Structural Basis for the Binding of Didemnins to Human Elongation Factor eEF1A and Rationale for the Potent Antitumor Activity of These Marine Natural Products

Abstract

Didemnins and tamandarins are closely related marine natural products with potent inhibitory effects on protein synthesis and cell viability. On the basis of available biochemical and structural evidence and results from molecular dynamics simulations, a model is proposed that accounts for the strong and selective binding of these compounds to human elongation factor eEF1A in the presence of GTP. We suggest that the p-methoxyphenyl ring of these cyclic depsipeptides is inserted into the same pocket in eEF1A that normally lodges either the 3′ terminal adenine of aminoacylated tRNA, as inferred from two prokaryotic EF-Tu‚GTP‚tRNA complexes, or the aromatic side chain of Phe/Tyr-163 from the nucleotide exchange factor eEF1BR, as observed in several X-ray crystal structures of a yeast eEF1A:eEF1BR complex. This pocket, which has a strong hydrophobic character, is formed by two protruding loops on the surface of eEF1A domain 2. Further stabilization of the bound depsipeptide is brought about by additional crucial interactions involving eEF1A domain 1 in such a way that the molecule fits snugly at the interface between these two domains. In the GDP-bound form of eEF1A, this binding site exists only as two separate halves, which accounts for the much greater affinity of didemnins for the GTP-bound form of this elongation factor. This binding mode is entirely different from those seen in the complexes of the homologous prokaryotic EF-Tu with kirromycin-type antibiotics or the cyclic thiazolyl peptide antibiotic GE2270A. Interestingly, the set of interactions used by didemnins to bind to eEF1A is also distinct from that used by eEF1BR or eEF1B , thus establishing a competition for binding to a common site that goes beyond simple molecular mimicry. The model presented here is consistent with both available biochemical evidence and known structure-activity relationships for these two classes of natural compounds and synthetic analogues and provides fertile ground for future research.

Inhibition of translation by cytotrienin A—a member of the ansamycin family

“…Both Cyt A and Did B inhibited translocation when aa-tRNA was loaded in an eEF1A-dependent manner ( Fig. 3D; SirDeshpande and Toogood 1995), which would be consistent with this model, since eEF2 and the ternary complex share binding sites on the ribosome (Marco et al 2004). Indeed, this mode of action has been suggested for Did B previously and is the mechanism of action of the antibiotic kirromycin (Wolf et al 1977;Ahuja et al 2000;Andersen et al 2003;Schmeing et al 2009).…”

Synthesis and Structure–Activity Relationship of Cytotoxic Marine Cyclodepsipeptide IB‐01212 Analogues

“…Drugs derived from marine organisms have recently inspired a new era in human therapy, offering vast potential for the treatment of a myriad diseases for which new, alternative therapies are desperately needed. Numerous marine compounds have been evaluated for cancer treatment, including ecteinascidin-743, [1] aplidine, [2][3][4][5] , variolin B, [6,7] lamellarins, [8] dolastatin 10, [9] jasplakinolide, [10,11] and kahalalide F. [12][13][14] In many cases, these promising compounds are peptides or depsipeptides with complex structures that favor conformational diversity. Specifically, rare residues such as d-amino acids, N-or C-alkylated amino acids, a,b-didehydroamino acids, hydroxyl acids, and structurally elaborate amino acids, such as the reverse prenyl (rPr) of two residues of Ser and Thr in Trunkamide A.…”

Overcoming the Inadequacies or Limitations of Experimental Structures as Drug Targets by Using Computational Modeling Tools and Molecular Dynamics Simulations

“…The desired structural rearrangement was achieved by progressively reducing each distance in a zipper-like fashion ( Figure 5) using a harmonic potential with a force constant that was progressively increased during several consecutive sMD runs. [107] As in the tMD Figure 4. Conformational changes in HIV-1 RT subunit p66 in going from the apo form in a covalently trapped catalytic complex (PDB entry 1rtd) to a non-nucleoside-bound inhibited form (PDB entry 1fk9).…”

“…Schematic of the steered molecular dynamics protocol implemented to drive the conformation of the catalytic domain of eEF-1A (residue numbers in pink) progressively from that found in the crystallographic complex with the guanine nucleotide exchange factor eEF-1Ba (left) to that adopted when it binds GTP (right), which is equivalent to the "GTP conformation" experimentally observed for its prokaryotic counterpart, EF-1A, also known as EF-Tu (residue numbers in cyan). [107] phate hydrolases characterized by a three-layer (aba) sandwich architecture and a Rossmann fold. Examination of the normal modes for these enzymes and exploration of the resulting structures with the CAVER tool [121] revealed that some internal motions coupled closure of the P-loop in the ATP binding site to the creation of a hydrophobic channel in the helical region that connected the deoxythymidine binding site with the bulk solvent.…”