The Microbiome Artificial Intelligence Drug ENabler (MAIDEN) takes advantage of a large database of disease biology and microbiome datasets to discovery small molecule therapeutics. MAIDEN integrates computational biology and chemistry to increase precision in drug candidate identification. Currently, approximately 50% of approved drugs utilised natural products as the genesis for the development of new therapeutics. Novel structural scaffolds/motifs harnessed from bioactive natural products facilitate the discovery of new molecules with high biological relevance. MAIDEN works with the promising field of microbiome yet delivers to Pharma with an actionable drug modality that complements the existing drug development and regulatory frameworks.