A Dual-Sensor-Based Screening System for In Vitro Selection of TDP1 Inhibitors.

Ann-Katrine Jakobsen,Francisco Palacios,Magnus Stougaard,Endika Martin-Encinas,Birgitta Ruth Knudsen,Concepcion Alonso,Josephine Geertsen Keller,María Gonzalez

doi:10.3390/s21144832

Abstract

DNA sensors can be used as robust tools for high-throughput drug screening of small molecules with the potential to inhibit specific enzymes. As enzymes work in complex biological pathways, it is important to screen for both desired and undesired inhibitory effects. We here report a screening system utilizing specific sensors for tyrosyl-DNA phosphodiesterase 1 (TDP1) and topoisomerase 1 (TOP1) activity to screen in vitro for drugs inhibiting TDP1 without affecting TOP1. As the main function of TDP1 is repair of TOP1 cleavage-induced DNA damage, inhibition of TOP1 cleavage could thus reduce the biological effect of the TDP1 drugs. We identified three new drug candidates of the 1,5-naphthyridine and 1,2,3,4-tetrahydroquinolinylphosphine sulfide families. All three TDP1 inhibitors had no effect on TOP1 activity and acted synergistically with the TOP1 poison SN-38 to increase the amount of TOP1 cleavage-induced DNA damage. Further, they promoted cell death even with low dose SN-38, thereby establishing two new classes of TDP1 inhibitors with clinical potential. Thus, we here report a dual-sensor screening approach for in vitro selection of TDP1 drugs and three new TDP1 drug candidates that act synergistically with TOP1 poisons.

Highlights

Accepted: 13 July 2021Modern small-molecule-based anticancer treatments, especially within precision medicine, are based on targeting specific cellular mechanisms or enzymatic reactions driving the cancer
In an unpublished study, screened 40 small molecular compounds for inhibitory effect on tyrosyl-DNA phosphodiesterase 1 (TDP1) activity to select the best compounds for this study
Based on the structural comparison of the most potent TDP1 inhibitors among the 40 compounds, seven small molecular compounds were selected from a library of compounds developed at Department of Organic Chemistry I, University of Basque Country (UPV/EHU), and resynthesized for investigation in this study

Summary

Introduction

Modern small-molecule-based anticancer treatments, especially within precision medicine, are based on targeting specific cellular mechanisms or enzymatic reactions driving the cancer. With the increased knowledge of the biological mechanisms driving different cancer types, specific anticancer targets are identified, and with the large amount of already synthesized small molecular compounds, the modern approach often is to perform a wide screen of small molecule panels for inhibitory effect of the relevant targets. DNA sensors capable of determining the effect of small molecular compounds in screening-based setups are becoming increasingly important for discovery, characterization, and validation of new anticancer drugs [1,2,3]. TDP1 is involved in many different DNA repair processes due to its ability to remove 30 -adducts by catalyzing the hydrolysis of 30 -phosphodiester bonds [21,22,23]. Several studies have indicated that TDP1 is involved in resolving double-stranded breaks by participation in the non-homologous

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Conclusion