Structural rationale for the cross-resistance of tumor cells bearing the A399V variant of elongation factor eEF1A1 to the structurally unrelated didemnin B, ternatin, nannocystin A and ansatrienin B

• Published in: Journal of computer-aided molecular design 2017-10, Vol.31 (10), p.915-928
• Main Authors: Sánchez-Murcia, Pedro A., Cortés-Cabrera, Álvaro, Gago, Federico
• Format: Article
• Language: English
• Subjects: Alanine; Animal Anatomy; Animals; Antineoplastic Agents - chemistry; Antineoplastic Agents - pharmacology; Atomic structure; Binding Sites; Cell Line, Tumor; Chemistry; Chemistry and Materials Science; Computer Applications in Chemistry; Crystallization; Depsipeptides - chemistry; Drug Resistance - drug effects; Drugs; Elongated structure; Flavonoids - chemistry; Histology; Homology; Humans; Macrocyclic Compounds - chemistry; Molecular Docking Simulation; Molecular dynamics; Morphology; Natural products; Oligomerization; Peptide Elongation Factor 1 - chemistry; Peptide Elongation Factor 1 - genetics; Peptide Elongation Factor 1 - metabolism; Physical Chemistry; Polyketides - chemistry; Protein Binding; Protein Conformation; Protein synthesis; Proteins; Quinones - chemistry; Rabbits; Valine
• ISSN: 0920-654X; 1573-4951
• DOI: 10.1007/s10822-017-0066-x

At least four classes of structurally distinct natural products with potent antiproliferative activities target the translation elongation factor eEF1A1, which is best known as the G-protein that delivers amino acyl transfer RNAs (aa-tRNAs) to ribosomes during mRNA translation. We present molecular models in atomic detail that provide a common structural basis for the high-affinity binding of didemnin B, ternatin, ansatrienin B and nannocystin A to eEF1A1, as well as a rationale based on molecular dynamics results that accounts for the deleterious effect of replacing alanine 399 with valine. The proposed binding site, at the interface between domains I and III, is eminently hydrophobic and exists only in the GTP-bound conformation. Drug binding at this site is expected to disrupt neither loading of aa-tRNAs nor GTP hydrolysis but would give rise to stabilization of this particular conformational state, in consonance with reported experimental findings. The experimental solution of the three-dimensional structure of mammalian eEF1A1 has proved elusive so far and the highly homologous eEF1A2 from rabbit muscle has been crystallized and solved only as a homodimer in a GDP-bound conformation. Interestingly, in this dimeric structure the large interdomain cavity where the drugs studied are proposed to bind is occupied by a mostly hydrophobic α-helix from domain I of the same monomer. Since binding of this α-helix and any of these drugs to domain III of eEF1A(1/2) is, therefore, mutually exclusive and involves two distinct protein conformations, one intriguing possibility that emerges from our study is that the potent antiproliferative effect of these natural products may arise not only from inhibition of protein synthesis, which is the current dogma, but also from interference with some other non-canonical functions. From this standpoint, this type of drugs could be considered antagonists of eEF1A1/2 oligomerization, a hypothesis that opens up novel areas of research.