Effects of the Protonation State of Titratable Residues and the Presence of Water Molecules on Nocodazole Binding to β‐Tubulin. (23rd November 2017) - Guzmán‐Ocampo, Dulce C.
Abstract: Regulation of microtubule assembly by antimitotic agents is a potential therapeutic strategy for the treatment of cancer, parasite infections, and neurodegenerative diseases. One of these agents is nocodazole (NZ), which inhibits microtubule polymerization by binding to β‐tubulin. NZ was recently co‐crystallized in Gallus gallus tubulin, providing new information about the features of interaction for ligand recognition and stability. In this work, we used state‐of‐the‐art computational approaches to evaluate the protonation effects of titratable residues and the presence of water molecules in the binding of NZ. Analysis of protonation states showed that residue E198 has the largest modification in its p K a value. The resulting E198 p K a value, calculated with pH‐REMD methodology (p K a =6.21), was higher than the isolated E amino acid (p K a =4.25), thus being more likely to be found in its protonated state at the binding site. Moreover, we identified an interaction between a water molecule and C239 and G235 as essential for NZ binding. Our results suggest that the protonation state of E198 and the structural water molecules play key roles in the binding of NZ to β‐tubulin. Abstract : NZ–β‐tubulin complex : Nocodazole (NZ) inhibits microtubule polymerization by binding to the β‐tubulin subunit. In this study we evaluated the effect of the protonated states of titratable residues and structural water molecules in the binding mode of NZ, using different computational approaches. Our results suggest that the protonated state of E198 and the water molecule located between G235 and C239 are key structural features for the binding of NZ to β‐tubulin.