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Setting up MD Simulations of Biomolecules
Stefan Boresch is professor in the Department of Computational Biological Chemistry of the Faculty of Chemistry since 2011. An expert in biomolecular MD simulations, his research interests encompass methods development and applications of MD based free energy simulations, extending free energy simulations to hybrid QM/MM descriptions of interactions, and optimization of MD on novel computer architectures. Presently, he employs above techniques to understand complications resulting from tautomerism in free energy simulations. He is a developer of the CHARMM biomolecular simulation package, regularly participates in the CHARMM developers’ meetings, which he also hosted 2015.
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Prof. Maurizio Botta obtained a degree with laude in Chemistry at University of Rome in 1974 and in December 1979 he was awarded with the title of PhD at the University of New Brunswick under the supervision of Prof. K. Wiesner. Between 1981 and 1987 he came back to Italy and held a position at the University of Rome as a Assistant Professor in Organic Chemistry. However, during this period he has spent two years at the University of Montreal as an invited researcher in Prof. S. Hanessian’s labs. In 1987 Prof. Botta moved to the University of Siena, where he was appointed with the position of Associate Professor first and of Full Professor of Medicinal Chemistry at the Department of Biotechnology Chemistry and Pharmacy in 2000. In the same University he has also covered the position Head of the Dipartimento Farmaco Chimico Tecnologico between November 2002 and October 2008, and the position of Dean of the Faculty of Pharmacy between November 2009 to December 2012. Furthermore, since January 2008 he is an Adjunct Professor in the Department of Biology in the Temple University College of Science and Technology, Philadelphia (USA). Prof. Maurizio Botta’s scientific research is supported by EU and national funds as well as industrial grants, which allow him to work on medicinal chemistry topics, in particular on the design, synthesis and in vitro ADME evaluation of anticancer, antiviral and antibiotic compounds. Thanks to the positive results he has obtained, he has also co-founded two spin-off companies: MoLiRom (molecular Links Rome) and LDS (Lead Discovery Siena). In his career, Prof. Maurizio Botta has been active in the publication of his results, being the author of more than 600 papers, 10 publications on volumes, 26 patents, and over 450 proceedings at congresses. He was also active in training and general dissemination, being a member of the Scientific and/or Organizing Committees of several scientific Schools and Meetings (European COST Meetings, European Workshop in Drug Design now at its 12th Edition, European Workshop in Drug Synthesis now at its 7th Edition). Moreover, he is an associate Editor of ACS Medicinal Chemistry Letters and is member of the Editorial Advisory Board of Journal of Medicinal Chemistry (ACS Publications), Journal of Chemical Information and Modeling (ACS Publications) and Chemistry and Medicinal Chemistry (Wiley). Prof. Botta’s achievements were recognized through five “Academic Development Program in Chemistry” Merck Research Laboratories Awards (in 1996, 1997, 1998, 2001 and 2002) and with the “Pietro Pratesi’s medal” for his research studies (Rende, September 2014 – XXV Congresso Nazionale della Società Chimica Italiana).
ADVANCED 3D-PHARMACOPHORES AND THEIR USE IN DRUG DISCOVERY RESEARCH
Sharon Bryant is CEO at Inte:Ligand GmbH, an Austrian company with 16 years of experience developing scientific software and providing bioactive molecule discovery research services for the pharmaceutical, cosmetic, nutrition, animal health and crop protection industries. Sharon is also a guest professor and regular staff member at the University of Vienna, Department of Pharmaceutical Chemistry teaching in the Pharmacy and Master in Preclinical Drug Discovery programs. Before joining Inte:Ligand, she was a Research Scientist at the National Institutes of Health (NIH) for 17 years where she collaboratively developed novel opioid derivatives. She is author of more than 130 articles, reviews, and reference volumes and holds patents for opioid inventions. Her long-term expertise involves 3D-pharmacophores, protein modeling, MD simulations, computer-aided drug design, mentoring and entrepreneurship. In 2010 she developed a training program involving 3D-pharmacophores for designing, discovering and triaging molecules using Inte:Ligand’s suite of software, that she has given worldwide to industry and academic scientists. Her passion is innovation, in the context of inspiring scientists to develop ideas into tangible products or services to address challenges that create value for society.
Thermodynamics and Kinetics of Drug-Target Binding via Molecular Simulations
Andrea Cavalli is Professor of Medicinal Chemistry at the University of Bologna and Director of Computational and Chemical Biology at the Italian Istitute of Tecnology, Genova (Italy), where he is also Deputy Director for the Research Domain ”Computational Sciences”. Prof. Cavalli received his PhD in Pharmaceutical Sciences from the University of Bologna in 1999 and did postdoctoral work at SISSA (Trieste, Italy) and ETH (Zurich, Switzerland). Prof. Cavalli’s research has combined computational chemistry with drug discovery, focusing on neurodegenerative diseases, cancer, and neglected tropical diseases. Recently, he has started research projects in the field of clinical machine learning, combining genomics with clinical data. He has developed and applied algorithms and protocols to accelerate and enhance the discovery of novel lead and drug candidates. In particular, he has been a pioneer in the use of molecular dynamics simulations and related approaches to drug discovery. In an interdisciplinary effort, these approaches led to the identification and characterization of lead candidates within the framework of multitarget drug discovery and polypharmacology. He is an author of more than 220 scientific papers and inventor in several international patents. He has delivered more than 120 invited lectures and seminars at international congresses and prestigious institutions. He is member of the Editorial Board of several international journals, and in 2014 he founded a high-tech startup company (BiKi Technologies) focused on molecular dynamics and enhanced sampling methods for drug discovery. In 2003, he was awarded the Farmindustria Prize for Pharmaceutical Research.
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Gerhard Ecker is Professor of Pharmacoinformatics and Head of the Pharmacoinformatics Research Group at the Department of Pharmaceutical Chemistry, University of Vienna. He also coordinates the research focus “Computational Life Sciences” of the Faculty of Life Sciences. Gerhard received his doctorate in natural sciences from the University of Vienna and performed his post-doctoral training at the group of J. Seydel in Borstel (Germany). His research focuses on computational drug design, with special emphasis on drug-transporter interaction and in silico safety assessment. He coordinated the Open PHACTS project, which created an Open Pharmacological Space by semantic integration of public databases. Gerhard served 2009 – 2011 as President of the European Federation for Medicinal Chemistry, and is currently Dean at the Faculty of Life Sciences. Very recently, he founded the company Phenaris, which leverages linked open data for safety assessment of drug candidates.
Hydrogens Matter – Considering Tautomers and Protomers in Drug Discovery
Stephan Ehrlich works as Senior Application Scientist for Schrödinger since 2016. Before that, he did a postdoc at the University of Bonn where he cooperated with Bayer HealthCare to predict protein-ligand binding affinities using graphics card based quantum mechanical methods. He received his PhD from the University of Münster, where he was working on non-covalent interactions in small organic systems in the Group of Prof. Dr. Stefan Grimme. A chemist by training, Stephan has a broad background in the field of computational chemistry with a focus on non-covalent interactions and quantum-mechanical methods.
Ligand bound proteins – the underestimated skill of template choice and analysis in homology based approaches.
Margot Ernst is Assoc. Prof. at the Medical University of Vienna, where she works since 2001 on the structure and pharmacology of GABAA receptors. Prior to her current computational focus – modelling of this protein family – she was trained as computational chemist and applied quantum chemical methods to diverse chemotypes. Her current research interests include the experimental calibration of computational scoring and ranking schemes, as well as the computational analysis of protein- ligand interactions. Course participants can expect to learn about homology modeling in the gray zone of low sequence similarity, dealing with variable regions, assessing protein functional states, treatment of highly mobile or flexible proteins, and efficient means to collaborate with experimental labs in the design of informative ligands or mini-libraries on the one hand, and informative mutational studies of the protein on the other hand.
PROTACs – a New Therapeutic Modality
Peter Ettmayer graduated at the Vienna University of Technology, Austria, in synthetic organic chemistry and received his doctoral degree there in 1990 (sub auspiciis praesidentis). After a postdoctoral stay at the Christian Doppler Laboratories for Chiral Compounds & Chemical Synthesis he joined the Novartis Research Institute in Vienna as a laboratory head in the antiviral therapy and immunopathology area in 1991. In 2005 Peter joined Boehringer-Ingelheim as a group leader in the Oncology Medicinal Chemistry Department. His main responsibilities span from heading the structural research group and analytics to heading NCE based external collaborations in the UK, Boston and Shanghai. Following the successful internalization of several first in class projects in 2014 Peter is now responsible for biophysical and function assays for compound profiling in the TA oncology. Peter is the author of numerous publication and patents and as the chairman of the medicinal chemistry section of the Austrian Chemical Society organized and chaired the JMMC 2005 and EFMC-ISMC in Vienna in 2008. His main research areas are in the areas of oncology and immunopathology covering many fields of medicinal chemistry, e.g. PPIs, kinase inhibitors, peptidomimetics, combinatorial chemistry, prodrugs and PROTACs.
Chemical Space Navigation — A Journey to 1020 Possibilities
Marcus Gastreich is BioSolveIT’s Director of Application Science acting as a strategic interface between pharma clients and IT development. BioSolveIT is a globally acting provider of drug modeling software and services. Gastreich holds a diploma degree in chemistry from the University of Bonn, Germany. He did his doctorate in Theoretical Chemistry under supervision of Prof. Christel M. Marian on ab initio NMR simulation of solids and force field development for amorphous materials, with a minor in Bioinformatics.
In the late 90’s, he went to London for a research stay with Julian Gale at Imperial College. In 1999, shortly before BioSolveIT had been founded as a spin-off from Fraunhofer Gesellschaft (FhG) in 2001, he joined Prof. Thomas Lengauer’s chem- and bioinformatics group in St. Augustin, Germany, where BioSolveIT’s popular FlexX molecular docking program had initially been developed.
Gastreich is (co-/)author of more than a dozen scientific publications and has contributed to several books. His major interests lay in user-centric interface design for scientific software, visualization of molecular information, and exploiting fast, interactive algorithms to help in drug design and development. His fingerprint can be clearly made out on tools such as LeadIT, SeeSAR, and PepSee, a new therapeutic peptide analysis and design software.
Marcus travels worldwide to understand users’ & clients’ needs, and to give presentations. He has insight into small and large organizations of both academic and industrial flavors. His responsibilities span from the US, across Europe, and to Japan.
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Dr. Gerhard Hessler is head of Structure, Design & Informatics at Sanofi in Frankfurt. His team supports computer-based drug design, structural biology and data management. Before, he headed teams in computer-aided drug design and structural biology since 2008. He joined Aventis in 2001 as a computational chemist, after working for four years in the computational chemistry group of the Central Research at Bayer AG. Dr. Gerhard Hessler did his Ph.D. at Technical University of Munich in NMR-based conformational analysis of biologically active peptides and oligonucleotides. During his industrial career the main focus of his work is the application of ligand- and structure-based design techniques to the development of drugs.
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Alexander Hillisch is a Director of Medicinal Chemistry and Head of Computational Chemistry at Bayer AG, Wuppertal, Germany. His team supports drug discovery in cardiology and ophthalmology indication areas with computational chemistry, chemoinformatics, in silico ADMET and structural bioinformatics techniques. From 1998 to 2003 he headed a research group at EnTec GmbH, Jena, Germany, a subsidiary of Schering AG, Berlin. There he was project manager in preclinical research and involved in the computer-aided design and pharmacological characterization of drugs against gynecological diseases and cancer. He conducted his Ph.D. thesis at the Institute of Molecular Biotechnology (IMB), Jena in the area of biophysics (NMR, FRET) and molecular modeling. Alexander Hillisch received his Ph.D. in Biochemistry with Prof. Peter Schuster in 1998 and his diploma in Pharmacy in 1995 from the University of Vienna, Austria. He is author of 43 research papers, 61 patents and 2 books. Alexander teaches “Molecular pharmacology and Drug Design” at the University of Cologne from which he received a honorary professorship in 2010.
NEW COMPUTATIONAL TOOLS AT THE MOLECULAR SCALE FOR PROTEIN-LIGAND BINDING IN DRUG DISCOVERY
Dušanka Janežič is full professor at the Faculty of Mathematics, Natural Sciences and Information Technologies at the University of Primorska (Slovenia). Has published 2 scientific books and 120 publications in SCI journals with over 2000 pure citations in Web of Science database, and h-index 19. One of the Editors in the ACS Journal of Chemical Information and Modeling (2001-2014). In 2013, Recipient of Žiga Zois Award for outstanding research achievements in mathematics in natural sciences. In 1999, Recipient of Ambassador in Science of the Republic of Slovenia Award. Since 2013 she is appointed by the government of Republic of Slovenia as council member of the National Agency of Qualitative Evaluation of Higher Education in Slovenia. She worked in the USA as a visiting researcher at the National Institute of Standards and Technology. As a Senior Fulbright Scholar she conducted research in the USA at the National Institutes of Health. She worked at the Technical University of Munich, Germany as a DAAD fellow. Her current research interests include graph theory development, prediction of protein-protein and protein-ligand binding sites, biomolecular simulations, and the application of these techniques to problems in pharmaceutical research and drug development.
In silico prediction of drug metabolism
Johannes Kirchmair is an associate professor in bioinformatics at the Department of Chemistry and the Computational Biology Unit (CBU) of the University of Bergen. He also is a group leader at the Center for Bioinformatics (ZBH) of the University of Hamburg. After earning his PhD from the University of Innsbruck (2007), Johannes started his career as an application scientist at Inte:Ligand GmbH (Vienna) and as a university assistant at his alma mater. In 2010 he joined BASF SE (Ludwigshafen) as a postdoctoral research fellow. Thereafter he worked as a research associate at the University of Cambridge (2010-2013) and ETH Zurich (2013-2014). From 2014 to 2018 Johannes held a junior professorship in applied bioinformatics at the University of Hamburg. Johannes has been a visiting professor or lecturer at the National Institute of Warangal (2016), the University of Cagliari (2017) and the University of Vienna (2018). His main research interests include the development and application of computational methods for the prediction of the biological activities, metabolic fate and toxicity of drugs, cosmetics and agrochemicals.
Reflections on Discovery in Science
Hugo Kubinyi studied chemistry in Vienna, Austria. After his Ph.D. thesis at the Max Planck Institute of Biochemistry in Munich he continued as PostDoc at the German Cancer Research Centre in Heidelberg. In 1966 he joined Knoll AG, later a subsidiary of BASF AG. Development of a partial synthetic cardiac glycoside (Meproscillarin, CLIFT; launched in 1978). In 1985 he moved to BASF AG. Since 1987, until his retirement, he was responsible for the Molecular Modelling, X-ray Crystallography and Drug Design group of BASF, since early 1998 also for Combinatorial Chemistry in the Life Sciences. In 1986 he was appointed as associate Professor of Pharmaceutical Chemistry at the University of Heidelberg. He is former Chair of the Cheminformatics and QSAR Society (1995-2000; from 2000-2007 Advisor to the Chair) and IUPAC Fellow. In 2006 he received the Herman Skolnik Award (CINF, ACS) and in 2008 the Nauta Award in Pharmacochemistry (EFMC) and the Nauta Chair (Vrije Universiteit, Amsterdam). In 2011 he became a Corresponding Member of the Brazilian Academy of Sciences (Academia Brasileira de Ciências).
From his scientific work resulted more than 100 publications and seven books on QSAR, 3D QSAR, Drug Design (the German book “Wirkstoffdesign” received the 1999 Book Award of the FCI, Association of Chemical Industry), Chemogenomics in Drug Discovery, and Drug Discovery Technologies (Volume 3 of Comprehensive Medicinal Chemistry II).
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Thierry Langer is full professor and head of the department of Pharmaceutical Chemistry at University of Vienna, Austria. Before that, he was CEO of Prestwick Chemical, France. He is author of more than 200 original papers and has long term expertise in computational medicinal chemistry. In 2003, with colleagues he founded the software development and consulting company Inte:Ligand GmbH. which he led until 2008. He was also the coordinator of the Austrian academic drug discovery initiative wings4innovation (www.w4i.org).
Applications of free energy calculations from molecular dynamics simulations
Chris Oostenbrink is professor at the University of Natural Resources and Life Sciences in Vienna and heads the Institute of Molecular Modelling and Simulation (BOKU). He has published more than 150 peer-reviewed papers involving computational approaches to describe complex biomolecular systems. He was brought to BOKU on a Vienna Science Chair by the Vienna Science and Technology Fund (WWTF) in 2009 and was a recipient of a Starting Grant of the European Research Council (ERC). He heads the doctoral program Biomolecular Technology of Proteins (BioToP) in which 50 doctoral candidate are currently enrolled. His main research interests are the structure and function of complex biomolecular systems, through molecular simulations and the accurate description of molecular interactions.
Cheminformatics in the open-source KNIME Analytics Platform
Martyna Pawletta is a data scientist in the Life Sciences team at KNIME GmbH in Berlin. Before that she worked in different research and IT projects at Bayer and Clarivate Analytics, where she analyzed data coming from various scientific areas like chemistry, toxicology, bioinformatics or clinical research. At Bayer, she supported the Innovative Medicine Initiative (IMI) eTOX project. There she worked mainly on data curation, quality management, development of ontologies and development of in silico models for toxicity prediction of new drugs. At Clarivate she worked as a data scientist on projects related to data mining and data integration, especially in the area of clinical informatics and bioinformatics.
She has a Master of Science in Bioinformatics from the Free University (FU) of Berlin, with a focus on evaluation of different in silico models to predict autofluorescence effects in biological high throughput assays during her master thesis. She is also a member of the German Society for Experimental and Clinical Pharmacology and Toxicology (DGPT).
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Prof. Schleifer studied pharmacy at the Freie Universität Berlin. After his PhD in experimental pharmaceutical chemistry he started a “Habilitation” in the computational working group of Prof. Höltje. In 2001 he changed from academia to industry and succeeded Prof. Kubinyi as head of the molecular modelling at BASF Ludwigshafen. Today he is heading Computational Chemistry and Bioinformatics with sites at San Diego (California), Raleigh (North Carolina), Ludwigshafen and Mumbai. Parallel to his work at BASF he is lecturer for Drug Design at the University of Düsseldorf where he was appointed as Professor for Pharmaceutical and Medicinal Chemistry (“apl. Prof.”) in 2008.
Extracting hidden design opportunities from protein structure ensembles
Philipp Schmalhorst is a postdoctoral researcher in computational chemistry at Boehringer Ingelheim. He received his doctorate in biochemistry from Hannover Medical School, Germany, for studies on fungal cell wall carbohydrates. In a subsequent postdoctoral stay in the lab of Carl-Philipp Heisenberg at the Institute of Science and Technology (IST) Austria, he worked on Molecular Dynamics simulations of carbohydrates. In collaboration with Mateusz Sikora he contributed to the improvement of the coarse-grained MARTINI force field.
In 2018, he joined the computational chemistry team of Andreas Bergner at Boehringer Ingelheim. His research focuses on the development of methods to extract and aggregate information from protein structure ensembles to fully exploit 3D structural data for drug design.
Multi-parameter Optimisation in Drug Discovery: Targeting compounds with a high chance of success
Matt is CEO of Optibrium. He has a Master of Science in computation from the University of Oxford and a Ph.D. in theoretical physics from the University of Cambridge. As Associate Director at Camitro (UK), ArQule Inc. and then Inpharmatica, he led a team developing predictive ADME models and state-of-the-art intuitive decision-support and visualization tools for drug discovery. In January 2006, he became responsible for management of Inpharmatica’s ADME business, including experimental ADME services and the StarDrop software platform. Following acquisition of Inpharmatica, Matt became Senior Director responsible for BioFocus DPI’s ADMET division and in 2009 led a management buyout of the StarDrop business to found Optibrium, which develops software for small molecule design, optimisation and data analysis. Matt has published over 30 peer-reviewed papers and book chapters on computational chemistry, cheminformatics and drug discovery.
Design of selective histone deacetylase inhibitors – lessons learned from X-ray crystallography and molecular modelling
Wolfgang Sippl is Professor for Medicinal Chemistry at the Martin-Luther-University of Halle-Wittenberg (Germany). He obtained a Ph. D. in 1997 in Pharmaceutical Chemistry at the University of Düsseldorf in the group of Hans-Dieter Höltje and was a post-doctoral fellow at the Université Louis-Pasteur in Strasbourg (France) where he worked with Camille G. Wermuth. Since 2003 he is Full Professor at the University of Halle-Wittenberg and since 2010 he is Director of the Institute of Pharmacy in Halle. He has published more than 180 articles mainly related to drug design, virtual screening and structure-based optimization of epigenetic modulators. He has edited four books including and gave more than 100 invited lectures. His research focuses on the drug design of epigenetic modulators, which not only led to the development of successful virtual screening methods, but also resulted in the development and biological characterization of novel epigenetic modulators for the treatment of cancer and parasitic diseases.
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Gunther Stahl received his license as pharmacist in 1996 after his study at the University of Bonn. He continued his education as Ph.D. student under Prof. Höltje at the University of Düsseldorf where he received his doctorate degree in 2001 focusing on Homology Modeling and Molecular Dynamics. He then joined Tripos GmbH as Application Scientist to work with industrial and academic customers to help them apply the different computational chemistry tools available. After different roles at Tripos (Application Scientist at the US East Coast and later again from Germany as manager of the PacRim distributors) he joined OpenEye in 2012 to work with all their European customers.
Computational studies on ion channels
Anna Weinzinger is Assistant Professor at the Department of Pharmacology and Toxicology at the Faculty of Life Science since 2016. She conducted her doctoral research at the Institute of Theoretical Chemistry, Vienna, in the area of molecular modeling, focusing on different membrane proteins including GPCRs and voltage gated calcium channels. Anna performed her post-doctoral training at the group of Bert de Groot, at the Max Planck Institute for Biophysical Chemistry in Göttingen (Germany), where she started to address the “off-target” pharmacology of the hERG K+ channel. She habilitated in Pharmacoinformatics in 2015 at the University of Vienna. Her fields of research are voltage and ligand gated ion channels. Her research combines computational methods such as homology modeling, molecular dynamics simulations and drug docking with a special focus on rare ion channel diseases such Cantú syndrome (funded by the ERARE initiative of the European Union), Long QT syndrome or Timothy syndrome.
Intertwining Data Science and Computational Molecular Design – Recent Examples from Modeling Hepatic Uptake Transporters
Barbara Zdrazil is a junior group leader working at the University of Vienna, Department of Pharmaceutical Chemistry. During her PhD (University of Vienna), Barbara was mainly engaged in QSAR and cheminformatics, and got some training in chemogenomics during an internship with Jordi Mestres (Barcelona). Barbara performed her postdoctoral training in the group of Hans-Dieter Höltje (University of Düsseldorf) where she gained knowledge in molecular dynamic simulations and other structure-based methods. From 2008 onwards Barbara was working in the Pharmacoinformatics Research Group (University of Vienna), being involved in National and European projects: SFB35 (FWF), eTOX (IMI), OpenPHACTS (IMI), and EU-ToxRisk (H2020 project). Barbara’s research is concentrated on integrating Data Science approaches into the Computational Molecular Design process. She is PI in an FWF funded project on “Elucidating hepatic Organic Anion Transporting Polypeptide (OATP) ligand interactions and selectivity”. As a second main research focus Barbara is performing large-scale data analyses with a special focus on time trend analyses of fragments and drug discovery relevant properties.