Enhancing Pharma Processes

1. Discovery

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This is a written summary of a live webinar presented on March 19, 2025. The recording and resources are available on the recording page.

Presented by:

Rigaku
Director of Scientific Support, Life Sciences
Amy Syverson
Presenter: Amy Syverson
Rigaku Reagents
General Manager

Webinar summary

This webinar, part of a series on enhancing pharmaceutical processes, focused on analytical techniques that support the early stages of pharmaceutical research, particularly compound discovery. It is tailored for professionals in the pharmaceutical industry who are familiar with analytical tools but may not have extensive experience with crystallographic methods.

Pierre Le Magueres presents single-crystal X-ray crystallography as the most definitive technique for determining the precise structure of a molecule. This method provides detailed, atomic-level information that confirms molecular identity, connectivity, absolute configuration, and crystal form. It can distinguish between salts and cocrystals, detect hydrates and solvates, and determine whether a compound has successfully bound to a target protein. These capabilities are particularly useful in structure-based drug design. While this technique is powerful, it requires crystals of at least one micron in size, and sample preparation can be time-consuming and complex.

When traditional crystallography is not feasible due to small crystal size, electron diffraction—also known as MicroED—offers a compelling alternative. Electron beams interact much more strongly with matter than X-rays, enabling the structural analysis of submicron crystals, often directly from a powder sample. Pierre highlights how this technique can provide crystal structures from nanogram-scale material and be used to perform high-throughput polymorph screening on many individual crystals automatically. This is particularly valuable in early stages of pharmaceutical discovery, where only small quantities of new compounds are available.

The combined use of X-ray and electron diffraction methods provides a powerful toolkit. X-ray diffraction remains the preferred option when suitable crystals are available, but electron diffraction, thanks to its capability to work on nanograms of powder grain by grain, allows researchers to push structural analysis earlier into the discovery timeline, minimizing delays due to characterization bottlenecks.

Following this technical discussion, Amy Syverson presented best practices for managing stock solutions in a research laboratory. She emphasized the importance of preparation and inventory control to maintain smooth and reproducible workflows, especially when using liquid-handling automation. She outlined a framework for understanding stock solution categories, such as buffers, salts, precipitants, and prepared reagent mixtures, and explained how organizing and standardizing these across teams can significantly improve laboratory efficiency. Amy also stressed the value of maintaining digital records, tracking expiration dates, using aseptic techniques, and forecasting chemical usage based on upcoming experimental needs.

Key questions answered in the webinar:

One of the main challenges in pharmaceutical research and quality control, besides funding, is time. Significant time can be lost in unambiguously characterizing new compounds, including understanding their molecular structure and crystal form. This process can be hindered if compounds are difficult to crystallize, require scaling up small amounts, purification, or characterization of polymorphs. Traditional methods like NMR, FTIR, and solid-state powder measurements may not provide complete structural information (e.g., absolute configuration) or are challenging to perform with limited sample amounts or impure bulk materials.

  • Crystal structures provide a clear picture of molecules in their pure crystal form and the arrangement of molecules within the crystal. Key information derived from crystal structures includes:
  • Unambiguous identification of a compound and its molecular connectivity (how atoms are linked).
  • Determination of the absolute configuration (handedness) of chiral drug candidates, which is crucial for their efficacy.
  • Distinguishing between salts and cocrystals based on the position of hydrogen atoms and resulting charge distribution.
  • Assessing whether a drug candidate has inserted itself into the active site of a target protein and how it binds, which is vital for structural biology and screening.
  • Identifying whether solvent or water molecules are incorporated into the crystal lattice (hydrates or solvates).
  • Determining the presence and nature of different polymorphs (different crystal forms of the same compound).

Single crystal X-ray crystallography involves directing a monochromatic and focused X-ray beam onto a single crystal. The interaction of the X-rays with the electrons in the crystal produces discrete reflections, which are recorded on a detector. By rotating the crystal and recording these reflections, the data is mathematically processed using Fourier transform to generate an electron density map. The maxima in this map reveal the positions of atoms, allowing for the determination of the molecular structure and crystal packing. The main limitations of X-ray crystallography relate to crystal quality and size. The tightness of molecular packing and the size of the crystal affect the quality of the diffraction data. X-ray crystallography typically requires crystals that are at least one micron in dimension. Below this size, the interaction of X-rays is too weak for effective analysis, necessitating alternative methods.

Electron diffraction is preferred when X-ray crystallography fails, particularly when dealing with very small crystals or crystalline powders. The interaction of electrons with crystalline matter is much stronger than that of X-ray photons, by several orders of magnitude. This allows electron diffraction to analyze submicron particles, even those with dimensions around 50 nanometers or less. Consequently, electron diffraction can be performed on crystalline powders, eliminating the need to grow larger single crystals. It requires only tiny amounts of sample, making it suitable for analyzing the very first solids obtained during synthesis when traditional methods might not have enough material.

The main advantages of using an electron diffractometer like the Rigaku XtaLAB Synergy-ED are related to crystal size and sample amount. Electron diffraction can analyze submicron crystals, including those found in crystalline powders. This removes the often-time-consuming step of growing larger single crystals. Because only one or a handful of submicron particles are needed, the technique requires only tiny amounts of material. Additionally, the ability to analyze multiple nanocrystals from a powder sample allows for high-throughput screening of polymorphs, which is crucial at any stage of drug research.

Stock solutions are concentrated solutions of common reagents prepared in advance for laboratory experiments. They are essential for many lab settings and can be categorized into types like salt solutions, buffers, precipitants, and prepared reagent solutions (which may contain multiple components). Having stock solutions readily available is important because they are often needed in multiple steps of an experiment. Preparing them ahead of time saves valuable time that would otherwise be spent mixing solutions from scratch for each experiment. This also helps reduce errors and ensures consistency across experiments, which is critical for reliable results.

The five best practices for managing stock solutions are:

  1. Knowing your lab's needs: Tracking and understanding the types and volumes of stock solutions required for upcoming projects, monitoring usage patterns, and establishing clear definitions of when a solution is considered "empty" to avoid running out.
  2. Planning for the future: Anticipating upcoming requirements for stock solutions based on the lab's growth, changes in schedule, and the needs of different instruments.
  3. Keeping an eye on your inventory regularly: Maintaining an accurate logbook or digital record of chemicals and stock solutions on hand, noting details like CAS numbers, grades, vendors, and lot numbers. This helps compare needs to available inventory and prevent using expired stock.
  4. Using a recipe repository: Having a designated place to store and update stock solution recipes, including details like weights, volumes, catalog/lot numbers, dissolution requirements, pH adjustments, and necessary PPE. This ensures consistent preparation and traceability.
  5. Setting team standards: Establishing clear protocols and documentation for stock solution preparation, storage, tracking, and usage. This ensures everyone on the team follows the same procedures, reduces mistakes, improves workflow, and facilitates smooth transitions when team members are unavailable.

Liquid handling instruments can significantly enhance research efficiency and accuracy. However, their performance is highly dependent on a consistent and adequate supply of stock solutions. Without proper stock solution management, inadequate or inconsistent supply can lead to errors in experiments, compromise data integrity, and potentially cause downstream issues. Therefore, effective management of stock solutions is crucial for maximizing the benefits of using liquid handling instrumentation, ensuring smooth workflow, and avoiding delays in high-throughput laboratories. Keeping accurate records of stock solution batches, even without automated systems, is important to track usage and maintain inventory.

Crystallography times editor

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