Chemical Biology Discussion Group

FREE

for Members

Chemical Biology Discussion Group

Monday, June 1, 2009

The New York Academy of Sciences

Presented By

 

Recent years have seen an increasing level of dialogue between chemists and biologists, the lines of communication consolidated by the availability of recombinant biotechnology tools for manipulating the chemical structure of genes, and the proteins they encode. This has led to an explosion of interdisciplinary activity at the chemistry/biology interface, now coined chemical biology. The Chemical Biology Discussion Group brings together chemists and biologists interested in hearing about the latest ideas in this rapidly growing field. Meetings of this group will provide a forum for lively discussion and for establishing connections, and perhaps collaborations, between chemists armed with novel technologies and biologists receptive to using these approaches to solve their chosen biological problem.

Speakers

Organizer

Peter Tonge

Stony Brook University

Peter Tonge is in the Department of Chemistry at Stony Brook University. He obtained his B.Sc. and Ph.D. degrees in biochemistry at the University of Birmingham and then moved to the National Research Council of Canada (NRC) in 1986 as a NATO-SERC postdoctoral fellow. After spells at NRC as a Research Associate and a Research Officer, followed by an appointment as a Staff Investigator at The Picower Institute for Medical Research, he joined the faculty at Stony Brook University in 1996 where he is currently a full Professor. His research involves the use of precise information on enzyme mechanisms to develop enzyme inhibitors with a specific focus on antibacterial drug discovery for diseases such as tuberculosis. He also uses steady state and ultrafast vibrational spectroscopy to understand the photochemistry of fluorescent and light-activated proteins. Efforts in his drug discovery program center on the development of slow-onset enzyme inhibitors based on the belief that the long residence times of these compounds on their cellular targets is critical for their in vivo activity (Lu et al, ACS Chem. Bio., 4, 221-231).

Keynote Speaker

Adrian Whitty

Boston University

Adrian Whitty is Associate Professor in the Department of Chemistry, Boston University, where he has worked since 2008. He spent the previous 14 years at Biogen Idec, most recently as Director of Physical Biochemistry leading a group responsible for the structural, biophysical and mechanistic study of drug targets and of protein and small molecules drug candidates. Adrian obtained a B.Sc. in Chemistry at King’s College, University of London and a Ph.D. in Organic Chemistry at the University of Illinois at Chicago, after which he did postdoctoral work with the joined Biogen (now Biogen Idec) in 1993. His research has included elucidation of enzyme mechanisms and enzyme-inhibitor interactions, as well as mechanistic investigations of integrins, immune cell co-stimulatory molecules, and a number of cytokine and growth factor receptors. The unifying theme of his work has been to understand how binding energy is generated through protein-protein or protein-small molecule interactions and how it is used to achieve biological function and specificity. A major focus of his current research is exploration of how the interactions between receptor components in the two-dimensional environment of the cell membrane govern the ability of cells to sense and respond to their extracellular environment (see, for example, Schlee et al., Nature Chemical Biology, 2, 636-44, 2006). A second area of focus is the development of small molecule inhibitors that block protein-protein interactions (see Whitty and Kumaravel, Nature Chemical Biology, 2, 112-18, 2006).

Short Presentations

Renato Bauer

Memorial Sloan-Kettering Cancer Center (Derek Tan Laboratory)

Renato Bauer is a graduate student in the Tri-Institutional Training Program in Chemical Biology (TPCB) at Cornell University. A native of Pepperell, Massachusetts, Bauer received his B.S. in Biochemistry with honors from Stonehill College in 2005. He is currently conducting his doctoral work in the laboratory of Derek Tan at Memorial Sloan–Kettering Cancer Institute in the areas of reaction discovery and method development for the purposes of diversity-oriented synthesis.

Mark Blenner

Columbia University (Scott Banta Laboratory)

Mark Blenner is a 5th year graduate student in the Department of Chemical Engineering at Columbia University. He works in the Protein and Metabolic Engineering Laboratory headed by Scott Banta. Mark will be defending his dissertation, “Design of Stimulus Responsive Peptide and Engineering Biomolecular Recognition into Stimulus Responsive Proteins” at the end of July. Mark will begin a postdoctoral fellowship at the Immune Disease Institute working with Timothy Springer this September.

Guillaume Charron

The Rockefeller University (Howard C. Hang Laboratory)

Guillaume Charron received his M.Sc. in Chemistry from Université de Montréal where he studied the structure-activity relationships of conformationally constrained drugs under the guidance of Professor Stephen Hanessian. He is now pursuing a Ph.D. in Biological Sciences at The Rockefeller University in the Hang Laboratory of Chemical Biology and Microbial Pathogenesis.

Angelo Guainazzi

Stony Brook University (Orlando D. Schärer Laboratory)

I completed my undergraduate and master studies at the Swiss federal Institute of Technology (ETH) in Zurich in 2003. My master thesis was performed in Donald Hilvert lab working on enzyme engineering. I then joint Orlando Schärer group in 2004 at the University of Zurich and moved with the whole group to Stony Brook University one year later where I have work on DNA damage and repair as a PhD student ever since.

Scott Lefurgy

Albert Einstein College of Medicine Yeshiva University (Tom Leyh Laboratory)

Dr. Scott Lefurgy is a postdoctoral fellow at the Albert Einstein College of Medicine in the laboratory of Tom Leyh. He received his Ph.D. from Columbia University, where he studied protein function using in vivo screening and selection methods in the laboratory of Virginia Cornish. Scott holds Bachelor of Science (Biochemistry) and Music (Voice Performance) degrees from the University of Michigan. An accomplished classical singer, he made his Carnegie Hall debut in 2003 and been reviewed by the international magazine Opera.

Tosan Omabegho

New York University (Nadrian C. Seeman Laboratory)

Tosan Omabegho is a doctoral candidate in the School of Engineering and Applied Science at Harvard University. In 2005 he moved to New York City to work with Nadrian Seeman at NYU as a visiting scholar. In the Seeman lab Tosan completed his doctoral research on a synthetic molecular motor constructed from DNA. He is graduating this Spring 09 and is currently looking for a postodoctoral research position.

Abstracts

Keynote Presentation

Expanding the Druggable Proteome: Finding Small Molecule Inhibitors of Protein-Protein Interactions

Adrian Whitty, Boston University

Developing small molecule inhibitors of protein-protein interaction (PPI) interfaces remains among the most difficult challenges facing contemporary drug discovery. In this talk I will discuss some of the factors that determine the "druggability" of PPI targets, what we have learned to date about the strengths and weaknesses of fragment-based approaches for addressing such targets, and what to look for in target sites and in fragment hits to determine which are most likely to be advanceable to pharmaceutically-relevant lead compounds. The talk will be illustrated using unpublished data obtained during a multi-target collaboration between Biogen Idec and Sunesis Pharmaceuticals, co-led by the author, in which Sunesis's proprietary Tethering® technology was used to search for leads against TNFa and other highly challenging protein-protein interaction targets.

Short Presentations

An Asymmetric Synthesis of a Multiscaffold Library for Discovery Screening: A Tethered Cycloaddition and Cycloisomerization Approach

Renato Bauer
Memorial Sloan-Kettering Cancer Center (Derek Tan Laboratory)

Diversity-oriented synthesis (DOS) is a major research area through which the potentials of organic synthesis are currently being tapped to impact biology and medicine. In practice, collections of compounds derived from DOS are screened in a high-throughput manner to find novel small molecules that interact with target proteins in biochemical assays or that modulate cellular pathways in phenotypic assays. Here, we present a DOS strategy that exploits optically active t-butylsulfinamides as lynchpins for the transition metal-mediated cyclizations of enynes or diynes. The required enynes and diynes were synthesized enantioselectively in three steps and, upon treatment with transition metal-based reagents, produced functionalized mono- and bicycles as end products. The present work addresses reactivity patterns of important cycloaddition and cycloisomerization reactions in terms of yield, regioselectivity, and diastereoselectivity, and also demonstrates how a strategically designed synthetic route can rapidly yield novel architectures for biological evaluation. Our particular strategy gives rise to eight different scaffolds based on those found in polycyclic terpenoid and alkaloid natural products.

Synthesis and Molecular Modeling of a New Nitrogen Mustards Interstrand Crosslink

Angelo Guainazzi
Stony Brook University (Orlando D. Schärer Laboratory)

Nitrogen mustards (NM) are a group of bifunctional alkylating agents that react with the N(7) atom of guanine residues forming interstrand crosslinks (ICLs). ICLs are very cytotoxic since they inhibit vital cellular processes such as transcription and replication by covalently linking two opposite DNA strands. Despite the importance of ICL-forming agents in cancer chemotherapy, the mechanism by which these lesions are repaired remains poorly understood. A major impediment in studying ICLs repair has been the limited availability of well-defined substrates. We have developed a new strategy that enables the synthesis of defined site-specific NM-like ICLs in high yields and purity. Our strategy relies on the incorporation of ICL precursors bearing reactive aldehyde functionality on complementary strands of DNA, followed by ICL formation via double reductive amination. The synthetic substrates, which bear chemical modification with respect to therapeutic NM ICLs, were validated through molecular dynamic studies, confirming that the mimic had identical structural features to its natural counterpart. Our synthetic approach furthermore allows for the synthesis of major groove ICLs with different amount of distortion, providing unique and valuable tools for biochemical and cell biological studies of ICL repair.

A Bipedal DNA Brownian Motor with Coordinated Legs

Tosan Omabegho
New York University (Nadrian C. Seeman Laboratory)

Biological bipedal motors, such as kinesin, myosin, and dynein are all examples of coordinated activity between two motor domains that lead to processive linear movement along directionally polar tracks. How such directed motion emerges from domain coordination is a major issue in the effort to create synthetic molecular motors that can cyclically bias Brownian motion using chemical energy as input (1). Synthetic DNA walking devices (2 - 5) are useful systems to explore these questions, due to DNA's programmability and structural robustness. A benchmark goal is the design and construction of controlled autonomous translocators, for example to use in synthetic molecular assembly procedures that emulate nucleic acid polymerases or the ribosome.

To address this problem, we have contructed an autonomous bipedal walker made of DNA that walks along a directionally polar DNA track that is consumed during the walking cycle. This device displays true motor behavior by coordinating the stepping cycle of its two legs as it walks along its track; it does this by having its leading leg catalyze the release of its trailing leg. The release signal, sent from the leading leg to the trailing leg, is mediated by metastable DNA fuel strand complexes (4 - 7), and aided by the structural asymmetry of the track. The basis of our demonstration entails crosslinking aliquots of the walker covalently to its track in successive walking states, showing that the walker can complete a full walking cycle on a stiff linear track whose length could be extended for longer walks.

Bacterial Isoprenoid Biosynthesis as an Antibiotic Target

Scott Lefurgy
Albert Einstein College of Medicine Yeshiva University (Tom Leyh Laboratory)

Streptococcus pneumoniae is a leading cause of death among children worldwide. The increasing prevalence of multi-drug resistant S. pneumoniae continually requires new approaches to combat this threat. Our laboratory has discovered an antibiotic target in this organism—mevalonate kinase (MK), which catalyzes the first step in the conversion of mevalonate to the isoprenoid building block, isopentenyl diphosphate. Mevalonate kinase is potently, allosterically inhibited by diphosphomevalonate (DPM), whereas human MK is not inhibited by DPM. To assess the spectrum of DPM inhibition, MK homologs from pathogenic bacteria were assessed for their sensitivity to DPM. Surprisingly, these homologs are inhibited via a completely different mechanism that appears to hinge on the oligomeric state of the enzyme. This result suggests that DPM may be an exquisitely narrow-spectrum antibiotic capable of killing numerous subspecies of S. pneumoniae without affecting even their closest bacterial relatives. To extend DPM inhibition to a downstream target in the mevalonate pathway, DPM analogs were designed to inactivate DPM decarboxylase by producing a highly reactive carbocation immediately prior to decarboxylation. The absence of covalent adduct formation suggests that, counter to existing dogma, the decarboxylation transition state is concerted. Determination of the transition state structure is underway.

Intrinsically Disordered RTX Motifs as Scaffolds for Engineering Allosterically Controlled Biomolecular Recognition

Mark Blenner
Columbia University (Scott Banta Laboratory)

Directed evolution techniques have matured over recent years and high affinity binders are readily discoverable using numerous protein scaffolds, such as peptides, antibodies and repeat proteins just to name a few. It would be advantageous to be able to control the binding event with an orthogonal effector. Intrinsically disordered proteins are able to form ordered secondary and tertiary structures upon binding a ligand. We describe a Repeat in Toxin (RTX) motif from the adenylate cyclase toxin of Bordetella pertussis. This motif is comprised of 8 glycine and aspartic acid rich nonamers. Calcium binding causes this unstructured protein to form a parallel beta-helix where the calcium binding causes the first six residues to form a turn and last three form a beta-strand. These assemble into a beta-helix, where the strands form parallel beta sheets that present two highly variable residues. This work explores the calcium-induced RTX transition from a disordered to ordered state. CD, FRET and fluorescent spectroscopic methods are used to study this RTX motif and assess potential application as a useful scaffold for designing allosterically controlled biomolecular recognition.

Chemical Reporters for the Visualization and Identification of Fatty-acylated Proteins in Mammalian Cells during Salmonella Infection

Guillaume Charron
The Rockefeller University (Howard C. Hang Laboratory)

Salmonella enterica serovars are a group of Gram-negative facultative intracellular bacteria that infect a wide variety of animals. Salmonella infections are common in humans, causing typhoid fever and gastrointestinal diseases, and are an important public health concern worldwide. Once inside macrophages, Salmonella reside in a niche for their proliferation, Salmonella-containing vacuoles (SCVs), maintained by secreted bacterial protein effectors that modulate the composition of SCVs. Protein lipidation is believed to be an important process in maintaining SCVs since lipidated protein in host cells are differentially recruited or excluded from the SCVs. The lipidation of proteins has traditionally been studied with radioactive lipids, which are cumbersome to use and present low specificity, limiting the detection of less abundant lipidated proteins. Here, we present new chemical tools designed for the detection and identification of fatty-acylated proteins during Salmonella infection. Proteomic analysis of these changes should reveal insights into the specific role of secreted bacterial proteins effectors in reorganizing SCVs.