08:00
09:00
Welcome word
Dr Henning STEINHAGEN
APTUIT, Verona, Italy
Session 1: Big Data Analysis and Precision Medicine
Session Chair
Prof. Modesto OROZCO
INSTITUTE FOR RESEARCH IN BIOMEDICINE (IRB), Barcelona, Spain
09:05
PL02 - Informatics Methods for Understanding Drug Binding and Action
Prof. Russ B. ALTMAN
STANFORD UNIVERSITY, Stanford, United States
Russ Biagio Altman is a professor of bioengineering, genetics, & medicine (and of computer science, by courtesy) and past chairman of the Bioengineering Department at Stanford University. His primary research interests are in the application of computing and informatics technologies to problems relevant to medicine. He is particularly interested in methods for understanding drug action at molecular, cellular, organism and population levels. His lab studies how human genetic variation impacts drug response (e.g. http://www.pharmgkb.org/). Other work focuses on the analysis of biological molecules to understand the action, interaction and adverse events of drugs (http://features.stanford.edu/). Dr. Altman holds an A.B. from Harvard College, and M.D. from Stanford Medical School, and a Ph.D. in Medical Information Sciences from Stanford. He received the U.S. Presidential Early Career Award for Scientists and Engineers and a National Science Foundation CAREER Award. He is a fellow of the American College of Physicians (ACP), the American College of Medical Informatics (ACMI), the American Institute of Medical and Biological Engineering (AIMBE), and the American Association for the Advancement of Science (AAAS). He is a member of the Institute of Medicine of the National Academies. He is a past-President, founding board member, and a Fellow of the International Society for Computational Biology (ISCB), and a past-President of the American Society for Clinical Pharmacology & Therapeutics (ASCPT). He has chaired the Science Board advising the FDA Commissioner, and currently serves on the NIH Director’s Advisory Committee. He is an organizer of the annual Pacific Symposium on Biocomputing (http://psb.stanford.edu/), and a founder of Personalis, Inc. Dr. Altman is board certified in Internal Medicine and in Clinical Informatics. He received the Stanford Medical School graduate teaching award in 2000, and mentorship award in 2014.
09:50
KL01 - Multi-Scale Structure-Based Drug Discovery
Prof. Rommie AMARO
UNIVERSITY OF CALIFORNIA, San Diego, United States
Rommie E. Amaro is an Associate Professor of Chemistry and Biochemistry at the University of California, San Diego. She received her B.S. (Chemical Engineering, 1999) and Ph.D. (Chemistry, 2005) from the University of Illinois at Urbana-Champaign. She was a NIH postdoctoral fellow with Andy McCammon (UCSD). Rommie is the recipient of an NIH New Innovator Award, the Presidential Early Career Award for Scientists and Engineers, the ACS COMP OpenEye Outstanding Junior Faculty Award, and the ACS Kavli Foundation Emerging Leader in Chemistry National Lecturer (Spring 2016). She is the director of the NIH P41 National Biomedical Computation Resource and a co-Director of the NIH U01 Drug Design Data Resource. Her research is broadly concerned with the development and application of state-of-the-art computational methods to address outstanding questions in drug discovery and molecular biophysics.
10:20
OC01 - Biosignature Based Drug Design: Impacts of a New Paradigm from a Pharma Perspective
Dr Joerg Kurt WEGNER
JOHNSON & JOHNSON, Beerse, Belgium
Joerg Kurt Wegner is a Principal Scientist working since ten years for Janssen Pharmaceutica, Beerse, Belgium.
He started as PostDoc in Structure-Based Drug Design (SBDD) modeling HIV virus mutations to Xray structures for translating viral resistance models into drug design suggestions. He moved then into computational chemistry project support for multiple years, including all aspects of Computer-Aided Drug Design (CADD) and Structural Biology, including Fragment-Based Drug Design (FBDD). Since 2011 he is working in the ComputationalSciences department coordinating and co-coordinating various leveraged funding projects with multiple academic partners, high-performance compute centers, and Intel.
His key role within Janssen is to ensure applications of high-dimensional biology data across multiple enterprise warehousing systems for therapeutic area projects for all therapeutic areas as well as within strategic initiatives. For enabling this we are utilizing big data analytics, high-performance computing, and large-scale machine learning. We coined the application Biosignature-Based Drug Design (BBDD) to reflect the application aspects highlighting alos the difference to traditional drug design paradigms.
10:40
OC02 - Chemical Reactions Mining: Big Data Challenge
Prof. Alexandre VARNEK
UNIVERSITY OF STRASBOURG, Strasbourg, France
11:00
Session 2: QSAR Tools and Applications
Session Chair
Prof. Gerhard ECKER
UNIVERSITY OF VIENNA, Vienna, Austria
11:25
PL03 - QSAR and Environmental Toxicology - From Chemical Structure to Environmental Hazard: Exploiting QSAR for Screening, Prioritization and Safer Alternative's Design
Prof. Paola GRAMATICA
INSUBRIA UNIVERSITY, Varese, Italy
Paola Gramatica is full professor of Environmental Chemistry at Department of Theoretical and Applied Sciences (DiSTA) in Insubria University (Varese), leader of the QSAR Research Unit in Environmental Chemistry and Ecotoxicology. She is an organic environmental chemist working on QSAR applied to compounds of environmental concern. Different classes of organic compounds (POPs, PBTs, PAHs, Pesticides, Endocrine Disruptors, Flame Retardants, Personal Care Products, Pharmaceuticals, etc.) have been studied modeling various physico-chemical properties or biological activities, such as toxicity, biodegradability, persistence, mutagenicity, endocrine disruptor and PBT properties, etc. She has developed the software QSARINS for QSAR OLS model development and validation.
PG is author of more than 150 scientific papers on referred international journals, with more than 6500 citations according to ISI Web of Science/8000 according to Google Scholar, some book chapters and about 250 meeting presentations. She was a selected member of the OECD Task Force of QSAR Experts for the definition of the famous “OECD principles for QSAR validation for regulation applicability”.
PG is member of the Editorial Board of Molecular Informatics, Sustainable Chemicals and Pharmaceuticals and The Open Applied Informatics Journal. Among other EU-Projects, she has been leader of a Workpackage on QSAR modeling in the recent EU-FP7 Project CADASTER for REACH.
12:10
KL02 - A Method for Incorporating Proprietary SAR Information to Improve (Q)SAR Models without Disclosing Underlying Compounds
Dr Catrin HASSELGREN
LEADSCOPE, Columbus, United States
Catrin Hasselgren has a background in the pharmaceutical industry, having spent 12 years at AstraZeneca working in computational toxicology with her last position being Associate Director of Computational ADME and Safety. After a short stop at the University of New Mexico followed by founding her own consultancy company, she is now Senior Principal Scientist at Leadscope.
12:40
OC03 - A Cheminformatics Story Behind 141,000,000$ Molecule
Prof. Artem CHERKASOV
UNIVERSITY OF BC, VANCOUVER PROSTATE CENTRE, Vancouver, Canada
Dr. Artem Cherkasov, PhD, DSc
Associate Professor at the Faculty of Medicine, University of British Columbia.
Research interests include computer-aided drug design, structure-activity modeling, drug reprofiling, new therapies and development of novel cheminformatics and bioinformatics tools.
Dr. Cherkasov authored more than 200 articles and conference proceedings, more than 60 patents, 6 book chapters.
During his tenure at the UBC, Dr. Cherkasov has been a principal applicant or co-applicant on a number of successful grants totalling over 43M dollars, and founded several spinoff biotech companies.
Dr. Cherkasov holds a number of current research grants from NSERC, CIHR, Genome BC, Prostate Cancer Canada, Prostate Cancer Canada BC, US Department of Defense, CCSRI and Prostate Cancer USA.
In December of 2015, the Androgen Receptor inhibitor developed by Dr. Cherkasov was licensed by Hoffman-LaRoche company for 142M dollars - a record amount for Canadian academic institutions..
13:00
OC04 - How Much Does a Molecule Cost? Molecular Statistics Explains the Big Data Problem In QSPR
Prof. Jaroslaw POLANSKI
UNIVERSITY OF SILESIA, Katowice, Poland
13:20
OC05 - How To Increase the Concordance of the Experimental Data for QSAR Modeling: Case Study for HIV-1 Reverse Transcriptase Inhibitors
Dr Olga TARASOVA
IBMC, Moscow, Russia
Olga A. Tarasova, 30 years old. Graduated from Russian State Medical University in 2008, got PhD in Bioinformatics in 2012 at the Institute of Biomedical Chemistry in Moscow, Russia. During PhD studies, she developed and validated fragment-based approach to a computer generation of the new chemical compounds with required biological activity profile. As a result, new thiazole derivatives with the potential anti-inflammatory activity were designed and their activity has been confirmed experimentally. She also took a part in several international projects for the search of prospective antineoplastic and anti-HIV agents using SAR/SPR models, molecular modeling (docking, pharmacophore analysis) and fragment-based drug design. Current study is a part of RFBR ongoing research project directed to the design of the new compounds with the potential activity against the variety of HIV resistant strains, taking into account the details of the biological assays used for the experimental testing.
13:40
Lunch and Poster session
14:10 - Workshop organised by OpenEye (75 min)
Session 3: Molecular Dynamics Simulations and Related Methods
Session Chair
Prof. Andrea CAVALLI
UNIVERSITY OF BOLOGNA AND IIT, Bologna, Italy
15:40
PL04 - Exploring Protein Dynamics for Ligand Design
Prof. Rebecca WADE
HEIDELBERG UNIVERSITY AND HITS, Heidelberg, Germany
Rebecca Wade is scientific director at Heidelberg Institute for Theoretical Studies (HITS) where she leads the Molecular and Cellular Modeling group. She also holds a professorship in “Computational Structural Biology” at the Center for Molecular Biology (ZMBH), Heidelberg University, Germany.
Rebecca Wade studied at Oxford University and received her doctorate in molecular biophysics in 1988. She was a group leader at the European Molecular Biology Laboratory (EMBL) in Heidelberg before moving to HITS in 2001. Her research is focused on the development and application of computer-aided methods to model and simulate biomolecular interactions. She is an author of over 200 scientific publications.
She is the recipient of the 2004 Hansch Award of the QSAR and Modelling Society.
URL: www.h-its.org/mcm.
16:25
KL03 - Mechanistic and Inhibition Studies of the ARP2/3 Complex Using Computational Techniques
Dr Zoe COURNIA
BIOMEDICAL RESEARCH FOUNDATION ACADEMY OF ATHENS, Athens, Greece
Dr. Zoe Cournia graduated from the Chemistry Department of the University of Athens in 2001 and then pursued doctoral studies with Professor Jeremy Smith in the University of Heidelberg, Germany in the field of computational biophysics, receiving her Ph.D. degree in 2006. She then performed post-doctoral studies in computer-aided drug design with Professor Bill Jorgensen in the Department of Chemistry, Yale University, and she also became a Lecturer in Yale College in 2009. Since 2009 she is an Assistant Professor at the Biomedical Research Foundation of the Academy of Athens working on drug discovery and drug delivery design. She has earned the AACR Fellowship for Cancer Research in Angiogenesis, the “Women of Innovation Award” from the Connecticut Technology Council, USA and the Outstanding Junior Faculty Award in Computational Chemistry from the American Chemical Society. She blogs frequently in her “Life is Chemistry” blog, which aims to promote public awareness and understanding of chemistry in everyday life.
16:55
17:25
OC06 - Hybrid Modeling Approach to Investigate Antibody Dynamics
Dr Michal VIETH
ELI LILLY & CO, Indianapolis, United States
Michal Vieth received MS in chemistry from University of Warsaw in 1991 and Ph.D. in chemistry from The Scripps Research Institute in 1996. During his graduate career he worked on the computational understanding of lecine zipper assembly under Prof. Jeffrey Skolnick. His postdoctoral work with Prof. Charles Brooks gave rise to the new generation of small molecule docking algorithm, utilized in industrial setting for over a decade. In 1998 he joined Computational group at Lilly, where he currently holds Senior Research Advisor title. His technical contributions impacted lead generation, computational toolkit and screening strategies currently implemented at Lilly. He authored 42 peer reviewed publications, presented over 30 invited lectures, co-organizes bi-annual Kinase meetings in Poland and contributes to Lilly MDR TB initiative. His current research focuses on the development and integration of new computational technologies in drug discovery through collaborations with multiple academic labs including molecular dynamics, hybrid modeling and de novo design of molecules through crowdsourcing game.
17:45
OC07 - Finding a Way Toward Binding: A MD Biasing Potential Leading to the Protein-Ligand Complex
Dr Walter ROCCHIA
FONDAZIONE ISTITUTO ITALIANO DI TECNOLOGIA, Genova, Italy
19:00
City Tour for participants