Takahashi DT, Gadelle D, Agama K, Kiselev E, Zhang H, Yab E. et al. Topoisomerase I (TOP1) dynamics: conformational transition from open to closed states. Nat Commun. 2022;13:59 https://doi.org/10.1038/s41467-021-27686-7.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Pommier Y, Pourquier P, Fan Y, Strumberg D. Mechanism of action of eukaryotic DNA topoisomerase I and drugs targeted to the enzyme. Biochim Biophys Acta. 1998;1400:83–106. 10.1016/S0167-4781(98)00129-8.

Article  CAS  PubMed  Google Scholar 

Xu Y, Her C. Inhibition of topoisomerase (DNA) I (TOP1): DNA damage repair and anticancer therapy. Biomolecules. 2015;5:1652–70. https://doi.org/10.3390/biom5031652

Article  CAS  PubMed  PubMed Central  Google Scholar 

Comeaux EQ, van Waardenburg RCAM. Tyrosyl-DNA phosphodiesterase I resolves both naturally and chemically induced DNA adducts and its potential as a therapeutic target. Drug Metab Rev 2014;46:494–507. https://doi.org/10.3109/03602532.2014.971957

Article  CAS  PubMed  Google Scholar 

Leung E, Patel J, Hollywood JA, Zafar A, Tomek P, Barker D, et al. Validating TDP1 as an inhibition target for the development of chemosensitizers for camptothecin-based chemotherapy drugs. Oncol Ther 2021;9:541–56. https://doi.org/10.1007/s40487-021-00158-0

Article  PubMed  PubMed Central  Google Scholar 

Barthelmes HU, Habermeyer M, Christensen MO, Mielke C, Interthal H, Pouliot JJ, et al. TDP1 overexpression in human cells counteracts DNA damage mediated by topoisomerases I and II. J Biol Chem 2004;279:55618–25. https://doi.org/10.1074/jbc.M405042200

Article  CAS  PubMed  Google Scholar 

Meisenberg C. TDP1/TOP1 ratio as a promising indicator for the response of small cell lung cancer to topotecan. J Cancer Sci Ther 2014;06:258–67. https://doi.org/10.4172/1948-5956.1000280

Article  CAS  Google Scholar 

Katyal S, El-Khamisy SF, Russell HR, Li Y, Ju L, Caldecott KW, et al. TDP1 facilitates chromosomal single-strand break repair in neurons and is neuroprotective in vivo. EMBO J. 2007;26:4720–31. https://doi.org/10.1038/sj.emboj.7601869

Article  CAS  PubMed  PubMed Central  Google Scholar 

Das BB, Antony S, Gupta S, Dexheimer TS, Redon CE, Garfield S, et al. Optimal function of the DNA repair enzyme TDP1 requires its phosphorylation by ATM and/or DNA-PK. EMBO J. 2009;28:3667–80. https://doi.org/10.1038/emboj.2009.302

Article  CAS  PubMed  PubMed Central  Google Scholar 

Ivankin DI, Kornienko TE, Mikhailova MA, Dyrkheeva NS, Zakharenko AL, Achara C, et al. Novel TDP1 inhibitors: disubstituted thiazolidine-2,4-diones containing monoterpene moieties. Int J Mol Sci 2023;24:3834. https://doi.org/10.3390/ijms24043834

Article  CAS  PubMed  PubMed Central  Google Scholar 

Chepanova AA, Zakharenko AL, Dyrkheeva NS, Chernyshova IA, Zakharova OD, Ilina ES, et al. Influence of tyrosyl-DNA phosphodiesterase 1 inhibitor on the proapoptotic and genotoxic effects of anticancer agent topotecan. Dokl Biochem Biophys 2023;508:25–30. https://doi.org/10.1134/S1607672922700077

Article  CAS  PubMed  PubMed Central  Google Scholar 

Salomatina OV, Popadyuk II, Zakharenko AL, Zakharova OD, Chepanova AA, Dyrkheeva NS, et al. Deoxycholic acid as a molecular scaffold for tyrosyl-DNA phosphodiesterase 1 inhibition: a synthesis, structure–activity relationship and molecular modeling study. Steroids. 2021;165:108771. https://doi.org/10.1016/j.steroids.2020.108771

Article  CAS  PubMed  Google Scholar 

Conda-Sheridan M, Reddy PVN, Morrell A, Cobb BT, Marchand C, Agama K, et al. Synthesis and biological evaluation of indenoisoquinolines that inhibit both tyrosyl-DNA phosphodiesterase I (Tdp1) and topoisomerase I (Top1). J Med Chem 2013;56:182–200. https://doi.org/10.1021/jm3014458

Article  CAS  PubMed  Google Scholar 

Yang H, Qin C, Wu M, Wang F, Wang W, Agama K, et al. Synthesis and biological activities of 11‐ and 12‐substituted benzophenanthridinone derivatives as DNA topoisomerase IB and tyrosyl‐DNA phosphodiesterase 1 inhibitors. ChemMedChem. 2023;18:1–16. https://doi.org/10.1002/cmdc.202200593

Article  CAS  Google Scholar 

Zhao XZ, Wang W, Lountos GT, Kiselev E, Tropea JE, Needle D, et al. Identification of multidentate tyrosyl-DNA phosphodiesterase 1 (TDP1) inhibitors that simultaneously access the DNA, protein and catalytic-binding sites by oxime diversification. RSC Chem Biol 2023;4:334–43. https://doi.org/10.1039/D2CB00230B

Article  CAS  PubMed  PubMed Central  Google Scholar 

Huang SN, Pommier Y, Marchand C. Tyrosyl-DNA phosphodiesterase 1 (Tdp1) inhibitors. Expert Opin Ther Pat 2011;21:1285–92. https://doi.org/10.1517/13543776.2011.604314

Article  CAS  PubMed  PubMed Central  Google Scholar 

Zakharenko AL, Luzina OA, Chepanova AA, Dyrkheeva NS, Salakhutdinov NF, Lavrik OI. Natural products and their derivatives as inhibitors of the DNA repair enzyme tyrosyl-DNA phosphodiesterase 1. Int J Mol Sci 2023;24:5781. https://doi.org/10.3390/ijms24065781

Article  CAS  PubMed  PubMed Central  Google Scholar 

Chepanova AA, Mozhaitsev ES, Munkuev AA, Suslov EV, Korchagina DV, Zakharova OD, et al. The development of tyrosyl-DNA phosphodiesterase 1 inhibitors. combination of monoterpene and adamantine moieties via amide or thioamide bridges. Appl Sci 2019;9:2767. https://doi.org/10.3390/app9132767

Article  CAS  Google Scholar 

Mozhaitsev ES, Zakharenko AL, Suslov EV, Korchagina DV, Zakharova OD, Vasil’eva IA, et al. Novel inhibitors of DNA repair enzyme TDP1 combining monoterpenoid and adamantane fragments. Anticancer Agents Med Chem 2019;19:463–72. https://doi.org/10.2174/1871520619666181207094243

Article  CAS  PubMed  Google Scholar 

Munkuev AA, Mozhaitsev ES, Chepanova AA, Suslov EV, Korchagina DV, Zakharova OD, et al. Novel Tdp1 inhibitors based on adamantane connected with monoterpene moieties via heterocyclic fragments. Molecules. 2021;26:3128. https://doi.org/10.3390/molecules26113128

Article  CAS  PubMed  PubMed Central  Google Scholar 

Munkuev AA, Dyrkheeva NS, Kornienko TE, Ilina ES, Ivankin DI, Suslov EV, et al. Adamantane-monoterpenoid conjugates linked via heterocyclic linkers enhance the cytotoxic effect of topotecan. Molecules. 2022;27:3374. https://doi.org/10.3390/molecules27113374

Article  CAS  PubMed  PubMed Central  Google Scholar 

Ramprasad J, Nayak N, Dalimba U. Design of new phenothiazine-thiadiazole hybrids via molecular hybridization approach for the development of potent antitubercular agents. Eur J Med Chem 2015;106:75–84. https://doi.org/10.1016/j.ejmech.2015.10.035

Article  CAS  PubMed  Google Scholar 

Cressier D, Prouillac C, Hernandez P, Amourette C, Diserbo M, Lion C, et al. Synthesis, antioxidant properties and radioprotective effects of new benzothiazoles and thiadiazoles. Bioorg Med Chem 2009;17:5275–84. https://doi.org/10.1016/j.bmc.2009.05.039

Article  CAS  PubMed  Google Scholar 

Zakharenko A, Khomenko T, Zhukova S, Koval O, Zakharova O, Anarbaev R, et al. Synthesis and biological evaluation of novel tyrosyl-DNA phosphodiesterase 1 inhibitors with a benzopentathiepine moiety. Bioorg Med Chem 2015;23:2044–52. https://doi.org/10.1016/j.bmc.2015.03.020

Article  CAS  PubMed  Google Scholar 

Zhao XZ, Kiselev E, Lountos GT, Wang W, Tropea JE, Needle D, et al. Small molecule microarray identifies inhibitors of tyrosyl-DNA phosphodiesterase 1 that simultaneously access the catalytic pocket and two substrate binding sites. Chem Sci 2021;12:3876–84. https://doi.org/10.1039/D0SC05411A

Article  CAS  PubMed  PubMed Central  Google Scholar 

Dyrkheeva NS, Filimonov AS, Luzina OA, Zakharenko AL, Ilina ES, Malakhova AA, et al. New hybrid compounds combining fragments of usnic acid and monoterpenoids for effective tyrosyl-DNA phosphodiesterase 1 inhibition. Biomolecules. 2021;11:973. https://doi.org/10.3390/biom11070973

Article  CAS  PubMed  PubMed Central  Google Scholar 

Jones G, Willett P, Glen RC, Leach AR, Taylor R. Development and validation of a genetic algorithm for flexible docking 1. J Mol Biol 1997;267:727–48. https://doi.org/10.1006/jmbi.1996.0897

Article  CAS  PubMed  Google Scholar 

Eldridge MD, Murray CW, Auton TR, Paolini GV, Mee RP. Empirical scoring functions: I. The development of a fast empirical scoring function to estimate the binding affinity of ligands in receptor complexes. J Comput Aided Mol Des 1997;11:425–45. https://doi.org/10.1023/a:1007996124545

Article  CAS  PubMed  Google Scholar 

Verdonk ML, Cole JC, Hartshorn MJ, Murray CW, Taylor RD. Improved protein-ligand docking using GOLD. Proteins 2003;52:609–23. https://doi.org/10.1002/prot.10465

Article  CAS  PubMed  Google Scholar 

Korb O, Stützle T, Exner TE. Empirical scoring functions for advanced protein−ligand docking with PLANTS. J Chem Inf Model 2009;49:84–96. https://doi.org/10.1021/ci800298z

Article  CAS  PubMed  Google Scholar 

Mooij WTM, Verdonk ML. General and targeted statistical potentials for protein-ligand interactions. Proteins 2005;61:272–87. https://doi.org/10.1002/prot.20588

Article  CAS