High-throughput Crystallization Research Articles

Influence of Chemical Modifications of the Crystallophore on Protein Nucleating Properties and Supramolecular Interactions Network.

Crystallophores are lanthanide complexes that have demonstrated outstanding induction of crystallization for various proteins. This article explores the effect of tailored modifications of the crystallophore first generation and their impact on the nucleating properties and protein crystal structures. Through high-throughput crystallization experiments and dataset analysis, we evaluated the effectiveness of these variants, in comparison to the first crystallophore generation G1. In particular, the V1 variant, featuring a propanol pendant arm, demonstrated the ability to produce new crystallization conditions for the proteins tested (hen-egg white lysozyme, proteinase K and thaumatin). Structural analysis performed in the case of hen egg-white lysozyme along with Molecular Dynamics simulations, highlights V1's unique behavior, taking advantage of the flexibility of its propanol arm to explore different protein surfaces and form versatile supramolecular interactions.

Exploration of the polymorphic solid-state landscape of an amide-linked organic cage using computation and automation.

Organic cages can possess complex, functionalised cavities that make them promising candidates for synthetic enzyme mimics. Conformationally flexible, chemically robust structures are needed for adaptable guest binding and catalysis, but rapidly exchanging systems are difficult to resolve in solution. Here, we use low-cost calculations and high-throughput crystallisation to identify accessible conformers of a recently reported organic cage by 'locking' them in the solid state. The conformers exhibit varying distances between the internal carboxylic acid groups, suggesting adaptability for binding a wide array of target guest molecules.

High-throughput nanoscale crystallization of dihydropyridine active pharmaceutical ingredients.

Single-crystal X-ray diffraction analysis of small molecule active pharmaceutical ingredients is a key technique in the confirmation of molecular connectivity, including absolute stereochemistry, as well as the solid-state form. However, accessing single crystals suitable for X-ray diffraction analysis of an active pharmaceutical ingredient can be experimentally laborious, especially considering the potential for multiple solid-state forms (solvates, hydrates and polymorphs). In recent years, methods for the exploration of experimental crystallization space of small molecules have undergone a `step-change', resulting in new high-throughput techniques becoming available. Here, the application of high-throughput encapsulated nanodroplet crystallization to a series of six dihydropyridines, calcium channel blockers used in the treatment of hypertension related diseases, is described. This approach allowed 288 individual crystallization experiments to be performed in parallel on each molecule, resulting in rapid access to crystals and subsequent crystal structures for all six dihydropyridines, as well as revealing a new solvate polymorph of nifedipine (1,4-dioxane solvate) and the first known solvate of nimodipine (DMSO solvate). This work further demonstrates the power of modern high-throughput crystallization methods in the exploration of the solid-state landscape of active pharmaceutical ingredients to facilitate crystal form discovery and structural analysis by single-crystal X-ray diffraction.

Identification of the nativeTorpedo californicanicotinic acetylcholine receptor's glycan compositionafter a multi-step sequential purification methodusing MALDI-ToF MS.

The Cys-loop pentameric ligand-gated ion channels comprise a dynamic group of proteins that have been extensively studied for decades, yielding a wealth of findings at both the structural and functional levels. The nicotinic acetylcholine receptor (nAChR) is no exception, as it is part of this large protein family involved in proper organismal function. Our efforts have successfully produced a highly pure nAChR in detergent complex (nAChR-DC), enabling more robust studies to be conducted on it, including beginning to experiment with high-throughput crystallization. Our homogeneous product has been identified and extensively characterized with 100% identity using Nano Lc MS/MS and MALDI ToF/ToF for each nAChR subunit. Additionally, the N-linked glycans in the Torpedo californica-nAChR (Tc-nAChR) subunits have been identified. To study this, the Tc-nAChR subunits were digested with PNGase F and the released glycans were analyzed by MALDI-ToF. The MS results showed the presence of high-mannose N-glycan in all native Tc-nAChR subunits. Specifically, the oligommanose population Man8-9GlcNac2 with peaks at m/z 1742 and 1904 ([M + Na]+ ions) were observed.

Membrane-Based Micro-Volume Dialysis Method for Rapid and High-Throughput Protein Crystallization

Membrane-Based Micro-Volume Dialysis Method for Rapid and High-Throughput Protein Crystallization

Operations of the National Crystallization Center: two decades of high-throughput crystallization efforts fueled by structural genomics

Operations of the National Crystallization Center: two decades of high-throughput crystallization efforts fueled by structural genomics

High-Throughput Crystallization Screening Technique with Transmission PXRD Analysis

The ability to quickly generate and identify crystalline solids for organic compounds in a parallel fashion requires a rapid, adaptable crystallization screening strategy that delivers reliable, valuable, and consistent results. The key to the system is a standard platform small-scale (0.5–2 mg) crystallizer screening array that reproducibly crystallizes compounds and facilitates the presentation of crystallization samples to both an automated polarized light microscope and an instrument capable of PXRD analysis. Data science technologies were leveraged to streamline the workflow of data visualization and processing. The fully developed workflow successfully used both single-crystal and PXRD analyses to identify multiple polymorphs of a test compound in a single screening experiment on 200 mg of input material with commercially available crystallizers and instruments to perform a highly detailed crystallization screening study. The methods and techniques described herein are fully transferrable to those working in the synthetic organic chemistry field.

High-Throughput Screening to Obtain Crystal Hits for Protein Crystallography.

X-ray crystallography is the most commonly employed technique to discern macromolecular structures, but the crucial step of crystallizing a protein into an ordered lattice amenable to diffraction remains challenging. The crystallization of biomolecules is largely experimentally defined, and this process can be labor-intensive and prohibitive to researchers at resource-limited institutions. At the National High-Throughput Crystallization (HTX) Center, highly reproducible methods have been implemented to facilitate crystal growth, including an automated high-throughput 1,536-well microbatch-under-oil plate setup designed to sample a wide breadth of crystallization parameters. Plates are monitored using state-of-the-art imaging modalities over the course of 6 weeks to provide insight into crystal growth, as well as to accurately distinguish valuable crystal hits. Furthermore, the implementation of a trained artificial intelligence scoring algorithm for identifying crystal hits, coupled with an open-source, user-friendly interface for viewing experimental images, streamlines the process of analyzing crystal growth images. Here, the key procedures and instrumentation are described for the preparation of the cocktails and crystallization plates, imaging the plates, and identifying hits in a way that ensures reproducibility and increases the likelihood of successful crystallization.

20 years of crystal hits: progress and promise in ultrahigh-throughput crystallization screening.

Diffraction-based structural methods contribute a large fraction of the biomolecular structural models available, providing a critical understanding of macromolecular architecture. These methods require crystallization of the target molecule, which remains a primary bottleneck in crystal-based structure determination. The National High-Throughput Crystallization Center at Hauptman-Woodward Medical Research Institute has focused on overcoming obstacles to crystallization through a combination of robotics-enabled high-throughput screening and advanced imaging to increase the success of finding crystallization conditions. This paper will describe the lessons learned from over 20 years of operation of our high-throughput crystallization services. The current experimental pipelines, instrumentation, imaging capabilities and software for image viewing and crystal scoring are detailed. New developments in the field and opportunities for further improvements in biomolecular crystallization are reflected on.

Polymorph prediction through observed structural isomorphism leading to a new crystalline form of cannabidiol

A new polymorph of cannabidiol (CBD, form 2), a bioactive phytocannabinoid, was discovered via high-throughput crystallisation. CBD form 2 fits within a series of crystal structures of CBD C-5′ homologues, forming a set of homologous isomorphs.

Exploring the Cocrystal Landscape of Posaconazole by Combining High-Throughput Screening Experimentation with Computational Chemistry.

The development of multicomponent crystal forms, such as cocrystals, represents a means to enhance the dissolution and absorption properties of poorly water-soluble drug compounds. However, the successful discovery of new pharmaceutical cocrystals remains a time- and resource-consuming process. This study proposes the use of a combined computational-experimental high-throughput approach as a tool to accelerate and improve the efficiency of cocrystal screening exemplified by posaconazole. First, we employed the COSMOquick software to preselect and rank cocrystal candidates (coformers). Second, high-throughput crystallization experiments (HTCS) were conducted on the selected coformers. The HTCS results were successfully reproduced by liquid-assisted grinding and reaction crystallization, ultimately leading to the synthesis of thirteen new posaconazole cocrystals (7 anhydrous, 5 hydrates, and 1 solvate). The posaconazole cocrystals were characterized by PXRD, 1H NMR, Fourier transform-Raman, thermogravimetry-Fourier transform infrared spectroscopy, and differential scanning calorimetry. In addition, the prediction performance of COSMOquick was compared to that of two alternative knowledge-based methods: molecular complementarity (MC) and hydrogen bond propensity (HBP). Although HBP does not perform better than random guessing for this case study, both MC and COSMOquick show good discriminatory ability, suggesting their use as a potential virtual tool to improve cocrystal screening.

Calibration-free PAT: Locating selective crystallization or precipitation sweet spot in screenings with multi-way PARAFAC models.

When developping selective crystallization or precipitation processes, biopharmaceutical modalities require empirical screenings and analytics tailored to the specific needs of the target molecule. The multi-way chemometric approach called parallel factor analysis (PARAFAC) coupled with ultraviolet visible light (UV/Vis) spectroscopy is able to predict specific concentrations and spectra from highly structured data sets without the need for calibration samples and reference analytics. These calculated models can provide exploratory information on pure species spectra and concentrations in all analyzed samples by representing one model component with one species. In this work, protein mixtures, monoclonal antibodies, and virus-like particles in chemically defined and complex solutions were investigated in three high-throughput crystallization or precipitation screenings with the aim to construct one PARAFAC model per case. Spectroscopic data sets of samples after the selective crystallization or precipitation, washing, and redissolution were recorded and arranged into a four-dimensional data set per case study. Different reference analytics and pure species spectra served as validation. Appropriate spectral preprocessing parameters were found for all case studies allowing even the application of this approach to the third case study in which quantitative concentration analytics are missing. Regardless of the modality or the number of species present in complex solutions, all models were able to estimate the specific concentration and find the optimal process condition regarding yield and product purity. It was shown that in complex solutions, species demonstrating similar phase behavior can be clustered as one component and described in the model. PARAFAC as a calibration-free approach coupled with UV/Vis spectroscopy provides a fast overview of species present in complex solution and of their concentration during selective crystallization or precipitation, washing, and redissolution.

Rapid high-throughput crystallisation of dihydropyridines

Rapid high-throughput crystallisation of dihydropyridines

The National High-Throughput Crystallization Center and coming hands-on workshops

The National High-Throughput Crystallization Center and coming hands-on workshops

Inhibition of acyl-ACP thioesterase as site of action of the commercial herbicides cumyluron, oxaziclomefone, bromobutide, methyldymron and tebutam.

Understanding the mode and site of action of a herbicide is key for its efficient development, the evaluation of its toxicological risk, efficient weed control and resistance management. Recently, the mode of action (MoA) of the herbicide cinmethylin was identified in lipid biosynthesis with acyl-ACP thioesterase (FAT) as the site of action (SoA). Cinmethylin was registered for selective use in cereal crops for the control of grass weeds in 2020. Here, we present a high-resolution co-crystal structure of FAT in complex with cumyluron identified by a high throughput crystallization screen. We show binding to and inhibition of FAT by cumyluron. Furthermore, in an array of experiments consisting of FAT binding assays, FAT inhibition assays, physiological and metabolic profiling, we tested compounds that are structurally related to cumyluron and identified the commercial herbicides oxaziclomefone, methyldymron, tebutam and bromobutide, with so far unknown sites of action, as FAT inhibitors. Additionally, we show that the previously described FAT inhibitors cinmethylin and methiozolin bind to FAT in a nanomolar range, inhibit FAT enzymatic activity and lead to similar metabolic changes. Based on presented data, we corroborate cinmethylin and methiozolin as potent FAT inhibitors and identify FAT as the SoA of the herbicides cumyluron, oxaziclomefone, bromobutide, methyldymron and tebutam. © 2022 Society of Chemical Industry.

Revealing the effects of microwell sizes on the crystal growth kinetics of active pharmaceutical ingredients by deep learning

In the pharmaceutical industry, high-throughput crystallization (HTC) is an emerging strategy to accelerate the discovery of active pharmaceutical ingredients (APIs) with appropriate crystallization properties. It is typically processed in 96- and 384-well plates, which offer parallel crystallization vessels with microliter-scaled volume. However, the microwell size effect on crystallization kinetics at the scale of microtiters has not been fully investigated and remains unsolved. To address the issue, we proposed a novel deep-learning-based approach to investigate the effects of microwell sizes on the crystal growth kinetics of APIs. With a combination of microscopic imaging and deep learning, the massive information of indomethacin crystals was successfully obtained and analyzed in a high-throughput manner. And the relationships between crystallization properties (the average size, crystal size distribution, and the growth rate of crystals) and the size of the crystallization vessels were successfully revealed, which were further validated by the crystallization of ibuprofen and the scale-up experiment. Our research demonstrated the powerful capability of deep learning in processing complicated crystalline images. Moreover, our findings in the relationships between the size of the crystallization vessels and crystal growth kinetics are of great value in guiding the manufacture of APIs in the pharmaceutical industry.

Abstract 1836: Structural basis for recognition of MUC16 expressed in various cancers

Abstract Background: Overexpressed Mucin 16 (MUC16) is highly related with cancer progression, metastasis, and therapy resistance in multiple malignancies. The proteolytic cleavages of MUC16 form independent bimodular fragments, a circulating shed form known as an ovarian cancer biomarker (CA 125) and a C-terminal tail-connected juxtamembrane region as an unshed form which is critical in determining the unique mechanistic roles of MUC16 and therapeutic interventions. Effective neutralizing antibody for MUC16-positive solid cancers is urgently needed for earlier diagnosis and immunotherapeutic approaches. Methods: The novel 4H11-scFv (single chain antibody) targeting MUC16-juxtamembrane was optimized for mammalian cell usage and Liter-scale cultures of HEK293T were infected with high-titer lentiviral stocks expressing the 4H11-scFv and the recombinant proteins were purified by a series of purification process and prepared for further characterization and crystallization. The sequence corresponding to human MUC16-juxtamembrane was cloned with maltose binding protein (MBP) and expressed by the bacterial system. The purified MBP-fused-MUC16 was prepared for co-crystallization with 4H11-scFv. A series of biochemical studies are performed: Thermal stability measurement of 4H11-scFv, MBP-pull down, Isothermal titration calorimetry (ITC) for interaction analysis, bioactivity of Alexa-labeled 4H11-scFv, analytical size-exclusion chromatography, multi-mutagenesis studies at the interface of 4H11-scFv-MUC16 complex. Crystallizations were performed using high-throughput crystallization screen kits, followed by extensive manual optimization. X-ray diffraction data were collected at the Advanced Photon Source (APS) and processed with HKL2000, PHENIX, CCP4 suite package and COOT. Results: We determined the crystal structures of 4H11-scFv at 2.36 Å and 4H11-scFv-MUC16 at 2.47 Å resolutions, respectively. Structural analysis of a 4H11-scFv demonstrated that all six complementarity-determining regions (CDRs) are composed of 5 loop-like coiled coil regions and 1 short-helix in VH (Heavy chain), while juxtamembrane portion showing flexible loop regions with β-Turns. The complex was stabilized through extensive hydrogen bond-mediated interaction, salt bridge, and cation-π interaction. We identified some specific residues of MUC16, critical to form the complex, from mutagenesis studies. Biochemical analysis demonstrated the 4H11-scFv potently neutralizes MUC16 and stable at the cancer microenvironmental and endosomal pH with a possibility of pre-clinical diagnosis/treatment in various cancers. Conclusion: We investigate the structures and the neutralizing mechanisms for 4H11-scFv targeting the MUC16. Our study offer insight into antibody to neutralize the non-cleaved cell surface retained portion of MUC16 and advance our ability to design anti-MUC16 antibody with improved therapeutic properties. Citation Format: Kwangkook Lee, Kay Perry, Oladapo O. Yeku, David R. Spriggs. Structural basis for recognition of MUC16 expressed in various cancers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 1836.

The Automated Crystallography Pipelines at the EMBL HTX Facility in Grenoble.

EMBL Grenoble operates the High Throughput Crystallization Laboratory (HTX Lab), a large-scale user facility offering high throughput crystallography services to users worldwide. The HTX lab has a strong focus in the development of new methods in macromolecular crystallography. Through the combination of a high throughput crystallization platform, the CrystalDirect technology for fully automated crystal mounting and cryocooling and the CRIMS software we have developed fully automated pipelines for macromolecular crystallography that can be remotely operated over the internet. These include a protein-to-structure pipeline for the determination of new structures, a pipeline for the rapid characterization of protein-ligand complexes in support of medicinal chemistry, and a large-scale, automated fragment screening pipeline enabling evaluation of libraries of over 1000 fragments. Here we describe how to access and use these resources.

The Automated Crystallography Pipelines at the EMBL HTX Facility in Grenoble

EMBL Grenoble operates the High Throughput Crystallization Laboratory (HTX Lab), a large-scale user facility offering high throughput crystallography services to users worldwide. The HTX lab has a strong focus in the development of new methods in macromolecular crystallography. Through the combination of a high throughput crystallization platform, the CrystalDirect technology for fully automated crystal mounting and cryocooling and the CRIMS software we have developed fully automated pipelines for macromolecular crystallography that can be remotely operated over the internet. These include a protein-to-structure pipeline for the determination of new structures, a pipeline for the rapid characterization of protein-ligand complexes in support of medicinal chemistry, and a large-scale, automated fragment screening pipeline enabling evaluation of libraries of over 1000 fragments. Here we describe how to access and use these resources.

Polo: an open-source graphical user interface for crystallization screening.

Polo is a Python-based graphical user interface designed to streamline viewing and analysis of images to monitor crystal growth, with a specific target to enable users of the High-Throughput Crystallization Screening Center at Hauptman-Woodward Medical Research Institute (HWI) to efficiently inspect their crystallization experiments. Polo aims to increase efficiency, reducing time spent manually reviewing crystallization images, and to improve the potential of identifying positive crystallization conditions. Polo provides a streamlined one-click graphical interface for the Machine Recognition of Crystallization Outcomes (MARCO) convolutional neural network for automated image classification, as well as powerful tools to view and score crystallization images, to compare crystallization conditions, and to facilitate collaborative review of crystallization screening results. Crystallization images need not have been captured at HWI to utilize Polo's basic functionality. Polo is free to use and modify for both academic and commercial use under the terms of the copyleft GNU General Public License v3.0.