Elucidating Immune and Inflammatory Diseases on the Atomic and Microbiome Scales
The driving purpose of biomedical science is to understand the molecular mechanisms of disease progression and design tools to enable disruption. In this dissertation, I leverage two disparate scientific fields -- computational chemistry and the microbiome -- to explore the environments that drugs interact with, with an eye toward improving therapeutic development prospects. On the atomic scale, I present our work using molecular dynamics simulations and Markov-state models to characterize the effect of small molecule inhibitors on CCR2, a critical protein target for the treatment of a number of immune or inflammatory diseases. On the microbiome scale, I present several studies investigating the interplay between health, immune and inflammatory diseases, diet, and the community of microbes that inhabit the human gut.