The Unique Binding Mode of Laulimalide to Two Tubulin Protofilaments

Abstract

Laulimalide, a cancer chemotherapeutic in preclinical development, has a unique binding site located on two adjacent β-tubulin units between tubulin protofilaments of a microtubule. Our extended protein model more accurately mimics the microtubule environment, and together with a 135 ns molecular dynamics simulation, identifies a new binding mode for laulimalide, which differs from the modes presented in work using smaller protein models. The new laulimalide-residue interactions that are computationally revealed explain the contacts observed via independent mass shift perturbation experiments. The inclusion of explicit solvent shows that many laulimalide-tubulin interactions are water mediated. The new contacts between the drug and the microtubule structure not only improve our understanding of laulimalide binding but also will be essential for efficient derivatization and optimization of this prospective cancer chemotherapy agent. Observed changes in secondary protein structure implicate the S7-H9 loop (M-loop) and H1'-S2 loop in the mechanism by which laulimalide stabilizes microtubules to exert its cytotoxic effects.

Molecular modeling study on the differential microtubule‐stabilizing effect in singly‐ and doubly‐bonded complexes with peloruside A and paclitaxel

“…Due to the large size of these simplified models, extending the computational system to larger tubulin arrangements (ie, octameric, dodecameric) is prohibitive considering our current resources. Nevertheless, tetrameric systems have proven to be reliable to describe MT‐based phenomena in recent molecular modeling studies …”

“…To this purpose, herein we propose the use of reduced MT models composed of two laterally arranged tubulin dimers to examine the structural and energetic effects induced by the association of stabilizing ligands in singly‐ and doubly‐bonded complexes using molecular dynamics (MD) simulations. The reduced MT models employed in this study have been previously reported in the literature, and correspond to a B‐type lattice configuration—which is the primary arrangement within MTs—describing homologous lateral contacts between αβ‐tubulin dimers (Figure ) . These reduced models are expected to provide a reliable description of the molecular events taking place at the lateral interface between PFs upon the association of MT stabilizers, in the search for structural and energetic evidence that could be related to the differential mechanism of action of PLA and TX at a molecular level …”

“…The reduced MT models employed in this study have been previously reported in the literature, and correspond to a B-type lattice configuration-which is the primary arrangement within MTs-describing homologous lateral contacts between αβ-tubulin dimers ( Figure 2). [16][17][18] These reduced models are expected to provide a reliable description of the molecular events taking place at the lateral interface between PFs upon the association of MT stabilizers, in the search for structural and energetic evidence that could be related to the differential mechanism of action of PLA and TX at a molecular level. [19][20][21][22] 2 | MATERIALS AND METHODS…”

Modulation of lateral and longitudinal interdimeric interactions in microtubule models by Laulimalide and Peloruside A association: A molecular modeling approach on the mechanism of microtubule stabilizing agents

“…In 2015, Churchill et al reported the use of an extended tubulin heterodimer model composed of two laterally arranged αβtubulin units to examine its interaction with LAU. [12] Authors claimed that this model is representative for the association of LAU ligands between two protofilaments in MTs. Nevertheless, the tubulin arrangement was built from the 2XRP reconstruction of MTs, which combines cryo-electron microscopy data with the low-resolution 1JFF structure of the αβ-tubulin complex with taxol, which does not account for the specific allosteric effects exerted by non-taxane ligands bonded to the LAU/PLA site.…”

“…In 2015, Churchill et al. reported the use of an extended tubulin heterodimer model composed of two laterally arranged αβ‐tubulin units to examine its interaction with LAU . Authors claimed that this model is representative for the association of LAU ligands between two protofilaments in MTs.…”