Syn-pentane Interactions Research Articles

Conformationally Controlled sp3 -Hydrocarbon-Based α-Helix Mimetics.

With over 60 % of protein-protein interfaces featuring an α-helix, the use of α-helix mimetics as inhibitors of these interactions is a prevalent therapeutic strategy. However, methods to control the conformation of mimetics, thus enabling maximum efficacy, can be restrictive. Alternatively, conformation can be controlled through the introduction of destabilizing syn-pentane interactions. This tactic, which is often adopted by Nature, is not a common feature of lead optimization owing to the significant synthetic effort required. Through assembly-line synthesis with NMR and computational analysis, we have shown that alternating syn-anti configured contiguously substituted hydrocarbons, by avoiding syn-pentane interactions, adopt well-defined conformations that present functional groups in an arrangement that mimics the α-helix. The design of a p53 mimetic that binds to Mdm2 with moderate to good affinity, demonstrates the therapeutic promise of these scaffolds.

Conformationally Controlled Linear and Helical Hydrocarbons Bearing Extended Side Chains.

Conformationally controlled flexible molecules are ideal for applications in medicine and materials, where shape matters but an ability to adapt to multiple and changing environments is often required. The conformation of flexible hydrocarbon chains bearing contiguous methyl substituents is controlled through the avoidance of syn-pentane interactions: alternating syn-anti isomers adopt a linear conformation while all-syn isomers adopt a helical conformation. From a simple diamond lattice analysis, larger substituents, which would be required for most potential applications, result in significant and unavoidable syn-pentane interactions, suggesting substantially reduced conformational control. Through a combination of computation, synthesis, and NMR analysis, we have identified a selection of substitution patterns that allow large groups to be incorporated on conformationally controlled linear and helical hydrocarbon chains. Surprisingly, when the methyl substituents of alternating syn-anti hydrocarbons are replaced with acetoxyethyl groups, the main chain of almost 95% of the population of molecules adopt a linear conformation. Here, the side chains adopt nonideal eclipsed conformations with the main chain, thus minimizing syn-pentane interactions. In the case of all-syn hydrocarbons, concurrent removal of some methyl groups on the main chain adjacent to the large substituents is required to maintain a high population of molecules adopting a helical conformation. This information can now be used to design flexible hydrocarbon chains displaying functional groups in a defined relative orientation for multivalent binding or cooperative reactivity, for example, in targeting the interfaces defined by disease-relevant protein-protein interactions.

Stereospecific Cross-Coupling Reactions Provide Conformationally-Biased Arylalkanes with Anti-Leukemia Activity.

A focused small library of carbamates and alcohols was prepared employing stereospecific Kumada-ring opening reactions of tetrahydropyrans. The core framework of the library members is acyclic and incorporates 1,3-substituents, to provide a conformational bias in avoiding syn-pentane interactions. A new compound with micromolar activity against MOLT-4, CCRF-CEM, and HL-60(TB) leukemia cell lines was identified from this series.

Syntheses of Unsymmetrical 1,4-Bifunctional Allylboron Reagents via Cu-catalyzed Highly Regio- and Stereoselective 1,4-Protoboration of Dienylboronates and Analysis of the Origin of Chemoselective Aldehyde syn-(Hydroxymethyl)allylation.

The syntheses of unsymmetrical 1,4-bifunctional allylboron reagents via Cu-catalyzed highly regio- and stereoselective 1,4-protoboration of dienylboronates were developed. The resulting allylboronates underwent chemoselective allylboration with aldehydes followed by oxidative workup to give diol products with high diastereoselectivity. Transition state analysis revealed that the disfavored transition states suffer from either a severe A1,3 allylic strain or 1,3- syn-pentane interactions. Minimization of such nonbonding 1,3- syn-pentane interactions is proposed to be the origin of observed chemoselectivity of the reaction.

Asymmetric Synthesis of the Antiviral Diterpene Wickerol A

Wickerol A (1) is an unusual diterpene with remarkable activity against the H1N1 influenza virus. Its tetracyclic skeleton contains three quaternary carbons and is marked by several syn-pentane interactions which force a six-membered ring into a twist-boat conformation. We present an asymmetric synthesis of wickerol A (1) that is based on a Jung Diels-Alder reaction, an intramolecular alkylation to complete the 6-5-6-6 ring system, and a conjugate addition, all of which overcome considerable steric strain. During the synthesis, we isolated an unexpected cyclopropane that presumably stems from a carbonium ion intermediate.

Stapled Peptides with γ-Methylated Hydrocarbon Chains for the Estrogen Receptor/Coactivator Interaction.

"Stapled" peptides are typically designed to replace two non-interacting residues with a constraining, olefinic staple. To mimic interacting leucine and isoleucine residues, we have created new amino acids that incorporate a methyl group in the γ-position of the stapling amino acid S5. We have incorporated them into a sequence derived from steroid receptor coactivator 2, which interacts with estrogen receptor α. The best peptide (IC50 =89 nm) replaces isoleucine 689 with an S-γ-methyl stapled amino acid, and has significantly higher affinity than unsubstituted peptides (390 and 760 nm). Through X-ray crystallography and molecular dynamics studies, we show that the conformation taken up by the S-γ-methyl peptide minimizes the syn-pentane interactions between the α- and γ-methyl groups.

Double diastereoselection in anti aldol reactions mediated by dicyclohexylchloroborane between an l-erythrulose derivative and chiral aldehydes

Anti aldol reactions of an l-erythrulose derivative with several α-chiral aldehydes mediated by dicyclohexylboron chloride are examined. Good yields and stereoselectivities are observed. The results are best explained when the reactions are assumed to occur via boat-like transition states with minimization of 1,3-allylic strain and avoidance of syn pentane interactions.

Importance of C−N Bond Rotation in N-Acyl Oxazolidinones in their SmI2-Promoted Coupling to Acrylamides

A detailed mechanistic investigation was undertaken to determine the dominating factors of the postelectron transfer steps in the SmI(2)-promoted carbon-carbon bond forming reaction between N-acyl oxazolidinones and acrylamides. Competition experiments were performed by reacting two N-acyl oxazolidinones with a limiting amount of N-t-butyl acrylamide, and from the product distribution, the relative reactivity values (RV) for a series of N-acyl oxazolidinones were then calculated against N-pivaloyl oxazolidinone as the reference. An almost linear correlation was obtained for the simple alkyl N-acyl oxazolidinones when ln RV was plotted against the activation barriers for C-N bond rotation (s-trans to s-cis) obtained by DFT calculations, implying that C-N bond rotation from the s-trans to s-cis conformation is one of the essential parameters controlling the reactivity. These results were substantiated by other competition experiments carried out for the corresponding imide derivatives, where rotation is not necessary for obtaining bidentate coordination and where no such correlation as described above was observable. The finding that the reactivity of the simple N-acyl oxazolidinones for these SmI(2)-mediated transformations correlates with the activation barriers for C-N bond rotation may have implications for other useful synthetic organic reactions involving similar substrates. Finally, these studies were extrapolated to understanding the poor reactivity of N-acyl oxazolidinones, as those derived from Evans chiral auxiliaries, with N-tert-butyl acrylamide. These couplings appear to be dominated by the activation energy for addition because of arising syn-pentane interactions in the transition-state for C-C bond formation. We demonstrate that the addition of Lewis acids can have a beneficial effect on the coupling yields.

Asymmetric Hydrogenation Routes to Deoxypolyketide Chirons

Asymmetric hydrogenations of monoenes and dienes were performed to obtain terminal deoxypolyketide fragments A and the corresponding internal chirons B and C. The chiral N-heterocyclic carbene catalyst 1 was used throughout. Modest selectivities for hydrogenations of simple monoenes relayed into high selectivities for preparations of the terminal deoxypolyketide fragments in which either two hydrogenations or one and an optically pure starting material were used. Curiously, the face selectivities for hydrogenation of alpha,beta-unsaturated esters were consistently opposite to those that had been observed for styrene and stilbene derivatives in previous work, and to closely related allylic alcohol and ether derivatives in this work. Plausible mechanisms for this differing behavior were deduced by using DFT calculations. It appears that the origin of the unusual stereoselectivity for the ester derivatives is transient metal-coordination of the ester carbonyl whereas there is no evidence that the allylic alcohol or ethers coordinate. The routes developed to alpha,omega-functionalized internal deoxypolyketide fragments are extremely practical. These begin with the Roche ester being converted into alkene and, in one case, diene derivatives. Catalyst control prevails in the hydrogenations of these substrates, but there is a significant "substrate vector" (a term we used to describe the influence of the substrate on a catalyst-controlled reaction). This is determined by minimization of 1,3-allylic strain and, in some cases, syn pentane interactions. This substrate vector can be constructively paired with the (dominant) catalyst vector by use of the appropriate enantiomer of 1. In the hydrogenation of a diene derivative, two chiral centers could be formed simultaneously with overall 11:1.0 selectivity; this is the first time this has been achieved in any asymmetric synthesis of a deoxypolyketide fragment. Throughout, diastereoselectivities of the crude material in the syntheses of alpha,omega-functionalized internal deoxypolyketide fragments were in excess of 11:1.0 and chromatographically purified samples could be isolated in high yields with dr (dr=diastereomeric ratio) values consistently in excess of 40:1.0.

Conformations of Laulimalide in DMSO-d6

Laulimalide is one of the newest naturally occurring macrolides known to act as a microtubule stabilizing agent with properties similar to Taxol. It also stands as being one of the most flexible with 18 rotatable bonds. This large number of rotatable bonds allows for approximately 3(18) potential conformers. To examine the conformational energy surface of laulimalide, we have performed an NAMFIS deconvolution analysis for laulimalide in DMSO-d6. The latter has been supplemented with a post-NAMFIS energy analysis at the Becke3LYP/6-31G level that examines the opposing effects of internal hydrogen bonding and syn-pentane interactions. In this way, we have identified 15 laulimalide conformations that can be classified into 5 different families: Supine, Convex, Cobra, Stretch, and Concave motifs.

Total synthesis of the cytotoxic cyclodepsipeptide (-)-doliculide: the "ester" effect in acyclic 1,3-induction of deoxypropionates.

The total synthesis of the marine cyclodepsipeptide (-)-doliculide is described. An acyclic (2S,4S,6R)-trimethyl alkanoic acid precursor to the "hydrocarbon" portion of doliculide was synthesized starting with l-ascorbic acid based on a stereocontrolled iterative conjugate addition of lithium dimethylcuprate to acyclic delta-Cmethyl alpha,beta-unsaturated ester derivatives. syn/syn selectivity was achieved by relying on 1,3-induction in preferred folded conformations that avoid 1,5-syn-pentane interactions in the transition states. The nature of the ester moiety seems to play an important role in determining the syn/anti ratios of C-methyl adducts. The 1-methyl-1-cyclopentyl ester group was found to confer the best syn selectivity to the cuprate addition products, especially in seven-carbon enoates.

Application of conformation design in acyclic stereoselection: total synthesis of borrelidin as the crystalline benzene solvate.

The total synthesis of (-)-borrelidin (treponemycin), a structurally distinct 18-membered macrolide antibiotic, has been achieved. It was isolated as the crystalline benzene solvate, and its structure was confirmed by a single-crystal X-ray analysis. The deoxypropionate subunit consisting of four alternating C-methyl groups with a C(4)-C(10) syn/syn/anti orientation was elaborated by a new method of iterative cuprate additions to acyclic alpha,beta-unsaturated esters relying on two consecutive 1,3-inductions and starting with d-glyceraldehyde as the chiral progenitor. The unique Z/E cyanodiene unit was obtained as a single isomer by application of the Still-Gennari olefination protocol. The gamma-hydroxycyclopentane carboxylic acid subunit was prepared from L-malic acid utilizing a sequential introduction of C-vinyl and C-allyl groups, capitalizing on 1,2-induction in an acyclic alpha,beta-unsaturated ester and carbocyclization by a Grubbs ring closure metathesis reaction. The prevalence of 1,3-syn-disposed deoxypropionate triads in the cuprate additions is rationalized on the basis of minimized syn-pentane interactions in the transition states. A virtual diamond lattice was used as a visual tool to portray the low-energy conformations of the acyclic substrates, and corroborated by (1)H NMR homodecoupling studies.

Laboratory emulation of polyketide biosynthesis: an iterative, aldol-based, synthetic entry to polyketide libraries using (R)- and (S )-1-(benzyloxy)-2-methylpentan-3-one, and conformational aspects of extended polypropionates

Iterative, one-directional, boron-mediated aldol chain extensions, using the dipropionyl reagent (R)-1-(benzyloxy)-2-methylpentan-3-one 7, have enabled the highly diastereoselective assembly of the stereoregular heptapropionates 5 and 6. The synthetic sequence developed permits structural diversity through variation in the stereochemical nature of the aldolisation and reduction steps, together with the choice of the chiral ketone employed at each iteration. The heptapropionate 5 has been shown to represent an example of a fully flexible molecule, whose backbone nevertheless adopts a single preferred conformation. It forms part of a family of conformationally controlled polyols, exploiting the avoidance of syn-pentane interactions and the preference for preorganisation through intramolecular hydrogen bonding.