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Cheraghi S, Şenel P, Dogan Topal B, Agar S, Majidian M, Yurtsever M, Bellur Atici E, Gölcü A, Ozkan SA. Elucidation of DNA-Eltrombopag Binding: Electrochemical, Spectroscopic and Molecular Docking Techniques. BIOSENSORS 2023; 13:300. [PMID: 36979512 PMCID: PMC10046231 DOI: 10.3390/bios13030300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 02/13/2023] [Accepted: 02/16/2023] [Indexed: 06/18/2023]
Abstract
Eltrombopag is a powerful adjuvant anticancer drug used in treating MS (myelodysplastic syndrome) and AML (acute myeloid leukemia) diseases. In this study, the interaction mechanism between eltrombopag and DNA was studied by voltammetry, spectroscopic techniques, and viscosity measurements. We developed a DNA-based biosensor and nano-biosensor using reduced graphene oxide-modified glassy carbon electrode to detect DNA-eltrombopag binding. The reduction of desoxyguanosine (dGuo) and desoxyadenosine (dAdo) oxidation signals in the presence of the drug demonstrated that a strong interaction could be established between the eltrombopag and dsDNA. The eltrombopag-DNA interaction was further investigated by UV absorption and fluorescence emission spectroscopy to gain more quantitative insight on binding. Viscosity measurements were utilized to characterize the binding mode of the drug. To shed light on the noncovalent interactions and binding mechanism of eltrombopag molecular docking and molecular dynamics (MD), simulations were performed. Through simultaneously carried out experimental and in silico studies, it was established that the eltrombopag binds onto the DNA via intercalation.
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Affiliation(s)
- Somaye Cheraghi
- Department of Analytical Chemistry, Faculty of Pharmacy, Ankara University, Ankara 06560, Turkey
- Department of Chemistry, Shahid Bahonar University of Kerman, Kerman 7616914111, Iran
| | - Pelin Şenel
- Department of Chemistry, Faculty of Science and Letters, Istanbul Technical University, Istanbul 34469, Turkey
| | - Burcu Dogan Topal
- Department of Analytical Chemistry, Faculty of Pharmacy, Ankara University, Ankara 06560, Turkey
| | - Soykan Agar
- Department of Chemistry, Faculty of Science and Letters, Istanbul Technical University, Istanbul 34469, Turkey
| | - Mahsa Majidian
- Department of Analytical Chemistry, Faculty of Pharmacy, Ankara University, Ankara 06560, Turkey
| | - Mine Yurtsever
- Department of Chemistry, Faculty of Science and Letters, Istanbul Technical University, Istanbul 34469, Turkey
| | | | - Ayşegül Gölcü
- Department of Chemistry, Faculty of Science and Letters, Istanbul Technical University, Istanbul 34469, Turkey
| | - Sibel A. Ozkan
- Department of Analytical Chemistry, Faculty of Pharmacy, Ankara University, Ankara 06560, Turkey
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2
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Bedwell E, McCarthy WJ, Coyne AG, Abell C. Development of potent inhibitors by fragment-linking strategies. Chem Biol Drug Des 2022; 100:469-486. [PMID: 35854428 DOI: 10.1111/cbdd.14120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 07/12/2022] [Accepted: 07/17/2022] [Indexed: 11/29/2022]
Abstract
Fragment-based drug discovery (FBDD) is a method of identifying small molecule hits that can be elaborated rationally through fragment growing, merging, and linking, to afford high affinity ligands for biological targets. Despite the promised theoretical potential of fragment linking, examples are still surprisingly sparse and remain overshadowed by the successes of fragment growing. The aim of this review is to outline a number of key examples of fragment linking strategies and discuss their strengths and limitations. Structure-based approaches including X-ray crystallography and in silico methods fragment optimisation are discussed, as well as fragment linking guided by NMR experiments. Target-guided approaches, exploiting the biological target to assemble its own inhibitors through dynamic combinatorial chemistry (DCC) and kinetic target-guided synthesis (KTGS), are identified as alternative efficient methods for fragment linking.
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Affiliation(s)
- Elizabeth Bedwell
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambrdige, United Kingdom
| | - William J McCarthy
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambrdige, United Kingdom
| | - Anthony G Coyne
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambrdige, United Kingdom
| | - Chris Abell
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambrdige, United Kingdom
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3
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Human Gammaherpesvirus 8 Oncogenes Associated with Kaposi’s Sarcoma. Int J Mol Sci 2022; 23:ijms23137203. [PMID: 35806208 PMCID: PMC9266852 DOI: 10.3390/ijms23137203] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 04/28/2022] [Accepted: 04/29/2022] [Indexed: 01/01/2023] Open
Abstract
Kaposi’s sarcoma-associated herpesvirus (KSHV), also known as human gammaherpesvirus 8 (HHV-8), contains oncogenes and proteins that modulate various cellular functions, including proliferation, differentiation, survival, and apoptosis, and is integral to KSHV infection and oncogenicity. In this review, we describe the most important KSHV genes [ORF 73 (LANA), ORF 72 (vCyclin), ORF 71 or ORFK13 (vFLIP), ORF 74 (vGPCR), ORF 16 (vBcl-2), ORF K2 (vIL-6), ORF K9 (vIRF 1)/ORF K10.5, ORF K10.6 (vIRF 3), ORF K1 (K1), ORF K15 (K15), and ORF 36 (vPK)] that have the potential to induce malignant phenotypic characteristics of Kaposi’s sarcoma. These oncogenes can be explored in prospective studies as future therapeutic targets of Kaposi’s sarcoma.
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Topkaya SN, Kaya HO, Cetin AE. Electrochemical Detection of Linagliptin and its Interaction with DNA. Turk J Pharm Sci 2021; 18:645-651. [PMID: 34719193 DOI: 10.4274/tjps.galenos.2021.71354] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Objectives Linagliptin (Lin) is a drug used in treatment of type 2 diabetes mellitus. In this study, the electrochemical detection of Lin and its interaction with DNA was analyzed for the first time using voltammetric methods by measuring the oxidation currents of the adenine bases of DNA before and after the interaction. In addition, the electrochemical properties of the Lin were studied. Materials and Methods The interaction between Lin and DNA was evaluated using differential pulse voltammetry. A three-electrode system comprising of a pencil graphite electrode as the working electrode, reference electrode (Ag/AgCl), and platinum wire as the auxiliary electrode was used in the electrochemical studies. Experimental conditions, such as the concentration, pH of the supporting electrolyte, and immobilization time were optimized to obtain maximum analytical signals. Results The adenine bases of DNA were evaluated as an analytical signal obtained at approximately +1.2 V vs. Ag/AgCl. After the Lin-DNA interaction, the oxidation currents of adenine decreased as proof of interaction. No reports have been published on Lin interacting with DNA. Based on our results, a diffusion-controlled irreversible redox process involving independent oxidation was revealed for Lin. Under optimum conditions, the detection limit was 6.7 µg/mL for DNA and 21.5 µg/mL for Lin. Based on the observations, Lin has a toxic effect on DNA. Conclusion We successfully demonstrated that Lin interacts with DNA, and its influence on DNA could play a vital role in the medical effect of the drug.
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Affiliation(s)
- Seda Nur Topkaya
- İzmir Katip Çelebi University Faculty of Pharmacy, Department of Analytical Chemistry, İzmir, Turkey
| | - Hüseyin Oğuzhan Kaya
- İzmir Katip Çelebi University Faculty of Pharmacy, Department of Analytical Chemistry, İzmir, Turkey
| | - Arif E Cetin
- İzmir Biomedicine and Genome Center, İzmir, Turkey
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Naimo E, Zischke J, Schulz TF. Recent Advances in Developing Treatments of Kaposi's Sarcoma Herpesvirus-Related Diseases. Viruses 2021; 13:1797. [PMID: 34578378 PMCID: PMC8473310 DOI: 10.3390/v13091797] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 08/30/2021] [Accepted: 09/01/2021] [Indexed: 12/27/2022] Open
Abstract
Kaposi-sarcoma-associated herpesvirus (KSHV) or human herpesvirus 8 (HHV-8) is the causative agent of several malignancies, including Kaposi's sarcoma (KS), primary effusion lymphoma (PEL), and multicentric Castleman's disease (MCD). Active KSHV replication has also been associated with a pathological condition called KSHV inflammatory cytokine syndrome (KICS), and KSHV may play a role in rare cases of post-transplant polyclonal lymphoproliferative disorders. Several commonly used herpesviral DNA polymerase inhibitors are active against KSHV in tissue culture. Unfortunately, they are not always efficacious against KSHV-induced diseases. To improve the outcome for the patients, new therapeutics need to be developed, including treatment strategies that target either viral proteins or cellular pathways involved in tumor growth and/or supporting the viral life cycle. In this review, we summarize the most commonly established treatments against KSHV-related diseases and review recent developments and promising new compounds that are currently under investigation or on the way to clinical use.
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Affiliation(s)
- Eleonora Naimo
- Institute of Virology, Hannover Medical School, 30625 Hannover, Germany; (E.N.); (J.Z.)
- German Centre for Infection Research, Hannover-Braunschweig Site, 38023 Braunschweig, Germany
| | - Jasmin Zischke
- Institute of Virology, Hannover Medical School, 30625 Hannover, Germany; (E.N.); (J.Z.)
- German Centre for Infection Research, Hannover-Braunschweig Site, 38023 Braunschweig, Germany
| | - Thomas F. Schulz
- Institute of Virology, Hannover Medical School, 30625 Hannover, Germany; (E.N.); (J.Z.)
- German Centre for Infection Research, Hannover-Braunschweig Site, 38023 Braunschweig, Germany
- Cluster of Excellence 2155 RESIST, Institute of Virology, Hannover Medical School, 30625 Hannover, Germany
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KSHV-specific antivirals targeting the protein-DNA interaction of the latency-associated nuclear antigen. Future Med Chem 2021; 13:1141-1151. [PMID: 34036806 DOI: 10.4155/fmc-2021-0059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The Kaposi sarcoma-associated herpesvirus (KSHV) is an oncogenic human herpesviruses that is responsible for cancer, especially in immunosuppressed people, such as patients with AIDS. So far, there are no KSHV-specifc antiviral agents available. In this review, we provide an overview on one particular target-centered approach toward novel anti-KSHV drugs focusing on interfering with the molecular functions of the latency-associated nuclear antigen (LANA). This review focuses on attempts to interfere with the LANA-DNA interaction mediated by the C-terminal domain. We describe the drug discovery approaches chosen for this endeavor as well as molecular structures that were identified in this innovative concept toward novel and KSHV-specific antiherpesviral agents.
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Balasubramaniam B, Prateek, Ranjan S, Saraf M, Kar P, Singh SP, Thakur VK, Singh A, Gupta RK. Antibacterial and Antiviral Functional Materials: Chemistry and Biological Activity toward Tackling COVID-19-like Pandemics. ACS Pharmacol Transl Sci 2021; 4:8-54. [PMID: 33615160 PMCID: PMC7784665 DOI: 10.1021/acsptsci.0c00174] [Citation(s) in RCA: 99] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Indexed: 12/12/2022]
Abstract
The ongoing worldwide pandemic due to COVID-19 has created awareness toward ensuring best practices to avoid the spread of microorganisms. In this regard, the research on creating a surface which destroys or inhibits the adherence of microbial/viral entities has gained renewed interest. Although many research reports are available on the antibacterial materials or coatings, there is a relatively small amount of data available on the use of antiviral materials. However, with more research geared toward this area, new information is being added to the literature every day. The combination of antibacterial and antiviral chemical entities represents a potentially path-breaking intervention to mitigate the spread of disease-causing agents. In this review, we have surveyed antibacterial and antiviral materials of various classes such as small-molecule organics, synthetic and biodegradable polymers, silver, TiO2, and copper-derived chemicals. The surface protection mechanisms of the materials against the pathogen colonies are discussed in detail, which highlights the key differences that could determine the parameters that would govern the future development of advanced antibacterial and antiviral materials and surfaces.
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Affiliation(s)
| | - Prateek
- Department
of Chemical Engineering, Indian Institute
of Technology Kanpur, Kanpur, Uttar Pradesh 208016, India
| | - Sudhir Ranjan
- Department
of Chemical Engineering, Indian Institute
of Technology Kanpur, Kanpur, Uttar Pradesh 208016, India
| | - Mohit Saraf
- Department
of Chemical Engineering, Indian Institute
of Technology Kanpur, Kanpur, Uttar Pradesh 208016, India
| | - Prasenjit Kar
- Department
of Chemical Engineering, Indian Institute
of Technology Kanpur, Kanpur, Uttar Pradesh 208016, India
| | - Surya Pratap Singh
- Department
of Chemistry, Indian Institute of Technology
Kanpur, Kanpur, Uttar Pradesh 208016, India
| | - Vijay Kumar Thakur
- Biorefining
and Advanced Materials Research Center, Scotland’s Rural College (SRUC), Kings Buildings, West Mains Road, Edinburgh EH9 3JG, United Kingdom
| | - Anand Singh
- Department
of Chemistry, Indian Institute of Technology
Kanpur, Kanpur, Uttar Pradesh 208016, India
| | - Raju Kumar Gupta
- Department
of Chemical Engineering, Indian Institute
of Technology Kanpur, Kanpur, Uttar Pradesh 208016, India
- Center
for Environmental Science and Engineering, Indian Institute of Technology Kanpur, Kanpur, Uttar Pradesh 208016, India
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8
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Calderon A, Soldan SS, De Leo A, Deng Z, Frase DM, Anderson EM, Zhang Y, Vladimirova O, Lu F, Leung JC, Murphy ME, Lieberman PM. Identification of Mubritinib (TAK 165) as an inhibitor of KSHV driven primary effusion lymphoma via disruption of mitochondrial OXPHOS metabolism. Oncotarget 2020; 11:4224-4242. [PMID: 33245718 PMCID: PMC7679036 DOI: 10.18632/oncotarget.27815] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 10/29/2020] [Indexed: 02/07/2023] Open
Abstract
KSHV-associated cancers have poor prognoses and lack therapeutics that selectively target viral gene functions. We developed a screening campaign to identify known drugs that could be repurposed for the treatment of KSHV-associated cancers. We focused on primary effusion lymphoma (PEL), which has particularly poor treatment outcomes. We developed a luciferase reporter assay to test the ability of drugs to inhibit DNA binding of the KSHV LANA DNA binding domain (DBD). In parallel, we screened drugs for selective inhibition of a KSHV+ PEL cells. While potent hits were identified in each assay, only one hit, Mubritinib, was found to score in both assays. Mubritinib caused PEL cells to undergo cell cycle arrest with accumulation of sub-G1 population and Annexin V. Mubritinib inhibited LANA binding to KSHV terminal repeat (TR) DNA in KSHV+ PEL cells, but did not lead to KSHV lytic cycle reactivation. Mubritinib was originally identified as a receptor tyrosine kinase (RTK) inhibitor selective for HER2/ErbB2. But recent studies have revealed that Mubritinib can also inhibit the electron transport chain (ETC) complex at nanomolar concentrations. We found that other related ETC complex inhibitors (Rotenone and Deguelin) exhibited PEL cell growth inhibition while RTK inhibitors failed. Seahorse analysis demonstrated that Mubritinib selectively inhibits the maximal oxygen consumption (OCR) in PEL cells and metabolomics revealed changes in ATP/ADP and ATP/AMP ratios. These findings indicate that PEL cells are selectively sensitive to ETC complex inhibitors and provide a rationale for repurposing Mubritinib for selective treatment of PEL.
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Affiliation(s)
| | | | | | - Zhong Deng
- The Wistar Institute, Philadelphia, PA 19146, USA
| | | | | | - Yue Zhang
- The Wistar Institute, Philadelphia, PA 19146, USA
| | | | - Fang Lu
- The Wistar Institute, Philadelphia, PA 19146, USA
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Kirsch P, Stein SC, Berwanger A, Rinkes J, Jakob V, Schulz TF, Empting M. Hit-to-lead optimization of a latency-associated nuclear antigen inhibitor against Kaposi’s sarcoma-associated herpesvirus infections. Eur J Med Chem 2020; 202:112525. [DOI: 10.1016/j.ejmech.2020.112525] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 05/25/2020] [Accepted: 05/30/2020] [Indexed: 12/15/2022]
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10
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Hartman AM, Jumde VR, Elgaher WAM, Te Poele EM, Dijkhuizen L, Hirsch AKH. Potential Dental Biofilm Inhibitors: Dynamic Combinatorial Chemistry Affords Sugar-Based Molecules that Target Bacterial Glucosyltransferase. ChemMedChem 2020; 16:113-123. [PMID: 32542998 PMCID: PMC7818428 DOI: 10.1002/cmdc.202000222] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 06/15/2020] [Indexed: 12/21/2022]
Abstract
We applied dynamic combinatorial chemistry (DCC) to find novel ligands of the bacterial virulence factor glucosyltransferase (GTF) 180. GTFs are the major producers of extracellular polysaccharides, which are important factors in the initiation and development of cariogenic dental biofilms. Following a structure‐based strategy, we designed a series of 36 glucose‐ and maltose‐based acylhydrazones as substrate mimics. Synthesis of the required mono‐ and disaccharide‐based aldehydes set the stage for DCC experiments. Analysis of the dynamic combinatorial libraries (DCLs) by UPLC‐MS revealed major amplification of four compounds in the presence of GTF180. Moreover, we found that derivatives of the glucose‐acceptor maltose at the C1‐hydroxy group act as glucose‐donors and are cleaved by GTF180. The synthesized hits display medium to low binding affinity (KD values of 0.4–10.0 mm) according to surface plasmon resonance. In addition, they were investigated for inhibitory activity in GTF‐activity assays. The early‐stage DCC study reveals that careful design of DCLs opens up easy access to a broad class of novel compounds that can be developed further as potential inhibitors.
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Affiliation(s)
- Alwin M Hartman
- Department of Drug Design and Optimization Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Campus Building E8.1, 66123, Saarbrücken, Germany.,Department of Pharmacy, Saarland University, Campus Building E8.1, 66123, Saarbrücken, Germany.,Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 7, 9747, AG Groningen, The Netherlands
| | - Varsha R Jumde
- Department of Drug Design and Optimization Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Campus Building E8.1, 66123, Saarbrücken, Germany.,Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 7, 9747, AG Groningen, The Netherlands
| | - Walid A M Elgaher
- Department of Drug Design and Optimization Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Campus Building E8.1, 66123, Saarbrücken, Germany
| | - Evelien M Te Poele
- Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 7, 9747 AG, Groningen (The, Netherlands.,CarbExplore Research BV, Zernikepark 1, 9747 AN, Groningen (The, Netherlands
| | - Lubbert Dijkhuizen
- Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 7, 9747 AG, Groningen (The, Netherlands.,CarbExplore Research BV, Zernikepark 1, 9747 AN, Groningen (The, Netherlands
| | - Anna K H Hirsch
- Department of Drug Design and Optimization Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), Campus Building E8.1, 66123, Saarbrücken, Germany.,Department of Pharmacy, Saarland University, Campus Building E8.1, 66123, Saarbrücken, Germany.,Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 7, 9747, AG Groningen, The Netherlands
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