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Chemical Biology in THE HUB Symposium
Sept 19th, 2019
Merck Research Laboratories 33 Avenue Louis Pasteur
Boston, MA 02115
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Many Thanks to our Sponsors!!
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Symposium Agenda
8:30-9:00 Check-in Atrium
9:00-9:10 Welcome - Introductory remarks Erik Hett (Merck) Auditorium
9:10-9:25 Who do we want to be when we grow up? Milka Kostic (DFCI) Auditorium
Introduction by: Paola Castaldi 9:25-10:05 The power and limitations of learned Regina Barzilay (MIT) Auditorium molecular representations Introduction by: John Tallarico 10:05-10:45 Applications of artificial intelligence in drug discovery- Pat Walters (Relay Therapeutics) Auditorium
separating hype from utility Introduction by: Donovan Chin
10:45-11:05 Coffee Break Atrium
11:05-11:45 Lysosome targeting chimeras (LYTACs) Carolyn Bertozzi (Stanford University) Auditorium as a new therapeutic modality Introduction by: Steve Canham
11:45-12:25 Mapping of immunomodulatory receptor protein Niyi Fadeyi and Rob Oslund (Merck) Auditorium Interactions via photoactivation-based proximity Introduction by: Erik Hett Labelling of the cell surface
12:25-1:30 Lunch Atrium
1:30-1:45 Small tools to answer big questions- Chris am Ende (Pfizer) Auditorium advancing chemical biology through innovative chemistry Introduction by: Jaimeen Majmudar
1:45-2:25 Chemical probes of transcription factors Angela Koehler (MIT) Auditorium Introduction by: Rhamy Zaid 2:25-3:05 Solving a 60 year mystery: SALL4 mediates Mary Matyskiela (Celgene) Auditorium tetratogenicity as a thalidomide-dependent Introduction by: Bob Kyne substrate of cereblon 3:05-3:25 Coffee Break Atrium 3:25-4:05 Quantitative chemical imaging in live cells Yamuna Krishnan (U of Chicago) Auditorium Introduction by: Olivier Bedel 4:05-4:45 Chemical Biology: An essential pillar in Drug Discovery? Mark Bunnage (Vertex) Auditorium Introduction by: Jeremy Barzya 4:45-4:55 Concluding remarks and looking to 2020 Erik Hett (Merck) Auditorium Jaimeen Majmudar (Pfizer) 5:00-6:30 Reception & Posters Atrium
Time Time Presentation Speaker Location
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Many thanks for the volunteers and support from:
Merck: o Kerrie Spencer o Jeanne Callinan o Sina Mohammadi o Daria Hazuda o Emma Parmee o FLIK catering
Northeastern Section of the American Chemical Society: o Leland Johnson, past-chair o Andrew Scholte, Chair o Anna Singer o Saha Ashis
2019 Chemical Biology in the Hub Board:
o Jeremy Baryza: [email protected] o Olivier Bedel: [email protected] o Steve Canham: [email protected] o Paola Castaldi: [email protected] o Donovan Chin: [email protected] o Erik Hett: [email protected] o Leland Johnson: [email protected] o Robert Kyne: [email protected] o Jaimeen Majmudar: [email protected] o Justin Rettenmaier: [email protected] o Kirti Sharma: [email protected] o Daniel Simard: [email protected] o Sue Swalley: [email protected] o John Tallarico: [email protected] o Rhamy Zeid: [email protected]
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Speaker Presentation Title and Biography
Milka Kostic Who do we want to be when we grow up?
Dr. Milka Kostic Program Director, Chemical Biology Program Dana-Farber Cancer Institute Boston, MA USA
Milka Kostic, PhD, is the Program Director responsible for setting the mission, vision, and strategy for our program, a home for more than 100 researchers. In a broader context, Dr. Kostic is dedicated to promoting and advocating for chemical biology and structural biology as integral research partners on the chemistry-biology-medicine continuum, as well as a vocal proponent, coach, and mentor of the next generation of a diverse biomedical workforce.
Professor Regina Barzilay The power and limitations of learned molecular representations Professor Regina Barzilay Department of Electrical Engineering and Computer Science Massachusetts Institute of Technology Cambridge, MA USA
Regina Barzilay is a professor in the Department of Electrical Engineering and Computer Science
and a member of the Computer Science and Artificial Intelligence Laboratory at the
Massachusetts Institute of Technology. Her research interests are in natural language processing.
Currently, Prof. Barzilay is focused on bringing the power of machine learning to oncology. In
collaboration with physicians and her students, she is devising deep learning models that utilize
imaging, free text, and structured data to identify trends that affect early diagnosis, treatment,
and disease prevention. Prof. Barzilay is poised to play a leading role in creating new models that
advance the capacity of computers to harness the power of human language data. Regina Barzilay
is a recipient of various awards including the MacArthur Fellowship, NSF Career Award, the MIT
Technology Review TR-35 Award, Microsoft Faculty Fellowship and several Best Paper Awards in
top NLP conferences. In 2017, she received a MacArthur fellowship, an ACL fellowship and an
AAAI fellowship. Prof. Barzilay received her MS and BS from Ben-Gurion University of the Negev.
Regina Barzilay received her PhD in Computer Science from Columbia University, and spent a
year as a postdoc at Cornell University.
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Pat Walters
Applications of artificial intelligence in drug discovery—separating hype from
utility
Dr. Pat Walters
Senior Vice President, Computation
Relay Therapeutics
Pat Walters heads the Computation & Informatics group at Relay Therapeutics in Cambridge, MA.
His group focuses on novel applications of computational methods that integrate computer
simulations and experimental data to provide insights that drive drug discovery programs. Prior
to joining Relay, he spent more than 20 years at Vertex Pharmaceuticals where he was Global
Head of Modeling & Informatics. Pat is a member of the editorial advisory board for the Journal
of Medicinal Chemistry, and previously held similar roles with Molecular Informatics, and Letters
in Drug Design & Discovery. He continues to play an active role in scientific community. Pat was
the Chair of 2017 Gordon Conference on Computer-Aided Drug Design. He has been
instrumental in a number of community driven efforts to evaluate computation methods
including the NIH funded Drug Design Data Resource (D3R) and the American Chemical Society
TDT initiative. Pat received his Ph.D. in Organic Chemistry from the University of Arizona where
he studied the application of artificial intelligence in conformational analysis. Prior to obtaining
his Ph.D., he worked at Varian Instruments as both a chemist and a software developer. Pat
received his B.S. in Chemistry from the University of California, Santa Barbara.
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Professor Carolyn Bertozzi
Lysosome targeting chimeras (LYTACs) as a new therapeutic modality
Professor Carolyn Bertozzi Anne T. and Robert M. Bass Professor of Chemistry &
Professor of Chemical and Systems Biology and Radiology
Stanford University Palo Alto, CA USA Carolyn Bertozzi is the Anne T. and Robert M. Bass Professor of Chemistry and Professor of
Chemical & Systems Biology and Radiology (by courtesy) at Stanford University, and an
Investigator of the Howard Hughes Medical Institute. She completed her undergraduate degree
in Chemistry from Harvard University in 1988 and her Ph.D. in Chemistry from UC Berkeley in
1993. After completing postdoctoral work at UCSF in the field of cellular immunology, she joined
the UC Berkeley faculty in 1996. In June 2015, she joined the faculty at Stanford University
coincident with the launch of Stanford's ChEM-H institute.
Prof. Bertozzi's research interests span the disciplines of chemistry and biology with an emphasis
on studies of cell surface glycosylation pertinent to disease states. Her lab focuses on profiling
changes in cell surface glycosylation associated with cancer, inflammation and bacterial infection,
and exploiting this information for development of diagnostic and therapeutic approaches, most
recently in the area of immuno-oncology. She has been recognized with many honors and
awards for her research accomplishments. She is an elected member of the Institute of
Medicine, National Academy of Sciences, and American Academy of Arts and Sciences. She has
been awarded the Lemelson-MIT Prize, the Heinrich Wieland Prize, and a MacArthur Foundation
Fellowship, among many others.
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Niyi Fadeyi & Rob Oslund
Mapping of Immunomodulatory Receptor Protein Interactions via Photoactivation-Based Proximity Labeling of the Cell Surface Dr. Niyi Fadeyi Merck Exploratory Science Center Cambridge, MA USA Originally from Nigeria, Niyi performed his doctoral studies at Vanderbilt University, under the mentorship of Prof. Craig Lindsley and did his postdoc at Harvard with Prof. Matthew Shair. After a few years at Pfizer, he joined the Molecular Discovery group at Merck Exploratory Science Center in Cambridge where he’s developing novel platforms that integrate chemistry and biology to study the underlying mechanisms of human diseases to develop new therapeutics. Dr Rob Oslund Merck Exploratory Science Center Cambridge, MA USA Rob Oslund is a chemical biologist at the Merck Exploratory Science Center
where he is involved in understanding novel biology for therapeutic
development. He obtained his PhD under Mike Gelb at the University of
Washington and did postdoc studies with Tom Muir at Princeton. He was raised out west in
fabulous Las Vegas.
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Chris am Ende
Small Tools to Answer Big Questions – Advancing Chemical Biology through Innovative
Chemistry
Dr Chris Am Ende Chemical Biology and Exploratory Project Synthesis Lead Internal Medicine Group Pfizer Cambridge, MA USA
Christopher W. am Ende is the Chemical Biology and Exploratory Project Synthesis lead in the
Internal Medicine group at Pfizer. Chris received a B.S. in Biochemistry from the University of
Delaware, conducting undergraduate research with Professor Neal J. Zondlo designing
lanthanide-binding peptides. He then pursued his graduate studies at Stony Brook University
working with Professor Peter J. Tonge where he developed slow, tight binding inhibitors of InhA,
the enoyl reductase from M. tuberculosis and under the direction of Kathlyn A. Parker, completed
the first total synthesis of the natural product bisabosqual A. Additionally, Chris has published
>50 journal articles and patents, serves as a steering committee member for the New York
Academy of Sciences Chemical Biology Discussion Group, is an Adjunct Assistant Professor of
Chemistry at Connecticut College and was named an American Chemical Society Young
Investigator.
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Angela Koehler
Chemical probes of transcription factors
Professor Angela Koehler
Goldblith Career Development Professor in Applied Biology
Department of Biological Engineering
Massachussetts Institute of Technology
Cambridge, MA USA
Angela Koehler is the Goldblith Career Development Professor in Applied Biology in the
Department of Biological Engineering at MIT and an intramural member of the David H. Koch
Institute for Integrative Cancer Research at MIT. She is also an Institute Member of the Broad
Institute and a Founding Member of the MIT Center for Precision Cancer Medicine. Her research
group aims to discover and develop functional small-molecule probes of transcriptional
regulators, including chromatin modifying enzymes and oncogenic transcription factors.
Angela received her B.A. in Biochemistry and Molecular Biology from Reed College in 1997. There
she worked under the guidance of Professor Arthur Glasfeld on structural and biochemical
studies of proteins that recognize tRNA or DNA. In 2003, she received her Ph.D. in Chemistry from
Harvard University where she worked with Professor Stuart Schreiber to develop novel
technologies for identifying and characterizing interactions between proteins and small
molecules. Upon graduation, she became an Institute Fellow in the Chemical Biology Program at
the Broad Institute and a Group Leader for the NCI Initiative for Chemical Genetics.
At MIT, Angela serves at the Faculty Director of the High-Throughput Sciences Facility in the
Swanson Biotechnology Center. She is also a co-Director of the MIT Biomedical Engineering
Undergraduate Program and a member of the Committee on Pre-Health Advising. Angela has
served on the Chemists in Cancer Research Executive Advisory Board for AACR. Awards include
being named a Genome Technology Young Investigator and a Broad Institute Merkin Fellow as
well as the Novartis Lectureship in Chemistry, the Ono Pharma Breakthrough Science Award, the
AACR-Bayer Innovation and Discovery Award and the Junior Bose Award for Excellence in
Teaching. Angela serves as a consultant or scientific advisory board member to several
pharmaceutical or biotechnology companies and has founded two biotechnology companies.
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Mary Matyskiela
Solving a 60 year mystery: SALL4 mediates teratogenicity as a thalidomide-dependent substrate
of cereblon.
Dr. Mary Matyskiela
Principal Scientist
Structural and Chemical Biology Department
Celgene
San Diego, CA USA
Mary Matyskiela is a Principal Scientist and group leader in the Structural and Chemical Biology
department at Celgene. She received a B.S. in Chemistry at Yale University, followed by Ph.D.
work at the University of California San Francisco and postdoctoral studies at the University of
California Berkeley focused on ubiquitin ligase and 26S proteasome structure and function. Her
work at Celgene includes biochemical and structural studies on small molecule modulation of the
cereblon-CRL4 ubiquitin ligase for therapeutic effect.
Yamuna Krishnan
Quantitative chemical imaging in live cells
Professor Yamuna Krishnan
Department of Chemistry
University of Chicago
Chicago, IL USA
Yamuna Krishnan is Professor at the Department of Chemistry at the University of Chicago since
2014. She received a PhD in Organic Chemistry in 2002 from the Indian Institute of Science,
Bangalore and was an 1851 Research Fellow at the University of Cambridge, UK. Her research
group pioneered the use of DNA-nanotechnology to study living cells and taking DNA-
nanotechnology into the world of precision medicine. Selected honors include the Infosys Prize
for Physical Sciences in 2017, the Shanti Swarup Bhatnagar Award, the Innovative Young
Biotechnologist Award, the INSA Young Scientist Medal, the Wellcome-Trust DBT Senior Research
Fellowship and the YIM Boston Young Scientist Award. She was featured on Cell’s top 40 under
40 of scientists that are shaping current and future trends in Biology and the LSDP’s Top 100.
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Mark Bunnage
Chemical Biology: An essential pillar in Drug Discovery? Dr Mark Bunnage Senior Vice President
Vertex Pharmaceuticals Boston, MA USA
Mark studied chemistry at the University of Durham and conducted postgraduate research with
Professor S G Davies at the University of Oxford. Mark then moved to The Scripps Research
Institute in La Jolla, USA to work with Professor K C Nicolaou.
Mark then joined Pfizer in the UK as a medicinal chemist and ultimately became Head of
Medicinal Chemistry, Sandwich Laboratories. In April 2011, Mark was appointed Vice President,
Worldwide Medicinal Chemistry, and relocated to Cambridge, MA. In August 2016, Mark moved
to his current position of Senior Vice President and Site Head for Boston Research at Vertex
Pharmaceuticals.
Mark has broad interests in Drug Discovery and is an author or inventor on over 50 publications
and patents. Mark is also a visiting Professor in Chemistry at the University of Oxford.
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SYMPOSIUM POSTERS
Name Affiliation Title Email
Alexander Loftis Massachusetts Institute of Technology
In vivo affinity selection of noncanonical erythrocyte-targeting peptides
Amissi Sadki Northeastern University
Novel Reversible Switches for Protein Bioconjugation: Modulate Protein Function by Light
Andrea Zuhl AstraZeneca Chemical Proteomics for ALS Phenotypic Screen Target Deconvolution
Anthony Varca Dana-Farber Cancer Institute / Harvard University
Identification of Deubiquitinase Inhibitors via Small Molecule Library Screening
Benjamin Ruprecht
Merck A mass spectrometry-based proteome map of drug action in lung adenocarcinoma cell lines
Dr. Liam Hudson Broad Institute/Novartis
DOSEDO: Diversity Oriented Synthesis Encoded by Deoxyoligonucleotides
Dr. Tyler Faust Dana-Farber Cancer Institute
Structural complementarity offsets low receptor affinity in E7820-mediated RBM39 degradation by DCAF15
Ghaith Hamza AstraZeneca From Chemical Proteomics to Translational Chemical Biology
Haibo Liu Celgene Discovery of Selective, Targeted Covalent FGFR4 Inhibitors with Anti-tumor Activity in Xenograft Models of Orthotopic and Sorafenib-resistant Hepatocellular Carcinoma (HCC)
Henry Kilgore Massachusetts Institute of Technology
Chemical Energy Driven Protein Internalization
Herschel Mukherjee
Arrakis Therapeutics Photoaffinity Probes for the Evaluation of Small Molecule-RNA Interactions
Jesús M. Dones Massachusetts Institute of Technology
AN OPTIMAL PEPTIDE FOR ANNEALING TO DAMAGED COLLAGEN
Jon Mortison Merck BiTSA: A Simplified NanoBiT Thermal Shift Assay for Determining Target Engagement in Live Cells
Justin Rettenmair and Matt Labenski
Jnana Therapeutics Building an SLC Drug Discovery Platform
Kaelyn Wilke Millipore Sigma Innovative Chemical Biology and Medicinal Chemistry Tools for Drug Discovery
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Kaitlin Chambers Tufts University Harnessing Bacterial Enzymes to Install Dehydrobutyrine
Kirk Donovan Biogen Using fluorescent activity probes to monitor lysosomal enzymatic activity in compound-treated neurons
Kirti Sharma Kymera Mapping the human E3 ligase atlas for developing next generation disease-specific targeted protein degraders
Marek Kobylarz Novartis VPS34 inhibition disrupts transferrin receptor trafficking and iron homeostasis
Mike Wuo Massachusetts Institute of Technology
Imaging antibiotic effects on mycobacteria
Nam Chu HMS and BWH Akt kinase activation mechanisms revealed using Expressed Protein Ligation
Natalia Kozlyuk Vanderbilt University Fragment-based Discovery of Small Molecule Inhibitors of RAGE-ligand Interactions
Olivier Bedel Sanofi 6-Alkynyl-F-ara-NAD: Versatile Tool Compound for CD38 related Chemical Biology
Peter Juhasz Pelago Biosciences Thermal stability changes for targets, off-targets and non-targets of small molecule drugs
Rebecca Gorelov Broad Institute Talazoparib treatment preferentially depletes cohesin-mutant clones in new in vivo models of cohesin-mutant myeloid diseases
Rob Wilson Massachusetts Institute of Technology
High-throughput chemical screening for inhibitors of RNA-binding proteins
Shalise Couvertier Biogen Investigation of DMF on signaling pathways in non-immune cells using chemoproteomics
Uthpala Seneviratne and Liang Xue
Pfizer Inc Quantitative Assessment of the Cellular Reactive Cysteinome
Vicky Luo Yale University Dynamic Profiling of Human mRNA Decapping Protein hDcp2 Reveals Guiding Rules of RNA Stability
Xiaofeng Jiang Harvard University A high content small molecule screening for intra-cellular hydrogen sulfide regulators
Xingyou Wang Brandeis University Leu413: a Flap Residue of Bacillus anthracis Inosine 5'-Monophosphate Dehydrogenase (BaIMPDH) Interacts with Inhibitors
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Attendees Associations
ACCRF Harvard Medical School
Amgen Harvard Medical School/McLean Hospital
Arrakis Therapeutics Brigham Women's Hospital
Arvinas Hybrigenics
AstraZeneca Jnana Therapeutics
Astrazeneca-Tufts lab for basic and translational neuroscience
Kymera Therapeutics
Biogen Massachusetts College of Pharmacy and Health Sciences
Boston Children's Hospital Massachusetts Institute of Technology
Brandeis University Merck Exploratory Sciences Center Cambridge
Broad Institute Merck Research Labs
C&EN - Chemical & Engineering News MilliporeSigma
C4 Therapeutics New England BioLab
Caldwell IP Law Novartis Institutes for Biomedical Research
Celgene Corp. Northeastern University
Cell Press Pelago Bioscience
Cogen Immune Medicine Pfizer Inc
CreaGen Inc. Relay Therapeutics
Cygnal Therapeutics Saha Discovery Solutions, Inc.
Dana Farber Cancer Institute Sanofi
Diaago The Rockefeller University
Discoverybytes The Scripps Research Institute
Faculty of Pharmacy, University of Porto, Portugal Third Rock Ventures
GlaxoSmithKline Tufts University
Vanderbilt university
Vertex Pharmaceuticals Inc
Yale University
