1
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Aishwarya S, Torres GC, Lopez-Saenz JA, Gutierrez DA, Kumar S, Madarakhandi A, Metikurki B, Teraiya N, Aguilera RJ, Karki SS. Synthesis of novel pyridazine and pyrimidine linked pyrazole derivatives as DNA ligase 1 and IV inhibitors that induce apoptosis. Chem Biol Interact 2025; 414:111509. [PMID: 40221125 PMCID: PMC12083462 DOI: 10.1016/j.cbi.2025.111509] [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: 11/30/2024] [Revised: 03/19/2025] [Accepted: 04/09/2025] [Indexed: 04/14/2025]
Abstract
Human ligase I and ligase IV have recently been recognized as potential targets and regulators of cancer. Novel pyrazole analogues were synthesized and evaluated for their anti-proliferation effects against lymphoma, breast and other cancer cell lines. The initial biological investigation resulted in the identification of lead compounds 7a and 8e. Compounds 7a and 8e were the most cytotoxic to acute lymphoblastic leukemia CEM cells, with CC50 values of 4.78 μM and 9.23 μM, respectively. Compound 8e was selected for further biological testing, whereas compound 7a was excluded from subsequent evaluations due to its poor solubility. To investigate the mechanism of action of 8e, it was tested for phosphatidylserine externalization, caspase-3 activation, mitochondrial membrane depolarization, reactive oxygen species generation (ROS) and its effects on the cell cycle. Results from these assays indicated that 8e induced the intrinsic apoptosis pathway and arrested cells in the S phase of the cell cycle. Furthermore, in silico docking and molecular dynamic simulation revealed a strong affinity of 7a and 8e for ligase I and ligase IV suggesting that the induction of apoptosis is likely due to direct inhibition of these ligases. Collectively, these findings indicate that 8e is a promising anticancer agent.
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Affiliation(s)
- S Aishwarya
- Department of Pharmaceutical Chemistry, KLE College of Pharmacy (A Constituent Unit of KLE Academy of Higher Education & Research-Belagavi), Rajajinagar, Bengaluru, Karnataka, 560010, India
| | - Gabriela C Torres
- Cellular Characterization and Biorepository Core Facility, Border Biomedical Research Center, Department of Biological Sciences, College of Science, The University of Texas at El Paso, 500 West University Avenue, El Paso, TX, 79968-0519, USA
| | - Jose A Lopez-Saenz
- Cellular Characterization and Biorepository Core Facility, Border Biomedical Research Center, Department of Biological Sciences, College of Science, The University of Texas at El Paso, 500 West University Avenue, El Paso, TX, 79968-0519, USA
| | - Denisse A Gutierrez
- Cellular Characterization and Biorepository Core Facility, Border Biomedical Research Center, Department of Biological Sciences, College of Science, The University of Texas at El Paso, 500 West University Avenue, El Paso, TX, 79968-0519, USA
| | - Sujeet Kumar
- Department of Pharmaceutical Chemistry, NITTE College of Pharmaceutical Sciences, Yelahanka, Bengaluru, Karnataka 560064, India
| | - Ashok Madarakhandi
- Department of Pharmaceutical Chemistry, KLE College of Pharmacy (A Constituent Unit of KLE Academy of Higher Education & Research-Belagavi), Rajajinagar, Bengaluru, Karnataka, 560010, India
| | - Basavaraj Metikurki
- Department of Pharmaceutical Chemistry, NITTE College of Pharmaceutical Sciences, Yelahanka, Bengaluru, Karnataka 560064, India
| | - Nishith Teraiya
- Department of Pharmaceutical Chemistry, K B Institute of Pharmaceutical Education and Research, KadiSarvaVishvavidhyalaya, Gandhinagar, Gujarath, 382023, India
| | - Renato J Aguilera
- Cellular Characterization and Biorepository Core Facility, Border Biomedical Research Center, Department of Biological Sciences, College of Science, The University of Texas at El Paso, 500 West University Avenue, El Paso, TX, 79968-0519, USA.
| | - Subhas S Karki
- Department of Pharmaceutical Chemistry, KLE College of Pharmacy (A Constituent Unit of KLE Academy of Higher Education & Research-Belagavi), Rajajinagar, Bengaluru, Karnataka, 560010, India.
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2
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Joy R, Siddiqua H, Sharma S, Raveendran M, John F, Hassan P, Gawali SL, Raghavan SC, George J. Block Copolymer Encapsulation of Disarib, an Inhibitor of BCL2 for Improved Chemotherapeutic Potential. ACS OMEGA 2023; 8:40729-40740. [PMID: 37929147 PMCID: PMC10621013 DOI: 10.1021/acsomega.3c05802] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 10/06/2023] [Accepted: 10/09/2023] [Indexed: 11/07/2023]
Abstract
A chemical inhibitor of antiapoptotic protein, BCL2, known as Disarib, suffers poor solubility in aqueous environments; thereby limiting its potential as a chemotherapeutic agent. To overcome this limitation and enhance the therapeutic efficacy of Disarib, we have employed the encapsulation of this small molecule inhibitor within P123 copolymer matrix. Micelles were synthesized using a thin-film hydration technique, and a comprehensive analysis was undertaken to evaluate the resulting micelle properties, including morphology, particle size, intermolecular interactions, encapsulation efficiency, and in vitro release characteristics. This assessment utilized various physicochemical techniques including UV spectroscopy, FTIR spectroscopy, dynamic light scattering (DLS), transmission electron microscopy (TEM), and small-angle X-ray scattering (SAXS). Disarib-loaded P123 micelle formulation denoted as P123D exhibited a well-defined particle size of approximately 29.2 nm spherical core-shell morphology. Our investigations revealed a notable encapsulation efficiency of 75%, and we observed a biphasic release pattern for the encapsulated Disarib. Furthermore, our cytotoxicity assessment of P123D micelles against mouse breast adenocarcinoma, mouse lymphoma, and human leukemic cell lines showed 40-45% increase in cytotoxicity compared with the administration of Disarib alone in the breast adenocarcinoma cell line. Enhancement in the cytotoxicity of P123D was found to be higher or limited; however, it is important to observe that the encapsulation method significantly enhanced the aqueous solubility of Disarib as it has the best solubility in dimethyl sulfoxide (DMSO) in the unencapsulated state.
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Affiliation(s)
- Reshma Joy
- Bio-organic
Laboratory, Department of Chemistry, Sacred
Heart College, Kochi 682013, India
| | - Humaira Siddiqua
- Department
of Biochemistry, Indian Institute of Science, Bangalore 560012, India
| | - Shivangi Sharma
- Department
of Biochemistry, Indian Institute of Science, Bangalore 560012, India
| | - Manthra Raveendran
- Department
of Biochemistry, Indian Institute of Science, Bangalore 560012, India
| | - Franklin John
- Bio-organic
Laboratory, Department of Chemistry, Sacred
Heart College, Kochi 682013, India
| | | | - Santosh L Gawali
- Chemistry
Division, Bhabha Atomic Research Centre, Mumbai 400085, India
| | - Sathees C. Raghavan
- Department
of Biochemistry, Indian Institute of Science, Bangalore 560012, India
| | - Jinu George
- Bio-organic
Laboratory, Department of Chemistry, Sacred
Heart College, Kochi 682013, India
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3
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Ray U, Gopinatha VK, Sharma S, Goyary L, Choudhary B, Mantelingu K, Rangappa KS, Raghavan SC. Identification and characterization of mercaptopyrimidine-based small molecules as inhibitors of nonhomologous DNA end joining. FEBS J 2023; 290:796-820. [PMID: 36048168 DOI: 10.1111/febs.16615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 07/21/2022] [Accepted: 08/31/2022] [Indexed: 02/04/2023]
Abstract
Mercaptopyrimidine derivatives are heterocyclic compounds with potent biological activities including antiproliferative, antibacterial, and anti-inflammatory properties. The present study describes the synthesis and characterization of several mercaptopyrimidine derivatives through condensation of 5,6-diamino-2-mercaptopyrimidin-4-ol with various heterocyclic and aromatic aldehydes. Previous studies have shown that SCR7, synthesized from 5,6-diamino-2-mercaptopyrimidin-4-ol, induced cytotoxicity by targeting cancer cells by primarily inhibiting DNA Ligase IV involved in nonhomologous end joining, one of the major DNA double-strand break repair pathways. Inhibition of DNA repair pathways is considered as an important strategy for cancer therapy. Due to limitations of SCR7 in terms of IC50 in cancer cells, here we have designed, synthesized, and characterized potent derivatives of SCR7 using 5,6-diamino-2-mercaptopyrimidin-4-ol as the starting material. Several synthesized imine compounds exhibited significant improvement in inhibition of end joining and cytotoxicity up to 27-fold lower concentrations than SCR7. Among these, two compounds, SCR116 and SCR132, showed increased cancer cell death in a Ligase IV-dependent manner. Treatment with the compounds also led to reduction in V(D)J recombination efficiency, cell cycle arrest at G2/M phase, accumulation of double-strand breaks inside cells, and improved anti-cancer potential when combined with γ-radiation and radiomimetic drugs. Thus, we describe novel inhibitors of NHEJ with higher efficacy and potential, which can be developed as cancer therapeutics.
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Affiliation(s)
- Ujjayinee Ray
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | - Vindya K Gopinatha
- Department of Biochemistry, Indian Institute of Science, Bangalore, India.,Department of Studies in Chemistry, University of Mysore, India
| | - Shivangi Sharma
- Department of Biochemistry, Indian Institute of Science, Bangalore, India.,Institute of Bioinformatics and Applied Biotechnology, Electronics City, Bangalore, India
| | - Laijau Goyary
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | - Bibha Choudhary
- Institute of Bioinformatics and Applied Biotechnology, Electronics City, Bangalore, India
| | | | - Kanchugarakoppal S Rangappa
- Department of Studies in Chemistry, University of Mysore, India.,Institution of Excellence, Vijnana Bhavana, University of Mysore, India
| | - Sathees C Raghavan
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
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4
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Joy R, George J, John F. Brief Outlook on Polymeric Nanoparticles, Micelles, Niosomes, Hydrogels and Liposomes: Preparative Methods and Action. ChemistrySelect 2022. [DOI: 10.1002/slct.202104045] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Reshma Joy
- Bioorganic Chemistry Laboratory Sacred Heart college (Autonomous), Thevara Kochi Kerala 682013 India
| | - Jinu George
- Bioorganic Chemistry Laboratory Sacred Heart college (Autonomous), Thevara Kochi Kerala 682013 India
| | - Franklin John
- Bioorganic Chemistry Laboratory Sacred Heart college (Autonomous), Thevara Kochi Kerala 682013 India
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5
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Shaikh SJ, Patel HS, Ray D, Aswal VK, Singh S, Vijayvargia R, Sheth U, Sharma RK. Enhanced Solubility and Oral Bioavailability of Hydrophobic Drugs Using Pluronic Nanomicelles: An In‐Vitro Evaluation. ChemistrySelect 2021. [DOI: 10.1002/slct.202102123] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Sofiya J. Shaikh
- Applied Chemistry Department Faculty of Technology and Engineering The Maharaja Sayajirao University of Baroda Vadodara 390001 Gujarat India
| | - Hemil S. Patel
- Applied Chemistry Department Faculty of Technology and Engineering The Maharaja Sayajirao University of Baroda Vadodara 390001 Gujarat India
| | - Debes Ray
- Solid State Physics Division Bhabha Atomic Research Centre Mumbai Maharashtra India
| | - Vinod K. Aswal
- Solid State Physics Division Bhabha Atomic Research Centre Mumbai Maharashtra India
| | - Sushmita Singh
- Department of Biochemistry Faculty of Science The Maharaja Sayajirao University of Baroda Vadodara 390001 Gujarat India
| | - Ravi Vijayvargia
- Department of Biochemistry Faculty of Science The Maharaja Sayajirao University of Baroda Vadodara 390001 Gujarat India
| | - Urjita Sheth
- C. G. Bhakta Institute of Biotechnology UkaTarsadia University Bardoli Gujarat India
| | - Rakesh K. Sharma
- Applied Chemistry Department Faculty of Technology and Engineering The Maharaja Sayajirao University of Baroda Vadodara 390001 Gujarat India
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6
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Ray U, Raghavan SC. Understanding the DNA double-strand break repair and its therapeutic implications. DNA Repair (Amst) 2021; 106:103177. [PMID: 34325086 DOI: 10.1016/j.dnarep.2021.103177] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Revised: 06/25/2021] [Accepted: 07/07/2021] [Indexed: 10/20/2022]
Abstract
Repair of DNA double-strand breaks (DSBs) and its regulation are tightly integrated inside cells. Homologous recombination, nonhomologous end joining and microhomology mediated end joining are three major DSB repair pathways in mammalian cells. Targeting proteins associated with these repair pathways using small molecule inhibitors can prove effective in tumors, especially those with deregulated repair. Sensitization of cancer to current age therapy including radio and chemotherapy, using small molecule inhibitors is promising and warrant further development. Although several are under clinical trial, till date no repair inhibitor is approved for commercial use in cancer patients, with the exception of PARP inhibitors targeting single-strand break repair. Based on molecular profiling of repair proteins, better prognostic and therapeutic output can be achieved in patients. In the present review, we highlight the different mechanisms of DSB repair, chromatin dynamics to provide repair accessibility and modulation of inhibitors in association with molecular profiling and current gold standard treatment modalities for cancer.
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Affiliation(s)
- Ujjayinee Ray
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India
| | - Sathees C Raghavan
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India.
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7
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Gopalakrishnan V, Sharma S, Ray U, Manjunath M, Lakshmanan D, Vartak SV, Gopinatha VK, Srivastava M, Kempegowda M, Choudhary B, Raghavan SC. SCR7, an inhibitor of NHEJ can sensitize tumor cells to ionization radiation. Mol Carcinog 2021; 60:627-643. [PMID: 34192388 DOI: 10.1002/mc.23329] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 06/01/2021] [Accepted: 06/07/2021] [Indexed: 12/30/2022]
Abstract
Nonhomologous end joining (NHEJ), one of the major DNA double-strand break repair pathways, plays a significant role in cancer cell proliferation and resistance to radio and chemotherapeutic agents. Previously, we had described a small molecule inhibitor, SCR7, which inhibited NHEJ in a DNA Ligase IV dependent manner. Here, we report that SCR7 potentiates the effect of γ-radiation (IR) that induces DNA breaks as intermediates to eradicate cancer cells. Dose fractionation studies revealed that coadministration of SCR7 and IR (0.5 Gy) in mice Dalton's lymphoma (DLA) model led to a significant reduction in mice tumor cell proliferation, which was equivalent to that observed for 2 Gy dose when both solid and liquid tumor models were used. Besides, co-treatment with SCR7 and 1 Gy of IR further improved the efficacy. Notably, there was no significant change in blood parameters, kidney and liver functions upon combinatorial treatment of SCR7 and IR. Further, the co-treatment of SCR7 and IR resulted in a significant increase in unrepaired DSBs within cancer cells compared to either of the agent alone. Anatomy, histology, and other studies in tumor models confirmed the cumulative effects of both agents in activating apoptotic pathways to induce cytotoxicity by modulating DNA damage response and repair pathways. Thus, we report that SCR7 has the potential to reduce the side effects of radiotherapy by lowering its effective dose ex vivo and in mice tumor models, with implications in cancer therapy.
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Affiliation(s)
- Vidya Gopalakrishnan
- Department of Biochemistry, Indian Institute of Science, Bangalore, Karnataka, India.,Institute of Bioinformatics and Applied Biotechnology, Electronics City, Bangalore, Karnataka, India.,Department of Zoology, St. Joseph's College (Autonomous), Irinjalakuda, Kerala, India
| | - Shivangi Sharma
- Department of Biochemistry, Indian Institute of Science, Bangalore, Karnataka, India.,Institute of Bioinformatics and Applied Biotechnology, Electronics City, Bangalore, Karnataka, India
| | - Ujjayinee Ray
- Department of Biochemistry, Indian Institute of Science, Bangalore, Karnataka, India
| | - Meghana Manjunath
- Institute of Bioinformatics and Applied Biotechnology, Electronics City, Bangalore, Karnataka, India.,Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Divya Lakshmanan
- Department of Biochemistry, Indian Institute of Science, Bangalore, Karnataka, India
| | - Supriya V Vartak
- Department of Biochemistry, Indian Institute of Science, Bangalore, Karnataka, India
| | - Vindya K Gopinatha
- Department of Biochemistry, Indian Institute of Science, Bangalore, Karnataka, India
| | - Mrinal Srivastava
- Department of Biochemistry, Indian Institute of Science, Bangalore, Karnataka, India.,Tata Institute of Fundamental Research, Hyderabad, Telangana, India
| | | | - Bibha Choudhary
- Institute of Bioinformatics and Applied Biotechnology, Electronics City, Bangalore, Karnataka, India
| | - Sathees C Raghavan
- Department of Biochemistry, Indian Institute of Science, Bangalore, Karnataka, India
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8
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Manjunath M, Choudhary B, Raghavan SC. SCR7, a potent cancer therapeutic agent and a biochemical inhibitor of nonhomologous DNA end-joining. Cancer Rep (Hoboken) 2021; 4:e1341. [PMID: 33496064 PMCID: PMC8222562 DOI: 10.1002/cnr2.1341] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 12/15/2020] [Accepted: 12/21/2020] [Indexed: 12/11/2022] Open
Abstract
Background DNA double‐strand breaks (DSBs) are harmful to the cell as it could lead to genomic instability and cell death when left unrepaired. Homologous recombination and nonhomologous end‐joining (NHEJ) are two major DSB repair pathways, responsible for ensuring genome integrity in mammals. There have been multiple efforts using small molecule inhibitors to target these DNA repair pathways in cancers. SCR7 is a very well‐studied anticancer molecule that blocks NHEJ by targeting one of the critical enzymes, Ligase IV. Recent findings In this review, we have highlighted the anticancer effects of SCR7 as a single agent and in combination with other chemotherapeutic agents and radiation. SCR7 blocked NHEJ effectively both in vitro and ex vivo. SCR7 has been used for biochemical studies like chromosomal territory resetting and in understanding the role of repair proteins in cell cycle phases. Various forms of SCR7 and its derivatives are discussed. SCR7 is also used as a potent biochemical inhibitor of NHEJ, which has found its application in improving genome editing using a CRISPR‐Cas system. Conclusion SCR7 is a potent NHEJ inhibitor with unique properties and wide applications as an anticancer agent. Most importantly, SCR7 has become a handy aid for improving genome editing across different model systems.
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Affiliation(s)
- Meghana Manjunath
- Institute of Bioinformatics and Applied Biotechnology, Bangalore, India.,Manipal Academy of Higher Education, Manipal, India
| | - Bibha Choudhary
- Institute of Bioinformatics and Applied Biotechnology, Bangalore, India
| | - Sathees C Raghavan
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
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9
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Kopa P, Macieja A, Pastwa E, Majsterek I, Poplawski T. DNA double-strand breaks repair inhibitors potentiates the combined effect of VP-16 and CDDP in human colorectal adenocarcinoma (LoVo) cells. Mol Biol Rep 2021; 48:709-720. [PMID: 33389482 DOI: 10.1007/s11033-020-06124-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 12/22/2020] [Indexed: 12/18/2022]
Abstract
I. BACKGROUND A combination of etoposide (VP-16) and cisplatin (CDDP) is the standard treatment for certain colon cancers. These drugs promote the death of cancer cells via direct and indirect induction of the most lethal DNA lesions - DNA double-stand breaks. However, cancer cells can reverse the DNA damaging effect of anticancer drugs by triggering DNA repair processes. In eukaryotic cells, the main DNA repair pathway responsible for DNA double-stand breaks repair is non-homologous end-joining (NHEJ). Inhibitors of DNA repair are of special interest in cancer research as they could break the cellular resistance to DNA-damaging agents and increase the efficiency of standard cancer treatments. In this study, we investigated the effect of two NHEJ inhibitors, SCR7 and NU7441, on the cytotoxic mechanism of VP-16/CDDP in a LoVo human colorectal adenocarcinoma cell line. SCR7 blocks Ligase IV-mediated joining by interfering with its DNA binding, whereas NU7441 is a highly potent and selective DNA-PK inhibitor.II. METHODS AND RESULTS Both inhibitors synergistically increased the cytotoxicity of CDDP and VP-16 when combined, but the effect of SCR7 was more pronounced. SCR7 and NU7441 also significantly increased VP-16; CDDP induced DNA double-stand breaks level and delayed drug-induced DSB repair, as seen on the comet assay and measured using H2AX foci. We also observed changes in cell cycle distribution and enhanced apoptosis ratio in colorectal adenocarcinoma cells treated with DNA repair inhibitors and VP-16/CDDP.III. CONCLUSIONS Our data support the hypothesis that NHEJ inhibitors could be used in conjunction with standard therapy to provide effective clinical improvement and allow reduction in drug doses.
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Affiliation(s)
- Paulina Kopa
- Faculty of Medicine, Department of Immunopathology, Division of Biomedical Science, Medical University of Lodz, Lodz, Poland
| | - Anna Macieja
- Department of Molecular Genetics, Faculty of Biology and Environmental Protection, University of Lodz, Lodz, Poland
| | - Elzbieta Pastwa
- Functional Genomics & Proteomics Unit, ITSI-Biosciences, Johnstown, PA, USA
| | - Ireneusz Majsterek
- Department of Clinical Chemistry and Biochemistry, Faculty of Medicine, Medical University of Lodz, Lodz, Poland
| | - Tomasz Poplawski
- Department of Molecular Genetics, Faculty of Biology and Environmental Protection, University of Lodz, Lodz, Poland.
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10
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Inhibitors of DNA double-strand break repair at the crossroads of cancer therapy and genome editing. Biochem Pharmacol 2020; 182:114195. [DOI: 10.1016/j.bcp.2020.114195] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 08/03/2020] [Accepted: 08/10/2020] [Indexed: 12/17/2022]
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11
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Modulation of DNA double-strand break repair as a strategy to improve precise genome editing. Oncogene 2020; 39:6393-6405. [PMID: 32884115 DOI: 10.1038/s41388-020-01445-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 08/07/2020] [Accepted: 08/21/2020] [Indexed: 12/11/2022]
Abstract
In the present day, it is possible to incorporate targeted mutations or replace a gene using genome editing techniques such as customisable CRISPR/Cas9 system. Although induction of DNA double-strand breaks (DSBs) by genome editing tools can be repaired by both non-homologous end joining (NHEJ) and homologous recombination (HR), the skewness of the former pathway in human and other mammals normally result in imprecise repair. Scientists working at the crossroads of DNA repair and genome editing have devised new strategies for using a specific pathway to their advantage. Refinement in the efficiency of precise gene editing was witnessed upon downregulation of NHEJ by knockdown or using small molecule inhibitors on one hand, and upregulation of HR proteins and addition of HR stimulators, other hand. The exploitation of cell cycle phase differences together with appropriate donor DNA length/sequence and small molecules has provided further improvement in precise genome editing. The present article reviews the mechanisms of improving the efficiency of precise genome editing in several model organisms and in clinics.
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12
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Ray U, Vartak SV, Raghavan SC. NHEJ inhibitor SCR7 and its different forms: Promising CRISPR tools for genome engineering. Gene 2020; 763:144997. [PMID: 32783992 DOI: 10.1016/j.gene.2020.144997] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 07/21/2020] [Indexed: 12/14/2022]
Abstract
The CRISPR-Cas system currently stands as one of the best multifaceted tools for site-specific genome engineering in mammals. An important aspect of research in this field focusses on improving the specificity and efficacy of precise genome editing in multiple model systems. The cornerstone of this mini-review is one of the extensively investigated small molecule inhibitor, SCR7, which abrogates NHEJ, a Ligase IV-dependent DSB repair pathway, thus guiding integration of the foreign DNA fragment via the more precise homology directed repair during genome editing. One of our recent studies sheds light on properties of different forms of SCR7. Here, we give a succinct account on the use of SCR7 and its different forms in CRISPR-Cas system, highlighting their chemical properties and biological relevance as potent efficiency-enhancing CRISPR tools.
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Affiliation(s)
- Ujjayinee Ray
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India
| | - Supriya V Vartak
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India
| | - Sathees C Raghavan
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India.
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13
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Amir M, Mohammad T, Dohare R, Islam A, Ahmad F, Imtaiyaz Hassan M. Structure, function and therapeutic implications of OB-fold proteins: A lesson from past to present. Brief Funct Genomics 2020; 19:377-389. [PMID: 32393969 DOI: 10.1093/bfgp/elaa008] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Oligonucleotide/oligosaccharide-binding (OB)-fold proteins play essential roles in the regulation of genome and its correct transformation to the subsequent generation. To maintain the genomic stability, OB-fold proteins are implicated in various cellular processes including DNA replication, DNA repair, cell cycle regulation and maintenance of telomere. The diverse functional spectrums of OB-fold proteins are mainly due to their involvement in protein-DNA and protein-protein complexes. Mutations and consequential structural alteration in the OB-fold proteins often lead to severe diseases. Here, we have investigated the structure, function and mode of action of OB-fold proteins (RPA, BRCA2, DNA ligases and SSBs1/2) in cellular pathways and their relationship with diseases and their possible use in therapeutic intervention. Due to the crucial role of OB-fold proteins in regulating the key physiological process, a detailed structural understanding in the context of underlying mechanism of action and cellular complexity offers a new avenue to target OB-proteins for therapeutic intervention.
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14
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Ray U, Raul SK, Gopinatha VK, Ghosh D, Rangappa KS, Mantelingu K, Raghavan SC. Identification and characterization of novel SCR7-based small-molecule inhibitor of DNA end-joining, SCR130 and its relevance in cancer therapeutics. Mol Carcinog 2020; 59:618-628. [PMID: 32189406 DOI: 10.1002/mc.23186] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 02/26/2020] [Accepted: 02/27/2020] [Indexed: 12/20/2022]
Abstract
Targeting DNA repair with small-molecule inhibitors is an attractive strategy for cancer therapy. Majority of DNA double-strand breaks in mammalian cells are repaired through nonhomologous end-joining (NHEJ). It has been shown that small-molecule inhibitors of NHEJ can block efficient repair inside cancer cells, leading to cell death. Previously, we have reported that SCR7, an inhibitor of NHEJ can induce tumor regression in mice. Later studies have shown that different forms of SCR7 can inhibit DNA end-joining in Ligase IV-dependent manner. Recently, we have derivatized SCR7 by introducing spiro ring into core structure. Here, we report the identification of a novel inhibitor of NHEJ, named SCR130 with 20-fold higher efficacy in inducing cytotoxicity in cancer cell lines. SCR130 inhibited DNA end-joining catalyzed by rat tissue extract. Specificity analysis revealed that while SCR130 was specific to Ligase IV, it showed minimal or no effect on Ligase III and Ligase I mediated joining. Importantly, SCR130 exhibited the least cytotoxicity in Ligase IV-null cell line as compared with wild type, confirming Ligase IV-specificity. Furthermore, we demonstrate that SCR130 can potentiate the effect of radiation in cancer cells when used in combination with γ-radiation. Various cellular assays in conjunction with Western blot analysis revealed that treatment with SCR130 led to loss of mitochondrial membrane potential leading to cell death by activating both intrinsic and extrinsic pathways of apoptosis. Thus, we describe a novel inhibitor of NHEJ with higher efficacy and may have the potential to be developed as cancer therapeutic.
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Affiliation(s)
- Ujjayinee Ray
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | - Sanjay Kumar Raul
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | - Vindya K Gopinatha
- Department of Studies in Chemistry, ManasaganFindo-frgotri, University of Mysore, Mysuru, India
| | - Dipayan Ghosh
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | | | - Kempegowda Mantelingu
- Department of Studies in Chemistry, ManasaganFindo-frgotri, University of Mysore, Mysuru, India
| | - Sathees C Raghavan
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
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15
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Devassy G, Ramachandran R, Jeena K, Junnuthula VR, Gopinatha VK, Manju C, Manohar M, Nair SV, Raghavan SC, Koyakutty M. Simultaneous release of two drugs from polymer nano-implant inhibits recurrence in glioblastoma spheroids. PRECISION NANOMEDICINE 2019. [DOI: 10.33218/prnano2(1).181122.1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Local implant-based delivery of rationally selected combination of chemotherapeutics has some major advantages for the treatment of glioblastoma such as: (a) 100 % bio-availability locally in brain can be achieved at the tumor site (b) avoid systemic leakage and associated toxicity, and (c) simultaneous inhibition of multiple, mutually exclusive cancer mechanisms is possible. Here, we report a polymeric brain implant capable of delivering two different drugs in recur-rent glioma cells. We have selected a combination of clinically used DNA alkylating agent, Te-mozolomide, and a DNA mismatch repair protein (Ligase IV) inhibitor, SCR-7, and delivered simultaneously into tumor spheroids formed by rat glioma cells, C6. The dual-drug loaded polymeric wafer, prepared by lyophilization method, could deliver both the drugs in a controlled fashion. To test the efficacy of this system, we have optimized an in vitro recurrent model of glioma spheroids wherein, the implant released both the drugs in a sustained fashion, thereby continuously exposing the cells to DNA methylation while inhibiting the DNA repair pathways. This leads to synergistic toxicity and inhibition of tumor recurrence for extended duration compared to free drug combination.
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16
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Vartak SV, Swarup HA, Gopalakrishnan V, Gopinatha VK, Ropars V, Nambiar M, John F, Kothanahally SKS, Kumari R, Kumari N, Ray U, Radha G, Dinesh D, Pandey M, Ananda H, Karki SS, Srivastava M, Charbonnier JB, Choudhary B, Mantelingu K, Raghavan SC. Autocyclized and oxidized forms of SCR7 induce cancer cell death by inhibiting nonhomologous DNA end joining in a Ligase IV dependent manner. FEBS J 2018; 285:3959-3976. [PMID: 30230716 DOI: 10.1111/febs.14661] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 08/23/2018] [Accepted: 09/17/2018] [Indexed: 12/17/2022]
Abstract
Nonhomologous DNA end joining (NHEJ) is the major DNA double-strand break (DSB) repair pathway in mammals. Previously, we have described a small molecule inhibitor, SCR7, which can inhibit NHEJ in a Ligase IV-dependent manner. Administration of SCR7 within the cells resulted in the accumulation of DNA breaks, cell death, and inhibition of tumor growth in mice. In the present study, we report that parental SCR7, which is unstable, can be autocyclized into a stable form. Both parental SCR7 and cyclized SCR7 possess the same molecular weight (334.09) and molecular formula (C18 H14 N4 OS), whereas its oxidized form, SCR7-pyrazine, possesses a different molecular formula (C18 H12 N4 OS), molecular weight (332.07), and structure. While cyclized form of SCR7 showed robust inhibition of NHEJ in vitro, both forms exhibited efficient cytotoxicity. Cyclized and oxidized forms of SCR7 inhibited DNA end joining catalyzed by Ligase IV, whereas their impact was minimal on Ligase III, Ligase I, and T4 DNA Ligase-mediated joining. Importantly, both forms inhibited V(D)J recombination, although the effect was more pronounced for SCR7-cyclized. Both forms blocked NHEJ in a Ligase IV-dependent manner leading to the accumulation of DSBs within the cells. Although cytotoxicity due to SCR7-cyclized was Ligase IV specific, the pyrazine form exhibited nonspecific cytotoxicity at higher concentrations in Ligase IV-null cells. Finally, we demonstrate that both forms can potentiate the effect of radiation. Thus, we report that cyclized and oxidized forms of SCR7 can inhibit NHEJ in a Ligase IV-dependent manner, although SCR7-pyrazine is less specific to Ligase IV inside the cell.
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Affiliation(s)
- Supriya V Vartak
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | | | - Vidya Gopalakrishnan
- Institute of Bioinformatics and Applied Biotechnology, Bangalore, India.,Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Vindya K Gopinatha
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | - Virginie Ropars
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris-Sud, Univ Paris-Saclay, Gif-sur-Yvette Cedex, France
| | - Mridula Nambiar
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | - Franklin John
- Department of Chemistry, Sacred Heart College, Kochi, India
| | | | - Rupa Kumari
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | - Nitu Kumari
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | - Ujjayinee Ray
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | - Gudapureddy Radha
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | - Depina Dinesh
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | - Monica Pandey
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | - Hanumappa Ananda
- Department of Biochemistry, Indian Institute of Science, Bangalore, India.,Department of Chemistry, University of Mysore, India
| | - Subhas S Karki
- KLE Academy of Higher Education and Research, KLE College of Pharmacy, Rajajinagar, Bengaluru, India
| | - Mrinal Srivastava
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | - Jean Baptiste Charbonnier
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris-Sud, Univ Paris-Saclay, Gif-sur-Yvette Cedex, France
| | - Bibha Choudhary
- Institute of Bioinformatics and Applied Biotechnology, Bangalore, India
| | | | - Sathees C Raghavan
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
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17
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Yang Z, Chen S, Xue S, Li X, Hu J, Sun Z, Cui H. Injection of an SV40 transcriptional terminator causes embryonic lethality: a possible zebrafish model for screening nonhomologous end-joining inhibitors. Onco Targets Ther 2018; 11:4945-4953. [PMID: 30154663 PMCID: PMC6103608 DOI: 10.2147/ott.s153576] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Introduction DNA repair by the nonhomologous end joining (NHEJ) pathway promotes tumor recurrence after chemotherapy and radiotherapy. Discovery of rapid and high-throughput techniques to screen for an effective NHEJ inhibitor drug is imperative for the suppression of NHEJ during tumor treatment. However, traditional screening methods are too cumbersome to meet the current need. Zebrafish is an ideal model for drug screening due to the specificity of its early embryonic development and similarity of tumor cell generation. By exploiting the high frequency of NHEJ in early embryonic development, we established a model that uses a transcriptional terminator signal fragment from the Simian virus 40 (SV40) to cause embryonic lethality. SV40 fragment-induced embryonic lethality was alleviated by 5,6-bis ((E)-benzylideneamino)-2-mercaptopyrimidin-4-ol or C18H14N4OS (SCR7), an NHEJ inhibitor. Materials and methods A 122 bp SV40 terminator fragment (10 ng/µL) was microinjected into zebrafish zygotes. SV40 fragment integration into the zebrafish embryonic genome was detected by Southern blot using a DNA probe for the SV40 terminator. Embryonic lethality rates were observed 24 and 48 h after microinjection. A nonhomologous recombinant inhibitor, SCR7 (5 µM), was used to alleviate embryonic lethality. Results Microinjection of zebrafish embryos with the SV40 terminator fragment (10 ng/µL) caused a progressive increase in mortality over time. Using Southern blots, we confirmed that SV40 terminator sequences were integrated into the zebrafish embryonic genome. This phenomenon was effectively alleviated by addition of SCR7. Conclusion Injection of an SV40 terminator into zebrafish embryos may cause embryonic lethality due to NHEJ during early zebrafish development. The high mortality of zebrafish embryos could be alleviated by using the NHEJ inhibitor, SCR7. The zebrafish model presented here is simpler and more convenient than traditional methods of screening for NHEJ inhibitors and can be utilized in large-scale drug screens for NHEJ inhibitors and for the development of novel anticancer drugs.
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Affiliation(s)
- Zhe Yang
- Institute of Epigenetics and Epigenomics, Yangzhou University, Yangzhou, Jiangsu 225009, People's Republic of China, .,College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu 225009, People's Republic of China,
| | - Shihao Chen
- Institute of Epigenetics and Epigenomics, Yangzhou University, Yangzhou, Jiangsu 225009, People's Republic of China, .,College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu 225009, People's Republic of China,
| | - Songlei Xue
- Institute of Epigenetics and Epigenomics, Yangzhou University, Yangzhou, Jiangsu 225009, People's Republic of China, .,College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu 225009, People's Republic of China,
| | - Xinxiu Li
- Institute of Epigenetics and Epigenomics, Yangzhou University, Yangzhou, Jiangsu 225009, People's Republic of China, .,College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu 225009, People's Republic of China,
| | - Jiang Hu
- Institute of Epigenetics and Epigenomics, Yangzhou University, Yangzhou, Jiangsu 225009, People's Republic of China, .,College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu 225009, People's Republic of China,
| | - Zhen Sun
- Institute of Epigenetics and Epigenomics, Yangzhou University, Yangzhou, Jiangsu 225009, People's Republic of China, .,College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu 225009, People's Republic of China,
| | - Hengmi Cui
- Institute of Epigenetics and Epigenomics, Yangzhou University, Yangzhou, Jiangsu 225009, People's Republic of China, .,College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu 225009, People's Republic of China, .,Institute of Comparative Medicine, Yangzhou University, Yangzhou, Jiangsu 225009, People's Republic of China, .,Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, Jiangsu 225009, People's Republic of China, .,Joint International Research Laboratory of Agricultural & Agri-Product Safety of Educational Ministry of China, Yangzhou University, Yangzhou, Jiangsu 225009, People's Republic of China,
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18
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Hegde M, Vartak SV, Kavitha CV, Ananda H, Prasanna DS, Gopalakrishnan V, Choudhary B, Rangappa KS, Raghavan SC. A Benzothiazole Derivative (5g) Induces DNA Damage And Potent G2/M Arrest In Cancer Cells. Sci Rep 2017; 7:2533. [PMID: 28566733 PMCID: PMC5451441 DOI: 10.1038/s41598-017-02489-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Accepted: 04/12/2017] [Indexed: 11/25/2022] Open
Abstract
Chemically synthesized small molecules play important role in anticancer therapy. Several chemical compounds have been reported to damage the DNA, either directly or indirectly slowing down the cancer cell progression by causing a cell cycle arrest. Direct or indirect reactive oxygen species formation causes DNA damage leading to cell cycle arrest and subsequent cell death. Therefore, identification of chemically synthesized compounds with anticancer potential is important. Here we investigate the effect of benzothiazole derivative (5g) for its ability to inhibit cell proliferation in different cancer models. Interestingly, 5g interfered with cell proliferation in both, cell lines and tumor cells leading to significant G2/M arrest. 5g treatment resulted in elevated levels of ROS and subsequently, DNA double-strand breaks (DSBs) explaining observed G2/M arrest. Consistently, we observed deregulation of many cell cycle associated proteins such as CDK1, BCL2 and their phosphorylated form, CyclinB1, CDC25c etc. Besides, 5g treatment led to decreased levels of mitochondrial membrane potential and activation of apoptosis. Interestingly, 5g administration inhibited tumor growth in mice without significant side effects. Thus, our study identifies 5g as a potent biochemical inhibitor to induce G2/M phase arrest of the cell cycle, and demonstrates its anticancer properties both ex vivo and in vivo.
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Affiliation(s)
- Mahesh Hegde
- Department of Biochemistry, Indian Institute of Science, Bangalore, 560012, India.,Department of Studies in Chemistry, University of Mysore, Mysuru, 570006, India
| | - Supriya V Vartak
- Department of Biochemistry, Indian Institute of Science, Bangalore, 560012, India
| | | | - Hanumappa Ananda
- Department of Biochemistry, Indian Institute of Science, Bangalore, 560012, India
| | - Doddakunche S Prasanna
- Department of Nanotechnology, Visvesvaraya Technological University, Center for Postgraduate Studies, Bengaluru Region, Muddenahalli, Chikkaballapur, Bangalore, 562101, India
| | - Vidya Gopalakrishnan
- Department of Biochemistry, Indian Institute of Science, Bangalore, 560012, India.,Institute of Bioinformatics and Applied Biotechnology, Electronics City, Bangalore, 560100, India
| | - Bibha Choudhary
- Institute of Bioinformatics and Applied Biotechnology, Electronics City, Bangalore, 560100, India
| | | | - Sathees C Raghavan
- Department of Biochemistry, Indian Institute of Science, Bangalore, 560012, India.
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19
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Zhao LY, Zhang WM. Recent progress in drug delivery of pluronic P123: pharmaceutical perspectives. J Drug Target 2017; 25:471-484. [PMID: 28135859 DOI: 10.1080/1061186x.2017.1289538] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
This review focuses on recent investigations that used Pluronic P123 (P123) as pharmaceutical ingredients in vesicle, micelle, mixed micelle, in situ gel, tablet and emulsion. The main results from these studies show that P123 can significantly increase the stability of incorporated hydrophobic drugs with enhanced in vitro cytotoxicity and cellular uptake of anticancer drugs. Moreover, modified forms of P123 with RGD, folate or other targeted marker have shown its therapeutic potentials in various types of tumors and cancers. Furthermore, modified forms of P123 alone and/or mixed with other copolymers have less toxic effects and more tumor-specific delivery of anticancer drugs. They are promising materials as a nanoplatform for the drug delivery. Finally, the future perspectives of the field are briefly discussed.
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Affiliation(s)
- Li-Yan Zhao
- a Department of Pharmacy , Hebei North University , Zhangjiakou , PR China
| | - Wan-Ming Zhang
- a Department of Pharmacy , Hebei North University , Zhangjiakou , PR China
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20
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Dehvari K, Lin KS, Hammouda B. Small-angle neutron scattering studies of microenvironmental and structural changes of Pluronic micelles upon encapsulation of paclitaxel. J Taiwan Inst Chem Eng 2017. [DOI: 10.1016/j.jtice.2016.11.027] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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21
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Pandey M, Kumar S, Goldsmith G, Srivastava M, Elango S, Shameem M, Bannerjee D, Choudhary B, Karki SS, Raghavan SC. Identification and characterization of novel ligase I inhibitors. Mol Carcinog 2016; 56:550-566. [PMID: 27312791 DOI: 10.1002/mc.22516] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2015] [Revised: 06/06/2016] [Accepted: 06/14/2016] [Indexed: 12/17/2022]
Abstract
The terminal step of ligation of single and/or double-strand breaks during physiological processes such as DNA replication, repair and recombination requires participation of DNA ligases in all mammals. DNA Ligase I has been well characterised to play vital roles during these processes. Considering the indispensable role of DNA Ligase I, a therapeutic strategy to impede proliferation of cancer cells is by using specific small molecule inhibitors against it. In the present study, we have designed and chemically synthesised putative DNA Ligase I inhibitors. Based on various biochemical and biophysical screening approaches, we identify two prospective DNA Ligase I inhibitors, SCR17 and SCR21. Both the inhibitors blocked ligation of nicks on DNA in a concentration-dependent manner, when catalysed by cell-free extracts or purified Ligase I. Docking studies in conjunction with biolayer interferometry and gel shift assays revealed that both SCR17 and SCR21 can bind to Ligase I, particularly to the DNA Binding Domain of Ligase I with KD values in nanomolar range. The inhibitors did not show significant affinity towards DNA Ligase III and DNA Ligase IV. Further, addition of Ligase I could restore the joining, when the inhibitors were treated with testicular cell-free extracts. Ex vivo studies using multiple assays showed that even though cell death was limited in the presence of inhibitors in cancer cells, their proliferation was compromised. Hence, we identify two promising DNA Ligase I inhibitors, which can be used in biochemical and cellular assays, and could be further modified and optimised to target cancer cells. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Monica Pandey
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | - Sujeet Kumar
- Department of Pharmaceutical Chemistry, KLE University's College of Pharmacy, Bangalore, India
| | - Gunaseelan Goldsmith
- Institute of Bioinformatics and Applied Biotechnology, Electronics City, Bangalore, India
| | - Mrinal Srivastava
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | - Santhini Elango
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | | | | | - Bibha Choudhary
- Institute of Bioinformatics and Applied Biotechnology, Electronics City, Bangalore, India
| | - Subhas S Karki
- Department of Pharmaceutical Chemistry, KLE University's College of Pharmacy, Bangalore, India
| | - Sathees C Raghavan
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
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22
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Hegde M, Mantelingu K, Pandey M, Pavankumar CS, Rangappa KS, Raghavan SC. Combinatorial Study of a Novel Poly (ADP-ribose) Polymerase Inhibitor and an HDAC Inhibitor, SAHA, in Leukemic Cell Lines. Target Oncol 2016; 11:655-665. [DOI: 10.1007/s11523-016-0441-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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23
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Vartak SV, Raghavan SC. Inhibition of nonhomologous end joining to increase the specificity of CRISPR/Cas9 genome editing. FEBS J 2015; 282:4289-94. [PMID: 26290158 DOI: 10.1111/febs.13416] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Revised: 08/02/2015] [Accepted: 08/04/2015] [Indexed: 12/22/2022]
Abstract
DNA repair, one of the fundamental processes occurring in a cell, safeguards the genome and maintains its integrity. Among various DNA lesions, double-strand breaks are considered to be the most deleterious, as they can lead to potential loss of genetic information, if not repaired. Nonhomologous end joining (NHEJ) and homologous recombination are two major double-strand break repair pathways. SCR7, a DNA ligase IV inhibitor, was recently identified and characterized as a potential anticancer compound. Interestingly, SCR7 was shown to have several applications, owing to its unique property as an NHEJ inhibitor. Here, we focus on three main areas of research in which SCR7 is actively being used, and discuss one of the applications, i.e. genome editing via CRISPR/Cas, in detail. In the past year, different studies have shown that SCR7 significantly increases the efficiency of precise genome editing by inhibiting NHEJ, and favouring the error-free homologous recombination pathway, both in vitro and in vivo. Overall, we discuss the current applications of SCR7 to shed light on the unique property of the small molecule of having distinct applications in normal and cancer cells, when used at different cellular concentrations.
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Affiliation(s)
- Supriya V Vartak
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | - Sathees C Raghavan
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
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24
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Javadekar SM, Raghavan SC. Snaps and mends: DNA breaks and chromosomal translocations. FEBS J 2015; 282:2627-45. [PMID: 25913527 DOI: 10.1111/febs.13311] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Revised: 03/29/2015] [Accepted: 04/23/2015] [Indexed: 01/11/2023]
Abstract
Integrity in entirety is the preferred state of any organism. The temporal and spatial integrity of the genome ensures continued survival of a cell. DNA breakage is the first step towards creation of chromosomal translocations. In this review, we highlight the factors contributing towards the breakage of chromosomal DNA. It has been well-established that the structure and sequence of DNA play a critical role in selective fragility of the genome. Several non-B-DNA structures such as Z-DNA, cruciform DNA, G-quadruplexes, R loops and triplexes have been implicated in generation of genomic fragility leading to translocations. Similarly, specific sequences targeted by proteins such as Recombination Activating Genes and Activation Induced Cytidine Deaminase are involved in translocations. Processes that ensure the integrity of the genome through repair may lead to persistence of breakage and eventually translocations if their actions are anomalous. An insufficient supply of nucleotides and chromatin architecture may also play a critical role. This review focuses on a range of events with the potential to threaten the genomic integrity of a cell, leading to cancer.
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Affiliation(s)
- Saniya M Javadekar
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | - Sathees C Raghavan
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
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25
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Katiyar A, Hegde M, Kumar S, Gopalakrishnan V, Bhatelia KD, Ananthaswamy K, Ramareddy SA, De Clercq E, Choudhary B, Schols D, Raghavan SC, Karki SS. Synthesis and evaluation of the biological activity of N′-[2-oxo-1,2 dihydro-3H-indol-3-ylidene] benzohydrazides as potential anticancer agents. RSC Adv 2015. [DOI: 10.1039/c5ra01528f] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
New N′-[2-oxo-1,2-dihydro-3H-indol-3-ylidene]benzohydrazide derivatives were synthesized and evaluated for their cytotoxic properties against murine leukemia, L1210, human leukemia, REH, K562 and CEM and human cervix carcinoma, HeLa cells.
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Affiliation(s)
- Arpit Katiyar
- Department of Pharmaceutical Chemistry
- KLE University's College of Pharmacy
- Bangalore-560 010
- India
- Department of Pharmacy and Medical Science
| | - Mahesh Hegde
- Department of Biochemistry
- Indian Institute of Science
- Bangalore-560012
- India
| | - Sujeet Kumar
- Department of Pharmaceutical Chemistry
- KLE University's College of Pharmacy
- Bangalore-560 010
- India
| | | | - Khyati D. Bhatelia
- Department of Biochemistry
- Indian Institute of Science
- Bangalore-560012
- India
| | - Kavya Ananthaswamy
- Department of Biochemistry
- Indian Institute of Science
- Bangalore-560012
- India
| | - Sureshbabu A. Ramareddy
- Department of Pharmaceutical Chemistry
- KLE University's College of Pharmacy
- Bangalore-560 010
- India
| | - Erik De Clercq
- Rega Institute for Medical Research
- KU Leuven
- B-3000 Leuven
- Belgium
| | - Bibha Choudhary
- Institute of Bioinformatics and Applied Biotechnology
- Bangalore 560 100
- India
| | - Dominique Schols
- Rega Institute for Medical Research
- KU Leuven
- B-3000 Leuven
- Belgium
| | | | - Subhas S. Karki
- Department of Pharmaceutical Chemistry
- KLE University's College of Pharmacy
- Bangalore-560 010
- India
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26
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John F, George J, Srivastava M, Hassan PA, Aswal VK, Karki SS, Raghavan SC. Pluronic copolymer encapsulated SCR7 as a potential anticancer agent. Faraday Discuss 2015; 177:155-61. [DOI: 10.1039/c4fd00176a] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Nonhomologous end joining (NHEJ) of DNA double strand breaks (DSBs) inside cells can be selectively inhibited by 5,6-bis-(benzylideneamino)-2-mercaptopyrimidin-4-ol (SCR7) which possesses anticancer properties. The hydrophobicity of SCR7 decreases its bioavailability which is a major setback in the utilization of this compound as a therapeutic agent. In order to circumvent the drawback of SCR7, we prepared a polymer encapsulated form of SCR7. The physical interaction of SCR7 and Pluronic® copolymer is evident from different analytical techniques. The in vitro cytotoxicity of the drug formulations is established using the MTT assay.
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Affiliation(s)
- Franklin John
- Biotechnology Laboratory
- PG and Research Department of Chemistry
- Sacred Heart College
- Kochi 682 013
- India
| | - Jinu George
- Biotechnology Laboratory
- PG and Research Department of Chemistry
- Sacred Heart College
- Kochi 682 013
- India
| | - Mrinal Srivastava
- Department of Biochemistry
- Indian Institute of Science
- Bangalore 560 012
- India
| | - P. A. Hassan
- Chemistry Division
- Bhabha Atomic Research Centre
- Mumbai 400 085
- India
| | - V. K. Aswal
- Solid State Physics Division
- Bhabha Atomic Research Centre
- Mumbai 400 085
- India
| | - Subhas. S. Karki
- Department of Pharmaceutical Chemistry
- KLE University
- Bangalore 560 010
- India
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