50 Years of NIGMS-Supported Chemistry Enabling Biomedical Research Abstracts

American Chemical Society Meeting

August 20, 2012

Advances in Palladium-Catalyzed Oxidation Reactions
Melanie Sanford
University of Michigan

This presentation will describe the evolution of and recent progress in an NIH-NIGMS supported project in the Sanford group involving the development of new catalytic processes for C-H and olefin oxidation reactions.

Backwards and Forwards with Molecular and Classical Pharmacology
Brian K. Shoichet
University of California, San Francisco

The recent determination of the structures of G-Protein Coupled Receptors enables the structure-based prediction of new ligands for these classic targets. Unbiased docking screens of over 3 Million ZINC library molecules against the ß2-Adrenergic, the Adenosine A2a, the Dopamine D3, and the Chemokine CXCR4 receptors, have all returned new scaffolds and sub-micromolar affinity ligands with hit rates ranging from 17 to 35%. The structural, computational and chemical space origins of this hit rate will be discussed, as will opportunities for using homology models of these targets (as done with the D3 receptor), for finding agonists as well as antagonists, and for de-orphanizing GPCRs using a structure-based approach.

In contrast to this molecular biology view of pharmacology, which begins with targets and seeks ligands, the pharmacology practiced in the classical period (~1930 to ~1985) began with ligands and used these to define receptors. As peculiar as this direction of information seems to us, in its day it was highly successful. Here we return to this classic idea, seeking unexpected similarities. Using a chemoinformatic method, we quantitatively compare over 3000 targets to one another based on the similarity of their ligands. The relationships that emerge predict previously unknown off-targets for specific drugs and reagents. Applications to predicting adverse drug reactions, identifying the molecular targets in phenotypic screens, and to understanding the targets underlying mechanism of action will be considered.

Defining the Transcriptional Initiation Interaction Network In Vivo
Anna Mapp
University of Michigan

Although it has long been known that proteins called transcriptional activators mediate the assembly of the transcriptional machinery as part of gene up-regulation, it has not been possible to define the direct activator binding events that lead to this assembly. This lack of specific information about activator-transcriptional machinery interactions has been a prominent obstacle in the discovery of pharmacological inhibitors that target particular promoters. To address this we have implemented a site-specific in vivo crosslinking methodology that has enabled the capture and characterization of the direct binding partners of three prototypical transcriptional activators: VP16, Gal4 and Gcn4. These results coupled with transient kinetic data suggest a model in which activators of this class stimulate assembly through a distinct but overlapping set of transient binding interactions. To define the activator-protein interactions targetable for inhibitor development, we have generated small-molecule covalent inhibitors targeted to specific binding surfaces within key coactivators such as CBP.

Complex Molecule Synthesis Enabling Studies at the Chemistry/Biomedical Interface
Daniel Romo
Texas A&M University

Natural products are essential tools for basic cellular studies leading to the identification of medically relevant protein targets and the discovery of potential therapeutic agents. Our total synthesis efforts and synthetic methodology studies are intrinsically coupled to our interests in probing the mode of action of targeted bioactive natural products. In the case of the marine sponge derived natural product, pateamine A, our synthetic and mechanism of action studies in collaboration with Jun Liu's lab (Johns Hopkins) led us to explore eukaryotic protein translation as a therapeutic approach to treat particular cancers that overexpress translation initiation factors and prosurvival proteins as key mechanisms for their uncontrolled proliferation. Our interest in beta-lactone synthesis led us to study novel strategies for inhibition of fatty acid synthase and the proteasome, two therapeutic targets for anticancer chemotherapy in collaboration with Jeff Smith's lab (Sanford-Burnham, La Jolla). In another project, we are studying the chemoselectivity of several reactions to be used as versatile tools for natural product derivatization and bioactive probe synthesis enabling, for example, activity-based protein profiling in collaboration with Ben Cravatt's Lab (Scripps). Selected short stories from these projects performed admirably by graduate/undergraduate students and post-doctoral fellows in my laboratory and generously supported by NIGMS will be described.

Palladium-Catalyzed Cross-Coupling Methods for Applications in Organic Synthesis
Stephen L. Buchwald
Massachusetts Institute of Technology

This talk will describe our work that involves the development of carbon-carbon, carbon-nitrogen, carbon-oxygen and carbon-halogen bond-forming processes of importance for organic synthesis. Our recent progress, applications of the methods and mechanistic studies will be detailed.

Sweet Chemical Signaling: Understanding the Structure-Function Relationships of Carbohydrates in Neurobiology and Cancer
Linda C. Hsieh-Wilson
California Institute of Technology

Carbohydrates comprise one of the largest and most diverse collections of biologically active molecules, and it is increasingly clear that they participate in nearly every aspect of biology. However, relative to their macromolecular peers (i.e., proteins and nucleic acids), carbohydrates remain relatively unexplored, and their structure-function relationships are still poorly understood. Several of the fundamental challenges inherent in studying carbohydrates include: (1) their chemical complexity; (2) the lack of efficient and sensitive analytical methods for their detection and quantification; and (3) their complex chemical synthesis and biosynthesis. We will describe the development of chemical approaches to overcome these fundamental challenges and how the principles and tools of chemistry can be used to uncover new functions for carbohydrates and their associated proteins in neurobiology and cancer.

Inorganic Chemistry Controlling Cellular Physiology and Development
Thomas V. O'Halloran
Northwestern University

Cells must acquire a variety of transition metal ions until they achieve a highly conserved ensemble of metal concentrations known as the metallome. While highly conserved over evolution, metallomes undergo temporal fluxes in pathogenesis, during cellular proliferation and at the earliest stage of development. Metallomes are controlled by metalloregulatory proteins, which sense changes in metal availability and adjust gene expression accordingly. Structural and thermodynamic studies of these metal receptors are providing new insights into the coordination chemistry and allosteric mechanisms that give rise to extreme sensitivity (i.e., zinc changes in femtomolar range and copper in zeptomolar range). Quantitative physical methods (STEM-EDS, ICP-MS, X-ray fluorescence microscopy and fluorescent metal-specific probes) reveal connections between fluxes in subcellular metals and key cellular decisions such as cell cycle entry and exit. New examples where metal fluxes trigger physiological change will be described including those controlling the earliest stage of mammalian development and infectious disease.

Coupling Activities of Helicase and Polymerase at the DNA Replication Fork
Smita S. Patel
UMDNJ-Robert Wood Johnson Medical School

DNA replication is catalyzed by the cooperative action of the DNA polymerase, primase and helicase enzymes. The helicase is a motor protein that uses the energy of NTP hydrolysis to unwind double-stranded DNA and create single-stranded templates for the DNA polymerase to copy. Our studies of phage T7 replication enzymes have shown that the isolated helicase does not efficiently unwind the DNA and its unwinding rate shows a strong dependence on GC-content or DNA stability. The DNA polymerase by itself does not unwind DNA nevertheless it is able to accelerate the helicase through GC-rich regions to enable a uniform rate of DNA synthesis. We are investigating the mechanism of coupling between the helicase and polymerase to understand their cooperative roles at the replication fork. We will discuss recent studies that provide new insights into how the two enzymes are physically and functionally coupled at the replication fork.

Fundamentals of Enzymatic Transition States and Use of the Information
Vern L Schramm
Albert Einstein College of Medicine

Our curiosity about enzymatic transition states led us to develop experimental and computational methods to generate static models of the transition state. The molecular electrostatic potential of the transition state contains sufficient information to provide a blueprint for the design of transition state analogues. Chemical synthesis based on transition state mimicry has provided some of the most powerful enzyme inhibitors known. Transition state analogues against selected targets in this research program have led to several analogues now in human clinical trials. Binding thermodynamics of picomolar and femtomolar transition state analogues with different enzymes show a surprising diversity in sources of binding energy. Crystal structures of enzymes in complexes with transition state analogues provide structural models of enzyme complexes with geometry near the transition state. By comparison with Michaelis complexes, the motions involved in bringing the Michaelis complex to the transition state are revealed. Computational chemistry with starting points from enzyme complexes with transition state analogues provides understanding of transition state lifetimes and protein motions coupled to barrier crossing.

Chemistry in Living Systems
Carolyn R. Bertozzi
University of California, Berkeley

Chemical reactions designed for orthogonality and compatibility with living systems can be harnessed to probe the spatiotemporal dynamics of biopolymers and their various modifications. This talk will focus on recent progress in the development of such bioorthogonal reactions and their applications toward profiling protein glycosylation dynamics associated with development and disease. This research, supported largely by NIGMS, highlights the synergies of "curiosity-driven" and "applications-driven" (i.e., translational) science.