Microscopy-based high-throughput screening of natural compounds to identify novel host-directed therapeutics for combating intracellular bacteria

• Grant number: 25/08144-9
• Support Opportunities: Research Grants - Young Investigators Grants
• Start date: December 01, 2025
• End date: November 30, 2029
• Field of knowledge: Biological Sciences - Microbiology - Applied Microbiology
• Principal Investigator: Caio Haddad Franco
• Grantee: Caio Haddad Franco
• Host Institution: Institut Pasteur de São Paulo (IPSP). São Paulo , SP, Brazil
• City of the host institution: São Paulo
• Associated researchers: Ana Sofia Bregieiro Eulalio ; Carolina Borsoi Moraes ; Laura Maria Alcântara ; Lucio Holanda Gondim de Freitas Junior ; Regildo Márcio Gonçalves da Silva ; Sergio Schenkman
• Associated scholarship(s): 25/26467-0 - Microscopy-based high-throughput screening of natural compounds to identify novel host-directed therapeutics for combating intracellular bacteria, BP.JP

Abstract

Infections caused by Staphylococcus aureus are the leading cause of death from bacterial pathogens, accounting for over one million deaths annually. The emergence of antibiotic-resistant strains, such as methicillin-resistant S. aureus (MRSA), further worsens the scenario, ranking as the second most deadly cause of antimicrobial resistance. This facultative intracellular pathogen can invade and replicate within professional and non-professional phagocytes, adopting distinct behaviours depending on the host cell and bacterial isolate. The intracellular environment protects the bacteria from immune defences and antibiotics, contributing to persistent and recurrent infections. Even under treatment, many antibiotics fail to penetrate or accumulate within host cells, resulting in ineffective bacterial clearance and contributing to antimicrobial resistance.Host-directed therapy (HDT) has emerged as a promising alternative to overcome the limitations of conventional therapies. Rather than directly targeting the pathogen, HDT modulates host cellular pathways essential for bacterial survival. Despite its success in other bacterial infections, HDT remains underexplored against S. aureus. Natural products represent valuable sources of bioactive molecules with high potential for HDT due to their structural and chemical diversity, polypharmacological properties, and evolutionary interaction with biological targets. Brazil's biodiversity, the richest in the world, greatly expands this potential, offering access to novel compounds with possible innovative mechanisms of action.The MICRONATIB project proposes an innovative HDT discovery approach through the screening of natural products from Brazilian biodiversity, aiming to modulate cellular pathways crucial for the intracellular survival of S. aureus. The project is structured into five key stages: (i) implementation of a phenotypic platform for testing drugs against intracellular S. aureus infection; (ii) screening of 2,000 natural products to evaluate activity against both intracellular and planktonic forms of S. aureus; (iii) characterisation of selected compounds in various host cells, against clinical isolates, and in combination with antibiotics; (iv) application of Cell Painting technology to elucidate mechanisms of action via similarity of phenotypic profiling with reference drugs, followed by molecular validation; and (v) in vivo evaluation of the most promising candidate in a murine model of staphylococcal sepsis.The Young Researcher and Associated Researchers (ARs) bring solid expertise in drug discovery, bacterial infection, natural products, high-content/high-throughput assays, in vivo models, and target deconvolution, key elements for this project's successful execution. The research team will also include a PD researcher, a PhD student, a Master's student, and a technical trainee, with additional institutional support. Essential resources, such as the compound library, clinical isolates, imaging and screening infrastructure, are already available or will be provided by the ARs. Additional equipment will be acquired to expand institutional capabilities. Preliminary tests conducted by the candidate demonstrate project's feasibility, validating the technical and scientific viability of the proposal.By the end of the project, we expect to identify compounds with novel mechanisms of action, characterise native natural products, and uncover previously unknown host-S. aureus interactions. Due to the multidisciplinary nature of the drug discovery pipeline, MICRONATIB will serve as a foundation for future work and collaborations in medicinal chemistry and natural product research, with the potential for patentable discoveries. The results will support the development of innovative antimicrobial therapies, especially against resistant strains, while establishing a new and competitive research line at the Host Institution. (AU)