Several members of the PandemicStop-AI consortium will be joining forces on a new project, ML-driven small molecule design of Klebsiella-specific antibiotics, which has received US$3.8 million in funding from the Gates Foundation (over 3 years). The team, co-led by PandemicStop-AI director Yves Brun and fellow member Mike Tyers, will tackle antimicrobial resistance in Klebsiella pneumoniae, a critical-priority pathogen responsible for nearly 20% of global deaths linked to AMR. Their efforts will contribute to a new international consortium, Gram-Negative Antibiotic Discovery Innovator (Gr-ADI), established by the Gates Foundation, Novo Nordisk Foundation and Wellcome, to accelerate discovery of the next-generation of antibiotics.
Benefiting from expertise and platforms in microbiology, AI, drug discovery, and medicinal chemistry, the project will explore new chemical spaces to design novel antimicrobials effective against Klebsiella, some strains of which resist all known antibiotics. Researchers will generate detailed cellular and molecular “fingerprints” of Klebsiella and its subcellular targets to train predictive and generative AI models, which in turn will propose new molecules effective against the bacterium. In parallel, medicinal chemists will synthesize the most promising candidates to test experimentally, enabling active learning loops to improve drug design. Finally, in collaboration with industry partner Simmunome Inc., the team will develop a digital twin of Klebsiella using AI models trained with experimental data, to understand the bacterium’s antibiotic responses and mechanisms of resistance. Ultimately, this new research initiative will complement PandemicStop-AI’s own activities, offering an additional testbed for the pandemic preparedness platforms developed by our present consortium.
The full Gates team includes PandemicStop-AI members Yves Brun (University of Montreal), Mike Tyers (The Hospital for Sick Children), Yoshua Bengio (University of Montreal), Anne Marinier (University of Montreal), Michal Koziarski (The Hospital for Sick Children), and Alex Hernández-García (University of Montreal), as well as industry partner Simmunome Inc., and a new collaborator Robert Batey (University of Toronto).