Structure‐based approaches for the design of benzimidazole‐2‐carbamate derivatives as tubulin polymerization inhibitors

Abstract

Microtubules are highly dynamic assemblies of α/β-tubulin heterodimers whose polymerization inhibition is among one of the most successful approaches for anticancer drug development. Overexpression of the class I (βI) and class III (βIII) β-tubulin isotypes in breast and lung cancers and the highly expressed class VI (βVI) β-tubulin isotype in normal blood cells have increased the interest for designing specific tubulin-binding anticancer therapies. To this end, we employed our previously proposed model of the β-tubulin-nocodazole complex, supported by the recently determined X-ray structure, to identify the fundamental structural differences between β-tubulin isotypes. Moreover, we employed docking and molecular dynamics (MD) simulations to determine the binding mode of a series of benzimidazole-2-carbamete (BzC) derivatives in the βI-, βIII-, and βVI-tubulin isotypes. Our results demonstrate that Ala198 in the βVI isotype reduces the affinity of BzCs, explaining the low bone marrow toxicity for nocodazole. Additionally, no significant differences in the binding modes between βI- and βIII-BzC complexes were observed; however, Ser239 in the βIII isotype might be associated with the low affinity of BzCs to this isotype. Finally, our study provides insight into the β-tubulin-BzC interaction features essential for the development of more selective and less toxic anticancer therapeutics.

Design, Synthesis and Evaluation of 2,4‐Diaminoquinazoline Derivatives as Potential Tubulin Polymerization Inhibitors

“…The quinazoline derivative formed three key H‐bonds in the NZ site with E198 side chain and V236 main chain. Interestingly, the interaction profile of 4 i in the NZ site is consistent with the previously proposed pharmacophore hypotesis . On the other hand, the acetamide group places the quinoline substituent at the COL site, where the chlorine group could form a H‐bond with the N256 side chain.…”

“…According to our previous pharmacophore hypothesis and the recent crystallographic data, the following pharmacophoric features should be addressed by a molecule to bind in the NZ site: an aromatic scaffold, an H‐bond acceptor, two nearby H‐bond donors, and a distal aromatic substituent (Figure B) . The protonated state of E198 residue favors the H‐bond interaction with the scaffold fused nitrogen, while the H‐bond donor groups interact with either E198 or Y200 side chains and with the main chain carbonyl of V236 .…”

“…Interestingly, the NZ site varies in sequence between tubulin isoforms, allowing the design of more selective molecules. A previous study performed by our research group showed that compounds that bind to NZ site have a low probability of being hematotoxic due to the inability to interact with the highly expressed βVI tubulin isoform in blood cells . The latter increased our interest in designing molecules that bind to the NZ binding site.…”

Effects of the Protonation State of Titratable Residues and the Presence of Water Molecules on Nocodazole Binding to β‐Tubulin

“…In previous computational studies, our group assessed the importance of key NZ binding site residues in the interaction and affinity of benzimidazole derivatives to different parasite and mammalian β‐tubulins . Those studies, along with experimental information, indicated that NZ and other derivatives interaction with E198 is responsible for its binding, and that substitutions or mutations at positions 165, 167, 200 or 239 exhibit minor alterations to the NZ affinity to the β subunit . Moreover, we suggested that the NZ‐1,6 tautomer might modify its interaction with E198 to interact with the main‐chain carbonyl group of V236.…”

Investigation of benzimidazole anthelmintics as oral anticancer agents

“…6 Studies have suggested that benzimidazole anthelmintic drugs inhibit microtubule dynamics by promoting microtubule depolymerization. [7][8][9][10] Because microtubules play a crucial role in mitosis, cell division, cell structure maintenance, and many other cellular events, reagents that disrupt microtubule dynamics can potentially serve as anticancer agents. [11][12][13][14][15] Although there are numerous publications regarding the anticancer activity and mechanism of action of benzimidazole anthelmintic drugs, there is no conclusive report on the anticancer profile.…”