Synthesis and evaluation of aryliden- and hetarylidenfuranone derivatives of usnic acid as highly potent Tdp1 inhibitors

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Abstract

Tyrosyl-DNA phosphodiesterase 1 (Tdp1) is a repair enzyme for stalled DNA-topoisomerase 1 (Top 1) cleavage complexes and other 3′-end DNA lesions. Tdp1 is a promising target for anticancer therapy, since it can repair DNA lesions caused by Top1 inhibitors leading to drug resistance. Hence, Tdp1 inhibition should result in synergistic effect with Top1 inhibitors. Twenty nine derivatives of (+)-usnic acid were tested for in vitro Tdp1 inhibitory activity using a fluorescent-based assay. Excellent activity was obtained, with derivative 6m demonstrating the lowest IC50 value of 25 nM. The established efficacy was verified using a gel-based assay, which gave close results to that of the fluorescent assay. In addition, molecular modeling in the Tdp1 substrate binding pocket suggested plausible binding modes for the active analogues. The synergistic effect of the Tdp1 inhibitors with topotecan, a Top1 poison in clinical use, was tested in two human cell lines, A-549 and HEK-293. Compounds 6k and 6x gave very promising results. In particular, 6x has a low cytotoxicity and an IC50 value of 63 nM, making it a valuable lead compound for the development of potent Tdp1 inhibitors for clinical use.

Introduction

Developing inhibitors of DNA repair enzymes is a promising approach to improve anticancer therapy, particularly for drug-resistant tumors. Radiation and chemotherapy of cancer usually induce DNA lesions; however, tumors can be resistant, or develop resistance, during treatment. Tyrosyl-DNA phosphodiesterase (Tdp1) plays a crucial role in repair of DNA lesions formed by antitumor drugs such as the Top1 inhibitors camptothecin, topotecan and irinotecan, making Tdp1 a promising target for adjunctive cancer treatment.[1], [2], [3] A relatively small number of Tdp1 inhibitors[4], [5], [6], [7], [8], [9], [10], [11], [12], [13] have been reported in literature; most of them exhibit moderate inhibiting activity, which makes discovering novel Tdp1 inhibitors a worthwhile undertaking. Natural products are an important source of compounds for the development of novel medicines, due to the high chemical diversity often lacking in libraries of synthetic molecules.[14], [15] Indeed, a number of effective Tdp1 inhibitors were identified from natural products.[16], [17], [18], [19] It has been previously demonstrated that inhibition of Tdp1 using terpene-coumarin based ligands (see analogue 1, Fig. 1), has a synergistic effect with camptothecin on the viability of the MCF-7 breast cancer cell line.[18], [20]

Usnic acid is a secondary metabolite commonly found in various types of lichens, which has a broad range of biological activities: antiviral, antibiotic, analgesic, antimycotic and insecticide.[21], [22] Research conducted over the past few decades has demonstrated that targeted synthesis of usnic acid derivatives yields various polycyclic compounds that exhibit potent biological activity for a number of important diseases, such as malaria, influenza and tuberculosis.[23], [24], [25]

It has been previously found that usnic acid derivatives, modified at ring C (general structure formula 3, Fig. 1), are effective Tdp1 inhibitors with significant synergistic effect on the viability of the MCF-7 breast cancer cell line.20 However, the presence of the native moieties on ring C is known to be important for the penetration of usnic acid derivatives through biological membranes.26 This study aimed to synthesize and test the Tdp1 inhibitory activity of usnic acid derivatives containing aryl- or hetarylidenfuranone moieties at ring A, keeping the triketone system in ring C of natural dibenzofurane intact.

Section snippets

Chemistry

We have previously proposed the three-step synthesis scheme of benzylidenefuranone derivatives from (+)-usnic acid that included the stage of electrophilic bromination with bromine in dioxane giving bromoderivative 4; subsequent intramolecular cyclization of compound 4 into furanone 5 in the presence of potassium hydroxide; and alkali-catalyzed condensation of 5 with appropriate aldehydes, resulting in compounds 6a-d, 6h-k (Scheme 1).27

Compounds 6a-k, m-z (Table 1) as well as compound 6zz with

Conclusion

Twenty nine usnic acid derivatives 6a-zz, 7m and 7x were synthesized, and evaluated for their in vitro Tdp1 inhibitory activity using a fluorescent based assay, which was verified with a gel-based assay for analogue 6g. It was found that the absolute configuration of the asymmetric center in usnic acid derivatives does not influence inhibitory activity of the compounds.

Compounds 6a-z, 7m and 7x exhibited very high to moderate inhibitory activity (IC50 = 0.025 − 6.7 μM), compared to the

Chemistry

The analytical and spectral studies were conducted in the Chemical Service Center for the collective use of SB RAS.

The 1H and 13C NMR spectra for solutions of the compounds in CDCl3 were recorded on a Bruker AV-400 spectrometer (400.13 and 100.61 MHz, respectively). The residual signals of the solvent were used as references (δH 2.48,δC 39.52). The mass spectra (70 eV) were recorded on a DFS Thermo Scientific high-resolution mass spectrometer. The melting points were measured using a Kofler

Acknowledgments

This work was supported by Russian Science Foundation (grant 16-13-10074), excluding the synthesis of the tyrosine-containing solid support and oligonucleotide, which was funded by Russian Science Foundation (grant 15-15-00121 to D. Stetsenko), and grant of Russian Foundation for Basic Research 16-03-00374 to O. Luzina for synthesis of compound 6zz.

References (50)

  • D.R. Davies et al.

    The Crystal Structure of Human Tyrosyl-DNA Phosphodiesterase, Tdp1

    Structure

    (2002)
  • H.M. Berman et al.

    The Protein Data Bank

    Nucl Acids Res

    (2000)
  • E.Q. Comeaux et al.

    Tyrosyl-DNA phosphodiesterase I resolves both naturally and chemically induced DNA adducts and its potential as a therapeutic target

    Drug Metab Rev

    (2014)
  • T.S. Dexheimer et al.

    Tyrosyl-DNA phosphodiesterase as a target for anticancer therapy

    Anticancer Agents Med Chem

    (2008)
  • F. Cortes Ledesma et al.

    A novel human 5’-tyrosyl DNA phosphodiesterase that repairs topoisomerase-mediated DNA damage

    Nature

    (2009)
  • S. Antony et al.

    Novel high-throughput electrochemiluminescent assay for identification of human tyrosyl-DNA phosphodiesterase (Tdp1) inhibitors and characterization of furamidine (NSC 305831) as an inhibitor of Tdp1

    Nucleic Acids Res

    (2007)
  • M. Conda-Sheridan et al.

    Synthesis and biological evaluation of Indenoisoquinolines that Inhibit Both tyrosyl-DNA phosphodiesterase I (Tdp1) and topoisomerase I (Top1)

    J Med Chem

    (2013)
  • V.R. Sirivolu et al.

    5-Arylidenethioxothiazolidinones as Inhibitors of Tyrosyl–DNA Phosphodiesterase I

    J Med Chem

    (2012)
  • P. Wang et al.

    Synthesis and biological evaluation of the first triple inhibitors of human topoisomerase 1, tyrosyl−DNA phosphodiesterase 1 (Tdp1), and tyrosyl−DNA phosphodiesterase 2 (Tdp2)

    J Med Chem

    (2017)
  • T.X. Nguyen et al.

    Synthesis and biological evaluation of nitrated 7-, 8-, 9-, and 10-hydroxyindenoisoquinolines as potential dual topoisomerase I (Top1) − tyrosyl-DNA phosphodiesterase I (TDP1) inhibitors

    J Med Chem

    (2015)
  • H.J. Arabshahi et al.

    A synthesis, in silico, in vitro and in vivo study of thieno[2,3-b]pyridine anticancer analogues

    Med Chem Commun

    (2015)
  • D.J. Newman et al.

    Natural products as sources of new drugs from 1981 to 2014

    J Nat Prod

    (2016)
  • N.F. Salakhutdinov et al.

    Monoterpenes as a renewable source of biologically active compounds

    Pure Appl Chem

    (2017)
  • T.S. Dexheimer et al.

    4-Pregnen-21-ol-3,20-dione-21-(4-bromobenzenesulfonate) (NSC 88915) and related novel steroid derivatives as tyrosyl-DNA phosphodiesterase (Tdp1) inhibitors

    J Med Chem

    (2009)
  • A.L. Zakharenko et al.

    Rus J Bioorg Chem

    (2015)
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