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.
Authors
- Daniel Maragno Trindade (ORCID: https://orcid.org/0000-0002-8005-8784)
- Agnes A. S. Takeda (ORCID: https://orcid.org/0000-0001-5000-6652)
- Clóvis A. Silva (ORCID: https://orcid.org/0000-0001-9250-6508)
- Thiago M. Cunha (ORCID: https://orcid.org/0000-0003-1084-0065)
- Daniela Barretto Barbosa Trivella (ORCID: https://orcid.org/0000-0002-7505-2345)
- Adriana Fernandes (ORCID: https://orcid.org/0000-0003-3890-5799)
- Evandro Ares de Araújo
- Roberto G. S. Berlinck (ORCID: https://orcid.org/0000-0003-0118-2523)
- Amanda Aparecida de Araújo (ORCID: https://orcid.org/0000-0003-4955-0356)
- Andrey Fabricio Ziem Nascimento (ORCID: https://orcid.org/0000-0003-4692-5263)
- Alisson C. Cardoso (ORCID: https://orcid.org/0000-0002-3051-9976)
- Joane K. Rustiguel (ORCID: https://orcid.org/0000-0002-0900-7175)
- Ariane F. Bertonha (ORCID: https://orcid.org/0000-0002-6651-8641)
- Juliana R. Gubiani (ORCID: https://orcid.org/0000-0002-0930-3628)
- Éverton L. F. Ferreira (ORCID: https://orcid.org/0000-0001-6091-4769)
- Raquel P. Morais Urano
- Rafael de Felício (ORCID: https://orcid.org/0000-0002-3698-940X)
- Raphael Meneghello
Institutions
- Universidade de Ribeirão Preto (BR)
- Universidade Federal de São Carlos (BR)
- Universidade de São Paulo (BR)
- Brazilian Center for Research in Energy and Materials (BR)
- Clinics Hospital of Ribeirão Preto (BR)
- Brazilian Biosciences National Laboratory (BR)
Publication Details
- Journal
- Acta Crystallographica Section F Structural Biology Communications
- Published
- 2025-04-16
- DOI
- https://doi.org/10.1107/s2053230x25001542
- Citations
- 1
- Primary Topic
- Enzyme Structure and Function
- Type
- article
- Field-Weighted Citation Impact
- 0.52
Funders
- Fundação de Amparo à Pesquisa do Estado de São Paulo
- Coordenação de Aperfeiçoamento de Pessoal de Nível Superior
- Ministério da Ciência, Tecnologia e Inovação
- Instituto Serrapilheira