Please click on the name in order to find more information about the Speaker and his / her talk.
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.
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.
Structure, Function and Ligand Discovery for Solute Carrier Transporters
Claire Colas is a postdoctoral scientist in the Pharmacoinformatics research group (University of Vienna). She completed her PhD in 2011 at the Pasteur Institute in Paris, France and worked for two years as a postdoctoral scientist at the Institut de Chimie des Substances Naturelles at Gif-sur-Yvette, France. Since 2013, Dr. Colas’ research has been focused on the structural characterization of Solute Carrier (SLC) transporters. In humans, there are over 450 SLCs that transport a broad range of substrates, including neurotransmitters, metabolites, and drugs. Thus, SLCs are emerging as important therapeutic targets. First at the mount Sinai School of Medicine in New-York City (2013-2018) and then in Vienna (2018-present), Dr Colas has been working on six distinct SLC families, involved in various diseases and disorders.
Dr Colas uses various computational methods such as homology modeling and molecular docking to explore the structural determinants defining the substrate specificities of SLCs.
Lessons learned from protein-ligand complex prediction and lead optimization with FEP in the D3R Challenge
Women at the Interface of Computational Chemistry and Drug Discovery
Dr. Cournia is a Researcher (Assistant Professor) at the Biomedical Research Foundation, Academy of Athens, where she works on computer-aided drug design (http://www.drugdesign.gr). She graduated from the Chemistry Department, University of Athens in 2001 and received her PhD in 2006 (University of Heidelberg, Germany). She was a postdoctoral researcher, Chemistry Department, Yale University, USA, on computer-aided drug design and in 2009 she became a Lecturer at Yale College. She has been awarded with the American Association for Cancer Research Angiogenesis Fellowship (2008), the “Woman of Innovation 2009” Award, Connecticut Technology Council, USA, the Marie Curie Fellowship, European Union (2010), the “Outstanding Junior Faculty Award”, American Chemical Society (2014) and the first “Ada Lovelace Award”, Partnership for Advanced Computing in Europe (2016). She is the Associate Editor of the Journal of Chemical information and Modeling, American Chemical Society, and a member of the Infrastructure Advisory Group (INFRAG) of the European High Performance Computing Joint Undertaking, European Commission. She is currently teaching at the Master’s program “Information Technologies in Technology and Medicine” at the Department of Informatics and Telecommunications, National University of Athens. She is the Founder of Ingredio, a mobile phone app that informs consumers on the potential hazards of chemical ingredients in food and cosmetics products using open, peer-reviewed data (http://www.ingred.io/android).
Accessing public databases with KNIME
Daniela Digles is post-doc as well as senior lecturer at the Department of Pharmaceutical Chemistry, University of Vienna. She completed her PhD studies with a DOC-fFORTE-fellowship of the Austrian Academy of Sciences at the University of Vienna, in the Pharmacoinformatics Research Group of Prof. Gerhard Ecker.
In 2012 she started her Post-doc within the Open PHACTS project (IMI), and later on within the Open PHACTS Foundation, where she was testing the developed system, creating KNIME workflows to access the data to answer research questions, as well as user support. Currently, she is involved in the “FAIRness for Life Science Data” project (FWF), and the RESOLUTE project (IMI).
Her main research interests are the usage and quality control of open data (especially for solute carrier proteins), classification schemes, and the application of workflow tools.
Virtual Screening Campaigns for the Identification of New Immunomodulatory Drugs Targeting AhR
Daniela Dolciami is a third-year PhD student in Pharmaceutical Sciences at the University of Perugia. She works in the group of Professor Antonio Macchiarulo dealing with computational and biophysical aspects of Aryl hydrocarbon Receptor. Both her Master thesis and PhD research projects have been devoted to the identification of new small molecules with immune modulation function. She has recently carried out an internship at the University of Cambridge under the supervision of Dr. Andreas Bender working on the development of Machine Learning models to predict drug toxicity. Her research interest is focused on the application of in silico methods, artificial intelligence and data analysis techniques to different steps of drug discovery projects. In 2017, she has successfully applied for the EUROPIN program.
Computational Toxicology – from models to workflows
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.
Representation of 3-D Pharmacophore Models Extracted from Molecular Dynamics Simulation
Arthur Garon studied Chemistry and Biology at the University of Clermont-Ferrand (France) and obtained a MSc degree in Chemoinformatics at University of Strasbourg (France) in 2016. During his studies he did a six months internship in the Chemoinformatics Research Group within the Department of Pharmaceutical Chemistry of University of Vienna (Austria). He then started his PhD in 2017 there, studying the development and implementation of new methods for pharmacophore-based analysis of molecular dynamics simulations used for computer assisted lead optimization in early drug development. This project is performed in collaboration between University of Vienna, Inte:Ligand GmbH, and Laboratoires Servier.
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.
Computational studies of molecular interactions in the human serotonin transporter
Eva Hellsberg is a PhD student at the University of Vienna since 2015, supervised by Gerhard F. Ecker and Anna Weinzinger. She is working on computational studies of molecular interactions in monoamine transporters with special focus on the human serotonin and dopamine transporters. As a full fellow of the MolTag PhD program, she was involved in collaborations with the Medical and Technical Universities of Vienna, participated in the organization of scientific events, presented her work on international conferences, and did a six-month research internship at NIH in Bethesda under supervision of Lucy R. Forrest.
Cover: Conformational OVERsampling of toxicological datasets for deep learning
Jennifer Hemmerich obtained a B.sc. in Molecular medicine and a M.sc. in Toxicology. Since 2017 she is working oh her PhD in the Pharmacoinformatics group of the University of Vienna under the supervision of Professor Gerhard F. Ecker. For her PhD she is researching the use of deep learning for in silico toxicology. Deep learning is widely researched but only limited data is available for toxicity predictions. Usually those datasets are very small and imbalanced and deep neural network training becomes unfeasible. For this reason she is researching techniques to facilitate training on toxicological datasets in order to utilize this powerful technique. She is a EUROPIN associate since 2017 and an associate fellow of the MolTag PhD program since 2019.
Efficient Mining of Chemical Space
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.
Bayer’s “Next Generation Library Initiative”: Selected Examples of Computational Compound Design
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.
Structural and molecular aspects of GABA transporter subtype selectivity
Stefanie Kickinger studied pharmacy and is currently working as a PhD student in the Pharmacoinformatics Research group at the University of Vienna, supervised by Gerhard F. Ecker. She is interested in elucidating the molecular determinants for subtype selectivity of GABA transporters (GATs). GATs are relevant drug targets as they are involved in many neurological diseases such as epilepsy. With the help of homology modeling, molecular docking and molecular dynamics simulations Stefanie tries to shed light on the binding mechanism of different GAT inhibitors with a particular focus on a possible new allosteric binding pocket. Her major focus is to understand the molecular interactions that drive subtype selectivity which will ultimately govern the design of new highly selective GAT inhibitors. Moreover, Stefanie is an associate fellow of the MolTag PhD program which funded her to conduct a six-month internship at Yale University under the supervision of William L. Jorgensen.
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).
Adventures in Computer-Assisted Molecular Design
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).
Computer-based approaches for the search of new Spindlin1 Inhibitors
Chiara Luise is a research assistant at the Institute of Pharmacy in Halle (Martin-Luther-University of Halle-Wittenberg, Germany) and she is currently at the final stage of her PhD program. After graduating in Pharmacy from the University of Perugia (Italy), she joined the Medicinal Chemistry Research group of Prof. Wolfgang Sippl in Halle. There she spent initially a period of 6 months as an Erasmus+ Traineeship fellow. At the end of the training period, she was offered the opportunity to continue her experience as a PhD student. Her current projects are mainly focused on the application of computer-based methods to design novel inhibitors for methyl-lysine reader proteins and histone acetyltransferases; two classes of epigenetic targets. To expand her knowledge on pharmacophore-based modelling, Chiara joined a 2 months Internship program at Inte:Ligand (Vienna, Austria) within the MuTaLig Cost Action framework. Also, she is involved in a 2-year DAAD bilateral project with the University of Ljubljana (Slovenia) titled “Algorithm Development & Application for Target Site Prediction in Drug Discovery”. Since 2017, she is a member of the EUROPIN program.
Targeting Cytochrome P450 4Z1 as Novel Cancer Target
David Machalz is a third-year PhD student in the group of Prof. Wolber at (FU) Freie Universität Berlin and EUROPIN associate since 2017. He graduated in Pharmacy from FU Berlin in 2014 and obtained his pharmacist license in 2016. He was introduced to modeling cytochrome P450s (CYP) during his eight-month stay at the Molecular and Computational Toxicology group (Vrije Universiteit Amsterdam) and summarized his findings in an additional diploma thesis in Pharmacy. He works on the characterization of orphaned CYPs in a strong collaborative network including the CYP expression expert Prof. Bureik (Tianjin University) and metabolism analytics expert Prof. Parr (FU Berlin). In his current project David is working on a mechanistic model for the promising anti-cancer target CYP4Z1 using dynamic pharmacophores derived from molecular dynamics simulations.
Deep learning for computational chemistry: compound representation, ADMET profiles and automatic optimization
Floriane Montanari is a research scientist with years of experience in cheminformatics. She has a passion for useful machine learning approaches applied at all stages of the drug discovery pipeline. Since May 2017 she is working at Bayer, where she has been lucky enough to improve the daily routine of chemists company-wide by productionizing her work on deep learning for ADMET properties. Floriane is co-author of more than fifteen scientific publications and in 2016 she received a PhD from the University of Vienna, with a thesis focusing on ABC-transporters inhibition and best practices in model validation. She enjoys participating in competitions and in 2014 she submitted the best predictive model in the Teach-Discover-Treat challenge on Malaria HTS prediction.
Dihedral angle dynamics of GPCR activation hotspots
Trung Ngoc Nguyen is a PhD student in the Molecular Design Lab of Prof. Gerhard Wolber at Freie Universität Berlin. He studied Pharmacy in Berlin from 2011-2015 and came in touch with molecular modelling for the first time in 2016 exploring structural determinants of Sphingosine-1-phosphate receptors (S1PR) important for subtype selectivity and used them for virtual screening. Now he strives to link subtle changes in G protein-coupled receptors to specific activation states combining molecular dynamics simulations and machine learning. Trung Ngoc Nguyen is part of the EUROPIN doctoral program since 2017 and is doing a lab rotation in the group of Prof. Jana Selent in Barcelona at the moment.
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.
Design of novel NS2B-NS3 flaviviral protease inhibitors
Szymon Pach is a PhD student in the group of Prof. Gerhard Wolber at Freie Universität Berlin. He studied Pharmacy in Berlin 2011-2015 and obtained his pharmacist license in 2017. Szymon is part of the EUROPIN doctoral program since 2017. His work focuses on the design of small molecule inhibitors of flaviviral proteases and characterization of covalent binding to enzymes. Besides inhibitor design, he is interested in understanding viral entry processes through computational studies on protein-protein 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).
Structure-activity relationship of the hERG activator ICA-105574
Eva-Maria Plessl is a postdoctoral scientist in the Department for Pharmacology and Toxicology, University of Vienna. She completed her PhD in chemistry in 2016 at the Institute of Theoretical Chemistry, University of Vienna, under the guidance of Prof. Hofacker and Ass.-Prof. Weinzinger, where she was associated to the doctoral program MolTag. Her research fields include the inward rectifier potassium channel (KIR) and the human ether-a-go-go related gene (hERG) channel, among others.
The method portfolio of Eva Plessl includes computational methods such as molecular dynamics simulations, homology modeling and molecular docking, as well as experimental methods such as the patch clamp technique. She is further collaborating with international experimentalists and crystallographers. Her main focus is to understand the conformational changes occurring during the gating process of ion channels and how these can be influenced by mutations within the channel as well as ligands.
Computational Chemistry @ BASF
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.
Integrating Interaction Hotspots of the Ras/SOS Complex to Rationalize Small Molecule Design
Doris Schuetz studied pharmacy at the University of Vienna. After she had finished her Masters, she went to work in different pharmacies for more than 5 years, before she returned to the Department of Pharmaceutical Chemistry. She finished her PhD in the Pharmacoinformatics Research Group beginning of 2018 and was furthermore working as an application scientist for Inte:Ligand in 2017 and 2018. In September 2018 she joined the computational chemistry team at the Institute for Research in Immunology and Cancer (IRIC) in Montréal, Canada. Doris is working as a postdoctoral researcher, focusing on structure-based drug design. She is mainly working on protein-protein interfaces, aiming to integrate structural information into small molecule and macrocycle design in a cancer context. She is participating in several multidisciplinary academic projects, in close collaboration with scientists from different domains, i.e. biology, synthetic chemistry, biophysics and bioinformatics. Furthermore, she is involved in cancer related projects of pharmaceutical companies, supporting their research by employing computational methods.
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.
Virtual Screening – do I REAL-ly need large scale?
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.
Combining structure- and ligand-based methods for toxicity prediction linked to human mitochondrial respiratory complex I inhibition and in vitro validation
Florentina Troger studied pharmacy and is a PhD student at University of Vienna in the Pharmacoinformatics Research group of Prof. Dr. Gerhard F. Ecker. She is focussing on mitochondrial toxicity predictions by using structure based methods such as docking and structure-based pharamcophore modeling. Her major interest is the first complex of the mitochondrial respiratory chain which is crucial for the oxidative phosphorylation and in this way for energy creation in form of ATP. Inhibition of human mitochondrial respiratory complex I is linked to Parkinson’s disease which makes it a relevant off-target. This study is conducted within the EU-ToxRisk project. Additionally, Florentina is performing structure-based modeling studies on SLC25 family members within RESOLUTE.
Multiscale Computer-based Studies to Identify Ligand Interactions and Selectivity Among Hepatic Organic Anion Transporting Polypeptides
Alžběta Türková is a PhD student in the group of Dr. Barbara Zdrazil at the University of Vienna. In 2015, Alžběta Türková graduated in bachelor study program Cheminformatics and Bioinformatics. Her bachelor thesis was focused on the calculations of partial atomic charges in proteins by means of Quantum Mechanics (QM) methods and Electronegativity Equalization Method. Within her master study in Biomolecular Chemistry (year 2015-2017), she switched from sub-atomistic QM calculations to the mesoscale (bio)physics of cell membranes and their interactions with antimicrobial peptides. Her primary focus was to identify optimal peptide properties for their pore-forming activity by means of multiscale coarse-grained simulations with enhanced sampling. In the meanwhile, she also contributed to the creating Complex Portal database of macromolecular complexes (in collaboration with EBI, Hinxton UK). In August 2017, Alžběta Türková moved to Vienna to start her dissertation project on exploring ligand interactions with hepatic Organic Anion Transporting Polypeptides (OATPs) by means of computational methods. Following a holistic in silico approach, linking multiscale data mining approaches with structure-based molecular modeling, Alžběta Türková seeks to unravel molecular determinants which would explain selectivity switches among the three hepatic OATPs. Her special research interest is also to treat protein flexibility in structure-based modeling pipeline by applying elastic network normal mode analysis which is an useful reduced-representation approach to unravel intrinsic conformational dynamics of proteins.
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.
Exploring dynamic 3D interaction patterns for mechanistic understanding of protein-ligand binding
Prof. Gerhard Wolber is professor for Pharmaceutical Chemistry and head of the computational chemistry group at the Institute of Pharmacy at the Freie Universitaet Berlin since 2010. After his studies of pharmacy at the University of Innsbruck and Computer Science at the Technical University of Vienna, he received his PhD in pharmaceutical chemistry at the University of Innsbruck. In 2003 he co-founded the molecular modeling software company Inte:Ligand together with Prof. Hermann Stuppner and Prof. Thierry Langer. In 2008 he changed back to academia as assistant professor and group head of the Computer-Aided drug design group at the University of Innsbruck before changing to the Freie Universitaet Berlin in 2010. His research focuses on computational drug design and the development of drug development and virtual screening tools. Gerhard Wolber is the initial author of the pharmacophore design and screening tool LigandScout, which is still actively developed.
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.