most active in this study against a wide range of antibiotic-resistant, and susceptible, Gram-positive, and Gram-negative bacterial strains. Time-kill assay experiments indicated that compound 13d was an effective bactericidal compound against the tested organisms at the log-phase of bacterial growth. Docking simulations were performed to assess in silico its mode of action regarding UPPS, KARI, and DNA as potential bacterial targets. Results unveiled the importance of structural features of compound 13d in its biological activity including central thiophene ring equipped with left and right pyrrolo[2,3-b]pyridine and phenyl moieties and two terminal amidines cyclized into 4,5-dihydro-1H-imidazol-2-yl functionalities. Collectively, compound 13d represents a possible hit for future development of potent antibacterial agents.
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Affiliation(s)
- Selwan M El-Sayed
- Department of Medicinal Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Delta University for Science and Technology, Gamasa 35712, Egypt
| | - Samar A Ahmed
- Department of Clinical and Administrative Sciences, College of Pharmacy, California Northstate University, Elk Grove, CA 95757, USA
| | - Kanika Gulia
- Master of Pharmaceutical Sciences Program, California Northstate University, 9700 W Taron Dr., Elk Grove, CA 95757, USA
| | - Justin R Lenhard
- Department of Clinical and Administrative Sciences, College of Pharmacy, California Northstate University, Elk Grove, CA 95757, USA
| | - Ahmed H E Hassan
- Department of Medicinal Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt
- Medicinal Chemistry Laboratory, College of Pharmacy, Kyung Hee University, Seoul 02447, Republic of Korea
| | - Abdelbasset A Farahat
- Master of Pharmaceutical Sciences Program, California Northstate University, 9700 W Taron Dr., Elk Grove, CA 95757, USA
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt
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13
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Ressler AJ, Frate M, Hontoria A, Ream A, Timms E, Li H, Stettler LD, Bollinger A, Poor JE, Parra MA, Ma H, Seeram NP, Meschwitz SM, Henry GE. Synthesis, anti-ferroptosis, anti-quorum sensing, antibacterial and DNA interaction studies of chromene-hydrazone derivatives. Bioorg Med Chem 2023; 90:117369. [PMID: 37320993 DOI: 10.1016/j.bmc.2023.117369] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 05/15/2023] [Accepted: 06/05/2023] [Indexed: 06/17/2023]
Abstract
Nineteen chromene-hydrazone derivatives containing a variety of structural modifications on the hydrazone moiety were synthesized. Structure-activity correlations were investigated to determine the influence of structural variations on anti-ferroptosis, anti-quorum sensing, antibacterial, DNA cleavage and DNA binding properties. Ferroptosis inhibitory activity was determined by measuring the ability of the derivatives to reverse erastin-induced ferroptosis. Several of the derivatives were more effective than fisetin at inhibiting ferroptosis, with the thiosemicarbazone derivative being the most effective. Quorum sensing inhibition was evaluated using Vibrio harveyi, and both V. harveyi and Staphylococcus aureus were used to determine antibacterial activity. The semicarbazone and benzensulfonyl hydrazone derivatives showed moderate quorum sensing inhibition with IC50 values of 27 μM and 22 μM, respectively, while a few aryl hydrazone and pyridyl hydrazone derivatives showed bacterial growth inhibition, with MIC values ranging from 3.9 to 125 μM. In addition, the interaction of the hydrazone derivatives with DNA was investigated by gel electrophoresis, UV-Vis spectroscopy and molecular docking. All of the derivatives cleaved plasmid DNA and showed favorable interaction with B-DNA through minor groove binding. Overall, this work highlights a broad range of pharmacological applications for chromene-hydrazone derivatives.
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Affiliation(s)
- Andrew J Ressler
- Department of Chemistry, Susquehanna University, 514 University Avenue, Selinsgrove, PA 17870, USA
| | - Marissa Frate
- Department of Chemistry, Salve Regina University, Newport, Rhode Island 02840, USA
| | - Ana Hontoria
- Department of Chemistry, Salve Regina University, Newport, Rhode Island 02840, USA
| | - Anna Ream
- Department of Chemistry, Susquehanna University, 514 University Avenue, Selinsgrove, PA 17870, USA
| | - Eliza Timms
- Department of Chemistry, Salve Regina University, Newport, Rhode Island 02840, USA
| | - Huifang Li
- Bioactive Botanical Research Laboratory, Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, Kingston, RI 02881, USA
| | - Lauren D Stettler
- Department of Chemistry, Susquehanna University, 514 University Avenue, Selinsgrove, PA 17870, USA
| | - Ashton Bollinger
- Department of Chemistry, Susquehanna University, 514 University Avenue, Selinsgrove, PA 17870, USA
| | - Jenna E Poor
- Department of Chemistry, Susquehanna University, 514 University Avenue, Selinsgrove, PA 17870, USA
| | - Michael A Parra
- Department of Chemistry, Susquehanna University, 514 University Avenue, Selinsgrove, PA 17870, USA
| | - Hang Ma
- Bioactive Botanical Research Laboratory, Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, Kingston, RI 02881, USA
| | - Navindra P Seeram
- Bioactive Botanical Research Laboratory, Department of Biomedical and Pharmaceutical Sciences, College of Pharmacy, University of Rhode Island, Kingston, RI 02881, USA
| | - Susan M Meschwitz
- Department of Chemistry, Salve Regina University, Newport, Rhode Island 02840, USA.
| | - Geneive E Henry
- Department of Chemistry, Susquehanna University, 514 University Avenue, Selinsgrove, PA 17870, USA.
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14
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Minneci M, Misevicius M, Rozas I. Green Synthesis of Nitroaryl Thioureas: Towards an Improved Preparation of Guanidinium DNA Binders. Bioorg Med Chem Lett 2023; 90:129346. [PMID: 37217024 DOI: 10.1016/j.bmcl.2023.129346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 05/12/2023] [Accepted: 05/19/2023] [Indexed: 05/24/2023]
Abstract
We present a general efficient green method for the preparation of nitro N,N'-diaryl thioureas via a one-pot method using cyrene as a solvent with almost quantitative yields. This confirmed the viability of cyrene as a green alternative to THF in the synthesis of thiourea derivatives. After screening different reducing conditions, the nitro N,N'-diaryl thioureas were selectively reduced using Zn dust in the presence of water and acid to the corresponding amino N,N'-diaryl thioureas. These were then used to test the installation of the Boc-protected guanidine group with N,N'-bis-Boc protected pyrazole-1-carboxamidine as a guanidylating reagent not requiring mercury(II) activation. Finally, the TFA salts obtained after Boc-deprotection of two sample compounds were tested for their affinity towards DNA showing no binding.
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Affiliation(s)
- Marco Minneci
- School of Chemistry, Trinity College Dublin, 152-160 Pearse Street, Dublin 2, Ireland
| | - Matas Misevicius
- School of Chemistry, Trinity College Dublin, 152-160 Pearse Street, Dublin 2, Ireland
| | - Isabel Rozas
- School of Chemistry, Trinity College Dublin, 152-160 Pearse Street, Dublin 2, Ireland.
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15
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Gulia K, Hassan AHE, Lenhard JR, Farahat AA. Escaping ESKAPE resistance: in vitro and in silico studies of multifunctional carbamimidoyl-tethered indoles against antibiotic-resistant bacteria. ROYAL SOCIETY OPEN SCIENCE 2023; 10:230020. [PMID: 37090961 PMCID: PMC10113819 DOI: 10.1098/rsos.230020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/22/2023] [Accepted: 03/24/2023] [Indexed: 05/03/2023]
Abstract
Combining the hybridization and repurposing strategies, six compounds from our in-house library and having a designed hybrid structure of MBX-1162, pentamidine and MMV688271 were repurposed as potential antibacterial agents. Among, compounds 1a and 1d elicited potential sub-µg ml-1 activity against the high-priority antibiotic-resistant Gram-positive members of ESKAPE bacteria as well as antibiotic-susceptible Gram-positive bacteria. Furthermore, they showed potential low µg ml-1 activity against the explored critical-priority antibiotic-resistant Gram-negative members of ESKAPE bacteria. In time-kill assay, compound 1a has effective 0.5 and 0.25 µg ml-1 antibacterial lethal concentrations against MRSA in exponential growth phase. In silico investigations predicted compounds 1a and 1d as inhibitors of the open conformation of undecaprenyl diphosphate synthase involved in bacterial isoprenoid synthesis. In addition, compounds 1a and 1d were predicted as inhibitors of NADPH-free but not NADPH-bound form of ketol-acid reductoisomerase and may also serve as potential B-DNA minor groove binders with possible differences in the molecular sequence recognition. Overall, compounds 1a and 1d are presented as multifunctional potential antibacterial agents for further development against high- and critical-priority Gram-positive and Gram-negative antibiotic-resistant ESKAPE bacterial pathogens as well as antibiotic-susceptible Gram-positive bacterial pathogens.
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Affiliation(s)
- Kanika Gulia
- Master of Pharmaceutical Sciences Program, California Northstate University, 9700 W Taron Dr., Elk Grove, CA 95757, USA
- College of Medicine, California Northstate University, 9700 W Taron Dr., Elk Grove, CA 95757, USA
| | - Ahmed H. E. Hassan
- Department of Medicinal Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt
| | - Justin R. Lenhard
- Department of Clinical and Administrative Sciences, College of Pharmacy, California Northstate University, Elk Grove, CA 95757, USA
| | - Abdelbasset A. Farahat
- Master of Pharmaceutical Sciences Program, California Northstate University, 9700 W Taron Dr., Elk Grove, CA 95757, USA
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt
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16
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DNA sequence-specific ligands. XX. Synthesis, spectral properties, virological and biochemical studies of fluorescent dimeric trisbenzimidazoles DB3P(n). Med Chem Res 2023. [DOI: 10.1007/s00044-023-03017-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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17
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Vijayaraj A, Prabu R, Suresh R, Sangeetha Kumari R, Kaviyarasan V, Narayanan V, Tamizhdurai P, Mangesh V, Ali Alasmary F, Rajaji U, Govindasamy M. DNA binding, Cleavage, Catalytic, Magnetic Active; 2,2–bipyridyl based d-f hetero binuclear Gd(III), Cu(II) Complexes and Their Electrochemical, Fluorescence Studies. ARAB J CHEM 2023. [DOI: 10.1016/j.arabjc.2023.104656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2023] Open
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18
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Schlosser J, Ihmels H. Ligands for Abasic Site-containing DNA and their Use as Fluorescent Probes. Curr Org Synth 2023; 20:96-113. [PMID: 35170411 DOI: 10.2174/1570179419666220216091422] [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: 08/14/2021] [Revised: 12/16/2021] [Accepted: 12/16/2021] [Indexed: 12/16/2022]
Abstract
Apurinic and apyrimidinic sites, also referred to as abasic or AP sites, are residues of duplex DNA in which one DNA base is removed from a Watson-Crick base pair. They are formed during the enzymatic repair of DNA and offer binding sites for a variety of guest molecules. Specifically, the AP site may bind an appropriate ligand as a substitute for the missing nucleic base, thus stabilizing the abasic site-containing DNA (AP-DNA). Notably, ligands that bind selectively to abasic sites may be employed for analytical and therapeutical purposes. As a result, there is a search for structural features that establish a strong and selective association of a given ligand with the abasic position in DNA. Against this background, this review provides an overview of the different classes of ligands for abasic site-containing DNA (AP-DNA). This review covers covalently binding substrates, namely amine and oxyamine derivatives, as well as ligands that bind to AP-DNA by noncovalent association, as represented by small heterocyclic aromatic compounds, metal-organic complexes, macrocyclic cyclophanes, and intercalator-nucleobase conjugates. As the systematic development of fluorescent probes for AP-DNA has been somewhat neglected so far, this review article contains a survey of the available reports on the fluorimetric response of the ligand upon binding to the AP-DNA. Based on these data, this compilation shall present a perspective for future developments of fluorescent probes for AP-DNA.
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Affiliation(s)
- Julika Schlosser
- Department of Chemistry and Biology, University of Siegen, Center of Micro- and Nanochemistry and (Bio)Technology (Cμ), Adolf-Reichwein-Str. 2, 57068 Siegen, Germany
| | - Heiko Ihmels
- Department of Chemistry and Biology, University of Siegen, Center of Micro- and Nanochemistry and (Bio)Technology (Cμ), Adolf-Reichwein-Str. 2, 57068 Siegen, Germany
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19
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Khan S, Ali A, Moinuddin, Mir AR, Khan RH, Alhumaydhi FA, Habib S. 4-Chloro-orthophenylenediamine alters DNA integrity and affects cell survival: inferences from a computational, biophysical/biochemical, microscopic and cell-based study. J Biomol Struct Dyn 2022; 40:14176-14187. [PMID: 34762004 DOI: 10.1080/07391102.2021.2001376] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The deleterious impact of toxic constituents of hair dyes over the human health has gained immense attention in the recent past. Their oncogenicity, mutagenicity, role in protein modification, impact on cellular metabolism has been documented. There is little information on the mechanism of reactivity of hair dye components with the nucleic acids and its implications. This work, therefore, uses computational, biophysical/biochemical, microscopic and cell-based study to analyze the interaction of monocyclic aromatic amine and a hair dye component, 4-chloro-orthophenylenediamine (4-Cl-OPD) with the DNA, its impact on DNA structure and cell survival. The results suggest that 4-Cl-OPD binds with the DNA in minor groove of the duplex involving three base pairs preferentially the G-C residues, induces strand breaks and makes DNA thermally labile through loss of hydrogen bonding/base unstacking. 4-Cl-OPD causes fragmentation of DNA, reduction in size of the molecule, alters B-DNA conformation and disrupts its secondary structure. The modified DNA gives fragmented appearance, shows broken strands and aggregation in ultra-structural analysis. 4-Cl-OPD induces ROS generation in lymphocytes, increases the comet's average tail length and reduces the viability of lymphocytes. This study forms a base for establishing the direct toxicity of 4-Cl-OPD at the molecular and cellular level through direct production of superoxide radicalCommunicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Shifa Khan
- Department of Biochemistry, Faculty of Medicine, Jawaharlal Nehru Medical College, Aligarh Muslim University, Aligarh, India
| | - Asif Ali
- Department of Biochemistry, Faculty of Medicine, Jawaharlal Nehru Medical College, Aligarh Muslim University, Aligarh, India
| | - Moinuddin
- Department of Biochemistry, Faculty of Medicine, Jawaharlal Nehru Medical College, Aligarh Muslim University, Aligarh, India
| | - Abdul Rouf Mir
- Department of Biochemistry, Faculty of Medicine, Jawaharlal Nehru Medical College, Aligarh Muslim University, Aligarh, India
| | - Rizwan Hasan Khan
- Interdisciplinary Biotechnology Unit, Faculty of Life Sciences, Aligarh Muslim University, Aligarh, India
| | - Fahad A Alhumaydhi
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah, Saudi Arabia
| | - Safia Habib
- Department of Biochemistry, Faculty of Medicine, Jawaharlal Nehru Medical College, Aligarh Muslim University, Aligarh, India
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20
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Selective delivery of pentamidine toward cancer cells by self-assembled nanoparticles. Int J Pharm 2022; 625:122102. [PMID: 35961419 DOI: 10.1016/j.ijpharm.2022.122102] [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: 05/01/2022] [Revised: 08/03/2022] [Accepted: 08/05/2022] [Indexed: 11/23/2022]
Abstract
Pentamidine (PTM) is an aromatic diamidine approved for the treatment of parasitic infections that has been recently proposed for possible repositioning as an anticancer drug. To this aim, efforts have been made to improve its therapeutic efficacy and reduce associated adverse effects through both covalent derivatization and association with nanocarriers. To efficiently encapsulate PTM into biocompatible nanoparticles and to enhance its selectivity toward cancer cells, a squalene (SQ) derivative (1,1',2-tris-norsqualenoic acid, SQ-COOH) was selected to prepare PTM-loaded nanocarriers. Indeed, SQ and its derivatives self-assemble into nanoparticles in aqueous media. Furthermore, SQ-bioconjugates strongly interact with low-density lipoproteins (LDL), thus favoring preferential accumulation in cells overexpressing the LDL receptor (LDLR). We report here the preparation of nanocarriers by ion-pairing between the negatively charged SQ-COOH and the positively charged PTM free base (PTM-B), which allowed the covalent grafting of SQ to PTM to be avoided. The nanoparticles were characterized (mean size < 200 nm and zeta potential < -20 mV for SQ-COOH/PTM-B 3:1 molar ratio) and molecular modelling studies of the SQ-COOH/PTM-B interaction confirmed the nanocarrier stability. Finally, the ability to indirectly target LDLR-overexpressing cancer cells was evaluated by in vitro cell viability assays and confirmed by LDLR silencing, serum privation and simvastatin treatment.
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21
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Synthesis and Evaluation of Novel DNA Minor Groove Binders as Antiamoebic Agents. Antibiotics (Basel) 2022; 11:antibiotics11070935. [PMID: 35884189 PMCID: PMC9312114 DOI: 10.3390/antibiotics11070935] [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] [Received: 05/30/2022] [Revised: 06/30/2022] [Accepted: 07/05/2022] [Indexed: 12/02/2022] Open
Abstract
The free-living amoeba Acanthamoeba castellanii is responsible for the central nervous infection granulomatous amoebic encephalitis and sight-threatening infection Acanthamoeba keratitis. Moreover, no effective treatment is currently present, and a combination drug therapy is used. In this study, twelve DNA minor groove binders (MGBs) were synthesized and tested for their antiamoebic activity via amoebicidal, encystation, excystation, and cytopathogenicity assays. It was found that the compounds MGB3, MGB6, MGB22, MGB24, and MGB16 significantly reduce amoeba viability to 76.20%, 59.45%, 66.5%, 39.32%, and 43.21%, respectively, in amoebicidal assays. Moreover, the compounds MGB6, MGB20, MGB22, MGB28, MGB30, MGB32, and MGB16 significantly inhibit Acanthamoeba cysts, leading to the development of only 46.3%, 39%, 30.3%, 29.6%, 27.8%, 41.5%, and 45.6% cysts. Additionally, the compounds MGB3, MGB4, MGB6, MGB22, MGB24, MGB28, MGB32, and MGB16 significantly reduce the re-emergence of cysts to trophozoites, with viable trophozoites being only 64.3%, 47.3%, 41.4%, 52.9%, 55.4%, 40.6%, 62.1%, and 51.7%. Moreover, the compounds MGB3, MGB4, and MGB6 exhibited the greatest reduction in amoeba-mediated host-cell death, with cell death reduced to 41.5%, 49.4%, and 49.5%. With the following determined, future in vivo studies can be carried out to understand the effect of the compounds on animal models such as mice.
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22
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Wamhoff EC, Romanov A, Huang H, Read BJ, Ginsburg E, Knappe GA, Kim HM, Farrell NP, Irvine DJ, Bathe M. Controlling Nuclease Degradation of Wireframe DNA Origami with Minor Groove Binders. ACS NANO 2022; 16:8954-8966. [PMID: 35640255 PMCID: PMC9649841 DOI: 10.1021/acsnano.1c11575] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Viruslike particles (VLPs) fabricated using wireframe DNA origami are emerging as promising vaccine and gene therapeutic delivery platforms due to their programmable nature that offers independent control over their size and shape, as well as their site-specific functionalization. As materials that biodegrade in the presence of endonucleases, specifically DNase I and II, their utility for the targeting of cells, tissues, and organs depends on their stability in vivo. Here, we explore minor groove binders (MGBs) as specific endonuclease inhibitors to control the degradation half-life of wireframe DNA origami. Bare, unprotected DNA-VLPs composed of two-helix edges were found to be stable in fetal bovine serum under typical cell culture conditions and in human serum for 24 h but degraded within 3 h in mouse serum, suggesting species-specific endonuclease activity. Inhibiting endonucleases by incubating DNA-VLPs with diamidine-class MGBs increased their half-lives in mouse serum by more than 12 h, corroborated by protection against isolated DNase I and II. Our stabilization strategy was compatible with the functionalization of DNA-VLPs with HIV antigens, did not interfere with B-cell signaling activity of DNA-VLPs in vitro, and was nontoxic to B-cell lines. It was further found to be compatible with multiple wireframe DNA origami geometries and edge architectures. MGB protection is complementary to existing methods such as PEGylation and chemical cross-linking, offering a facile protocol to control DNase-mediated degradation rates for in vitro and possibly in vivo therapeutic and vaccine applications.
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Affiliation(s)
- Eike-Christian Wamhoff
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Anna Romanov
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Hellen Huang
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Benjamin J Read
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Eric Ginsburg
- Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia 23284-2006, United States
| | - Grant A Knappe
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Hyun Min Kim
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Nicholas P Farrell
- Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia 23284-2006, United States
| | - Darrell J Irvine
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts 02139, United States
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, United States
| | - Mark Bathe
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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23
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4-Phenylbutyric acid based homo-heteroleptic Zn(II) carboxylates: Synthesis, structural elucidation, DNA interaction through spectroscopic and computational methods as well as ALP inhibition study. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.119031] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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24
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Multitargeted anti-infective drugs: resilience to resistance in the antimicrobial resistance era. FUTURE DRUG DISCOVERY 2022; 4:FDD73. [PMID: 35600289 PMCID: PMC9112235 DOI: 10.4155/fdd-2022-0001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2022] [Accepted: 04/08/2022] [Indexed: 12/23/2022] Open
Abstract
The standard drug discovery paradigm of single molecule – single biological target – single biological effect is perhaps particularly unsuitable for anti-infective drug discovery. This is due to the rapid evolution of resistance likely to be observed with single target drugs. Multitargeted anti-infective drugs are likely to be superior due to their lower susceptibility to target-related resistance mechanisms. Strathclyde minor groove binders are a class of compounds which have been developed by adopting the multitargeted anti-infective drugs paradigm, and their effectiveness against a wide range of pathogenic organisms is discussed. The renaming of this class to Strathclyde nucleic acid binders is also presented due to their likely targets including both DNA and RNA.
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25
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Costas-Lago MC, Vila N, Rahman A, Besada P, Rozas I, Brea J, Loza MI, González-Romero E, Terán C. Novel Pyridazin-3(2 H)-one-Based Guanidine Derivatives as Potential DNA Minor Groove Binders with Anticancer Activity. ACS Med Chem Lett 2022; 13:463-469. [PMID: 35300077 PMCID: PMC8919506 DOI: 10.1021/acsmedchemlett.1c00633] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 02/04/2022] [Indexed: 02/08/2023] Open
Abstract
Novel aryl guanidinium analogues containing the pyridazin-3(2H)-one core were proposed as minor groove binders (MGBs) with the support of molecular docking studies. The target dicationic or monocationic compounds, which show the guanidium group at different positions of the pyridazinone moiety, were synthesized using the corresponding silyl-protected pyridazinones as key intermediates. Pyridazinone scaffolds were converted into the adequate bromoalkyl derivatives, which by reaction with N,N'-di-Boc-protected guanidine followed by acid hydrolysis provided the hydrochloride salts 1-14 in good yields. The ability of new pyridazin-3(2H)-one-based guanidines as DNA binders was studied by means of DNA UV-thermal denaturation experiments. Their antiproliferative activity was also explored in three cancer cell lines (NCI-H460, A2780, and MCF-7). Compounds 1-4 with a bis-guanidinium structure display a weak DNA binding affinity and exhibit a reasonable cellular viability inhibition percentage in the three cancer cell lines studied.
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Affiliation(s)
- María Carmen Costas-Lago
- Departamento de Química Orgánica, Universidade de Vigo, 36310 Vigo, España
- Instituto de Investigación Sanitaria Galicia Sur, Hospital Álvaro Cunqueiro, 36213 Vigo, España
| | - Noemí Vila
- Departamento de Química Orgánica, Universidade de Vigo, 36310 Vigo, España
- Instituto de Investigación Sanitaria Galicia Sur, Hospital Álvaro Cunqueiro, 36213 Vigo, España
| | - Adeyemi Rahman
- School of Chemistry, Trinity Biomedical Sciences Institute, Trinity College Dublin, 152-160 Pearse Street, Dublin 2, Ireland
| | - Pedro Besada
- Departamento de Química Orgánica, Universidade de Vigo, 36310 Vigo, España
- Instituto de Investigación Sanitaria Galicia Sur, Hospital Álvaro Cunqueiro, 36213 Vigo, España
| | - Isabel Rozas
- School of Chemistry, Trinity Biomedical Sciences Institute, Trinity College Dublin, 152-160 Pearse Street, Dublin 2, Ireland
| | - José Brea
- Drug Screening Platform/Biofarma Research Group, CIMUS Research Center. Departamento de Farmacoloxía, Farmacia e Tecnoloxía Farmacéutica. Universidade de Santiago de Compostela, 15782 Santiago de Compostela, España
| | - María Isabel Loza
- Drug Screening Platform/Biofarma Research Group, CIMUS Research Center. Departamento de Farmacoloxía, Farmacia e Tecnoloxía Farmacéutica. Universidade de Santiago de Compostela, 15782 Santiago de Compostela, España
| | - Elisa González-Romero
- Departamento de Química Analítica y Alimentaria, Universidade de Vigo, 36310 Vigo, España
| | - Carmen Terán
- Departamento de Química Orgánica, Universidade de Vigo, 36310 Vigo, España
- Instituto de Investigación Sanitaria Galicia Sur, Hospital Álvaro Cunqueiro, 36213 Vigo, España
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26
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Abstract
Pentamidine (PTM), which is a diamine that is widely known for its antimicrobial activity, is a very interesting drug whose mechanism of action is not fully understood. In recent years, PTM has been proposed as a novel potential drug candidate for the treatment of mental illnesses, myotonic dystrophy, diabetes, and tumors. Nevertheless, the systemic administration of PTM causes severe side effects, especially nephrotoxicity. In order to efficiently deliver PTM and reduce its side effects, several nanosystems that take advantage of the chemical characteristics of PTM, such as the presence of two positively charged amidine groups at physiological pH, have been proposed as useful delivery tools. Polymeric, lipidic, inorganic, and other types of nanocarriers have been reported in the literature for PTM delivery, and they are all in different development phases. The available approaches for the design of PTM nanoparticulate delivery systems are reported in this review, with a particular emphasis on formulation strategies and in vitro/in vivo applications. Furthermore, a critical view of the future developments of nanomedicine for PTM applications, based on recent repurposing studies, is provided. Created with BioRender.com.
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27
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Guo P, Farahat AA, Paul A, Boykin DW, Wilson WD. Engineered modular heterocyclic-diamidines for sequence-specific recognition of mixed AT/GC base pairs at the DNA minor groove. Chem Sci 2021; 12:15849-15861. [PMID: 35024109 PMCID: PMC8672716 DOI: 10.1039/d1sc04720e] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 10/28/2021] [Indexed: 12/20/2022] Open
Abstract
This report describes a breakthrough in a project to design minor groove binders to recognize any sequence of DNA. A key goal is to invent synthetic chemistry for compound preparation to recognize an adjacent GG sequence that has been difficult to target. After trying several unsuccessful compound designs, an N-alkyl-benzodiimidazole structure was selected to provide two H-bond acceptors for the adjacent GG-NH groups. Flanking thiophenes provide a preorganized structure with strong affinity, DB2831, and the structure is terminated by phenyl-amidines. The binding experimental results for DB2831 with a target AAAGGTTT sequence were successful and include a high ΔT m, biosensor SPR with a K D of 4 nM, a similar K D from fluorescence titrations and supporting competition mass spectrometry. MD analysis of DB2831 bound to an AAAGGTTT site reveals that the two unprotonated N of the benzodiimidazole group form strong H-bonds (based on distance) with the two central G-NH while the central -CH of the benzodiimidazole is close to the -C[double bond, length as m-dash]O of a C base. These three interactions account for the strong preference of DB2831 for a -GG- sequence. Surprisingly, a complex with one dynamic, interfacial water is favored with 75% occupancy.
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Affiliation(s)
- Pu Guo
- Department of Chemistry, Center for Diagnostics and Therapeutics, Georgia State University 50 Decatur St SE Atlanta GA 30303 USA +1 404-413-5503
| | - Abdelbasset A Farahat
- Department of Chemistry, Center for Diagnostics and Therapeutics, Georgia State University 50 Decatur St SE Atlanta GA 30303 USA +1 404-413-5503
- Department of Pharmaceutical Organic Chemistry, Faculty of Pharmacy, Mansoura University Mansoura 35516 Egypt
| | - Ananya Paul
- Department of Chemistry, Center for Diagnostics and Therapeutics, Georgia State University 50 Decatur St SE Atlanta GA 30303 USA +1 404-413-5503
| | - David W Boykin
- Department of Chemistry, Center for Diagnostics and Therapeutics, Georgia State University 50 Decatur St SE Atlanta GA 30303 USA +1 404-413-5503
| | - W David Wilson
- Department of Chemistry, Center for Diagnostics and Therapeutics, Georgia State University 50 Decatur St SE Atlanta GA 30303 USA +1 404-413-5503
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28
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The analysis of interactions between DNA and small molecules: proposals for binding mechanisms based on computational data. MONATSHEFTE FUR CHEMIE 2021. [DOI: 10.1007/s00706-021-02872-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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29
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Fudickar W, Bauch M, Ihmels H, Linker T. DNA-Triggered Enhancement of Singlet Oxygen Production by Pyridinium Alkynylanthracenes. Chemistry 2021; 27:13591-13604. [PMID: 34263955 DOI: 10.1002/chem.202101918] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Indexed: 12/23/2022]
Abstract
There is an ongoing interest in 1 O2 sensitizers, whose activity is selectively controlled by their interaction with DNA. To this end, we synthesized three isomeric pyridinium alkynylanthracenes 2 o-p and a water-soluble trapping reagent for 1 O2 . In water and in the absence of DNA, these dyes show a poor efficiency to sensitize the photooxygenation of the trapping reagent as they decompose due to electron transfer processes. In contrast, in the presence of DNA 1 O2 is generated from the excited DNA-bound ligand. The interactions of 2 o-p with DNA were investigated by thermal DNA melting studies, UV/vis and fluorescence spectroscopy, and linear and circular dichroism spectroscopy. Our studies revealed an intercalative binding with an orientation of the long pyridyl-alkynyl axis parallel to the main axis of the DNA base pairs. In the presence of poly(dA : dT), all three isomers show an enhanced formation of singlet oxygen, as indicated by the reaction of the latter with the trapping reagent. With green light irradiation of isomer 2 o in poly(dA : dT), the conversion rate of the trapping reagent is enhanced by a factor >10. The formation of 1 O2 was confirmed by control experiments under anaerobic conditions, in deuterated solvents, or by addition of 1 O2 quenchers. When bound to poly(dG : dC), the opposite effect was observed only for isomers 2 o and 2 m, namely the trapping reagent reacted significantly slower. Overall, we showed that pyridinium alkynylanthracenes are very useful intercalators, that exhibit an enhanced photochemical 1 O2 generation in the DNA-bound state.
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Affiliation(s)
- Werner Fudickar
- Department of Chemistry, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476, Potsdam, Germany
| | - Marcel Bauch
- Department of Chemistry, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476, Potsdam, Germany
| | - Heiko Ihmels
- Department of Chemistry and Biology, University of Siegen, Adolf-Reichwein-Str. 2, 57068, Siegen, Germany
| | - Torsten Linker
- Department of Chemistry, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476, Potsdam, Germany
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30
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Ganguly S, Murugan NA, Ghosh D, Narayanaswamy N, Govindaraju T, Basu G. DNA Minor Groove-Induced cis- trans Isomerization of a Near-Infrared Fluorescent Probe. Biochemistry 2021; 60:2084-2097. [PMID: 34142803 DOI: 10.1021/acs.biochem.1c00281] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The discovery of small molecules that exhibit turn-on far-red or near-infrared (NIR) fluorescence upon DNA binding and understanding how they bind DNA are important for imaging and bioanalytical applications. Here we report the DNA-bound structure and the DNA binding mechanism of quinone cyanine dithiazole (QCy-DT), a recently reported AT-specific turn-on NIR fluorescent probe for double-stranded DNA. The nuclear magnetic resonance (NMR)-derived structure showed minor groove binding but no specific ligand-DNA interactions, consistent with an endothermic and entropy-driven binding mechanism deduced from isothermal titration calorimetry. Minor groove binding is typically fast because it minimally perturbs the DNA structure. However, QCy-DT exhibited unusually slow DNA binding. The cyanine-based probe is capable of cis-trans isomerization due to overlapping methine bridges, with 16 possible slowly interconverting cis/trans isomers. Using NMR, density functional theory, and free energy calculations, we show that the DNA-free and DNA-bound environments of QCy-DT prefer distinctly different isomers, indicating that the origin of the slow kinetics is a cis-trans isomerization and that the minor groove preferentially selects an otherwise unstable cis/trans isomer of QCy-DT. Flux analysis showed the conformational selection pathway to be the dominating DNA binding mechanism at low DNA concentrations, which switches to the induced fit pathway at high DNA concentrations. This report of cis/trans isomerization of a ligand, upon binding the DNA minor groove, expands the prevailing understanding of unique discriminatory powers of the minor groove and has an important bearing on using polymethine cyanine dyes to probe the kinetics of molecular interactions.
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Affiliation(s)
- Sudakshina Ganguly
- Department of Biophysics, Bose Institute, P-1/12 CIT Scheme VIIM, Kolkata 700054, West Bengal, India
| | - N Arul Murugan
- Division of Theoretical Chemistry and Biology, School of Biotechnology, KTH Royal Institute of Technology, S-106 91 Stockholm, Sweden
| | - Debasis Ghosh
- Bioorganic Chemistry Laboratory, New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur P.O., Bengaluru 560064, Karnataka, India
| | - Nagarjun Narayanaswamy
- Bioorganic Chemistry Laboratory, New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur P.O., Bengaluru 560064, Karnataka, India
| | - Thimmaiah Govindaraju
- Bioorganic Chemistry Laboratory, New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur P.O., Bengaluru 560064, Karnataka, India
| | - Gautam Basu
- Department of Biophysics, Bose Institute, P-1/12 CIT Scheme VIIM, Kolkata 700054, West Bengal, India
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31
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Sharma V, Gupta M, Kumar P, Sharma A. A Comprehensive Review on Fused Heterocyclic as DNA Intercalators: Promising Anticancer Agents. Curr Pharm Des 2021; 27:15-42. [PMID: 33213325 DOI: 10.2174/1381612826666201118113311] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 08/02/2020] [Indexed: 12/09/2022]
Abstract
Since the discovery of DNA intercalating agents (by Lerman, 1961), a growing number of organic, inorganic, and metallic compounds have been developed to treat life-threatening microbial infections and cancers. Fused-heterocycles are amongst the most important group of compounds that have the ability to interact with DNA. DNA intercalators possess a planar aromatic ring structure that inserts itself between the base pairs of nucleic acids. Once inserted, the aromatic structure makes van der Waals interactions and hydrogen-bonding interactions with the base pairs. The DNA intercalator may also contain an ionizable group that can form ionic interactions with the negatively charged phosphate backbone. After the intercalation, other cellular processes could take place, leading ultimately to cell death. The heterocyclic nucleus present in the DNA intercalators can be considered as a pharmacophore that plays an instrumental role in dictating the affinity and selectivity exhibited by these compounds. In this work, we have carried out a revision of small organic molecules that bind to the DNA molecule via intercalation and cleaving and exert their antitumor activity. A general overview of the most recent results in this area, paying particular attention to compounds that are currently under clinical trials, is provided. Advancement in spectroscopic techniques studying DNA interaction can be examined in-depth, yielding important information on structure-activity relationships. In this comprehensive review, we have focused on the introduction to fused heterocyclic agents with DNA interacting features, from medicinal point of view. The structure-activity relationships points, cytotoxicity data, and binding data and future perspectives of medicinal compounds have been discussed in detail.
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Affiliation(s)
- Vikas Sharma
- IIMT College of Pharmacy, Knowledge Park III, Greater Noida, Uttar Pradesh-201308, India
| | - Mohit Gupta
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Robertson Life Sciences Building, 2730 South Moody Avenue, Portland, OR 97201, United States
| | - Pradeep Kumar
- Department of Pharmacy and Pharmacology, School of Therapeutic Sciences, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, 2193, South Africa
| | - Atul Sharma
- School of Chemistry, Monash University, Clayton, Victoria, 3800, Australia
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32
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Ma H, Liang H, Cai S, O'Keefe BR, Mooberry SL, Cichewicz RH. An Integrated Strategy for the Detection, Dereplication, and Identification of DNA-Binding Biomolecules from Complex Natural Product Mixtures. JOURNAL OF NATURAL PRODUCTS 2021; 84:750-761. [PMID: 33226219 PMCID: PMC9229839 DOI: 10.1021/acs.jnatprod.0c00946] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
A fundamental factor in natural product drug discovery programs is the necessity to identify the active component(s) from complex chemical mixtures. Whereas this has traditionally been accomplished using bioassay-guided fractionation, we questioned whether alternative techniques could supplement and, in some cases, even supplant this approach. We speculated that a combination of ligand-fishing methods and modern analytical tools (e.g., LC-MS and online natural product databases) offered a route to enhance natural product drug discovery. Herein, a candidate solution referred to as the lickety-split ligand-affinity-based molecular angling system (LLAMAS) is described. This approach utilizes an ultrafiltration-based LC-PDA-MS/MS-guided DNA-binding assay in combination with the (i) Global Natural Products Social Molecular Networking, (ii) Dictionary of Natural Products, and (iii) SciFinder platforms to identify DNA binders in complex chemical mixtures. LLAMAS was initially vetted in tests using known small-molecule DNA binders and then optimized to a 96-well plate-based format. A set of 332 plant samples used in traditional Chinese medicine was screened for DNA-binding activity with LLAMAS, resulting in the identification of seven DNA-binding molecules, including berberine (12), palmatine (13), coptisine (14), fangchinoline (15), tetrandrine (16), daurisoline (17), and dauricine (18). These results demonstrate that LLAMAS is an effective natural product discovery platform for the efficient identification and dereplication of DNA-binding molecules from complex mixtures.
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Affiliation(s)
- Hongyan Ma
- Department of Chemistry and Biochemistry, Stephenson Life Sciences Research Center, and Natural Products Discovery Group and Institute for Natural Products Applications and Research Technologies, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Huiyun Liang
- Department of Pharmacology, University of Texas Health Science Center, San Antonio, Texas 78229, United States
| | - Shengxin Cai
- Department of Chemistry and Biochemistry, Stephenson Life Sciences Research Center, and Natural Products Discovery Group and Institute for Natural Products Applications and Research Technologies, University of Oklahoma, Norman, Oklahoma 73019, United States
| | - Barry R O'Keefe
- Natural Products Branch, Developmental Therapeutics Program, Division of Cancer Treatment and Diagnosis, and Molecular Targets Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland 21702, United States
| | - Susan L Mooberry
- Department of Pharmacology, University of Texas Health Science Center, San Antonio, Texas 78229, United States
| | - Robert H Cichewicz
- Department of Chemistry and Biochemistry, Stephenson Life Sciences Research Center, and Natural Products Discovery Group and Institute for Natural Products Applications and Research Technologies, University of Oklahoma, Norman, Oklahoma 73019, United States
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33
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Lam AYF, Vuong D, Jex AR, Piggott AM, Lacey E, Emery-Corbin SJ. TriTOX: A novel Trichomonas vaginalis assay platform for high-throughput screening of compound libraries. INTERNATIONAL JOURNAL FOR PARASITOLOGY-DRUGS AND DRUG RESISTANCE 2021; 15:68-80. [PMID: 33601283 PMCID: PMC7897990 DOI: 10.1016/j.ijpddr.2021.01.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 12/22/2020] [Accepted: 01/12/2021] [Indexed: 11/25/2022]
Abstract
Trichomonas vaginalis is a neglected urogenital parasitic protist that causes 170 million cases of trichomoniasis annually, making it the most prevalent non-viral, sexually transmitted disease. Trichomoniasis treatment relies on nitroheterocyclics, such as metronidazole. However, with increasing drug-resistance, there is an urgent need for novel anti-trichomonals. Little progress has been made to translate anti-trichomonal research into commercialised therapeutics, and the absence of a standardised compound-screening platform is the immediate stumbling block for drug-discovery. Herein, we describe a simple, cost-effective growth assay for T. vaginalis and the related Tritrichomonas foetus. Tracking changes in pH were a valid indicator of trichomonad growth (T. vaginalis and T. foetus), allowing development of a miniaturised, chromogenic growth assay based on the phenol red indicator in 96- and 384-well microtiter plate formats. The outputs of this assay can be quantitatively and qualitatively assessed, with consistent dynamic ranges based on Z' values of 0.741 and 0.870 across medium- and high-throughput formats, respectively. We applied this high-throughput format within the largest pure-compound microbial metabolite screen (812 compounds) for T. vaginalis and identified 43 hit compounds. We compared these identified compounds to mammalian cell lines, and highlighted extensive overlaps between anti-trichomonal and anti-tumour activity. Lastly, observing nanomolar inhibition of T. vaginalis by fumagillin, and noting this compound has reported activity in other protists, we performed in silico analyses of the interaction of fumagillin with its molecular target methionine aminopeptidase 2 for T. vaginalis, Giardia lamblia and Entamoeba histolytica, highlighting potential for fumagillin as a broad-spectrum anti-protistal against microaerophilic protists. Together, this new platform will accelerate drug-discovery efforts, underpin drug-resistance screening in trichomonads, and contributing to a growing body of evidence highlighting the potential of microbial natural products as novel anti-protistals.
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Affiliation(s)
- Alexander Y F Lam
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia; Department of Medical Biology, The University of Melbourne, Parkville, VIC, Australia
| | - Daniel Vuong
- Microbial Screening Technologies, Smithfield, NSW, Australia
| | - Aaron R Jex
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia; Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC, Australia; Department of Medical Biology, The University of Melbourne, Parkville, VIC, Australia
| | - Andrew M Piggott
- Department of Molecular Sciences, Faculty of Science and Engineering, Macquarie University, North Ryde, NSW, Australia
| | - Ernest Lacey
- Microbial Screening Technologies, Smithfield, NSW, Australia; Department of Molecular Sciences, Faculty of Science and Engineering, Macquarie University, North Ryde, NSW, Australia
| | - Samantha J Emery-Corbin
- Population Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC, Australia; Department of Medical Biology, The University of Melbourne, Parkville, VIC, Australia.
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34
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Bortolozzi R, Ihmels H, Schulte R, Stremmel C, Viola G. Synthesis, DNA-binding and antiproliferative properties of diarylquinolizinium derivatives. Org Biomol Chem 2021; 19:878-890. [PMID: 33410854 DOI: 10.1039/d0ob02298e] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
A series of ten 2,7- and 2,8-diarylquinolizinium derivatives was synthesized and their DNA-binding and cytotoxic properties were investigated. Except for one nitro-substituted derivative all tested diarylquinolizinium ions bind to DNA with sufficient affinity (2 × 104 M-1-2 × 105 M-1). It was shown with photometric, fluorimetric and polarimetric titrations as well as with flow-LD analysis that the ligands bind mainly by intercalation to duplex DNA, however, depending on the ligand-DNA ratio, groove binding and backbone association were also observed with some derivatives. The biological activity was further investigated with tests of cytotoxicity and antiproliferative properties towards non-tumor cells and selected cancer cells, along with cell cycle analysis and an annexin-V assay. Notably, substrates that carry donor-functionalities in the 4-position of the phenyl substituents revealed a strong, and in some cases selective, antiproliferative activity as quantified by the growth inhibition, GI50, at very low micromolar and even submicromolar level both in leukemia and solid tumors.
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Affiliation(s)
- Roberta Bortolozzi
- Department of Women's and Child's health, Oncohematology laboratory, University of Padova, Via Giustiniani 2, I-35128 Padova, Italy. giampietro,
| | - Heiko Ihmels
- Department of Chemistry and Biology, University of Siegen, Adolf-Reichwein-Str. 2, 57068 Siegen, Germany.
| | - Robin Schulte
- Department of Chemistry and Biology, University of Siegen, Adolf-Reichwein-Str. 2, 57068 Siegen, Germany.
| | - Christopher Stremmel
- Department of Chemistry and Biology, University of Siegen, Adolf-Reichwein-Str. 2, 57068 Siegen, Germany.
| | - Giampietro Viola
- Department of Women's and Child's health, Oncohematology laboratory, University of Padova, Via Giustiniani 2, I-35128 Padova, Italy. giampietro,
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Bai S, Wang J, Yang K, Zhou C, Xu Y, Song J, Gu Y, Chen Z, Wang M, Shoen C, Andrade B, Cynamon M, Zhou K, Wang H, Cai Q, Oldfield E, Zimmerman SC, Bai Y, Feng X. A polymeric approach toward resistance-resistant antimicrobial agent with dual-selective mechanisms of action. SCIENCE ADVANCES 2021; 7:eabc9917. [PMID: 33571116 PMCID: PMC7840121 DOI: 10.1126/sciadv.abc9917] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Accepted: 12/08/2020] [Indexed: 05/19/2023]
Abstract
Antibiotic resistance is now a major threat to human health, and one approach to combating this threat is to develop resistance-resistant antibiotics. Synthetic antimicrobial polymers are generally resistance resistant, having good activity with low resistance rates but usually with low therapeutic indices. Here, we report our solution to this problem by introducing dual-selective mechanisms of action to a short amidine-rich polymer, which can simultaneously disrupt bacterial membranes and bind to bacterial DNA. The oligoamidine shows unobservable resistance generation but high therapeutic indices against many bacterial types, such as ESKAPE strains and clinical isolates resistant to multiple drugs, including colistin. The oligomer exhibited excellent effectiveness in various model systems, killing extracellular or intracellular bacteria in the presence of mammalian cells, removing all bacteria from Caenorhabditis elegans, and rescuing mice with severe infections. This "dual mechanisms of action" approach may be a general strategy for future development of antimicrobial polymers.
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Affiliation(s)
- Silei Bai
- Institute of Chemical Biology and Nanomedicine, Hunan University, Changsha, Hunan 410082, China
- State Key Laboratory of Chem/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha, Hunan 410082, China
- School of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, China
| | - Jianxue Wang
- Institute of Chemical Biology and Nanomedicine, Hunan University, Changsha, Hunan 410082, China
- State Key Laboratory of Chem/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha, Hunan 410082, China
- School of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, China
| | - Kailing Yang
- Institute of Chemical Biology and Nanomedicine, Hunan University, Changsha, Hunan 410082, China
- State Key Laboratory of Chem/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha, Hunan 410082, China
- School of Biology, Hunan University, Changsha, Hunan 410082, China
| | - Cailing Zhou
- Institute of Chemical Biology and Nanomedicine, Hunan University, Changsha, Hunan 410082, China
- State Key Laboratory of Chem/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha, Hunan 410082, China
- School of Biology, Hunan University, Changsha, Hunan 410082, China
| | - Yangfan Xu
- Institute of Chemical Biology and Nanomedicine, Hunan University, Changsha, Hunan 410082, China
- State Key Laboratory of Chem/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha, Hunan 410082, China
- School of Biology, Hunan University, Changsha, Hunan 410082, China
| | - Junfeng Song
- Institute of Chemical Biology and Nanomedicine, Hunan University, Changsha, Hunan 410082, China
- State Key Laboratory of Chem/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha, Hunan 410082, China
- School of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, China
| | - Yuanxin Gu
- Institute of Chemical Biology and Nanomedicine, Hunan University, Changsha, Hunan 410082, China
- State Key Laboratory of Chem/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha, Hunan 410082, China
- School of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, China
| | - Zheng Chen
- Institute of Chemical Biology and Nanomedicine, Hunan University, Changsha, Hunan 410082, China
- State Key Laboratory of Chem/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha, Hunan 410082, China
- School of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, China
| | - Min Wang
- Institute of Chemical Biology and Nanomedicine, Hunan University, Changsha, Hunan 410082, China
- State Key Laboratory of Chem/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha, Hunan 410082, China
- School of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, China
| | - Carolyn Shoen
- Veterans Affairs Medical Center, Syracuse, NY 13210, USA
| | - Brenda Andrade
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | | | - Kai Zhou
- Shenzhen Institute of Respiratory Diseases, The First Affiliated Hospital of Southern University of Science and Technology (Shenzhen People's Hospital), Shenzhen, Guangdong 518035, China
- The Second Clinical Medical College of Jinan University (Shenzhen People's Hospital), Shenzhen, Guangdong 518020, China
| | - Hui Wang
- Department of Clinical Laboratories, Peking University People's Hospital, Beijing, 100044, China
| | - Qingyun Cai
- School of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, China
| | - Eric Oldfield
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Steven C Zimmerman
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Yugang Bai
- Institute of Chemical Biology and Nanomedicine, Hunan University, Changsha, Hunan 410082, China.
- State Key Laboratory of Chem/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha, Hunan 410082, China
- School of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, China
| | - Xinxin Feng
- Institute of Chemical Biology and Nanomedicine, Hunan University, Changsha, Hunan 410082, China.
- State Key Laboratory of Chem/Biosensing and Chemometrics, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology, Hunan University, Changsha, Hunan 410082, China
- School of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan 410082, China
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Pegoraro S, Ros G, Sgubin M, Petrosino S, Zambelli A, Sgarra R, Manfioletti G. Targeting the intrinsically disordered architectural High Mobility Group A (HMGA) oncoproteins in breast cancer: learning from the past to design future strategies. Expert Opin Ther Targets 2020; 24:953-969. [PMID: 32970506 DOI: 10.1080/14728222.2020.1814738] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
INTRODUCTION Triple-negative breast cancer (TNBC) is the most difficult breast cancer subtype to treat because of its heterogeneity and lack of specific therapeutic targets. High Mobility Group A (HMGA) proteins are chromatin architectural factors that have multiple oncogenic functions in breast cancer, and they represent promising molecular therapeutic targets for this disease. AREAS COVERED We offer an overview of the strategies that have been exploited to counteract HMGA oncoprotein activities at the transcriptional and post-transcriptional levels. We also present the possibility of targeting cancer-associated factors that lie downstream of HMGA proteins and discuss the contribution of HMGA proteins to chemoresistance. EXPERT OPINION Different strategies have been exploited to counteract HMGA protein activities; these involve interfering with their nucleic acid binding properties and the blocking of HMGA expression. Some approaches have provided promising results. However, some unique characteristics of the HMGA proteins have not been exploited; these include their extensive protein-protein interaction network and their intrinsically disordered status that present the possibility that HMGA proteins could be involved in the formation of proteinaceous membrane-less organelles (PMLO) by liquid-liquid phase separation. These unexplored characteristics could open new pharmacological avenues to counteract the oncogenic contributions of HMGA proteins.
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Affiliation(s)
- Silvia Pegoraro
- Department of Life Sciences, University of Trieste , Trieste, Italy
| | - Gloria Ros
- Department of Life Sciences, University of Trieste , Trieste, Italy
| | - Michela Sgubin
- Department of Life Sciences, University of Trieste , Trieste, Italy
| | - Sara Petrosino
- Department of Life Sciences, University of Trieste , Trieste, Italy
| | | | - Riccardo Sgarra
- Department of Life Sciences, University of Trieste , Trieste, Italy
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Carraro ML, Marques S, Silva AS, Freitas B, Silva PMA, Pedrosa J, De Marco P, Bousbaa H, Fernandes C, Tiritan ME, Silva AMS, Pinto MMM. Synthesis of New Chiral Derivatives of Xanthones with Enantioselective Effect on Tumor Cell Growth and DNA Crosslinking. ChemistrySelect 2020. [DOI: 10.1002/slct.202002588] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Maria L. Carraro
- Department of Chemical Sciences Laboratory of Organic and Pharmaceutical Chemistry Faculty of Pharmacy University of Porto Rua de Jorge Viterbo Ferreira 228 4050-313 Porto Portugal
| | - Sandra Marques
- CESPU Instituto de Investigação e Formação Avançada em Ciências e Tecnologias da Saúde (IINFACTS) Rua Central de Gandra, 1317 4585-116 Gandra PRD Portugal
| | - Ana Sofia Silva
- Department of Chemical Sciences Laboratory of Organic and Pharmaceutical Chemistry Faculty of Pharmacy University of Porto Rua de Jorge Viterbo Ferreira 228 4050-313 Porto Portugal
| | - Bruno Freitas
- Department of Chemical Sciences Laboratory of Organic and Pharmaceutical Chemistry Faculty of Pharmacy University of Porto Rua de Jorge Viterbo Ferreira 228 4050-313 Porto Portugal
| | - Patrícia M. A. Silva
- CESPU Instituto de Investigação e Formação Avançada em Ciências e Tecnologias da Saúde (IINFACTS) Rua Central de Gandra, 1317 4585-116 Gandra PRD Portugal
| | - Joel Pedrosa
- CESPU Instituto de Investigação e Formação Avançada em Ciências e Tecnologias da Saúde (IINFACTS) Rua Central de Gandra, 1317 4585-116 Gandra PRD Portugal
| | - Paolo De Marco
- CESPU Instituto de Investigação e Formação Avançada em Ciências e Tecnologias da Saúde (IINFACTS) Rua Central de Gandra, 1317 4585-116 Gandra PRD Portugal
| | - Hassan Bousbaa
- CESPU Instituto de Investigação e Formação Avançada em Ciências e Tecnologias da Saúde (IINFACTS) Rua Central de Gandra, 1317 4585-116 Gandra PRD Portugal
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR) Edifício do Terminal de Cruzeiros do Porto de Leixões Av. General Norton de Matos s/n 4050-208 Matosinhos Portugal
| | - Carla Fernandes
- Department of Chemical Sciences Laboratory of Organic and Pharmaceutical Chemistry Faculty of Pharmacy University of Porto Rua de Jorge Viterbo Ferreira 228 4050-313 Porto Portugal
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR) Edifício do Terminal de Cruzeiros do Porto de Leixões Av. General Norton de Matos s/n 4050-208 Matosinhos Portugal
| | - Maria Elizabeth Tiritan
- Department of Chemical Sciences Laboratory of Organic and Pharmaceutical Chemistry Faculty of Pharmacy University of Porto Rua de Jorge Viterbo Ferreira 228 4050-313 Porto Portugal
- CESPU Instituto de Investigação e Formação Avançada em Ciências e Tecnologias da Saúde (IINFACTS) Rua Central de Gandra, 1317 4585-116 Gandra PRD Portugal
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR) Edifício do Terminal de Cruzeiros do Porto de Leixões Av. General Norton de Matos s/n 4050-208 Matosinhos Portugal
| | - Artur M. S. Silva
- QOPNA & LAQV-REQUIMTE Departamento de Química Universidade de Aveiro Aveiro 3810-103 Aveiro Portugal
| | - Madalena M. M. Pinto
- Department of Chemical Sciences Laboratory of Organic and Pharmaceutical Chemistry Faculty of Pharmacy University of Porto Rua de Jorge Viterbo Ferreira 228 4050-313 Porto Portugal
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR) Edifício do Terminal de Cruzeiros do Porto de Leixões Av. General Norton de Matos s/n 4050-208 Matosinhos Portugal
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Kolade SO, Izunobi JU, Hosten EC, Olasupo IA, Ogunlaja AS, Familoni OB. Synthesis, crystal structure and docking studies of tetracyclic 10-iodo-1,2-dihydroisoquinolino[2,1-b][1,2,4]benzothiadiazine 12,12-dioxide and its precursors. Acta Crystallogr C Struct Chem 2020; 76:810-820. [PMID: 32756044 DOI: 10.1107/s2053229620009626] [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: 05/28/2020] [Accepted: 07/15/2020] [Indexed: 11/10/2022] Open
Abstract
The title compound, 10-iodo-1,2-dihydroisoquinolino[2,1-b][1,2,4]benzothiadiazine 12,12-dioxide, C15H11IN2O2S (8), was synthesized via the metal-free intramolecular N-iodosuccinimide (NIS)-mediated radical oxidative sp3-C-H aminative cyclization of 2-(2'-aminobenzenesulfonyl)-1,3,4-trihydroisoquinoline, C15H16N2O2S (7). The amino adduct 7 was prepared via a two-step reaction, starting from the condensation of 2-nitrobenzenesulfonyl chloride (4) with 1,2,3,4-tetrahydroisoquinoline (5), to afford 2-(2'-nitrobenzenesulfonyl)-1,3,4-trihydroisoquinoline, C15H14N2O4S (6), in 82% yield. The catalytic hydrogenation of 6 with hydrogen gas, in the presence of 10% palladium-on-charcoal catalyst, furnished 7. Products 6-8 were characterized by their melting points, IR and NMR (1H and 13C) spectroscopy, and single-crystal X-ray diffraction. The three compounds crystallized in the monoclinic space group, with 7 exhibiting classical intramolecular hydrogen bonds of 2.16 and 2.26 Å. All three crystal structures exhibit centrosymmetric pairs of intermolecular C-H...π(ring) and/or π-π stacking interactions. The docking studies of molecules 6, 7 and 8 with deoxyribonucleic acid (PDB id: 1ZEW) revealed minor-groove binding behaviours without intercalation, with 7 presenting the most favourable global energy of the three molecules. Nonetheless, molecule 8 interacted strongly with the DNA macromolecule, with an attractive van der Waals energy of -15.53 kcal mol-1.
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Affiliation(s)
- Sherif O Kolade
- Chemistry, University of Lagos, Akoka-Yaba, Lagos 100001, Nigeria
| | | | - Eric C Hosten
- Chemistry, Nelson Mandela University, PO Box 77000, Port Elizabeth 6031, South Africa
| | - Idris A Olasupo
- Chemistry, University of Lagos, Akoka-Yaba, Lagos 100001, Nigeria
| | - Adeniyi S Ogunlaja
- Chemistry, Nelson Mandela University, PO Box 77000, Port Elizabeth 6031, South Africa
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Berdnikova DV, Heider J, Ihmels H, Sewald N, Pithan PM. Photoinduced Release of DNA‐Binding Ligands from the [4+4] Dimers of Benzo[ b]quinolizinium and Anthracene Derivatives. CHEMPHOTOCHEM 2020. [DOI: 10.1002/cptc.202000015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Daria V. Berdnikova
- Department of Chemistry-BiologyUniversity of Siegen Adolf-Reichwein-Str. 2 57068 Siegen Germany
| | - Josef Heider
- Department of Chemistry-BiologyUniversity of Siegen Adolf-Reichwein-Str. 2 57068 Siegen Germany
| | - Heiko Ihmels
- Department of Chemistry-BiologyUniversity of Siegen Adolf-Reichwein-Str. 2 57068 Siegen Germany
| | - Norbert Sewald
- Department of Chemistry, Organic and Bioorganic ChemistryBielefeld University PO Box 100121 33501 Bielefeld Germany
| | - Phil M. Pithan
- Department of Chemistry-BiologyUniversity of Siegen Adolf-Reichwein-Str. 2 57068 Siegen Germany
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Choi PJ, Park TI, Cooper E, Dragunow M, Denny WA, Jose J. Heptamethine Cyanine Dye Mediated Drug Delivery: Hype or Hope. Bioconjug Chem 2020; 31:1724-1739. [DOI: 10.1021/acs.bioconjchem.0c00302] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Peter J. Choi
- Auckland Cancer Society Research Centre, School of Medical Sciences, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
| | - Thomas I−H. Park
- Department of Pharmacology & The Centre for Brain Research, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
- Neurosurgical Research Unit, The Centre for Brain Research, University of Auckland, Private Bag
92019, Auckland 1142, New Zealand
| | - Elizabeth Cooper
- Auckland Cancer Society Research Centre, School of Medical Sciences, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
- Department of Pharmacology & The Centre for Brain Research, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
- Neurosurgical Research Unit, The Centre for Brain Research, University of Auckland, Private Bag
92019, Auckland 1142, New Zealand
| | - Mike Dragunow
- Department of Pharmacology & The Centre for Brain Research, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
- Neurosurgical Research Unit, The Centre for Brain Research, University of Auckland, Private Bag
92019, Auckland 1142, New Zealand
| | - William A. Denny
- Auckland Cancer Society Research Centre, School of Medical Sciences, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
| | - Jiney Jose
- Auckland Cancer Society Research Centre, School of Medical Sciences, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
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Nafie MS, Arafa K, Sedky NK, Alakhdar AA, Arafa RK. Triaryl dicationic DNA minor-groove binders with antioxidant activity display cytotoxicity and induce apoptosis in breast cancer. Chem Biol Interact 2020; 324:109087. [PMID: 32294457 DOI: 10.1016/j.cbi.2020.109087] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 03/17/2020] [Accepted: 04/02/2020] [Indexed: 12/18/2022]
Abstract
Despite advances in cancer treatment modalities, DNA still stands as one of the targets for anticancer agents. DNA minor groove binders (MGBs) represent an important investigational chemotherapeutic class with promising cytotoxic capacity. Herein this study reports the potent cytotoxic effect of a series of repurposed flexible bis-imidamides 1-4, triaryl bis-guanidine 5 and bis-N-substituted guanidines 6,7 having a 1,4-diphenoxybenzene scaffold backbone on MCF-7 and MDA-MB-231 breast cancer cell lines. Of these compounds, imidamide 4 was chosen for further in-vitro, in-vivo and molecular dynamics (MD) studies owing to its promising anti-tumor activity, with IC50 values on MCF-7 and MDA-MB-231 breast cancer cell lines of 1.9 and 2.08 μM, respectively. Annexin V/propidium iodide apoptosis assay revealed apoptosis induction on imidamide 4 treated MCF-7 cells. RT-PCR assay results demonstrated the proapoptotic effect of compound 4 through increase of mRNA levels of the pro-apoptotic genes; p53, PUMA, and Bax, and inhibiting the anti-apoptotic Bcl-2 gene expression in MCF-7 cells. Moreover, compound 4 induced a G0/G1 cell-cycle arrest in MCF-7 in a dose-dependent manner. Corroborating in-vivo experiments on Ehrlich ascites carcinoma (EAC)-bearing mice, reflected the anticancer strength of derivative 4. For further target validation, molecular dynamics (MD) studies demonstrated an energetically favorable binding of imidamide 4 with the DNA minor groove AT rich site. In effect, imidamide 4 can be viewed as a promising hit dicationic compound with good cytotoxic and apoptotic inducing activity against breast cancer that can be adopted for future optimization.
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Affiliation(s)
- Mohamed S Nafie
- Chemistry Department, Faculty of Science Suez Canal University, Ismailia, 41522, Egypt
| | - Kholoud Arafa
- Center for Materials Science, Zewail City of Science and Technology, 12578, Cairo, Egypt
| | - Nada K Sedky
- Drug Design and Discovery Laboratory, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, 12578, Cairo, Egypt; Biochemistry Department, Faculty of Pharmacy, Sinai University, East Kantara Branch, New City, El Ismailia, 41611, Cairo, Egypt
| | - Amira A Alakhdar
- Drug Design and Discovery Laboratory, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, 12578, Cairo, Egypt
| | - Reem K Arafa
- Drug Design and Discovery Laboratory, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, 12578, Cairo, Egypt; Biomedical Sciences Program, University of Science and Technology, Zewail City of Science and Technology, 12578, Cairo, Egypt.
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42
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Fudickar W, Linker T. Structural motives controlling the binding affinity of 9,10-bis(methylpyridinium)anthracenes towards DNA. Bioorg Med Chem 2020; 28:115432. [DOI: 10.1016/j.bmc.2020.115432] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 02/20/2020] [Accepted: 03/02/2020] [Indexed: 10/24/2022]
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Chernikova EY, Ruleva AY, Tsvetkov VB, Fedorov YV, Novikov VV, Aliyeu TM, Pavlov AA, Shepel NE, Fedorova OA. Cucurbit[7]uril-driven modulation of ligand-DNA interactions by ternary assembly. Org Biomol Chem 2020; 18:755-766. [PMID: 31912862 DOI: 10.1039/c9ob02543j] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The design of small organic molecules with a predictable and desirable DNA-binding mechanism is a topical research task for biomedicine application. Herein, we demonstrate an attractive supramolecular strategy for controlling the non-covalent ligand-DNA interaction by binding with cucurbituril as a synthetic receptor. With a combination of UV/vis, CD and NMR experiments, we demonstrate that the bis-styryl dye with two suitable binding sites can involve double stranded DNA and cucurbituril in the formation of the supramolecular triad. The ternary assembly is formed as a result of the interaction of macrocyclic cucurbituril with one pyridinium fragment of the bis-styryl dye, while the second pyridinium fragment of the dye is effectively associated with DNA backbones, which leads to a change in the ligand-DNA binding mode from aggregation to a minor groove. This exciting outcome was supported by molecular docking studies that help to understand the molecular orientation of the supramolecular triad and elucidate the destruction of dye aggregates caused by cucurbituril. These studies provide valuable information on the mechanisms of DNA binding to small molecules and recognition processes in bioorganic supramolecular assemblies constructed from multiple non-covalent interactions.
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Affiliation(s)
- Ekaterina Y Chernikova
- Laboratory of Photoactive Supramolecular Systems, A.N. Nesmeyanov Institute of Organoelement Compounds of Russian Academy of Sciences, Vavilova St. 28, Moscow, 119991, Russia.
| | - Anna Y Ruleva
- Laboratory of Photoactive Supramolecular Systems, A.N. Nesmeyanov Institute of Organoelement Compounds of Russian Academy of Sciences, Vavilova St. 28, Moscow, 119991, Russia.
| | - Vladimir B Tsvetkov
- Computational Oncology Group, I.M. Sechenov First Moscow State Medical University, Trubetskaya str, 8/2, Moscow, 119146 Russia and Biophysics Department, Research and Clinical Center for Physical Chemical Medicine, Malaya Pirogovskaya str. 1a, Moscow 119435, Russia and Polyelectrolytes and Biomedical Polymers Laboratory, A.V. Topchiev Institute of Petrochemical Synthesis, Russian Academy of Sciences, Leninsky prospect str. 29, Moscow, 119991, Russia
| | - Yuri V Fedorov
- Laboratory of Photoactive Supramolecular Systems, A.N. Nesmeyanov Institute of Organoelement Compounds of Russian Academy of Sciences, Vavilova St. 28, Moscow, 119991, Russia.
| | - Valentin V Novikov
- Laboratory of Nuclear Magnetic Resonances, A.N. Nesmeyanov Institute of Organoelement Compounds of Russian Academy of Sciences, Vavilova St. 28, Moscow, 119991, Russia
| | - Tseimur M Aliyeu
- Center for Molecule Composition Studies, A.N. Nesmeyanov Institute of Organoelement Compounds of Russian Academy of Sciences, Vavilova St. 28, Moscow, 119991, Russia
| | - Alexander A Pavlov
- Laboratory of Nuclear Magnetic Resonances, A.N. Nesmeyanov Institute of Organoelement Compounds of Russian Academy of Sciences, Vavilova St. 28, Moscow, 119991, Russia
| | - Nikolay E Shepel
- Laboratory of Photoactive Supramolecular Systems, A.N. Nesmeyanov Institute of Organoelement Compounds of Russian Academy of Sciences, Vavilova St. 28, Moscow, 119991, Russia.
| | - Olga A Fedorova
- Laboratory of Photoactive Supramolecular Systems, A.N. Nesmeyanov Institute of Organoelement Compounds of Russian Academy of Sciences, Vavilova St. 28, Moscow, 119991, Russia.
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Kölsch S, Ihmels H, Mattay J, Sewald N, Patrick BO. Reversible photoswitching of the DNA-binding properties of styrylquinolizinium derivatives through photochromic [2 + 2] cycloaddition and cycloreversion. Beilstein J Org Chem 2020; 16:111-124. [PMID: 32082430 PMCID: PMC7006495 DOI: 10.3762/bjoc.16.13] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 01/08/2020] [Indexed: 12/17/2022] Open
Abstract
It was demonstrated that styrylquinolizinium derivatives may be applied as photoswitchable DNA ligands. At lower ligand:DNA ratios (≤1.5), these compounds bind to duplex DNA by intercalation, with binding constants ranging from K b = 4.1 × 104 M to 2.6 × 105 M (four examples), as shown by photometric and fluorimetric titrations as well as by CD and LD spectroscopic analyses. Upon irradiation at 450 nm, the methoxy-substituted styrylquinolizinium derivatives form the corresponding syn head-to-tail cyclobutanes in a selective [2 + 2] photocycloaddition, as revealed by X-ray diffraction analysis of the reaction products. These photodimers bind to DNA only weakly by outside-edge association, but they release the intercalating monomers upon irradiation at 315 nm in the presence of DNA. As a result, it is possible to switch between these two ligands and likewise between two different binding modes by irradiation with different excitation wavelengths.
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Affiliation(s)
- Sarah Kölsch
- Department of Chemistry and Biology, Organic Chemistry II, University of Siegen, Adolf-Reichwein-Str. 2, D-57068 Siegen, Germany
| | - Heiko Ihmels
- Department of Chemistry and Biology, Organic Chemistry II, University of Siegen, Adolf-Reichwein-Str. 2, D-57068 Siegen, Germany
| | - Jochen Mattay
- Department of Chemistry, Organic and Bioorganic Chemistry, Bielefeld University, PO Box 100121, D-33501 Bielefeld, Germany
| | - Norbert Sewald
- Department of Chemistry, Organic and Bioorganic Chemistry, Bielefeld University, PO Box 100121, D-33501 Bielefeld, Germany
| | - Brian O Patrick
- Department of Chemistry, Structural Chemistry Facility, The University of British Columbia, 2036 Main Mall, V6T 1Z1, Vancouver, BC, Canada
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Müller S, Paulus J, Mattay J, Ihmels H, Dodero VI, Sewald N. Photocontrolled DNA minor groove interactions of imidazole/pyrrole polyamides. Beilstein J Org Chem 2020; 16:60-70. [PMID: 31976017 PMCID: PMC6964667 DOI: 10.3762/bjoc.16.8] [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: 10/26/2019] [Accepted: 12/20/2019] [Indexed: 12/21/2022] Open
Abstract
Azobenzenes are photoswitchable molecules capable of generating significant structural changes upon E-to-Z photoisomerization in peptides or small molecules, thereby controlling geometry and functionality. E-to-Z photoisomerization usually is achieved upon irradiation at 350 nm (π–π* transition), while the Z-to-E isomerization proceeds photochemically upon irradiation at >400 nm (n–π* transition) or thermally. Photoswitchable compounds have frequently been employed as modules, e.g., to control protein–DNA interactions. However, their use in conjunction with minor groove-binding imidazole/pyrrole (Im/Py) polyamides is yet unprecedented. Dervan-type Im/Py polyamides were equipped with an azobenzene unit, i.e., 3-(3-(aminomethyl)phenyl)azophenylacetic acid, as the linker between two Im/Py polyamide strands. Only the (Z)-azobenzene-containing polyamides bound to the minor groove of double-stranded DNA hairpins. Photoisomerization was exemplarily evaluated by 1H NMR experiments, while minor groove binding of the (Z)-azobenzene derivatives was proven by CD titration experiments. The resulting induced circular dichroism (ICD) bands of the bound ligands, together with the photometric determination of the dsDNA melting temperature, revealed a significant stabilization of the DNA upon association with the ligand. The (Z)-azobenzene acted as a building block inducing a reverse turn, which favored hydrogen bonds between the pyrrole/imidazole amide and the DNA bases. In contrast, the E-configured polyamides did not induce any ICD characteristic for minor groove binding. The incorporation of the photoswitchable azobenzene unit is a promising strategy to obtain photoswitchable Im/Py hairpin polyamides capable of interacting with the dsDNA minor groove only in the Z-configuration.
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Affiliation(s)
- Sabrina Müller
- Organic and Bioorganic Chemistry, Department of Chemistry, Bielefeld University, PO Box 100131, D-33501 Bielefeld, Germany
| | - Jannik Paulus
- Organic and Bioorganic Chemistry, Department of Chemistry, Bielefeld University, PO Box 100131, D-33501 Bielefeld, Germany
| | - Jochen Mattay
- Organic Chemistry I, Department of Chemistry, Bielefeld University, PO Box 100131, D-33501 Bielefeld, Germany
| | - Heiko Ihmels
- Organic Chemistry II, Department Chemistry - Biology, Siegen University, Adolf-Reichwein-Str. 2, D-57068 Siegen, Germany
| | - Veronica I Dodero
- Organic and Bioorganic Chemistry, Department of Chemistry, Bielefeld University, PO Box 100131, D-33501 Bielefeld, Germany
| | - Norbert Sewald
- Organic and Bioorganic Chemistry, Department of Chemistry, Bielefeld University, PO Box 100131, D-33501 Bielefeld, Germany
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Collings CK, Little DW, Schafer SJ, Anderson JN. HIV chromatin is a preferred target for drugs that bind in the DNA minor groove. PLoS One 2019; 14:e0216515. [PMID: 31887110 PMCID: PMC6936835 DOI: 10.1371/journal.pone.0216515] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Accepted: 12/03/2019] [Indexed: 12/25/2022] Open
Abstract
The HIV genome is rich in A but not G or U and deficient in C. This nucleotide bias controls HIV phenotype by determining the highly unusual composition of all major HIV proteins. The bias is also responsible for the high frequency of narrow DNA minor groove sites in the double-stranded HIV genome as compared to cellular protein coding sequences and the bulk of the human genome. Since drugs that bind in the DNA minor groove disrupt nucleosomes on sequences that contain closely spaced oligo-A tracts which are prevalent in HIV DNA because of its bias, it was of interest to determine if these drugs exert this selective inhibitory effect on HIV chromatin. To test this possibility, nucleosomes were reconstituted onto five double-stranded DNA fragments from the HIV-1 pol gene in the presence and in the absence of several minor groove binding drugs (MGBDs). The results demonstrated that the MGBDs inhibited the assembly of nucleosomes onto all of the HIV-1 segments in a manner that was proportional to the A-bias, but had no detectable effect on the formation of nucleosomes on control cloned fragments or genomic DNA from chicken and human. Nucleosomes preassembled onto HIV DNA were also preferentially destabilized by the drugs as evidenced by enhanced nuclease accessibility in physiological ionic strength and by the preferential loss of the histone octamer in hyper-physiological salt solutions. The drugs also selectively disrupted HIV-containing nucleosomes in yeast as revealed by enhanced nuclease accessibility of the in vivo assembled HIV chromatin and reductions in superhelical densities of plasmid chromatin containing HIV sequences. A comparison of these results to the density of A-tracts in the HIV genome indicates that a large fraction of the nucleosomes that make up HIV chromatin should be preferred in vitro targets for the MGBDs. These results show that the MGBDs preferentially disrupt HIV-1 chromatin in vitro and in vivo and raise the possibility that non-toxic derivatives of certain MGBDs might serve as a novel class of anti-HIV agents.
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Affiliation(s)
- Clayton K Collings
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA, United States of America.,Broad Institute of MIT and Harvard, Cambridge, MA, United States of America
| | - Donald W Little
- University of Michigan Medical School, Ann Arbor, MI, United States of America
| | - Samuel J Schafer
- Department of Reproductive and Developmental Sciences, University of British Columbia, Vancouver, BC, Canada
| | - John N Anderson
- Department of Biological Sciences, Purdue University, West Lafayette, IN, United States of America
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A New Generation of Minor-Groove-Binding-Heterocyclic Diamidines That Recognize G·C Base Pairs in an AT Sequence Context. Molecules 2019; 24:molecules24050946. [PMID: 30866557 PMCID: PMC6429135 DOI: 10.3390/molecules24050946] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Revised: 02/28/2019] [Accepted: 03/01/2019] [Indexed: 12/17/2022] Open
Abstract
We review the preparation of new compounds with good solution and cell uptake properties that can selectively recognize mixed A·T and G·C bp sequences of DNA. Our underlying aim is to show that these new compounds provide important new biotechnology reagents as well as a new class of therapeutic candidates with better properties and development potential than other currently available agents. In this review, entirely different ways to recognize mixed sequences of DNA by modifying AT selective heterocyclic cations are described. To selectively recognize a G·C base pair an H-bond acceptor must be incorporated with AT recognizing groups as with netropsin. We have used pyridine, azabenzimidazole and thiophene-N-methylbenzimidazole GC recognition units in modules crafted with both rational design and empirical optimization. These modules can selectively and strongly recognize a single G·C base pair in an AT sequence context. In some cases, a relatively simple change in substituents can convert a heterocyclic module from AT to GC recognition selectivity. Synthesis and DNA interaction results for initial example lead modules are described for single G·C base pair recognition compounds. The review concludes with a description of the initial efforts to prepare larger compounds to recognize sequences of DNA with more than one G·C base pairs. The challenges and initial successes are described along with future directions.
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