New Hybrid Compounds Combining Fragments of Usnic Acid and Monoterpenoids for Effective Tyrosyl-DNA Phosphodiesterase 1 Inhibition

Abstract

Usnic acid (UA) is a secondary metabolite of lichens that exhibits a wide range of biological activities. Previously, we found that UA derivatives are effective inhibitors of tyrosyl-DNA phosphodiesterase 1 (TDP1). It can remove covalent complex DNA-topoisomerase 1 (TOP1) stabilized by the TOP1 inhibitor topotecan, neutralizing the effect of the drugs. TDP1 removes damage at the 3′ end of DNA caused by other anticancer agents. Thus, TDP1 is a promising therapeutic target for the development of drug combinations with topotecan, as well as other drugs for cancer treatment. Ten new UA enamino derivatives with variation in the terpene fragment and substituent of the UA backbone were synthesized and tested as TDP1 inhibitors. Four compounds, 11a-d, had IC50 values in the 0.23–0.40 μM range. Molecular modelling showed that 11a-d, with relatively short aliphatic chains, fit to the important binding domains. The intrinsic cytotoxicity of 11a-d was tested on two human cell lines. The compounds had low cytotoxicity with CC50 ≥ 60 μM for both cell lines. 11a and 11c had high inhibition efficacy and low cytotoxicity, and they enhanced topotecan’s cytotoxicity in cancerous HeLa cells but reduced it in the non-cancerous HEK293A cells. This “protective” effect from topotecan on non-cancerous cells requires further investigation.

New Deoxycholic Acid Derived Tyrosyl-DNA Phosphodiesterase 1 Inhibitors Also Inhibit Tyrosyl-DNA Phosphodiesterase 2

“…DCA derivatives 1-18 were docked into the binding site of the TDP1 (PDB ID: 6W7K, resolution 1.70 Å) [35] and TDP2 (PDB ID: 5J3S, resolution 3.40 Å) [36] enzymes. The robustness of the TDP1 docking scaffold has been previously established [19]; the robustness of the TDP2 docking scaffold was confirmed and further discussion (see Supplementary Materials, Molecular modeling section).…”

“…Molecular dynamics simulations have suggested that the TDP1 inhibitors occupy an allosteric binding pocket next to the catalytic site, as shown in Figure 4 A [ 18 ]. The existence of the allosteric site was further supported by combined molecular modeling and structural activity relationship study of usnic acid derivatives, combined with monoterpenoids [ 19 ]. The occupancy of the allosteric site was shown to be very advantageous to the overall binding efficacy.…”

“…Several studies have reported the development of TDP1 inhibitors of organic chemical matter [ 6 , 7 , 8 , 9 ] as well as natural product derivatives: steroids ( A – C ) ( Figure 1 ) [ 10 , 11 , 12 ], coumarins [ 13 , 14 ], usnic acids [ 15 , 16 , 17 , 18 , 19 ], and aminoadamantanes containing monoterpene-derived fragments [ 20 , 21 , 22 , 23 ]. Known TDP2 inhibitors are represented by isoquinoline-1,3-diones ( J ) [ 24 ], deazaflavins ( E ), and toxoflavins ( F ) [ 25 ].…”

New Hybrid Compounds Combining Fragments of Usnic Acid and Thioether Are Inhibitors of Human Enzymes TDP1, TDP2 and PARP1

“…We showed that Tdp1 knockout cells were more sensitive to Tpc compared to WT cells. The data on the HEK293FT mutants were of low reproducibility [48], which is why we decided to change the basic cell line to HEK293A [49]. In this work, we created new PARP1-/-HEK293A cells using the CRISPR-Cas9 approach (Figure S27).…”

“…In our previous works, we checked the cytotoxic effect of Tpc and the TDP1 inhibitors -monoterpene 3-carene-derived compounds [48,49] and UA combined with monoterpenoids [49], measured separately and jointly with Tpc-using a panel of HEK293FT and HEK293A Tdp1 knockout isogenic clones. We showed that Tdp1 knockout cells were more sensitive to Tpc compared to WT cells.…”