UC San Diego

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.