Ahead of protein and antibody engineering conference PEGS Europe 2023 in Lisbon, DDW’s Megan Thomas looks at what to expect from each track of the annual biologics technology meeting. On Day 3, Thursday 16 November 2023, the tracks include: the second part of machine learning for protein engineering, antibodies against membrane protein targets, engineering bispecific antibodies, next-generation immunotherapies, protein stability and formulation, and protein process development.
Machine learning for protein engineering: Part 2
The first track of PEGS Europe 2023 is ‘Machine learning for protein engineering: Part 2’, which will feature a range of sessions made up of presentations, talks and posters which address PLM and generative modelling for de novo design, structure, docking and dynamics fundamentals, and novel/alternative ML-enables screening technologies for higher POS.
PLM and generative modelling for de novo degisn
This session will begin with chairperson’s remarks from Victor Greiff, PhD, Associate Professor, Immunology, University of Oslo. Thereafter, the following presentations will take place:
- Melody Shahsavarian, PhD, Digital Biologics Platform, Large Molecules Research, Sanofi, on: ‘Enhancing antibody discovery with generative AI’.
- Enkelejda Miho, PhD, Professor, University of Applied Sciences and Arts Northwestern Switzerland, and Managing Director, aiNET, on: ‘The singular immune response to dengue and machine learning identification of antibodies in high-throughput sequences’.
- Ali Madani, PhD, Founder and CEO, Profluent Bio, on: ‘Protein engineering with large language models’.
- Stefan Ewert, PhD, Associate Director, Biologics Center, Novartis Institutes for Biomedical Research, on: ‘Computational counterselection identifies nonspecific therapeutic biologic candidates’.
- Hiroki Shirai, PhD, Coordinator, RIKEN Center for Computational Science, on: ‘Applying deep learning anomaly detection to antibody structures’.
- Anne Goupil-Lamy, PhD, Science Council Fellow at BIOVIA, BIOVIA, Dassault Systèmes, on: ‘Computational nanobody binding epitope prediction and re-epitoping’.
Structure, docking and dynamics fundamentals
Following Greiff’s chairperson remarks, this session will include two presentations:
- Rahmad Akbar, PhD, Researcher, Computational Systems Immunology, University of Oslo, on: ‘Unconstrained generation of synthetic antibody-antigen structures to guide machine learning methodology for antibody specificity prediction’.
- Pietro Sormanni, PhD, Group Leader, Royal Society University Research Fellow, Chemistry of Health, Yusuf Hamied Department of Chemistry, University of Cambridge, on: ‘Third-generation approaches of antibody discovery and optimisation’.
Novel/alternative ML-enabled screening technologies for higher POS
Following chairperson’s remarks from M Frank Erasmus, PhD, Head, Bioinformatics, Specifica, there will be four presentations and a panel discussion. The presentations are as follows:
- Fabian Schmich, PhD, Senior Data Scientist, pRED Informatics, Roche Diagnostics Deutschland, on: ‘scifAI: An explainable machine learning framework applied to functional characterisation of therapeutic antibodies’.
- Jannick Bendtsen, CEO, PipeBio, on: ‘Accelerating antibody development: Advancing discovery through integrated bioinformatics and machine learning’.
- Brajesh Rai, PhD, Senior Director, Machine Learning Computational Sciences, Pfizer, on: ‘Low-data interpretable deep learning prediction of antibody viscosity using a biophysically meaningful representation’.
- Alexander Yermanos, PhD, Lecturer, Systems & Synthetic Immunology, ETH Zurich, on: ‘Integrating single-cell immune repertoire sequencing, machine learning, and biophysical properties of antibodies’.
The panel discussion will be hosted by chairperson Erasmus and Greiff on the current state of AI in antibody therapeutics. It will cover methods currently presented in ML tracks, which AI approaches currently exhibit the greatest savings in time/cost savings relative to existing capabilities, which AI methodologies are likely to be most disruptive to existing capabilities and how soon will this occur, and whether panellists think AI-based approaches may enhance our regulatory approval systems and reduce the time/cost of the time to clinic. Panellists include:
- Andrew Bradbury, PhD, CSO, Specifica
- Rebecca Croasdale-Wood, PhD, Director, Augmented Biologics Discovery & Design, Biologics Engineering, Oncology, AstraZeneca
- René Hoet, PhD, Chief Innovation Officer, FairJourney Biologics
- Enkelejda Miho, PhD, Professor, University of Applied Sciences and Arts Northwestern Switzerland, and Managing Director, aiNET
Antibodies against membrane protein targets
The second track of PEGS Europe 2023 is ‘Antibodies against membrane protein targets’, which will feature a range of sessions made up of presentations, talks and posters which address discovery strategies, biotherapeutics for membrane protein targets, and include a number of roundtable breakout discussions.
After chairperson remarks from Catherine Hutchings, PhD, Independent Consultant, there will be a keynote presentation from Benjamin Hackel, PhD, Professor, Chemical Engineering & Materials Science, University of Minnesota. He will discuss selection technologies for membrane targets using advances in whole cell panning and comparative deep sequencing. Thereafter, there will be five presentations as follows:
- Keenan Taylor, PhD, Senior Scientist, AbbVie, on: ‘GPCR production strategies to enable antibody discovery and characterisation’.
- Jens Frauenfeld, PhD, Founder, CEO, Salipro Biotech, on: ‘Structure-function studies of salipro-CXCRs for antibody development’.
- Jendrik Schöppe, PhD, Senior Scientist, Novo Nordisk, on: ‘Stablised GPCRs for antibody discovery’.
- Noel Pauli, PhD, Group Leader, Antibody Engineering, Adimab, on: ‘Harnessing in vivo diversities with a yeast-based platform for the discovery of antibodies against multi-pass membrane proteins’.
- Jorge Lerma Romero, Graduate Student, Biochemistry, Technical University of Darmstadt, on: ‘Featured poster presentation: conformation locking scFvs for the research and discovery of FKBP51 selective ligands’.
Roundtable breakout discussions
Breakout Discussions are informal, moderated discussions, which allow participants to exchange ideas and experiences and develop future collaborations around a focused topic. These topics include: Membrane protein discovery challenges, and characterisation of antibodies against membrane proteins. Respectively, they will be moderated by previous speaker Noel Pauli, and Joseph Rucker, PhD, Vice President, Research and Development, Integral Molecular.
Biotherapeutics for membrane protein targets
After Noel Pauli has given his chairperson’s remarks, the following presentations will take place:
- Trevor Wilkinson, PhD, Director, Biologics Engineering, AstraZeneca, on: ‘Strategies for discovery of functional antibodies to membrane protein targets’.
- Savanna Skeeters, PhD, Scientist, Cyrus Biotechnology, on: ‘Computer-aided design of deimmunised membrane protein ligands with controlled affinities’.
- Dorien De Vlieger, PhD, Scientist, Molecular Engineering, Confo Therapeutics, on: ‘ConfoBodies for parallel discovery of GPCR agonistic antibodies’.
- Oliver Hartley, PhD, Vice President, Drug Discovery, Orion Biotechnology, on: ‘Targeting small protein GPCRs by engineering their natural ligands’.
- Laura Mele, PhD, Investigator, GlaxoSmithKline, on: ‘Discovery and characterisation of highly potent Fc-enhanced anti-GPCR mAbs’.
Engineering bispecific antibodies
The third track of PEGS Europe 2023 is ‘Engineering bispecific antibodies’, which will feature a range of sessions made up of presentations, talks and posters which address immunocytokines, novel approaches and formats, novel approaches and formats, and effector cell redirection.
Following chairperson’s remarks from Stefan Zielonka, PhD, Global Head of Antibody Discovery and Protein Engineering, Merck Healthcare KGaA; Professor of Biomolecular Immunotherapy, Technical University of Darmstadt, there will be a keynote presentation from Roberto De Luca, PhD, Head, Therapeutic Antibodies, Philochem. De Luca will present on Tripkin, a best-in-class potential for tumour-targeted interleukin-2 (IL2) potentiated by tumour necrosis facor (TNF).
Thereafter, the following presentations will take place:
- Bertolt Kreft, PhD, CSO, Bright Peak Therapeutics, on: ‘PD1-IL18 IC (BPT567) — A first-in-class and highly potent immunocytokine specifically targeting of PD-1+/IL18R+/CD8+ T effector cells enriched in the tumour microenvironment’.
- Dennis Verzijl, PhD, Principal Scientist, Genmab, on: ‘Kinetic antibody characterisation on challenging targets’.
Novel approaches and formats
After chairperson’s remarks from Harald Kolmar, PhD, Professor and Head, Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, the following presentations will take place:
- Christine Engeland, MD, PhD, Researcher, Immunotherapy, German Cancer Research Center, DKFZ, on: ‘oncolytic viral vaccines: Platforms for targeted cancer immunotherapy’.
- Shohei Koide, PhD, Professor, Biochemistry & Molecular Pharmacology, New York University School of Medicine; Perlmutter Cancer Center, NYU Langone Health, on: ‘Creating and targeting cancer-specific neoantigens by design’.
- Jens Fischer, PhD, Program Manager, Large Molecule Research Therapeutic Modalities, Roche Pharma Research and Early Development (pRED), on: ‘
- Bispecific and next-generation antibodies for non-oncology indications such as ophthalmologic and neurologic diseases’.
- Yuchih Lin, Doctor, Sino Biological Europe, on: ‘Accelerating drug discovery using advanced antibody development platforms’.
- Ellen Hilgenberg, PhD, Senior Business Development Manager, Business Development, ProBioGen, on: ‘DirectedLuck for bispecifics – a transposase system streamlines cell line development’.
Thereafter, the following luncheon presentations will take place:
- Kent Bondensgaard, PhD, Senior Vice President of Antibody Discovery Service, Antibody Discovery Services, Alloy Therapeutics, on: ‘Accelerating bispecifics discovery with the alloy common light chain fully human transgenic mouse platform’.
- Ankita Srivastava, PhD, Vice President, Antibody Engineering and Protein Sciences, AlivaMab Biologics, on: ‘Bispecific antibody engineering integrated with AlivaMab platform to deliver selectively functional antibodies’.
The session will conclude with a presentation from Steffen Goletz, PhD, Full Professor, Deputy Head, Vice Director, Biotechnology & Biomedicine, Danish Technical University, on IgG-VHH fusions with a focus on technology.
Effector cell redirection
After chairperson remarks from G Jonah Rainey, PhD, Senior Director, Protein Engineering, Eli Lilly and Company, the following presentations will take place in this session:
- Oliver Seifert, PhD, Senior Scientist, Institute of Cell Biology and Immunology, University of Stuttgart, on: ‘eIg-based bispecific T cell-engagers: Format matters’.
- Felix Unverdorben, PhD, Associate Director, Immatics Biotechnologies, on: ‘TCER: Next-generation, half-life extended TCR bispecifics designed to maximise efficacy while minimising toxicities for patients’.
- Jeremy Fry, Dr, Director of Sales, ProImmune, on: ‘Mastering immunogenicity and biologics development’.
- Christopher Rowley, PhD, Principal Research Scientist, Protein Science Pipeline, Immunocore, on: ‘ImmTAC: A high-affinity soluble TCR bispecific platform to target cancers’.
- Jürgen Kuball, PhD, Head, Hematology, University Medical Center Utrecht, on: ‘gdT cell inspired therapies’.
- Matthias Peipp, PhD, Research Head & Mildred Scheel Professor, Stem Cell Transplantation & Immunotherapy, University of Kiel, on: ‘Activating NK cell receptors as trigger molecules for bispecific antibodies to enhance anti-tumour NK cell responses’.
The fourth track of PEGS Europe 2023 on the third day is ‘Next-generation immunotherapies’, which will feature a range of sessions made up of presentations, talks and posters which address cell-based immunotherapies, vaccines, and checkpoints and agonists. The track will be opened by chairperson remarks from Daniel Chen, MD, PhD, Founder, Engenuity Life Sciences, which will be followed by the track’s keynote presentation by Bent Jakobsen, PhD, FMedSci, CEO & Founder, Accession Therapeutics. It is called, ‘An unexpected future for immune oncology therapies?’
This session will feature the following presentations:
- Viktor Lemgart, PhD, Research Fellow, Tidal Therapeutics, a Sanofi Company, on: ‘Reprogramming CAR T cells in vivo using targeted LNPs’.
- Yunying Chen, Vice President, Biologics Innovation & Discovery (BID), WuXi Biologics, on: ‘Targeting TAAs to fight cancers: Choice between TCE and ADC’.
- Michael Traxlmayr, PhD, Group leader, CD Laboratory for Next-Generation CAR T Cells, University of Natural Resources & Life Sciences, on: ‘Novel concepts to regulate CAR T cell activity with small molecule drugs in vivo’.
- Gabriela de Medeiros Silva, PhD, Research Investigator, Animal Cell Technology, iBET Instituto de Biologia Experimental Tecnologica, on: ‘Novel scFv against notch ligand JAG1 suitable for development of cell therapies toward JAG1-positive tumours’.
- Paul-Joseph Aspuria, PhD, Director, Cell Therapy, Cell Therapy, Synthekine, on: ‘SYNCAR: Engineered human IL-2/IL-2Rβ orthogonal pairs that selectively enhance CAR T cell anti-tumour efficacy in liquid and solid tumour models’.
- Bárbara Schlicht, Head of Product Management, Commercial Operations, Samplix, on: ‘Droplet based flowcytometry for function-based screening of single immune cells in Xdrop DE50 droplets’.
Thereafter, there will be two luncheon presentations:
- Joseph Rucker, PhD, Vice President, Research & Development, Integral Molecular, on: ‘A humanised chicken antibody platform that delivers diverse and developable therapeutic candidates’.
- Steven Quistad, PhD, Senior Applications Scientist, DNA Script, on: ‘Rapidly assemble genes in your laboratory using automated enzymatic oligo synthesis’.
In his session, there will be two presentations following chairperson’s remarks from Viktor Lemgart, PhD, Research Fellow, Tidal Therapeutics, a Sanofi Company. They include:
- Nicolas Poirier, PhD, CSO, OSE Immunotherapeutics, on: ‘Neoepitopes cancer vaccine monotherapy positive efficacy in non-small cell lung cancer with resistance to immunotherapy randomised Phase III’.
- Nageatte Ibrahim, MD, Vice President, Oncology & Global Clinical Development, MSD, on: ‘The new age of immunotherapy: From checkpoint inhibitors to vaccines’.
Checkpoints and agonists
This final session in the track will feature five presentations, which include:
- Timo Van den Berg, PhD, Senior Director, Immuno-Oncology Research, Byondis, on: ‘
- The CD47-SIRPα myeloid immune checkpoint: Considerations for targeting and preclinical characterisation of BYON4228’.
- Mattias Levin, PhD, Director, Antibody Technology Innovation, Alligator Bioscience, on: ‘Design and engineering of ATOR-4066 using the RUBY format: A novel Neo-X-Prime bsab Targeting CD40 and CEA’.
- Weisheng Chen, PhD, Founder and CEO, Leveragen, on: ‘Singularity sapiens: A next generation mouse model for developing fully human single domain antibodies’.
- Stefan Warmuth, PhD, Vice President, Head CMC, Numab Therapeutics, on: ‘Update on Numab’s affinity-balanced PD-L1x4-1BBxHSA trispecific tumour-targeted immunotherapy’.
- Wouter Verdurmen, PhD, Assistant Professor, Medical Biosciences, Radboud University Nijmegen, on: ‘Adenovial vector-mediated local IgA production: A novel anti-cancer immunotherapy’.
Protein stability and formulation
The fifth track of PEGS Europe 2023 is ‘Protein stability and formulation’, which will feature a range of sessions made up of presentations, talks and posters which address aggregation risks and stability prediction, formulation development and challenges for IV and subcutaneous administration, and a series of breakout sessions.
Aggregation risks and stability prediction
After chairperson’s remarks from Bernhard Valldorf, PhD, Targeting Director, Targeted mRNA Delivery, EMD Serono, this session will include the following presentations:
- Nathalie Heuze-Vourc’h, PhD, Research Professor, Research Center for Respiratory Diseases, Inserm, UMR, on: ‘Aggregation of antibody during inhalation delivery: Risk, countermeasure, and potential adverse effects’.
- Stefano Cucuzza, PhD, Postdoctoral Researcher, TRD Biologics & CGT, Novartis Pharma, on: ‘Not the usual suspects: Alternative surfactants for biopharmaceuticals’.
- Andre Mueller, PhD, Marketing Manager, Biologics Solutions, Unchained Labs, said: ‘Tackle high-concentration biologics with the right toolkit’.
Next, the keynote presentation will take place by Andrew Kosky, PhD, Sr Director, Technical Development, Genentech. He will present on science and risk-based shelf-life prediction for protein biologics. Thereafter, the following presentations will take place:
- Hristo Svilenov, PhD, Associate Professor, Ghent University, on: ‘Extrinsic stabilisation of antiviral ACE2-Fc fusion proteins targeting SARS-CoV-2’.
- Mitja Zidar, PhD, Senior Expert Science and Technology, Novartis, on: ‘Analytical characterisation meets molecular modeling: In silico forced degradation studies’.
- Racha Majed, Technical Sales Specialist, Sales, Refeyn, on: ‘Mass photometry – a fast and accurate mass characterisation of biomolecules’.
- Felix Gloge, PhD, Field Application Scientist, Waters | Wyatt Technology, on: ‘Spotlight on light scattering – How MALS and DLS help with measuring product parameters from research to production’.
The session will conclude with a luncheon presentation by Ana Carreras González, Ms, Analytical Development, Viralgen, on breaking through the challenges of rAAV purity characterisation by capillary electrophoresis (CE-SDS).
Roundtable breakout discussions
Breakout Discussions are informal, moderated discussions, which allow participants to exchange ideas and experiences and develop future collaborations around a focused topic. These topics include: subcutaneous administration and immunogenicity risk- current understanding and future considerations including novel modalities; and challenges and outlook of mRNA delivery and formulation. Respectively, they will be moderated by Karoline Bechtold-Peters, PhD, Senior Strategy & Technology Leader, Pharmaceuticals & Biopharma Process, Novartis Pharma, and Bernhard Valldorf, PhD, Targeting Director, Targeted mRNA Delivery, EMD Serono.
Formulation development and challenges for iv and subcutaneous administration
After Karoline Bechtold-Peters, PhD, Senior Strategy & Technology Leader, Pharmaceuticals & Biopharma Process, Novartis Pharma, has given her chairperson’s remarks, the following presentations will conclude this track:
- Michael Siedler, PhD, Section Head, NBE Formulation Sciences & Process Development, Abbvie Deutschland, on: ‘Case studies on the application of new tools and approaches for current challenges in formulation development of antibody-based drugs’.
- Ramesh Kumar Shanmugam, PhD, MBA, Associate Director, Biopharmaceutical Development, AstraZeneca, on: ‘Interactions between preservatives and an IgG1 mAb in support of multi-dose formulation development for biologics’.
- Lisa Dietel, PhD, Scientist, Pharmaceutical and Processing Department, Novel Formats, F Hoffmann-La Roche, on: ‘Understanding and overcoming surfactant-related stability challenges’.
- Kathya Rashida de la Luz Hernandez, PhD, Head, Analytical, Center of Molecular Immunology, on: ‘Development of a new high-concentrated formulation of anti-tumour mAbs for subcutaneous administration: Anti-EGFR mAb study case’.
- Qingyan Hu, PhD, Associate Director, Protein Formulation Development, Regeneron Pharmaceuticals, on: ‘Improving safety and dose accuracy of IV administration for protein drug products’.
Protein process development
The sixth track of PEGS Europe 2023 is ‘Protein process development’, which will feature a range of sessions made up of presentations, talks and posters which address quality control, protein purification, automation and process optimisation, and roundtable breakout discussions.
After chairperson remarks by Nicola Burgess-Brown, PhD, Director of Enzymology and Protein Engineering, Exact Sciences Innovation, the following presentations will take place in this session:
- Julieta Maria Sanchez, Instituto de Biotecnologia y Biomedicina, Universidad Autonoma de Barcelona (UAB), on: ‘Protein quality after the release from microparticles’.
- Opher Gileadi, PhD, Head, Protein Science SGC, Karolinska Institute, on: ‘Targeting every human protein: Challenges and prospects’.
- Fabian Mohr, PhD, Vice President Research & Development, IBA Lifesciences, on: ‘Developing a robust affinity tag platform using engineered streptavidin’.
- Zana Kapustina, PhD, Director of Product Management, Product Management, Atrandi Biosciences, ‘Platform integration for high-throughput functional screening applications’.
This session will begin with two presentations:
- David Reczek, PhD, Head of US Biologics Research, Large Molecules Platform, Sanofi, on: ‘Rapid purification of multi-specific antibodies enabled by introduction of engineered mutations’.
- Sandeep Talapatra, PhD, Leader Protein Science, Protein Cell & Structural Sciences, GSK, on: ‘Enhancing success rates and throughput of protein purification for drug discovery: A medium-scale approach’.
There will then be a keynote presentation from Kim Remans, PhD, Head, Protein Expression & Purification Core Facility, EMBL Heidelberg, which covers the need to condiser protein purification strategies for downstream applications and individual biological characteristics. This will be followed by a presentation from Anis Larbi, PhD, Senior Manager Medical & Scientific Affairs, Beckman Coulter Life Sciences, on: ‘Reducing the complexity of protein manufacturing: Streamlining the workflow’.
Roundtable breakout discussions
Breakout Discussions are informal, moderated discussions, which allow participants to exchange ideas and experiences and develop future collaborations around a focused topic. These topics include: High-throughput (HTP) protein production and AI and automation in bioprocess development. Respectively, they will be moderated by previous speaker Nicola Burgess-Brown, and Peter Herr Neubauer, PhD, Lab Head, Bioprocess Engineering, TU Berlin.
Automation and process optimisation
This session will begin with chairperson’s remarks from James Love, PhD, Vice President, Automation & Process Optimisation, Novo Nordisk. This will be followed by six presentations:
- Adam Brown, PhD, Associate Professor, Chemical & Biological Engineering, University of Sheffield, on: ‘Expanding the manufacturing solution space: Harnessing gene therapy technology innovation for recombinant protein production’.
- Augusto Pedro, PhD, Researcher, CICECO, Department of Chemistry, University of Aveiro, on: ‘Development of an integrated messenger RNA manufacturing process using thermoreversible aqueous biphasic systems’.
- Jana Langhoff, Tecan, on: ‘Opportunities and challenges of automating high throughput protein purification’.
- Ana Rebocho, Manager, BioP R&D, Revvity, on: ‘Accelerating biologic development programs with a state-of-the-art CHO expression system’.
- Jonathan Jones, Manager, Upstream Microbial, CPI Biologics, on: ‘An integrated approach for the process development and scale-up of recombinant proteins’.
- Miguel Pupo, PhD, Process Modelling Engineer, DataHow, on: ‘Using machine-learning to transfer learnings across development stages towards a digital platform process’.
This session will close with a featured presentation from James Love, PhD, Vice President, Automation & Process Optimization, Novo Nordisk, on automation and closed loop optimisation of protein development processes.