Analysis of the binding mode of laulimalide to microtubules: Establishing a laulimalide–tubulin pharmacophore

Abstract

Laulimalide (LA) is a microtubule-stabilizing agent, currently in preclinical studies. However, studying the binding of this species and successfully synthesizing potent analogues have been challenging. The LA binding site is located between tubulin protofilaments, and therefore LA is in contact with two adjacent -tubulin units. Here, an improved model of the binding mode of LA in microtubules is presented, using the newly available crystal structure pose and an extended tubulin heterodimer complex, as well as molecular dynamics simulations. With this model, a series of LA analogues developed by Mooberry and coworkers are also analyzed in order to establish important pharmacophores in LA binding and cytotoxicity. In the side chain, – interactions are important contributors to LA binding, as are water-mediated hydrogen bonds. An intramolecular hydrogen bond is correlated with high cytotoxicity, and is dependent on macrocycle conformation. Therefore, while the epoxide and olefin groups in the macrocycle do not engage in specific interactions with the protein, they are essential contributions to an active macrocycle conformation, and therefore potency. Calculations reveal that a balance in binding affinity is important for LA activity, where the more potent compounds have larger interactions with the adjacent tubulin unit than the less-active analogs. Several modifications are suggested for the rational design of LA analogues that should not disrupt the active macrocycle conformation.

Keywords:

• laulimalide
• isolaulimalide
• rational drug design
• cytotoxicity
• microtubule
• tubulin heterodimer

Acknowledgements

J.A.T. acknowledges the support of the Allard Foundation, the Alberta Cancer Foundation, the National Sciences and Engineering Research Council (NSERC), and Alberta Advanced Education and Technology. M.K. thanks NSERC. C.D.M.C. thanks NSERC, Alberta Innovates–Technology Futures, the Killam Trust, the IODE War Memorial Scholarship and the University of Alberta for funding. Computations were performed using in-house GPUs and WestGrid resources. The authors are grateful to Dr. Susan Mooberry and coworkers, who performed the important experimental work on which this study is based.

Notes

No potential conflict of interest was reported by the authors.

Supplemental data for this article can be accessed http://dx.doi.org/10.1080/07391102.2015.1078115.

1 The decomposition of the total MM/GBSA binding energy (neglecting the entropy component) is not pairwise decomposable. Therefore, the sum of the drug-residue interactions does not equal the total binding energy.

Additional information

Funding

This work was supported by Natural Sciences and Engineering Research Council of Canadaand Discovery grants awarded to JAT and MK.