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Article ; Online: Understanding the DNA double-strand break repair and its therapeutic implications.

Ray, Ujjayinee / Raghavan, Sathees C

2021 Volume 106, Page(s) 103177

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 ...

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.
MeSH term(s)	Animals ; Antineoplastic Agents/pharmacology ; Antineoplastic Agents/therapeutic use ; Chromatin/metabolism ; DNA/drug effects ; DNA/metabolism ; DNA/radiation effects ; DNA Breaks, Double-Stranded ; DNA End-Joining Repair ; DNA Repair ; Humans ; Neoplasms/drug therapy ; Neoplasms/genetics ; Neoplasms/metabolism ; Poly(ADP-ribose) Polymerase Inhibitors/pharmacology ; Poly(ADP-ribose) Polymerase Inhibitors/therapeutic use ; Recombinational DNA Repair
Chemical Substances	Antineoplastic Agents ; Chromatin ; Poly(ADP-ribose) Polymerase Inhibitors ; DNA (9007-49-2)
Language	English
Publishing date	2021-07-09
Publishing country	Netherlands
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	2071608-4
ISSN	1568-7856 ; 1568-7864
ISSN (online)	1568-7856
ISSN	1568-7864
DOI	10.1016/j.dnarep.2021.103177
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Article ; Online: Modulation of DNA double-strand break repair as a strategy to improve precise genome editing.

Ray, Ujjayinee / Raghavan, Sathees C

Oncogene

2020 Volume 39, Issue 41, Page(s) 6393–6405

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 ... ...

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.
MeSH term(s)	Animals ; CRISPR-Cas Systems/genetics ; DNA Breaks, Double-Stranded ; DNA End-Joining Repair/drug effects ; DNA End-Joining Repair/genetics ; DNA Repair Enzymes/antagonists & inhibitors ; DNA Repair Enzymes/metabolism ; DNA-Binding Proteins/antagonists & inhibitors ; DNA-Binding Proteins/metabolism ; Gene Editing/methods ; Gene Knockdown Techniques ; Homologous Recombination/drug effects ; Homologous Recombination/genetics ; Humans ; Models, Animal ; Oligonucleotides, Antisense/pharmacology ; Pyrimidines/pharmacology ; Schiff Bases/pharmacology
Chemical Substances	5,6-bis(benzylideneamino)-2-mercaptopyrimidin-4-ol ; DNA-Binding Proteins ; Oligonucleotides, Antisense ; Pyrimidines ; Schiff Bases ; DNA Repair Enzymes (EC 6.5.1.-)
Language	English
Publishing date	2020-09-03
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	639046-8
ISSN	1476-5594 ; 0950-9232
ISSN (online)	1476-5594
ISSN	0950-9232
DOI	10.1038/s41388-020-01445-2
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Article ; Online: Inhibitors of DNA double-strand break repair at the crossroads of cancer therapy and genome editing.

Ray, Ujjayinee / Raghavan, Sathees C

Biochemical pharmacology

2020 Volume 182, Page(s) 114195

Abstract: Conventional cancer treatment modalities such as radiation and chemotherapy, cause cancer cell death by inducing DNA damage, particularly DNA strand breaks. Over the years, newer avenues have emerged for overcoming radio/chemoresistance by harnessing ... ...

Abstract	Conventional cancer treatment modalities such as radiation and chemotherapy, cause cancer cell death by inducing DNA damage, particularly DNA strand breaks. Over the years, newer avenues have emerged for overcoming radio/chemoresistance by harnessing repair proteins as targets for small molecule inhibitors. Analysis of genome-wide expression data in cancer subtypes and understanding synthetic lethal interactions among repair pathways are important stepping-stones. Several inhibitors targeting DNA strand break repair proteins have yielded good effects in preclinical studies, and have the potential to be developed as therapeutics in cancer as monotherapy or in combination with radiation and chemotherapy. Furthermore, these small molecule inhibitors can aid in precise genome editing (using CRISPR) by harnessing the differential levels of repair inside cells. Shifting the repair balance towards homology-directed repair using inhibitors of NHEJ or stimulators of HR has yielded promising effects alongside CRISPR in cells and several disease models. In short, DNA strand break repair inhibitors are the forerunners in cancer therapy and genome editing, working in concert with the established artillery in the field.
MeSH term(s)	Animals ; Antineoplastic Agents/pharmacology ; Antineoplastic Agents/therapeutic use ; DNA Breaks, Double-Stranded/drug effects ; DNA End-Joining Repair/drug effects ; DNA Repair/drug effects ; DNA Repair/genetics ; Gene Editing/methods ; Gene Editing/trends ; Humans ; Neoplasms/drug therapy ; Neoplasms/genetics ; Neoplasms/metabolism
Chemical Substances	Antineoplastic Agents
Language	English
Publishing date	2020-08-13
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	208787-x
ISSN	1873-2968 ; 0006-2952
ISSN (online)	1873-2968
ISSN	0006-2952
DOI	10.1016/j.bcp.2020.114195
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Article ; Online: NHEJ inhibitor SCR7 and its different forms: Promising CRISPR tools for genome engineering.

Ray, Ujjayinee / Vartak, Supriya V / Raghavan, Sathees C

Gene

2020 Volume 763, Page(s) 144997

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 ... ...

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.
MeSH term(s)	Animals ; CRISPR-Cas Systems ; DNA Ligase ATP/antagonists & inhibitors ; Enzyme Inhibitors/chemistry ; Enzyme Inhibitors/pharmacology ; Gene Editing/methods ; Humans ; Pyrimidines/chemistry ; Pyrimidines/pharmacology ; Recombinational DNA Repair/drug effects ; Schiff Bases/chemistry ; Schiff Bases/pharmacology
Chemical Substances	5,6-bis(benzylideneamino)-2-mercaptopyrimidin-4-ol ; Enzyme Inhibitors ; Pyrimidines ; Schiff Bases ; DNA Ligase ATP (EC 6.5.1.1)
Language	English
Publishing date	2020-08-09
Publishing country	Netherlands
Document type	Journal Article ; Review
ZDB-ID	391792-7
ISSN	1879-0038 ; 0378-1119
ISSN (online)	1879-0038
ISSN	0378-1119
DOI	10.1016/j.gene.2020.144997
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Article: NHEJ inhibitor SCR7 and its different forms: Promising CRISPR tools for genome engineering

Ray, Ujjayinee / Vartak, Supriya V / Raghavan, Sathees C

Gene. 2020 Dec. 30, v. 763

2020

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.
Keywords	DNA fragmentation ; DNA repair ; gene editing ; genes ; ligases ; light ; mammals ; models ; physicochemical properties ; research ; sheds
Language	English
Dates of publication	2020-1230
Publishing place	Elsevier B.V.
Document type	Article
Note	NAL-light
ZDB-ID	391792-7
ISSN	1879-0038 ; 0378-1119
ISSN (online)	1879-0038
ISSN	0378-1119
DOI	10.1016/j.gene.2020.144997
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Article ; Online: Design and Synthesis of Ketenimine Sulfonamide Conjugates through Multicomponent Reactions; A Combined Cytotoxic Analysis and Computational Exploration.

Prabhu, Deepak J / Ray, Ujjayinee / Rajeev, Anjaly / Joy, Reshma / George, Abi Thoppilan / George, Jinu / Raghavan, Sathees C / John, Franklin

ACS omega

2023 Volume 8, Issue 41, Page(s) 38619–38631

Abstract: Multicomponent reactions involving zwitterion generated from dimethyl acetylenedicarboxylate, aryl sulfonamide, and isocyanide to generate sulfonamide-conjugated ketenimines is reported. The synthetic strategy adopted is highly atom economical and ... ...

Abstract	Multicomponent reactions involving zwitterion generated from dimethyl acetylenedicarboxylate, aryl sulfonamide, and isocyanide to generate sulfonamide-conjugated ketenimines is reported. The synthetic strategy adopted is highly atom economical and stereoselective. Ketenimine sulfonamide analogues are key intermediates for further synthetic conversions to generate a combinatorial library of compounds. Furthermore, sulfonamide compounds are known to possess a broad spectrum of biological applications. All the novel molecules synthesized exhibit the potential to target the nonhomologous DNA end-joining (NHEJ) pathway with cytotoxic ability. Computational studies compliment the in vitro biological assays of the 8 small-molecule inhibitors. DNA double-strand breaks (DSBs) are considered as the most lethal among different DNA damages. NHEJ repairs about 70% of the DSBs generated in cells within mammals. The DNA-dependent protein kinase catalytic subunit is one of the PI3 kinases associated with NHEJ. Compounds DK01-DK08 were investigated for their ability to induce cancer cell death by treating with two leukemic cell lines where NHEJ is high. Results showed that bromoaryl (DK04)- and nitroaryl (DK05)-conjugated molecules showed excellent biological activity, having IC
Language	English
Publishing date	2023-10-05
Publishing country	United States
Document type	Journal Article
ISSN	2470-1343
ISSN (online)	2470-1343
DOI	10.1021/acsomega.3c05816
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Article ; Online: Correction to "Design and Synthesis of Ketenimine Sulfonamide Conjugates through Multicomponent Reactions; A Combined Cytotoxic Analysis and Computational Exploration".

Prabhu, Deepak J / Ray, Ujjayinee / Rajeev, Anjaly / Joy, Reshma / George, Abi Thoppilan / George, Jinu / Raghavan, Sathees C / John, Franklin

ACS omega

2023 Volume 8, Issue 49, Page(s) 47315

Abstract: This corrects the article DOI: 10.1021/acsomega.3c05816.]. ...

Abstract	[This corrects the article DOI: 10.1021/acsomega.3c05816.].
Language	English
Publishing date	2023-11-29
Publishing country	United States
Document type	Published Erratum
ISSN	2470-1343
ISSN (online)	2470-1343
DOI	10.1021/acsomega.3c08691
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Article ; Online: Identification and characterization of mercaptopyrimidine‐based small molecules as inhibitors of nonhomologous DNA end joining

Ray, Ujjayinee / Gopinatha, Vindya K. / Sharma, Shivangi / Goyary, Laijau / Choudhary, Bibha / Mantelingu, Kempegowda / Rangappa, Kanchugarakoppal S. / Raghavan, Sathees C.

The FEBS Journal. 2023 Feb., v. 290, no. 3 p.796-820

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 ... ...

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.
Keywords	DNA ; DNA repair ; cancer therapy ; cell cycle checkpoints ; cell death ; cytotoxicity ; heterocyclic compounds ; imines ; ligases ; neoplasm cells
Language	English
Dates of publication	2023-02
Size	p. 796-820.
Publishing place	John Wiley & Sons, Ltd
Document type	Article ; Online
Note	JOURNAL ARTICLE
ZDB-ID	2173655-8
ISSN	1742-4658 ; 1742-464X
ISSN (online)	1742-4658
ISSN	1742-464X
DOI	10.1111/febs.16615
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Article ; Online: Identification and characterization of mercaptopyrimidine-based small molecules as inhibitors of nonhomologous DNA end joining.

Ray, Ujjayinee / Gopinatha, Vindya K / Sharma, Shivangi / Goyary, Laijau / Choudhary, Bibha / Mantelingu, Kempegowda / Rangappa, Kanchugarakoppal S / Raghavan, Sathees C

The FEBS journal

2022 Volume 290, Issue 3, Page(s) 796–820

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 ... ...

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 IC
MeSH term(s)	Humans ; DNA End-Joining Repair ; Neoplasms/genetics ; DNA Repair ; DNA Breaks, Double-Stranded ; DNA/metabolism
Chemical Substances	DNA (9007-49-2)
Language	English
Publishing date	2022-09-11
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2173655-8
ISSN	1742-4658 ; 1742-464X
ISSN (online)	1742-4658
ISSN	1742-464X
DOI	10.1111/febs.16615
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Article ; Online: G4 DNA present at human telomeric DNA contributes toward reduced sensitivity to γ-radiation induced oxidative damage, but not bulky adduct formation.

Ray, Ujjayinee / Sharma, Shivangi / Kapoor, Indu / Kumari, Susmita / Gopalakrishnan, Vidya / Vartak, Supriya V / Kumari, Nitu / Varshney, Umesh / Raghavan, Sathees C

International journal of radiation biology

2021 Volume 97, Issue 9, Page(s) 1166–1180

Abstract: Purpose: DNA, the hereditary material of a human cell generally exists as Watson-Crick base paired double-stranded B-DNA. Studies suggest that DNA can also exist in non-B forms, such as four stranded G-quadruplexes (G4 DNA). Recently, our studies ... ...

Abstract	Purpose: DNA, the hereditary material of a human cell generally exists as Watson-Crick base paired double-stranded B-DNA. Studies suggest that DNA can also exist in non-B forms, such as four stranded G-quadruplexes (G4 DNA). Recently, our studies revealed that the regions of DNA that can fold into G-quadruplex structures are less sensitive to ionizing radiation (IR) compared to B-DNA. Importantly, we reported that the planar G-quartet of a G4 structure is shielded from radiation induced DNA breaks, while the single- and double-stranded DNA regions remained susceptible. Thus, in the present study, we investigate whether telomeric repeat DNA present at the end of telomere, known to fold into G4 DNA can protect from radiation induced damages including strand breaks, oxidation of purines and bulky adduct formation on DNA. Materials and methods: For plasmid irradiation assay, plasmids containing human telomeric repeat DNA sequence TTAGGG (0.8 kb or 1.8 kb) were irradiated with increasing doses of IR along with appropriate control plasmids and products were resolved on 1% agarose gel. Radioprotection was evaluated based on extent of conversion of supercoiled to nicked or linear forms of the DNA following irradiation. Formation of G-quadruplex structure on supercoiled DNA was evaluated based on circular dichroism (CD) spectroscopy studies. Cleavage of radiation induced oxidative damage and extent of formation of nicks was further evaluated using base and nucleotide excision repair proteins. Results: Results from CD studies showed that the plasmid DNA harboring human telomeric repeats (TTAGGG) can fold into G-quadruplex DNA structures. Further, results showed that human telomeric repeat sequence when present on a plasmid can protect the plasmid DNA against IR induced DNA strand breaks, unlike control plasmids bearing random DNA sequence. Conclusions: Human telomeric repeat sequence when present on plasmids can fold into G-quadruplex DNA structures, and can protect the DNA against IR induced DNA strand breaks and oxidative damage. These results in conjunction with our previous studies suggest that telomeric repeat sequence imparts less sensitivity to IR and thus telomeres of chromosomes are protected from radiation.
MeSH term(s)	Base Sequence ; DNA Adducts/genetics ; DNA Adducts/radiation effects ; G-Quadruplexes/radiation effects ; Gamma Rays/adverse effects ; Humans ; Oxidative Stress/genetics ; Oxidative Stress/radiation effects ; Telomere/genetics ; Telomere/radiation effects
Chemical Substances	DNA Adducts
Language	English
Publishing date	2021-08-06
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	3065-x
ISSN	1362-3095 ; 0020-7616 ; 0955-3002
ISSN (online)	1362-3095
ISSN	0020-7616 ; 0955-3002
DOI	10.1080/09553002.2021.1955997
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