Identification and characterization of novel ligase I inhibitors.
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.
Department of Biochemistry, Indian Institute of Science, Bangalore, India.
Monica
M
Pandey
Department of Pharmaceutical Chemistry, KLE University's College of Pharmacy, Bangalore, India.
Sujeet
S
Kumar
Institute of Bioinformatics and Applied Biotechnology, Electronics City, Bangalore, India.
Gunaseelan
G
Goldsmith
Department of Biochemistry, Indian Institute of Science, Bangalore, India.
Mrinal
M
Srivastava
Department of Biochemistry, Indian Institute of Science, Bangalore, India.
Santhini
S
Elango
Central Drug Research Institute, Lucknow, Uttar Pardesh, India.
Mohammad
M
Shameem
Central Drug Research Institute, Lucknow, Uttar Pardesh, India.
Dibyendu
D
Bannerjee
Institute of Bioinformatics and Applied Biotechnology, Electronics City, Bangalore, India.
Bibha
B
Choudhary
Department of Pharmaceutical Chemistry, KLE University's College of Pharmacy, Bangalore, India.
Subhas S
SS
Karki
Department of Biochemistry, Indian Institute of Science, Bangalore, India.
Sathees C
SC
Raghavan
D000818:Animals; D002453:Cell Cycle / Q000187:drug effects; D045744:Cell Line, Tumor; D049109:Cell Proliferation / Q000187:drug effects; D000072481:DNA Ligase ATP / Q000037:antagonists & inhibitors* / Q000737:chemistry / Q000378:metabolism; D004261:DNA Replication / Q000187:drug effects; D015195:Drug Design; D004791:Enzyme Inhibitors / Q000737:chemistry* / Q000494:pharmacology*; D057809:HEK293 Cells; D006801:Humans; D008297:Male; D062105:Molecular Docking Simulation; D051381:Rats; D017208:Rats, Wistar; D054852:Small Molecule Libraries / Q000737:chemistry* / Q000494:pharmacology*
D004791:Enzyme Inhibitors; D054852:Small Molecule Libraries; D000072481:DNA Ligase ATP
DNA double-strand break; DNA repair; NHEJ; ligase inhibitor; ligation