New sources of chemical diversity inspired by biosynthesis: rational design of a potent epothilone analogue

Synthesis and Biological Evaluation of 7-Deoxy-Epothilone Analogues

The synthesis of two deoxygenated analogues of potent epothilones is reported in an effort to analyze the relative importance of molecular conformation and ligand-target interactions to biological activity. 7-deoxy-epothilone D and 7-deoxy-(S)-14-methoxy-epothilone D were prepared through total synthesis and shown to maintain the conformational preferences of their biologically active parent congeners through computer modeling and nuclear magnetic resonance (NMR) studies. The significant decrease in observed potency for each compound suggests that a hydrogen bond between the C7-hydroxyl group and the tubulin binding site plays a critical role in the energetics of binding in the epothilone class of polyketides.

Dihedral Angle-Based Sampling of Natural Product Polyketide Conformations: Application to Permeability Prediction

Macrocycles pose challenges for computer-aided drug design due to their conformational complexity. One fundamental challenge is identifying all low-energy conformations of the macrocyclic ring, which is important for modeling target binding, passive membrane permeation, and other conformation-dependent properties. Macrocyclic polyketides are medically and biologically important natural products characterized by structural and functional diversity. Advances in synthetic biology and semisynthetic methods may enable creation of an even more diverse set of non-natural product polyketides for drug discovery and other applications. However, the conformational sampling of these flexible compounds remains demanding. We developed and optimized a dihedral angle-based macrocycle conformational sampling method for macrocycles of arbitrary structure, and here we apply it to diverse polyketide natural products. First, we evaluated its performance using a data set of 37 polyketides with available crystal structures, with 9-22 rotatable bonds in the macrocyclic ring. Our optimized protocol was able to reproduce the crystal structure of polyketides' aglycone backbone within 0.50 Å RMSD for 31 out of 37 polyketides. Consistent with prior structural studies, our analysis suggests that polyketides tend to have multiple distinct low-energy structures, including the bioactive (target-bound) conformation as well as others of unknown significance. For this reason, we also introduce a strategy to improve both efficiency and accuracy of the conformational search by utilizing torsional restraints derived from NMR vicinal proton couplings to restrict the conformational search. Finally, as a first application of the method, we made blinded predictions of the passive membrane permeability of a diverse set of polyketides, based on their predicted structures in low- and high-dielectric media.

Conformation-activity relationships of polyketide natural products

Polyketides represent an important class of secondary metabolites that interact with biological targets connected to a variety of disease-associated pathways. Remarkably, nature's assembly lines, polyketide synthases, manufacture these privileged structures through a combinatorial mixture of just a few structural units. This review highlights the role of these structural elements in shaping a polyketide's conformational preferences, the use of computer-based molecular modeling and solution NMR studies in the identification of low-energy conformers, and the importance of conformational analogues in probing the bound conformation. In particular, this review covers several examples wherein conformational analysis complements classic structure-activity relationships in the design of biologically active natural product analogues.

Selected hybrid natural products as tubulin modulators

Modulators of microtubule dynamics have received increasing attention because of their potential to stop cancer growth. Although it belongs to the category of complex protein-protein interactions (PPIs), which are generally considered difficult to modulate through small molecules, the use of microtubule is considered a well-validated target. There are a number of bioactive natural products and related compounds that are currently in use as drugs or in clinical trials as next generation anti-cancer agents. The present review article is focused on two such bioactive natural products, epothilone and halichondrin B, and covers some of the key papers published after 2005 that outline various synthetic approaches to obtain next generation structural analogs as well as the synthesis of hybrid compounds.

Epothilone D and its 9-Methyl analogues: combinatorial syntheses, conformation, and biological activities

Epothilone D (Epo D) and its 9-Methyl conformational analogues were synthesized through a highly efficient combinatorial approach. The fragment E was synthesized in 11 total steps with 6 longest linear steps, and each aldehyde B was prepared via a 3-step sequence. Starting from the common precursor E and a suitable aldehydes B, each target molecule were obtained in only 4 steps. The 9-(S)-epo D and 9-(R)-epo D demonstrated significant difference in inhibition activities against cancer cell lines and in conformational analysis.

Thermodynamic control of 1,3-boratropic shifts of α- and γ-stannyl-substituted allylboranes: hyperconjugation outweighs steric effects

(E)-δ-Stannyl homoallylic alcohols are prepared by an allene hydroboration-aldehyde allylboration sequence ( Chen , M. et al. J. Am. Chem. Soc. 2010 , 132, 7881 ). Key to this reaction sequence is that the kinetic allene hydroboration product, 2a, is less stable than and isomerizes to the more sterically congested α-stannylallylborane 3a (see abstract figure). An M06-2X density functional analysis shows that the C-Sn to boron σ-π hyperconjugation interaction is sufficiently stabilizing to override the steric congestion in 3a.

Enantioselective synthesis of (E)-delta-stannyl homoallylic alcohols via aldehyde allylboration using alpha-stannylallylboranes generated by allene hydroboration followed by a highly diastereoselective 1,3-boratropic shift

A highly enantioselective synthesis of (E)-delta-stannyl homoallylic alcohols 4 via aldehyde allylboration reactions of the double-chiral allylborane reagent 2a is reported. Allylborane 2a was generated from the hydroboration of commercially available allenylstannane 1 with ((d)Ipc)(2)BH at -40 to -20 degrees C followed by a kinetically controlled and highly diastereoselective 1,3-boratropic shift in intermediate 3a.