Absolute Structure Determination of API Molecules by MicroED analysis of Cocrystals formed based on Cocrystal Propensity Prediction Calculations

Chandler Greenwell
Applications Scientist

Harsh Shah
Senior Scientist

Jessica Bruhn
Principal Scientist
NanoImaging Services

Of the 35 small molecule drugs approved in 2020, 43% were chiral compounds formulated as enantiopure products. For most chiral small molecule drugs, only one enantiomer is biologically active, while the other enantiomer can potentially lead to unwanted side-effects/toxicity (e.g. thalidomide). Therefore, it is critical that researchers establish ways to purify only the desired enantiomer and use structural characterization techniques to understand which enantiomer is biologically active. Historically, single crystal X-ray diffraction (scXRD) has been the gold standard for establishing the absolute configuration of active pharmaceutical ingredients (APIs), either directly from the measured intensities or by co-crystallization with a chiral probe. Unfortunately, this technique is limited by the need to grow suitably sized crystals, which can be challenging for many APIs. Here, we present a method for obtaining absolute configuration from chiral co-crystals that are too small for scXRD by using microcrystal electron diffraction (MicroED). In order to streamline this approach, we have also employed computational methods to guide co-crystal formation. These computational methods combine a conductor-like model for realistic solvents (COSMO-RS), machine learning (ML) and pKa considerations to virtually screen a large list of potential co-formers. The top co-former hits were then employed in cocrystal screens and potential co-crystals were characterized by light microscopy, X-ray powder diffraction and NMR. Crystalline material was then sent for MicroED structure determination without the need to optimize for the growth of large crystals, resulting in a rapid structure determination and establishment of the absolute configuration of the API. This strategy was employed to determine the absolute configuration of two pharmaceutical compounds: Finafloxacin and Ipragliflozin.