High-throughput protein crystallography to empower natural product-based drug discovery

Nature is a rich and largely untapped reservoir of small molecules, the latter historically being the main source of new drugs. Three-dimensional structures of proteins in complex with small-molecule ligands represent key information to progress drug-discovery projects, in particular in the hit-to-lead phase. High-throughput crystallography has been of extensive use in recent years, especially to obtain crystallographic complexes of synthetic ligands and fragments. However, the process of discovering novel bioactive natural products has experienced limitations that have long prevented large drug-discovery programs using this outstanding source of molecules. Recent technologies have contributed to the re-emergence of natural products in modern drug discovery. We present the use of high-throughput protein crystallography to directly capture bioactive natural products from unpurified biota chemical samples using protein crystals. These routines, which are currently in use at the Brazilian Centre for Research in Energy and Materials (CNPEM), are introduced with a description of crystal preparation, automated data collection and processing at the MANACÁ beamline (Sirius, LNLS, CNPEM), along with case examples of bioactive natural product capture using protein crystals. The usefulness of this pipeline, which accelerates the discovery and structural elucidation of both known and previously unknown bioactive natural products, paves the way for the development of innovative therapeutic agents, thus contributing to the new era of natural product-based drug discovery.