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Speakers

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Christopher Gemski, MSc., BSc.
Translation Bioassay and Immunogenicity Risk Assessment, Global DMPK Oncology & Rare Diseases
Takeda

Workshop

November 19, 2019

1:00 pm | In-silico Immunogenicity Predictions (Hands-on Session)

Monica Wang
Principal Technology Lead, Project and Program Manager, Scientific Informatics
Takeda

Workshop

November 19, 2019

1:00 pm | In-silico Immunogenicity Predictions (Hands-on Session)

Karen Khar
Computational Protein Scientist
Cyrus Biotechnology

Workshop

November 19, 2019

1:00 pm | In-silico Immunogenicity Predictions (Hands-on Session)

Anna Vangone
Postdoctoral Scientist
Roche

Anna Vangone carried out her PhD in Structural Bioinformatics at University of Salerno (Italy) and University of Oxford. With a Marie Sklodowska-Curie postdoctoral fellowship, she moved to Utrecht University (NL) for a postdoc, hosted in a world-leading lab for the docking technique. After a period as visiting scientist in Australia (University of Queensland) and Saudi Arabia (KAUST), she joined Roche in 2018 as Postdoctoral Scientist. Her expertise falls into the field of in silico proteins interaction studies, modelling and design, with particular focus to antibody-antigen systems.

Day One

Tuesday November 20, 2019

11:30 am | Roche Antibody Formats: Predict the Epitope to Generate Adequate Bi-specifics or Bi-paratopics

Dana I. Filoti, Ph.D.
Senior Scientist
AbbVie

Dana Filoti is currently a member of the NBE Analytical R&D group at AbbVie, where she leads the analytical clinical development of ADC therapeutics along with preclinical candidate selection, drug delivery systems and subvisible particle characterization of protein therapeutics. She received her Ph.D. in Physics/Materials Science from University of New Hampshire. As a Post-Doctoral fellow, she worked with Dr. Thomas Laue at the Biomolecular Interaction Technologies Center (BITC) on the development of instrumentation and methods for examining macromolecular interactions via charge measurements to address colloidal stability issues associated with high concentration formulation development. She has about 10 years of experience in protein formulation, analytical development and biophysical characterization.  

Dea Shahinas
Director
Aivie

Dea Shahinas has over 10 years experience in protein structural biology and bioinformatics applications to innovate solutions that circumvent antimicrobial resistance. She currently designs single domain antibodies with applications in food safety, animal and human health. Dr. Shahinas has been a principal scientist on combination therapy against various infectious diseases, overcoming vaccine escape events and cataloguing microbiome shift events after recurrent infection at AbCelex Technologies Inc and previously at Public Health Ontario.   Dr. Shahinas completed her post-doctoral fellowship and PhD at Mount Sinai Hospital and the University of Toronto with focus on protein biochemistry, molecular microbiology and applied bioinformatics.

Day One

Tuesday November 20, 2019

4:00 pm | Panel Session: Predictive Tools for Optimizing Antibody Structure Function and Developability Attributes

Day Two

Wednesday November 21, 2019

2:00 pm | Computational Design of Single Domain Antibodies

Hubert Kettenberger
Senior Principal Scientist
Roche

Hubert Kettenberger holds a PhD in biochemistry from the University of Munich. After a PostDoc at the Max-Planck-Institute for Biochemistry he joined the Large Molecule Research unit of Roche in Penzberg/Germany in the year 2006 and is now a Senior Principal Scientist in the field of protein engineering. His areas of expertise include the biochemical and biophysical characterization of therapeutic proteins. Moreover, HK developed strategies, in-vitro and in-silico methods for the assessment of new drug candidates (antibodies, bispecifics, next-generation biotherapeutics).

Day One

Tuesday November 20, 2019

3:00 pm | Scope and Limitations of In Silico Feature Prediction in Therapeutic Proteins

John Gunn
Senior Research Scientist
Chemical Computing Group

John Gunn joined Chemical Computing Group in 2015 as a Senior Research Scientist specializing in protein modeling. John has been working in the chemical software industry since 1999, principally at Schrödinger Inc, where he developed several protein modeling applications. Dr. Gunn obtained his Ph.D. in 1992 at the University of California (Berkeley) studying the structure and phase transitions of semi-ordered liquids before being drawn into the world of proteins during a post-doc at Columbia University and then as a professor of theoretical chemistry at the Université de Montréal.

Day Two

Wednesday November 21, 2019

9:30 am | Modeling Protein Properties using pH-dependent Conformational Sampling

Johannes Maier
Principal Scientist
Schrodinger

Day One

Tuesday November 20, 2019

11:00 am | Improved Scoring Function to Reliably Detect Antigen Binding Sites

Katrina Lexa
Pathway Leader
Denali Therapeutics

Katrina Lexa received her PhD in Medicinal Chemistry from the University of Michigan with Prof. Heather Carlson, then performed F32-funded postdoctoral research with Prof. Matt Jacobson at UCSF. After her postdoc, Katrina joined Merck’s newly formed Chemical Biotechnology department, where her research focused on (bio)-catalyst optimization and structure-based design in Process and Discovery Chemistry. In 2017, Katrina joined Denali Therapeutics, where she now leads the Modeling & Informatics group and supports efforts across Discovery to develop breakthrough therapies for neurodegenerative diseases.

Day Two

Wednesday November 21, 2019

10:00 am | Building a Computational Pipeline for Early Developability Assessment and Optimization

Klaus R. Liedl
Professor
University of Innsbruck

Klaus R. Liedl is full professor of Theoretical Chemistry and heads the Department of General, Inorganic and Theoretical Chemistry at the University of Innsbruck. He holds degrees in mathematics and chemistry (1989, 1992) and wrote his PhD (1995) about a QM/MM-algorithm allowing particle to cross the QM/MM-border. He got his tenure (1998) for work on nuclear quantum effects in concerted proton transfer reactions. He obtain a degree in laws (2003) and wrote a juridical science doctorate thesis (2006) about the European Community Patent and Patent Litigation in Europe. His current research focusses on physics based understanding of biomolecular interfaces like antibodies, allergens and proteases by computer simulations and quantum mechanics. Klaus R. Liedl’s key academic figures are 312 publications, 6695 citations (<10% self-citations) and h-index of 43.

Day Two

Wednesday November 21, 2019

2:30 pm | Antibody Dynamics from the Nanosecond to Millisecond Timescale – Implications for Affinity Maturation and Humanization

Marc Bailly
Associate Principal Scientist
Merck

Marc Bailly obtained his PhD in Biochemistry from University Louis Pasteur in Strasbourg, France in Pr. Daniel Kern’s team. After two postdocs in bioinformatics and human T cell development, Marc joined Merck in 2015 where he focused on high throughput analytical characterization technologies enabling lead candidate selection for biologics programs. Marc also worked at MacroGenics focussing on the DART bispecific platforms. Currently Marc is co-leading the analytical characterization group at Merck South San Francisco site. He is focussing on analytical characterization and high throughput data management using bioassays to facilitate the development of machine learning algorithms aiming at predicting developability profiles of antibodies and other biologics modalities. 

Day Two

Wednesday November 21, 2019

11:30 am | Modifying Discovery Workflow to Utilize Machine Learning Algorithms for Better and Faster Optimization of Biologics

Monica Fernández Quintero
PhD Student
University of Innsbruck

Monica L. Fernández Quintero is last-year PhD student both at the University and at the Medical School in Innsbruck and works on antibodies and ion channels. Already since her Bachelor thesis 2015 she is working on the dynamics of antibodies and graduated in 2017. She already authored several papers, gave talks and presented posters on international conferences featuring various aspects of antibody and T-cell receptor dynamics. She is very active in establishing and fostering a wide network of collaborations both in academia and industry.

Day Two

Wednesday November 21, 2019

3:00 pm | CDR-H3 Loop Dynamics – Implications for Antibody Design and Structure predictions

Naresh Chennamsetty
Senior Scientist
BMS

Naresh is a senior scientist in BMS with 10 years of experience in developing computational tools for higher order structural characterization of biologics.  Naresh got his Ph.D in Chemical and Bio-molecular Engineering from North Carolina State University, and then a post doctorate from MIT.  While at MIT, he developed the Spatial-Aggregation-Propensity (SAP) model for protein aggregation of biologics that is well known in the industry.  He is currently working in the Bio-physical and Chemical Characterization Centre of Excellence at BMS where he develops in silico models to predict molecular liabilities for biologics and assess their impact on function. 

Day Two

Wednesday November 21, 2019

9:00 am | Computational Tools to Aid in Developability and Early Risk Assessment of Biologics

Pankaj Agarwal
Senior Member
ISCB

Dr. Pankaj Agarwal, has 22+ years strategic and tactical experience utilizing bioinformatics to enable drug discovery and create pipeline value. He has collaborated extensively with numerous pharmaceutical project teams, academic/biotech partners, and top informatics talent. Dr. Agarwal has 50+ publications in top journals, including Nature Rev Drug Discovery, Nature Biotechnology, and Clinical Pharmacology & Therapeutics, and multiple methodological and gene patents. He has successfully led an internal biotech at GSK  on computational and experimental drug repurposing. In 2016, he was among a group of select few scientists appointed as senior fellows at GSK. Dr. Agarwal has also served on NSF, NIH, FDA and PhRMA panels. He possesses a B.Tech. in Computer Science & Engineering from IIT, Delhi and a Ph.D. in Computer Science from the Courant Institute of Mathematical Sciences at NYU. He is a founder and senior member of the International Society for Computational Biology (ISCB). Most importantly, Dr. Agarwal is passionate about drug discovery, rare diseases, and helping patients.

Day Two

Wednesday November 21, 2019

12:00 pm | AI & Machine Learning for High Quality Targets and Disease Indications for Both Biologics and Small Molecules

Rafael Depetris
Principal Scientist
Abbvie

Rafael obtained his Ph.D. from NYU in 2008 working with Stevan Hubbard in the field of X-Ray crystallography, specifically focusing on the structural analysis of proteins that interact with the insulin receptor. His post-graduate work was done at Weill Cornell Medical College where he focused in the structural analysis of the HIV-1 Envelope proteins as well as of the HIV-1 neutralizing antibodies. Rafael went on to assume a position of a Senior Scientist at Pfizer CTI in New York, where he initiated his work focused on modeling of targets and therapeutic antibody candidates. He was also commanding the efforts for the humanization of the lead antibody candidates based on the modeling analyses. Rafael is continuing to explore structural features of biologics and their targets in his current position as a Principal Scientist at the Kadmon Corporation in NYC. At Kadmon he is combining his expertise in structural biology with in silico approaches to drive forward discovery projects. He has participated in many symposia, speaking about the interplay of structural analysis and computational tools.

Day One

Tuesday November 20, 2019

4:00 pm | Panel Session: Predictive Tools for Optimizing Antibody Structure Function and Developability Attributes

Maria Wendt
Head, Biologics
Sanofi

Day One

Tuesday November 20, 2019

9:00 am | Keynote: Realizing Digitally Driven Drug Development – A Call to Action

Stanley Krystek
Research Fellow
BMS

Dr. Krystek received his M.S. (1986) and PhD. in Biochemistry from Albany Medical College in 1989. Dr. Krystek joined Bristol-Myers Squibb (BMS) in 1989 and has remained at BMS throughout his 30 year career.  Dr. Krystek focused his efforts developing computational methods for protein modeling and drug discovery. He applied computational methods to understanding protein-ligand interactions for important therapeutic targets such as GPCRs, proteases, and NHRs. Dr. Krystek has published over 65 papers in the area of protein structure and modeling including application of QSAR methods to drug discovery, structure-based drug design and GPCR modeling. He is the co-inventor on over 25 patents.  Currently Dr. Krystek is a Research Fellow in the department of Molecular Structure and Design where he leads a team that is focused on design and engineering of protein therapeutics.

Day One

Tuesday November 20, 2019

1:30 pm | Engineering Safer Antibodies: In Silico Design of Antibody Prodrugs

Vanita Sood
Senior Director
EMD Serono

Vanita Sood trained molecular biology & computational protein design at the University of Toronto and the University of Washington. She joined EMD Serono as a Scientist in 2008. Since 2016 she has been a member of the Discovery & Development Technologies leadership team at EMD Serono, and leads a global department dedicated to improving the way we discover and optimize the molecules that will become the medications of tomorrow. The Design, Structure, Prediction & Data science department provides expertise in X-ray crystallography, NMR, cryo-EM, Computational Chemistry, Antibody Informatics, Machine learning and Artificial intelligence.  All these approaches are utilized in support of discovery projects covering diverse molecular modalities, including NBEs, NCEs and ADCs.

Day One

Tuesday November 20, 2019

3:30 pm | Designing Superior Scaffolds Using Genetic Algorithms

Vinodh Kurella
Senior Scientist
Voyager Therapeutics

Vinodh Kurella currently is a Senior Scientist at Voyager Therapeutics within the Antibody discovery and design group in the Vector Engineering department. He is a protein engineer with a focus on antibody and antigen designs via structure guided computational modeling-based approach. At Merrimack Pharmaceuticals, he was team lead for structure guided antibody engineering, humanization designs and validations. At Intrexon corporation, lead the antibody CAR-T cell designs and optimizations in the Immuno_Oncology division at Intrexon Corporation. He completed his post-doctoral training at Dana Farber Cancer Institute and Harvard Medical school in Dr. Wayne Marasco laboratory and received Ph.D. in Dr. David Worthylake lab from Dept. of Biochemistry at LSU Health Sciences Center in the field of protein X-ray crystallography.

Workshop

November 19, 2019

1:00 pm | In-silico Immunogenicity Predictions (Hands-on Session)

Day One

Tuesday November 20, 2019

1:00 pm | Structure Guided Homology Model-Based Humanization of a Mouse Antibody Against Leukemia(B-CLL)

Yao Fan
Senior Scientist III
Abbvie

Yao Fan is currently a Senior Scientist in Global Biologics at AbbVie.  He works on the drug-like properties and developability of biologics molecules to facilitate their transition from discovery to development, using a combination of structural, biophysical and computational approaches.  He received his PhD in computational chemistry at University of Minnesota and was trained in X-ray crystallography and small-molecule drug discovery before joining the biologics field.  He enjoys bridging the gaps between theory and experiments and hopes to get the best of both worlds.

Day One

Tuesday November 20, 2019

4:00 pm | Panel Session: Predictive Tools for Optimizing Antibody Structure Function and Developability Attributes

Bernhardt Trout
Professor, Chemical Engineering
MIT

Bernhardt L. Trout is the Raymond F. Baddour, ScD, (1949) Professor of Chemical Engineering and Director of the Novartis-MIT Center for Continuous Manufacturing. He received his S.B. and S.M. degrees from MIT and his Ph.D. from the University of California at Berkeley. In addition, he performed post-doctoral research at the Max-Planck Institute. Trout’s research focuses on molecular engineering, specifically the development and application of both computational and experimental molecular-based methods, including machine learning, to engineering pharmaceutical formulations and processes with unprecedented specificity. Since 1999, he has focused on molecular engineering for biopharmaceutical formulation, primarily liquid formulation, but also lyophilized formulation. A major aspect of his research focuses on developing both microscopic and macroscopic models to design stable formulations efficiently. In 2007, with several colleagues from MIT, he set up the Novartis-MIT Center for Continuous Manufacturing, a $85 million partnership with the objective of transforming pharmaceutical manufacturing. In addition to Novartis, he has worked with many other pharmaceutical companies in research or consulting. He has published over 200 papers and currently has 20 patents pending or issued. (Photo by Jon Sachs – MIT SHASS Communication)