Integrating Synthetic, Bioanalytical, and Computational Approaches to Drug Design

With its origins from a casual hallway conversation between Professor Roger Acey and Kensaku Nakayama some years ago, these two began a collaboration focused on examining the development of inhibitors that targeted butyrylcholinesterase (BChE) at a time when researchers were largely focused on inhibiting acetylcholinesterase (AChE) to treat cognitive loss among patients suffering from Alzheimer's disease (AD). Professors Acey and Nakayama soon realized that simple structural modifications to organophosphorus inhibitors could greatly enhance the selectivity of BChE inhibition over that of AChE. These early observations encouraged their collaboration to search for more effective organophosphorus inhibitors, leading to their initial collaborative publication in 2007.

Soon thereafter, Professor Eric Sorin was enlisted to complement the synthetic and biochemical methods being employed with computer-based modeling and, more recently, this collaboration expanded to include Professor Jason Schwans. The Nakayama, Schwans, and Sorin labs recently published their first collaborative article, "Synthesis, biochemical evaluation, and molecular modeling studies of aryl and arylalkyl di-n-butyl phosphates, effective butyrylcholinesterase inhibitors", in Bioorganic & Medicinal Chemistry (2017, 25, 3171-3181), illustrating the sensitivity of inhibitor activity to chemical modification and providing a structural basis for the striking changes in inhibitor potency. The article was co-authored by five CNSM undergraduate and graduate students.

These observations serve as the basis for additional families of derivatives now under investigation, as well as motivating much more time-consuming and computationally intensive studies to better understand the dynamic nature of the BChE-inhibitor complex. In addition, Professor Kevin Sinchak is contributing his expertise via animal studies to evaluate the potential of previous and future compounds of investigation to treat AD-related cognitive loss. This multi-pronged approach represents a fruitful integration of subfields within our Department aimed at the singular goal of identifying new compounds for potential use in mitigating neurodegenerative diseases.

In 2019 and 2020 this collaboration led to the computationally-driven Journal of Biomolecular Structure & Dynamics article titled "Understanding the enzyme-ligand complex: insights from all-atom simulations of butyrylcholinesterase inhibition", which was co-first-authored by MS Physics graduate Walter Alvarado and MS Chemistry graduate Parker Bremer, and the follow-up to that article titled "Overcoming the Heuristic Nature of k-Means Clustering: Identification and Characterization of Binding Modes from Simulations of Molecular Recognition Complexes" authored by Parker Bremer, undergraduate Chem major Danna De Boer, and undergrad CompSci major Xavier Martinez, which was published in the ACS Journal of Chemical Information and Modeling.  Walter is now a Ph.D. candidate at the University of Chicago and a fellow at NASA, and Parker is pursuing further cheminformatics work in the Ph.D. program at UC Davis.