Structural and Thermodynamic Basis of the Enhanced Interaction between Kinesin Spindle Protein Eg5 and STLC-type Inhibitors

Abstract

For a better understanding of protein–inhibitor interactions, we report structural, thermodynamic, and biological analyses of the interactions between S -trityl- l -cysteine (STLC) derivatives and the motor domain of kinesin spindle protein Eg5. Binding of STLC-type inhibitors to Eg5 was enthalpically driven and entropically unfavorable. The introduction of a para -methoxy substituent in one phenyl ring of STLC enhances its inhibitory activity resulting from a larger enthalpy gain possibly due to the increased shape complementarity. The substituent fits to a recess in the binding pocket. To avoid steric hindrance, the substituted STLC is nudged toward the side opposite to the recess, which enhances the interaction of Eg5 with the remaining part of the inhibitor. Further introduction of an ethylene linkage between two phenyl rings enhances Eg5 inhibitory activity by reducing the loss of entropy in forming the complex. This study provides valuable examples of enhancing protein–inhibitor interactions without forming additional hydrogen bonds.

Structure and comparison of the motor domain of centromere-associated protein E

“…To date, a large number of Eg5 inhibitors, such as STLC and PVZB1194, have been reported (Ogo et al, 2007;Matsuno et al, 2009). A large amount of structural information on Eg5 in complex with its inhibitors has also been reported (Yokoyama et al, 2015(Yokoyama et al, , 2018Myers & Collins, 2016). However, Eg5 inhibitors have not found clinical use because they target not only cancer cells but also other actively proliferating cells.…”

RAB11A and RAB11B control mitotic spindle function in intestinal epithelial progenitor cells

“…There are well‐characterized KIF11 inhibitors that bind allosteric pockets of KIF11 and inhibit the release of ADP (Yokoyama et al , 2018 ) (Mayer et al , 1999 ; Tcherniuk et al , 2010 ; Venere et al , 2015 ; Wu et al , 2018 ). Previous studies reported a tighter KIF11‐association by S‐trityl‐L‐cysteine (STLC) than monastrol (Skoufias et al , 2006 ), and a better pocket‐fitting by ispinesib than monastrol (Zhang et al , 2008a ).…”

Crystal structure of the motor domain of centromere‐associated protein E in complex with a non‐hydrolysable ATP analogue

“…Considering the helix a0 and loop L1, a0 and L1 regions of CENP-E have two more residues than that of other kinesins. Although the B factor of these kinesins is below 30 A 2 , the B factors of some residues of CENP-E-MgAMPPNP are over 40 A 2 . We consider that the a0 region and loop L1 of CENP-E-MgAMPPNP are less stable than other kinesins because two residues or more of the longer loop L1 are more flexible.…”

“…Recently, numerous small‐molecule inhibitors targeting the motor domain of Kinesin‐5, a kinesin essential for mitosis, have been developed for new anticancer agents. Many researchers have elucidated the structures of the inhibitor‐bound Kinesin‐5 motor domain by using X‐ray crystallography, which has helped in rational design of more effective Kinesin‐5 inhibitors [2]. However, inhibitors targeting the Kinesin‐5 motor domain have not been approved for use in clinical practice because of facing with the problem that most inhibitors tested exhibited only limited efficacy [3].…”