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Sadat SMA, Vakili MR, Abd-El Hafeez SI, Paladino M, Hall DG, Weinfeld M, Lavasanifar A. Synergistic Nanomedicine Delivering Topoisomerase I Toxin (SN-38) and Inhibitors of Polynucleotide Kinase 3'-Phosphatase (PNKP) for Enhanced Treatment of Colorectal Cancer. Mol Pharm 2024. [PMID: 38785196 DOI: 10.1021/acs.molpharmaceut.4c00007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2024]
Abstract
Inhibitors of a DNA repair enzyme known as polynucleotide kinase 3'-phosphatase (PNKP) are expected to show synergistic cytotoxicity in combination with topoisomerase I (TOP1) inhibitors in cancer. In this study, the synergistic cytotoxicity of a novel inhibitor of PNKP, i.e., A83B4C63, with a potent TOP1 inhibitor, i.e., SN-38, against colorectal cancer cells was investigated. Polymeric micelles (PMs) for preferred tumor delivery of A83B4C63, developed through physical encapsulation of this compound in methoxy poly(ethylene oxide)-poly(α-benzyl carboxylate-ε-caprolactone) (mPEO-b-PBCL) micelles, were combined with SN-38 in free or PM form. The PM form of SN-38 was prepared through chemical conjugation of SN-38 to the functional end group of mPEO-b-PBCL and further assembly of mPEO-b-PBCL-SN-38 in water. Moreover, mixed micelles composed of mPEO-b-PBCL and mPEO-b-PBCL-SN-38 were used to co-load A83B4C63 and SN-38 in the same nanoformulation. The loading content (% w/w) of the SN-38 and A83B4C63 to mPEO-b-PBCL in the co-loaded formulation was 7.91 ± 0.66 and 16.13 ± 0.11% (w/w), respectively, compared to 15.67 ± 0.34 (% w/w) and 23.06 ± 0.63 (% w/w) for mPEO-b-PBCL micelles loading individual drugs. Notably, the average diameter of PMs co-encapsulating both SN-38 and A83B4C63 was larger than that of PMs encapsulating either of these compounds alone but still lower than 60 nm. The release of A83B4C63 from PMs co-encapsulating both drugs was 76.36 ± 1.41% within 24 h, which was significantly higher than that of A83B4C63-encapsulated micelles (42.70 ± 0.72%). In contrast, the release of SN-38 from PMs co-encapsulating both drugs was 44.15 ± 2.61% at 24 h, which was significantly lower than that of SN-38-conjugated PMs (74.16 ± 3.65%). Cytotoxicity evaluations by the MTS assay as analyzed by the Combenefit software suggested a clear synergy between PM/A83B4C63 (at a concentration range of 10-40 μM) and free SN-38 (at a concentration range of 0.001-1 μM). The synergistic cytotoxic concentration range for SN-38 was narrowed down to 0.1-1 or 0.01-1 μM when combined with PM/A83B4C63 at 10 or 20-40 μM, respectively. In general, PMs co-encapsulating A83B4C63 and SN-38 at drug concentrations within the synergistic range (10 μM for A83B4C63 and 0.05-1 μM for SN-38) showed slightly less enhancement of SN-38 anticancer activity than a combination of individual micelles, i.e., A83B4C63 PMs + SN-38 PMs at the same molar concentrations. This was attributed to the slower release of SN-38 from the SN-38 and A83B4C63 co-encapsulated PMs compared to PMs only encapsulating SN-38. Cotreatment of cells with TOP1 inhibitors and A83B4C63 formulation enhanced the expression level of γ-HA2X, cleaved PARP, caspase-3, and caspase-7 in most cases. This trend was more consistent and notable for PMs co-encapsulating both A83B4C63 and SN-38. The overall result from the study shows a synergy between PMs of SN-38 and A83B4C63 as a mixture of two PMs for individual drugs or PMs co-encapsulating both drugs.
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Affiliation(s)
- Sams M A Sadat
- Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, Alberta T6G 2R3, Canada
| | - Mohammad Reza Vakili
- Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, Alberta T6G 2R3, Canada
| | - Sara I Abd-El Hafeez
- Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, Alberta T6G 2R3, Canada
- Department of Pharmaceutics, Faculty of Pharmacy, Assiut University, Assiut 71515, Egypt
| | - Marco Paladino
- Department of Chemistry, Faculty of Science, University of Alberta, Edmonton, Alberta T6G 2R3, Canada
| | - Dennis G Hall
- Department of Chemistry, Faculty of Science, University of Alberta, Edmonton, Alberta T6G 2R3, Canada
| | - Michael Weinfeld
- Department of Oncology, Cross Cancer Institute, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta T6G 2R3, Canada
| | - Afsaneh Lavasanifar
- Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, Alberta T6G 2R3, Canada
- Department of Chemical and Material Engineering, University of Alberta, Edmonton, Alberta T6G 2R3, Canada
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Islam A, Chakraborty A, Sarker AH, Aryal UK, Pan L, Sharma G, Boldogh I, Hazra T. Site-specific acetylation of polynucleotide kinase 3'-phosphatase regulates its distinct role in DNA repair pathways. Nucleic Acids Res 2024; 52:2416-2433. [PMID: 38224455 PMCID: PMC10954452 DOI: 10.1093/nar/gkae002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 12/21/2023] [Accepted: 01/01/2024] [Indexed: 01/16/2024] Open
Abstract
Mammalian polynucleotide kinase 3'-phosphatase (PNKP), a DNA end-processing enzyme with 3'-phosphatase and 5'-kinase activities, is involved in multiple DNA repair pathways, including base excision (BER), single-strand break (SSBR), and double-strand break repair (DSBR). However, little is known as to how PNKP functions in such diverse repair processes. Here we report that PNKP is acetylated at K142 (AcK142) by p300 constitutively but at K226 (AcK226) by CBP, only after DSB induction. Co-immunoprecipitation analysis using AcK142 or AcK226 PNKP-specific antibodies showed that AcK142-PNKP associates only with BER/SSBR, and AcK226 PNKP with DSBR proteins. Despite the modest effect of acetylation on PNKP's enzymatic activity in vitro, cells expressing non-acetylable PNKP (K142R or K226R) accumulated DNA damage in transcribed genes. Intriguingly, in striatal neuronal cells of a Huntington's Disease (HD)-based mouse model, K142, but not K226, was acetylated. This is consistent with the reported degradation of CBP, but not p300, in HD cells. Moreover, transcribed genomes of HD cells progressively accumulated DSBs. Chromatin-immunoprecipitation analysis demonstrated the association of Ac-PNKP with the transcribed genes, consistent with PNKP's role in transcription-coupled repair. Thus, our findings demonstrate that acetylation at two lysine residues, located in different domains of PNKP, regulates its distinct role in BER/SSBR versus DSBR.
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Affiliation(s)
- Azharul Islam
- Department of Internal Medicine, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Anirban Chakraborty
- Department of Internal Medicine, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Altaf H Sarker
- Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Uma K Aryal
- Purdue Proteomics Facility, Bindley Bioscience Center, Purdue University, IN 47907, USA
| | - Lang Pan
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Gulshan Sharma
- Department of Internal Medicine, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Istvan Boldogh
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Tapas Hazra
- Department of Internal Medicine, University of Texas Medical Branch, Galveston, TX 77555, USA
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3
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Su A, Luo D, Li S, Zhang Y, Wang H, Yang L, Yang W, Pang P. An electrochemical biosensor for T4 polynucleotide kinase activity assay based on host-guest recognition between phosphate pillar[5]arene@MWCNTs and thionine. Analyst 2024; 149:1271-1279. [PMID: 38226548 DOI: 10.1039/d3an01863f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2024]
Abstract
T4 polynucleotide kinase helps with DNA recombination and repair. In this study, an electrochemical biosensor was developed for a T4 polynucleotide kinase activity assay and inhibitor screening based on phosphate pillar[5]arene and multi-walled carbon nanotube nanocomposites. The water-soluble pillar[5]arene was employed as the host to complex thionine guest molecules. The substrate DNA with a 5'-hydroxyl group initially self-assembled on the gold electrode surface through chemical adsorption of the thiol group, which was phosphorylated in the presence of T4 polynucleotide kinase. Titanium dioxide nanoparticles served as a bridge to link phosphorylated DNA and phosphate pillar[5]arene and multi-walled carbon nanotube composite due to strong phosphate-Ti4+-phosphate chemistry. Through supramolecular host-guest recognition, thionine molecules were able to penetrate the pillar[5]arene cavity, resulting in an enhanced electrochemical response signal. The electrochemical signal is proportional to the T4 polynucleotide kinase concentration in the range of 10-5 to 15 U mL-1 with a detection limit of 5 × 10-6 U mL-1. It was also effective in measuring HeLa cell lysate-related T4 polynucleotide kinase activity and inhibitor screening. The proposed method offers a unique sensing platform for kinase activity measurement, holding great potential in nucleotide kinase-target drug development, clinical diagnostics, and inhibitor screening.
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Affiliation(s)
- Aiwen Su
- Key Laboratory of Environmental Functional Materials of Yunnan Province Education Department, Yunnan Minzu University, Kunming 650504, P. R. China.
| | - Dan Luo
- Key Laboratory of Environmental Functional Materials of Yunnan Province Education Department, Yunnan Minzu University, Kunming 650504, P. R. China.
| | - Shixuan Li
- Key Laboratory of Environmental Functional Materials of Yunnan Province Education Department, Yunnan Minzu University, Kunming 650504, P. R. China.
| | - Yanli Zhang
- Key Laboratory of Environmental Functional Materials of Yunnan Province Education Department, Yunnan Minzu University, Kunming 650504, P. R. China.
| | - Hongbin Wang
- Key Laboratory of Environmental Functional Materials of Yunnan Province Education Department, Yunnan Minzu University, Kunming 650504, P. R. China.
| | - Lijuan Yang
- Key Laboratory of Environmental Functional Materials of Yunnan Province Education Department, Yunnan Minzu University, Kunming 650504, P. R. China.
| | - Wenrong Yang
- School of Life and Environmental Sciences, Deakin University, Geelong, VIC 3217, Australia
| | - Pengfei Pang
- Key Laboratory of Environmental Functional Materials of Yunnan Province Education Department, Yunnan Minzu University, Kunming 650504, P. R. China.
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Luo D, Liu Z, Su A, Zhang Y, Wang H, Yang L, Yang W, Pang P. An electrochemical biosensor for detection of T4 polynucleotide kinase activity based on host-guest recognition between phosphate pillar[5]arene and methylene blue. Talanta 2024; 266:124956. [PMID: 37499362 DOI: 10.1016/j.talanta.2023.124956] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Revised: 07/12/2023] [Accepted: 07/15/2023] [Indexed: 07/29/2023]
Abstract
T4 polynucleotide kinase (T4 PNK) is an important DNA repair-related enzyme that plays a crucial role in DNA recombination, replication and damage repair. Herein, an electrochemical biosensor was developed for detection of T4 PNK activity and inhibitor screening based on supramolecular host-guest recognition between phosphate pillar (Dumitrache and McKinnon, 2017) [5] arene (PP5) and methylene blue (MB). The water-soluble PP5 employed as the host for complexation of MB guest molecules. The substrate DNA with 5'-hydroxyl group was first self-assembled on the gold electrode surface through the chemical adsorption of the thiol group, which was phosphorylated in the presence of T4 PNK and adenosine triphosphate (ATP). TiO2 served as a bridge to link phosphorylated DNA and PP5 via the robust phosphate-Ti4+-phosphate chemistry. The immobilized PP5 captured the MB on electrode surface via the supramolecular host-guest recognition interaction, resulting in an enhanced electrochemical response signal. The electrochemical signal is proportional to the T4 PNK concentration in the range of 2 × 10-4 to 5 U mL-1 with a detection limit of 1 × 10-4 U mL-1. It was also successfully used for PNK inhibitor screening and PNK activity assay in HeLa cell lysates sample. The proposed strategy provides a novel sensing platform for kinase activity assay and inhibitor screening, holding a great potential in clinical diagnostics, inhibitor screening, and nucleotide kinase-target drug discovery.
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Affiliation(s)
- Dan Luo
- Key Laboratory of Environmental Functional Materials of Yunnan Province Education Department, Yunnan Minzu University, Kunming, 650504, PR China
| | - Zaiqiong Liu
- Key Laboratory of Environmental Functional Materials of Yunnan Province Education Department, Yunnan Minzu University, Kunming, 650504, PR China
| | - Aiwen Su
- Key Laboratory of Environmental Functional Materials of Yunnan Province Education Department, Yunnan Minzu University, Kunming, 650504, PR China
| | - Yanli Zhang
- Key Laboratory of Environmental Functional Materials of Yunnan Province Education Department, Yunnan Minzu University, Kunming, 650504, PR China.
| | - Hongbin Wang
- Key Laboratory of Environmental Functional Materials of Yunnan Province Education Department, Yunnan Minzu University, Kunming, 650504, PR China
| | - Lijuan Yang
- Key Laboratory of Environmental Functional Materials of Yunnan Province Education Department, Yunnan Minzu University, Kunming, 650504, PR China.
| | - Wenrong Yang
- School of Life and Environmental Sciences, Deakin University, Geelong, VIC, 3217, Australia
| | - Pengfei Pang
- Key Laboratory of Environmental Functional Materials of Yunnan Province Education Department, Yunnan Minzu University, Kunming, 650504, PR China.
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Gohil D, Sarker AH, Roy R. Base Excision Repair: Mechanisms and Impact in Biology, Disease, and Medicine. Int J Mol Sci 2023; 24:14186. [PMID: 37762489 PMCID: PMC10531636 DOI: 10.3390/ijms241814186] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 09/12/2023] [Accepted: 09/14/2023] [Indexed: 09/29/2023] Open
Abstract
Base excision repair (BER) corrects forms of oxidative, deamination, alkylation, and abasic single-base damage that appear to have minimal effects on the helix. Since its discovery in 1974, the field has grown in several facets: mechanisms, biology and physiology, understanding deficiencies and human disease, and using BER genes as potential inhibitory targets to develop therapeutics. Within its segregation of short nucleotide (SN-) and long patch (LP-), there are currently six known global mechanisms, with emerging work in transcription- and replication-associated BER. Knockouts (KOs) of BER genes in mouse models showed that single glycosylase knockout had minimal phenotypic impact, but the effects were clearly seen in double knockouts. However, KOs of downstream enzymes showed critical impact on the health and survival of mice. BER gene deficiency contributes to cancer, inflammation, aging, and neurodegenerative disorders. Medicinal targets are being developed for single or combinatorial therapies, but only PARP and APE1 have yet to reach the clinical stage.
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Affiliation(s)
- Dhara Gohil
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC 20057, USA;
| | - Altaf H. Sarker
- Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA;
| | - Rabindra Roy
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC 20057, USA;
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Wu Y, Yi J, Su A, Zhang Y, Wang H, Yang L, Yang W, Pang P. An electrochemical biosensor for T4 polynucleotide kinase activity identification according to host-guest recognition among phosphate pillar[5]arene@palladium nanoparticles@reduced graphene oxide nanocomposite and toluidine blue. Mikrochim Acta 2023; 190:394. [PMID: 37715009 DOI: 10.1007/s00604-023-05983-w] [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: 06/11/2023] [Accepted: 09/02/2023] [Indexed: 09/17/2023]
Abstract
T4 polynucleotide kinase (T4 PNK) helps with DNA recombination and repair. In this work, a phosphate pillar[5]arene@palladium nanoparticles@reduced graphene oxide nanocomposite (PP5@PdNPs@rGO)-based electrochemical biosensor was created to identify T4 PNK activities. The PP5 used to complex toluidine blue (TB) guest molecules is water-soluble. With T4 PNK and ATP, the substrate DNA, which included a 5'-hydroxyl group, initially self-assembled over the gold electrode surface by chemical adsorption of the thiol units. Strong phosphate-Zr4+-phosphate chemistry allowed Zr4+ to act as a bridge between phosphorylated DNA and PP5@PdNPs@rGO. Through a supramolecular host-guest recognition connection, TB molecules were able to penetrate the PP5 cavity, where they produced a stronger electrochemical response. With a 5 × 10-7 U mL-1 detection limit, the electrochemical signal is linear in the 10-6 to 1 U mL-1 T4 PNK concentration range. It was also effective in measuring HeLa cell lysate-related PNK activities and screening PNK inhibitors. Nucleotide kinase-target drug development, clinical diagnostics, and screening for inhibitors all stand to benefit greatly from the suggested technology, which offers a unique sensing mechanism for kinase activity measurement.
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Affiliation(s)
- Yongju Wu
- Key Laboratory of Environmental Functional Materials of Yunnan Province Education Department, Yunnan Minzu University, Kunming, 650504, People's Republic of China
| | - Jinfei Yi
- Key Laboratory of Environmental Functional Materials of Yunnan Province Education Department, Yunnan Minzu University, Kunming, 650504, People's Republic of China
| | - Aiwen Su
- Key Laboratory of Environmental Functional Materials of Yunnan Province Education Department, Yunnan Minzu University, Kunming, 650504, People's Republic of China
| | - Yanli Zhang
- Key Laboratory of Environmental Functional Materials of Yunnan Province Education Department, Yunnan Minzu University, Kunming, 650504, People's Republic of China.
| | - Hongbin Wang
- Key Laboratory of Environmental Functional Materials of Yunnan Province Education Department, Yunnan Minzu University, Kunming, 650504, People's Republic of China
| | - Lijuan Yang
- Key Laboratory of Environmental Functional Materials of Yunnan Province Education Department, Yunnan Minzu University, Kunming, 650504, People's Republic of China
| | - Wenrong Yang
- School of Life and Environmental Sciences, Deakin University, Geelong, VIC, 3217, Australia
| | - Pengfei Pang
- Key Laboratory of Environmental Functional Materials of Yunnan Province Education Department, Yunnan Minzu University, Kunming, 650504, People's Republic of China
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Islam A, Chakraborty A, Sarker AH, Aryal UK, Sharma G, Boldogh I, Hazra T. Site-specific acetylation of polynucleotide kinase 3'-phosphatase (PNKP) regulates its distinct role in DNA repair pathways. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.21.545973. [PMID: 37645927 PMCID: PMC10461918 DOI: 10.1101/2023.06.21.545973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Mammalian polynucleotide kinase 3'-phosphatase (PNKP) is a dual-function DNA end-processing enzyme with 3'-phosphatase and 5'-kinase activities, which generate 3'-OH and 5'-phosphate termini respectively, as substrates for DNA polymerase and DNA ligase to complete DNA repair. PNKP is thus involved in multiple DNA repair pathways, including base excision (BER), single-strand break (SSBR), and double-strand break repair (DSBR). However, little is known as to how PNKP functions in such diverse repair processes, which involve distinct sets of proteins. In this study, we report that PNKP is acetylated at two lysine (K142 and K226) residues. While K142 (AcK142) is constitutively acetylated by p300, CBP acetylates K226 (AcK226) only after DSB induction. Co-immunoprecipitation analysis using antibodies specific for PNKP peptides containing AcK142 or AcK226 of PNKP showed that AcK142-PNKP associates only with BER/SSBR, and AcK226 PNKP only with DSBR proteins. Although acetylation at these residues did not significantly affect the enzymatic activity of PNKP in vitro, cells expressing nonacetylable PNKP (K142R or K226R) accumulated DNA damage, specifically in transcribed genes. Intriguingly, in striatal neuronal cells of a Huntington's Disease (HD)-based mouse model, K142, but not K226, was acetylated. This observation is consistent with the reported degradation of CBP but not p300 in HD cells. Moreover, genomes of HD cells progressively accumulated DSBs specifically in the transcribed genes. Chromatin-immunoprecipitation analysis using anti-AcK142 or anti-AcK226 antibodies demonstrated an association of Ac-PNKP with the transcribed genes, consistent with PNKP's role in transcription-coupled repair. Thus, our findings collectively demonstrate that acetylation at two lysine residues located in different domains of PNKP regulates its functionally distinct role in BER/SSBR vs. DSBR.
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Affiliation(s)
- Azharul Islam
- Department of Internal Medicine, University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - Anirban Chakraborty
- Department of Internal Medicine, University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - Altaf H Sarker
- Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Uma K Aryal
- Purdue Proteomics Facility, Bindley Bioscience Center, Purdue University, IN 47907, USA
| | - Gulshan Sharma
- Department of Internal Medicine, University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - Istvan Boldogh
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Tapas Hazra
- Department of Internal Medicine, University of Texas Medical Branch, Galveston, TX, 77555, USA
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Islam A, Chakraborty A, Gambardella S, Campopiano R, Sarker AH, Boldogh I, Hazra T. Functional analysis of a conserved site mutation in the DNA processing enzyme PNKP leading to Ataxia with Oculomotor Apraxia type 4 (AOA4) in humans. J Biol Chem 2023; 299:104714. [PMID: 37061005 DOI: 10.1016/j.jbc.2023.104714] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 04/06/2023] [Accepted: 04/07/2023] [Indexed: 04/17/2023] Open
Abstract
Polynucleotide kinase 3'-phosphatase (PNKP), an essential DNA end-processing enzyme in mammals with 3'-phosphatase and 5'-kinase activities, plays a pivotal role in multiple DNA repair pathways. Its functional deficiency has been etiologically linked to various neurological disorders. Recent reports have shown that mutation at a conserved Glutamine (Gln) in PNKP leads to late-onset Ataxia with Oculomotor Apraxia type 4 (AOA4) in humans, and embryonic lethality in pigs. However, the molecular mechanism underlying such phenotypes remains elusive. Here, we report that the enzymatic activities of the mutant vs. wild-type PNKP are comparable; however, cells expressing mutant PNKP as well as Peripheral Blood Mononuclear Cells (PBMCs) of AOA4 patients showed a significant amount of DNA double-strand break (DSB) accumulation and consequent activation of the DNA damage response (DDR). Further investigation revealed that the nuclear localization of mutant PNKP is severely abrogated, and the mutant proteins remain primarily in the cytoplasm. Western blot analysis of AOA4 patient-derived PBMCs also revealed the presence of mutated PNKP predominantly in the cytoplasm. To understand the molecular determinants, we identified that mutation at a conserved Gln residue impedes the interaction of PNKP with importin alpha, but not with importin beta, two highly conserved proteins that mediate the import of proteins from the cytoplasm into the nucleus. Collectively, our data suggest that the absence of PNKP in the nucleus leads to constant activation of the DDR due to persistent accumulation of DSBs in the mutant cells, triggering death of vulnerable brain cells-a potential cause of neurodegeneration in AOA4 patients.
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Affiliation(s)
- Azharul Islam
- Department of Internal Medicine, University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - Anirban Chakraborty
- Department of Internal Medicine, University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - Stefano Gambardella
- IRCCS Neuromed & Department of Biomolecular Sciences, University of Urbino "Carlo Bo", Urbino, Italy
| | - Rosa Campopiano
- IRCCS Neuromed & Department of Biomolecular Sciences, University of Urbino "Carlo Bo", Urbino, Italy
| | - Altaf H Sarker
- Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Istvan Boldogh
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Tapas Hazra
- Department of Internal Medicine, University of Texas Medical Branch, Galveston, TX, 77555, USA.
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Liu XW, Liu WJ, Meng Y, Hu J, Zhang CY. Development of a tandem signal amplification strategy for label-free sensing polynucleotide kinase activity in cancer cells. Talanta 2023. [DOI: 10.1016/j.talanta.2022.124001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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10
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Cui W, Fan X, Zhao W, Liu J, Zheng L, Zhou L, Zhang J, Zhang X, Wang X. A label-free fluorescent biosensor for amplified detection of T4 polynucleotide kinase activity based on rolling circle amplification and catalytic hairpin assembly. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2023; 285:121938. [PMID: 36209712 DOI: 10.1016/j.saa.2022.121938] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 09/06/2022] [Accepted: 09/28/2022] [Indexed: 06/16/2023]
Abstract
T4 polynucleotide kinase (PNK) plays a key role in maintaining genome integrity and repairing DNA damage. In this paper, we proposed a label-free fluorescent biosensor for amplified detection of T4 PNK activity based on rolling circle amplification (RCA) and catalytic hairpin assembly (CHA). Firstly, we designed a padlock probe with a 5'-hydroxyl terminus for phosphorylation reaction, a complementary sequence of the primer for initiating RCA, and a complementary sequence of the trigger for triggering CHA. T4 PNK catalyzed the phosphorylation reaction by adding a phosphate group to the 5'-hydroxyl terminus of padlock probe, generating a phosphorylated padlock probe. Then it hybridized with the primer to generate a circular probe under the action of ligase. Subsequently, the primer initiated an RCA reaction along the circular probe to synthesize a large molecular weight product with repetitive trigger sequences. The triggers then triggered the cyclic assembly reactions between hairpin probe 1 and hairpin probe 2 to generate a large amount of complexes with free G-rich sequences. The free G-rich sequences folded into G-quadruplex structures, and the N-methylmesoporphyrin IXs were inserted into them to produce an amplified fluorescent signal. Benefiting from high amplification efficiency of RCA and CHA, this fluorescent biosensor could detect T4 PNK as low as 6.63 × 10-4 U mL-1, and was successfully applied to detect its activity in HeLa cell lysates. Moreover, this fluorescent biosensor could effectively distinguish T4 PNK from other alternatives and evaluate the inhibitory effect of inhibitor, indicating that it had great potential in drug screening and disease treatment.
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Affiliation(s)
- Wanling Cui
- Shandong Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou 253023, PR China.
| | - Xiaoyang Fan
- Shandong Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou 253023, PR China
| | - Wenqi Zhao
- Shandong Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou 253023, PR China
| | - Jinrong Liu
- Shandong Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou 253023, PR China
| | | | - Libing Zhou
- Laoling People's Hospital, Dezhou 253600, PR China
| | - Junye Zhang
- Shandong Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou 253023, PR China
| | - Xiumei Zhang
- College of Physics and Electronic Information, Dezhou University, Dezhou 253023, PR China
| | - Xiaoxin Wang
- College of Physics and Electronic Information, Dezhou University, Dezhou 253023, PR China
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Construction of a simple, localized and homogeneous fluorescence detection platform for T4 PNK activity based on tetrahedral DNA nanostructure-mediated primer exchange reaction. Microchem J 2022. [DOI: 10.1016/j.microc.2022.107989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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12
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Glycolytic flux control by drugging phosphoglycolate phosphatase. Nat Commun 2022; 13:6845. [PMID: 36369173 PMCID: PMC9652372 DOI: 10.1038/s41467-022-34228-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Accepted: 10/14/2022] [Indexed: 11/13/2022] Open
Abstract
Targeting the intrinsic metabolism of immune or tumor cells is a therapeutic strategy in autoimmunity, chronic inflammation or cancer. Metabolite repair enzymes may represent an alternative target class for selective metabolic inhibition, but pharmacological tools to test this concept are needed. Here, we demonstrate that phosphoglycolate phosphatase (PGP), a prototypical metabolite repair enzyme in glycolysis, is a pharmacologically actionable target. Using a combination of small molecule screening, protein crystallography, molecular dynamics simulations and NMR metabolomics, we discover and analyze a compound (CP1) that inhibits PGP with high selectivity and submicromolar potency. CP1 locks the phosphatase in a catalytically inactive conformation, dampens glycolytic flux, and phenocopies effects of cellular PGP-deficiency. This study provides key insights into effective and precise PGP targeting, at the same time validating an allosteric approach to control glycolysis that could advance discoveries of innovative therapeutic candidates.
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13
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A multiple primers-mediated exponential rolling circle amplification strategy for highly sensitive detection of T4 polynucleotide kinase and T4 DNA ligase activity. Microchem J 2022. [DOI: 10.1016/j.microc.2022.107403] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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14
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Shams F, Bayat H, Mohammadian O, Mahboudi S, Vahidnezhad H, Soosanabadi M, Rahimpour A. Advance trends in targeting homology-directed repair for accurate gene editing: An inclusive review of small molecules and modified CRISPR-Cas9 systems. BIOIMPACTS 2022; 12:371-391. [PMID: 35975201 PMCID: PMC9376165 DOI: 10.34172/bi.2022.23871] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 11/21/2021] [Accepted: 11/21/2021] [Indexed: 11/25/2022]
Abstract
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Introduction: Clustered regularly interspaced short palindromic repeat and its associated protein (CRISPR-Cas)-based technologies generate targeted modifications in host genome by inducing site-specific double-strand breaks (DSBs) that can serve as a substrate for homology-directed repair (HDR) in both in vitro and in vivo models. HDR pathway could enhance incorporation of exogenous DNA templates into the CRISPR-Cas9-mediated DSB site. Owing to low rate of HDR pathway, the efficiency of accurate genome editing is diminished. Enhancing the efficiency of HDR can provide fast, easy, and accurate technologies based on CRISPR-Cas9 technologies.
Methods: The current study presents an overview of attempts conducted on the precise genome editing strategies based on small molecules and modified CRISPR-Cas9 systems.
Results: In order to increase HDR rate in targeted cells, several logical strategies have been introduced such as generating CRISPR effector chimeric proteins, anti-CRISPR proteins, modified Cas9 with donor template, and using validated synthetic or natural small molecules for either inhibiting non-homologous end joining (NHEJ), stimulating HDR, or synchronizing cell cycle. Recently, high-throughput screening methods have been applied for identification of small molecules which along with the CRISPR system can regulate precise genome editing through HDR.
Conclusion: The stimulation of HDR components or inhibiting NHEJ can increase the accuracy of CRISPR-Cas-mediated engineering systems. Generating chimeric programmable endonucleases provide this opportunity to direct DNA template close proximity of CRISPR-Cas-mediated DSB. Small molecules and their derivatives can also proficiently block or activate certain DNA repair pathways and bring up novel perspectives for increasing HDR efficiency, especially in human cells. Further, high throughput screening of small molecule libraries could result in more discoveries of promising chemicals that improve HDR efficiency and CRISPR-Cas9 systems.
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Affiliation(s)
- Forough Shams
- Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Hadi Bayat
- Department of Molecular Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
- Department of Tissue Engineering and Applied Cell Sciences, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Omid Mohammadian
- Medical Nano-Technology and Tissue Engineering Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Department of Tissue Engineering and Applied Cell Sciences, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Somayeh Mahboudi
- Department of Food Science and Technology, School of Agriculture, Shiraz University, Shiraz, Iran
| | - Hassan Vahidnezhad
- Department of Dermatology and Cutaneous Biology, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, USA
- Jefferson Institute of Molecular Medicine, Thomas Jefferson University, Philadelphia, PA, USA
| | - Mohsen Soosanabadi
- Department of Medical Genetics, Semnan University of Medical Sciences, Semnan, Iran
| | - Azam Rahimpour
- Medical Nano-Technology and Tissue Engineering Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Department of Tissue Engineering and Applied Cell Sciences, School of Advanced Technologies in Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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15
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Zika Virus Induces Mitotic Catastrophe in Human Neural Progenitors by Triggering Unscheduled Mitotic Entry in the Presence of DNA Damage While Functionally Depleting Nuclear PNKP. J Virol 2022; 96:e0033322. [PMID: 35412344 PMCID: PMC9093132 DOI: 10.1128/jvi.00333-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Vertical transmission of Zika virus (ZIKV) leads with high frequency to congenital ZIKV syndrome (CZS), whose worst outcome is microcephaly. However, the mechanisms of congenital ZIKV neurodevelopmental pathologies, including direct cytotoxicity to neural progenitor cells (NPC), placental insufficiency, and immune responses, remain incompletely understood. At the cellular level, microcephaly typically results from death or insufficient proliferation of NPC or cortical neurons. NPC replicate fast, requiring efficient DNA damage responses to ensure genome stability. Like congenital ZIKV infection, mutations in the polynucleotide 5′-kinase 3′-phosphatase (PNKP) gene, which encodes a critical DNA damage repair enzyme, result in recessive syndromes often characterized by congenital microcephaly with seizures (MCSZ). We thus tested whether there were any links between ZIKV and PNKP. Here, we show that two PNKP phosphatase inhibitors or PNKP knockout inhibited ZIKV replication. PNKP relocalized from the nucleus to the cytoplasm in infected cells, colocalizing with the marker of ZIKV replication factories (RF) NS1 and resulting in functional nuclear PNKP depletion. Although infected NPC accumulated DNA damage, they failed to activate the DNA damage checkpoint kinases Chk1 and Chk2. ZIKV also induced activation of cytoplasmic CycA/CDK1 complexes, which trigger unscheduled mitotic entry. Inhibition of CDK1 activity inhibited ZIKV replication and the formation of RF, supporting a role of cytoplasmic CycA/CDK1 in RF morphogenesis. In brief, ZIKV infection induces mitotic catastrophe resulting from unscheduled mitotic entry in the presence of DNA damage. PNKP and CycA/CDK1 are thus host factors participating in ZIKV replication in NPC, and pathogenesis to neural progenitor cells. IMPORTANCE The 2015–2017 Zika virus (ZIKV) outbreak in Brazil and subsequent international epidemic revealed the strong association between ZIKV infection and congenital malformations, mostly neurodevelopmental defects up to microcephaly. The scale and global expansion of the epidemic, the new ZIKV outbreaks (Kerala state, India, 2021), and the potential burden of future ones pose a serious ongoing risk. However, the cellular and molecular mechanisms resulting in microcephaly remain incompletely understood. Here, we show that ZIKV infection of neuronal progenitor cells results in cytoplasmic sequestration of an essential DNA repair protein itself associated with microcephaly, with the consequent accumulation of DNA damage, together with an unscheduled activation of cytoplasmic CDK1/Cyclin A complexes in the presence of DNA damage. These alterations result in mitotic catastrophe of neuronal progenitors, which would lead to a depletion of cortical neurons during development.
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16
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de Paiva IM, Vakili MR, Soleimani AH, Tabatabaei Dakhili SA, Munira S, Paladino M, Martin G, Jirik FR, Hall DG, Weinfeld M, Lavasanifar A. Biodistribution and Activity of EGFR Targeted Polymeric Micelles Delivering a New Inhibitor of DNA Repair to Orthotopic Colorectal Cancer Xenografts with Metastasis. Mol Pharm 2022; 19:1825-1838. [PMID: 35271294 PMCID: PMC9175178 DOI: 10.1021/acs.molpharmaceut.1c00918] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The disruption of polynucleotide kinase/phosphatase (PNKP) in colorectal cancer (CRC) cells deficient in phosphatase and tensin homolog (PTEN) is expected to lead to the loss of cell viability by a process known as synthetic lethality. In previous studies, we have reported on the encapsulation of a novel inhibitor of PNKP, namely, A83B4C63, in polymeric micelles and its activity in slowing the growth of PTEN-deficient CRC cells as well as subcutaneous xenografts. In this study, to enhance drug delivery and specificity to CRC tumors, the surface of polymeric micelles carrying A83B4C63 was modified with GE11, a peptide targeting epidermal growth factor receptor (EGFR) overexpressed in about 70% of CRC tumors. Using molecular dynamics (MD) simulations, we assessed the binding site and affinity of GE11 for EGFR. The GE11-modified micelles, tagged with a near-infrared fluorophore, showed enhanced internalization by EGFR-overexpressing CRC cells in vitro and a trend toward increased primary tumor homing in an orthotopic CRC xenograft in vivo. In line with these observations, the GE11 modification of polymeric micelles was shown to positively contribute to the improved therapeutic activity of encapsulated A83B4C63 against HCT116-PTEN-/- cells in vitro and that of orthotopic CRC xenograft in vivo. In conclusion, our results provided proof of principle evidence for the potential benefit of EGFR targeted polymeric micellar formulations of A83B4C63 as monotherapeutics for aggressive and metastatic CRC tumors but at the same time highlighted the need for the development of EGFR ligands with improved physiological stability and EGFR binding.
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Affiliation(s)
- Igor Moura de Paiva
- Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, AB T6G 2EZ, Canada
| | - Mohammad Reza Vakili
- Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, AB T6G 2EZ, Canada
| | - Amir Hasan Soleimani
- Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, AB T6G 2EZ, Canada
| | | | - Sirazum Munira
- Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, AB T6G 2EZ, Canada
| | - Marco Paladino
- Department of Chemistry, Faculty of Science, University of Alberta, Edmonton, AB T6G 2G2, Canada
| | | | | | - Dennis G Hall
- Department of Chemistry, Faculty of Science, University of Alberta, Edmonton, AB T6G 2G2, Canada
| | - Michael Weinfeld
- Department of Oncology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G 1Z2, Canada
| | - Afsaneh Lavasanifar
- Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, AB T6G 2EZ, Canada.,Department of Chemical and Materials Engineering, Faculty of Engineering, University of Alberta, Edmonton, AB T6G 2H5, Canada
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17
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Hydrazonoyl chlorides possess promising antitumor properties. Life Sci 2022; 295:120380. [DOI: 10.1016/j.lfs.2022.120380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 02/01/2022] [Accepted: 02/02/2022] [Indexed: 11/23/2022]
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18
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Sadat SMA, Wuest M, Paiva IM, Munira S, Sarrami N, Sanaee F, Yang X, Paladino M, Binkhathlan Z, Karimi-Busheri F, Martin GR, Jirik FR, Murray D, Gamper AM, Hall DG, Weinfeld M, Lavasanifar A. Nano-Delivery of a Novel Inhibitor of Polynucleotide Kinase/Phosphatase (PNKP) for Targeted Sensitization of Colorectal Cancer to Radiation-Induced DNA Damage. Front Oncol 2022; 11:772920. [PMID: 35004293 PMCID: PMC8733593 DOI: 10.3389/fonc.2021.772920] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 11/24/2021] [Indexed: 12/29/2022] Open
Abstract
Inhibition of the DNA repair enzyme polynucleotide kinase/phosphatase (PNKP) increases the sensitivity of cancer cells to DNA damage by ionizing radiation (IR). We have developed a novel inhibitor of PNKP, i.e., A83B4C63, as a potential radio-sensitizer for the treatment of solid tumors. Systemic delivery of A83B4C63, however, may sensitize both cancer and normal cells to DNA damaging therapeutics. Preferential delivery of A83B4C63 to solid tumors by nanoparticles (NP) was proposed to reduce potential side effects of this PNKP inhibitor to normal tissue, particularly when combined with DNA damaging therapies. Here, we investigated the radio-sensitizing activity of A83B4C63 encapsulated in NPs (NP/A83) based on methoxy poly(ethylene oxide)-b-poly(α-benzyl carboxylate-ε-caprolactone) (mPEO-b-PBCL) or solubilized with the aid of Cremophor EL: Ethanol (CE/A83) in human HCT116 colorectal cancer (CRC) models. Levels of γ-H2AX were measured and the biodistribution of CE/A83 and NP/A83 administered intravenously was determined in subcutaneous HCT116 CRC xenografts. The radio-sensitization effect of A83B4C63 was measured following fractionated tumor irradiation using an image-guided Small Animal Radiation Research Platform (SARRP), with 24 h pre-administration of CE/A83 and NP/A83 to Luc+/HCT116 bearing mice. Therapeutic effects were analyzed by monitoring tumor growth and functional imaging using Positron Emission Tomography (PET) and [18F]-fluoro-3’-deoxy-3’-L:-fluorothymidine ([18F]FLT) as a radiotracer for cell proliferation. The results showed an increased persistence of DNA damage in cells treated with a combination of CE/A83 or NP/A83 and IR compared to those only exposed to IR. Significantly higher tumor growth delay in mice treated with a combination of IR and NP/A83 than those treated with IR plus CE/A83 was observed. [18F]FLT PET displayed significant functional changes for tumor proliferation for the drug-loaded NP. This observation was attributed to the higher A83B4C63 levels in the tumors for NP/A83-treated mice compared to those treated with CE/A83. Overall, the results demonstrated a potential for A83B4C63-loaded NP as a novel radio-sensitizer for the treatment of CRC.
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Affiliation(s)
- Sams M A Sadat
- Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, AB, Canada
| | - Melinda Wuest
- Department of Oncology, Cross Cancer Institute, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
| | - Igor M Paiva
- Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, AB, Canada
| | - Sirazum Munira
- Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, AB, Canada
| | - Nasim Sarrami
- Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, AB, Canada
| | - Forughalsadat Sanaee
- Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, AB, Canada
| | - Xiaoyan Yang
- Department of Oncology, Cross Cancer Institute, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
| | - Marco Paladino
- Department of Chemistry, Faculty of Science, University of Alberta, Edmonton, AB, Canada
| | - Ziyad Binkhathlan
- Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, AB, Canada.,Department of Pharmaceutics, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Feridoun Karimi-Busheri
- Department of Oncology, Cross Cancer Institute, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
| | - Gary R Martin
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, AB, Canada
| | - Frank R Jirik
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, AB, Canada.,Department of Medicine, University of Calgary, Calgary, AB, Canada
| | - David Murray
- Department of Oncology, Cross Cancer Institute, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
| | - Armin M Gamper
- Department of Oncology, Cross Cancer Institute, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
| | - Dennis G Hall
- Department of Chemistry, Faculty of Science, University of Alberta, Edmonton, AB, Canada
| | - Michael Weinfeld
- Department of Oncology, Cross Cancer Institute, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
| | - Afsaneh Lavasanifar
- Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, AB, Canada.,Department of Chemical and Material Engineering, University of Alberta, Edmonton, AB, Canada
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19
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Base excision repair and its implications to cancer therapy. Essays Biochem 2021; 64:831-843. [PMID: 32648895 PMCID: PMC7588666 DOI: 10.1042/ebc20200013] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 06/16/2020] [Accepted: 06/19/2020] [Indexed: 12/15/2022]
Abstract
Base excision repair (BER) has evolved to preserve the integrity of DNA following cellular oxidative stress and in response to exogenous insults. The pathway is a coordinated, sequential process involving 30 proteins or more in which single strand breaks are generated as intermediates during the repair process. While deficiencies in BER activity can lead to high mutation rates and tumorigenesis, cancer cells often rely on increased BER activity to tolerate oxidative stress. Targeting BER has been an attractive strategy to overwhelm cancer cells with DNA damage, improve the efficacy of radiotherapy and/or chemotherapy, or form part of a lethal combination with a cancer specific mutation/loss of function. We provide an update on the progress of inhibitors to enzymes involved in BER, and some of the challenges faced with targeting the BER pathway.
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20
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A synthetically lethal nanomedicine delivering novel inhibitors of polynucleotide kinase 3'-phosphatase (PNKP) for targeted therapy of PTEN-deficient colorectal cancer. J Control Release 2021; 334:335-352. [PMID: 33933518 DOI: 10.1016/j.jconrel.2021.04.034] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 04/24/2021] [Accepted: 04/27/2021] [Indexed: 11/21/2022]
Abstract
Phosphatase and TENsin homolog deleted on chromosome 10 (PTEN) is a major tumor-suppressor protein that is lost in up to 75% of aggressive colorectal cancers (CRC). The co-depletion of PTEN and a DNA repair protein, polynucleotide kinase 3'-phosphatase (PNKP), has been shown to lead to synthetic lethality in several cancer types including CRC. This finding inspired the development of novel PNKP inhibitors as potential new drugs against PTEN-deficient CRC. Here, we report on the in vitro and in vivo evaluation of a nano-encapsulated potent, but poorly water-soluble lead PNKP inhibitor, A83B4C63, as a new targeted therapeutic for PTEN-deficient CRC. Our data confirmed the binding of A83B4C63, as free or nanoparticle (NP) formulation, to intracellular PNKP using the cellular thermal shift assay (CETSA), in vitro and in vivo. Dose escalating toxicity studies in healthy CD-1 mice, based on measurement of animal weight changes and biochemical blood analysis, revealed the safety of both free and nano-encapsulated A83B4C63, at assessed doses of ≤50 mg/kg. Nano-carriers of A83B4C63 effectively inhibited the growth of HCT116/PTEN-/- xenografts in NIH-III nude mice following intravenous (IV) administration, but not that of wild-type HCT116/PTEN+/+ xenografts. This was in contrast to IV administration of A83B4C63 solubilized with the aid of Cremophor EL: Ethanol (CE), which led to similar tumor growth to that of formulation excipients (NP or CE without drug) or 5% dextrose. This observation was attributed to the higher levels of A83B4C63 delivered to tumor tissue by its NP formulation. Our data provide evidence for the success of NPs of A83B4C63, as novel synthetically lethal nano-therapeutics in the treatment of PTEN-deficient CRC. This research also highlights the potential of successful application of nanomedicine in the drug development process.
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21
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Saigal, Ghanem YSA, Uddin A, Khan S, Abid M, Khan MM. Synthesis, Biological Evaluation and Docking Studies of Functionalized Pyrrolo[3,4‐
b
]pyridine Derivatives. ChemistrySelect 2021. [DOI: 10.1002/slct.202004781] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Saigal
- Department of Chemistry Aligarh Muslim University Aligarh 202002, U.P India
| | | | - Amad Uddin
- Medicinal Chemistry Laboratory Department of Biosciences, Jamia Millia Islamia New Delhi India 110025
| | - Sarfaraz Khan
- Department of Chemistry Aligarh Muslim University Aligarh 202002, U.P India
| | - Mohammad Abid
- Medicinal Chemistry Laboratory Department of Biosciences, Jamia Millia Islamia New Delhi India 110025
| | - Md. Musawwer Khan
- Department of Chemistry Aligarh Muslim University Aligarh 202002, U.P India
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22
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The FHA domain of PNKP is essential for its recruitment to DNA damage sites and maintenance of genome stability. Mutat Res 2020; 822:111727. [PMID: 33220551 DOI: 10.1016/j.mrfmmm.2020.111727] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 09/28/2020] [Accepted: 10/26/2020] [Indexed: 01/08/2023]
Abstract
Polynucleotide kinase phosphatase (PNKP) has dual enzymatic activities as kinase and phosphatase for DNA ends, which are the prerequisite for the ligation, and thus is involved in base excision repair, single-strand break repair and non-homologous end joining for double-strand break (DSB) repair. In this study, we examined mechanisms for the recruitment of PNKP to DNA damage sites by laser micro-irradiation and live-cell imaging analysis using confocal microscope. We show that the forkhead-associated (FHA) domain of PNKP is essential for the recruitment of PNKP to DNA damage sites. Arg35 and Arg48 within the FHA domain are required for interactions with XRCC1 and XRCC4. PNKP R35A/R48A mutant failed to accumulate on the laser track and siRNA-mediated depletion of XRCC1 and/or XRCC4 reduced PNKP accumulation on the laser track, indicating that PNKP is recruited to DNA damage sites via the interactions between its FHA domain and XRCC1 or XRCC4. Furthermore, cells expressing PNKP R35A/R48A mutant exhibited increased sensitivity toward ionizing radiation in association with delayed SSB and DSB repair and genome instability, represented by micronuclei and chromosome bridges. Taken together, these findings revealed the importance of PNKP recruitment to DNA damage sites via its FHA domain for DNA repair and maintenance of genome stability.
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23
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Zhang J, Si J, Gan L, Zhou R, Guo M, Zhang H. Harnessing the targeting potential of differential radiobiological effects of photon versus particle radiation for cancer treatment. J Cell Physiol 2020; 236:1695-1711. [PMID: 32691425 DOI: 10.1002/jcp.29960] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 07/09/2020] [Indexed: 01/04/2023]
Abstract
Radiotherapy is one of the major modalities for malignancy treatment. High linear energy transfer (LET) charged-particle beams, like proton and carbon ions, exhibit favourable depth-dose distributions and radiobiological enhancement over conventional low-LET photon irradiation, thereby marking a new era in high precision medicine. Tumour cells have developed multicomponent signal transduction networks known as DNA damage responses (DDRs), which initiate cell-cycle checkpoints and induce double-strand break (DSB) repairs in the nucleus by nonhomologous end joining or homologous recombination pathways, to manage ionising radiation (IR)-induced DNA lesions. DNA damage induction and DSB repair pathways are reportedly dependent on the quality of radiation delivered. In this review, we summarise various types of DNA lesion and DSB repair mechanisms, upon irradiation with low and high-LET radiation, respectively. We also analyse factors influencing DNA repair efficiency. Inhibition of DNA damage repair pathways and dysfunctional cell-cycle checkpoint sensitises tumour cells to IR. Radio-sensitising agents, including DNA-PK inhibitors, Rad51 inhibitors, PARP inhibitors, ATM/ATR inhibitors, chk1 inhibitors, wee1 kinase inhibitors, Hsp90 inhibitors, and PI3K/AKT/mTOR inhibitors have been found to enhance cell killing by IR through interference with DDRs, cell-cycle arrest, or other cellular processes. The cotreatment of these inhibitors with IR may represent a promising therapeutic strategy for cancer.
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Affiliation(s)
- Jinhua Zhang
- Department of Medical Physics, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
- Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Sciences, Lanzhou, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Jing Si
- Department of Medical Physics, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
- Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Sciences, Lanzhou, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Lu Gan
- Department of Medical Physics, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
- Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Sciences, Lanzhou, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Rong Zhou
- Research Center for Ecological Impacts and Environmental Health Effects of Toxic and Hazardous Chemicals, Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment of the People's Republic of China, Nanjing, China
| | - Menghuan Guo
- School of Pharmacy, Lanzhou University, Lanzhou, China
| | - Hong Zhang
- Department of Medical Physics, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, China
- Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Sciences, Lanzhou, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
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24
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Radiation resistance in head and neck squamous cell carcinoma: dire need for an appropriate sensitizer. Oncogene 2020; 39:3638-3649. [PMID: 32157215 PMCID: PMC7190570 DOI: 10.1038/s41388-020-1250-3] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2019] [Revised: 02/18/2020] [Accepted: 02/25/2020] [Indexed: 01/11/2023]
Abstract
Radiation is a significant treatment for patients with head and neck cancer. Despite advances to improve treatment, many tumors acquire radiation resistance resulting in poor survival. Radiation kills cancer cells by inducing DNA double-strand breaks. Therefore, radiation resistance is enhanced by efficient repair of damaged DNA. Head and neck cancers overexpress EGFR and have a high frequency of p53 mutations, both of which enhance DNA repair. This review discusses the clinical criteria for radiation resistance in patients with head and neck cancer and summarizes how cancer cells evade radiation-mediated apoptosis by p53- and epidermal growth factor receptor (EGFR)-mediated DNA repair. In addition, we explore the role of cancer stem cells in promoting radiation resistance, and how the abscopal effect provides rationale for combination strategies with immunotherapy.
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25
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Shang J, Wei J, Wang Q, Wang J, Zhou Y, Yu S, Liu X, Wang F. Adaption of an autonomously cascade DNA circuit for amplified detection and intracellular imaging of polynucleotide kinase with ultralow background. Biosens Bioelectron 2020; 152:111994. [DOI: 10.1016/j.bios.2019.111994] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 12/15/2019] [Accepted: 12/23/2019] [Indexed: 12/20/2022]
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26
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Jin T, Zhang J, Zhao Y, Huang X, Tan C, Sun S, Tan Y. Magnetic bead-gold nanoparticle hybrids probe based on optically countable gold nanoparticles with dark-field microscope for T4 polynucleotide kinase activity assay. Biosens Bioelectron 2020; 150:111936. [DOI: 10.1016/j.bios.2019.111936] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Revised: 11/12/2019] [Accepted: 11/27/2019] [Indexed: 12/12/2022]
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27
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Liu X, Yu S, Feng C, Mao D, Li J, Zhu X. In situ Analysis of Cancer Cells Based on DNA Signal Amplification and DNA Nanodevices. Crit Rev Anal Chem 2019; 51:8-19. [PMID: 31613139 DOI: 10.1080/10408347.2019.1674631] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Cancer is a global disease which has been disturbing researchers in medicine and seriously threatens patients' health and lifetime around the world in the past several decades. Due to the characteristics of cancer cells, such as uncontrollable cell proliferation, cell invasion and metastasis to surrounding tissues, lower grade of differentiation, higher telomerase activity and others, it has been one of the most usual lethal factors, next to heart disease in incidence. Cancer mortality can be decreased by early diagnosis, and the people who with treatment at an early stage have an obvious improved survival rate. Consequently, early detection is significant for better understanding the pathogenesis of cancer and improving the prognosis of patients. In situ detection technique is a vital tool for imaging and cellular pathology research, which can provide effective information about tumor markers in the early cancer detection. In view of low expression of most tumor markers in the early stage of cancers, detection techniques based on DNA signal amplification and DNA nanodevices can provide a strong support for the diagnosis and detection of cancers. In this review, we summarize the research progress of different analytical techniques for detecting various tumor markers that have been reported in recent years. We compare different DNA amplification and nanodevices, then provide guidance and suggestions for better understanding in situ analysis of cancer cells.
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Affiliation(s)
- Xiaohao Liu
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai, P. R. China
| | - Sinuo Yu
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai, P. R. China
| | - Chang Feng
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai, P. R. China
| | - Dongsheng Mao
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai, P. R. China
| | - Jinlong Li
- Department of Laboratory Medicine, the Second Hospital of Nanjing, Nanjing University of Chinese Medicine, Nanjing, P. R. China
| | - Xiaoli Zhu
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, Shanghai, P. R. China
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28
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Kopa P, Macieja A, Galita G, Witczak ZJ, Poplawski T. DNA Double Strand Breaks Repair Inhibitors: Relevance as Potential New Anticancer Therapeutics. Curr Med Chem 2019; 26:1483-1493. [PMID: 29446719 DOI: 10.2174/0929867325666180214113154] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Revised: 01/22/2018] [Accepted: 01/23/2018] [Indexed: 12/19/2022]
Abstract
DNA double-strand breaks are considered one of the most lethal forms of DNA damage. Many effective anticancer therapeutic approaches used chemical and physical methods to generate DNA double-strand breaks in the cancer cells. They include: IR and drugs which mimetic its action, topoisomerase poisons, some alkylating agents or drugs which affected DNA replication process. On the other hand, cancer cells are mostly characterized by highly effective systems of DNA damage repair. There are two main DNA repair pathways used to fix double-strand breaks: NHEJ and HRR. Their activity leads to a decreased effect of chemotherapy. Targeting directly or indirectly the DNA double-strand breaks response by inhibitors seems to be an exciting option for anticancer therapy and is a part of novel trends that arise after the clinical success of PARP inhibitors. These trends will provide great opportunities for the development of DNA repair inhibitors as new potential anticancer drugs. The main objective of this article is to address these new promising advances.
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Affiliation(s)
- Paulina Kopa
- Department of Immunopathology, Faculty of Biomedical Sciences and Postgraduate Training, Medical University of Lodz, Lodz 90-752, Poland
| | - Anna Macieja
- Department of Molecular Genetics, Faculty of Biology and Environmental Protection, University of Lodz, Lodz 90-236, Poland
| | - Grzegorz Galita
- Department of Molecular Genetics, Faculty of Biology and Environmental Protection, University of Lodz, Lodz 90-236, Poland
| | - Zbigniew J Witczak
- Department of Pharmaceutical Sciences, Nesbitt School of Pharmacy, Wilkes University, Wilkes-Barre, PA 18766, United States
| | - Tomasz Poplawski
- Department of Molecular Genetics, Faculty of Biology and Environmental Protection, University of Lodz, Lodz 90-236, Poland
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29
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Abstract
A snapshot of noteworthy recent developments in the patent literature of relevance to pharmaceutical and medical research and development.
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30
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Zhou H, Tong C, Zou W, Yang Y, Liu Y, Li B, Qin Y, Dang W, Liu B, Wang W. A novel fluorescence method for activity assay and drug screening of T4 PNK by coupling rGO with ligase reaction. Analyst 2019; 144:1187-1196. [DOI: 10.1039/c8an02147c] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
T4 polynucleotide kinase (PNK) is the primary member of the 5′-kinase family that can transfer the γ-phosphate residue of ATP to the 5′-hydroxyl group of oligonucleotides.
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Affiliation(s)
| | - Chunyi Tong
- College of Biology
- Hunan University
- Changsha
- China
| | - Wei Zou
- NHC key laboratory of birth defects research
- prevention and treatment
- Hunan Provincial Maternal and Child Health Care Hospital
- Changsha 410008
- PR China
| | - Yupei Yang
- TCM and Ethnomedicine Innovation & Development International Laboratory
- Innovative Material Medical Research Institute
- School of Pharmacy
- Hunan University of Chinese Medicine
- Changsha
| | - Yongbei Liu
- TCM and Ethnomedicine Innovation & Development International Laboratory
- Innovative Material Medical Research Institute
- School of Pharmacy
- Hunan University of Chinese Medicine
- Changsha
| | - Bin Li
- TCM and Ethnomedicine Innovation & Development International Laboratory
- Innovative Material Medical Research Institute
- School of Pharmacy
- Hunan University of Chinese Medicine
- Changsha
| | - Yan Qin
- TCM and Ethnomedicine Innovation & Development International Laboratory
- Innovative Material Medical Research Institute
- School of Pharmacy
- Hunan University of Chinese Medicine
- Changsha
| | - Wenya Dang
- College of Biology
- Hunan University
- Changsha
- China
| | - Bin Liu
- College of Biology
- Hunan University
- Changsha
- China
- TCM and Ethnomedicine Innovation & Development International Laboratory
| | - Wei Wang
- TCM and Ethnomedicine Innovation & Development International Laboratory
- Innovative Material Medical Research Institute
- School of Pharmacy
- Hunan University of Chinese Medicine
- Changsha
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31
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Zagorac I, Fernandez-Gaitero S, Penning R, Post H, Bueno MJ, Mouron S, Manso L, Morente MM, Alonso S, Serra V, Muñoz J, Gómez-López G, Lopez-Acosta JF, Jimenez-Renard V, Gris-Oliver A, Al-Shahrour F, Piñeiro-Yañez E, Montoya-Suarez JL, Apala JV, Moreno-Torres A, Colomer R, Dopazo A, Heck AJR, Altelaar M, Quintela-Fandino M. In vivo phosphoproteomics reveals kinase activity profiles that predict treatment outcome in triple-negative breast cancer. Nat Commun 2018; 9:3501. [PMID: 30158526 PMCID: PMC6115463 DOI: 10.1038/s41467-018-05742-z] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Accepted: 07/19/2018] [Indexed: 01/25/2023] Open
Abstract
Triple-negative breast cancer (TNBC) lacks prognostic and predictive markers. Here, we use high-throughput phosphoproteomics to build a functional TNBC taxonomy. A cluster of 159 phosphosites is upregulated in relapsed cases of a training set (n = 34 patients), with 11 hyperactive kinases accounting for this phosphoprofile. A mass-spectrometry-to-immunohistochemistry translation step, assessing 2 independent validation sets, reveals 6 kinases with preserved independent prognostic value. The kinases split the validation set into two patterns: one without hyperactive kinases being associated with a >90% relapse-free rate, and the other one showing ≥1 hyperactive kinase and being associated with an up to 9.5-fold higher relapse risk. Each kinase pattern encompasses different mutational patterns, simplifying mutation-based taxonomy. Drug regimens designed based on these 6 kinases show promising antitumour activity in TNBC cell lines and patient-derived xenografts. In summary, the present study elucidates phosphosites and kinases implicated in TNBC and suggests a target-based clinical classification system for TNBC. Triple-negative breast cancer (TNBC) lacks prognostic and predictive markers. Here, the authors use phosphoproteomics to define kinases with distinct activity profiles in TNBC, demonstrating their prognostic value as well as their utility for simplifying TNBC classification and designing drug regimens.
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Affiliation(s)
- Ivana Zagorac
- Breast Cancer Clinical Research Unit, CNIO - Spanish National Cancer Research Center, 28029, Madrid, Spain
| | - Sara Fernandez-Gaitero
- Breast Cancer Clinical Research Unit, CNIO - Spanish National Cancer Research Center, 28029, Madrid, Spain
| | - Renske Penning
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands.,Netherlands Proteomics Center, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Harm Post
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands.,Netherlands Proteomics Center, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Maria J Bueno
- Breast Cancer Clinical Research Unit, CNIO - Spanish National Cancer Research Center, 28029, Madrid, Spain
| | - Silvana Mouron
- Breast Cancer Clinical Research Unit, CNIO - Spanish National Cancer Research Center, 28029, Madrid, Spain
| | - Luis Manso
- Medical Oncology, Hospital 12 de Octubre, Madrid, 28029, Spain
| | - Manuel M Morente
- Biobank, CNIO - Spanish National Cancer Research Center, Madrid, 28029, Spain
| | - Soledad Alonso
- Pathology Department, Hospital Universitario de Guadalajara, Guadalajara, 19002, Spain
| | - Violeta Serra
- Experimental Therapeutics Group, VHIO - Vall d'Hebron Institute of Oncology, Barcelona, 08035, Spain
| | - Javier Muñoz
- Proteomics Unit, CNIO - Spanish National Cancer Research Center, Madrid, 28029, Spain
| | - Gonzalo Gómez-López
- Bioinformatics Unit, CNIO - Spanish National Cancer Research Center, Madrid, 28029, Spain
| | | | - Veronica Jimenez-Renard
- Breast Cancer Clinical Research Unit, CNIO - Spanish National Cancer Research Center, 28029, Madrid, Spain
| | - Albert Gris-Oliver
- Experimental Therapeutics Group, VHIO - Vall d'Hebron Institute of Oncology, Barcelona, 08035, Spain
| | - Fatima Al-Shahrour
- Bioinformatics Unit, CNIO - Spanish National Cancer Research Center, Madrid, 28029, Spain
| | - Elena Piñeiro-Yañez
- Bioinformatics Unit, CNIO - Spanish National Cancer Research Center, Madrid, 28029, Spain
| | | | - Juan V Apala
- Breast Cancer Clinical Research Unit, CNIO - Spanish National Cancer Research Center, 28029, Madrid, Spain
| | - Amalia Moreno-Torres
- Pathology Department, Hospital Universitario de Fuenlabrada, Fuenlabrada, 28942, Spain
| | - Ramon Colomer
- Medical Oncology, Hospital La Princesa, Madrid, 28006, Spain
| | - Ana Dopazo
- Genomics Unit, CNIC - Spanish National Center for Cardiovascular Research, Madrid, 28029, Spain
| | - Albert J R Heck
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands.,Netherlands Proteomics Center, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Maarten Altelaar
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands.,Netherlands Proteomics Center, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Miguel Quintela-Fandino
- Breast Cancer Clinical Research Unit, CNIO - Spanish National Cancer Research Center, 28029, Madrid, Spain. .,Medical Oncology, Hospital Universitario Fuenlabrada, Madrid, 28942, Spain. .,Medical Oncology, Hospital Universitario Quirón, Madrid, 28223, Spain.
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32
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Shire Z, Vakili MR, Morgan TDR, Hall DG, Lavasanifar A, Weinfeld M. Nanoencapsulation of Novel Inhibitors of PNKP for Selective Sensitization to Ionizing Radiation and Irinotecan and Induction of Synthetic Lethality. Mol Pharm 2018; 15:2316-2326. [PMID: 29688721 DOI: 10.1021/acs.molpharmaceut.8b00169] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
There is increasing interest in developing and applying DNA repair inhibitors in cancer treatment to augment the efficacy of radiation and conventional genotoxic chemotherapy. However, targeting the inhibitor is required to avoid reducing the repair capacity of normal tissue. The aim of this study was to develop nanodelivery systems for the encapsulation of novel imidopiperidine-based inhibitors of the DNA 3'-phosphatase activity of polynucleotide kinase/phosphatase (PNKP), a DNA repair enzyme that plays a critical role in rejoining DNA single- and double-strand breaks. For this purpose, newly identified hit compounds with potent PNKP inhibitory activity, imidopiperidines A12B4C50 and A83B4C63 were encapsulated in polymeric micelles of different poly(ethylene oxide)- b-poly(ε-caprolactone) (PEO- b-PCL)-based structures. Our results showed efficient loading of A12B4C50 and A83B4C63 in PEO- b-PCLs with pendent carboxyl and benzyl carboxylate groups, respectively, and relatively slow release over 24 h. Both free and encapsulated inhibitors were able to sensitize HCT116 cells to radiation and the topoisomerase I poison, irinotecan. In addition, the encapsulated inhibitors were capable of inducing synthetic lethalilty in phosphatase and tensin homologue (PTEN)-deficient cells. We also established the validity of the peptide GE11 as a suitable ligand for active targeted delivery of nanoencapsulated drugs to colorectal cancer cells overexpressing epidermal growth factor receptor (EGFR). Our results show the potential of nanoencapsulated inhibitors of PNKP as either mono or combined therapeutic agents for colorectal cancer.
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Affiliation(s)
- Zahra Shire
- Department of Oncology, Faculty of Medicine and Dentistry , University of Alberta , Edmonton , AB , Canada T6G 1Z2.,Faculty of Pharmacy and Pharmaceutical Sciences , University of Alberta , Edmonton , AB , Canada T6G 2E1
| | - Mohammad Reza Vakili
- Faculty of Pharmacy and Pharmaceutical Sciences , University of Alberta , Edmonton , AB , Canada T6G 2E1
| | - Timothy D R Morgan
- Department of Chemistry, Faculty of Science , University of Alberta , Edmonton , AB , Canada T6G 2G2
| | - Dennis G Hall
- Department of Chemistry, Faculty of Science , University of Alberta , Edmonton , AB , Canada T6G 2G2
| | - Afsaneh Lavasanifar
- Faculty of Pharmacy and Pharmaceutical Sciences , University of Alberta , Edmonton , AB , Canada T6G 2E1
| | - Michael Weinfeld
- Department of Oncology, Faculty of Medicine and Dentistry , University of Alberta , Edmonton , AB , Canada T6G 1Z2
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33
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Gu L, Yan W, Liu L, Wang S, Zhang X, Lyu M. Research Progress on Rolling Circle Amplification (RCA)-Based Biomedical Sensing. Pharmaceuticals (Basel) 2018; 11:E35. [PMID: 29690513 PMCID: PMC6027247 DOI: 10.3390/ph11020035] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Revised: 04/10/2018] [Accepted: 04/10/2018] [Indexed: 12/26/2022] Open
Abstract
Enhancing the limit of detection (LOD) is significant for crucial diseases. Cancer development could take more than 10 years, from one mutant cell to a visible tumor. Early diagnosis facilitates more effective treatment and leads to higher survival rate for cancer patients. Rolling circle amplification (RCA) is a simple and efficient isothermal enzymatic process that utilizes nuclease to generate long single stranded DNA (ssDNA) or RNA. The functional nucleic acid unit (aptamer, DNAzyme) could be replicated hundreds of times in a short period, and a lower LOD could be achieved if those units are combined with an enzymatic reaction, Surface Plasmon Resonance, electrochemical, or fluorescence detection, and other different kinds of biosensor. Multifarious RCA-based platforms have been developed to detect a variety of targets including DNA, RNA, SNP, proteins, pathogens, cytokines, micromolecules, and diseased cells. In this review, improvements in using the RCA technique for medical biosensors and biomedical applications were summarized and future trends in related research fields described.
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Affiliation(s)
- Lide Gu
- College of Marine Life and Fisheries, Huahai Institute of Technology, Lianyungang 222005, China.
| | - Wanli Yan
- College of Marine Life and Fisheries, Huahai Institute of Technology, Lianyungang 222005, China.
| | - Le Liu
- College of Marine Life and Fisheries, Huahai Institute of Technology, Lianyungang 222005, China.
| | - Shujun Wang
- Marine Resources Development Institute of Jiangsu, Lianyungang 222005, China.
- Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Huaihai Institute of Technology, Lianyungang 222005, China.
| | - Xu Zhang
- Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Huaihai Institute of Technology, Lianyungang 222005, China.
- Verschuren Centre for Sustainability in Energy & the Environment, Cape Breton University, Sydney, NS B1P 6L2, Canada.
| | - Mingsheng Lyu
- College of Marine Life and Fisheries, Huahai Institute of Technology, Lianyungang 222005, China.
- Marine Resources Development Institute of Jiangsu, Lianyungang 222005, China.
- Co-Innovation Center of Jiangsu Marine Bio-industry Technology, Huaihai Institute of Technology, Lianyungang 222005, China.
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34
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Srivastava P, Sarma A, Chaturvedi CM. Targeting DNA repair with PNKP inhibition sensitizes radioresistant prostate cancer cells to high LET radiation. PLoS One 2018; 13:e0190516. [PMID: 29320576 PMCID: PMC5762163 DOI: 10.1371/journal.pone.0190516] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Accepted: 12/15/2017] [Indexed: 12/19/2022] Open
Abstract
High linear energy transfer (LET) radiation or heavy ion such as carbon ion radiation is used as a method for advanced radiotherapy in the treatment of cancer. It has many advantages over the conventional photon based radiotherapy using Co-60 gamma or high energy X-rays from a Linear Accelerator. However, charged particle therapy is very costly. One way to reduce the cost as well as irradiation effects on normal cells is to reduce the dose of radiation by enhancing the radiation sensitivity through the use of a radiomodulator. PNKP (polynucleotide kinase/phosphatase) is an enzyme which plays important role in the non-homologous end joining (NHEJ) DNA repair pathway. It is expected that inhibition of PNKP activity may enhance the efficacy of the charged particle irradiation in the radioresistant prostate cancer cell line PC-3. To test this hypothesis, we investigated cellular radiosensitivity by clonogenic cell survival assay in PC-3 cells.12Carbon ion beam of62 MeVenergy (equivalent 5.16 MeV/nucleon) and with an entrance LET of 287 kev/μm was used for the present study. Apoptotic parameters such as nuclear fragmentation and caspase-3 activity were measured by DAPI staining, nuclear ladder assay and colorimetric caspase-3method. Cell cycle arrest was determined by FACS analysis. Cell death was enhanced when carbon ion irradiation is combined with PNKPi (PNKP inhibitor) to treat cells as compared to that seen for PNKPi untreated cells. A low concentration (10μM) of PNKPi effectively radiosensitized the PC-3 cells in terms of reduction of dose in achieving the same survival fraction. PC-3 cells underwent significant apoptosis and cell cycle arrest too was enhanced at G2/M phase when carbon ion irradiation was combined with PNKPi treatment. Our findings suggest that combined treatment of carbon ion irradiation and PNKP inhibition could enhance cellular radiosensitivity in a radioresistant prostate cancer cell line PC-3. The synergistic effect of PNKPi and carbon ion irradiation could be used as a promising method for carbon-ion therapy in radioresistant cells.
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Affiliation(s)
- Pallavi Srivastava
- Department of Zoology, Banaras Hindu University, Varanasi, Uttar Pradesh, India
| | - Asitikantha Sarma
- Radiation Biology Laboratory, Inter University Accelerator Centre, New Delhi, India
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35
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Aceytuno RD, Piett CG, Havali-Shahriari Z, Edwards RA, Rey M, Ye R, Javed F, Fang S, Mani R, Weinfeld M, Hammel M, Tainer JA, Schriemer DC, Lees-Miller SP, Glover JNM. Structural and functional characterization of the PNKP-XRCC4-LigIV DNA repair complex. Nucleic Acids Res 2017; 45:6238-6251. [PMID: 28453785 PMCID: PMC5449630 DOI: 10.1093/nar/gkx275] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Accepted: 04/25/2017] [Indexed: 01/14/2023] Open
Abstract
Non-homologous end joining (NHEJ) repairs DNA double strand breaks in non-cycling eukaryotic cells. NHEJ relies on polynucleotide kinase/phosphatase (PNKP), which generates 5΄-phosphate/3΄-hydroxyl DNA termini that are critical for ligation by the NHEJ DNA ligase, LigIV. PNKP and LigIV require the NHEJ scaffolding protein, XRCC4. The PNKP FHA domain binds to the CK2-phosphorylated XRCC4 C-terminal tail, while LigIV uses its tandem BRCT repeats to bind the XRCC4 coiled-coil. Yet, the assembled PNKP-XRCC4–LigIV complex remains uncharacterized. Here, we report purification and characterization of a recombinant PNKP–XRCC4–LigIV complex. We show that the stable binding of PNKP in this complex requires XRCC4 phosphorylation and that only one PNKP protomer binds per XRCC4 dimer. Small angle X-ray scattering (SAXS) reveals a flexible multi-state complex that suggests that both the PNKP FHA and catalytic domains contact the XRCC4 coiled-coil and LigIV BRCT repeats. Hydrogen-deuterium exchange indicates protection of a surface on the PNKP phosphatase domain that may contact XRCC4–LigIV. A mutation on this surface (E326K) causes the hereditary neuro-developmental disorder, MCSZ. This mutation impairs PNKP recruitment to damaged DNA in human cells and provides a possible disease mechanism. Together, this work unveils multipoint contacts between PNKP and XRCC4–LigIV that regulate PNKP recruitment and activity within NHEJ.
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Affiliation(s)
- R Daniel Aceytuno
- Department of Biochemistry, University of Alberta, Edmonton, AB T6G-2H7, Canada
| | - Cortt G Piett
- Department of Biochemistry & Molecular Biology, Robson DNA Science Centre, Arnie Charbonneau Cancer Institute, University of Calgary, Calgary, AB T2N 1N4, Canada
| | | | - Ross A Edwards
- Department of Biochemistry, University of Alberta, Edmonton, AB T6G-2H7, Canada
| | - Martial Rey
- Department of Biochemistry & Molecular Biology, Robson DNA Science Centre, Arnie Charbonneau Cancer Institute, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Ruiqiong Ye
- Department of Biochemistry & Molecular Biology, Robson DNA Science Centre, Arnie Charbonneau Cancer Institute, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Fatima Javed
- Department of Biochemistry, University of Alberta, Edmonton, AB T6G-2H7, Canada
| | - Shujuan Fang
- Department of Biochemistry & Molecular Biology, Robson DNA Science Centre, Arnie Charbonneau Cancer Institute, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Rajam Mani
- Department of Oncology, University of Alberta, Cross Cancer Institute, 11560 University Avenue, Edmonton, Alberta T6G 1Z2, Canada
| | - Michael Weinfeld
- Department of Oncology, University of Alberta, Cross Cancer Institute, 11560 University Avenue, Edmonton, Alberta T6G 1Z2, Canada
| | - Michal Hammel
- Molecular Biophysics & Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - John A Tainer
- Molecular Biophysics & Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.,Department of Molecular and Cellular Oncology, The University of Texas M. D. Anderson Cancer Center, Houston, TX 77030, USA
| | - David C Schriemer
- Department of Biochemistry & Molecular Biology, Robson DNA Science Centre, Arnie Charbonneau Cancer Institute, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Susan P Lees-Miller
- Department of Biochemistry & Molecular Biology, Robson DNA Science Centre, Arnie Charbonneau Cancer Institute, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - J N Mark Glover
- Department of Biochemistry, University of Alberta, Edmonton, AB T6G-2H7, Canada
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36
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Havali-Shahriari Z, Weinfeld M, Glover JNM. Characterization of DNA Substrate Binding to the Phosphatase Domain of the DNA Repair Enzyme Polynucleotide Kinase/Phosphatase. Biochemistry 2017; 56:1737-1745. [PMID: 28276686 DOI: 10.1021/acs.biochem.6b01236] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Polynucleotide kinase/phosphatase (PNKP) is a DNA strand break repair enzyme that uses separate 5' kinase and 3' phosphatase active sites to convert damaged 5'-hydroxyl/3'-phosphate strand termini to ligatable 5'-phosphate/3'-hydroxyl ends. The phosphatase active site has received particular attention as a target of inhibition in cancer therapy development. The phosphatase domain dephosphorylates a range of single- and double-stranded substrates; however, structural studies have shown that the phosphatase catalytic cleft can bind only single-stranded substrates. Here we use a catalytically inactive but structurally intact phosphatase mutant to probe interactions between PNKP and a variety of single- and double-stranded DNA substrates using an electrophoretic mobility shift assay. This work indicates that the phosphatase domain binds 3'-phosphorylated single-stranded DNAs in a manner that is highly dependent on the presence of the 3'-phosphate. Double-stranded substrate binding, in contrast, is not as dependent on the 3'-phosphate. Experiments comparing blunt-end, 3'-overhanging, and frayed-end substrates indicate that the predicted loss of energy due to base pair disruption upon binding of the phosphatase active site is likely balanced by favorable interactions between the liberated complementary strand and PNKP. Comparison of the effects on substrate binding of mutations within the phosphatase active site cleft with mutations in surrounding positively charged surfaces suggests that the surrounding surfaces are important for binding to double-stranded substrates. We further show that while fluorescence polarization methods can detect specific binding of single-stranded DNAs with the phosphatase domain, this method does not detect specific interactions between the PNKP phosphatase and double-stranded substrates.
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Affiliation(s)
| | - Michael Weinfeld
- Department of Oncology, University of Alberta, Cross Cancer Institute , 11560 University Avenue, Edmonton, Alberta T6G 1Z2, Canada
| | - J N Mark Glover
- Department of Biochemistry, University of Alberta , Edmonton, Alberta T6G 2H7, Canada
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37
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Hall DG, Rybak T, Verdelet T. Multicomponent Hetero-[4 + 2] Cycloaddition/Allylboration Reaction: From Natural Product Synthesis to Drug Discovery. Acc Chem Res 2016; 49:2489-2500. [PMID: 27753496 DOI: 10.1021/acs.accounts.6b00403] [Citation(s) in RCA: 89] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Multicomponent reactions (MCR), transformations employing three or more simple substrates in a single and highly atom-economical operation, are very attractive in both natural product synthesis and diversity-oriented synthesis of druglike molecules. Several popular multicomponent reactions were designed by combining two well-established individual reactions that utilize mutually compatible substrates. In this regard, it is not surprising that the merging of two reactions deemed as workhorses of stereoselective synthesis, the Diels-Alder cycloaddition and carbonyl allylboration, would produce a powerful and highly versatile tandem MCR process. The idea of using 1,3-dienylboronates in [4 + 2] cycloadditions as a means to produce cyclic allylic boronates was first reported by Vaultier and Hoffmann in 1987. In their seminal study, a 1-boronodiene was reacted with electron-poor alkenes, and the intermediate cycloadducts were isolated and added to aldehydes in a separate step leading to α-hydroxyalkylated carbocycles via a highly diastereoselective allylboration reaction. The one-pot three-component variant was realized in 1999 by Lallemand and co-workers, and soon after groups led by Hall and Carboni reported heterocyclic variants of the tandem [4 + 2] cycloaddition/allylboration to prepare α-hydroxyalkylated piperidine and pyran containing compounds, respectively. These classes of heterocycles are ubiquitous in Nature and are important components of pharmaceuticals. This Account summarizes the development and evolution of this powerful multicomponent reaction for accessing nonaromatic heterocycles and its many applications in natural products synthesis and drug discovery. The aza[4 + 2]cycloaddition/allylboration MCR was first optimized in our laboratory using 4-boronylhydrazonobutadienes and N-substituted maleimides, and it was exploited in the preparation of combinatorial libraries of polysubstituted imidopiperidines that feature as many as four elements of chemical diversity. Biological screening of these druglike imidopiperidine libraries unveiled promising bioactive agents such as A12B4C3, the first reported inhibitor of the human DNA repair enzyme, polynucleotide kinase-phosphatase (hPNKP). Related applications of this MCR in target-oriented synthesis also led to total syntheses of palustrine alkaloids. The inverse electron-demand oxa[4 + 2] cycloaddition/allyboration variant can take advantage of Jacobsen's chiral Cr(III)salen catalyst, affording a rare example of catalytic enantioselective MCR, one that provides a rapid access to α-hydroxyalkyl dihydropyrans in high enantio- and diastereoselectivity. This process exploits 3-boronoacrolein pinacolate as the heterodiene with ethyl vinyl ether or various 2-substituted enol ethers, along with a wide variety of aldehydes in the allylation stage. This versatile methodology was deployed in total syntheses of thiomarinol antibiotics, goniodiol and its derivatives, and the complex anticancer macrolide palmerolide A. More recent work from our laboratory centered on the regio- and stereoselective Suzuki-Miyaura cross-coupling of the dihydropyranyl boronates, thus providing a glimpse of the potential for new multicomponent variants that merge hetero[4 + 2] cycloadditions of 1-borylated heterodienes with transition metal-catalyzed transformations. This stereoselective MCR strategy holds great promise for provoking continuing applications in complex molecule synthesis and drug discovery, and is likely to inspire new and innovative MCR-based approaches to nonaromatic heterocycles.
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Affiliation(s)
- Dennis G. Hall
- Department of Chemistry, University of Alberta, 4-010 Centennial Centre for Interdisciplinary Science, Edmonton, Alberta, Canada, T6G 2G2
| | - Taras Rybak
- Department of Chemistry, University of Alberta, 4-010 Centennial Centre for Interdisciplinary Science, Edmonton, Alberta, Canada, T6G 2G2
| | - Tristan Verdelet
- Department of Chemistry, University of Alberta, 4-010 Centennial Centre for Interdisciplinary Science, Edmonton, Alberta, Canada, T6G 2G2
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Zhang H, Zhao Z, Lei Z, Wang Z. Sensitive Detection of Polynucleotide Kinase Activity by Paper-Based Fluorescence Assay with λ Exonuclease Assistance. Anal Chem 2016; 88:11358-11363. [DOI: 10.1021/acs.analchem.6b03567] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- Hua Zhang
- State
Key Laboratory of Electroanalytical Chemistry, Changchun Institute
of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, People’s Republic of China
| | - Zhen Zhao
- State
Key Laboratory of Electroanalytical Chemistry, Changchun Institute
of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, People’s Republic of China
- University
of
Chinese Academy of Sciences, No. 19A
Yuquan Road, Beijing, 100049, People’s Republic of China
| | - Zhen Lei
- State
Key Laboratory of Electroanalytical Chemistry, Changchun Institute
of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, People’s Republic of China
- University
of
Chinese Academy of Sciences, No. 19A
Yuquan Road, Beijing, 100049, People’s Republic of China
| | - Zhenxin Wang
- State
Key Laboratory of Electroanalytical Chemistry, Changchun Institute
of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, People’s Republic of China
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Xu J, Gao Y, Li B, Jin Y. Cyclic up-regulation fluorescence of pyrene excimer for studying polynucleotide kinase activity based on dual amplification. Biosens Bioelectron 2016; 80:91-97. [DOI: 10.1016/j.bios.2016.01.046] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Revised: 01/14/2016] [Accepted: 01/16/2016] [Indexed: 11/16/2022]
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End-processing nucleases and phosphodiesterases: An elite supporting cast for the non-homologous end joining pathway of DNA double-strand break repair. DNA Repair (Amst) 2016; 43:57-68. [PMID: 27262532 DOI: 10.1016/j.dnarep.2016.05.011] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Accepted: 05/05/2016] [Indexed: 11/20/2022]
Abstract
Nonhomologous end joining (NHEJ) is an error-prone DNA double-strand break repair pathway that is active throughout the cell cycle. A substantial fraction of NHEJ repair events show deletions and, less often, insertions in the repair joints, suggesting an end-processing step comprising the removal of mismatched or damaged nucleotides by nucleases and other phosphodiesterases, as well as subsequent strand extension by polymerases. A wide range of nucleases, including Artemis, Metnase, APLF, Mre11, CtIP, APE1, APE2 and WRN, are biochemically competent to carry out such double-strand break end processing, and have been implicated in NHEJ by at least circumstantial evidence. Several additional DNA end-specific phosphodiesterases, including TDP1, TDP2 and aprataxin are available to resolve various non-nucleotide moieties at DSB ends. This review summarizes the biochemical specificities of these enzymes and the evidence for their participation in the NHEJ pathway.
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Auger electron-emitting 111 In-DTPA-NLS-CSL360 radioimmunoconjugates are cytotoxic to human acute myeloid leukemia (AML) cells displaying the CD123 + /CD131 − phenotype of leukemia stem cells. Appl Radiat Isot 2016; 110:1-7. [DOI: 10.1016/j.apradiso.2015.12.043] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Revised: 11/18/2015] [Accepted: 12/14/2015] [Indexed: 11/19/2022]
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Gavande NS, VanderVere-Carozza PS, Hinshaw HD, Jalal SI, Sears CR, Pawelczak KS, Turchi JJ. DNA repair targeted therapy: The past or future of cancer treatment? Pharmacol Ther 2016; 160:65-83. [PMID: 26896565 DOI: 10.1016/j.pharmthera.2016.02.003] [Citation(s) in RCA: 258] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The repair of DNA damage is a complex process that relies on particular pathways to remedy specific types of damage to DNA. The range of insults to DNA includes small, modest changes in structure including mismatched bases and simple methylation events to oxidized bases, intra- and interstrand DNA crosslinks, DNA double strand breaks and protein-DNA adducts. Pathways required for the repair of these lesions include mismatch repair, base excision repair, nucleotide excision repair, and the homology directed repair/Fanconi anemia pathway. Each of these pathways contributes to genetic stability, and mutations in genes encoding proteins involved in these pathways have been demonstrated to promote genetic instability and cancer. In fact, it has been suggested that all cancers display defects in DNA repair. It has also been demonstrated that the ability of cancer cells to repair therapeutically induced DNA damage impacts therapeutic efficacy. This has led to targeting DNA repair pathways and proteins to develop anti-cancer agents that will increase sensitivity to traditional chemotherapeutics. While initial studies languished and were plagued by a lack of specificity and a defined mechanism of action, more recent approaches to exploit synthetic lethal interaction and develop high affinity chemical inhibitors have proven considerably more effective. In this review we will highlight recent advances and discuss previous failures in targeting DNA repair to pave the way for future DNA repair targeted agents and their use in cancer therapy.
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Affiliation(s)
- Navnath S Gavande
- Department of Medicine, Indiana University School of Medicine, Indianapolis, IN 46202, United States
| | | | - Hilary D Hinshaw
- Department of Obstetrics and Gynecology, Indiana University School of Medicine, Indianapolis, IN 46202, United States
| | - Shadia I Jalal
- Department of Medicine, Indiana University School of Medicine, Indianapolis, IN 46202, United States
| | - Catherine R Sears
- Department of Medicine, Indiana University School of Medicine, Indianapolis, IN 46202, United States
| | | | - John J Turchi
- Department of Medicine, Indiana University School of Medicine, Indianapolis, IN 46202, United States; NERx Biosciences, Indianapolis, IN 46202, United States; Department of Biochemistry & Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, United States.
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Codini M, Cataldi S, Lazzarini A, Tasegian A, Ceccarini MR, Floridi A, Lazzarini R, Ambesi-Impiombato FS, Curcio F, Beccari T, Albi E. Why high cholesterol levels help hematological malignancies: role of nuclear lipid microdomains. Lipids Health Dis 2016; 15:4. [PMID: 26754536 PMCID: PMC4709975 DOI: 10.1186/s12944-015-0175-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2015] [Accepted: 12/24/2015] [Indexed: 12/11/2022] Open
Abstract
Background Diet and obesity are recognized in the scientific literature as important risk factors for cancer development and progression. Hypercholesterolemia facilitates lymphoma lymphoblastic cell growth and in time turns in hypocholesterolemia that is a sign of tumour progression. The present study examined how and where the cholesterol acts in cancer cells when you reproduce in vitro an in vivo hypercholesterolemia condition. Methods We used non-Hodgkin’s T cell human lymphoblastic lymphoma (SUP-T1 cell line) and we studied cell morphology, aggressiveness, gene expression for antioxidant proteins, polynucleotide kinase/phosphatase and actin, cholesterol and sphingomyelin content and finally sphingomyelinase activity in whole cells, nuclei and nuclear lipid microdomains. Results We found that cholesterol changes cancer cell morphology with the appearance of protrusions together to the down expression of β-actin gene and reduction of β-actin protein. The lipid influences SUP-T1 cell aggressiveness since stimulates DNA and RNA synthesis for cell proliferation and increases raf1 and E-cadherin, molecules involved in invasion and migration of cancer cells. Cholesterol does not change GRX2 expression but it overexpresses SOD1, SOD2, CCS, PRDX1, GSR, GSS, CAT and PNKP. We suggest that cholesterol reaches the nucleus and increases the nuclear lipid microdomains known to act as platform for chromatin anchoring and gene expression. Conclusion The results imply that, in hypercholesterolemia conditions, cholesterol reaches the nuclear lipid microdomains where activates gene expression coding for antioxidant proteins. We propose the cholesterolemia as useful parameter to monitor in patients with cancer.
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Affiliation(s)
- Michela Codini
- Department of Pharmaceutical Sciences, University of Perugia, Perugia, Italy
| | - Samuela Cataldi
- Department of Pharmaceutical Sciences, University of Perugia, Perugia, Italy
| | - Andrea Lazzarini
- Laboratory of Nuclear Lipid BioPathology, CRABiON, Perugia, Italy
| | - Anna Tasegian
- Department of Pharmaceutical Sciences, University of Perugia, Perugia, Italy
| | | | | | - Remo Lazzarini
- Laboratory of Nuclear Lipid BioPathology, CRABiON, Perugia, Italy
| | | | - Francesco Curcio
- Department of Clinical and Biological Sciences, University of Udine, Udine, Italy
| | - Tommaso Beccari
- Department of Pharmaceutical Sciences, University of Perugia, Perugia, Italy
| | - Elisabetta Albi
- Department of Pharmaceutical Sciences, University of Perugia, Perugia, Italy.
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Jiang YH, Xiao M, Yan CG. Convenient synthesis of functionalized pyrrolo[3,4-b]pyridines and pyrrolo[3,4-b]quinolines via three-component reactions. RSC Adv 2016. [DOI: 10.1039/c6ra03165j] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
A simple protocol for convenient construction of pyrrolo[3,4-b]pyridine skeleton was successfully developed by base promoted three-component reaction of β-enamino imide, aromatic aldehydes and malononitrile as well as its ester and amide derivatives.
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Affiliation(s)
- Yan-Hong Jiang
- College of Chemistry & Chemical Engineering
- Yangzhou University
- Yangzhou 225002
- China
| | - Man Xiao
- College of Chemistry & Chemical Engineering
- Yangzhou University
- Yangzhou 225002
- China
| | - Chao-Guo Yan
- College of Chemistry & Chemical Engineering
- Yangzhou University
- Yangzhou 225002
- China
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45
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Label-free and sensitive detection of T4 polynucleotide kinase activity via coupling DNA strand displacement reaction with enzymatic-aided amplification. Biosens Bioelectron 2015; 73:138-145. [DOI: 10.1016/j.bios.2015.05.059] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Revised: 05/05/2015] [Accepted: 05/26/2015] [Indexed: 01/04/2023]
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46
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Knobloch G, Jabari N, Stadlbauer S, Schindelin H, Köhn M, Gohla A. Synthesis of hydrolysis-resistant pyridoxal 5′-phosphate analogs and their biochemical and X-ray crystallographic characterization with the pyridoxal phosphatase chronophin. Bioorg Med Chem 2015; 23:2819-27. [DOI: 10.1016/j.bmc.2015.02.049] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2015] [Revised: 02/24/2015] [Accepted: 02/25/2015] [Indexed: 12/12/2022]
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47
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Kelley MR, Logsdon D, Fishel ML. Targeting DNA repair pathways for cancer treatment: what's new? Future Oncol 2015; 10:1215-37. [PMID: 24947262 DOI: 10.2217/fon.14.60] [Citation(s) in RCA: 130] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Disruptions in DNA repair pathways predispose cells to accumulating DNA damage. A growing body of evidence indicates that tumors accumulate progressively more mutations in DNA repair proteins as cancers progress. DNA repair mechanisms greatly affect the response to cytotoxic treatments, so understanding those mechanisms and finding ways to turn dysregulated repair processes against themselves to induce tumor death is the goal of all DNA repair inhibition efforts. Inhibition may be direct or indirect. This burgeoning field of research is replete with promise and challenge, as more intricacies of each repair pathway are discovered. In an era of increasing concern about healthcare costs, use of DNA repair inhibitors can prove to be highly effective stewardship of R&D resources and patient expenses.
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Affiliation(s)
- Mark R Kelley
- Department of Pediatrics, Herman B Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN, USA
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48
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49
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Wang Y, Wu Y, Wang Y, Zhou B, Wu S. A sensitive immobilization-free electrochemical assay for T4PNK activity based on exonuclease III-assisted recycling. RSC Adv 2015. [DOI: 10.1039/c5ra12849h] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
This work develops a novel, immobilization-free, simple and sensitive electrochemical platform for the detection of T4PNK activity based on λ-exo and exonuclease III-assisted signal amplification.
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Affiliation(s)
- Yonghong Wang
- College of Life Science and Technology
- Central South University of Forestry and Technology
- Changsha
- China
- State Key Laboratory of Chemo/Biosensing and Chemometrics
| | - Yaohui Wu
- College of Life Science and Technology
- Central South University of Forestry and Technology
- Changsha
- China
| | - Yuanqing Wang
- College of Life Science and Technology
- Central South University of Forestry and Technology
- Changsha
- China
| | - Bo Zhou
- College of Life Science and Technology
- Central South University of Forestry and Technology
- Changsha
- China
| | - Shun Wu
- College of Life Science and Technology
- Central South University of Forestry and Technology
- Changsha
- China
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50
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Du J, Xu Q, Lu X, Zhang CY. A label-free bioluminescent sensor for real-time monitoring polynucleotide kinase activity. Anal Chem 2014; 86:8481-8. [PMID: 25048013 DOI: 10.1021/ac502240c] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Polynucleotide kinase (PNK) plays a crucial role in maintaining the genomic stability of cells and is becoming a potential target in the radio-therapeutic treatment of cancers. The fluorescent method is usually used to measure the PNK activity, but it is impossible to obtain the real-time monitoring without the employment of the labeled DNA probes. Here, we report a label-free bioluminescent sensor for PNK activity assay through real-time monitoring of the phosphorylation-dependent DNA ligation reaction. In this bioluminescent sensor, two hairpin DNA probes with 5'-protruding terminal are designed as the phosphate acceptor, and the widely used phosphate donor of ATP is substituted by dCTP. In the absence of PNK, the ligation reaction cannot be triggered due to the lack of 5'-phosphoryl groups in the probes, and the background signal is negligible. With the addition of PNK, the phosphorylation-ligation reaction of the probes is initiated with the release of AMP, and the subsequent conversion of AMP to ATP leads to the generation of distinct bioluminescence signal. The PNK activity assay can be performed in real time by continuously monitoring the bioluminescence signal. This bioluminescent sensor is much simpler, label-free, cost-effective, and free from the autofluorescence interference of biological matrix, and can be further used for quantitative, kinetic, and inhibition assay.
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Affiliation(s)
- Jiao Du
- Key Laboratory of Bioelectrochemistry & Environmental analysis of Gansu Province, College of Chemistry & Chemical Engineering, Northwest Normal University , Lanzhou 730070, China
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