There are three parallel workshops on Monday, Tuesday and Wednesday, either from 15:00 to 16:30 or 17:00 to 18:30. Please register via the link provided by email as soon as you received it. For each time slot on every day, you can choose first, second and third priority. We will then try our best to allocate you to your favourite workshops each day.
| MONDAY | TUESDAY | WEDNESDAY | |
|---|---|---|---|
| 15:00 – 16:30 | inte:ligand + Optibrium + OpenEye | inte:ligand + Schrödinger + Pharmacelera | inte:ligand + BioSolveIT + Pharmacelera |
| 16:30 | Coffee | Coffee | Coffee |
| 17:00 – 18:30 | inte:ligand + BioSolveIT + OpenEye | inte:ligand + Schrödinger + BioSolveIT | inte:ligand + OpenEye |
| 19:30 | Dinner | Dinner | Dinner |
expect actives!
Monday 17:00 – 18:30 and Wednesday 15:00 – 16:30 sessions
Introduction into 3D compound design using SeeSAR
Computational methods have become indispensable in all stages of drug discovery, particularly with identifying potential drug candidates and guiding optimization processes to enhance molecule properties and selectivity.
This course offers comprehensive knowledge and practical skills in utilizing drug discovery software to craft new ideas, predict ligand binding modes, and understand drug design fundamentals from a medicinal chemistry perspective.
In the first part of the course, we will delve into structure-based methods aimed at enhancing the binding affinity of lead-like compounds through the strategic utilization of rational drug design techniques.
Later, we will explore fragment-based approaches. Through practical exercises, participants will engage with concepts such as fragment growing, linking, and merging to improve pharmacological and physicochemical properties using diverse ideation methods.
Finally, a short sneak peek into BioSolveIT’s second pillar of technology: Chemical Space exploration. BioSolveIT has a new technology that competes with classical enumerated libraries. These new “.Space” files will give participants the opportunity to rethink their horizons in the fast-changing world of CADD.
Tuesday 17:00 – 18:30 session
From Bits to Beakers: Integrating FBDD with Synthetic Feasibility and Chemical Space Exploration
Leveraging own medicinal chemistry knowledge is one of the most important resources to evolve a small fragment binder. In this workshop, we will apply techniques such as fragment growing, linking, and merging, to explore the chemical space around fragment binders to enhance their binding affinity, selectivity, and physicochemical properties with SeeSAR.
Furthermore, we will spotlight the pivotal role of synthetic accessibility of promising compounds in the early stages of the drug discovery process. Using the freshly designed lead compounds, we will dive into ultra-large Chemical Spaces using the infiniSee platform to retrieve relevant and synthesizable molecules.
We will provide insights on the concept of similarity between compounds as it can alter based on the goal of the project. This entails:
- Mining for compounds based on fuzzy pharmacophore features for scaffold hopping;
- Retrieval of close analogs for SAR exploration;
- Screening for compounds containing a substructure of interest.
Finally, with a comprehensive analysis of the iterative SeeSAR and infiniSee process, participants, whether seasoned researchers or newcomers, will gain invaluable insights into decision-making processes crucial for lead optimization.
LigandScout: Advanced Workflows for Molecular Design and Discovery
Inte:Ligand, known for the development of LigandScout, is the leader in the field for 3D-pharmacophore modeling and virtual screening. We support scientists worldwide with innovative software and consulting services for molecular design and drug discovery. Join our workshops to learn innovative, and inspiring workflows using LigandScout. We will cover advanced 3D-pharmacophore modeling and hit finding workflows, including use of our unique molecular dynamics simulation analysis tools, ligand-activity profiling, docking, fragment-based design, model generation in detected protein cavities, novel compound library design and de-risking neurotoxic adverse outcomes.
Monday and Tuesday Sessions:
- 15:00 – 16:30 (each day): Structure-based modeling and virtual screening workflows. 3D-pharmacophore editing; understanding structure-activity (SAR) relationships, VS strategies, ligand activity profiling, docking and VS results analysis.
- 17:00 – 18:30 (each day): Advanced workflows including analysis of MD simulations and dynamic pharmacophores for VS, Apo site pharmacophore strategies, ligand-based modeling, parallel screening, and interactive molecule design.
Wednesday Sessions (15:00 – 16:30 & 17:00 – 18:30):
- People’s choice open sessions. Everything you wanted to know but didn’t have time to ask!
We will explore creative workflows in these sessions to support and maximize your interests and results from your own projects. We will also demonstrate how to derisk chemical structures for neurotoxic adverse outcomes with the NeuroDeRisk IL Profiler.
Improving lives through computational molecular design
Who is this course for?
This tutorial is for researchers who are interested in conducting a structure and ligand-based virtual screening on a massive scale. (1,2) Together we will deepen your knowledge of concepts like protein structure and ligands.
The content will provide you with an understanding how to perform a large-scale virtual screening and its analysis with the help of OpenEye’s Orion® platform.
What will you achieve?
By the end of the course, you will be acquainted with:
- Orion’s interface, basic concepts, and workflows
- Preparing your protein structure for a virtual screening run and examine it interactively in 3D space.
- Large-scale workflows searching on a massive scale.
- https://docs.eyesopen.com/floe/modules/classic-floes/docs/source/tutorials/spruce.html#
- https://docs.eyesopen.com/floe/modules/large-scale-floes/docs/source/tutorial.html
In Silico Prediction of Phase I and II Metabolism: Guiding Optimisation of Drug Metabolism
For success as a drug, compounds must reach the target site at a sufficient concentration and for an appropriate duration whilst also being metabolised and excreted within a reasonable timeframe without creating reactive or toxic metabolites. We will describe unique mechanistic in silico models that help researchers design drugs in the early stages to satisfy all these requirements.
The StarDrop™ Metabolism module is a new precision modelling environment which helps you to determine Phase I and II metabolic routes, sites, products and lability for your compound. It enables users to quickly identify metabolic pathways and likely metabolites and guide compound design to avoid metabolic liabilities.
In this workshop, you’ll have the chance to follow along with our practical demonstration of the Metabolism module within the cloud-based StarDrop drug discovery platform. Together, we will use a range of case studies to:
- Determine how to design new compounds for greater metabolic stability.
- Identify the routes and products of metabolism to reduce the risk of drug-drug interactions, issues due to genetic polymorphisms, or the formation of reactive or toxic metabolites.
- Pinpoint the most important enzymes to ensure coverage during preclinical studies.
This workshop is suitable for anyone looking to achieve a practical understanding of predicting drug metabolism and applying the results in their projects.
Pushing the limits of computational chemistry
Tuesday, 15:00 – 16:30: Unlocking Chemical Diversity with Advanced 3D Ligand-Based Screening
Chemical diversity is a key aspect when screening virtual libraries of compounds. Hit identification must be accompanied by a scaffold diversity, exploring new chemical solutions that allow the identification of the right hit with drug-like properties while maintaining the same Mechanism of Action (MoA). Using different and accurate molecular descriptors is key to find novel chemical matter.
In this workshop we will compare the capabilities of our advanced 3D molecular field descriptors, derived from quantum mechanic calculations with respect classical 2D fingerprints. Our approach describes with high accuracy the factors that determine ligand / receptor interactions. To run this comparison we will use KNIME platform showcasing how PharmScreen – our 3D virtual screening tool – measures against similarity search workflows driven by 2D fingerprints.
Wednesday, 15:00 – 16:30: Novel synthesizable compounds from ultra-large chemical libraries
The ever-expanding accessible chemical universe harbours trillions of synthesizable compounds, offering a wealth of novel and diverse possibilities. Accessing this uncharted territory is crucial, yet the immense computational demands make accurate exploration a formidable challenge. Innovative solutions are needed to efficiently navigate and mine this untapped space, ensuring both, accuracy and synthesizability, to fuel the future of drug discovery and development.
In this workshop we will apply exaScreen to explore ultra-large chemical libraries using our proprietary 3D molecular field descriptors, explaining how the technology works and how it can mine billions of compounds on your workstation in a few hours. We will use KNIME platform to run a screening campaign on Enamine REAL.
Opening new worlds for molecular discovery
Tuesday, 15:00 – 16:30: A beginners’ guide to Structure Based Modeling
If you are interested in learning how to navigate the Maestro interface and how to perform design and docking of small molecules, join us for a hands-on workshop designed for beginners at using Schrödinger software.
The main Maestro interface contains all the tools that are required to bring in your starting small molecules and protein system, so that they can be properly prepared. We will explore ligand design in an automated fashion using the Ligand Designer GUI which facilitates on-the-fly ideation through ‘build and dock’ workflows. Through the use of embedded libraries of building blocks, users can modify their initial idea in many intuitive ways: from attachment points on the bound ligand, the free and viable space in the binding site, through to selecting specific residues in the protein or specific waters in the binding cavity to guide the design process.
Finally, we will set up and run docking calculations with Glide, and analyze how the resulting docked compounds satisfy the basic criteria of shape and molecular interactions that lead to the final Glide scoring term.
Tuesday, 17:00 – 18:30: Running and analyzing MD Simulations with Desmond
If you are interested in running molecular dynamics simulations, join us for a hands-on workshop designed for intermediate users of the Schrödinger software.
In this workshop you will learn how to use the Schrödinger platform to run and analyze the results of a molecular dynamics simulation using Desmond and Maestro. We will focus on a protein-ligand complex to look at the preparation of the system, the setup of an MD simulation and to go through different methods and tools to analyze a simulation. The analysis will improve our understanding of the binding pocket and the interactions between protein and ligand. Finally, we will discuss the different ways in which MD simulations with Desmond can be used as part of more complex workflows.