Research in the Du Bois Laboratory spans a broad arc of discovery science – from catalyst and reagent design, mechanistic physical organic chemistry, natural product synthesis, and molecular and cellular biology.  All research projects are connected to long range programmatic goals in chemical synthesis and ion channel chemical biology.  Members of the lab are given the intellectual freedom to develop their own ideas and are encouraged to forge collaborative partnerships within and external to the Department of Chemistry.  The physical proximity of our lab to the Stanford School of Medicine greatly facilitates our close interactions with both research and clinical labs interested in neurobiology and neurophysiology.

Reaction Development and Total Synthesis

Methods Development, Catalysts Design, Mechanistic Investigations, Chemical Synthesis

We have described selective processes and new catalyst systems that enable site-specific modification of aliphatic C–H bonds. Such methods have the potential to alter the practice of assembling small molecules, which we have tried to demonstrate in syntheses of the puffer fish toxin, tetrodotoxin, manzacidins, and agelastatin. We have witnessed an explosion of activity over the past 10 years in the general problem area of C–H functionalization. Nevertheless, supreme challenges remain to be solved if these technologies are to become part of the standard lexicon of chemical synthesis. In particular, the ability to control at the reagent-level with high precision the site of C–H bond modification in complex structures remains an unsolved problem. Borrowing from Nature, we wish to integrate molecular recognition elements within our catalyst complexes as a means for ‘directing’ site selectivity. We have investigated novel dirhodium and diruthenium complexes for C–H amination and both ruthenium and non-metal-based oxidants for C–H hydroxylation, and are attempting to use each of these platforms to further our ideas in molecular recognition. Detailed mechanistic investigations to identify factors that influence catalyst performance are central to this research. Efforts to utilize both amination and hydroxylation methods for the synthesis of molecules such as pactamycin and anisatin are on-going. These problems serve to demonstrate both at the strategic and tactical level the manner in which C–H functionalization can be employed to assemble molecules.

FIGURE 1. Intra- and intermolecular C–H oxidation methods developed by the Du Bois lab.

Ion Channels

Chemical Design & Synthesis, Molecular Biology, Electrophysiology, Imaging, Animal Behavioral Models


FIGURE 2. Live-cell NaV imaging with modified toxins.

We wish to understand at the systems level the role of specific ion channels in electrogenesis and nerve cell conduction. Some of the underlying questions that we are attempting to answer include: 1) what is the rate at which channels are being made and degraded, and are such rates context dependent (i.e., is protein turnover affected by increased neural activity, nerve cell damage, etc.); 2) how are the membrane concentrations and cellular distributions of functional channels changing as a result of nerve insult; and 3) is channel function regulated by neighboring glial cells. Answers to these types of questions will better inform our understanding of molecular mechanisms by which nerve cells respond to external stimuli and to injury. While small molecule chemical design and synthesis play an integral role in this evolving story, as a lab, we are resolved to use any tool necessary for our investigations. To this end, we have spent the past 10 years educating ourselves in neurobiology and developing the necessary skills in molecular biology and electrophys-iology to evaluate selective chemical probes of ion channel function. We conduct experiments across all facets of this work, which include complex small molecule design and synthesis, molecular and cellular biology, whole-cell voltage-clamp electrophysiology, fluorescent and radio-imaging, and murine behavioral studies. These investigations are uniquely enabled through collaborations with the Barres (Neurobiology), Biswal (Radiology), Maduke (MCP), Moerner, Pande, Yeomans (Anesthesiology), & Zare labs.

Our lab has described multi-step chemical syntheses of some of the world’s most infamous neurotoxins. Tetrodotoxin stands as arguably our greatest work, demonstrating the power of methods for C–H functionalization to alter strategic planning in small molecule assembly. This molecule, which acts a potent inhibitor of ion flux through voltage-gated Na+ channels (NaV), has inspired subsequent efforts in my lab to prepare other known modifiers of NaV function, including saxitoxin, gonyautoxins, zetekitoxin AB, batrachotoxin, and aconitine. Each of these natural products poses its own unique set of challenges in total synthesis, and each has provided a framework for shaping our research in methods development. For example, interest in the guanidinium toxins has motivated us to develop oxidative tools for preparing 5-membered ring cyclic guanidine structures. These reactions rely on our expertise and our years of effort in the general problem area of C–H bond functionalization. Batrachotoxin and related steroidal derivatives have led us to consider novel reaction processes for carbocyclic ring formation. And finally, a desire to synthesize aconitine, with its heavily oxygenated frame, has compelled us to seek selective methods for C–H hydroxylation in addition to new, convergent means for poly-carbocyclic ring construction. The uniqueness of these natural products as pharmacological agents for studying NaV structure/function is at the core of our interest in such molecules. The inability to access sufficient quantities of the guanidinium toxins and batrachotoxin and the difficulties associated with semi-synthetic manipulation of such compounds necessitates effective, modular synthetic protocols for their preparation.

FIGURE 3. Naturally occurring modulators of voltage-gated sodium ion channels (NaVs).