Altering mammalian transcription networking with ADAADi: An inhibitor of ATP-dependent chromatin remodeling

Radhakrishnan Rakesh,Pynskhem Bok Swer,Ketki Patne,Rohini Muthuswami,Deepa Bisht,Kaveri Goel,Upasana Bedi Chanana,Saddam Hussain,Soni Sharma,Joel W Hockensmith,Srinivas Saladi

doi:10.1371/journal.pone.0251354

Radhakrishnan Rakesh, Pynskhem Bok Swer + Show 9 more

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https://doi.org/10.1371/journal.pone.0251354

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Journal: PloS one	Publication Date: May 17, 2021
Citations: 5	License type: CC BY 4.0

Affiliation: University of Virginia

Abstract

Active DNA-dependent ATPase A Domain inhibitor (ADAADi) is the only known inhibitor of ATP-dependent chromatin remodeling proteins that targets the ATPase domain of these proteins. The molecule is synthesized by aminoglycoside phosphotransferase enzyme in the presence of aminoglycosides. ADAADi interacts with ATP-dependent chromatin remodeling proteins through motif Ia present in the conserved helicase domain, and thus, can potentially inhibit all members of this family of proteins. We show that mammalian cells are sensitive to ADAADi but with variable responses in different cell lines. ADAADi can be generated from a wide variety of aminoglycosides; however, cells showed differential response to ADAADi generated from various aminoglycosides. Using HeLa and DU145 cells as model system we have explored the effect of ADAADi on cellular functions. We show that the transcriptional network of a cell type is altered when treated with sub-lethal concentration of ADAADi. Although ADAADi has no known effects on DNA chemical and structural integrity, expression of DNA-damage response genes was altered. The transcripts encoding for the pro-apoptotic proteins were found to be upregulated while the anti-apoptotic genes were found to be downregulated. This was accompanied by increased apoptosis leading us to hypothesize that the ADAADi treatment promotes apoptotic-type of cell death by upregulating the transcription of pro-apoptotic genes. ADAADi also inhibited migration of cells as well as their colony forming ability leading us to conclude that the compound has effective anti-tumor properties.

Highlights

We quickly realized that quantitation of the effect of Active DNA-dependent ATPase A Domain inhibitor (ADAADi) on mammalian cells required an investigation of the timeframe required for its action on cellular processes
Mammalian cell lines were treated with neomycin derived ADAADi (ADAADiN) for 24 hr and 48 hr and the viability of the cells was measured at the two points
Mammalian cancer cell lines were treated with ADAADi generated from neomycin (ADAADiN) or kanamycin (ADAADiK) for 48 hr and we found that cell lines displayed differential sensitivity to the inhibitor, for example, in case of DU145 cells (S1B Fig; Table 1)

Summary

Introduction

Some examples include: PFI-3 targeting the bromodomain of BRG1; orally active small molecule allosteric inhibitors that target the ATPase domain reported by Novartis; and small molecule inhibitors identified by highthroughput screening that target the bromodomain [9,10,11] In addition to these inhibitors, we had earlier reported that the enzyme aminoglycoside (neomycin) phosphotransferase catalyzes the formation of a small molecule called Active DNA-dependent ATPase A domain inhibitor (ADAADi) that effectively inhibits the ATPase activity of the ATP-dependent chromatin remodeling proteins [12]. ADAADi is a small molecule inhibitor generated from aminolygcosides that inhibits the ATPase activity, and the nucleosome remodeling activity of ATP-dependent chromatin remodeling proteins. We demonstrate that ADAADi inhibits cell migration as well as anchorage-independent growth

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