BioExcel continues its direct support to industry through site visits. In late May we were pleased to visit UCB’s research site in Braine D’Alleud, Belgium for an exciting day of in depth discussions.
The morning started with our host, Dr Zara Sands of the Computer Aided drug Design group, giving us a live demonstration of the UnityMol 3D molecular viewer. The viewer uses the HTC Vive virtual reality (VR) platform developed by Marc Baaden’s group at the LBT laboratory in the IBPC institute of CNRS in Paris (http://www.baaden.ibpc.fr/umol).
Next, presentations were given by the BioExcel partners, beginning with a short introduction to BioExcel by Dr Ian Harrow. This was followed by a presentation by Prof. Erik Lindahl on the MD engine GROMACS which included insights into getting best performance. Next, Dr Vytautas Gapsys presented PMX, a tool for automation of topology generation during free energy calculations with GROMACS. Finally, Prof. Alexandre Bonvin presented on the docking tool, HADDOCK (bioexcel.eu/software/haddock) which included top predictions in the blind challenges of D3R (drugdesigndata.org) and CAPRI (ebi.ac.uk/msd-srv/capri).
After lunch, a number of presentations were given by investigators at the UCB sites of Braine and Slough, UK who joined us by teleconference. This started with an overview of the available compute resources and capabilities for molecular modelling and simulations using local or remote hardware.
We went on to consider use case applications which ranged from virtual screening and modelling small ligand interactions with molecular targets such as G protein-couple receptors. A further application is antibody engineering, such as for Olokizumab, the humanised antibody targeting interleukin-6 and neutralizing gp130-signaling (doi: 10.4161/mabs.28612).
Part of Figure 3. Crystal structure of the Fab portion of olokizumab in complex with IL-6. (A) The crystal structure of the antibody: target complex. The heavy chain is shown in pink, the light chain is shown in blue, and IL-6 is shown in green.
Our in depth discussions during the afternoon also considered the current challenges for molecular modellers in Pharma. This determined what gaps, if addressed, would help extraction of more value from molecular modelling approaches. These included a brainstorm session to understand how to get more value from BioExcel’s molecular modelling tools, and potential collaborative activities that may help to bridge unresolved gaps.
Throughout the day a number of potential opportunities for collaboration were identified to strengthen the relationship between the Computer Aided Drug Design group at UCB and BioExcel partners.