Nature has developed eloquent mechanisms for producing molecules through complex biosynthetic pathways consisting of enzymes as the primary molecular machines. Our goal is to hijack these metabolic pathways to create custom molecules for solving problems related to human health and the environment. The major challenges lie in understanding the mechanism of these dynamic pathways and decoding the relationship between enzyme sequence, structure, and function. Building upon state-of-the-art technologies, we use enhanced sampling molecular dynamics, machine learning, and computational models tightly coupled to experimental results for protein and small molecule design. Recent breakthroughs include uncovering molecular recognition mechanisms in carrier-protein dependent biosynthesis pathways and understanding viral infection.