Chemical Biology Discussion Group Year-End Symposium

Chemical Biology Discussion Group Year-End Symposium

Wednesday, May 25, 2016

The New York Academy of Sciences

Post-translational modification of proteins play a critical role in wide ranging cellular process, increasing the diversity and function of the proteome. Elucidating the mechanisms underlying these processes is thus critical to our understanding of biology, and human health and disease. In 2016, the annual Chemical Biology Year-End symposium will feature distinguished keynote speakers Dr Philip Cole, from Johns Hopkins University Medical School, and Dr Kenneth Duncan, from Epizyme; bringing together academic and industry perspectives in the study of post-translational modification and epigenetics. This will be preceded by shorter, cutting-edge talks that span the scope of chemical biology by graduate students and postdoctoral fellows selected from abstract submissions, and a poster session.

Chemical biology is a diverse and dynamic field involving chemical approaches to studying and manipulating biological systems. The goal of the Academy's Chemical Biology Discussion Group meetings is to enhance interactions among local-area laboratories working in chemical biology and to feature forefront research in chemical biology to the wider community. The meeting traditionally covers a range of current topics in chemical biology, including chemical probe development, organic synthesis, biosynthesis, protein engineering, and drug discovery.

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Member (Student / Postdoc / Resident / Fellow) $0
Nonmember (Academia) $65
Nonmember (Corporate) $75
Nonmember (Non-profit) $65
Nonmember (Student / Postdoc / Resident / Fellow) $30

This event will also be broadcast as a webinar; registration is required.

Please note: Transmission of presentations via the webinar is subject to individual consent by the speakers. Therefore, we cannot guarantee that every speaker's presentation will be broadcast in full via the webinar. To access all speakers' presentations in full, we invite you to attend the live event in New York City where possible.

Webinar Pricing

Member $0
Member (Student / Postdoc / Resident / Fellow) $0
Nonmember (Academia) $20
Nonmember (Corporate) $35
Nonmember (Non-profit) $20
Nonmember (Student / Postdoc / Resident / Fellow) $10

Agenda

* Presentation titles and times are subject to change.


May 25, 2016

11:30 AM

Registration and Poster Set-Up

12:00 PM

Welcome and Introduction
Caitlin McOmish PhD, The New York Academy of Sciences
Christopher am Ende, PhD, Pfizer

12:15 PM

Keynote Presentation
Targeting Arginine Methyltransferases: Identification of First-In-Class PRMT5 Inhibitor EPZ015666
Kenneth W. Duncan, PhD, Epizyme

1:00 PM

Development of ‘Clickable’ Fluorescent Sensors for Targeted Mg2+ Detection in Cellular Organelles
Jessica Gruskos, New York University

1:15 PM

Synthesis and Photophysical Studies of Azetidinyl Rhodamines Tailored for Biological Imaging
Anand Muthusamy, Janelia Research Campus, Howard Hughes Medical Institute

1:30 PM

siRNA Nanotechnology: A Self-Assembled Platform for Cancer Gene Therapy
Mayurbhai Patel, Seton Hall University

1:45 PM

Networking Coffee Break

2:15 PM

Targeting Nucleic Acid Junctions Using Triptycene-Based Molecules
Stephanie A. Barros, PhD, University of Pennsylvania

2:30 PM

Small-Molecule-Induced Oxidation of Protein Disulfide Isomerase is Neuroprotective
Anna Kaplan, PhD, Columbia University

2:45 PM

Keynote Presentation
Chemical Approaches to Sorting Out Reversible Protein Lys Modifications
Philip Cole, MD PhD, Johns Hopkins University Medical School
* Presenter slides will not be included as part of the Webinar broadcast.

3:30 PM

Poster Session and Networking Reception

4:50 PM

F1000Research Outstanding Poster Presentation Awards
Scott Priestly, PhD, Bristol-Meyers Squibb

5:00 PM

Adjourn

Organizers

Christopher am Ende, PhD

Pfizer Inc.

Christopher W. am Ende received his BS in Biochemistry from the University of Delaware, conducting undergraduate research with Professor Neal J. Zondlo designing lanthanide-binding peptides. Chris then pursued his graduate studies at Stony Brook University working with Professor Peter J. Tonge where he developed long residence time inhibitors of InhA, the enoyl reductase in M. tuberculosis. After completion of an MS in Chemistry, he began his career in the Neuroscience Medicinal Chemistry group at Pfizer in Groton, CT. In this role, he contributed to several projects across the portfolio, helping to advance a clinical candidate for the treatment of Alzheimer's disease. Concurrent with his work at Pfizer, Chris earned his PhD at Stony Brook University under the direction of Kathlyn A. Parker, completing the first total synthesis of the natural product bisabosqual A. Chris currently is the Chemical Biology and PET synthesis laboratory head in the Neuroscience and Pain Group. He has published more than 25 journal articles, patents and book chapters, as well as presented at numerous external venues. In addition, Chris is an Adjunct Assistant Professor of Chemistry at Connecticut College.

E. Scott Priestley, PhD

Bristol-Myers Squibb

E. Scott Priestley is currently a Senior Principal Scientist in the Cardiovascular Chemistry group at Bristol-Myers Squibb. He leads several ongoing cardiovascular drug discovery projects. His research interests include thrombosis and heart failure therapies, antivirals, G-protein coupled receptor modulators, serine protease inhibitors, and oligonucleotide therapeutics. Scott received his BS in 1991 from Texas A&M University and his PhD in 1996 from the California Institute of Technology, where he worked with Professor Peter Dervan on non-natural nucleosides in DNA triple helix formation. He then moved to Scripps Research Institute and carried out post-doctoral research with Professor Chi-Huey Wong on aminoglycoside-RNA interactions. He joined DuPont-Merck Pharmaceuticals in 1998, and moved to Bristol-Myers Squibb in 2001 when it acquired DuPont Pharmaceuticals.

Sonya Dougal, PhD

The New York Academy of Sciences

Caitlin McOmish, PhD

The New York Academy of Sciences

Speakers

Stephanie A. Barros, PhD

New York University

Stephanie Barros received her BS in Chemistry and Biochemistry from Montclair State University in 2010. She obtained her PhD in 2015 from the University of Pennsylvania in the laboratory of David Chenoweth. At Penn, she worked on the synthesis and evaluation of triptycene-based molecules to target nucleic acid junctions. She is currently a postdoctoral researcher in the lab of Paramjit Arora at NYU.

Philip A. Cole, MD PhD

Johns Hopkins University School of Medicine

Phil Cole graduated from Yale University with a BS in Chemistry in 1984 and then spent a year as a Churchill Scholar at the University of Cambridge. Cole went on to obtain MD and PhD degrees from Johns Hopkins where he pursued research in bioorganic chemistry in 1991. Cole then entered post-doctoral training at Harvard Medical School prior to joining Rockefeller University in 1996 as a junior lab head. In 1999, Cole moved back to Johns Hopkins as the Marshall-Maren professor and director of pharmacology. His research interests are in the area of protein post-translational modifications and chemical biology. With Tom Muir, his group developed the method of expressed protein ligation. His team also reported the first potent and selective histone acetyltransferase inhibitors which led to the founding of Acylin Therapeutics Inc. His honors include election as an AAAS fellow and receipt of an NIH MERIT Award.

Kenneth W. Duncan, PhD

Epizyme, Inc.

Dr. Duncan received his BSc and PhD at the University of Strathclyde in Glasgow, Scotland. His post graduate work focused on the development of synthetic methodologies to produce a range of novel non-steroidal bile acid analogs as chemical probes for orphan nuclear receptors implicated in atherosclerosis. He moved directly from academia to a small biotech company in 2001 in the UK, where he leads medicinal chemistry efforts on kinase projects focused on oncology and diabetes indications. After moving to Cambridge MA in 2006 he has continued to work for small biotech companies including Epizyme whom he's worked for since 2011 as program and research alliance leader delivering multiple programs into development.

Jessica Gruskos

New York University

Jessica Gruskos was born in New Jersey. She attended The College of New Jersey where she performed undergraduate research developing peptide mimics in the lab of Professor Danielle Guarracino. After receiving a BS in Chemistry in 2013, Jessica began her PhD graduate studies in the laboratory of Professor Daniela Buccella at New York University, where she focuses on developing new tools for studying magnesium homeostasis.

Anna Kaplan, PhD

Columbia University

Anna Kaplan is a postdoctoral research scientist at Columbia University, focusing on strategies to tackle undruggable proteins in cancer with small molecules. She received her BS in Biochemistry and Biology from Brandeis University, conducting undergraduate research with Dr. Irene M. Pepperberg. Kaplan went on to obtain her PhD degree in 2015 from Columbia University, under the supervision of Dr. Brent R. Stockwell. Her doctoral work focused on the identification and biophysical characterization of small molecules modulating proteins in neurodegenerative diseases.

Anand K. Muthusamy

Howard Hughes Medical Institute

Anand K. Muthusamy is on the research staff of Dr. Luke Lavis' lab at Janelia Research Campus of the Howard Hughes Medical Institute. He earned his BA at the University of Pennsylvania and worked under Prof. E. James Petersson developing unnatural amino acid tools for biophysical studies. This experience was formative for his interest in science. Anand currently synthesizes and characterizes molecular probes, primarily fluorophores, for biological studies. He is generally interested in molecular life science, materials, and computing.

Mayurbhai R. Patel

Seton Hall University

Mayurbhai Patel received his BSc, MSc degree in Chemistry from Sardar Patel University, India. He traveled to United States to continue his education 2008. He obtained MSc in Chemistry from New Jersey Institute of Technology (NJIT) where he developed DNA aptamer based biosensor and further joined PhD program at Seton Hall University in 2011. During course of his PhD, Mayurbhai acquired in-depth knowledge in both oligonucleotide Chemistry and Chemical Biology. His research interests are in the area of developing novel siRNA Nanostructures for stable and potent gene knockdown for cancer gene therapy application. He is also working in numerous project like siRNA conjugation with phthalocyanine and peptides for cancer therapy application. In addition, his research focuses on studying chaperone proteins function and mechanism of action of followed by novel siRNA treatment. His honors include Dr. Robert DeSimone fellowship and university department nominee for ACS 2016–Irving Sigal Postdoctoral Fellowship.

Sponsors

Grant Support

This program is supported by an educational grant from Bristol-Myers Squibb

Promotional Partners

Current Opinion in Chemical Biology

The Chemical Biology Discussion Group is proudly supported by the American Chemical Society

Abstracts

Targeting Arginine Methyltransferases: Identification of First-In-Class PRMT5 Inhibitor EPZ015666
Kenneth W. Duncan, PhD, Epizyme, Inc., Cambridge

Protein Arginine Methyltransferase-5 (PRMT5) has been reported to play a role in multiple diverse cellular processes including tumorigenesis. Overexpression of PRMT5 has been observed in cell lines and primary patient samples derived from lymphomas, particularly Mantle Cell Lymphoma (MCL). Here, we will describe the identification and characterization of EPZ015666 (GSK3235025), a potent, selective and orally available inhibitor of PRMT5. This novel inhibitor is SAM-uncompetitive, peptide-competitive and interacts with the PRMT5:MEP50 complex through a unique inhibition mode not previously observed for any SAM-dependent enzyme. Treatment of MCL cell lines with EPZ015666 led to robust inhibition of PRMT5 mediated methylation and cell killing, with IC50 values in the nM range. Oral dosing of EPZ015666 demonstrated dose-dependent anti-tumor activity in multiple MCL xenograft models. In a Z-138 MCL xenograft model 93% tumor growth inhibition was observed after 21 days of dosing accompanied by a corresponding decrease in symmetrically dimethylated levels of PRMT5 substrates. In summary, we have developed the first potent and selective small molecule inhibitor of PRMT5 that has cellular activity as well as in vivo efficacy and used it as a chemical probe to confirm reports that MCL cells are dependent on PRMT5 activity for their survival. EPZ015666 represents a validated PRMT5:MEP50 chemical probe for the further study of PRMT5 biology and arginine methylation in cancer and other diseases.
 
Coauthors: Elayne Chan-Penebre1, Kristy G. Kuplast1, Christina R. Majer1, P. Ann Boriack-Sjodin1, Tim J. Wigle1, L. Danielle Johnston1, Nathalie Rioux1, Michael J. Munchhof1, Lei Jin1, Suzanne L. Jacques1, Kip A. West1, Trupti Lingaraj1, Kimberly Stickland1, Scott A. Ribich1, Alejandra Raimondi1, Margaret Porter-Scott1, Nigel J. Waters1, Roy M. Pollock1, Jesse J. Smith1, Olena Barbash2, Melissa Pappalardi2, Thau F. Ho3, Kelvin Nurse3, Khyati P. Oza3, Kathleen T. Gallagher4, Ryan Kruger2, Mikel P. Moyer1, Robert A. Copeland1, Richard Chesworth1.
 
1. Epizyme, Inc., Cambridge.
2. Cancer Epigenetics DPU, GlaxoSmithKline, Collegeville, Pennsylvania.
3. Department of Biological Reagents and Assay Development, GlaxoSmithKline.
4. Discovery Core Technologies and Capabilities, GlaxoSmithKline. 

Development of 'Clickable' Fluorescent Sensors for Targeted Mg2+ Detection in Cellular Organelles
Jessica Gruskos, New York University

Organelle-targeted fluorescent sensors enable the study of intracellular ion compartmentalization and trafficking in the context of both physiological and pathological cellular processes. We describe a new molecular tool for site-specific anchoring and activation of ratiometric Mg2+ sensors for subcellular detection by fluorescence microscopy. Our strategy capitalizes on the fast response of small-molecule indicators and the ease of localization of genetically encoded fusion proteins for subcellular targeting of probes. Organelle-targeted self-labeling protein tags are covalently labeled with ligands bearing a reactive moiety for click chemistry. The anchored reactive moiety serves as an attachment point to site-specifically anchor and activate, in a fluorogenic fashion, sensors decorated with tetrazines through the inverse electron demand Diels–Alder reaction. We demonstrate the utility of our tool to anchor APTRA-based Mg2+ sensors in intracellular compartments for the study of subcellular Mg2+ distribution and mobilization. Our strategy can be easily adapted to other metal ion indicators for subcellular imaging.
 
Coauthors: Guangqian Zhang and Daniela Buccella, New York University. 

Synthesis and Photophysical Studies of Azetidinyl Rhodamines Tailored for Biological Imaging
Anand K. Muthusamy, BA, Janelia Research Campus, Howard Hughes Medical Institute

As biological imaging modalities such as super-resolution imaging and single-particle tracking increase in sophistication, fluorophore chemistry should provide robust tools to interrogate living systems. We found that replacing the ubiquitous N, N-dimethylamino group in rhodamine dyes with azetidines affords significant increases in quantum yield and photostability. Moreover, substitutions on the azetidine ring tune photophysical properties and offer handles for further modification. Heteroatom substitutions for oxygen in the xanthene moiety offer more dramatic tuning. Combining these two findings has yielded a fluorinated azetidine-carbon/silicon rhodamine conjugated to Halo/SNAP-tag that transitions to its quinoid/fluorescent form only when bound to its target. Additionally, the 3-carboxy azetidine offers a handle to append photochemically active molecules which can alter photostability. The synthesis of these fluorophores has been accessed in a modular fashion, using palladium-catalyzed cross couplings to install the key azetidine moiety. We have created a library of dyes spanning the visible spectrum combined with tags such as SNAP/CLIP/Halo-Tag ligands and reactive chemical handles. With our fluorogenic probes, this library enables robust multi-color, no-wash imaging with a large photon budget. The utility of these dyes has been demonstrated in neurobiology imaging experiments. We freely share our dyes with the academic community and have received positive feedback. We have begun computational studies and spectroscopic experiments for modeling non-radiative decay to explain the "azetidine effect" and for modeling solvation to explain fluorogenic properties aforementioned. Our goal is to build a physical organic intuition connecting probe properties to the parameters of biological experiments.
 
Coauthors: Jonathan B. Grimm, Timothy A. Brown, Luke D. Lavis, Janelia Research Campus, Howard Hughes Medical Institute. 

siRNA Nanotechnology: A Self-Assembled Platform for Cancer Gene Therapy
Mayurbhai R. Patel, MSc, Program in Molecular Pharmacology & Chemistry and Department of Medicine, Memorial Sloan-Kettering Cancer Center; Department of Chemistry and Biochemistry, Seton Hall University

The emerging field of RNA nanotechnology has ushered-in a new wave of programmable self-assembled nanostructures. Among the most significant examples, are the nanoparticle formulations that incorporate multiple short-interfering RNA (siRNA). These discrete higher-ordered nanostructures function to synergize the RNA interference (RNAi) gene knockdown effect, leading to significant biological responses in cells. Significantly, siRNA nanotechnology has been successfully applied in the treatment of cancer. In this presentation, a library of self-assembled siRNA nanostructures have been formulated for potent cancer gene therapy applications in endometrial cancer. The siRNAs were designed to target the Glucose Regulated Protein of 78 kilodalton (GRP78) oncogene. The solid-phase synthesis of linear, V-shape and Y-shape RNA templates effectively formed functional scaffolds for siRNA hybridization and self-assembly. The higher-order siRNA nanostructures were found to display distinct sizes and shapes which effected potent anti-cancer activity within a GRP78-overexpressing AN3CA endometrial cancer cell line. Thus, the development of this novel siRNA nanotechnology strategy has effectively expanded the repertoire of functional siRNAs for fruitful applications in cancer gene therapy and for potentially screening important oncogene targets.
 
Coauthors: Stephen D. Kozuch3, Christopher N. Cultrara3, Reeta Yadav2, Suiying Huang2, Uri Samuni2, John Koren, 3rd1, Gabriela Chiosis1, and David Sabatino3.
 
1. Program in Molecular Pharmacology & Chemistry and Department of Medicine, Memorial Sloan-Kettering Cancer Center.
2. Department of Chemistry and Biochemistry, Queens College, City University of New York; and the PhD Programs in Chemistry and Biochemistry, The Graduate Center of the City University of New York.
3. Department of Chemistry and Biochemistry, Seton Hall University. 

Targeting Nucleic Acid Junctions Using Triptycene-Based Molecules
Stephanie A. Barros, PhD, University of Pennsylvania

Small molecule modulation of nucleic acid structure is critical to several processes in biological systems. Targeting nucleic acids specifically with small molecules remains a significant challenge in chemical biology. The selective modulation of a subset of nucleic acid structures using small molecules would allow for precise chemical control of cellular processes. Nucleic acid junctions are ubiquitous structures found in DNA and RNA involved in several biological processes and viral genomes. We demonstrate a new class of structure-specific nucleic acid junction binders based on triptycene. These triptycene molecules significantly stabilize DNA three-way junctions over double helical DNA. This new class of molecules also has the ability to modulate junctions in trinucleotide repeat expansions implicated in neurodegenerative diseases as well as bacterial mRNA temperature sensors. Triptycene is a versatile scaffold to target higher-order nucleic acid junctions.
 
Coauthor: David M. Chenoweth, University of Pennsylvania. 

Small-Molecule-Induced Oxidation of Protein Disulfide Isomerase is Neuroprotective
Anna Kaplan, PhD, Department of Biological Sciences, Columbia University

Protein disulfide isomerase (PDI) is a chaperone protein in the endoplasmic reticulum that is upregulated in mouse models of, and brains of patients with, neurodegenerative diseases involving protein misfolding. PDI's role in these diseases, however, is not fully understood. Here, we report the discovery of a reversible, neuroprotective compound, LOC14, as a modulator of PDI. LOC14 was identified using a high-throughput screen of ~10,000 lead-optimized compounds for potent rescue of PC12 cells expressing mutant huntingtin protein, followed by an evaluation of effects of compounds on PDI reductase activity in an in vitro screen. Isothermal titration calorimetry and fluorescence experiments revealed that binding to PDI was reversible with a Kd of 61.7 nM, suggesting LOC14 to be the most potent PDI inhibitor reported to date. Using chemical shift perturbations from 2D-NMR experiments, we were able to map the binding site of LOC14 as being adjacent to the active site, and to observe by HSQC NMR that binding of LOC14 forces PDI to adopt an oxidized conformation. Furthermore, we found that LOC14-induced oxidation of PDI has a neuroprotective effect not only in cell culture, but also in corticostriatal brain slice cultures. LOC14 exhibited high stability in mouse liver microsomes and blood plasma, low intrinsic microsome clearance, and low plasma-protein binding. These results suggest that LOC14 is a promising lead compound to evaluate the potential therapeutic effects of modulating PDI in animal models of disease.
 
Coauthors: Michael M. Gaschler2, Denise E. Dunn3, Ryan Colligan1,4, Lewis M. Brown1,4, Arthur G. Palmer III5, Donald C. Lo3, and Brent R. Stockwell1,2.
 
1. Department of Biological Sciences, Columbia University.
2. Department of Chemistry, Columbia University.
3. Duke University Medical Center.
4. Quantitative Proteomics Center, Columbia University.
5. Department of Biochemistry and Molecular Biophysics, Columbia University. 

Chemical Approaches to Sorting Out Reversible Protein Lys Modifications
Philip A. Cole, MD, PhD, Johns Hopkins University School of Medicine

The histone lysine demethylase LSD1 is a flavin-dependent amine oxidase that selectively cleaves one or two methyl groups from histone H3 that is mono- or di-methylated at the Lys4 position. Cellular LSD1 is prominently located in the gene silencing CoREST complex that includes the scaffolding protein CoREST and the histone deacetylase HDAC1. LSD1, HDAC1, and the CoREST complex are considered anti-tumor targets for cancer drug discovery. We will discuss our approaches and progress to design selective inhibitors of LSD1 and the CoREST complex using suicide inactivation strategies.
 

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