Retrieving neuronal orientations using 3D scanning SAXS and comparison with diffusion MRI.

While diffusion MRI (dMRI) is currently the method of choice to non-invasively probe tissue microstructure and study structural connectivity in the brain, its spatial resolution is limited and its results need structural validation. Current ex vivo methods employed to provide 3D fiber orientations have limitations, including tissue-distorting sample preparation, small field of view or inability to quantify 3D fiber orientation distributions. 3D fiber orientation in tissue sections can be obtained from 3D scanning small-angle X-ray scattering (3D sSAXS) by analyzing the anisotropy of scattering signals. Here we adapt the 3D sSAXS method for use in brain tissue, exploiting the high sensitivity of the SAXS signal to the ordered molecular structure of myelin. We extend the characterization of anisotropy from vectors to tensors, employ the Funk-Radon-Transform for converting scattering information to real space fiber orientations, and demonstrate the feasibility of the method in thin sections of mouse brain with minimal sample preparation. We obtain a second rank tensor representing the fiber orientation distribution function (fODF) for every voxel, thereby generating fODF maps. Finally, we illustrate the potential of 3D sSAXS by comparing the result with diffusion MRI fiber orientations in the same mouse brain. We show a remarkably good correspondence, considering the orthogonality of the two methods, i.e. the different physical processes underlying the two signals. 3D sSAXS can serve as validation method for microstructural MRI, and can provide novel microstructural insights for the nervous system, given the method's orthogonality to dMRI, high sensitivity to myelin sheath's orientation and abundance, and the possibility to extract myelin-specific signal and to perform micrometer-resolution scanning.

A novel method to remove the background from x-ray diffraction signal.

The first step that is required to extract the correct information from a two-dimensional (2D) diffraction signature is to remove the background accurately. However, direct background subtraction inevitably overcorrects the signal as it does not take into account the attenuation by the sample. Other traditional background removal methods, such as the rolling ball technique, can separate sharp diffraction peaks of crystalline materials from their background. These methods are unsuitable for biological tissue, which is amorphous and does not have sharp diffraction peaks. This technical note proposes a novel method that combines peak fitting and experimental results to estimate the background for 2D XRD signals.

Characterization of the NISTmAb Reference Material using small-angle scattering and molecular simulation : Part I: Dilute protein solutions.

Both conformational and colloidal stability of therapeutic proteins must be closely monitored and thoroughly characterized to assess the long-term viability of drug products. We characterized the IgG1 NISTmAb reference material in its histidine formulation buffer and report our findings on the higher order structure and interactions of NISTmAb under a range of conditions. In this paper we present the analysis of experimental small-angle scattering data with atomistic molecular simulations to characterize the monodisperse dilute solution of NISTmAb. In part II we describe the characterization of the NISTmAb at high protein concentration (Castellanos et al. 2018). The NISTmAb was found to be a flexible protein with a radius of gyration of 49.0 ± 1.2 Å in histidine formulation buffer using a variety of neutron and X-ray scattering measurements. Scattering data were then modeled using molecular simulation. After building and validating a starting NISTmAb structure from the Fc and Fab crystallographic coordinates, molecular dynamics and torsion-angle Monte Carlo simulations were performed to explore the configuration space sampled in the NISTmAb and obtain ensembles of structures with atomistic detail that are consistent with the experimental data. Our results indicate that the small-angle scattering profiles of the NISTmAb can be modeled using ensembles of flexible structures that explore a wide configuration space. The NISTmAb is flexible in solution with no single preferred orientation of Fc and Fab domains, but with some regions of configuration space that are more consistent with measured scattering profiles. Analysis of inter-domain atomistic contacts indicated that all ensembles contained configurations where residues between domains are ≤ 4 Å, although few contacts were observed for variable and C H 3 regions. Graphical Abstract Heavy atom self contact maps of the NISTmAb indicate a highly-flexible structure.

Sample and Buffer Preparation for SAXS.

In this book chapter, a practical approach for conducting small angle X-ray scattering (SAXS) experiments is given. Our aim is to guide SAXS users through a three-step process of planning, preparing and performing a basic SAXS measurement. The minimal requirements necessary to prepare samples are described specifically for protein and other macromolecular samples in solution. We address the very important aspects in terms of sample characterization using additional techniques as well as the essential role of accurately subtracting background scattering contributions. At the end of the chapter some advice is given for trouble-shooting problems that may occur during the course of the SAXS measurements. Automated pipelines for data processing are described which are useful in allowing users to evaluate the quality of the data 'on the spot' and consequently react to events such as radiation damage, the presence of unwanted sample aggregates or miss-matched buffers.

Considerations for Sample Preparation Using Size-Exclusion Chromatography for Home and Synchrotron Sources.

The success of a SAXS experiment for structural investigations depends on two precise measurements, the sample and the buffer background. Buffer matching between the sample and background can be achieved using dialysis methods but in biological SAXS of monodisperse systems, sample preparation is routinely being performed with size exclusion chromatography (SEC). SEC is the most reliable method for SAXS sample preparation as the method not only purifies the sample for SAXS but also almost guarantees ideal buffer matching. Here, I will highlight the use of SEC for SAXS sample preparation and demonstrate using example proteins that SEC purification does not always provide for ideal samples. Scrutiny of the SEC elution peak using quasi-elastic and multi-angle light scattering techniques can reveal hidden features (heterogeneity) of the sample that should be considered during SAXS data analysis. In some cases, sample heterogeneity can be controlled using a small molecule additive and I outline a simple additive screening method for sample preparation.

How to Analyze and Present SAS Data for Publication.

SAS is a powerful technique to investigate oligomeric state and domain organization of macromolecules, e.g. proteins and nucleic acids, under physiological, functional and even time resolved conditions. However, reconstructing three dimensional structures from SAS data is inherently ambiguous, as no information about orientation and phase is available. In addition experimental artifacts such as radiation damage, concentration effects and incorrect background subtraction can hinder the interpretation of even lead to wrong results. In this chapter, explanations on how to analyze data and how to assess and minimize the influence of experimental artifacts on the data. Furthermore, guidelines on how to present the resulting data and models to demonstrate the data supports the conclusion being made and that it is not biased by artifacts, will be given.

A Successful Combination: Coupling SE-HPLC with SAXS.

A monodispersed and ideal solution is a central (unique?) requirement of SAXS to allow one to extract structural information from the recorded pattern. On-line Size Exclusion Chromatography (SEC) marked a major breakthrough, separating particles present in solution according to their size. Identical frames under an elution peak can be averaged and further processed free from contamination. However, this is not always straightforward, separation is often incomplete and software have been developed to deconvolve the contributions from the different species (molecules or oligomeric forms) within the sample. In this chapter, we present the general workflow of a SEC-SAXS experiment. We present recent instrumental and data analysis improvements that have improved the quality of recorded data, extended its potential and turn it into a mainstream approach. We describe into some details two specific applications of SEC-SAXS that provide more than just separating associated forms from the particle of interest.

Cross-Validation of Data Compatibility Between Small Angle X-ray Scattering and Cryo-Electron Microscopy.

Cryo-electron microscopy (EM) and small angle X-ray scattering (SAXS) are two different data acquisition modalities often used to glean information about the structure of large biomolecular complexes in their native states. A SAXS experiment is generally considered fast and easy but unveils the structure at very low resolution, whereas a cryo-EM experiment needs more extensive preparation and postacquisition computation to yield a three-dimensional (3D) density map at higher resolution. In certain applications, we may need to verify whether the data acquired in the SAXS and cryo-EM experiments correspond to the same structure (e.g., before reconstructing the 3D density map in EM). In this article, a simple and fast method is proposed to verify the compatibility of the SAXS and EM experimental data. The method is based on averaging the two-dimensional correlation of EM images and the Abel transform of the SAXS data. Orientational preferences are known to exist in cryo-EM experiments, and we also consider these effects on our method. The results are verified on simulations of conformational states of large biomolecular complexes.

Portable near-infrared instruments: Application for quality control of polymorphs in pharmaceutical raw materials and calibration transfer.

This work presents an evaluation of the analytical performance of three different portable near-infrared (NIR) instruments (denominated Port.1, Port.2 and Port.3) for quantifying mebendazole polymorphs (A, B and C) in pharmaceutical raw materials using multivariate calibration models. The performance of the portable instruments was compared with a benchtop one (FT-NIR Frontier spectrometer). In addition, calibration transfer between the benchtop and one of the portable instruments was also performed. For polymorph A, the Port.1 presented the lowest RMSEP value (1.01% w/w) even when compared to the FT-NIR instrument. For polymorphs B and C, the same Port.1 instrument presented RMSEP values of 2.09% w/w and 2.41% w/w, respectively, which were statistically similar to those obtained with the benchtop instrument. The LOD ranges (3.9-5.5 for polymorph A, 3.6-5.1 for polymorph B and 5.7-7.7 for polymorph C) obtained with the Port.1 was higher than those achieved with the benchtop NIR instrument, with high spectral resolution, signal-to-noise ratio and better wavelength reproducibility. Calibration transfer was performed between the benchtop NIR and Port.1 instruments. According to the results, the transferability of models is possible. The results obtained for complete recalibration of the portable instrument and those for the benchtop are comparable. The methods developed demonstrated a flexible, easy, cheap and fast way for quality control of MBZ polymorphs in incoming material, mainly in pharmaceutical laboratory chains.

An integrated pipeline for sample preparation and characterization at the EMBL@PETRA3 synchrotron facilities.

The characterization of macromolecular samples at synchrotrons has traditionally been restricted to direct exposure to X-rays, but beamline automation and diversification of the user community has led to the establishment of complementary characterization facilities off-line. The Sample Preparation and Characterization (SPC) facility at the EMBL@PETRA3 synchrotron provides synchrotron users access to a range of biophysical techniques for preliminary or parallel sample characterization, to optimize sample usage at the beamlines. Here we describe a sample pipeline from bench to beamline, to assist successful structural characterization using small angle X-ray scattering (SAXS) or macromolecular X-ray crystallography (MX). The SPC has developed a range of quality control protocols to assess incoming samples and to suggest optimization protocols. A high-throughput crystallization platform has been adapted to reach a broader user community, to include chemists and biologists that are not experts in structural biology. The SPC in combination with the beamline and computational facilities at EMBL Hamburg provide a full package of integrated facilities for structural biology and can serve as model for implementation of such resources for other infrastructures.

Optimisation of X-ray emission from a laser plasma source for the realisation of microbeam in sub-keV region.

In this work, the X-ray emission generated from a plasma produced by focusing Nd-YAG laser beam on the Mylar and Yttrium targets will be characterised. The goal is to reach the best condition that optimises the X-ray conversion efficiency at 500 eV (pre-edge of the Oxigen K-shell), strongly absorbed by carbon-based structures. The characteristics of the microbeam optical system, the software/hardware control and the preliminary measurements of the X-ray fluence will be presented.

Assessment of respirable crystalline silica analysis using Proficiency Analytical Testing results from 2003-2013.

Analysis of Proficiency Analytical Testing (PAT) results between 2003 and 2013 suggest that the variation in respirable crystalline silica analysis is much smaller today than it was in the period 1990-1998, partly because of a change in sample production procedure and because the colorimetric method has been phased out, although quality improvements in the x-ray diffraction (XRD) or infrared (IR) methods may have also played a role. There is no practical difference between laboratories using XRD or IR methods or between laboratories which are accredited or those which are not. Reference laboratory means (assigned values) are not different from the means of all participants across the current range of mass loading, although there is a small difference in variance in the ratios of all participants to reference laboratory means based on method because the reference laboratories are much more likely to use XRD than are the others. Matrix interference does not lead to biases or substantially larger variances for either XRD or IR methods. Data from proficiency test sample analyses that include results from poorly performing laboratories should not be used to determine the validity of a method. PAT samples are not produced below 40 µg and variance may increase with lower masses, although this is not particularly predictable. PAT data from lower mass loadings will be required to evaluate analytical performance if exposure limits are lowered without change in sampling method. Task-specific exposure measurements for periods shorter than a full shift typically result in lower mass loadings and the quality of these analyses would also be better assured from being within the range of PAT mass loadings. High flow rate cyclones, whose performance has been validated, can be used to obtain higher mass loadings in environments of lower concentrations or where shorter sampling times are desired.

A quality comparison of protein crystals grown under containerless conditions generated by diamagnetic levitation, silicone oil and agarose gel.

High-quality crystals are key to obtaining accurate three-dimensional structures of proteins using X-ray diffraction techniques. However, obtaining such protein crystals is often a challenge. Several containerless crystallization techniques have been reported to have the ability to improve crystal quality, but it is unknown which is the most favourable way to grow high-quality protein crystals. In this paper, a quality comparison of protein crystals which were grown under three containerless conditions provided by diamagnetic levitation, silicone oil and agarose gel was conducted. A control experiment on a vessel wall was also simultaneously carried out. Seven different proteins were crystallized under the four conditions, and the crystal quality was assessed in terms of the resolution limit, the mosaicity and the Rmerge. It was found that the crystals grown under the three containerless conditions demonstrated better morphology than those of the control. X-ray diffraction data indicated that the quality of the crystals grown under the three containerless conditions was better than that of the control. Of the three containerless crystallization techniques, the diamagnetic levitation technique exhibited the best performance in enhancing crystal quality. This paper is to our knowledge the first report of improvement of crystal quality using a diamagnetic levitation technique. Crystals obtained from agarose gel demonstrated the second best improvement in crystal quality. The study indicated that the diamagnetic levitation technique is indeed a favourable method for growing high-quality protein crystals, and its utilization is thus potentially useful in practical efforts to obtain well diffracting protein crystals.

Identification of critical process parameters and its interplay with nanosuspension formulation prepared by top down media milling technology--a QbD perspective.

The purpose of this study was to optimize the process parameters of a poorly soluble drug by top down media milling process using different polymer systems. Process parameters including agitation rate (RPM), size of grinding media and drug content were studied through a Quality by Design (QbD) approach, using three different polymeric stabilizers (HPMC 3 cps, PVP K-30 and HPC-EXF) with the addition of Vitamin E TPGS as a surface active agent. From the statistical analysis, the RPM of the media milling was determined to be the most significant process parameter with respect to influence on particle size. The effects of varying the size of grinding media or drug content were not found to be as significant as the effects of RPM. Finally, the polymeric stabilizer played an important role in the production of nanoparticles. Among the different polymers, HPMC stabilized systems demonstrated superior results with regards to the consistency in producing successful nanoparticles and inhibition of crystal growth during storage. This study established the interplay among the formulation parameters in order to select the design space, which helped us in the identification and rank ordering of critical and noncritical variables related to the quality attributes of nanosuspension formulation during the early phase of product development.

A new generation of crystallographic validation tools for the protein data bank.

This report presents the conclusions of the X-ray Validation Task Force of the worldwide Protein Data Bank (PDB). The PDB has expanded massively since current criteria for validation of deposited structures were adopted, allowing a much more sophisticated understanding of all the components of macromolecular crystals. The size of the PDB creates new opportunities to validate structures by comparison with the existing database, and the now-mandatory deposition of structure factors creates new opportunities to validate the underlying diffraction data. These developments highlighted the need for a new assessment of validation criteria. The Task Force recommends that a small set of validation data be presented in an easily understood format, relative to both the full PDB and the applicable resolution class, with greater detail available to interested users. Most importantly, we recommend that referees and editors judging the quality of structural experiments have access to a concise summary of well-established quality indicators.

Polymorph transformation in paracetamol monitored by in-line NIR spectroscopy during a cooling crystallization process.

The reliable in-line monitoring of pharmaceutical processes has been regarded as a key tool toward the full implementation of process analytical technology. In this study, near-infrared (NIR) spectroscopy was examined for use as an in-line monitoring method of the paracetamol cooling crystallization process. The drug powder was dissolved in ethanol-based cosolvent at 60°C and was cooled by 1°C/min for crystallization. NIR spectra acquired by in-line measurement were interpreted by principal component analysis combined with off-line characterizations via X-ray diffraction, optical microscopy, and transmission electron microscopy. The whole crystallization process appeared to take place in three steps. A metastable form II polymorph of paracetamol was formed and transformed into the stable form I polymorph on the way to the growth of pure form I by cooling crystallization. These observations are consistent with a previous focused beam reflectance method-based study (Barthe et al., Cryst Growth Des 8:3316-3322, 2008).

Complexation and full characterization of the tretinoin and dimethyl-ß-cyclodextrin complex.

The aim of this work is to prepare tretinoin/dimethyl-beta-cyclodextrin complexes and fully characterize them through various analytical techniques. According to the phase solubility studies performed, the equilibrium for maximum complexation is reached in about 8 days presenting an A(L)-type diagram (soluble complexes) corresponding mainly to 1:1 stoichiometry (K(s) = 13,600 M(-1)), although the possibility of the presence of 1:2 complexes was mathematically proven. Differential scanning calorimetry, X-ray diffraction and all the other analytical techniques have proven the presence of true complex formation in all the preparation methods tested. H-NMR and FTIR spectra allowed the selection of the best complexation method. The comparison between Raman spectra revealed that the more relevant feature is the band at 1,573 cm(-1), which corresponds to the entire delocalization of the superconjugated system, and after inclusion is observed as a positive frequency shift. Based on these results and the data obtained by molecular modelling calculations, it is proposed that the structure of the drug included into the cyclodextrin corresponds to the side chain including the functional group COOH. The complex was also analysed by atomic force microscopy to determine its size distribution which was heterogeneous and polymodal. However, it could be observed that they all have the same phase constitution.

A kinetic study of the polymorphic transformation of nimodipine and indomethacin during high shear granulation.

The objective of the present study was to investigate the mechanism, kinetics, and factors affecting the polymorphic transformation of nimodipine (NMD) and indomethacin (IMC) during high shear granulation. Granules containing active pharmaceutical ingredient, microcrystalline cellulose, and low-substituted hydroxypropylcellulose were prepared with ethanolic hydroxypropylcellulose solution, and the effects of independent process variables including impeller speed and granulating temperature were taken into consideration. Two polymorphs of the model drugs and granules were characterized by X-ray powder diffraction analysis and quantitatively determined by differential scanning calorimetry. A theoretical kinetic method of ten kinetic models was applied to analyze the polymorphic transformation of model drugs. The results obtained revealed that both the transformation of modification I to modification II of NMD and the transformation of the α form to the γ form of IMC followed a two-dimensional nuclei growth mechanism. The activation energy of transformation was calculated to be 7.933 and 56.09 kJ·mol(-1) from Arrhenius plot, respectively. Both the granulating temperature and the impeller speed affected the transformation rate of the drugs and, in particular, the high shear stress significantly accelerated the transformation process. By analyzing the growth mechanisms of granules in high-shear mixer, it was concluded that the polymorphic transformation of NMD and IMC took place in accordance with granule growth in a high-shear mixer.

Bioadhesive microspheres for bioavailability enhancement of raloxifene hydrochloride: formulation and pharmacokinetic evaluation.

Raloxifene hydrochloride (R-HCl), a BCS class II drug, remains a mainstay in the prevention and pharmacologic therapy of osteoporosis. Its absolute bioavailability, however, is 2% due to poor solubility and extensive first pass metabolism. The present study describes two simultaneous approaches to improve its bioavailability, complexation of R-HCl with cyclodextrin(s), and formulation of mucoadhesive microspheres of the complex using different proportions of carbopol and HPMC. Microspheres were pale yellow in color, free-flowing, spherical, and porous in outline. The particle size ranged between 3 and 15 µm, and entrapment efficiency was found to be within 81.63% to 87.73%. A significant improvement in the solubility of R-HCl was observed, and it differed with the combination of excipients used. X-ray diffraction and differential scanning calorimetry studies revealed that enhancement in drug solubility was resulted due to a change in its crystallinity within the formulation. Microspheres possessed remarkable mucoadhesion and offered controlled drug release, lasting up to 24 h. They produced a sharp plasma concentration-time profile of R-HCl within 30 min post-administration to Wistar rats. [AUC](0-24 h) was found to be 1,722.34 ng h/ml, and it differed significantly to that of pure drug powder (318.28 ng h/ml). More than fivefold increase in AUC and more than twofold increase in MRT were observed. FT-IR studies evidenced no interaction among drug and excipients. The results of this study showed that mucoadhesive microspheres could be a viable approach to improve the pharmacokinetic profile of R-HCl.

Rietveld refinement in the routine quantitative analysis of famotidine polymorphs.

Accurate, precise and reliable X-ray powder diffraction method was developed for the quantitative determination of famotidine polymorphic forms in their binary mixtures, which slightly outperforms the previously established Raman method. The study highlights the advantage of focused beam transmission geometry in diminishing the effect of preferred orientation in general, and the straightforward transmission foil sample preparation technique in facilitating high-throughput measurements in particular. This combination can provide good quality data for Rietveld refinement which assures more reliable quantitative results than utilizing intensity ratios of selected single reflections. After careful adjustment of profile parameters, simple routine application of the method was achieved.