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Zhang Q, Liu Q, Fu G, Huang F, Tang Y, Qiu Y, Ge A, Hu J, Wang W, Li B, Wang H. Dual-driven AND molecular logic gates for label-free and sensitive ratiometric fluorescence sensing and inhibitors screening. J Colloid Interface Sci 2024; 674:841-851. [PMID: 38955015 DOI: 10.1016/j.jcis.2024.06.202] [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: 06/11/2024] [Accepted: 06/26/2024] [Indexed: 07/04/2024]
Abstract
Due to the complexity of regulatory networks of disease-related biomarkers, developing simple, sensitive, and accurate methods has remained challenging for precise diagnosis. Herein, an "AND" logic gates DNA molecular machine (LGDM) was constructed, which was powered by the catalytic hairpin assembly (CHA). It was coupled with dual-emission CdTe quantum dots (QDs)-based cation exchange reaction (CER) for label-free, sensitive, and ratiometric fluorescence detection of APE1 and miRNA biomarkers. Benefiting from synergistic signal amplification strategies and a ratiometric fluorometric output mode, this LGDM enables accurate logic computing with robust and significant output signals from weak inputs. It offers improved sensitivity and selectivity even in cell extracts. Using dual-emission spectra CdTe QDs, with a ratiometric signal output mode, ensured good stability and effectively prevented false-positive signals from intrinsic biological interferences compared to the approach relying on a single signal output mode, which enabled the LGDM to achieve rapid, efficient, and accurate natural drug screening against APE1 inhibitors in vitro and cells. The developed method provides impetus to streamline research related to miRNA and APE1, offering significant promise for widespread application in drug development and clinical analysis.
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Affiliation(s)
- Qiongdan Zhang
- TCM and Ethnomedicine Innovation & Development International Laboratory, School of Pharmacy, Hunan·University of Chinese Medicine, Changsha, China
| | - Qingyi Liu
- TCM and Ethnomedicine Innovation & Development International Laboratory, School of Pharmacy, Hunan·University of Chinese Medicine, Changsha, China
| | - Gang Fu
- TCM and Ethnomedicine Innovation & Development International Laboratory, School of Pharmacy, Hunan·University of Chinese Medicine, Changsha, China
| | - Feibing Huang
- TCM and Ethnomedicine Innovation & Development International Laboratory, School of Pharmacy, Hunan·University of Chinese Medicine, Changsha, China
| | - Yanfu Tang
- TCM and Ethnomedicine Innovation & Development International Laboratory, School of Pharmacy, Hunan·University of Chinese Medicine, Changsha, China
| | - Yixing Qiu
- TCM and Ethnomedicine Innovation & Development International Laboratory, School of Pharmacy, Hunan·University of Chinese Medicine, Changsha, China
| | - Anqi Ge
- The First Affiliated Hospital of Hunan University of Chinese Medicine, Changsha, China
| | - Jinhui Hu
- The First Affiliated Hospital of Hunan University of Chinese Medicine, Changsha, China
| | - Wei Wang
- TCM and Ethnomedicine Innovation & Development International Laboratory, School of Pharmacy, Hunan·University of Chinese Medicine, Changsha, China.
| | - Bin Li
- TCM and Ethnomedicine Innovation & Development International Laboratory, School of Pharmacy, Hunan·University of Chinese Medicine, Changsha, China.
| | - Huizhen Wang
- TCM and Ethnomedicine Innovation & Development International Laboratory, School of Pharmacy, Hunan·University of Chinese Medicine, Changsha, China.
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Minko IG, Luzadder MM, McCullough AK, Lloyd RS. Interactions of pixantrone with apurinic/apyrimidinic sites in DNA. MICROPUBLICATION BIOLOGY 2024; 2024:10.17912/micropub.biology.001207. [PMID: 38911437 PMCID: PMC11193111 DOI: 10.17912/micropub.biology.001207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Figures] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Revised: 05/23/2024] [Accepted: 06/04/2024] [Indexed: 06/25/2024]
Abstract
Pixantrone and mitoxantrone are structurally related anticancer drugs which have been shown to generate covalent conjugates at apurinic/apyrimidinic (AP) sites in DNA. Mitoxantrone binding to AP sites induces DNA strand cleavage and inhibits the endonuclease activity of human AP endonuclease 1 (APE1). Here, pixantrone was demonstrated to have similar properties, but relative to mitoxantrone, it was significantly less potent in both DNA incision and APE1 inhibition. Consistent with these observations, pixantrone had ~ 15-fold lower affinity for DNA containing an AP site analogue, tetrahydrofuran, as measured by a Thiazole Orange (ThO) displacement assay.
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Affiliation(s)
- Irina G. Minko
- Oregon Institute of Occupational Health Sciences, Oregon Health & Science University, Portland, Oregon, United States
| | - Michael M. Luzadder
- Oregon Institute of Occupational Health Sciences, Oregon Health & Science University, Portland, Oregon, United States
| | - Amanda K. McCullough
- Oregon Institute of Occupational Health Sciences, Oregon Health & Science University, Portland, Oregon, United States
- Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, Oregon, United States
| | - R. Stephen Lloyd
- Oregon Institute of Occupational Health Sciences, Oregon Health & Science University, Portland, Oregon, United States
- Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, Oregon, United States
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3
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Verrelle P, Gestraud P, Poyer F, Soria A, Tessier S, Lescure A, Anthony E, Corbé M, Heinrich S, Beauvineau C, Chaput L, Granzhan A, Piguel S, Perez F, Teulade-Fichou MP, Megnin-Chanet F, Del Nery E. Integrated High-Throughput Screening and Large-Scale Isobolographic Analysis to Accelerate the Discovery of Radiosensitizers With Greater Selectivity for Cancer Cells. Int J Radiat Oncol Biol Phys 2024; 118:1294-1307. [PMID: 37778425 DOI: 10.1016/j.ijrobp.2023.09.044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 09/15/2023] [Accepted: 09/19/2023] [Indexed: 10/03/2023]
Abstract
PURPOSE High-throughput screening (HTS) platforms have been widely used to identify candidate anticancer drugs and drug-drug combinations; however, HTS-based identification of new drug-ionizing radiation (IR) combinations has rarely been reported. Herein, we developed an integrated approach including cell-based HTS and computational large-scale isobolographic analysis to accelerate the identification of radiosensitizing compounds acting strongly and more specifically on cancer cells. METHODS AND MATERIALS In a 384-well plate format, 160 compounds likely to interfere with the cell response to radiation were screened on human glioblastoma (U251-MG) and cervix carcinoma (ME-180) cell lines, as well as on normal fibroblasts (CCD-19Lu). After drug exposure, cells were irradiated or not and short-term cell survival was assessed by high-throughput cell microscopy. Computational large-scale dose-response and isobolographic approach were used to identify promising synergistic drugs radiosensitizing cancer cells rather than normal cells. Synergy of a promising compound was confirmed on ME-180 cells by an independent 96-well assay protocol, and finally, by the gold-standard colony forming assay. RESULTS We retained 4 compounds synergistic at 2 isoeffects in U251-MG and ME-180 cell lines and 11 compounds synergistically effective in only one cancer cell line. Among these 15 promising radiosensitizers, 5 compounds showed limited toxicity combined or not with IR on normal fibroblasts. CONCLUSIONS Overall, this study demonstrated that HTS chemoradiation screening together with large-scale computational analysis is an efficient tool to identify synergistic drug-IR combinations, with concomitant assessment of unwanted toxicity on normal fibroblasts. It sparks expectations to accelerate the discovery of highly desired agents improving the therapeutic index of radiation therapy.
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Affiliation(s)
- Pierre Verrelle
- Radiation Oncology Department, Institut Curie Hospital, Paris, France; Chemistry and Modelisation for the Biology of Cancer, CNRS UMR9187, INSERM U1196, Institut Curie, Université Paris Saclay, 91405 Orsay, France.
| | - Pierre Gestraud
- Chemistry and Modelisation for the Biology of Cancer, CNRS UMR9187, INSERM U1196, Institut Curie, Université Paris Saclay, 91405 Orsay, France
| | - Florent Poyer
- Chemistry and Modelisation for the Biology of Cancer, CNRS UMR9187, INSERM U1196, Institut Curie, Université Paris Saclay, 91405 Orsay, France
| | - Adèle Soria
- Biophenics High-Content Screening Laboratory, Department of Translational Research, PSL Research University, PICT-IBiSa, Institut Curie Research Center, Paris, France
| | - Sarah Tessier
- Biophenics High-Content Screening Laboratory, Department of Translational Research, PSL Research University, PICT-IBiSa, Institut Curie Research Center, Paris, France
| | - Aurianne Lescure
- Biophenics High-Content Screening Laboratory, Department of Translational Research, PSL Research University, PICT-IBiSa, Institut Curie Research Center, Paris, France
| | - Elodie Anthony
- Biophenics High-Content Screening Laboratory, Department of Translational Research, PSL Research University, PICT-IBiSa, Institut Curie Research Center, Paris, France
| | - Maxime Corbé
- Biophenics High-Content Screening Laboratory, Department of Translational Research, PSL Research University, PICT-IBiSa, Institut Curie Research Center, Paris, France
| | - Sophie Heinrich
- Experimental Radiotherapy Platform (RadeXp), Translational Research Department, Institut Curie, Orsay, France; Inserm U1021-CNRS UMR 3347, Institut Curie, Paris Saclay University
| | - Claire Beauvineau
- Bioinformatics and Computational Systems Biology of Cancer, PSL Research University, Mines Paris Tech, INSERM U900, Paris, France
| | - Ludovic Chaput
- Bioinformatics and Computational Systems Biology of Cancer, PSL Research University, Mines Paris Tech, INSERM U900, Paris, France
| | - Anton Granzhan
- Bioinformatics and Computational Systems Biology of Cancer, PSL Research University, Mines Paris Tech, INSERM U900, Paris, France
| | - Sandrine Piguel
- Bioinformatics and Computational Systems Biology of Cancer, PSL Research University, Mines Paris Tech, INSERM U900, Paris, France; BioCIS UMR8076, Université Paris-Saclay, Faculté de Pharmacie, Orsay, France
| | - Franck Perez
- Biophenics High-Content Screening Laboratory, Department of Translational Research, PSL Research University, PICT-IBiSa, Institut Curie Research Center, Paris, France; Cell Biology and Cancer UMR144, Institut Curie, PSL Research University, Paris, France
| | - Marie-Paule Teulade-Fichou
- Chemistry and Modelisation for the Biology of Cancer, CNRS UMR9187, INSERM U1196, Institut Curie, Université Paris Saclay, 91405 Orsay, France
| | - Frédérique Megnin-Chanet
- Bioinformatics and Computational Systems Biology of Cancer, PSL Research University, Mines Paris Tech, INSERM U900, Paris, France
| | - Elaine Del Nery
- Biophenics High-Content Screening Laboratory, Department of Translational Research, PSL Research University, PICT-IBiSa, Institut Curie Research Center, Paris, France.
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Minko IG, Moellmer SA, Luzadder MM, Tomar R, Stone MP, McCullough AK, Lloyd RS. Interaction of mitoxantrone with abasic sites - DNA strand cleavage and inhibition of apurinic/apyrimidinic endonuclease 1, APE1. DNA Repair (Amst) 2024; 133:103606. [PMID: 38039951 PMCID: PMC11257150 DOI: 10.1016/j.dnarep.2023.103606] [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: 06/05/2023] [Revised: 10/04/2023] [Accepted: 11/15/2023] [Indexed: 12/03/2023]
Abstract
Mitoxantrone (1,4-dihydroxy-5,8-bis[2-(2-hydroxyethylamino)ethylamino]-anthracene-9,10-dione) is a clinically-relevant synthetic anthracenedione that functions as a topoisomerase II poison by trapping DNA double-strand break intermediates. Mitoxantrone binds to DNA via both stacking interactions with DNA bases and hydrogen bonding with the sugar-phosphate backbone. It has been shown that mitoxantrone inhibits apurinic/apyrimidinic (AP) endonuclease 1 (APE1)-catalyzed incision of DNA containing a tetrahydrofuran (THF) moiety and more recently, that mitoxantrone forms Schiff base conjugates at AP sites in DNA. In this study, mitoxantrone-mediated inhibition of APE1 at THF sites was shown to be consistent with preferential binding to, and thermal stabilization of DNA containing a THF site as compared to non-damaged DNA. Investigations into the properties of mitoxantrone at AP and 3' α,β-unsaturated aldehyde sites demonstrated that in addition to being a potent inhibitor of APE1 at these biologically-relevant substrates (∼ 0.5 μM IC50 on AP site-containing DNA), mitoxantrone also incised AP site-containing DNA by catalyzing β- and β/δ-elimination reactions. The efficiency of these reactions to generate the 3' α,β-unsaturated aldehyde and 3' phosphate products was modulated by DNA structure. Although these cell-free reactions revealed that mitoxantrone can generate 3' phosphates, cells lacking polynucleotide kinase phosphatase did not show increased sensitivity to mitoxantrone treatment. Consistent with its ability to inhibit APE1 activity on DNAs containing either an AP site or a 3' α,β-unsaturated aldehyde, combined exposures to clinically-relevant concentrations of mitoxantrone and a small molecule APE1 inhibitor revealed additive cytotoxicity. These data suggest that in a cellular context, mitoxantrone may interfere with APE1 DNA repair functions.
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Affiliation(s)
- Irina G Minko
- Oregon Institute of Occupational Health Sciences, Oregon Health & Science University, Portland, OR 97239, USA
| | - Samantha A Moellmer
- Oregon Institute of Occupational Health Sciences, Oregon Health & Science University, Portland, OR 97239, USA
| | - Michael M Luzadder
- Oregon Institute of Occupational Health Sciences, Oregon Health & Science University, Portland, OR 97239, USA
| | - Rachana Tomar
- Department of Chemistry and the Vanderbilt-Ingram Cancer Center, Vanderbilt University, Station B Box 351822, Nashville, TN 37235, USA
| | - Michael P Stone
- Department of Chemistry and the Vanderbilt-Ingram Cancer Center, Vanderbilt University, Station B Box 351822, Nashville, TN 37235, USA
| | - Amanda K McCullough
- Oregon Institute of Occupational Health Sciences, Oregon Health & Science University, Portland, OR 97239, USA; Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR 97239, USA
| | - R Stephen Lloyd
- Oregon Institute of Occupational Health Sciences, Oregon Health & Science University, Portland, OR 97239, USA; Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR 97239, USA.
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5
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Das D, Duncton MAJ, Georgiadis TM, Pellicena P, Clark J, Sobol RW, Georgiadis MM, King-Underwood J, Jobes DV, Chang C, Gao Y, Deacon AM, Wilson DM. A New Drug Discovery Platform: Application to DNA Polymerase Eta and Apurinic/Apyrimidinic Endonuclease 1. Int J Mol Sci 2023; 24:16637. [PMID: 38068959 PMCID: PMC10706420 DOI: 10.3390/ijms242316637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 10/26/2023] [Accepted: 10/27/2023] [Indexed: 12/18/2023] Open
Abstract
The ability to quickly discover reliable hits from screening and rapidly convert them into lead compounds, which can be verified in functional assays, is central to drug discovery. The expedited validation of novel targets and the identification of modulators to advance to preclinical studies can significantly increase drug development success. Our SaXPyTM ("SAR by X-ray Poses Quickly") platform, which is applicable to any X-ray crystallography-enabled drug target, couples the established methods of protein X-ray crystallography and fragment-based drug discovery (FBDD) with advanced computational and medicinal chemistry to deliver small molecule modulators or targeted protein degradation ligands in a short timeframe. Our approach, especially for elusive or "undruggable" targets, allows for (i) hit generation; (ii) the mapping of protein-ligand interactions; (iii) the assessment of target ligandability; (iv) the discovery of novel and potential allosteric binding sites; and (v) hit-to-lead execution. These advances inform chemical tractability and downstream biology and generate novel intellectual property. We describe here the application of SaXPy in the discovery and development of DNA damage response inhibitors against DNA polymerase eta (Pol η or POLH) and apurinic/apyrimidinic endonuclease 1 (APE1 or APEX1). Notably, our SaXPy platform allowed us to solve the first crystal structures of these proteins bound to small molecules and to discover novel binding sites for each target.
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Affiliation(s)
- Debanu Das
- XPose Therapeutics, Inc., San Carlos, CA 94070, USA
- Accelero Biostructures, Inc., San Carlos, CA 94070, USA
| | | | | | | | - Jennifer Clark
- Mitchell Cancer Institute and Department of Pharmacology, University of South Alabama, Mobile, AL 36604, USA
| | - Robert W. Sobol
- Mitchell Cancer Institute and Department of Pharmacology, University of South Alabama, Mobile, AL 36604, USA
- Department of Pathology & Laboratory Medicine, Warrant Alpert Medical School & Legorreta Cancer Center, Brown University, Providence, RI 02912, USA
| | - Millie M. Georgiadis
- XPose Therapeutics, Inc., San Carlos, CA 94070, USA
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA
| | | | - David V. Jobes
- XPose Therapeutics, Inc., San Carlos, CA 94070, USA
- Mid-Atlantic BioTherapeutics, Inc., Doylestown, PA 18902, USA
| | - Caleb Chang
- Department of BioSciences, Rice University, Houston, TX 77251, USA
| | - Yang Gao
- Department of BioSciences, Rice University, Houston, TX 77251, USA
| | - Ashley M. Deacon
- XPose Therapeutics, Inc., San Carlos, CA 94070, USA
- Accelero Biostructures, Inc., San Carlos, CA 94070, USA
| | - David M. Wilson
- XPose Therapeutics, Inc., San Carlos, CA 94070, USA
- Biomedical Research Institute, Hasselt University, 3500 Diepenbeek, Belgium
- Belgium & Boost Scientific, 3550 Heusden-Zolder, Belgium
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Malfatti MC, Bellina A, Antoniali G, Tell G. Revisiting Two Decades of Research Focused on Targeting APE1 for Cancer Therapy: The Pros and Cons. Cells 2023; 12:1895. [PMID: 37508559 PMCID: PMC10378182 DOI: 10.3390/cells12141895] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 07/06/2023] [Accepted: 07/14/2023] [Indexed: 07/30/2023] Open
Abstract
APE1 is an essential endodeoxyribonuclease of the base excision repair pathway that maintains genome stability. It was identified as a pivotal factor favoring tumor progression and chemoresistance through the control of gene expression by a redox-based mechanism. APE1 is overexpressed and serum-secreted in different cancers, representing a prognostic and predictive factor and a promising non-invasive biomarker. Strategies directly targeting APE1 functions led to the identification of inhibitors showing potential therapeutic value, some of which are currently in clinical trials. Interestingly, evidence indicates novel roles of APE1 in RNA metabolism that are still not fully understood, including its activity in processing damaged RNA in chemoresistant phenotypes, regulating onco-miRNA maturation, and oxidized RNA decay. Recent data point out a control role for APE1 in the expression and sorting of onco-miRNAs within secreted extracellular vesicles. This review is focused on giving a portrait of the pros and cons of the last two decades of research aiming at the identification of inhibitors of the redox or DNA-repair functions of APE1 for the definition of novel targeted therapies for cancer. We will discuss the new perspectives in cancer therapy emerging from the unexpected finding of the APE1 role in miRNA processing for personalized therapy.
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Affiliation(s)
- Matilde Clarissa Malfatti
- Laboratory of Molecular Biology and DNA Repair, Department of Medicine, University of Udine, 33100 Udine, Italy
| | - Alessia Bellina
- Laboratory of Molecular Biology and DNA Repair, Department of Medicine, University of Udine, 33100 Udine, Italy
| | - Giulia Antoniali
- Laboratory of Molecular Biology and DNA Repair, Department of Medicine, University of Udine, 33100 Udine, Italy
| | - Gianluca Tell
- Laboratory of Molecular Biology and DNA Repair, Department of Medicine, University of Udine, 33100 Udine, Italy
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7
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Malfatti MC, Antoniali G, Tell G. In Vitro Assay to Measure APE1 Enzymatic Activity on Ribose Monophosphate Abasic Site. Methods Mol Biol 2023; 2701:21-38. [PMID: 37574473 DOI: 10.1007/978-1-0716-3373-1_2] [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] [Indexed: 08/15/2023]
Abstract
APE1 (apurinic/apyrimidinic endodeoxyribonuclease 1) is a central enzyme of the base excision repair (BER) pathway playing a pivotal role in protecting mammalian cells against genotoxins and in safeguarding genome stability. Recently, we demonstrated the APE1 ability to process abasic ribonucleotides embedded in DNA. Here, we provide a pipeline of protocols to quantify endodeoxyribonuclease activity by APE1 on these substrates, by using recombinant protein and whole-cell extracts. The repair capacity is measured by using fluorescent oligonucleotide substrates, which are then separated by polyacrylamide gel electrophoresis and detected by imaging scanning. The specificity of APE1 action is demonstrated using specific APE1 enzymatic inhibitors.
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Affiliation(s)
- Matilde Clarissa Malfatti
- Laboratory of Molecular Biology and DNA repair, Department of Medicine (DAME), University of Udine, Udine, Italy
| | - Giulia Antoniali
- Laboratory of Molecular Biology and DNA repair, Department of Medicine (DAME), University of Udine, Udine, Italy
| | - Gianluca Tell
- Laboratory of Molecular Biology and DNA repair, Department of Medicine (DAME), University of Udine, Udine, Italy.
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8
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Pidugu LS, Servius HW, Sevdalis SE, Cook ME, Varney KM, Pozharski E, Drohat AC. Characterizing inhibitors of human AP endonuclease 1. PLoS One 2023; 18:e0280526. [PMID: 36652434 PMCID: PMC9847973 DOI: 10.1371/journal.pone.0280526] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 12/30/2022] [Indexed: 01/19/2023] Open
Abstract
AP endonuclease 1 (APE1) processes DNA lesions including apurinic/apyrimidinic sites and 3´-blocking groups, mediating base excision repair and single strand break repair. Much effort has focused on developing specific inhibitors of APE1, which could have important applications in basic research and potentially lead to clinical anticancer agents. We used structural, biophysical, and biochemical methods to characterize several reported inhibitors, including 7-nitroindole-2-carboxylic acid (CRT0044876), given its small size, reported potency, and widespread use for studying APE1. Intriguingly, NMR chemical shift perturbation (CSP) experiments show that CRT0044876 and three similar indole-2-carboxylic acids bind a pocket distal from the APE1 active site. A crystal structure confirms these findings and defines the pose for 5-nitroindole-2-carboxylic acid. However, dynamic light scattering experiments show the indole compounds form colloidal aggregates that could bind (sequester) APE1, causing nonspecific inhibition. Endonuclease assays show the compounds lack significant APE1 inhibition under conditions (detergent) that disrupt aggregation. Thus, binding of the indole-2-carboxylic acids at the remote pocket does not inhibit APE1 repair activity. Myricetin also forms aggregates and lacks APE1 inhibition under aggregate-disrupting conditions. Two other reported compounds (MLS000552981, MLS000419194) inhibit APE1 in vitro with low micromolar IC50 and do not appear to aggregate in this concentration range. However, NMR CSP experiments indicate the compounds do not bind specifically to apo- or Mg2+-bound APE1, pointing to a non-specific mode of inhibition, possibly DNA binding. Our results highlight methods for rigorous interrogation of putative APE1 inhibitors and should facilitate future efforts to discover compounds that specifically inhibit this important repair enzyme.
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Affiliation(s)
- Lakshmi S. Pidugu
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Hardler W. Servius
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Spiridon E. Sevdalis
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Mary E. Cook
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Kristen M. Varney
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Edwin Pozharski
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
- Center for Biomolecular Therapeutics, Institute for Bioscience and Biotechnology Research, Rockville, Maryland, United States of America
- * E-mail: (EP); (ACD)
| | - Alexander C. Drohat
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
- * E-mail: (EP); (ACD)
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Benítez D, Franco J, Sardi F, Leyva A, Durán R, Choi G, Yang G, Kim T, Kim N, Heo J, Kim K, Lee H, Choi I, Radu C, Shum D, No JH, Comini MA. Drug-like molecules with anti-trypanothione synthetase activity identified by high throughput screening. J Enzyme Inhib Med Chem 2022; 37:912-929. [PMID: 35306933 PMCID: PMC8942522 DOI: 10.1080/14756366.2022.2045590] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Trypanothione synthetase (TryS) catalyses the synthesis of N1,N8-bis(glutathionyl)spermidine (trypanothione), which is the main low molecular mass thiol supporting several redox functions in trypanosomatids. TryS attracts attention as molecular target for drug development against pathogens causing severe and fatal diseases in mammals. A drug discovery campaign aimed to identify and characterise new inhibitors of TryS with promising biological activity was conducted. A large compound library (n = 51,624), most of them bearing drug-like properties, was primarily screened against TryS from Trypanosoma brucei (TbTryS). With a true-hit rate of 0.056%, several of the TbTryS hits (IC50 from 1.2 to 36 µM) also targeted the homologue enzyme from Leishmania infantum and Trypanosoma cruzi (IC50 values from 2.6 to 40 µM). Calmidazolium chloride and Ebselen stand out for their multi-species anti-TryS activity at low µM concentrations (IC50 from 2.6 to 13.8 µM). The moieties carboxy piperidine amide and amide methyl thiazole phenyl were identified as novel TbTryS inhibitor scaffolds. Several of the TryS hits presented one-digit µM EC50 against T. cruzi and L. donovani amastigotes but proved cytotoxic against the human osteosarcoma and macrophage host cells (selectivity index ≤ 3). In contrast, seven hits showed a significantly higher selectivity against T. b. brucei (selectivity index from 11 to 182). Non-invasive redox assays confirmed that Ebselen, a multi-TryS inhibitor, induces an intracellular oxidative milieu in bloodstream T. b. brucei. Kinetic and mass spectrometry analysis revealed that Ebselen is a slow-binding inhibitor that modifies irreversible a highly conserved cysteine residue from the TryS’s synthetase domain. The most potent TbTryS inhibitor (a singleton containing an adamantine moiety) exerted a non-covalent, non-competitive (with any of the substrates) inhibition of the enzyme. These data feed the drug discovery pipeline for trypanosomatids with novel and valuable information on chemical entities with drug potential.
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Affiliation(s)
- Diego Benítez
- Laboratory Redox Biology of Trypanosomes, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Jaime Franco
- Laboratory Redox Biology of Trypanosomes, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Florencia Sardi
- Laboratory Redox Biology of Trypanosomes, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Alejandro Leyva
- Analytical Biochemistry and Proteomics Unit, Institut Pasteur de Montevideo, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
| | - Rosario Durán
- Analytical Biochemistry and Proteomics Unit, Institut Pasteur de Montevideo, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo, Uruguay
| | - Gahee Choi
- Host-Parasite Research Laboratory, Institut Pasteur Korea, Gyeonggi-do, Republic of Korea
| | - Gyongseon Yang
- Host-Parasite Research Laboratory, Institut Pasteur Korea, Gyeonggi-do, Republic of Korea
| | - Taehee Kim
- Assay Development and Screening, Institut Pasteur Korea, Gyeonggi-do, Republic of Korea
| | - Namyoul Kim
- Assay Development and Screening, Institut Pasteur Korea, Gyeonggi-do, Republic of Korea
| | - Jinyeong Heo
- Assay Development and Screening, Institut Pasteur Korea, Gyeonggi-do, Republic of Korea
| | - Kideok Kim
- Automation and Logistics Management, Institut Pasteur Korea, Gyeonggi-do, Republic of Korea
| | - Honggun Lee
- Automation and Logistics Management, Institut Pasteur Korea, Gyeonggi-do, Republic of Korea
| | - Inhee Choi
- Medicinal Chemistry, Institut Pasteur Korea, Gyeonggi-do, Republic of Korea
| | - Constantin Radu
- Automation and Logistics Management, Institut Pasteur Korea, Gyeonggi-do, Republic of Korea
| | - David Shum
- Assay Development and Screening, Institut Pasteur Korea, Gyeonggi-do, Republic of Korea
| | - Joo Hwan No
- Host-Parasite Research Laboratory, Institut Pasteur Korea, Gyeonggi-do, Republic of Korea
| | - Marcelo A Comini
- Laboratory Redox Biology of Trypanosomes, Institut Pasteur de Montevideo, Montevideo, Uruguay
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10
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Wu Z, Duan H, Cheng Y, Guo D, Peng L, Hu Y, Hu J, Luo T. A novel ligand swing-mediated active site coordination change of human apurinic/apyrimidinic endonuclease 1: A potential cytotoxic mechanism of nickel ion in the base excision repair. Chem Phys 2022. [DOI: 10.1016/j.chemphys.2022.111456] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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11
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Ebenezer O, Damoyi N, Shapi M. Predicting New Anti-Norovirus Inhibitor With the Help of Machine Learning Algorithms and Molecular Dynamics Simulation-Based Model. Front Chem 2021; 9:753427. [PMID: 34869204 PMCID: PMC8636098 DOI: 10.3389/fchem.2021.753427] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 10/13/2021] [Indexed: 12/30/2022] Open
Abstract
Hepatitis C virus (HCV) inhibitors are essential in the treatment of human norovirus (HuNoV). This study aimed to map out HCV NS5B RNA-dependent RNA polymerase inhibitors that could potentially be responsible for the inhibitory activity of HuNoV RdRp. It is necessary to develop robust machine learning and in silico methods to predict HuNoV RdRp compounds. In this study, Naïve Bayesian and random forest models were built to categorize norovirus RdRp inhibitors from the non-inhibitors using their molecular descriptors and PubChem fingerprints. The best model observed had accuracy, specificity, and sensitivity values of 98.40%, 97.62%, and 97.62%, respectively. Meanwhile, an external test set was used to validate model performance before applicability to the screened HCV compounds database. As a result, 775 compounds were predicted as NoV RdRp inhibitors. The pharmacokinetics calculations were used to filter out the inhibitors that lack drug-likeness properties. Molecular docking and molecular dynamics simulation investigated the inhibitors' binding modes and residues critical for the HuNoV RdRp receptor. The most active compound, CHEMBL167790, closely binds to the binding pocket of the RdRp enzyme and depicted stable binding with RMSD 0.8-3.2 Å, and the RMSF profile peak was between 1.0-4.0 Å, and the conformational fluctuations were at 450-460 residues. Moreover, the dynamic residue cross-correlation plot also showed the pairwise correlation between the binding residues 300-510 of the HuNoV RdRp receptor and CHEMBL167790. The principal component analysis depicted the enhanced movement of protein atoms. Moreover, additional residues such as Glu510 and Asn505 interacted with CHEMBL167790 via water bridge and established H-bond interactions after the simulation. http://zinc15.docking.org/substances/ZINC000013589565.
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Affiliation(s)
- Oluwakemi Ebenezer
- Department of Chemistry, Faculty of Natural Science, Mangosuthu University of Technology, Durban, South Africa
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12
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Wilson DM, Deacon AM, Duncton MAJ, Pellicena P, Georgiadis MM, Yeh AP, Arvai AS, Moiani D, Tainer JA, Das D. Fragment- and structure-based drug discovery for developing therapeutic agents targeting the DNA Damage Response. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2021; 163:130-142. [PMID: 33115610 PMCID: PMC8666131 DOI: 10.1016/j.pbiomolbio.2020.10.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 10/13/2020] [Accepted: 10/23/2020] [Indexed: 12/12/2022]
Abstract
Cancer will directly affect the lives of over one-third of the population. The DNA Damage Response (DDR) is an intricate system involving damage recognition, cell cycle regulation, DNA repair, and ultimately cell fate determination, playing a central role in cancer etiology and therapy. Two primary therapeutic approaches involving DDR targeting include: combinatorial treatments employing anticancer genotoxic agents; and synthetic lethality, exploiting a sporadic DDR defect as a mechanism for cancer-specific therapy. Whereas, many DDR proteins have proven "undruggable", Fragment- and Structure-Based Drug Discovery (FBDD, SBDD) have advanced therapeutic agent identification and development. FBDD has led to 4 (with ∼50 more drugs under preclinical and clinical development), while SBDD is estimated to have contributed to the development of >200, FDA-approved medicines. Protein X-ray crystallography-based fragment library screening, especially for elusive or "undruggable" targets, allows for simultaneous generation of hits plus details of protein-ligand interactions and binding sites (orthosteric or allosteric) that inform chemical tractability, downstream biology, and intellectual property. Using a novel high-throughput crystallography-based fragment library screening platform, we screened five diverse proteins, yielding hit rates of ∼2-8% and crystal structures from ∼1.8 to 3.2 Å. We consider current FBDD/SBDD methods and some exemplary results of efforts to design inhibitors against the DDR nucleases meiotic recombination 11 (MRE11, a.k.a., MRE11A), apurinic/apyrimidinic endonuclease 1 (APE1, a.k.a., APEX1), and flap endonuclease 1 (FEN1).
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Affiliation(s)
- David M Wilson
- Hasselt University, Biomedical Research Institute, Diepenbeek, Belgium; Boost Scientific, Heusden-Zolder, Belgium; XPose Therapeutics Inc., San Carlos, CA, USA
| | - Ashley M Deacon
- Accelero Biostructures Inc., San Francisco, CA, USA; XPose Therapeutics Inc., San Carlos, CA, USA
| | | | | | - Millie M Georgiadis
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, USA; XPose Therapeutics Inc., San Carlos, CA, USA
| | - Andrew P Yeh
- Accelero Biostructures Inc., San Francisco, CA, USA
| | - Andrew S Arvai
- Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Davide Moiani
- Department of Cancer Biology, MD Anderson Cancer Center, Houston, TX, USA; Department of Molecular and Cellular Oncology, MD Anderson Cancer Center, Houston, TX, USA
| | - John A Tainer
- Department of Cancer Biology, MD Anderson Cancer Center, Houston, TX, USA; Department of Molecular and Cellular Oncology, MD Anderson Cancer Center, Houston, TX, USA
| | - Debanu Das
- Accelero Biostructures Inc., San Francisco, CA, USA; XPose Therapeutics Inc., San Carlos, CA, USA.
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13
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Liu TC, Guo KW, Chu JW, Hsiao YY. Understanding APE1 cellular functions by the structural preference of exonuclease activities. Comput Struct Biotechnol J 2021; 19:3682-3691. [PMID: 34285771 PMCID: PMC8258793 DOI: 10.1016/j.csbj.2021.06.036] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Revised: 06/21/2021] [Accepted: 06/22/2021] [Indexed: 12/17/2022] Open
Abstract
Mammalian apurinic/apyrimidinic (AP) endonuclease 1 (APE1) has versatile enzymatic functions, including redox, endonuclease, and exonuclease activities. APE1 is thus broadly associated with pathways in DNA repair, cancer cell growth, and drug resistance. Unlike its AP site-specific endonuclease activity in Base excision repair (BER), the 3′-5′ exonucleolytic cleavage of APE1 using the same active site exhibits complex substrate selection patterns, which are key to the biological functions. This work aims to integrate molecular structural information and biocatalytic properties to deduce the substrate recognition mechanism of APE1 as an exonuclease and make connection to its diverse functionalities in the cell. In particular, an induced space-filling model emerges in which a bridge-like structure is formed by Arg177 and Met270 (RM bridge) upon substrate binding, causing the active site to adopt a long and narrow product pocket for hosting the leaving group of an AP site or the 3′-end nucleotide. Rather than distinguishing bases as other exonucleases, the hydrophobicity and steric hindrance due to the APE1 product pocket provides selectivity for substrate structures, such as matched or mismatched blunt-ended dsDNA, recessed dsDNA, gapped dsDNA, and nicked dsDNA with 3′-end overhang shorter than 2 nucleotides. These dsDNAs are similar to the native substrates in BER proofreading, BER for trinucleotide repeats (TNR), Nucleotide incision repair (NIR), DNA single-strand breaks (SSB), SSB with damaged bases, and apoptosis. Integration of in vivo studies, in vitro biochemical assays, and structural analysis is thus essential for linking the APE1 exonuclease activity to the specific roles in cellular functions.
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Affiliation(s)
- Tung-Chang Liu
- Institute of Molecular Medicine and Bioengineering, National Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan.,Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu, Taiwan 30068, Taiwan
| | - Kai-Wei Guo
- Institute of Molecular Medicine and Bioengineering, National Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan.,Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu, Taiwan 30068, Taiwan
| | - Jhih-Wei Chu
- Institute of Molecular Medicine and Bioengineering, National Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan.,Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu, Taiwan 30068, Taiwan.,Institute of Bioinformatics and Systems Biology, National Yang Ming Chiao Tung University, Hsinchu, 30068, Taiwan.,Center For Intelligent Drug Systems and Smart Bio-devices (IDSB), National Yang Ming Chiao Tung University, Hsinchu, Taiwan
| | - Yu-Yuan Hsiao
- Institute of Molecular Medicine and Bioengineering, National Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan.,Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu, Taiwan 30068, Taiwan.,Institute of Bioinformatics and Systems Biology, National Yang Ming Chiao Tung University, Hsinchu, 30068, Taiwan.,Center For Intelligent Drug Systems and Smart Bio-devices (IDSB), National Yang Ming Chiao Tung University, Hsinchu, Taiwan.,Drug Development and Value Creation Research Center, Center for Cancer Research, Kaohsiung Medical University, Kaohsiung, Taiwan
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14
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HMCES Maintains Replication Fork Progression and Prevents Double-Strand Breaks in Response to APOBEC Deamination and Abasic Site Formation. Cell Rep 2021; 31:107705. [PMID: 32492421 PMCID: PMC7313144 DOI: 10.1016/j.celrep.2020.107705] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 04/28/2020] [Accepted: 05/06/2020] [Indexed: 01/12/2023] Open
Abstract
5-Hydroxymethylcytosine (5hmC) binding, ES-cell-specific (HMCES) crosslinks to apurinic or apyrimidinic (AP, abasic) sites in single-strand DNA (ssDNA). To determine whether HMCES responds to the ssDNA abasic site in cells, we exploited the activity of apolipoprotein B mRNA-editing enzyme catalytic polypeptide-like 3A (APOBEC3A). APOBEC3A preferentially deaminates cytosines to uracils in ssDNA, which are then converted to abasic sites by uracil DNA glycosylase. We find that HMCES-deficient cells are hypersensitive to nuclear APOBEC3A localization. HMCES relocalizes to chromatin in response to nuclear APOBEC3A and protects abasic sites from processing into double-strand breaks (DSBs). Abasic sites induced by APOBEC3A slow both leading and lagging strand synthesis, and HMCES prevents further slowing of the replication fork by translesion synthesis (TLS) polymerases zeta (Polζ) and kappa (Polκ). Thus, our study provides direct evidence that HMCES responds to ssDNA abasic sites in cells to prevent DNA cleavage and balance the engagement of TLS polymerases. Mehta et al. use APOBEC3A to demonstrate that HMCES responds to ssDNA abasic sites in cells and prevents replication fork collapse. APOBEC3A-induced abasic sites slow both leading and lagging strand polymerization, and HMCES engagement prevents further fork slowing because of the action of TLS polymerases zeta (Polζ) and kappa (Polκ).
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15
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Prendergast L, McClurg UL, Hristova R, Berlinguer-Palmini R, Greener S, Veitch K, Hernandez I, Pasero P, Rico D, Higgins JMG, Gospodinov A, Papamichos-Chronakis M. Resolution of R-loops by INO80 promotes DNA replication and maintains cancer cell proliferation and viability. Nat Commun 2020; 11:4534. [PMID: 32913330 PMCID: PMC7484789 DOI: 10.1038/s41467-020-18306-x] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 08/18/2020] [Indexed: 02/04/2023] Open
Abstract
Collisions between the DNA replication machinery and co-transcriptional R-loops can impede DNA synthesis and are a major source of genomic instability in cancer cells. How cancer cells deal with R-loops to proliferate is poorly understood. Here we show that the ATP-dependent chromatin remodelling INO80 complex promotes resolution of R-loops to prevent replication-associated DNA damage in cancer cells. Depletion of INO80 in prostate cancer PC3 cells leads to increased R-loops. Overexpression of the RNA:DNA endonuclease RNAse H1 rescues the DNA synthesis defects and suppresses DNA damage caused by INO80 depletion. R-loops co-localize with and promote recruitment of INO80 to chromatin. Artificial tethering of INO80 to a LacO locus enabled turnover of R-loops in cis. Finally, counteracting R-loops by INO80 promotes proliferation and averts DNA damage-induced death in cancer cells. Our work suggests that INO80-dependent resolution of R-loops promotes DNA replication in the presence of transcription, thus enabling unlimited proliferation in cancers.
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Affiliation(s)
- Lisa Prendergast
- Cancer Research UK Newcastle Drug Discovery Unit, Newcastle University Centre for Cancer, Newcastle University, Paul O'Gorman Building, Newcastle upon Tyne, NE2 4HH, UK
- Drug Discovery Unit, Cancer Research UK Manchester Institute, The University of Manchester, Alderley Park, SK10 4TG, Manchester, UK
| | - Urszula L McClurg
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Rossitsa Hristova
- Roumen Tsanev Institute of Molecular Biology, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | | | - Sarah Greener
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Katie Veitch
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Inmaculada Hernandez
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, 08028, Spain
| | - Philippe Pasero
- Institute of Human Genetics, CNRS UMR9002 and University of Montpellier, Equipe Labéllisée Ligue Contre le Cancer, 34090, Montpellier, France
| | - Daniel Rico
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | | | - Anastas Gospodinov
- Roumen Tsanev Institute of Molecular Biology, Bulgarian Academy of Sciences, Sofia, Bulgaria.
| | - Manolis Papamichos-Chronakis
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK.
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle Upon Tyne, NE2 4HH, UK.
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16
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Liu XQ, Ohsaki E, Ueda K. Establishment of a system for finding inhibitors of ε RNA binding with the HBV polymerase. Genes Cells 2020; 25:523-537. [PMID: 32415897 PMCID: PMC7496097 DOI: 10.1111/gtc.12778] [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: 01/09/2020] [Revised: 04/14/2020] [Accepted: 05/08/2020] [Indexed: 12/18/2022]
Abstract
Although several nucleo(s)tide analogs are available for treatment of HBV infection, long‐term treatment with these drugs can lead to the emergence of drug‐resistant viruses. Recent HIV‐1 studies suggest that combination therapies using nucleo(s)tide reverse transcriptase inhibitors (NRTIs) and non‐nucleo(s)tide reverse transcriptase inhibitors (NNRTIs) could drastically inhibit the viral genome replication of NRTI‐resistant viruses. In order to carry out such combinational therapy against HBV, several new NRTIs and NNRTIs should be developed. Here, we aimed to identify novel NNRTIs targeting the HBV polymerase terminal protein (TP)‐reverse transcriptase (RT) (TP‐RT) domain, which is a critical domain for HBV replication. We expressed and purified the HBV TP‐RT with high purity using an Escherichia coli expression system and established an in vitro ε RNA‐binding assay system. Then, we used TP‐RT in cell‐free assays to screen candidate inhibitors from a chemical compound library, and identified two compounds, 6‐hydroxy‐DL‐DOPA and N‐oleoyldopamine, which inhibited the binding of ε RNA with the HBV polymerase. Furthermore, these drugs reduced HBV DNA levels in cell‐based assays as well by inhibiting packaging of pregenome RNA into capsids. The novel screening system developed herein should open a new pathway the discovery of drugs targeting the HBV TP‐RT domain to treat HBV infection.
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Affiliation(s)
- Xiao-Quan Liu
- Division of Virology, Department of Microbiology and Immunology, Osaka University Graduate School of Medicine, Suita, Japan
| | - Eriko Ohsaki
- Division of Virology, Department of Microbiology and Immunology, Osaka University Graduate School of Medicine, Suita, Japan
| | - Keiji Ueda
- Division of Virology, Department of Microbiology and Immunology, Osaka University Graduate School of Medicine, Suita, Japan
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17
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Hamza A, Driessen MRM, Tammpere E, O'Neil NJ, Hieter P. Cross-Species Complementation of Nonessential Yeast Genes Establishes Platforms for Testing Inhibitors of Human Proteins. Genetics 2020; 214:735-747. [PMID: 31937519 PMCID: PMC7054014 DOI: 10.1534/genetics.119.302971] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 01/13/2020] [Indexed: 01/09/2023] Open
Abstract
Cross-species complementation can be used to generate humanized yeast, which is a valuable resource with which to model and study human biology. Humanized yeast can be used as an in vivo platform to screen for chemical inhibition of human protein drug targets. To this end, we report the systematic complementation of nonessential yeast genes implicated in chromosome instability (CIN) with their human homologs. We identified 20 human-yeast complementation pairs that are replaceable in 44 assays that test rescue of chemical sensitivity and/or CIN defects. We selected a human-yeast pair (hFEN1/yRAD27), which is frequently overexpressed in cancer and is an anticancer therapeutic target, to perform in vivo inhibitor assays using a humanized yeast cell-based platform. In agreement with published in vitro assays, we demonstrate that HU-based PTPD is a species-specific hFEN1 inhibitor. In contrast, another reported hFEN1 inhibitor, the arylstibonic acid derivative NSC-13755, was determined to have off-target effects resulting in a synthetic lethal phenotype with yRAD27-deficient strains. Our study expands the list of human-yeast complementation pairs to nonessential genes by defining novel cell-based assays that can be utilized as a broad resource to study human drug targets.
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Affiliation(s)
- Akil Hamza
- Michael Smith Laboratories, University of British Columbia, Vancouver V6T 1Z4, Canada
| | - Maureen R M Driessen
- Michael Smith Laboratories, University of British Columbia, Vancouver V6T 1Z4, Canada
| | - Erik Tammpere
- Michael Smith Laboratories, University of British Columbia, Vancouver V6T 1Z4, Canada
| | - Nigel J O'Neil
- Michael Smith Laboratories, University of British Columbia, Vancouver V6T 1Z4, Canada
| | - Philip Hieter
- Michael Smith Laboratories, University of British Columbia, Vancouver V6T 1Z4, Canada
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18
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Wang JY, Zhao MP. [Fluorescence assay for the detection of apurinic/apyrimidinic endonuclease 1 (APE1) activity in human blood samples]. JOURNAL OF PEKING UNIVERSITY. HEALTH SCIENCES 2019; 51:487-492. [PMID: 31209420 DOI: 10.19723/j.issn.1671-167x.2019.03.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
OBJECTIVE To develop a simple, sensitive and robust method for rapid detection of human apurinic/apyrimidinic endonuclease 1 (APE1) in various biological samples. METHODS An abasic site-containing DNA probe with a sequence of 5'-T*T*C*C*T*C*T(ROX)AGAGXCGTT (BHQ2)C*A*C*T*G*T*AGTTTATA*C*A*G*T*GAATCTCTCTAG*T*C*T-3' ["X" represents AP site; The phosphorothioated nucleotides (at 3' side) are indicated with an asterisk after the nucleotides; ROX is 6-carboxy-X-rhodamine and BHQ2 is Black Hole quencher 2] was synthesized and used for the detection. In the presence of APE1, the DNA probe could be specifically hydrolyzed by the enzyme and release the fluorophore, resulting in strong fluorescence emission. The activity of APE1 was determined according to the rate of increase in fluorescence intensity. In this work, we modified the reaction buffer and significantly improved the performance of the method. Moreover, the method was further extended to measure the contents of APE1 in the protein extraction from peripheral blood mononuclear cells (PBMCs) extracted from human whole blood samples by density gradient centrifugation. The assay was also applied to measure the activity of APE1 in human serum samples. RESULTS With a new reaction buffer composed of 0.04% (V/V) Triton X-100, 50 mmol/L KAc, 20 mmol/L Tris-Ac, 10 mmol/L Mg(Ac)2 and 1 mmol/L dithiothreitol (DTT), the method achieved a detection limit of 0.005 U/mL (3 pg/mL) and a linear response ranging from 6 pg/mL to 1.2 ng/mL. The contents of APE1 in the protein extraction from PBMCs of eight blood samples were measured to be in the range from 0.061 to 0.40 ng/μg protein, with an average of 0.16 ng/μg protein. The recovery was 98%±5% (n=3). The levels of APE1 in the sera from 102 normal individuals (51 male and 51 female, age range: 59-75 years) were observed to be from 0.13 to 0.34 ng/mL, with a recovery of 96%±15% (n=3). CONCLUSION The new fluorescence assay was simple, rapid and sensitive, providing a practical tool to measure the activity of APE1 in serum samples and cell extracts. It also holds great potential in measurement of APE1 in many other biological samples for clinical test and laboratory research.
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Affiliation(s)
- J Y Wang
- Beijing National Laboratory for Molecular Sciences, MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - M P Zhao
- Beijing National Laboratory for Molecular Sciences, MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
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19
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Zhang Y, Deng Y, Wang C, Li L, Xu L, Yu Y, Su X. Probing and regulating the activity of cellular enzymes by using DNA tetrahedron nanostructures. Chem Sci 2019; 10:5959-5966. [PMID: 31360402 PMCID: PMC6566069 DOI: 10.1039/c9sc01912j] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Accepted: 05/03/2019] [Indexed: 01/14/2023] Open
Abstract
Given the essential role of apurinic/apyrimidinic endonuclease (APE1) in gene repair and cancer progression, we report a novel approach for probing and regulating cellular APE1 activity by using DNA tetrahedrons.
Given the essential role of apurinic/apyrimidinic endonuclease (APE1) in gene repair and cancer progression, we report a novel approach for probing and regulating cellular APE1 activity by using DNA tetrahedrons. The tetrahedron with an AP site-containing antenna exhibits high sensitivity and specificity to APE1. It is suitable for APE1 in vitro detection (detection limit 5 pM) and cellular fluorescence imaging without any auxiliary transfection reagents, which discriminates the APE1 expression level of cancer cells and normal cells. In contrast, the tetrahedron with an AP site on its scaffold exhibits high binding affinity to APE1 but limits enzymatic catalysis making this nanostructure an APE1 inhibitor with an IC50 of 14.8 nM. It suppresses the APE1 activity in living cells and sensitizes cancer cells to anticancer drugs. We also demonstrate that the APE1 probe and inhibitor can be switched allosterically via stand displacement, which holds potential for reversible inhibition of APE1. Our approach provides a new way for fabricating enzyme probes and regulators and new insights into enzyme–substrate interactions, and it can be expanded to regulate other nucleic acid related enzymes.
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Affiliation(s)
- Yi Zhang
- College of Life Science and Technology , Beijing University of Chemical Technology , Beijing 100029 , China .
| | - Yingnan Deng
- College of Life Science and Technology , Beijing University of Chemical Technology , Beijing 100029 , China .
| | - Congshan Wang
- College of Life Science and Technology , Beijing University of Chemical Technology , Beijing 100029 , China .
| | - Lidan Li
- College of Life Science and Technology , Beijing University of Chemical Technology , Beijing 100029 , China .
| | - Lida Xu
- College of Life Science and Technology , Beijing University of Chemical Technology , Beijing 100029 , China .
| | - Yingjie Yu
- Department of Biomedical Engineering , Tufts University , Medford , MA 02155 , USA .
| | - Xin Su
- College of Life Science and Technology , Beijing University of Chemical Technology , Beijing 100029 , China .
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20
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Netzler NE, Enosi Tuipulotu D, White PA. Norovirus antivirals: Where are we now? Med Res Rev 2019; 39:860-886. [PMID: 30584800 PMCID: PMC7168425 DOI: 10.1002/med.21545] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2018] [Revised: 10/02/2018] [Accepted: 10/04/2018] [Indexed: 12/24/2022]
Abstract
Human noroviruses inflict a significant health burden on society and are responsible for approximately 699 million infections and over 200 000 estimated deaths worldwide each year. Yet despite significant research efforts, approved vaccines or antivirals to combat this pathogen are still lacking. Safe and effective antivirals are not available, particularly for chronically infected immunocompromised individuals, and for prophylactic applications to protect high-risk and vulnerable populations in outbreak settings. Since the discovery of human norovirus in 1972, the lack of a cell culture system has hindered biological research and antiviral studies for many years. Recent breakthroughs in culturing human norovirus have been encouraging, however, further development and optimization of these novel methodologies are required to facilitate more robust replication levels, that will enable reliable serological and replication studies, as well as advances in antiviral development. In the last few years, considerable progress has been made toward the development of norovirus antivirals, inviting an updated review. This review focuses on potential therapeutics that have been reported since 2010, which were examined across at least two model systems used for studying human norovirus or its enzymes. In addition, we have placed emphasis on antiviral compounds with a defined chemical structure. We include a comprehensive outline of direct-acting antivirals and offer a discussion of host-modulating compounds, a rapidly expanding and promising area of antiviral research.
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Affiliation(s)
- Natalie E. Netzler
- School of Biotechnology and Biomolecular Sciences, Faculty of Science, University of New South Wales, SydneyNew South WalesAustralia
| | - Daniel Enosi Tuipulotu
- School of Biotechnology and Biomolecular Sciences, Faculty of Science, University of New South Wales, SydneyNew South WalesAustralia
| | - Peter A. White
- School of Biotechnology and Biomolecular Sciences, Faculty of Science, University of New South Wales, SydneyNew South WalesAustralia
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21
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Li M, Dai N, Wang D, Zhong Z. Distinct APE1 Activities Affect the Regulation of VEGF Transcription Under Hypoxic Conditions. Comput Struct Biotechnol J 2019; 17:324-332. [PMID: 30906512 PMCID: PMC6411614 DOI: 10.1016/j.csbj.2019.02.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 02/14/2019] [Accepted: 02/15/2019] [Indexed: 01/17/2023] Open
Abstract
Angiogenesis is essential for tumor growth. Vascular endothelial growth factor (VEGF), a crucial factor in tumor angiogenesis, has been reported to be transcriptionally regulated by hypoxia-inducible factor-1 (HIF-1). An 8-oxo-G or apurinic/apyrimidinic (AP) site, which is frequently associated with DNA damage, has been identified in the promoter region of VEGF. However, the detailed molecular mechanisms by which AP sites regulate VEGF gene transcription are largely unknown. The dual functional protein apurinic/apyrimidinic endonuclease 1 (APE1) is both the key enzyme in DNA base excision repair and the redox factor shown to regulate HIF-1 DNA-binding activity. In the present study, we tested the involvement of both the AP endonuclease and redox activity of APE1 in regulating HIF-1 DNA binding and VEGF transcription in HUVECs. By employing two APE1 activity-specific inhibitors and AP-site-containing reporter constructs, we confirmed that both activities of APE1 were involved in regulating VEGF expression under hypoxic conditions. Furthermore, we found that the interaction between APE1 and its downstream repair enzyme, DNA polymerase β, was compromised when the N-terminal structure of APE1 was distorted under oxidative conditions. Our data suggest that the DNA repair and redox activity of APE1 can play a collaborative role in regulating the transcriptional initiation of the AP-site-containing promoter.
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Key Words
- AP site
- AP sites, Apurinic/apyrimidinic sites
- APE1
- APE1, Apurinic/apyrimidinic endonuclease
- BER, Base excision repair
- Co-IP, Coimmunoprecipitation
- EMSA, Electrophoretic mobility-shift assay
- Egr-1, Early growth response protein-1
- Fapy, Formamidopyrimidine
- HIF-1
- HIF-1, Hypoxia-induced factor-1
- HRE, Hypoxic response element
- HUVEC, Human umbilical vein endothelial cells
- Hypoxia
- NF-κB, Nuclear factor-kappa B
- OGG1, DNA Oxoguanine glycosylase 1
- Pol β, DNA Polymerase β
- Redox
- VEGF, Vascular endothelial growth factor
- qPCR, Quantitative PCR
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Affiliation(s)
- Mengxia Li
- Cancer Center, The Third Affiliated Hospital and Research Institute of Surgery of Army Medical University (Third Military Medical University), Chongqing 400042, PR China
| | - Nan Dai
- Cancer Center, The Third Affiliated Hospital and Research Institute of Surgery of Army Medical University (Third Military Medical University), Chongqing 400042, PR China
| | - Dong Wang
- Cancer Center, The Third Affiliated Hospital and Research Institute of Surgery of Army Medical University (Third Military Medical University), Chongqing 400042, PR China
| | - Zhaoyang Zhong
- Cancer Center, The Third Affiliated Hospital and Research Institute of Surgery of Army Medical University (Third Military Medical University), Chongqing 400042, PR China
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22
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Trilles R, Beglov D, Chen Q, He H, Wireman R, Reed A, Chennamadhavuni S, Panek JS, Brown LE, Vajda S, Porco JA, Kelley MR, Georgiadis MM. Discovery of Macrocyclic Inhibitors of Apurinic/Apyrimidinic Endonuclease 1. J Med Chem 2019; 62:1971-1988. [PMID: 30653918 DOI: 10.1021/acs.jmedchem.8b01529] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Apurinic/apyrimidinic endonuclease 1 (APE1) is an essential base excision repair enzyme that is upregulated in a number of cancers, contributes to resistance of tumors treated with DNA-alkylating or -oxidizing agents, and has recently been identified as an important therapeutic target. In this work, we identified hot spots for binding of small organic molecules experimentally in high resolution crystal structures of APE1 and computationally through the use of FTMAP analysis ( http://ftmap.bu.edu/ ). Guided by these hot spots, a library of drug-like macrocycles was docked and then screened for inhibition of APE1 endonuclease activity. In an iterative process, hot-spot-guided docking, characterization of inhibition of APE1 endonuclease, and cytotoxicity of cancer cells were used to design next generation macrocycles. To assess target selectivity in cells, selected macrocycles were analyzed for modulation of DNA damage. Taken together, our studies suggest that macrocycles represent a promising class of compounds for inhibition of APE1 in cancer cells.
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Affiliation(s)
- Richard Trilles
- Department of Chemistry and Center for Molecular Discovery (BU-CMD) , Boston University , Boston , Massachusetts 02215 , United States
| | - Dmitri Beglov
- Department of Biomedical Engineering , Boston University , Boston , Massachusetts 02215 , United States
| | | | | | | | | | - Spandan Chennamadhavuni
- Department of Chemistry and Center for Molecular Discovery (BU-CMD) , Boston University , Boston , Massachusetts 02215 , United States
| | - James S Panek
- Department of Chemistry and Center for Molecular Discovery (BU-CMD) , Boston University , Boston , Massachusetts 02215 , United States
| | - Lauren E Brown
- Department of Chemistry and Center for Molecular Discovery (BU-CMD) , Boston University , Boston , Massachusetts 02215 , United States
| | - Sandor Vajda
- Department of Biomedical Engineering , Boston University , Boston , Massachusetts 02215 , United States
| | - John A Porco
- Department of Chemistry and Center for Molecular Discovery (BU-CMD) , Boston University , Boston , Massachusetts 02215 , United States
| | | | - Millie M Georgiadis
- Department of Chemistry and Chemical Biology, Purdue School of Science , Indiana University-Purdue University Indianapolis , Indianapolis , Indiana 46202 , United States
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23
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Targeting the DNA Repair Endonuclease ERCC1-XPF with Green Tea Polyphenol Epigallocatechin-3-Gallate (EGCG) and Its Prodrug to Enhance Cisplatin Efficacy in Human Cancer Cells. Nutrients 2018; 10:nu10111644. [PMID: 30400270 PMCID: PMC6267282 DOI: 10.3390/nu10111644] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Revised: 10/24/2018] [Accepted: 10/29/2018] [Indexed: 11/17/2022] Open
Abstract
The 5′-3′ structure-specific endonuclease ERCC1/XPF (Excision Repair Cross-Complementation Group 1/Xeroderma Pigmentosum group F) plays critical roles in the repair of cisplatin-induced DNA damage. As such, it has been identified as a potential pharmacological target for enhancing clinical response to platinum-based chemotherapy. The goal of this study was to follow up on our previous identification of the compound NSC143099 as a potent inhibitor of ERCC1/XPF activity by performing an in silico screen to identify structural analogues that could inhibit ERCC1/XPF activity in vitro and in vivo. Using a fluorescence-based DNA-endonuclease incision assay, we identified the green tea polyphenol (-)-epigallocatechin-3-gallate (EGCG) as a potent inhibitor of ERCC1/XPF activity with an IC50 (half maximal inhibitory concentration) in the nanomolar range in biochemical assays. Using DNA repair assays and clonogenic survival assays, we show that EGCG can inhibit DNA repair and enhance cisplatin sensitivity in human cancer cells. Finally, we show that a prodrug of EGCG, Pro-EGCG (EGCG octaacetate), can enhance response to platinum-based chemotherapy in vivo. Together these data support a novel target of EGCG in cancer cells, namely ERCC1/XPF. Our studies also corroborate previous observations that EGCG enhances sensitivity to cisplatin in multiple cancer types. Thus, EGCG or its prodrug makes an ideal candidate for further pharmacological development with the goal of enhancing cisplatin response in human tumors.
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24
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Ferreira J, Ramos AA, Almeida T, Azqueta A, Rocha E. Drug resistance in glioblastoma and cytotoxicity of seaweed compounds, alone and in combination with anticancer drugs: A mini review. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2018; 48:84-93. [PMID: 30195884 DOI: 10.1016/j.phymed.2018.04.062] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Accepted: 04/19/2018] [Indexed: 06/08/2023]
Abstract
BACKGROUND Glioblastomas (GBM) are one of the most aggressive tumor of the central nervous system with an average life expectancy of only 1-2 years after diagnosis, even with the use of advanced treatments with surgery, radiation, and chemotherapy. There are several anticancer drugs with alkylating properties that have been used in the therapy of malignant gliomas. Temozolomide (TMZ) is one of them, widely used even in combination with ionizing radiation. However, the main disadvantage of using these types of drugs in the treatment of GBM is the development of cancer drug resistance. Research of bioactive compounds with anticancer activity has been heavily explored. PURPOSE This review focuses on a carotenoid and a phlorotannin present in seaweed, namely fucoxanthin and phloroglucinol, and their anticancer activity against glioblastoma. The combination of natural compounds with conventional drugs is also discussed. CONCLUSION Several natural compounds existing in seaweeds, such as fucoxanthin and phoroglucinol, have shown cytotoxic activity in models in vitro and in vivo, acting through different molecular mechanisms, such as antioxidant, antiproliferative, DNA damage/DNA repair, proapoptotic, antiangiogenic and antimetastic. Within the scope of interactions with conventional drugs, there are evidences that some seaweed compounds could be used to potentiate the action of anticancer drugs. However, their effects and mechanisms of action, alone or in combination with anticancer drugs, namely TMZ, in glioblastoma cell, still few explored and require more attention due to the unquestionable high potential of these marine compounds.
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Affiliation(s)
- Joana Ferreira
- Team of Histomorphology, Physiopathology and Applied Toxicology, CIIMAR - Interdisciplinary Center for Marine and Environmental Research, U.Porto - University of Porto, Avenida General Norton de Matos s/n, Matosinhos 4450-208, Portugal; Laboratory of Histology and Embryology, Department of Microscopy, ICBAS - Institute of Biomedical Sciences Abel Salazar, U.Porto - University of Porto, Rua de Jorge Viterbo Ferreira, n° 228, Porto 4050-313, Portugal; FCUP - Faculty of Sciences, U.Porto - University of Porto (U.Porto), Rua do Campo Alegre, Porto 4169-007, Portugal
| | - Alice Abreu Ramos
- Team of Histomorphology, Physiopathology and Applied Toxicology, CIIMAR - Interdisciplinary Center for Marine and Environmental Research, U.Porto - University of Porto, Avenida General Norton de Matos s/n, Matosinhos 4450-208, Portugal; Laboratory of Histology and Embryology, Department of Microscopy, ICBAS - Institute of Biomedical Sciences Abel Salazar, U.Porto - University of Porto, Rua de Jorge Viterbo Ferreira, n° 228, Porto 4050-313, Portugal.
| | - Tânia Almeida
- Team of Histomorphology, Physiopathology and Applied Toxicology, CIIMAR - Interdisciplinary Center for Marine and Environmental Research, U.Porto - University of Porto, Avenida General Norton de Matos s/n, Matosinhos 4450-208, Portugal; Laboratory of Histology and Embryology, Department of Microscopy, ICBAS - Institute of Biomedical Sciences Abel Salazar, U.Porto - University of Porto, Rua de Jorge Viterbo Ferreira, n° 228, Porto 4050-313, Portugal; FCUP - Faculty of Sciences, U.Porto - University of Porto (U.Porto), Rua do Campo Alegre, Porto 4169-007, Portugal
| | - Amaya Azqueta
- Department of Pharmacology and Toxicology, University of Navarra, C/ Irunlarrea, CP 31008 Pamplona, Navarra, Spain
| | - Eduardo Rocha
- Team of Histomorphology, Physiopathology and Applied Toxicology, CIIMAR - Interdisciplinary Center for Marine and Environmental Research, U.Porto - University of Porto, Avenida General Norton de Matos s/n, Matosinhos 4450-208, Portugal; Laboratory of Histology and Embryology, Department of Microscopy, ICBAS - Institute of Biomedical Sciences Abel Salazar, U.Porto - University of Porto, Rua de Jorge Viterbo Ferreira, n° 228, Porto 4050-313, Portugal
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25
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Visnes T, Grube M, Hanna BMF, Benitez-Buelga C, Cázares-Körner A, Helleday T. Targeting BER enzymes in cancer therapy. DNA Repair (Amst) 2018; 71:118-126. [PMID: 30228084 DOI: 10.1016/j.dnarep.2018.08.015] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Base excision repair (BER) repairs mutagenic or genotoxic DNA base lesions, thought to be important for both the etiology and treatment of cancer. Cancer phenotypic stress induces oxidative lesions, and deamination products are responsible for one of the most prevalent mutational signatures in cancer. Chemotherapeutic agents induce genotoxic DNA base damage that are substrates for BER, while synthetic lethal approaches targeting BER-related factors are making their way into the clinic. Thus, there are three strategies by which BER is envisioned to be relevant in cancer chemotherapy: (i) to maintain cellular growth in the presence of endogenous DNA damage in stressed cancer cells, (ii) to maintain viability after exogenous DNA damage is introduced by therapeutic intervention, or (iii) to confer synthetic lethality in cancer cells that have lost one or more additional DNA repair pathways. Here, we discuss the potential treatment strategies, and briefly summarize the progress that has been made in developing inhibitors to core BER-proteins and related factors.
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Affiliation(s)
- Torkild Visnes
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, S-171 76 Stockholm, Sweden; Department of Biotechnology and Nanomedicine, SINTEF Industry, N-7034 Trondheim, Norway
| | - Maurice Grube
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, S-171 76 Stockholm, Sweden
| | - Bishoy Magdy Fekry Hanna
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, S-171 76 Stockholm, Sweden
| | - Carlos Benitez-Buelga
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, S-171 76 Stockholm, Sweden
| | - Armando Cázares-Körner
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, S-171 76 Stockholm, Sweden
| | - Thomas Helleday
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, S-171 76 Stockholm, Sweden; Sheffield Cancer Centre, Department of Oncology and Metabolism, University of Sheffield, Sheffield S10 2RX, UK.
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26
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Ferla S, Netzler NE, Ferla S, Veronese S, Tuipulotu DE, Guccione S, Brancale A, White PA, Bassetto M. In silico screening for human norovirus antivirals reveals a novel non-nucleoside inhibitor of the viral polymerase. Sci Rep 2018. [PMID: 29515206 PMCID: PMC5841303 DOI: 10.1038/s41598-018-22303-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Human norovirus causes approximately 219,000 deaths annually, yet there are currently no antivirals available. A virtual screening of commercially available drug-like compounds (~300,000) was performed on the suramin and PPNDS binding-sites of the norovirus RNA-dependent RNA polymerase (RdRp). Selected compounds (n = 62) were examined for inhibition of norovirus RdRp activity using an in vitro transcription assay. Eight candidates demonstrated RdRp inhibition (>25% inhibition at 10 µM), which was confirmed using a gel-shift RdRp assay for two of them. The two molecules were identified as initial hits and selected for structure-activity relationship studies, which resulted in the synthesis of novel compounds that were examined for inhibitory activity. Five compounds inhibited human norovirus RdRp activity (>50% at 10 µM), with the best candidate, 54, demonstrating an IC50 of 5.6 µM against the RdRp and a CC50 of 62.8 µM. Combinational treatment of 54 and the known RdRp site-B inhibitor PPNDS revealed antagonism, indicating that 54 binds in the same binding pocket. Two RdRps with mutations (Q414A and R419A) previously shown to be critical for the binding of site-B compounds had no effect on inhibition, suggesting 54 interacts with distinct site-B residues. This study revealed the novel scaffold 54 for further development as a norovirus antiviral.
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Affiliation(s)
- Salvatore Ferla
- School of Pharmacy and Pharmaceutical Sciences, Cardiff University, Cardiff, United Kingdom.
| | - Natalie E Netzler
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Sebastiano Ferla
- School of Pharmacy and Pharmaceutical Sciences, Cardiff University, Cardiff, United Kingdom.,Dipartimento di Scienze del Farmaco, Università degli Studi di Catania, Catania, Italy
| | - Sofia Veronese
- School of Pharmacy and Pharmaceutical Sciences, Cardiff University, Cardiff, United Kingdom
| | - Daniel Enosi Tuipulotu
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Salvatore Guccione
- Dipartimento di Scienze del Farmaco, Università degli Studi di Catania, Catania, Italy
| | - Andrea Brancale
- School of Pharmacy and Pharmaceutical Sciences, Cardiff University, Cardiff, United Kingdom
| | - Peter A White
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Marcella Bassetto
- School of Pharmacy and Pharmaceutical Sciences, Cardiff University, Cardiff, United Kingdom
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27
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Sengupta S, Mantha AK, Song H, Roychoudhury S, Nath S, Ray S, Bhakat KK. Elevated level of acetylation of APE1 in tumor cells modulates DNA damage repair. Oncotarget 2018; 7:75197-75209. [PMID: 27655688 PMCID: PMC5342734 DOI: 10.18632/oncotarget.12113] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Accepted: 09/02/2016] [Indexed: 12/20/2022] Open
Abstract
Apurinic/apyrimidinic (AP) sites are frequently generated in the genome by spontaneous depurination/depyrimidination or after removal of oxidized/modified bases by DNA glycosylases during the base excision repair (BER) pathway. Unrepaired AP sites are mutagenic and block DNA replication and transcription. The primary enzyme to repair AP sites in mammalian cells is AP endonuclease (APE1), which plays a key role in this repair pathway. Although overexpression of APE1 in diverse cancer types and its association with chemotherapeutic resistance are well documented, alteration of posttranslational modification of APE1 and modulation of its functions during tumorigenesis are largely unknown. Here, we show that both classical histone deacetylase HDAC1 and NAD+-dependent deacetylase SIRT1 regulate acetylation level of APE1 and acetylation of APE1 enhances its AP-endonuclease activity both in vitro and in cells. Modulation of APE1 acetylation level in cells alters AP site repair capacity of the cell extracts in vitro. Primary tumor tissues of diverse cancer types have higher level of acetylated APE1 (AcAPE1) compared to adjacent non-tumor tissue and exhibit enhanced AP site repair capacity. Importantly, in the absence of APE1 acetylation, cells accumulate AP sites in the genome and show increased sensitivity to DNA damaging agents. Together, our study demonstrates that elevation of acetylation level of APE1 in tumor could be a novel mechanism by which cells handle the elevated levels of DNA damages in response to genotoxic stress and maintain sustained proliferation.
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Affiliation(s)
- Shiladitya Sengupta
- Department of Biochemistry & Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA.,Department of Radiation Oncology, Houston Methodist Research Institute, Houston, TX 77030 , USA
| | - Anil K Mantha
- Department of Biochemistry & Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA.,Center for Animal Sciences, School of Basic and Applied Sciences, Central University of Punjab, Bathinda 151001, Punjab, India
| | - Heyu Song
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Shrabasti Roychoudhury
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Somsubhra Nath
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE 68198, USA.,Molecular Biology Research & Diagnostic Laboratory, Saroj Gupta Cancer Centre & Research Institute, Kolkata 700063, India
| | - Sutapa Ray
- Department of Pediatrics, Hematology/Oncology Division, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Kishor K Bhakat
- Department of Biochemistry & Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA.,Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE 68198, USA
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28
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Barabutis N, Dimitropoulou C, Gregory B, Catravas JD. Wild-type p53 enhances endothelial barrier function by mediating RAC1 signalling and RhoA inhibition. J Cell Mol Med 2018; 22:1792-1804. [PMID: 29363851 PMCID: PMC5824363 DOI: 10.1111/jcmm.13460] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Accepted: 10/02/2017] [Indexed: 12/13/2022] Open
Abstract
Inflammation is the major cause of endothelial barrier hyper‐permeability, associated with acute lung injury and acute respiratory distress syndrome. This study reports that p53 “orchestrates” the defence of vascular endothelium against LPS, by mediating the opposing actions of Rac1 and RhoA in pulmonary tissues. Human lung microvascular endothelial cells treated with HSP90 inhibitors activated both Rac1‐ and P21‐activated kinase, which is an essential element of vascular barrier function. 17AAG increased the phosphorylation of both LIMK and cofilin, in contrast to LPS which counteracted those effects. Mouse lung microvascular endothelial cells exposed to LPS exhibited decreased expression of phospho‐cofilin. 17AAG treatment resulted in reduced levels of active cofilin. Silencing of cofilin pyridoxal phosphate phosphatase (PDXP) blocked the LPS‐induced hyper‐permeability, and P53 inhibition reversed the 17AAG‐induced PDXP down‐regulation. P190RHOGAP suppression enhanced the LPS‐triggered barrier dysfunction in endothelial monolayers. 17AAG treatment resulted in P190RHOGAP induction and blocked the LPS‐induced pMLC2 up‐regulation in wild‐type mice. Pulmonary endothelial cells from “super p53” mice, which carry additional p53‐tg alleles, exhibited a lower response to LPS than the controls. Collectively, our findings help elucidate the mechanisms by which p53 operates to enhance barrier function.
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Affiliation(s)
- Nektarios Barabutis
- Frank Reidy Research Center for Bioelectrics, Old Dominion University, Norfolk, VA, USA
| | | | - Betsy Gregory
- Frank Reidy Research Center for Bioelectrics, Old Dominion University, Norfolk, VA, USA
| | - John D Catravas
- Frank Reidy Research Center for Bioelectrics, Old Dominion University, Norfolk, VA, USA.,School of Medical Diagnostic & Translational Sciences, College of Health Sciences, Old Dominion University, Norfolk, VA, USA
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29
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Lee IW, Yoon J, Lee G, Lee M. Identification of New Potential APE1 Inhibitors by Pharmacophore Modeling and Molecular Docking. Genomics Inform 2017; 15:147-155. [PMID: 29307141 PMCID: PMC5769857 DOI: 10.5808/gi.2017.15.4.147] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Revised: 12/01/2017] [Accepted: 12/01/2017] [Indexed: 02/05/2023] Open
Abstract
Apurinic/apyrimidinic endonuclease 1 (APE1) is an enzyme responsible for the initial step in the base excision repair pathway and is known to be a potential drug target for treating cancers, because its expression is associated with resistance to DNA-damaging anticancer agents. Although several inhibitors already have been identified, the identification of novel kinds of potential inhibitors of APE1 could provide a seed for the development of improved anticancer drugs. For this purpose, we first classified known inhibitors of APE1. According to the classification, we constructed two distinct pharmacophore models. We screened more than 3 million lead-like compounds using the pharmacophores. Hits that fulfilled the features of the pharmacophore models were identified. In addition to the pharmacophore screen, we carried out molecular docking to prioritize hits. Based on these processes, we ultimately identified 1,338 potential inhibitors of APE1 with predicted binding affinities to the enzyme.
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Affiliation(s)
- In Won Lee
- Department of Biological Science, Sangji University, Wonju 26339, Korea
| | - Jonghwan Yoon
- Department of Biomedicine & Health Sciences, Graduate School, The Catholic University of Korea, Seoul 06591, Korea
| | - Gunhee Lee
- Department of Biomedicine & Health Sciences, Graduate School, The Catholic University of Korea, Seoul 06591, Korea
| | - Minho Lee
- Catholic Precision Medicine Research Center, College of Medicine, The Catholic University of Korea, Seoul 06591, Korea
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30
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Netzler NE, Enosi Tuipulotu D, Eltahla AA, Lun JH, Ferla S, Brancale A, Urakova N, Frese M, Strive T, Mackenzie JM, White PA. Broad-spectrum non-nucleoside inhibitors for caliciviruses. Antiviral Res 2017; 146:65-75. [PMID: 28757394 DOI: 10.1016/j.antiviral.2017.07.014] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Revised: 07/19/2017] [Accepted: 07/24/2017] [Indexed: 02/06/2023]
Abstract
Viruses of the Caliciviridae cause significant and sometimes lethal diseases, however despite substantial research efforts, specific antivirals are lacking. Broad-spectrum antivirals could combat multiple viral pathogens, offering a rapid solution when no therapies exist. The RNA-dependent RNA polymerase (RdRp) is an attractive antiviral target as it is essential for viral replication and lacks mammalian homologs. To focus the search for pan-Caliciviridae antivirals, the RdRp was probed with non-nucleoside inhibitors (NNIs) developed against hepatitis C virus (HCV) to reveal both allosteric ligands for structure-activity relationship enhancement, and highly-conserved RdRp pockets for antiviral targeting. The ability of HCV NNIs to inhibit calicivirus RdRp activities was assessed using in vitro enzyme and murine norovirus cell culture assays. Results revealed that three NNIs which bound the HCV RdRp Thumb I (TI) site also inhibited transcriptional activities of six RdRps spanning the Norovirus, Sapovirus and Lagovirus genera of the Caliciviridae. These NNIs included JTK-109 (RdRp inhibition range: IC50 4.3-16.6 μM), TMC-647055 (IC50 range: 18.8-45.4 μM) and Beclabuvir (IC50 range: 23.8->100 μM). In silico studies and site-directed mutagenesis indicated the JTK-109 binding site was within the calicivirus RdRp thumb domain, in a pocket termed Site-B, which is highly-conserved within all calicivirus RdRps. Additionally, RdRp inhibition assays revealed that JTK-109 was antagonistic with the previously reported RdRp inhibitor pyridoxal-5'-phosphate-6-(2'-naphthylazo-6'-nitro-4',8'-disulfonate) tetrasodium salt (PPNDS), that also binds to Site-B. Moreover, like JTK-109, PPNDS was also a potent inhibitor of polymerases from six viruses spanning the three Caliciviridae genera tested (IC50 range: 0.1-2.3 μM). Together, this study demonstrates the potential for de novo development of broad-spectrum antivirals that target the highly-conserved RdRp thumb pocket, Site-B. We also revealed three broad-spectrum HCV NNIs that could be used as antiviral scaffolds for further development against caliciviruses and other viruses.
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Affiliation(s)
- Natalie E Netzler
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Daniel Enosi Tuipulotu
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Auda A Eltahla
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia; School of Medical Sciences, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia
| | - Jennifer H Lun
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Salvatore Ferla
- School of Pharmacy and Pharmaceutical Sciences, Cardiff University, Cardiff, United Kingdom
| | - Andrea Brancale
- School of Pharmacy and Pharmaceutical Sciences, Cardiff University, Cardiff, United Kingdom
| | - Nadya Urakova
- CSIRO Health and Biosecurity, Canberra, ACT, Australia; Invasive Animals Cooperative Research Centre, University of Canberra, ACT, Australia; Health Research Institute, University of Canberra, ACT, Australia
| | - Michael Frese
- CSIRO Health and Biosecurity, Canberra, ACT, Australia; Invasive Animals Cooperative Research Centre, University of Canberra, ACT, Australia; Health Research Institute, University of Canberra, ACT, Australia; Institute for Applied Ecology, University of Canberra, ACT, Australia
| | - Tanja Strive
- CSIRO Health and Biosecurity, Canberra, ACT, Australia; Health Research Institute, University of Canberra, ACT, Australia; Institute for Applied Ecology, University of Canberra, ACT, Australia
| | - Jason M Mackenzie
- Department of Microbiology and Immunology, School of Biomedical Sciences, University of Melbourne, VIC, Australia; The Peter Doherty Institute for Infection and Immunity, VIC, Australia
| | - Peter A White
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia.
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31
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Human Apurinic/Apyrimidinic Endonuclease (APE1) Is Acetylated at DNA Damage Sites in Chromatin, and Acetylation Modulates Its DNA Repair Activity. Mol Cell Biol 2017; 37:MCB.00401-16. [PMID: 27994014 PMCID: PMC5335514 DOI: 10.1128/mcb.00401-16] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 12/14/2016] [Indexed: 11/20/2022] Open
Abstract
Apurinic/apyrimidinic (AP) sites, the most frequently formed DNA lesions in the genome, inhibit transcription and block replication. The primary enzyme that repairs AP sites in mammalian cells is the AP endonuclease (APE1), which functions through the base excision repair (BER) pathway. Although the mechanism by which APE1 repairs AP sites in vitro has been extensively investigated, it is largely unknown how APE1 repairs AP sites in cells. Here, we show that APE1 is acetylated (AcAPE1) after binding to the AP sites in chromatin and that AcAPE1 is exclusively present on chromatin throughout the cell cycle. Positive charges of acetylable lysine residues in the N-terminal domain of APE1 are essential for chromatin association. Acetylation-mediated neutralization of the positive charges of the lysine residues in the N-terminal domain of APE1 induces a conformational change; this in turn enhances the AP endonuclease activity of APE1. In the absence of APE1 acetylation, cells accumulated AP sites in the genome and showed higher sensitivity to DNA-damaging agents. Thus, mammalian cells, unlike Saccharomyces cerevisiae or Escherichia coli cells, require acetylation of APE1 for the efficient repair of AP sites and base damage in the genome. Our study reveals that APE1 acetylation is an integral part of the BER pathway for maintaining genomic integrity.
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32
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Laev SS, Salakhutdinov NF, Lavrik OI. Inhibitors of nuclease and redox activity of apurinic/apyrimidinic endonuclease 1/redox effector factor 1 (APE1/Ref-1). Bioorg Med Chem 2017; 25:2531-2544. [PMID: 28161249 DOI: 10.1016/j.bmc.2017.01.028] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Revised: 01/16/2017] [Accepted: 01/18/2017] [Indexed: 01/15/2023]
Abstract
Human apurinic/apyrimidinic endonuclease 1/redox effector factor 1 (APE1/Ref-1) is a multifunctional protein which is essential in the base excision repair (BER) pathway of DNA lesions caused by oxidation and alkylation. This protein hydrolyzes DNA adjacent to the 5'-end of an apurinic/apyrimidinic (AP) site to produce a nick with a 3'-hydroxyl group and a 5'-deoxyribose phosphate moiety or activates the DNA-binding activity of certain transcription factors through its redox function. Studies have indicated a role for APE1/Ref-1 in the pathogenesis of cancer and in resistance to DNA-interactive drugs. Thus, this protein has potential as a target in cancer treatment. As a result, major efforts have been directed to identify small molecule inhibitors against APE1/Ref-1 activities. These agents have the potential to become anticancer drugs. The aim of this review is to present recent progress in studies of all published small molecule APE1/Ref-1 inhibitors. The structures and activities of APE1/Ref-1 inhibitors, that target both DNA repair and redox activities, are presented and discussed. To date, there is an urgent need for further development of the design and synthesis of APE1/Ref-1 inhibitors due to high importance of this protein target.
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Affiliation(s)
- Sergey S Laev
- Vorozhtsov Institute of Organic Chemistry, Siberian Division, Russian Academy of Sciences, pr. akademika Lavrent'eva 9, Novosibirsk 630090, Russian Federation.
| | - Nariman F Salakhutdinov
- Vorozhtsov Institute of Organic Chemistry, Siberian Division, Russian Academy of Sciences, pr. akademika Lavrent'eva 9, Novosibirsk 630090, Russian Federation; Novosibirsk State University, Pirogova Str. 2, Novosibirsk 630090, Russian Federation
| | - Olga I Lavrik
- Novosibirsk State University, Pirogova Str. 2, Novosibirsk 630090, Russian Federation; Novosibirsk Institute of Chemical Biology and Fundamental Medicine, Siberian Division, Russian Academy of Sciences, pr. akademika Lavrent'eva 8, Novosibirsk 630090, Russian Federation
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33
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Sawant A, Floyd AM, Dangeti M, Lei W, Sobol RW, Patrick SM. Differential role of base excision repair proteins in mediating cisplatin cytotoxicity. DNA Repair (Amst) 2017; 51:46-59. [PMID: 28110804 DOI: 10.1016/j.dnarep.2017.01.002] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Revised: 12/01/2016] [Accepted: 01/03/2017] [Indexed: 02/04/2023]
Abstract
Interstrand crosslinks (ICLs) are covalent lesions formed by cisplatin. The mechanism for the processing and removal of ICLs by DNA repair proteins involves nucleotide excision repair (NER), homologous recombination (HR) and fanconi anemia (FA) pathways. In this report, we monitored the processing of a flanking uracil adjacent to a cisplatin ICL by the proteins involved in the base excision repair (BER) pathway. Using a combination of extracts, purified proteins, inhibitors, functional assays and cell culture studies, we determined the specific BER proteins required for processing a DNA substrate with a uracil adjacent to a cisplatin ICL. Uracil DNA glycosylase (UNG) is the primary glycosylase responsible for the removal of uracils adjacent to cisplatin ICLs, whereas other uracil glycosylases can process uracils in the context of undamaged DNA. Repair of the uracil adjacent to cisplatin ICLs proceeds through the classical BER pathway, highlighting the importance of specific proteins in this redundant pathway. Removal of uracil is followed by the generation of an abasic site and subsequent cleavage by AP endonuclease 1 (APE1). Inhibition of either the repair or redox domain of APE1 gives rise to cisplatin resistance. Inhibition of the lyase domain of Polymerase β (Polβ) does not influence cisplatin cytotoxicity. In addition, lack of XRCC1 leads to increased DNA damage and results in increased cisplatin cytotoxicity. Our results indicate that BER activation at cisplatin ICLs influences crosslink repair and modulates cisplatin cytotoxicity via specific UNG, APE1 and Polβ polymerase functions.
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Affiliation(s)
- Akshada Sawant
- Department of Oncology, Karmanos Cancer Institute, Wayne State University, Detroit, MI 48201, United States
| | - Ashley M Floyd
- Department of Oncology, Karmanos Cancer Institute, Wayne State University, Detroit, MI 48201, United States
| | - Mohan Dangeti
- Department of Biochemistry and Cancer Biology, University of Toledo - Health Science Campus, Toledo, OH 43614, United States
| | - Wen Lei
- Department of Oncology, Karmanos Cancer Institute, Wayne State University, Detroit, MI 48201, United States
| | - Robert W Sobol
- Department of Oncologic Sciences, Molecular & Metabolic Oncology Program, Mitchell Cancer Institute, University of South Alabama,1660 Springhill Avenue, Mobile, AL 36604, United States
| | - Steve M Patrick
- Department of Oncology, Karmanos Cancer Institute, Wayne State University, Detroit, MI 48201, United States.
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34
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Rideout MC, Liet B, Gasparutto D, Berthet N. A high-throughput screen for detection of compound-dependent phosphodiester bond cleavage at abasic sites. Anal Biochem 2016; 513:93-97. [PMID: 27594348 DOI: 10.1016/j.ab.2016.08.028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Revised: 07/28/2016] [Accepted: 08/30/2016] [Indexed: 11/20/2022]
Abstract
We have employed a DNA molecular beacon with a real abasic site, namely a 2-deoxyribose, in a fluorescent high-throughput assay to identify artificial nucleases that cleave at abasic sites. We screened a 1280 compound chemical library and identified a compound that functions as an artificial nuclease. We validated a key structure-activity relationship necessary for abasic site cleavage using available analogs of the identified artificial nuclease. We also addressed the activity of the identified compound with dose titrations in the absence and presence of a source of non-specific DNA. Finally, we characterized the phosphodiester backbone cleavage at the abasic site using denaturing gel electrophoresis. This study provides a useful template for researchers seeking to rapidly identify new artificial nucleases.
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Affiliation(s)
- Marc C Rideout
- Département de Chimie Moléculaire (DCM), Laboratoire Ingénierie et Interactions BioMoléculaires (I2BM), UMR-5250, ICMG FR-2607, CNRS, Université Grenoble Alpes (UGA), 570 Rue de la Chimie, BP-53, 38041 Grenoble Cedex 9, France.
| | - Benjamin Liet
- Département de Chimie Moléculaire (DCM), Laboratoire Ingénierie et Interactions BioMoléculaires (I2BM), UMR-5250, ICMG FR-2607, CNRS, Université Grenoble Alpes (UGA), 570 Rue de la Chimie, BP-53, 38041 Grenoble Cedex 9, France
| | - Didier Gasparutto
- Institut des Nanosciences & Cryogénie (INAC), SPrAM - UMR 5819 CEA/CNRS/Université Grenoble Alpes, Commissariat à l'Energie Atomique, 17 rue des Martyrs, F-38054 Grenoble Cedex 9, France
| | - Nathalie Berthet
- Département de Chimie Moléculaire (DCM), Laboratoire Ingénierie et Interactions BioMoléculaires (I2BM), UMR-5250, ICMG FR-2607, CNRS, Université Grenoble Alpes (UGA), 570 Rue de la Chimie, BP-53, 38041 Grenoble Cedex 9, France.
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35
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Guerreiro PS, Estácio SG, Antunes F, Fernandes AS, Pinheiro PF, Costa JG, Castro M, Miranda JP, Guedes RC, Oliveira NG. Structure-based virtual screening toward the discovery of novel inhibitors of the DNA repair activity of the human apurinic/apyrimidinic endonuclease 1. Chem Biol Drug Des 2016; 88:915-925. [DOI: 10.1111/cbdd.12826] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Revised: 05/10/2016] [Accepted: 07/11/2016] [Indexed: 01/21/2023]
Affiliation(s)
- Patrícia S. Guerreiro
- Research Institute for Medicines (iMed.ULisboa); Faculty of Pharmacy; Universidade de Lisboa; Lisbon Portugal
| | - Sílvia G. Estácio
- BioISI - Biosystems and Integrative Sciences Institute; Faculdade de Ciências; Universidade de Lisboa; Lisbon Portugal
| | - Fernando Antunes
- Departamento de Química e Bioquímica and Centro de Química e Bioquímica; Faculdade de Ciências; Universidade de Lisboa; Lisbon Portugal
| | - Ana S. Fernandes
- Research Institute for Medicines (iMed.ULisboa); Faculty of Pharmacy; Universidade de Lisboa; Lisbon Portugal
- CBIOS; Universidade Lusófona Research Center for Biosciences and Health Technologies; Lisbon Portugal
| | - Pedro F. Pinheiro
- Research Institute for Medicines (iMed.ULisboa); Faculty of Pharmacy; Universidade de Lisboa; Lisbon Portugal
- Centro de Química Estrutural (CQE); Instituto Superior Técnico; Universidade de Lisboa; Lisbon Portugal
| | - João G. Costa
- Research Institute for Medicines (iMed.ULisboa); Faculty of Pharmacy; Universidade de Lisboa; Lisbon Portugal
- CBIOS; Universidade Lusófona Research Center for Biosciences and Health Technologies; Lisbon Portugal
| | - Matilde Castro
- Research Institute for Medicines (iMed.ULisboa); Faculty of Pharmacy; Universidade de Lisboa; Lisbon Portugal
| | - Joana P. Miranda
- Research Institute for Medicines (iMed.ULisboa); Faculty of Pharmacy; Universidade de Lisboa; Lisbon Portugal
| | - Rita C. Guedes
- Research Institute for Medicines (iMed.ULisboa); Faculty of Pharmacy; Universidade de Lisboa; Lisbon Portugal
| | - Nuno G. Oliveira
- Research Institute for Medicines (iMed.ULisboa); Faculty of Pharmacy; Universidade de Lisboa; Lisbon Portugal
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36
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Kuznetsov NA, Kupryushkin MS, Abramova TV, Kuznetsova AA, Miroshnikova AD, Stetsenko DA, Pyshnyi DV, Fedorova OS. New oligonucleotide derivatives as unreactive substrate analogues and potential inhibitors of human apurinic/apyrimidinic endonuclease APE1. MOLECULAR BIOSYSTEMS 2016; 12:67-75. [PMID: 26548492 DOI: 10.1039/c5mb00692a] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Human apurinic/apyrimidinic endonuclease APE1 is one of the key enzymes of the base excision DNA repair system. The main biological function of APE1 is the hydrolysis of the phosphodiester bond on the 5'-side of an apurinic/apyrimidinic site (AP-site) to give the 5'-phosphate and 3'-hydroxyl group. It has long been known that AP-sites have mutagenic and cytotoxic effects and their accumulation in DNA is a potential hazard to the cell lifecycle. The structural and biochemical studies of APE1 are complicated by its high catalytic activity towards the AP-site and its cyclic or acyclic analogues. This work has focussed on the design, synthesis and analysis of oligonucleotide derivatives as potentially unreactive APE1 substrates. We have shown that the replacement of oxygen atoms in the phosphate group on the 5'-side from the AP-site analogue tetrahydrofuran (F) considerably decreases the rate of enzymatic hydrolysis of modified oligonucleotides. We have calculated that a N3'-P5' phosphoramidate linkage is hydrolysed about 30 times slower than the native phosphodiester bond while phosphorothioate or primary phosphoramidate linkages are cleaved more than three orders of magnitude slower. The value of IC50 of the oligonucleotide duplex containing a primary phosphoramidate linkage is 2.5 × 10(-7) M, which is in accordance with the APE1 association constant of DNA duplexes containing AP-sites. Thus, it is demonstrated that oligonucleotide duplexes with chemical modifications could be used as unreactive substrates and potential competitive inhibitors of APE1.
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Affiliation(s)
- Nikita A Kuznetsov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia. and Department of Natural Sciences, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Maxim S Kupryushkin
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia.
| | - Tatyana V Abramova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia.
| | - Alexandra A Kuznetsova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia.
| | - Anastasia D Miroshnikova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia.
| | - Dmitry A Stetsenko
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia. and Department of Natural Sciences, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Dmitrii V Pyshnyi
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia. and Department of Natural Sciences, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Olga S Fedorova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia. and Department of Natural Sciences, Novosibirsk State University, Novosibirsk 630090, Russia
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37
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Foley TL, Dorjsuren D, Dexheimer TS, Burkart MD, Wight WC, Simeonov A. A Platform to Enable the Pharmacological Profiling of Small Molecules in Gel-Based Electrophoretic Mobility Shift Assays. ACTA ACUST UNITED AC 2016; 21:1125-1131. [PMID: 27269812 DOI: 10.1177/1087057116652895] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
We describe a polyacrylamide gel casting cassette that overcomes limitations of commercially available gel electrophoresis equipment. This apparatus molds a single polyacrylamide gel that can evaluate more than 200 samples in parallel, is loaded with a multichannel pipettor, and is flexible with respect to composition of the separating matrix. We demonstrate its use to characterize inhibitors of enzymes that modify protein and nucleic acid substrates. Throughputs of greater than 1000 samples per day were achieved when this system was paired with a quantitative laser-based imaging system, yielding data of remarkable quality.
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Affiliation(s)
- Timothy L Foley
- 1 Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA.,Primary Pharmacology Group, Pharmacokinetics, Dynamics & Metabolism-New Chemical Entities, Pfizer, Groton, CT, USA
| | - Dorjbal Dorjsuren
- 1 Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
| | - Thomas S Dexheimer
- 1 Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA.,Assay Development and Drug Repurposing Core Facility, Department of Pharmacology & Toxicology, Michigan State University, East Lansing, MI, USA
| | - Michael D Burkart
- 2 Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, USA
| | | | - Anton Simeonov
- 1 Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
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38
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Georgiadis MM, Chen Q, Meng J, Guo C, Wireman R, Reed A, Vasko MR, Kelley MR. Small molecule activation of apurinic/apyrimidinic endonuclease 1 reduces DNA damage induced by cisplatin in cultured sensory neurons. DNA Repair (Amst) 2016; 41:32-41. [PMID: 27078577 DOI: 10.1016/j.dnarep.2016.03.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Revised: 03/23/2016] [Accepted: 03/24/2016] [Indexed: 11/18/2022]
Abstract
Although chemotherapy-induced peripheral neuropathy (CIPN) affects approximately 5-60% of cancer patients, there are currently no treatments available in part due to the fact that the underlying causes of CIPN are not well understood. One contributing factor in CIPN may be persistence of DNA lesions resulting from treatment with platinum-based agents such as cisplatin. In support of this hypothesis, overexpression of the base excision repair (BER) enzyme, apurinic/apyrimidinic endonuclease 1 (APE1), reduces DNA damage and protects cultured sensory neurons treated with cisplatin. Here, we address stimulation of APE1's endonuclease through a small molecule, nicorandil, as a means of mimicking the beneficial effects observed for overexpression of APE1. Nicorandil, was identified through high-throughput screening of small molecule libraries and found to stimulate APE1 endonuclease activity by increasing catalytic efficiency approximately 2-fold. This stimulation is primarily due to an increase in kcat. To prevent metabolism of nicorandil, an approved drug in Europe for the treatment of angina, cultured sensory neurons were pretreated with nicorandil and daidzin, an aldehyde dehydrogenase 2 inhibitor, resulting in decreased DNA damage but not altered transmitter release by cisplatin. This finding suggests that activation of APE1 by nicorandil in cisplatin-treated cultured sensory neurons does not imbalance the BER pathway in contrast to overexpression of the kinetically faster R177A APE1. Taken together, our results suggest that APE1 activators can be used to reduce DNA damage induced by cisplatin in cultured sensory neurons, although further studies will be required to fully assess their protective effects.
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Affiliation(s)
- Millie M Georgiadis
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, United States; Department of Chemistry and Chemical Biology, Indiana University Purdue University at Indianapolis, Indianapolis, IN, United States.
| | - Qiujia Chen
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, United States
| | - Jingwei Meng
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, United States
| | - Chunlu Guo
- Department of Pharmacology and Toxicology, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Randall Wireman
- Department of Pediatrics, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, United States
| | - April Reed
- Department of Pediatrics, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Michael R Vasko
- Department of Pharmacology and Toxicology, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Mark R Kelley
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, United States; Department of Pharmacology and Toxicology, Indiana University School of Medicine, Indianapolis, IN, United States; Department of Pediatrics, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, United States
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39
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Ramdzan ZM, Pal R, Kaur S, Leduy L, Bérubé G, Davoudi S, Vadnais C, Nepveu A. The function of CUX1 in oxidative DNA damage repair is needed to prevent premature senescence of mouse embryo fibroblasts. Oncotarget 2016; 6:3613-26. [PMID: 25682875 PMCID: PMC4414141 DOI: 10.18632/oncotarget.2919] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Accepted: 12/11/2014] [Indexed: 12/19/2022] Open
Abstract
Despite having long telomeres, mouse embryo fibroblasts (MEFs) senesce more rapidly than human diploid fibroblasts because of the accumulation of oxidative DNA damage. The CUX1 homeodomain protein was recently found to prevent senescence in RAS-driven cancer cells that produce elevated levels of reactive-oxygen species. Here we show that Cux1-/- MEFs are unable to proliferate in atmospheric (20%) oxygen although they can proliferate normally in physiological (3%) oxygen levels. CUX1 contains three domains called Cut repeats. Structure/function analysis established that a single Cut repeat domain can stimulate the DNA binding, Schiff-base formation, glycosylase and AP-lyase activities of 8-oxoguanine DNA glycosylase 1, OGG1. Strikingly and in contrast to previous reports, OGG1 exhibits efficient AP-lyase activity in the presence of a Cut repeat. Repair of oxidative DNA damage and proliferation in 20% oxygen were both rescued in Cux1-/- MEFs by ectopic expression of CUX1 or of a recombinant Cut repeat protein that stimulates OGG1 but is devoid of transcription activation potential. These findings reinforce the causal link between oxidative DNA damage and cellular senescence and suggest that the role of CUX1 as an accessory factor in DNA repair will be critical in physiological situations that generate higher levels of reactive oxygen species.
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Affiliation(s)
- Zubaidah M Ramdzan
- Goodman Cancer Centre, McGill University, Montreal, Quebec H3A 1A3, Canada
| | - Ranjana Pal
- Goodman Cancer Centre, McGill University, Montreal, Quebec H3A 1A3, Canada.,Department of Biological Sciences, Presidency University, Kolkata 700073, India
| | - Simran Kaur
- Goodman Cancer Centre, McGill University, Montreal, Quebec H3A 1A3, Canada.,Department of Biochemistry, McGill University, Montreal, Quebec H3A 1A3, Canada
| | - Lam Leduy
- Goodman Cancer Centre, McGill University, Montreal, Quebec H3A 1A3, Canada
| | - Ginette Bérubé
- Goodman Cancer Centre, McGill University, Montreal, Quebec H3A 1A3, Canada
| | - Sayeh Davoudi
- Goodman Cancer Centre, McGill University, Montreal, Quebec H3A 1A3, Canada.,Department of Biochemistry, McGill University, Montreal, Quebec H3A 1A3, Canada
| | - Charles Vadnais
- Goodman Cancer Centre, McGill University, Montreal, Quebec H3A 1A3, Canada.,Department of Biochemistry, McGill University, Montreal, Quebec H3A 1A3, Canada
| | - Alain Nepveu
- Goodman Cancer Centre, McGill University, Montreal, Quebec H3A 1A3, Canada.,Department of Biochemistry, McGill University, Montreal, Quebec H3A 1A3, Canada.,Department of Medicine, McGill University, Montreal, Quebec H3A 1A3, Canada.,Department of Oncology, McGill University, Montreal, Quebec H3A 1A3, Canada
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40
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Lebedeva NA, Anarbaev RO, Kupryushkin MS, Rechkunova NI, Pyshnyi DV, Stetsenko DA, Lavrik OI. Design of a New Fluorescent Oligonucleotide-Based Assay for a Highly Specific Real-Time Detection of Apurinic/Apyrimidinic Site Cleavage by Tyrosyl-DNA Phosphodiesterase 1. Bioconjug Chem 2015; 26:2046-53. [PMID: 26335988 DOI: 10.1021/acs.bioconjchem.5b00451] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Tyrosyl-DNA phosphodiesterase 1 (Tdp1) promotes catalytic scission of a phosphodiester bond between the 3'-end of DNA and the hydroxyl group of a tyrosine residue, as well as cleaving off a variety of other 3'-terminal phosphate-linked DNA substituents. We have shown recently that Tdp1 can initiate an apurinic/apyrimidinic (AP) site repair pathway that is independent from the one mediated by AP endonuclease 1 (APE1). Until recently, there was no method available of tracking the AP-site cleaving activity of Tdp1 by real-time fluorescence assay. In the present study we demonstrate a highly specific real-time detection of the AP-site cleaving activity of Tdp1 which allows one to distinguish it from the activity of APE1 by using a short hairpin oligonucleotide with a 1,12-dodecanediol loop, a 5'-fluorophore, and a 3'-quencher. Specific phosphodiesterase activity of Tdp1, which is usually able to remove quencher from the 3'-end of DNA, was suppressed in our approach by introducing a noncleavable phosphate group mimic between the 3'-end and the quencher. As a nondigestible 3'-phosphate analogue, we have used a new uncharged tetramethyl phosphoryl guanidine (Tmg) group, which is resistant to 3'-phosphodiesterase cleavage.
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Affiliation(s)
- Natalia A Lebedeva
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences , 8 Lavrentiev Avenue, Novosibirsk 630090, Russia.,Department of Natural Sciences, Novosibirsk State University , 2 Pirogov Street, Novosibirsk 630090, Russia
| | - Rashid O Anarbaev
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences , 8 Lavrentiev Avenue, Novosibirsk 630090, Russia.,Department of Natural Sciences, Novosibirsk State University , 2 Pirogov Street, Novosibirsk 630090, Russia
| | - Maxim S Kupryushkin
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences , 8 Lavrentiev Avenue, Novosibirsk 630090, Russia
| | - Nadejda I Rechkunova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences , 8 Lavrentiev Avenue, Novosibirsk 630090, Russia.,Department of Natural Sciences, Novosibirsk State University , 2 Pirogov Street, Novosibirsk 630090, Russia
| | - Dmitrii V Pyshnyi
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences , 8 Lavrentiev Avenue, Novosibirsk 630090, Russia.,Department of Natural Sciences, Novosibirsk State University , 2 Pirogov Street, Novosibirsk 630090, Russia
| | - Dmitry A Stetsenko
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences , 8 Lavrentiev Avenue, Novosibirsk 630090, Russia
| | - Olga I Lavrik
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences , 8 Lavrentiev Avenue, Novosibirsk 630090, Russia.,Department of Natural Sciences, Novosibirsk State University , 2 Pirogov Street, Novosibirsk 630090, Russia
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41
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Evison BJ, Sleebs BE, Watson KG, Phillips DR, Cutts SM. Mitoxantrone, More than Just Another Topoisomerase II Poison. Med Res Rev 2015; 36:248-99. [PMID: 26286294 DOI: 10.1002/med.21364] [Citation(s) in RCA: 135] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Revised: 07/13/2015] [Accepted: 07/14/2015] [Indexed: 02/06/2023]
Abstract
Mitoxantrone is a synthetic anthracenedione originally developed to improve the therapeutic profile of the anthracyclines and is commonly applied in the treatment of breast and prostate cancers, lymphomas, and leukemias. A comprehensive overview of the drug's molecular, biochemical, and cellular pharmacology is presented here, beginning with the cardiotoxic nature of its predecessor doxorubicin and how these properties shaped the pharmacology of mitoxantrone itself. Although mitoxantrone is firmly established as a DNA topoisomerase II poison within mammalian cells, it is now clear that the drug interacts with a much broader range of biological macromolecules both covalently and noncovalently. Here, we consider each of these interactions in the context of their wider biological relevance to cancer therapy and highlight how they may be exploited to further enhance the therapeutic value of mitoxantrone. In doing so, it is now clear that mitoxantrone is more than just another topoisomerase II poison.
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Affiliation(s)
- Benny J Evison
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Victoria, 3086, Australia
| | - Brad E Sleebs
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, 3052, Australia.,Department of Medical Biology, The University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Keith G Watson
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, 3052, Australia.,Department of Medical Biology, The University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Don R Phillips
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Victoria, 3086, Australia
| | - Suzanne M Cutts
- Department of Biochemistry and Genetics, La Trobe Institute for Molecular Science, La Trobe University, Victoria, 3086, Australia
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42
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Quinn BA, Lee NA, Kegelman TP, Bhoopathi P, Emdad L, Das SK, Pellecchia M, Sarkar D, Fisher PB. The Quest for an Effective Treatment for an Intractable Cancer: Established and Novel Therapies for Pancreatic Adenocarcinoma. Adv Cancer Res 2015; 127:283-306. [PMID: 26093904 DOI: 10.1016/bs.acr.2015.04.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
With therapies that date back to the 1950s, and few newly approved treatments in the last 20 years, pancreatic cancer remains a significant challenge for the development of novel therapeutics. Current regimens have successfully extended patient survival, although they still lead to prognoses measured in months rather than years. The genetic diversity inherent in pancreatic tumors forms the roadblocks that must be overcome in future therapeutics. Recent insight into the genetic patterns found in tumor cells may provide clues leading to better understanding of the challenges hindering the development of treatments. Here, we review currently used drugs and established combination therapies that comprise the standard of care for a highly recalcitrant disease. Novel approaches can improve upon current therapies in a variety of ways. Enhancing specificity, such that growth inhibition and cytotoxic effects act preferentially on tumor cells, is one approach to advance treatments. This can be accomplished through the targeting of extracellular markers specific to cancer cells. Additionally, enlisting natural defenses and overcoming tumor-driven immune suppression could prove to be a useful tactic. Recent studies utilizing these approaches have yielded promising results and could contribute to an ongoing effort battling a particularly difficult cancer.
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Affiliation(s)
- Bridget A Quinn
- Department of Human and Molecular Genetics, Virginia Commonwealth University, School of Medicine, Richmond, Virginia, USA
| | - Nathaniel A Lee
- Department of Human and Molecular Genetics, Virginia Commonwealth University, School of Medicine, Richmond, Virginia, USA; Department of Surgery, Virginia Commonwealth University, School of Medicine, Richmond, Virginia, USA
| | - Timothy P Kegelman
- Department of Human and Molecular Genetics, Virginia Commonwealth University, School of Medicine, Richmond, Virginia, USA
| | - Praveen Bhoopathi
- Department of Human and Molecular Genetics, Virginia Commonwealth University, School of Medicine, Richmond, Virginia, USA
| | - Luni Emdad
- Department of Human and Molecular Genetics, Virginia Commonwealth University, School of Medicine, Richmond, Virginia, USA; VCU Institute of Molecular Medicine, Virginia Commonwealth University, School of Medicine, Richmond, Virginia, USA; VCU Massey Cancer Center, Virginia Commonwealth University, School of Medicine, Richmond, Virginia, USA
| | - Swadesh K Das
- Department of Human and Molecular Genetics, Virginia Commonwealth University, School of Medicine, Richmond, Virginia, USA; VCU Institute of Molecular Medicine, Virginia Commonwealth University, School of Medicine, Richmond, Virginia, USA; VCU Massey Cancer Center, Virginia Commonwealth University, School of Medicine, Richmond, Virginia, USA
| | | | - Devanand Sarkar
- Department of Human and Molecular Genetics, Virginia Commonwealth University, School of Medicine, Richmond, Virginia, USA; VCU Institute of Molecular Medicine, Virginia Commonwealth University, School of Medicine, Richmond, Virginia, USA; VCU Massey Cancer Center, Virginia Commonwealth University, School of Medicine, Richmond, Virginia, USA
| | - Paul B Fisher
- Department of Human and Molecular Genetics, Virginia Commonwealth University, School of Medicine, Richmond, Virginia, USA; VCU Institute of Molecular Medicine, Virginia Commonwealth University, School of Medicine, Richmond, Virginia, USA; VCU Massey Cancer Center, Virginia Commonwealth University, School of Medicine, Richmond, Virginia, USA.
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43
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Feng Z, Kochanek S, Close D, Wang L, Srinivasan A, Almehizia AA, Iyer P, Xie XQ, Johnston PA, Gold B. Design and activity of AP endonuclease-1 inhibitors. J Chem Biol 2015; 8:79-93. [PMID: 26101550 DOI: 10.1007/s12154-015-0131-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Accepted: 03/25/2015] [Indexed: 12/12/2022] Open
Abstract
Apurinic/apyrimidinic endonuclease-1/redox effector factor-1 (APE-1) is a critical component of base excision repair that excises abasic lesions created enzymatically by the action of DNA glycosylases on modified bases and non-enzymatically by hydrolytic depurination/depyrimidination of nucleobases. Many anticancer drugs generate DNA adducts that are processed by base excision repair, and tumor resistance is frequently associated with enhanced APE-1 expression. Accordingly, APE-1 is a potential therapeutic target to treat cancer. Using computational approaches and the high resolution structure of APE-1, we developed a 5-point pharmacophore model for APE-1 small molecule inhibitors. One of the nM APE-1 inhibitors (AJAY-4) that was identified based on this model exhibited an overall median growth inhibition (GI50) of 4.19 μM in the NCI-60 cell line panel. The mechanism of action is shown to be related to the buildup of abasic sites that cause PARP activation and PARP cleavage, and the activation of caspase-3 and caspase-7, which is consistent with cell death by apoptosis. In a drug combination growth inhibition screen conducted in 10 randomly selected NCI-60 cell lines and with 20 clinically used non-genotoxic anticancer drugs, a synergy was flagged in the SK-MEL-5 melanoma cell line exposed to combinations of vemurafenib, which targets melanoma cells with V600E mutated BRAF, and AJAY-4, our most potent APE-1 inhibitor. The synergy between AJAY-4 and vemurafenib was not observed in cell lines expressing wild-type B-Raf protein. This synergistic combination may provide a solution to the resistance that develops in tumors treated with B-Raf-targeting drugs.
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Affiliation(s)
- Zhiwei Feng
- Department of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, PA 15261 USA
| | - Stanton Kochanek
- Department of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, PA 15261 USA
| | - David Close
- Department of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, PA 15261 USA
| | - LiRong Wang
- Department of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, PA 15261 USA
| | - Ajay Srinivasan
- Malaria Vaccine Development Program, New Delhi, 110067 India
| | | | - Prema Iyer
- Department of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, PA 15261 USA
| | - Xiang-Qun Xie
- Department of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, PA 15261 USA
| | - Paul A Johnston
- Department of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, PA 15261 USA
| | - Barry Gold
- Department of Pharmaceutical Sciences, University of Pittsburgh, Pittsburgh, PA 15261 USA
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44
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Doherty R, Madhusudan S. DNA Repair Endonucleases: Physiological Roles and Potential as Drug Targets. ACTA ACUST UNITED AC 2015; 20:829-41. [PMID: 25877151 DOI: 10.1177/1087057115581581] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Accepted: 03/22/2015] [Indexed: 12/15/2022]
Abstract
Genomic DNA is constantly exposed to endogenous and exogenous damaging agents. To overcome these damaging effects and maintain genomic stability, cells have robust coping mechanisms in place, including repair of the damaged DNA. There are a number of DNA repair pathways available to cells dependent on the type of damage induced. The removal of damaged DNA is essential to allow successful repair. Removal of DNA strands is achieved by nucleases. Exonucleases are those that progressively cut from DNA ends, and endonucleases make single incisions within strands of DNA. This review focuses on the group of endonucleases involved in DNA repair pathways, their mechanistic functions, roles in cancer development, and how targeting these enzymes is proving to be an exciting new strategy for personalized therapy in cancer.
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Affiliation(s)
- Rachel Doherty
- Laboratory of Molecular Oncology, Academic Unit of Oncology, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham, Nottingham University Hospitals, Nottingham, UK
| | - Srinivasan Madhusudan
- Laboratory of Molecular Oncology, Academic Unit of Oncology, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham, Nottingham University Hospitals, Nottingham, UK
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45
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Poletto M, Malfatti MC, Dorjsuren D, Scognamiglio PL, Marasco D, Vascotto C, Jadhav A, Maloney DJ, Wilson DM, Simeonov A, Tell G. Inhibitors of the apurinic/apyrimidinic endonuclease 1 (APE1)/nucleophosmin (NPM1) interaction that display anti-tumor properties. Mol Carcinog 2015; 55:688-704. [PMID: 25865359 DOI: 10.1002/mc.22313] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Revised: 02/10/2015] [Accepted: 02/21/2015] [Indexed: 12/23/2022]
Abstract
The apurinic/apyrimidinic endonuclease 1 (APE1) is a protein central to the base excision DNA repair pathway and operates in the modulation of gene expression through redox-dependent and independent mechanisms. Aberrant expression and localization of APE1 in tumors are recurrent hallmarks of aggressiveness and resistance to therapy. We identified and characterized the molecular association between APE1 and nucleophosmin (NPM1), a multifunctional protein involved in the preservation of genome stability and rRNA maturation. This protein-protein interaction modulates subcellular localization and endonuclease activity of APE1. Moreover, we reported a correlation between APE1 and NPM1 expression levels in ovarian cancer, with NPM1 overexpression being a marker of poor prognosis. These observations suggest that tumors that display an augmented APE1/NPM1 association may exhibit increased aggressiveness and resistance. Therefore, targeting the APE1/NPM1 interaction might represent an innovative strategy for the development of anticancer drugs, as tumor cells relying on higher levels of APE1 and NPM1 for proliferation and survival may be more sensitive than untransformed cells. We set up a chemiluminescence-based high-throughput screening assay in order to find small molecules able to interfere with the APE1/NPM1 interaction. This screening led to the identification of a set of bioactive compounds that impair the APE1/NPM1 association in living cells. Interestingly, some of these molecules display anti-proliferative activity and sensitize cells to therapeutically relevant genotoxins. Given the prognostic significance of APE1 and NPM1, these compounds might prove effective in the treatment of tumors that show abundant levels of both proteins, such as ovarian or hepatic carcinomas.
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Affiliation(s)
- Mattia Poletto
- Department of Medical and Biological Sciences, University of Udine, Udine, Italy
| | - Matilde C Malfatti
- Department of Medical and Biological Sciences, University of Udine, Udine, Italy
| | - Dorjbal Dorjsuren
- NIH Chemical Genomics Center, National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, Maryland
| | - Pasqualina L Scognamiglio
- Department of Pharmacy, CIRPEB (Centro Interuniversitario di Ricerca sui Peptidi Bioattivi), University of Naples 'Federico II', Naples, Italy.,Center for Advanced Biomaterials for Healthcare@CRIB, Istituto Italiano di Tecnologia (IIT), Naples, Italy
| | - Daniela Marasco
- Department of Pharmacy, CIRPEB (Centro Interuniversitario di Ricerca sui Peptidi Bioattivi), University of Naples 'Federico II', Naples, Italy
| | - Carlo Vascotto
- Department of Medical and Biological Sciences, University of Udine, Udine, Italy
| | - Ajit Jadhav
- NIH Chemical Genomics Center, National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, Maryland
| | - David J Maloney
- NIH Chemical Genomics Center, National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, Maryland
| | - David M Wilson
- Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health, Baltimore, Maryland
| | - Anton Simeonov
- NIH Chemical Genomics Center, National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, Maryland
| | - Gianluca Tell
- Department of Medical and Biological Sciences, University of Udine, Udine, Italy
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46
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Sharbeen G, McCarroll J, Goldstein D, Phillips PA. Exploiting base excision repair to improve therapeutic approaches for pancreatic cancer. Front Nutr 2015; 2:10. [PMID: 25988138 PMCID: PMC4428371 DOI: 10.3389/fnut.2015.00010] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Accepted: 03/10/2015] [Indexed: 12/13/2022] Open
Abstract
Pancreatic ductal adenocarcinoma (PDA) is a highly chemoresistant and metastatic disease with a dismal 5-year survival rate of 6%. More effective therapeutic targets and approaches are urgently needed to tackle this devastating disease. The base excision repair (BER) pathway has been identified as a predictor of therapeutic response, prognostic factor, and therapeutic target in a variety of cancers. This review will discuss our current understanding of BER in PDA and its potential to improve PDA treatment.
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Affiliation(s)
- George Sharbeen
- Pancreatic Cancer Translational Research Group, Lowy Cancer Research Centre, Prince of Wales Clinical School, UNSW Australia , Sydney, NSW , Australia
| | - Joshua McCarroll
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW Australia , Sydney, NSW , Australia
| | - David Goldstein
- Pancreatic Cancer Translational Research Group, Lowy Cancer Research Centre, Prince of Wales Clinical School, UNSW Australia , Sydney, NSW , Australia
| | - Phoebe A Phillips
- Pancreatic Cancer Translational Research Group, Lowy Cancer Research Centre, Prince of Wales Clinical School, UNSW Australia , Sydney, NSW , Australia
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47
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Fluorogenic DNA ligase and base excision repair enzyme assays using substrates labeled with single fluorophores. Anal Biochem 2015; 477:69-77. [PMID: 25728944 DOI: 10.1016/j.ab.2015.02.022] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Accepted: 02/19/2015] [Indexed: 01/27/2023]
Abstract
Continuing our work on fluorogenic substrates labeled with single fluorophores for nucleic acid modifying enzymes, here we describe the development of such substrates for DNA ligases and some base excision repair enzymes. These substrates are hairpin-type synthetic DNA molecules with a single fluorophore located on a base close to the 3' ends, an arrangement that results in strong fluorescence quenching. When such substrates are subjected to an enzymatic reaction, the position of the dyes relative to that end of the molecules is altered, resulting in significant fluorescence intensity changes. The ligase substrates described here were 5' phosphorylated and either blunt-ended or carrying short, self-complementary single-stranded 5' extensions. The ligation reactions resulted in the covalent joining of the ends of the molecules, decreasing the quenching effect of the terminal bases on the dyes. To generate fluorogenic substrates for the base excision repair enzymes formamido-pyrimidine-DNA glycosylase (FPG), human 8-oxo-G DNA glycosylase/AP lyase (hOGG1), endonuclease IV (EndoIV), and apurinic/apyrimidinic endonuclease (APE1), we introduced abasic sites or a modified nucleotide, 8-oxo-dG, at such positions that their enzymatic excision would result in the release of a short fluorescent fragment. This was also accompanied by strong fluorescence increases. Overall fluorescence changes ranged from approximately 4-fold (ligase reactions) to more than 20-fold (base excision repair reactions).
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48
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Kotera N, Poyer F, Granzhan A, Teulade-Fichou MP. Efficient inhibition of human AP endonuclease 1 (APE1) via substrate masking by abasic site-binding macrocyclic ligands. Chem Commun (Camb) 2015; 51:15948-51. [DOI: 10.1039/c5cc06084b] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Bis-naphthalene macrocycles bind to abasic sites in DNA, leading to efficient inhibition of their cleavage by human AP endonuclease 1 (APE1).
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Affiliation(s)
- Naoko Kotera
- CNRS UMR9187/INSERM U1196 “Chemistry, Modelling and Imaging for Biology”
- Centre de Recherche
- Institut Curie
- 91405 Orsay
- France
| | - Florent Poyer
- CNRS UMR9187/INSERM U1196 “Chemistry, Modelling and Imaging for Biology”
- Centre de Recherche
- Institut Curie
- 91405 Orsay
- France
| | - Anton Granzhan
- CNRS UMR9187/INSERM U1196 “Chemistry, Modelling and Imaging for Biology”
- Centre de Recherche
- Institut Curie
- 91405 Orsay
- France
| | - Marie-Paule Teulade-Fichou
- CNRS UMR9187/INSERM U1196 “Chemistry, Modelling and Imaging for Biology”
- Centre de Recherche
- Institut Curie
- 91405 Orsay
- France
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49
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Chohan M, Mackedenski S, Li WM, Lee CH. Human apurinic/apyrimidinic endonuclease 1 (APE1) has 3' RNA phosphatase and 3' exoribonuclease activities. J Mol Biol 2014; 427:298-311. [PMID: 25498387 DOI: 10.1016/j.jmb.2014.12.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Revised: 12/02/2014] [Accepted: 12/02/2014] [Indexed: 10/24/2022]
Abstract
Apurinic/apyrimidinic endonuclease 1 (APE1) is the predominant mammalian enzyme in DNA base excision repair pathway that cleaves the DNA backbone immediately 5' to abasic sites. In addition to its abasic endonuclease activity, APE1 has 3' phosphatase and 3'-5' exonuclease activities against DNA. We recently identified APE1 as an endoribonuclease that preferentially cleaves at UA, UG, and CA sites in single-stranded regions of RNAs and can regulate c-myc mRNA level and half-life in cells. APE1 can also endonucleolytically cleave abasic single-stranded RNA. Here, we show for the first time that the human APE1 has 3' RNA phosphatase and 3' exoribonuclease activities. Using three distinct RNA substrates, we show that APE1, but not RNase A, can remove the phosphoryl group from the 3' end of RNA decay products. Studies using various site-directed APE1 mutant proteins (H309N, H309S, D283N, N68A, D210N, Y171F, D308A, F266A, and D70A) suggest that the 3' RNA phosphatase activity shares the same active center as its other known nuclease activities. A number of APE1 variants previously identified in the human population, including the most common D148E variant, have greater than 80% reduction in the 3' RNA phosphatase activity. APE1 can remove a ribonucleotide from the 3' overhang of RNA decay product, but its 3'-5' exoribonuclease activity against unstructured poly(A), poly(C), and poly(U) RNAs is relatively weak. This study further underscores the significance of understanding the role of APE1 in RNA metabolism in vivo.
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Affiliation(s)
- Manbir Chohan
- Chemistry Program, University of Northern British Columbia, 3333 University Way, Prince George, British Columbia, V2N 4Z9, Canada
| | - Sebastian Mackedenski
- Chemistry Program, University of Northern British Columbia, 3333 University Way, Prince George, British Columbia, V2N 4Z9, Canada
| | - Wai-Ming Li
- Chemistry Program, University of Northern British Columbia, 3333 University Way, Prince George, British Columbia, V2N 4Z9, Canada
| | - Chow H Lee
- Chemistry Program, University of Northern British Columbia, 3333 University Way, Prince George, British Columbia, V2N 4Z9, Canada.
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50
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Oxidatively induced DNA damage and its repair in cancer. MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH 2014; 763:212-45. [PMID: 25795122 DOI: 10.1016/j.mrrev.2014.11.002] [Citation(s) in RCA: 173] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Revised: 11/03/2014] [Accepted: 11/04/2014] [Indexed: 12/28/2022]
Abstract
Oxidatively induced DNA damage is caused in living organisms by endogenous and exogenous reactive species. DNA lesions resulting from this type of damage are mutagenic and cytotoxic and, if not repaired, can cause genetic instability that may lead to disease processes including carcinogenesis. Living organisms possess DNA repair mechanisms that include a variety of pathways to repair multiple DNA lesions. Mutations and polymorphisms also occur in DNA repair genes adversely affecting DNA repair systems. Cancer tissues overexpress DNA repair proteins and thus develop greater DNA repair capacity than normal tissues. Increased DNA repair in tumors that removes DNA lesions before they become toxic is a major mechanism for development of resistance to therapy, affecting patient survival. Accumulated evidence suggests that DNA repair capacity may be a predictive biomarker for patient response to therapy. Thus, knowledge of DNA protein expressions in normal and cancerous tissues may help predict and guide development of treatments and yield the best therapeutic response. DNA repair proteins constitute targets for inhibitors to overcome the resistance of tumors to therapy. Inhibitors of DNA repair for combination therapy or as single agents for monotherapy may help selectively kill tumors, potentially leading to personalized therapy. Numerous inhibitors have been developed and are being tested in clinical trials. The efficacy of some inhibitors in therapy has been demonstrated in patients. Further development of inhibitors of DNA repair proteins is globally underway to help eradicate cancer.
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