Crystal Structure and NMR of an α,δ-Peptide Foldamer Helix Shows Side-Chains are Well Placed for Bifunctional Catalysis: Application as a Minimalist Aldolase Mimic

We report the first NMR and X-ray diffraction (XRD) structures of an unusual 13/11-helix (alternating i, i+1 {NH-O=C} and i, i+3 {C=O-H-N} H-bonds) formed by a heteromeric 1 : 1 sequence of α- and δ-amino acids, and demonstrate the application of this framework towards catalysis. Whilst intramolecular hydrogen bonds (IMHBs) are the clear driver of helix formation in this system, we also observe an apolar interaction between the ethyl residue of one δ-amino acid and the cyclohexyl group of the next δ-residue in the sequence that seems to stabilize one type of helix over another. To the best of our knowledge this type of additional stabilization leading to a specific helical preference has not been observed before. Critically, the helix type realized places the α-residue functionalities in positions proximal enough to engage in bifunctional catalysis as demonstrated in the application of our system as a minimalist aldolase mimic.

Crystal Structure and NMR of an α,δ-Peptide Foldamer Helix Shows Side-Chains are Well Placed for Bifunctional Catalysis: Application as a Minimalist Aldolase Mimic

We report the first NMR and X-ray diffraction (XRD) structures of an unusual 13/11-helix (alternating i, i+1 {NH-O=C} and i, i+3 {C=O-H-N} H-bonds) formed by a heteromeric 1 : 1 sequence of α- and δ-amino acids, and demonstrate the application of this framework towards catalysis. Whilst intramolecular hydrogen bonds (IMHBs) are the clear driver of helix formation in this system, we also observe an apolar interaction between the ethyl residue of one δ-amino acid and the cyclohexyl group of the next δ-residue in the sequence that seems to stabilize one type of helix over another. To the best of our knowledge this type of additional stabilization leading to a specific helical preference has not been observed before. Critically, the helix type realized places the α-residue functionalities in positions proximal enough to engage in bifunctional catalysis as demonstrated in the application of our system as a minimalist aldolase mimic.

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.

Prediction of 15 N chemical shifts by machine learning

We demonstrate the potential for machine learning systems to predict three-dimensional (3D)-relevant NMR properties beyond traditional ¹ H- and ¹³ C-based data, with comparable accuracy to density functional theory (DFT) (but orders of magnitude faster). Predictions of DFT-calculated ¹⁵ N chemical shifts for 3D molecular structures can be achieved using a machine learning system-IMPRESSION (Intelligent Machine PREdiction of Shift and Scalar information Of Nuclei), with an accuracy of 6.12-ppm mean absolute error (∼1% of the δ¹⁵ N chemical shift range) and an error of less than 20 ppm for 95% of the chemical shifts. It provides less accurate raw predictions of experimental chemical shifts, due to the limited size and chemical space diversity of the training dataset used in its creation, coupled with the limitations of the underlying DFT methodology in reproducing experiment.

Accelerating quantitative 13C NMR spectra using an EXtended ACquisition Time (EXACT) method

Accurate quantitative ¹³C NMR spectra can be accelerated by using EXACT (EXtended ACquisition Time) NMR methods which reduce Nuclear Overhauser Enhancement (NOE) during the FID. This allows 30-50% shorter experiment times to be used when achieving a given level of quantitative accuracy.

Monitoring off-resonance signals with SHARPER NMR - the MR-SHARPER experiment

We demonstrate an extension to the SHARPER (Sensitive Homogenous and Refocussed Peaks in Real Time) NMR experiment which allows more than one signal to be monitored simultaneously, while still giving ultra-sharp, homo- and hetero-decoupled NMR signals. This is especially valuable in situations where magnetic field inhomogeneity would normally make NMR a problematic tool, for example when gas evolution is occurring during reaction monitoring. The originally reported SHARPER experiment only works for a single, on-resonance NMR signal, but here we demonstrate the Multiple Resonance SHARPER approach can be developed, which in principle can acquire multiple on-/off-resonance signals simultaneously while retaining the desirable properties of the parent sequence. In practice, the case of two resonances, e.g. those of a reactant and a product, will most of the time be considered for MR-SHARPER, as illustrated here.

Synthesis and pharmacological characterisation of arctigenin analogues as antagonists of AMPA and kainate receptors

(-)-Arctigenin and a series of new analogues have been synthesised and then tested for their potential as AMPA and kainate receptor antagonists of human homomeric GluA1 and GluK2 receptors expressed in HEK293 cells using a Ca²⁺ influx assay. In general, these compounds showed antagonist activity at both receptors with greater activity evident at AMPARs. Schild analysis indicates that a spirocyclic analogue 6c acts as a non-competitive antagonist. Molecular docking studies in which 6c was docked into the X-ray crystal structure of the GluA2 tetramer suggest that (-)-arctigenin and its analogues bind in the transmembrane domain in a similar manner to the known AMPA receptor non-competitive antagonists GYKI53655 and the antiepileptic drug perampanel. The arctigenin derivatives described herein may serve as novel leads for the development of drugs for the treatment of epilepsy.

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.

3× Axial vs 3× Equatorial: The ΔGGA Value Is a Robust Computational Measure of Substituent Steric Effects

We define ΔG_GA as the free energy change for the formal equilibrium: [13]G-H + 1-X-adamantane → [13]G-X + adamantane, where [13]G-H is the C₁₃H₂₂ fragment of all-trans graphane with 3-fold symmetry. This compares with a situation where the group X is equatorial to three cyclohexane rings with one where it is axial to three rings. ΔG_GA values vary from 2.9 (CN) to 145.7 kJ mol^-1 (CCl₃), and this wide range means that ΔG can be calculated with confidence. ΔG_GA values for Me, Et, i-Pr, and t-Bu form a regular series, 34.9, 63.3, 101.6, and 142.0, and clearly reflect the steric size of the groups. We propose a model where the six axial hydrogens surrounding X on [13]G-X provide a nearly circular constriction on the substituent close to its point of attachment but which does not extend far above this. We compare these results with A values and with calculations on 2- and 7-substituted [1(2,3)4]pentamantanes. We show that electronic effects on ΔG_GA values are negligible but that they correlate well with computed cone and solid angles subtended by the substituent.

A community-powered search of machine learning strategy space to find NMR property prediction models

The rise of machine learning (ML) has created an explosion in the potential strategies for using data to make scientific predictions. For physical scientists wishing to apply ML strategies to a particular domain, it can be difficult to assess in advance what strategy to adopt within a vast space of possibilities. Here we outline the results of an online community-powered effort to swarm search the space of ML strategies and develop algorithms for predicting atomic-pairwise nuclear magnetic resonance (NMR) properties in molecules. Using an open-source dataset, we worked with Kaggle to design and host a 3-month competition which received 47,800 ML model predictions from 2,700 teams in 84 countries. Within 3 weeks, the Kaggle community produced models with comparable accuracy to our best previously published 'in-house' efforts. A meta-ensemble model constructed as a linear combination of the top predictions has a prediction accuracy which exceeds that of any individual model, 7-19x better than our previous state-of-the-art. The results highlight the potential of transformer architectures for predicting quantum mechanical (QM) molecular properties.

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.

IMPRESSION - prediction of NMR parameters for 3-dimensional chemical structures using machine learning with near quantum chemical accuracy

The IMPRESSION (Intelligent Machine PREdiction of Shift and Scalar information Of Nuclei) machine learning system provides an efficient and accurate method for the prediction of NMR parameters from 3-dimensional molecular structures. Here we demonstrate that machine learning predictions of NMR parameters, trained on quantum chemical computed values, can be as accurate as, but computationally much more efficient (tens of milliseconds per molecular structure) than, quantum chemical calculations (hours/days per molecular structure) starting from the same 3-dimensional structure. Training the machine learning system on quantum chemical predictions, rather than experimental data, circumvents the need for the existence of large, structurally diverse, error-free experimental databases and makes IMPRESSION applicable to solving 3-dimensional problems such as molecular conformation and stereoisomerism.

Accelerated acquisition in pure-shift spectra based on prior knowledge from 1H NMR

Pure shift NMR with maximum performance by non-uniform sampling with prior knowledge.

High Resolution for Chemical Shifts and Scalar Coupling Constants: The 2D Real-Time J-Upscaled PSYCHE-DIAG

The facile determination of chemical shift and scalar coupling constants in NMR spectra is often prevented by spectral overlap and limited resolution. Here, we present a high-resolution NMR experiment for the simultaneous detection of both resonance frequencies and coupling patterns even with small J-values. A PSYCHE-decoupled DIAG (Pure Shift Yielded by Chirp Excitation- DIAGonal) experiment, which resolves chemical shift in the indirect dimension of a 2D experiment is combined with real-time J-upscaling in order to visualize small coupling constants that would otherwise be hidden in the linewidth of a regular proton or DIAG spectrum.

Genetic and chemical characterisation of the cornexistin pathway provides further insight into maleidride biosynthesis

The biosynthesis of the herbicide cornexistin in the fungus Paecilomyces variotii was investigated by full sequencing of its genome, knockout of key genes within its biosynthetic gene cluster and isolation and identification of intermediate compounds. The general biosynthetic pathway resembles that of byssochlamic acid and other nonadrides in the early stages, but differs in requiring fewer enzymes in the key nonadride dimerisation step, and in the removal of one maleic anhydride moiety.

Improved NOE fitting for flexible molecules based on molecular mechanics data – a case study with S-adenosylmethionine

Using the important biomolecule S-adenosyl methionine as an exemplar, we provide a new, enhanced approach for fitting MD data to high-accuracy NOE data, providing improvements in structure determination.

Perhydrohelicenes and other diamond-lattice based hydrocarbons: the choreography of inversion

Overall inversion in fused cyclohexane oligomers 2, 3, and 4 (all based on cis-decalin 1) occurs by a rolling process involving no more than two adjacent rings in twist-boat conformations at any time. These inverting rings move along the oligomer in processes that are precisely choreographed by the adjacent chairs. Actual inversion mechanisms can be stepwise [CC → TC → TT → C'T → C'C'], as for cis-decalin, but it is shown that a concerted alternative [CC → TC → C'T → C'C'] is enforced in 2. The all-cis,anti,cis-isomers of perhydrohelicenes 4 are based on the diamond lattice and have remarkably low strain energies. Helix inversion in 4 is compared with that in helicenes 5. For both, the intermediates and transition states have shapes broadly like kinked old-style telephone cables. In both cases barriers increase with the length of the system to eventually reach a plateau value of ca. 120 kJ mol-1 for 4, much lower than that for 5 (320-350 kJ mol-1). While rolling inversion only requires two adjacent rings in twist-boat conformations at any instant, inversion in propellane 6 requires all three rings be converted to twist-boats, and the S4 symmetric hydrocarbon 7 requires all four rings to be converted to twist-boats. As a consequence, 7 probably has the highest barrier of any non-oligomeric cis-decalin derived structure (87.3 kJ mol-1 at B3LYP/6-31G*).

Convection enhanced delivery of panobinostat (LBH589)-loaded pluronic nano-micelles prolongs survival in the F98 rat glioma model

Background

The pan-histone deacetylase inhibitor panobinostat is a potential therapy for malignant glioma, but it is water insoluble and does not cross the blood–brain barrier when administered systemically. In this article, we describe the in vitro and in vivo efficacy of a novel water-soluble nano-micellar formulation of panobinostat designed for administration by convection enhanced delivery (CED).

Materials and methods

The in vitro efficacy of panobinostat-loaded nano-micelles against rat F98, human U87-MG and M059K glioma cells and against patient-derived glioma stem cells was measured using a cell viability assay. Nano-micelle distribution in rat brain was analyzed following acute CED using rhodamine-labeled nano-micelles, and toxicity was assayed using immunofluorescent microscopy and synaptophysin enzyme-linked immunosorbent assay. We compared the survival of the bioluminescent syngenic F98/Fischer344 rat glioblastoma model treated by acute CED of panobinostat-loaded nano-micelles with that of untreated and vehicle-only-treated controls.

Results

Nano-micellar panobinostat is cytotoxic to rat and human glioma cells in vitro in a dose-dependent manner following short-time exposure to drug. Fluorescent rhodamine-labelled nano-micelles distribute with a volume of infusion/volume of distribution (Vi/Vd) ratio of four and five respectively after administration by CED. Administration was not associated with any toxicity when compared to controls. CED of panobinostat-loaded nano-micelles was associated with significantly improved survival when compared to controls (n=8 per group; log-rank test, P<0.001). One hundred percent of treated animals survived the 60-day experimental period and had tumour response on post-mortem histological examination.

Conclusion

CED of nano-micellar panobinostat represents a potential novel therapeutic option for malignant glioma and warrants translation into the clinic.

A tendril perversion in a helical oligomer: trapping and characterizing a mobile screw-sense reversal

Helical oligomers of achiral monomers adopt domains of uniform screw sense, which are occasionally interrupted by screw-sense reversals. These rare, elusive, and fast-moving features have eluded detailed characterization. We now describe the structure and habits of a screw-sense reversal trapped within a fragment of a helical oligoamide foldamer of the achiral quaternary amino acid 2-aminoisobutyric acid (Aib). The reversal was enforced by compelling the amide oligomer to adopt a right-handed screw sense at one end and a left-handed screw sense at the other. The trapped reversal was characterized by X-ray crystallography, and its dynamic properties were monitored by NMR and circular dichroism, and modelled computationally. Raman spectroscopy indicated that a predominantly helical architecture was maintained despite the reversal. NMR and computational results indicated a stepwise shift from one screw sense to another on moving along the helical chain, indicating that in solution the reversal is not localised at a specific location, but is free to migrate across a number of residues. Analogous unconstrained screw-sense reversals that are free to move within a helical structure are likely to provide the mechanism by which comparable helical polymers and foldamers undergo screw-sense inversion.

Accurate measurement of long range proton–carbon scalar coupling constants

The accuracy and ease-of-use of various experimental NMR methods for measuringⁿJ_CHvalues is assessed.

The hydrolysis of geminal ethers: a kinetic appraisal of orthoesters and ketals

A novel approach to protecting jet fuel against the effects of water contamination is predicated upon the coupling of the rapid hydrolysis reactions of lipophilic cyclic geminal ethers, with the concomitant production of a hydrophilic acyclic hydroxyester with de-icing properties (Fuel Dehydrating Icing Inhibitors - FDII). To this end, a kinetic appraisal of the hydrolysis reactions of representative geminal ethers was undertaken using a convenient surrogate for the fuel-water interface (D2O/CD3CN 1:4). We present here a library of acyclic and five/six-membered cyclic geminal ethers arranged according to their hydroxonium catalytic coefficients for hydrolysis, providing for the first time a framework for the development of FDII. A combination of (1)H NMR, labelling and computational studies was used to assess the effects that may govern the observed relative rates of hydrolyses.

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.

Plakilactones G and H from a marine sponge. Stereochemical determination of highly flexible systems by quantitative NMR-derived interproton distances combined with quantum mechanical calculations of (13)C chemical shifts

In this paper the stereostructural investigation of two new oxygenated polyketides, plakilactones G and H, isolated from the marine sponge Plakinastrella mamillaris collected at Fiji Islands, is reported. The stereostructural studies began on plakilactone H by applying an integrated approach of the NOE-based protocol and quantum mechanical calculations of (13)C chemical shifts. In particular, plakilactone H was used as a template to extend the application of NMR-derived interproton distances to a highly flexible molecular system with simultaneous assignment of four non-contiguous stereocenters. Chemical derivatization and quantum mechanical calculations of (13)C on plakilactone G along with a plausible biogenetic interconversion between plakilactone G and plakilactone H allowed us to determine the absolute configuration in this two new oxygenated polyketides.

Oxidative dearomatisation: the key step of sorbicillinoid biosynthesis†Electronic supplementary information (ESI) available: Containing all experimental details. See DOI: 10.1039/c3sc52911hClick here for additional data file

A new biosynthetic pathway to the sorbicillinoid natural products is proposed based on the observation of oxidative dearomatisation of dihydrosorbicillin 10b.

An FAD-dependent monooxygenase encoding gene (SorbC) was cloned from Penicillium chrysogenum E01-10/3 and expressed as a soluble protein in Escherichia coli. The enzyme efficiently performed the oxidative dearomatisation of sorbicillin and dihydrosorbicillin to give sorbicillinol and dihydrosorbicillinol respectively. Bioinformatic examination of the gene cluster surrounding SorbC indicated the presence of two polyketide synthase (PKS) encoding genes designated sorbA and sorbB. The gene sorbA-encodes a highly reducing iterative PKS while SorbB encodes a non-reducing iterative PKS which features a reductive release domain usually involved in the production of polyketide aldehydes. Using these observations and previously reported results from isotopic feeding experiments a new and simpler biosynthetic route to the sorbicillin class of secondary metabolites is proposed which is consistent with all reported experimental results.

Properties of new magnetic surfactants

This Article describes the synthesis and detailed characterization of a new set of magnetic surfactants containing lanthanide metal counterions. SQUID magnetometry has been used to elucidate the magnetic phase behavior, and small-angle neutron scattering (SANS) provides evidence of micellar aggregation in aqueous media. This study also reveals that for cationic surfactants in aqueous systems there appears to be no significant increase in magnetic susceptibility after micellization.

Magnetizing DNA and proteins using responsive surfactants

DNA chains and their movement in solvent may now be controlled simply by surfactant binding and the switching "on" and "off" of a magnetic field adding a new paradigm to the study and control, condensation and manipulation of DNA (and other biomolecules). Such control is essential for biotechnological applications such as transfection and the regulation of gene suppression, as well as in materials science concerning soft molecular self-assemblies.

Shear and extensional rheology of cellulose/ionic liquid solutions

In this study, we characterize the shear and extensional rheology of dilute to semidilute solutions of cellulose in the ionic liquid 1-ethyl-3-methylimidazolium acetate (EMIAc). In steady shear flow, the semidilute solutions exhibit shear thinning, and the high-frequency complex modulus measured in small amplitude oscillatory shear flow exhibits the characteristic scaling expected for solutions of semiflexible chains. Flow curves of the steady shear viscosity plotted against shear rate closely follow the frequency dependence of the complex viscosity acquired using oscillatory shear, thus satisfying the empirical Cox-Merz rule. We use capillary thinning rheometry (CaBER) to characterize the relaxation times and apparent extensional viscosities of the semidilute cellulose solutions in a uniaxial extensional flow that mimics the dynamics encountered in the spin-line during fiber spinning processes. The apparent extensional viscosity and characteristic relaxation times of the semidilute cellulose/EMIAc solutions increase dramatically as the solutions enter the entangled concentration regime at which fiber spinning becomes viable.

Anionic surfactant ionic liquids with 1-butyl-3-methyl-imidazolium cations: characterization and application

For the first time a series of anionic surfactant ionic liquids (SAILs) has been synthesized based on organic surfactant anions and 1-butyl-3-methyl-imidazolium cations. These compounds are more environmentally friendly and chemically tunable as compared to other common ionic liquids. A detailed investigation of physicochemical properties highlights potential applications from battery design to reaction control, and studies into aqueous aggregation behavior, as well as structuring in pure ILs, point to possible uses in electrochemistry.