High-throughput Small-angle X-ray Research Articles

Physicochemical and structural insights into lyophilized mRNA-LNP from lyoprotectant and buffer screenings

The surge in RNA therapeutics has revolutionized treatments for infectious diseases like COVID-19 and shows the potential to expand into other therapeutic areas. However, the typical requirement for ultra-cold storage of mRNA-LNP formulations poses significant logistical challenges for global distribution. Lyophilization serves as a potential strategy to extend mRNA-LNP stability while eliminating the need for ultra-cold supply chain logistics. Although recent advancements have demonstrated the promise of lyophilization, the choice of lyoprotectant is predominately focused on sucrose, and there remains a gap in comprehensive evaluation and comparison of lyoprotectants and buffers. Here, we aim to systematically investigate the impact of a diverse range of excipients including oligosaccharides, polymers, amino acids, and various buffers, on the quality and performance of lyophilized mRNA-LNPs. From the screening of 45 mRNA-LNP formulations under various lyoprotectant and buffer conditions for lyophilization, we identified previously unexplored formulation compositions, e.g., polyvinylpyrrolidone (PVP) in Tris or acetate buffers, as promising alternatives to the commonly used oligosaccharides to maintain the physicochemical stability of lyophilized mRNA-LNPs. Further, we delved into how physicochemical and structural properties influence the functionality of lyophilized mRNA-LNPs. Leveraging high-throughput small-angle X-ray scattering (SAXS) and cryogenic transmission electron microscopy (cryo-TEM), we showed that there is complex interplay between mRNA-LNP structural features and cellular translation efficacy. We also assessed innate immune responses of the screened mRNA-LNPs in human peripheral blood mononuclear cells (PBMCs), and showed minimal alterations of cytokine secretion profiles induced by lyophilized formulations. Our results provide valuable insights into the structure-activity relationship of lyophilized formulations of mRNA-LNP therapeutics, paving the way for rational design of these formulations. This work creates a foundation for a comprehensive understanding of mRNA-LNP properties and in vitro performance change resulting from lyophilization.

Chemical screening by time-resolved X-ray scattering to discover allosteric probes.

Drug discovery relies on efficient identification of small-molecule leads and their interactions with macromolecular targets. However, understanding how chemotypes impact mechanistically important conformational states often remains secondary among high-throughput discovery methods. Here, we present a conformational discovery pipeline integrating time-resolved, high-throughput small-angle X-ray scattering (TR-HT-SAXS) and classic fragment screening applied to allosteric states of the mitochondrial import oxidoreductase apoptosis-inducing factor (AIF). By monitoring oxidized and X-ray-reduced AIF states, TR-HT-SAXS leverages structure and kinetics to generate a multidimensional screening dataset that identifies fragment chemotypes allosterically stimulating AIF dimerization. Fragment-induced dimerization rates, quantified with time-resolved SAXS similarity analysis (kVR), capture structure-activity relationships (SAR) across the top-ranked 4-aminoquinoline chemotype. Crystallized AIF-aminoquinoline complexes validate TR-SAXS-guided SAR, supporting this conformational chemotype for optimization. AIF-aminoquinoline structures and mutational analysis reveal active site F482 as an underappreciated allosteric stabilizer of AIF dimerization. This conformational discovery pipeline illustrates TR-HT-SAXS as an effective technology for targeting chemical leads to important macromolecular states.

High-throughput small-angle X-ray scattering (HT-SAXS) pipeline for lipid nanoparticle (LNP) development on the SIBYLS beamline

High-throughput small-angle X-ray scattering (HT-SAXS) pipeline for lipid nanoparticle (LNP) development on the SIBYLS beamline

Investigation of Nucleation and Growth at a Liquid-Liquid Interface by Solvent Exchange and Synchrotron Small-Angle X-Ray Scattering.

Hybrid nanomaterials possess complex architectures that are driven by a self-assembly process between an inorganic element and an organic ligand. The properties of these materials can often be tuned by organic ligand variation, or by swapping the inorganic element. This enables the flexible fabrication of tailored hybrid materials with a rich variety of properties for technological applications. Liquid-liquid interfaces are useful for synthesizing these compounds as precursors can be segregated and allowed to interact only at the interface. Although procedurally straightforward, this is a complex reaction in an environment that is not easy to probe. Here, we explore the interfacial crystallization of mithrene, a supramolecular multi-quantum well. This material sandwiches a well-defined silver-chalcogenide layer between layers of organic ligands. Controlling mithrene crystal size and morphology to be useful for applications requires understanding details of its crystal growth, but the specific mechanism for this reaction remain only lightly investigated. We performed a study of mithrene crystallization at an oil-water interfaces to elucidate how the interfacial free energy affects nucleation and growth. We exchanged the oil solvent on the basis of solvent viscosity and surface tension, modifying the dynamic contact angle and interfacial free energy. We isolated and characterized the reaction byproducts via scanning electron microscopy (SEM). We also developed a high-throughput small angle X-ray scattering (SAXS) technique to measure crystallization at short reaction timescales (minutes). Our results showed that modifying interfacial surface energy affects both the reaction kinetics and product size homogeneity and yield. Our SAXS measurements reveal the onset of crystallinity after only 15 min. These results provide a template for exploring directed synthesis of complex materials via experimental methods.

Novel Amphiphilic Block Copolymers for the Formation of Stimuli-Responsive Non-Lamellar Lipid Nanoparticles.

Non-lamellar lyotropic liquid crystalline (LLC) lipid nanoparticles contain internal multidimensional nanostructures such as the inverse bicontinuous cubic and the inverse hexagonal mesophases, which can respond to external stimuli and have the potential of controlling drug release. To date, the internal LLC mesophase responsiveness of these lipid nanoparticles is largely achieved by adding ionizable small molecules to the parent lipid such as monoolein (MO), the mixture of which is then dispersed into nanoparticle suspensions by commercially available poly(ethylene oxide)–poly(propylene oxide) block copolymers. In this study, the Reversible Addition-Fragmentation chain Transfer (RAFT) technique was used to synthesize a series of novel amphiphilic block copolymers (ABCs) containing a hydrophilic poly(ethylene glycol) (PEG) block, a hydrophobic block and one or two responsive blocks, i.e., poly(4-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)benzyl acrylate) (PTBA) and/or poly(2-(dimethylamino)ethyl methacrylate) (PDMAEMA). High throughput small angle X-ray scattering studies demonstrated that the synthesized ABCs could simultaneously stabilize a range of LLC MO nanoparticles (vesicles, cubosomes, hexosomes, inverse micelles) and provide internal particle nanostructure responsiveness to changes of hydrogen peroxide (H2O2) concentrations, pH and temperature. It was found that the novel functional ABCs can substitute for the commercial polymer stabilizer and the ionizable additive in the formation of next generation non-lamellar lipid nanoparticles. These novel formulations have the potential to control drug release in the tumor microenvironment with endogenous H2O2 and acidic pH conditions.

µDrop: a system for high-throughput small-angle X-ray scattering measurements of microlitre samples.

An automatic sample changer system for measurements of large numbers of liquid samples - the µDrop Sample Changer - is presented. It is based on a robotic arm equipped with a pipetting mechanism, which is combined with a novel drop-based sample holder. In this holder a drop of liquid is suspended between two parallel plates by surface tension. The absence of a transfer line benefits the cleaning, improving the background as well as making it faster and more efficient than most comparable capillary-based systems. The µDrop Sample Changer reaches cycle times below 35 s and can process up to 480 samples in a single run. Sample handling is very reliable, with a drop misplacement chance of about 0.2%. Very low sample volumes (<20 µl) are needed and repeatable measurements were performed down to 6 µl. Using measurements of bovine serum albumin and lysozyme, the performance of the instrument and quality of the gathered data of low and high concentrations of proteins are presented. The temperature of samples can also be controlled during storage and during measurement, which is demonstrated by observing a phase transition of a mesophase-forming lipid solution. The instrument has been developed for use in small-angle X-ray scattering experiments, which is a well established technique for measuring (macro-)molecules. It is commonly used in biological studies, where often large sets of rare samples have to be measured.

Beamline B21: high-throughput small-angle X-ray scattering at Diamond Light Source.

B21 is a small-angle X-ray scattering (SAXS) beamline with a bending magnet source in the 3 GeV storage ring at the Diamond Light Source Ltd synchrotron in the UK. The beamline utilizes a double multi-layer monochromator and a toroidal focusing optic to deliver 2 × 1012 photons per second to a 34 × 40 µm (FWHM) focal spot at the in-vacuum Eiger 4M (Dectris) detector. A high-performance liquid chromatography system and a liquid-handling robot make it possible to load solution samples into a temperature-controlled in-vacuum sample cell with a high level of automation. Alternatively, a range of viscous or solid materials may be loaded manually using a range of custom sample cells. A default scattering vector range from 0.0026 to 0.34 Å-1 and low instrument background make B21 convenient for measuring a wide range of biological macromolecules. The beamline has run a full user programme since 2013.

Micellar Fd3m cubosomes from monoolein – long chain unsaturated fatty acid mixtures: Stability on temperature and pH response

HypothesisControl of the nanostructure of self-assembled systems may be achieved through manipulation of surfactant molecular packing and interfacial curvature. In order to phase engineer the inverse micellar cubosomes in some monoolein-fatty acid systems, lipids with wedge shaped molecular geometry were incorporated to promote the formation of this phase, that is of interest as potential sustained released nanocarriers. ExperimentsLiquid crystalline nanoparticle dispersions of monoolein with some cis unsaturated fatty acids were prepared and their partial temperature-composition phase diagrams and structure were established using high throughput Small Angle X-ray Scattering (SAXS) and cryogenic transmission electron microscopy (cryo-TEM). The pH responsiveness of these systems was evaluated in the presence of phosphate buffered saline (PBS). FindingsThe partial temperature-composition phase diagrams of five nanoparticle formulations containing monoolein and unsaturated fatty acids were established and identified the presence of micellar cubosomes in each of these systems. The results indicate that temperature, fatty acid concentration and structure, as well as pH all directly impact the formation and stability of this phase. Low energy inverse micellar cubic to emulsion phase transformations were identified in the monoolein with oleic acid and vaccenic acid systems at physiological temperatures that may be advantageous for staged therapeutic release strategies in nanomedicine.

Inverse hexagonal and cubic micellar lyotropic liquid crystalline phase behaviour of novel double chain sugar-based amphiphiles

The lyotropic phase behaviour of a library of sugar-based amphiphiles was investigated using high-throughput small-angle X-ray scattering (SAXS). Double unsaturated-chain monosaccharide amphiphiles formed inverse hexagonal and cubic micellar (Fd3m) lyotropic phases under excess water conditions. A galactose-oleyl amphiphile from the library was subsequently formulated into hexosome nanoparticles, which have potential uses as drug delivery vehicles. The nanoparticles were shown to be stable at elevated temperatures and non-cytotoxic up to at least 200μgmL−1.

Online data analysis at the ESRF bioSAXS beamline, BM29

High-throughput small-angle X-ray scattering on proteins in solution (bioSAXS) at synchrotron sources is a commonly used technique in structural biology, which relies on highly automated data acquisition. Data reduction and primary analysis for bioSAXS experiments consist of a well defined series of individual tasks, the automation of which allows a first easy assessment of the quality of collected data and the adjustment of collection strategies if necessary. This article describes both the logic and the technical implementation of the automated processing pipeline for bioSAXS data at the ESRF BM29 beamline using theEDNAframework.

Predicting the Effect of Lipid Structure on Mesophase Formation during in Meso Crystallization

Bicontinuous cubic lipidic materials are increasingly used as crystallization media for in meso crystallization of membrane proteins (MPs). Varying the lipid architecture may assist with encapsulation of larger proteins and promote crystal growth. However, not all lipids are compatible with the components of typical crystallization screens, and compatibility must therefore be checked prior to crystallization trials. The method currently used, high-throughput small-angle X-ray scattering (HT SAXS), may be time-consuming and is costly in valuable MP. We have therefore employed a modeling approach using Bayesian regularized neural networks to accurately predict the complex phase behavior of lipid materials under the influence of the PACT crystallization screen and determine the lipid characteristics that allow a lipid to retain a cubic phase under the multiple components required during an in meso crystallization trial. This information will be used to select robust lipids for use in crystallization trials a...

Characterization of lipid matrices for membrane protein crystallization by high-throughput small angle X-ray scattering

The lipidic cubic phase (LCP) has repeatedly proven to serve as a successful membrane–mimetic matrix for a variety of difficult-to-crystallize membrane proteins. While monoolein has been the predominant lipid of choice, there is a growing need for the characterization and use of other LCP host lipids, allowing exploration of a range of structural parameters such as bilayer thickness and curvature for optimal insertion, stability and crystallogenesis of membrane proteins. Here, we describe the development of a high-throughput (HT) pipeline to employ small angle X-ray scattering (SAXS) – the most direct technique to identify lipid mesophases and measure their structural parameters – to interrogate rapidly a large number of lipid samples under a variety of conditions, similar to those encountered during crystallization. Leveraging the identical setup format for LCP crystallization trials, this method allows the quickly assessment of lipid matrices for their utility in membrane protein crystallization, and could inform the tailoring of lipid and precipitant conditions to overcome specific crystallization challenges. As proof of concept, we present HT LCP–SAXS analysis of lipid samples made of monoolein with and without cholesterol, and of monovaccenin, equilibrated with solutions used for crystallization trials and LCP fluorescence recovery after photobleaching (FRAP) experiments.

High-Throughput Small Angle X-ray Scattering from Proteins in Solution Using a Microfluidic Front-End

This manuscript presents, for the first time, the method of automated structural analysis of biomolecules in solution on a microfluidic chip. A polymer-based micrototal analysis system for high-throughput Small-Angle X-ray Scattering (SAXS) data collection from biological macromolecules has been developed. The bioXTAS chip features an integrated X-ray transparent 200 nL sample chamber and diffusion-based mixing of protein and buffer solutions. Software for fully automated fluidic control, data acquisition, and data analysis has been developed. The proof-of concept is based on data using bovine serum albumin as the model system. It confirms the quality of SAXS data generated from small sample volumes and furthermore validates the on-chip mixing capabilities. SAXS data on the gradual unfolding of BSA induced by an anionic surfactant exemplifies how the bioXTAS chip can be used to follow and identify structural changes and proves the feasibility of high-throughput structural analysis in solution. In total, this shows that the bioXTAS chip has the potential for becoming a powerful tool for automated high-throughput structural analysis of macromolecular systems.