Synthesis of fluorinated tubastatin A derivatives with bi-, tri-, and tetracyclic cap groups: molecular docking with HDAC6 and evaluation of in vitro antitumor activity

Herein, the creation of 16 modified versions of tubastatin A, each featuring cap groups with two, three, or four rings and containing fluorine atoms, is detailed. A majority of these modified compounds displayed significant anticancer activity in laboratory tests, achieving effectiveness at micromolar or even sub-micromolar concentrations. The most notable compound, identified as 4-(6-bromo-3,3-difluoro-1,2,3,4-tetrahydro-9H-carbozol-9-yl)methyl)-N-hydroxybenzamide (designated as 14f), showed strong inhibition of growth in human nasopharyngeal carcinoma cells (SUNE1) and human breast cancer cells (MDA-MB-231), with concentrations required to inhibit 50% of cell growth being 0.51 μM and 0.52 μM, respectively. Interestingly, another compound, 4-((8-fluoroindeno[2,1-b]indol-5(6H)-yl)-N-hydroxybenzamide (designated as 13c), exhibited substantial anticancer activity against pancreatic cancer cells (SW1990), with a 50% inhibitory concentration of 2.06 μM, while demonstrating low toxicity to normal cells. In general, changes to the cap group, progressing from two to three and then to four rings, along with the incorporation of fluorine atoms, enhanced the anticancer activity of these modified compounds. Among them, tricyclic compounds modified with a difluoromethyl group showed a broad range of anticancer effects in laboratory tests. Computer simulations of molecular docking suggest that these modified compounds bind to Histone Deacetylase 6 with low energy requirements, ranging from -6.54 to -9.84 kcal mol-1, through interactions involving metal complexation, hydrogen bonds, pi-pi stacking, and pi-cation interactions. This binding behavior correlates with their observed good anticancer activity. The compound 4-((2-fluoro-5,6-dihydro-7H-benzo[c]carbazol-7-yl)methyl)-N-hydroxybenzamide (designated as 13a), which exhibited the lowest binding energy of -9.84 kcal mol-1, also demonstrated the best anticancer activity in laboratory tests against MCF-7 cells, with a 50% inhibitory concentration of 1.98 μM.