Session 9 - Predicting Off-Target Pharmacology
09:00
Session Chair
Prof. Fred HAMPRECHT
HEIDELBERG UNIVERSITY, Heidelberg, Germany
09:05
Promiscuity of Ligand Binding:
From Off-target Prediction to Fragment-based Design
(PL08)
Prof. Oliver KOCH
UNIVERSITY OF MÜNSTER, Münster, Germany
PD Dr Oliver Koch is currently an independent group leader for computational medicinal chemistry and molecular design at the University of Münster. He studied pharmacy and computer science at the University of Marburg, where he also received his PhD in pharmaceutical chemistry. After a postdoctoral research stay at the Cambridge Crystallographic Data Centre in 2008, he joined MSD Animal Health Innovation GmbH, before becoming a junior group leader at TU Dortmund University. Since January 2019, he is a member of the Institute of Pharmaceutical and Medicinal Chemistry, University of Münster, where he recently received the Venia Legendi for Pharmaceutical and Medicinal Chemistry.
His research interests lie in the development and application of computational methods in rational drug design with focus on structure-based design and ‘big data’ driven decisions combined with artificial intelligence in order to develop bioactive molecules and to understand selectivity, promiscuity and polypharmacology of protein-ligand interactions
09:45
Assessing the Suitability of 3D QM-Derived Atomic Hydrophobicity Patterns for Ligand-Target Interactions (SL12)
Prof. F. Javier LUQUE
UNIVERSITY OF BARCELONA, Barcelona, Spain
F. Javier Luque obtained his PhD in Chemistry at Universitat Autònoma de Barcelona in 1989. He carried out post-doctoral stays at the Swiss Federal Institute of Technology in Zurich (1992), University of Pisa (1994) and University of Nancy (1998). In 1991 he was appointed Full Professor at the University of Barcelona (UB) in 2003. He is also member leading the Computational Biology and Drug Design research team at the UB. He is also member of the Institute of Biomedicine (IBUB) and Institute of Theoretical and Computational Chemistry (IQTCUB), both pertaining to the UB. His research interest are focused on the study of biomolecular systems with the aim to explore the relationships between structure, dynamics and function, understand the molecular determinants involved in biomolecular recognition, and apply this knowledge in the design of new bioactive compounds.
10:15
The Use of Deep Neural Networks on Molecular Dynamics Simulations for the Prediction of Binding Affinities (OC06)
Mr Pierre-Yves LIBOUBAN
INSTITUTE OF ORGANIC AND ANALYTICAL CHEMISTRY, Orléans, France
After obtaining a master’s degree at the University of Rennes in the field of Pharmacy (2016-2019) and a master degree at the University of Paris Diderot In the field of in-silico drug design (2018-2019), I attended an internship in Bioinformatics at Institut Pasteur in Paris for 6 months. In 2019, I started my PhD studies at the Institute of Organic and Analytical Chemistry (ICOA) under the supervision of the professor Pascal Bonnet in the Structural Bioinformatics and Chemoinformatics group. In collaboration with the drug discovery company Janssen, my PhD project focuses on improving binding affinity prediction using recent deep learning algorithms combined to molecular dynamics simulations.
10:35
Session 10 - Artificial Intelligence in Drug Discovery
11:05
Session Chair
Prof. Tudor I. OPREA
ROIVANT SCIENCES INC., Albuquerque, United States
Tudor Oprea is currently Vice President, Translational Informatics at Roivant Sciences Inc, in Boston MA (USA). He is also Emeritus Professor of Medicine at the University of New Mexico Health Sciences Center in Albuquerque, New Mexico (USA). He served as Guest Professor at the Gothenburg University in Sweden and at the University of Copenhagen, Denmark between 2018 and 2022. Dr Oprea holds an MD (general medicine) and a PhD (molecular physiology) from the University of Medicine and Pharmacy, Timişoara, Romania. He previously held positions at the University of Utrecht, Washington University in St. Louis, Los Alamos National Laboratory and AstraZeneca Gothenburg.
Dr Oprea’s translational research led to clinical trials, most notably R-ketorolac as Cdc42/Rac1b inhibitor in ovarian cancer; and LNS8801, a selective GPER agonist for melanoma. He served as Principal Investigator for the “Illuminating the Druggable Genome” Knowledge Management Center, and has co-developed several databases including Pharos (pharos.nih.gov) and DrugCentral (drugcentral.org). He has co-authored over 300 publications, 10 granted US patents and co-edited 2 books on informatics in drug discovery.
His current research is in the development of validated artificial intelligence models for target selection in drug discovery, by combining numerical and free-text information to model human health via knowledge graphs.
11:10
Towards Machine Learning-Driven Drug Development (PL09)
Prof. Olivier ELEMENTO
CORNELL UNIVERSITY, New York, United States
Research Field
Precision Medicine, AI, Computational Biomedicine
Education
BS, Mechanical Engineering / University Paul Sabatier, Toulouse (FR)
MS, Mechanical Engineering / INSA Toulouse (FR) / University of Nottingham (UK)
MS, Intelligent Systems (Artificial Intelligence) / University of Paris Dauphine (FR)
PhD, Computational Biology / University of Montpellier (FR) / CNRS / LIRMM
Former professional experience
2009-2014 Assistant Professor, Dept of Physiology and Biophysics, Weill Cornell Medical College, NY
2009-2014 Assistant Professor, Institute for Computational Biomedicine, Weill Cornell Medical College, NY
2014-2019 Associate Professor, Dept of Physiology and Biophysics, Weill Cornell Medical College, NY
11:50
The Challenges Associated with Building Accurate Predictive Cytochrome P450 Inhibition Models Using Machine Learning Approaches (SL13)
Dr Petrina KAMYA
INSILICO MEDICINE, Hong Kong, Hong Kong
12:20
Fragment-Based and Pocket-Focused Library Design by Protein-Applied Computer Vision and Deep Generative Linking (OC07)
Dr Didier ROGNAN
CNRS, Illkirch, France
Didier Rognan heads the Laboratory of Therapeutic Innovation (LIT) at the Faculty of Pharmacy of Strasbourg (France). He studied Pharmacy at the University of Rennes (France) and did a Ph.D. in Medicinal Chemistry in Strasbourg (France) under the supervision of Prof. C.G. Wermuth. After a post-doctoral fellow at the University of Tübingen (Germany, supervisor PD. Dr. G. Folkers), he moved as an Assistant Professor at the Swiss Federal Institute of Technology (ETH, Supervisor: Prof. G. Folkers) until October 2000. He was then appointed Research Director at the CNRS to build a new laboratory in Strasbourg. Dr. Rognan is scientific consultant for several pharmaceutical companies (e.g. Lilly, Sanofi, Servier, Solvay) and has created two start-up companies (IDEALP Pharma, medchem CRO) and BIODOL Therapeutics (innovative treatment of chronic pain). He is author of 190 publications and is mainly interested in all aspects of structure-based design and synthesis of bioactive compounds.
12:40
13:05
QCMS General Meeting (Open to all attendees)
Session 11 - New Modes of Target Interaction
14:10
Session Chair
Prof. Christian KLEIN
HEIDELBERG UNIVERSITY, Heidelberg, Germany
14:15
Exploring Alchemical Binding Free Energy Calculations in Drug Discovery (PL10)
Dr Gary TRESADERN
JANSSEN, Beerse, Belgium
Gary Tresadern is a Scientific Director in the European CADD group at Janssen R&D and heads a team of 8 people. He joined Janssen in 2005 and has held various positions and responsibilities: head of the EU molecular informatics group, head of the global kinase platform, co-lead on neuroscience hit-generation group, responsible for external structural biology support, global lead on MD/FE activities. Throughout his time at Janssen he has worked as a molecular modeler in drug discovery programs for different therapeutic areas and contributed to over a half a dozen projects reaching clinical evaluation. He has a broad interest in hit and lead generation and at Janssen has been responsible for initiating and leading collaborations in areas beyond computational chemistry, such as fragment screening, protein NMR, novel screening approaches, and structural biology. In the early part of his career his scientific interests leaned towards virtual screening while during the last ten years he has developed expertise in MD and free energy calculations and helped explore and introduce the methods to drug discovery projects at Janssen. In the early 2000’s, prior to joining Janssen, he worked at Tripos in the UK and prior to that graduated with a PhD in computational chemistry from the University of Manchester focused on QM/MM and enzyme dynamics and kinetics. He is co-author of over 90 scientific articles and co-inventor on 25 patents.
14:55
Covalent Reversible Inhibition of Rhodesain; A Key Player in African Sleeping Sickness (SL14)
Prof. Tanja SCHIRMEISTER
UNIVERSITY OF MAINZ, Mainz, Germany
15:25
In Silico Design of Tubulin Activity Modulators (OC08)
Dr Dragos HORVATH
CNRS , Strasbourg, France
Dragos Horvath graduated in 1991 as a chemical engineer at the University of Cluj-Napoca, Romania, where he continued as teaching assistant until departure (1992-1996) for MSc and PhD studies in Lille (Institut Pasteur, Prof. Andrè Tartar) and Brussels (Université Libre, Prof. Shoshana Wodak). As co-founder of the combinatorial chemistry team of Cerep, he acted as Head of Molecular Modeling (worldwide) for this company until 2003, when he returned to academic research as a CNRS Scientist (2003) and then Research Director (2011). Since 2007 he joined Alexandre Varnek’s Chemoinformatics Laboratory at the University of Strasbourg. He is active in both methodological development and applications of 3D modeling (conformational sampling, docking) and 2D chemoinformatics (molecular descriptors, QSAR, chemical space mapping, chemical reactivity, etc.)
15:45
Session 12 - New Trends in Quantum Mechanics
16:15
Session Chair
Prof. Frauke GRÄTER
HEIDELBERG UNIVERSITY & HITS, Heidelberg, Germany
16:20
Enhanced Sampling Atomistic Simulations for The Estimation of Drug Binding Kinetics (PL11)
Prof. Paolo CARLONI
FORSCHUNGSZENTRUM JÜLICH, Jülich, Germany
Paolo Carloni is Chair on Theoretical Biophysics at RWTH Aachen University, Germany, Director of the Computational Biomedicine section (INM-9/IAS-5) of the Institute for Neuroscience and Medicine (INM) and Institute for Advanced Simulation (IAS), and Co-Director of the JARA-Institute Molecular Neuroscience and Neuroimaging (INM-11), Forschungszentrum Jülich, Germany.
He got his PhD at the University of Florence, Italy in 1994, under the supervision of Lucia Banci, Pier Luigi Orioli and Michele Parrinello (then at the IBM Research Laboratory in Zurich, Switzerland) on “Molecular simulations of metalloproteins”. His research focuses on development and application of HPC-based molecular simulation to problems of neurobiological interest (https://scholar.google.com/citations?user=G2 R_F1sAAAAJ&hl=en). He has published more than 310 papers and given more than 280 talks in conferences, universities and research institutes. He has supervised more than 55 PhD students. He is part of several EU projects, from the Human Brain Project to the Center for Computational Biology “BioExcel” and to the ITN program “Stimulate“.
17:00
QRNN: Transferable Neural Network for Potential Energy Surfaces of Closed-Shell Organic Molecules Including Ions (OC09)
Dr Stephan EHRLICH
SCHRÖDINGER GMBH, Mannheim, Germany
17:20
Multiscale Molecular Dynamics: An Efficient Tool for Assessing the Affinity and Specificity of Covalent Inhibitors (OC10)
Dr Levente Márk MIHALOVITS
RESEARCH CENTRE FOR NATURAL SCIENCES, Budapest, Hungary
Levente Márk Mihalovits studied chemical engineering at the Budapest University of Technology and Economics. He finished the pharmaceutical engineer MSc in 2018. Thereafter, he started his PhD studies under the guidance of Prof. György G. Ferenczy at the Medicinal Chemistry Research Group (Research Centre of Natural Sciences, Budapest) led by Prof. György Miklós Keserű as a student of the György Oláh Doctoral School. During the four years of PhD, his main focus was the computational characterization of covalent inhibition using a wide scope of computational chemistry methods including quantum chemical and hybrid QM/MM calculations. He received his PhD in 2022.
17:45
Erasmus public seminar: An Intuitive Drug Design Suite of Web Applications for Ligand-Based and Structure-Based Studies – Part 1 (1h15)
Prof. Rino RAGNO
SAPIENZA ROME UNIVERSITY, Roma, Italy
20:00