Structure-based design generated novel hydroxamic acid based preferential HDAC6 lead inhibitor with on-target cytotoxic activity against primary choroid plexus carcinoma

Abstract

Histone deacetylase 6 (HDAC6) is an attractive target for cancer therapeutic intervention. Selective HDAC6 inhibitors is important to minimise the side effects of pan inhibition. Thus, new class of hydroxamic acid-based derivatives were designed on structural basis to perform preferential activity against HDAC6 targeting solid tumours. Interestingly, 1-benzylbenzimidazole-2-thio- N -hydroxybutanamide 10a showed impressive preference with submicromolar potency against HDAC6 (IC 50 = 510 nM). 10a showed cytotoxic activity with interesting profile against CCHE-45 at (IC 50 = 112.76 µM) when compared to standard inhibitor Tubacin (IC 50 = 20 µM). Western blot analysis of acetylated-α-tubulin verified the HDAC6 inhibiting activity of 10a . Moreover, the insignificant difference in acetylated-α-tubulin induced by 10a and Tubacin implied the on-target cytotoxic activity of 10a . Docking of 10a in the binding site of HDAC6 attributed the activity of 10a to π-π stacking with the amino acids of the hydrophobic channel of HDAC6 and capture of zinc metal in bidentate fashion. The therapeutic usefulness besides the on-target activity may define 10a as an interesting safe-lead inhibitor for future development.

Molecular design, synthesis and in vitro biological evaluation of thienopyrimidine–hydroxamic acids as chimeric kinase HDAC inhibitors: a challenging approach to combat cancer

“…In ( Scheme 3 ), the synthesised key intermediates (5a–d) were then coupled with the previously prepared chloro derivative (3) 25 to yield (6a-d). The first novel series of the target hydroxamic acid derivatives (7a-d) was obtained through the reaction of the ethyl ester group in compounds (6a-d) with freshly prepared hydroxylamine in absolute ethanol to give (7a-d) 26 , 27 , ( Scheme 3 ). Compounds (7a-d) were confirmed by many spectral data, in which 1 HNMR signals were consistent with protons of the targeted compounds (7a-d).…”

“…Finally, the route adopted for the synthesis of the three target novel series of hydroxamic acid derivatives bearing aniline moiety (15a-d, 19 b-d and 20 b-d) ( Scheme 4 ) is the same route depicted in ( Scheme 3 ) with the same reagents and conditions. The first novel series of the target hydroxamic acid derivatives (15a-d) was obtained through the reaction of the ethyl ester group in compounds (14a-d) with freshly prepared hydroxylamine in absolute ethanol to give (15a-d) 26 , 27 , ( Scheme 4 ). Then, the hydrolysis of the carboxylate ethyl ester of the previously prepared compounds (14b-d) ( Scheme 4 ), through refluxing it with Li(OH) 2 in THF and water to prepare the intermediate carboxylic acid derivatives (16b-d) 28 .…”

“…Initially, all synthesised compounds were screened against HDAC6 at 10 μM concentration. HDAC6 enzyme inhibition assay was selected since our newly synthesised hydroxamic acid compounds have a large capping group suitable for fitting in the large hydrophobic channel of HDAC6, which is unique to the HDAC6 receptor 26 . The newly designed compounds were synthesized either having short hydrocarbon linkers between the zinc-binding group (ZBG) and the connecting amide unit or having no linear hydrocarbon linker between the hydroxamic acid moiety and the thieno[2,3- d ]pyrimidine fragment, as the previously reported potent HDAC6 inhibitors 19 , 20 .…”

“…The reaction is monitored by TLC till the complete disappearance of starting compounds using an appropriate eluting system [DCM: MeOH (9.5:0.5)]. The solvent was removed under vacuum to afford crude products, washed with water, and crystallised from ethanol to yield target compounds (11a-c, 19 b-d, 12a-c, 20b-d) 26 , 27 .…”

Hybrid inhibitors of DNA and HDACs remarkably enhance cytotoxicity in leukaemia cells

“…Apart from histone modification, HDACs also regulate the deacetylation of non-histone proteins, including transcription factors, chaperones, signalling molecules, and DNA repair proteins [19][20][21] . In recent years, inhibition of HDACs has emerged as a promising therapeutic target for cancers and several other diseases [22][23][24][25][26] . As a result, significant efforts have been made to identify HDAC inhibitors, leading to the approval of SAHA (vorinostat), FK228 (romidepsin), LBH589 (panobinostat), and PXD101 (belinostat) as anticancer drugs ( Figure 2) [27][28][29][30][31][32][33][34][35][36] .…”