Structural insight into the role of Gln293Met mutation on the Peloruside A/Laulimalide association with αβ-tubulin from molecular dynamics simulations, binding free energy calculations and weak interactions analysis

Abstract

Peloruside A (PLA) and Laulimalide (LAU) are novel microtubule-stabilizing agents with promising properties against different cancer types. These ligands share a non-taxoid binding site at the outer surface of β-tubulin and promote microtubule stabilization by bridging two adjacent αβ-tubulin dimers from parallel protofilaments. Recent site-directed mutagenesis experiments confirmed the existence of a unique β-tubulin site mutation (Gln293Met) that specifically increased the activity of PLA and caused resistance to LAU, without affecting the stability of microtubules in the absence of the ligands. In this work, fully atomistic molecular dynamics simulations were carried out to examine the PLA and LAU association with native and mutated αβ-tubulin in the search for structural and energetic evidence to explain the role of Gln293Met mutation on determining the activity of these ligands. Our results revealed that Gln293Met mutation induced the loss of relevant LAU-tubulin contacts but exerted negligible changes in the interaction networks responsible for PLA-tubulin association. Binding free energy calculations (MM/GBSA and MM/PBSA), and weak interaction analysis (aNCI) predicted an increased affinity for PLA, and a weakened association for LAU after mutation, thus suggesting that Gln293Met mutation exerts its action by a modulation of drug-tubulin interactions. These results are valuable to increase understanding about PLA and LAU activity and to assist the future design of novel agents targeting the PLA/LAU binding pocket.

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

“…The residues of β 2 that are relevant for the interaction with the ligand are β 2 Asp120, β 2 Arg123, β 2 Lys124, and β 2 Glu125, as described earlier in the case of the LAU complex with laterally arranged MT models. Regarding longitudinal MT models, the binding modes and ligand–protein interactions found in these systems are highly consistent with the 4O4H and 4O4J models and with previously reported theoretical predictions . The consistency between our current MD results, available crystallographic information, and previous simulation reports validates the quality of our simulation approach and the use of MD trajectories to retrieve structural and energetic information regarding the effect of PLA and LAU binding on the interaction between tubulin dimers in lateral and longitudinal arrangement, as detailed next.…”

“…To address this issue, reliable models and suitable computational approaches must be employed to take into consideration the structural and energetic aspects involved in MTs stabilization by LAU and PLA association. To date, numerous reports have dealt with the study of MSA–tubulin interactions using molecular docking, pharmacophore modeling, molecular dynamics (MD) simulations, and binding free energy calculations, among others . The systems under study have been restricted mostly to MSA complexes with β‐tubulin subunits or αβ‐tubulin heterodimers.…”

“…To date, numerous reports have dealt with the study of MSAtubulin interactions using molecular docking, pharmacophore modeling, molecular dynamics (MD) simulations, and binding free energy calculations, among others. [6][7][8][9][10][11] The systems under study have been restricted mostly to MSA complexes with β-tubulin subunits or αβ-tubulin heterodimers. 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.…”

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

“…GB calculations were carried out using the modified GB model (igb = 5) with mbondi2, and α , β , and γ values of 1.0, 0.8, and 4.85, respectively. The validity of the igb = 5 model in dealing with ligand‐protein and protein‐protein interactions in tubulin‐related systems has already been tested in our past work and is expected to afford reliable results dealing with the structural and energetic effects induced by the double PLA‐TX association on the dimer‐dimer interaction in reduced MT models . Dielectric constants for the solvent and the protein were set to 80 and 1, respectively.…”

“…GB calculations were carried out using the modified GB model reliable results dealing with the structural and energetic effects induced by the double PLA-TX association on the dimer-dimer interaction in reduced MT models. 18,28 Dielectric constants for the solvent and the protein were set to 80 and 1, respectively. The entropic term was not included in our calculations due to the size of the systems under study.…”