Flexible Molecules with Defined Shape?Conformational Design

Controlled interconversion of macrocyclic atropisomers via defined intermediates

Macrocyclic conformations play a crucial role in regulating their properties. Our understanding of the determinants to control macrocyclic conformation interconversion is still in its infancy. Here we present a macrocycle, octamethyl cyclo[4](1,3-(4,6)-dimethylbenzene)[4]((4,6-benzene)(1,3-dicarboxylate) (OC-4), that can exist at 298 K as two stable atropisomers with C2v and C4v symmetry denoted as C2v-OC-4 and C4v-OC-4, respectively. Heating induces the efficient stepwise conversion of C2v- to C4v-OC-4 via a Cs-symmetric intermediate (Cs-OC-4). It differs from the typical transition state-mediated processes of simple C-C single bond rotations. Hydrolysis and further esterification with a countercation dependence promote the generation of C2v- and Cs-OC-4 from C4v-OC-4. In contrast to C2v-OC-4, C4v-OC-4 can bind linear guests to form pseudo-rotaxans, or bind C60 or C70 efficiently. The present study highlights the differences in recognition behavior that can result from conformational interconversion, as well as providing insights into the basic parameters that govern coupled molecular rotations.

Photoinduced dual bond rotation of a nitrogen-containing system realized by chalcogen substitution

Photoinduced concerted multiple-bond rotation has been proposed in some biological systems. However, the observation of such phenomena in synthetic systems, in other words, the synthesis of molecules that undergo photoinduced multiple-bond rotation upon photoirradiation, has been a challenge in the photochemistry field. Here we describe a chalcogen-substituted benzamide system that exhibits photoinduced dual bond rotation in heteroatom-containing bonds. Introduction of the chalcogen substituent into a sterically hindered benzamide system provides sufficient kinetic stability and photosensitivity to enable the photoinduced concerted rotation. The presence of two different substituents on the phenyl ring in the thioamide derivative enables the generation of a pair of enantiomers and E/Z isomers. Using these four stereoisomers as indicators of which bonds are rotated, we monitor the photoinduced C-N/C-C concerted bond rotation in the thioamide derivative depending on external stimuli such as temperature and photoirradiation. Theoretical calculations provide insight on the mechanism of this selective photoinduced C-N/C-C concerted rotation.

Catalytic Ring Expanding Difluorination: An Enantioselective Platform to Access β,β-Difluorinated Carbocycles

Cyclic β,β-difluoro-carbonyl compounds have a venerable history as drug discovery leads, but limitations in the synthesis arsenal continue to impede chemical space exploration. This challenge is particularly acute in the arena of fluorinated medium rings where installing the difluoromethylene unit subtly alters the ring conformation by expanding the internal angle (∠C-CF2-C>∠C-CH2-C): this provides a handle to modulate physicochemistry (e.g. pKa). To reconcile this disparity, a highly modular ring expansion has been devised that leverages simple α,β-unsaturated esters and amides, and processes them to one-carbon homologated rings with concomitant geminal difluorination (6 to 10 membered rings, up to 95 % yield). This process is a rare example of the formal difluorination of an internal alkene and is enabled by sequential I(III)-enabled O-activation. Validation of enantioselective catalysis in the generation of unprecedented medium ring scaffolds is reported (up to 93 : 7 e.r.) together with X-ray structural analyses and product derivatization.

Synthesis and structure-activity relationship of novel thiazole aminoguanidines against MRSA and Escherichia coli

Novel lead thiazole aminoguanidines exhibited strong activity against Gram-positive bacteria. The potential targets of these substances are undecaprenyl diphosphate synthase (UPPS) and undecaprenyl diphosphate phosphatase (UPPP). Here, we report the synthesis and antibacterial evaluation of a library of thiazole aminoguanidines analogues, wherein the rotatable bond is inserted between the C2 position of thiazole and hydrophobic group. The molecular flexibility is increased, and new analogues with strong activity against MRSA and E. coli are produced. The best compound 4i showed rapid sterilization and low tendency to induce bacterial resistance. The IC50 of compound 4i to EcUPPS enzyme is 145 μmol L-1 (58 μg mL-1). Compound 4i can also inhibit and destroy bacterial biofilms. These thiazole aminoguanidines can be developed as potential therapeutic candidates in the future.

First synthesis of (±)-halichonadins A-D

Described herein is the first total synthesis of a marine isocyanide terpene, (±)-halichonadin C. Our synthetic strategy features nitrile-to-isocyanide interconversion utilizing hypervalent iodine-promoted Hofmann rearrangement. This approach led to successful construction of an isocyanide group at the stereochemically encumbered C-6 position in (±)-halichonadin C. Furthermore, in accord with a scenario we propose for the biosynthesis of halichonadins A-D, (±)-halichonadin C was transformed to halichonadins A and B via the missing link intermediate, halichonadin isocyanate.

Theoretical models of staurosporine and analogs uncover detailed structural information in biological solution

Staurosporine and its analogs (STA-analogs) are indolocarbazoles (ICZs) compounds able to inhibit kinase proteins in a non-specific way, while present antimicrobial and cytostatic properties. The knowledge of molecular features associated to the complexation, including the ligand shape in solution and thermodynamics of complexation, is substantial to the development of new bioactive ICZs with improved therapeutic properties. In this context, the empirical approach of GROMOS force field is able to accurately reproduce condensed phase physicochemical properties of molecular systems after parameterization. Hence, through parameterization under GROMOS force field and molecular simulations, we assessed STA-analogs dynamics in aqueous solution, as well as its interaction with water to probe conformational and structural features involved in complexation to therapeutic targets. The coexistence of multiple conformers observed in simulations, and confirmed by metadynamics calculations, expanding the conformational space knowledge of these ligands with potential implications in understanding the ligand conformational selection during complexation. Also, changes in availability to H-bonding concerning the different substituents and water can reflect on effects at complexation free energy due to variation at the desolvation energetic costs. Based on these results, we expect the obtained structural data provide systemic framework for rational chemical modification of STA-analogs.

First-Principles Study of the Dispersion Effects in the Structures and Keto-Enol Tautomerization of Curcumin

Noncovalent interactions, such as dispersion, play a significant role in the stability of flexible molecules, such as curcumin. This study revealed the importance of dispersion correction in the structure and keto-enol tautomerization of curcumin, which has rarely been addressed in computational studies. We rigorously constructed all possible unique curcumin conformers in the enol and keto forms within the first-principles framework. Regardless of the different environments, we carefully explained the agreement between the computational geometry (in the gas phase) and the experimental measurement (in the polymorph) by using dispersion correction. The calculation results for the aqueous solution of conformational abundance, thermochemistry, and reaction kinetics support the experimental observations after considering the dispersion correction. The study also suggests a water-catalyzed mechanism for keto-enol tautomerization, where dispersion correction plays a role in decreasing the energy barrier and making the keto form thermochemically and kinetically favorable. Our results could be helpful in future computational studies to find a method for increasing the aqueous solubility of curcumin; hence, the potential of curcumin as a multifunctional medicine can be fully achieved.

The Role of Allylic Strain for Conformational Control in Medicinal Chemistry

It is axiomatic in medicinal chemistry that optimization of the potency of a small molecule at a macromolecular target requires complementarity between the ligand and target. In order to minimize the conformational penalty on binding, both enthalpically and entropically, it is therefore preferred to have the ligand preorganized in the bound conformation. In this Perspective, we highlight the role of allylic strain in controlling conformational preferences. Allylic strain was originally described for carbon-based allylic systems, but the same principles apply to other types of structure with sp² or pseudo-sp² arrangements. These systems include benzylic (including heteroaryl methyl) positions, amides, N-aryl groups, aryl ethers, and nucleotides. We have derived torsion profiles from small molecule X-ray structures for these systems. Through multiple examples, we show how these effects have been applied in drug discovery and how they can be used prospectively to influence conformation in the design process.

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.

Determination of the Absolute Configuration of Ballonigrin Lactone A Using Density Functional Theory Calculations

We report the determination of the absolute configuration of a diterpenoid, namely, ballonigrin lactone A (BLA), by comparison of the computed optical rotations, [α]_D, of its two diastereomers using density functional theory (DFT) calculations to the experimental [α]_D value of +22.4. One of the diastereomers having configurations 4S, 5R, 6S, 10S, 15S was named "α-BLA," and the other one with configuration 4S, 5R, 6S, 10S, 15R was called "β-BLA". Six conformers for each diastereomer (α-BLA and β-BLA) of BLA were identified through their conformational analysis. [α]_D values of these six conformations for each diastereomer were calculated using DFT at the mPW1PW91/6-311G(d,p)/SMD_Chloroform level of theory, leading to the conformationally averaged [α]_D values of -96.8 for α-BLA and +65.1 for β-BLA. Thus, it was found that the experimental [α]_D value of +22.4 was of 4S, 5R, 6S, 10S, 15R, i.e., β-BLA. Experimental and computed nuclear magnetic resonance (NMR) data were also compared, and this comparison was in accordance with the conclusion drawn from the comparison of [α]_D values. Finally, the results were augmented with the calculation of the DP4 analysis, and the probability obtained also endorsed our earlier calculations.

Towards the engineering of a photon-only two-stroke rotary molecular motor

The rational engineering of photoresponsive materials, e.g., light-driven molecular motors, is a challenging task. Here, we use structure-related design rules to prepare a prototype molecular rotary motor capable of completing an entire revolution using, exclusively, the sequential absorption of two photons; i.e., a photon-only two-stroke motor. The mechanism of rotation is then characterised using a combination of non-adiabatic dynamics simulations and transient absorption spectroscopy measurements. The results show that the rotor moiety rotates axially relative to the stator and produces, within a few picoseconds at ambient T, an intermediate with the same helicity as the starting structure. We discuss how such properties, that include a 0.25 quantum efficiency, can help overcome the operational limitations of the classical overcrowded alkene designs.

Navigating complex peptide structures using macrocycle conformational maps

Identification of turn motifs that are stabilized by intramolecular hydrogen bonds can be useful in describing the conformation of peptide systems. However, this approach is somewhat insufficient for cyclic peptides because peptide regions that are not positioned within a hydrogen bond can be left with no description. Furthermore, non-regular secondary structures and other rarely-observed conformations can be left without detailed evaluation. Herein, we describe “higher-order” ϕ/ψ plots termed macrocycle conformational maps (MCMs) as a tool for evaluating and comparing the conformations of a series of structurally related macrocyclic peptides.

Identification of turn motifs that are stabilized by hydrogen bonds can be useful in describing the conformation of peptides. Herein, we describe “higher-order” ϕ/ψ plots termed macrocycle conformational maps (MCMs) as a tool to evaluate and compare the conformations of related macrocycles.

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.

Regio- and Diastereoselective Copper-Catalyzed Carbomagnesiation for the Synthesis of Penta- and Hexa-Substituted Cyclopropanes

Despite the highly strained nature of cyclopropanes possessing three vicinal quaternary carbon stereocenters, the regio- and diastereoselective copper-catalyzed carbomagnesiation reaction of cyclopropenes provides an easy and efficient access to these novel persubstituted cyclopropyl cores with a complete regio- and diastereoselectivity.

Illuminating the dark conformational space of macrocycles using dominant rotors

Three-dimensional conformation is the primary determinant of molecular properties. The thermal energy available at room temperature typically equilibrates the accessible conformational states. Here, we introduce a method for isolating unique and previously understudied conformations of macrocycles. The observation of unusual conformations of 16- to 22-membered rings has been made possible by controlling their interconversion using dominant rotors, which represent tunable atropisomeric constituents with relatively high rotational barriers. Density functional theory and in situ NMR measurements suggest that dominant rotor candidates for the amino-acid-based structures considered here should possess a rotational energy barrier of at least 25 kcal mol^-1. Notable differences in the geometries of the macrocycle conformations were identified by NMR spectroscopy and X-ray crystallography. There is evidence that amino acid residues can be forced into rare turn motifs not observed in the corresponding linear counterparts and homodetic rings. These findings should unlock new avenues for studying the conformation-activity relationships of bioactive molecules.

Insight into Out-of-Layer Fluctuations in the Smectic A Stability of 3,5-Diarylisoxazole Liquid Crystals

Polar-terminated 3,5-diarylisoxazole liquid crystals (ILCs) were synthetized and characterized. ILCs are composed by rigid core 3,5-diarylisoxazol, alkyl chain and polar-terminated flexible spacer. Hydroxyl-, ketal- and 1,2-diol-terminated ILCs rendered smectic C and A mesophase, while bromine-terminated ILCs showed smectic A and B mesophase, for monosubstituted and linear ILCs. For branched alkyl chain monotropic SmA was detected and for disubstituted ILCs no mesophase was detected. Out-of-layer fluctuations (OLFs) are discussed based on X-ray diffraction date and textures. The OLFs are dependent on the bromine atom hardness, hydrogen bonding through collective actions and conformational effects at the interface between layers. Smectic translational order parameter (TOP) Σ was also obtained for orientated bromine- and hydroxyl-terminated ILCs and related it with OLFs. For 1,2-diol-terminated ILCs two SmC sublayers were founded, probably related to the intramolecular hydrogen bond favoring the 5-membered and 6-membered formation.

How Do Branched Detergents Stabilize GPCRs in Micelles?

The structural and functional properties of G protein-coupled receptors (GPCRs) are often studied in a detergent micellar environment, but many GPCRs tend to denature or aggregate in short alkyl chain detergents. In our previous work [Lee, S., et al. (2016) J. Am. Chem. Soc.138, 15425–15433], we showed that GPCRs in alkyl glucosides were highly dynamic, resulting in the penetration of detergent molecules between transmembrane α-helices, which is the initial step in receptor denaturation. Although this was not observed for GPCRs in dodecyl maltoside (DDM, also known as lauryl maltoside), even this detergent is not mild enough to preserve the integrity of many GPCRs during purification. Lauryl maltose neopentylglycol (LMNG) detergents have been found to have significant advantages for purifying GPCRs in a native state as they impart more stability to the receptor than DDM. To gain insights into how they stabilize GPCRs, we used atomistic molecular dynamics simulations of wild type adenosine A_2A receptor (WT-A_2AR), thermostabilized A_2AR (tA_2AR), and wild type β₂-adrenoceptor (β₂AR) in a variety of detergents (LMNG, DMNG, OGNG, and DDM). Analysis of molecular dynamics simulations of tA_2AR in LMNG, DMNG, and OGNG showed that this series of detergents exhibited behavior very similar to that of an analogous series of detergents DDM, DM, and OG in our previous study. However, there was a striking difference upon comparison of the behavior of LMNG to that of DDM. LMNG showed considerably less motion than DDM, which resulted in the enhanced density of the aliphatic chains around the hydrophobic regions of the receptor and considerably more hydrogen bond formation between the head groups. This contributed to enhanced interaction energies between both detergent molecules and between the receptor and detergent, explaining the enhanced stability of GPCRs purified in this detergent. Branched detergents occlude between transmembrane helices and reduce their flexibility. Our results provide a rational foundation to develop detergent variants for stabilizing membrane proteins.

Odd-even alternations in helical propensity of a homologous series of hydrocarbons

Odd and even homologues of some n-alkane-based systems are known to exhibit notably different trends in solid-state properties; a well-known illustration is the zigzag plot of their melting point versus chain length. Odd-even effects in the solid state often arise from intermolecular interactions that involve fully extended molecules. These effects have also been observed in less condensed phases, such as self-assembled monolayers; however, the origins of these effects in such systems can be difficult to determine. Here we combined NMR and computational analysis to show that all-syn contiguously methyl-substituted hydrocarbons, with chain lengths from C6 to C11, exhibit a dramatic odd-even effect in helical propensity. The even- and odd-numbered hydrocarbons populate regular and less-controlled helical conformations, respectively. This knowledge will guide the design of helical hydrocarbons as rigid scaffolds or as hydrophobic components in soft materials.

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.

Rapid Access to the Structural Core of Aflavinines via Stereoselective Tandem Intramolecular Diels-Alder Cycloaddition Controlled by the Allylic 1,3-Strain

An expedient route to access the functionalized structural core of aflavinines has been developed starting from three readily available fragments over 12 steps in 29.1% overall yield without using any transition metal catalysis. The key feature of this approach is a tandem intramolecular Diels-Alder cycloaddition to complete the hexacyclic framework with the correct stereochemistry and all the requisite structural elements in place to achieve the total synthesis of aflavinine and its congeners.

Inverting Small Molecule-Protein Recognition by the Fluorine Gauche Effect: Selectivity Regulated by Multiple H→F Bioisosterism

Fluorinated motifs have a venerable history in drug discovery, but as C(sp3 )-F-rich 3D scaffolds appear with increasing frequency, the effect of multiple bioisosteric changes on molecular recognition requires elucidation. Herein we demonstrate that installation of a 1,3,5-stereotriad, in the substrate for a commonly used lipase from Pseudomonas fluorescens does not inhibit recognition, but inverts stereoselectivity. This provides facile access to optically active, stereochemically well-defined organofluorine compounds (up to 98 % ee). Whilst orthogonal recognition is observed with fluorine, the trend does not hold for the corresponding chlorinated substrates or mixed halogens. This phenomenon can be placed on a structural basis by considering the stereoelectronic gauche effect inherent to F-C-C-X systems (σ→σ*). Docking reveals that this change in selectivity (H versus F) with a common lipase results from inversion in the orientation of the bound substrate being processed as a consequence of conformation. This contrasts with the stereochemical interpretation of the biogenetic isoprene rule, whereby product divergence from a common starting material is also a consequence of conformation, albeit enforced by two discrete enzymes.

Rapid mass spectral fingerprinting of complex mixtures of decomposed lignin: Data-processing methods for high-resolution full-scan mass spectra

Lignin is the second most abundant natural biopolymer and its wastes are significant sources for renewable chemicals as an alternative to conventional fossil fuels. Consequently, chemical characterization methods are required to assess the content of valuable chemicals contained in these complex lignin wastes. This short overview summarizes rapid data-processing methods developed in our laboratory for application to full-scan raw data from high-resolution mass spectrometry experiments of decomposed lignin samples. The discussed graphical and statistical methods support the initial classification and elucidation of the main structural features of the lignin components without the need for time-consuming tandem mass spectrometry analyses.

Lewis Acid-Promoted Regio- and Diastereoselective Cross-Coupling of Aryl-Substituted 1,2-Diols and Boronic Acids

A Lewis acid-promoted highly regio- and diastereoselective C(sp³)-C(sp²) cross-coupling reaction between unprotected aryl-substituted 1,2-diols and styryl-, aryl-, heteroaryl-, and polyarylboronic acids has been developed in a one-pot procedure. The regioselective opening of aryl-substituted cyclic boronic esters promoted by a Lewis acid followed by subsequent intramolecular 1,4-transfer of the carbon ligand from boron to a resonance-stabilized benzylic carbenium ion minimizing the allylic 1,3-strain in a stereoselective fashion led to the corresponding α-substituted syn-phenylethyl alcohols. The synthetic utility of the method was illustrated by a short and efficient enantioselective synthesis of cherylline diethyl ether (-)-16.

Bicyclic acetals: biological relevance, scaffold analysis, and applications in diversity-oriented synthesis

The chemoinformatics analysis of fused, spiro, and bridged bicyclic acetals is instrumental for the DOS of natural product-inspired molecular collections.

Informing Molecular Design by Stereoelectronic Theory: The Fluorine Gauche Effect in Catalysis

The axioms of stereoelectronic theory constitute an atlas to navigate the contours of molecular space. All too rarely lauded, the advent and development of stereoelectronic theory has been one of organic chemistry's greatest triumphs. Inevitably, however, in the absence of a comprehensive treatise, many of the field's pioneers do not receive the veneration that they merit. Rather their legacies are the stereoelectronic pillars that persist in teaching and research. This ubiquity continues to afford practitioners of organic chemistry with an abundance of opportunities for creative endeavor in reaction design, in conceiving novel activation modes, in preorganizing intermediates, or in stabilizing productive transition states and products. Antipodal to steric governance, which mitigates destabilizing nonbonding interactions, stereoelectronic control allows well-defined, often complementary, conformations to be populated. Indeed, the prevalence of stabilizing hyperconjugative interactions in biosynthetic processes renders this approach to molecular preorganization decidedly biomimetic and, by extension, expansive. In this Account, the evolution and application of a simple donor-acceptor model based on the fluorine gauche effect is delineated. Founded on reinforcing hyperconjugative interactions involving C(sp³)-H bonding orbitals and C(sp³)-X antibonding orbitals [σ_C-H → σ_C-X*], this general stratagem has been used in conjunction with an array of secondary noncovalent interactions to achieve acyclic conformational control (ACC) in structures of interest. These secondary effects range from 1,3-allylic strain (A^1,3) through to electrostatic charge-dipole and cation-π interactions. Synergy between these interactions ensures that rotation about strategic C(sp³)-C(sp³) bonds is subject to the stereoelectronic requirement for antiperiplanarity (180°). Logically, in a generic [X-CH₂-CH₂-Y] system (X, Y = electron withdrawing groups) conformations in which the two C(sp³)-X bonds are synclinal (i.e., gauche) are significantly populated. As such, simple donor-acceptor models are didactically and predictively powerful in achieving topological preorganization. In the case of the gauche effect, the low steric demand of fluorine ensures that the remaining substituents at the C(sp³) hybridized center are placed in a predictable area of molecular space: An exit vector analogy is thus appropriate. Furthermore, the intrinsic chemical stability of the C-F bond is advantageous, thus it may be considered as an inert conformational steering group: This juxtaposition of size and electronegativity renders fluorinated organic molecules unique among the organo-halogen series. Cognizant that the replacement of one fluorine atom in the difluoroethylene motif by another electron withdrawing group preserves the gauche conformation, it was reasoned that β-fluoroamines would be intriguing candidates for investigation. The burgeoning field of Lewis base catalysis, particularly via iminium ion activation, provided a timely platform from which to explore a postulated fluorine-iminium ion gauche effect. Necessarily, activation of this stereoelectronic effect requires a process of intramolecularization to generate the electron deficient neighboring group: Examples include protonation, condensation to generate iminium salts, or acylation. This process, akin to substrate binding, has obvious parallels with enzymatic catalysis, since it perturbs the conformational dynamics of the system [ synclinal-endo, antiperiplanar, synclinal-exo]. This Account details the development of conformationally predictable small molecules based on the [X-C_α-C_β-F] motif through a logical process of molecular design and illustrates their synthetic value in enantioselective catalysis.

Iriomoteolides: novel chemical tools to study actin dynamics

Despite its promising biological profile, the cellular targets of iriomoteolide-3a, a novel 15-membered macrolide isolated from Amphidinium sp., have remained unknown. A small library of non-natural iriomoteolide-3a analogues is presented here as a result of a novel, highly convergent, catalysis-based scaffold-diversification campaign, which revealed the suitable sites for chemical editing in the original core. We provide compelling experimental evidence for actin as one of iriomoteolides' primary cellular targets, establishing the ability of these secondary metabolites to inhibit cell migration, induce severe morphological changes in cells and cause a reversible cytoplasmic retraction and reduction of F-actin fibers in a time and dose dependent manner. These results are interpreted in light of the ability of iriomoteolides to stabilize F-actin filaments. Molecular dynamics simulations provide evidence for iriomoteolide-3a binding to the barbed end of G-actin. These results showcase iriomoteolides as novel and easily tunable chemical probes for the in vitro study of actin dynamics in the context of cell motility processes including cell invasion and division.

Electrophile-Dependent Alkylations of Lithiated 4-Alkoxyalk-4-enenitriles

Alkylations of acyclic, lithiated 4-alkoxyalk-4-enenitriles are highly diastereoselective with an unusual electrophile-dependent preference. Alkyl halides, sulfur, chlorine, and acyl cyanide electrophiles intercept a series of lithiated 4-alkoxyalk-4-enenitriles to install contiguous tertiary-quaternary stereocenters with high diastereoselectivity, whereas acylations with ester and carbonate electrophiles are modestly selective. The diastereoselectivity is consistent with electrophilic attack on the most accessible face of the lithated nitrile for most electrophiles except ester and carbonate electrophiles, which likely precoordinate the lithiated nitrile before acylation. Intercepting the lithiated 4-alkoxyalk-4-enenitriles with a range of electrophiles provide insight into the criteria for otherwise challenging diastereoselective alkylations and acylations of acyclic nitriles.

Stereochemistry and biological activity of chlorinated lipids: a study of danicalipin A and selected diastereomers

The syntheses of (+)-16-epi- and (+)-11,15-di-epi-danicalipin A (2 and 3) are reported. The conformations of the parent diols 5 and 6 as well as the corresponding disulfates 2 and 3 were determined on the basis of J-based configuration analysis and supported by calculations. The impact of configuration on membrane permeability in Gram-negative bacteria and mammalian cell lines was assessed as well as cytotoxicity. Although diastereomer 2 showed similar behavior to natural (+)-danicalipin A (1), strikingly, the more flexible C11,C15-epimer 3 had no effect on permeability and proved equally or more toxic towards multiple cell lines.

Catalytic 1,3-Difunctionalization via Oxidative C-C Bond Activation

Electronegative substituents arrayed in 1,3-relationships along saturated carbon frameworks can exert strong influence over molecular conformation due to dipole minimization effects. Simple and general methods for incorporation of such functional group relationships could thus provide a valuable tool for modulating molecular shape. Here, we describe a general strategy for the 1,3-oxidation of cyclopropanes using aryl iodine(I-III) catalysis, with emphasis on 1,3-difluorination reactions. These reactions make use of practical, commercially available reagents and can engage a variety of substituted cyclopropane substrates. Analysis of crystal and solution structures of several of the products reveal the consistent effect of 1,3-difluorides in dictating molecular conformation. The generality of the 1,3-oxidation strategy is demonstrated through the catalytic oxidative ring-opening of cyclopropanes for the synthesis of 1,3-fluoroacetoxylated products, 1,3-diols, 1,3-amino alcohols, and 1,3-diamines.

Emulating Natural Product Conformation by Cooperative, Non-Covalent Fluorine Interactions

Pervasive in Nature, the propane unit is an essential component of numerous bioactive molecules. These range from acyclic systems, such as the neurotransmitter γ-aminobutyric acid, through to the bicyclic nuclei of various chromanes and dihydrobenzofurans. In the latter case, cyclisation via cyclic ether formation ensures a highly pre-organised structure, whilst linear scaffolds display more dynamic conformational behaviour resulting from rotation about the two internal C(sp³ )-C(sp³ ) bonds. In this study, the replacement of -[CH₂ ]- units by -[CHF]- centres is evaluated as a strategy to achieve acyclic conformational control by hindering these internal rotations. Reinforcing, non-covalent fluorine interactions are validated as powerful design features that result in programmable conformational behaviours: These are encoded by the relative configuration of each centre. By exploiting cooperative neighbouring stereoelectronic effects in a multi-vicinal fluoroalkane it is possible to emulate the overall conformation of the dihydrobenzofuran scaffold found in a variety of natural products with an acyclic mimic. This is described as a function of two bond vectors at the chain termini and validated by combined theoretical, crystallographic and spectroscopic analyses. In view of the favourable physicochemical properties associated with fluorine introduction, this approach to bioactive scaffold design may prove to be expansive.

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.

Assembly-line synthesis of organic molecules with tailored shapes

Molecular assembly lines, where molecules undergo iterative processes involving chain elongation and functional group manipulation are hallmarks of many processes found in Nature. We have sought to emulate Nature in the development of our own molecular assembly line through iterative homologations of boronic esters. Here we report a reagent (α-lithioethyl triispopropylbenzoate) which inserts into carbon-boron bonds with exceptionally high fidelity and stereocontrol. Through repeated iteration we have converted a simple boronic ester into a complex molecule (a carbon chain with ten contiguous methyl groups) with remarkably high precision over its length, its stereochemistry and therefore its shape. Different stereoisomers were targeted and it was found that they adopted different shapes (helical/linear) according to their stereochemistry. This work should now enable scientists to rationally design and create molecules with predictable shape, which could have an impact in all areas of molecular sciences where bespoke molecules are required.

Generation of stereochemically defined tetrasubstituted enolborinates by 1,4-hydroboration of α,β-unsaturated morpholine carboxamides with (diisopinocampheyl)borane

On all fours: The title reaction with (Ipc)2 BH provides tetrasubstituted enolborinates which undergo aldol reactions with aldehydes to form products with all-carbon quaternary centers with exceptional diastereo- and enantioselectivity. A change to the substitution pattern of the starting amide leads to either diastereomer of the α-methyl-α-ethyl-β-hydroxy carboxamide (1 or 2).

Crotylboron-based synthesis of the polypropionate units of chaxamycins A/D, salinisporamycin, and rifamycin S

Syntheses of the C(15)-C(27) fragments of chaxamycins A/D, rifamycin S, and the C(12)-C(24) fragment of salinisporamycin have been accomplished in 10 steps from commercially available starting materials. Three crotylboron reagents were utilized to construct the seven contiguous stereocenters in these fragments with excellent stereoselectivity.

A biomimetic polyketide-inspired approach to small-molecule ligand discovery

The discovery of new compounds for the pharmacological manipulation of protein function often embraces the screening of compound collections, and it is widely recognized that natural products offer beneficial characteristics as protein ligands. Much effort has therefore been focused on “natural product-like” libraries, yet the synthesis and screening of such libraries is often limited by one or more of the following: modest library sizes and structural diversity, conformational heterogeneity, and the costs associated with the substantial infrastructure of modern high-throughput screening centers. Here, we describe the design and execution of an approach to this broad problem by merging principles associated biologically-inspired oligomerization and the structure of polyketide-derived natural products. A novel class of chiral and conformationally-constrained oligomers is described (termed “chiral oligomers of pentenoic amides” – COPAs) that offers compatibility with split-and-pool methods and can be screened en masse in a batch mode. We demonstrate that a COPA library containing 160,000 compounds is a useful source of novel protein ligands by identifying a non-covalent synthetic ligand to the DNA-binding domain of the p53 transcription factor.

Solution- and solid-state conformations of C(α)-alkyl analogues of methylphenidate (Ritalin) salts: avoidance of gauche(+)gauche(-) interactions

Alkyl analogues of methylphenidate (Ritalin) salts are slow onset, long duration dopamine reuptake inhibitors with a potential use as a cocaine abuse pharmacotherapy. X-ray crystallographic studies and nuclear magnetic resonance (NMR) investigations strongly suggest that avoidance of sterically unfavorable gauche(-)gauche(+) orientations effectively influences both the C(α)-alkyl side chain conformation and the formation of a predominant rotamer about the CH-CH bond ligating piperidine and C(Ar)R moieties. The favored CH-CH rotamer in D(2)O and in CD(2)Cl(2) of the pharmacologically interesting i-Bu and CH(2)-cyc-Pnt (RS,RS)-salts has the same antiperiplanar arrangement that was found in the crystal structures, although there clearly is a fast equilibrium involving smaller amounts of synclinal partners. While the rotamer in the (RS,SR)-i-Bu HCl crystal structure exhibits a synclinal orientation for the vicinal pair of adjacent methine protons, the weighted time-averaged arrangement for these protons becomes almost completely antiperiplanar when the crystals are dissolved in D(2)O. Increased steric congestion around the CH-CH bond in the analogous N-methyl tertiary ammonium salts seems to augment the quantity of the preferred rotamer within the mixture. The stereochemistry of the species observed via NMR seems to arise from specific combinations of N-methyl orientation and avoidance of sterically unfavorable gauche(-)gauche(+) arrangements.